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Regina Malveste Ito C, Santos MO, de Oliveira Cunha M, de Araújo KM, de Souza GRL, Rézio GS, de Brito PN, Rezende APC, Fonseca JG, Wastowski IJ, Gonçalves Vieira JD, Gomes Avelino MA, Carneiro LC. Rhinovirus infection and co-infection in children with severe acute respiratory infection during the COVID-19 pandemic period. Virulence 2024; 15:2310873. [PMID: 38384141 PMCID: PMC10885176 DOI: 10.1080/21505594.2024.2310873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Rhinovirus causes respiratory tract infections in children and is found in co-infections. The objective of this research was to study the clinical profile of rhinovirus infection and co-infection in children with severe acute respiratory infection (SARI) during the COVID-19 pandemic period. We included 606 children ranging in age from 0.1 to 144 months of age from March 2020 to December 2021, hospitalized in the Pediatric Intensive Care Unit (PICU). The samples were collected by secretion from the nasopharynx region. A total of 259 children were tested positive for viral infection, 153 (59.07%) of them had a single rhinovirus infection and, 56 (36.6%) were aged between 60.1 and 144 months. Nine types of co-infections were identified and were found coinfection with three or more viruses (22/104, 21.15%). Observing the seasonality, the number of cases was similar between 2020 (49.53%) and 2021 (51.47%). Patients with a single infection (86.88%) and coinfection (67.30%) were more likely to have coughed. Patients with co-infection required the use of O2 for longer than those with a single rhinovirus infection. Hemogram results obtained from individuals with a single infection had higher levels of urea when compared to patients with co-infection with and other respiratory viruses. Multiple correspondence analyses indicated different clinical symptoms and comorbidities in patients with co-infection compared to those with single infection. The results found that the rhinovirus was much prevalent virus during the pandemic period and was found in co-infection with other virus types, what is important to diagnostic for the correct treatment of patients.
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Affiliation(s)
- Célia Regina Malveste Ito
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás- 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Mônica Oliveira Santos
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás- 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Marcos de Oliveira Cunha
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás- 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Kelliane Martins de Araújo
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás- 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Guilherme Rocha Lino de Souza
- Biochemistry and Molecular Biology Laboratory, Biologic Science Institute, Federal University of Goiás, Samambaia Camp, Goiânia, Goiás, Brazil
| | - Geovana Sôffa Rézio
- State Emergency Hospital of the Northwest Region of Goiânia Governador Otávio Lage de Siqueira (HUGOL), Goiânia, Goiás, Brazil
| | - Pollyanna Neta de Brito
- State Emergency Hospital of the Northwest Region of Goiânia Governador Otávio Lage de Siqueira (HUGOL), Goiânia, Goiás, Brazil
| | - Alana Parreira Costa Rezende
- State Emergency Hospital of the Northwest Region of Goiânia Governador Otávio Lage de Siqueira (HUGOL), Goiânia, Goiás, Brazil
| | - Jakeline Godinho Fonseca
- State Emergency Hospital of the Northwest Region of Goiânia Governador Otávio Lage de Siqueira (HUGOL), Goiânia, Goiás, Brazil
| | - Isabela Jubé Wastowski
- Molecular Immunology Laboratory of Goiás State University, Laranjeiras Unity Prof. Alfredo de Castro neighborhood, Goiânia, Goiás, Brazil
| | - José Daniel Gonçalves Vieira
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás- 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Melissa Ameloti Gomes Avelino
- Department of Pediatrics, Federal University of Goiás, Universitaria Avenue, Leste Universitário neighborhood, Goiânia, Goiás, Brazil
| | - Lilian Carla Carneiro
- Microorganism Biotechnology Laboratory of Institute of Tropical Pathology and Public Health, Federal University of Goiás- 235 St. Leste Universitário neighborhood, Goiânia, Goiás, Brazil
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Almoammar S, Kamran MA, Alnazeh AA, Almagbol M, Al Jearah MM, Mannakandath ML. Orthodontic adhesive loaded with different proportions of ZrO 2 silver-doped nanoparticles: An in vitro μTBS, SEM, EDX, FTIR, and antimicrobial analysis. Microsc Res Tech 2024; 87:1146-1156. [PMID: 38278778 DOI: 10.1002/jemt.24503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/30/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
Zirconium dioxide silver-doped nanoparticles (ZrO2AgDNPs) impacts the adhesive material in terms of its physical characteristics, antimicrobial properties, degree of conversion (DC), and micro-tensile bond strength (μTBS) of orthodontic brackets to the enamel surface. A comprehensive methodological analysis utilizing a range of analytical techniques, including scanning electron microscopy coupled with energy-dispersive x-ray spectroscopy (EDX), Fourier-transform infrared (FTIR) spectroscopy, DC analysis, and μTBS testing. A light-curable orthodontic adhesive, specifically Transbond XT, was combined with ZrO2AgDNPs at 2.5% and 5%. As a control, an adhesive with no incorporation of ZrO2AgDNPs was also prepared. The tooth samples were divided into three groups based on the weightage of NPs: group 1: 0% ZrO2AgDNPs (control), group 2: 2.5 wt% ZrO2AgDNPs, and group 3: 5 wt% ZrO2AgDNPs. EDX graph demonstrated silver (Ag), Zirconium (Zr), and Oxygen (O2), The antibacterial efficacy of adhesives with different concentrations of NPs (0%, 2.5%, and 5%) was assessed using the pour plate method. The FTIR spectra were analyzed to identify peaks at 1607 cm-1 corresponding to aromatic CC bonds and the peaks at 1638 cm-1 indicating the presence of aliphatic CC bonds. The μTBS was assessed using universal testing machine (UTM) and bond failure of orthodontic brackets was seen using adhesive remanent index (ARI) analysis. Kruskal-Wallis test assessed the disparities in survival rates of Streptococcus mutans. Analysis of variance (ANOVA) and post hoc Tukey multiple comparisons test calculated μTBS values. The lowest μTBS was observed in group 1 adhesive loaded with 0% ZrO2AgDNPs (21.25 ± 1.22 MPa). Whereas, the highest μTBS was found in group 3 (26.19 ± 1.07 MPa) adhesive loaded with 5% ZrO2AgDNPs. ZrO2AgDNPs in orthodontic adhesive improved μTBS and has acceptable antibacterial activity against S mutans. ZrO2AgDNPs at 5% by weight can be used in orthodontic adhesive alternative to the conventional method of orthodontic adhesive for bracket bonding. RESEARCH HIGHLIGHTS: The highest μTBS was found in orthodontic adhesive loaded with 5% ZrO2AgDNPs. ARI analysis indicates that the majority of the failures fell between 0 and 1 among all investigated groups. The colony-forming unit count of S. mutans was significantly less in orthodontic adhesive loaded with nanoparticles compared with control. The 0% ZrO2AgDNPs adhesive showed the highest DC.
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Affiliation(s)
- Salem Almoammar
- Department of Pedodontics and Orthodontic Sciences, College of Dentistry, King Khalid University, Abha, Saudi Arabia
| | - Muhammad Abdullah Kamran
- Department of Pedodontics and Orthodontic Sciences, College of Dentistry, King Khalid University, Abha, Saudi Arabia
| | - Abdullah A Alnazeh
- Department of Pedodontics and Orthodontic Sciences, College of Dentistry, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Almagbol
- Department of Community and Periodontics, Faculty of Dentistry, King Khalid University, Abha, Saudi Arabia
| | | | - Master Luqman Mannakandath
- Department of Oral Diagnosis and Oral Biology, College of Dentistry, King Khalid University, Abha, Saudi Arabia
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Bartoš O, Chmel M, Swierczková I. The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification. Sci Rep 2024; 14:9067. [PMID: 38643216 PMCID: PMC11032355 DOI: 10.1038/s41598-024-59667-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/12/2024] [Indexed: 04/22/2024] Open
Abstract
The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA-protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.
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Affiliation(s)
- Oldřich Bartoš
- Military Health Institute, Military Medical Agency, 16200, Prague, Czech Republic.
| | - Martin Chmel
- Military Health Institute, Military Medical Agency, 16200, Prague, Czech Republic
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108, Prague, Czech Republic
| | - Iva Swierczková
- Military Health Institute, Military Medical Agency, 16200, Prague, Czech Republic
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Duan H, Li S, Li C, Tian L, Ma Y, Cai X. Alfalfa xeno-miR159a regulates bovine mammary epithelial cell proliferation and milk protein synthesis by targeting PTPRF. Sci Rep 2024; 14:9117. [PMID: 38643232 PMCID: PMC11032358 DOI: 10.1038/s41598-024-59948-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/17/2024] [Indexed: 04/22/2024] Open
Abstract
Milk protein content is an important index to evaluate the quality and nutrition of milk. Accumulating evidence suggests that microRNAs (miRNAs) play important roles in bovine lactation, but little is known regarding the cross-kingdom regulatory roles of plant-derived exogenous miRNAs (xeno-miRNAs) in milk protein synthesis, particularly the underlying molecular mechanisms. The purpose of this study was to explore the regulatory mechanism of alfalfa-derived xeno-miRNAs on proliferation and milk protein synthesis in bovine mammary epithelial cells (BMECs). Our previous study showed that alfalfa miR159a (mtr-miR159a, xeno-miR159a) was highly expressed in alfalfa, and the abundance of mtr-miR159a was significantly lower in serum and whey from high-protein-milk dairy cows compared with low-protein-milk dairy cows. In this study, mRNA expression was detected by real-time quantitative PCR (qRT-PCR), and casein content was evaluated by enzyme-linked immunosorbent assay (ELISA). Cell proliferation and apoptosis were detected using the cell counting kit 8 (CCK-8) assay, 5-ethynyl-2'-deoxyuridine (EdU) staining, western blot, and flow cytometry. A dual-luciferase reporter assay was used to determine the regulation of Protein Tyrosine Phosphatase Receptor Type F (PTPRF) by xeno-miR159a. We found that xeno-miR159a overexpression inhibited proliferation of BMEC and promoted cell apoptosis. Besides, xeno-miR159a overexpression decreased β-casein abundance, and increased α-casein and κ-casein abundance in BMECs. Dual-luciferase reporter assay result confirmed that PTPRF is a target gene of xeno-miR159a. These results provide new insights into the mechanism by which alfalfa-derived miRNAs regulate BMECs proliferation and milk protein synthesis.
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Affiliation(s)
- Hongjuan Duan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Shaojin Li
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Chuangwei Li
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Lan Tian
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Xiaoyan Cai
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China.
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Hill LJ, Messias CSMDA, Vilela CLS, Garritano AN, Villela HDM, do Carmo FL, Thomas T, Peixoto RS. Bacteria associated with the in hospite Symbiodiniaceae's phycosphere. iScience 2024; 27:109531. [PMID: 38585661 PMCID: PMC10995889 DOI: 10.1016/j.isci.2024.109531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/23/2023] [Accepted: 03/16/2024] [Indexed: 04/09/2024] Open
Abstract
Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.
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Affiliation(s)
- Lilian Jorge Hill
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Helena Dias Muller Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Flavia Lima do Carmo
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Raquel S. Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
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Sacco MD, Hammond LR, Noor RE, Bhattacharya D, McKnight LJ, Madsen JJ, Zhang X, Butler SG, Kemp MT, Jaskolka-Brown AC, Khan SJ, Gelis I, Eswara P, Chen Y. Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB. eLife 2024; 13:e85579. [PMID: 38639993 DOI: 10.7554/elife.85579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
In the Firmicutes phylum, GpsB is a membrane associated protein that coordinates peptidoglycan synthesis with cell growth and division. Although GpsB has been studied in several bacteria, the structure, function, and interactome of Staphylococcus aureus GpsB is largely uncharacterized. To address this knowledge gap, we solved the crystal structure of the N-terminal domain of S. aureus GpsB, which adopts an atypical, asymmetric dimer, and demonstrates major conformational flexibility that can be mapped to a hinge region formed by a three-residue insertion exclusive to Staphylococci. When this three-residue insertion is excised, its thermal stability increases, and the mutant no longer produces a previously reported lethal phenotype when overexpressed in Bacillus subtilis. In S. aureus, we show that these hinge mutants are less functional and speculate that the conformational flexibility imparted by the hinge region may serve as a dynamic switch to finetune the function of the GpsB complex and/or to promote interaction with its various partners. Furthermore, we provide the first biochemical, biophysical, and crystallographic evidence that the N-terminal domain of GpsB binds not only PBP4, but also FtsZ, through a conserved recognition motif located on their C-termini, thus coupling peptidoglycan synthesis to cell division. Taken together, the unique structure of S. aureus GpsB and its direct interaction with FtsZ/PBP4 provide deeper insight into the central role of GpsB in S. aureus cell division.
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Affiliation(s)
- Michael D Sacco
- Department of Molecular Medicine, University of South Florida, Tampa, United States
| | - Lauren R Hammond
- Department of Molecular Biosciences, University of South Florida, Tampa, United States
| | - Radwan E Noor
- Global and Planetary Health, University of South Florida, Tampa, United States
| | | | - Lily J McKnight
- Department of Molecular Biosciences, University of South Florida, Tampa, United States
| | - Jesper J Madsen
- Department of Molecular Medicine, University of South Florida, Tampa, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida, Tampa, United States
| | - Shane G Butler
- Department of Molecular Medicine, University of South Florida, Tampa, United States
| | - M Trent Kemp
- Department of Molecular Medicine, University of South Florida, Tampa, United States
| | | | - Sebastian J Khan
- Department of Molecular Biosciences, University of South Florida, Tampa, United States
| | - Ioannis Gelis
- Department of Chemistry, University of South Florida, Tampa, United States
| | - Prahathees Eswara
- Department of Molecular Biosciences, University of South Florida, Tampa, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida, Tampa, United States
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Shaku MT, Um PK, Ocius KL, Apostolos AJ, Pires MM, Bishai WR, Kana BD. A modified BCG with depletion of enzymes associated with peptidoglycan amidation induces enhanced protection against tuberculosis in mice. eLife 2024; 13:e89157. [PMID: 38639995 DOI: 10.7554/elife.89157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 04/17/2024] [Indexed: 04/20/2024] Open
Abstract
Mechanisms by which Mycobacterium tuberculosis (Mtb) evades pathogen recognition receptor activation during infection may offer insights for the development of improved tuberculosis (TB) vaccines. Whilst Mtb elicits NOD-2 activation through host recognition of its peptidoglycan-derived muramyl dipeptide (MDP), it masks the endogenous NOD-1 ligand through amidation of glutamate at the second position in peptidoglycan side-chains. As the current BCG vaccine is derived from pathogenic mycobacteria, a similar situation prevails. To alleviate this masking ability and to potentially improve efficacy of the BCG vaccine, we used CRISPRi to inhibit expression of the essential enzyme pair, MurT-GatD, implicated in amidation of peptidoglycan side-chains. We demonstrate that depletion of these enzymes results in reduced growth, cell wall defects, increased susceptibility to antibiotics, altered spatial localization of new peptidoglycan and increased NOD-1 expression in macrophages. In cell culture experiments, training of a human monocyte cell line with this recombinant BCG yielded improved control of Mtb growth. In the murine model of TB infection, we demonstrate that depletion of MurT-GatD in BCG, which is expected to unmask the D-glutamate diaminopimelate (iE-DAP) NOD-1 ligand, yields superior prevention of TB disease compared to the standard BCG vaccine. In vitro and in vivo experiments in this study demonstrate the feasibility of gene regulation platforms such as CRISPRi to alter antigen presentation in BCG in a bespoke manner that tunes immunity towards more effective protection against TB disease.
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Affiliation(s)
- Moagi Tube Shaku
- DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Peter K Um
- Department of Medicine, Johns Hopkins University, Baltimore, United States
| | - Karl L Ocius
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - William R Bishai
- Department of Medicine, Johns Hopkins University, Baltimore, United States
| | - Bavesh D Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, University of the Witwatersrand, Johannesburg, South Africa
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Fortun M, L'hirondel J. [Use of LDBIO Diagnostics ® TOXOPLASMA ICT IGG-IGM in association with Siemens Atellica ® IM in toxoplasmosis serological screening]. Ann Biol Clin (Paris) 2024; 82:81-92. [PMID: 38638021 DOI: 10.1684/abc.2024.1875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
According to French recommendations for serological screening of toxoplasmosis, some profiles must be confirmed by additional methods, extending the time taken to produce results. Thus, the Laborizon Bretagne technical platform in Nantes studied the place of the LDBIO Diagnostics® TOXOPLASMA ICT IGG-IGM (ICT) test in addition to Siemens Atellica® serology. IgG-/IgM+ and equivocal or weak positive IgG/IgM- (IgGEq/IgM-) profiles on Atellica® will be confirmed by ICT, Alinity® Abbott and Platelia® Biorad. Among the 66 IgGEq/IgM- profiles, the concordance is perfect between ICT and complementary techniques: 21 weak positives were confirmed positive, 8 equivocal were considered negative and 37 were confirmed positive. Concerning the 76 IgG-/IgM+ profiles, 68 are negative and 7 are positive by complementary techniques and ICT. One discordance was observed. The Atellica®/ICT combination allows excellent discrimination of IgG-/IgM+ and IgGEq/IgM serological profiles with consistent diagnostic orientation in 99.3% of cases. Only 1 sample was found to be discordant but required monitoring at 15 days. The observed performances are compatible with routine use. This test simplifies the analytical process, improves the time to obtain results, while guaranteeing an excellent level of quality.
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Thapa S, Rathnaiah G, Zinniel DK, Barletta RG, Bannantine JP, Huebner M, Sreevatsan S. The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation. Sci Rep 2024; 14:8941. [PMID: 38637716 PMCID: PMC11026511 DOI: 10.1038/s41598-024-59691-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024] Open
Abstract
Johne's disease (JD) is a chronic enteric infection of dairy cattle worldwide. Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of JD, is fastidious often requiring eight to sixteen weeks to produce colonies in culture-a major hurdle in the diagnosis and therefore in implementation of optimal JD control measures. A significant gap in knowledge is the comprehensive understanding of the metabolic networks deployed by MAP to regulate iron both in-vitro and in-vivo. The genome of MAP carries MAP3773c, a putative metal regulator, which is absent in all other mycobacteria. The role of MAP3773c in intracellular iron regulation is poorly understood. In the current study, a field isolate (K-10) and an in-frame MAP3773c deletion mutant (ΔMAP3773c) derived from K-10, were exposed to iron starvation for 5, 30, 60, and 90 min and RNA-Seq was performed. A comparison of transcriptional profiles between K-10 and ΔMAP3773c showed 425 differentially expressed genes (DEGs) at 30 min time post-iron restriction. Functional analysis of DEGs in ΔMAP3773c revealed that pantothenate (Pan) biosynthesis, polysaccharide biosynthesis and sugar metabolism genes were downregulated at 30 min post-iron starvation whereas ATP-binding cassette (ABC) type metal transporters, putative siderophore biosynthesis, PPE and PE family genes were upregulated. Pathway analysis revealed that the MAP3773c knockout has an impairment in Pan and Coenzyme A (CoA) biosynthesis pathways suggesting that the absence of those pathways likely affect overall metabolic processes and cellular functions, which have consequences on MAP survival and pathogenesis.
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Affiliation(s)
- Sajani Thapa
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, STEG300, East Lansing, MI, 48824, USA
| | - Govardhan Rathnaiah
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
- University Of Nebraska, Eppley Institute for Cancer Research, Lincoln, USA
| | - Denise K Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
| | - Raul G Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
| | | | - Marianne Huebner
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, STEG300, East Lansing, MI, 48824, USA.
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Vandepol NS, Shade A. Is everything everywhere? A hands-on activity to engage undergraduates with key concepts in quantitative microbial biogeography. J Microbiol Biol Educ 2024:e0017023. [PMID: 38634606 DOI: 10.1128/jmbe.00170-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
The ubiquity and ease with which microbial cells disperse over space is a key concept in microbiology, especially in microbial ecology. The phenomenon prompted Baas Becking's famous "everything is everywhere" statement that now acts as the null hypothesis in studies that test the dispersal limitation of microbial taxa. Despite covering the content in lectures, exam performance indicated that the concepts of dispersal and biogeography challenged undergraduate students in an upper-level Microbial Ecology course. Therefore, we iteratively designed a hands-on classroom activity to supplement the lecture content and reinforce fundamental microbial dispersal and biogeography concepts while also building quantitative reasoning and teamwork skills. In a class period soon after the lecture, the students formed three-to-five-person teams to engage in the activity, which included a hands-on dispersal simulation and worksheet to guide discussion. The simulation involved stepwise neutral immigration or emigration and then environmental selection on a random community of microbial taxa represented by craft poms. The students recorded the results at each step as microbial community data. A field guide was provided to identify the taxonomy based on the pom phenotype and a reference to each taxon's preferred environmental niches. The worksheet guided a reflection of student observations during the simulation. It also sharpened quantitative thinking by prompting the students to summarize and visualize their and other teams' microbial community data and then to compare the observed community distributions to the idealized expectation given only selection without dispersal. We found that the activity improved student performance on exam questions and general student satisfaction and comfort with the biogeography concepts. Activity instructions and a list of needed materials are included for instructors to reproduce for their classrooms.
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Affiliation(s)
- Natalie S Vandepol
- Dean's Office, Broad College of Business, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Ecologie Microbienne: CNRS UMR5557, INRAE UMR1418, VetAgro Sup, Universite Claude Bernard Lyon 1, 69622 Villeurbanne, France
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11
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Hartsough EM, Foreman RK, Martinez-Lage M, Branda J, Sohani AR, Zukerberg L. Dematiaceous fungal infections: clinical and pathologic conundrums. J Clin Pathol 2024; 77:352-357. [PMID: 38272660 DOI: 10.1136/jcp-2023-209239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
Dematiaceous fungi are defined by pigment within their cell walls. They are increasingly recognised human pathogens, causing a wide range of clinical presentations, from localised subcutaneous infections to disseminated disease in rare cases. We report our institutional experience with diagnosis of dematiaceous fungal infections from 2005 to 2022 and highlight four instructive cases that clinically and pathologically mimicked other diseases for which the diagnosis was confirmed by fungal culture (one case) or supported by PCR with 28S rRNA and internal transcribed spacer primers (three cases). Two patients were immunocompromised and two had presumed exposure to the organism. In each highlighted case, fungal infection was not clinically suspected, and the pathologist was critical in making the diagnosis and ensuring appropriate clinical management, which was supplemented by fungal stains and novel molecular methods.
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Affiliation(s)
- Emily Mae Hartsough
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ruth K Foreman
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Maria Martinez-Lage
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John Branda
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Aliyah R Sohani
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lawerence Zukerberg
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
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12
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Thiermann R, Sandler M, Ahir G, Sauls JT, Schroeder J, Brown S, Le Treut G, Si F, Li D, Wang JD, Jun S. Tools and methods for high-throughput single-cell imaging with the mother machine. eLife 2024; 12:RP88463. [PMID: 38634855 PMCID: PMC11026091 DOI: 10.7554/elife.88463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning-based segmentation, 'what you put is what you get' (WYPIWYG) - that is, pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother machine-based high-throughput imaging and analysis methods in their research.
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Affiliation(s)
- Ryan Thiermann
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Michael Sandler
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Gursharan Ahir
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - John T Sauls
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn ArborUnited States
| | - Steven Brown
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | | | - Fangwei Si
- Department of Physics, Carnegie Mellon UniversityPittsburghUnited States
| | - Dongyang Li
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | - Suckjoon Jun
- Department of Physics, University of California, San DiegoLa JollaUnited States
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13
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Wyatt NJ, Watson H, Anderson CA, Kennedy NA, Raine T, Ahmad T, Allerton D, Bardgett M, Clark E, Clewes D, Cotobal Martin C, Doona M, Doyle JA, Frith K, Hancock HC, Hart AL, Hildreth V, Irving PM, Iqbal S, Kennedy C, King A, Lawrence S, Lees CW, Lees R, Letchford L, Liddle T, Lindsay JO, Maier RH, Mansfield JC, Marchesi JR, McGregor N, McIntyre RE, Ostermayer J, Osunnuyi T, Powell N, Prescott NJ, Satsangi J, Sharma S, Shrestha T, Speight A, Strickland M, Wason JM, Whelan K, Wood R, Young GR, Zhang X, Parkes M, Stewart CJ, Jostins-Dean L, Lamb CA. Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine. BMJ Open 2024; 14:e073639. [PMID: 38631839 PMCID: PMC11029295 DOI: 10.1136/bmjopen-2023-073639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 02/20/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients.Current understanding of IBD pathogenesis implicates complex interactions between host genetics and the gut microbiome. Most cohorts studying the gut microbiota to date have been underpowered, examined single treatments and produced heterogeneous results. Lack of cross-treatment comparisons and well-powered independent replication cohorts hampers the ability to infer real-world utility of predictive signatures.IBD-RESPONSE will use multi-omic data to create a predictive tool for treatment response. Future patient benefit may include development of biomarker-based treatment stratification or manipulation of intestinal microbial targets. IBD-RESPONSE and downstream studies have the potential to improve quality of life, reduce patient risk and reduce expenditure on ineffective treatments. METHODS AND ANALYSIS This prospective, multicentre, observational study will identify and validate a predictive model for response to advanced IBD therapies, incorporating gut microbiome, metabolome, single-cell transcriptome, human genome, dietary and clinical data. 1325 participants commencing advanced therapies will be recruited from ~40 UK sites. Data will be collected at baseline, week 14 and week 54. The primary outcome is week 14 clinical response. Secondary outcomes include clinical remission, loss of response in week 14 responders, corticosteroid-free response/remission, time to treatment escalation and change in patient-reported outcome measures. ETHICS AND DISSEMINATION Ethical approval was obtained from the Wales Research Ethics Committee 5 (ref: 21/WA/0228). Recruitment is ongoing. Following study completion, results will be submitted for publication in peer-reviewed journals and presented at scientific meetings. Publications will be summarised at www.ibd-response.co.uk. TRIAL REGISTRATION NUMBER ISRCTN96296121.
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Affiliation(s)
- Nicola J Wyatt
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Hannah Watson
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Tim Raine
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Dean Allerton
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Michelle Bardgett
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Emma Clark
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Dawn Clewes
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | | | - Mary Doona
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jennifer A Doyle
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katherine Frith
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Helen C Hancock
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Ailsa L Hart
- Department of Gastroenterology, St Mark's Hospital and Academic Institute, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Victoria Hildreth
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' NHS Foundation Trust, London, UK
- School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sameena Iqbal
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ciara Kennedy
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew King
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sarah Lawrence
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Charlie W Lees
- Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Edinburgh IBD Unit, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Robert Lees
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Laura Letchford
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Trevor Liddle
- Research Informatics Team, Clinical Research, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - James O Lindsay
- Department of Gastroenterology, Barts Health NHS Trust, London, UK
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
| | - Rebecca H Maier
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - John C Mansfield
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital, Imperial College London, London, UK
| | - Naomi McGregor
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | | | | | | | - Nick Powell
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital, Imperial College London, London, UK
- Department of Gastroenterology, Imperial College Healthcare NHS Trust, London, UK
| | - Natalie J Prescott
- Department of Medical and Molecular Genetics, Guy's Hospital, King's College London, London, UK
| | - Jack Satsangi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Shriya Sharma
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Tara Shrestha
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Ally Speight
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - James Ms Wason
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Kevin Whelan
- Department of Nutritional Sciences, King's College London, London, UK
| | - Ruth Wood
- Newcastle Clinical Trials Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Gregory R Young
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Xinyue Zhang
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Miles Parkes
- Department of Gastroenterology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christopher J Stewart
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Christopher A Lamb
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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14
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Hossain Z, Zhao S, Liu K, Li L, Hubbard M. Deciphering Aphanomyces euteiches-pea-biocontrol bacterium interactions through untargeted metabolomics. Sci Rep 2024; 14:8877. [PMID: 38632368 PMCID: PMC11024177 DOI: 10.1038/s41598-024-52949-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/25/2024] [Indexed: 04/19/2024] Open
Abstract
Aphanomyces euteiches causes root rot in pea, leading to significant yield losses. However, the metabolites involved in this pathosystem have not been thoroughly studied. This study aimed to fill this gap and explore mechanisms of bacterial suppression of A. euteiches via untargeted metabolomics using pea grown in a controlled environment. Chemical isotope labeling (CIL), followed by liquid chromatography-mass spectrometry (LC-MS), was used for metabolite separation and detection. Univariate and multivariate analyses showed clear separation of metabolites from pathogen-treated pea roots and roots from other treatments. A three-tier approach positively or putatively identified 5249 peak pairs or metabolites. Of these, 403 were positively identified in tier 1; 940 were putatively identified with high confidence in tier 2. There were substantial changes in amino acid pool, and fatty acid and phenylpropanoid pathway products. More metabolites, including salicylic and jasmonic acids, were upregulated than downregulated in A. euteiches-infected roots. 1-aminocyclopropane-1-carboxylic acid and 12-oxophytodienoic acid were upregulated in A. euteiches + bacterium-treated roots compared to A. euteiches-infected roots. A great number of metabolites were up- or down-regulated in response to A. euteiches infection compared with the control and A. euteiches + bacterium-treated plants. The results of this study could facilitate improved disease management.
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Affiliation(s)
- Zakir Hossain
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, Swift Current, Saskatchewan, S9H 3X2, Canada.
| | - Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Kui Liu
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, Swift Current, Saskatchewan, S9H 3X2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Michelle Hubbard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, Swift Current, Saskatchewan, S9H 3X2, Canada.
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15
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Chen S, Hu Z, Tang J, Zhu H, Zheng Y, Xiao J, Xu Y, Wang Y, Luo Y, Mo X, Wu Y, Guo J, Zhang Y, Luo H. High temperature and humidity in the environment disrupt bile acid metabolism, the gut microbiome, and GLP-1 secretion in mice. Commun Biol 2024; 7:465. [PMID: 38632312 PMCID: PMC11024098 DOI: 10.1038/s42003-024-06158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
High temperature and humidity in the environment are known to be associated with discomfort and disease, yet the underlying mechanisms remain unclear. We observed a decrease in plasma glucagon-like peptide-1 levels in response to high-temperature and humidity conditions. Through 16S rRNA gene sequencing, alterations in the gut microbiota composition were identified following exposure to high temperature and humidity conditions. Notably, changes in the gut microbiota have been implicated in bile acid synthesis. Further analysis revealed a decrease in lithocholic acid levels in high-temperature and humidity conditions. Subsequent in vitro experiments demonstrated that lithocholic acid increases glucagon-like peptide-1 secretion in NCI-H716 cells. Proteomic analysis indicated upregulation of farnesoid X receptor expression in the ileum. In vitro experiments revealed that the combination of lithocholic acid with farnesoid X receptor inhibitors resulted in a significant increase in GLP-1 levels compared to lithocholic acid alone. In this study, we elucidate the mechanism by which reduced lithocholic acid suppresses glucagon-like peptide 1 via farnesoid X receptor activation under high-temperature and humidity condition.
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Affiliation(s)
- Song Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zongren Hu
- Department of Rehabilitation and Healthcare, Hunan University of Medicine, Huaihua, China
| | - Jianbang Tang
- Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Chinese Medicine, Zhongshan, China
| | | | - Yuhua Zheng
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiedong Xiao
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Youhua Xu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macao, China
| | - Yao Wang
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yi Luo
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoying Mo
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yalan Wu
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jianwen Guo
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China.
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Yongliang Zhang
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Immunology Programme, The Life Science Institute, National University of Singapore, Singapore, Singapore.
| | - Huanhuan Luo
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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16
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Kamari F, Eller E, Bøgebjerg ME, Capella IM, Galende BA, Korim T, Øland P, Borup ML, Frederiksen AR, Ranjouriheravi A, Al-Jwadi AF, Mansour M, Hansen S, Diethelm I, Burek M, Alvarez F, Buch AG, Mojtahedi N, Röttger R, Segtnan EA. Clinical performance of AI-integrated risk assessment pooling reveals cost savings even at high prevalence of COVID-19. Sci Rep 2024; 14:8853. [PMID: 38632289 PMCID: PMC11024139 DOI: 10.1038/s41598-024-59068-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/06/2024] [Indexed: 04/19/2024] Open
Abstract
Individual testing of samples is time- and cost-intensive, particularly during an ongoing pandemic. Better practical alternatives to individual testing can significantly decrease the burden of disease on the healthcare system. Herein, we presented the clinical validation of Segtnan™ on 3929 patients. Segtnan™ is available as a mobile application entailing an AI-integrated personalized risk assessment approach with a novel data-driven equation for pooling of biological samples. The AI was selected from a comparison between 15 machine learning classifiers (highest accuracy = 80.14%) and a feed-forward neural network with an accuracy of 81.38% in predicting the rRT-PCR test results based on a designed survey with minimal clinical questions. Furthermore, we derived a novel pool-size equation from the pooling data of 54 published original studies. The results demonstrated testing capacity increase of 750%, 60%, and 5% at prevalence rates of 0.05%, 22%, and 50%, respectively. Compared to Dorfman's method, our novel equation saved more tests significantly at high prevalence, i.e., 28% (p = 0.006), 40% (p = 0.00001), and 66% (p = 0.02). Lastly, we illustrated the feasibility of the Segtnan™ usage in clinically complex settings like emergency and psychiatric departments.
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Affiliation(s)
- Farzin Kamari
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | | | - Mathias Emil Bøgebjerg
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | | | - Borja Arroyo Galende
- Grupo de Aplicación de Telecomunicaciones Visuales, Universidad Politécnica de Madrid, Madrid, Spain
| | | | | | | | | | - Amir Ranjouriheravi
- Research Center for Translational Medicine (KUTTAM), Graduate School of Sciences and Engineering, Koç University, Istanbul, Turkey
| | | | - Mostafa Mansour
- SDU Health Informatics and Technology, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Sara Hansen
- SDU Health Informatics and Technology, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Isabella Diethelm
- SDU Health Informatics and Technology, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Marta Burek
- SDU Health Informatics and Technology, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Federico Alvarez
- Grupo de Aplicación de Telecomunicaciones Visuales, Universidad Politécnica de Madrid, Madrid, Spain
| | - Anders Glent Buch
- Department of Engineering, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Nima Mojtahedi
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Eivind Antonsen Segtnan
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark.
- Synaptic ApS, Copenhagen, Denmark.
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17
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Nhu NTK, Phan MD, Hancock SJ, Peters KM, Alvarez-Fraga L, Forde BM, Andersen SB, Miliya T, Harris PNA, Beatson SA, Schlebusch S, Bergh H, Turner P, Brauner A, Westerlund-Wikström B, Irwin AD, Schembri MA. High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection. eLife 2024; 12:RP91853. [PMID: 38622998 PMCID: PMC11021048 DOI: 10.7554/elife.91853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
Neonatal meningitis is a devastating disease associated with high mortality and neurological sequelae. Escherichia coli is the second most common cause of neonatal meningitis in full-term infants (herein NMEC) and the most common cause of meningitis in preterm neonates. Here, we investigated the genomic relatedness of a collection of 58 NMEC isolates spanning 1974-2020 and isolated from seven different geographic regions. We show NMEC are comprised of diverse sequence types (STs), with ST95 (34.5%) and ST1193 (15.5%) the most common. No single virulence gene profile was conserved in all isolates; however, genes encoding fimbrial adhesins, iron acquisition systems, the K1 capsule, and O antigen types O18, O75, and O2 were most prevalent. Antibiotic resistance genes occurred infrequently in our collection. We also monitored the infection dynamics in three patients that suffered recrudescent invasive infection caused by the original infecting isolate despite appropriate antibiotic treatment based on antibiogram profile and resistance genotype. These patients exhibited severe gut dysbiosis. In one patient, the causative NMEC isolate was also detected in the fecal flora at the time of the second infection episode and after treatment. Thus, although antibiotics are the standard of care for NMEC treatment, our data suggest that failure to eliminate the causative NMEC that resides intestinally can lead to the existence of a refractory reservoir that may seed recrudescent infection.
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Affiliation(s)
- Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Kate M Peters
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Laura Alvarez-Fraga
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of QueenslandBrisbaneAustralia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
| | - Patrick NA Harris
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Sanmarie Schlebusch
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
- Q-PHIRE Genomics and Public Health Microbiology, Forensic and Scientific Services, Coopers PlainsBrisbaneAustralia
| | - Haakon Bergh
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Annelie Brauner
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University HospitalStockholmSweden
| | | | - Adam D Irwin
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Infection Management Prevention Service, Queensland Children's HospitalBrisbaneAustralia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
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18
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Levin BR, Berryhill BA, Gil-Gil T, Manuel JA, Smith AP, Choby JE, Andersson DI, Weiss DS, Baquero F. Theoretical considerations and empirical predictions of the pharmaco- and population dynamics of heteroresistance. Proc Natl Acad Sci U S A 2024; 121:e2318600121. [PMID: 38588431 PMCID: PMC11032463 DOI: 10.1073/pnas.2318600121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024] Open
Abstract
Antibiotics are considered one of the most important contributions to clinical medicine in the last century. Due to the use and overuse of these drugs, there have been increasing frequencies of infections with resistant pathogens. One form of resistance, heteroresistance, is particularly problematic; pathogens appear sensitive to a drug by common susceptibility tests. However, upon exposure to the antibiotic, resistance rapidly ascends, and treatment fails. To quantitatively explore the processes contributing to the emergence and ascent of resistance during treatment and the waning of resistance following cessation of treatment, we develop two distinct mathematical and computer-simulation models of heteroresistance. In our analysis of the properties of these models, we consider the factors that determine the response to antibiotic-mediated selection. In one model, heteroresistance is progressive, with each resistant state sequentially generating a higher resistance level. In the other model, heteroresistance is non-progressive, with a susceptible population directly generating populations with different resistance levels. The conditions where resistance will ascend in the progressive model are narrower than those of the non-progressive model. The rates of reversion from the resistant to the sensitive states are critically dependent on the transition rates and the fitness cost of resistance. Our results demonstrate that the standard test used to identify heteroresistance is insufficient. The predictions of our models are consistent with empirical results. Our results demand a reevaluation of the definition and criteria employed to identify heteroresistance. We recommend that the definition of heteroresistance should include a consideration of the rate of return to susceptibility.
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Affiliation(s)
- Bruce R. Levin
- Department of Biology, Emory University, Atlanta, GA30322
- Emory Antibiotic Resistance Center, Atlanta, GA30322
| | - Brandon A. Berryhill
- Department of Biology, Emory University, Atlanta, GA30322
- Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA30322
| | - Teresa Gil-Gil
- Department of Biology, Emory University, Atlanta, GA30322
| | | | | | - Jacob E. Choby
- Emory Antibiotic Resistance Center, Atlanta, GA30322
- Emory Vaccine Center, Atlanta, GA30322
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, UppsalaSE-75123, Sweden
| | - David S. Weiss
- Emory Antibiotic Resistance Center, Atlanta, GA30322
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA30322
- Georgia Emerging Infections Program, Georgia Department of Public Health, Atlanta, GA30322
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, and Centro de Investigación Biomédica en Red Epidemiología y Salud Pública, Madrid28034, Spain
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19
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Kim JH, Kim T, Kim W, Kim SH, Hong YJ, Lim E, Bae DW, Noh SM, Lee J. The incidence and predictors of antibiotic-associated encephalopathy: a multicenter hospital-based study. Sci Rep 2024; 14:8747. [PMID: 38627483 PMCID: PMC11021399 DOI: 10.1038/s41598-024-59555-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
This study aimed to evaluate the incidence and likelihood of antibiotic-associated encephalopathy (AAE), comparing rates among the classes of antibiotics in monotherapy or in combination therapy. We also investigated the associations between the incidence of AAE and the glomerular filtration rate (GFR) and electroencephalogram features. Consecutive admissions that used any kind of antibiotics to treat infectious diseases were identified from six hospitals. We classified antibiotics according to three distinct pathophysiologic mechanisms and clinical subtypes. We searched for the incidence of AAE as the primary outcome. A total of 97,433 admission cases among 56,038 patients was identified. Cases that received type 1 antibiotics had significantly more frequent AAE compared to those that received type 2 antibiotics (adjusted odds ratio [OR], 2.62; 95% confidence interval [CI] 1.15-5.95; P = 0.021). Combined use of type 1 + 2 antibiotics was associated with a significantly higher incidence of AAE compared to the use of type 2 antibiotics alone (adjusted OR, 3.44; 95% CI 1.49-7.93; P = 0.004). Groups with GFR < 60 mL/min/1.73 m2 had significantly higher incidence rates of AAE compared to those with GFRs ≥ 90 mL/min/1.73 m2 among cases that received type 1 + 2 antibiotics. Detection of spike-and-wave or sharp-and-wave patterns on electroencephalogram was significantly more common in the combination therapy group. Combination use of antibiotics was associated with a higher incidence of AAE compared to monotherapy. The incidence of AAE significantly increased as renal function decreased, and epileptiform discharges were more likely to be detected in cases receiving combined antibiotics.
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Affiliation(s)
- Jean Hee Kim
- Department of Neurology, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Taewon Kim
- Department of Neurology, Incheon St. Mary's Hospital, The Catholic University of Korea, #56 Dongsu-Ro, Bupyeong-Gu, Incheon, 21431, South Korea.
| | - Woojun Kim
- Department of Neurology, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Seong-Hoon Kim
- Department of Neurology, Uijeongbu St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Yun Jeong Hong
- Department of Neurology, Uijeongbu St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Eunyae Lim
- Department of Neurology, Yeouido St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Dae Woong Bae
- Department of Neurology, St. Vincent's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Sang-Mi Noh
- Department of Neurology, St. Vincent's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Jieun Lee
- Department of Neurology, Bucheon St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
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20
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Chau CW, To A, Au-Yeung RKH, Tang K, Xiang Y, Ruan D, Zhang L, Wong H, Zhang S, Au MT, Chung S, Song E, Choi DH, Liu P, Yuan S, Wen C, Sugimura R. SARS-CoV-2 infection activates inflammatory macrophages in vascular immune organoids. Sci Rep 2024; 14:8781. [PMID: 38627497 PMCID: PMC11021416 DOI: 10.1038/s41598-024-59405-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
SARS-CoV-2 provokes devastating tissue damage by cytokine release syndrome and leads to multi-organ failure. Modeling the process of immune cell activation and subsequent tissue damage is a significant task. Organoids from human tissues advanced our understanding of SARS-CoV-2 infection mechanisms though, they are missing crucial components: immune cells and endothelial cells. This study aims to generate organoids with these components. We established vascular immune organoids from human pluripotent stem cells and examined the effect of SARS-CoV-2 infection. We demonstrated that infections activated inflammatory macrophages. Notably, the upregulation of interferon signaling supports macrophages' role in cytokine release syndrome. We propose vascular immune organoids are a useful platform to model and discover factors that ameliorate SARS-CoV-2-mediated cytokine release syndrome.
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Affiliation(s)
- Chiu Wang Chau
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Alex To
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rex K H Au-Yeung
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yang Xiang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Degong Ruan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lanlan Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Hera Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Shihui Zhang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Man Ting Au
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | | | | | | | - Pentao Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Centre for Translational Stem Cell Biology, Sha Tin, Hong Kong
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Chunyi Wen
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.
| | - Ryohichi Sugimura
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
- Centre for Translational Stem Cell Biology, Sha Tin, Hong Kong.
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21
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Upadhyay M, Nair D, Moseley GW, Srivastava S, Kondabagil K. Giant Virus Global Proteomics Innovation: Comparative Evaluation of In-Gel and In-Solution Digestion Methods. OMICS 2024. [PMID: 38621149 DOI: 10.1089/omi.2024.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
With their unusually large genome and particle sizes, giant viruses (GVs) defy the conventional definition of viruses. Although most GVs isolated infect unicellular protozoans, such as amoeba, studies in the last decade have established their much wider prevalence infecting most eukaryotic supergroups and some giant viral families with the potential to be human pathogens. Their complexity, almost autonomous life cycle, and enigmatic evolution necessitate the study of GVs. The accurate assessment of GV proteome is a veritable challenge. We have compared the coverage of global protein identification using different methods for GVs isolated in Mumbai, Mimivirus Bombay (MVB), Powai Lake Megavirus (PLMV), and Kurlavirus (KV), along with two previously studied GVs, Acanthamoeba polyphaga Mimivirus (APMV) and Marseillevirus (MV). Our study shows that the simultaneous use of in-gel and in-solution digestion methods can significantly increase the coverage of protein identification in the global proteome analysis of purified GV particles. Combining the two methods of analyses, we identified an additional 72 proteins in APMV and 114 in MV compared with what have been previously reported. Similarly, proteomes of MVB, PLMV, and KV were analyzed, and a total of 242 proteins in MVB, 287 proteins in PLMV, and 174 proteins in KV were identified. Our results suggest that a combined methodology of in-gel and in-solution methods is more efficient and opens up new avenues for innovation in global proteome analysis of GVs. Future planetary health research on GVs can benefit from consideration of a broader range of proteomics methodologies as illustrated by the present study.
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Affiliation(s)
- Monica Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Gregory W Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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22
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Jain S, Uritskiy G, Mahalingam M, Batra H, Chand S, Trinh HV, Beck C, Shin WH, Alsalmi W, Kijak G, Eller LA, Kim J, Kihara D, Tovanabutra S, Ferrari G, Robb ML, Rao M, Rao VB. A remarkable genetic shift in a transmitted/founder virus broadens antibody responses against HIV-1. eLife 2024; 13:RP92379. [PMID: 38619110 PMCID: PMC11018346 DOI: 10.7554/elife.92379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Abstract
A productive HIV-1 infection in humans is often established by transmission and propagation of a single transmitted/founder (T/F) virus, which then evolves into a complex mixture of variants during the lifetime of infection. An effective HIV-1 vaccine should elicit broad immune responses in order to block the entry of diverse T/F viruses. Currently, no such vaccine exists. An in-depth study of escape variants emerging under host immune pressure during very early stages of infection might provide insights into such a HIV-1 vaccine design. Here, in a rare longitudinal study involving HIV-1 infected individuals just days after infection in the absence of antiretroviral therapy, we discovered a remarkable genetic shift that resulted in near complete disappearance of the original T/F virus and appearance of a variant with H173Y mutation in the variable V2 domain of the HIV-1 envelope protein. This coincided with the disappearance of the first wave of strictly H173-specific antibodies and emergence of a second wave of Y173-specific antibodies with increased breadth. Structural analyses indicated conformational dynamism of the envelope protein which likely allowed selection of escape variants with a conformational switch in the V2 domain from an α-helix (H173) to a β-strand (Y173) and induction of broadly reactive antibody responses. This differential breadth due to a single mutational change was also recapitulated in a mouse model. Rationally designed combinatorial libraries containing 54 conformational variants of V2 domain around position 173 further demonstrated increased breadth of antibody responses elicited to diverse HIV-1 envelope proteins. These results offer new insights into designing broadly effective HIV-1 vaccines.
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Affiliation(s)
- Swati Jain
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Gherman Uritskiy
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Marthandan Mahalingam
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Himanshu Batra
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Subhash Chand
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Hung V Trinh
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Charles Beck
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Woong-Hee Shin
- Department of Biological Sciences, Purdue UniversityWest LafayetteUnited States
- Department of Chemistry Education, Sunchon National UniversitySuncheonRepublic of Korea
- Department of Advanced Components and Materials Engineering, Sunchon National UniversitySuncheonRepublic of Korea
| | - Wadad Alsalmi
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
| | - Gustavo Kijak
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Leigh A Eller
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
| | - Jerome Kim
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue UniversityWest LafayetteUnited States
- Department of Computer Science, Purdue UniversityWest LafayetteUnited States
| | - Sodsai Tovanabutra
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Guido Ferrari
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Merlin L Robb
- Henry M. Jackson Foundation for the Advancement of Military MedicineBethesdaUnited States
| | - Mangala Rao
- Laboratory of Adjuvant and Antigen Research, U.S. Military HIV Research Program, Walter Reed Army Institute of ResearchSilver SpringUnited States
| | - Venigalla B Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of AmericaWashingtonUnited States
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23
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Liu H, Wang S, Chen M, Ji H, Zhang D. Effects of Lactobacillus-fermented low-protein diets on the growth performance, nitrogen excretion, fecal microbiota and metabolomic profiles of finishing pigs. Sci Rep 2024; 14:8612. [PMID: 38616198 PMCID: PMC11016537 DOI: 10.1038/s41598-024-58832-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024] Open
Abstract
This study investigated the effects of Lactobacillus-fermented low-protein diet on the growth performance, nitrogen balance, fecal microbiota, and metabolomic profiles of finishing pigs. A total of 90 finishing pigs were assigned to one of three dietary treatments including a normal protein diet (CON) as well as two experimental diets in which a low-protein diet supplemented with 0 (LP) or 1% Lactobacillus-fermented low-protein feed (FLP). In comparison with CON, the LP and FLP significantly increased average daily gain (P = 0.044), significantly decreased feed to gain ratio (P = 0.021), fecal nitrogen (P < 0.01), urine nitrogen (P < 0.01), and total nitrogen (P < 0.01), respectively. The LP group exhibited increased abundances of unclassified_f_Selenomonadaceae, Coprococcus, Faecalibacterium, and Butyricicoccus, while the abundances of Verrucomicrobiae, Verrucomicrobiales, Akkermansiaceae, and Akkermansia were enriched in the FLP group. Low-protein diet-induced metabolic changes were enriched in sesquiterpenoid and triterpenoid biosynthesis and Lactobacillus-fermented low-protein feed-induced metabolic changes were enriched in phenylpropanoid biosynthesis and arginine biosynthesis. Overall, low-protein diet and Lactobacillus-fermented low-protein diet improved the growth performance and reduce nitrogen excretion, possibly via altering the fecal microbiota and metabolites in the finishing pigs. The present study provides novel ideas regarding the application of the low-protein diet and Lactobacillus-fermented low-protein diet in swine production.
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Affiliation(s)
- Hui Liu
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Sixin Wang
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Meixia Chen
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Haifeng Ji
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Dongyan Zhang
- Institute of Animal Science and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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24
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Jambhulkar PP, Singh B, Raja M, Ismaiel A, Lakshman DK, Tomar M, Sharma P. Genetic diversity and antagonistic properties of Trichoderma strains from the crop rhizospheres in southern Rajasthan, India. Sci Rep 2024; 14:8610. [PMID: 38616195 PMCID: PMC11016547 DOI: 10.1038/s41598-024-58302-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 03/27/2024] [Indexed: 04/16/2024] Open
Abstract
There are fewer studies on Trichoderma diversity in agricultural fields. The rhizosphere of 16 crops was analyzed for Trichoderma species in 7 districts of Rajasthan state of India. Based on DNA sequence of translation elongation factor 1α (tef-1α), and morphological characteristics, 60 isolates were identified as 11 species: Trichoderma brevicompactum, species in Harzianum clade identified as T. afroharzianum, T. inhamatum, T. lentiforme, T. camerunense, T. asperellum, T. asperelloides, T. erinaceum, T. atroviride, T. ghanense, and T. longibrachiatum. T. brevicompactum is the most commonly occurring strain followed by T. afroharzianum. No new species were described in this study. T. lentiforme, showed its first occurrence outside the South American continent. The morphological and cultural characteristics of the major species were observed, described, and illustrated in detail. The isolates were tested for their antagonistic effect against three soilborne plant pathogens fungi: Sclerotium rolfsii, Rhizoctonia solani, and Fusarium verticillioides in plate culture assays. One of the most potent strains was T. afroharzianum BThr29 having a maximum in vitro inhibition of S. rolfsii (76.6%), R. solani (84.8%), and F. verticillioides (85.7%). The potential strain T. afroharzianum BThr29 was also found to be efficient antagonists against soil borne pathogens in in vivo experiment. Such information on crop selectivity, antagonistic properties, and geographic distribution of Trichoderma species will be beneficial for developing efficient Trichoderma-based biocontrol agents.
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Affiliation(s)
- Prashant P Jambhulkar
- Department of Plant Pathology, College of Agriculture, Rani Lakshmi Bai Central Agricultural University (RLBCAU), Jhansi, Uttar Pradesh, 284003, India.
- Agricultural Research Station, Banswara, Rajasthan, 327001, India.
| | - Bhumica Singh
- Agricultural Research Station, Banswara, Rajasthan, 327001, India
| | - M Raja
- Department of Plant Pathology, Sri Karan Narendra Agriculture University, Jobner-Jaipur, Rajasthan, 303328, India
| | - Adnan Ismaiel
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Dilip K Lakshman
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
| | - Maharishi Tomar
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Pratibha Sharma
- Department of Plant Pathology, Sri Karan Narendra Agriculture University, Jobner-Jaipur, Rajasthan, 303328, India
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25
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Sijmons D, Collett S, Soliman C, Guy AJ, Scott AM, Durrant LG, Elbourne A, Walduck AK, Ramsland PA. Probing the expression and adhesion of glycans involved in Helicobacter pylori infection. Sci Rep 2024; 14:8587. [PMID: 38615147 PMCID: PMC11016089 DOI: 10.1038/s41598-024-59234-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/08/2024] [Indexed: 04/15/2024] Open
Abstract
Helicobacter pylori infects approximately half the human population and has an unusual infective niche of the human stomach. Helicobacter pylori is a major cause of gastritis and has been classified as a group 1 carcinogen by the WHO. Treatment involves triple or quadruple antibiotic therapy, but antibiotic resistance is becoming increasingly prevalent. Helicobacter pylori expresses certain blood group related antigens (Lewis system) as a part of its lipopolysaccharide (LPS), which is thought to assist in immune evasion. Additionally, H. pylori LPS participates in adhesion to host cells alongside several adhesion proteins. This study profiled the carbohydrates of H. pylori reference strains (SS1 and 26695) using monoclonal antibodies (mAbs) and lectins, identifying interactions between two carbohydrate-targeting mAbs and multiple lectins. Atomic force microscopy (AFM) scans were used to probe lectin and antibody interactions with the bacterial surfaces. The selected mAb and lectins displayed an increased adhesive force over the surface of the curved H. pylori rods. Furthermore, this study demonstrates the ability of anti-carbohydrate antibodies to reduce the adhesion of H. pylori 26695 to human gastric adenocarcinoma cells via AFM. Targeting bacterial carbohydrates to disrupt crucial adhesion and immune evasion mechanisms represents a promising strategy for combating H. pylori infection.
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Affiliation(s)
- Daniel Sijmons
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Simon Collett
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Caroline Soliman
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Andrew J Guy
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
- ZiP Diagnostics, Collingwood, VIC, 3066, Australia
| | - Andrew M Scott
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Melbourne, VIC, Australia
- Department of Molecular Imaging and Therapy, Austin Health and Faculty of Medicine, The University of Melbourne, Melbourne, VIC, Australia
| | - Lindy G Durrant
- Scancell Limited, University of Nottingham Biodiscovery Institute, Nottingham, UK
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Aaron Elbourne
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Anna K Walduck
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia.
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
| | - Paul A Ramsland
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia.
- Department of Immunology, Monash University, Melbourne, VIC, 3004, Australia.
- Department of Surgery, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia.
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26
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Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy M, Biswas S, Byrnes J, Kreitler DF, Cheng JF, Ghosh A, Almo SC, Iwai M, Niyogi KK, Pakrasi HB, Sarangi R, van Dam H, Yang L, Blaby IK, Blaby-Haas CE. A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nat Commun 2024; 15:3167. [PMID: 38609367 PMCID: PMC11014987 DOI: 10.1038/s41467-024-47486-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.
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Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA
| | - Macon Abernathy
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO, USA
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masakazu Iwai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hubertus van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ian K Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Mowery MA, Rosenwald LC, Chapman E, Lubin Y, Segoli M, Khoza T, Lyle R, White JA. Endosymbiont diversity across native and invasive brown widow spider populations. Sci Rep 2024; 14:8556. [PMID: 38609398 PMCID: PMC11014918 DOI: 10.1038/s41598-024-58723-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
The invasive brown widow spider, Latrodectus geometricus (Araneae: Theridiidae), has spread in multiple locations around the world and, along with it, brought associated organisms such as endosymbionts. We investigated endosymbiont diversity and prevalence across putative native and invasive populations of this spider, predicting lower endosymbiont diversity across the invasive range compared to the native range. First, we characterized the microbial community in the putative native (South Africa) and invasive (Israel and the United States) ranges via high throughput 16S sequencing of 103 adult females. All specimens were dominated by reads from only 1-3 amplicon sequence variants (ASV), and most individuals were infected with an apparently uniform strain of Rhabdochlamydia. We also found Rhabdochlamydia in spider eggs, indicating that it is a maternally-inherited endosymbiont. Relatively few other ASV were detected, but included two variant Rhabdochlamydia strains and several Wolbachia, Spiroplasma and Enterobacteriaceae strains. We then diagnostically screened 118 adult female spiders from native and invasive populations specifically for Rhabdochlamydia and Wolbachia. We found Rhabdochlamydia in 86% of individuals and represented in all populations, which suggests that it is a consistent and potentially important associate of L. geometricus. Wolbachia was found at lower overall prevalence (14%) and was represented in all countries, but not all populations. In addition, we found evidence for geographic variation in endosymbiont prevalence: spiders from Israel were more likely to carry Rhabdochlamydia than those from the US and South Africa, and Wolbachia was geographically clustered in both Israel and South Africa. Characterizing endosymbiont prevalence and diversity is a first step in understanding their function inside the host and may shed light on the process of spread and population variability in cosmopolitan invasive species.
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Affiliation(s)
- Monica A Mowery
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel.
- Department of Biology, York College, The City University of New York, Jamaica, NY, USA.
| | - Laura C Rosenwald
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Eric Chapman
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Yael Lubin
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Michal Segoli
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Thembile Khoza
- South African National Biodiversity Institute, Biosystematics Division, Pretoria, South Africa
| | - Robin Lyle
- Agricultural Research Council-Plant Health and Protection, Biosystematics Division, Queenswood, South Africa
| | - Jennifer A White
- Department of Entomology, University of Kentucky, Lexington, KY, USA
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Luong QXT, Hoang PT, Lee Y, Ayun RQ, Na K, Park S, Lin C, Ho PT, Lee TK, Lee S. An RNA-hydrolyzing recombinant minibody prevents both influenza A virus and coronavirus in co-infection models. Sci Rep 2024; 14:8472. [PMID: 38605110 PMCID: PMC11009316 DOI: 10.1038/s41598-024-52810-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/23/2024] [Indexed: 04/13/2024] Open
Abstract
With the lifting of COVID-19 non-pharmaceutical interventions, the resurgence of common viral respiratory infections was recorded in several countries worldwide. It facilitates viral co-infection, further burdens the already over-stretched healthcare systems. Racing to find co-infection-associated efficacy therapeutic agents need to be rapidly established. However, it has encountered numerous challenges that necessitate careful investigation. Here, we introduce a potential recombinant minibody-associated treatment, 3D8 single chain variable fragment (scFv), which has been developed as a broad-spectrum antiviral drug that acts via its nucleic acid catalytic and cell penetration abilities. In this research, we demonstrated that 3D8 scFv exerted antiviral activity simultaneously against both influenza A viruses (IAVs) and coronaviruses in three established co-infection models comprising two types of coronaviruses [beta coronavirus-human coronavirus OC43 (hCoV-OC43) and alpha coronavirus-porcine epidemic diarrhea virus (PEDV)] in Vero E6 cells, two IAVs [A/Puerto Rico/8/1934 H1N1 (H1N1/PR8) and A/X-31 (H3N2/X-31)] in MDCK cells, and a combination of coronavirus and IAV (hCoV-OC43 and adapted-H1N1) in Vero E6 cells by a statistically significant reduction in viral gene expression, proteins level, and approximately around 85%, 65%, and 80% of the progeny of 'hCoV-OC43-PEDV', 'H1N1/PR8-H3N2/X-31', and 'hCoV-OC43-adapted-H1N1', respectively, were decimated in the presence of 3D8 scFv. Taken together, we propose that 3D8 scFv is a promising broad-spectrum drug for treatment against RNA viruses in co-infection.
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Affiliation(s)
- Quynh Xuan Thi Luong
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Phuong Thi Hoang
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yongjun Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | | | - Kyungho Na
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seonhyeon Park
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chengmin Lin
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Phuong Thi Ho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea
| | - Taek-Kyun Lee
- Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje, 53201, Korea.
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, 16419, Korea.
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Eriksen C, Boustedt K, Sonne SB, Dahlgren J, Kristiansen K, Twetman S, Brix S, Roswall J. Early life factors and oral microbial signatures define the risk of caries in a Swedish cohort of preschool children. Sci Rep 2024; 14:8463. [PMID: 38605085 PMCID: PMC11009336 DOI: 10.1038/s41598-024-59126-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 04/08/2024] [Indexed: 04/13/2024] Open
Abstract
The oral cavity harbors complex communities comprising bacteria, archaea, fungi, protozoa, and viruses. The oral microbiota is establish at birth and develops further during childhood, with early life factors such as birth mode, feeding practices, and oral hygiene, reported to influence this development and the susceptibility to caries. We here analyzed the oral bacterial composition in saliva of 260 Swedish children at two, three and five years of age using 16S rRNA gene profiling to examine its relation to environmental factors and caries development at five years of age. We were able to assign the salivary bacterial community in each child at each time point to one of seven distinct clusters. We observed an individual dynamic in the development of the oral microbiota related to early life factors, such as being first born, born by C-section, maternal perinatal antibiotics use, with a distinct transition between three and five years of age. Different bacterial signatures depending on age were related to increased caries risk, while Peptococcus consistently linked to reduced risk of caries development.
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Affiliation(s)
- Carsten Eriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Katarina Boustedt
- Department of Paediatrics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Maxillofacial Unit, Halland Hospital, Halmstad, Sweden
| | - Si Brask Sonne
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jovanna Dahlgren
- Department of Paediatrics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Pediatrics, Queen Silvia Children's Hospital, Västra Götalandsregionen, Gothenburg, Sweden
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- BGI-Shenzhen, Shenzhen, 518083, China.
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, 266555, Shandong, China.
| | - Svante Twetman
- Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Josefine Roswall
- Department of Paediatrics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Department of Paediatrics, Halland Hospital, Halmstad, Sweden.
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30
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Jeffrey MP, Saleem L, MacPherson CW, Tompkins TA, Clarke ST, Green-Johnson JM. A Lacticaseibacillus rhamnosus secretome induces immunoregulatory transcriptional, functional and immunometabolic signatures in human THP-1 monocytes. Sci Rep 2024; 14:8379. [PMID: 38600116 PMCID: PMC11006683 DOI: 10.1038/s41598-024-56420-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
Macrophage responses to activation are fluid and dynamic in their ability to respond appropriately to challenges, a role integral to host defence. While bacteria can influence macrophage differentiation and polarization into pro-inflammatory and alternatively activated phenotypes through direct interactions, many questions surround indirect communication mechanisms mediated through secretomes derived from gut bacteria, such as lactobacilli. We examined effects of secretome-mediated conditioning on THP-1 human monocytes, focusing on the ability of the Lacticaseibacillus rhamnosus R0011 secretome (LrS) to drive macrophage differentiation and polarization and prime immune responses to subsequent challenge with lipopolysaccharide (LPS). Genome-wide transcriptional profiling revealed increased M2-associated gene transcription in response to LrS conditioning in THP-1 cells. Cytokine and chemokine profiling confirmed these results, indicating increased M2-associated chemokine and cytokine production (IL-1Ra, IL-10). These cells had increased cell-surface marker expression of CD11b, CD86, and CX3CR1, coupled with reduced expression of the M1 macrophage-associated marker CD64. Mitochondrial substrate utilization assays indicated diminished reliance on glycolytic substrates, coupled with increased utilization of citric acid cycle intermediates, characteristics of functional M2 activity. LPS challenge of LrS-conditioned THP-1s revealed heightened responsiveness, indicative of innate immune priming. Resting stage THP-1 macrophages co-conditioned with LrS and retinoic acid also displayed an immunoregulatory phenotype with expression of CD83, CD11c and CD103 and production of regulatory cytokines. Secretome-mediated conditioning of macrophages into an immunoregulatory phenotype is an uncharacterized and potentially important route through which lactic acid bacteria and the gut microbiota may train and shape innate immunity at the gut-mucosal interface.
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Affiliation(s)
- Michael P Jeffrey
- Applied Bioscience Graduate Program and the Faculty of Science, Ontario Tech University, Oshawa, ON, L1G 0C5, Canada
| | - Lin Saleem
- Applied Bioscience Graduate Program and the Faculty of Science, Ontario Tech University, Oshawa, ON, L1G 0C5, Canada
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, N1G 5C9, Canada
| | - Chad W MacPherson
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada
| | | | - Sandra T Clarke
- Applied Bioscience Graduate Program and the Faculty of Science, Ontario Tech University, Oshawa, ON, L1G 0C5, Canada
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, N1G 5C9, Canada
| | - Julia M Green-Johnson
- Applied Bioscience Graduate Program and the Faculty of Science, Ontario Tech University, Oshawa, ON, L1G 0C5, Canada.
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31
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Nouioura G, El Fadili M, El Barnossi A, Loukili EH, Laaroussi H, Bouhrim M, Giesy JP, Aboul-Soud MAM, Al-Sheikh YA, Lyoussi B, Derwich EH. Comprehensive analysis of different solvent extracts of Ferula communis L. fruit reveals phenolic compounds and their biological properties via in vitro and in silico assays. Sci Rep 2024; 14:8325. [PMID: 38594363 PMCID: PMC11004150 DOI: 10.1038/s41598-024-59087-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 04/07/2024] [Indexed: 04/11/2024] Open
Abstract
Although giant fennel is recognized as a "superfood" rich in phytochemicals with antioxidant activity, research into the antibacterial properties of its fruits has been relatively limited, compared to studies involving the root and aerial parts of the plant. In this study, seven solvents-acetone, methanol, ethanol, ethyl acetate, chloroform, water, and hexane-were used to extract the chemical constituents of the fruit of giant fennel (Ferula communis), a species of flowering plant in the carrot family Apiaceae. Specific attributes of these extracts were investigated using in silico simulations and in vitro bioassays. High-performance liquid chromatography equipped with a diode-array detector (HPLC-DAD) identified 15 compounds in giant fennel extract, with p-coumaric acid, 3-hydroxybenzoic acid, sinapic acid, and syringic acid being dominant. Among the solvents tested, ethanol demonstrated superior antioxidant activity and phenolic and flavonoid contents. F. communis extracts showed advanced inhibition of gram-negative pathogens (Escherichia coli and Proteus mirabilis) and variable antifungal activity against tested strains. Molecular docking simulations assessed the antioxidative, antibacterial, and antifungal properties of F. communis, facilitating innovative therapeutic development through predicted compound-protein interactions. In conclusion, the results validate the ethnomedicinal use and potential of F. communis. This highlights its significance in natural product research and ethnopharmacology.
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Affiliation(s)
- Ghizlane Nouioura
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, 30 000, Fez, Morocco.
| | - Mohamed El Fadili
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, 30 000 Fez, Morocco
| | - Azeddin El Barnossi
- Biological Engineering Laboratory, Faculty of Sciences and Techniques, Sultan Moulay Slimane University, Beni Mellal, Morocco
- Laboratory of Biotechnology, Environment, Agri-Food and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, 30050, Fez, Morocco
| | - El Hassania Loukili
- Euromed Research Center, Euromed Polytechnic School, Euromed University of Fes, 30 000, Fez, Morocco
| | - Hassan Laaroussi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, 30 000, Fez, Morocco
| | - Mohammed Bouhrim
- Laboratory of Biological Engineering, Team of Functional and Pathological Biology, University Sultan Moulay Slimane, 23000, Beni Mellal, Morocco
| | - John P Giesy
- Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
- Department of Integrative Biology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, 48895, USA
- Department of Environmental Science, Baylor University, Waco, TX, 76798, USA
| | - Mourad A M Aboul-Soud
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, 11433, Riyadh, Saudi Arabia
| | - Yazeed A Al-Sheikh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, 11433, Riyadh, Saudi Arabia
| | - Badiaa Lyoussi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, 30 000, Fez, Morocco
| | - El Houssine Derwich
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, 30 000, Fez, Morocco
- Unity of GC/MS and GC, City of Innovation, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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32
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Gäb F, Bierbaum G, Wirth R, Bultmann C, Palmer B, Janssen K, Karačić S. Enzymatic phosphatization of fish scales-a pathway for fish fossilization. Sci Rep 2024; 14:8347. [PMID: 38594297 PMCID: PMC11003971 DOI: 10.1038/s41598-024-59025-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024] Open
Abstract
Phosphatized fish fossils occur in various locations worldwide. Although these fossils have been intensively studied over the past decades they remain a matter of ongoing research. The mechanism of the permineralization reaction itself remains still debated in the community. The mineralization in apatite of a whole fish requires a substantial amount of phosphate which is scarce in seawater, so the origin of the excess is unknown. Previous research has shown that alkaline phosphatase, a ubiquitous enzyme, can increase the phosphate content in vitro in a medium to the degree of saturation concerning apatite. We applied this principle to an experimental setup where fish scales were exposed to commercial bovine alkaline phosphatase. We analyzed the samples with SEM and TEM and found that apatite crystals had formed on the remaining soft tissue. A comparison of these newly formed apatite crystals with fish fossils from the Solnhofen and Santana fossil deposits showed striking similarities. Both are made up of almost identically sized and shaped nano-apatites. This suggests a common formation process: the spontaneous precipitation from an oversaturated solution. The excess activity of alkaline phosphatase could explain that effect. Therefore, our findings could provide insight into the formation of well-preserved fossils.
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Affiliation(s)
- Fabian Gäb
- Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Richard Wirth
- Deutsches GeoForschungsZentrum (GFZ), Section 3.5 Interface Geochemistry, Potsdam, Germany
| | - Christoph Bultmann
- Radiomed Group Practice for Radiology and Nuclear Medicine, Wiesbaden, Germany
| | - Brianne Palmer
- Bonn Institute of Organismic Biology, Division of Palaeontology, University of Bonn, Bonn, Germany
| | - Kathrin Janssen
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Sabina Karačić
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany.
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Ferrari L, Ruggiero A, Stefani C, Benedetti L, Piermatteo L, Andreassi E, Caldara F, Zace D, Pagliari M, Ceccherini-Silberstein F, Jones C, Iannetta M, Geretti AM. Utility of accessible SARS-CoV-2 specific immunoassays in vaccinated adults with a history of advanced HIV infection. Sci Rep 2024; 14:8337. [PMID: 38594459 PMCID: PMC11003986 DOI: 10.1038/s41598-024-58597-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/01/2024] [Indexed: 04/11/2024] Open
Abstract
Accessible SARS-CoV-2-specific immunoassays may inform clinical management in people with HIV, particularly in case of persisting immunodysfunction. We prospectively studied their application in vaccine recipients with HIV, purposely including participants with a history of advanced HIV infection. Participants received one (n = 250), two (n = 249) or three (n = 42) doses of the BNT162b2 vaccine. Adverse events were documented through questionnaires. Sample collection occurred pre-vaccination and a median of 4 weeks post-second dose and 14 weeks post-third dose. Anti-spike and anti-nucleocapsid antibodies were measured with the Roche Elecsys chemiluminescence immunoassays. Neutralising activity was evaluated using the GenScript cPass surrogate virus neutralisation test, following validation against a Plaque Reduction Neutralization Test. T-cell reactivity was assessed with the Roche SARS-CoV-2 IFNγ release assay. Primary vaccination (2 doses) was well tolerated and elicited measurable anti-spike antibodies in 202/206 (98.0%) participants. Anti-spike titres varied widely, influenced by previous SARS-CoV-2 exposure, ethnicity, intravenous drug use, CD4 counts and HIV viremia as independent predictors. A third vaccine dose significantly boosted anti-spike and neutralising responses, reducing variability. Anti-spike titres > 15 U/mL correlated with neutralising activity in 136/144 paired samples (94.4%). Three participants with detectable anti-S antibodies did not develop cPass neutralising responses post-third dose, yet displayed SARS-CoV-2 specific IFNγ responses. SARS-CoV-2 vaccination is well-tolerated and immunogenic in adults with HIV, with responses improving post-third dose. Anti-spike antibodies serve as a reliable indicator of neutralising activity. Discordances between anti-spike and neutralising responses were accompanied by detectable IFN-γ responses, underlining the complexity of the immune response in this population.
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Affiliation(s)
- Ludovica Ferrari
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Department of Infectious Diseases, Fondazione PTV, University of Rome Tor Vergata, Viale Oxford 81, 00133, Rome, Italy
| | - Alessandra Ruggiero
- Department of Neurosciences, Biomedicine and Movement Sciences, School of Medicine, University of Verona, Verona, Italy
| | - Chiara Stefani
- Department of Neurosciences, Biomedicine and Movement Sciences, School of Medicine, University of Verona, Verona, Italy
| | - Livia Benedetti
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Eleonora Andreassi
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Federica Caldara
- Department of Infectious Diseases, Fondazione PTV, University of Rome Tor Vergata, Viale Oxford 81, 00133, Rome, Italy
| | - Drieda Zace
- Department of Infectious Diseases, Fondazione PTV, University of Rome Tor Vergata, Viale Oxford 81, 00133, Rome, Italy
| | - Matteo Pagliari
- Laboratory of Experimental Animal Models, Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, Italy
| | | | - Christopher Jones
- Department of Primary Care and Public Health, Brighton and Sussex Medical School, Falmer, UK
| | - Marco Iannetta
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Department of Infectious Diseases, Fondazione PTV, University of Rome Tor Vergata, Viale Oxford 81, 00133, Rome, Italy
| | - Anna Maria Geretti
- Department of Infectious Diseases, Fondazione PTV, University of Rome Tor Vergata, Viale Oxford 81, 00133, Rome, Italy.
- Department of Infection, North Middlesex University Hospital, London, UK.
- School of Immunity & Microbial Sciences, King's College London, London, UK.
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Lateef AA, Azeez AA, Ren W, Hamisu HS, Oke OA, Asiegbu FO. Bacterial biota associated with the invasive insect pest Tuta absoluta (Meyrick). Sci Rep 2024; 14:8268. [PMID: 38594362 PMCID: PMC11003966 DOI: 10.1038/s41598-024-58753-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Tuta absoluta (the tomato pinworm) is an invasive insect pest with a highly damaging effect on tomatoes causing between 80 and 100% yield losses if left uncontrolled. Resistance to chemical pesticides have been reported in some T. absoluta populations. Insect microbiome plays an important role in the behavior, physiology, and survivability of their host. In a bid to explore and develop an alternative control method, the associated microbiome of this insect was studied. In this study, we unraveled the bacterial biota of T. absoluta larvae and adults by sequencing and analyzing the 16S rRNA V3-V4 gene regions using Illumina NovaSeq PE250. Out of 2,092,015 amplicon sequence variants (ASVs) recovered from 30 samples (15 larvae and 15 adults), 1,268,810 and 823,205 ASVs were obtained from the larvae and adults, respectively. A total of 433 bacterial genera were shared between the adults and larval samples while 264 and 139 genera were unique to the larvae and adults, respectively. Amplicon metagenomic analyses of the sequences showed the dominance of the phylum Proteobacteria in the adult samples while Firmicutes and Proteobacteria dominated in the larval samples. Linear discriminant analysis effect size (LEfSe) comparison revealed the genera Pseudomonas, Delftia and Ralstonia to be differentially enriched in the adult samples while Enterococcus, Enterobacter, Lactococcus, Klebsiella and Wiessella were differentially abundant in the larvae. The diversity indices showed that the bacterial communities were not different between the insect samples collected from different geographical regions. However, the bacterial communities significantly differed based on the sample type between larvae and adults. A co-occurrence network of significantly correlated taxa revealed a strong interaction between the microbial communities. The functional analysis of the microbiome using FAPROTAX showed that denitrification, arsenite oxidation, methylotrophy and methanotrophy as the active functional groups of the adult and larvae microbiomes. Our results have revealed the core taxonomic, functional, and interacting microbiota of T. absoluta and these indicate that the larvae and adults harbor a similar but transitory set of bacteria. The results provide a novel insight and a basis for exploring microbiome-based biocontrol strategy for this invasive insect pest as well as the ecological significance of some of the identified microbiota is discussed.
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Affiliation(s)
- A A Lateef
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland.
- Department of Plant Biology, University of Ilorin, Kwara State, Ilorin, Nigeria.
| | - A A Azeez
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Rainforest Research Station, Forestry Research Institute of Nigeria, Jericho Hill, Ibadan, Nigeria
| | - W Ren
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - H S Hamisu
- National Horticultural Research Institute, Ibadan, Nigeria
| | - O A Oke
- National Horticultural Research Institute, Ibadan, Nigeria
| | - F O Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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Poulsen CS, Hesse D, Fernandes GR, Hansen TH, Kern T, Linneberg A, Van Espen L, Jørgensen T, Nielsen T, Alibegovic AC, Matthijnssens J, Pedersen O, Vestergaard H, Hansen T, Andersen MK. Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults. Sci Rep 2024; 14:8315. [PMID: 38594375 PMCID: PMC11003976 DOI: 10.1038/s41598-024-58985-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/05/2024] [Indexed: 04/11/2024] Open
Abstract
Latent autoimmune diabetes in adults (LADA) is a heterogeneous disease characterized by autoantibodies against insulin producing pancreatic beta cells and initial lack of need for insulin treatment. The aim of the present study was to investigate if individuals with LADA have an altered gut microbiota relative to non-diabetic control subjects, individuals with type 1 diabetes (T1D), and individuals with type 2 diabetes (T2D). Bacterial community profiling was performed with primers targeting the variable region 4 of the 16S rRNA gene and sequenced. Amplicon sequence variants (ASVs) were generated with DADA2 and annotated to the SILVA database. The gut virome was sequenced, using a viral particle enrichment and metagenomics approach, assembled, and quantified to describe the composition of the viral community. Comparison of the bacterial alpha- and beta-diversity measures revealed that the gut bacteriome of individuals with LADA resembled that of individuals with T2D. Yet, specific genera were found to differ in abundance in individuals with LADA compared with T1D and T2D, indicating that LADA has unique taxonomical features. The virome composition reflected the stability of the most dominant order Caudovirales and the families Siphoviridae, Podoviridae, and Inoviridae, and the dominant family Microviridae. Further studies are needed to confirm these findings.
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Affiliation(s)
- Casper S Poulsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dan Hesse
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Novo Nordisk A/S, Soeborg, Denmark
| | - Gabriel R Fernandes
- Biosystems Informatics, Institute René Rachou-Fiocruz Minas, Belo Horizonte, Brazil
| | - Tue H Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Timo Kern
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical Microbiomics A/S, Copenhagen, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lore Van Espen
- Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Clinical & Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Amra C Alibegovic
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Novo Nordisk A/S, Soeborg, Denmark
| | - Jelle Matthijnssens
- Department of Microbiology, Immunology & Transplantation, Rega Institute, Laboratory of Clinical & Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Clinical Metabolic Research, Department of Medicine, Gentofte University Hospital, Copenhagen, Denmark
| | - Henrik Vestergaard
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Medicine, Bornholms Hospital, Rønne, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Mette K Andersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Kwiatkowska M, Gołębiewski M, Sikora M, Rycharska EŁ, Krogulska A. The oral cavity and intestinal microbiome in children with functional constipation. Sci Rep 2024; 14:8283. [PMID: 38594374 PMCID: PMC11004141 DOI: 10.1038/s41598-024-58642-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/01/2024] [Indexed: 04/11/2024] Open
Abstract
Constipation is a widespread problem in paediatric practice, affecting almost 30% of children. One of the key causal factors of constipation may be disturbances in the homeostasis of the gastrointestinal microbiome. The aim of the study was to determine whether the oral and fecal microbiomes differ between children with and without constipation. A total of 91 children over three years of age were included in the study. Of these, 57 were qualified to a group with constipation, and 34 to a group without. The saliva and stool microbiomes were evaluated using 16S rRNA gene amplicon sequencing. Functional constipation was associated with characteristic bacterial taxa in the fecal microbiota. Statistically significant differences were found at the family level: Burkholderiaceae (q = 0.047), Christensenellaceae (q = 0.047), Chlostridiaceae (q = 0.047) were significantly less abundant in the constipation group, while the Tannerellaceae (q = 0.007) were more abundant. At the genus level, the significant differences were observed for rare genera, including Christensenellaceae r-7 (q = 2.88 × 10-2), Fusicatenibacter (q = 2.88 × 10-2), Parabacteroides (q = 1.63 × 10-2), Romboutsia (q = 3.19 × 10-2) and Subdoligranulum (q = 1.17 × 10-2). All of them were less abundant in children with constipation. With the exception of significant taxonomic changes affecting only feces, no differences were found in the alpha and beta diversity of feces and saliva. Children with functional constipation demonstrated significant differences in the abundance of specific bacteria in the stool microbiome compared to healthy children. It is possible that the rare genera identified in our study which were less abundant in the constipated patients (Christensellaceae r-7, Fusicatenibacter, Parabacteroides, Romboutsia and Subdoligranulum) may play a role in protection against constipation. No significant differences were observed between the two groups with regard to the saliva microbiome.
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Affiliation(s)
- Monika Kwiatkowska
- Department of Paediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100, Torun, Poland.
- , Bydgoszcz, Poland.
| | - Marcin Gołębiewski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, 87-100, Torun, Poland
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100, Torun, Poland
| | - Marcin Sikora
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 87-100, Torun, Poland
| | - Ewa Łoś Rycharska
- Department of Paediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100, Torun, Poland
| | - Aneta Krogulska
- Department of Paediatrics, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100, Torun, Poland
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Boon M, Buntic I, Ahmed K, Dopffel N, Peters C, Hajibeygi H. Microbial induced wettability alteration with implications for Underground Hydrogen Storage. Sci Rep 2024; 14:8248. [PMID: 38589617 PMCID: PMC11001864 DOI: 10.1038/s41598-024-58951-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/04/2024] [Indexed: 04/10/2024] Open
Abstract
Characterization of the microbial activity impacts on transport and storage of hydrogen is a crucial aspect of successful Underground Hydrogen Storage (UHS). Microbes can use hydrogen for their metabolism, which can then lead to formation of biofilms. Biofilms can potentially alter the wettability of the system and, consequently, impact the flow dynamics and trapping mechanisms in the reservoir. In this study, we investigate the impact of microbial activity on wettability of the hydrogen/brine/rock system, using the captive-bubble cell experimental approach. Apparent contact angles are measured for bubbles of pure hydrogen in contact with a solid surface inside a cell filled with living brine which contains sulphate reducing microbes. To investigate the impact of surface roughness, two different solid samples are used: a "rough" Bentheimer Sandstone sample and a "smooth" pure Quartz sample. It is found that, in systems where buoyancy and interfacial forces are the main acting forces, the impact of biofilm formation on the apparent contact angle highly depends on the surface roughness. For the "rough" Bentheimer sandstone, the apparent contact angle was unchanged by biofilm formation, while for the smooth pure Quartz sample the apparent contact angle decreased significantly, making the system more water-wet. This decrease in apparent contact angle is in contrast with an earlier study present in the literature where a significant increase in contact angle due to microbial activity was reported. The wettability of the biofilm is mainly determined by the consistency of the Extracellular Polymeric Substances (EPS) which depends on the growth conditions in the system. Therefore, to determine the impact of microbial activity on the wettability during UHS will require accurate replication of the reservoir conditions including surface roughness, chemical composition of the brine, the microbial community, as well as temperature, pressure and pH-value conditions.
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Affiliation(s)
- Maartje Boon
- Delft University of Technology, Faculty of Civil Engineering and Geosciences, 2600, Delft, GA, The Netherlands.
- University of Stuttgart, Institute of Applied Mechanics, Stuttgart, 70569, Germany.
| | - Ivan Buntic
- University of Stuttgart, Department of Hydromechanics and Modelling of Hydrosystems, 70569, Stuttgart, Germany
| | - Kadir Ahmed
- Delft University of Technology, Faculty of Civil Engineering and Geosciences, 2600, Delft, GA, The Netherlands
| | - Nicole Dopffel
- NORCE Norwegian Research Centre AS, 5008, Bergen, Norway
| | - Catherine Peters
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey, USA
| | - Hadi Hajibeygi
- Delft University of Technology, Faculty of Civil Engineering and Geosciences, 2600, Delft, GA, The Netherlands
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38
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Wei N, Ju M, Su X, Zhang Y, Huang Y, Rao X, Cui L, Lin Z, Dong Y. Transplantation of gut microbiota derived from patients with schizophrenia induces schizophrenia-like behaviors and dysregulated brain transcript response in mice. Schizophrenia (Heidelb) 2024; 10:44. [PMID: 38589422 PMCID: PMC11001608 DOI: 10.1038/s41537-024-00460-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/06/2024] [Indexed: 04/10/2024]
Abstract
Schizophrenia (SCZ), as a neurodevelopmental disorder and devastating disease, affects approximately 1% of the world population. Although numerous studies have attempted to elucidate the causes of SCZ occurrence, it is not clearly understood. Recently, the emerging roles of the gut microbiota in a range of brain disorders, including SCZ, have attracted much attention. While the molecular mechanism of gut microbiota in regulating the pathogenesis of SCZ is still lacking. Here, we first confirmed the difference of gut microbiome between SCZ patients and healthy controls, and then, we performed fecal microbiota transplantation (FMT) to clarify the roles of SCZ patients-derived microbiota in a specific pathogen free (SPF) mice model. 16 S rDNA sequencing confirmed that a significant difference of gut microbiome was present between two groups of FMT mice, which has a similar trend with the above human gut microbiome. Furthermore, we found that transplantation of fecal microbiota from SCZ patients into SPF mice was sufficient to induce schizophrenia-like (SCZ-like) symptoms, such as deficits in sociability and hyperactivity. Furthermore, the brains of mice colonized with SCZ microbiota displayed dysregulated transcript response and alternative splicing of SCZ-relevant genes. Moreover, 10 key genes were identified to be correlated with SCZ by an integrative transcriptome data analysis. Finally, 4 key genes were identified to be correlated with the 12 differential genera between two groups of FMT mice. Our results thus demonstrated that the gut microbiome might modify the transcriptomic profile in the brain, thereby modulating social behavior, and our present study can help better understand the link between gut microbiota and SCZ pathogenesis through the gut-brain axis.
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Affiliation(s)
- Nana Wei
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, 200241, Shanghai, China
| | - Mingliang Ju
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, 200030, Shanghai, China
| | - Xichen Su
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Yan Zhang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, 200241, Shanghai, China
| | - Yonghe Huang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, 200241, Shanghai, China
| | - Xinyue Rao
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Li Cui
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China.
| | - Zhibing Lin
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China.
| | - Yi Dong
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, 200241, Shanghai, China.
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39
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Uchendu CG, Guan Z, Klein EA. Spatial organization of bacterial sphingolipid synthesis enzymes. J Biol Chem 2024:107276. [PMID: 38588805 DOI: 10.1016/j.jbc.2024.107276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/16/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024] Open
Abstract
Sphingolipids are produced by nearly all eukaryotes where they play significant roles in cellular processes such as cell growth, division, programmed cell death, angiogenesis, and inflammation. While it was previously believed that sphingolipids were quite rare among bacteria, bioinformatic analysis of the recently identified bacterial sphingolipid synthesis genes suggests that these lipids are likely to be produced by a wide range of microbial species. The sphingolipid synthesis pathway consists of three critical enzymes. Serine palmitoyltransferase catalyzes the condensation of serine with palmitoyl-CoA (or palmitoyl-acyl carrier protein), ceramide synthase adds the second acyl chain, and a reductase reduces the ketone present on the long-chain base. While there is general agreement regarding the identity of these bacterial enzymes, the precise mechanism and order of chemical reactions for microbial sphingolipid synthesis is more ambiguous. Two mechanisms have been proposed. First, the synthesis pathway may follow the well characterized eukaryotic pathway in which the long-chain base is reduced prior to the addition of the second acyl chain. Alternatively, our previous work suggests that addition of the second acyl chain precedes the reduction of the long-chain base. To distinguish between these two models, we investigated the subcellular localization of these three key enzymes. We found that serine palmitoyltransferase and ceramide synthase are localized to the cytoplasm whereas the ceramide reductase is in the periplasmic space. This is consistent with our previously proposed model wherein the second acyl chain is added in the cytoplasm prior to export to the periplasm where the lipid molecule is reduced.
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Affiliation(s)
- Chioma G Uchendu
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Eric A Klein
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA; Biology Department, Rutgers University-Camden, Camden, NJ 08102, USA; Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA.
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de Moraes Pires WM, Cruz ACR, de Souza AJS, Silva SP, Souza Barbosa Coelho TF, Dias DD, Rosa Júnior JW, Mendes SB, da Costa Fraga E, Barros MC, Sampaio I. Genomic characterization of a novel Hepatovirus identified in Maranhão state, Brazil. Sci Rep 2024; 14:7981. [PMID: 38575654 PMCID: PMC10995186 DOI: 10.1038/s41598-024-58171-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bats are efficient reservoirs of a number of viruses with zoonotic potential, and are involved directly in the transmission cycle of many zoonoses. In the present study, which is part of a larger project that is documenting the viromes of the bat species found in the Mid-North states of Maranhão and Piauí, we analyzed 16 pooled samples obtained from four species of bat of the genus Artibeus-Artibeus obscurus, Artibeus cinereus, Artibeus lituratus and Artibeus planirostris. We describe and identify a Hepatovirus, denominated Hepatovirus H isolate sotense, which was found in a pool of internal organs (liver and lungs) extracted from a specimen of A. planirostris, a frugivorous bat, collected in the Cerrado biome of Maranhão state. This material was analyzed using new generation sequencing, which produced a contig of 7390 nucleotides and presented a degree of identity with a number of existing Hepatovirus sequences available for bats (amino acid identity of 61.5% with Bat hepatovirus C of Miniopterus cf. manavi, 66.6% with Bat hepatovirus G of Coleura afra, 67.4% with Hepatovirus G2 of Rhinolophus landeri, and 75.3% with Hepatovirus H2 of Rhinolophus landeri). The analysis of the functional domains of this contig confirmed a pattern consistent with the characteristics of the genus Hepatovirus (Picornaviridae). In the phylogenetic tree with several other Hepatovirus species, this genome also grouped in a monophyletic clade with Hepatovirus H (HepV-H1; HepV-H2, and HepV-H3) albeit on an external branch, which suggests that it may be a distinct genotype within this species. This is the first isolate of Hepatovirus H identified in bats from South America, and represents an important discovery, given that most studies of viruses associated with bats in the state of Maranhão have focused on the family Rhabdoviridae.
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Affiliation(s)
| | - Ana Cecília Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - Alex Junior Souza de Souza
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, Brazil
| | - Sandro Patroca Silva
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | | | - Daniel Damous Dias
- Laboratory of Medical Entomology, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - José Wilson Rosa Júnior
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - Samira Brito Mendes
- Graduate Program in Biodiversity and Biotechnology-Bionorte Network, Laboratory of Genetics and Molecular Biology, Universidade Estadual do Maranhão, São Luís, Maranhão, 65055-310, Brazil
| | - Elmary da Costa Fraga
- Laboratory of Genetics and Molecular Biology-GENBIMOL, Universidade Estadual Do Maranhão-Campus Caxias, Caxias, Maranhão, 65604-380, Brazil
| | - Maria Claudene Barros
- Laboratory of Genetics and Molecular Biology-GENBIMOL, Universidade Estadual Do Maranhão-Campus Caxias, Caxias, Maranhão, 65604-380, Brazil
| | - Iracilda Sampaio
- Laboratory of Evolution, Institute of Coastal Studies, Universidade Federal do Pará-UFPA-UFPA, Bragança, Pará, 68600-000, Brazil
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41
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Santangelo BE, Apgar M, Colorado ASB, Martin CG, Sterrett J, Wall E, Joachimiak MP, Hunter LE, Lozupone CA. Integrating biological knowledge for mechanistic inference in the host-associated microbiome. Front Microbiol 2024; 15:1351678. [PMID: 38638909 PMCID: PMC11024261 DOI: 10.3389/fmicb.2024.1351678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 04/20/2024] Open
Abstract
Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.
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Affiliation(s)
- Brook E. Santangelo
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Madison Apgar
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | | | - Casey G. Martin
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - John Sterrett
- Department of Integrative Physiology, University of Colorado, Boulder, CO, United States
| | - Elena Wall
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Marcin P. Joachimiak
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Biosystems Data Science Department, Berkeley, CA, United States
| | - Lawrence E. Hunter
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, United States
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Abate A, Munshea A, Nibret E, Alemayehu DH, Alemu A, Abdissa A, Mihret A, Abebe M, Mulu A. Characterization of human papillomavirus genotypes and their coverage in vaccine delivered to Ethiopian women. Sci Rep 2024; 14:7976. [PMID: 38575600 PMCID: PMC10995144 DOI: 10.1038/s41598-024-57085-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024] Open
Abstract
Cervical cancer is a significant public health concern in Ethiopia. It is mainly caused by persistent infection with the human papillomaviruses. The aim of this study was to assess the relationship between carcinogenic risk of probable, possible and low risk HPV infection and those of cervical intraepithelial neoplasia (CIN) and cervical cancer. A cross sectional study nested from prospective cohort study was conducted in Bahir Dar, northwest Ethiopia. Statistical analyses were performed using SPSSversion 26.0. HPV-16 was associated with a relatively higher risk of CIN II+, (AOR = 15.42; 95% CI 6.81-34.91). In addition, HPV-52, -18, -53 and -58, were significantly associated with an increased risk of CIN II+, (AOR = 7.38 (1.73-31.54), 5.42 (1.61-18.31), 4.08 (1.53-10.87), and 3.17 (1.00-10.03)), respectively. The current study shows high rate of HPV with predominance of HPV-16, -53, -58, -18, -35, and -52. The quadrivalent and nonavalent vaccine had only covered 27.1% and 45% of the circulating HPV genotypes. Ethiopia may need to consider introduction of nonavalent vaccine into the national public health strategy. Polyvalent vaccine which includes the genotypes not covered by existing approved vaccines should be considered.
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Affiliation(s)
- Alemayehu Abate
- Department of Health Biotechnology, Institute of Biotechnology, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia.
- Amhara Public Health Institute, Bahir Dar, Ethiopia.
| | - Abaineh Munshea
- Department of Health Biotechnology, Institute of Biotechnology, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia
- Department of Biology, College of Science, Bahir Dar University, P. O Box 79, Bahir Dar, Ethiopia
| | - Endalkachew Nibret
- Department of Health Biotechnology, Institute of Biotechnology, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia
- Department of Biology, College of Science, Bahir Dar University, P. O Box 79, Bahir Dar, Ethiopia
| | | | - Ashenafi Alemu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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Duveau F, Cordier C, Chiron L, Le Bec M, Pouzet S, Séguin J, Llamosi A, Sorre B, Di Meglio JM, Hersen P. Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability. eLife 2024; 12:RP88750. [PMID: 38568203 PMCID: PMC10990491 DOI: 10.7554/elife.88750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival, and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer, and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.
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Affiliation(s)
- Fabien Duveau
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364LyonFrance
| | - Céline Cordier
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Lionel Chiron
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Matthias Le Bec
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Sylvain Pouzet
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Julie Séguin
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Artémis Llamosi
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Benoit Sorre
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
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Stone JK, von Muhlinen N, Zhang C, Robles AI, Flis AL, Vega-Valle E, Miyanaga A, Matsumoto M, Greathouse KL, Cooks T, Trinchieri G, Harris CC. Acidovorax temperans skews neutrophil maturation and polarizes Th17 cells to promote lung adenocarcinoma development. Oncogenesis 2024; 13:13. [PMID: 38570533 PMCID: PMC10991269 DOI: 10.1038/s41389-024-00513-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
Change within the intratumoral microbiome is a common feature in lung and other cancers and may influence inflammation and immunity in the tumor microenvironment, affecting growth and metastases. We previously characterized the lung cancer microbiome in patients and identified Acidovorax temperans as enriched in tumors. Here, we instilled A. temperans in an animal model driven by mutant K-ras and Tp53. This revealed A. temperans accelerates tumor development and burden through infiltration of proinflammatory cells. Neutrophils exposed to A. temperans displayed a mature, pro-tumorigenic phenotype with increased cytokine signaling, with a global shift away from IL-1β signaling. Neutrophil to monocyte and macrophage signaling upregulated MHC II to activate CD4+ T cells, polarizing them to an IL-17A+ phenotype detectable in CD4+ and γδ populations (T17). These T17 cells shared a common gene expression program predictive of poor survival in human LUAD. These data indicate bacterial exposure promotes tumor growth by modulating inflammation.
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Affiliation(s)
- Joshua K Stone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Natalia von Muhlinen
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Chenran Zhang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Amy L Flis
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Eleazar Vega-Valle
- Laboratory Animal Science Program, Laboratory of Human Carcinogenesis, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Akihiko Miyanaga
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Masaru Matsumoto
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - K Leigh Greathouse
- Human Science and Design, Robbins College of Health and Human Sciences, Baylor University, Waco, TX, 76798, USA
| | - Tomer Cooks
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.
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Rybina AA, Glushak RA, Bessonova TA, Dakhnovets AI, Rudenko AY, Ozhiganov RM, Kaznadzey AD, Tutukina MN, Gelfand MS. Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli. Sci Rep 2024; 14:7852. [PMID: 38570624 PMCID: PMC10991401 DOI: 10.1038/s41598-024-58492-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/29/2024] [Indexed: 04/05/2024] Open
Abstract
CsqR (YihW) is a local transcription factor that controls expression of yih genes involved in degradation of sulfoquinovose in Escherichia coli. We recently showed that expression of the respective gene cassette might be regulated by lactose. Here, we explore the phylogenetic and functional traits of CsqR. Phylogenetic analysis revealed that CsqR had a conserved Met25. Western blot demonstrated that CsqR was synthesized in the bacterial cell as two protein forms, 28.5 (CsqR-l) and 26 kDa (CsqR-s), the latter corresponding to start of translation at Met25. CsqR-s was dramatically activated during growth with sulfoquinovose as a sole carbon source, and displaced CsqR-l in the stationary phase during growth on rich medium. Molecular dynamic simulations revealed two possible states of the CsqR-s structure, with the interdomain linker being represented by either a disordered loop or an ɑ-helix. This helix allowed the hinge-like motion of the N-terminal domain resulting in a switch of CsqR-s between two conformational states, "open" and "compact". We then modeled the interaction of both CsqR forms with putative effectors sulfoquinovose, sulforhamnose, sulfoquinovosyl glycerol, and lactose, and revealed that they all preferred the same pocket in CsqR-l, while in CsqR-s there were two possible options dependent on the linker structure.
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Affiliation(s)
- Anna A Rybina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205.
| | - Roman A Glushak
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Tatiana A Bessonova
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
| | | | - Alexander Yu Rudenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Ratislav M Ozhiganov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Anna D Kaznadzey
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Maria N Tutukina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
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46
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Golaz D, Papenfuhs CK, Bellés-Sancho P, Eberl L, Egli M, Pessi G. RNA-seq analysis in simulated microgravity unveils down-regulation of the beta-rhizobial siderophore phymabactin. NPJ Microgravity 2024; 10:44. [PMID: 38570513 PMCID: PMC10991261 DOI: 10.1038/s41526-024-00391-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
Exploiting the symbiotic interaction between crops and nitrogen-fixing bacteria is a simple and ecological method to promote plant growth in prospective extraterrestrial human outposts. In this study, we performed an RNA-seq analysis to investigate the adaptation of the legume symbiont Paraburkholderia phymatum STM815T to simulated microgravity (s0-g) at the transcriptome level. The results revealed a drastic effect on gene expression, with roughly 23% of P. phymatum genes being differentially regulated in s0-g. Among those, 951 genes were upregulated and 858 downregulated in the cells grown in s0-g compared to terrestrial gravity (1 g). Several genes involved in posttranslational modification, protein turnover or chaperones encoding were upregulated in s0-g, while those involved in translation, ribosomal structure and biosynthesis, motility or inorganic ions transport were downregulated. Specifically, the whole phm gene cluster, previously bioinformatically predicted to be involved in the production of a hypothetical malleobactin-like siderophore, phymabactin, was 20-fold downregulated in microgravity. By constructing a mutant strain (ΔphmJK) we confirmed that the phm gene cluster codes for the only siderophore secreted by P. phymatum as assessed by the complete lack of iron chelating activity of the P. phymatum ΔphmJK mutant on chrome azurol S (CAS) agar plates. These results not only provide a deeper understanding of the physiology of symbiotic organisms exposed to space-like conditions, but also increase our knowledge of iron acquisition mechanisms in rhizobia.
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Affiliation(s)
- Daphné Golaz
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland
| | - Chad K Papenfuhs
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland
| | - Paula Bellés-Sancho
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland
| | - Marcel Egli
- School of Engineering and Architecture, Institute of Medical Engineering, Space Biology Group, Lucerne University of Applied Sciences and Arts, Hergiswil, Switzerland
- National Center for Biomedical Research in Space, Innovation Cluster Space and Aviation, University of Zurich, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial biology, University of Zurich, Zurich, Switzerland.
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Eisenhofer R, Nesme J, Santos-Bay L, Koziol A, Sørensen SJ, Alberdi A, Aizpurua O. A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics. Microbiol Spectr 2024; 12:e0359023. [PMID: 38451230 DOI: 10.1128/spectrum.03590-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.
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Affiliation(s)
- Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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48
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Brar NK, Dhariwal A, Åmdal HA, Junges R, Salvadori G, Baker JL, Edlund A, Petersen FC. Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome. NPJ Biofilms Microbiomes 2024; 10:37. [PMID: 38565843 PMCID: PMC10987642 DOI: 10.1038/s41522-024-00507-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.
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Affiliation(s)
- N K Brar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - A Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - H A Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - R Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - G Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - J L Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health & Science University, Portland, OR, USA
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - A Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - F C Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway.
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49
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Wang WJ, Dong XM, Li GB. Macrocyclic peptides: up-and-coming weapons to combat antimicrobial resistance. Signal Transduct Target Ther 2024; 9:81. [PMID: 38565549 PMCID: PMC10987554 DOI: 10.1038/s41392-024-01813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- Wen-Jing Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Xiang-Min Dong
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China.
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50
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Wang PC, Rajput D, Wang XF, Huang CM, Chen CC. Exploring the possible relationship between skin microbiome and brain cognitive functions: a pilot EEG study. Sci Rep 2024; 14:7774. [PMID: 38565877 PMCID: PMC10987680 DOI: 10.1038/s41598-024-57649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Human microbiota mainly resides on the skin and in the gut. Human gut microbiota can produce a variety of short chain fatty acids (SCFAs) that affect many physiological functions and most importantly modulate brain functions through the bidirectional gut-brain axis. Similarly, skin microorganisms also have identical metabolites of SCFAs reported to be involved in maintaining skin homeostasis. However, it remains unclear whether these SCFAs produced by skin bacteria can affect brain cognitive functions. In this study, we hypothesize that the brain's functional activities are associated with the skin bacterial population and examine the influence of local skin-bacterial growth on event-related potentials (ERPs) during an oddball task using EEG. Additionally, five machine learning (ML) methods were employed to discern the relationship between skin microbiota and cognitive functions. Twenty healthy subjects underwent three rounds of tests under different conditions-alcohol, glycerol, and water. Statistical tests confirmed a significant increase in bacterial population under water and glycerol conditions when compared to the alcohol condition. The metabolites of bacteria can turn phenol red from red-orange to yellow, confirming an increase in acidity. P3 amplitudes were significantly enhanced in response to only oddball stimulus at four channels (Fz, FCz, and Cz) and were observed after the removal of bacteria when compared with that under the water and glycerol manipulations. By using machine learning methods, we demonstrated that EEG features could be separated with a good accuracy (> 88%) after experimental manipulations. Our results suggest a relationship between skin microbiota and brain functions. We hope our findings motivate further study into the underlying mechanism. Ultimately, an understanding of the relationship between skin microbiota and brain functions can contribute to the treatment and intervention of diseases that link with this pathway.
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Affiliation(s)
- Po-Chun Wang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Daniyal Rajput
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Central University and Academia Sinica, Taipei, Taiwan
| | - Xin-Fu Wang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Chun-Ming Huang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Chun-Chuan Chen
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan.
- Institute of Cognitive Neuroscience, National Central University, Taoyuan, Taiwan.
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