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Arega AM, Dhal AK, Pattanaik KP, Nayak S, Mahapatra RK. An Immunoinformatics-Based Study of Mycobacterium tuberculosis Region of Difference-2 Uncharacterized Protein (Rv1987) as a Potential Subunit Vaccine Candidate for Preliminary Ex Vivo Analysis. Appl Biochem Biotechnol 2024; 196:2367-2395. [PMID: 37498378 DOI: 10.1007/s12010-023-04658-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 07/28/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is the pathogen that causes tuberculosis and develops resistance to many of the existing drugs. The sole licensed TB vaccine, BCG, is unable to provide a comprehensive defense. So, it is crucial to maintain the immunological response to eliminate tuberculosis. Our previous in silico study reported five uncharacterized proteins as potential vaccine antigens. In this article, we considered the uncharacterized Mtb H37Rv regions of difference (RD-2) Rv1987 protein as a promising vaccine candidate. The vaccine quality of the protein was analyzed using reverse vaccinology and immunoinformatics-based quality-checking parameters followed by an ex vivo preliminary investigation. In silico analysis of Rv1987 protein predicted it as surface localized, secretory, single helix, antigenic, non-allergenic, and non-homologous to the host protein. Immunoinformatics analysis of Rv1987 by CD4 + and CD8 + T-cells via MHC-I and MHC-II binding affinity and presence of B-cell epitope predicted its immunogenicity. The docked complex analysis of the 3D model structure of the protein with immune cell receptor TLR-4 revealed the protein's capability for potential interaction. Furthermore, the target protein-encoded gene Rv1987 was cloned, over-expressed, purified, and analyzed by mass spectrometry (MS) to report the target peptides. The qRT-PCR gene expression analysis shows that it is capable of activating macrophages and significantly increasing the production of a number of key cytokines (TNF-α, IL-1β, and IL-10). Our in-silico analysis and ex vivo preliminary investigations revealed the immunogenic potential of the target protein. These findings suggest that the Rv1987 be undertaken as a potent subunit vaccine antigen and that further animal model immuno-modulation studies would boost the novel TB vaccine discovery and/or BCG vaccine supplement pipeline.
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Affiliation(s)
- Aregitu Mekuriaw Arega
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
- National Veterinary Institute, Debre Zeit, Ethiopia
| | - Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
| | | | - Sasmita Nayak
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India
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Burgan W. Creation of an Isogenic H/N/KRAS-Less Mouse Embryonic Fibroblast Cell Line Panel Derived from a Size-Sorted Diploid Clone. Methods Mol Biol 2024; 2797:323-336. [PMID: 38570470 DOI: 10.1007/978-1-0716-3822-4_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Cell line panels have proven to be an invaluable tool for investigators researching a range of topics from drug mechanism or drug sensitivity studies to disease-specific etiology. The cell lines used in these panels may range from heterogeneous tumor populations grown from primary tumor isolations to genetically engineered clonal cell lines which express specific gene isoforms. Mouse embryonic fibroblast (MEF) cells are a commonly used cell line for biological research due to their accessibility and ease of genetic manipulation. This chapter will describe the process of creating a size-sorted diploid (SSDC) clonal cell panel expressing specific RAS isoforms from a previously engineered RAS-less MEF cell line pool.
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Affiliation(s)
- William Burgan
- Cell Line Development Group, Protein Expression Laboratory, NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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Ren R, Shi J, Zeng M, Tang Z, Xie S, Zhang Z. Inter- and intra-varietal genetic variations co-shape the polyphenol profiles of Vitis vinifera L. grapes and wines. Food Chem X 2023; 20:101030. [PMID: 38144762 PMCID: PMC10740138 DOI: 10.1016/j.fochx.2023.101030] [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: 06/20/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
Inheritance and mutations are important factors affecting grape phenolic composition. To investigate the inter- and intra-varietal differences in polyphenolic compounds among grapes and wines, 27 clones belonging to eight varieties of Vitis vinifera L. were studied over two consecutive years. A total of 24 polyphenols (nine anthocyanins, three flavanols, five flavonols, and seven phenolic acids) were analyzed, and the physicochemical parameters of the grapes and wines were determined. Polyphenol profiles showed significant varietal and clonal polymorphisms, and malvidin-3-O-glucoside, peonidin-3-O- glucoside, and epicatechin were identified as key biomarkers distinguishing different grapes and wines when using an orthogonal partial least squares discriminant analysis. Further multivariate analysis classified these genotypes into three subclasses, and a somatic variant of 'Malbec', MBVCR6, had the most abundant polyphenolic compounds that were related to the titratable acid content. The current results reveal that varietal and clonal variations are important for obtaining wines with high polyphenol content.
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Affiliation(s)
- Ruihua Ren
- College of Enology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Jingjing Shi
- College of Enology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Maoyu Zeng
- College of Enology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Zizhu Tang
- College of Enology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Sha Xie
- College of Enology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Zhenwen Zhang
- College of Enology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
- China Wine Industry Technology Institute, Room 1606, Zhongguancun Innovation Center, Yinchuan, Ningxia 750021, China
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Potter GE, Callier V, Shrestha B, Joshi S, Dwivedi A, Silva JC, Laurens MB, Follmann DA, Deye GA. Can incorporating genotyping data into efficacy estimators improve efficiency of early phase malaria vaccine trials? Malar J 2023; 22:383. [PMID: 38115002 PMCID: PMC10729369 DOI: 10.1186/s12936-023-04802-0] [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: 09/19/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Early phase malaria vaccine field trials typically measure malaria infection by PCR or thick blood smear microscopy performed on serially sampled blood. Vaccine efficacy (VE) is the proportion reduction in an endpoint due to vaccination and is often calculated as VEHR = 1-hazard ratio or VERR = 1-risk ratio. Genotyping information can distinguish different clones and distinguish multiple infections over time, potentially increasing statistical power. This paper investigates two alternative VE endpoints incorporating genotyping information: VEmolFOI, the vaccine-induced proportion reduction in incidence of new clones acquired over time, and VEC, the vaccine-induced proportion reduction in mean number of infecting clones per exposure. METHODS Power of VEmolFOI and VEC was compared to that of VEHR and VERR by simulations and analytic derivations, and the four VE methods were applied to three data sets: a Phase 3 trial of RTS,S malaria vaccine in 6912 African infants, a Phase 2 trial of PfSPZ Vaccine in 80 Burkina Faso adults, and a trial comparing Plasmodium vivax incidence in 466 Papua New Guinean children after receiving chloroquine + artemether lumefantrine with or without primaquine (as these VE methods can also quantify effects of other prevention measures). By destroying hibernating liver-stage P. vivax, primaquine reduces subsequent reactivations after treatment completion. RESULTS In the trial of RTS,S vaccine, a significantly reduced number of clones at first infection was observed, but this was not the case in trials of PfSPZ Vaccine or primaquine, although the PfSPZ trial lacked power to show a reduction. Resampling smaller data sets from the large RTS,S trial to simulate phase 2 trials showed modest power gains from VEC compared to VEHR for data like those from RTS,S, but VEC is less powerful than VEHR for trials in which the number of clones at first infection is not reduced. VEmolFOI was most powerful in model-based simulations, but only the primaquine trial collected enough serial samples to precisely estimate VEmolFOI. The primaquine VEmolFOI estimate decreased after most control arm liver-stage infections reactivated (which mathematically resembles a waning vaccine), preventing VEmolFOI from improving power. CONCLUSIONS The power gain from the genotyping methods depends on the context. Because input parameters for early phase power calculations are often uncertain, these estimators are not recommended as primary endpoints for small trials unless supported by targeted data analysis. TRIAL REGISTRATIONS NCT00866619, NCT02663700, NCT02143934.
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Affiliation(s)
- Gail E Potter
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Viviane Callier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Biraj Shrestha
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sudhaunshu Joshi
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ankit Dwivedi
- Institute for Genomic Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genomic Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew B Laurens
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dean A Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Gregory A Deye
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- AstraZeneca PLC, Gaithersburg, MD, USA
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Paganelli A, Felici M, Turini L, Baragli P, Carlucci L, Recchia FA, Sgorbini M. Detour test performance of cloned minipigs from three different clone populations. Vet Res Commun 2023; 47:2137-2144. [PMID: 37452229 DOI: 10.1007/s11259-023-10168-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Genetics, the uterine environment, maternal behavior, and rearing conditions can all influence animal behavioral phenotypes. Some studies on cloned pigs have found no differences between the behavioral patterns of cloned and non-cloned animals. Other studies conducted on dogs have reported similarities in the behavior of cloned subjects. This study evaluated the performance of 12 cloned minipigs from three different clone populations (A, B, C) in a detour test around symmetric and asymmetric barriers. We measured the detour time and patterns, in order to investigate the pigs' cognitive abilities.The detour time and the detour entry/exit pattern were recorded. All the animals tended to keep a fixed entry/exit pattern instead of modifying it to accommodate changes in the working set. Significant differences in detour time were found among the populations, with animals belonging to population B being faster than the others, and also within each population.Our study is one of the few to assess the cognitive abilities of cloned minipigs. The results indicate that even animals belonging to the same cloned population may develop different cognitive, hence behavioral characteristics. Whether cloning can be utilized to obtain similar behavioral phenotypes therefore remains a matter of debate.
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Affiliation(s)
- Aurora Paganelli
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33, Pisa, 56127, Italy
| | - Martina Felici
- Department of Agricultural and Food Science, Viale Giuseppe Fanin, 40-50, Bologna, 40127, Italy
| | - Luca Turini
- Department of Agriculture, Food and Environment, Via del Borghetto 80, Pisa, 56124, Italy.
| | - Paolo Baragli
- Department of Veterinary Sciences, Viale delle Piagge 2, Pisa, 56122, Italy
| | - Lucia Carlucci
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33, Pisa, 56127, Italy
| | - Fabio Anastasio Recchia
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33, Pisa, 56127, Italy
- Institute of Clinical Physiology, National Research Council of Italy, Pisa, Italy
| | - Micaela Sgorbini
- Department of Veterinary Sciences, Viale delle Piagge 2, Pisa, 56122, Italy
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Wan M, Yang X, He L, Meng H. Elucidating the clonal relationship of esophageal second primary tumors in patients with laryngeal squamous cell carcinoma. Infect Agent Cancer 2023; 18:75. [PMID: 38017473 PMCID: PMC10685475 DOI: 10.1186/s13027-023-00558-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023] Open
Abstract
Laryngeal cancer ranks as the second most prevalent upper airway malignancy, following Lung cancer. Although some progress has been made in managing laryngeal cancer, the 5-year survival rate is disappointing. The gradual increase in the incidence of second primary tumors (SPTs) plays a crucial role in determining survival outcomes during long-term follow-up, and the esophagus was the most common site with a worse prognosis. In clinical practice, the treatment of esophageal second primary tumors (ESPT) in patients with laryngeal squamous cell carcinoma (LSCC) has always been challenging. For patients with synchronous tumors, several treatment modalities, such as radiotherapy, chemotherapy and potentially curative surgery are necessary but are typically poorly tolerated. Secondary cancer therapy options for metachronous patients are always constrained by index cancer treatment indications. Therefore, understanding the clonal origin of the second primary tumor may be an important issue in the treatment of patients. LSCC cells demonstrate genetic instability because of two distinct aetiologies (human papillomavirus (HPV)-negative and HPV-positive) disease. Various etiologies exhibit distinct oncogenic mechanisms, which subsequently impact the tissue microenvironment. The condition of the tissue microenvironment plays a crucial role in determining the destiny and clonal makeup of mutant cells during the initial stages of tumorigenesis. This review focuses on the genetic advances of LSCC, the current research status of SPT, and the influence of key carcinogenesis of HPV-positive and HPV-negative LSCC on clonal evolution of ESPT cells. The objective is to gain a comprehensive understanding of the molecular basis underlying the clonal origins of SPT, thereby offering novel perspectives for future investigations in this field.
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Affiliation(s)
- Meixuan Wan
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Xinxin Yang
- Precision Medicine Center, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Lin He
- Department of Stomatology, Heilongjiang Province Hospital, Harbin, 150081, China
| | - Hongxue Meng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
- Precision Medicine Center, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
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Das S, Mallick A, Barik M, Sarkar S, Saha P. The emergence of clonally diverse carbapenem-resistant Enterobacter cloacae complex in West Bengal, India: a dockyard of β-lactamases periling nosocomial infections. Int Microbiol 2023:10.1007/s10123-023-00451-0. [PMID: 37985632 DOI: 10.1007/s10123-023-00451-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]
Abstract
Carbapenem-resistant Enterobacter cloacae complex (CRECC) constitutes a global public health threat challenging clinical treatment and infection control, especially in low- and middle-income countries such as India. We analyzed the antimicrobial susceptibility, major β-lactamase genes, plasmid profiles, and genetic relatedness to understand the molecular epidemiology of CRECC clinical isolates (n = 44) in West Bengal, India, during 2021-2022. The majority (> 55%) of the isolates were resistant to fluoroquinolones, aminoglycosides, and co-trimoxazole, even > 20% for tigecycline and > 35% were extensively drug-resistant. Co-β-lactamase production was categorized into twenty-seven types, importantly NDM (84%), OXA-48 (40%), TEM (61%), CTX-M (46%), OXA-1 (55%), and MIR (27%). The NDM-1 and OXA-181 were major variants with the first observations of NDM-24 and -29 variants in India. Wide-range of plasmids (2 to > 212 kb) were harbored by the β-lactamase-producing isolates: small (91%), medium (27%), large (9%), and mega (71%). IncX3, ColE1, and HI2 were noted in about 30% of isolates, while IncF and R were carried by < 20% of isolates. The clonally diverse CRECC isolates were noted to cause cross-infections, especially at superficial site, bloodstream, and urinary-tract. This is the first molecular surveillance on CRECC in India. The study isolates serve as the dockyard of NDM, TEM, and CTX-M harboring a wide range of plasmids. The outcomes of the study may strengthen local and national policies for infection prevention and control practices, clarifying the genetic diversity among CRECC. Extensive genomic study may further intersect the relationships between these different plasmids, especially with their sizes, types, and antibiotic resistance markers.
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Affiliation(s)
- Surojit Das
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Abhi Mallick
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Mili Barik
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Soma Sarkar
- Department of Microbiology at Nil Ratan Sirkar Medical College Hospital, Kolkata, West Bengal, India
- Department of Microbiology at Infectious Diseases & Beleghata General Hospital, Kolkata, West Bengal, India
| | - Puranjoy Saha
- Department of Microbiology, Malda Medical College and Hospital, Malda, West Bengal, India
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Mugisa I, Karungi J, Musana P, Odama R, Anyanga MO, Edema R, Gibson P, Ssali RT, Campos H, Oloka BM, Yencho GC, Yada B. Heterotic gains, transgressive segregation and fitness cost of sweetpotato weevil resistance expression in a partial diallel cross of sweetpotato. Euphytica 2023; 219:110. [PMID: 37780031 PMCID: PMC10533626 DOI: 10.1007/s10681-023-03225-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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/06/2023] [Indexed: 10/03/2023]
Abstract
Heterosis-exploiting breeding schemes are currently under consideration as a means of accelerating genetic gains in sweetpotato (Ipomoea batatas) breeding. This study was aimed at establishing heterotic gains, fitness costs and transgressive segregation associated with sweetpotato weevil (SPW) resistance in a partial diallel cross of sweetpotato. A total of 1896 clones were tested at two sites, for two seasons each in Uganda. Data on weevil severity (WED), weevil incidence (WI), storage root yield (SRY) and dry matter content (DM) were obtained. Best linear unbiased predictors (BLUPs) for each clone across environments were used to estimate heterotic gains and for regression analyses to establish relationships between key traits. In general, low mid-parent heterotic gains were detected with the highest favorable levels recorded for SRY (14.7%) and WED (- 7.9%). About 25% of the crosses exhibited desirable and significant mid-parent heterosis for weevil resistance. Over 16% of the clones displayed superior transgressive segregation, with the highest percentages recorded for SRY (21%) and WED (18%). A yield penalty of 10% was observed to be associated with SPW resistance whereas no decline in DM was detected in relation to the same. Chances of improving sweetpotato through exploiting heterosis in controlled crosses using parents of mostly similar background are somewhat minimal, as revealed by the low heterotic gains. The yield penalty detected due to SPW resistance suggests that a trade-off may be necessary between maximizing yields and developing weevil-resistant cultivars if the current needs for this crop are to be met in weevil-prone areas.
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Affiliation(s)
- Immaculate Mugisa
- National Crops Resources Research Institute (NaCRRI), NARO, Kampala, Uganda
- Department of Agricultural production, Makerere University, Kampala, Uganda
| | - Jeninah Karungi
- Department of Agricultural production, Makerere University, Kampala, Uganda
| | - Paul Musana
- National Crops Resources Research Institute (NaCRRI), NARO, Kampala, Uganda
| | - Roy Odama
- National Crops Resources Research Institute (NaCRRI), NARO, Kampala, Uganda
| | - Milton O. Anyanga
- National Crops Resources Research Institute (NaCRRI), NARO, Kampala, Uganda
| | - Richard Edema
- Department of Agricultural production, Makerere University, Kampala, Uganda
| | - Paul Gibson
- Department of Agricultural production, Makerere University, Kampala, Uganda
| | | | | | - Bonny M. Oloka
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - G. Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC USA
| | - Benard Yada
- National Crops Resources Research Institute (NaCRRI), NARO, Kampala, Uganda
- National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Namulonge, Kampala, Uganda
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Maeshima AM, Taniguchi H, Furukawa H, Hattori D, Sasaki H, Makita S, Iwaki N, Fukuhara S, Munakata W, Izutsu K. Diagnostic clues of BCL2-negative, faint, or controversial follicular lymphomas: a study of 103 cases. Hum Pathol 2023; 135:84-92. [PMID: 36702355 DOI: 10.1016/j.humpath.2023.01.006] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023]
Abstract
BCL2 positivity by immunohistochemistry is helpful for the diagnosis of follicular lymphoma (FL); however, a minority of FL cases are BCL2-negative, and the diagnosis is thus challenging. We retrospectively analyzed the incidence, morphology, immunophenotype, and genetic status of BCL21+ (weakly/focally positive by clone 124), BCL20 (negative), and BCL2controversial FLs compared with BCL22+ (strongly positive) FLs to clarify diagnostic clues. In 1068 FL cases, 103 (10%) with BCL21+ (37 cases, 4%), BCL20 (61 cases, 6%), or BCL2controversial (5 cases, 0.5%) were included in the final analysis. BCL21+ and BCL20 FLs tended to have limited stage disease, nodal disease, and grades 3A/3B histology and showed a higher complete response rate than BCL22+ FLs. Among 103 BCL20, BCL21+, or BCL2controversial FL cases, 34 (33%) had a diffuse area composed of CD20-positive small-to medium-sized lymphoid cells, a feature of low-grade B-cell lymphoma. Interfollicular dense CD20-positive cells and interfollicular clusters of CD10-positive cells were observed in 59% and 37% of cases, respectively. In remaining 13/40 cases (33%), BCL2 was converted to BCL22+ by other clones E17/SP66. CD23 and MUM1 were positive in 10/40 (25%) and 1/40 (3%) cases, respectively. IGH/BCL2 fusion and clonality were detected in 6/37 (16%) and 31/34 (91%) cases, respectively. In conclusion, morphological examination of the distribution of CD20-and/or CD10-positive cells and the presence of diffuse area could be used to diagnose FL in most cases. The majority of the remaining FL cases could be diagnosed using other BCL2 clones and clonality analyses.
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Affiliation(s)
| | - Hirokazu Taniguchi
- Department of Diagnostic Pathology, Tokyo 104-0045, Japan; Department of Pathology and Clinical Laboratory, JR Tokyo General Hospital, Tokyo 151-8528, Japan
| | - Haruhi Furukawa
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Daiki Hattori
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Hirokazu Sasaki
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Shinichi Makita
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Noriko Iwaki
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Suguru Fukuhara
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Wataru Munakata
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Koji Izutsu
- Department of Hematology, National Cancer Center Hospital, Tokyo 104-0045, Japan
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Shibata K, Kuroda M, Yamaha E, Arai K, Fujimoto T. Nucleotide Sequence and Chromosome Mapping of 5S Ribosomal DNA from the Dojo Loach, Misgurnus anguillicaudatus. Cytogenet Genome Res 2023; 162:570-578. [PMID: 36682354 DOI: 10.1159/000529150] [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: 08/25/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023] Open
Abstract
There are 2 genetically divergent groups in the dojo loach Misgurnus anguillicaudatus: A and B. Although most wild-type diploids reproduce sexually, clonal diploids (clonal loach) reproduce gynogenetically in certain areas. Clonal loaches produce unreduced isogenic eggs by premeiotic endomitosis, and such diploid eggs develop gynogenetically following activation by the sperm of sympatric wild-type diploids. These clonal loaches have presumably arisen from past hybridization events between 2 different ancestors. The genomic differences between these 2 groups have not been completely elucidated. Thus, new genetic and cytogenetic markers are required to distinguish between these 2 groups. Here, we compared the 5S rDNA region to develop markers for the identification of different dojo loach groups. The nontranscribed sequence (NTS) of the 5S rDNA was highly polymorphic and group-specific. NTSs were found in clades of 2 different groups in clonal loaches. In contrast, we did not find any group-specific sequences in the coding region of the 5S rRNA gene. Sequences were located near the centromere of the short arm of the largest submetacentric chromosomes in groups A and B and clonal loaches. Thus, the 5S rDNA of the dojo loach is conserved at the chromosomal location. Whereas, the sequences of the NTS regions evolved group-specifically in the dojo loach, with the sequences of both groups being conserved in clonal loaches.
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Affiliation(s)
- Kiko Shibata
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Masamichi Kuroda
- Department of Ocean and Fisheries Sciences, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Japan
| | - Etsuro Yamaha
- Nanae Freshwater Station, Field Science Center for Northern Biosphere, Hokkaido University, Nanae, Japan
| | - Katsutoshi Arai
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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Alarcon ZK, Prada D, Gabastou JM, Sanabria O, Duarte C, Moreno J. Population structure of Neisseria meningitidis ST-9493 identified in Colombian isolates. Enferm Infecc Microbiol Clin (Engl Ed) 2023; 41:290-293. [PMID: 36681574 DOI: 10.1016/j.eimce.2022.01.005] [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] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/26/2022] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Neisseria meningitidis is associated with invasive infections causing high mortality rates. The objective of this study was to describe the population structure of Colombian invasive isolates with ST-9493, a potentially emerging clonal group in the country. METHODS The complete genomes of 34 invasive isolates of serogroup B with ST-9493 and its variants at one or two loci were sequenced by Illumina to describe the phenotypic and genotypic characteristics of these isolates. RESULTS The relationship of a clonal group associated with ST-136 CC41/44 was phylogenetically established, identifying two main clades composed of isolates from an outbreak or endemic. The most frequent alleles and peptides included porA 17, porB 44, fHbp 2.24, NHBA 10, and the FetA F5-17 variant. Most of the isolates were susceptible to the antibiotics evaluated. CONCLUSION This study shows that meningococcal isolates with ST-9493 are an autochthonous clonal group with population dynamics and the capacity to cause endemic and epidemic meningococcal disease in Colombia.
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Affiliation(s)
| | - Diego Prada
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
| | | | - Olga Sanabria
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Jaime Moreno
- Grupo de Microbiología, Instituto Nacional de Salud (INS), Bogotá, Colombia.
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Abstract
Repertoire sequencing of B cells is the high-throughput profiling of B cell receptors (BCR) expressed on the surface of B cells and of immunoglobulins (Ig) expressed by antibody secreting cells. Each BCR/Ig transcript has a unique complementarity-determining region 3 (CDR3) sequence that can be used to identify and track individual B cell lymphocytes over time and throughout different compartments of the human body. B cell differentiation can be further tracked by assessing the point mutations acquired during affinity maturation via somatic hypermutation (SHM). Here we describe a method for high-throughput sequencing of the variable region of Ig heavy-chain transcripts for repertoire analysis of human B cells on the Illumina Miseq platform.
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Affiliation(s)
- Jennifer R Hom
- Lowance Center for Human Immunology, Division of Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Tomar
- Lowance Center for Human Immunology, Division of Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, GA, USA
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Division of Rheumatology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, GA, USA.
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Rosenfeld AM, Meng W, Horne KI, Chen EC, Bagnara D, Stervbo U, Luning Prak ET; AIRR Community. Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community. Methods Mol Biol 2022; 2453:317-43. [PMID: 35622334 DOI: 10.1007/978-1-0716-2115-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this method we illustrate how to amplify, sequence, and analyze antibody/immunoglobulin (IG) heavy-chain gene rearrangements from genomic DNA that is derived from bulk populations of cells by next-generation sequencing (NGS). We focus on human source material and illustrate how bulk gDNA-based sequencing can be used to examine clonal architecture and networks in different samples that are sequenced from the same individual. Although bulk gDNA-based sequencing can be performed on both IG heavy (IGH) or kappa/lambda light (IGK/IGL) chains, we focus here on IGH gene rearrangements because IG heavy chains are more diverse, tend to harbor higher levels of somatic hypermutations (SHM), and are more reliable for clone identification and tracking. We also provide a procedure, including code, and detailed instructions for processing and annotation of the NGS data. From these data we show how to identify expanded clones, visualize the overall clonal landscape, and track clonal lineages in different samples from the same individual. This method has a broad range of applications, including the identification and monitoring of expanded clones, the analysis of blood and tissue-based clonal networks, and the study of immune responses including clonal evolution.
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14
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Wu J, Liu W, Lu J, Xu R, Xie J, Zha L. Cloning, prokaryotic expression, and purification of acetyl-CoA C-acetyltransferase from Atractylodes lancea. Protein Pept Lett 2021; 29:156-165. [PMID: 34825863 DOI: 10.2174/0929866528666211126162838] [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: 08/24/2021] [Revised: 10/09/2021] [Accepted: 10/26/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cangzhu (Atractylodes lancea), a valuable and common traditional Chinese medicinal herb, is primarily used as an effective medicine with various health-promoting effects. The main pharmacological bioactive ingredients in the rhizome of A. lancea are terpenoids. Acetyl-CoA C-acetyltransferase (AACT) is the first enzyme in the terpenoid synthesis pathway and catalyzes two units of acetyl-CoA into acetoacetyl-CoA. OBJECTIVE The objective of the present work was to clone and identify function of AlAACT from Atractylodes lancea. METHOD A full-length cDNA clone of AlAACT was isolated using PCR and expressed in Escherichia coli. The expressed protein was purified using Ni-NTA agarose column using standard protocols. AlAACT was transiently expressed in N. benthamiana leaves to determine their subcellular location. The difference in growth between recombinant bacteria and control bacteria under different stresses was observed using the droplet plate experiment. Results:In this study, a full-length cDNA of AACT (AlAACT) was cloned from A. lancea, which contains a 1,227 bp open reading frame and encodes a protein with 409 amino acids. Bioinformatic and phylogenetic analysis clearly suggested that AlAACT shared high similarity with AACTs from other plants. The recombinant protein pET32a(+)/AlAACT was successfully expressed in Escherichia coli BL21(DE3) cells induced with 0.4 mM IPTG at 30°C as the optimized condition. The recombinant enzyme pET-32a-AlAACT was purified using the Ni-NTA column based on the His-tag, and the molecular weight was determined to be 62 kDa through SDS-PAGE and Western Blot analysis. The recombinant protein was eluted with 100, 300, and 500 mM imidazole; most of the protein was eluted with 300 mM imidazole. Under mannitol stress, the recombinant pET-32a-AlAACT protein showed a substantial advantage in terms of growth rates compared to the control. However, this phenomenon was directly opposite under NaCl abiotic stress. Subcellular localization showed that AlAACT localizes to the nucleus and cytoplasm. Conclusion:The expression and purification of recombinant enzyme pET-32a-AlAACT were successful, and the recombinant strain pET-32a-AlAACT in showed better growth in a drought stress. The expression of AlAACT-EGFP fusion protein revealed its localization in both nuclear and cytoplasm compartments. This study provides an important foundation for further research into the effects of terpenoid biosynthesis in A. lancea.
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Affiliation(s)
- Junxian Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Weiwei Liu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Jimei Lu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Rui Xu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Jin Xie
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
| | - Liangping Zha
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
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Ferreira CM, Filho RAAB, Ferreira GMA, de Lacerda MVG, de Oliveira CMC, de Souza Sampaio V, Silva LM, Pascoal AG, Ferreira WA. Molecular epidemiology of methicillin resistant Staphylococcus species in healthcare workers of a blood bank in the Brazilian Amazon. BMC Microbiol 2021; 21:306. [PMID: 34736414 PMCID: PMC8567558 DOI: 10.1186/s12866-021-02365-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/22/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Healthcare workers are susceptible to colonization by multiresistant bacteria, which can increase the risk of outbreaks. METHODS Samples were collected from the nasopharynx, hands, and lab coats of healthcare workers. The phenotypic identification was carried out using a VITEK®2 rapid test system. PCR tests for the mecA gene and the sequencing of the amplicons were performed. Staphylococcus epidermidis and Staphylococcus aureus phylogenies were reconstructed using the Bayesian inference. RESULTS A total of 225 healthcare workers participated in this study. Of these, 21.3% were male and 78.7% female. S. epidermidis and S.aureus showed high levels of resistance to penicillin, ampicillin, erythromycin, tetracycline and cefoxitin. The prevalence of methicillin resistant S. aureus was 3.16% and methicillin resistant S. epidermidis was 100%. Multilocus sequence typing identified 23 new S. epidermidis sequence types, and one new allele and sequence type for S. aureus. The frequency of methicillin-resistant S. epidermidis in nursing and hemotherapy technicians as a percentage of the total number of healthcare workers was 5.8-3.1%, while the frequency of methicillin resistant S. aureus in hemotherapy technicians and biomedics, as a percentage of the total number of healthcare workers was 4.2-8.9%%. CONCLUSIONS The healthcare workers at the city's blood bank, even when taking the necessary care with their hands, body and clothes, harbour methicillin-resistant S. aureus and S. epidermidis sequence types, which, as a potential source of multidrug resistant bacteria, can contribute to nosocomial infections among hematological patients.
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Affiliation(s)
| | | | - Guilherme Motta Antunes Ferreira
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas - HEMOAM, Manaus, Brazil.,Programa de Pós-Graduação em Hematologia, Universidade do Estado do Amazonas - UEA, Manaus, Brazil
| | | | | | - Vanderson de Souza Sampaio
- Universidade do Estado do Amazonas - Programa de Pós-Graduação em Medicina Tropical, Manaus, Brazil.,Fundação de Vigilância em Saúde do Amazonas, Manaus, Brazil
| | - Lucyane Mendes Silva
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas - HEMOAM, Manaus, Brazil.,Programa de Pós-Graduação em Hematologia, Universidade do Estado do Amazonas - UEA, Manaus, Brazil
| | - Andreza Gomes Pascoal
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas - HEMOAM, Manaus, Brazil
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Kunos Á, Maróti M, Zádori L. Critical Relations of Crowns in Critical Times of Coronavirus Depression. Order (Dordr) 2021; 39:229-241. [PMID: 34248236 PMCID: PMC8260343 DOI: 10.1007/s11083-021-09571-6] [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: 07/01/2020] [Accepted: 06/04/2021] [Indexed: 06/13/2023]
Abstract
The critical relations are the building blocks of the relational clone of a relational structure with respect to the relational operations intersection and direct product. In this paper we describe the critical relations of crowns. As a consequence, we obtain that the subpower membership problem for any crown is polynomial-time solvable.
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Affiliation(s)
- Ádám Kunos
- Bolyai Institute, University of Szeged, Szeged, Hungary
| | - Miklós Maróti
- Bolyai Institute, University of Szeged, Szeged, Hungary
| | - László Zádori
- Bolyai Institute, University of Szeged, Szeged, Hungary
- Alfréd Rényi Institute of Mathematics, Budapest, Hungary
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17
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Zabelina V, Yonemura N, Uchino K, Iizuka T, Mochida Y, Takemura Y, Klymenko V, Sezutsu H, Sehnal F, Tamura T. Production of cloned transgenic silkworms by breeding non-diapausing parthenogenetic strains. J Insect Physiol 2021; 132:104265. [PMID: 34097982 DOI: 10.1016/j.jinsphys.2021.104265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 06/12/2023]
Abstract
Clonal transgenic silkworms are useful for the functional analysis of insect genes and for the production of recombinant proteins. Such silkworms have previously been created using an existing ameiotic parthenogenetic strain. However, the process was labor intensive, and the efficiency of producing transgenic silkworms was very low. To overcome this issue, we developed a more convenient and efficient method by breeding non-diapausing parthenogenetic strains. The strains produced non-diapausing eggs only when the embryogenesis of the parent eggs was performed at low temperatures, which could then be used for injecting vector plasmids. This demonstrated that transgenic silkworms could be produced with greater ease and efficiency. To breed the strains, we crossed the existing parthenogenetic strains with bivoltine strains and made F1 and F2 from each cross. Then we selected the silkworms whose eggs have a high ability of parthenogenesis and became non-diapausing. We also demonstrated that the germplasm could be cryopreserved in liquid nitrogen. Thus, this method increases the efficiency and ease of using genetically engineered silkworms to analyze gene function and produce recombinant proteins, potentially impacting various industries.
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Affiliation(s)
- Valeriya Zabelina
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
| | - Naoyuki Yonemura
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
| | - Keiro Uchino
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
| | - Tetsuya Iizuka
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
| | - Yuji Mochida
- Institute of Sericulture, Iikura 1053, 300-0324 Ami-machi, Ibaraki, Japan
| | - Yoko Takemura
- Institute of Sericulture, Iikura 1053, 300-0324 Ami-machi, Ibaraki, Japan
| | | | - Hideki Sezutsu
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki 305-8634, Japan
| | | | - Toshiki Tamura
- Institute of Sericulture, Iikura 1053, 300-0324 Ami-machi, Ibaraki, Japan.
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Dridi M, Boutonnat J, Dumollard JM, Peoc'h M, Karpathiou G. Patterns of brachyury expression in chordomas. Ann Diagn Pathol 2021; 53:151760. [PMID: 33989961 DOI: 10.1016/j.anndiagpath.2021.151760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Chordomas are rare malignant midline tumors, presumed to arise from notochordal remnants. This was further suggested by the discovery of the brachyury in chordomas pathogenesis. Its immunohistochemical expression has become the principal adjunct in the diagnosis of chordomas. However, studies about brachyury expression in chordomas are not fully comparable, mainly because they use different primary antibodies. Thus, the aim of this study is to investigate the expression of brachyury expression in a series of chordomas in conjunction to clinicopathological characteristics and to review the relevant literature providing all the details needed in the immunohistochemical study of brachyury. MATERIALS AND METHODS This is a retrospective study of 62 chordomas, diagnosed over a 22-year period. No dedifferentiated or poorly differentiated cases were included. A monoclonal primary antibody (clone A-4) was used and brachyury expression was evaluated by the H-score. Clinicopathological parameters studied were age, sex, tumor localization, decalcification status and tissue age. Fetal notochords were used for comparison. RESULTS Mean H-score of nuclear brachyury expression was 129.8. The tissue age significantly influenced brachyury expression, the older samples expressing less brachyury. Decalcification demonstrated a trend to weaken brachyury expression. Clinical characteristics were not correlated with the patterns of brachyury expression. Notochords were negative. Literature review reveals several polyclonal antibodies used and a positivity of 75%-100% in chordomas with even more variable results in notochords. CONCLUSION In chordomas, as in other tumor types, an uniformization of studies about brachyury expression is needed, by considering the clone used, and the decalcification and the age of the sample, given the growing importance of brachyury in diagnosis and therapeutic steps.
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Affiliation(s)
- Maroa Dridi
- Pathology Departments, University Hospital of Saint-Etienne, France
| | | | | | - Michel Peoc'h
- Pathology Departments, University Hospital of Saint-Etienne, France
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Pimentel de Araujo F, Monaco M, Del Grosso M, Pirolo M, Visca P, Pantosti A. Staphylococcus aureus clones causing osteomyelitis: a literature review (2000-2020). J Glob Antimicrob Resist 2021; 26:29-36. [PMID: 33965630 DOI: 10.1016/j.jgar.2021.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/07/2020] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES Staphylococcus aureus is the most common causative organism of osteomyelitis (OM). Nevertheless, the molecular epidemiology of S. aureus causing OM remains ill-defined. This study aimed to address the global epidemiology of S. aureus clones from OM patients. METHODS Literature databases were searched for studies reporting the molecular typing of S. aureus involved in OM published between 1 January 2000 and 29 July 2020. Data from 32 articles that fulfilled the inclusion criteria were analysed for year of publication, country of patients, methicillin susceptibility and genotypic characteristics of S. aureus isolates. RESULTS Pandemic clones CC5, CC8, CC22, CC30 and CC45 were the most common in OM. The distribution of clones differed greatly among studies owing to the local epidemiology of S. aureus and the MSSA heterogeneity. PVL-positive MRSA clones belonging to ST80/CC80 and ST8/CC8/USA300 were the most common among paediatric patients in Europe and the USA; greater variability was observed in the adult population. In Europe, MRSA belonged to PVL-negative CC5, CC8 and CC22 indicating a nosocomial origin of infections; in Asia PVL-positive ST59/CC59 MRSA was the most frequent. PVL-positive clones were often detected in haematogenous OM in children and adults. Although MSSA were polyclonal, PVL-negative ST398/CC398 MSSA was the most prevalent clone in diabetic foot OM. CONCLUSION All major S. aureus clones circulating both in hospital and community settings appear to be capable of causing OM. Future studies reporting molecular typing and genomic data will provide more insights into the epidemiology and pathobiology of S. aureus clones causing OM.
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Affiliation(s)
- Fernanda Pimentel de Araujo
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy; Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Monica Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Maria Del Grosso
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Mattia Pirolo
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
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Li X, Li Y, Song W, Xie D, Zhu F, Yang M, Li Y. cDNA cloning, expression and bioinformatical analysis of Tssk genes in tree shrews. Comput Biol Chem 2021; 92:107474. [PMID: 33765466 DOI: 10.1016/j.compbiolchem.2021.107474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/20/2019] [Revised: 10/09/2020] [Accepted: 03/02/2021] [Indexed: 11/17/2022]
Abstract
Tree shrews are more closely related to primate animals than rodents in many aspects. In addition, they also possess several advantageous characteristics including small body size, high brain-to-body mass ratio, low cost of feeding and maintenance, short reproductive cycle and life span, which make them promising novel laboratory animals to replace more precious larger primate animals. Testis-specific serine/threonine kinase (Tssk) plays important roles in spermatogenesis and/or the regulation of sperm function. However, studies on Tssk in tree shrews have not been reported yet. In the present study, the full-length sequences of five members of the Tssk family in tree shrews were cloned and their CDS region sequences were analyzed by basic bioinformatics. The phylogenetic tree and prokaryotic protein expression system of Tssk gene of tree shrews were constructed. The mRNA expressions of Tssk genes in 11 tissues/organs from tree shrews were studied. The results showed that: 1. the length of the CDS region of tree shrew Tssk gene for Tssk1B, Tssk2, Tssk3 (variant X1 / X2), Tssk4 (variant X1 / X2) and Tssk6 is 1080bp, 1077bp, 867 / 807bp, 1014 / 984bp, 822bp, respectively, encoding 359, 358, 288/268, 337/327 and 273 amino acids, respectively; the cloned sequences of Tssk genes have been submitted to GenBank with the following accession numbers: KX091161(Tssk1B), KX091162(Tssk2), KX091163(Tssk3 variant X1)/KX091164(Tssk3 variant X2), KX091165(Tssk4variant X1)/KX091166(Tssk4variant X2), KX091160(Tssk6). 2. All tree shrew Tssk proteins distribute in cytoplasm, indicating that they are hydrophilic and non-secretory proteins, with multiple phosphorylation sites of serine and/or threonine. In addition, they are all mixed proteins with similar tertiary structures sharing a highly conserved functional domain of S_TKc (Serine/Threonine protein kinases, catalytic domain). 3.The molecular phylogenetic tree of five Tssk genes in tree shrews indicates that they are neither rodent nor primate animal, but are closely related to primate animals. 4. Five members of the Tssk recombinant proteins in tree shrews were successfully obtained using the constructed prokaryotic protein expression system. 5. Five Tssk genes are specifically expressed in the testis and/or sperm of tree shrews. Additionally, small amount of Tssk1B was expressed in several tissues other than testis and sperm. Limited mRNA levels of Tssk2 and Tssk4 were expressed in the brain, while mRNA of Tssk3 or Tssk6 could only be detected in the testis and sperm. This study will provide fundamental data on reproductive biology of tree shrews, which paves a way for further studying Tssk's biological function in this novel model animal.
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Affiliation(s)
- Xue Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Yuanji Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Wenfei Song
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China; Institute of Sericultural and Apiculture, Yunnan Academy of Agricultural Sciences, Mengzi, 661101, China
| | - Daohao Xie
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Fangfang Zhu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Minghua Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Yahui Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
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Nasr-Esfahani MH, Ahmad-Khanbeigi KH, Hasannia A. Qur'anic Views on Human Cloning (I): Doctrinal and Theological Evidences. Int J Fertil Steril 2021; 15:73-79. [PMID: 33497051 PMCID: PMC7838753 DOI: 10.22074/ijfs.2020.134415] [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] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/20/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Human cloning is a recent occurrence that is not confined to bio-issues; rather, it has provoked numerous questions worldwide and presented scientific and religious challenges. These series of articles aim to examine the proposed approaches and analyze the aspects of human cloning in terms of tenets, morals, jurisprudence, and laws. In this paper, we analyze the ideological and theological evidences, regardless of scientific, ethical and legal problems that exist in the reproduction method. MATERIALS AND METHODS We used a descriptive-analytical method to consider the challenges of human cloning according to the "system of Divine creativity" and "the will of God", as well as the "pairing system" and "diversity in nature" with emphasis on the Holy Qur'an and Qur'anic commentaries. RESULTS According to the Qur'an, although any type of physical changes and retouching of the human body are forbidden, the alteration of God's creation may not prove the prohibition of cloning. Cloning is not contradictory to the principle, precedent, and rule of coupling, and it may be one of the hidden precedents of creation. Therefore, not only does a clone not contradict the precedent of the variety of men, but this variety is a sign for men and not a precedent predominated over the order of nature. CONCLUSION It is proven that cloning does not give life; instead, it utilizes the life bestowed by God. This technique does not contradict the precedents of existence. It is a way to discover some precedents of God and is under the order of cause and effect of the world. Cloning is not considered as a challenge to human beliefs, nor is it a change in Divine creation. Moreover, cloning does not contradict the theological teachings and concepts of the Holy Qur'an and Shiite Muslims.
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Affiliation(s)
- Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - K Hadijeh Ahmad-Khanbeigi
- Department of Jurisprudence and Law, Research Institute of Imam Khomeini and Islamic Revolution, Tehran, Iran.
| | - Ali Hasannia
- Department of Qur'an and Hadith Sciences, Shahed University, Tehran, Iran
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Yang N, Liu B, Yang P, Chen X, Li H, Wang W, Li Q, Wang S. Molecular cloning, characterization and expression analysis of CbPLDδ gene from Chorispora bungeana in low temperature. Cryobiology 2021; 98:119-26. [PMID: 33290735 DOI: 10.1016/j.cryobiol.2020.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/30/2020] [Accepted: 11/24/2020] [Indexed: 11/21/2022]
Abstract
Chorispora bungeana (C. bungeana) is a rare alpine subnival species that is highly tolerant to low temperature stress. Phospholipase D (PLD) is a key enzyme involved in membrane phospholipid catabolism during plant growth and the stress response. In this study, one member of CbPLD gene family, CbPLDδ, was cloned from C. bungeana and was introduced into tobacco. This gene encodes an 864-amino acid protein with two catalytic HxKxxxxD motifs which are essential for phospholipase D activity. After the CbPLDδ gene is fused with the vector containing the GFP tag, subcellular localization showed that CbPLDδ was predominately located in the cell membrane. RT-qPCR and histochemical GUS assays showed that CbPLDδ gene was induced by low temperature and expressed predominantly in leaf and root. Compared with wild-type tobacco, CbPLDδ transgenic tobacco showed higher activities of antioxidant enzymes, and lower levels of malonidiadehyde and electrolyte leakage under low temperature stress. These results reflected that CbPLDδ is involved in the response to low temperature stress, and has the potential to improve the low temperature tolerance of plants.
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Rehner SA. Genetic structure of Metarhizium species in western USA: Finite populations composed of divergent clonal lineages with limited evidence for recent recombination. J Invertebr Pathol 2020; 177:107491. [PMID: 33069670 DOI: 10.1016/j.jip.2020.107491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 12/06/2019] [Revised: 10/01/2020] [Accepted: 10/10/2020] [Indexed: 01/25/2023]
Abstract
Globally distributed, soil associated Metarhizium species used in insect biological control are evidently facultatively sexual and obligately outcrossing, yet sexual morphs have not been observed for most species and corroboration that they recombine in nature remains limited. Community-wide genetic diversity of Metarhizium species among 480 soil isolates from 14 states of western USA was investigated to assess the contributions of clonality and recombination in determining each species' population structure. Seven species, varying greater than 100-fold in relative abundance, were identified by phylogenetic analysis of 5' EF1-α (5TEF), including M. robertsii (n = 372), M. guizhouense (n = 37), M. brunneum (n = 37), M. lepidiotae (n = 14), M. pemphigi (n = 11), M. anisopliae (n = 7) and M. pingshaense (n = 2). Analyses of composite multilocus genotypes integrating 5TEF sequences, multilocus microsatellites and mating type idiomorphs conducted on a subset of 239 isolates revealed that all species populations display pronounced clonal structure. Following clone-correction procedures to remove redundant clonal genotypes and collapse clonal lineages, each species' population sample was determined to be composed of a dozen or fewer genetically unique individuals. Thus, the Metarhizium community inhabiting western USA is conservatively estimated to comprise as few as 34 distinct genetic individuals, with a single, geographically ubiquitous clonal lineage of M. robertsii constituting 45% of total isolates. M. robertsii was the only population determined to be in linkage equilibrium. However, the high proportion of private alleles differentiating most M. robertsii clonal lineages argues against contemporary panmixia, thus the recombination signal detected may be historical. Nevertheless, within M. robertsii, M. brunneum and M. guizhouense there are closely related genotypes of opposite mating type, which suggests that if recombination is contemporary, it likely occurs between closely related individuals. The restricted number of genetic individuals observed throughout western North American Metarhizium species may signify that these represent peripheral populations descended from limited numbers of founders among which there has been little recombination relative to the extent of clone expansion and within-clone genetic divergence.
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Affiliation(s)
- Stephen A Rehner
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705, USA.
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24
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Liu D, Wang F, Cao L, Wang L, Su S, Hou Z, Xu J, Hu J, Tao J. Identification and characterization of a cDNA encoding a gametocyte-specific protein of the avian coccidial parasite Eimeria necatrix. Mol Biochem Parasitol 2020; 240:111318. [PMID: 32956771 DOI: 10.1016/j.molbiopara.2020.111318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 06/27/2019] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 11/20/2022]
Abstract
Gametocyte proteins of Eimeria spp. are essential components of the oocyst wall, and some of these proteins have been analysed to identify targets of transmission-blocking vaccines against avian coccidiosis. In the present study, a cDNA from E. necatrix gametocytes was cloned and sequenced. The cDNA is 1473 bp in length and encodes a 490-amino-acid protein containing a tyrosine-serine (Tyr/Ser)-rich domain and a proline-methionine (Pro/Met)-rich domain. A quantitative real-time PCR (qPCR) analysis showed that the cDNA is expressed only during gametogenesis. A fragment containing the Tyr/Ser-rich domain (rEnGAM59) was expressed in Escherichia coli BL21 (DE3) cells. Immunoblotting showed that rEnGAM59 was recognized by the serum of convalescent chickens after infection with E. necatrix, and that an anti-rEnGAM59 antibody recognized a ∼59 kDa protein and two other proteins (∼35 kDa and ∼33 kDa) in gametocyte extracts. An immunofluorescence assay showed that the anti-rEnGAM59 antibody recognized wall-forming bodies in the macrogametocytes and oocyst walls. An in vivo vaccination and challenge trial was conducted to test the potential utility of rEnGAM59 as a vaccine. Immunized chickens performed better than the unimmunized and challenged (positive control) chickens. The intestinal lesion scores were significantly lower in the immunized groups than in the positive control group (P < 0.05). In contrast, the body weight gains (BWG) were significantly higher in the immunized groups than in the positive control group (P < 0.05). There were no significant differences in the lesion scores and BWG between the groups immunized with rEnGAM59 protein or with live oocysts (P> 0.05). Chickens immunized with rEnGAM59 protein had a significantly higher antigen-specific serum IgY response (P < 0.05). rEnGAM59 protein can be used as candidate antigen to develop a recombinant coccidiosis vaccine.
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Affiliation(s)
- Dandan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Feiyan Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Liqin Cao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Lele Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Shijie Su
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Zhaofeng Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Jinjun Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Junjie Hu
- Biology Department, Yunnan University, Kunming, 650500, China.
| | - Jianping Tao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Konno S, Wakayama S, Ito D, Kazama K, Hirose N, Ooga M, Wakayama T. Removal of remodeling/reprogramming factors from oocytes and the impact on the full-term development of cloned embryos. Development 2020; 147:dev.190777. [PMID: 32665239 DOI: 10.1242/dev.190777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 03/19/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
Abstract
The reason for the poor development of cloned embryos is not yet clear. Several reports have suggested that some nuclear remodeling/reprogramming factors (RRFs) are removed from oocytes at the time of enucleation, which might cause the low success rate of animal cloning. However, there is currently no method to manipulate the amount of RRFs in oocytes. Here, we describe techniques we have developed to gradually reduce RRFs in mouse oocytes by injecting somatic cell nuclei into oocytes. These injected nuclei were remodeled and reprogrammed using RRFs, and then RRFs were removed by subsequent deletion of somatic nuclei from oocytes. The size of the metaphase II spindle reduced immediately, but did recover when transferred into fresh oocytes. Though affected, the full-term developmental potential of these RRF-reduced oocytes with MII-spindle shrinkage was not lost after fertilization. When somatic cell nuclear transfer was performed, the successful generation of cloned mice was somewhat improved and abnormalities were reduced when oocytes with slightly reduced RRF levels were used. These results suggest that a change in RRFs in oocytes, as achieved by the method described in this paper or by enucleation, is important but not the main reason for the incomplete reprogramming of somatic cell nuclei.
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Affiliation(s)
- Shunsuke Konno
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, 400-8510, Japan
| | - Sayaka Wakayama
- Advanced Biotechnology Center, University of Yamanashi, Yamanashi, 400-8510, Japan
| | - Daiyu Ito
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, 400-8510, Japan
| | - Kousuke Kazama
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, 400-8510, Japan
| | - Naoki Hirose
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, 400-8510, Japan
| | - Masatoshi Ooga
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, 400-8510, Japan
| | - Teruhiko Wakayama
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, 400-8510, Japan .,Advanced Biotechnology Center, University of Yamanashi, Yamanashi, 400-8510, Japan
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Ortega-Peña S, Franco-Cendejas R, Aquino-Andrade A, Betanzos-Cabrera G, Sharma A, Rodríguez-Martínez S, Cancino-Diaz ME, Cancino-Diaz JC. Genotypic and phenotypic changes of Staphylococcus epidermidis during relapse episodes in prosthetic joint infections. Braz J Microbiol 2019; 51:601-612. [PMID: 31828715 DOI: 10.1007/s42770-019-00190-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 08/09/2019] [Accepted: 11/13/2019] [Indexed: 01/14/2023] Open
Abstract
Staphylococcus epidermidis is a coagulase-negative bacterium capable of causing recurrent relapses in prosthetic joint infection (PJI). The aim of this study was to determine if Staphylococcus epidermidis isolates from patients with recurrent relapses of prosthetic joint infection (PJI) changed genotypically (pulsed-field gel electrophoresis (PFGE) pattern analysis and genes involved in biofilm formation) and phenotypically (antimicrobial resistance, biofilm formation) during the different episodes. Four patients with PJI recurrent relapses were evaluated clinically and microbiologically. Genotypic and phenotypic characteristics of 31 S. epidermidis isolates were determined. In all cases, PJI was treated with antimicrobial therapy and resection of the prosthesis without reimplantation. Months later, all patients had a relapse episode and treated with rifampin plus vancomycin and surgical debridement. Changes in the antibiotics resistance profile in isolates from patients 1 and 2 were observed in the two episodes. Patient 1 had four clones A, B, C, and D that were distributed differentially in the two episodes. Similarly, patients 2 and 3 had two clones and subclones (E-E1 and F-F1, respectively), and patient 4 had only the clone G in both episodes. The clone F formed small-colony variants (SCVs). High level of biofilm formation was found in all clones, except for clones D and G. Clones/subclones showed a genotypic variation in icaA, sdrF, bap, sesI, and embp genes. The principal coordinate analysis showed that all clones/subclones were different. These results showed that the initial infective clone of S. epidermidis from PJI, changed genotypically and phenotypically after a second relapse as a response to the treatment.
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Affiliation(s)
- Silvestre Ortega-Peña
- Laboratory of Infectology, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", 11340, Mexico City, Mexico
- Microbiology and Immunology Departments of Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Col. Santo Tomas, Mexico City, Mexico
| | - Rafael Franco-Cendejas
- Laboratory of Infectology, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", 11340, Mexico City, Mexico
| | | | - Gabriel Betanzos-Cabrera
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro, Mexico
- Área Académica de Nutrición and Toxicología Clínica, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca, Hidalgo, Mexico
| | - Ashutosh Sharma
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro, Mexico
| | - Sandra Rodríguez-Martínez
- Microbiology and Immunology Departments of Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Col. Santo Tomas, Mexico City, Mexico
| | - Mario E Cancino-Diaz
- Microbiology and Immunology Departments of Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Col. Santo Tomas, Mexico City, Mexico.
| | - Juan Carlos Cancino-Diaz
- Microbiology and Immunology Departments of Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Col. Santo Tomas, Mexico City, Mexico.
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Zhang Y, Chen W, Li M, Yang L, Chen X. Cloning, phylogenetic research, and prokaryotic expression study of the metabolic detoxification gene EoGSTs1 in Empoasca onukii Matsuda. PeerJ 2019; 7:e7641. [PMID: 31534862 PMCID: PMC6733243 DOI: 10.7717/peerj.7641] [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: 03/06/2019] [Accepted: 08/07/2019] [Indexed: 11/20/2022] Open
Abstract
Due to the misuse of chemical pesticides, small green leafhoppers (Empoasca onukii Matsuda) have developed resistance to pesticides, thereby posing a serious problem to the tea industry. Glutathione S-transferases (GSTs) are an important family of enzymes that are involved in pesticide resistance in Empoasca onukii Matsuda. Empoasca onukii GST sigma 1 (EoGSTs1, GenBank: MK443501) is a member of the GST family. In this study, the full-length cDNA of EoGSTs1 was cloned by reverse transcription polymerase chain reaction (qPCR), and its taxonomic identity was examined. Furthermore, we performed bioinformatics and phylogenetic analyses of the gene and structural and functional domain prediction of the protein. The results demonstrate that EoGSTS1 belongs to the Sigma family of GSTs; the full-length EoGSTs1 cDNA is 841 bp with a 624-bp coding region that encodes a 23.68932-kDa protein containing 207 amino acids. The theoretical isoelectric point (IEP) was calculated to be 6.00. Phylogenetic analysis indicates that EoGSTS1 is closely related to the Sub psaltriayangi subfamily of the Cicadoidea superfamily in order Hemiptera, whereas it is distantly related to Periplaneta americana of order Blattodea. Amino acid sequence alignment of EoGSTS1 and GSTs from four other insects of order Hemiptera revealed protein sequence conservation. Tertiary structure analysis and structural domain functional predictions of the protein revealed that EoGSTS1 contains nine α helices and two β sheets with one conserved GST domain. The results of enzyme activity assay showed that recombinant EoGSTs1 (rEoGSTs1) protein had catalytic activity for substrate 1-chloro-2,4-dinitrobenzene (CDNB) and exhibited the highest activity at pH 7 and 25 °C. The Michaelis constant Km of rEoGSTs1 protein was 0.07782 ± 0.01990 mmol/L, and the maximum reaction rate Vmax was 12.15 ± 1.673 µmol/min⋅mg. Our study clarified the taxonomic identity of small green leafhopper EoGSTs1 and revealed some properties of the gene and its encoded protein sequence. According to the catalytic activity of the rEoGSTs1 enzyme on the model substrate CDNB, we infer that it functions in the degradation of exogenous substances.
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Affiliation(s)
- Yujie Zhang
- Institute of Entomology, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Plant Pest Management of Mountainous Region, Guizhou University, Guiyang, China
| | - Wenlong Chen
- Institute of Entomology, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Plant Pest Management of Mountainous Region, Guizhou University, Guiyang, China
| | - Ming Li
- The Provincial Special Key Laboratory for Development and Utilization of Insect Resources of Guizhou, Guiyang, China
| | - Lin Yang
- Institute of Entomology, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Plant Pest Management of Mountainous Region, Guizhou University, Guiyang, China
| | - Xiangsheng Chen
- Institute of Entomology, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Plant Pest Management of Mountainous Region, Guizhou University, Guiyang, China
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28
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Gao L, Tian Y, Chen MC, Wei L, Gao TG, Yin HJ, Zhang JL, Kumar T, Liu LB, Wang SM. Cloning and functional characterization of epidermis-specific promoter MtML1 from Medicago truncatula. J Biotechnol 2019; 300:32-39. [PMID: 31085201 DOI: 10.1016/j.jbiotec.2019.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 01/29/2019] [Revised: 04/23/2019] [Accepted: 05/09/2019] [Indexed: 01/21/2023]
Abstract
Epidermis-specific promoters are necessary for ectopic expression of specific functional genes such as the cuticle-related genes. Previous studies indicated that both ECERIFERUM 6 (AtCER6) and MERISTEM L1 LAYER (ATML1) promoters from Arabidopsis thaliana can drive gene expression specifically in the epidermis of shoot apical meristems (SAMs) and leaves. However, the epidermis-specific promoters from legume plants have not been reported. Here, we cloned a 5' flanking sequence from the upstream -2150 bp to the translational start ATG codon of MtML1 gene of legume model plant Medicago truncatula. PlantCARE analysis indicated that this sequence matches the characteristics of a promoter, having TATA box and CAAT box, as well as contains some conserved elements of epidermis-specific promoters like AtCER6 and ATML1 promoters. The β-glucuronidase (GUS) histochemical analysis showed that MtML1 promoter can drive GUS gene expression in transiently transformed Nicotiana tabacum leaves under non-inducing condition. Furthermore, it can also control GUS expression in leaves and siliques rather than roots of the stably transformed Arabidopsis. More importantly, the leaf cross-section observations indicated that MtML1 exclusively expressed in the epidermis of leaves. These results suggested that MtML1 promoter performed the epidermis-specific in plant shoot. Our study establishes the foundation for driving the cuticle-related gene to express in epidermis, which may be very useful in genetic engineering of legume plants.
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Affiliation(s)
- Li Gao
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Ye Tian
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Meng-Ci Chen
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Li Wei
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Tian-Ge Gao
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Hong-Ju Yin
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Jin-Lin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Tanweer Kumar
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Lin-Bo Liu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China
| | - Suo-Min Wang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, P.R. China.
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Martín-Pardillos A, Valls Chiva Á, Bande Vargas G, Hurtado Blanco P, Piñeiro Cid R, Guijarro PJ, Hümmer S, Bejar Serrano E, Rodriguez-Casanova A, Diaz-Lagares Á, Castellvi J, Miravet-Verde S, Serrano L, Lluch-Senar M, Sebastian V, Bribian A, López-Mascaraque L, López-López R, Ramón Y Cajal S. The role of clonal communication and heterogeneity in breast cancer. BMC Cancer 2019; 19:666. [PMID: 31277602 PMCID: PMC6612119 DOI: 10.1186/s12885-019-5883-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 05/28/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
Background Cancer is a rapidly evolving, multifactorial disease that accumulates numerous genetic and epigenetic alterations. This results in molecular and phenotypic heterogeneity within the tumor, the complexity of which is further amplified through specific interactions between cancer cells. We aimed to dissect the molecular mechanisms underlying the cooperation between different clones. Methods We produced clonal cell lines derived from the MDA-MB-231 breast cancer cell line, using the UbC-StarTrack system, which allowed tracking of multiple clones by color: GFP C3, mKO E10 and Sapphire D7. Characterization of these clones was performed by growth rate, cell metabolic activity, wound healing, invasion assays and genetic and epigenetic arrays. Tumorigenicity was tested by orthotopic and intravenous injections. Clonal cooperation was evaluated by medium complementation, co-culture and co-injection assays. Results Characterization of these clones in vitro revealed clear genetic and epigenetic differences that affected growth rate, cell metabolic activity, morphology and cytokine expression among cell lines. In vivo, all clonal cell lines were able to form tumors; however, injection of an equal mix of the different clones led to tumors with very few mKO E10 cells. Additionally, the mKO E10 clonal cell line showed a significant inability to form lung metastases. These results confirm that even in stable cell lines heterogeneity is present. In vitro, the complementation of growth medium with medium or exosomes from parental or clonal cell lines increased the growth rate of the other clones. Complementation assays, co-growth and co-injection of mKO E10 and GFP C3 clonal cell lines increased the efficiency of invasion and migration. Conclusions These findings support a model where interplay between clones confers aggressiveness, and which may allow identification of the factors involved in cellular communication that could play a role in clonal cooperation and thus represent new targets for preventing tumor progression. Electronic supplementary material The online version of this article (10.1186/s12885-019-5883-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Martín-Pardillos
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain. .,CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain.
| | - Ángeles Valls Chiva
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Gemma Bande Vargas
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Roberto Piñeiro Cid
- CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain.,Cancer Modelling Lab, Roche-CHUS Joint Unit, Santiago de Compostela, Spain
| | - Pedro J Guijarro
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Stefan Hümmer
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain.,CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain
| | - Eva Bejar Serrano
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain.,CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Ángel Diaz-Lagares
- CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain.,Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Josep Castellvi
- Hospital Vall d'Hebron, Anatomía Patológica, Barcelona, Spain
| | - Samuel Miravet-Verde
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - María Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Institute of Science and Technology, Barcelona, Spain
| | - Víctor Sebastian
- Department of Chemical Engineering, Aragon Institute of Nanoscience (INA), University of Zaragoza, Zaragoza, Spain.,Networking Research Centre on Bioengineering, Biomaterials and Nanomedicine, CIBER-BBN, Madrid, Spain
| | - Ana Bribian
- Department of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal-CSIC, Madrid, Spain
| | - Laura López-Mascaraque
- Department of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal-CSIC, Madrid, Spain
| | - Rafael López-López
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain.,Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Santiago Ramón Y Cajal
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain. .,CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain. .,Hospital Vall d'Hebron, Anatomía Patológica, Barcelona, Spain.
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Aithammou R, Harrouni C, Aboudlou L, Hallouti A, Mlouk M, Elasbahani A, Daoud S. Effect of clones, year of harvest and geographical origin of fruits on quality and chemical composition of Argan oil. Food Chem 2019; 297:124749. [PMID: 31253289 DOI: 10.1016/j.foodchem.2019.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 10/18/2018] [Revised: 04/10/2019] [Accepted: 05/05/2019] [Indexed: 12/11/2022]
Abstract
Argan oil is precious oil with food and cosmetic uses. In recent years, this oil has been subject to an increasing national and international demand. The present work aims at studying the effect of clones and age, year of harvest and geographical origin on Argan oil quality and chemical composition. The results indicate that age does not affect Argan oil quality and fatty acids content. However, clones had a significant effect on fatty acids and tocopherol levels. Saturated and unsaturated fatty acids were highly influenced by the year of harvest and geographical origin, presumably due to climatic conditions. Unsaturated fatty acids varied from 78.28% to 81.77%. Depending on clones, total tocopherols varied from 687.40 mg/kg to 1068 mg/kg. This study is useful for the choice of clones with the aim of developing Argan trees orchards destined to oil production.
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Affiliation(s)
- Rachid Aithammou
- Laboratory of Microbial Biotechnology and Plant Protection, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco; Direction des Domaines Agricoles (Les Arômes du Maroc), Casablanca, Morocco.
| | - Cherif Harrouni
- Department of Landscape Architecture and Environment, I.A.V. Hassan II, Agadir, Morocco
| | - Leila Aboudlou
- Etablissement Autonome de Contrôle et de Coordination des Exportations, Agadir, Morocco
| | - Ayoub Hallouti
- Laboratory of Microbial Biotechnology and Plant Protection, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Mohamed Mlouk
- Direction des Domaines Agricoles (Les Arômes du Maroc), Casablanca, Morocco
| | - Abdelhafed Elasbahani
- Laboratory Lacape- Bio-organic Chemistry and Natural Substances, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Salma Daoud
- Laboratory of Microbial Biotechnology and Plant Protection, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
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Park SH, Jeong J, Lee SH, Yoo DW, Choi Y, Jo JC, Lim JH. Comparison of High Sensitivity and Conventional Flow Cytometry for Diagnosing Overt Paroxysmal Nocturnal Hemoglobinuria and Detecting Minor Paroxysmal Nocturnal Hemoglobinuria Clones. Ann Lab Med 2019; 39:150-157. [PMID: 30430777 PMCID: PMC6240522 DOI: 10.3343/alm.2019.39.2.150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/09/2018] [Revised: 03/15/2018] [Accepted: 09/20/2018] [Indexed: 01/08/2023] Open
Abstract
Background High sensitivity flow cytometry (HS-FCM) was recently developed for diagnosing paroxysmal nocturnal hemoglobinuria (PNH). We compared its performance with conventional flow cytometry (C-FCM) for diagnosing overt PNH and detecting minor (0.1–1%) PNH clones in aplastic anemia (AA)/low-grade myelodysplastic syndrome (MDS) patients. Methods C-FCM and HS-FCM were performed simultaneously on 41 samples from healthy controls and 23 peripheral blood samples from 15 AA/low-grade MDS and eight PNH patients, using a Navios flow cytometer (Beckman Coulter, Miami, FL, USA). Results were compared. Results No healthy control samples had PNH clone size >0.01%. For granulocytes, C-FCM detected a smaller PNH clone size than HS-FCM (mean difference: 0.7–1.7%). In AA/low-grade MDS patients, three samples showed >1% PNH clones with C-FCM but not with HS-FCM. Seven samples showed minor PNH clones by C-FCM, but HS-FCM showed negative results for all these samples. In PNH patients, C-FCM detected a smaller PNH clone size than HS-FCM (mean difference: 1.9–5.0%). For red blood cells, C-FCM detected a greater PNH clone size than HS-FCM (mean difference: 1.5%). In AA/low-grade MDS patients, C-FCM showed >1% PNH clones in six samples, but HS-FCM showed >1% PNH clones in none of the samples. C-FCM detected minor PNH clones in nine samples, but six of them were negative by HS-FCM. In PNH patients, C-FCM detected a greater PNH clone size than HS-FCM (mean difference: 2.5%). Conclusions HS-FCM can sensitively detect minor PNH clones and reduce false-positive C-FCM minor PNH clone cases in AA/low-grade MDS patients.
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Affiliation(s)
- Sang Hyuk Park
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Joseph Jeong
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Seon Ho Lee
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Dong Won Yoo
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Yunsuk Choi
- Department of Hematology and Cellular Therapy, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Jae Cheol Jo
- Department of Hematology and Cellular Therapy, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea
| | - Ji Hun Lim
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea.
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Hu B, Xiao J, Yi P, Hu C, Zhu M, Yin S, Wen C, Wu J. Cloning and characteristic of MMP1 gene from Hyriopsis cumingii and collagen hydrolytic activity of its recombinant protein. Gene 2019; 693:92-100. [PMID: 30716434 DOI: 10.1016/j.gene.2018.12.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/08/2018] [Revised: 12/04/2018] [Accepted: 12/27/2018] [Indexed: 10/27/2022]
Abstract
Matrix metalloproteinases (MMPs) play an essential role in a variety of biological processes including wound healing, inflammation, cell invasion, angiogenesis and immune defense. In this study, a putative MMP1 cDNA was cloned and characterized from Hyriopsis cumingii (designated as HcMMP1). The cDNA was 1822 bp in length and encoded a putative protein of 510 amino acids, with a predicted molecular mass of 58.28 kDa and an isoelectric point (pI) of 9.27. HcMMP1 contained all prototype MMPs family signatures, such as signal peptide, prodomain, catalytic center, hinge region, and hemopexin like domain. Quantitative real time-PCR (qRT-PCR) revealed that in mussels HcMMP1 mRNA was expressed in all tissues tested, and the transcriptional expression levels were significantly up-regulated in hepatopancreas and hemocytes after Aeromonas hydrophila, peptidoglycan stimulations and in mantle after wounding. Moreover, the recombination HcMMP1 protein, successfully expressed in Escherichia coli, was purified by affinity chromatography with the concentration of final yield at 0.3 mg/mL. The recombinase had an essentially hydrolytic activity toward rat type I collagen, mouse II and IV collagen after renaturation.
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Affiliation(s)
- Baoqing Hu
- College of Life Science, Nanchang University, Nanchang 330031, China.
| | - Jun Xiao
- Jiangxi Fisheries Research Institute, Nanchang 330039, China
| | - Peipei Yi
- College of Life Science, Nanchang University, Nanchang 330031, China
| | - Chenxi Hu
- College of Life Science, Nanchang University, Nanchang 330031, China
| | - Mingxing Zhu
- College of Life Science, Nanchang University, Nanchang 330031, China
| | - Shuyuan Yin
- College of Life Science, Nanchang University, Nanchang 330031, China
| | - Chungen Wen
- College of Life Science, Nanchang University, Nanchang 330031, China.
| | - Jielian Wu
- College of Life Science, Nanchang University, Nanchang 330031, China
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Sui X, Zhao M, Han X, Zhao L, Xu Z. RrGT1, a key gene associated with anthocyanin biosynthesis, was isolated from Rosa rugosa and identified via overexpression and VIGS. Plant Physiol Biochem 2019; 135:19-29. [PMID: 30500515 DOI: 10.1016/j.plaphy.2018.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/29/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
At present, research on the flower color of Rosa rugosa requires very innovative and practical studies. Glycosylation plays an important role in increasing the stability and solubility of anthocyanins in plants. In this study, a gene with a full-length cDNA of 1161 bp encoding 386 amino acids, designated RrGT1 (MK034140), was isolated from the flowers of R. rugosa 'Zizhi' and then functionally characterized. Sequence alignment revealed that the coding regions of RrGT1 were highly specific among different species but still contained typical conserved amino acid residues that are crucial for RrGT1 enzyme activity. RrGT1 transcripts were detected in various tissues of R. rugosa 'Zizhi' and Rosa davurica, and their expression patterns corresponded with the accumulation of anthocyanins. Additionally, the in vivo function of RrGT1 was investigated via its overexpression in Arabidopsis thaliana. Transgenic Arabidopsis plants expressing RrGT1 regained red color pigmentation of their leaves and flower stems, indicating that RrGT1 could encode a functional glycosyltransferase (GT) protein for anthocyanin biosynthesis and could function in other species. The functional verification of RrGT1 for anthocyanin biosynthesis in R. rugosa was performed via virus-induced gene silencing (VIGS). This was the first time that a VIGS system was developed for use with perennial Rosa plants grown naturally in the field as experimental materials to study a key color-controlling gene in Rosa. When the RrGT1 gene was silenced, the Rosa plants displayed a pale petal color phenotype. The detection results showed that the expression of the endogenous RrGT1 gene was significantly downregulated while the six key structural genes in its upstream were normally expressed, and the contents of all anthocyanins also decreased significantly. Therefore, we speculated that glycosylation of RrGT1 plays a crucial role in anthocyanin biosynthesis in R. rugosa.
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Affiliation(s)
- Xiaoming Sui
- College of Forestry, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, China
| | - Mingyuan Zhao
- College of Forestry, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, China
| | - Xu Han
- College of Forestry, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, China
| | - Lanyong Zhao
- College of Forestry, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, China.
| | - Zongda Xu
- College of Forestry, Shandong Agricultural University, 61 Daizong Street, Taian, 271018, China.
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Sui X, Zhao M, Xu Z, Zhao L, Han X. RrGT2, A Key Gene Associated with Anthocyanin Biosynthesis in Rosa rugosa, Was Identified Via Virus-Induced Gene Silencing and Overexpression. Int J Mol Sci 2018; 19:E4057. [PMID: 30558205 PMCID: PMC6321322 DOI: 10.3390/ijms19124057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/06/2018] [Accepted: 12/12/2018] [Indexed: 12/20/2022] Open
Abstract
In this study, a gene with a full-length cDNA of 1422 bp encoding 473 amino acids, designated RrGT2, was isolated from R. rugosa 'Zizhi' and then functionally characterized. RrGT2 transcripts were detected in various tissues and were proved that their expression patterns corresponded with anthocyanins accumulation. Functional verification of RrGT2 in R. rugosa was performed via VIGS. When RrGT2 was silenced, the Rosa plants displayed a pale petal color phenotype. The detection results showed that the expression of RrGT2 was significantly downregulated, which was consistent with the decrease of all anthocyanins; while the expression of six key upstream structural genes was normal. Additionally, the in vivo function of RrGT2 was investigated via its overexpression in tobacco. In transgenic tobacco plants expressing RrGT2, anthocyanin accumulation was induced in the flowers, indicating that RrGT2 could encode a functional GT protein for anthocyanin biosynthesis and could function in other species. The application of VIGS in transgenic tobacco resulted in the treated tobacco plants presenting flowers whose phenotypes were lighter in color than those of normal plants. These results also validated and affirmed previous conclusions. Therefore, we speculated that glycosylation of RrGT2 plays a crucial role in anthocyanin biosynthesis in R. rugosa.
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Affiliation(s)
- Xiaoming Sui
- Flower Research Laboratory, College of Forestry, Shandong Agricultural University, Taian 271018, China.
| | - Mingyuan Zhao
- Flower Research Laboratory, College of Forestry, Shandong Agricultural University, Taian 271018, China.
| | - Zongda Xu
- Flower Research Laboratory, College of Forestry, Shandong Agricultural University, Taian 271018, China.
| | - Lanyong Zhao
- Flower Research Laboratory, College of Forestry, Shandong Agricultural University, Taian 271018, China.
| | - Xu Han
- Flower Research Laboratory, College of Forestry, Shandong Agricultural University, Taian 271018, China.
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Bekele S, Derese Y, Hailu E, Mihret A, Dagne K, Yamuah L, Hailu T, Ayele S, Beyene D, Berg S, Aseffa A. Line-probe assay and molecular typing reveal a potential drug resistant clone of Mycobacterium tuberculosis in Ethiopia. Trop Dis Travel Med Vaccines 2018; 4:15. [PMID: 30534412 PMCID: PMC6280437 DOI: 10.1186/s40794-018-0075-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/25/2018] [Indexed: 11/30/2022]
Abstract
Background Antimicrobial resistance is a global concern of increasing significance. Multidrug resistant tuberculosis (MDR-TB) is spreading worldwide. It is important to monitor trends of antimycobacterial resistance. This is particularly true for high TB burden countries such as Ethiopia where disproportionally less drug sensitivity data are reported from. Methods The prevalence of drug resistance was assessed with the line probe assay GenoType MTBDRplus in a set of 161 M. tuberculosis strains that were selected from four common lineages and sub-lineages previously identified in Ethiopia. Most of the tested M. tuberculosis isolates had been genotyped by established Spoligotyping and MIRU-VNTR typing methods. Results The proportion of MDR-TB among the isolates was 3.1%. Mono-resistance was 1.2% to rifampicin and 4.3% to isoniazid, and resistance to either of the two first line drugs was 8.7%. Strains of Lineage 4 had the highest resistance rate (13.6%) followed by Lineage 3 (4.9%). None of the isolates representing Lineages 1 and Lineage 7 were drug resistant. Multidrug resistance among pulmonary TB and TB lymphadenitis clinical isolates was 2.8 and 3.7%, respectively. Drug resistance of strains carrying the most prevalent spoligotype in Ethiopia - SIT149 - was further explored. Stratification by MIRU-VNTR identified one genotype with a high rate of drug resistance against Rifampicin and Isoniazid and circulation of a potential MDR-TB clone is proposed. Conclusion Although the strain selection was not fully randomized, the overall M. tuberculosis drug resistance rate in this strain set was 8.7% while the rate of MDR was 3.1%. In parallel, we identified a sub-lineage that showed a high rate of resistance to both rifampicin and isoniazid. These resistant strains may belong to a clone of M. tuberculosis that is circulating in the highlands of Ethiopia. Electronic supplementary material The online version of this article (10.1186/s40794-018-0075-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shiferaw Bekele
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia.,2Department of Microbial, Cellular and Molecular Biology, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia.,4Present address: J. Craig Venter Institute, Rockville, MD USA
| | - Yohannes Derese
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia
| | - Elena Hailu
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia
| | - Adane Mihret
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia
| | - Kifle Dagne
- 2Department of Microbial, Cellular and Molecular Biology, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lawrence Yamuah
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia
| | - Tsegaye Hailu
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia
| | - Samuel Ayele
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia
| | - Demissew Beyene
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia
| | - Stefan Berg
- 3Animal and Plant Health Agency, New Haw, Surrey, UK
| | - Abraham Aseffa
- 1Armauer Hansen Research Institute, Jima Road, Addis Ababa, Ethiopia.,4Present address: J. Craig Venter Institute, Rockville, MD USA
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Peng S, Deng D, He P, Xu X, Zhang C, Cao J, Liu Q, Zhang T. Effects of Microcystis aeruginosa on the life history traits and SOD activity of Daphnia similoides sinensis. Environ Sci Pollut Res Int 2018; 25:30696-30707. [PMID: 30178409 DOI: 10.1007/s11356-018-3040-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
With water eutrophication and global warming, cyanobacteria blooms have occurred frequently, and the interaction between M. aeruginosa and Daphnia has been widely paid attention by researchers. However, the effects of toxic M. aeruginosa on the SOD activity of Daphnia are poorly known. Six D. similoides sinensis clones collected from Lake Junshan and the offspring of two clones were employed. The effects of toxic M. aeruginosa on the life history traits and SOD activities of D. similoides sinensis in the mother and their offspring were studied. Toxic M. aeruginosa could significantly inhibit the life history traits (e.g., body lengths, offspring numbers at first reproduction, cumulative offspring numbers, and the intrinsic rate of population) and induce higher SOD activities of D. similoides sinensis. Compared with the mother, the effects of toxic M. aeruginosa on the life history traits and SOD activities of D. similoides sinensis in the offspring showed obvious differences. Moreover, the adaptability of the offspring to M. aeruginosa indicated also the differences between two clones. Our results suggested that the mother exposed to toxic M. aeruginosa could enhance the fitness of their offspring to Microcystis by maternal effect and was also affected by the D. similoides sinensis genotypes.
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Affiliation(s)
- Shuixiu Peng
- School of Life Science, Anhui Key Laboratory of Resource and Plant Biology, Huaibei Normal University, Huaibei, 235000, China
| | - Daogui Deng
- School of Life Science, Anhui Key Laboratory of Resource and Plant Biology, Huaibei Normal University, Huaibei, 235000, China.
| | - Ping He
- School of Life Science, Anhui Key Laboratory of Resource and Plant Biology, Huaibei Normal University, Huaibei, 235000, China
| | - Xiaoxue Xu
- School of Life Science, Anhui Key Laboratory of Resource and Plant Biology, Huaibei Normal University, Huaibei, 235000, China
| | - Chenchen Zhang
- School of Life Science, Anhui Key Laboratory of Resource and Plant Biology, Huaibei Normal University, Huaibei, 235000, China
| | - Jie Cao
- School of Life Science, Anhui Key Laboratory of Resource and Plant Biology, Huaibei Normal University, Huaibei, 235000, China
| | - Qi Liu
- School of Life Science, Anhui Key Laboratory of Resource and Plant Biology, Huaibei Normal University, Huaibei, 235000, China
| | - Tingting Zhang
- School of Life Science, Anhui Key Laboratory of Resource and Plant Biology, Huaibei Normal University, Huaibei, 235000, China
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Dai YJ, Liu WB, Li XF, Zhou M, Xu C, Qian Y, Jiang GZ. Molecular cloning of adipose triglyceride lipase (ATGL) gene from blunt snout bream and its expression after LPS-induced TNF-α factor. Fish Physiol Biochem 2018; 44:1143-1157. [PMID: 29705966 DOI: 10.1007/s10695-018-0502-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
The aims of the present study were to clone the full-length cDNA of adipose triglyceridelipase (ATGL) and to analyze its expression after lipopolysaccharide (LPS)-induced tumor necrosis factor alpha (TNF-α). The cDNA obtained covered 1801 bp with an open reading frame of 1500 bp encoding 499 amino acids. Sequence alignment and phylogenetic analysis show the best identity with Cyprinus carpio (86%). The ATGL protein shared a highly conserved 169-amino acid patatin domain, containing a glycine-rich motif, an active serine hydrolase motif, and an aspartic active site. The highest ATGL expression was observed in the liver followed by muscle, whereas relatively low values were detected in the brain and adipose. TNF-α is regarded as an important factor in regulating fat metabolism. Here, LPS was used to induce TNF-α in vivo to verify whether TNF-α can affect ATGL expression. TNF-α expression in liver and muscle is increased and remains unchanged in adipose tissue and brain. The variation of ATGL activity is consistent with that of TNF-α gene expression. Next, we explored the mechanism by which LPS-induced TNF-α mediates the mRNA expression of ATGL in the liver and muscle. For liver, the mRNA levels of c-Jun N-terminal kinase (JNK), nuclear factor kappa B (NF-κB), Sirtuin 1 (SIRT1), and AMP-activated protein kinase (AMPK) were increased by LPS-induced TNF-α. Differencing from the situation in the liver, there was a near-significant decrease trend in the expression of SIRT1 in muscle. Those results indicated that the ATGL gene of blunt snout bream shared a high similarity with the other vertebrates. The expression level of ATGL in tissues with high-fat content was intended to be high. LPS can induce ATGL expression perhaps related to TNF-α.
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Affiliation(s)
- Yong-Jun Dai
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Wen-Bin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Xiang-Fei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Man Zhou
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Chao Xu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Yu Qian
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China
| | - Guang-Zhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, No.1 Weigang Road, Nanjing, 210095, People's Republic of China.
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Zhao X, Hong X, Chen R, Yuan L, Zha J, Qin J. New cytokines and TLR pathway signaling molecules in Chinese rare minnow (Gobiocypris rarus): Molecular characterization, basal expression, and their response to chlorpyrifos. Chemosphere 2018; 199:26-34. [PMID: 29427811 DOI: 10.1016/j.chemosphere.2018.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 06/08/2023]
Abstract
In this study, the cDNA fragments of cytokines (il-8) and toll-like receptor (TLR) pathway signaling molecules (myd88, irak-1, irf5, and irf7) in the Chinese rare minnow were cloned and exhibited a high amino-acid sequence identity compared to other cyprinid fish orthologs. The mRNA expressions of these genes in the different tissues (liver, brain, spleen, kidney, and skin) were observed. The highest expression levels of myd88, irak-1, and irf5 were detected in the spleen, whereas il-8 and irf7 were detected in the kidney and liver respectively. The mRNA expression of irak-1, irf5, and irf7 in the liver from 0.1 μg/L and 0.5 μg/L CPF treatments were significantly increased on day 7 (p < 0.05), whereas the levels of only irak-1 and irf7 were markedly increased on day 28 (p < 0.05). Moreover, the mRNA expression of il-8 in the spleen following 0.5 μg/L CPF treatments was significantly decreased on day 7 (p < 0.05), whereas significantly decrease were observed in the levels of irf7 in the spleen at 2.5 μg/L CPF on days 7 and 28 (p < 0.05). The 0.1 μg/L and 0.5 μg/L of CPF significantly induced the levels of irak-1 and myd88 in the spleen after 28 d exposure (p < 0.05). Therefore, the high induction of cytokines and TLR pathway signaling molecules demonstrated that Chinese rare minnow was immune-compromised exposed to CPF. Moreover, our finding indicated that these immune-related genes could be feasible to screen for substances hazardous to the immune system of fish.
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Affiliation(s)
- Xu Zhao
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan 430070, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiangsheng Hong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100085, China
| | - Rui Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lilai Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jianhui Qin
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan 430070, China.
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Revollo JR, Dad A, McDaniel LP, Pearce MG, Dobrovolsky VN. Genome-wide mutation detection by interclonal genetic variation. Mutat Res Genet Toxicol Environ Mutagen 2018; 829-830:61-69. [PMID: 29704995 DOI: 10.1016/j.mrgentox.2018.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/10/2018] [Accepted: 03/10/2018] [Indexed: 12/20/2022]
Abstract
Genetic toxicology assays estimate mutation frequencies by phenotypically screening for the activation or inactivation of endogenous or exogenous reporter genes. These reporters can only detect mutations in narrow areas of the genome and their use is often restricted to certain in vitro and in vivo models. Here, we show that Interclonal Genetic Variation (ICGV) can directly identify mutations genome-wide by comparing sequencing data of single-cell clones derived from the same source or organism. Upon ethyl methanesulfonate (EMS) exposure, ICGV detected greater levels of mutation in a dose- and time-dependent manner in E. coli. In addition, ICGV was also able to identify a ∼20-fold increase in somatic mutations in T-cell clones derived from an N-ethyl-N-nitrosourea (ENU)-treated rat vs. a vehicle-treated rat. These results demonstrate that the genetic differences of single-cell clones can be used for genome-wide mutation detection.
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Affiliation(s)
- Javier R Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA.
| | - Azra Dad
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Lea P McDaniel
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Mason G Pearce
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Vasily N Dobrovolsky
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
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Sauvage T, Plouviez S, Schmidt WE, Fredericq S. TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees. BMC Res Notes 2018; 11:164. [PMID: 29506565 PMCID: PMC5838971 DOI: 10.1186/s13104-018-3268-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 01/11/2018] [Accepted: 02/24/2018] [Indexed: 11/16/2022] Open
Abstract
Objective The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets. Results We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content. Electronic supplementary material The online version of this article (10.1186/s13104-018-3268-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Sauvage
- Department of Biology, University of Louisiana at Lafayette, 410 E. Saint Mary Boulevard, Lafayette, LA, 70503, USA. .,Smithsonian Marine Station, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.
| | - Sophie Plouviez
- Department of Biology, University of Louisiana at Lafayette, 410 E. Saint Mary Boulevard, Lafayette, LA, 70503, USA
| | - William E Schmidt
- Department of Biology, University of Louisiana at Lafayette, 410 E. Saint Mary Boulevard, Lafayette, LA, 70503, USA
| | - Suzanne Fredericq
- Department of Biology, University of Louisiana at Lafayette, 410 E. Saint Mary Boulevard, Lafayette, LA, 70503, USA
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Arrizabalaga M, Morales F, Oyarzun M, Delrot S, Gomès E, Irigoyen JJ, Hilbert G, Pascual I. Tempranillo clones differ in the response of berry sugar and anthocyanin accumulation to elevated temperature. Plant Sci 2018; 267:74-83. [PMID: 29362101 DOI: 10.1016/j.plantsci.2017.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/29/2017] [Accepted: 11/22/2017] [Indexed: 05/21/2023]
Abstract
The intra-varietal genetic diversity of grapevine (Vitis vinifera L.) may be exploited to maintain grape quality under future warm conditions, which may alter grape berry development and composition. The present study assesses the effects of elevated temperature on the development of berry, grape composition and anthocyanins:sugars ratio of thirteen clones of V. vinifera. cv. Tempranillo that differed in length of the ripening period (time from veraison to berry total soluble solids, mainly sugars, of ca. 22 °Brix). Two temperature regimes (24 °C/14 °C or 28 °C/18 °C, day/night) were imposed to grapevine fruit-bearing cuttings from fruit set to maturity under greenhouse-controlled conditions. Elevated temperature hastened berry development, with a greater influence before the onset of ripening, and reduced anthocyanin concentration, colour intensity and titratable acidity. The clones significantly differed in the number of days that elapsed between fruit set and maturity. At the same concentration of total soluble solids, the anthocyanin concentration was lower at 28 °C/18 °C than 24 °C/14 °C, indicating a decoupling effect of elevated temperature during berry ripening. Thermal decoupling was explained by changes in the relative rate of response of anthocyanin and sugar build-up, rather than delayed onset of anthocyanin accumulation. Clones differed in the degree of thermal decoupling, but it was directly associated with differences neither in the length of their ripening period nor in plant vigour.
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Affiliation(s)
- Marta Arrizabalaga
- Universidad de Navarra, Faculty of Sciences, Plant Stress Physiology Group, Associated Unit to CSIC (EEAD, Zaragoza, and ICVV, Logroño), Irunlarrea, 1, 31008, Pamplona, Spain; Unité Mixte de Recherche, 1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), Bordeaux Sciences Agro, INRA, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, 33883, Villenave d'Ornon, France
| | - Fermín Morales
- Estación Experimental de Aula Dei (EEAD), CSIC, Department of Plant Nutrition, Apdo, 13034, 50080 Zaragoza, Spain
| | - Mónica Oyarzun
- Universidad de Navarra, Faculty of Sciences, Plant Stress Physiology Group, Associated Unit to CSIC (EEAD, Zaragoza, and ICVV, Logroño), Irunlarrea, 1, 31008, Pamplona, Spain
| | - Serge Delrot
- Unité Mixte de Recherche, 1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), Bordeaux Sciences Agro, INRA, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, 33883, Villenave d'Ornon, France
| | - Eric Gomès
- Unité Mixte de Recherche, 1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), Bordeaux Sciences Agro, INRA, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, 33883, Villenave d'Ornon, France
| | - Juan José Irigoyen
- Universidad de Navarra, Faculty of Sciences, Plant Stress Physiology Group, Associated Unit to CSIC (EEAD, Zaragoza, and ICVV, Logroño), Irunlarrea, 1, 31008, Pamplona, Spain
| | - Ghislaine Hilbert
- Unité Mixte de Recherche, 1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), Bordeaux Sciences Agro, INRA, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, 33883, Villenave d'Ornon, France
| | - Inmaculada Pascual
- Universidad de Navarra, Faculty of Sciences, Plant Stress Physiology Group, Associated Unit to CSIC (EEAD, Zaragoza, and ICVV, Logroño), Irunlarrea, 1, 31008, Pamplona, Spain.
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Tsugawa S, Hervieux N, Kierzkowski D, Routier-Kierzkowska AL, Sapala A, Hamant O, Smith RS, Roeder AHK, Boudaoud A, Li CB. Clones of cells switch from reduction to enhancement of size variability in Arabidopsis sepals. Development 2017; 144:4398-4405. [PMID: 29183944 PMCID: PMC5769632 DOI: 10.1242/dev.153999] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 04/30/2017] [Accepted: 10/20/2017] [Indexed: 12/16/2022]
Abstract
Organs form with remarkably consistent sizes and shapes during development, whereas a high variability in growth is observed at the cell level. Given this contrast, it is unclear how such consistency in organ scale can emerge from cellular behavior. Here, we examine an intermediate scale, the growth of clones of cells in Arabidopsis sepals. Each clone consists of the progeny of a single progenitor cell. At early stages, we find that clones derived from a small progenitor cell grow faster than those derived from a large progenitor cell. This results in a reduction in clone size variability, a phenomenon we refer to as size uniformization. By contrast, at later stages of clone growth, clones change their growth pattern to enhance size variability, when clones derived from larger progenitor cells grow faster than those derived from smaller progenitor cells. Finally, we find that, at early stages, fast growing clones exhibit greater cell growth heterogeneity. Thus, cellular variability in growth might contribute to a decrease in the variability of clones throughout the sepal. Summary: Growth analyses of Arabidopsis sepals identify a tipping point in organ development, at which clones of cells change their growth pattern from size uniformization to size variability enhancement.
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Affiliation(s)
- Satoru Tsugawa
- Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan
| | - Nathan Hervieux
- Laboratoire de Reproduction et Développement des Plantes, Universiteé de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Daniel Kierzkowski
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Anne-Lise Routier-Kierzkowska
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Aleksandra Sapala
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Universiteé de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Arezki Boudaoud
- Laboratoire de Reproduction et Développement des Plantes, Universiteé de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, INRA, CNRS, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Chun-Biu Li
- Department of Mathematics, Stockholm University, 106 91 Stockholm, Sweden
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Zheng J, Yamada Y, Fung TS, Huang M, Chia R, Liu DX. Identification of N-linked glycosylation sites in the spike protein and their functional impact on the replication and infectivity of coronavirus infectious bronchitis virus in cell culture. Virology 2018; 513:65-74. [PMID: 29035787 DOI: 10.1016/j.virol.2017.10.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/25/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022]
Abstract
Spike (S) glycoprotein on the viral envelope is the main determinant of infectivity. The S protein of coronavirus infectious bronchitis virus (IBV) contains 29 putative asparagine(N)-linked glycosylation sites. These post-translational modifications may assist in protein folding and play important roles in the functionality of S protein. In this study, we used bioinformatics tools to predict N-linked glycosylation sites and to analyze their distribution in IBV strains and variants. Among these sites, 8 sites were confirmed in the S protein extracted from partially purified virus particles by proteomics approaches. N-D and N-Q substitutions at 13 predicted sites were introduced into an infectious clone system. The impact on S protein-mediated cell-cell fusion, viral recovery and infectivity was assessed, leading to the identification of sites essential for the functions of IBV S protein. Further characterization of these and other uncharacterized sites may reveal novel aspects of N-linked glycosylation in coronavirus replication and pathogenesis.
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Li Z, Wang Y, Tian X, Shang P, Chen H, Kang X, Tian Y, Han R. Characterization of the visfatin gene and its expression pattern and effect on 3T3-L1 adipocyte differentiation in chickens. Gene 2017; 632:16-24. [PMID: 28851613 DOI: 10.1016/j.gene.2017.08.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/04/2017] [Accepted: 08/25/2017] [Indexed: 12/18/2022]
Abstract
Visfatin is a newly identified adipocytokine that plays an important role in the determination of fat traits. In this study, we investigated the characterization of visfatin and the relationship between gene expression and chicken development to provide a theoretical basis for studying visfatin functions. The main results are summarized as follows: The 1482-bp full coding sequence of the visfatin gene of silky fowl was obtained and found to encode 493 amino acids. This gene contains 26 phosphorylation sites and a conserved domain of the NAPRTase family but no signal peptide sequence. It exhibits six functional motifs, including an amidation site. In chickens, visfatin is a highly conserved protein. The highest expression of visfatin was found in breast muscle and the lowest in bone marrow. There was no difference in expression between visceral fat and subcutaneous fat. However, the expression of visfatin in the bone marrow, liver, kidneys, and subcutaneous and visceral fat of broiler chickens was significantly higher than that in silky fowl (P<0.05). Visfatin mRNA levels in the bone marrow decreased with development (P<0.05) but increased in the liver and leg muscle. Visfatin gene expression in the liver, heart and bone marrow did not differ in silky fowl according to sex. A visfatin fusion protein caused a significant increase in the expression of adipocyte differentiation markers (PPARγ, aP2, C/EBPα, and FAS) compared with the control group and a decrease compared with the insulin group. Taken together, the results of the present study contribute to a better understanding of the expression and role of the visfatin gene in chickens.
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Li X, Niu M, Su J, Ma Z, Jin M, Qiao W, Zhang Y, Feng Y, An N, Hou Y, Yang S, Chuan S, Lei Z. Cloning and expression patterns of neuromedin U and its receptors in pigs. Neuropeptides 2017; 64:47-60. [PMID: 28434792 DOI: 10.1016/j.npep.2017.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 11/19/2022]
Abstract
Neuromedin U (NMU) is a highly conserved neuropeptide that performs a variety of physiological functions in animals via neuromedin U receptor-1 (NMUR1) and neuromedin U receptor-2 (NMUR2). In this study, we cloned the pig NMU, NMUR1 and NMUR2 genes. Bioinformatics analysis demonstrated that the pig NMU cDNA encoded the amino acids Phe-Leu-Phe-Arg-Pro-Arg-Asn-NH2 at the C-terminus and that the NMU receptors, which are G-protein-coupled receptors (GPCRs), contained the seven transmembrane domains typical of GPCRs. Systemic NMU, NMUR1 and NMUR2 mRNA expression was investigated in various pig tissues using real-time RT-PCR. NMU mRNA was expressed both in the central nervous system (CNS) and in peripheral tissues. NMUR1 mRNA was widely expressed in peripheral tissues, whereas NMUR2 mRNA was mainly expressed in the CNS. Immunohistochemistry (IHC) was used to determine the expression patterns of NMU and NMUR1, which were predominantly located in the gastrointestinal tract, genitourinary organs, and immune organs. This study presents molecular and morphological data to aid in additional NMU research in pigs.
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Affiliation(s)
- Xiang Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China; College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, Henan, PR China
| | - Mingfu Niu
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, Henan, PR China
| | - Juan Su
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Zhiyu Ma
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Mengmeng Jin
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Wenna Qiao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Ying Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Yanyan Feng
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Na An
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Yuanlong Hou
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Sheng Yang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Suo Chuan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Zhihai Lei
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.
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Feng Y, Chen HL, Chen CJ, Chen CL, Chiu CH. Genome comparisons of two Taiwanese community-associated methicillin-resistant Staphylococcus aureus ST59 clones support the multi-origin theory of CA-MRSA. Infect Genet Evol 2017. [PMID: 28642157 DOI: 10.1016/j.meegid.2017.06.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Sequence type (ST) 59 is an epidemic lineage of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) in Asia. Two ST59 clones are prevalent in Taiwan: the Taiwan clone (TW) causes severe infections, whereas the Asian-Pacific clone (AP) is usually commensal. In this study, we sequenced the genome and transcriptome of the representative strains of these two clones and found their differences to focus on three mobile genetic elements: TW carries SCCmec Type VT, Panton-Valentine leucocidin (PVL)-encoding prophage ΦSa2, whereas AP carries SCCmec Type IV and staphylokinase (SAK)-encoding prophage ΦSa3. The anti-virulent role of SAK was confirmed using murine skin and bloodstream infection models. ΦSa3 usually integrates into the hlb gene, but in AP was found to be integrated at the genomic island νSaβ. The mutation of the attB site "TGTATCCAAACTGG" to "TGTATCCGAATTGG" led to a failure in the integration of ΦSa3 in hlb, prompting atypical integration at other sites. The sak gene possessed remarkably different patterns of distribution among the different STs of S. aureus. We conclude that the atypical integration of ΦSa3 may help S. aureus adapt to the human host habitat and that the subsequent loss of ΦSa3 contributes toward the development of a virulent CA-MRSA lineage for wider horizontal transmission.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Hsiu-Ling Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chih-Jung Chen
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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Abstract
In biology, the term "clone" is most widely used to designate genetically identical cells or organisms that are asexually descended from a common progenitor. The concept of clonality in hematology-oncology has received much attention in recent years, as the advent of next-generation sequencing platforms has provided new tools for detection of clonal populations in patients, and experiments on primary cells have provided fascinating new insights into the clonal architecture of human malignancies. The term "clone" is used more loosely by the general public to mean any close or identical copy. Cloning of humans has been a staple of science fiction films and dystopian novels since Aldous Huxley's Brave New World was published in 1932. Here I trace the origin and evolution of the word clone, from its first use as an agricultural and botanical term in 1903, to its widespread adoption in biology, adaptation by artists, and contemporary use in hematology-oncology.
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Ruppé E, Olearo F, Pires D, Baud D, Renzi G, Cherkaoui A, Goldenberger D, Huttner A, François P, Harbarth S, Schrenzel J. Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing. Clin Microbiol Infect 2017; 23:470-5. [PMID: 28143787 DOI: 10.1016/j.cmi.2017.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/11/2017] [Accepted: 01/21/2017] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Whole-genome sequencing (WGS) is a promising tool for identifying transmission pathways in outbreaks caused by multidrug-resistant bacteria. However, it is uncertain how the data produced by WGS can be best integrated into epidemiologic investigations. METHODS We tested various genomic analyses to identify clonal groups in two distinct outbreaks of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae that occurred in Switzerland in 2013 and 2015. In blinded fashion, we sequenced 12 strains involved in the two outbreaks, respectively, and six that were epidemiologically unrelated. We analysed genomic commonalities from conserved genes to plasmid-borne antibiotic resistance genes (ARGs) and contrasted these results with available epidemiologic evidence. RESULTS Using WGS, blinded analysts correctly identified the two clusters of strains from the two outbreaks. Nonetheless, the 2015 index strain was found to be slightly different (1-3 single nucleotide variants) from the strains recovered from secondary cases, likely because prior long-term carriage (3 years) by the index patient allowed for genetic mutations over time. Also, we observed occasional loss of ARG-bearing plasmidic fragments in outbreak-causing strains. CONCLUSIONS Retrospective WGS analysis was successful in identifying clonal groups in both outbreaks. Still, data should be analysed with caution in cases of previous long-term carriage of the studied bacteria.
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? Adv Parasitol 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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Tortosa I, Escalona JM, Bota J, Tomás M, Hernández E, Escudero EG, Medrano H. Exploring the genetic variability in water use efficiency: Evaluation of inter and intra cultivar genetic diversity in grapevines. Plant Sci 2016; 251:35-43. [PMID: 27593461 DOI: 10.1016/j.plantsci.2016.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 05/21/2023]
Abstract
Genetic improvement of crop Water Use Efficiency (WUE) is a general goal because the increasing water scarcity and the trend to a more sustainable agriculture. For grapevines, this subject is relevant and need an urgent response because their wide distribution in semi-arid areas. New cultivars are difficult to introduce in viticulture due to the narrow dependency of consumer appreciation often linked to a certain particular wine taste. Clones of reputed cultivars would presumably be more accepted but little is known on the intra-cultivar genetic variability of the WUE. The present work compares, on the basis of two field assays, the variability of intrinsic water use efficiency (WUEi) in a large collection of cultivars in contrast with a collection of clones of Tempranillo cultivar. The results show that clonal variability of WUEi was around 80% of the inter-cultivar, thus providing a first assessment on the opportunity for clonal selection by WUE. Plotting the WUEi data against stem water potential or stomatal conductance it was possible to identify cultivars and clones out of the confidence intervals of this linear regression thus with significantly higher and lower WUEi values. The present results contribute to open the expectative for a genetic improvement of grapevine WUE.
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Affiliation(s)
- Ignacio Tortosa
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - José Mariano Escalona
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - Josefina Bota
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - Magdalena Tomás
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | - Esther Hernández
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain
| | | | - Hipólito Medrano
- Research Group on Plant Biology Under Mediterranean Conditions, Department of Biology, IMEDEA (CSIC-Universitat de les Illes Balears), Carretera de Valldemossa Km 7.5, 07122 Palma de Mallorca, Spain.
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