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Steinhauser S, Estoppey D, Buehler DP, Xiong Y, Pizzato N, Rietsch A, Wu F, Leroy N, Wunderlin T, Claerr I, Tropberger P, Müller M, Davison LM, Sheng Q, Bergling S, Wild S, Moulin P, Liang J, English WJ, Williams B, Knehr J, Altorfer M, Reyes A, Mickanin C, Hoepfner D, Nigsch F, Frederiksen M, Flynn CR, Fodor BD, Brown JD, Kolter C. The transcription factor ZNF469 regulates collagen production in liver fibrosis. bioRxiv 2024:2024.04.25.591188. [PMID: 38712281 PMCID: PMC11071482 DOI: 10.1101/2024.04.25.591188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world's population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.
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Villabona N, Moran N, Hammer T, Reyes A. Conserved, yet disruption-prone, gut microbiomes in neotropical bumblebees. mSphere 2023; 8:e0013923. [PMID: 37855643 PMCID: PMC10732019 DOI: 10.1128/msphere.00139-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/05/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Social bees are an important model for the ecology and evolution of gut microbiomes. These bees harbor ancient, specific, and beneficial gut microbiomes and are crucial pollinators. However, most of the research has concentrated on managed honeybees and bumblebees in the temperate zone. Here we used 16S rRNA gene sequencing to characterize gut microbiomes in wild neotropical bumblebee communities from Colombia. We also analyzed drivers of microbiome structure across our data and previously published data from temperate bumblebees. Our results show that lineages of neotropical bumblebees not only retained their ancient gut bacterial symbionts during dispersal from North America but also are prone to major disruption, a shift that is strongly associated with parasite infection. Finally, we also found that microbiomes are much more strongly structured by host phylogeny than by geography, despite the very different environmental conditions and plant communities in the two regions.
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Affiliation(s)
- Nickole Villabona
- Research Group on Computational Biology and Microbial Ecology, Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Nancy Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Tobin Hammer
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Alejandro Reyes
- Research Group on Computational Biology and Microbial Ecology, Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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Byun H, Singh GB, Xu WK, Das P, Reyes A, Battenhouse A, Wylie DC, Lozano MM, Dudley JP. Apobec-Mediated Retroviral Hypermutation In Vivo is Dependent on Mouse Strain. bioRxiv 2023:2023.11.02.565355. [PMID: 37961113 PMCID: PMC10635078 DOI: 10.1101/2023.11.02.565355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Replication of the complex retrovirus mouse mammary tumor virus (MMTV) is antagonized by murine Apobec3 (mA3), a member of the Apobec family of cytidine deaminases. We have shown that MMTV-encoded Rem protein inhibits proviral mutagenesis by the Apobec enzyme, activation-induced cytidine deaminase (AID) during viral replication in BALB/c mice. To further study the role of Rem in vivo , we have infected C57BL/6 (B6) mice with a superantigen-independent lymphomagenic strain of MMTV (TBLV-WT) or a mutant strain (TBLV-SD) that is defective in Rem and its cleavage product Rem-CT. Unlike MMTV, TBLV induced T-cell tumors in µMT mice, indicating that mature B cells, which express the highest AID levels, are not required for TBLV replication. Compared to BALB/c, B6 mice were more susceptible to TBLV infection and tumorigenesis. The lack of Rem expression accelerated B6 tumorigenesis at limiting doses compared to TBLV-WT in either wild-type B6 or AID-deficient mice. However, unlike proviruses from BALB/c mice, high-throughput sequencing indicated that proviral G-to-A or C-to-T changes did not significantly differ in the presence and absence of Rem expression. Ex vivo stimulation showed higher levels of mA3 relative to AID in B6 compared to BALB/c splenocytes, but effects of agonists differed in the two strains. RNA-Seq revealed increased transcripts related to growth factor and cytokine signaling in TBLV-SD-induced tumors relative to those from TBLV-WT, consistent with a third Rem function. Thus, Rem-mediated effects on tumorigenesis in B6 mice are independent of Apobec-mediated proviral hypermutation.
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Fernández-Barrés S, Perez G, Piñero M, Reyes A, Pérez K, Artazcoz L, Borrell C. Effect of COVID-19 prevention as part of an urban renewal programme. Public Health 2023; 223:179-182. [PMID: 37666182 DOI: 10.1016/j.puhe.2023.07.014] [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: 05/23/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 09/06/2023]
Abstract
OBJECTIVES To address existing inequalities, the Barcelona City Council launched a Neighbourhood Plan in 2016-2020. During the first wave of the COVID-19 pandemic, the Neighbourhood Plan interventions were intensified. This study aimed to assess the effect of the plan on the incidence of COVID-19 during the first wave of the pandemic in Barcelona. STUDY DESIGN We used a quasi-experimental design with 16 intervention neighbourhoods and 17 neighbourhoods in the comparison group with similar socioeconomic characteristics. METHODS We calculated the cumulative incidence rate (CIR) of COVID-19 per 100,000 inhabitants by sex, age groups, and neighbourhood of residence. Poisson regression models were fitted to estimate the crude relative risk and relative risk adjusted by socioeconomic status (cRR and aRR) and their 95% confidence intervals (CIs). RESULTS The CIR of COVID-19 was lower in the intervention neighbourhoods (CIR: 841 per 100,000 inhabitants) than in the comparison group (CIR: 973 per 100,000 inhabitants). On multivariate analysis, the aRR was 0.77 (CI: 0.70-0.83) for men and 0.89 (CI: 0.83-0.96) for women. Among men older than 75 years (aRR = 0.73; CI: 0.62-0.86), statistically significant differences were found in the intervention neighbourhoods compared to the comparison group. This pattern was not observed in women older than 75 years (aRR = 1.13; CI: 0.99-1.30). CONCLUSION This research finds positive short-term effect in the intervention neighbourhoods. We conclude that the COVID-19 control and prevention interventions are likely to explain the better performance in the neighbourhoods included in the Neighbourhood Plan.
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Affiliation(s)
| | - G Perez
- Agència de Salut Pública de Barcelona (ASPB), Barcelona, Spain; Institut D'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Universitat Pompeu Fabra, Barcelona, Spain.
| | - M Piñero
- Agència de Salut Pública de Barcelona (ASPB), Barcelona, Spain
| | - A Reyes
- Agència de Salut Pública de Barcelona (ASPB), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - K Pérez
- Agència de Salut Pública de Barcelona (ASPB), Barcelona, Spain; Institut D'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - L Artazcoz
- Agència de Salut Pública de Barcelona (ASPB), Barcelona, Spain; Institut D'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - C Borrell
- Agència de Salut Pública de Barcelona (ASPB), Barcelona, Spain; Institut D'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Universitat Pompeu Fabra, Barcelona, Spain
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Orr ME, Hopper AB, Salans MA, Reyes A, Stasenko A, Sanghvi P, McDonald C, Hattangadi-Gluth JA, Karunamuni R. Quantitative Analysis of BrainAge using Neuroimaging Data to Estimate Radiation-Induced Brain Aging and Associations with Cognitive Changes in Brain Metastases Patients. Int J Radiat Oncol Biol Phys 2023; 117:e143. [PMID: 37784718 DOI: 10.1016/j.ijrobp.2023.06.955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiotherapy is critical in brain tumor management yet causes accelerated aging via irreparable damage to white matter, cortex, and subcortical areas. BrainAGE is an open-source machine learning tool that analyses morphology from raw quantitative structural MRI to generate a predictive 'BrainAge' value, enabling analyses of patients with neurodegenerative diseases. We assessed the utility of this algorithm in measuring brain age morphology in brain metastases patients on a clinical trial, analyzed differences in BrainAge and chronological age, and explored associations with cognitive performance. MATERIALS/METHODS We analyzed pre-SRS high-resolution T1-weighted noncontrast volumetric MRI in patients with brain metastases (n = 57, median age 63 years, range 20-87) treated on a prospective clinical trial of cognitive-sparing SRS. The BrainAGE machine learning tool processed images to derive a BrainAge; it reliably generates this value using a Gaussian Processes regression, with a robust neurotypical training cohort. We examined correlations between BrainAge and chronological age with regression. Brain-predicted age gap (Brain-Gap) was calculated, defined as the difference between a patient's BrainAge and chronological age. We assessed cognitive function at baseline pre-SRS with a comprehensive battery of validated tests across multiple domains performed by a neuropsychologist, including memory (HVLT total), executive function (COWAT category fluency), and language (COWAT letter fluency). Raw test scores were scaled to T-scores adjusting for age, sex, and education level per testing norms. We examined if Brain-Gap was associated with cognitive performance pre-SRS. RESULTS BrainAGE software was robust, estimating a BrainAge for all input MRI sequences. We found a strong correlation between BrainAge and chronological age (r-squared = 0.82). The Brain-Gap median value was 0.84 and the mean was -0.90, in years (range -18.30-11.36 years). Brain-Gap was not significantly associated with cognitive performance across the three tests at the pre-SRS timepoint. Among patients with impaired cognition (T<35), there was no significant difference in BrainAge relative to chronological age. CONCLUSION To our knowledge, this is the first study utilizing the BrainAGE model as a biomarker of neuroanatomical age for brain tumors patients. Existing publications had lesion-free cohorts. Our results show that BrainAge was reliably associated with chronologic age in brain metastases patients pre-SRS. The Brain-Gap difference was minimal at baseline, and we found no significant association with pre-SRS cognitive performance. Future studies will examine this biomarker after SRS to look for individual aging radiation effects and prediction for cognitive changes after therapy.
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Affiliation(s)
- M E Orr
- Department of Radiation Medicine and Applied Sciences, UC San Diego, La Jolla, CA
| | - A B Hopper
- Department of Radiation Medicine and Applied Sciences, UC San Diego, La Jolla, CA
| | - M A Salans
- University of California San Francisco, San Francisco, CA
| | - A Reyes
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - A Stasenko
- Department of Psychiatry, University of California San Diego, La Jolla, CA
| | - P Sanghvi
- Department of Radiation Medicine and Applied Sciences, UC San Diego, La Jolla, CA
| | - C McDonald
- Department of Radiation Medicine and Applied Sciences, UC San Diego, La Jolla, CA
| | - J A Hattangadi-Gluth
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - R Karunamuni
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA; Department of Computer Science and Engineering, UC San Diego, La Jolla, CA
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Ciampi E, Soler B, Uribe-San-Martin R, Jürgensen L, Guzman I, Keller K, Reyes A, Bravo-Grau S, Cruz JP, Cárcamo C. Socioeconomic, health-care access and clinical determinants of disease severity in Multiple Sclerosis in Chile. Mult Scler Relat Disord 2023; 78:104918. [PMID: 37562199 DOI: 10.1016/j.msard.2023.104918] [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: 04/12/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND MS severity may be affected by genetic, patient-related, disease-related and environmental factors. Socioeconomic status, including income and healthcare access, amongst others, may also have a role in affecting diagnostic delay or therapy prescription. In Chile, two main healthcare systems exist, public-healthcare and private-healthcare, nonetheless universal care laws (e.g., access to High Efficacy Therapy-HET), including both systems, have been recently enacted for people with MS. OBJECTIVE To assess the role of Socioeconomic Conditions (SEC), clinical variables and public health policies on the impact of disease severity of MS patients in Chile. METHODS Multicentric, observational, cross-sectional study including patients from two reference centres (1 national reference centre from the private-health system and 1 regional reference centre from the public-health system). SEC and clinical variables included healthcare insurance (private or public), subclassification of health insurance according to monthly income, sex, age at onset, diagnostic delay, disease duration, diagnosis before HET law (as a proxy of HET delay), and current HET treatment. Progression Index (PI), EDSS ≥6.0 and Progressive MS diagnosis were used as outcome measures. Multivariable binary logistic regression was performed. RESULTS We included 604 patients (460 private-health, 144 public-health), 67% women, 100% white/mestizo, 88% RRMS, mean age 42±12 years, mean age at onset 32±11 years, mean disease duration 10±6 years, median diagnostic delay 0 (0-34) years, 86% currently receiving any DMT, 55% currently receiving HET, median EDSS at last visit of 2.0 (0-10), and median PI 0.17 (0-4.5). Lower monthly income was associated with higher EDSS and higher PI. In the multivariable analysis, public-healthcare (OR 10.2), being diagnosed before HET-law (OR 4.89), longer diagnostic delay (OR 1.26), and older age at onset (OR 1.05) were associated with a higher risk of PI>0.2, while current HET (OR 0.39) was a protective factor. Diagnosis before HET-law (OR 7.59), public-healthcare (OR 6.49), male sex (OR 2.56), longer disease duration (OR 1.2) and older age at onset (OR 1.1) were associated with a higher risk of Progressive MS. Public-healthcare (OR 5.54), longer disease duration (OR 1.14) and older age at onset (OR 1.08) were associated with a higher risk of EDSS ≥6.0 while current treatment with HET had a trend as being a protective factor (OR 0.44, p = 0.05). CONCLUSION MS severity is impacted by non-modifiable factors such as sex and age at onset. Interventions focused on shortening diagnostic delay and encouraging early access to high-efficacy therapies, as well as initiatives that may reduce the disparities inherent to lower socioeconomic status, may improve outcomes in people with MS.
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Affiliation(s)
- E Ciampi
- Neurology Department, Pontificia Universidad Católica de Chile, Santiago, Chile; Neurology Service, Hospital Sótero del Río, Santiago, Chile.
| | - B Soler
- Neurology Department, Pontificia Universidad Católica de Chile, Santiago, Chile; Neurology Service, Hospital Sótero del Río, Santiago, Chile
| | - R Uribe-San-Martin
- Neurology Department, Pontificia Universidad Católica de Chile, Santiago, Chile; Neurology Service, Hospital Sótero del Río, Santiago, Chile
| | - L Jürgensen
- Neurology Department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - I Guzman
- Neurology Department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - K Keller
- Neurology Department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - A Reyes
- Neurology Department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - S Bravo-Grau
- Neurorradiology Department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - J P Cruz
- Neurorradiology Department, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - C Cárcamo
- Neurology Department, Pontificia Universidad Católica de Chile, Santiago, Chile
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7
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Hopper AB, Connor M, Salans MA, Unnikrishnan S, Huynh-Le MP, Tibbs MD, Qian AS, Reyes A, Stasenko A, McDonald C, Moiseenko V, Hattangadi-Gluth JA. Evidence-Based Multivariate Normal Tissue Complication Probability (NTCP) Study of Domain-Specific Cognitive Decline after Partial Brain RT. Int J Radiat Oncol Biol Phys 2023; 117:S75-S76. [PMID: 37784568 DOI: 10.1016/j.ijrobp.2023.06.388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Beyond the hippocampus, there are no evidence-based dose constraints for eloquent brain structures which subserve memory and attention/processing speed. We performed a multivariate normal tissue complication probability analysis of post-RT neurocognitive decline, examining dosimetric predictors of eloquent brain regions. MATERIALS/METHODS Data were analyzed from a prospective longitudinal clinical trial. Patients (n = 78) with primary brain tumors receiving fractionated RT complete a comprehensive neurocognitive evaluation and high-resolution volumetric and diffusion MRI at baseline and 6 months post-RT. Image processing using robust, validated automated segmentation parcellated individual WM tracts, cortical regions, and hippocampi. Well-validated neurocognitive tests including Delis-Kaplan Executive Function System and Wechsler Adult Intelligence Scale-IV coding (attention/processing), Boston Naming Test (language) and Hopkins Verbal Learning Test and Brief Visuospatial Memory Test (verbal/visuospatial memory) were assessed. Reliable change indices adjusted for practice effects (RCI-PE) were calculated for each patient between baseline and 6 months; a negative RCI-PE was scored as decline. Univariate logistic regression was performed with mean and max dose to structures of interest as well as clinical variables. Multivariate model building was performed using automated bootstrapped logistic regression, LASSO and random forest modeling. RESULTS On univariate analysis mean and max dose to multiple regions of the corpus callosum (CC) were correlated with attention/processing speed decline; most significantly in WAIS coding, including Dmax to the anterior CC (p = 0.011) and central CC (p = 0.010), and Dmax and Dmean to the mid anterior CC (p = 0.006 and 0.010). Mean dose to the left fornix was associated with decline in memory (p = 0.023, cutoff 12.9 Gy), as were increasing age and both concurrent and adjuvant chemotherapy. On multivariate analysis for attention, automated bootstrapped logistic regression showed the most frequently selected variable was mean dose to the mid anterior CC. Performance at nested cross-validation by AUC was 0.80 (0.75-0.84); LASSO model performance by AUC was 0.76 (0.72-0.81) with Dmean to the mid anterior CC being the most frequent variable. The top five most important variables in the Random Forest as ranked by mean decrease in Gini coefficient were mean dose to mid anterior CC, all white matter, combined CC and max dose to CC and posterior CC. Model performance by AUC was 0.66 (0.60-0.71). CONCLUSION Here, we present the first, to our knowledge, NTCP model for decline in attention/processing speed, along with dosimetric predictors of memory decline beyond the hippocampus. We found that after partial brain RT, dose to several ROIs significantly correlated with post-RT impairment. These data can guide future cognitive-sparing strategies for brain RT.
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Affiliation(s)
- A B Hopper
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - M Connor
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - M A Salans
- University of California San Francisco, San Francisco, CA
| | - S Unnikrishnan
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - M P Huynh-Le
- Radiation Oncology, The Brooklyn Cancer Center, Brooklyn, NY
| | - M D Tibbs
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - A S Qian
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - A Reyes
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - A Stasenko
- Department of Psychiatry, University of California San Diego, La Jolla, CA
| | - C McDonald
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA; Department of Psychiatry, University of California San Diego, La Jolla, CA
| | - V Moiseenko
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
| | - J A Hattangadi-Gluth
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, CA
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Adriaenssens EM, Roux S, Brister JR, Karsch-Mizrachi I, Kuhn JH, Varsani A, Yigang T, Reyes A, Lood C, Lefkowitz EJ, Sullivan MB, Edwards RA, Simmonds P, Rubino L, Sabanadzovic S, Krupovic M, Dutilh BE. Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification. Nat Biotechnol 2023; 41:1346. [PMID: 37608068 DOI: 10.1038/s41587-023-01952-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Affiliation(s)
- Evelien M Adriaenssens
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, UK.
| | - Simon Roux
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Tong Yigang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, CH, the Netherlands
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Castellanos A, Restrepo L, Bajaña L, Betancourt I, Bayot B, Reyes A. Genomic and Evolutionary Features of Nine AHPND Positive Vibrio parahaemolyticus Strains Isolated from South American Shrimp Farms. Microbiol Spectr 2023; 11:e0485122. [PMID: 37272817 PMCID: PMC10433878 DOI: 10.1128/spectrum.04851-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Vibrio parahaemolyticus is a bacterial pathogen that becomes lethal to Penaeus shrimps when acquiring the pVA1-type plasmid carrying the PirABvp genes, causing acute hepatopancreatic necrosis disease (AHPND). This disease causes significant losses across the world, with outbreaks reported in Southeast Asia, Mexico, and South America. Virulence level and mortality differences have been reported in isolates from different locations, and whether this phenomenon is caused by plasmid-related elements or genomic-related elements from the bacteria remains unclear. Here, nine genomes of South American AHPND-causing V. parahaemolyticus (VPAHPND) isolates were assembled and analyzed using a comparative genomics approach at (i) whole-genome, (ii) secretion system, and (iii) plasmid level, and then included for a phylogenomic analysis with another 86 strains. Two main results were obtained from our analyses. First, all isolates contained pVA1-type plasmids harboring the toxin coding genes, and with high similarity with the prototypical sequence of Mexican-like origin, while phylogenomic analysis showed some level of heterogeneity with discrete clusters and wide diversity compared to other available genomes. Second, although a high genomic similarity was observed, variation in virulence genes and clusters was observed, which might be relevant in the expression of the disease. Overall, our results suggest that South American pathogenic isolates are derived from various genetic lineages which appear to have acquired the plasmid through horizontal gene transfer. Furthermore, pathogenicity seems to be a multifactorial trait where the degree of virulence could be altered by the presence or variations of several virulence factors. IMPORTANCE AHPND have caused losses of over $2.6 billion to the aquaculture industry around the world due to its high mortality rate in shrimp farming. The most common etiological agent is V. parahaemolyticus strains possessing the pVA1-type plasmid carrying the PirABvp toxin. Nevertheless, complete understanding of the role of genetic elements and their impact in the virulence of this pathogen remains unclear. In this work, we analyzed nine South American AHPND-causing V. parahaemolyticus isolates at a genomic level, and assessed their evolutionary relationship with other 86 strains. We found that all our isolates were highly similar and possessed the Mexican-type plasmid, but their genomic content did not cluster with other Mexican strains, but instead were spread across all isolates. These results suggest that South American VPAHPND have different genetic backgrounds, and probably proceed from diverse geographical locations, and acquire the pVA1-type plasmid via horizontal gene transfer at different times.
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Affiliation(s)
- Alejandro Castellanos
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Leda Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
- Postdoctoral Training in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Guayaquil, Ecuador
| | - Leandro Bajaña
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Guayaquil, Ecuador
| | - Irma Betancourt
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Guayaquil, Ecuador
| | - Bonny Bayot
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Guayaquil, Ecuador
- Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ingeniería Marítima y Ciencias del Mar, FIMCM, Guayaquil, Ecuador
| | - Alejandro Reyes
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
- Center for Genome Sciences and Systems Biology, Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, Missouri, USA
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10
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Smitherman EA, Chahine RA, Beukelman T, Lewandowski LB, Rahman AKMF, Wenderfer SE, Curtis JR, Hersh AO, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar‐Smiley F, Barillas‐Arias L, Basiaga M, Baszis K, Becker M, Bell‐Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang‐Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel‐Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie‐Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui‐Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein‐Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PM, McGuire S, McHale I, McMonagle A, McMullen‐Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O'Brien B, O'Brien T, Okeke O, Oliver M, Olson J, O'Neil K, Onel K, Orandi A, Orlando M, Osei‐Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan‐Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas‐Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth‐Wojcicki E, Rouster – Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert‐Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner‐Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Childhood-Onset Lupus Nephritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: Short-Term Kidney Status and Variation in Care. Arthritis Care Res (Hoboken) 2023; 75:1553-1562. [PMID: 36775844 PMCID: PMC10500561 DOI: 10.1002/acr.25002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/14/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE The goal was to characterize short-term kidney status and describe variation in early care utilization in a multicenter cohort of patients with childhood-onset systemic lupus erythematosus (cSLE) and nephritis. METHODS We analyzed previously collected prospective data from North American patients with cSLE with kidney biopsy-proven nephritis enrolled in the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry from March 2017 through December 2019. We determined the proportion of patients with abnormal kidney status at the most recent registry visit and applied generalized linear mixed models to identify associated factors. We also calculated frequency of medication use, both during induction and ever recorded. RESULTS We identified 222 patients with kidney biopsy-proven nephritis, with 64% class III/IV nephritis on initial biopsy. At the most recent registry visit at median (interquartile range) of 17 (8-29) months from initial kidney biopsy, 58 of 106 patients (55%) with available data had abnormal kidney status. This finding was associated with male sex (odds ratio [OR] 3.88, 95% confidence interval [95% CI] 1.21-12.46) and age at cSLE diagnosis (OR 1.23, 95% CI 1.01-1.49). Patients with class IV nephritis were more likely than class III to receive cyclophosphamide and rituximab during induction. There was substantial variation in mycophenolate, cyclophosphamide, and rituximab ever use patterns across rheumatology centers. CONCLUSION In this cohort with predominately class III/IV nephritis, male sex and older age at cSLE diagnosis were associated with abnormal short-term kidney status. We also observed substantial variation in contemporary medication use for pediatric lupus nephritis between pediatric rheumatology centers. Additional studies are needed to better understand the impact of this variation on long-term kidney outcomes.
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11
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Adriaenssens EM, Roux S, Brister JR, Karsch-Mizrachi I, Kuhn JH, Varsani A, Yigang T, Reyes A, Lood C, Lefkowitz EJ, Sullivan MB, Edwards RA, Simmonds P, Rubino L, Sabanadzovic S, Krupovic M, Dutilh BE. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification. Nat Biotechnol 2023; 41:898-902. [PMID: 37430074 PMCID: PMC10526704 DOI: 10.1038/s41587-023-01844-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Affiliation(s)
- Evelien M Adriaenssens
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, UK.
| | - Simon Roux
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Tong Yigang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, CH, the Netherlands
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12
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Oliveira LS, Reyes A, Dutilh BE, Gruber A. Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons. Viruses 2023; 15:519. [PMID: 36851733 PMCID: PMC9966878 DOI: 10.3390/v15020519] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profile HMMs. These methods were implemented on TABAJARA, a program that can be used to either detect all biological sequences of a group or discriminate specific groups of sequences. By calculating position-specific information scores along a multiple sequence alignment, TABAJARA automatically identifies the most informative sequence motifs and uses them to construct profile HMMs. As a proof-of-principle, we applied TABAJARA to generate profile HMMs for the detection and classification of two viral groups presenting different evolutionary rates: bacteriophages of the Microviridae family and viruses of the Flavivirus genus. We obtained conserved models for the generic detection of any Microviridae or Flavivirus sequence, and profile HMMs that can specifically discriminate Microviridae subfamilies or Flavivirus species. In another application, we constructed Cas1 endonuclease-derived profile HMMs that can discriminate CRISPRs and casposons, two evolutionarily related transposable elements. We believe that the protocols described here, and implemented on TABAJARA, constitute a generic toolbox for generating profile HMMs for the highly sensitive and specific detection of sequence classes.
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Affiliation(s)
- Liliane S. Oliveira
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Arthur Gruber
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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13
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Sutcliffe SG, Reyes A, Maurice CF. Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota. iScience 2023; 26:106007. [PMID: 36798434 PMCID: PMC9926308 DOI: 10.1016/j.isci.2023.106007] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/28/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Bacteriophages, viruses specific to bacteria, coexist with their bacterial hosts with limited diversity fluctuations in the guts of healthy individuals where they replicate mostly via lysogenic replication. This favors 'piggy-back-the-winner' over 'kill-the-winner' dynamics which are driven by lytic bacteriophage replication. Revisiting the deep-viral sequencing data of a healthy individual sampled over 2.4 years, we explore how these dynamics occur. Prophages found in assembled bacterial metagenomes were also found extra-cellularly, as induced phage particles (iPPs), likely derived from prophage activation. These iPPs were diverse and continually present in low abundance, relative to the highly abundant but less diverse lytic phage population. The continuous detection of low levels of iPPs suggests that spontaneous induction regularly occurs in this healthy individual, possibly allowing prophages to maintain their ability to replicate and avoiding degradation and loss from the gut microbiota.
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Affiliation(s)
- Steven G. Sutcliffe
- McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA,Corresponding author
| | - Corinne F. Maurice
- McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada,Corresponding author
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14
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Thorndyke MP, Guimaraes O, Medrado M, Loh HY, Tangredi BV, Reyes A, Barrington RK, Schmidt K, Tillquist NM, Li L, Ippolito JA, Zervoudakis JT, Wagner JJ, Engle TE. The Effects of Long-term Molybdenum Exposure in Drinking Water on Molybdenum Metabolism and Production Performance of Beef Cattle Consuming a High Forage Diet. Biol Trace Elem Res 2023:10.1007/s12011-022-03532-9. [PMID: 36600169 DOI: 10.1007/s12011-022-03532-9] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023]
Abstract
Fifty-four multiparous beef cows with calves were used to evaluate the effects of Mo source (feed or water) on reproduction, mineral status, and performance over two cow-calf production cycles (553 days). Cows were stratified by age, body weight, liver Cu, and Mo status and were then randomly assigned to one of six treatment groups. Treatments were (1) negative control (NC; basal diet with no supplemental Mo or Cu), (2) positive control (NC + Cu; 3 mg of supplemental Cu/kg DM), (3) NC + 500 µg Mo/L from Na2MoO4·2H2O supplied in drinking water, (4) NC + 1000 µg Mo/L of Na2MoO4·2H2O supplied in drinking water, (5) NC + Mo 1000-water + 3 mg of supplemental Cu/kg DM, and (6) NC + 3.0 mg of supplemental Mo/kg diet DM from Na2MoO4·2H2O. Animals were allowed ad libitum access to both harvested grass hay (DM basis: 6.6% crude protein; 0.15% S, 6.7 mg Cu/kg, 2.4 mg Mo/kg) and water throughout the experiment. Calves were weaned at approximately 6 months of age each year. Dietary Cu concentration below 10.0 mg Cu/kg DM total diet reduced liver and plasma Cu concentrations to values indicative of a marginal Cu deficiency in beef cows. However, no production parameters measured in this experiment were affected by treatment. Results suggest that Mo supplemented in water or feed at the concentrations used in this experiment had minimal impact on Cu status and overall performance.
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Affiliation(s)
- M P Thorndyke
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - O Guimaraes
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - M Medrado
- Department of Animal Science, Faculdade de Ciências Agrárias E Jaboticabal, Jaboticabal, Sao Paulo, Brasil
| | - H Y Loh
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - B V Tangredi
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - A Reyes
- Department of Animal Science, University of WI - River Falls, River Falls, USA
| | - R K Barrington
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - K Schmidt
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - N M Tillquist
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - L Li
- Department of Environmental Science, Henan University of Technology, Zhengzhou, Henan, China
| | - J A Ippolito
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - J T Zervoudakis
- Department of Animal Science, Universidade Federal de Mato Grosso, Cuiaba, Mato Grosso, Brazil
| | - J J Wagner
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA
| | - T E Engle
- Department of Animal Science, Colorado State University, Fort Collins, CO, USA.
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15
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Hahn T, Daymont C, Beukelman T, Groh B, Hays K, Bingham CA, Scalzi L, Abel N, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar-Smiley F, Barillas-Arias L, Basiaga M, Baszis K, Becker M, Bell-Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang-Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel-Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie-Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui-Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein-Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PMC, McGuire S, McHale I, McMonagle A, McMullen-Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O’Brien B, O’Brien T, Okeke O, Oliver M, Olson J, O’Neil K, Onel K, Orandi A, Orlando M, Osei-Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan-Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas-Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth-Wojcicki E, Rouster-Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert-Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner-Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Intraarticular steroids as DMARD-sparing agents for juvenile idiopathic arthritis flares: Analysis of the Childhood Arthritis and Rheumatology Research Alliance Registry. Pediatr Rheumatol Online J 2022; 20:107. [PMID: 36434731 PMCID: PMC9701017 DOI: 10.1186/s12969-022-00770-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/08/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Children with juvenile idiopathic arthritis (JIA) who achieve a drug free remission often experience a flare of their disease requiring either intraarticular steroids (IAS) or systemic treatment with disease modifying anti-rheumatic drugs (DMARDs). IAS offer an opportunity to recapture disease control and avoid exposure to side effects from systemic immunosuppression. We examined a cohort of patients treated with IAS after drug free remission and report the probability of restarting systemic treatment within 12 months. METHODS We analyzed a cohort of patients from the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry who received IAS for a flare after a period of drug free remission. Historical factors and clinical characteristics and of the patients including data obtained at the time of treatment were analyzed. RESULTS We identified 46 patients who met the inclusion criteria. Of those with follow up data available 49% had restarted systemic treatment 6 months after IAS injection and 70% had restarted systemic treatment at 12 months. The proportion of patients with prior use of a biologic DMARD was the only factor that differed between patients who restarted systemic treatment those who did not, both at 6 months (79% vs 35%, p < 0.01) and 12 months (81% vs 33%, p < 0.05). CONCLUSION While IAS are an option for all patients who flare after drug free remission, it may not prevent the need to restart systemic treatment. Prior use of a biologic DMARD may predict lack of success for IAS. Those who previously received methotrexate only, on the other hand, are excellent candidates for IAS.
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Affiliation(s)
- Timothy Hahn
- Department of Pediatrics, Penn State Children's Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA, 17033-0855, USA.
| | - Carrie Daymont
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | - Timothy Beukelman
- grid.265892.20000000106344187Department of Pediatrics, University of Alabama at Birmingham, CPPN G10, 1600 7th Ave South, Birmingham, AL 35233 USA
| | - Brandt Groh
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | | | - Catherine April Bingham
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | - Lisabeth Scalzi
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
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Gudipati S, Salans M, Karunamuni R, Unnikrishnan S, Yu J, Tibbs M, Huynh-Le M, Qian A, Hermann G, Connor M, Reyes A, Stasenko A, McDonald C, Hattangadi-Gluth J. Role of Thalamus and Thalamic Nuclei in Mediating Post-Treatment Cognitive Changes in Primary Brain Tumor Patients. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Unnikrishnan S, Karunamuni R, Salans M, Gudipati S, Qian A, Yu J, Connor M, Huynh-Le M, Tibbs M, Hermann G, Reyes A, Stasenko A, Seibert T, McDonald C, Hattangadi-Gluth J. Prospective Longitudinal Analysis of Amygdala Volumes and Association with Mood and Memory Outcomes in Brain Tumor Patients. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Qian A, Karunamuni R, Unnikrishnan S, Salans M, Gudipati S, Yu J, Connor M, Hermann G, Huynh-Le M, Tibbs M, Reyes A, Stasenko A, McDonald C, Hattangadi-Gluth J. Beyond the Hippocampus: White Matter Memory Network Implicated in Post-Radiation Memory Decline in Primary Brain Tumor Patients. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Andrade-Martínez JS, Camelo Valera LC, Chica Cárdenas LA, Forero-Junco L, López-Leal G, Moreno-Gallego JL, Rangel-Pineros G, Reyes A. Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiol Mol Biol Rev 2022; 86:e0000421. [PMID: 35311574 PMCID: PMC9199400 DOI: 10.1128/mmbr.00004-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.
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Affiliation(s)
- Juan Sebastián Andrade-Martínez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Carolina Camelo Valera
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Luis Alberto Chica Cárdenas
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Forero-Junco
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Gamaliel López-Leal
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J. Leonardo Moreno-Gallego
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Guillermo Rangel-Pineros
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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Moore B, Carvajal-López P, Abel Chauke P, Cristancho M, Dominguez Del Angel V, Fernandez-Valverde SL, Ghouila A, Gopalasingam P, Guerfali FZ, Matimba A, Morgan SL, Oliveira G, Ras V, Reyes A, De Las Rivas J, Mulder N. Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries. PLoS Comput Biol 2022; 18:e1010197. [PMID: 35613071 PMCID: PMC9132329 DOI: 10.1371/journal.pcbi.1010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Castro-Guarda M, Arancibia Y, Chipón C, Matamala C, Oyarzo P, Vargas G, Reyes A, Salas M, Morera FJ, Zambrano A. Metabolic changes induced by DNA damage in Ramos cells: Exploring the role of mTORC1 complex. FEBS Open Bio 2022; 12:1509-1522. [PMID: 35538662 PMCID: PMC9340868 DOI: 10.1002/2211-5463.13436] [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: 09/16/2021] [Revised: 02/26/2022] [Accepted: 05/09/2022] [Indexed: 11/09/2022] Open
Abstract
DNA damage induces the activation of many different signals associated with repair or cell death, but it is also connected with physiological events, such as adult neurogenesis and B‐cell differentiation. DNA damage induces different signaling pathways, some of them linked to important metabolic changes. The mTORC1 pathway has a central role in the regulation of growth processes and cell division in response to environmental changes and also controls protein synthesis, lipid biogenesis, nucleotide synthesis, and expression of glycolytic genes. Here, we report that double‐strand breaks induced with etoposide affect the expression of genes encoding different enzymes associated with specific metabolic pathways in Ramos cells. We also analyzed the role of mTOR signaling, demonstrating that double‐strand breaks induce downregulation of mTOR signaling. Specific inhibition of mTORC1 using rapamycin also induced changes in the expression of metabolic genes. Finally, we demonstrated that DNA damage and rapamycin can regulate glucose uptake. In summary, our findings show that etoposide and rapamycin affect the expression of metabolic genes as well as apoptotic and proliferation markers in Ramos cells, increasing our understanding of cancer metabolism.
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Affiliation(s)
- Marcos Castro-Guarda
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Yennyfer Arancibia
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Carina Chipón
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Christofer Matamala
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Paola Oyarzo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Gabriela Vargas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Alejandro Reyes
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile.,Campus Patagonia, Universidad Austral de Chile, Coyhaique, 5950000, Chile
| | - Mónica Salas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Francisco J Morera
- Instituto de Farmacología y Morfofisiología, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, 5090000, Chile
| | - Angara Zambrano
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile.,Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia, Chile
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Hernández R, Chaib De Mares M, Jimenez H, Reyes A, Caro-Quintero A. Functional and Phylogenetic Characterization of Bacteria in Bovine Rumen Using Fractionation of Ruminal Fluid. Front Microbiol 2022; 13:813002. [PMID: 35401437 PMCID: PMC8992543 DOI: 10.3389/fmicb.2022.813002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 11/11/2021] [Accepted: 02/01/2022] [Indexed: 01/08/2023] Open
Abstract
Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem.
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Affiliation(s)
- Ruth Hernández
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Maryam Chaib De Mares
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hugo Jimenez
- Animal Microbiology Laboratory, Agrodiversity Department, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.,The Edison Family Center for Genome Science and Systems Biology, Washington University School of Medicine, Saint Louis, MO, United States
| | - Alejandro Caro-Quintero
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
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Garcia-Ledesma O, Mantilla D, Correa-Ruiz PA, D Vera D, Valenzuela-Santos C, Serrano-Gómez S, Reyes A, Galvis M, Ferreira-Prada CA, Vargas O. Proximal balloon-guided catheter with flow inversion vs. distal filter protection during the carotid stent placement, a seven years experience in a Colombian reference center. Interv Neuroradiol 2022:15910199221085363. [PMID: 35285737 PMCID: PMC10369106 DOI: 10.1177/15910199221085363] [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] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND PURPOSE The carotid stent placement as a therapeutic option for carotid stenosis has been increasing among years; therefore, studies are required to evaluate the security and efficacy of its materials. The purpose of this study was to evaluate the distal filter and the proximal balloon-guided catheter with flow inversion as protection devices during carotid angioplasty and stenting. METHODS This is a retrospective, observational study of patients diagnosed with carotid stenosis treated with angioplasty between January 1, 2014, and June 30, 2020; we analyzed a radiology service database to compare the distal filter and the proximal balloon-guided catheter as protection devices during angioplasty. RESULTS One hundred seventy-five angioplasties were performed, the distal filter was the most prevalent embolic protection device used (66%), patients baseline characteristics did not differ between groups with different embolic protection devices, except for history of dyslipidemia (p < 0.000). As well, we did not find any significant differences between the groups in the device related complications, intervention time (p = 0.140), unrelated complications (p = 0.693) and functional independence at 90 days (p = 0.096). CONCLUSIONS In our study the proximal balloon-guided catheter and the distal filter protection device as protection devices during the carotid stenting didn't show significant differences regarding complications related to the system.
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Affiliation(s)
- O Garcia-Ledesma
- Interventional radiology Department. 536071Fundación oftalmológica de Santander - Clínica Ardila Lülle. Floridablanca, Colombia.,Radiology Department. 67597Fundación Valle del Lili. Cali, Colombia
| | - D Mantilla
- Interventional radiology Department. 536071Fundación oftalmológica de Santander - Clínica Ardila Lülle. Floridablanca, Colombia.,Interventional radiology Department. 27968Universidad Autónoma de Bucaramanga. Bucaramanga, Colombia
| | | | - D D Vera
- Universidad Autónoma de Bucaramanga. Bucaramanga, Colombia
| | - C Valenzuela-Santos
- Radiology Department. 536071Fundación oftalmológica de Santander - Clínica Ardila Lülle. Floridablanca, Colombia
| | - S Serrano-Gómez
- Clinical Research Group-UNAB, 27968Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
| | - A Reyes
- Clinical Research Group-UNAB, 27968Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
| | - M Galvis
- Interventional radiology Department. 536071Fundación oftalmológica de Santander - Clínica Ardila Lülle. Floridablanca, Colombia.,Interventional radiology Department. 27968Universidad Autónoma de Bucaramanga. Bucaramanga, Colombia
| | - C A Ferreira-Prada
- Interventional radiology Department. 536071Fundación oftalmológica de Santander - Clínica Ardila Lülle. Floridablanca, Colombia.,Interventional radiology Department. 27968Universidad Autónoma de Bucaramanga. Bucaramanga, Colombia
| | - O Vargas
- Interventional radiology Department. 536071Fundación oftalmológica de Santander - Clínica Ardila Lülle. Floridablanca, Colombia.,Interventional radiology Department. 27968Universidad Autónoma de Bucaramanga. Bucaramanga, Colombia
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Soulsby WD, Balmuri N, Cooley V, Gerber LM, Lawson E, Goodman S, Onel K, Mehta B, Abel N, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar-Smiley F, Barillas-Arias L, Basiaga M, Baszis K, Becker M, Bell-Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang-Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel-Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie-Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui-Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein-Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PMC, McGuire S, McHale I, McMonagle A, McMullen-Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O’Brien B, O’Brien T, Okeke O, Oliver M, Olson J, O’Neil K, Onel K, Orandi A, Orlando M, Osei-Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan-Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas-Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth-Wojcicki E, Rouster-Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert-Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner-Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Social determinants of health influence disease activity and functional disability in Polyarticular Juvenile Idiopathic Arthritis. Pediatr Rheumatol Online J 2022; 20:18. [PMID: 35255941 PMCID: PMC8903717 DOI: 10.1186/s12969-022-00676-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/07/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Social determinants of health (SDH) greatly influence outcomes during the first year of treatment in rheumatoid arthritis, a disease similar to polyarticular juvenile idiopathic arthritis (pJIA). We investigated the correlation of community poverty level and other SDH with the persistence of moderate to severe disease activity and functional disability over the first year of treatment in pJIA patients enrolled in the Childhood Arthritis and Rheumatology Research Alliance Registry. METHODS In this cohort study, unadjusted and adjusted generalized linear mixed effects models analyzed the effect of community poverty and other SDH on disease activity, using the clinical Juvenile Arthritis Disease Activity Score-10, and disability, using the Child Health Assessment Questionnaire, measured at baseline, 6, and 12 months. RESULTS One thousand six hundred eighty-four patients were identified. High community poverty (≥20% living below the federal poverty level) was associated with increased odds of functional disability (OR 1.82, 95% CI 1.28-2.60) but was not statistically significant after adjustment (aOR 1.23, 95% CI 0.81-1.86) and was not associated with increased disease activity. Non-white race/ethnicity was associated with higher disease activity (aOR 2.48, 95% CI: 1.41-4.36). Lower self-reported household income was associated with higher disease activity and persistent functional disability. Public insurance (aOR 1.56, 95% CI 1.06-2.29) and low family education (aOR 1.89, 95% CI 1.14-3.12) was associated with persistent functional disability. CONCLUSION High community poverty level was associated with persistent functional disability in unadjusted analysis but not with persistent moderate to high disease activity. Race/ethnicity and other SDH were associated with persistent disease activity and functional disability.
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Affiliation(s)
- William Daniel Soulsby
- University of California, San Francisco, 550 16th Street, 4th Floor, Box #0632, San Francisco, CA, 94158, USA.
| | - Nayimisha Balmuri
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Victoria Cooley
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Linda M. Gerber
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Erica Lawson
- grid.266102.10000 0001 2297 6811University of California, San Francisco, 550 16th Street, 4th Floor, Box #0632, San Francisco, CA 94158 USA
| | - Susan Goodman
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Karen Onel
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Bella Mehta
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
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Keller CG, Shin Y, Monteys AM, Renaud N, Beibel M, Teider N, Peters T, Faller T, St-Cyr S, Knehr J, Roma G, Reyes A, Hild M, Lukashev D, Theil D, Dales N, Cha JH, Borowsky B, Dolmetsch R, Davidson BL, Sivasankaran R. An orally available, brain penetrant, small molecule lowers huntingtin levels by enhancing pseudoexon inclusion. Nat Commun 2022; 13:1150. [PMID: 35241644 PMCID: PMC8894458 DOI: 10.1038/s41467-022-28653-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/27/2022] [Indexed: 02/07/2023] Open
Abstract
Huntington's Disease (HD) is a progressive neurodegenerative disorder caused by CAG trinucleotide repeat expansions in exon 1 of the huntingtin (HTT) gene. The mutant HTT (mHTT) protein causes neuronal dysfunction, causing progressive motor, cognitive and behavioral abnormalities. Current treatments for HD only alleviate symptoms, but cerebral spinal fluid (CSF) or central nervous system (CNS) delivery of antisense oligonucleotides (ASOs) or virus vectors expressing RNA-induced silencing (RNAi) moieties designed to induce mHTT mRNA lowering have progressed to clinical trials. Here, we present an alternative disease modifying therapy the orally available, brain penetrant small molecule branaplam. By promoting inclusion of a pseudoexon in the primary transcript, branaplam lowers mHTT protein levels in HD patient cells, in an HD mouse model and in blood samples from Spinal Muscular Atrophy (SMA) Type I patients dosed orally for SMA (NCT02268552). Our work paves the way for evaluating branaplam's utility as an HD therapy, leveraging small molecule splicing modulators to reduce expression of dominant disease genes by driving pseudoexon inclusion.
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Affiliation(s)
| | - Youngah Shin
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Alex Mas Monteys
- The Raymond G Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Nicole Renaud
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Natalia Teider
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Thomas Peters
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Thomas Faller
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sophie St-Cyr
- The Raymond G Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alejandro Reyes
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marc Hild
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Diethilde Theil
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Natalie Dales
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jang-Ho Cha
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Beverly L Davidson
- The Raymond G Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA.
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Matiz-Ceron L, Reyes A, Anzola J. Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier. Front Plant Sci 2022; 12:782663. [PMID: 35185949 PMCID: PMC8850773 DOI: 10.3389/fpls.2021.782663] [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: 09/24/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.
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Affiliation(s)
- Luisa Matiz-Ceron
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
| | - Juan Anzola
- Research Group in Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
- Department of Engineering and Natural Sciences, Universidad Central, Bogotá, Colombia
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SIASAT A, Ilagan B, Reyes A, Ronquillo R, Clemente C, Chan A, Baltazar G. POS-875 THE CLINICAL PROFILE AND OUTCOME OF PATIENTS WITH COVID 19 WHO UNDERWENT HEMOPERFUSION IN BATAAN GENERAL HOSPITAL AND MEDICAL CENTER. Kidney Int Rep 2022. [PMCID: PMC8854936 DOI: 10.1016/j.ekir.2022.01.913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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28
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Varunjikar MS, Moreno-Ibarguen C, Andrade-Martinez JS, Tung HS, Belghit I, Palmblad M, Olsvik PA, Reyes A, Rasinger JD, Lie KK. Comparing novel shotgun DNA sequencing and state-of-the-art proteomics approaches for authentication of fish species in mixed samples. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Rangel-Pineros G, Millard A, Michniewski S, Scanlan D, Sirén K, Reyes A, Petersen B, Clokie MR, Sicheritz-Pontén T. From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs. Phage (New Rochelle) 2021; 2:194-203. [PMID: 36147515 PMCID: PMC9041511 DOI: 10.1089/phage.2021.0008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Background: Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large and diverse phage sequence space. Here, we present PhageClouds, a novel approach using a graph database of phage genomic sequences and their intergenomic distances to explore the phage genomic sequence space. Methods: A total of 640,000 phage genomic sequences were retrieved from a variety of databases and public virome assemblies. Intergenomic distances were calculated with dashing, an alignment-free method suitable for handling massive data sets. These data were used to build a Neo4j® graph database. Results: PhageClouds supported the search of related phages among all complete phage genomes from GenBank for a single query phage in just 10 s. Moreover, PhageClouds expanded the number of closely related phage sequences detected for both finished and draft phage genomes, in comparison with searches exclusively targeting phage entries from GenBank. Conclusions: PhageClouds is a novel resource that will facilitate the analysis of phage genomic sequences and the characterization of assembled phage genomes.
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Affiliation(s)
- Guillermo Rangel-Pineros
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogota, Colombia
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Slawomir Michniewski
- Warwick Medical School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - David Scanlan
- Warwick Medical School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogota, Colombia
| | - Bent Petersen
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martha R.J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Thomas Sicheritz-Pontén
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Address correspondence to: Thomas Sicheritz-Pontén, PhD, Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Bygning 7, Room 7.1.20a, Copenhagen 1353, Denmark
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Yu J, Salans M, Karunamuni R, Tibbs M, Huynh-Le M, Unnikrishnan S, Connor M, Qian A, Reyes A, Stasenko A, Seibert T, McDonald C, Hattangadi-Gluth J. Entorhinal Cortical Volume is Associated With Verbal and Visuospatial Memory Performance in Primary Brain Tumor Patients. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Unnikrishnan S, Karunamuni R, Kim G, Connor M, Salans M, Sanghvi P, Bruggeman A, Simpson D, Yu J, Reyes A, Stasenko A, Moore K, Moiseenko V, McDonald C, Hattangadi-Gluth J. Phase II Clinical Trial of Image-Guided Cognitive-Sparing SRS in Patients With Brain Metastases. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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Krupovic M, Turner D, Morozova V, Dyall-Smith M, Oksanen HM, Edwards R, Dutilh BE, Lehman SM, Reyes A, Baquero DP, Sullivan MB, Uchiyama J, Nakavuma J, Barylski J, Young MJ, Du S, Alfenas-Zerbini P, Kushkina A, Kropinski AM, Kurtböke I, Brister JR, Lood C, Sarkar BL, Yigang T, Liu Y, Huang L, Wittmann J, Chanishvili N, van Zyl LJ, Rumnieks J, Mochizuki T, Jalasvuori M, Aziz RK, Łobocka M, Stedman KM, Shkoporov AN, Gillis A, Peng X, Enault F, Knezevic P, Lavigne R, Rhee SK, Cvirkaite-Krupovic V, Moraru C, Moreno Switt AI, Poranen MM, Millard A, Prangishvili D, Adriaenssens EM. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021. Arch Virol 2021; 166:3239-3244. [PMID: 34417873 PMCID: PMC8497307 DOI: 10.1007/s00705-021-05205-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratified by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 genera and 1845 species were newly created or redefined (moved/promoted).
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Affiliation(s)
- Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol, UK
| | - Vera Morozova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Mike Dyall-Smith
- Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Rob Edwards
- Flinders Accelerator for Microbiome Exploration, Adelaide, Australia
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Susan M Lehman
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20903, USA
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA.,Department Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Jumpei Uchiyama
- School of Veterinary Medicine, Azabu University, Sagamihara, Japan
| | - Jesca Nakavuma
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznan, Collegium Biologicum-Umultowska 89, 61-614, Poznan, Poland
| | - Mark J Young
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Shishen Du
- Department of Microbiology, College of Life Sciences, Wuhan University, Wuhan, China
| | | | - Alla Kushkina
- Zabolotny Institute of Microbiology and Virology, NAS of Ukraine, Kyiv, Ukraine
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, Canada.,Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Ipek Kurtböke
- University of the Sunshine Coast, Sippy Downs, Australia
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA
| | | | - B L Sarkar
- Emeritus ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India
| | - Tong Yigang
- Beijing University of Chemical Technology, Beijing, China
| | - Ying Liu
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Berlin, Germany
| | - Nina Chanishvili
- The Eliava Institute of Bacteriophage, MIcrobiology and Virology, Tbilisi, Georgia
| | | | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Tomohiro Mochizuki
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University and Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
| | - Małgorzata Łobocka
- Laboratory of Bacteriophage Biology, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Kenneth M Stedman
- Biology Department and Center for Life in Extreme Environments, Portland State University, Portland, USA
| | | | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UC Louvain, Louvain-la-Neuve, Belgium
| | - Xu Peng
- Microbial Immunity Group, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGE, 63000, Clermont-Ferrand, France
| | - Petar Knezevic
- Faculty of Sciences Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | | | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, South Korea
| | | | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrea I Moreno Switt
- Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Moore B, Carvajal-López P, Chauke PA, Cristancho M, Dominguez Del Angel V, Fernandez-Valverde SL, Ghouila A, Gopalasingam P, Guerfali FZ, Matimba A, Morgan SL, Oliveira G, Ras V, Reyes A, De Las Rivas J, Mulder N. Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries. PLoS Comput Biol 2021; 17:e1009218. [PMID: 34411091 PMCID: PMC8375989 DOI: 10.1371/journal.pcbi.1009218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail: (BM); (NM)
| | - Patricia Carvajal-López
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paballo Abel Chauke
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Marco Cristancho
- Vicerrectoria de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | | | - Selene L. Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Amel Ghouila
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Piraveen Gopalasingam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Fatma Zahra Guerfali
- Institut Pasteur de Tunis, Laboratory of Transmission, Control and Immunobiology of Infections, Tunis-Belvédère, Tunisia
| | - Alice Matimba
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sarah L. Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - Verena Ras
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Alejandro Reyes
- Universidad de los Andes, Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Javier De Las Rivas
- Cancer Research Center, Consejo Superior de Investigaciones Científicas and University of Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail: (BM); (NM)
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Hernández R, Jimenez H, Vargas-Garcia C, Caro-Quintero A, Reyes A. Disentangling the Complexity of the Rumen Microbial Diversity Through Fractionation Using a Sucrose Density Gradient. Front Microbiol 2021; 12:664754. [PMID: 34305833 PMCID: PMC8297521 DOI: 10.3389/fmicb.2021.664754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/05/2021] [Accepted: 06/15/2021] [Indexed: 12/29/2022] Open
Abstract
The ruminal microbial community is an important element in health, nutrition, livestock productivity, and climate impact. Despite the historic and current efforts to characterize this microbial diversity, many of its members remain unidentified, making it challenging to associate microbial groups with functions. Here we present a low-cost methodology for rumen sample treatment that separates the microbial community based on cell size, allowing for the identification of subtle compositional changes. In brief, the sample is centrifuged through a series of sucrose density gradients, and cells migrate to their corresponding density fraction. From each fraction, DNA is extracted and 16S rRNA gene amplicons are sequenced. We tested our methodology on four animals under two different conditions, fasting, and post-feeding. Each fraction was examined by confocal microscopy showing that the same sucrose fraction consistently separated similar cell-sized microorganisms independent of the animal or treatment. Microbial composition analysis using metabarcoding showed that our methodology detected low abundance bacterial families and population changes between fasting and post-feeding treatments that could not be observed by bulk DNA analysis. In conclusion, the sucrose-based method is a powerful low-cost approximation to untwine, enrich, and potentially isolate uncharacterized members of the ruminal microbiome.
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Affiliation(s)
- Ruth Hernández
- Computational Biology and Microbial Ecology Group, Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.,Animal Microbiology Laboratory, Agrodiversity Department, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá, Colombia
| | - Hugo Jimenez
- Animal Microbiology Laboratory, Agrodiversity Department, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá, Colombia
| | - Cesar Vargas-Garcia
- Grupo de Investigación en Sistemas Agropecuarios Sostenibles, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá, Colombia
| | - Alejandro Caro-Quintero
- Animal Microbiology Laboratory, Agrodiversity Department, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá, Colombia.,Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Alejandro Reyes
- Computational Biology and Microbial Ecology Group, Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
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Abstract
Viruses, far from being just parasites affecting hosts' fitness, are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison with public databases. In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs (Eukaryotic Viruses and Phages Orthologous Groups). To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. The clustering of domains and unannotated regions into orthologous groups was done using cogSoft. Finally, we employed a random forest implementation to classify genomes into their taxonomy and found that the presence or absence of ViPhOGs is significantly associated with their taxonomy. Furthermore, we established a set of 1457 ViPhOGs that given their importance for the classification could be considered as markers or signatures for the different taxonomic groups defined by the ICTV at the order, family, and genus levels.
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Affiliation(s)
- Jaime Leonardo Moreno-Gallego
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
- Correspondence:
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36
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Restrepo L, Domínguez-Borbor C, Bajaña L, Betancourt I, Rodríguez J, Bayot B, Reyes A. Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus). Microbiome 2021; 9:88. [PMID: 33845910 PMCID: PMC8042889 DOI: 10.1186/s40168-021-01043-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 12/07/2020] [Accepted: 03/05/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp bacterial disease caused by some Vibrio species. The severity of the impact of this disease on aquaculture worldwide has made it necessary to develop alternatives to prophylactic antibiotics use, such as the application of probiotics. To assess the potential to use probiotics in order to limit the detrimental effects of AHNPD, we evaluated the effect of the ILI strain, a Vibrio sp. bacterium and efficient shrimp probiotic, using metabarcoding (16S rRNA gene) on the gastrointestinal microbiota of shrimp after being challenged with AHPND-causing V. parahaemolyticus. RESULTS We showed how the gastrointestinal microbiome of shrimp varied between healthy and infected organisms. Nevertheless, a challenge of working with AHPND-causing Vibrio pathogens and Vibrio-related bacteria as probiotics is the potential risk of the probiotic strain becoming pathogenic. Consequently, we evaluated whether ILI strain can acquire the plasmid pV-AHPND via horizontal transfer and further cause the disease in shrimp. Conjugation assays were performed resulting in a high frequency (70%) of colonies harboring the pv-AHPND. However, no shrimp mortality was observed when transconjugant colonies of the ILI strain were used in a challenge test using healthy shrimp. We sequenced the genome of the ILI strain and performed comparative genomics analyses using AHPND and non-AHPND Vibrio isolates. Using available phylogenetic and phylogenomics analyses, we reclassified the ILI strain as Vibrio diabolicus. In summary, this work represents an effort to study the role that probiotics play in the normal gastrointestinal shrimp microbiome and in AHPND-infected shrimp, showing that the ILI probiotic was able to control pathogenic bacterial populations in the host's gastrointestinal tract and stimulate the shrimp's survival. The identification of probiotic bacterial species that are effective in the host's colonization is important to promote animal health and prevent disease. CONCLUSIONS This study describes probiotic bacteria capable of controlling pathogenic populations of bacteria in the shrimp gastrointestinal tract. Our work provides new insights into the complex dynamics between shrimp and the changes in the microbiota. It also addresses the practical application of probiotics to solve problems with pathogens that cause high mortality-rate in shrimp farming around the world. Video Abstract.
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Affiliation(s)
- Leda Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Cristóbal Domínguez-Borbor
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Leandro Bajaña
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Irma Betancourt
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Jenny Rodríguez
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ciencias de la Vida, FCV, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Bonny Bayot
- Escuela Superior Politécnica del Litoral, ESPOL, Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador.
- Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ingeniería Marítima y Ciencias del Mar, FIMCM, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador.
| | - Alejandro Reyes
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
- Max Planck Tandem Group in Computational Biology, Universidad de los Andes, Bogotá, Colombia.
- Center for Genome Sciences and Systems Biology, Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO, USA.
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Quiroga-González C, Cardenas LAC, Ramírez M, Reyes A, González C, Stevenson PR. Monitoring the variation in the gut microbiota of captive woolly monkeys related to changes in diet during a reintroduction process. Sci Rep 2021; 11:6522. [PMID: 33753830 PMCID: PMC7985493 DOI: 10.1038/s41598-021-85990-0] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Microbiome is known to play an important role in the health of organisms and different factors such as diet have been associated with modifications in microbial communities. Differences in the microbiota composition of wild and captive animals has been evaluated; however, variation during a reintroduction process in primates has never been reported. Our aim was to identify changes in the bacterial composition of three individuals of reintroduced woolly monkeys (Lagothrix lagothricha) and the variables associated with such changes. Fecal samples were collected and the V4 region of the 16S rRNA gene was sequenced to determine gut microbial composition and functionality. Individual samples from released individuals showed a higher microbial diversity after being released compared to before liberation, associated with changes in their diet. Beta diversity and functionality analysis showed separation of samples from released and captive conditions and the major factor of variation was the moment of liberation. This study shows that intestinal microbiota varies depending on site conditions and is mainly associated with diet diversity. The intake of food from wild origin by released primates may promote a positive effect on gut microbiota, improving health, and potentially increasing success in reintroduction processes.
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Affiliation(s)
- Camilo Quiroga-González
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia.
| | - Luis Alberto Chica Cardenas
- Grupo de Investigación en Biología Computacional y Ecología Microbiana (BCEM), Max Planck Tandem Research Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
| | - Mónica Ramírez
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Grupo de Investigación en Biología Computacional y Ecología Microbiana (BCEM), Max Planck Tandem Research Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Camila González
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
| | - Pablo R Stevenson
- Laboratorio de Ecología de Bosques Tropicales y Primatología (LEBTYP), Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de Los Andes, Bogotá, Colombia
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Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O’Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform 2021; 22:642-663. [PMID: 33147627 PMCID: PMC7665365 DOI: 10.1093/bib/bbaa232] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [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: 05/27/2020] [Revised: 07/28/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Christian Brandt
- Institute of Infectious Disease and Infection Control at Jena University Hospital, Germany
| | - Marco Cacciabue
- Consejo Nacional de Investigaciones Científicas y Tócnicas (CONICET) working on FMDV virology at the Instituto de Agrobiotecnología y Biología Molecular (IABiMo, INTA-CONICET) and at the Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Argentina
| | | | - Oliver Drechsel
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Adrian Fritz
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research, Germany
| | - Stephan Fuchs
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Georges Hattab
- Bioinformatics Division at Philipps-University Marburg, Germany
| | | | - Dominik Heider
- Data Science in Biomedicine at the Philipps-University of Marburg, Germany
| | | | | | - Stefan Hoops
- Biocomplexity Institute and Initiative at the University of Virginia, USA
| | - Lars Kaderali
- Bioinformatics and head of the Institute of Bioinformatics at University Medicine Greifswald, Germany
| | | | - Max von Kleist
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Renó Kmiecinski
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Gorka Lasso
- Chandran Lab, Albert Einstein College of Medicine, USA
| | | | | | | | | | | | | | - Alice C McHardy
- Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig, Germany
| | - Pedro Mendes
- Center for Quantitative Medicine of the University of Connecticut School of Medicine, USA
| | | | - Vincent Navratil
- Bioinformatics and Systems Biology at the Rhône Alpes Bioinformatics core facility, Universitó de Lyon, France
| | | | | | | | | | | | - Nicole Redaschi
- Development of the Swiss-Prot group at the SIB for UniProt and SIB resources that cover viral biology (ViralZone)
| | - Susanne Reimering
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research
| | | | | | | | | | - Sepideh Sadegh
- Chair of Experimental Bioinformatics at Technical University of Munich, Germany
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | | | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | | | | | - Manja Marz
- Friedrich Schiller University Jena, Germany
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Gradaschi V, Payaslian F, Dieterle ME, Rondón Salazar L, Urdániz E, Di Paola M, Peña Cárcamo J, Zon F, Allievi M, Sosa E, Fernandez Do Porto D, Dunne M, Goeller P, Klumpp J, Raya RR, Reyes A, Piuri M. Genome Sequence and Characterization of Lactobacillus casei Phage, vB_LcaM_Lbab1 Isolated from Raw Milk. Phage (New Rochelle) 2021; 2:57-63. [PMID: 36148441 PMCID: PMC9041484 DOI: 10.1089/phage.2020.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Introduction: Only a few Lactobacillus casei phages have so far been characterized. As several L. casei strains are part of probiotic formulations, bacteriophage outbreaks targeting these strains can lead to critical losses within the dairy industry. Materials and Methods: A new L. casei phage was isolated from raw milk obtained from a milking yard from the province of Buenos Aires. The phage genome was sequenced, annotated, and analyzed. Morphology was determined by electron microscopy and the host range was established. Results: Lactobacillus phage vB_LcaM_Lbab1 is a member of the Herelleviridae family and features a host range including L. casei/Lactobacillus paracasei and Lactobacillus kefiri strains. We further analyzed the baseplate proteins in silico and found putative carbohydrate binding modules that are responsible for host recognition in other Lactobacillus phages. Conclusions: A new Lactobacillus phage was isolated and characterized. The focus was made on its host recognition mechanism, pointing toward the development of future strategies to avoid deleterious infections in the dairy industry.
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Affiliation(s)
- Victoria Gradaschi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Florencia Payaslian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Maria Eugenia Dieterle
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Liliana Rondón Salazar
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Estefanía Urdániz
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Matias Di Paola
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - José Peña Cárcamo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Fabio Zon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Mariana Allievi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Ezequiel Sosa
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Darío Fernandez Do Porto
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Pauline Goeller
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Payaslian F, Gradaschi V, Rondón Salazar L, Dieterle ME, Urdániz E, Di Paola M, Peña Cárcamo J, Zon F, Sosa E, Fernandez Do Porto D, Dunne M, Goeller P, Klumpp J, Raya RR, Reyes A, Piuri M. Isolation and Characterization of vB_MsmS_Celfi: A New Mycobacterium tuberculosis Bacteriophage. Phage (New Rochelle) 2021; 2:43-49. [PMID: 36148439 PMCID: PMC9041486 DOI: 10.1089/phage.2020.0030] [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] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Introduction: Because of the clinical relevance of Mycobacteria, and from a therapeutic perspective, there is an increasing interest to study phages that infect bacteria belonging to this genus. Materials and Methods: A phage was isolated from a soil sample, using Mycobacterium smegmatis as host. Its characterization included sequencing, annotation, and analysis of the genome, host range determination, and electron microscopy imaging. Results: Mycobacterium phage vB_MsmS_Celfi is a temperate phage able to infect Mycobacterium tuberculosis with high efficiency. From electron microscopy images, Celfi belongs to the Siphoviridae family. Genome analysis classified phage Celfi into cluster L, subcluster L2 of Actinobacteriophage clusters. Mycobacterium phage Celfi exhibits a Lysin B distant to those present in other members of the subcluster and other mycobacteriophages. Conclusions: The discovery of new phages that infect M. tuberculosis could contribute to the development of novel tools for detection systems and future treatment of the disease.
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Affiliation(s)
- Florencia Payaslian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Victoria Gradaschi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Liliana Rondón Salazar
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Maria Eugenia Dieterle
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Estefanía Urdániz
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Matias Di Paola
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - José Peña Cárcamo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Fabio Zon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Ezequiel Sosa
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Darío Fernandez Do Porto
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Pauline Goeller
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Payaslian F, Gradaschi V, Rondón Salazar L, Dieterle ME, Urdániz E, Di Paola M, Zon F, Allievi M, Sanchez Rivas C, Raya RR, Reyes A, Piuri M. Tightening Bonds in Latin America Through Phage Discovery. Phage (New Rochelle) 2021; 2:7-10. [PMID: 36148437 PMCID: PMC9041481 DOI: 10.1089/phage.2020.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Between 2015 and 2019, we hosted an International Phage Course at Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina. The 2-week full-time course was hands-on and included lectures from renowned phage biologists. Participating students were able to meet and discuss with recognized experts from around the world in a familiar setting, facilitating the establishment of scientific collaborations and the expansion of their networks. Eighty-four students from 14 Latin American countries have participated in the course, which included isolation, characterization, genome sequencing, and annotation of novel phages. We have successfully created a coursework that enabled the acquisition of new knowledge and expertise in bacteriophage biology and strengthened ties among Latin American colleagues.
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Affiliation(s)
- Florencia Payaslian
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Victoria Gradaschi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Liliana Rondón Salazar
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Maria Eugenia Dieterle
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Estefanía Urdániz
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Matias Di Paola
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Fabio Zon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Mariana Allievi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Carmen Sanchez Rivas
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Abstract
Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.
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Affiliation(s)
- Luis Alberto Chica Cardenas
- Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia.,Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
| | - Viviana Clavijo
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Martha Vives
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia.,Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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Orta N, Sampol C, Reyes A, Martín A, Torrent A, Amengual J, Rioja J, Repetto A, Luna B, Peña C. Selective sentinel lymph node biopsy in squamous vulvar cancer. Ten-year follow-up analysis. Rev Esp Med Nucl Imagen Mol 2020. [DOI: 10.1016/j.remnie.2020.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Salans M, Tibbs M, Yip A, Karunamuni R, Huynh-Le M, Macari A, Reyes A, Tringale K, Seibert T, McDonald C, Hattangadi-Gluth J. Quantitative Imaging Biomarkers Associated With Fine Motor Coordination After Brain Radiotherapy (RT). Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Díaz VP, Reyes A, Calzadilla A, Torres PA, González E, Bilbao JL, González F, Estrada N, Fortich N, Sepúlveda W, Silva-Vetri MG, Bullen M, Erazo AM. Psychometry and estimation of cutoff points of Jefferson Scale of empathy in dental students. J Dent Educ 2020; 85:322-330. [PMID: 33035381 DOI: 10.1002/jdd.12444] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/10/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The objective of this study was to determine the psychometric properties of the 3-dimensional latent model of empathy on the Jefferson Scale of Physician Empathy instrument (version S), and to verify the existence of cutoff points capable of differentiating empathy measures classified as: "high," "medium," and "low" using data collected from observations of students from 11 dental faculties of 5 Central American and Caribbean countries (n = 3082) between 2015 and 2019. METHODS This is an exploratory, "a posteriori," and non-experimental study. Factor structure and factor invariance by country and gender were analyzed. Hierarchical cluster analysis and bifactorial analysis were applied, and the data were normalized by cluster and by percentiles within them. RESULTS Confirmatory factor analysis showed that the original model was replicable and fit the data, while multigroup analysis allowed assuming an invariant factor structure by country and by gender. There is reliability in the measurement made by the scale and its dimensions. CONCLUSIONS The instrument has adequate psychometric properties, and cutoff values obtained allow people with lower or higher levels of empathy and its components to be classified. Therefore, these results solve the problem of comparing the scores and observed levels of empathy between dental schools within and between countries and between genders. Such comparisons were only possible since the original data of each study were made available for traditional statistical methods.
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Affiliation(s)
- Víctor P Díaz
- Dentistry Faculty, Universidad Andres Bello, Santiago, Chile
| | - Alejandro Reyes
- Faculty of Social Sciences and communications, Universidad Santo Tomás, Concepción, Chile
| | - Aracelis Calzadilla
- Faculty of Health, Universidad Bernardo OHiggins, Santiago, Chile.,Faculty of Health Sciences, Universidad Autónoma de Chile, Chile
| | - Pilar A Torres
- Dentistry Faculty, Universidad San Sebastián, Concepción, Chile
| | - Eugenia González
- Dentistry Faculty, Universidad Central del Este, Dominican Republic
| | - Jorge L Bilbao
- Research Department, Universidad Metropolitana, Barranquilla, Colombia
| | | | - Nuvia Estrada
- Dentistry Faculty, Universidad Evangélica de El Salvador, El Salvador
| | - Natalia Fortich
- Dentistry Faculty, Corporación Universitaria Rafael Núñez, Cartagena, Colombia
| | | | - María G Silva-Vetri
- Dentistry Faculty, Universidad Nacional Pedro Henríquez Ureña, Dominican Republic
| | | | - Ana M Erazo
- Research Department, Universidad Metropolitana, Barranquilla, Colombia
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46
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Qi Y, Reyes A, Johnstone SE, Aryee MJ, Bernstein BE, Zhang B. Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization. Biophys J 2020; 119:1905-1916. [PMID: 33086041 DOI: 10.1016/j.bpj.2020.09.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Chromosomes are positioned nonrandomly inside the nucleus to coordinate with their transcriptional activity. The molecular mechanisms that dictate the global genome organization and the nuclear localization of individual chromosomes are not fully understood. We introduce a polymer model to study the organization of the diploid human genome. It is data-driven because all parameters can be derived from Hi-C data; it is also a mechanistic model because the energy function is explicitly written out based on a few biologically motivated hypotheses. These two features distinguish the model from existing approaches and make it useful both for reconstructing genome structures and for exploring the principles of genome organization. We carried out extensive validations to show that simulated genome structures reproduce a wide variety of experimental measurements, including chromosome radial positions and spatial distances between homologous pairs. Detailed mechanistic investigations support the importance of both specific interchromosomal interactions and centromere clustering for chromosome positioning. We anticipate the polymer model, when combined with Hi-C experiments, to be a powerful tool for investigating large-scale rearrangements in genome structure upon cell differentiation and tumor progression.
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Affiliation(s)
- Yifeng Qi
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Alejandro Reyes
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Data Sciences, Dana Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Sarah E Johnstone
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Martin J Aryee
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Bin Zhang
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell 2020; 182:1474-1489.e23. [PMID: 32841603 PMCID: PMC7575124 DOI: 10.1016/j.cell.2020.07.030] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 05/04/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
Widespread changes to DNA methylation and chromatin are well documented in cancer, but the fate of higher-order chromosomal structure remains obscure. Here we integrated topological maps for colon tumors and normal colons with epigenetic, transcriptional, and imaging data to characterize alterations to chromatin loops, topologically associated domains, and large-scale compartments. We found that spatial partitioning of the open and closed genome compartments is profoundly compromised in tumors. This reorganization is accompanied by compartment-specific hypomethylation and chromatin changes. Additionally, we identify a compartment at the interface between the canonical A and B compartments that is reorganized in tumors. Remarkably, similar shifts were evident in non-malignant cells that have accumulated excess divisions. Our analyses suggest that these topological changes repress stemness and invasion programs while inducing anti-tumor immunity genes and may therefore restrain malignant progression. Our findings call into question the conventional view that tumor-associated epigenomic alterations are primarily oncogenic.
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Affiliation(s)
- Sarah E Johnstone
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Alejandro Reyes
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA
| | - Yifeng Qi
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carmen Adriaens
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Esmat Hegazi
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Karin Pelka
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Jonathan H Chen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Luli S Zou
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA
| | - Yotam Drier
- The Lautenberg Center for Immunology and Cancer Research, The Hebrew University, Jerusalem, Israel
| | - Vivian Hecht
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Noam Shoresh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Martin K Selig
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Caleb A Lareau
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02215, USA
| | - Sowmya Iyer
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Son C Nguyen
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric F Joyce
- Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Rafael A Irizarry
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA
| | - Bin Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martin J Aryee
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA.
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA.
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Cazorla BP, Cabello J, Peñas J, Garcillán PP, Reyes A, Alcaraz-Segura D. Incorporating Ecosystem Functional Diversity into Geographic Conservation Priorities Using Remotely Sensed Ecosystem Functional Types. Ecosystems 2020. [DOI: 10.1007/s10021-020-00533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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49
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Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernández J, Salgado H, Collado-Torres L, Reyes A. Programmatic access to bacterial regulatory networks with regutools. Bioinformatics 2020; 36:4532-4534. [PMID: 32573705 DOI: 10.1093/bioinformatics/btaa575] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 04/29/2020] [Accepted: 06/15/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools gives researchers the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks. AVAILABILITY AND IMPLEMENTATION regutools is an R package available through Bioconductor at bioconductor.org/packages/regutools.
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Affiliation(s)
- Joselyn Chávez
- Departamento de Microbiología Molecular, Instituto de Biotecnología
| | - Carmina Barberena-Jonas
- Programa de Genómica Computacional, Centro de Ciencias Genómicas.,Licenciatura de Ciencias Genómicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico 62210.,National Laboratory of Genomics for Biodiversity, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 36821, Mexico
| | - Jesus E Sotelo-Fonseca
- Programa de Genómica Computacional, Centro de Ciencias Genómicas.,Licenciatura de Ciencias Genómicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico 62210.,National Laboratory of Genomics for Biodiversity, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 36821, Mexico
| | - José Alquicira-Hernández
- Programa de Genómica Computacional, Centro de Ciencias Genómicas.,Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia.,Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Heladia Salgado
- Programa de Genómica Computacional, Centro de Ciencias Genómicas
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Alejandro Reyes
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
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50
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Botero D, Monk J, Rodríguez Cubillos MJ, Rodríguez Cubillos A, Restrepo M, Bernal-Galeano V, Reyes A, González Barrios A, Palsson BØ, Restrepo S, Bernal A. Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. Front Genet 2020; 11:837. [PMID: 32849823 PMCID: PMC7432306 DOI: 10.3389/fgene.2020.00837] [Citation(s) in RCA: 2] [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: 09/20/2019] [Accepted: 07/10/2020] [Indexed: 01/05/2023] Open
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reconstruction of the genome-scale model of Xpm metabolism and the insights it provides into plant-pathogen interactions. The model, iXpm1556, displayed 1,556 reactions, 1,527 compounds, and 890 genes. Metabolic maps of central amino acid and carbohydrate metabolism, as well as xanthan biosynthesis of Xpm, were reconstructed using Escher (https://escher.github.io/) to guide the curation process and for further analyses. The model was constrained using the RNA-seq data of a mutant of Xpm for quorum sensing (QS), and these data were used to construct context-specific models (CSMs) of the metabolism of the two strains (wild type and QS mutant). The CSMs and flux balance analysis were used to get insights into pathogenicity, xanthan biosynthesis, and QS mechanisms. Between the CSMs, 653 reactions were shared; unique reactions belong to purine, pyrimidine, and amino acid metabolism. Alternative objective functions were used to demonstrate a trade-off between xanthan biosynthesis and growth and the re-allocation of resources in the process of biosynthesis. Important features altered by QS included carbohydrate metabolism, NAD(P)+ balance, and fatty acid elongation. In this work, we modeled the xanthan biosynthesis and the QS process and their impact on the metabolism of the bacterium. This model will be useful for researchers studying host-pathogen interactions and will provide insights into the mechanisms of infection used by this and other Xanthomonas species.
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Affiliation(s)
- David Botero
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Biología Computacional y Ecología Microbiana, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Jonathan Monk
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - María Juliana Rodríguez Cubillos
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | | | - Mariana Restrepo
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Vivian Bernal-Galeano
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Universidad de Los Andes, Bogotá, Colombia
- Grupo de Biología Computacional y Ecología Microbiana, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Bernhard Ø. Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Silvia Restrepo
- Laboratory of Mycology and Plant Pathology (LAMFU), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - Adriana Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes, LIMMA, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
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