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Abstract
Improving human healthspan in our rapidly aging population has never been more imperative. Telomeres, protective "caps" at the ends of linear chromosomes, are essential for maintaining genome stability of eukaryotic genomes. Due to their physical location and the "end-replication problem" first envisioned by Dr. Alexey Olovnikov, telomeres shorten with cell division, the implications of which are remarkably profound. Telomeres are hallmarks and molecular drivers of aging, as well as fundamental integrating components of the cumulative effects of genetic, lifestyle, and environmental factors that erode telomere length over time. Ongoing telomere attrition and the resulting limit to replicative potential imposed by cellular senescence serves a powerful tumor suppressor function, and also underlies aging and a spectrum of age-related degenerative pathologies, including reduced fertility, dementias, cardiovascular disease and cancer. However, very little data exists regarding the extraordinary stressors and exposures associated with long-duration space exploration and eventual habitation of other planets, nor how such missions will influence telomeres, reproduction, health, disease risk, and aging. Here, we briefly review our current understanding, which has advanced significantly in recent years as a result of the NASA Twins Study, the most comprehensive evaluation of human health effects associated with spaceflight ever conducted. Thus, the Twins Study is at the forefront of personalized space medicine approaches for astronauts and sets the stage for subsequent missions. We also extrapolate from current understanding to future missions, highlighting potential biological and biochemical strategies that may enable human survival, and consider the prospect of longevity in the extreme environment of space.
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Affiliation(s)
- Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Maria A Sierra
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Henry J Feng
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
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Wu J, Hu Y, Perlin MH, Danko D, Lu J, Oliveira M, Werner J, Zambrano MM, Sierra MA, Osuolale OO, Łabaj P, Rascovan N, Hazrin-Chong NH, Jang S, Suzuki H, Nieto-Caballero M, Prithiviraj B, Lee PKH, Chmielarczyk A, Różańska A, Zhao Y, Wang L, Mason CE, Shi T. Landscape of global urban environmental resistome and its association with local socioeconomic and medical status. Sci China Life Sci 2024:10.1007/s11427-023-2504-1. [PMID: 38489008 DOI: 10.1007/s11427-023-2504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/06/2023] [Indexed: 03/17/2024]
Abstract
Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.
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Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yige Hu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, 40292, USA
| | - David Danko
- Weill Cornell Medicine, New York, 10065, USA
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA
| | - Jun Lu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4050-290, Portugal
- Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, 4200-465, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4050-290, Portugal
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Maria A Sierra
- Weill Cornell Medicine, New York, 10065, USA
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, 340271, Nigeria
| | - Paweł Łabaj
- Maopolska Centre of Biotechnology, Jagiellonian University, Kraków, 30-005, Poland
| | - Nicolás Rascovan
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, 83041, France
| | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia UKM, 43600, Bangi, Selangor, Malaysia
| | - Soojin Jang
- Institut Pasteur Korea, Seoul, 13488, Republic of Korea
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
| | - Marina Nieto-Caballero
- Civil, Environmental and Architectural Department, University of Colorado at Boulder, Boulder, 80303, USA
| | | | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, 999077, China
| | - Agnieszka Chmielarczyk
- Department of Microbiology, Faculty of Medicine, Jagiellonian University, Krakow, 30-005, Poland
| | - Anna Różańska
- Department of Microbiology, Faculty of Medicine, Jagiellonian University, Krakow, 30-005, Poland
| | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China.
| | - Lan Wang
- College of Architecture and Urban Planning, Tongji University, Shanghai, 200092, China.
| | - Christopher E Mason
- Weill Cornell Medicine, New York, 10065, USA.
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA.
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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Olarte-Castillo XA, Licitra BN, André NM, Sierra MA, Mason CE, Goodman LB, Whittaker GR. Intra-host variation in the spike S1/S2 region of a feline coronavirus type-1 in a cat with persistent infection. bioRxiv 2023:2023.07.31.551356. [PMID: 37577589 PMCID: PMC10418068 DOI: 10.1101/2023.07.31.551356] [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: 08/15/2023]
Abstract
Feline coronavirus type 1 (FCoV-1) is widely known for causing feline infectious peritonitis (FIP), a systemic infection that is often fatal, with the virus known as the FIPV biotype. However, subclinical disease also occurs, in which cats may not show signs and intermittently shed the virus, including in feces, possibly for long periods of time. This virus is known as the FECV biotype. Progression of FECV to FIPV has been linked to several genomic changes, however a specific region of the viral spike protein at the interface of the spike S1 and S2 domains has been especially implicated. In this study, we followed a cat (#576) for six years from 2017, at which time FCoV-1 was detected in feces and conjunctival swabs, until 2022, when the animal was euthanized based on a diagnosis of alimentary small cell lymphoma. Over this time period, the cat was clinically diagnosed with inflammatory bowel disease and chronic rhinitis, and cardiac problems were also suspected. Using hybridization capture targeting the spike (S) gene of FCoV followed by next-generation sequencing, we screened 27 clinical samples. We detected FCoV-1 in 4 samples taken in 2017 (intestine and nasal tissue, feces, and conjunctiva), and 3 samples taken in 2022 (feces, and intestinal and heart tissue), but not in fecal samples taken in 2019 and 2020. Next, we focused on the S1/S2 region within S, which contains the furin cleavage site (FCS), a key regulator of viral transmission and pathogenesis. We show that the FCoV-1 variants obtained from feces in 2017 and 2022 were identical, while the ones from conjunctiva (2017), heart (2022), and intestine (2017 and 2022) were distinct. Sequence comparison of all the variants obtained showed that most of the non-synonymous changes in the S1/S2 region occur within the FCS. In the heart, we found two variants that differed by a single nucleotide, resulting in distinct FCS motifs that differ in one amino acid. It is predicted that one of these FCS motifs will down-regulate spike cleavability. The variant from the conjunctiva (2017) had a 6-nucleotide in-frame insertion that resulted in a longer and more exposed S1/S2 loop, which is predicted to be more accessible to the furin protease. Our studies indicate that FCoV-1 can independently persist in the gastrointestinal tract and heart of a cat over a long period of time without evidence of typical FIP signs, with intermittent viral shedding from the gastrointestinal and respiratory tracts.
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Shiwa Y, Baba T, Sierra MA, Kim J, Mason CE, Suzuki H. Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces. BMC Res Notes 2023; 16:142. [PMID: 37420286 DOI: 10.1186/s13104-023-06417-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVE Metatranscriptomic analysis of RNA viromes on built-environment surfaces is hampered by low RNA yields and high abundance of rRNA. Therefore, we evaluated the quality of libraries, efficiency of rRNA depletion, and viral detection sensitivity using a mock community and a melamine-coated table surface RNA with levels below those required (< 5 ng) with a library preparation kit (NEBNext Ultra II Directional RNA Library Prep Kit). RESULTS Good-quality RNA libraries were obtained from 0.1 ng of mock community and table surface RNA by changing the adapter concentration and number of PCR cycles. Differences in the target species of the rRNA depletion method affected the community composition and sensitivity of virus detection. The percentage of viral occupancy in two replicates was 0.259 and 0.290% in both human and bacterial rRNA-depleted samples, a 3.4 and 3.8-fold increase compared with that for only bacterial rRNA-depleted samples. Comparison of SARS-CoV-2 spiked-in human rRNA and bacterial rRNA-depleted samples suggested that more SARS-CoV-2 reads were detected in bacterial rRNA-depleted samples. We demonstrated that metatranscriptome analysis of RNA viromes is possible from RNA isolated from an indoor surface (representing a built-environment surface) using a standard library preparation kit.
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Affiliation(s)
- Yuh Shiwa
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan.
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan.
| | - Tomoya Baba
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
- Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Tokyo, Japan
| | - Maria A Sierra
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.
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Sierra MA, Ryon KA, Tierney BT, Foox J, Bhattacharya C, Afshin E, Butler D, Green SJ, Thomas WK, Ramsdell J, Bivens NJ, McGrath K, Mason CE, Tighe SW. Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations. Environ Microbiome 2022; 17:60. [PMID: 36544228 PMCID: PMC9768965 DOI: 10.1186/s40793-022-00455-9] [Citation(s) in RCA: 1] [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] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Through metagenomic sequencing and culture-based approaches, our results evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate that the microbiome in Lake Hillier is composed of multiple pigment-producer microbes, including Dunaliella, Salinibacter, Halobacillus, Psychroflexus, Halorubrum, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria (N = 14) and archaea (N = 7), only 2 of which could be taxonomically annotated to previously observed species. Our findings provide the first metagenomic study to decipher the source of the pink color of Australia's Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.
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Affiliation(s)
- Maria A Sierra
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Krista A Ryon
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Braden T Tierney
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jonathan Foox
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chandrima Bhattacharya
- Tri-Institutional Computational Biology and Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Evan Afshin
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University, New York, IL, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, College of Life Sciences and Agriculture, University of New Hampshire, Durham, NH, USA
| | | | - Nathan J Bivens
- DNA Core Facility, University of Missouri, Columbia, MO, USA
| | | | - Christopher E Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Scott W Tighe
- Advanced Genomics Laboratory, University of Vermont Cancer Center, University of Vermont, Burlington, VT, USA.
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Cifuentes EA, Sierra MA, Yepes AF, Baldión AM, Rojas JA, Álvarez-Moreno CA, Anzola JM, Zambrano MM, Huertas MG. Endotracheal tube microbiome in hospitalized patients defined largely by hospital environment. Respir Res 2022; 23:168. [PMID: 35751068 PMCID: PMC9233342 DOI: 10.1186/s12931-022-02086-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Background Studies of the respiratory tract microbiome primarily focus on airway and lung microbial diversity, but it is still unclear how these microbial communities may be affected by intubation and long periods in intensive care units (ICU), an aspect that today could aid in the understanding of COVID19 progression and disease severity. This study aimed to explore and characterize the endotracheal tube (ETT) microbiome by analyzing ETT-associated microbial communities. Methods This descriptive study was carried out on adult patients subjected to invasive mechanical ventilation from 2 to 21 days. ETT samples were obtained from 115 patients from ICU units in two hospitals. Bacteria isolated from endotracheal tubes belonging to the ESKAPE group were analyzed for biofilm formation using crystal violet quantification. Microbial profiles were obtained using Illumina sequencing of 16S rRNA gene. Results The ETT microbiome was mainly composed by the phyla Proteobacteria, Firmicutes and Bacteroidetes. Microbiome composition correlated with the ICU in which patients were hospitalized, while intubation time and diagnosis of ventilator-associated pneumonia (VAP) did not show any significant association. Conclusion These results suggest that the ICU environment, or medical practices, could be a key to microbial colonization and have a direct influence on the ETT microbiomes of patients that require mechanical ventilation. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02086-7.
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Affiliation(s)
| | - Maria A Sierra
- Corporación CorpoGen Research Center, Bogotá, Colombia.,Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | - Juan Manuel Anzola
- Corporación CorpoGen Research Center, Bogotá, Colombia.,Universidad Central, Bogotá, Colombia
| | - María Mercedes Zambrano
- Corporación CorpoGen Research Center, Bogotá, Colombia.,Universidad Central, Bogotá, Colombia
| | - Monica G Huertas
- Corporación CorpoGen Research Center, Bogotá, Colombia. .,Universidad Pedagógica y Tecnológica de Colombia, Tunja, Boyacá, Colombia.
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Leinwand JC, Paul B, Chen R, Xu F, Sierra MA, Paluru MM, Nanduri S, Alcantara Hirsch CG, Shadaloey SA, Yang F, Adam SA, Li Q, Bandel M, Gakhal I, Appiah L, Guo Y, Vardhan M, Flaminio ZJ, Grodman ER, Mermelstein A, Wang W, Diskin B, Aykut B, Khan M, Werba G, Pushalkar S, McKinstry M, Kluger Z, Park JJ, Hsieh B, Dancel-Manning K, Liang FX, Park JS, Saxena A, Li X, Theise ND, Saxena D, Miller G. Intrahepatic microbes govern liver immunity by programming NKT cells. J Clin Invest 2022; 132:151725. [PMID: 35175938 PMCID: PMC9012289 DOI: 10.1172/jci151725] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
The gut microbiome shapes local and systemic immunity. The liver is presumed to be a protected sterile site. As such, a hepatic microbiome has not been examined. Here, we showed a liver microbiome in mice and humans that is distinct from the gut and is enriched in Proteobacteria. It undergoes dynamic alterations with age and is influenced by the environment and host physiology. Fecal microbial transfer experiments revealed that the liver microbiome is populated from the gut in a highly selective manner. Hepatic immunity is dependent on the microbiome, specifically Bacteroidetes species. Targeting Bacteroidetes with oral antibiotics reduced hepatic immune cells by ~90%, prevented APC maturation, and mitigated adaptive immunity. Mechanistically, our findings are consistent with presentation of Bacteroidetes-derived glycosphingolipids to NKT cells promoting CCL5 signaling, which drives hepatic leukocyte expansion and activation, among other possible host-microbe interactions. Collectively, we reveal a microbial - glycosphingolipid - NKT - CCL5 axis that underlies hepatic immunity.
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Affiliation(s)
- Joshua C Leinwand
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Bidisha Paul
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Ruonan Chen
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Fangxi Xu
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Maria A Sierra
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Madan M Paluru
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Sumant Nanduri
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | | | - Sorin Aa Shadaloey
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Fan Yang
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Salma A Adam
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Qianhao Li
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Michelle Bandel
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Inderdeep Gakhal
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Lara Appiah
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Yuqi Guo
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Mridula Vardhan
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Zia J Flaminio
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Emilie R Grodman
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Ari Mermelstein
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Wei Wang
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Brian Diskin
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Berk Aykut
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Mohammed Khan
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Gregor Werba
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Smruti Pushalkar
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Mia McKinstry
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Zachary Kluger
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Jaimie J Park
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
| | - Brandon Hsieh
- Department of Medicine, NYU Langone Medical Center, New York, United States of America
| | - Kristen Dancel-Manning
- Department of Cell Biology, NYU Langone Medical Center, New York, United States of America
| | - Feng-Xia Liang
- Department of Cell Biology, NYU Langone Medical Center, New York, United States of America
| | - James S Park
- Department of Medicine, NYU Langone Medical Center, New York, United States of America
| | - Anjana Saxena
- Department of Biology, City University of New York, New York, United States of America
| | - Xin Li
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - Neil D Theise
- Department of Pathology, NYU Langone Medical Center, New York, United States of America
| | - Deepak Saxena
- Department of Molecular Pathobiology, NYU College of Dentistry, New York, United States of America
| | - George Miller
- Department of Surgery, NYU Langone Medical Center, New York, United States of America
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Bijlani S, Parker C, Singh NK, Sierra MA, Foox J, Wang CCC, Mason CE, Venkateswaran K. Genomic Characterization of the Titan-like Cell Producing Naganishia tulchinskyi, the First Novel Eukaryote Isolated from the International Space Station. J Fungi (Basel) 2022; 8:jof8020165. [PMID: 35205919 PMCID: PMC8875396 DOI: 10.3390/jof8020165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 12/25/2022] Open
Abstract
Multiple strains of a novel yeast belonging to genus Naganishia were isolated from environmental surfaces aboard the International Space Station (ISS). These strains exhibited a phenotype similar to Titan cell (~10 µm diameter) morphology when grown under a combination of simulated microgravity and 5% CO2 conditions. Confocal, scanning, and transmission electron microscopy revealed distinct morphological differences between the microgravity-grown cells and the standard Earth gravity-grown cells, including larger cells and thicker cell walls, altered intracellular morphology, modifications to extracellular fimbriae, budding, and the shedding of bud scars. Phylogenetic analyses via multi-locus sequence typing indicated that these ISS strains represented a single species in the genus Naganishia and were clustered with Naganishia diffluens. The name Naganishia tulchinskyi is proposed to accommodate these strains, with IF6SW-B1T as the holotype. The gene ontologies were assigned to the cell morphogenesis, microtubule-based response, and response to UV light, suggesting a variety of phenotypes that are well suited to respond to microgravity and radiation. Genomic analyses also indicated that the extracellular region, outer membrane, and cell wall were among the highest cellular component results, thus implying a set of genes associated with Titan-like cell plasticity. Finally, the highest molecular function matches included cytoskeletal motor activity, microtubule motor activity, and nuclear export signal receptor activity.
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Affiliation(s)
- Swati Bijlani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; (S.B.); (C.C.C.W.)
| | - Ceth Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
| | - Maria A. Sierra
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA;
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Jonathan Foox
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; (S.B.); (C.C.C.W.)
| | - Christopher E. Mason
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
- Correspondence: (C.E.M.); (K.V.); Tel.: +1-(203)-668-1448 (C.E.M.); +1-(818)-393-1481 (K.V.); Fax: +1-(646)-962-00383 (C.E.M.); +1-(818)-393-4176 (K.V.)
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
- Correspondence: (C.E.M.); (K.V.); Tel.: +1-(203)-668-1448 (C.E.M.); +1-(818)-393-1481 (K.V.); Fax: +1-(646)-962-00383 (C.E.M.); +1-(818)-393-4176 (K.V.)
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9
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Ruff RR, Paul B, Sierra MA, Xu F, Li X, Crystal YO, Saxena D. Predicting Treatment Nonresponse in Hispanic/Latino Children Receiving Silver Diamine Fluoride for Caries Arrest: A Pilot Study Using Machine Learning. Front Oral Health 2022; 2:695759. [PMID: 35048036 PMCID: PMC8757842 DOI: 10.3389/froh.2021.695759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment non-response using machine learning. Methods: An observational pilot study (N = 20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment non-response was assessed using lasso regression and artificial neural networks. Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between non-responders and those who responded to SDF therapy. No differences were found between non-responders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron. Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.
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Affiliation(s)
- Ryan Richard Ruff
- Department of Epidemiology and Health Promotion, New York University College of Dentistry, New York, NY, United States
| | - Bidisha Paul
- Department of Molecular Pathobiology, New York, NY, United States
| | - Maria A Sierra
- Department of Molecular Pathobiology, New York, NY, United States
| | - Fangxi Xu
- Department of Molecular Pathobiology, New York, NY, United States
| | - Xin Li
- Department of Molecular Pathobiology, New York, NY, United States
| | - Yasmi O Crystal
- Department of Epidemiology and Health Promotion, New York University College of Dentistry, New York, NY, United States
| | - Deepak Saxena
- Department of Molecular Pathobiology, New York, NY, United States
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10
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Xu F, Pushalkar S, Lin Z, Thomas SC, Persaud JK, Sierra MA, Vardhan M, Vasconcelos R, Akapo A, Guo Y, Gordon T, Corby PM, Kamer AR, Li X, Saxena D. Electronic cigarette use enriches periodontal pathogens. Mol Oral Microbiol 2022; 37:63-76. [PMID: 34997976 DOI: 10.1111/omi.12361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/03/2022] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Abstract
The effect of electronic cigarette (e-cigarette) smoking, especially its long-term impact on oral health, is poorly understood. Here, we conducted a longitudinal clinical study with two study visits, 6 months apart, to investigate the effect of e-cigarette use on the bacterial community structure in the saliva of 101 periodontitis patients. Our data demonstrated that e-cigarette use altered the oral microbiome in periodontitis patients, enriching members of the Filifactor, Treponema, and Fusobacterium taxa. For patients at the same periodontal disease stage, cigarette smokers and e-cigarette smokers shared more similarities in their oral bacterial composition. E-cigarette smoking may have a similar potential as cigarette smoking at altering the bacterial composition of saliva over time, leading to an increase in the relative abundance of periodontal disease-associated pathogens such as Porphyromonas gingivalis and Fusobacterium nucleatum. The correlation analysis showed that certain genera, such as Dialister, Selenomonas, and Leptotrichia in the e-cigarette smoking group, were positively correlated with the levels of proinflammatory cytokines, including IFN-γ, IL-1β, and TNF-α. E-cigarette use was also associated with elevated levels of proinflammatory cytokines such as IFN-γ and TNF-α, which contribute to oral microbiome dysbiosis and advanced disease state. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fangxi Xu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Smruti Pushalkar
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Ziyan Lin
- Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Scott C Thomas
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Julia Kishanie Persaud
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Maria A Sierra
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Mridula Vardhan
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Rebeca Vasconcelos
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Adenike Akapo
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Yuqi Guo
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Terry Gordon
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Patricia M Corby
- Department of Oral Medicine, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Angela R Kamer
- Department of Periodontology and Implant Dentistry, New York University College of Dentistry, New York, NY, United States
| | - Xin Li
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
| | - Deepak Saxena
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, United States
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11
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Danko D, Malli Mohan GB, Sierra MA, Rucker M, Singh NK, Regberg AB, Bell MS, O’Hara NB, Ounit R, Mason CE, Venkateswaran K. Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions. Front Microbiol 2021; 12:608478. [PMID: 34394013 PMCID: PMC8358432 DOI: 10.3389/fmicb.2021.608478] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied. RESULTS To evaluate the microbial colonization of spacesuits, NASA used an Extravehicular Activity swab kit to examine viable microbial populations of 48 samples from spacesuits using both traditional microbiological methods and molecular sequencing methods. The cultivable microbial population ranged from below the detection limit to 9 × 102 colony forming units per 25 cm2 of sample and also significantly varied by the location. The cultivable microbial diversity was dominated by members of Bacillus, Arthrobacter, and Ascomycota. However, 16S rRNA-based viable bacterial burden ranged from 105 to 106 copies per 25 cm2 of sample. Shotgun metagenome sequencing revealed the presence of a diverse microbial population on the spacesuit surfaces, including Curtobacterium and Methylobacterium from across all sets of spacesuits in high abundance. Among bacterial species identified, higher abundance of Cutibacterium acnes, Methylobacterium oryzae, and M. phyllosphaerae reads were documented. CONCLUSION The results of this study provide evidence that identical microbial strains may live on the wrist joint, inner gauntlet, and outer gauntlet of spacesuits. This raises the possibility, but does not confirm that microbial contaminants on the outside of the suits could contaminate planetary science operations unless additional measures are taken. Overall, these data provide the first estimate of microbial distribution associated with spacesuit surfaces, which will help future mission planners develop effective planetary protection strategies.
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Affiliation(s)
- David Danko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Ganesh Babu Malli Mohan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Maria A. Sierra
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Michelle Rucker
- Exploration Mission Planning Office, Johnson Space Center, Houston, TX, United States
| | - Nitin K. Singh
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
| | - Aaron B. Regberg
- Astromaterials Research and Exploration Science Division, Johnson Space Center, Houston, TX, United States
| | - Mary S. Bell
- Jacobs@NASA/Johnson Space Center, Houston, TX, United States
| | - Niamh B. O’Hara
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA, United States
| | - Christopher E. Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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12
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Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021; 184:3376-3393.e17. [PMID: 34043940 PMCID: PMC8238498 DOI: 10.1016/j.cell.2021.05.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023]
Abstract
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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Affiliation(s)
- David Danko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Evan E Afshin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Chandrima Bhattacharya
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniel J Butler
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Kern Rei Chng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Daisy Donnellan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Katelyn Jackson
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Katerina Kuchin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Mikhail Karasikov
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail Lyons
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Lauren Mak
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dmitry Meleshko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Harun Mustafa
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Beth Mutai
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya
| | - Russell Y Neches
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Ng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | | | | | - Eileen Png
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Krista A Ryon
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jorge L Sanchez
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Heba Shaaban
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Maria A Sierra
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dominique Thomas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Ben Young
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Omar O Abudayyeh
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Josue Alicea
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | | | - Eduardo Castro-Nallar
- Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Ana M Cañas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Aspassia D Chatziefthimiou
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Youping Deng
- University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Christelle Desnues
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Emmanuel Dias-Neto
- Medical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil
| | - Marius Dybwad
- Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Dennis Gankin
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | | | - David C Green
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Iman Hajirasouliha
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jaden J A Hastings
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago, Chile; Wellcome Sanger Institute, Hinxton, UK
| | | | - Andre Kahles
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; Kyiv Academic University, Kyiv, Ukraine; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Frank J Kelly
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Kaymisha Knights
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paweł P Łabaj
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Boku University Viennna, Vienna, Austria
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Ken McGrath
- Microba, 388 Queen St, Brisbane City, QLD 4000, Australia
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | | | - Houtan Noushmehr
- University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto - SP, Brazil
| | - Manuela Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
| | - Orhan Özcan
- Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicolás Rascovan
- Microbial Paleogenomics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - Hugues Richard
- Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France; Robert Koch Institute, Berlin, Germany
| | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Rania Siam
- University of Medicine and Health Sciences, St. Kitts, West Indies and American University in Cairo, Cairo, Egypt
| | - Le Huu Song
- 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | | | - Denise Syndercombe Court
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | | | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Klas I Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; SciLife EVP, Department of Aquatic Sciences Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Brandon Valentine
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dimitar I Vassilev
- Faculty of Mathematics and Informatics, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Elena M Vayndorf
- Institute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, AK, USA
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Univeristätsklinikum Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam
| | - Jun Wu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Jifeng Zhu
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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Danko DC, Sierra MA, Benardini JN, Guan L, Wood JM, Singh N, Seuylemezian A, Butler DJ, Ryon K, Kuchin K, Meleshko D, Bhattacharya C, Venkateswaran KJ, Mason CE. A comprehensive metagenomics framework to characterize organisms relevant for planetary protection. Microbiome 2021; 9:82. [PMID: 33795001 PMCID: PMC8016160 DOI: 10.1186/s40168-021-01020-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 08/12/2020] [Accepted: 02/02/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Clean rooms of the Space Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL) at NASA are the final step of spacecraft cleaning and assembly before launching into space. Clean rooms have stringent methods of air-filtration and cleaning to minimize microbial contamination for exoplanetary research and minimize the risk of human pathogens, but they are not sterile. Clean rooms make a selective environment for microorganisms that tolerate such cleaning methods. Previous studies have attempted to characterize the microbial cargo through sequencing and culture-dependent protocols. However, there is not a standardized metagenomic workflow nor analysis pipeline for spaceflight hardware cleanroom samples to identify microbial contamination. Additionally, current identification methods fail to characterize and profile the risk of low-abundance microorganisms. RESULTS A comprehensive metagenomic framework to characterize microorganisms relevant for planetary protection in multiple cleanroom classifications (from ISO-5 to ISO-8.5) and sample types (surface, filters, and debris collected via vacuum devices) was developed. Fifty-one metagenomic samples from SAF clean rooms were sequenced and analyzed to identify microbes that could potentially survive spaceflight based on their microbial features and whether the microbes expressed any metabolic activity or growth. Additionally, an auxiliary testing was performed to determine the repeatability of our techniques and validate our analyses. We find evidence that JPL clean rooms carry microbes with attributes that may be problematic in space missions for their documented ability to withstand extreme conditions, such as psychrophilia and ability to form biofilms, spore-forming capacity, radiation resistance, and desiccation resistance. Samples from ISO-5 standard had lower microbial diversity than those conforming to ISO-6 or higher filters but still carried a measurable microbial load. CONCLUSIONS Although the extensive cleaning processes limit the number of microbes capable of withstanding clean room condition, it is important to quantify thresholds and detect organisms that can inform ongoing Planetary Protection goals, provide a biological baseline for assembly facilities, and guide future mission planning. Video Abstract.
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Affiliation(s)
- David C Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Maria A Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - James N Benardini
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Lisa Guan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Jason M Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Nitin Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Arman Seuylemezian
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Daniel J Butler
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Katerina Kuchin
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Dmitry Meleshko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chandrima Bhattacharya
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kasthuri J Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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Paul B, Sierra MA, Xu F, Crystal YO, Li X, Saxena D, Ruff RR. Microbial population shift and metabolic characterization of silver diamine fluoride treatment failure on dental caries. PLoS One 2021; 16:e0242396. [PMID: 33720954 PMCID: PMC7959385 DOI: 10.1371/journal.pone.0242396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/22/2021] [Indexed: 11/25/2022] Open
Abstract
The objective of this pilot study was to describe the microbial profiles present in the plaque and saliva of children who continued to develop new carious lesions following treatment with silver diamine fluoride ("nonresponders") compared to caries active, caries-free, and children immediately receiving SDF treatment for untreated caries in order to identify potential microbial differences that may relate to a re-incidence of caries. Saliva and plaque samples from infected and contralateral sites were obtained from twenty children who were either caries free, had active carious lesions, were caries active and received SDF treatment immediately before sampling, or had previously received SDF treatment and developed new caries. In total, 8,057,899 Illumina-generated sequence reads from 60 samples were obtained. Reads were processed using the Quantitative Insights Into Microbial Ecology pipeline. Group differences were assessed using Analysis of Variance Models and Tukey Honest Significant Differences. To identify significant taxa between treatment groups, Linear discriminant analysis Effect Size (LefSe) and Analysis of Differential Abundance Taking Sample Variation Into Account were used. Differential abundant analysis indicated that members of the Lachnospiraceae family were significantly enriched in non-responders and the genus Tannerella and species Granulicatella adiances were also highly abundant in this group. LefSe analysis between non-responders and SDF-treated groups revealed that genera Leptotrichia and Granulicatella were enriched in non-responders. We observed the highest abundance of phosphotransferase system and lowest abundance of lipopolysaccharide synthesis in non-responders. The microbiome in dental biofilms is responsible for initiation and progression of dental caries. SDF has been shown to be effective in arresting the progression carious lesions, in part due to its antimicrobial properties. Findings suggest that the differential abundance of select microbiota and specific pathway functioning in individuals that present with recurrent decay after SDF treatment may contribute to a potential failure of silver diamine fluoride to arrest dental caries. However, the short duration of sample collection following SDF application and the small sample size emphasize the need for further data and additional analysis.
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Affiliation(s)
- Bidisha Paul
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, United States of America
| | - Maria A. Sierra
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, United States of America
| | - Fangxi Xu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, United States of America
| | - Yasmi O. Crystal
- Department of Pediatric Dentistry, New York University College of Dentistry, New York, New York, United States of America
| | - Xin Li
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, United States of America
| | - Deepak Saxena
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, United States of America
| | - Ryan Richard Ruff
- Department of Epidemiology and Health Promotion, New York University College of Dentistry, New York, New York, United States of America
- New York University College of Global Public Health, New York, New York, United States of America
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Sierra MA, Li Q, Pushalkar S, Paul B, Sandoval TA, Kamer AR, Corby P, Guo Y, Ruff RR, Alekseyenko AV, Li X, Saxena D. The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community. Genes (Basel) 2020; 11:genes11080878. [PMID: 32756341 PMCID: PMC7465726 DOI: 10.3390/genes11080878] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 06/06/2020] [Revised: 07/11/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.
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Affiliation(s)
- Maria A. Sierra
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Qianhao Li
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Smruti Pushalkar
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Bidisha Paul
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Angela R. Kamer
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Patricia Corby
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Yuqi Guo
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Ryan Richard Ruff
- Department of Epidemiology & Health Promotion, New York University College of Dentistry, New York, NY 10010, USA;
| | - Alexander V. Alekseyenko
- The Biomedical Informatics Center, Program for Human Microbiome Research, Department of Public Health Sciences, Department of Oral Health Sciences, Department of Healthcare Leadership and Management, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Xin Li
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Deepak Saxena
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
- S. Arthur Localio Laboratory, Departments of Surgery New York University School of Medicine, New York, NY 10016, USA
- Correspondence: ; Tel.: +1-212-9989256
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Sierra MA, Danko DC, Sandoval TA, Pishchany G, Moncada B, Kolter R, Mason CE, Zambrano MM. The Microbiomes of Seven Lichen Genera Reveal Host Specificity, a Reduced Core Community and Potential as Source of Antimicrobials. Front Microbiol 2020; 11:398. [PMID: 32265864 PMCID: PMC7105886 DOI: 10.3389/fmicb.2020.00398] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/17/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in Colombian Paramos using 16S rRNA gene amplicon sequencing and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes varied in diversity indexes and number of OTUs, but were composed predominantly by the phyla Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia. In the case of Cora and Cladonia, the microbiomes were distinguished based on the identity of the lichen host. While the majority of the lichen-associated microorganisms were not present in all lichens sampled, sixteen taxa shared among this diverse group of lichens suggest a core lichen microbiome that broadens our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant microbial strains. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.
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Affiliation(s)
- Maria A. Sierra
- Molecular Genetics, Corporación CorpoGen – Research Center, Bogotá, Colombia
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - David C. Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Gleb Pishchany
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Bogotá, Colombia
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
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Sierra E, Espinosa de Los Monteros A, Fernández A, Díaz-Delgado J, Suárez-Santana C, Arbelo M, Sierra MA, Herráez P. Muscle Pathology in Free-Ranging Stranded Cetaceans. Vet Pathol 2016; 54:298-311. [PMID: 27538973 DOI: 10.1177/0300985816660747] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Despite the profound impact that skeletal muscle disorders may pose for the daily activities of wild terrestrial and marine mammals, such conditions have been rarely described in cetaceans. In this study, the authors aimed to determine the nature and prevalence of skeletal muscle lesions in small and large odontocetes and mysticetes ( n = 153) from 19 different species. A macroscopic evaluation of the epaxial muscle mass and a histologic examination of the longissimus dorsi muscle were performed in all cases. The only macroscopically evident change was variable degrees of atrophy of the epaxial muscles ( longissimus dorsi, multifidus, spinalis) in emaciated specimens. The histopathological study revealed single or combined morphological changes in 91.5% of the cases. These changes included the following: degenerative lesions (75.2%), muscle atrophy (37.9%), chronic myopathic changes (25.5%), parasitic infestation (9.2%), and myositis (1.9%). The skeletal muscle is easily sampled during a necropsy and provides essential microscopic information that reflects both local and systemic conditions. Thus, skeletal muscle should be systematically sampled, processed, and examined in all stranded cetaceans.
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Affiliation(s)
- E Sierra
- 1 Department of Veterinary Pathology, Institute for Animal Health, Veterinary School, University of Las Palmas de Gran Canaria, Arucas, Spain
| | - A Espinosa de Los Monteros
- 1 Department of Veterinary Pathology, Institute for Animal Health, Veterinary School, University of Las Palmas de Gran Canaria, Arucas, Spain
| | - A Fernández
- 1 Department of Veterinary Pathology, Institute for Animal Health, Veterinary School, University of Las Palmas de Gran Canaria, Arucas, Spain
| | - J Díaz-Delgado
- 1 Department of Veterinary Pathology, Institute for Animal Health, Veterinary School, University of Las Palmas de Gran Canaria, Arucas, Spain
| | - C Suárez-Santana
- 1 Department of Veterinary Pathology, Institute for Animal Health, Veterinary School, University of Las Palmas de Gran Canaria, Arucas, Spain
| | - M Arbelo
- 1 Department of Veterinary Pathology, Institute for Animal Health, Veterinary School, University of Las Palmas de Gran Canaria, Arucas, Spain
| | - M A Sierra
- 2 Department of Anatomy and Comparative Pathology, Veterinary Faculty, University of Córdoba, Córdoba, Spain
| | - P Herráez
- 1 Department of Veterinary Pathology, Institute for Animal Health, Veterinary School, University of Las Palmas de Gran Canaria, Arucas, Spain
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Abstract
The sudden death of five sulphur-crested cockatoos (Cacatua galerita) with no apparent clinical signs was investigated. The birds had hepatitis with intranuclear inclusion bodies (IIBs), as well as IIBs in mononuclear spleen cells, epithelial cells of the kidney tubules and endothelial cells of the glomerular capillaries. Ultrastructurally, icosahedral herpesvirus-like particles, 110 to 115 nm in diameter were found consistent with Pacheco's disease. This is the first time the disease has been reported in cockatoos in Spain.
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Sánchez-Cordón PJ, Gómez-Villamandos JC, Gutiérrez J, Sierra MA, Pedrera M, Bautista MJ. Atoxoplasma spp. Infection in Captive Canaries (Serinus canaria). ACTA ACUST UNITED AC 2007; 54:23-6. [PMID: 17359450 DOI: 10.1111/j.1439-0442.2007.00909.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clinical signs, histopathological and ultrastructural findings associated with Atoxoplasma spp. natural infection in captive canaries (Serinus canaria) are described. Intracytoplasmic Atoxoplasma-like protozoa were found in the liver and lung. In the liver, protozoa were found in hepatocytes and Kupffer's cells and were associated with granulomatous hepatitis and a marked bile duct hyperplasia. An usual finding was the presence of infected mononuclear cells adhered to the endothelium of the blood vessels in lung. The diagnosis was confirmed by ultrastructural examination of reprocessed paraffin-embedded tissues.
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Affiliation(s)
- P J Sánchez-Cordón
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Edificio de Sanidad Animal, Campus de Rabanales, 14014 Córdoba, Spain.
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Salguero FJ, Sánchez-Cordón PJ, Sierra MA, Jover A, Núñez A, Gómez-Villamandos JC. Apoptosis of thymocytes in experimental African Swine Fever virus infection. Histol Histopathol 2004; 19:77-84. [PMID: 14702174 DOI: 10.14670/hh-19.77] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper report on the lesions occurred in the thymus in experimental acute African swine fever (ASF). Twenty-one pigs were inoculated with the highly virulent ASF virus (ASFV) isolate Spain-70. Animals were slaughtered from 1 to 7 days post infection (dpi). Three animals with similar features were used as controls. Thymus samples were fixed in 10% buffered formalin solution for histological and immunohistochemical study and in 2.5% glutaraldehyde for ultrastructural examination. For immunohistochemical study, the avidin-biotin-peroxidase complex (ABC) technique was used to demonstrate viral protein 73 and porcine myeloid-histiocyte antigen SWC3 using specific monoclonal antibodies. Cell apoptosis was evaluated by the TUNEL assay. Blood samples were taken daily from all pigs and were used for leukocyte counts. The results of this study show a severe thymocyte apoptosis not related to the direct action of ASFV on these cells, but probably to a quantitative increase in macrophages in the thymus and their activation. A decrease in the percentage of blood lymphocytes was observed at the same time No significant vascular changes were observed in the study. With these results we suggest that ASFV infection of the thymus does not seem to play a critical role in the acute disease. Although severe apoptosis was observed, animals died because of the severe lesions found in the other organs.
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Affiliation(s)
- F J Salguero
- Departamento de Anatomía Patológica, Facultad de Veterinaria, Universidad de Córdoba, Campus Universitario de Rabanales, Edificio de Sanidad Animal, Córdoba, Spain
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Gómez-Villamandos JC, Carrasco L, Bautista MJ, Sierra MA, Quezada M, Hervas J, Chacón MDLF, Ruiz-Villamor E, Salguero FJ, Sónchez-Cordón PJ, Romanini S, Núñez A, Mekonen T, Méndez A, Jover A. African swine fever and classical swine fever: a review of the pathogenesis. Dtsch Tierarztl Wochenschr 2003; 110:165-9. [PMID: 12756959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
This paper describes major pathogenetic mechanisms of African and Classical Swine Fever virus infections. The interactions between both viruses and the monocyte-macrophage-system result in the release of mediator molecules, which are important for the further progression of the diseases. The causes of the thrombocytopenia and the mechanisms of the haemorrhages, which are characteristic in both infections, are described. Apoptotic cell death is regarded as the predominant cause of lymphopenia in both virus infections.
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Abstract
Twenty pigs were inoculated with a virulent isolate (Quillota strain) of classical swine fever (CSF) virus to determine the chronological development of lesions in bone marrow. Histopathologic, ultrastructural and immunohistochemical (detection of viral antigen gp55, myeloid-histiocyte antigen, CD3 antigen, and FVIII-rag), and morphometric techniques were employed. Viral antigen was detected from 2 days postinfection (dpi) in stromal and haematopoitic cells, and severe atrophy related to apoptosis of haematopoitic cells was observed. Megakaryocytes (MKs) did not show significant changes in number, but there were important qualitative changes including 1) increased numbers of cloud-nuclei MKs, microMKs, apoptotic MKs, and atypical nucleated MKs and 2) decreased number of typical nucleated MKs. Morphometric study of these cells showed a decrease in cytoplasmic area. MK infection was detected from 2 dpi, but in a small percentage of cells. Myeloid cells showed quantitative changes, with an increase in granulocyte numbers. Apoptosis of lymphocytes and viral infection of erythroblasts were also observed. The main changes in stroma were depletion of T lymphocytes in the middle phase of the experiment and macrophages. Viral infection was also observed in these cells. MK lesions suggest dysmegakaryocytopoiesis, which would aggravate the thrombocytopenia already present and could be responsible for it. Granulocyte changes would lead to the appearance of circulating immature forms, whereas lymphocyte apoptosis in bone marrow would contribute to lymphopenia.
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Affiliation(s)
- J C Gomez-Villamandos
- Departamento Anatomía y Anatomía Patológica Comparadas, Edificio de Sanidad Animal, Campus Universitario de Rabanales, Córdoba, Spain.
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Sierra MA, Gómez-Gallego M, Mancheño MJ, Martínez-Alvarez R, Ramírez-López P, Kayali N, González A. Electrospray mass spectra of group 6 (Fischer) carbenes in the presence of electron-donor compounds. J Mass Spectrom 2003; 38:151-156. [PMID: 12577281 DOI: 10.1002/jms.424] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fischer carbene complexes 1-7 are not ionized under standard electrospray ionization (ESI) conditions. We report here that unsaturated chromium and tungsten (Fischer) carbene complexes can be ionized in an electrospray ion source in the presence of electron-donor compounds such as hydroquinone (HQ) or tetrathiafulvalene (TTF). The addition of these compounds, which seem to act as electron transfer agents, permits the recording and study of their ESI mass spectra in the negative mode of detection. Both chromium and tungsten(0) carbene complexes undergo in the first fragmentation stage a double simultaneous decarbonylation process.
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Affiliation(s)
- M A Sierra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense, E-28040 Madrid, Spain
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Carrasco L, Núñez A, Salguero FJ, Díaz San Segundo F, Sánchez-Cordón P, Gómez-Villamandos JC, Sierra MA. African swine fever: Expression of interleukin-1 alpha and tumour necrosis factor-alpha by pulmonary intravascular macrophages. J Comp Pathol 2002; 126:194-201. [PMID: 11945008 DOI: 10.1053/jcpa.2001.0543] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To determine, in the acute form of African swine fever (ASF), the relationship between the appearance of pulmonary oedema and viral replication and expression of cytokines by pulmonary intravascular macrophages (PIMs), 14 pigs were inoculated intramuscularly with ASF virus (strain España'70) and killed in pairs on days 1-7 post-inoculation. Samples of lung were examined immunohistochemically and ultrastructurally. The immunohistochemical study was carried out with antibodies against interleukin-1 alpha (IL-1alpha), tumour necrosis factor-alpha (TNF-alpha), viral antigen of ASF (Vp73) and a myeloid marker (SWC3). Viral replication was observed mainly in PIMs, which at the same time showed intense activation, accompanied by the expression of IL-1alpha and TNF-alpha. The occurrence of interstitial oedema, neutrophil sequestration and fibrin microthrombi in septal capillaries coincided with high degrees of cytokine expression by infected PIMs. Alveolar macrophages did not show a significant change in cytokine expression as a result of ASF infection, and viral replication was detected in only a low percentage of these cells.
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Affiliation(s)
- L Carrasco
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Spain
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25
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Abstract
The photochemical reaction of alkoxychromium(0)carbene complexes and ferrocene mono- and disubstituted imines formed 2-azetidinones having one or two ferrocene moieties in good yields. Yields decrease when the carbene moiety bears an aminoferrocene moiety attached to the carbene carbon, while complex 9 having the ferrocene directly bonded to the carbene carbon was totally inert in these reactions. Access to beta-lactams with the ferrocene tethered to the C3 position through a methylene group was gained using the lithium enolate derived from ethyl 3-ferrocenylpropanoate. The reaction of this enolate produced two unexpected processes. Thus, 2-azetidinone 15 having an hydroxyl group at the C3 position was obtained together with the expected beta-lactam 14, by reaction of the lithium enolate of ethyl 3-ferrocenylpropenoate and imine 1. Additionally, unsaturated amide 17 was obtained by base-promoted Hoffmann-like breakage of the beta-lactam ring formed in the reaction of the same enolate and imine 2. Oxidation of the anion at the C3 of the 2-azetidinone ring on compound 14, as well as the sterically driven ring-breakage of the C3 anion derived from the nonisolated 2-azetidinone 18, should be responsible for this behavior.
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Affiliation(s)
- M A Sierra
- Departamento de Química Orgánica, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain.
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26
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Sierra MA, del Amo JC, Mancheño MJ, Gómez-Gallego M. Pd-catalyzed inter- and intramolecular carbene transfer from group 6 metal-carbene complexes. J Am Chem Soc 2001; 123:851-61. [PMID: 11456618 DOI: 10.1021/ja002497i] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The use of group 6 metal-carbene complexes in inter- and intramolecular carbene transfer reactions has been studied. Thus, pentacarbonyl[(aryl)(methoxy)carbene]chromium(0) and tungsten complexes, 10, efficiently dimerize at room temperature in the presence of diverse Pd(0) and Pd(II)/Et(3)N catalysts. The effect of additives (PPh(3), AsPh(3), or SbPh(3)) on the nature and the isomeric ratio of the reaction products is negligible. The nature of the reaction products is more catalyst-dependent for metal carbenes 12 bearing alkyl groups attached to the carbene carbon. In these cases, either carbene ligand dimerization or beta-hydrogen elimination reactions are observed, depending on the catalyst. The carbene ligand dimerization reaction can be used to prepare conjugated polyenes, including those having metal moieties at both ends of the polyene system, as well as enediyne derivatives. The intramolecular carbene ligand dimerization of chromium bis-carbene complexes 28 and 30 allows the preparation of mono- and bicyclic derivatives, with ring sizes from six to nine members. For bis-carbene derivatives the beta-hydrogen elimination reaction is inhibited, provided that both metal centers are tethered by an o-xylylene group. Other alkyl complexes 32 form new mononuclear carbene complexes 37 or decompose to complex reaction mixtures. The results obtained in these reactions may be explained by transmetalation from Cr(0) to Pd(0) and the intermediacy of Pd-carbene complexes. Aminocarbene-chromium(0) complexes 15, need harsher reaction conditions to transfer the carbene ligand, and this transfer occurs only in the presence of deactivated olefins. The corresponding insertion/hydrolysis products 48 resulted in these cases. A catalytic cycle involving transmetalation from a chromacyclobutane to a palladacyclobutane is proposed to explain these results.
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Affiliation(s)
- M A Sierra
- Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain.
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27
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Carrasco L, Ruiz-Villamor E, Gómez-Villamandos JC, Bautista MJ, Nuñez A, Quezada M, Sierra MA. Atypical cilia in the bronchiolar epithelium of pigs experimentally infected with hog cholera virus. J Comp Pathol 2001; 124:29-35. [PMID: 11428186 DOI: 10.1053/jcpa.2000.0424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To study the effect of hog cholera virus on the epithelial cells of the bronchiolar mucosa, 12 pigs were inoculated with a highly virulent strain. Immunohistochemical and ultrastructural examination of the ciliated epithelial cells demonstrated an increase in the number of atypical cilia. The latter showed alterations in the microtubular pattern, possibly resulting from viral interference with the normal metabolism of the epithelial cells.
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Affiliation(s)
- L Carrasco
- Departamento de Anatomía y Anatomía Patológica Comparadas, Edificio de Sanidad Animal, Facultad de Veterinaria, Universidad de Córdoba, Campus Universitario de Rabanales, 14014 Córdoba, Spain
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28
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Affiliation(s)
- M A Sierra
- Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, 28040-Madrid, Spain
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Quezada M, Cayo L, Carrasco L, Islas A, Lecocq C, Gómez-Villamandos JC, Sierra MA. Characterization of lesions caused by a South American virulent isolate ('Quillota') of the hog cholera virus. J Vet Med B Infect Dis Vet Public Health 2000; 47:411-22. [PMID: 11014061 DOI: 10.1046/j.1439-0450.2000.00376.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study, macroscopic and histopathological lesions produced by a virulent South American isolate ('Quillota') of hog cholera virus were studied. The virus was inoculated in doses of 10(5)TCID50 in each of 35 pigs of 20 kg live weight. The animals were slaughtered from 4 to 18 days post-inoculation. The presence of virus antigens in lymphatic tissue was confirmed by both direct immunofluorescence and Avidin-Biotin-Peroxidase techniques in formalin-embedded tissue samples. Histological sections were stained with haematoxylin-eosin and Mallory's phosphotungstic acid haematoxylin methods. The 'Quillota' isolate used in this study caused a disease characterized by vascular lesions (splenic infarcts, haemorrhages in the lymph nodes and the urinary system and disseminated microthrombosis), and necrosis of lymphocytes, particularly in the B-areas of the lymphoid organs, lesions that are characteristic of the acute form of the disease. Other lesions observed were a non-purulent meningoencephalitis, the necrosis of the epithelial cells of tonsils, the presence of fibrin nets in the red pulp and a marked thickening of the alveolar septa.
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Affiliation(s)
- M Quezada
- Department of Pathology, Veterinary Faculty, University of Concepción, Chillán, Chile
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30
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Gómez-Villamandos JC, Ruiz-Villamor E, Bautista MJ, Quezada M, Sánchez CP, Salguero FJ, Sierra MA. Pathogenesis of classical swine fever: renal haemorrhages and erythrodiapedesis. J Comp Pathol 2000; 123:47-54. [PMID: 10906255 DOI: 10.1053/jcpa.2000.0385] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Thirty pigs were inoculated with a virulent isolate (Quillota strain) of classical swine fever (hog cholera) virus to establish the chronological occurrence of lesions in the kidney and to determine the mechanism responsible for renal haemorrhages. The study included the use of histopathological, ultrastructural, immunohistochemical (detection of viral antigen gp55, MAC387, lambda chains, CD3 and C1q) and morphometrical techniques (vascular area). Renal interstitial oedema and haemorrhages were detected from 7 days post-inoculation (dpi), associated with a slight interstitial mononuclear infiltrate and evidence of viral infection in macrophages and fibroblasts, and in a small proportion of lymphocytes. Viral infection was not detected in capillary endothelial cells. An intense mononuclear infiltrate, with B cells, T cells and small numbers of macrophages, was detected from 10 dpi. In the final phase of the experiment (14 dpi), slight proliferation and degranulation of mast cells were observed. Increased expression of the C1q component of complement was also detected. A significant increase in vascular area was observed from 7 dpi. These results suggest that haemorrhages observed in the kidneys of pigs inoculated with the Quillota strain resulted from erythrodiapedesis and increased vascular permeability, probably aggravated by mast cell degranulation in the final stage of the experiment. The results suggested that mast cell degranulation was linked to activation of the complement system.
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Affiliation(s)
- J C Gómez-Villamandos
- Departamento de Anatomía Patológica, Universidad de Córdoba, Campus Universitario de Rabanales, Carretera de Madrid, 14014 Córdoba, Spain
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31
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Abstract
From the very beginning organic chemistry and total synthesis have been intimately joined. In fact, one of the first things that freshmen in organic chemistry learn is how to join two molecules together to obtain a more complex one. Of course they still have a long way to go to become fully mature synthetic chemists, but they must have the primary instinct to build molecules, as synthesis is the essence of organic chemistry. With the different points of view that actually coexist in the chemical community about the maturity of the science (art, or both) of organic synthesis, it is clear that nowadays we know how to make almost all of the most complex molecules ever isolated. The primary question is how easy is it to accomplish? For the readers of papers describing the total synthesis of either simple or complex molecules, it appears that the routes followed are, most of the time, smooth and free of troubles. The synthetic scheme written on paper is, apparently, done in the laboratory with few, if any, modifications and these, essentially, seem to be based on finding the optimal experimental conditions to effect the desired reaction. Failures in the planned synthetic scheme to achieve the goal, detours imposed by unexpected reactivity, or the absence of reactivity are almost never discussed, since they may diminish the value of the work reported. This review attempts to look at total synthesis from a different side; it will focus on troubles found during the synthetic work that cause detours from the original synthetic plan, or on the dead ends that eventually may force redesign. From there, the evolution from the original route to the final successful one that achieves the synthetic target will be presented. The syntheses discussed in this paper have been selected because they contain explicit information about the failures of the original synthetic plan, together with the evolution of the final route to the target molecule. Therefore, they contain a lot of useful negative information that may otherwise be lost.
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Affiliation(s)
- MA Sierra
- Departamento de Química Orgánica I Facultad de Química, Universidad Complutense 28040 Madrid (Spain)
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Carrasco L, Segalés J, Bautista MJ, Gómez-Villamandos JC, Rosell C, Ruiz-Villamor E, Sierra MA. Intestinal chlamydial infection concurrent with postweaning multisystemic wasting syndrome in pigs. Vet Rec 2000; 146:21-3. [PMID: 10661458 DOI: 10.1136/vr.146.1.21] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- L Carrasco
- Departmento Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Spain
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Pérez J, Astorga R, Carrasco L, Méndez A, Perea A, Sierra MA. Outbreak of salmonellosis in farmed European wild boars (Sus scrofa ferus). Vet Rec 1999; 145:464-5. [PMID: 10576283 DOI: 10.1136/vr.145.16.464] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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34
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Gómez-Villamandos JC, Sánchez C, Carrasco L, Laviada MM, Bautista MJ, Martínez-Torrecuadrada J, Sánchez-Vizcaíno JM, Sierra MA. Pathogenesis of African horse sickness: ultrastructural study of the capillaries in experimental infection. J Comp Pathol 1999; 121:101-16. [PMID: 10405303 DOI: 10.1053/jcpa.1999.0305] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
African horse sickness (AHS) was induced in five horses by inoculation, to determine the ultrastructural changes in endothelial cells of capillaries in the myocardium, lung, spleen and liver. The animals developed cardiac and mixed forms of the disease. Alterations detected in the endothelial cells of the vessels of infected animals included: the presence of structures associated with viral infection, hypertrophy, degenerative changes, appearance of cytoplasmic projections, changes in permeability, alteration of intercellular junctions, loss of endothelium, subendothelial deposition of cell debris and fibrin, and vascular repair. In association with these changes, oedema, haemorrhages and microthromboses were detected, particularly in the myocardium and lung. This study showed that infection of, and changes to, the capillary endothelial cells of the organs under study was independent of the form in which the disease manifested itself but was dependent on the organ and blood vessel type. Thus, different levels of viral tropism were observed for the endothelial cells of the vessels in different organs. Viral infection was commonest in the endothelial cells of myocardial vessels, followed by those in the lung, whereas in the spleen and liver, endothelial cell infection was rare and, in the case of the liver, limited to the interstitial capillaries.
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Affiliation(s)
- J C Gómez-Villamandos
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Avenida de Medina Azahara 7, Córdoba, 14005, USA
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35
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Carrasco L, Sánchez C, Gómez-Villamandos JC, Laviada MD, Bautista MJ, Martínez-Torrecuadrada J, Sánchez-Vizcaíno JM, Sierra MA. The role of pulmonary intravascular macrophages in the pathogenesis of African horse sickness. J Comp Pathol 1999; 121:25-38. [PMID: 10373291 DOI: 10.1053/jcpa.1998.0293] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
African horse sickness (AHS) is a disease of equids, characterized by severe pulmonary oedema and caused by an orbivirus. To determine the role of pulmonary intravascular macrophages (PIMs) in the development of pulmonary microvascular changes in this disease, five horses were given an intravenous inoculation of 10(6)TCID50of serotype 4 of AHS virus. Viral replication was detected in endothelial cells, PIMs, interstitial macrophages and fibroblasts. Alveolar and interstitial oedema, and changes in pulmonary microvasculature, consisting mainly of the sequestration of neutrophils and the formation of platelet aggregates and fibrinous microthrombi, were related to endothelial changes and to a high degree of PIM activation. This suggested that the PIMs, once activated, contributed to these vascular changes by releasing chemical inflammatory mediators.
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Affiliation(s)
- L Carrasco
- Departmento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Avenida Medina Azahara s/n, Córdoba, 14005, Spain
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36
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Méndez A, Scarlata E, Carrasco L, Pérez J, Gómez-Villamandos JC, Sierra MA. Rupture of the gracilis muscle in Iberian pigs at slaughter. Vet Rec 1999; 144:294-6. [PMID: 10204226 DOI: 10.1136/vr.144.11.294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- A Méndez
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad Veterinaria, Universidad de Córdoba, Spain
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37
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Abstract
Two 3-week-old Limousin x Retinta calves from extensive farms in the south of Spain died suddenly. Microscopic examination of the spleen and lymph nodes revealed an intense lymphoid proliferation; the germinal centres were prominent and were surrounded by areas of haemorrhage. Parasitic forms, similar to Koch's bodies, were observed in only a small number of lymphoid cells and macrophages. In the myocardium a severe myocarditis was found. Inflammatory cells were in close contact with damaged myocytes, sometimes surrounding fragments of cells. In some areas the vessels had intraluminal deposits of fibrin. The endothelial damage and thrombosis may have contributed to the damage observed in the myocytes, together with the cytotoxic mechanism associated with the presence of an intense inflammatory infiltrate. The active multiplication of parasites may be due to the age of the animals and their breed, since they are not an autochthonous breed and present low resistance to infection.
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Affiliation(s)
- J Hervás
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Cordoba, Spain
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38
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Gómez-Villamandos JC, Ruiz-Villamor E, Salguero FJ, Bautista MJ, Carrasco L, Sánchez C, Quezada M, Sierra MA. Immunohistochemical and ultrastructural evidence of hog cholera virus infection of megakaryocytes in bone marrow and spleen. J Comp Pathol 1998; 119:111-9. [PMID: 9749356 DOI: 10.1016/s0021-9975(98)80056-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Twelve pigs were inoculated with a highly virulent strain of hog cholera virus (HCV) to study viral infection of megakaryocytes in the bone marrow and spleen. Immunohistochemical and ultrastructural examination revealed HCV infection in a small proportion (2.5-9.0%) of these cells from the 2nd to the 9th day after inoculation, at which time the experiment was terminated. Megakaryocyte infection accounts for the presence of viral antigens in platelets. The latter may represent a passive vehicle for spreading the virus in the animal.
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Affiliation(s)
- J C Gómez-Villamandos
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Spain
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39
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Pérez J, Fernández AI, Sierra MA, Herráez P, Fernández A, Martín de las Mulas J. Serological and immunohistochemical study of African swine fever in wild boar in Spain. Vet Rec 1998; 143:136-9. [PMID: 9725185 DOI: 10.1136/vr.143.5.136] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A serological and immunohistochemical study of African swine fever was carried out in wild boar killed in seven municipalities in the north of the province of Córdoba during two hunting seasons (1991-92 and 1992-93), when the area was affected by the disease. Fourteen of 147 wild boar analysed by ELISA and immunoblotting had antibodies to African swine fever virus. The immunohistochemical study revealed that four cases (two seropositive and two seronegative) showed immunoreactivity to the anti-VP73 monoclonal antibody. Two of the VP73+ wild boar had severe generalised haemorrhages consistent with the acute from of the disease, and another had lesions consistent with subacute African swine fever, but none of the remaining 144 animals had gross or microscopic changes suggestive of the disease. These results indicate that wild boar can suffer from African swine fever without showing clinical signs. The disease in wild boar was associated with the disease in domestic pigs. Thus, no African swine fever-positive boar were found either in one municipality with no out-breaks in domestic pigs or in three municipalities with only one outbreak in pigs during the hunting seasons and during the previous year. These results suggest that European wild boar do not play an important role as carriers of the virus of African swine fever.
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Affiliation(s)
- J Pérez
- Department of Comparative Pathology, Córdoba, Spain
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40
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Bautista MJ, Gómez-Villamandos JC, Carrasco L, Ruíz-Villamor E, Salguero FJ, Sierra MA. Ultrastructural pathology of the bone marrow in pigs inoculated with a moderately virulent strain (DR'78) of African swine fever virus. Histol Histopathol 1998; 13:713-20. [PMID: 9690128 DOI: 10.14670/hh-13.713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interpretation of changes in bone marrow during infectious processes is quite complex. This paper reports bone marrow lesions observed in pigs inoculated with a moderately virulent ASF virus strain and studies their relationship to the pathogenesis of the disease. In this work, we have carried out the structural and ultrastructural study of the bone marrow of 14 Large White x Landrace pigs that were inoculated by the intramuscular route with 10(5) 50% hemodsorbing doses (HAD50) of the Dominican Republic'78 ASF virus strain. The inoculated pigs were killed at 3, 5, 7, 9, 11, 13, 15 and 17 days postinjection. Analysis of cells and structures belonging to the two main bone-marrow compartments, the hematopoietic cells and the hematopoietic micro-environment, showed that after inoculation with a moderately virulent strain, the most significant changes occurred in macrophages and megakaryocytes, consisting in virus replication in these cell populations and apoptosis of megakaryocytes, related with the sudden and transitory thrombocytopenia detected in the subacute ASF.
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Affiliation(s)
- M J Bautista
- Department of Pathology, Faculty of Veterinary, University of Córdoba, Spain
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41
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Gómez-Villamandos JC, Bautista MJ, Carrasco L, Chacón-Manrique de Lara F, Hervás J, Wilkinson PJ, Sierra MA. Thrombocytopenia associated with apoptotic megakaryocytes in a viral haemorrhagic syndrome induced by a moderately virulent strain of African swine fever virus. J Comp Pathol 1998; 118:1-13. [PMID: 9500234 DOI: 10.1016/s0021-9975(98)80023-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A viral haemorrhagic syndrome was induced in 14 pigs by inoculation with an African swine fever (ASF) virus strain of moderate virulence, to determine changes in megakaryocyte (MK) numbers and morphology and thus to assess the role of these cells in the thrombocytopenia characteristic of subacute ASF. The strain tested induced changes in the proportion of different types of MK (typical nucleated MKs, apoptotic MKs and immature MKs); it also caused subcellular lesions over the first 7 days post-inoculation (dpi). At 7 dpi, severe thrombocytopenia was observed. There was a statistically significant increase in apoptotic MK numbers. The MKs showed three stages in the course of the disease: a compensatory stage, represented by cytoplasmic projections, a hypermaturity stage, represented by apoptotic MKs, and a regenerative stage, represented by clusters of immature MKs. These changes, especially the presence of numerous apoptotic MKs, may explain the early and transitory thrombocytopenia detected in subacute ASF. The large number of apoptotic MKs observed may be associated with the accelerated maturation of these cells, resulting from the action of cytokines, or peripheral platelet consumption, or both.
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Affiliation(s)
- J C Gómez-Villamandos
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Spain
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Holste JE, Colwell DD, Kumar R, Lloyd JE, Pinkall NP, Sierra MA, Waggoner JW, Langholff WK, Barrick RA, Eagleson JS. Efficacy of eprinomectin against Hypoderma spp in cattle. Am J Vet Res 1998; 59:56-8. [PMID: 9442244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To determine the efficacy of a topical formulation of eprinomectin against natural infestations of first (L1)-stage, and second and third (L2/L3)-stage larvae of Hypoderma spp. ANIMALS 140 approximately 6- to 18-month-old cattle of various breeds. PROCEDURE Cattle, selected from herds with high prevalence of Hypoderma infestation, were treated in 4 experiments: within each replicate, 1 animal received eprinomectin at a dosage of 500 micrograms/kg of body weight against first-stage larvae (L1). The second animal received the same treatment against second or third-stage larvae (L2/L3). The third animal served as an untreated control. In a fifth experiment, visible warbles were treated on half of the cattle. Remaining cattle served as vehicle-treated controls. In 1 experiment, warbles were examined from time of treatment until all lesions were resolved. In 4 experiments, emerging Hypoderma larvae were recovered, speciated, and enumerated, and viability was determined. RESULTS Eprinomectin (500 micrograms/kg) efficacy was complete against L1. Hypoderma L2/L3 eradication approached 100% efficacy (1 live larva was recorded). Warbles in treated cattle resolved in a significantly shorter time than did those in controls. Adverse reactions related to treatment were not observed in any of the trials. CONCLUSIONS Eprinomectin (500 micrograms/kg) applied topically was safe and highly efficacious for treatment of all larval stages of Hypoderma spp in these trials. CLINICAL RELEVANCE Attributes of eprinomectin besides antiparasite efficacy allow treatment of all classes of cattle with no need for meat or milk withdrawal.
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Pérez J, Quezada M, López J, Casquet O, Sierra MA, Martín de las Mulas J. Immunohistochemical detection of Brucella abortus antigens in tissues from aborted bovine fetuses using a commercially available polyclonal antibody. J Vet Diagn Invest 1998; 10:17-21. [PMID: 9526855 DOI: 10.1177/104063879801000104] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A commercially available polyclonal antibody and an avidin-biotin-peroxidase immunohistochemical technique were used to detect Brucella abortus antigens in formalin-fixed, paraffin-embedded tissues of lung and liver from 20 aborted bovine fetuses. Thirteen fetuses were obtained from farms with a previous history of brucellosis, and 7 were collected from farms without a history of brucellosis. Among the 13 aborted bovine fetuses obtained from farms with a history of brucellosis, immunoreactivity to B. abortus was detected in lung (9 fetuses) and in liver (1 fetus), whereas Brucella was cultured from abomasal contents in 9 fetuses (8 were immunohistochemically positive). In addition, 11 dams of these 13 aborted bovine fetuses had antibodies to Brucella. Brucella abortus was not detected by immunohistochemistry in the 7 aborted bovine fetuses collected from farms without a history of brucellosis. Bacteriologic culture and serologic tests were also negative for Brucella. The results of this study revealed that the immunohistochemical technique was sufficiently sensitive for detecting B. abortus antigens in formalin-fixed lung tissues from naturally aborted bovine fetuses. Although additional studies are necessary to rule out cross-reaction of the polyclonal antibody with other microorganisms that cause bovine abortion, this immunohistochemical technique could be a complementary tool to serology and bacteriology for the diagnosis of brucellosis.
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Affiliation(s)
- J Pérez
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Spain
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Pérez J, Bautista MJ, Rodríguez F, Wilkinson PJ, Sierra MA, Martín de las Mulas J. Double-labelling immunohistochemical study of megakaryocytes in African swine fever. Vet Rec 1997; 141:386-90. [PMID: 9364707 DOI: 10.1136/vr.141.15.386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bone marrow samples from pigs infected with the highly virulent Malawi'83 or moderately virulent Dominican Republic (DR'78) isolates of African swine fever virus were studied by means of a double labelling immunohistochemical technique which stained the major structural protein VP73 of the virus and megakaryocytes simultaneously. In pigs infected with the highly virulent Malawi'83 isolate, 2.2 per cent of megakaryocytes were VP73+ five days after inoculation, and at six and seven days 2.5 and 9.5 per cent of megakaryocytes were VP73+. Some infected and uninfected megakaryocytes showed pyknosis and karyorrhexis, particularly at seven days after inoculation. However, in comparison with uninfected pigs, the number of megakaryocytes decreased only at seven days after inoculation. In pigs infected with the moderately virulent DR'78 isolate, only 0.2 per cent of megakaryocytes were VP73+ at eight days after inoculation. However, at eight, nine and 10 days after inoculation the total number of megakaryocytes was significantly lower (P < 0.01) than in control uninfected pigs, and the majority of the megakaryocytes showed signs of cell death such as pyknosis and karyorrhexis. The fact that this greater destruction of megakaryocytes was associated with the lower rate of infection of this cell type suggests that indirect damage to megakaryocytes is an additional mechanism of thrombocytopenia in acute and subacute African swine fever.
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Affiliation(s)
- J Pérez
- Department of Comparative Pathology, Faculty of Veterinary Medicine, Córdoba, Spain
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Hervás J, Gómez-Villamandos JC, Pérez J, Carrasco L, Sierra MA. Focal mesangial-sclerosing glomerulonephritis and acute-spontaneous infectious canine hepatitis: structural, immunohistochemical and subcellular studies. Vet Immunol Immunopathol 1997; 57:25-32. [PMID: 9239835 DOI: 10.1016/s0165-2427(96)05764-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The glomerular alterations observed in a dog with acute spontaneous infectious canine hepatitis (ICH) are described. Histologic changes of the glomeruli were enlargement of the mesangium with presence of intranuclear inclusion bodies and without proliferation of mesangial cells. Electron microscopy revealed adenovirus replication sites in glomerular mesangial cells and in endothelial cells of glomerular capillaries, as well as a focal mesangial-sclerosing glomerulonephritis associated with electron dense deposits which were closely related with extracellular ICH viral particles and immunohistochemically reactive for immunoglobulin (Ig) G, IgA, IgM and C3c complement components.
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Affiliation(s)
- J Hervás
- Dpto. Anatomía Patológica, Facultad de Veterinaria, Cordoba, Spain
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Carrasco L, Chàcón-M de Lara F, Martín de Las Mulas J, Gómez-Villamandos JC, Sierra MA, Villeda CJ, Wilkinson PJ. Ultrastructural changes related to the lymph node haemorrhages in acute African swine fever. Res Vet Sci 1997; 62:199-204. [PMID: 9300534 DOI: 10.1016/s0034-5288(97)90190-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In order to determine the pathogenic mechanisms involved in lymph node haemorrhages in acute African swine fever (ASF), eight pigs were inoculated with ASF virus, strain Malawi'83. Lymph node haemorrhages were observed from three days post infection (dpi) onwards, coinciding with ASF virus replication in monocytes and macrophages adjacent to stimulated endothelial cells, phagocytic stimulation of capillary and small-vessel endothelial cells, increase in the number of fenestrations of endothelial cells, and endothelial cell loss, as well as clusters of blood cells and necrotic material beneath the endothelium. Vascular lumina were blocked by platelet plugs and fibrin microthrombi. These phenomena became more marked as the disease progressed. At five dpi, virus replication was also found in circulating neutrophils. At seven dpi, lesions were more intense and were accompanied by virus replication in sinus and capillary endothelial cells, and in other cell populations including pericytes, fibroblasts, smooth muscle fibres and reticular cells. The results obtained in this study suggest that lymph node haemorrhages are related to endothelial stimulation and the onset of disseminated intravascular coagulation. Virus replication in vessel wall cells occurs only in the final stages of the disease and plays a secondary role.
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Affiliation(s)
- L Carrasco
- Departamento de Anatomía y Anatomía Patológica Comparadas, Facultad de Veterinaria, Universidad de Córdoba, Spain
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Abstract
The ultrastructure of several stages of Hepatozoon canis found in dogs with clinically and histologically diagnosed infections was determined using transmission electron microscopy. Merozoites, macro- and microschizonts and gamonts were found in spleen, liver, kidneys and lungs. Macro- and micromeronts were characterized by their size and by the presence of intracytoplasmic amylopectin granules. Gamonts, which provide the basis for clinical diagnosis of the disease, were observed within mononuclear cells (monocytes/macrophages); they were butterfly-shaped and exhibited varying electron densities. On the basis of the microscopic observations reported here, it is clear that the life cycle of H. canis is a complex one.
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Affiliation(s)
- J Hervás
- Departamento de Anatomía Patológica, Facultad de Veterinaria, Córdoba, Spain
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Gómez-Villamandos JC, Bautista MJ, Carrasco L, Caballero MJ, Hervás J, Villeda CJ, Wilkinson PJ, Sierra MA. African swine fever virus infection of bone marrow: lesions and pathogenesis. Vet Pathol 1997; 34:97-107. [PMID: 9066076 DOI: 10.1177/030098589703400202] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The effects of African swine fever (ASF) virus infection on bone marrow hematopoiesis and microenvironment were determined by studying the sequential development of ultrastructural lesions of bone marrow and blood cell changes. Eight pigs (two pigs/infected group) were inoculated by intramuscular route with 10(5) 50% hemadsorbing doses (HAD50) of the Malawi'83 ASF virus isolate. Two uninfected pigs were used as controls. Ultrastructural changes developed by day 3 postinoculation (PI), persisted through day 7 PI, and were characterized by activation of macrophages. From day 5 PI, viral replication was observed in monocytes/macrophages, reticular cells, immature neutrophils, and promonocytes. Also viral replication was detected in megakaryocytes, endothelial cells, and pericytes at day 7 PI. Vascular alterations consisted of activation of sinusoidal endothelial cells, intravascular coagulation, and fibrin strands interspersed among microenvironment and hematopoietic cells. No significant changes were observed in total white blood cells counts, percentage of monocytes, and platelet counts; however, severe lymphopenia and neutrophilia were detected from day 3 PI. Results of this experiment indicate that there is increased hematopoiesis in bone marrow during acute ASF, coinciding with macrophage activation. Neither vascular changes nor viral replication in different bone marrow cell populations gave rise to impaired bone marrow function. Increased hematopoiesis would exert a positive influence by preventing the early onset of thrombocytopenia and would exert a negative influence by stimulating the spread of the virus via neutrophils. Increased hematopoiesis would be unable to compensate for the lymphopenia.
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Affiliation(s)
- J C Gómez-Villamandos
- Departamento Anatomía y Anatomía Patológica, Facultad de Veterinaria, Universidad de Córdoba, Spain
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Carrasco L, Hervás J, Gómez-Villamandos JC, de Lara FC, Sierra MA. Massive Filaroides hirthi infestation associated with canine distemper in a puppy. Vet Rec 1997; 140:72-3. [PMID: 9023910 DOI: 10.1136/vr.140.3.72] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- L Carrasco
- Department of Anatomy and Comparative Pathology, Faculty of Veterinary Medicine, University of Córdoba, Spain
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de las Mulas JM, Ruiz-Villamor E, Donoso S, Quezada M, Lecocq C, Sierra MA. Immunohistochemical detection of hog cholera viral glycoprotein 55 in paraffin-embedded tissues. J Vet Diagn Invest 1997; 9:10-6. [PMID: 9087919 DOI: 10.1177/104063879700900103] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Formalin-fixed, paraffin embedded tissues obtained from 40 pigs inoculated with a field isolate of hog cholera virus were examined for the presence of Gp55, a major structural protein of the virus envelope, using a monoclonal antibody-based immunohistochemical test with the avidin-biotin-peroxidase complex method. Immunoreactivity was detected in hog cholera virus-infected tissues but not in control pigs tissues, African swine fever virus-infected tissues, or bovine viral diarrhea virus-infected porcine or bovine tissues. The first positive reactions were seen in lymphatic tissues, digestive tract and skin on postinoculation day (pid) 4, respiratory and urinary tissues on pid 5, nervous tissues on pid 6, and endocrine tissues on pid 7. These staining reactions persisted until the last observation on pid 18. Hog cholera virus antigen was not detected in heart tissue at any time. The highest levels of antigen detection were found in tonsils, spleen, and pancreas, although the esophageal mucosa and skin epithelial cells were also intensely and widely stained. The cellular staining pattern of Gp55 had a ubiquitous distribution. It was found in epithelial cells, macrophages and circulating monocytes, endothelial cells, lymphoid cells, and glial cells. The results showed a high specificity and high sensitivity for detecting hog cholera Gp55 in formalin-fixed, paraffin embedded tissue samples. This method allows precise association of Gp55 with specific cells, tissues, and histologic lesions, making the technique suitable for use in routine diagnosis of hog cholera.
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Affiliation(s)
- J M de las Mulas
- Department of Comparative Pathology, Veterinary Faculty, University of Córdoba, Spain
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