1
|
Nejthardt MB, Alexandris P, Bechan S, Bijli MFA, Chetty S, Dippenaar JM, Gibbs M, Johnson M, Kluyts H, Llewellyn R, Motiang M, Mogane P, Motshabi P, Mrara B, Roodt F, Singh U, Spijkerman S, Turton E, Van der Westhuizen J, Biccard B. The development of a nurse-led preoperative anaesthesia screening tool by Delphi consensus. S Afr Med J 2024; 114:e1306. [PMID: 38525581 DOI: 10.7196/samj.2024.v114i2.1306] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Low- and middle-income countries have a critical shortage of specialist anaesthetists. Most patients arriving for surgery are of low perioperative risk. Without immediate access to preoperative specialist care, an appropriate interim strategy may be to ensure that only high-risk patients are seen preoperatively by a specialist. Matching human resources to the burden of disease with a nurse-administered pre-operative screening tool to identify high-risk patients who might benefit from specialist review prior to the day of surgery may be an effective strategy. OBJECTIVE To develop a nurse-administered preoperative anaesthesia screening tool to identify patients who would most likely benefit from a specialist review before the day of surgery, and those patients who could safely be seen by the anaesthetist on the day of surgery. This would ensure adequate time for optimisation of high-risk patients preoperatively and limit avoidable day-of-surgery cancellations. METHODS A systematic review was conducted to identify preoperative screening questions for use in a three-round Delphi consensus process. A panel of 16 experienced full-time clinical anaesthetists representing all university-affiliated anaesthesia departments in South Africa participated to define a nurses' screening tool for preoperative assessment. RESULTS Ninety-eight studies were identified, which generated 79 questions. An additional 14 items identified by the facilitators were added to create a list of 93 questions for the first round. The final screening tool consisted of 81 questions, of which 37 were deemed critical to identify patients who should be seen by a specialist prior to the day of surgery. CONCLUSION A structured nurse-administered preoperative screening tool is proposed to identify high-risk patients who are likely to benefit from a timely preoperative specialist anaesthetist review to avoid cancellation on the day of surgery.
Collapse
Affiliation(s)
- M B Nejthardt
- Department of Anaesthesia and Perioperative Medicine, Faculty of Health Sciences, University of Cape Town, South Africa; Department of Anaesthesia and Perioperative Medicine, Groote Schuur Hospital, Cape Town, South Africa.
| | - P Alexandris
- Department of Anaesthesia, Faculty of Health Sciences, Nelson Mandela University, Gqeberha, South Africa.
| | - S Bechan
- Discipline of Anaesthesiology and Critical Care, Nelson R Mandela School of Medicine, University of Kwa-Zulu Natal, Albert Luthuli Academic Hospital, Durban, South Africa.
| | - M F A Bijli
- Department of Anaesthesia and Perioperative Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - S Chetty
- Department of Anaesthesia and Critical Care, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa.
| | - J M Dippenaar
- Department of Anaesthesiology, Steve Biko Academic Hospital, University of Pretoria, South Africa.
| | - M Gibbs
- Department of Anaesthesia and Perioperative Medicine, Faculty of Health Sciences, University of Cape Town, South Africa; Department of Anaesthesia and Perioperative Medicine, Groote Schuur Hospital, Cape Town, South Africa.
| | - M Johnson
- Department of Anaesthesia and Critical Care, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa.
| | - H Kluyts
- Department of Anaesthesiology and Critical Care, Sefako Makgatho Health Sciences University, Pretoria, South Africa.
| | - R Llewellyn
- Department of Anaesthesia and Perioperative Medicine, Faculty of Health Sciences, University of Cape Town, South Africa; Department of Anaesthesia and Perioperative Medicine, Groote Schuur Hospital, Cape Town, South Africa.
| | - M Motiang
- Department of Anaesthesiology and Critical Care, Sefako Makgatho Health Sciences University, Pretoria, South Africa.
| | - P Mogane
- Department of Anaesthesiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Anaesthesia, Chris Hani Baragwanath Hospital, Soweto, South Africa.
| | - P Motshabi
- Department of Anaesthesiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Anaesthesia, Charlotte Maxeke Hospital, Johannesburg, South Africa.
| | - B Mrara
- Department of Anaesthesia and Critical Care, Nelson Mandela Academic Hospital, Walter Sisulu University, Mthatha, South Africa.
| | - F Roodt
- Department of Anaesthesia and Perioperative Medicine, Faculty of Health Sciences, University of Cape Town, South Africa; George Provincial Hospital, George, South Africa.
| | - U Singh
- Discipline of Anaesthesiology and Critical Care, Nelson R Mandela School of Medicine, University of Kwa-Zulu Natal, Albert Luthuli Academic Hospital, Durban, South Africa.
| | - S Spijkerman
- Department of Anaesthesiology, Steve Biko Academic Hospital, University of Pretoria, South Africa.
| | - E Turton
- Department of Anaesthesia, University of the Free State, Universitas Hospital, Bloemfontein, South Africa.
| | - J Van der Westhuizen
- Department of Anaesthesia, University of the Free State, Universitas Hospital, Bloemfontein, South Africa.
| | - B Biccard
- Department of Anaesthesia and Perioperative Medicine, Faculty of Health Sciences, University of Cape Town, South Africa; Department of Anaesthesia and Perioperative Medicine, Groote Schuur Hospital, Cape Town, South Africa.
| |
Collapse
|
2
|
Haltom J, Trovao NS, Guarnieri J, Vincent P, Singh U, Tsoy S, O'Leary CA, Bram Y, Widjaja GA, Cen Z, Meller R, Baylin SB, Moss WN, Nikolau BJ, Enguita FJ, Wallace DC, Beheshti A, Schwartz R, Wurtele ES. SARS-CoV-2 Orphan Gene ORF10 Contributes to More Severe COVID-19 Disease. medRxiv 2023:2023.11.27.23298847. [PMID: 38076862 PMCID: PMC10705665 DOI: 10.1101/2023.11.27.23298847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The orphan gene of SARS-CoV-2, ORF10, is the least studied gene in the virus responsible for the COVID-19 pandemic. Recent experimentation indicated ORF10 expression moderates innate immunity in vitro. However, whether ORF10 affects COVID-19 in humans remained unknown. We determine that the ORF10 sequence is identical to the Wuhan-Hu-1 ancestral haplotype in 95% of genomes across five variants of concern (VOC). Four ORF10 variants are associated with less virulent clinical outcomes in the human host: three of these affect ORF10 protein structure, one affects ORF10 RNA structural dynamics. RNA-Seq data from 2070 samples from diverse human cells and tissues reveals ORF10 accumulation is conditionally discordant from that of other SARS-CoV-2 transcripts. Expression of ORF10 in A549 and HEK293 cells perturbs immune-related gene expression networks, alters expression of the majority of mitochondrially-encoded genes of oxidative respiration, and leads to large shifts in levels of 14 newly-identified transcripts. We conclude ORF10 contributes to more severe COVID-19 clinical outcomes in the human host.
Collapse
Affiliation(s)
- Jeffrey Haltom
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Nidia S Trovao
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Pan Vincent
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
| | - Sergey Tsoy
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Collin A O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zimu Cen
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Meller
- Morehouse School of Medicine, Atlanta, GA , 30310-1495, USA
| | - Stephen B Baylin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231
- Van Andel Research Institute, Grand Rapids, MI 49503
| | - Walter N Moss
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Basil J Nikolau
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Blue Marble Space Institute of Science, Seattle, WA, 98104 USA
| | - Robert Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| |
Collapse
|
3
|
Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Soto Albrecht Y, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Zhang S, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Bram Y, Kidane Y, Priebe W, Emmett MR, Meller R, Demharter S, Stentoft-Hansen V, Salvatore M, Galeano D, Enguita FJ, Grabham P, Trovao NS, Singh U, Haltom J, Heise MT, Moorman NJ, Baxter VK, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts. Sci Transl Med 2023; 15:eabq1533. [PMID: 37556555 DOI: 10.1126/scitranslmed.abq1533] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/20/2023] [Indexed: 08/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed mitochondrial gene expression in nasopharyngeal and autopsy tissues from patients with coronavirus disease 2019 (COVID-19). In nasopharyngeal samples with declining viral titers, the virus blocked the transcription of a subset of nuclear DNA (nDNA)-encoded mitochondrial OXPHOS genes, induced the expression of microRNA 2392, activated HIF-1α to induce glycolysis, and activated host immune defenses including the integrated stress response. In autopsy tissues from patients with COVID-19, SARS-CoV-2 was no longer present, and mitochondrial gene transcription had recovered in the lungs. However, nDNA mitochondrial gene expression remained suppressed in autopsy tissue from the heart and, to a lesser extent, kidney, and liver, whereas mitochondrial DNA transcription was induced and host-immune defense pathways were activated. During early SARS-CoV-2 infection of hamsters with peak lung viral load, mitochondrial gene expression in the lung was minimally perturbed but was down-regulated in the cerebellum and up-regulated in the striatum even though no SARS-CoV-2 was detected in the brain. During the mid-phase SARS-CoV-2 infection of mice, mitochondrial gene expression was starting to recover in mouse lungs. These data suggest that when the viral titer first peaks, there is a systemic host response followed by viral suppression of mitochondrial gene transcription and induction of glycolysis leading to the deployment of antiviral immune defenses. Even when the virus was cleared and lung mitochondrial function had recovered, mitochondrial function in the heart, kidney, liver, and lymph nodes remained impaired, potentially leading to severe COVID-19 pathology.
Collapse
Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph M Dybas
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Hossein Fazelinia
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Man S Kim
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Justin Frere
- Icahn School of Medicine at Mount Sinai, New York, NY 10023, USA
| | - Yuanchao Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Yentli Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Deborah G Murdock
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Scott L Weiss
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sonja M Best
- COVID-19 International Research Team, Medford, MA 02155, USA
- Rocky Mountain Laboratory, National Institute of Allergy and Infectious Disease, NIH, Hamilton, MT 59840, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Chicago, Chicago, IL 60615, USA
- Clever Research Lab, Springfield, IL 62704, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team, Medford, MA 02155, USA
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Yaron Bram
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Yared Kidane
- COVID-19 International Research Team, Medford, MA 02155, USA
- Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team, Medford, MA 02155, USA
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | | | | | - Diego Galeano
- COVID-19 International Research Team, Medford, MA 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Central, Paraguay
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA 02155, USA
- Faculdade de Medicina, Universidade de Lisboa, Instituto de Medicina Molecular João Lobo Antunes, 1649-028 Lisboa, Portugal
| | - Peter Grabham
- College of Physicians and Surgeons, Columbia University, New York, NY 19103, USA
| | - Nidia S Trovao
- COVID-19 International Research Team, Medford, MA 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Urminder Singh
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Jeffrey Haltom
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Mark T Heise
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Victoria K Baxter
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily A Madden
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Wes A Sanders
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Stephen B Baylin
- COVID-19 International Research Team, Medford, MA 02155, USA
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Campinas, Campinas, SP, Brazil
| | - Deanne Taylor
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
- New York Genome Center, New York, NY 10013, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Division of Human Genetics, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
4
|
Chakrabarti D, Qayoom S, Kukreja D, Goel M, Singh U, Verma M, Srivastava K, Bhatt M. PO-1359 Cancer stem cell biomarkers SOX2 and Oct4 in cervical cancer patients undergoing radiotherapy. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)03323-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
5
|
Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Albrecht YS, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Kidane YH, Priebe W, Emmett MR, Meller R, Singh U, Bram Y, tenOever BR, Heise MT, Moorman NJ, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baxter VK, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. TARGETED DOWN REGULATION OF CORE MITOCHONDRIAL GENES DURING SARS-COV-2 INFECTION. bioRxiv 2022:2022.02.19.481089. [PMID: 35233572 PMCID: PMC8887073 DOI: 10.1101/2022.02.19.481089] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.
Collapse
Affiliation(s)
- Joseph W. Guarnieri
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Joseph M. Dybas
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Hossein Fazelinia
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Man S. Kim
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | | | - Yuanchao Zhang
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Yentli Soto Albrecht
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | | | - Alessia Angelin
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Larry N. Singh
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Scott L. Weiss
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Sonja M. Best
- COVID-19 International Research Team
- Rocky Mountain Laboratories NIAID, Hamilton, MT 59840
| | - Marie T. Lott
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Viktorija Zaksas
- COVID-19 International Research Team
- University of Chicago, Chicago, IL, 60615, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | | | | | - Yared H. Kidane
- COVID-19 International Research Team
- Scottish Rite for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team
- University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark R. Emmett
- COVID-19 International Research Team
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Urminder Singh
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | | | - Mark T. Heise
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | - Emily A. Madden
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Wes A. Sanders
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Stephen B. Baylin
- COVID-19 International Research Team
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | - Deanne Taylor
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Christopher E. Mason
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
- New York Genome Center, NY, USA
| | - Jonathan C. Schisler
- COVID-19 International Research Team
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Robert E. Schwartz
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- KBR, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Douglas C. Wallace
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- University of Pennsylvania, Philadelphia, PA 19104 USA
| |
Collapse
|
6
|
Park J, Foox J, Hether T, Danko DC, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshin EE, MacKay M, Rendeiro AF, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti NP, Shapira S, Salvatore M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Rice CM, Borczuk AC, Meydan C, Schwartz RE, Mason CE. System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Rep Med 2022; 3:100522. [PMID: 35233546 PMCID: PMC8784611 DOI: 10.1016/j.xcrm.2022.100522] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/22/2021] [Accepted: 01/16/2022] [Indexed: 01/07/2023]
Abstract
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body-wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states. Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.
Collapse
Affiliation(s)
- Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan Foox
- Department of Physiology, Biophysics and Systems Biology, 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
| | | | - David C. Danko
- Department of Physiology, Biophysics and Systems Biology, 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
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | | | - Youngmi Kim
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Daniel J. Butler
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Evan E. Afshin
- Department of Physiology, Biophysics and Systems Biology, 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
| | - Matthew MacKay
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - André F. Rendeiro
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yaron Bram
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology, Biophysics and Systems Biology, 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
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Saravia-Butler
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Logyx, LLC, Mountain View, CA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA
| | - Jonathan Schisler
- McAllister Heart Institute at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, and Department of Pathology and Lab Medicine at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | | | - Steven Salvatore
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Nicholas P. Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison J. Kriegel
- Department of Physiology, Cardiovascular Center, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Olivier Elemento
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alain C. Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology, Biophysics and Systems Biology, 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
| | - Robert E. Schwartz
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E. Mason
- Department of Physiology, Biophysics and Systems Biology, 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
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
7
|
Venkataraman S, Benny R, Chanu A, Singh U, Kandasamy D, Lingaiah R. A randomized controlled trial to compare the effect of ultrasound-guided, single-dose platelet-rich plasma and corticosteroid injection in patients with carpal tunnel syndrome. J Int Soc Phys Rehabil Med 2022. [DOI: 10.4103/jisprm.jisprm-000164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
8
|
Li J, Singh U, Bhandary P, Campbell J, Arendsee Z, Seetharam AS, Wurtele ES. Foster thy young: enhanced prediction of orphan genes in assembled genomes. Nucleic Acids Res 2021; 50:e37. [PMID: 34928390 PMCID: PMC9023268 DOI: 10.1093/nar/gkab1238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Proteins encoded by newly-emerged genes ('orphan genes') share no sequence similarity with proteins in any other species. They provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Here, we systematically assess the ability of five gene prediction pipelines to accurately predict genes in genomes according to phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer gene structures by machine learning. Direct Inference is an evidence-based pipeline we developed to predict gene structures from alignments of RNA-Seq data. The BIND pipeline integrates ab initio predictions of BRAKER and Direct inference; MIND combines Direct Inference and MAKER predictions. We use highly-curated Arabidopsis and yeast annotations as gold-standard benchmarks, and cross-validate in rice. Each pipeline under-predicts orphan genes (as few as 11 percent, under one prediction scenario). Increasing RNA-Seq diversity greatly improves prediction efficacy. The combined methods (BIND and MIND) yield best predictions overall, BIND identifying 68% of annotated orphan genes, 99% of ancient genes, and give the highest sensitivity score regardless dataset in Arabidopsis. We provide a light weight, flexible, reproducible, and well-documented solution to improve gene prediction.
Collapse
Affiliation(s)
- Jing Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA
| | - Urminder Singh
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Priyanka Bhandary
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Jacqueline Campbell
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agriculture Research Service, Ames, IA 50014, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA 50014, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| |
Collapse
|
9
|
Neogy A, Garg T, Kumar A, Dwivedi AK, Singh H, Singh U, Singh Z, Prasad K, Jain M, Yadav SR. Corrigendum to: Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development. Plant Cell Physiol 2021; 62:1786. [PMID: 34893895 DOI: 10.1093/pcp/pcab100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
|
10
|
McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler JC, Mason CE, Chatterjee A, Meller R, Beheshti A. Role of miR-2392 in driving SARS-CoV-2 infection. Cell Rep 2021; 37:109839. [PMID: 34624208 PMCID: PMC8481092 DOI: 10.1016/j.celrep.2021.109839] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/13/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provide an exciting avenue toward antiviral therapeutics. From patient transcriptomic data, we determined that a circulating miRNA, miR-2392, is directly involved with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia, as well as promoting many symptoms associated with coronavirus disease 2019 (COVID-19) infection. We demonstrate that miR-2392 is present in the blood and urine of patients positive for COVID-19 but is not present in patients negative for COVID-19. These findings indicate the potential for developing a minimally invasive COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we design a miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters, and may potentially inhibit a COVID-19 disease state in humans.
Collapse
Affiliation(s)
- J Tyson McDonald
- COVID-19 International Research Team; Georgetown University School of Medicine, Washington, DC 20007, USA
| | - Francisco J Enguita
- COVID-19 International Research Team; Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Deanne Taylor
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert J Griffin
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Waldemar Priebe
- COVID-19 International Research Team; University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team; University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Anthony D Harris
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jean Clement
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joseph M Dybas
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Joseph W Guarnieri
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter Grabham
- COVID-19 International Research Team; Columbia University, New York, NY 10032, USA
| | - Stephen B Baylin
- COVID-19 International Research Team; Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Aliza Yousey
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | - Peter M Corry
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team; Logyx LLC, Mountain View, CA 94043, USA; NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Sadhana Sharma
- University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA
| | - Prashant Nagpal
- Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA; Quantum Biology Inc., Boulder, CO 80301, USA
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Bianca Cerqueira
- COVID-19 International Research Team; KBR Space & Science, San Antonio, TX 78235, USA; United States Air Force School of Aerospace Medicine, Lackland AFB, San Antonio, TX 78236, USA
| | - Viktorija Zaksas
- COVID-19 International Research Team; University of Chicago, Chicago, IL 60615, USA
| | - Urminder Singh
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | | | | | - Diego Galeano
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Alberto Paccanaro
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; University of London, Egham Hill, Egham, UK
| | - Suzanne L Meinig
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert S Hagan
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie M Bowman
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Selin Altinok
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | | | - Douglas C Wallace
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher E Mason
- COVID-19 International Research Team; Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY, USA
| | - Anushree Chatterjee
- COVID-19 International Research Team; University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA
| | - Robert Meller
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Afshin Beheshti
- COVID-19 International Research Team; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.
| |
Collapse
|
11
|
McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler J, Mason CE, Chatterjee A, Meller R, Beheshti A. The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection. bioRxiv 2021. [PMID: 33948587 DOI: 10.1101/2021.04.23.441024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we have discovered a circulating miRNA, miR-2392, that is directly involved with SARS-CoV-2 machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia as well as promoting many symptoms associated with COVID-19 infection. We demonstrate miR-2392 is present in the blood and urine of COVID-19 positive patients, but not detected in COVID-19 negative patients. These findings indicate the potential for developing a novel, minimally invasive, COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we have developed a novel miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters and may potentially inhibit a COVID-19 disease state in humans.
Collapse
|
12
|
Li J, Singh U, Arendsee Z, Wurtele ES. Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data. Front Genet 2021; 12:722981. [PMID: 34484307 PMCID: PMC8415361 DOI: 10.3389/fgene.2021.722981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
The "dark transcriptome" can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression of 6,692 annotated genes and 29,354 unannotated open reading frames (ORFs) in the Saccharomyces cerevisiae genome across diverse environmental, genetic and developmental conditions (3,457 RNA-Seq samples). Over 30% of the highly transcribed ORFs have translation evidence. Phylostratigraphic analysis infers most of these transcribed ORFs would encode species-specific proteins ("orphan-ORFs"); hundreds have mean expression comparable to annotated genes. These data reveal unannotated ORFs most likely to be protein-coding genes. We partitioned a co-expression matrix by Markov Chain Clustering; the resultant clusters contain 2,468 orphan-ORFs. We provide the aggregated RNA-Seq yeast data with extensive metadata as a project in MetaOmGraph (MOG), a tool designed for interactive analysis and visualization. This approach enables reuse of public RNA-Seq data for exploratory discovery, providing a rich context for experimentalists to make novel, experimentally testable hypotheses about candidate genes.
Collapse
Affiliation(s)
- Jing Li
- Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Urminder Singh
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
| | - Zebulun Arendsee
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
| | - Eve Syrkin Wurtele
- Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
| |
Collapse
|
13
|
Singh U, Li J, Seetharam A, Wurtele ES. pyrpipe: a Python package for RNA-Seq workflows. NAR Genom Bioinform 2021; 3:lqab049. [PMID: 34085037 PMCID: PMC8168212 DOI: 10.1093/nargab/lqab049] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/06/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023] Open
Abstract
The availability of terabytes of RNA-Seq data and continuous emergence of new analysis tools, enable unprecedented biological insight. There is a pressing requirement for a framework that allows for fast, efficient, manageable, and reproducible RNA-Seq analysis. We have developed a Python package, (pyrpipe), that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in Python, in an object-oriented manner. pyrpipe provides access to popular RNA-Seq tools, within Python, via high-level APIs. Pipelines can be customized by integrating new Python code, third-party programs, or Python libraries. Users can create checkpoints in the pipeline or integrate pyrpipe into a workflow management system, thus allowing execution on multiple computing environments, and enabling efficient resource management. pyrpipe produces detailed analysis, and benchmark reports which can be shared or included in publications. pyrpipe is implemented in Python and is compatible with Python versions 3.6 and higher. To illustrate the rich functionality of pyrpipe, we provide case studies using RNA-Seq data from GTEx, SARS-CoV-2-infected human cells, and Zea mays. All source code is freely available at https://github.com/urmi-21/pyrpipe; the package can be installed from the source, from PyPI (https://pypi.org/project/pyrpipe), or from bioconda (https://anaconda.org/bioconda/pyrpipe). Documentation is available at (http://pyrpipe.rtfd.io).
Collapse
Affiliation(s)
- Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50014, USA
| | - Jing Li
- Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50014, USA
| | - Arun Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA 50014, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50014, USA
| |
Collapse
|
14
|
Alyethodi RR, Singh U, Kumar S, Alex R, Sengar GS, Raja TV, Deb R, Prakash B. Designing, optimization, and validation of whole blood direct T-ARMS PCR for precise and rapid genotyping of complex vertebral malformation in cattle. BMC Biotechnol 2021; 21:36. [PMID: 34022869 PMCID: PMC8141239 DOI: 10.1186/s12896-021-00696-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/11/2021] [Indexed: 12/04/2022] Open
Abstract
Background DNA testing in the cattle industry undergoes multiple hurdles. Successful genotyping involves the transportation of samples from the field to the laboratory in a chilled environment followed by DNA extraction, and finally, a specific genotyping protocol is followed. Various researches are focused on overcoming these issues. Microcards offer blood transportation at ambient temperature. Direct PCR methods can save the time of DNA extraction but available only for simplex PCR. Tetra Primer-Amplification Refractory Mutation System based Polymerase Chain Reaction (T-ARMS PCR) can make DNA testing faster in a low-cost setting. The present study was aimed to design, optimize, and validate a T-ARMS PCR for faster DNA testing of SNP responsible for Complex Vertebral Malformation (CVM)-an important genetic disease of the cattle industry. Further, a direct T-ARMS PCR from whole blood was developed to avoid the DNA extraction steps. Lastly, using the optimized protocol, genotyping of blood spotted on Microcard eliminates the need for cold chain maintenance in the transportation of samples. Results The present study demonstrated a novel T-ARMS PCR-based genotyping of the SNP rs438228855, which is responsible for CVM. Here, wild genotypes were recognized by 389 bp and 199 bp bands in agarose gel, while the carrier genotype showed an additional 241 bp band. The developed protocol was validated using PCR-Primer Introduced Restriction Analysis (PCR-PIRA) and sequencing. The present study further established a direct T-ARMS PCR for this SNP from whole blood. Different conditions such as heparin and EDTA treated blood, the need for pre-treatment, and two different DNA Polymerases for the direct PCR were optimized. Finally, our optimized protocol successfully genotyped the whole blood samples dried on Insta™DNA cards. Conclusions The present study reported the usefulness of primer modified T-ARMS PCR for detecting CVM for the first time. To the best of our knowledge, direct PCR in T-ARMS PCR has never been reported. Lastly, the use of microcards in the developed protocol can make the assay useful in the DNA testing of field samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00696-5.
Collapse
Affiliation(s)
- R R Alyethodi
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Garacharma, Andaman and Nicobar Islands, 744101, India.
| | - U Singh
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - S Kumar
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - R Alex
- Animal genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - G S Sengar
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - T V Raja
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - R Deb
- ICAR-National Research centre on Pig, Guwahati, Assam, India
| | - B Prakash
- Animal genetics & Breeding Division, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| |
Collapse
|
15
|
Singh U, Castle J, Greenhalgh S, Hussain U, Descamps T, Nash S, Wilson M, Hunt R, Kirwan CC. O44: WOUND HEALING INFLAMMATORY MARKERS PREDICT PROGNOSIS AND SURVIVAL IN EARLY BREAST CANCER. Br J Surg 2021. [DOI: 10.1093/bjs/znab117.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Introduction
Cancer is likened to a non-healing wound. There is limited evidence on the expression of wound healing tissue inflammatory markers, CD68(pan-macrophage marker), HO-1(tumour cell marker) and FAP(cancer-associated fibroblast marker) in human breast cancer.
Method
In 201 invasive breast cancer and 58 DCIS patients, CD68+TAM expression, tumour HO-1 and fibroblast FAP expression, quantified by immunohistochemistry(dichotomised: high/present vs low/absent), was correlated with tumour factors (grade, proliferation(Ki67), ER, HER2); demographic factors, behavioural factors (smoking, alcohol) and survival status(DFS, OS)
Result
High CD68+macrophage expression was increased in invasive breast cancer, compared to DCIS, and normal tissue distant from the tumour(59%,41%and 6% respectively; p<0.001).In invasive cancer,CD68+TAM expression increased with increasing tumour grade(Grade 1:42%, Grade 2:58%, Grade 3:72%; p=0.006), high Ki67(71%vs.47%; p=0.004), ER negativity(79.4%vs.55.4%; p=0.01) and HER2(HER2 positive 81.8% vs. HER2 negative 56.3%; p=0.03). CD68+TAM expression was higher in high compared to low/intermediate grade DCIS(44% % vs. 31% p=0.52). CD68+TAM expression was increased in patients who self-reported alcohol intake(non-drinker 43% vs. drinker 62%; p=0.01). HO-1 was associated with shorter DFS(HR:3.22,p=0.027) and OS(HR:2.86,p=0.029).FAP fibroblast expression correlated with longer DFS (HR:0.296,p=0.029) and OS (HR:0.271,p=0.008).
Conclusion
Tumour inflammation as assessed by CD68+TAM expression shows utility in identifying aggressive breast cancer sub-types. The association reported between CD68+TAM density and alcohol intake suggests a possible mechanism for alcohol as a risk factor for breast cancer. The prognostic value of HO-1 and FAP expression demonstrated here suggests a functional role of these wound healing markers in breast cancer. HO-1:Heme-oxygenase-1; FAP:Fibroblast activation protein; TAM:Tumour associated macrophage; DCIS: Ductal carcinoma in situ
Take-home message
Wound healing pathways of inflammation may be implicated in early breast cancer development
Collapse
Affiliation(s)
- U Singh
- Division of Cancer Sciences, The University of Manchester
| | - J Castle
- Division of Cancer Sciences, The University of Manchester
| | | | - U Hussain
- Manchester University NHS Foundation Trust
| | | | - S Nash
- Manchester University NHS Foundation Trust
| | - M Wilson
- Manchester University NHS Foundation Trust
| | - R Hunt
- Manchester University NHS Foundation Trust
| | - CC Kirwan
- Division of Cancer Sciences, The University of Manchester
- Manchester University NHS Foundation Trust
| |
Collapse
|
16
|
Singh U, Castle J, Shaker H, Greenhalgh S, Hussain U, Descamps T, Nash S, Wilson M, Hunt R, Kirwan C. PO-75 The relationship between the coagulation and inflammatory phases of wound healing in early breast cancer. Thromb Res 2021. [DOI: 10.1016/s0049-3848(21)00248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
17
|
Park J, Foox J, Hether T, Danko D, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti N, Shapira S, Salvatore M, Loda M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Borczuk AC, Meydan C, Schwartz RE, Mason CE. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps. bioRxiv 2021. [PMID: 33758858 DOI: 10.1101/2021.03.08.434433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.
Collapse
|
18
|
Abstract
SUMMARY Searching for open reading frames is a routine task and a critical step prior to annotating protein coding regions in newly sequenced genomes or de novo transcriptome assemblies. With the tremendous increase in genomic and transcriptomic data, faster tools are needed to handle large input datasets. These tools should be versatile enough to fine-tune search criteria and allow efficient downstream analysis. Here we present a new python based tool, orfipy, which allows the user to flexibly search for open reading frames in genomic and transcriptomic sequences. The search is rapid and is fully customizable, with a choice of FASTA and BED output formats. AVAILABILITY AND IMPLEMENTATION orfipy is implemented in python and is compatible with python v3.6 and higher. Source code: https://github.com/urmi-21/orfipy. Installation: from the source, or via PyPi (https://pypi.org/project/orfipy) or bioconda (https://anaconda.org/bioconda/orfipy). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA,Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA,Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA,To whom correspondence should be addressed. or
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA,Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA,Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA,To whom correspondence should be addressed. or
| |
Collapse
|
19
|
Jaiswal A, Goswami K, Haldar P, Salve HR, Singh U. Prevalence of knee osteoarthritis, its determinants, and impact on the quality of life in elderly persons in rural Ballabgarh, Haryana. J Family Med Prim Care 2021; 10:354-360. [PMID: 34017753 PMCID: PMC8132764 DOI: 10.4103/jfmpc.jfmpc_1477_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/17/2020] [Accepted: 10/20/2020] [Indexed: 11/25/2022] Open
Abstract
Background: Osteoarthritis (OA) is the most common type of arthritis and a very common disease of elderly. It is one of the leading causes of disability. The present study was conducted to estimate the burden of the knee OA among rural elderly. Methods: A community-based cross-sectional study was conducted among 500 randomly selected elderly resident of rural Ballabgarh, Haryana. A semi-structured interview schedule was used by a trained investigator for face-to-face interview, clinical examination of knee using American College of Rheumatology criteria, and quality of life assessment using WHOQOL-BREF. Results: Almost two-third of the participants among 454 elderly recruited, suffered from knee OA (292, 64.3%) had knee OA. History of a knee injury, a family history of knee pain, current physical activity and smoking status were found to be significantly associated with knee OA, in multivariate logistic regression model. Elderly suffering from knee OA had significantly lower quality-of-life scores contrasted to those not (p-value < 0.001). The scores were significantly lower for all the domains (P-value <0.001) among elderly suffering with the knee OA, with the maximum effect seen in psychological, and physical domain. Conclusion: Rural elderly of Ballabgarh, Haryana, had a high burden of knee OA. Elderly suffering from knee OA had significantly lower perception of their quality of life most affected is the psychological and physical domains of quality of life.
Collapse
Affiliation(s)
- Abhishek Jaiswal
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Kiran Goswami
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Partha Haldar
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Harshal Ramesh Salve
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - U Singh
- Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
20
|
Khemka NK, Singh U, Dwivedi AK, Jain M. Machine Learning-Based Annotation of Long Noncoding RNAs Using PLncPRO. Methods Mol Biol 2021; 2107:253-260. [PMID: 31893451 DOI: 10.1007/978-1-0716-0235-5_12] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) are noncoding RNAs with transcript length more than 200 nucleotides. Although poorly conserved, lncRNAs are expressed across diverse species, including plants and animals, and are known to be involved in regulation of various biological processes. To understand their biological significance, we first need to identify the lncRNAs accurately. However, distinguishing lncRNAs from coding transcripts is still a challenging task. Here, we describe a machine learning-based approach to accurately identify the plant lncRNAs. We describe the usage of plant long noncoding RNA prediction by random forests (PLncPRO), which employs machine learning-based random forest algorithm to recognize the lncRNAs from the set of given transcript sequences. Stepwise instructions have been provided to use PLncPRO to annotate the lncRNA sequences.
Collapse
Affiliation(s)
- Niraj K Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Urminder Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Anuj K Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
21
|
Adamczewski-Musch J, Arnold O, Behnke C, Belounnas A, Belyaev A, Berger-Chen JC, Blanco A, Blume C, Böhmer M, Bordalo P, Chernenko S, Chlad L, Ciepal I, Deveaux C, Dreyer J, Epple E, Fabbietti L, Fateev O, Filip P, Fonte P, Franco C, Friese J, Fröhlich I, Galatyuk T, Garzón JA, Gernhäuser R, Golosov O, Golubeva M, Greifenhagen R, Guber F, Gumberidze M, Harabasz S, Heinz T, Hennino T, Hlavac S, Höhne C, Holzmann R, Ierusalimov A, Ivashkin A, Kämpfer B, Karavicheva T, Kardan B, Koenig I, Koenig W, Kohls M, Kolb BW, Korcyl G, Kornakov G, Kornas F, Kotte R, Kugler A, Kunz T, Kurepin A, Kurilkin A, Kurilkin P, Ladygin V, Lalik R, Lapidus K, Lebedev A, Lopes L, Lorenz M, Mahmoud T, Maier L, Malige A, Mamaev M, Mangiarotti A, Markert J, Matulewicz T, Maurus S, Metag V, Michel J, Mihaylov DM, Morozov S, Müntz C, Münzer R, Naumann L, Nowakowski K, Parpottas Y, Pechenov V, Pechenova O, Petukhov O, Piasecki K, Pietraszko J, Przygoda W, Pysz K, Ramos S, Ramstein B, Rathod N, Reshetin A, Rodriguez-Ramos P, Rosier P, Rost A, Rustamov A, Sadovsky A, Salabura P, Scheib T, Schuldes H, Schwab E, Scozzi F, Seck F, Sellheim P, Selyuzhenkov I, Siebenson J, Silva L, Singh U, Smyrski J, Sobolev YG, Spataro S, Spies S, Ströbele H, Stroth J, Sturm C, Svoboda O, Szala M, Tlusty P, Traxler M, Tsertos H, Usenko E, Wagner V, Wendisch C, Wiebusch MG, Wirth J, Wójcik D, Zanevsky Y, Zumbruch P. Directed, Elliptic, and Higher Order Flow Harmonics of Protons, Deuterons, and Tritons in Au+Au Collisions at sqrt[s_{NN}]=2.4 GeV. Phys Rev Lett 2020; 125:262301. [PMID: 33449792 DOI: 10.1103/physrevlett.125.262301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/07/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Flow coefficients v_{n} of the orders n=1-6 are measured with the High-Acceptance DiElectron Spectrometer (HADES) at GSI for protons, deuterons, and tritons as a function of centrality, transverse momentum, and rapidity in Au+Au collisions at sqrt[s_{NN}]=2.4 GeV. Combining the information from the flow coefficients of all orders allows us to construct for the first time, at collision energies of a few GeV, a multidifferential picture of the angular emission pattern of these particles. It reflects the complicated interplay between the effect of the central fireball pressure on the emission of particles and their subsequent interaction with spectator matter. The high precision information on higher order flow coefficients is a major step forward in constraining the equation of state of dense baryonic matter.
Collapse
Affiliation(s)
- J Adamczewski-Musch
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - O Arnold
- Excellence Cluster "Origin and Structure of the Universe," 85748 Garching, Germany
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - C Behnke
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - A Belounnas
- Laboratoire de Physique des 2 infinis Irène Joliot-Curie, Université Paris-Saclay, CNRS-IN2P3, F-91405 Orsay, France
| | - A Belyaev
- Joint Institute of Nuclear Research, 141980 Dubna, Russia
| | - J C Berger-Chen
- Excellence Cluster "Origin and Structure of the Universe," 85748 Garching, Germany
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - A Blanco
- LIP-Laboratório de Instrumentação e Física Experimental de Partículas, 3004-516 Coimbra, Portugal
| | - C Blume
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - M Böhmer
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - P Bordalo
- LIP-Laboratório de Instrumentação e Física Experimental de Partículas, 3004-516 Coimbra, Portugal
| | - S Chernenko
- Joint Institute of Nuclear Research, 141980 Dubna, Russia
| | - L Chlad
- Nuclear Physics Institute, The Czech Academy of Sciences, 25068 Rez, Czech Republic
| | - I Ciepal
- Institute of Nuclear Physics, Polish Academy of Sciences, 31342 Kraków, Poland
| | - C Deveaux
- II.Physikalisches Institut, Justus Liebig Universität Giessen, 35392 Giessen, Germany
| | - J Dreyer
- Institut für Strahlenphysik, Helmholtz-Zentrum Dresden-Rossendorf, 01314 Dresden, Germany
| | - E Epple
- Excellence Cluster "Origin and Structure of the Universe," 85748 Garching, Germany
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - L Fabbietti
- Excellence Cluster "Origin and Structure of the Universe," 85748 Garching, Germany
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - O Fateev
- Joint Institute of Nuclear Research, 141980 Dubna, Russia
| | - P Filip
- Institute of Physics, Slovak Academy of Sciences, 84228 Bratislava, Slovakia
| | - P Fonte
- LIP-Laboratório de Instrumentação e Física Experimental de Partículas, 3004-516 Coimbra, Portugal
| | - C Franco
- LIP-Laboratório de Instrumentação e Física Experimental de Partículas, 3004-516 Coimbra, Portugal
| | - J Friese
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - I Fröhlich
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - T Galatyuk
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - J A Garzón
- LabCAF. F. Física, Universidad de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - R Gernhäuser
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - O Golosov
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia
| | - M Golubeva
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - R Greifenhagen
- Institut für Strahlenphysik, Helmholtz-Zentrum Dresden-Rossendorf, 01314 Dresden, Germany
| | - F Guber
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - M Gumberidze
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - S Harabasz
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - T Heinz
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - T Hennino
- Laboratoire de Physique des 2 infinis Irène Joliot-Curie, Université Paris-Saclay, CNRS-IN2P3, F-91405 Orsay, France
| | - S Hlavac
- Institute of Physics, Slovak Academy of Sciences, 84228 Bratislava, Slovakia
| | - C Höhne
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
- II.Physikalisches Institut, Justus Liebig Universität Giessen, 35392 Giessen, Germany
| | - R Holzmann
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - A Ierusalimov
- Joint Institute of Nuclear Research, 141980 Dubna, Russia
| | - A Ivashkin
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - B Kämpfer
- Institut für Strahlenphysik, Helmholtz-Zentrum Dresden-Rossendorf, 01314 Dresden, Germany
| | - T Karavicheva
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - B Kardan
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - I Koenig
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - W Koenig
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - M Kohls
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - B W Kolb
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - G Korcyl
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - G Kornakov
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - F Kornas
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - R Kotte
- Institut für Strahlenphysik, Helmholtz-Zentrum Dresden-Rossendorf, 01314 Dresden, Germany
| | - A Kugler
- Nuclear Physics Institute, The Czech Academy of Sciences, 25068 Rez, Czech Republic
| | - T Kunz
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - A Kurepin
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - A Kurilkin
- Joint Institute of Nuclear Research, 141980 Dubna, Russia
| | - P Kurilkin
- Joint Institute of Nuclear Research, 141980 Dubna, Russia
| | - V Ladygin
- Joint Institute of Nuclear Research, 141980 Dubna, Russia
| | - R Lalik
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - K Lapidus
- Excellence Cluster "Origin and Structure of the Universe," 85748 Garching, Germany
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - A Lebedev
- Institute of Theoretical and Experimental Physics, 117218 Moscow, Russia
| | - L Lopes
- LIP-Laboratório de Instrumentação e Física Experimental de Partículas, 3004-516 Coimbra, Portugal
| | - M Lorenz
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - T Mahmoud
- II.Physikalisches Institut, Justus Liebig Universität Giessen, 35392 Giessen, Germany
| | - L Maier
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - A Malige
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - M Mamaev
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia
| | - A Mangiarotti
- LIP-Laboratório de Instrumentação e Física Experimental de Partículas, 3004-516 Coimbra, Portugal
| | - J Markert
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - T Matulewicz
- Uniwersytet Warszawski, Wydział Fizyki, Instytut Fizyki Doświadczalnej, 02-093 Warszawa, Poland
| | - S Maurus
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - V Metag
- II.Physikalisches Institut, Justus Liebig Universität Giessen, 35392 Giessen, Germany
| | - J Michel
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - D M Mihaylov
- Excellence Cluster "Origin and Structure of the Universe," 85748 Garching, Germany
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - S Morozov
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia
| | - C Müntz
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - R Münzer
- Excellence Cluster "Origin and Structure of the Universe," 85748 Garching, Germany
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - L Naumann
- Institut für Strahlenphysik, Helmholtz-Zentrum Dresden-Rossendorf, 01314 Dresden, Germany
| | - K Nowakowski
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - Y Parpottas
- Department of Physics, University of Cyprus, 1678 Nicosia, Cyprus
| | - V Pechenov
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - O Pechenova
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - O Petukhov
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - K Piasecki
- Uniwersytet Warszawski, Wydział Fizyki, Instytut Fizyki Doświadczalnej, 02-093 Warszawa, Poland
| | - J Pietraszko
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - W Przygoda
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - K Pysz
- Institute of Nuclear Physics, Polish Academy of Sciences, 31342 Kraków, Poland
| | - S Ramos
- LIP-Laboratório de Instrumentação e Física Experimental de Partículas, 3004-516 Coimbra, Portugal
| | - B Ramstein
- Laboratoire de Physique des 2 infinis Irène Joliot-Curie, Université Paris-Saclay, CNRS-IN2P3, F-91405 Orsay, France
| | - N Rathod
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - A Reshetin
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - P Rodriguez-Ramos
- Nuclear Physics Institute, The Czech Academy of Sciences, 25068 Rez, Czech Republic
| | - P Rosier
- Laboratoire de Physique des 2 infinis Irène Joliot-Curie, Université Paris-Saclay, CNRS-IN2P3, F-91405 Orsay, France
| | - A Rost
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - A Rustamov
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - A Sadovsky
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - P Salabura
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - T Scheib
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - H Schuldes
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - E Schwab
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - F Scozzi
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Laboratoire de Physique des 2 infinis Irène Joliot-Curie, Université Paris-Saclay, CNRS-IN2P3, F-91405 Orsay, France
| | - F Seck
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - P Sellheim
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - I Selyuzhenkov
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia
| | - J Siebenson
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - L Silva
- LIP-Laboratório de Instrumentação e Física Experimental de Partículas, 3004-516 Coimbra, Portugal
| | - U Singh
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - J Smyrski
- Smoluchowski Institute of Physics, Jagiellonian University of Cracow, 30-059 Kraków, Poland
| | - Yu G Sobolev
- Nuclear Physics Institute, The Czech Academy of Sciences, 25068 Rez, Czech Republic
| | - S Spataro
- Dipartimento di Fisica and INFN, Università di Torino, 10125 Torino, Italy
| | - S Spies
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - H Ströbele
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - J Stroth
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - C Sturm
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - O Svoboda
- Nuclear Physics Institute, The Czech Academy of Sciences, 25068 Rez, Czech Republic
| | - M Szala
- Institut für Kernphysik, Goethe-Universität, 60438 Frankfurt, Germany
| | - P Tlusty
- Nuclear Physics Institute, The Czech Academy of Sciences, 25068 Rez, Czech Republic
| | - M Traxler
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - H Tsertos
- Department of Physics, University of Cyprus, 1678 Nicosia, Cyprus
| | - E Usenko
- Institute for Nuclear Research, Russian Academy of Science, 117312 Moscow, Russia
| | - V Wagner
- Nuclear Physics Institute, The Czech Academy of Sciences, 25068 Rez, Czech Republic
| | - C Wendisch
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - M G Wiebusch
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| | - J Wirth
- Excellence Cluster "Origin and Structure of the Universe," 85748 Garching, Germany
- Physik Department E62, Technische Universität München, 85748 Garching, Germany
| | - D Wójcik
- Uniwersytet Warszawski, Wydział Fizyki, Instytut Fizyki Doświadczalnej, 02-093 Warszawa, Poland
| | - Y Zanevsky
- Joint Institute of Nuclear Research, 141980 Dubna, Russia
| | - P Zumbruch
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
| |
Collapse
|
22
|
Hazra S, Venkataraman S, Handa G, Yadav SL, Wadhwa S, Singh U, Kochhar KP, Deepak KK, Sarkar K. A Cross-Sectional Study on Central Sensitization and Autonomic Changes in Fibromyalgia. Front Neurosci 2020; 14:788. [PMID: 32848561 PMCID: PMC7417433 DOI: 10.3389/fnins.2020.00788] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
Fibromyalgia is a multi-symptomatic disorder characterized by generalized pain. The pathophysiology of fibromyalgia is supposedly an interplay between central nervous system hyper-responsiveness, autonomic dysfunction, and peripheral pain. In this cross-sectional study, the objective was to assess central sensitization and autonomic activity in patients with fibromyalgia compared with control. Fifty adults diagnosed with fibromyalgia by the modified American College of Rheumatology 2010 criteria and an equal number of age- and sex-matched controls participated in the study in an urban tertiary care hospital. Central sensitization was assessed by history and by evidence of increased prefrontal cortical activity as measured by cortical oxygenation using functional near-infrared spectroscopy. Autonomic activity was assessed by heart rate variability, electrodermal activity, and deep breathing test in three physiological states: rest, sympathetic stress (cold pressor test), and deep breathing. Mann–Whitney U-test, paired t-test, Wilcoxon test, and Friedman test with Bonferroni a priori were used to analyze the data. Cortical activity was significantly higher in the fibromyalgia group than control. There was no significant difference in autonomic activity between the fibromyalgia and control groups. In the fibromyalgia group, variable degrees of sympathetic hyperactivity and normal parasympathetic activity were observed. Central sensitization may be playing a primary role in the pathophysiology of generalized pain in fibromyalgia.
Collapse
Affiliation(s)
- Sandipan Hazra
- Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences, Jodhpur, India
| | - Srikumar Venkataraman
- Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences, New Delhi, India
| | - Gita Handa
- Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences, New Delhi, India
| | - S L Yadav
- Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Wadhwa
- Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences, New Delhi, India
| | - U Singh
- Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences, New Delhi, India
| | - K P Kochhar
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - K K Deepak
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Kaushik Sarkar
- Department of Electronics and Communication Engineering, Narula Institute of Technology, Kolkata, India
| |
Collapse
|
23
|
Arendsee Z, Li J, Singh U, Seetharam A, Dorman K, Wurtele ES. phylostratr: a framework for phylostratigraphy. Bioinformatics 2020; 35:3617-3627. [PMID: 30873536 DOI: 10.1093/bioinformatics/btz171] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION The goal of phylostratigraphy is to infer the evolutionary origin of each gene in an organism. This is done by searching for homologs within increasingly broad clades. The deepest clade that contains a homolog of the protein(s) encoded by a gene is that gene's phylostratum. RESULTS We have created a general R-based framework, phylostratr, to estimate the phylostratum of every gene in a species. The program fully automates analysis: selecting species for balanced representation, retrieving sequences, building databases, inferring phylostrata and returning diagnostics. Key diagnostics include: detection of genes with inferred homologs in old clades, but not intermediate ones; proteome quality assessments; false-positive diagnostics, and checks for missing organellar genomes. phylostratr allows extensive customization and systematic comparisons of the influence of analysis parameters or genomes on phylostrata inference. A user may: modify the automatically generated clade tree or use their own tree; provide custom sequences in place of those automatically retrieved from UniProt; replace BLAST with an alternative algorithm; or tailor the method and sensitivity of the homology inference classifier. We show the utility of phylostratr through case studies in Arabidopsis thaliana and Saccharomyces cerevisiae. AVAILABILITY AND IMPLEMENTATION Source code available at https://github.com/arendsee/phylostratr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Zebulun Arendsee
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
| | - Jing Li
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Arun Seetharam
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Department of Statistics, Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
| |
Collapse
|
24
|
Singh U, Hur M, Dorman K, Wurtele ES. MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. Nucleic Acids Res 2020; 48:e23. [PMID: 31956905 PMCID: PMC7039010 DOI: 10.1093/nar/gkz1209] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
The diverse and growing omics data in public domains provide researchers with tremendous opportunity to extract hidden, yet undiscovered, knowledge. However, the vast majority of archived data remain unused. Here, we present MetaOmGraph (MOG), a free, open-source, standalone software for exploratory analysis of massive datasets. Researchers, without coding, can interactively visualize and evaluate data in the context of its metadata, honing-in on groups of samples or genes based on attributes such as expression values, statistical associations, metadata terms and ontology annotations. Interaction with data is easy via interactive visualizations such as line charts, box plots, scatter plots, histograms and volcano plots. Statistical analyses include co-expression analysis, differential expression analysis and differential correlation analysis, with significance tests. Researchers can send data subsets to R for additional analyses. Multithreading and indexing enable efficient big data analysis. A researcher can create new MOG projects from any numerical data; or explore an existing MOG project. MOG projects, with history of explorations, can be saved and shared. We illustrate MOG by case studies of large curated datasets from human cancer RNA-Seq, where we identify novel putative biomarker genes in different tumors, and microarray and metabolomics data from Arabidopsis thaliana. MOG executable and code: http://metnetweb.gdcb.iastate.edu/ and https://github.com/urmi-21/MetaOmGraph/.
Collapse
Affiliation(s)
- Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
25
|
Abstract
Analysis of yeast, fly and human genomes suggests that sequence divergence is not the main source of orphan genes.
Collapse
Affiliation(s)
- Urminder Singh
- Department of Genetics, Developmental and Cell Biology, Iowa State UniversityAmesUnited States
| | - Eve Syrkin Wurtele
- Department of Genetics, Developmental and Cell Biology, Iowa State UniversityAmesUnited States
| |
Collapse
|
26
|
Singh U, Mani A, James K, Rao MB, Bhattacharya A. Effects of Heat Exposure from Live-Burn Fire Training on Postural Stability of Firefighters. Ergon Int J 2019; 3. [PMID: 31815252 DOI: 10.23880/eoji-16000213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Firefighters perform physically intensive jobs in suboptimal environments, making it even more important for them to maintain good functional postural balance or stability. As part of their training, firefighters are required to perform physically demanding tasks under high stress and high heat environments. These demanding tasks lead to increased physical fatigue which can then result in poor performance and/or postural instability. The objectives of this study were to 1) investigate the effect of live-firefighting training-induced heat stress on static postural balance, and 2) investigate the association between commonly monitored physiological responses (core body temperature, heart rate, oxygen saturation and blood pressure) and measures of static postural balance. Twenty-six firefighters (mean ± SD: age 36.0 years ±5.2, weight 216 lbs. ± 34, BMI 29.7 ± 4.2) participated in live firefighting training while performing following tasks: search and rescue, hose advancement, and backup. Prior to heat exposure (PRE) and following each scenario (POST1, POST2, POST3), firefighters' postural balance was assessed with a wearable 3-D inertial sensor system quantifying time dependent changes in linear acceleration (LIN ACC) and angular velocity (AV) about three orthogonal axes [Anterior-Posterior (AP), Medial-Lateral (ML), and vertical (V)] during one foot balance tests for 30 seconds under eyes open and eyes closed conditions. The outcome variables from 3-D wearable sensors were used to create 3-D Phase-Plane based postural stability metrics. Physiological measurement of core body temperature (CBT) (measured with a radio pill) as well as perception of heat increased significantly during the live fire-training exercise. In addition, firefighters also perceived an increase in physical fatigue and respiratory distress. Angular combined stability parameters (ACSP), RMS angular velocity around ML axis were significantly correlated with CBT. In the multivariate analysis adjusted for the scenarios, height and weight of the firefighters, these measures of static postural balance were significantly associated with CBT. As per the model results, static postural balance, as indicated by ACSP, worsened with an increase in CBT. Future studies should place sensors at body extremities along with close to center of mass to capture the kinematic movements more comprehensively influencing postural balance.
Collapse
Affiliation(s)
- U Singh
- Dept of Internal Medicine, University of Cincinnati College of Medicine, USA
| | - A Mani
- Dept of Environmental Health, University of Cincinnati College of Medicine, USA
| | - K James
- Dept of Environmental Health, University of Cincinnati College of Medicine, USA
| | - M B Rao
- Dept of Environmental Health, University of Cincinnati College of Medicine, USA
| | - A Bhattacharya
- Dept of Environmental Health, University of Cincinnati College of Medicine, USA
| |
Collapse
|
27
|
Arnold C, Kadaria D, Iyer P, Jackson C, Khan A, McDonald A, Pattanaik D, Shrestha R, Singh U, VanValkinburgh D, Sodhi A. 76 Airway Complications in Angioedema. Ann Emerg Med 2019. [DOI: 10.1016/j.annemergmed.2019.08.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
28
|
Neogy A, Garg T, Kumar A, Dwivedi AK, Singh H, Singh U, Singh Z, Prasad K, Jain M, Yadav SR. Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development. Plant Cell Physiol 2019; 60:2343-2355. [PMID: 31318417 DOI: 10.1093/pcp/pcz132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/01/2019] [Indexed: 05/09/2023]
Abstract
Unlike dicots, the robust root system in grass species largely originates from stem base during postembryonic development. The mechanisms by which plant hormone signaling pathways control the architecture of adventitious root remain largely unknown. Here, we studied the modulations in global genes activity in developing rice adventitious root by genome-wide RNA sequencing in response to external auxin and cytokinin signaling cues. We further analyzed spatiotemporal regulations of key developmental regulators emerged from our global transcriptome analysis. Interestingly, some of the key cell fate determinants such as homeodomain transcription factor (TF), OsHOX12, no apical meristem protein, OsNAC39, APETALA2/ethylene response factor, OsAP2/ERF-40 and WUSCHEL-related homeobox, OsWOX6.1 and OsWOX6.2, specifically expressed in adventitious root primordia. Functional analysis of one of these regulators, an auxin-induced TF containing AP2/ERF domain, OsAP2/ERF-40, demonstrates its sufficiency to confer the adventitious root fate. The ability to trigger the root developmental program is largely attributed to OsAP2/ERF-40-mediated dose-dependent transcriptional activation of genes that can facilitate generating effective auxin response, and OsERF3-OsWOX11-OsRR2 pathway. Our studies reveal gene regulatory network operating in response to hormone signaling pathways and identify a novel TF regulating adventitious root developmental program, a key agronomically important quantitative trait, upstream of OsERF3-OsWOX11-OsRR2 pathway.
Collapse
Affiliation(s)
- Ananya Neogy
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Tushar Garg
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Anil Kumar
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Anuj K Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Harshita Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Urminder Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Zeenu Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shri Ram Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| |
Collapse
|
29
|
Arendsee Z, Li J, Singh U, Bhandary P, Seetharam A, Wurtele ES. fagin: synteny-based phylostratigraphy and finer classification of young genes. BMC Bioinformatics 2019; 20:440. [PMID: 31455236 PMCID: PMC6712868 DOI: 10.1186/s12859-019-3023-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022] Open
Abstract
Background With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic regions of the genome. If some of these genes survive across speciations, then extant organisms will contain a patchwork of genes whose ancestors first appeared at different times. Standard phylostratigraphy, the technique of partitioning genes by their age, is based solely on protein similarity algorithms. However, this approach relies on negative evidence ─ a failure to detect a homolog of a query gene. An alternative approach is to limit the search for homologs to syntenic regions. Then, genes can be positively identified as de novo orphans by tracing them to non-coding sequences in related species. Results We have developed a synteny-based pipeline in the R framework. Fagin determines the genomic context of each query gene in a focal species compared to homologous sequence in target species. We tested the fagin pipeline on two focal species, Arabidopsis thaliana (plus four target species in Brassicaseae) and Saccharomyces cerevisiae (plus six target species in Saccharomyces). Using microsynteny maps, fagin classified the homology relationship of each query gene against each target genome into three main classes, and further subclasses: AAic (has a coding syntenic homolog), NTic (has a non-coding syntenic homolog), and Unknown (has no detected syntenic homolog). fagin inferred over half the “Unknown” A. thaliana query genes, and about 20% for S. cerevisiae, as lacking a syntenic homolog because of local indels or scrambled synteny. Conclusions fagin augments standard phylostratigraphy, and extends synteny-based phylostratigraphy with an automated, customizable, and detailed contextual analysis. By comparing synteny-based phylostrata to standard phylostrata, fagin systematically identifies those orphans and lineage-specific genes that are well-supported to have originated de novo. Analyzing within-species genomes should distinguish orphan genes that may have originated through rapid divergence from de novo orphans. Fagin also delineates whether a gene has no syntenic homolog because of technical or biological reasons. These analyses indicate that some orphans may be associated with regions of high genomic perturbation. Electronic supplementary material The online version of this article (10.1186/s12859-019-3023-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zebulun Arendsee
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA, 50010, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, 50011, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50011, USA
| | - Jing Li
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA, 50010, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, 50011, USA
| | - Urminder Singh
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA, 50010, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, 50011, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50011, USA
| | - Priyanka Bhandary
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA, 50010, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, 50011, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50011, USA
| | - Arun Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Eve Syrkin Wurtele
- Department of Genetics Development and Cell Biology, Iowa State University, Ames, IA, 50010, USA. .,Center for Metabolic Biology, Iowa State University, Ames, IA, 50011, USA. .,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, 50011, USA.
| |
Collapse
|
30
|
Agarwal A, Dhiraaj S, Raza M, Singhal V, Gupta D, Ranjan R, Singh PK, Singh U. Pain during Injection of Propofol: The Effect of Prior Administration of Ephedrine. Anaesth Intensive Care 2019; 32:657-60. [PMID: 15535489 DOI: 10.1177/0310057x0403200508] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 11/16/2022]
Abstract
Propofol causes pain on intravenous injection in 28 to 90% of patients. A number of techniques have been tried to minimize propofol-induced pain, with variable results. In a randomized, double-blind, placebo-controlled trial, we compared the efficacy of ephedrine 30 μg/kg pretreatment to lignocaine 40 mg for prevention of propofol-induced pain. Ninety-three adult patients, ASA 1 and 2, undergoing elective laparoscopic cholecystectomy were randomly assigned to three groups of 31 each. Group 1 received normal saline, group 2 received lignocaine 2% (40 mg) and group 3 received 30 μg/kg ephedrine. All pretreatment drugs were made up to 2 ml. Pain at the time of propofol injection was assessed on a four-point scale: 0=no pain, 1=mild pain, 2=moderate pain, and 3=severe pain. Twenty-seven patients (87%) of ephedrine pretreatment patients had pain during intravenous injection of propofol as compared to 24 (77%) in the normal saline group. In the lignocaine group, propofol-induced pain was observed in only 13 (42%) when compared with other study groups (P<0.05). Pretreatment with ephedrine 30 μg/kg did not attenuate pain associated with intravenous injection of propofol, nor did it improve haemodynamic stability during induction. However, pretreatment with 2% lignocaine (40 mg) was effective in attenuating propofol-associated pain.
Collapse
Affiliation(s)
- A Agarwal
- Department of Anesthesia, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Singh U, Cui Y, Dimaano N, Mehta S, Pruitt SK, Yearley J, Laterza OF, Juco JW, Dogdas B. Analytical validation of quantitative immunohistochemical assays of tumor infiltrating lymphocyte biomarkers. Biotech Histochem 2018; 93:411-423. [PMID: 29863904 DOI: 10.1080/10520295.2018.1445290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Tumor infiltrating lymphocytes (TIL), especially T-cells, have both prognostic and therapeutic applications. The presence of CD8+ effector T-cells and the ratio of CD8+ cells to FOXP3+ regulatory T-cells have been used as biomarkers of disease prognosis to predict response to various immunotherapies. Blocking the interaction between inhibitory receptors on T-cells and their ligands with therapeutic antibodies including atezolizumab, nivolumab, pembrolizumab and tremelimumab increases the immune response against cancer cells and has shown significant improvement in clinical benefits and survival in several different tumor types. The improved clinical outcome is presumed to be associated with a higher tumor infiltration; therefore, it is thought that more accurate methods for measuring the amount of TIL could assist prognosis and predict treatment response. We have developed and validated quantitative immunohistochemistry (IHC) assays for CD3, CD8 and FOXP3 for immunophenotyping T-lymphocytes in tumor tissue. Various types of formalin fixed, paraffin embedded (FFPE) tumor tissues were immunolabeled with anti-CD3, anti-CD8 and anti-FOXP3 antibodies using an IHC autostainer. The tumor area of stained tissues, including the invasive margin of the tumor, was scored by a pathologist (visual scoring) and by computer-based quantitative image analysis. Two image analysis scores were obtained for the staining of each biomarker: the percent positive cells in the tumor area and positive cells/mm2 tumor area. Comparison of visual vs. image analysis scoring methods using regression analysis showed high correlation and indicated that quantitative image analysis can be used to score the number of positive cells in IHC stained slides. To demonstrate that the IHC assays produce consistent results in normal daily testing, we evaluated the specificity, sensitivity and reproducibility of the IHC assays using both visual and image analysis scoring methods. We found that CD3, CD8 and FOXP3 IHC assays met the fit-for-purpose analytical acceptance validation criteria and that they can be used to support clinical studies.
Collapse
Affiliation(s)
- U Singh
- a Translational Medicine , Merck & Co., Inc ., Kenilworth
| | - Y Cui
- a Translational Medicine , Merck & Co., Inc ., Kenilworth
| | - N Dimaano
- a Translational Medicine , Merck & Co., Inc ., Kenilworth
| | - S Mehta
- b Applied Mathematics and Modeling, Data Science , Merck & Co. Inc ., Rahway , New Jersey
| | - S K Pruitt
- a Translational Medicine , Merck & Co., Inc ., Kenilworth
| | - J Yearley
- c Anatomic Pathology , Merck & Co., Inc , Palo Alto , California
| | - O F Laterza
- a Translational Medicine , Merck & Co., Inc ., Kenilworth
| | - J W Juco
- a Translational Medicine , Merck & Co., Inc ., Kenilworth
| | - B Dogdas
- b Applied Mathematics and Modeling, Data Science , Merck & Co. Inc ., Rahway , New Jersey
| |
Collapse
|
32
|
Singh R, Sengar GS, Singh U, Deb R, Junghare V, Hazra S, Kumar S, Tyagi S, Das AK, Raja TV, Kumar A. Functional proteomic analysis of crossbred (Holstein Friesian × Sahiwal) bull spermatozoa. Reprod Domest Anim 2018; 53:588-608. [DOI: 10.1111/rda.13146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/10/2018] [Indexed: 12/15/2022]
Affiliation(s)
- R Singh
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| | - GS Sengar
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| | - U Singh
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| | - R Deb
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| | - V Junghare
- Department of Biotechnology; Indian Institute of Technology; Roorkee Uttarakhand India
| | - S Hazra
- Department of Biotechnology; Indian Institute of Technology; Roorkee Uttarakhand India
- Center of Nanotechnology; Indian Institute of Technology; Roorkee Uttarakhand India
| | - S Kumar
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| | - S Tyagi
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| | - AK Das
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| | - TV Raja
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| | - A Kumar
- Molecular Genetics Laboratory; ICAR-Central Institute for Research on Cattle; Meerut Uttar Pradesh India
| |
Collapse
|
33
|
Singh U, Khemka N, Rajkumar MS, Garg R, Jain M. PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. Nucleic Acids Res 2018; 45:e183. [PMID: 29036354 PMCID: PMC5727461 DOI: 10.1093/nar/gkx866] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 09/16/2017] [Indexed: 12/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) make up a significant portion of non-coding RNAs and are involved in a variety of biological processes. Accurate identification/annotation of lncRNAs is the primary step for gaining deeper insights into their functions. In this study, we report a novel tool, PLncPRO, for prediction of lncRNAs in plants using transcriptome data. PLncPRO is based on machine learning and uses random forest algorithm to classify coding and long non-coding transcripts. PLncPRO has better prediction accuracy as compared to other existing tools and is particularly well-suited for plants. We developed consensus models for dicots and monocots to facilitate prediction of lncRNAs in non-model/orphan plants. The performance of PLncPRO was quite better with vertebrate transcriptome data as well. Using PLncPRO, we discovered 3714 and 3457 high-confidence lncRNAs in rice and chickpea, respectively, under drought or salinity stress conditions. We investigated different characteristics and differential expression under drought/salinity stress conditions, and validated lncRNAs via RT-qPCR. Overall, we developed a new tool for the prediction of lncRNAs in plants and showed its utility via identification of lncRNAs in rice and chickpea.
Collapse
Affiliation(s)
- Urminder Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Niraj Khemka
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar 201314, Uttar Pradesh, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
34
|
Alex R, Ramesha KP, Singh U, Kumar S, Alyethodi RR, Deb R, Rai S, Sharma S, Sengar GS, Kumar A, Prakash B. Association analysis of novel polymorphisms in 2', 5'-oligoadenylate synthetase gene with reproductive traits in indigenous and cross-bred cattle of Indian Origin. Reprod Domest Anim 2017; 53:442-449. [PMID: 29277982 DOI: 10.1111/rda.13129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022]
Abstract
2', 5'-Oligoadenylate synthetases (OAS) are important components of an interferon-mediated antiviral pathway. No polymorphisms in exonic regions of bovine OAS1 gene have been identified and associated with reproduction traits. The objective of the study was to detect and evaluate the effects of mutations in exonic region of bovine OAS1 gene with reproduction traits in cattle. DNA samples collected from 250 individual cows of two Indian dairy breeds (Sahiwal and Frieswal) of cattle were used in the study. The genetic variants of the OAS1 gene were identified with polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and sequence analysis using seven set of primer pairs. The PCR-SSCP analysis revealed polymorphism in the fragments comprising of exon 2, exon 5 and first fragment of exon 6 while the fragments of exons 1, 3, 4 and second fragment of exon 6 were monomorphic in Sahiwal and Frieswal cattle. The mutations in the amplified region comprising of exon 2 were found to have significant association with age at first breeding and calving, service period, dry period and pregnancy rate. Significant associations were found between SNPs in the exon 5 and service and dry periods of the animal, whereas the genetic variants in the first fragment of the exon 6 showed significant association with age at first breeding and calving. To our knowledge, this study demonstrated for the first time that the polymorphisms in OAS1 gene were associated with reproductive traits and it can be chosen as a candidate gene for improvement of reproductive performance of cattle.
Collapse
Affiliation(s)
- R Alex
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - K P Ramesha
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India.,Dairy Production, SRS, ICAR-National Dairy Research Institute, Banglore, India
| | - U Singh
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - S Kumar
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - R R Alyethodi
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - R Deb
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - S Rai
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India.,ERS, ICAR-National Dairy Research Institute, Kalyani, West Bengal, India
| | - S Sharma
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - G S Sengar
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - A Kumar
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - B Prakash
- Animal Genetics and Breeding Section, ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| |
Collapse
|
35
|
Singh U, Verma A, Bhat H. Discovery of novel 1,3,5-triazine-thiozolidine (DDDL-251) based dual PI3K/mTOR inhibitor against breast cancer. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx652.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
36
|
Kalinderis M, Singh U. Umbilical endometriosis: a rare case of spontaneous cutaneous umbilical endometriosis. CLIN EXP OBSTET GYN 2017. [DOI: 10.12891/ceog3839.2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
37
|
Singh U, Athavale S, Lalwani R. Bilateral tortuous internal carotid artery: A case report. J ANAT SOC INDIA 2017. [DOI: 10.1016/j.jasi.2017.08.322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
38
|
Sharma SK, Yadav SL, Singh U, Wadhwa S. Muscle Activation Profiles and Co-Activation of Quadriceps and Hamstring Muscles around Knee Joint in Indian Primary Osteoarthritis Knee Patients. J Clin Diagn Res 2017; 11:RC09-RC14. [PMID: 28658860 DOI: 10.7860/jcdr/2017/26975.9870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/09/2017] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Osteoarthritis (OA) of knee is a common joint disease. It is associated with reduced knee joint stability due to impaired quadriceps strength, pain, and an altered joint structure. There is altered muscle activation in knee OA patients, which interferes with normal load distribution around the knee and facilitates disease progression. AIM Our primary aim was to determine activation patterns of the muscles i.e., quadriceps and hamstrings in knee OA patients during walking. We also studied co-activation of muscles around knee joint in primary OA knee patients including directed medial and lateral co-contractions. MATERIALS AND METHODS This observational study was done at Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences, New Delhi, India. Fourty-four patients with medial compartment primary knee OA were included in study after satisfying inclusion and exclusion criteria. All the patients were assessed for mean, peak and integrated Root Mean Square (RMS), EMG values, muscle activation patterns and co-activation of muscles around knee joint by surface Electromyography (EMG) analysis of Vastus Medialis Obliques (VMO), Vastus Lateralis (VL), Semitendinosus (SMT) and Biceps Femoris (BF) muscles during gait cycle. The EMG waveform for each muscle was amplitude normalized and time normalized to 100% of gait cycle and plotted on graph. Quantitative variables were assessed for normal distribution and accordingly mean±SD or median (range), as appropriate, was computed. RESULTS For primary OA knee, mean age 61±5 years, mean weight 63.7±10.1 kg, mean height 153.9±7.2 cm, and mean Body Mass Index (BMI) 26.8±3.0 kg/m2 was found. The muscle activity of hamstrings (SMT muscle and BF) was increased during midstance, late stance and early swing phase of gait cycle as compared to quadriceps (VMO and VL) muscle activity respectively, suggesting co-contraction of opposing muscles around knee joint. CONCLUSION Patients with knee OA walk with increased hamstring muscle activity (during late stance and early swing phase) and reduced quadriceps recruitment. Altered neuro-muscular control around knee interferes with normal load distribution and facilitates disease progression in knee joint.
Collapse
Affiliation(s)
- Sanjeev Kumar Sharma
- Assistant Professor, Department of Physical Medicine and Rehabilitation, RUHS College of Medical Sciences, Jaipur, Rajasthan, India
| | - Shiv Lal Yadav
- Professor, Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - U Singh
- Professor, Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sanjay Wadhwa
- Professor, Department of Physical Medicine and Rehabilitation, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| |
Collapse
|
39
|
Kumar S, Singh U, Goswami C, Singru PS. Transient receptor potential vanilloid 5 (TRPV5), a highly Ca 2+ -selective TRP channel in the rat brain: relevance to neuroendocrine regulation. J Neuroendocrinol 2017; 29. [PMID: 28235149 DOI: 10.1111/jne.12466] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 11/28/2022]
Abstract
Recent studies suggest an important role for transient receptor potential vanilloid (TRPV) ion channels in neural and neuroendocrine regulation. The TRPV subfamily consists of six members: TRPV1-6. While the neuroanatomical and functional correlates of TRPV1-4 have been studied extensively, relevant information about TRPV5 and TRPV6, which are highly selective for Ca2+ , is limited. We detected TRPV5 mRNA expression in the olfactory bulb, cortex, hypothalamus, hippocampus, midbrain, brainstem and cerebellum of the rat. TRPV5-immunoreactive neurones were conspicuously seen in the hypothalamic paraventricular (PVN), supraoptic (SON), accessory neurosecretory (ANS), supraoptic nucleus, retrochiasmatic part (SOR), arcuate (ARC) and medial tuberal nuclei, hippocampus, midbrain, brainstem and cerebellum. Glial cells also showed TRPV5-immunoreactivity. To test the neuroendocrine relevance of TRPV5, we focused on vasopressin, oxytocin and cocaine- and amphetamine-regulated transcript (CART) as representative candidate markers with which TRPV5 may co-exist. In the hypothalamic neurones, co-expression of TRPV5 was observed with vasopressin (PVN: 50.73±3.82%; SON: 75.91±2.34%; ANS: 49.12±4.28%; SOR: 100%) and oxytocin (PVN: 6.88±1.21; SON: 63.34±5.69%; ANS: 20.4±4.14; SOR: 86.5±1.74%). While ARC neurones express oestrogen receptors, 17β-oestradiol regulates TRPV5, as well as CART neurones and astrocytes, in the ARC. Furthermore, ARC CART neurones are known to project to the preoptic area, and innervate and regulate GnRH neurones. Using double-immunofluorescence, glial fibrillary acidic protein-labelled astrocytes and the majority of CART neurones in the ARC showed TRPV5-immunoreactivity. Following iontophoresis of retrograde neuronal tracer, cholera toxin β (CtB) into the anteroventral periventricular nucleus and median preoptic nucleus, retrograde accumulation of CtB was observed in most TRPV5-equipped ARC CART neurones. Next, we determined the response of TRPV5-elements in the ARC during the oestrous cycle. Compared to pro-oestrus, a significant increase (P<.001) in the percentage of TRPV5-expressing CART neurones was observed during oestrus, metoestrus, and dioestrus. TRPV5-immunoreactivity in the astrocytes, however, showed a significant increase during metoestrus and dioestrus. We suggest that the TRPV5 ion channel may serve as an important regulator of neural and neuroendocrine pathways in the brain.
Collapse
Affiliation(s)
- S Kumar
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - U Singh
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - C Goswami
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| | - P S Singru
- School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, India
| |
Collapse
|
40
|
Prakash J, Ganiger V, Prakash S, Sivasankar M, Sunder S, Singh U. Kidney Disease in Human Immunodeficiency Virus-seropositive Patients: Absence of Human Immunodeficiency Virus-associated Nephropathy was a Characteristic Feature. Indian J Nephrol 2017; 27:271-276. [PMID: 28761228 PMCID: PMC5514822 DOI: 10.4103/0971-4065.202400] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection can cause a broad spectrum of renal diseases. However, there is paucity of Indian data on the patterns of renal lesions in HIV-seropositive patients. The aim of the present study was to delineate the spectrum of renal lesions in HIV/acquired immunodeficiency syndrome patients. In this prospective study, all HIV-positive patients of both genders aged >18 years were screened for renal disease. Patients with proteinuria of more than 1 g/24 h were subjected to renal biopsy. A total of 293 HIV-positive patients were screened; of these, 136 (46.4%) patients found to have renal involvement. Dipstick-positive proteinuria of 1+ or more was observed in 112 (38.2%) patients, and 16 (14.2%) patients had proteinuria of more than 1 g/24 h. Renal biopsy in 14 cases revealed glomerulonephritis (GN) in 12 (85.7%) (isolated GN in 4 [28.5%] and GN mixed with chronic TIN in 8 [57.1%]) patients. These include mesangioproliferative GN in 5 (35.7%), membranoproliferative GN in 2 (14.2%), focal segmental glomerulosclerosis in 2 (14.2%), diffuse proliferative GN in 2 (14.2%), and diabetic nephropathy in 1 (7.1%) patients. Chronic interstitial nephritis was noted in 10 (71.42%) (superimposed on GN in 8 [57.1%], isolated in 2 [14.2%]) patients. Granulomatous interstitial nephritis was seen in 3 (24.1%) cases. GN and chronic interstitial nephritis were noted in 85.7% and 71.42% of patients, respectively, mostly superimposed on each other. Mesangioproliferative GN was the most common glomerular lesion, but classical HIV-associated nephropathy was not observed.
Collapse
Affiliation(s)
- J Prakash
- Department of Nephrology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - V Ganiger
- Department of Nephrology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - S Prakash
- Department of Medicine, TNMC, Mumbai, Maharashtra, India
| | - M Sivasankar
- Department of Nephrology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - S Sunder
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - U Singh
- Department of Pathology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| |
Collapse
|
41
|
Deb R, Sengar GS, Singh U, Kumar S, Raja TV, Alex R, Alyethodi RR, Prakash B. LAMP assay for rapid diagnosis of cow DNA in goat milk and meat samples. Iran J Vet Res 2017; 18:134-137. [PMID: 28775755 PMCID: PMC5534258] [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] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/19/2016] [Accepted: 11/26/2016] [Indexed: 06/07/2023]
Abstract
Animal species detection is one of the crucial steps for consumer's food analysis. In the present study we developed an in-house built loop-mediated isothermal amplification (LAMP) assay for rapid detection of adulterated cow DNA in goat milk/meat samples. The cow milk/tissue DNA in goat milk/meat samples were identified in the developed LAMP assay by either naked eye visualizing with SYBR Green I dyes or by detecting the typical ladder pattern on gel electrophoresis. This test can detect up to minimum 5% level of cow components admixed in goat milk/meat samples and can be completed within 1 h 40 min starting from DNA extraction from milk/meat samples and can be performed in a water bath. Developed LAMP methodology is simple; rapid and sensitive techniques that can detect adulterant like cow components in goat milk/meat are more accurate than other existing DNA based technologies.
Collapse
Affiliation(s)
- R. Deb
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut-250 001, Uttar Pradesh, India
| | - G. S. Sengar
- MSc in Biotechnology, Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut-250 001, Uttar Pradesh, India
| | - U. Singh
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut-250 001, Uttar Pradesh, India
| | - S. Kumar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut-250 001, Uttar Pradesh, India
| | - T. V. Raja
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut-250 001, Uttar Pradesh, India
| | - R. Alex
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut-250 001, Uttar Pradesh, India
| | - R. R. Alyethodi
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut-250 001, Uttar Pradesh, India
| | - B. Prakash
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut-250 001, Uttar Pradesh, India
| |
Collapse
|
42
|
Singh O, Kumar S, Singh U, Bhute Y, Singru PS. Role of Isotocin in the Regulation of the Hypophysiotropic Dopamine Neurones in the Preoptic Area of the Catfish, Clarias batrachus. J Neuroendocrinol 2016; 28. [PMID: 27805784 DOI: 10.1111/jne.12441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 10/28/2016] [Accepted: 10/28/2016] [Indexed: 11/28/2022]
Abstract
Dopamine (DA) has emerged as a potent inhibitory neuromodulator of luteinsing hormone (LH) secretion and reproduction in teleosts. The DA neurones located in the anterior subdivision of nucleus preopticus periventricularis (NPPa) in the preoptic area (POA) innervate the pituitary gland and regulate LH cells. Although a reduction in the inhibitory DAergic tone is crucial for stimulatory action of gonadotrophin-releasing hormone (GnRH) on LH cells, the role of other hypothalamic factors is suggested but not fully understood. Nonapeptide, isotocin (IST) has emerged as a likely candidate that may also influence the LH cell function. IST neurones reside in the nucleus preopticus and innervate LH cells. While IST treatment dramatically elevated LH secretion, the IST levels in brain peaked during spawning. In a pilot study on the catfish, Clarias batrachus, we observed a dense network of IST-immunoreactive (IST-IR) fibres in the NPPa, the region known to harbour hypophysiotropic DA neurones. Application of the double immunofluorescence method showed a dense IST-IR fibre network around the tyrosine hydroxylase-immunoreactive (TH-IR) neurones in the NPPa region. A great majority of the TH-IR neurones in the NPPa were contacted by IST-IR fibres during the spawning phase. The NPPa therefore appears to be a site for the intense interaction of DA and IST. IST-IR fibre innervation in NPPa showed reproduction phase-dependent changes. The percent fluorescent area of IST-IR fibres showed a gradual increase from the resting through prespawning phases (resting: 7.5 ± 1.04; preparatory: 8.6 ± 0.8; prespawning: 15.5 ± 1.4), reaching a peak in the spawning phase (28 ± 2.3; P < 0.001). Compared to the spawning phase, a drastic reduction in IST-IR fibres in the NPPa was observed during the postspawning phase (8.4 ± 0.9; P < 0.001). Superfused slices of the POA of C. batrachus treated with IST peptide resulted in a significant reduction in TH immunoreactivity in the NPPa (Control: 45.3 ± 4.2; IST peptide, 5 μm: 29.4 ± 4.7; P < 0.05). We suggest that the intense interaction between IST and DA in the NPPa, most probably of an inhibitory nature, may be critical for the regulation of LH cells and reproduction in teleosts.
Collapse
Affiliation(s)
- O Singh
- School of Biological Sciences, National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni, Odisha, India
- Training School Complex, Homi Bhabha National Institute, Mumbai, India
| | - S Kumar
- School of Biological Sciences, National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni, Odisha, India
- Training School Complex, Homi Bhabha National Institute, Mumbai, India
| | - U Singh
- School of Biological Sciences, National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni, Odisha, India
- Training School Complex, Homi Bhabha National Institute, Mumbai, India
| | - Y Bhute
- Department of Zoology, DRB Sindhu Mahavidyalaya, Nagpur, India
| | - P S Singru
- School of Biological Sciences, National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni, Odisha, India
- Training School Complex, Homi Bhabha National Institute, Mumbai, India
| |
Collapse
|
43
|
Affiliation(s)
- S. K. Maurya
- Department of Statistics, Banaras Hindu University, Varanasi, India
| | - A. Kaushik
- Department of Statistics, Banaras Hindu University, Varanasi, India
| | - S. K. Singh
- Department of Statistics, Banaras Hindu University, Varanasi, India
| | - U. Singh
- Department of Statistics, Banaras Hindu University, Varanasi, India
| |
Collapse
|
44
|
Abstract
BACKGROUND Orbital involvement in Wegener's Granulomatosis (WG) is rare and has an overall good prognosis. CASE A 60-year-old hypertensive Indian female presented with vision loss and painful proptosis of left eye. Orbital incisional biopsy suggested necrotising small vessel inflammation. The saddle nose deformity and pedal nodulo- ulcerative lesions further consolidated the diagnosis of Wegener's granulomatosis. Systemic immunosuppressant provided remission and the only relapse was managed successfully with intravenous Rituximab. CONCLUSION Wegener's granulomatosis should be kept in the differential diagnosis of painful proptosis with a diffuse orbital mass in an elderly patient presenting with profound vision loss. Newer immune modulating agents are useful adjuncts in preventing relapses of this fatal disease.
Collapse
Affiliation(s)
- M Singh
- Department of Ophthalmic Plastic and Reconstructive Surgery Post Graduate Institute of Medical Education and Research, Sector-12, Chandigarh, India
| | | | | |
Collapse
|
45
|
Prakash J, Pant P, Prakash S, Sivasankar M, Vohra R, Doley PK, Pandey LK, Singh U. Changing picture of acute kidney injury in pregnancy: Study of 259 cases over a period of 33 years. Indian J Nephrol 2016; 26:262-7. [PMID: 27512298 PMCID: PMC4964686 DOI: 10.4103/0971-4065.161018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The incidence of acute kidney injury (AKI) in pregnancy is declining in developing countries but still remains a major cause of maternal and fetal morbidity and mortality. The aim of the study was to analyze the changing trends in pregnancy related AKI (PR-AKI) over a period of thirty-three years. Clinical characteristics of PR-AKI with respect to incidence, etiology and fetal and maternal outcomes were compared in three study periods, namely 1982-1991,1992-2002 and 2003-2014. The incidence of PR-AKI decreased to 10.4% in 1992-2002, from 15.2% in 1982-1991, with declining trend continuing in 2003-2014 (4.68%).Postabortal AKI decreased to 1.49% in 2003-2014 from 9.4% in 1982-1991of total AKI cases. The AKI related to puerperal sepsis increased to 1.56% of all AKI cases in 2003-2014 from 1.4% in 1982-1991. Preeclampsia/eclampsia associated AKI decreased from 3.5% of total AKI cases in 1982-1991 to 0.54% in 2003-2014. Pregnancy associated – thrombotic microangiopathy and acute fatty liver of pregnancy were uncommon causes of AKI. Hyperemesis gravidarum associated AKI was not observed in our study. Incidence of renal cortical necrosis (RCN) decreased to 1.4% in 2003-2014 from 17% in 1982-1991.Maternal mortality reduced to 5.79% from initial high value 20% in 1982-1991. The progression of PR-AKI to ESRD decreased to1.4% in 2003-2014 from 6.15% in 1982-1991. The incidence of PR-AKI has decreased over last three decades, mainly due to decrease in incidence of postabortal AKI. Puerperal sepsis and obstetric hemorrhage were the major causes of PR-AKI followed by preeclampsia in late pregnancy. Maternal mortality and incidence and severity of RCN have significantly decreased in PR-AKI. The progression to CKD and ESRD has decreased in women with AKI in pregnancy in recent decade. However, the perinatal mortality did not change throughout study period.
Collapse
Affiliation(s)
- J Prakash
- Department of Nephrology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - P Pant
- Department of Nephrology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - S Prakash
- Department of Medicine, Topiwala National Medical College, Mumbai, Maharashtra, India
| | - M Sivasankar
- Department of Nephrology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - R Vohra
- Department of Nephrology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - P K Doley
- Department of Nephrology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - L K Pandey
- Department of Obstetric and Gynaecology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - U Singh
- Department of Pathology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| |
Collapse
|
46
|
Abstract
Diabetes mellitus is a major source of mortality and morbidity along with an economic menace all over the world. In 2000, prevalence of diabetes worldwide was 171,000,000 and in 2030, it will be 366,000,000, nearly one in ten people globally will have some form of diabetes by 2035. There are some 382 million people living with the disease, but that could jump 55% by 2035. The total number of people in India with diabetes to be around 50.8 million in 2010, rising to 87.0 million by 2030 and it is estimated that by 2040 the numbers will increase upto 123.5 million. It has estimated that the prevalence of diabetes in rural populations is one-quarter that of urban population for India and other Indian sub-continent countries such as Bangladesh, Nepal, Bhutan, and Sri Lanka. Indian Council of Medical research (ICMR) revealed that a lower proportion of the population is affected in states of Northern India (Chandigarh 0.12 million, Jharkhand 0.96 million) as compared to Maharashtra (9.2 million) and Tamil Nadu (4.8 million). The National Urban Survey conducted across the metropolitan cities of India reported similar trend: 11.7 per cent in Kolkata (Eastern India), 6.1 per cent in Kashmir Valley (Northern India), 11.6 per cent in New Delhi (Northern India), and 9.3 per cent in West India (Mumbai) compared with (13.5 per cent in Chennai (South India), 16.6 per cent in Hyderabad (south India), and 12.4 per cent Bangalore (South India). Strengthening of health promotion activitiesin different settings, preventive health screening package, better treatment facilities and effective implementation can cure these problems worldwide.
Collapse
|
47
|
Murugesan S, Singh U, Perumal N, Ramanathan V, Krishnan P. High level mupirocin resistance among CoNS from nasal carriers of End stage renal disease patients and hospital personnel from tertiary care centre, Chennai. Indian J Med Microbiol 2016; 34:114-5. [DOI: 10.4103/0255-0857.167672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
48
|
Pandey CM, Mishra S, Singh U. Determinants and Trends of Anaemia among Children in Empowered Action Group States of India. Int J Epidemiol 2015. [DOI: 10.1093/ije/dyv096.193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
49
|
Jain A, Diwakar P, Singh U. Declining trend of resistance to first-line anti-tubercular drugs in clinical isolates of Mycobacterium tuberculosis in a tertiary care north Indian hospital after implementation of revised national Tuberculosis control programme. Indian J Med Microbiol 2015; 32:430-3. [PMID: 25297031 DOI: 10.4103/0255-0857.142257] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Trends showing drug-resistance pattern are needed to understand direction of tuberculosis (TB) control programme. The drug-resistance pattern in state of Uttar Pradesh, India, is not documented. Here we are reporting the prevalence of multi-drug-resistant (MDR) and drug-resistant TB in previously treated cases of pulmonary tuberculosis following launch of revised national TB control programme (RNTCP) in whole of Uttar Pradesh. Isolates of Mycobacterium tuberculosis, from patients of pulmonary tuberculosis, who were treated with antitubercular drugs for more than 4 weeks, were tested for resistance to first-line drugs; streptomycin (S), Ethambutol (E), Rifampicin (R) and isoniazid (H) over a period of 4 years, 2009-2012. Total 2496 isolates of M. tuberculosis were tested, of which 1139 isolates (45.6%) were pan-sensitive and 370 (14.8%) were pan-resistant. Total 695 isolates (27.8%) were MDR. Maximum resistance was with Isoniazid (n=1069, 42.8%) followed by streptomycin (n=840, 33.7%), rifampicin (n=742, 29.7%), and ethambutol (n=613, 24.6%). A decline in number of MDR strains and individual drug resistance was seen. Total MDR strains in the year 2009, 2010, 2011 and 2012 were 35.6%, 30.8%, 26.7% and 22.8% respectively. The drug resistance pattern reported from time to time may vary substantially. The decline in drug resistance visible over last four years, after implementation of DOTS, appears promising.
Collapse
Affiliation(s)
- A Jain
- Department of Microbiology, Tuberculosis Laboratory, King George's Medical University, Lucknow, Uttar Pradesh, India
| | | | | |
Collapse
|
50
|
Kumar S, Deb R, Singh U, Ganguly I, Mandal DK, Tyagi S, Kumar M, Sengar G, Sharma S, Singh R, Singh R. Bovine Circadian Locomotor Output Cycles Kaput (CLOCK) and Clusterin (CLU) mRNA Quantitation in Ejaculated Crossbred Bull Spermatozoa. Reprod Domest Anim 2015; 50:505-9. [PMID: 25845404 DOI: 10.1111/rda.12522] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 03/17/2015] [Indexed: 12/22/2022]
Abstract
Mammalian circadian locomotor output cycles kaput (CLOCK) gene encodes a transcription factor that affects both the persistence and the period of circadian rhythms. Earlier reports suggested that CLOCK gene might be associated with male infertility in human. Present investigation, for the first time, reports that CLOCK gene expresses differentially between good and poor quality crossbred bull semen. The relative expression of CLOCK was significantly (p < 0.05) higher among good quality bull semen than motility-impaired ones. Clusterins (CLU) are series of genes associated with a variety of physiological activities including spermatogenesis, apoptosis and degenerative disease conditions. In the present context, we also investigated that the expression of CLU gene was significantly (p < 0.05) higher among motility-impaired crossbred bull semen compared to the good quality one.
Collapse
Affiliation(s)
- S Kumar
- Indian Council of Agricultural Research- Central Institute for Research on Cattle, Meerut, India
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|