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Garcia A, Rivera R, Simpson AC, Singh NK, Green S, Venkateswaran K. Whole-genome sequencing of Paenibacillus phoenicis isolated from the Phoenix Mars Lander spacecraft assembly facility. Microbiol Resour Announc 2024:e0126523. [PMID: 38742883 DOI: 10.1128/mra.01265-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
The genome of Paenibacillus phoenicis, a spore-forming bacterium isolated from the spacecraft assembly facility of the Phoenix mission, was generated via hybrid assembly by merging short and long reads. Examining this genome may shed light on strategies to minimize the risk of contaminating extraterrestrial environments with Earth-based microorganisms.
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Affiliation(s)
- Andrew Garcia
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Oregon State University, Corvallis, Oregon, USA
| | - Romar Rivera
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Anna C Simpson
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Stefan Green
- Rush University Medical Center, Genomics and Microbiome Core Facility, Chicago, Illinois, USA
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Covington JK, Torosian N, Cook AM, Palmer M, Bryan SG, Nou NO, Mewalal R, Harmon-Smith M, Blaby IK, Cheng JF, Hess M, Brumm PJ, Singh NK, Venkateswaran K, Hedlund BP. Biochemical characterization of Fsa16295Glu from "Fervidibacter sacchari," the first hyperthermophilic GH50 with β-1,3-endoglucanase activity and founding member of the subfamily GH50_3. Front Microbiol 2024; 15:1355444. [PMID: 38725686 PMCID: PMC11079163 DOI: 10.3389/fmicb.2024.1355444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
The aerobic hyperthermophile "Fervidibacter sacchari" catabolizes diverse polysaccharides and is the only cultivated member of the class "Fervidibacteria" within the phylum Armatimonadota. It encodes 117 putative glycoside hydrolases (GHs), including two from GH family 50 (GH50). In this study, we expressed, purified, and functionally characterized one of these GH50 enzymes, Fsa16295Glu. We show that Fsa16295Glu is a β-1,3-endoglucanase with optimal activity on carboxymethyl curdlan (CM-curdlan) and only weak agarase activity, despite most GH50 enzymes being described as β-agarases. The purified enzyme has a wide temperature range of 4-95°C (optimal 80°C), making it the first characterized hyperthermophilic representative of GH50. The enzyme is also active at a broad pH range of at least 5.5-11 (optimal 6.5-10). Fsa16295Glu possesses a relatively high kcat/KM of 1.82 × 107 s-1 M-1 with CM-curdlan and degrades CM-curdlan nearly completely to sugar monomers, indicating preferential hydrolysis of glucans containing β-1,3 linkages. Finally, a phylogenetic analysis of Fsa16295Glu and all other GH50 enzymes revealed that Fsa16295Glu is distant from other characterized enzymes but phylogenetically related to enzymes from thermophilic archaea that were likely acquired horizontally from "Fervidibacteria." Given its functional and phylogenetic novelty, we propose that Fsa16295Glu represents a new enzyme subfamily, GH50_3.
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Affiliation(s)
| | - Nicole Torosian
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Allison M. Cook
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Scott G. Bryan
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Nancy O. Nou
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Ritesh Mewalal
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Miranda Harmon-Smith
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ian K. Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Matthias Hess
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | | | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
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Miliotis G, Sengupta P, Hameed A, Chuvochina M, McDonagh F, Simpson AC, Parker CW, Singh NK, Rekha PD, Morris D, Raman K, Kyrpides NC, Hugenholtz P, Venkateswaran K. Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio 2024; 15:e0018124. [PMID: 38477597 PMCID: PMC11005411 DOI: 10.1128/mbio.00181-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HST, exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HST is most closely related to Virgibacillus halophilus 5B73CT, sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HST is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HST = DSM 115946T = NRRL B-65666T), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73CT = DSM 21623T = JCM 21758T = KCTC 13935T). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6T = DSM 22952T = CCM 7714T). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins. IMPORTANCE The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.
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Affiliation(s)
- Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Punchappady D. Rekha
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Nikos C. Kyrpides
- US Department of Energy Joint Genome Institute, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Spry JA, Siegel B, Bakermans C, Beaty DW, Bell MS, Benardini JN, Bonaccorsi R, Castro-Wallace SL, Coil DA, Coustenis A, Doran PT, Fenton L, Fidler DP, Glass B, Hoffman SJ, Karouia F, Levine JS, Lupisella ML, Martin-Torres J, Mogul R, Olsson-Francis K, Ortega-Ugalde S, Patel MR, Pearce DA, Race MS, Regberg AB, Rettberg P, Rummel JD, Sato KY, Schuerger AC, Sefton-Nash E, Sharkey M, Singh NK, Sinibaldi S, Stabekis P, Stoker CR, Venkateswaran KJ, Zimmerman RR, Zorzano-Mier MP. Planetary Protection Knowledge Gap Closure Enabling Crewed Missions to Mars. Astrobiology 2024; 24:230-274. [PMID: 38507695 DOI: 10.1089/ast.2023.0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
As focus for exploration of Mars transitions from current robotic explorers to development of crewed missions, it remains important to protect the integrity of scientific investigations at Mars, as well as protect the Earth's biosphere from any potential harmful effects from returned martian material. This is the discipline of planetary protection, and the Committee on Space Research (COSPAR) maintains the consensus international policy and guidelines on how this is implemented. Based on National Aeronautics and Space Administration (NASA) and European Space Agency (ESA) studies that began in 2001, COSPAR adopted principles and guidelines for human missions to Mars in 2008. At that point, it was clear that to move from those qualitative provisions, a great deal of work and interaction with spacecraft designers would be necessary to generate meaningful quantitative recommendations that could embody the intent of the Outer Space Treaty (Article IX) in the design of such missions. Beginning in 2016, COSPAR then sponsored a multiyear interdisciplinary meeting series to address planetary protection "knowledge gaps" (KGs) with the intent of adapting and extending the current robotic mission-focused Planetary Protection Policy to support the design and implementation of crewed and hybrid exploration missions. This article describes the outcome of the interdisciplinary COSPAR meeting series, to describe and address these KGs, as well as identify potential paths to gap closure. It includes the background scientific basis for each topic area and knowledge updates since the meeting series ended. In particular, credible solutions for KG closure are described for the three topic areas of (1) microbial monitoring of spacecraft and crew health; (2) natural transport (and survival) of terrestrial microbial contamination at Mars, and (3) the technology and operation of spacecraft systems for contamination control. The article includes a KG data table on these topic areas, which is intended to be a point of departure for making future progress in developing an end-to-end planetary protection requirements implementation solution for a crewed mission to Mars. Overall, the workshop series has provided evidence of the feasibility of planetary protection implementation for a crewed Mars mission, given (1) the establishment of needed zoning, emission, transport, and survival parameters for terrestrial biological contamination and (2) the creation of an accepted risk-based compliance approach for adoption by spacefaring actors including national space agencies and commercial/nongovernment organizations.
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Affiliation(s)
| | | | - Corien Bakermans
- Department of Biology, Penn. State University (Altoona), Altoona, Pennsylvania, USA
| | - David W Beaty
- Jet Propulsion Laboratory/California Institute of Technology, Pasadena, California, USA
| | | | | | - Rosalba Bonaccorsi
- SETI Institute, Mountain View, California, USA
- NASA Ames Research Center, Moffett Field, California, USA
| | | | - David A Coil
- School of Medicine, University of California, Davis, Davis, California, USA
| | | | - Peter T Doran
- Department of Geology & Geophysics, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Lori Fenton
- SETI Institute, Mountain View, California, USA
| | - David P Fidler
- Council on Foreign Relations, Washington, District of Columbia, USA
| | - Brian Glass
- NASA Ames Research Center, Moffett Field, California, USA
| | | | - Fathi Karouia
- NASA Ames Research Center, Moffett Field, California, USA
| | - Joel S Levine
- College of William & Mary, Williamsburg, Virginia, USA
| | | | - Javier Martin-Torres
- School of Geoscience, University of Aberdeen, Aberdeen, United Kingdom
- Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Armilla, Spain
| | - Rakesh Mogul
- California Polytechnic (Pomona), Pomona, California, USA
| | - Karen Olsson-Francis
- School of Environment, Earth and Ecosystem Sciences, Open University, Milton Keynes, United Kingdom
| | | | - Manish R Patel
- School of Environment, Earth and Ecosystem Sciences, Open University, Milton Keynes, United Kingdom
| | - David A Pearce
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | | | | | | | - John D Rummel
- Friday Harbor Associates LLC, Friday Harbor, Washington, USA
| | | | - Andrew C Schuerger
- Department of Plant Pathology, University of Florida, Merritt Island, Florida, USA
| | | | - Matthew Sharkey
- US Department of Health & Human Services, Washington, District of Columbia, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory/California Institute of Technology, Pasadena, California, USA
| | | | | | - Carol R Stoker
- NASA Ames Research Center, Moffett Field, California, USA
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Hage N, Kappagantu KM, Singh NK, Ramamourthy B. Anomalous Posterior Branching of the Internal Jugular Vein: A Report of Two Patients. Int J Oral Maxillofac Surg 2023:S0901-5027(23)00881-0. [PMID: 38101987 DOI: 10.1016/j.ijom.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/08/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]
Abstract
The internal jugular vein (IJV) is an important vein encountered during most routine major head and neck surgeries. The IJV is known to infrequently present with anatomical variations, commonly duplication and fenestration. This report presents two cases that highlight an unusual anatomical variation of the IJV, namely the posterior tributary, which was encountered during neck dissection for papillary carcinoma of the thyroid and metastatic cervical lymph nodes. The first case was a 50-year-old woman with papillary carcinoma of the thyroid and regional metastasis, who underwent extensive neck dissection. During dissection, an anomalous posterior tributary of the IJV was discovered, originating around 3 cm above the omohyoid tendon-IJV junction. In case 2, a 40-year-old woman with a history of thyroidectomy exhibited a similar anomaly during neck dissection. In both cases, the posterior tributary was observed branching into two divisions. These cases emphasize the significance of recognizing anatomical variations to avoid inadvertent damage during surgical procedures. Anomalies like the posterior IJV tributary could have implications for surgical planning, emphasizing the importance of thorough exploration and understanding of individual variations. Awareness of such variations will help facilitate surgeons in safely performing neck dissections.
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Affiliation(s)
- N Hage
- Department of Otorhinolaryngology and Head and Neck Surgery, All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana, India.
| | - K M Kappagantu
- Department of Otorhinolaryngology and Head and Neck Surgery, All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana, India
| | - N K Singh
- Department of Otorhinolaryngology and Head and Neck Surgery, All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana, India
| | - B Ramamourthy
- Department of Otorhinolaryngology and Head and Neck Surgery, All India Institute of Medical Sciences, Bibinagar, Hyderabad, Telangana, India
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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes. Sci Rep 2023; 13:19207. [PMID: 37932283 PMCID: PMC10628120 DOI: 10.1038/s41598-023-44172-w] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023] Open
Abstract
With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (= NRRL B-65660T = DSM 115933T), Leifsonia virtsii F6_8S_P_1AT (= NRRL B-65661T = DSM 115931T), Leifsonia williamsii F6_8S_P_1BT (= NRRL B-65662T = DSM 115932T), Paenibacillus vandeheii F6_3S_P_1CT (= NRRL B-65663T = DSM 115940T), and Sporosarcina highlanderae F6_3S_P_2T (= NRRL B-65664T = DSM 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Ceth W Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Nitin K Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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7
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Yadava YK, Chaudhary P, Yadav S, Rizvi AH, Kumar T, Srivastava R, Soren KR, Bharadwaj C, Srinivasan R, Singh NK, Jain PK. Genetic mapping of quantitative trait loci associated with drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 2023; 13:17623. [PMID: 37848483 PMCID: PMC10582051 DOI: 10.1038/s41598-023-44990-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Elucidation of the genetic basis of drought tolerance is vital for genomics-assisted breeding of drought tolerant crop varieties. Here, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) derived from a cross between a drought tolerant chickpea variety, Pusa 362 and a drought sensitive variety, SBD 377. The GBS identified a total of 35,502 SNPs and subsequent filtering of these resulted in 3237 high-quality SNPs included in the eight linkage groups. Fifty-one percent of these SNPs were located in the genic regions distributed throughout the genome. The high density linkage map has total map length of 1069 cm with an average marker interval of 0.33 cm. The linkage map was used to identify 9 robust and consistent QTLs for four drought related traits viz. membrane stability index, relative water content, seed weight and yield under drought, with percent variance explained within the range of 6.29%-90.68% and LOD scores of 2.64 to 6.38, which were located on five of the eight linkage groups. A genomic region on LG 7 harbors quantitative trait loci (QTLs) explaining > 90% phenotypic variance for membrane stability index, and > 10% PVE for yield. This study also provides the first report of major QTLs for physiological traits such as membrane stability index and relative water content for drought stress in chickpea. A total of 369 putative candidate genes were identified in the 6.6 Mb genomic region spanning these QTLs. In-silico expression profiling based on the available transcriptome data revealed that 326 of these genes were differentially expressed under drought stress. KEGG analysis resulted in reduction of candidate genes from 369 to 99, revealing enrichment in various signaling pathways. Haplotype analysis confirmed 5 QTLs among the initially identified 9 QTLs. Two QTLs, qRWC1.1 and qYLD7.1, were chosen based on high SNP density. Candidate gene-based analysis revealed distinct haplotypes in qYLD7.1 associated with significant phenotypic differences, potentially linked to pathways for secondary metabolite biosynthesis. These identified candidate genes bolster defenses through flavonoids and phenylalanine-derived compounds, aiding UV protection, pathogen resistance, and plant structure.The study provides novel genomic regions and candidate genes which can be utilized in genomics-assisted breeding of superior drought tolerant chickpea cultivars.
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Affiliation(s)
- Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Pooja Chaudhary
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Aqeel Hasan Rizvi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Tapan Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rachna Srivastava
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - K R Soren
- ICAR-Indian Institute of Pulses Research, Kanpur, 208024, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - R Srinivasan
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India.
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Simpson AC, Tighe S, Wong S, Leo P, Parker C, Chander AM, Williams M, Wu HW, Venkateswaran K, Singh NK. Analysis of Microbiomes from Ultra-Low Biomass Surfaces Using Novel Surface Sampling and Nanopore Sequencing. J Biomol Tech 2023; 34:3fc1f5fe.bac4a5b3. [PMID: 37969875 PMCID: PMC10644977 DOI: 10.7171/3fc1f5fe.bac4a5b3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The rapid assessment of microbiomes from ultra-low biomass environments such as cleanrooms or hospital operating rooms has a number of applications for human health and spacecraft manufacturing. Current techniques often employ lengthy protocols using short-read DNA sequencing technology to analyze amplified DNA and have the disadvantage of a longer analysis time and lack of portability. Here, we demonstrate a rapid (~24 hours) on-site nanopore-based sequencing approach to characterize the microbiome of a NASA Class 100K cleanroom where spacecraft components are assembled. This approach employs a modified protocol of Oxford Nanopore's Rapid PCR Barcoding Kit in combination with the recently developed Squeegee-Aspirator for Large Sampling Area (SALSA) surface sampling device. Results for these ultra-low biomass samples revealed DNA amplification ~1 to 2 orders of magnitude above process control samples and were dominated primarily by Paracoccus and Acinetobacter species. Negative control samples were collected to provide critical data on background contamination, including Cutibacerium acnes, which most likely originated from the sampling reagents-associated microbiome (kitome). Overall, these results provide data on a novel approach for rapid low-biomass DNA profiling using the SALSA sampler combined with modified nanopore sequencing. These data highlight the critical need for employing multiple negative controls, along with using DNA-free reagents and techniques, to enable a proper assessment of ultra-low biomass samples.
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Affiliation(s)
- Anna C. Simpson
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Scott Tighe
- Vermont Integrative GenomicsUniversity of VermontBurlingtonVermont
| | | | - Patrick Leo
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Ceth Parker
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Atul M. Chander
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Michael Williams
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Hao-Wei Wu
- AI Biosciences, Inc.College StationTexas
| | - Kasthuri Venkateswaran
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
| | - Nitin K. Singh
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyBiotechnology and Planetary Protection GroupPasadenaCalifornia91109USA
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Leo P, de Melo Texeira M, Chander AM, Singh NK, Simpson AC, Yurkov A, Karouia F, Stajich JE, Mason CE, Venkateswaran K. Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities. IMA Fungus 2023; 14:15. [PMID: 37568226 PMCID: PMC10422843 DOI: 10.1186/s43008-023-00119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/20/2023] [Indexed: 08/13/2023] Open
Abstract
During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3T, isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1T, isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3T = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1T = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.
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Affiliation(s)
- Patrick Leo
- Department of Environmental Sciences, Informatics and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Mestre, Italy
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'università snc, 01100, Viterbo, Italy
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Marcus de Melo Texeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - Atul M Chander
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Nitin K Singh
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Anna C Simpson
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Fathi Karouia
- Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, PO BOX 1 MS 239/4, Moffett Field, CA, 94035, USA
- Space Research Within Reach, San Francisco, CA, 941110, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of CA-Riverside, Riverside, CA, 92521, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kasthuri Venkateswaran
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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10
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Simpson AC, Sengupta P, Zhang F, Hameed A, Parker CW, Singh NK, Miliotis G, Rekha PD, Raman K, Mason CE, Venkateswaran K. Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station. Res Sq 2023:rs.3.rs-3126314. [PMID: 37461605 PMCID: PMC10350232 DOI: 10.21203/rs.3.rs-3126314/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS). Results The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Conclusions Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10T (=NRRL B-65660T), Leifsonia virtsii, F6_8S_P_1AT (=NRRL B-65661T), Leifsonia williamsii, F6_8S_P_1BT (=NRRL B- 65662T and DSMZ 115932T), Paenibacillus vandeheii, F6_3S_P_1CT(=NRRL B-65663T and DSMZ 115940T), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664T and DSMZ 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
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Affiliation(s)
- Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Flora Zhang
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Asif Hameed
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Punchappady D. Rekha
- Yenepoya Research Centre, Yenepoya Deemed to be University, Mangalore 575018, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Christopher E. Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Gaikwad K, Ramakrishna G, Srivastava H, Saxena S, Kaila T, Tyagi A, Sharma P, Sharma S, Sharma R, Mahla HR, Kumar K, Sv AM, Solanke AU, Kalia P, Rao AR, Rai A, Sharma TR, Singh NK. The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes. Sci Rep 2023; 13:9941. [PMID: 37336893 DOI: 10.1038/s41598-023-33762-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/18/2023] [Indexed: 06/21/2023] Open
Abstract
Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.
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Affiliation(s)
- Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, India.
| | | | | | - Swati Saxena
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Priya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - R Sharma
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
| | - H R Mahla
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Amitha Mithra Sv
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Pritam Kalia
- Division of Vegetable Sciences, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - A R Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - T R Sharma
- DDG (CS), Indian Council of Agricultural Research, New Delhi, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
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Bejoy NB, Singh RK, Singh NK, Pananghat B, Patwari GN. Dynamics of Hydrogen Bond Breaking Induced by Outer-Valence Intermolecular Coulombic Decay. J Phys Chem Lett 2023:5718-5726. [PMID: 37318228 DOI: 10.1021/acs.jpclett.3c01039] [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: 06/16/2023]
Abstract
The photoexcitation of weakly bound complexes can lead to several decay pathways, depending on the nature of the potential energy surfaces. Upon excitation of a chromophore in a weakly bound complex, ionization of its neighbor upon energy transfer can occur due to a unique relaxation process known as intermolecular Coulombic decay (ICD), a phenomenon of renewed focus owing to its relevance in biological systems. Herein, we report the evidence for outer-valence ICD induced by multiphoton excitation by near-ultraviolet radiation of 4.4 eV photons, hitherto unknown in molecular systems. In the binary complexes of 2,6-difluorophenylacetylene with aliphatic amines, a resonant two-photon excitation localized on the 2,6-difluorophenylacetylene chromophore results in the formation of an amine cation following an outer-valence ICD process. The unique trends in experimentally observed translational energy distribution profiles of the amine cations following hydrogen bond dissociation, analyzed with the help of electronic structure and ab initio molecular dynamics calculations, revealed the presence of a delicate interplay of roaming dynamics, methyl-rotor dynamics, and binding energy.
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Affiliation(s)
- Namitha Brijit Bejoy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Reman Kumar Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nitin K Singh
- Indian Institute of Science Education and Research (IISER) Mohali, S. A. S Nagar, Mohali 140306, India
| | - Balanarayan Pananghat
- Indian Institute of Science Education and Research (IISER) Mohali, S. A. S Nagar, Mohali 140306, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Simpson AC, Eedara VVR, Singh NK, Damle N, Parker CW, Karouia F, Mason CE, Venkateswaran K. Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station. Front Microbiol 2023; 14:1166013. [PMID: 37396358 PMCID: PMC10308117 DOI: 10.3389/fmicb.2023.1166013] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1T. The 16S sequence of the F6_2S_P_1T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1T are anteiso-C15:0 (51.7%), iso-C16:0 (23.1%), and iso-C15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1T (=NRRL B-65657T and DSMZ 115098T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1T, C. rhizosphaerae, and C. ginsengisoli, along with two uncharacterized Cohnella strains, possess a shared set of 332 gene clusters which are not shared with any other WGS of Cohnella species, and form a distinct clade branching off from C. nanjingensis. Functional traits were predicted for the genomes of strain F6_2S_P_1T and other members of this clade.
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Affiliation(s)
- Anna C. Simpson
- California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States
| | - V. V. Ramprasad Eedara
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Nitin K. Singh
- California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States
| | - Namita Damle
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Ceth W. Parker
- California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States
| | | | - Christopher E. Mason
- Department of Physiology and Biophysics, and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- California Institute of Technology, Jet Propulsion Laboratory, Pasadena, CA, United States
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14
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Singh NK, Wood JM, Patane J, Moura LMS, Lombardino J, Setubal JC, Venkateswaran K. Characterization of metagenome-assembled genomes from the International Space Station. Microbiome 2023; 11:125. [PMID: 37264385 DOI: 10.1186/s40168-023-01545-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the microbial population. However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics. RESULTS In total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP generated 26 MAGs. Among 46 MAGs retrieved, 18 bacterial species were identified, including one novel genus/species combination (Kalamiella piersonii) and one novel bacterial species (Methylobacterium ajmalii). In addition, four bins exhibited fungal genomes; this is the first-time fungal genomes were assembled from ISS metagenomes. Phylogenetic analyses of five bacterial species showed ISS-specific evolution. The genes pertaining to cell membranes, such as transmembrane transport, cell wall organization, and regulation of cell shape, were enriched. Variations in the antimicrobial-resistant (AMR) and virulence genes of the selected 20 MAGs were characterized to predict the ecology and evolution of biosafety level (BSL) 2 microorganisms in space. Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. Among these 20 MAGs characterized, AMR genes were more prevalent in the Enterobacter bugandensis MAG, which has been predominantly isolated from clinical samples. MAGs were further used to analyze if genes involved in AMR and biofilm formation of viable microbes in ISS have variation due to generational evolution in microgravity and radiation pressure. CONCLUSIONS Comparative analyses of MAGs and whole-genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. The Pantoea/Kalamiella strains have the maximum single-nucleotide polymorphisms found within the ISS strains examined. This may suggest that Pantoea/Kalamiella strains are much more subjective to microgravity changes. The reconstructed genomes will enable researchers to study the evolution of genomes under microgravity and low-dose irradiation compared to the evolution of microbes here on Earth. Video Abstract.
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Affiliation(s)
- Nitin K Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Jason M Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Jose Patane
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Livia Maria Silva Moura
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jonathan Lombardino
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA.
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15
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Saxena A, Dariya SS, Chandra KP, Patil A, Kumar D, Gupta M, Singh NK, Patni B, Sheohara R, Meenakshisundaram L, Hiramath VS, Maheshwari A, Aslam M, Surajeet SK. LDL cholesterol an unmet target in diabetic, hypertensive population pan India exposing susceptive cardiovascular disorder risk. Eur Heart J 2023. [DOI: 10.1093/eurheartj/ehac779.102] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: None.
Background
Management and pathophysiology of diabetes and hypertension has always been the centre of research, with new insights being found consistently. CVD is the major cause of mortality in patients with type 2 diabetes and affects approximately 32.2% of people with type 2 diabetes. Southeast Asia stands out with a higher prevalence of CAD (29.4%) compared with other regions.
Purpose
The purpose of this EHR based real world study was to identify the proportion of patients with LDL-C out of control in people living with diabetes and hypertension who were under regular care of physicians. Specialized clinical care by super-specialists ensures management of specific disorders, yet risk factors for overall cardiovascular health continue to be expressed uncontrolled.
Methods
Patients reporting for routine care in 14 centers across the country were eligible to participate in the study. Patient recruitment at each site required informed consent signature, history of at least 6 months of diabetes mellitus type 2, was sequential and independent of other sites. An EMR (Medeva) integrated research proforma was created only for this study which collected data on medical history, comorbidities, diabetic complications, medications and laboratory values of relevance to the study. The recruitment started in March 2022 and ended in August 2022 (6 months).
Results
Average age of these patients was 54.36 years, and 1238 were male and 964 were female patients. Out of this sample, 1388 patients were only diabetic and 814 patients had diabetes as well as hypertension. 256 patients 44.8% patients had LDL-C within acceptable limits and the remaining 51.2% had hyperdyslipidemia. Average LDL-C value for all patients was 107.07, average LDL-C levels in only diabetic patients was 116.51, and LDL in patients with diabetes and hypertension is 90.97. In diabetes only patients, 37% patients had LDL-C under control whereas in diabetes and hypertension group 58% patients had LDL-C under control.
Conclusion
Although diabetic patients are under regular clinical care, their LDL-C values were higher in 55.2% of the patients. This is an alarming signal that calls all the stakeholders - diabetologists, researchers, educators, dieticians, policymakers, government agencies and people with diabetes must contribute towards the management of lipid profile for prevention of cardiovascular events. Also, the proportion of patients with LDL-C under control is lesser in patients who are only diabetic as compared to patients who are both diabetic and hypertensive. This finding suggests that there is either lesser focus or inadequate on lipid profile of patients who are only diabetic; more holistic management is an unprecedented requirement. More research is needed in this direction to recognize the loopholes, manage them and prevent them adequately.
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Affiliation(s)
- A Saxena
- Diabetes and Heart Center , Ludhiana , India
| | | | - K P Chandra
- Health City Hospital, Gomti Nagar, Medicine , Lucknow , India
| | - A Patil
- ARPAN POLYCLINIC, Diebetology , Mumbai , India
| | - D Kumar
- Harsha Clinic and Diabetes Center, Medicine , Lucknow , India
| | - M Gupta
- Udayaan Health Care, Medicine , Lucknow , India
| | - N K Singh
- Diabetes and Heart Research Center, Diebetology , Dhanbad , India
| | - B Patni
- Shanti Wellness Care, Medicine , Kolkatta , India
| | - R Sheohara
- Madhumeet Diabetes Center, Non Invasive Cardiology, Medicine , Raipur , India
| | | | | | - A Maheshwari
- Hind institute of Medical Science, Professor Medicine , Lucknow , India
| | - M Aslam
- Asian Hospital , Hyderabad , India
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Highlander SK, Wood JM, Gillece JD, Folkerts M, Fofanov V, Furstenau T, Singh NK, Guan L, Seuylemezian A, Benardini JN, Engelthaler DM, Venkateswaran K, Keim PS. Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition. PLoS One 2023; 18:e0282428. [PMID: 36947490 PMCID: PMC10032485 DOI: 10.1371/journal.pone.0282428] [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] [Received: 12/12/2022] [Accepted: 02/14/2023] [Indexed: 03/23/2023] Open
Abstract
The National Aeronautics and Space Administration (NASA) has been monitoring the microbial burden of spacecraft since the 1970's Viking missions. Originally culture-based and then focused 16S sequencing techniques were used, but we have now applied whole metagenomic sequencing to a variety of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools to contrast marker, k-mer, and true alignment approaches. Hierarchical clustering analysis of the data separated vacuum particles from other SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO (International Standards Organization) compliant facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals Cutibacterium acnes and Corynebacterium spp. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particles and SAF samples contained strong signals of the tricarboxylic acid cycle and of amino acid biosynthesis, suggesting that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 samples generated high quality metagenome assembled genomes (MAG), which were dominated by Moraxella osloensis or Malassezia restricta. One M. osloensis MAG was assembled into a single circular scaffold and gene annotated. This study includes a rigorous quantitative determination of microbial loads and a qualitative dissection of microbial composition. Assembly of multiple specimens led to greater confidence for the identification of particular species and their predicted functional roles.
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Affiliation(s)
- Sarah K Highlander
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jason M Wood
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - John D Gillece
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Megan Folkerts
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Viacheslav Fofanov
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Tara Furstenau
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Lisa Guan
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Arman Seuylemezian
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - James N Benardini
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - David M Engelthaler
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Paul S Keim
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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17
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Tierney BT, Singh NK, Simpson AC, Hujer AM, Bonomo RA, Mason CE, Venkateswaran K. Multidrug-resistant Acinetobacter pittii is adapting to and exhibiting potential succession aboard the International Space Station. Microbiome 2022; 10:210. [PMID: 36503581 PMCID: PMC9743659 DOI: 10.1186/s40168-022-01358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/11/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND Monitoring the adaptation of microorganisms to the extreme environment of the International Space Station (ISS) is crucial to understanding microbial evolution and infection prevention. Acinetobacter pittii is an opportunistic nosocomial pathogen, primarily impacting immunocompromised patients, that was recently isolated from two missions aboard the ISS. RESULTS Here, we report how ISS-associated A. pittii (n = 20 genomes) has formed its own genetically and functionally discrete clade distinct from most Earth-bound isolates (n = 291 genomes). The antimicrobial susceptibility testing of ISS strains and two related clinical isolates demonstrated that ISS strains acquired more resistance, specifically with regard to expanded-spectrum cephalosporins, despite no prediction of increased resistance based on genomic analysis of resistance genes. By investigating 402 longitudinal environmental and host-associated ISS metagenomes, we observed that viable A. pittii is increasing in relative abundance and therefore potentially exhibiting succession, being identified in >2X more metagenomic samples in back-to-back missions. ISS strains additionally contain functions that enable them to survive in harsh environments, including the transcriptional regulator LexA. Via a genome-wide association study, we identified a high level of mutational burden in methionine sulfoxide reductase genes relative to the most closely related Earth strains. CONCLUSIONS Overall, these results indicated a step forward in understanding how microorganisms might evolve and alter their antibiotic resistance phenotype in extreme, resource-limited, human-built environments. Video Abstract.
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Affiliation(s)
- Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Anna C Simpson
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, 44106, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, 44106, USA
- Departments of Biochemistry, Pharmacology, Molecular Biology and Microbiology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, 44106, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA.
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Madrigal P, Singh NK, Wood JM, Gaudioso E, Hernández-Del-Olmo F, Mason CE, Venkateswaran K, Beheshti A. Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome. Microbiome 2022; 10:134. [PMID: 35999570 PMCID: PMC9400218 DOI: 10.1186/s40168-022-01332-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/22/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) has a detrimental impact on human health on Earth and it is equally concerning in other environments such as space habitat due to microgravity, radiation and confinement, especially for long-distance space travel. The International Space Station (ISS) is ideal for investigating microbial diversity and virulence associated with spaceflight. The shotgun metagenomics data of the ISS generated during the Microbial Tracking-1 (MT-1) project and resulting metagenome-assembled genomes (MAGs) across three flights in eight different locations during 12 months were used in this study. The objective of this study was to identify the AMR genes associated with whole genomes of 226 cultivable strains, 21 shotgun metagenome sequences, and 24 MAGs retrieved from the ISS environmental samples that were treated with propidium monoazide (PMA; viable microbes). RESULTS We have analyzed the data using a deep learning model, allowing us to go beyond traditional cut-offs based only on high DNA sequence similarity and extending the catalog of AMR genes. Our results in PMA treated samples revealed AMR dominance in the last flight for Kalamiella piersonii, a bacteria related to urinary tract infection in humans. The analysis of 226 pure strains isolated from the MT-1 project revealed hundreds of antibiotic resistance genes from many isolates, including two top-ranking species that corresponded to strains of Enterobacter bugandensis and Bacillus cereus. Computational predictions were experimentally validated by antibiotic resistance profiles in these two species, showing a high degree of concordance. Specifically, disc assay data confirmed the high resistance of these two pathogens to various beta-lactam antibiotics. CONCLUSION Overall, our computational predictions and validation analyses demonstrate the advantages of machine learning to uncover concealed AMR determinants in metagenomics datasets, expanding the understanding of the ISS environmental microbiomes and their pathogenic potential in humans. Video Abstract.
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Affiliation(s)
- Pedro Madrigal
- Jeffrey Cheah Biomedical Centre, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Present Address: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK.
| | - Nitin K Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Jason M Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Elena Gaudioso
- Department of Artificial Intelligence, Computer Science School, Universidad Nacional de Educación a Distancia (UNED), 28040, Madrid, Spain
| | - Félix Hernández-Del-Olmo
- Department of Artificial Intelligence, Computer Science School, Universidad Nacional de Educación a Distancia (UNED), 28040, Madrid, Spain
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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Malik A, Kumar A, Ellur RK, Krishnan S G, Dixit D, Bollinedi H, Vinod KK, Nagarajan M, Bhowmick PK, Singh NK, Singh AK. Molecular mapping of QTLs for grain dimension traits in Basmati rice. Front Genet 2022; 13:932166. [PMID: 35983411 PMCID: PMC9379801 DOI: 10.3389/fgene.2022.932166] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Basmati rice is known for its extra-long slender grains, exceptional kernel dimensions after cooking, high volume expansion, and strong aroma. Developing high yielding Basmati rice varieties with good cooking quality is a gigantic task. Therefore, identifying the genomic regions governing the grain and cooked kernel dimension traits is of utmost importance for its use in marker-assisted breeding. Although several QTLs governing grain dimension traits have been reported, limited attempts have been made to map QTLs for grain and cooked kernel dimension traits of Basmati rice. In the current study, a population of recombinant inbred lines (RIL) was generated from a cross of Sonasal and Pusa Basmati 1121 (PB1121). In the RIL population, there was a significant positive correlation among the length (RRL: rough rice length, MRL: milled rice length, CKL: cooked kernel length) and breadth (RRB: rough rice breadth, MRB: milled rice breadth and CKB: cooked kernel breadth) of the related traits, while there was significant negative correlation between them. QTL mapping has led to the identification of four major genomic regions governing MRL and CKL. Two QTLs co-localize with the earlier reported major gene GS3 and a QTL qGRL7.1, while the remaining two QTLs viz., qCKL3.2 (qMRL3.2) and qCKL4.1 (qMRL4.1) were novel. The QTL qCKL3.2 has been bracketed to a genomic region of 0.78 Mb between the markers RM15247 and RM15281. Annotation of this region identified 18 gene models, of which the genes predicted to encode pentatricopeptides and brassinosteroid insensitive 1-associated receptor kinase 1 precursor may be the putative candidate genes. Furthermore, we identified a novel QTL qKER2.1 governing kernel elongation ratio (KER) in Basmati rice.
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Affiliation(s)
- Ankit Malik
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Aruna Kumar
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India
| | - Gopala Krishnan S
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India
| | - Deepshikha Dixit
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India
| | - Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India
| | - KK Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India
| | - M Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-IARI, Aduthurai, India
| | - PK Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India
| | - NK Singh
- ICAR-National Institute for Plant Biotechnology, IARI, New Delhi, India
| | - AK Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India
- *Correspondence: AK Singh,
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Lombardino J, Bijlani S, Singh NK, Wood JM, Barker R, Gilroy S, Wang CCC, Venkateswaran K. Genomic Characterization of Potential Plant Growth-Promoting Features of Sphingomonas Strains Isolated from the International Space Station. Microbiol Spectr 2022; 10:e0199421. [PMID: 35019675 PMCID: PMC8754149 DOI: 10.1128/spectrum.01994-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 11/20/2022] Open
Abstract
In an ongoing microbial tracking investigation of the International Space Station (ISS), several Sphingomonas strains were isolated. Based on the 16S rRNA gene sequence, phylogenetic analysis identified the ISS strains as Sphingomonas sanguinis (n = 2) and one strain isolated from the Kennedy Space Center cleanroom (used to assemble various Mars mission spacecraft components) as Sphingomonas paucimobilis. Metagenomic sequence analyses of different ISS locations identified 23 Sphingomonas species. An abundance of shotgun metagenomic reads were detected for S. sanguinis in the location from where the ISS strains were isolated. A complete metagenome-assembled genome was generated from the shotgun reads metagenome, and its comparison with the whole-genome sequences (WGS) of the ISS S. sanguinis isolates revealed that they were highly similar. In addition to the phylogeny, the WGS of these Sphingomonas strains were compared with the WGS of the type strains to elucidate genes that can potentially aid in plant growth promotion. Furthermore, the WGS comparison of these strains with the well-characterized Sphingomonas sp. LK11, an arid desert strain, identified several genes responsible for the production of phytohormones and for stress tolerance. Production of one of the phytohormones, indole-3-acetic acid, was further confirmed in the ISS strains using liquid chromatography-mass spectrometry. Pathways associated with phosphate uptake, metabolism, and solubilization in soil were conserved across all the S. sanguinis and S. paucimobilis strains tested. Furthermore, genes thought to promote plant resistance to abiotic stress, including heat/cold shock response, heavy metal resistance, and oxidative and osmotic stress resistance, appear to be present in these space-related S. sanguinis and S. paucimobilis strains. Characterizing these biotechnologically important microorganisms found on the ISS and harnessing their key features will aid in the development of self-sustainable long-term space missions in the future. IMPORTANCESphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth. This study describes the isolation and identification of Sphingomonas members from the ISS, which are capable of producing the phytohormone indole-3-acetic acid. Microbial production of phytohormones will help future in situ studies, grow plants beyond low earth orbit, and establish self-sustainable life support systems. Beyond phytohormone production, stable genomic elements of abiotic stress resistance, heavy metal resistance, and oxidative and osmotic stress resistance were identified, rendering the ISS Sphingomonas isolate a strong candidate for biotechnology-related applications.
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Affiliation(s)
| | - Swati Bijlani
- University of Southern California, Los Angeles, California, USA
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Jason M. Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Richard Barker
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Simon Gilroy
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Clay C. C. Wang
- University of Southern California, Los Angeles, California, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Bijlani S, Parker C, Singh NK, Sierra MA, Foox J, Wang CCC, Mason CE, Venkateswaran K. Genomic Characterization of the Titan-like Cell Producing Naganishia tulchinskyi, the First Novel Eukaryote Isolated from the International Space Station. J Fungi (Basel) 2022; 8:jof8020165. [PMID: 35205919 PMCID: PMC8875396 DOI: 10.3390/jof8020165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 12/25/2022] Open
Abstract
Multiple strains of a novel yeast belonging to genus Naganishia were isolated from environmental surfaces aboard the International Space Station (ISS). These strains exhibited a phenotype similar to Titan cell (~10 µm diameter) morphology when grown under a combination of simulated microgravity and 5% CO2 conditions. Confocal, scanning, and transmission electron microscopy revealed distinct morphological differences between the microgravity-grown cells and the standard Earth gravity-grown cells, including larger cells and thicker cell walls, altered intracellular morphology, modifications to extracellular fimbriae, budding, and the shedding of bud scars. Phylogenetic analyses via multi-locus sequence typing indicated that these ISS strains represented a single species in the genus Naganishia and were clustered with Naganishia diffluens. The name Naganishia tulchinskyi is proposed to accommodate these strains, with IF6SW-B1T as the holotype. The gene ontologies were assigned to the cell morphogenesis, microtubule-based response, and response to UV light, suggesting a variety of phenotypes that are well suited to respond to microgravity and radiation. Genomic analyses also indicated that the extracellular region, outer membrane, and cell wall were among the highest cellular component results, thus implying a set of genes associated with Titan-like cell plasticity. Finally, the highest molecular function matches included cytoskeletal motor activity, microtubule motor activity, and nuclear export signal receptor activity.
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Affiliation(s)
- Swati Bijlani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; (S.B.); (C.C.C.W.)
| | - Ceth Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
| | - Maria A. Sierra
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA;
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Jonathan Foox
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; (S.B.); (C.C.C.W.)
| | - Christopher E. Mason
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10021, USA;
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
- Correspondence: (C.E.M.); (K.V.); Tel.: +1-(203)-668-1448 (C.E.M.); +1-(818)-393-1481 (K.V.); Fax: +1-(646)-962-00383 (C.E.M.); +1-(818)-393-4176 (K.V.)
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.P.); (N.K.S.)
- Correspondence: (C.E.M.); (K.V.); Tel.: +1-(203)-668-1448 (C.E.M.); +1-(818)-393-1481 (K.V.); Fax: +1-(646)-962-00383 (C.E.M.); +1-(818)-393-4176 (K.V.)
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Parker CW, Teixeira MDM, Singh NK, Raja HA, Cank KB, Spigolon G, Oberlies NH, Barker BM, Stajich JE, Mason CE, Venkateswaran K. Genomic Characterization of Parengyodontium torokii sp. nov., a Biofilm-Forming Fungus Isolated from Mars 2020 Assembly Facility. J Fungi (Basel) 2022; 8:jof8010066. [PMID: 35050006 PMCID: PMC8778116 DOI: 10.3390/jof8010066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
A fungal strain (FJII-L10-SW-P1) was isolated from the Mars 2020 spacecraft assembly facility and exhibited biofilm formation on spacecraft-qualified Teflon surfaces. The reconstruction of a six-loci gene tree (ITS, LSU, SSU, RPB1 and RPB2, and TEF1) using multi-locus sequence typing (MLST) analyses of the strain FJII-L10-SW-P1 supported a close relationship to other known Parengyodontium album subclade 3 isolates while being phylogenetically distinct from subclade 1 strains. The zig-zag rachides morphology of the conidiogenous cells and spindle-shaped conidia were the distinct morphological characteristics of the P. album subclade 3 strains. The MLST data and morphological analysis supported the conclusion that the P. album subclade 3 strains could be classified as a new species of the genus Parengyodontium and placed in the family Cordycipitaceae. The name Parengyodontium torokii sp. nov. is proposed to accommodate the strain, with FJII-L10-SW-P1 as the holotype. The genome of the FJII-L10-SW-P1 strain was sequenced, annotated, and the secondary metabolite clusters were identified. Genes predicted to be responsible for biofilm formation and adhesion to surfaces were identified. Homology-based assignment of gene ontologies to the predicted proteome of P. torokii revealed the presence of gene clusters responsible for synthesizing several metabolic compounds, including a cytochalasin that was also verified using traditional metabolomic analysis.
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Affiliation(s)
- Ceth W. Parker
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.W.P.); (N.K.S.)
| | - Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (M.d.M.T.); (B.M.B.)
- School of Medicine, University of Brasilia, Brasilia 70910-900, Brazil
| | - Nitin K. Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.W.P.); (N.K.S.)
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (H.A.R.); (K.B.C.); (N.H.O.)
| | - Kristof B. Cank
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (H.A.R.); (K.B.C.); (N.H.O.)
| | - Giada Spigolon
- Biological Imaging Facility, California Institute of Technology, Pasadena, CA 91125, USA;
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA; (H.A.R.); (K.B.C.); (N.H.O.)
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (M.d.M.T.); (B.M.B.)
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California—Riverside, Riverside, CA 92521, USA;
| | - Christopher E. Mason
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA; (C.W.P.); (N.K.S.)
- Correspondence: ; Tel.: +1-(818)-393-1481; Fax: +1-(818)-393-4176
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Choudhury DR, Kumar R, S VD, Singh K, Singh NK, Singh R. Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers. Front Genet 2021; 12:726152. [PMID: 34899828 PMCID: PMC8655924 DOI: 10.3389/fgene.2021.726152] [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: 06/16/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.
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Affiliation(s)
| | - Ramesh Kumar
- Division of Genomic Resources, NBPGR, New Delhi, India
| | - Vimala Devi S
- Division of Germplasm Conservation, NBPGR, New Delhi, India
| | | | | | - Rakesh Singh
- Division of Genomic Resources, NBPGR, New Delhi, India
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Singh NK, Lavire C, Nesme J, Vial L, Nesme X, Mason CE, Lassalle F, Venkateswaran K. Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov. Front Microbiol 2021; 12:765943. [PMID: 34938279 PMCID: PMC8685578 DOI: 10.3389/fmicb.2021.765943] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Strains of Agrobacterium genomospecies 3 (i.e., genomovar G3 of the Agrobacterium tumefaciens species complex) have been previously isolated from diverse environments, including in association with plant roots, with algae, as part of a lignocellulose degrading community, from a hospital environment, as a human opportunistic pathogen, or as reported in this study, from a surface within the International Space Station. Polyphasic taxonomic methods revealed the relationship of Agrobacterium G3 strains to other Agrobacterium spp., which supports the description of a novel species. The G3 strains tested (n = 9) were phenotypically distinguishable among the strains from other genomospecies of the genus Agrobacterium. Phylogenetic analyses of the 16S rRNA gene, gyrB gene, multi-locus sequence analysis, and 1,089-gene core-genome gene concatenate concur that tested G3 strains belong to the Agrobacterium genus and they form a clade distinct from other validly described Agrobacterium species. The distinctiveness of this clade was confirmed by average nucleotide identity (ANI) and in silico digital DNA-DNA hybridization (dDDH) comparisons between the G3 tested strains and all known Agrobacterium species type strains, since obtained values were considerably below the 95% (ANI) and 70% (dDDH) thresholds used for the species delineation. According to the core-genome phylogeny and ANI comparisons, the closest relatives of G3 strains were Agrobacterium sp. strains UGM030330-04 and K599, members of a novel genomospecies we propose to call genomovar G21. Using this polyphasic approach, we characterized the phenotypic and genotypic synapomorphies of Agrobacterium G3, showing it is a bona fide bacterial species, well separated from previously named Agrobacterium species or other recognized genomic species. We thus propose the name Agrobacterium tomkonis for this species previously referred to as Agrobacterium genomospecies 3. The type strain of A. tomkonis is IIF1SW-B1T (= LMG 32164 = NRRL B-65602). Comparative genomic analysis show A. tomkonis strains have species-specific genes associated with secretion of secondary metabolites, including an exopolysaccharide and putative adhesins and resistance to copper. A. tomkonis specific gene functions notably relate to surface adhesion and could be involved to colonize nutrient-poor and harsh habitats. The A. tomkonis strains from the ISS showed presence of a 40-kbp plasmid and several other potential mobile genetic elements detected that could also be part of conjugative elements or integrated prophages.
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Affiliation(s)
- Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Céline Lavire
- CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Vial
- CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Xavier Nesme
- CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Florent Lassalle
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Wood JM, Singh NK, Guan L, Seuylemezian A, Benardini JN, Venkateswaran K. Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility. Front Microbiol 2021; 12:685254. [PMID: 34650522 PMCID: PMC8508200 DOI: 10.3389/fmicb.2021.685254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/24/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022] Open
Abstract
NASA planetary protection (PP) requires an assessment of the biological contamination of the potential microbial burden on spacecraft destined to explore planetary bodies that may harbor signs of life, like Mars and Europa. To help meet these goals, the performance of multiple metagenomic pipelines were compared and assessed for their ability to detect microbial diversity of a low-biomass clean room environment used to build spacecraft destined to these planetary bodies. Four vendors were chosen to implement their own metagenomic analysis pipeline on the shotgun sequences retrieved from environmental surfaces in the relevant environments at NASA's Jet Propulsion Laboratory. None of the vendors showed the same microbial profile patterns when analyzing same raw dataset since each vendor used different pipelines, which begs the question of the validity of a single pipeline to be recommended for future NASA missions. All four vendors detected species of interest, including spore-forming and extremotolerant bacteria, that have the potential to hitch-hike on spacecraft and contaminate the planetary bodies explored. Some vendors demonstrated through functional analysis of the metagenomes that the molecular mechanisms for spore-formation and extremotolerance were represented in the data. However, relative abundances of these microorganisms varied drastically between vendor analyses, questioning the ability of these pipelines to quantify the number of PP-relevant microorganisms on a spacecraft surface. Metagenomics offers tantalizing access to the genetic and functional potential of a microbial community that may offer NASA a viable method for microbial burden assays for planetary protection purposes. However, future development of technologies such as streamlining the processing of shotgun metagenome sequence data, long read sequencing, and all-inclusive larger curated and annotated microbial genome databases will be required to validate and translate relative abundances into an actionable assessment of PP-related microbes of interest. Additionally, the future development of machine learning and artificial intelligence techniques could help enhance the quality of these metagenomic analyses by providing more accurate identification of the genetic and functional potential of a microbial community.
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Affiliation(s)
| | | | | | | | | | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Singh NK, Agrawal PK, Gautam A, Pursnani N, Parihar A. Diabetic Dysglycemia During Lockdown an Unsung Journey (DDLJ) - An Online Survey. J Assoc Physicians India 2021; 69:11-12. [PMID: 34472823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- N K Singh
- Director, Diabetes and Heart Research Centre, Dhanbad, Jharkhand;P.G. Department of Medicine, S.N. Medical College, Agra, Uttar Pradesh
| | | | - Ashish Gautam
- Associate Professor, P.G. Department of Medicine, S.N. Medical College, Agra, Uttar Pradesh
| | - Nikhil Pursnani
- Assistant Professor, P.G. Department of Medicine, S.N. Medical College, Agra, Uttar Pradesh
| | - Awantika Parihar
- MBBS student, P.G. Department of Medicine, S.N. Medical College, Agra, Uttar Pradesh
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Danko D, Malli Mohan GB, Sierra MA, Rucker M, Singh NK, Regberg AB, Bell MS, O’Hara NB, Ounit R, Mason CE, Venkateswaran K. Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions. Front Microbiol 2021; 12:608478. [PMID: 34394013 PMCID: PMC8358432 DOI: 10.3389/fmicb.2021.608478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Crewed National Aeronautics and Space Administration (NASA) missions to other solar system bodies are currently being planned. One high-profile scientific focus during such expeditions would be life detection, specifically the discovery of past or present microbial life, if they exist. However, both humans and associated objects typically carry a high microbial burden. Thus, it is essential to distinguish between microbes brought with the expedition and those present on the exploring planets. Modern spacesuits are unique, customized spacecraft which provide protection, mobility and life support to crew during spacewalks, yet they vent, and the mobility of microbes through spacesuits has not been studied. RESULTS To evaluate the microbial colonization of spacesuits, NASA used an Extravehicular Activity swab kit to examine viable microbial populations of 48 samples from spacesuits using both traditional microbiological methods and molecular sequencing methods. The cultivable microbial population ranged from below the detection limit to 9 × 102 colony forming units per 25 cm2 of sample and also significantly varied by the location. The cultivable microbial diversity was dominated by members of Bacillus, Arthrobacter, and Ascomycota. However, 16S rRNA-based viable bacterial burden ranged from 105 to 106 copies per 25 cm2 of sample. Shotgun metagenome sequencing revealed the presence of a diverse microbial population on the spacesuit surfaces, including Curtobacterium and Methylobacterium from across all sets of spacesuits in high abundance. Among bacterial species identified, higher abundance of Cutibacterium acnes, Methylobacterium oryzae, and M. phyllosphaerae reads were documented. CONCLUSION The results of this study provide evidence that identical microbial strains may live on the wrist joint, inner gauntlet, and outer gauntlet of spacesuits. This raises the possibility, but does not confirm that microbial contaminants on the outside of the suits could contaminate planetary science operations unless additional measures are taken. Overall, these data provide the first estimate of microbial distribution associated with spacesuit surfaces, which will help future mission planners develop effective planetary protection strategies.
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Affiliation(s)
- David Danko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Ganesh Babu Malli Mohan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Maria A. Sierra
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Michelle Rucker
- Exploration Mission Planning Office, Johnson Space Center, Houston, TX, United States
| | - Nitin K. Singh
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, Manhattan, NY, United States
| | - Aaron B. Regberg
- Astromaterials Research and Exploration Science Division, Johnson Space Center, Houston, TX, United States
| | - Mary S. Bell
- Jacobs@NASA/Johnson Space Center, Houston, TX, United States
| | - Niamh B. O’Hara
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA, United States
| | - Christopher E. Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Ramakrishna G, Kaur P, Singh A, Yadav SS, Sharma S, Singh NK, Gaikwad K. Comparative transcriptome analyses revealed different heat stress responses in pigeonpea (Cajanus cajan) and its crop wild relatives. Plant Cell Rep 2021; 40:881-898. [PMID: 33837822 DOI: 10.1007/s00299-021-02686-5] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Comparative transcriptome analyses accompanied by biochemical assays revealed high variability in heat stress response in Cajanus species. Among the studied species, C. scarabaeoides was the most thermotolerant followed by C. cajanifolius, C. cajan, and C. acutifolius. Pigeonpea is one of the climate-resilient grain legumes. Though the optimum temperature for cultivated pigeonpea is ~ 25-35 °C, its wild relatives grow in temperatures ranging between 18 and 45 °C. To gain insight into molecular mechanisms responsible for the heat stress tolerance in pigeonpea, we conducted time-series transcriptome analysis of one pigeonpea cultivar (Cajanus cajan) and two wild relatives, Cajanus acutifolius, and Cajanus scarabaeoides subjected to heat stress at 42 ± 2 ºC for 30 min and 3 h. A total of 9521, 12,447, and 5282 identified transcripts were differentially expressed in C. cajan, C. acutifolius, and C. scarabaeoides, respectively. In this study, we observed that a significant number of genes undergo alternative splicing in a species-specific pattern during heat stress. Gene expression profiling analysis, histochemical assay, chlorophyll content, and electrolyte leakage assay showed that C. scarabaeoides has adaptive features for heat stress tolerance. The gene set enrichment analyses of differentially expressed genes in these Cajanus species during heat stress revealed that oxidoreductase activity, transcription factor activity, oxygen-evolving complex, photosystem-II, thylakoid, phenylpropanoid biosynthetic process, secondary metabolic process, and flavonoid biosynthetic process were highly affected. The histochemical assay showed more lipid peroxidation in C. acutifolius compared to other Cajanus species inferring the presence of higher quantities of polyunsaturated fatty acids in the plasma membrane which might have led to severe damage of membrane-bound organelles like chloroplast, and high electrolyte leakage during heat stress. This study paves the way for the identification of candidate genes, which can be useful for the development of thermo-tolerant pigeonpea cultivars.
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Affiliation(s)
- G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Parampreet Kaur
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- School of Organic Farming, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Anupam Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Sunishtha S Yadav
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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Bijlani S, Singh NK, Eedara VVR, Podile AR, Mason CE, Wang CCC, Venkateswaran K. Methylobacterium ajmalii sp. nov., Isolated From the International Space Station. Front Microbiol 2021; 12:639396. [PMID: 33790880 PMCID: PMC8005752 DOI: 10.3389/fmicb.2021.639396] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 12/08/2020] [Accepted: 02/22/2021] [Indexed: 11/22/2022] Open
Abstract
Four strains belonging to the family of Methylobacteriaceae were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three were identified as Gram-negative, rod-shaped, catalase-positive, oxidase-positive, motile bacteria, designated as IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, whereas the fourth was identified as Methylorubrum rhodesianum. The sequence similarity of these three ISS strains, designated as IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, was <99.4% for 16S rRNA genes and <97.3% for gyrB gene, with the closest being Methylobacterium indicum SE2.11T. Furthermore, the multi-locus sequence analysis placed these three ISS strains in the same clade of M. indicum. The average nucleotide identity (ANI) values of these three ISS strains were <93% and digital DNA-DNA hybridization (dDDH) values were <46.4% with any described Methylobacterium species. Based on the ANI and dDDH analyses, these three ISS strains were considered as novel species belonging to the genus Methylobacterium. The three ISS strains showed 100% ANI similarity and dDDH values with each other, indicating that these three ISS strains, isolated during various flights and from different locations, belong to the same species. These three ISS strains were found to grow optimally at temperatures from 25 to 30°C, pH 6.0 to 8.0, and NaCl 0 to 1%. Phenotypically, these three ISS strains resemble M. aquaticum and M. terrae since they assimilate similar sugars as sole carbon substrate when compared to other Methylobacterium species. Fatty acid analysis showed that the major fatty acid produced by the ISS strains are C18:1−ω7c and C18:1−ω6c. The predominant quinone was ubiquinone 10, and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and an unidentified lipid. Therefore, based on genomic, phylogenetic, biochemical, and fatty acid analyses, strains IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, are assigned to a novel species within the genus Methylobacterium, and the name Methylobacterium ajmalii sp. nov. is proposed. The type strain is IF7SW-B2T (NRRL B-65601T and LMG 32165T).
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Affiliation(s)
- Swati Bijlani
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - V V Ramprasad Eedara
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Appa Rao Podile
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Christopher E Mason
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Singh AK, Bhol S, Singh NK, Kumar MS, Kakti A, Madhumitha M. Assessment of Remineralization Capacity of Various Remineralizing Agents on Artificial Enamel Lesions Using Confocal Laser Scanning Microscope: An In Vitro Study. J Contemp Dent Pract 2021; 22:237-241. [PMID: 34210921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
AIM AND OBJECTIVE The present study aimed at evaluating the effectiveness of diverse remineralizing agents on artificial enamel lesion using confocal laser scanning microscope (CLSM). MATERIALS AND METHODS Totally 80 mandibular premolars which were single rooted were included. All teeth were suspended in a demineralizing solution to create artificial enamel lesions on the exposed enamel. The samples were separated randomly into four groups (20 each) depending on the application of the remineralizing agents as follows: group 1: control; group 2: calcium sucrose phosphate (CaSP); group 3: fluoride varnish; and group 4: casein phosphopeptides-amorphous calcium phosphate (CPP-ACP). The samples in individual group were treated with the corresponding remineralizing agent (except for the control group) two times a day for 14 days. The experimental and control groups were exposed to CLSM assessment to analyze the data of remineralization and demineralization. RESULTS The mean depth of remineralization of fluoride varnish group was slightly more compared to other groups. The highest mean depth of remineralization was found in the fluoride varnish group (122.26 ± 0.28) followed by CaSP (110.58 ± 1.34), CPP-ACP (107.08 ± 0.48), and control (157.78 ± 0.46) groups. The different comparisons among the remineralization material groups showed a statistically significant difference (p < 0.05) in almost all groups except group 2 vs group 4. CONCLUSION This study concluded that improved remineralization of artificial enamel lesion could be achieved with the fluoride varnish group when compared to the CaSP and CPP-ACP groups. CLINICAL SIGNIFICANCE Remineralization as a treatment technique has received a lot of consideration from clinicians. The process of remineralization and demineralization is considered an active process categorized by the movement of calcium and phosphate in and out of the enamel. Presently, the attention has changed toward increasing the resistance of the tooth by applying remineralizing agents topically, which has led to the notable fall in dental caries.
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Affiliation(s)
- Abhinav K Singh
- Department of Conservative Dentistry and Endodontics, Buddha Institute of Dental Sciences and Hospital, Patna, Bihar, India, Phone: +91 9576969374, e-mail:
| | - Subhasmita Bhol
- Department of Pedodontics, Hi-Tech Dental College and Hospital, Bhubaneswar, Odisha, India
| | - Nitin K Singh
- Department of Conservative Dentistry and Endodontics, Kalka Dental College and Hospital, Meerut, Uttar Pradesh, India
| | - Mayakkannan Senthil Kumar
- Department of Pedodontics and Preventive Dentistry, RVS Dental College and Hospital, Coimbatore, Tamil Nadu, India
| | - Ateet Kakti
- Pediatric Dentistry, Preventive Department, Riyadh Elm University, Riyadh, Kingdom of Saudi Arabia
| | - Mohanraj Madhumitha
- Department of Pedodontics and Preventive Dentistry, RVS Dental College and Hospital, Coimbatore, Tamil Nadu, India
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Shekhar H, Kant G, Tripathi R, Sharma S, Mani A, Singh NK, Srivastava S. Structural insight of two 4-Coumarate CoA ligase ( 4CL) isoforms in Leucaena suggests targeted genetic manipulations could lead to better lignin extractability from the pulp. 3 Biotech 2020; 10:383. [PMID: 32802725 DOI: 10.1007/s13205-020-02375-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/31/2020] [Indexed: 11/26/2022] Open
Abstract
4-Coumarate: coenzyme A ligase (4CL) is a key enzyme involved in the early steps of the monolignol biosynthetic pathway. It is hypothesized to modulate S and G monolignol content in the plant. Lignin removal is imperative to the paper industry and higher S/G ratio governs better extractability of lignin and economics of the pulping process. This background prompted us to predict 3D structure of two isoforms of 4CL in Leucaena leucocephala and evaluate their substrate preferences. The 3D structure of Ll4CL1 and Ll4CL2 protein were created by homology modeling and further refined by loop refinement. Molecular docking studies suggested differential substrate preferences of both the isoforms. Ll4CL1 preferred sinapic acid (- 4.91 kcal/mole), ferulic acid (- 4.84 kcal/mole), hydroxyferulic acid (- 4.72 kcal/mole), and caffeic acid (- 4.71 kcal/mole), in their decreasing order. Similarly, Ll4CL2 preferred caffeic acid (- 6.56 kcal/mole, 4 H bonds), hydroxyferulic acid (- 6.56 kcal/mole, 3 H bonds), and ferulic acid (- 6.32 kcal/mole) and sinapic acid (- 5.00 kcal/mole) in their decreasing order. Further, active site residues were identified in both the isoforms and in silico mutation and docking analysis was performed. Our analysis suggested that ASP228, TYR262, and PRO326 for Ll4CL1 and SER165, LYS247 and PRO315 for Ll4CL2 were important for their functional activity. Based on differential substrate preferences of the two isoforms, as a first step towards genetically modified Leuaena having the desired phenotype, it can be proposed that over-expression of Ll4CL1 gene and/or down-regulation of Ll4CL2 gene could yield higher S/G ratio leading to better extractability of lignin.
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Affiliation(s)
- Himanshu Shekhar
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004 India
| | - Gaurav Kant
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004 India
| | - Rahul Tripathi
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004 India
| | - Shivesh Sharma
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004 India
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004 India
| | - N K Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004 India
| | - Sameer Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, 211004 India
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Urbaniak C, Wong S, Tighe S, Arumugam A, Liu B, Parker CW, Wood JM, Singh NK, Skorupa DJ, Peyton BM, Jenson R, Karouia F, Dragon J, Venkateswaran K. Validating an Automated Nucleic Acid Extraction Device for Omics in Space Using Whole Cell Microbial Reference Standards. Front Microbiol 2020; 11:1909. [PMID: 32973700 PMCID: PMC7472602 DOI: 10.3389/fmicb.2020.01909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 11/13/2022] Open
Abstract
NASA has made great strides in the past five years to develop a suite of instruments for the International Space Station in order to perform molecular biology in space. However, a key piece of equipment that has been lacking is an instrument that can extract nucleic acids from an array of complex human and environmental samples. The Omics in Space team has developed the μTitan (simulated micro(μ) gravity tested instrument for automated nucleic acid) system capable of automated, streamlined, nucleic acid extraction that is adapted for use under microgravity. The μTitan system was validated using a whole cell microbial reference (WCMR) standard comprised of a suspension of nine bacterial strains, titrated to concentrations that would challenge the performance of the instrument, as well as to determine the detection limits for isolating DNA. Quantitative assessment of system performance was measured by comparing instrument input challenge dose vs recovery by Qubit spectrofluorometry, qPCR, Bioanalyzer, and Next Generation Sequencing. Overall, results indicate that the μTitan system performs equal to or greater than a similar commercially available, earth-based, automated nucleic acid extraction device. The μTitan system was also tested in Yellowstone National Park (YNP) with the WCMR, to mimic a remote setting, with limited resources. The performance of the device at YNP was comparable to that in a laboratory setting. Such a portable, field-deployable, nucleic extraction system will be valuable for environmental microbiology, as well as in health care diagnostics.
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Affiliation(s)
- Camilla Urbaniak
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Season Wong
- AI Biosciences, College Station, TX, United States
| | - Scott Tighe
- University of Vermont, Burlington, VT, United States
| | | | - Bo Liu
- AI Biosciences, College Station, TX, United States
| | - Ceth W Parker
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Jason M Wood
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K Singh
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | | | | | | | - Fathi Karouia
- NASA Ames Research Center, Moffett Field, CA, United States
| | - Julie Dragon
- University of Vermont, Burlington, VT, United States
| | - Kasthuri Venkateswaran
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Mhatre S, Singh NK, Wood JM, Parker CW, Pukall R, Verbarg S, Tindall BJ, Neumann-Schaal M, Venkateswaran K. Description of Chloramphenicol Resistant Kineococcus rubinsiae sp. nov. Isolated From a Spacecraft Assembly Facility. Front Microbiol 2020; 11:1957. [PMID: 32973710 PMCID: PMC7472656 DOI: 10.3389/fmicb.2020.01957] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 07/24/2020] [Indexed: 11/13/2022] Open
Abstract
A Gram-positive, coccoid, motile, aerobic bacterium, designated strain B12T was isolated from a Jet Propulsion Laboratory spacecraft assembly cleanroom, Pasadena, CA, United States. Strain B12T was resistant to chloramphenicol (100 μg/mL), and is a relatively slow grower (3-5 days optimal). Strain B12T was found to grow optimally at 28 to 32°C, pH 7 to 8, and 0.5% NaCl. Fatty acid methyl ester analysis showed that the major fatty acid of the strain B12T was anteiso C15 : 0 (66.3%), which is also produced by other Kineococcus species. However, arachidonic acid (C20 : 4 ω6,9,12,16c) was present in strain B12T and Kineococcus glutinatus YIM 75677T but absent in all other Kineococcus species. 16S rRNA analysis revealed that strain B12T was 97.9% similar to Kineococcus radiotolerans and falls within the Kineococcus clade. Low 16S rRNA gene sequence similarities (<94%) with other genera in the family Kineosporiaceae, including Angustibacter (93%), Kineosporia (94% to 95%), Pseudokineococcus (93%), Quadrisphaera (93%), and Thalassiella (94%) demonstrated that the strain B12T does not belong to these genera. Phylogenetic analysis of the gyrB gene show that all known Kineococcus species exhibited <86% sequence similarity with B12T. Multi-locus sequence and whole genome sequence analyses confirmed that B12T clades with other Kineococcus species. Average nucleotide identity of strain B12T were 75-78% with other Kineococcus species, while values ranged from 72-75% with species from other genera within family Kineosporiaceae. Average amino-acid identities were 66-72% with other Kineococcus species, while they ranged from 50-58% with species from other genera. The dDDH comparison of strain B12T genome with members of genera Kineococcus showed 20-22% similarity, again demonstrating that B12T is distantly related to other members of the genus. Furthermore, analysis of whole proteome deduced from WGS places strain B12T in order Kineosporiales, confirming that strain B12T is a novel member of family Kineosporiaceae. Based on these analyses and other genome characteristics, strain B12T is assigned to a novel species within the genus Kineococcus, and the name Kineococcus rubinsiae sp. nov., is proposed. The type strain is B12T (=FJII-L1-CM-PAB2T; NRRL B-65556T, DSM 110506T).
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Affiliation(s)
- Snehit Mhatre
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Jason M. Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Susanne Verbarg
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Singh NK, Bhattacharya R, Borrok DM. A Bayesian framework to unravel food, groundwater, and climate linkages: A case study from Louisiana. PLoS One 2020; 15:e0236757. [PMID: 32730317 PMCID: PMC7392305 DOI: 10.1371/journal.pone.0236757] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/12/2020] [Indexed: 11/19/2022] Open
Abstract
Advancing our understanding of the connections among groundwater, food, and climate is critical to meet global food demands while optimizing water resources usage. However, our understanding of the linkages among groundwater, food, and climate is still limited. Here, we offer a Bayesian framework to simulate crop yield at a regional scale and quantify its relationships and associated uncertainty with climate, groundwater, agricultural, and energy-related variables. We implemented the framework in the rice-producing regions of Louisiana from 1960-2015. To build a parsimonious model, we used a probability-based variable selection approach to detect the key drivers of rice yield. Rice yield increased, groundwater declined, and area planted declined or did not change over 56yrs. The number of irrigation wells, groundwater level, air temperature, and area planted were found to be the key drivers of rice yield. The regression coefficients showed that rice yield was positively related to groundwater level, and negatively related to area planted and the number of irrigation wells. The limited influence of N fertilizer was noted on rice yield for the period when fertilizer data were available. The inverse relationship between rice yield and area planted pointed to the adaption of efficient crop management practices that maintained or increased yield, despite the decline in area planted. The farmers' ability to install irrigation wells during droughts sustained the yields over long-term but not short-term. This decline in rice yield in response to drought over the short-term might explain the negative relation between yield and irrigation wells. Overall, this work highlighted the uncertainty in relationships between rice yield and key drivers and quantified the intimate connection between food and groundwater. This work may have implications for managing two highly competing commodities (i.e., groundwater and food) in agricultural regions.
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Affiliation(s)
- Nitin K. Singh
- Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
- Geosciences and Geological and Petroleum Engineering, Missouri University of Science and Technology, Rolla, MO, United States of America
| | - Ruchi Bhattacharya
- Earth and Environmental Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - David M. Borrok
- Geosciences and Geological and Petroleum Engineering, Missouri University of Science and Technology, Rolla, MO, United States of America
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Dubey H, Kiran K, Jaswal R, Bhardwaj SC, Mondal TK, Jain N, Singh NK, Kayastha AM, Sharma TR. Identification and characterization of Dicer-like genes in leaf rust pathogen (Puccinia triticina) of wheat. Funct Integr Genomics 2020; 20:711-721. [PMID: 32705366 DOI: 10.1007/s10142-020-00745-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 10/23/2022]
Abstract
Puccinia triticina (P. triticina) is one of the most devastating fungal pathogens of wheat which causes significant annual yield loss to the crop. Understanding the gene regulatory mechanism of the biotrophic pathogen is one of the important aspects of host-pathogen interaction studies. Dicer-like genes are considered as important mediators of RNAi-based gene regulation. In this study, we report the presence of three Dicer-like genes (Pt-DCL1, Pt-DCL2, Pt-DCL3) in P. triticina genome identified through computational and biological analyses. Quantitative real-time PCR studies revealed an increase in the expression of these genes in germinating spore stages. Heterologous expression combined with mass spectrometry analysis of Pt-DCL2 confirmed the presence of a canonical Dicer-like gene in P. triticina. Phylogenetic analysis of the Pt-DCLs with the Dicer-like proteins from other organisms showed a distinct cluster of rust pathogens from the order Pucciniales. The results indicated a species-specific duplication of Dicer-like genes within the wheat rust pathogens. This study, for the first time, reports the presence of Dicer-dependent RNAi pathway in P. triticina that may play a role in gene regulatory mechanism of the pathogen during its development. Our study serves as a vital source of information for further RNAi-based molecular studies for better understanding and management of the wheat leaf rust disease.
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Affiliation(s)
- Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India.,School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.,Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, Karnataka, 560035, India
| | - Kanti Kiran
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - Rajdeep Jaswal
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - Subhash C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, 171009, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - Neha Jain
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
| | - Tilak Raj Sharma
- ICAR-National Institute for Plant Biotechnology (formerly ICAR-National Research Centre on Plant Biotechnology), Pusa Campus, New Delhi, 110012, India. .,Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110001, India.
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Kaur P, Jindal S, Yadav B, Yadav I, Mahato A, Sharma P, Kaur S, Gupta OP, Vrána J, Šimková H, Doležel J, Gill BS, Meyer KFX, Khurana JP, Singh NK, Chhuneja P, Singh K. Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat. Mol Biol Rep 2020; 47:1991-2003. [PMID: 32034627 DOI: 10.1007/s11033-020-05295-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/30/2020] [Indexed: 11/26/2022]
Abstract
Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.
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Affiliation(s)
- Parampreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India.
- School of Organic Farming, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Suruchi Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Bharat Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Inderjit Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Ajay Mahato
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Priti Sharma
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - O P Gupta
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | | | - Klaus F X Meyer
- MIPS/IBIS, Helmholtz- Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - J P Khurana
- University of Delhi, South Campus, New Delhi, 110021, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, 141004, India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
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37
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Das A, Nigam D, Junaid A, Tribhuvan KU, Kumar K, Durgesh K, Singh NK, Gaikwad K. Expressivity of the key genes associated with seed and pod development is highly regulated via lncRNAs and miRNAs in Pigeonpea. Sci Rep 2019; 9:18191. [PMID: 31796783 PMCID: PMC6890743 DOI: 10.1038/s41598-019-54340-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 05/02/2018] [Accepted: 10/21/2019] [Indexed: 12/18/2022] Open
Abstract
Non-coding RNA’s like miRNA, lncRNA, have gained immense importance as a significant regulatory factor in different physiological and developmental processes in plants. In an effort to understand the molecular role of these regulatory agents, in the present study, 3019 lncRNAs and 227 miRNAs were identified from different seed and pod developmental stages in Pigeonpea, a major grain legume of Southeast Asia and Africa. Target analysis revealed that 3768 mRNAs, including 83 TFs were targeted by lncRNAs; whereas 3060 mRNA, including 154 TFs, were targeted by miRNAs. The targeted transcription factors majorly belong to WRKY, MYB, bHLH, etc. families; whereas the targeted genes were associated with the embryo, seed, and flower development. Total 302 lncRNAs interact with miRNAs and formed endogenous target mimics (eTMs) which leads to sequestering of the miRNAs present in the cell. Expression analysis showed that notably, Cc_lncRNA-2830 expression is up-regulated and sequestrates miR160h in pod leading to higher expression of the miR160h target gene, Auxin responsive factor-18. A similar pattern was observed for SPIKE, Auxin signaling F-box-2, Bidirectional sugar transporter, and Starch synthetase-2 eTMs. All the identified target mRNAs code for transcription factor and genes are involved in the processes like cell division, plant growth and development, starch synthesis, sugar transportation and accumulation of storage proteins which are essential for seed and pod development. On a combinatorial basis, our study provides a lncRNA and miRNA based regulatory insight into the genes governing seed and pod development in Pigeonpea.
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Affiliation(s)
- Antara Das
- ICAR- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Deepti Nigam
- ICAR- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Alim Junaid
- ICAR- National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - Kuldeep Kumar
- ICAR- National Research Centre on Plant Biotechnology, New Delhi, India
| | | | - N K Singh
- ICAR- National Research Centre on Plant Biotechnology, New Delhi, India
| | - Kishor Gaikwad
- ICAR- National Research Centre on Plant Biotechnology, New Delhi, India.
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38
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Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst 2019; 9:600-608.e4. [PMID: 31629686 DOI: 10.1016/j.cels.2019.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [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: 01/11/2019] [Revised: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.
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Affiliation(s)
- Liu Cao
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, USA
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Tiago Leão
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Robby Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA
| | - Rodolfo A S Benitez
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA
| | - Luke R Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA; Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, CA, USA
| | - Md-Nafiz Hamid
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - James T Morton
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alexander Shlemov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | | | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA
| | - Hosein Mohimani
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA.
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Abstract
Groundwater depletion in many areas of the world has been broadly attributed to irrigation. However, more formal, data-driven, causal mechanisms of long-term groundwater patterns have not been assessed. Here, we conducted the first Granger causality analysis to identify the “causes” of groundwater patterns using the rice-producing parishes of Louisiana, USA, as an example. Trend analysis showed a decline of up to 6 m in groundwater level over 51 years. We found that no single cause explained groundwater patterns for all parishes. Causal linkages were noted between groundwater and area harvested, number of irrigation wells, summer precipitation totals, and drought. Bi-directional linkages were noted between groundwater and rice yield, suggesting feedback between both time series. Causal linkages were absent between groundwater and many drivers where significant correlations were noted, highlighting the importance of using robust causal relationships over illusive correlations to detect the cause. These results advance our understanding of groundwater dynamics and can reveal a key connection between food and groundwater.
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Affiliation(s)
- Nitin K Singh
- Geosciences and Geological and Petroleum Engineering, Missouri University of Science and Technology, Rolla, MO, 65409, USA.
| | - David M Borrok
- Geosciences and Geological and Petroleum Engineering, Missouri University of Science and Technology, Rolla, MO, 65409, USA
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40
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Kumar P, Singh NK, Gargeshwari A, S R, Jha R. Changes in middle ear transmission characteristics secondary to altered bone remodelling. Osteoporos Int 2019; 30:863-870. [PMID: 30652218 DOI: 10.1007/s00198-019-04834-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/02/2019] [Indexed: 12/12/2022]
Abstract
UNLABELLED Alteration in the process of bone remodelling results in conditions like osteopenia and osteoporosis in which the bones become susceptible to fracture. The functioning of middle ear bones in such individuals were assessed in this study and it was found that the middle ear bones are equally susceptible to micro-fractures and can cause reduction in the transmission of sound energy. INTRODUCTION Alteration in the process of bone remodelling or increase in the number of osteoclasts cells as it occurs in osteoporosis and osteopenia are likely to affect the middle ear bones in the same way it affects the skeletal bones. Whether these micro-structural changes occurring at the level of the middle ear secondary to altered bone remodelling cause any significant impairment in its functioning is not explored. Thus, the present study aimed at assessing the different aspects of middle ear functioning in individuals with reduced BMD. METHODS The study included 25 normal, 39 osteopenic and 40 osteoporotic participants. The participants underwent pure-tone audiometry, otoscopic examination, conventional immittance evaluation using a 226 Hz probe tone, multi-component and multi-frequency tympanometry and acoustic reflex threshold testing. None of the participants had any current or previous history of middle ear effusion. RESULTS A significantly higher proportion of participants in the clinical group had hearing loss compared to the normal group. The clinical group participants also had reduced middle ear resonance frequency, elevated static compliance values and elevated or absent acoustic reflexes compared to the normal participants. There was no difference among the three groups for the proportion of participants having conductive hearing loss. CONCLUSIONS There is a detrimental impact of reduction in bone mineral density on middle ear transmission characteristics which may go unnoticed initially. Treatment of osteoporosis may potentially mitigate hearing loss from middle ear fractures due to reduced bone mineral density. Absence of significant air-bone gap with the presence of reduced middle ear resonance frequency may be early signs of reduced BMD.
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Affiliation(s)
- P Kumar
- Department of Audiology, All India Institute of Speech and Hearing, Manasagangothri, Mysore, Karnataka, 570006, India
| | - N K Singh
- Department of Audiology, All India Institute of Speech and Hearing, Manasagangothri, Mysore, Karnataka, 570006, India
| | - A Gargeshwari
- Department of Audiology, All India Institute of Speech and Hearing, Manasagangothri, Mysore, Karnataka, 570006, India
| | - R S
- Manasa Orthopaedic Centre, Manasagangothri, Mysore, 570006, India
| | - R Jha
- Department of Audiology, All India Institute of Speech and Hearing, Manasagangothri, Mysore, Karnataka, 570006, India.
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Goel S, Singh K, Singh B, Grewal S, Dwivedi N, Alqarawi AA, Abd Allah EF, Ahmad P, Singh NK. Analysis of genetic control and QTL mapping of essential wheat grain quality traits in a recombinant inbred population. PLoS One 2019; 14:e0200669. [PMID: 30840619 PMCID: PMC6402682 DOI: 10.1371/journal.pone.0200669] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 07/13/2018] [Accepted: 02/04/2019] [Indexed: 11/17/2022] Open
Abstract
Wheat cultivars are genetically crossed to improve end-use quality for traits as per demands of baking industry and broad consumer preferences. The processing and baking qualities of bread wheat are influenced by a variety of genetic make-ups, environmental factors and their interactions. Two wheat cultivars, WL711 and C306, derived recombinant inbred lines (RILs) with a population of 206, were used for phenotyping of quality-related traits. The genetic analysis of quality traits showed considerable variation for measurable quality traits, with normal distribution and transgressive segregation across the years. From the 206 RILs, few RILs were found to be superior to those of the parental cultivars for key quality traits, indicating their potential use for the improvement of end-use quality and suggesting the probability of finding new alleles and allelic combinations from the RIL population. Mapping analysis identified 38 putative QTLs for 13 quality-related traits, with QTLs explaining 7.9-16.8% phenotypic variation spanning over 14 chromosomes, i.e., 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4A, 4B, 4D, 5D, 6A, 7A and 7B. In-silico analysis based on homology to the annotated wheat genes present in database, identified six putative candidate genes within QTL for total grain protein content, qGPC.1B.1 region. Major QTL regions for other quality traits such as TKW have been identified on 1B, 2A, and 7A chromosomes in the studied RIL population. This study revealed the importance of the combination of stable QTLs with region-specific QTLs for better phenotyping, and the QTLs presented in our study will be useful for the improvement of wheat grain and bread-making quality.
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Affiliation(s)
- Sonia Goel
- ICAR-National Research centre on Plant Biotechnology, New Delhi, India
| | - Kalpana Singh
- Water Technology Centre, Indian Agriculture Research Institute, New Delhi, India
| | - Balwant Singh
- ICAR-National Research centre on Plant Biotechnology, New Delhi, India
| | - Sapna Grewal
- ICAR-National Research centre on Plant Biotechnology, New Delhi, India
| | - Neeta Dwivedi
- Water Technology Centre, Indian Agriculture Research Institute, New Delhi, India
| | - Abdulaziz A Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Parvaiz Ahmad
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Botany, S.P. College, Srinagar, Jammu and Kashmir, India
| | - N K Singh
- ICAR-National Research centre on Plant Biotechnology, New Delhi, India
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Reddy A, Garg G, Janardhanan S, Uthappa R, Arora S, Singh NK. An In Vitro Evaluation of Apical Leakage in Gutta-percha/ AH Plus and Resilon/Epiphany-filled Root Canals Using Two Dye Penetration Techniques. J Contemp Dent Pract 2019; 20:152-157. [PMID: 31058628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
AIM Aim of the present study was to evaluate the apical leakage in gutta-percha/AH plus and resilon/epiphany filled root canals using two dye penetration techniques. MATERIALS AND METHODS Sixty freshly extracted human single-rooted teeth were collected. The crown portion of each tooth was sectioned from the cementoenamel junction using a diamond disk. The canals were instrumented using Step back technique up to a caliber of 40. The roots were randomly divided into four experimental groups of 15 sample units each. All the groups are obturated using lateral compaction technique. Samples were placed in India ink and stored in an incubator for 7 days after which they were thoroughly washed under tap water and dried. The roots were divided into longitudinal splitting technique with diamond disks and using clearing technique was checked for linear dye penetration using stereomicroscope. The surfaces were scanned and surfaces with greatest dye penetration were measured by using De winter Biowizard software system. RESULTS The mean leakage for groups I, II, III, and IV are 2.31980, 2.68140, 4.11567, and 4.21047 respectively. One-way ANOVA was applied to the mean leakage scores of different groups, found a significant difference between mean leakage scores. F value of 3.266 and it was found to be significant with a p value of 0.028. Significant differences were obtained for mean comparisons of groups I and III, groups I and IV and groups III and IV. Further, between groups I and II, groups II and III, and groups III and IV no significant differences were observed. CONCLUSION In conclusion, gutta-percha/AH Plus sealed root canals showed lesser leakage than the Resilon Epiphany groups and there was no significant difference in the two different methodologies used for dye penetration. CLINICAL SIGNIFICANCE Tightly adapted endodontic filling material is one of the goals in successful clinical endodontics and Improvements in the adhesive technology have fostered attempts to reduce apical and coronal leakage by bonding to the root canal walls to obtain a solid monoblock.
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Affiliation(s)
- Asha Reddy
- Department of Conservative Dentistry and Endodontics, Sri Balaji Dental College, Moinabad, Telangana, India, Phone: +919676077601, e-mail:
| | - Gaurav Garg
- Department of Restorative Dental Sciences, College of Dentistry, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Sreeja Janardhanan
- Department of Conservative Dentistry and Endodontics, Government Dental College, Alappuzha, Kerala, India
| | - Roshan Uthappa
- Department of Restorative Dental Sciences, College of Dentistry, Majmaah University, Al Zulfi, Kingdom of Saudi Arabia
| | - Suraj Arora
- Department of Restorative Dental Sciences, College of Dentistry, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Nitin K Singh
- Department of Conservative Dentistry and Endodontics, Kalka Dental College and Hospital, Meerut, Uttar Pradesh, India
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Suttles KM, Singh NK, Vose JM, Martin KL, Emanuel RE, Coulston JW, Saia SM, Crump MT. Assessment of hydrologic vulnerability to urbanization and climate change in a rapidly changing watershed in the Southeast U.S. Sci Total Environ 2018; 645:806-816. [PMID: 30032080 DOI: 10.1016/j.scitotenv.2018.06.287] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
This study assessed the combined effects of increased urbanization and climate change on streamflow in the Yadkin-Pee Dee watershed (North Carolina, USA) and focused on the conversion from forest to urban land use, the primary land use transition occurring in the watershed. We used the Soil and Water Assessment Tool to simulate future (2050-2070) streamflow and baseflow for four combined climate and land use scenarios across the Yadkin-Pee Dee River watershed and three subwatersheds. The combined scenarios pair land use change and climate change scenarios together. Compared to the baseline, projected streamflow increased in three out of four combined scenarios and decreased in one combined scenario. Baseflow decreased in all combined scenarios, but decreases were largest in subwatersheds that lost the most forest. The effects of land use change and climate change were additive, amplifying the increases in runoff and decreases in baseflow. Streamflow was influenced more strongly by climate change than land use change. However, for baseflow the reverse was true; land use change tended to drive baseflow more than climate change. Land use change was also a stronger driver than climate in the most urban subwatershed. In the most extreme land use and climate projection the volume of the 1-day, 100 year flood nearly doubled at the watershed outlet. Our results underscore the importance of forests as hydrologic regulators buffering streamflow and baseflow from hydrologic extremes. Additionally, our results suggest that land managers and policy makers need to consider the implications of forest loss on streamflow and baseflow when planning for future urbanization and climate change adaptation options.
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Affiliation(s)
- Kelly M Suttles
- Center for Integrated Forest Science, USDA Forest Service Southern Research Station, Raleigh, NC, United States of America; Department of Forestry and Environmental Resources, North Carolina State University, Campus Box 8008, Raleigh, NC 27695, United States of America.
| | - Nitin K Singh
- Rubenstein School for Environment and Natural Resources, 617 Main Street, The University of Vermont, Burlington, VT, 05405, United States of America; Gund Institute for Environment, The University of Vermont, United States of America
| | - James M Vose
- Center for Integrated Forest Science, USDA Forest Service Southern Research Station, Raleigh, NC, United States of America; Department of Forestry and Environmental Resources, North Carolina State University, Campus Box 8008, Raleigh, NC 27695, United States of America
| | - Katherine L Martin
- Department of Forestry and Environmental Resources, North Carolina State University, Campus Box 8008, Raleigh, NC 27695, United States of America; Center for Geospatial Analytics, North Carolina State University, United States of America
| | - Ryan E Emanuel
- Department of Forestry and Environmental Resources, North Carolina State University, Campus Box 8008, Raleigh, NC 27695, United States of America; Center for Geospatial Analytics, North Carolina State University, United States of America
| | - John W Coulston
- Forest Inventory and Analysis Program, USDA Forest Service Southern Research Station, 1710 Research Center Drive, Blacksburg, VA 24060-6349, United States of America
| | - Sheila M Saia
- Center for Integrated Forest Science, USDA Forest Service Southern Research Station, Raleigh, NC, United States of America; Department of Forestry and Environmental Resources, North Carolina State University, Campus Box 8008, Raleigh, NC 27695, United States of America
| | - Michael T Crump
- Mark Twain National Forest, USDA Forest Service, 401 Fairgrounds Road, Rolla, MO 65401, United States of America
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Junaid A, Kumar H, Rao AR, Patil AN, Singh NK, Gaikwad K. Unravelling the epigenomic interactions between parental inbreds resulting in an altered hybrid methylome in pigeonpea. DNA Res 2018; 25:361-373. [PMID: 29566130 PMCID: PMC6105106 DOI: 10.1093/dnares/dsy008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/21/2018] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation. Identification of differentially methylated regions (DMRs) in the sterile and fertile parent revealed remarkable differences between their methylation patterns. Investigation of methylation status of parental DMRs in hybrid revealed non-additive methylation patterns resulting from trans-chromosomal methylation and trans-chromosomal demethylation events. Furthermore, we discovered several DMRs negatively associated with gene expression in the hybrid and fertile parent. Interestingly, many of those DMRs belonged to transposable elements and genes encoding pentatricopeptide repeats associated proteins, which may mediate a role in modulating the genes impacting pollen fertility. Overall, our findings provide an understanding of two parental epigenomes interacting to give rise to an altered methylome in pigeonpea hybrids, from genome-wide point of view.
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Affiliation(s)
- Alim Junaid
- National Research Centre on Plant Biotechnology, LBS Centre, PUSA Campus, New Delhi, India
| | - Himanshu Kumar
- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A R Rao
- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A N Patil
- Pulse Reaserch Unit, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, P.O. Krishi Nagar, Akola, Maharashtra, India
| | - N K Singh
- National Research Centre on Plant Biotechnology, LBS Centre, PUSA Campus, New Delhi, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, LBS Centre, PUSA Campus, New Delhi, India
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Singh NK, Wemple BC, Bomblies A, Ricketts TH. Simulating stream response to floodplain connectivity and revegetation from reach to watershed scales: Implications for stream management. Sci Total Environ 2018; 633:716-727. [PMID: 29597165 DOI: 10.1016/j.scitotenv.2018.03.198] [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] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/13/2018] [Accepted: 03/17/2018] [Indexed: 06/08/2023]
Abstract
Natural-infrastructures (e.g., floodplains) can offer multiple ecosystem services (ES), including flood-resilience and water quality improvement. In order to maintain these ES, state and non-profit organizations consider various stream interventions, including increased floodplain connectivity and revegetation. However, the effect of these interventions is rarely quantified. We build a hydraulic model to simulate the influence of above-mentioned interventions on stream power and water depth during 5 yr and 100 yr flood return-intervals for two watersheds in Vermont, USA. Simulated revegetation of floodplains increased water depth and decreased stream power, whereas increasing connectivity resulted in decline of both responses. Combination of increased connectivity and floodplain revegetation showed greatest reduction in stream-power suggesting that interventions may influence stream response in diverse ways. Across all three interventions, 14% and 48% of altered reaches showed increase in stream power and water depth over baseline, indicating that interventions may lead to undesirable outcomes and their apparent effectiveness can vary with the measure chosen for evaluation. Interventions also influenced up to 16% of unaltered reaches (i.e., in which no interventions were implemented), indicating the consequences of interventions can spread both up and downstream. Multivariate analysis showed that up to 50% of variance in stream response to interventions is attributable to characteristics of reaches, indicating that these characteristics could mediate the effectiveness of interventions. This study offers a framework to evaluate the potential ES provided by natural infrastructure. All stream interventions involve tradeoffs among responses and between target and non-target areas, so careful evaluation is therefore needed to compare benefits and costs among interventions. Such assessments can lead to more effective management of stream-floodplain ecosystems both in Vermont and elsewhere.
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Affiliation(s)
- Nitin K Singh
- Rubenstein School for Environment and Natural Resources, The University of Vermont, Burlington, VT 05405, United States; Gund Institute for Environment, 617 Main Street, The University of Vermont, Burlington, VT 05405, United States.
| | - Beverley C Wemple
- Department of Geography, The University of Vermont, Burlington, VT 05405, United States; Gund Institute for Environment, 617 Main Street, The University of Vermont, Burlington, VT 05405, United States
| | - Arne Bomblies
- Department of Civil & Environmental Engineering, The University of Vermont, Burlington, VT 05405, United States; Gund Institute for Environment, 617 Main Street, The University of Vermont, Burlington, VT 05405, United States
| | - Taylor H Ricketts
- Rubenstein School for Environment and Natural Resources, The University of Vermont, Burlington, VT 05405, United States; Gund Institute for Environment, 617 Main Street, The University of Vermont, Burlington, VT 05405, United States
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Bajpai A, Khan K, Muthukumar M, Rajan S, Singh NK. Molecular analysis of anthocyanin biosynthesis pathway genes and their differential expression in mango peel. Genome 2018; 61:157-166. [PMID: 29338343 DOI: 10.1139/gen-2017-0205] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mango fruit is cherished by masses for its taste and nutrition, contributed by color, flavor, and aroma. Among these, peel color is an important trait contributing to fruit quality and market value. We attempted to elucidate the role of key genes of the anthocyanin biosynthesis pathway related to fruit peel color from the leaf transcriptome of mango cultivar Amrapali. A total of 108 mined transcript sequences were assigned to the phenylpropanoid-flavonoid pathway from which 15 contigs representing anthocyanin biosynthesis genes were annotated. Alternate splice variants were identified by mapping against genes of Citrus clementina and Vitis vinifera (closest relatives) and protein subcellular localization was determined. Phylogenetic analysis of these pathway genes clustered them into distinct groups aligning with homologous genes of Magnifera indica, C. clementina, and V. vinifera. Expression profiling revealed higher relative fold expressions in mature fruit peel of red-colored varieties (Arunika, Ambika, and Tommy Atkins) in comparison with the green-peeled Amrapali. MiCHS, MiCHI, and MiF3H alternate splice variants revealed differential gene expression. Functionally divergent variants indicate availability of an allelic pool programmed to play critical roles in peel color. This study provides insight into the molecular genetic basis of peel color and offers scope for development of biomarkers in varietal improvement programs.
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Affiliation(s)
- Anju Bajpai
- a ICAR-Central Institute for Subtropical Horticulture, Lucknow-226101, India
| | - Kasim Khan
- a ICAR-Central Institute for Subtropical Horticulture, Lucknow-226101, India
| | - M Muthukumar
- a ICAR-Central Institute for Subtropical Horticulture, Lucknow-226101, India
| | - S Rajan
- a ICAR-Central Institute for Subtropical Horticulture, Lucknow-226101, India
| | - N K Singh
- b ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi-110012, India
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Upadhyay AK, Singh NK, Bankoti NS, Rai UN. Designing and construction of simulated constructed wetland for treatment of sewage containing metals. Environ Technol 2017; 38:2691-2699. [PMID: 27974042 DOI: 10.1080/09593330.2016.1273396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A simulated horizontal flow constructed wetland (CW) has been designed with gravel medium and aquatic plants Typha latifolia and Polygonum hydropiper to assess its performance efficiency for sewage treatment. Monitoring of fully developed CW revealed a high removal of nutrients and metals from sewage after treatment at varying retention times. The percent (%) removal of biological oxygen demand, total dissolved solids, total suspended solids, PO4-P and total nitrogen in CW planted with T. latifolia were 88.20, 61.9, 72.12, 74.23 and 66.78%; however, with P. hydropiper, reductions were 79.47, 53.47, 55.46, 60.40 and 52.87%, respectively, at 8 d retention time. In addition, T. latifolia and P. hydropiper accumulated substantial amount of metals in their tissues particularly in roots. T. latifolia root accumulated maximum amount of Zn (40.44 µg/g dw) followed by Cu (39.24 µg/g dw), Pb (37.78 µg/g dw) and Cr (19.95 µg/g dw) as compared to P. hydropiper, which was 17.85, 33.43, 36.19 and 9.67 µg/g dw, respectively. Further, plant-specific high translocation factor (>1) of metals were observed at different retention times. Results suggest that simulated CW may be applied as an ecofriendly and low-cost tool to treat sewage before discharge into a fresh water body.
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Affiliation(s)
- A K Upadhyay
- a Plant Ecology and Environmental Science Division , CSIR-National Botanical Research Institute , Lucknow , India
- b Department of Botany, L.S.M. Govt. P.G. College, Pithoragarh , Kumaun University , Nainital , India
| | - N K Singh
- c Institute of Environment and Sustainable Development , Banaras Hindu University , Varanasi , India
| | - N S Bankoti
- b Department of Botany, L.S.M. Govt. P.G. College, Pithoragarh , Kumaun University , Nainital , India
| | - U N Rai
- a Plant Ecology and Environmental Science Division , CSIR-National Botanical Research Institute , Lucknow , India
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Eliash N, Singh NK, Thangarajan S, Sela N, Leshkowitz D, Kamer Y, Zaidman I, Rafaeli A, Soroker V. Chemosensing of honeybee parasite, Varroa destructor: Transcriptomic analysis. Sci Rep 2017; 7:13091. [PMID: 29026097 PMCID: PMC5638865 DOI: 10.1038/s41598-017-13167-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [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: 05/31/2017] [Accepted: 09/04/2017] [Indexed: 01/05/2023] Open
Abstract
Chemosensing is a primary sense in nature, however little is known about its mechanism in Chelicerata. As a model organism we used the mite Varroa destructor, a key parasite of honeybees. Here we describe a transcriptomic analysis of two physiological stages for the Varroa foreleg, the site of primary olfactory organ. The transcriptomic analysis revealed transcripts of chemosensory related genes belonging to several groups. These include Niemann-Pick disease protein, type C2 (NPC2), gustatory receptors (GRs), ionotropic receptors (IRs), sensory neuron membrane proteins (SNMPs) and odorant binding proteins (OBP). However, no insect odorant receptors (ORs) and odorant co-receptors (ORcos) were found. In addition, we identified a homolog of the most ancient IR co-receptor, IR25a, in Varroa as well as in other members of Acari. High expression of this transcript in the mite’s forelegs, while not detectable in the other pairs of legs, suggests a function for this IR25a-like in Varroa chemosensing.
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Affiliation(s)
- Nurit Eliash
- Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel.,Institute of Agroecology and Plant Health, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Nitin K Singh
- Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Starlin Thangarajan
- Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Noa Sela
- Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Dena Leshkowitz
- Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
| | - Yosi Kamer
- Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ilia Zaidman
- Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Ada Rafaeli
- Department of Food Quality and Safety, Institute of Postharvest and Food Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Victoria Soroker
- Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel.
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Subi S, Lee SJ, Shiwani S, Singh NK. Differential characterization of myogenic satellite cells with linolenic and retinoic acid in the presence of thiazolidinediones from prepubertal Korean black goats. Asian-Australas J Anim Sci 2017; 31:439-448. [PMID: 28920418 PMCID: PMC5838350 DOI: 10.5713/ajas.17.0257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/15/2017] [Accepted: 08/31/2017] [Indexed: 12/27/2022]
Abstract
Objective Myogenic satellite cells were isolated from semitendinosus muscle of prepubertal Korean black goat to observe the differential effect of linolenic and retinoic acid in thepresence of thiazolidinediones (TZD) and also to observe the production insulin sensitive preadipocyte. Methods Cells were characterized for their stemness with cluster of differentiation 34 (CD34), CD13, CD106, CD44, Vimentin surface markers using flow cytometry. Cells characterized themselves as possessing significant (p<0.05) levels of CD13, CD34, CD106, Vimentin revealing their stemness potential. Goat myogenic satellite cells also exhibited CD44, indicating that they possessed a % of stemness factors of adipose lineage apart from their inherent stemness of paxillin factors 3/7. Results Cells during proliferation stayed absolutely and firmly within the myogenic fate without any external cues and continued to show a significant (p<0.05) fusion index % to express myogenic differentiation, myosin heavy chain, and smooth muscle actin in 2% horse serum. However, confluent myogenic satellite cells were the ones easily turning into adipogenic lineage. Intriguingly, upregulation in adipose specific genetic markers such as peroxisome proliferation-activated receptor γ, adiponectin, lipoprotein lipase, and CCAAT/enhancer binding protein α were observed and confirmed in all given treatments. However, the amount of adipogenesis was found to be statistically significant (p<0.01) with linolenic acid as compared to retinoic acid in combination with TZD’s. Conclusion Retinoic acid was found to produce smaller preadipocytes which have been assumed to have insulin sensitization and hence retinoic acid could be used as a potential agent to sensitize tissues to insulin in combination with TZD’s to treat diabetic conditions in humans and animals in future.
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Affiliation(s)
- S Subi
- College of Animal life sciences, Kangwon National University, Chuncheon 24341, Korea
| | - S J Lee
- College of Animal life sciences, Kangwon National University, Chuncheon 24341, Korea
| | - S Shiwani
- College of Animal life sciences, Kangwon National University, Chuncheon 24341, Korea
| | - N K Singh
- Department of Veterinary Surgery and Radiology, Faculty of Veterinary and Animal Sciences, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
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Nigam D, Saxena S, Ramakrishna G, Singh A, Singh NK, Gaikwad K. De novo Assembly and Characterization of Cajanus scarabaeoides (L.) Thouars Transcriptome by Paired-End Sequencing. Front Mol Biosci 2017; 4:48. [PMID: 28748187 PMCID: PMC5506216 DOI: 10.3389/fmolb.2017.00048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/26/2017] [Indexed: 11/13/2022] Open
Abstract
Pigeonpea [Cajanus cajan (L.) Millsp.] is a heat and drought resilient legume crop grown mostly in Asia and Africa. Pigeonpea is affected by various biotic (diseases and insect pests) and abiotic stresses (salinity and water logging) which limit the yield potential of this crop. However, resistance to all these constraints is not readily available in the cultivated genotypes and some of the wild relatives have been found to withstand these resistances. Thus, the utilization of crop wild relatives (CWR) in pigeonpea breeding has been effective in conferring resistance, quality and breeding efficiency traits to this crop. Bud and leaf tissue of Cajanus scarabaeoides, a wild relative of pigeon pea were used for transcriptome profiling. Approximately 30 million clean reads filtered from raw reads by removal of adaptors, ambiguous reads and low-quality reads (3.02 gigabase pairs) were generated by Illumina paired-end RNA-seq technology. All of these clean reads were pooled and assembled de novo into 1,17,007 transcripts using the Trinity. Finally, a total of 98,664 unigenes were derived with mean length of 396 bp and N50 values of 1393. The assembly produced significant mapping results (73.68%) in BLASTN searches of the Glycine max CDS sequence database (Ensembl). Further, uniprot database of Viridiplantae was used for unigene annotation; 81,799 of 98,664 (82.90%) unigenes were finally annotated with gene descriptions or conserved protein domains. Further, a total of 23,475 SSRs were identified in 27,321 unigenes. This data will provide useful information for mining of functionally important genes and SSR markers for pigeonpea improvement.
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Affiliation(s)
- Deepti Nigam
- Indian Council of Agricultural Research-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Swati Saxena
- Indian Council of Agricultural Research-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - G Ramakrishna
- Indian Council of Agricultural Research-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Archana Singh
- Division of Biochemistry, Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi, India
| | - N K Singh
- Indian Council of Agricultural Research-National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Kishor Gaikwad
- Indian Council of Agricultural Research-National Research Centre on Plant BiotechnologyNew Delhi, India
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