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Yadav M, Maiwal R, Kumar Br V, Tripathi G, Sharma N, Sharma N, Bindal V, Mathew B, Pandey S, Singh SP, Tevathia HV, Maras JS, Sarin SK. Comparative metabolome analysis reveals higher potential of haemoperfusion adsorption in providing favourable outcome in ACLF patients. Liver Int 2024; 44:1189-1201. [PMID: 38358068 DOI: 10.1111/liv.15858] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 01/02/2024] [Accepted: 01/21/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND AND AIMS Acute-on-chronic liver failure (ACLF) is a serious illness associated with altered metabolome, organ failure and high mortality. Need for therapies to improve the metabolic milieu and support liver regeneration are urgently needed. METHODS We investigated the ability of haemoperfusion adsorption (HA) and therapeutic plasma exchange (TPE) in improving the metabolic profile and survival in ACLF patients. Altogether, 45 ACLF patients were randomized into three groups: standard medical therapy (SMT), HA and TPE groups. Plasma metabolomics was performed at baseline, post-HA and TPE sessions on days 7 and 14 using high-resolution mass spectrometry. RESULTS The baseline clinical/metabolic profiles of study groups were comparable. We identified 477 metabolites. Of these, 256 metabolites were significantly altered post 7 days of HA therapy (p < .05, FC > 1.5) and significantly reduced metabolites linked to purine (12 metabolites), tryptophan (7 metabolites), primary bile acid (6 metabolites) and arginine-proline metabolism (6 metabolites) and microbial metabolism respectively (p < .05). Metabolites linked to taurine-hypotaurine and histidine metabolism were reduced and temporal increase in metabolites linked to phenylalanine and tryptophan metabolism was observed post-TPE therapy (p < .05). Finally, weighted metabolite correlation network analysis (WMCNA) along with inter/intragroup analysis confirmed significant reduction in inflammatory (tryptophan, arachidonic acid and bile acid metabolism) and secondary energy metabolic pathways post-HA therapy compared to TPE and SMT (p < .05). Higher baseline plasma level of 11-deoxycorticosterone (C03205; AUROC > 0.90, HR > 3.2) correlated with severity (r2 > 0.5, p < .05) and mortality (log-rank-p < .05). Notably, 51 of the 64 metabolite signatures (ACLF non-survivor) were reversed post-HA treatment compared to TPE and SMT(p < .05). CONCLUSION HA more potentially (~80%) improves plasma milieu compared to TPE and SMT. High baseline plasma 11-deoxycorticosterone level correlates with early mortality in ACLF patients.
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Affiliation(s)
- Manisha Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Rakhi Maiwal
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Vinay Kumar Br
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Gaurav Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Neha Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Nupur Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Vasundhra Bindal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Babu Mathew
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Sushmita Pandey
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Satender Pal Singh
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | | | - Jaswinder Singh Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
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Yadav M, Gowda M, Navya C, Deodhare K, Murugesan S. Prenatal presentation and diagnosis of a case of fetal varicella syndrome. Clin Dysmorphol 2024; 33:99-103. [PMID: 38363857 DOI: 10.1097/mcd.0000000000000480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Affiliation(s)
- Manisha Yadav
- Department of Obstetrics and Gynecology, Jawaharlal Institute of Postgraduate Medical Education and Research, Dhanvantri Nagar, Gorimedu, Pondicherry, India
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Chhillar B, Kadian R, Kumar M, Yadav M, Sodhi N, Xavier da Silva TN, Friedmann Angeli JP, Singh VP. Aminic Organoselenium Compounds as Glutathione Peroxidase Mimics and Inhibitors of Ferroptosis. Chembiochem 2024; 25:e202400074. [PMID: 38293899 DOI: 10.1002/cbic.202400074] [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: 10/23/2023] [Revised: 12/03/2023] [Accepted: 01/29/2024] [Indexed: 02/01/2024]
Abstract
The synthesis of diarylamine-based organoselenium compounds via the nucleophilic substitution reactions has been described. Symmetrical monoselenides and diselenides were conveniently synthesized by the reduction of their corresponding selenocyanates using sodium borohydride. Selenocyanates were obtained from 2-chloro acetamides by the nucleophilic displacement with potassium selenocyanate. Selenides were synthesized by treating the 2-chloro acetamides with in situ generated sodium butyl selenolate as nucleophile. Further, the newly synthesized organoselenium compounds were evaluated for their glutathione peroxidase (GPx)-like activity in thiophenol assay. This study revealed that the methoxy-substituted organoselenium compounds showed significant effect on the GPx-like activity. The catalytic parameters for the most efficient catalysts were also determined. The anti-ferroptotic activity for all GPx-mimics evaluated in a 4-OH-tamoxifen (TAM) inducible GPx4 knockout cell line using liproxstatin as standard.
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Affiliation(s)
- Babli Chhillar
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh, 160 014, India
| | - Rajni Kadian
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh, 160 014, India
| | - Manish Kumar
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh, 160 014, India
| | - Manisha Yadav
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh, 160 014, India
| | - Nikhil Sodhi
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh, 160 014, India
| | - Thamara Nishida Xavier da Silva
- Rudolf Virchow Zentrum, Centre for Integrative and Translational Bioimaging, Julius-Maximillian, University of Wurzburg, 97080, Wurzburg, Germany
| | - Jose Pedro Friedmann Angeli
- Rudolf Virchow Zentrum, Centre for Integrative and Translational Bioimaging, Julius-Maximillian, University of Wurzburg, 97080, Wurzburg, Germany
| | - Vijay P Singh
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh, 160 014, India
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Challa A, Maras JS, Nagpal S, Tripathi G, Taneja B, Kachhawa G, Sood S, Dhawan B, Acharya P, Upadhyay AD, Yadav M, Sharma R, Bajpai M, Gupta S. Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis. J Eur Acad Dermatol Venereol 2024. [PMID: 38284174 DOI: 10.1111/jdv.19805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/06/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery. OBJECTIVES The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model. METHODS Vaginal samples obtained from reproductive-age group women with (n = 40) and without BV (n = 40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy. RESULTS Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84 ± 0.21 and accuracy of 0.79 ± 0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97 ± 0.07 and an accuracy of 0.92 ± 0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97 ± 0.07 and accuracy of 0.94 ± 0.08 with diagnostic performance only slightly superior to the metabolite-based model. CONCLUSION Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.
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Affiliation(s)
- A Challa
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - J S Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Nagpal
- TCS Research, Tata Consultancy Services Ltd, Pune, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - B Taneja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Kachhawa
- Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - S Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - B Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - P Acharya
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - A D Upadhyay
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - M Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - R Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - M Bajpai
- Department of Transfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Gupta
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
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5
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Jeong GH, Yadav M, Lee SS, Chung BY, Cho JH, Lee IC, Bai HW, Kim TH. Novel Dihydrocoumarins Induced by Radiolysis as Potent Tyrosinase Inhibitors. Molecules 2024; 29:341. [PMID: 38257254 PMCID: PMC10820468 DOI: 10.3390/molecules29020341] [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: 12/26/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
A representative naturally occurring coumarin, 4-methylumbelliferone (5), was exposed to 50 kGy of gamma ray, resulting in four newly generated dihydrocoumarin products 1-4 induced by the gamma irradiation. The structures of these new products were elucidated by interpretation of spectroscopic data (NMR, MS, [α]D, and UV). The unusual bisdihydrocoumarin 4 exhibited improved tyrosinase inhibitory capacity toward mushroom tyrosinase with IC50 values of 19.8 ± 0.5 μM as compared to the original 4-methylumbelliferone (5). A kinetic analysis also exhibited that the potent metabolite 4 had non-competitive modes of action. Linkage of the hydroxymethyl group in the C-3 and C-4 positions on the lactone ring probably enhances the tyrosinase inhibitory effect of 4-methylumbelliferone (5). Thus, the novel coumarin analog 4 is an interesting new class of tyrosinase inhibitory candidates that requires further examination.
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Affiliation(s)
- Gyeong Han Jeong
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea; (G.H.J.); (S.S.L.); (B.Y.C.)
- Center for Companion Animal New Drug Development, Korea Institute of Toxicology (KIT), Jeongeup 56212, Republic of Korea
| | - Manisha Yadav
- Department of Food Science and Biotechnology, Daegu University, Gyeongsan 38453, Republic of Korea;
| | - Seung Sik Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea; (G.H.J.); (S.S.L.); (B.Y.C.)
- Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Byung Yeoup Chung
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea; (G.H.J.); (S.S.L.); (B.Y.C.)
| | - Jae-Hyeon Cho
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - In-Chul Lee
- Department of Cosmetic Science and Technology, Seowon University, Cheongju 28674, Republic of Korea;
| | - Hyoung-Woo Bai
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea; (G.H.J.); (S.S.L.); (B.Y.C.)
- Center for Companion Animal New Drug Development, Korea Institute of Toxicology (KIT), Jeongeup 56212, Republic of Korea
- Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Tae Hoon Kim
- Department of Food Science and Biotechnology, Daegu University, Gyeongsan 38453, Republic of Korea;
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6
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Tonnetti L, Groves JA, Self D, Yadav M, Spencer BR, Livezey K, Linnen JM, Stramer SL. A novel mitigation strategy for the prevention of transfusion-transmitted malaria. Transfusion 2024; 64:94-103. [PMID: 38018462 DOI: 10.1111/trf.17612] [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: 10/09/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Malaria is caused by protozoa of the genus Plasmodium and transmitted by Anopheles mosquitos. In the US, blood donors are assessed for malaria risk, including donor travel or previous residence in endemic areas and history of malaria by questionnaire and deferred for three months or three years, respectively. METHODS The Procleix Plasmodium Assay is a qualitative nucleic acid test based on transcription-mediated amplification (TMA) for the detection of 18S ribosomal RNA of P. falciparum, P. ovale, P. vivax, P. malariae, and P. knowlesi for use on the Procleix Panther system. Analytical sensitivity was evaluated with in vitro transcripts and infected red blood cells. For clinical specificity, 12,800 individual donations and 283 pools of 16 samples from routine US donors were screened. Malaria risk was evaluated by testing 862 donors deferred for 3 years. Reactive results were confirmed with in-house real-time TMA assay and serology. RESULTS Assay sensitivity was 8.47-11.89 RNA copies/mL and 2.10-6.82 infected red cells/mL. Specificity was 99.99% in 12,800 individual donations and 100% in 283 pools of 16. Of 862 tested deferred donor samples, one donor (0.12%) confirmed positive individually and in pools; he remained confirmed positive for 13 months. The infected donor was a prior resident of a malaria-endemic area in West Africa. CONCLUSIONS The Procleix Plasmodium Assay showed high sensitivity and specificity and detected Plasmodium RNA in an asymptomatic presenting donor. This assay may prove helpful as a screening test versus the use of risk questions to reduce the number of donors deferred for malaria risk.
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Affiliation(s)
- Laura Tonnetti
- Scientific Affairs, American Red Cross, Rockville and Gaithersburg, Maryland, USA
| | - Jamel A Groves
- Scientific Affairs, American Red Cross, Rockville and Gaithersburg, Maryland, USA
| | - Deanna Self
- Grifols Diagnostic Solutions Inc., San Diego, California, USA
| | - Manisha Yadav
- Grifols Diagnostic Solutions Inc., San Diego, California, USA
| | - Bryan R Spencer
- Scientific Affairs, American Red Cross, Dedham, Massachusetts, USA
| | - Kristin Livezey
- Grifols Diagnostic Solutions Inc., San Diego, California, USA
| | | | - Susan L Stramer
- Scientific Affairs, American Red Cross, Rockville and Gaithersburg, Maryland, USA
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Bajaj M, Muddassir M, Choi B, Singh P, Park JB, Singh S, Yadav M, Kumar R, Eom K, Sharma D. Single-molecule analysis of osmolyte-mediated nanomechanical unfolding behavior of a protein domain. Int J Biol Macromol 2023; 253:126849. [PMID: 37717878 DOI: 10.1016/j.ijbiomac.2023.126849] [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: 06/09/2023] [Revised: 08/25/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
The small organic molecules, known as osmolytes being ubiquitously present in different cell types, affect protein folding, stability and aggregation. However, it is unknown how the osmolytes affect the nanomechanical unfolding behavior of protein domain. Here, we show the osmolyte-dependent mechanical unfolding properties of protein titin immunoglobulin-27 (I27) domain using an atomic force microscopy (AFM)-based single-molecule force spectroscopy. We found that amines and methylamines improved the mechanical stability of I27 domain, whereas polyols had no effect. Interestingly, glycine betaine (GB) or trimethylamine-N-oxide (TMAO) increased the average unfolding force of the protein domain. The kinetic parameters analyzed at single-molecule level reveal that stabilizing effect of osmolytes is due to a decrease in the unfolding rate constant of I27, which was confirmed by molecular dynamics simulations. Our study reveals different effects that diverse osmolytes have on the mechanical properties of the protein, and suggests the potential use of osmolytes in modulating the mechanical stability of proteins required for various nano-biotechnological applications.
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Affiliation(s)
- Manish Bajaj
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Mohd Muddassir
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India; Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bumjoon Choi
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Digial Bio R&D Center, Mediazen, Seoul 07789, Republic of Korea
| | - Priyanka Singh
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Jong Bum Park
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Surjeet Singh
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Manisha Yadav
- School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Rajesh Kumar
- School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Deepak Sharma
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India; Academy of Scientific & Innovative Research, India.
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8
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Yadav M, Singh VP. Glutathione Peroxidase-like Antioxidant Activity of 1,3-Benzoselenazoles: Synthesis and In Silico Molecular Docking Studies as Pancreatic Lipase Inhibitors. J Org Chem 2023; 88:16934-16948. [PMID: 38008916 DOI: 10.1021/acs.joc.3c01762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
The synthesis of 1,3-benzoselenazoles was achieved by the reaction of corresponding bis[3-amino-N-(p-tolyl)benzamide-2-yl] diselenide, bis[3-amino-N-(4-methoxyphenyl)benzamide-2-yl] diselenide, and bis[3-amino-N-(4-(dimethylamino)phenyl) benzamide-2-yl] diselenide with aryl aldehydes. The 1,3-benzoselenazoles continued to exist as planar molecules due to the presence of secondary Se···O interactions as revealed by the single-crystal X-ray analysis. The presence of secondary Se···O interactions in 1,3-benzoselenazoles was confirmed using natural bond orbital (NBO) and atoms in molecules (AIM) calculations. Nucleus-independent chemical shift (NICS) values suggested the presence of aromatic character in a five-membered benzoselenazole heterocyclic ring. The glutathione peroxidase (GPx)-like antioxidant activity of all 1,3-benzoselenazoles was assessed using a thiophenol assay, exhibiting greater antioxidant activity than Ph2Se2 used as a reference. The most active catalyst carrying a strong electron-donating group (-NMe2) at the ortho-position to the benzoselenazole ring was further investigated at different concentrations of thiophenol, H2O2, and 1,3-benzoselenazoles as catalyst for determining their catalytic parameters. Moreover, the potential applications of all 1,3-benzoselenazoles against pancreatic lipase (PL) have been identified using in silico interactions between the active sites of the 1LPB protein as evaluated using a molecular docking study.
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Affiliation(s)
- Manisha Yadav
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160 014, India
| | - Vijay P Singh
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160 014, India
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Yadav M, Panwar R, Rustagi A, Chakraborty A, Roy A, Singh IK, Singh A. Comprehensive and evolutionary analysis of Spodoptera litura-inducible Cytochrome P450 monooxygenase gene family in Glycine max elucidate their role in defense. Front Plant Sci 2023; 14:1221526. [PMID: 38023937 PMCID: PMC10654349 DOI: 10.3389/fpls.2023.1221526] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023]
Abstract
Plants being sessile organisms and lacking both circulating phagocytic cells and somatic adaptive immune response, have thrived on various defense mechanisms to fend off insect pests and invasion of pathogens. CYP450s are the versatile enzymes, which thwart plants against insect pests by ubiquitous biosynthesis of phytohormones, antioxidants, and secondary metabolites, utilizing them as feeding deterrents and direct toxins. Therefore, a comprehensive analysis of biotic stress-responsive CYPs from Glycine max was performed to ascertain their function against S. litura-infestation. Phylogenetic analysis and evolutionary studies on conserved domains and motifs disclosed the evolutionary correspondence of these GmCYPs with already characterized members of the CYP450 superfamily and close relatedness to Medicago truncatula. These GmCYPs were mapped on 13 chromosomes; they possess 1-8 exons; they have evolved due to duplication and are localized in endoplasmic reticulumn. Further, identification of methyl-jasmonate, salicylic acid, defense responsive and flavonoid biosynthesis regulating cis-acting elements, their interaction with biotic stress regulating proteins and their differential expression in diverse types of tissues, and during herbivory, depicted their responsiveness to biotic stress. Three-dimensional homology modelling of GmCYPs, docking with heme cofactor required for their catalytic activity and enzyme-substrate interactions were performed to understand the functional mechanism of their action. Moreover, to gain insight into their involvement in plant defense, gene expression analysis was evaluated, which revealed differential expression of 11 GmCYPs upon S. litura-infestation, 12 GmCYPs on wounding while foliar spray of ethylene, methyl-jasmonate and salicylic acid differentially regulated 11 GmCYPs, 6 GmCYPs, and 10 GmCYPs respectively. Our study comprehensively analysed the underlying mechanism of GmCYPs function during S. litura-infestation, which can be further utilized for functional characterization to develop new strategies for enhancing soybean resistance to insect pests.
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Affiliation(s)
- Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
| | - Ruby Panwar
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Anjana Rustagi
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Amrita Chakraborty
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Amit Roy
- Forest Molecular Entomology Lab, EXTEMIT-K, EVA 4.0, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Department of Botany, Gargi College, University of Delhi, Delhi, India
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
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Yadav M, Gowda M, Chinta N, Deodhare K, Murugesan S. Factors associated with late gestational age of diagnosis and/or delayed referral of fetuses with major structural malformations: A study in a tertiary care hospital in South India. Prenat Diagn 2023; 43:1406-1415. [PMID: 37649210 DOI: 10.1002/pd.6431] [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: 04/23/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
OBJECTIVES To evaluate the factors related to delayed diagnosis or referral of women with major congenital malformations in a tertiary care hospital in South India, with a specific emphasis on the socioeconomic and psychosocial aspects. METHODS A retrospective analysis was conducted on 107 pregnant women with confirmed fetal anomalies at Jawaharlal Institute of Postgraduate Medical Education and Research. Both qualitative and quantitative data were collected on factors related to the patient, physician, and healthcare system that could have contributed to the delay. RESULTS In our study of 107 patients, 98.1% had at least one antenatal check-up before 20 weeks. Among them, 75.2% (79/107) were advised to undergo a mid-trimester anomaly scan, and 70.8% (56/79) actually underwent the scan. However, 62.5% (35/56) of those who had the scan performed at the appropriate time had undetected abnormalities. Retrospective analysis showed that 28.5% (10/35) of these anomalies could have been detected as early as 12-14 weeks of gestation. Additionally, 24.3% (26/107) of women were advised to undergo scans at or after 20 weeks and 4.7% (5/107) had anomalies detected during the scan but were unaware about the findings until subsequent visits. Inadequate healthcare professional training, busy schedules, lack of awareness, and communication gaps were identified as potential reasons for delayed diagnosis. Psychosocial factors such as denial, fear, emotional distress, and anxiety also influenced decision-making and contributed to delayed medical care. CONCLUSION Addressing healthcare provider training, communication between the healthcare professionals and the patients, and psychosocial factors are essential to prevent delays and improve pregnancy management. Future interventions should focus on awareness, providing comprehensive information, and support for parents facing fetal anomalies.
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Affiliation(s)
- Manisha Yadav
- Department of Obstetrics and Gynecology, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
| | - Mamatha Gowda
- Department of Obstetrics and Gynecology, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
| | - Navya Chinta
- Department of Obstetrics and Gynecology, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
| | - Kirti Deodhare
- Department of Obstetrics and Gynecology, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
| | - Sneha Murugesan
- Department of Obstetrics and Gynecology, Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, India
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Sharma N, Pandey S, Yadav M, Mathew B, Bindal V, Sharma N, Tripathi G, Bhat SH, Gupta A, Maiwall R, Sharma S, Sarin SK, Maras JS. Biomolecular map of albumin identifies signatures of severity and early mortality in acute liver failure. J Hepatol 2023; 79:677-691. [PMID: 37116716 DOI: 10.1016/j.jhep.2023.04.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/24/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND & AIMS Acute liver failure (ALF) is associated with high mortality. Alterations in albumin structure and function have been shown to correlate with outcomes in cirrhosis. We undertook a biomolecular analysis of albumin to determine its correlation with hepatocellular injury and early mortality in ALF. METHODS Altogether, 225 participants (200 patients with ALF and 25 healthy controls [HC]) were enrolled. Albumin was purified from the baseline plasma of the training cohort (ALF, n = 40; survivors, n = 8; non-survivors, n = 32; and HC, n = 5); analysed for modifications, functionality, and bound multi-omics signatures; and validated in a test cohort (ALF, n = 160; survivors, n = 53; non-survivors, n = 107; and HC, n = 20). RESULTS In patients with ALF, albumin is more oxidised and glycosylated with a distinct multi-omics profile than that in HC, more so in non-survivors (p <0.05). In non-survivors, albumin was more often bound (p <0.05, false discovery rate <0.01) to proteins associated with inflammation, advanced glycation end product, metabolites linked to arginine, proline metabolism, bile acid, and mitochondrial breakdown products. Increased bacterial taxa (Listeria, Clostridium, etc.) correlated with lipids (triglycerides [4:0/12:0/12:0] and phosphatidylserine [39:0]) and metabolites (porphobilinogen and nicotinic acid) in non-survivors (r2 >0.7). Multi-omics signature-based probability of detection for non-survival was >90% and showed direct correlation with albumin functionality and clinical parameters (r2 >0.85). Probability-of-detection metabolites built on the top five metabolites, namely, nicotinic acid, l-acetyl carnitine, l-carnitine, pregnenolone sulfate, and N-(3-hydroxybutanoyl)-l-homoserine lactone, showed diagnostic accuracy of 98% (AUC 0.98, 95% CI 0.95-1.0) and distinguish patients with ALF predisposed to early mortality (log-rank <0.05). On validation using high-resolution mass spectrometry and five machine learning algorithms in test cohort 1 (plasma and paired one-drop blood), the metabolome panel showed >92% accuracy/sensitivity and specificity for prediction of mortality. CONCLUSIONS In ALF, albumin is hyperoxidised and substantially dysfunctional. Our study outlines distinct 'albuminome' signatures capable of distinguishing patients with ALF predisposed to early mortality or requiring emergency liver transplantation. IMPACTS AND IMPLICATIONS Here, we report that the biomolecular map of albumin is distinct and linked to severity and outcome in patients with acute liver failure (ALF). Detailed structural, functional, and albumin-omics analysis in patients with ALF led to the identification and classification of albumin-bound biomolecules, which could segregate patients with ALF predisposed to early mortality. More importantly, we found albumin-bound metabolites indicative of mitochondrial damage and hyperinflammation as a putative indicator of <30-day mortality in patients with ALF. This preclinical study validates the utility of albuminome analysis for understanding the pathophysiology and development of poor outcome indicators in patients with ALF.
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Affiliation(s)
- Neha Sharma
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Sushmita Pandey
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Manisha Yadav
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Babu Mathew
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Vasundhra Bindal
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Nupur Sharma
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Gaurav Tripathi
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Sadam H Bhat
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Abhishak Gupta
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Rakhi Maiwall
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shvetank Sharma
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India.
| | - Jaswinder Singh Maras
- Departments of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India.
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Kumar R, Adhikary A, Saini R, Khan SA, Yadav M, Kumar S. Drought priming induced thermotolerance in wheat (Triticum aestivum L.) during reproductive stage; a multifaceted tolerance approach against terminal heat stress. Plant Physiol Biochem 2023; 201:107840. [PMID: 37379659 DOI: 10.1016/j.plaphy.2023.107840] [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] [Received: 02/02/2023] [Revised: 04/18/2023] [Accepted: 06/13/2023] [Indexed: 06/30/2023]
Abstract
In wheat (Triticum aestivum L.), terminal heat stress obstructs reproductive functioning eventually leading to yield loss. Drought priming during the vegetative stage can trigger a quicker and effective defense response against impending high temperature stress and improve crop production. In the present study, two contrasting wheat cultivars (PBW670 and C306) were subjected to moderate drought stress of 50-55% field capacity for eight days during the jointing stage to generate drought priming (DP) response. Fifteen days after anthesis heat stress (36 °C) was imposed for three days and physiological response of primed, and non-primed plants was assessed by analyzing membrane damage, water status and antioxidative enzymes. Heat shock transcription factors (14 TaHSFs), calmodulin (TaCaM5), antioxidative genes (TaSOD, TaPOX), polyamine biosynthesis genes and glutathione biosynthesis genes were analyzed. GC-MS based untargeted metabolite profiling was carried out to underpin the associated metabolic changes. Yield related parameters were recorded at maturity to finally assess the priming response. Heat stress response was visible from day one of exposure in terms of membrane damage and elevated antioxidative enzymes activity. DP reduced the impact of heat stress by lowering the membrane damage (ELI, MDA & LOX) and enhancing antioxidative enzyme activity except APX in both the cultivars. Drought priming upregulated the expression of HSFs, calmodulin, antioxidative genes, polyamines, and the glutathione biosynthesis genes. Drought priming altered key amino acids, carbohydrate, and fatty acid metabolism in PBW670 but also promoted thermotolerance in C306. Overall, DP provided a multifaceted approach against heat stress and positive association with yield.
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Affiliation(s)
- Rashpal Kumar
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Arindam Adhikary
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Rashmi Saini
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Shahied Ahmed Khan
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Manisha Yadav
- Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Sanjeev Kumar
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India; Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, India.
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Jafarzadeh A, Nemati M, Salarkia E, Yadav S, Aminizadeh N, Jafarzadeh S, Yadav M. Inflammatory responses during trichomoniasis: The role of Toll-like receptors and inflammasomes. Parasite Immunol 2023:e13000. [PMID: 37338019 DOI: 10.1111/pim.13000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Toll-like receptors (TLRs) and inflammasomes belong to the pattern recognition receptors (PRRs) of innate immunity identifying conserved compounds produced by pathogens or discharged by injured cells. Different cell subsets in the human urogenital system, such as epithelial cells and infiltrating leukocytes, express different kinds of TLRs (such as TLR2, TLR3, TLR4, TLR5 and TLR9) as well as inflammasomes (such as NLRP3, NLRC4 and AIM2). Various types of the Trichomonas vaginalis-derived components such as glycosyl-phosphatidylinositol (GPI), T. vaginalis virus (TVV), Lipophosphoglycan (LPG) and flagellin can be recognized by TLR2, TLR3, TLR4 and TLR5, respectively, leading to the production of proinflammatory cytokines and chemokines in the cervicovaginal mucosa. The T. vaginalis-induced inflammasomes can lead to pyroptosis as well as the release of IL-1β and IL-18 promoting innate and adaptive immune responses. The PRR-mediated responses to T. vaginalis may contribute to the induction of protective immune responses, local inflammation, promotion of co-infections, or even the development of malignancies, for example, prostate cancer. The protective or pathogenic roles of the TLRs and inflammasomes during trichomoniasis are highlighted in this review. A better understanding of PRR-mediated responses provides invaluable insights to develop effective immunotherapeutic strategies against T. vaginalis infection.
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Affiliation(s)
- Abdollah Jafarzadeh
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Maryam Nemati
- Immunology of Infectious Diseases Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
- Department of Laboratory Sciences, School of Para-Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Ehsan Salarkia
- Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Sonal Yadav
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
| | - Najmeh Aminizadeh
- Department of Histology, School of Medicine, Islamic Azad University Branch of Kerman, Kerman, Iran
| | - Sara Jafarzadeh
- Student Research Committee, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Manisha Yadav
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India
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Yadav M, Akhtar MN, Mishra M, Kumar S, Kumar R, Shubham, Nandal A, Sen P. Leishmania donovani Attenuates Dendritic Cell Trafficking to Lymph Nodes by Inhibiting C-Type Lectin Receptor 2 Expression via Transforming Growth Factor-β. Microbiol Spectr 2023; 11:e0412222. [PMID: 37125906 PMCID: PMC10269552 DOI: 10.1128/spectrum.04122-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/10/2023] [Indexed: 05/02/2023] Open
Abstract
To initiate an antileishmanial adaptive immune response, dendritic cells (DCs) must carry Leishmania antigens from peripheral tissues to local draining lymph nodes. However, the migratory capacity of DCs is largely compromised during Leishmania donovani infection. The molecular mechanism underlying this defective DC migration is not yet fully understood. Here, we demonstrate that L. donovani infection impaired the lymph node homing ability of DCs by decreasing C-type lectin receptor 2 (CLEC-2) expression. L. donovani exerted this inhibitory effect by inducing transforming growth factor-β (TGF-β) secretion from DCs. Indeed, TGF-β produced in this manner inhibited nuclear factor-κB (NF-κB)-mediated CLEC-2 expression on DCs by activating c-Src. Notably, suppression of c-Src expression significantly improved the arrival of DCs in draining lymph nodes by preventing L. donovani-induced CLEC-2 downregulation on DCs. These findings reveal a unique mechanism by which L. donovani inhibits DC migration to lymph nodes and suggest a key role for TGF-β, c-Src, and CLEC-2 in regulating this process. IMPORTANCE Dendritic cells (DCs) play a key role in initiating T cell-mediated protective immunity against visceral leishmaniasis (VL), the second most lethal parasitic disease in the world. However, the T cell-inducing ability of DCs critically depends on the extent of DC migration to regional lymph nodes. Notably, the migration of DCs is reported to be impaired during VL. The cause of this impaired DC migration, however, remains ill-defined. Here, we provide the first evidence that L. donovani, the causative agent of VL, attenuates the lymph node homing capacity of DCs by decreasing C-type lectin receptor 2 (CLEC-2) expression on DCs. Additionally, we have demonstrated how L. donovani mediates this inhibitory effect. Overall, our work has revealed a unique mechanism underlying L. donovani-induced impairment of DC migration and suggests a potential strategy to improve antileishmanial T cell activity by increasing DC arrival in lymph nodes.
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Affiliation(s)
- Manisha Yadav
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research—Institute of Microbial Technology, Chandigarh, India
| | - Md. Naushad Akhtar
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research—Institute of Microbial Technology, Chandigarh, India
| | - Manish Mishra
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research—Institute of Microbial Technology, Chandigarh, India
| | - Sandeep Kumar
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research—Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raj Kumar
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research—Institute of Microbial Technology, Chandigarh, India
| | - Shubham
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research—Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anil Nandal
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research—Institute of Microbial Technology, Chandigarh, India
| | - Pradip Sen
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research—Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Verma N, Yadav M, Yadav G, Arya S. Managing Multiple Schwannomatosis of Vagus and Hypoglossal Nerves: The Unanticipated Complications. Indian J Otolaryngol Head Neck Surg 2023; 75:1162-1168. [PMID: 37275115 PMCID: PMC10235340 DOI: 10.1007/s12070-022-03460-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/28/2022] [Indexed: 01/08/2023] Open
Abstract
Schwannomas are rare benign tumours of the nerve sheath. Extracranial schwannomas are usually found solitary, in the absence of other features of neurofibromatosis. The non NF1/2 multiple schwannomas are collectively described as the clinical scenario called schwannomatosis. We present a rare case of two extracranial schwannomas involving vagus and hypoglossal nerves in a 22-year-old female along with an unusual surgical complication of CSF leak presenting as post-op neck mass and a review of previously reported similar cases. A thorough literature search using the MeSH terms-'schwannomatosis' or 'Multiple Schwannoma' and 'Vagal Schwannoma' and 'Hypoglossal Schwannoma', was conducted using online databases and augmentated by hand search. A total of 13 reported cases were found and reviewed. Of the 14 cases described from review of literature and our case, 50% had involvement of vagus nerve as one of the components. 12.5% had hypoglossal and cervical sympathetic plexus involvement each. All patients underwent surgical excision. Half of the patients suffered intraoperative nerve sacrifice with resultant severe functional deficits like vocal cord paralysis, Horners syndrome, hypoglossal palsy, facial palsy and eleventh nerve palsy. In our case, there was un-unusual complication of CSF leak presenting as a cervical neck mass. Multiple extracranial head and neck schwannomas are rare and their management is fraught with several complications. Decision to operate is often perplexing. However, early planned surgical excision and preservation of nerve of origin minimizes the impact on quality of life postoperatively.
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Affiliation(s)
- Neha Verma
- Department of Otorhinolaryngology, University College of Medical Sciences and GTB Hospital, Delhi, India
| | - Manisha Yadav
- Department of Otorhinolaryngology, University College of Medical Sciences and GTB Hospital, Delhi, India
- Department of Otorhinolaryngology, Dr Baba Saheb Ambedkar Medical College and Hospital, Delhi, India
| | - Garima Yadav
- Department of Otorhinolaryngology, University College of Medical Sciences and GTB Hospital, Delhi, India
- Department of Otorhinolaryngology, Shaheed Hasan Khan Mewati, Government Medical College, Nalhar, Nuh, Haryana India
| | - Suvercha Arya
- Department of Otorhinolaryngology, University College of Medical Sciences and GTB Hospital, Delhi, India
- Department of Otorhinolaryngology, Maulana Azad Medical College, LNJP Hospital, Delhi, India
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Mishra M, Yadav M, Kumar S, Kumar R, Sen P. TIM-3 increases the abundance of type-2 dendritic cells during Leishmania donovani infection by enhancing IL-10 production via STAT3. Cell Death Dis 2023; 14:331. [PMID: 37202419 PMCID: PMC10195822 DOI: 10.1038/s41419-023-05848-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023]
Abstract
The outcome of the disease visceral leishmaniasis (VL), caused by Leishmania donovani (LD), largely relies on the relative dominance of host-protective type-1 T helper (Th1) cell response versus disease-promoting type-2 T helper (Th2) cell response. The Th1 and Th2 responses, in turn, are believed to be elicited by type-1 conventional dendritic cells (cDC1) and type-2 conventional DCs (cDC2), respectively. However, it is still unknown which DC subtype (cDC1 or cDC2) predominates during chronic LD infection and the molecular mechanism governing such occurrence. Here we report that in chronically infected mice, the splenic cDC1-cDC2 balance shifted toward the cDC2 subtype and that the receptor T cell immunoglobulin and mucin protein-3 (TIM-3) expressed by DCs played a key role in mediating this effect. Transfer of TIM-3-silenced DCs in fact prevented the predominance of the cDC2 subtype in mice with chronic LD infection. We also found that LD actually upregulated TIM-3 expression on DCs by triggering a TIM-3-mediated signaling pathway STAT3 (signal transducer and activator of transcription 3)→interleukin (IL)-10→c-Src→transcription factors Ets1, Ets2, USF1, and USF2. Notably, TIM-3 promoted STAT3 activation via a non-receptor tyrosine kinase Btk. Adoptive transfer experiments further demonstrated a critical role for STAT3-driven TIM-3 upregulation on DCs in increasing cDC2 abundance in chronically infected mice, which ultimately aided disease pathogenesis by augmenting Th2 responses. These findings document a new immunoregulatory mechanism contributing to disease pathology during LD infection and define TIM-3 as a key mediator of this process.
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Affiliation(s)
- Manish Mishra
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Manisha Yadav
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Sandeep Kumar
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raj Kumar
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Pradip Sen
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Yadav M, Eswari JS. LppDB - a Comprehensive Database for Lipopeptide based drugs: Exploring potential drug discovery aspects. Curr Pharm Biotechnol 2023:CPB-EPUB-130722. [PMID: 37038708 DOI: 10.2174/1389201024666230406084753] [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: 08/31/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 04/12/2023]
Abstract
AIM Lipopeptides are amphiphilic compounds consisting of a cyclic peptide attached to a fatty acid side chain. These are found with various medicinal properties ranging from broad-spectrum antimicrobial to anticancer properties. INTRODUCTION Elaborated studies on the therapeutic properties of peptides are hindered due to a lack of databases specifically dedicated to such classes of compounds where all the medicinal information of compounds is collectively studied in one place, which can accelerate the future scope of research on peptidolipidic compounds. METHOD The chemical information was retrieved from the PubChem compound database, and their metabolism information was generated through Swiss ADME. The application information about their particular pathways was obtained from different kinds of literature. RESULTS A python script was developed to extract the information about lipopeptides from a CSV file, and the information was stored in MySQL Database. The database contains information for 70 lipopeptides and their biochemical information, structure, chemical and physical properties, information on industrial and medicinal applications, functions and references for lipopeptides. CONCLUSION The development of web-based database applications allows the data stored in the database to be accessed and viewed publicly.
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Affiliation(s)
- Manisha Yadav
- Department of Biotechnology, National Institute of Technology Raipur, C.G., 492010, India
| | - J Satya Eswari
- Department of Biotechnology, National Institute of Technology Raipur, C.G., 492010, India
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Yadav M, Kumar M, Chahal A, Sodhi N, Chhillar B, Alajangi HK, Barnwal RP, Singh VP. Synthesis, Reactions, and Antioxidant Properties of Bis(3-amino-1-hydroxybenzyl)diselenide. J Org Chem 2023; 88:3509-3522. [PMID: 36847416 DOI: 10.1021/acs.joc.2c02739] [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: 03/01/2023]
Abstract
Bis(3-amino-1-hydroxybenzyl)diselenide containing two ortho groups was synthesized from 7-nitro-3H-2,1-benzoxaselenole and in situ generated sodium benzene tellurolate (PhTeNa). One-pot synthesis of 1,3-benzoselenazoles was achieved from bis(3-amino-1-hydroxybenzyl)diselenide and aryl aldehydes using acetic acid as a catalyst. The X-ray crystal structure of chloro-substituted benzoselenazole revealed a planar structure with T-shaped geometry around the Se atom. Both natural bond orbital and atoms in molecules calculations confirmed the presence of secondary Se···H interactions in bis(3-amino-1-hydroxybenzyl)diselenide and Se···O interactions in benzoselenazoles, respectively. The glutathione peroxidase (GPx)-like antioxidant activities of all compounds were evaluated using a thiophenol assay. Bis(3-amino-1-hydroxybenzyl)diselenide and benzoselenazoles showed better GPx-like activity compared to that of the diphenyl diselenide and ebselen, used as references, respectively. Based on 77Se{1H} NMR spectroscopy, a catalytic cycle for bis(3-amino-1-hydroxybenzyl)diselenide using thiophenol and hydrogen peroxide was proposed involving selenol, selenosulfide, and selenenic acid as intermediates. The potency of all GPx mimics was confirmed by their in vitro antibacterial properties against the biofilm formation of Bacillus subtilis and Pseudomonas aeruginosa. Additionally, molecular docking studies were used to evaluate the in silico interactions between the active sites of the TsaA and LasR-based proteins found in Bacillus subtilis and Pseudomonas aeruginosa.
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Affiliation(s)
- Manisha Yadav
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160 014, India
| | - Manish Kumar
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160 014, India
| | - Alka Chahal
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160 014, India
| | - Nikhil Sodhi
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160 014, India
| | - Babli Chhillar
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160 014, India
| | - Hema Kumari Alajangi
- Department of Biophysics, Panjab University, Sector-25, Chandigarh 160 014, India
| | - Ravi Pratap Barnwal
- Department of Biophysics, Panjab University, Sector-25, Chandigarh 160 014, India
| | - Vijay P Singh
- Department of Chemistry & Centre of Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160 014, India
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Burgos A, Acevedo Alvarez M, Chen Y, Gevelinger M, Nwachokor J, Yadav M, Mueller E, Adams W, Pham T. The use of the ipop model for the improvement of resident performance of the pop-q exam. Am J Obstet Gynecol 2023. [DOI: 10.1016/j.ajog.2022.12.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
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20
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Kumar D, Singhal C, Yadav M, Joshi P, Patra P, Tanwar S, Das A, Kumar Pramanik S, Chaudhuri S. Colistin potentiation in multidrug-resistant Acinetobacter baumannii by a non-cytotoxic guanidine derivative of silver. Front Microbiol 2023; 13:1006604. [PMID: 36687622 PMCID: PMC9846554 DOI: 10.3389/fmicb.2022.1006604] [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: 07/29/2022] [Accepted: 11/23/2022] [Indexed: 01/06/2023] Open
Abstract
A novel nano-formulation (NF) that sensitizes Acinetobacter baumannii (AB) to otherwise ineffective colistin is described in the present study. Infections due to multidrug resistant (MDR) AB represent a major therapeutic challenge, especially in situations of pre-existing colistin resistance (colR). Subsequently, boosting the effectiveness of colistin would be a better alternative tactic to treat AB infections rather than discovering a new class of antibiotics. We have previously demonstrated an NF comprising self-assembled guanidinium and ionic silver nanoparticles [AD-L@Ag(0)] to have anti-biofilm and bactericidal activity. We report NF AD-L@Ag(0) for the very first time for the potentiation of colistin in Gram-negative colistin-resistant bacteria. Our results implied that a combination of clinically relevant concentrations of colistin and AD-L@Ag(0) significantly decreased colistin-resistant AB bacterial growth and viability, which otherwise was elevated in the presence of only colistin. In this study, we have described various combinations of minimum inhibitory concentration (MIC) of colistin (MICcol, 1/2 MICcol, and 1/4 MICcol) and that of AD-L@Ag(0) [MICAD-L@Ag(0), 1/2 MICAD-L@Ag(0), and 1/4 MICAD-L@Ag(0)] and tested them against MDR AB culture. The results (in broth as well as in solid media) signified that AD-L@Ag(0) was able to potentiate the anti-microbial activity of colistin at sub-MIC concentrations. Furthermore, the viability and metabolic activity of bacterial cells were also measured by CTC fluorescence assay and ATP bioluminescence assay. The results of these assays were in perfect concordance with the scores of cultures (colony forming unit and culture turbidity). In addition, quantitative real-time PCR (qRT-PCR) was performed to unveil the expression of selected genes, DNAgyrA, DNAgyrB, and dac. These genes introduce negative supercoiling in the DNA, and hence are important for basic cellular processes. These genes, due to mutation, modified the Lipid A of bacteria, further resisting the uptake of colistin. Therefore, the expression of these genes was upregulated when AB was treated with only colistin, substantiating that AB is resistant to colistin, whereas the combinations of MICcol + MICAD-L@Ag(0) downregulated the expression of these genes, implying that the developed formulation can potentiate the efficiency of colistin. In conclusion, AD-L@Ag(0) can potentiate the proficiency of colistin, further enhancing colistin-mediated death of AB by putatively disrupting the outer membrane (OM) and facilitating bacterial death.
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Affiliation(s)
- Deepak Kumar
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Chaitali Singhal
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Manisha Yadav
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Pooja Joshi
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Priyanka Patra
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India
| | - Subhash Tanwar
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Amitava Das
- Indian Institute of Science Education and Research Kolkata, Mohanpur, India,*Correspondence: Amitava Dasc,
| | - Sumit Kumar Pramanik
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, India,Sumit Kumar Pramanikb,
| | - Susmita Chaudhuri
- Translational Health Science and Technology Institute (THSTI), Faridabad, India,Susmita Chaudhuria,
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21
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Bø K, Anglès-Acedo S, Batra A, Brækken IH, Chan YL, Jorge CH, Kruger J, Yadav M, Dumoulin C. Are hypopressive and other exercise programs effective for the treatment of pelvic organ prolapse? Int Urogynecol J 2023; 34:43-52. [PMID: 36418569 PMCID: PMC9834161 DOI: 10.1007/s00192-022-05407-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/03/2022] [Indexed: 11/27/2022]
Abstract
INTRODUCTION AND HYPOTHESIS Pelvic floor muscle training (PFMT) is effective for the treatment of pelvic organ prolapse (POP), but other exercise programs have also been promoted and used. The aim of this review was to evaluate the effect of hypopressive and other exercise programs besides PFMT for POP. METHODS A literature search was conducted on Ovid Medline, EMBASE, CINAHL, Cochrane, PEDro, and Scopus databases from January 1996 to 30 December 2021. Only randomized controlled trials (RCTs) were included. The keywords were combinations of "pelvic organ prolapse" or "urogenital prolapse," and "exercise therapy," "hypopressive exercise," "Kegel," "pelvic floor muscle training," "pelvic floor muscle exercises," "Pilates," "treatment," "yoga," "Tai Chi." Methodological quality was assessed using the PEDro rating scale (0-10). RESULTS Seven RCTs containing hypopressive exercise, yoga or breathing and hip muscle exercises in an inverted position were retrieved and analyzed. PEDro score ranged from 4 to 7. There was no additional effect of adding hypopressive exercise to PFMT, and PFMT was more effective than hypopressive exercise alone. The studies that included the term "yoga" included regular PFMT and thus can be classified as PFMT. Hip exercises in an inverted position added to PFMT vs PFMT alone showed better improvement in some secondary outcomes but not in the primary outcome, POP stage. CONCLUSIONS There are few RCTs assessing the effects of other exercise programs besides PFMT in the treatment of POP. To date, there is no evidence that other exercise programs are more effective than PFMT for POP.
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Affiliation(s)
- Kari Bø
- Department of Sports Medicine, The Norwegian School of Sport Sciences, PO Box 4014, Ullevål stadion, 0806, Oslo, Norway.
- Department of Obstetrics and Gynecology, Akershus University Hospital, Lørenskog, Norway.
| | | | - Achla Batra
- Department of Obstetrics & Gynaecology, VMMC & Safdarjung Hospital, New Delhi, India
| | - Ingeborg H Brækken
- Kolbotn Physical Institute, Nordre Follo Municipality, Norway
- The Pelvic Floor Centre, Division of Surgery, Akershus University Hospital, Lørenskog, Norway
| | - Yi Ling Chan
- Department of Obstetrics and Gynaecology, Calderdale and Huddersfield NHS Foundation Trust, Huddersfield, UK
| | - Cristine Homsi Jorge
- Department of Health Science Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Jennifer Kruger
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Manisha Yadav
- Paropakar Maternity and Women's Hospital, Kathmandu, Thapathali, Nepal
| | - Chantale Dumoulin
- School of Rehabilitation, Faculty of Medicine, Université de Montréal, Montréal, Canada
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22
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Yadav M, Singh IK, Singh A. Dhurrin: A naturally occurring phytochemical as a weapon against insect herbivores. Phytochemistry 2023; 205:113483. [PMID: 36279963 DOI: 10.1016/j.phytochem.2022.113483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Dhurrin, a cyanogenic glucoside, is a plant defensive chemical synthesized from aliphatic amino acids and consists of β-d-glucopyranose linked to α-hydroxy nitrile. It is catabolized by the consecutive action of hydroxynitrilase and β-glucosidase to release hydrogen cyanide on tissue disruption during herbivory. These phytoanticipins are widely distributed across various monocot and dicot plants such as Sorghum, Macadamia, Ostrya sp., and many other plant species with ornamental, pharmaceutical, medicinal, and food value. Although repellent properties of dhurrin against herbivores are often reported, less is known about its distribution, metabolism, mode of action against insects, and application for pest control. Herein, we highlight recent updates on dhurrin distribution, biosynthesis, and catabolism along with the cyanide detoxification pathway. Additionally, this article focuses on biological activities of dhurrin against various herbivores and opportunities to explore the utilization of dhurrin as a natural pest control agent and a substitute for chemically synthesized pesticides.
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Affiliation(s)
- Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India; Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, 110007, India.
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Yadav M, Eswari JS. Opportunistic Challenges of Computer-aided Drug Discovery of Lipopeptides: New Insights for Large Molecule Therapeutics. Avicenna J Med Biotechnol 2023; 15:3-13. [PMID: 36789119 PMCID: PMC9895984 DOI: 10.18502/ajmb.v15i1.11419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/27/2022] [Indexed: 12/27/2022] Open
Abstract
Computer-aided drug designing is a promising approach to defeating the dry pipeline of drug discovery. It aims at reduced experimental efforts with cost-effectiveness. Naturally occurring large molecules with molecular weight higher than 500 Dalton such as cationic peptides, cyclic peptides, glycopeptides and lipopeptides are a few examples of large molecules which have successful applications as the broad spectrum antibacterial, anticancer, antiviral, antifungal and antithrombotic drugs. Utilization of microbial metabolites as potential drug candidates incur cost effectiveness through large scale production of such molecules rather than a synthetic approach. Computational studies on such compounds generate tremendous possibilities to develop novel leads with challenges to handle these complex molecules with available computational tools. The opportunities begin with the desired structural modifications in the parent drug molecule. Virtual modifications followed by molecular interaction studies at the target site through molecular modeling simulations and identification of structure-activity relationship models to develop more prominent and potential drug molecules. Lead optimization studies to develop novel compounds with increased specificity and reduced off targeting is a big challenge computationally for large molecules. Prediction of optimized pharmacokinetic properties facilitates development of a compound with lower toxicity as compared to the natural compounds. Generating the library of compounds and studies for target specificity and ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) for large molecules are laborious and incur huge cost and chemical wastage through in-vitro methods. Hence, computational methods need to be explored to develop novel compounds from natural large molecules with higher specificity. This review article is focusing on possible challenges and opportunities in the pathway of computer-aided drug discovery of large molecule therapeutics.
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Affiliation(s)
- Manisha Yadav
- Department of Biotechnology, National Institute of Technology Raipur, C.G., India
| | - J. Satya Eswari
- Department of Biotechnology, National Institute of Technology Raipur, C.G., India
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24
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Yadav M, Dhyani S, Joshi P, Awasthi S, Tanwar S, Gupta V, Rathore DK, Chaudhuri S. Formic acid, an organic acid food preservative, induces viable-but-non-culturable state, and triggers new Antimicrobial Resistance traits in Acinetobacter baumannii and Klebsiella pneumoniae. Front Microbiol 2022; 13:966207. [PMID: 36504816 PMCID: PMC9730046 DOI: 10.3389/fmicb.2022.966207] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
Numerous human pathogens, especially Gram-negative bacteria, are able to enter the viable-but-non-culturable (VBNC) state when they are exposed to environmental stressors and pose the risk of being resuscitated and causing infection after the removal of the trigger. Widely used food preservatives like weak organic acids are potential VBNC inducers in food processing and packaging facilities but have only been reported for food-borne pathogens. In the present study, it is demonstrated for the first time that one such agent, formic acid (FA), can induce a VBNC state at food processing, storage, and distribution temperatures (4, 25, and 37°C) with a varied time of treatment (days 4-10) in pathogenic Gram-negative bacteria Acinetobacter baumannii and Klebsiella pneumoniae. The use of hospital-associated pathogens is critical based on the earlier reports that demonstrated the presence of these bacteria in hospital kitchens and commonly consumed foods. VBNC induction was validated by multiple parameters, e.g., non-culturability, metabolic activity as energy production, respiratory markers, and membrane integrity. Furthermore, it was demonstrated that the removal of FA was able to resuscitate VBNC with an increased expression of multiple virulence and Antimicrobial Resistance (AMR) genes in both pathogens. Since food additives/preservatives are significantly used in most food manufacturing facilities supplying to hospitals, contamination of these packaged foods with pathogenic bacteria and the consequence of exposure to food additives emerge as pertinent issues for infection control, and control of antimicrobial resistance in the hospital setting.
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Affiliation(s)
| | | | | | | | | | | | | | - Susmita Chaudhuri
- Department of Multidisciplinary Clinical and Translational Research, Translational Health Science and Technology Institute, Faridabad, Haryana, India
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25
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Rathi B, Gupta S, Kumar P, Kesarwani V, Dhanda RS, Kushwaha SK, Yadav M. Anti-biofilm activity of caffeine against uropathogenic E. coli is mediated by curli biogenesis. Sci Rep 2022; 12:18903. [PMID: 36344808 PMCID: PMC9640630 DOI: 10.1038/s41598-022-23647-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Biofilms are assemblages of sessile microorganisms that form an extracellular matrix around themselves and mediate attachment to surfaces. The major component of the extracellular matrix of Uropathogenic E. coli and other Enterobacteriaceae are curli fibers, making biofilms robust and resistant to antimicrobials. It is therefore imperative to screen antibiofilm compounds that can impair biofilm formation. In the present study, we investigated the curli-dependent antibiofilm activity of caffeine against UPEC strain CFT073 and commensal strain E. coli K-12MG1655.Caffeine significantly reduced the biofilm formation of both UPEC and E. coli K-12 by 86.58% and 91.80% respectively at 48 mM caffeine as determined by Crystal Violet assay. These results were further confirmed by fluorescence microscopy and Scanning Electron Microscope (SEM). Caffeine significantly reduced the cytotoxicity and survivability of UPEC. Molecular docking analysis revealed a strong interaction between caffeine and curli regulator protein (Csg D) of E. coli. The qRT-PCR data also showed significant downregulation in the expression of CsgBA and the CsgDEFG operon at both 24 mM and 48 mM caffeine. The findings revealed that caffeine could inhibit E. coli biofilm formation by regulating curli assembly and thus may be used as an alternative therapeutic strategy for the treatment of chronic E. coli biofilm-related infections.
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Affiliation(s)
- Bhawna Rathi
- grid.8195.50000 0001 2109 4999Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, 110007 India
| | - Surbhi Gupta
- grid.8195.50000 0001 2109 4999Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, 110007 India
| | - Parveen Kumar
- grid.265892.20000000106344187Department of Urology, University of Alabama at Birmingham, Birmingham, AL USA
| | | | | | - Sandeep Kumar Kushwaha
- grid.508105.90000 0004 1798 2821DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, India
| | - Manisha Yadav
- grid.8195.50000 0001 2109 4999Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, 110007 India ,grid.4514.40000 0001 0930 2361Department of Clinical Sciences, Lund University, Malmö, Sweden
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Sharma N, Yadav M, Tripathi G, Mathew B, Bindal V, Falari S, Pamecha V, Maras JS. Bile multi-omics analysis classifies lipid species and microbial peptides predictive of carcinoma of gallbladder. Hepatology 2022; 76:920-935. [PMID: 35357716 DOI: 10.1002/hep.32496] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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] [Received: 01/05/2022] [Revised: 03/14/2022] [Accepted: 03/27/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND AIMS Histopathological examination is the gold standard for detection of gallstone (GS) or gallbladder carcinoma (CAGB). Bile concentrated in the gallbladder (GB) is expected to recapitulate metagenomics and molecular changes associated with development of CAGB. APPROACH AND RESULTS Bile samples were screened for lipidomics and metaproteome (metagenomics) signatures capable of early detection of cancer in GB anomalies. Analysis of the training cohort (n = 87) showed that metastability of bile was reduced in CAGB (p < 0.05). CAGB bile showed significant alteration of lipidome and microbiome as indicated by multivariate partial least squares regression analysis and alpha-diversity and beta-diversity indexes (p < 0.05). Significant reduction of lipid species and increase in bacterial taxa were found to be associated with patients with CAGB, CAGB with GS, and GS (p < 0.05, log fold change >1.5). A multimodular correlation network created using weighted lipid/metaproteomic correlation network analysis showed striking associations between lipid and metaproteomic modules and functionality. CAGB-linked metaproteomic modules/functionality directly correlated with lipid modules, species, clinical parameters, and bile acid profile (p < 0.05). Increased bacterial taxa (Leptospira, Salmonella enterica, Mycoplasma gallisepticum) and their functionality showed a direct correlation with lipid classes such as lysophosphatidylinositol, ceramide 1-phosphate, and lysophosphatidylethanolamine and development of CAGB (r2 > 0.85). Lipid/metaproteomic signature-based probability of detection for CAGB was > 90%, whereas that for GS was > 80% (p < 0.05). Validation of eight lipid species using four machine learning algorithms in two separate cohorts (n = 38; bile [test cohort 1] and paired plasma [test cohort 2]) showed accuracy (99%) and sensitivity/specificity (>98%) for CAGB detection. CONCLUSIONS Bile samples of patients with CAGB showed significant reduction in lipid species and increase in bacterial taxa. Our study identifies a core set of bile lipidome and metaproteome signatures which may offer universal utility for early diagnosis of CAGB.
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Affiliation(s)
- Nupur Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Manisha Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Gaurav Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Babu Mathew
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Vasundhra Bindal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Sanyam Falari
- Department of Hepatobiliary Surgery, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Viniyendra Pamecha
- Department of Hepatobiliary Surgery, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Jaswinder Singh Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
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27
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Bø K, Anglès-Acedo S, Batra A, Brækken IH, Chan YL, Jorge CH, Kruger J, Yadav M, Dumoulin C. International urogynecology consultation chapter 3 committee 2; conservative treatment of patient with pelvic organ prolapse: Pelvic floor muscle training. Int Urogynecol J 2022; 33:2633-2667. [PMID: 35980443 PMCID: PMC9477909 DOI: 10.1007/s00192-022-05324-0] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 02/05/2023]
Abstract
INTRODUCTION AND HYPOTHESIS This manuscript from Chapter 3 of the International Urogynecology Consultation (IUC) on Pelvic Organ Prolapse (POP) describes the current evidence and suggests future directions for research on the effect of pelvic floor muscle training (PFMT) in prevention and treatment of POP. METHODS An international group of four physical therapists, four urogynecologists and one midwife/basic science researcher performed a search of the literature using pre-specified search terms on randomized controlled trials (RCTs) in Ovid Medline, EMBASE, CINAHL, Cochrane, PEDro and Scopus databases for publications between 1996 and 2021. Full publications or expanded abstracts in English or in other languages with abstracts in English were included. The PEDro rating scale (0-10) was used to evaluate study quality. Included RCTs were reviewed to summarize the evidence in six key sections: (1) evidence for PFMT in prevention of POP in the general female population; (2) evidence for early intervention of PFMT in the peripartum period for prevention and treatment of POP; (3) evidence for PFMT in treatment of POP in the general female population; (4) evidence for perioperative PFMT; (5) evidence for PFMT on associated conditions in women with POP; (6) evidence for the long-term effect of PFMT on POP. Full publications in English or in other languages with abstracts in English and expanded abstracts presented at international condition specific societies were included. Internal validity was examined by the PEDro rating scale (0-10). RESULTS After exclusion of duplicates and irrelevant trials, we classified and included 2 preventive trials, 4 trials in the post-partum period, 11 treatment trials of PFMT for POP in the general female population in comparison with no treatment or lifestyle interventions, 10 on PFMT as an adjunct treatment to POP surgery and 9 long-term treatment trials. Only three treatment studies compared PFMT with the use of a pessary. The RCTs scored between 4 and 8 on the PEDro scale. No primary prevention studies were found, and there is sparse and inconsistent evidence for early intervention in the postpartum period. There is good evidence/recommendations from 11 RCTs that PFMT is effective in reducing POP symptoms and/or improving POP stage (by one stage) in women with POP-Q stage I, II and III in the general female population, but no evidence from 9/10 RCTs that adding PFMT pre- and post -surgery for POP is effective. There are few long-term follow-up studies, and results are inconsistent. There are no serious adverse effects or complications reported related to PFMT. CONCLUSIONS There are few studies on prevention and in the postpartum period, and the effect is inconclusive. There is high-level evidence from 11 RCTs to recommend PFMT as first-line treatment for POP in the general female population. PFMT pre- and post-POP surgery does not seem to have any additional effect on POP. PFMT is effective and safe but needs thorough instruction and supervision to be effective.
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Affiliation(s)
- Kari Bø
- Department of Sports Medicine, The Norwegian School of Sport Sciences, PO Box 4014, Ullevål stadion, 0806, Oslo, Norway.
- Department of Obstetrics and Gynecology, Akershus University Hospital, Lørenskog, Norway.
| | | | - Achla Batra
- Department of Obstetrics & Gynaecology, VMMC & Safdarjung Hospital, New Delhi, India
| | - Ingeborg Hoff Brækken
- Kolbotn Physical Institute, Nordre Follo Municipality, Nordre Follo, Norway
- The Pelvic Floor Centre, Division of Surgery, Akershus University Hospital, Lørenskog, Norway
| | - Yi Ling Chan
- Department of Obstetrics and Gynaecology, Calderdale and Huddersfield NHS Foundation Trust, Huddersfield, UK
| | - Cristine Homsi Jorge
- Department of Health Science Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Jennifer Kruger
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Manisha Yadav
- Paropakar Maternity and women's hospital, Thapathali, Kathmandu, Nepal
| | - Chantale Dumoulin
- School of rehabilitation, Faculty of Medicine, Université de Montréal, Montréal, Canada
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Sharma N, Yadav M, Tripathi G, Mathew B, Bindal V, Falari S, Pamecha V, Maras JS. Reply. Hepatology 2022; 76:E76-E77. [PMID: 35477894 DOI: 10.1002/hep.32541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 12/08/2022]
Affiliation(s)
- Nupur Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Manisha Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Gaurav Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Babu Mathew
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Vasundhra Bindal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Sanyam Falari
- Department of Hepatobiliary Surgery, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Viniyendra Pamecha
- Department of Hepatobiliary Surgery, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Jaswinder Singh Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
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Oezkan F, Hilz S, Grindheim J, Wallace A, Seweryn M, Reuben A, Zhang J, Owen D, Nicholas A, Yadav M, Nagarkar D, de Almeida P, Ebert P, Osborne E, Johnson A, Lee J, Bunn P, Johnson B, Chaft J, Kris M, Rusch V, Schulze K, Kwiatkowski D, Wistuba I, Carbone D. OA14.06 T-Cell Dynamics in Response to Neoadjuvant Atezolizumab in Early NSCLC by Antigen Response and T-Cell Receptor Sequencing. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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30
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Dey A, Yadav M, Kumar D, Dey AK, Samal S, Tanwar S, Sarkar D, Pramanik SK, Chaudhuri S, Das A. A combination therapy strategy for treating antibiotic resistant biofilm infection using a guanidinium derivative and nanoparticulate Ag(0) derived hybrid gel conjugate. Chem Sci 2022; 13:10103-10118. [PMID: 36128224 PMCID: PMC9430544 DOI: 10.1039/d2sc02980d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 05/28/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteria organized in biofilms show significant tolerance to conventional antibiotics compared to their planktonic counterparts and form the basis for chronic infections. Biofilms are composites of different types of extracellular polymeric substances that help in resisting several host-defense measures, including phagocytosis. These are increasingly being recognized as a passive virulence factor that enables many infectious diseases to proliferate and an essential contributing facet to anti-microbial resistance. Thus, inhibition and dispersion of biofilms are linked to addressing the issues associated with therapeutic challenges imposed by biofilms. This report is to address this complex issue using a self-assembled guanidinium-Ag(0) nanoparticle (AD-L@Ag(0)) hybrid gel composite for executing a combination therapy strategy for six difficult to treat biofilm-forming and multidrug-resistant bacteria. Improved efficacy was achieved primarily through effective biofilm inhibition and dispersion by the cationic guanidinium ion derivative, while Ag(0) contributes to the subsequent bactericidal activity on planktonic bacteria. Minimum Inhibitory Concentration (MIC) of the AD-L@Ag(0) formulation was tested against Acinetobacter baumannii (25 μg mL-1), Pseudomonas aeruginosa (0.78 μg mL-1), Staphylococcus aureus (0.19 μg mL-1), Klebsiella pneumoniae (0.78 μg mL-1), Escherichia coli (clinical isolate (6.25 μg mL-1)), Klebsiella pneumoniae (clinical isolate (50 μg mL-1)), Shigella flexneri (clinical isolate (0.39 μg mL-1)) and Streptococcus pneumoniae (6.25 μg mL-1). Minimum bactericidal concentration, and MBIC50 and MBIC90 (Minimum Biofilm Inhibitory Concentration at 50% and 90% reduction, respectively) were evaluated for these pathogens. All these results confirmed the efficacy of the formulation AD-L@Ag(0). Minimum Biofilm Eradication Concentration (MBEC) for the respective pathogens was examined by following the exopolysaccharide quantification method to establish its potency in inhibition of biofilm formation, as well as eradication of mature biofilms. These effects were attributed to the bactericidal effect of AD-L@Ag(0) on biofilm mass-associated bacteria. The observed efficacy of this non-cytotoxic therapeutic combination (AD-L@Ag(0)) was found to be better than that reported in the existing literature for treating extremely drug-resistant bacterial strains, as well as for reducing the bacterial infection load at a surgical site in a small animal BALB/c model. Thus, AD-L@Ag(0) could be a promising candidate for anti-microbial coatings on surgical instruments, wound dressing, tissue engineering, and medical implants.
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Affiliation(s)
- Ananta Dey
- CSIR - Central Salt and Marine Chemical Research Institute Bhavnagar Gujarat India
- Indian Institute of Science Education and Research Kolkata Mohanpur 741246 West Bengal India
| | - Manisha Yadav
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Deepak Kumar
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Anik Kumar Dey
- CSIR - Central Salt and Marine Chemical Research Institute Bhavnagar Gujarat India
| | - Sweety Samal
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Subhash Tanwar
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Debrupa Sarkar
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Sumit Kumar Pramanik
- CSIR - Central Salt and Marine Chemical Research Institute Bhavnagar Gujarat India
| | - Susmita Chaudhuri
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Amitava Das
- Indian Institute of Science Education and Research Kolkata Mohanpur 741246 West Bengal India
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Kataria B, Sharma A, Pramanik R, Sahoo R, Thulkar S, Yadav M, Mishra S, Prasad C, Vishnubhatla S. PD-9 Three-arm phase II/III randomized controlled trial in patients with unresectable/metastatic gall bladder cancer with poor performance status: Erlotinib or capecitabine v/s best supportive care. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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32
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Singh RS, Vidhyasagar V, Yang S, Arna AB, Yadav M, Aggarwal A, Aguilera AN, Shinriki S, Bhanumathy KK, Pandey K, Xu A, Rapin N, Bosch M, DeCoteau J, Xiang J, Vizeacoumar FJ, Zhou Y, Misra V, Matsui H, Ross SR, Wu Y. DDX41 is required for cGAS-STING activation against DNA virus infection. Cell Rep 2022; 39:110856. [PMID: 35613581 PMCID: PMC9205463 DOI: 10.1016/j.celrep.2022.110856] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 12/27/2022] Open
Abstract
Upon binding double-stranded DNA (dsDNA), cyclic GMP-AMP synthase (cGAS) is activated and initiates the cGAS-stimulator of IFN genes (STING)-type I interferon pathway. DEAD-box helicase 41 (DDX41) is a DEAD-box helicase, and mutations in DDX41 cause myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). Here, we show that DDX41-knockout (KO) cells have reduced type I interferon production after DNA virus infection. Unexpectedly, activations of cGAS and STING are affected in DDX41 KO cells, suggesting that DDX41 functions upstream of cGAS. The recombinant DDX41 protein exhibits ATP-dependent DNA-unwinding activity and ATP-independent strand-annealing activity. The MDS/AML-derived mutant R525H has reduced unwinding activity but retains normal strand-annealing activity and stimulates greater cGAS dinucleotide-synthesis activity than wild-type DDX41. Overexpression of R525H in either DDX41-deficient or -proficient cells results in higher type I interferon production. Our results have led to the hypothesis that DDX41 utilizes its unwinding and annealing activities to regulate the homeostasis of dsDNA and single-stranded DNA (ssDNA), which, in turn, regulates cGAS-STING activation. cGAS is activated by dsDNA. Singh et al. find DDX41 regulates cGAS activation through unwinding and annealing activities on dsDNA and ssDNA, respectively, and MDS/AML patient mutant R525H causes overactivation of innate immune response due to its unbalanced activities. This DDX41-cGAS-STING pathway may be related to molecular pathogenesis of MDS/AML.
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Affiliation(s)
- Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | | | - Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Ananna Bhadra Arna
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Manisha Yadav
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Aanchal Aggarwal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada
| | - Alexya N Aguilera
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Satoru Shinriki
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | | | - Kannupriya Pandey
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Aizhang Xu
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - Noreen Rapin
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Mark Bosch
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - John DeCoteau
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Jim Xiang
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada
| | - Franco J Vizeacoumar
- Saskatchewan Cancer Agency, Saskatoon, SK S7N 5E5, Canada; Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Vikram Misra
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Susan R Ross
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon SK S7N 5E5, Canada.
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Abstract
Drought is the most prevalent environmental stress that affects plants' growth, development, and crop productivity. However, plants have evolved adaptive mechanisms to respond to the harmful effects of drought. They reprogram their: transcriptome, proteome, and metabolome that alter their cellular and physiological processes and establish cellular homeostasis. One of the crucial regulatory processes that govern this reprogramming is post-transcriptional regulation by microRNAs (miRNAs). miRNAs are small non-coding RNAs, involved in the downregulation of the target mRNA via translation inhibition/mRNA degradation/miRNA-mediated mRNA decay/ribosome drop off/DNA methylation. Many drought-inducible miRNAs have been identified and characterized in plants. Their main targets are regulatory genes that influence growth, development, osmotic stress tolerance, antioxidant defense, phytohormone-mediated signaling, and delayed senescence during drought stress. Overexpression of drought-responsive miRNAs (Osa-miR535, miR160, miR408, Osa-miR393, Osa-miR319, and Gma-miR394) in certain plants has led to tolerance against drought stress indicating their vital role in stress mitigation. Similarly, knock down (miR166/miR398c) or deletion (miR169 and miR827) of miRNAs has also resulted in tolerance to drought stress. Likewise, engineered Arabidopsis plants with miR165, miR166 using short tandem target mimic strategy, exhibited drought tolerance. Since miRNAs regulate the expression of an array of drought-responsive genes, they can act as prospective targets for genetic manipulations to enhance drought tolerance in crops and achieve sustainable agriculture. Further investigations toward functional characterization of diverse miRNAs, and understanding stress-responses regulated by these miRNAs and their utilization in biotechnological applications is highly recommended.
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Affiliation(s)
- Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Deepti Jain
- Department of Plant Molecular Biology, Interdisciplinary Centre for Plant Genomics, Delhi University South Campus, New Delhi, India
| | - Jyotsna Pandey
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Kailash C Bansal
- The Alliance of Bioversity International and CIAT (CGIAR), New Delhi, India
| | - Indrakant K Singh
- Department of Zoology, Molecular Biology Research Lab, Deshbandhu College, University of Delhi, New Delhi, India.,DBC i4 Center, Deshbandhu College, University of Delhi, New Delhi, India
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Yadav M, Pundir S, Kumari R, Kumar A, Venugopal SJ, Panigrahy R, Tak V, Chunchanur SK, Gautam H, Kapil A, Das B, Sood S, Salve HR, Malhotra S, Kant S, Hari P, Chaudhuri S, Mohapatra S. Virulence gene mutations as a differentiator of clinical phenotypes: insights from community-acquired uropathogenic Escherichia coli. Microbiology (Reading) 2022; 168. [PMID: 35380532 DOI: 10.1099/mic.0.001161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) remains an important cause of urinary tract infection during pregnancy. Multiple molecular virulence determinants and antibiotic resistant genes facilitate its pathogenesis and virulence phenotype. Hence it is hypothesized that there will be considerable variation in genes among the isolates from symptomatic as well as asymptomatic bacteriuria (ABU) during pregnancy. The aim of this study was to decipher the genetic variation among the two phenotypes. Six different UPEC isolates collected from urine specimens of consecutive pregnant females (five, symptomatic bacteriuria and one, ABU) were tested for their growth kinetics, and biofilm formation. A total of 87 virulence determinants and 56 antibiotic resistance genes were investigated using whole-genome sequencing, to identify putative drives of virulence phenotype. In this analysis, we identified eight different types of fully functional toxin antitoxin (TA) systems [HipAB, YefM-YoeB, YeeU-YeeV (CbtA), YhaV-PrlF, ChpBS, HigAB, YgiUT and HicAB] in the isolates from symptomatic bacteriuria; whereas partially functional TA system with mutations were observed in the asymptomatic one. Isolates of both the groups showed equivalent growth characteristics and biofilm-formation ability. Genes for an iron transport system (Efe UOB system, Fhu system except FhuA) were observed functional among all symptomatic and asymptomatic isolates, however functional mutations were observed in the latter group. Gene YidE was observed predominantly associated with the biofilm formation along with few other genes (BssR, BssS, YjgK, etc.). This study outlines putative critical relevance of specific variations in the genes for the TA system, biofilm formation, cell adhesion and colonization among UPEC isolates from symptomatic and asymptomatic bacteriuria among pregnant women. Further functional genomic study in the same cohort is warranted to establish the pathogenic role of these genes.
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Affiliation(s)
- Manisha Yadav
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Swati Pundir
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Kumari
- Department of Obstetrics and Gynaecology, All India Institute of Medical Science, New Delhi, India
| | - Arvind Kumar
- Department of Medicine, All India Institute of Medical Science, New Delhi, India
| | - Shwetha J Venugopal
- Department of Microbiology, Bangalore Medical College and Research Institute, Bangalore, India
| | - Rajashree Panigrahy
- Department of Microbiology, Institute of Medical Sciences and SUM Hospital, Bhubaneswar, India
| | - Vibhor Tak
- Department of Microbiology, All India Institute of Medical Science, Jodhpur, India
| | - Sneha K Chunchanur
- Department of Microbiology, Bangalore Medical College and Research Institute, Bangalore, India
| | - Hitender Gautam
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Bimal Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Harshal Ramesh Salve
- Centre for Community Medicine, All India Institute of Medical Science, New Delhi, India
| | - Sumit Malhotra
- Centre for Community Medicine, All India Institute of Medical Science, New Delhi, India
| | - Shashi Kant
- Centre for Community Medicine, All India Institute of Medical Science, New Delhi, India
| | - Pankaj Hari
- Department of Pediatrics, All India Institute of Medical Science, New Delhi, India
| | - Susmita Chaudhuri
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Sarita Mohapatra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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Sharma N, Bhat SH, Tripathi G, Yadav M, Mathew B, Bindal V, Sharma S, Gupta E, Maras JS, Sarin SK. Global metabolome profiling of COVID-19 respiratory specimen using high-resolution mass spectrometry (HRMS). STAR Protoc 2022; 3:101051. [PMID: 34877545 PMCID: PMC8639449 DOI: 10.1016/j.xpro.2021.101051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Here we describe a protocol for identifying metabolites in respiratory specimens of patients that are SARS-CoV-2 positive, SARS-CoV-2 negative, or H1N1 positive. This protocol provides step-by-step instructions on sample collection from patients, followed by metabolite extraction. We use ultra-high-pressure liquid chromatography (UHPLC) coupled with high-resolution mass spectrometry (HRMS) for data acquisition and describe the steps for data analysis. The protocol was standardized with specific customization for SARS-CoV-2-containing respiratory specimens. For complete details on the use and execution of this protocol, please refer to Maras et al. (2021).
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Affiliation(s)
- Nupur Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Sadam H Bhat
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Gaurav Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Manisha Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Babu Mathew
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Vasundhra Bindal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Shvetank Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Ekta Gupta
- Departments of Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Jaswinder Singh Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi 110070, India
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Tripathi G, Sharma N, Bindal V, Yadav M, Mathew B, Sharma S, Gupta E, Singh Maras J, Sarin SK. Protocol for global proteome, virome, and metaproteome profiling of respiratory specimen (VTM) in COVID-19 patient by LC-MS/MS-based analysis. STAR Protoc 2022; 3:101045. [PMID: 34870243 PMCID: PMC8626227 DOI: 10.1016/j.xpro.2021.101045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In this protocol, we describe global proteome profiling for the respiratory specimen of COVID-19 patients, patients suspected with COVID-19, and H1N1 patients. In this protocol, details for identifying host, viral, or bacterial proteome (Meta-proteome) are provided. Major steps of the protocol include virus inactivation, protein quantification and digestion, desalting of peptides, high-resolution mass spectrometry (HRMS)-based analysis, and downstream bioinformatics analysis. For complete details on the use and execution of this profile, please refer to Maras et al. (2021).
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Affiliation(s)
- Gaurav Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Nupur Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Vasundhra Bindal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Manisha Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Babu Mathew
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Shvetank Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
| | - Ekta Gupta
- Department of Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Jaswinder Singh Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi 110070, India
- Corresponding author
| | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
- Corresponding author
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Singh S, Yadav M. Gestational Diabetes Mellitus among Pregnant Women Delivering in a Tertiary Care Hospital: A Descriptive Cross-sectional Study. JNMA J Nepal Med Assoc 2022; 60:229-233. [PMID: 35633259 PMCID: PMC9226727 DOI: 10.31729/jnma.7304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/11/2022] [Indexed: 11/01/2022] Open
Abstract
Introduction: Gestational diabetes mellitus is increasing globally leading to significant maternal and foetal morbidity. This study aimed to find out the prevalence of gestational diabetes mellitus among pregnant women delivering in a tertiary care hospital.
Methods: A descriptive cross-sectional study on a total of 3034 pregnant women was conducted in a tertiary care hospital from 14th April 2017 to 13th April 2018 with ethical approval from Research and Institutional Review Committee (Reference number: 061-077/078) of the hospital. Pregnant women who met the eligibility criteria were included in the study. Convenience sampling was done. Data were analysed using the Statistical Package for the Social Sciences version 24.0 and Microsoft Excel. Point estimate at 99% Confidence Interval was calculated along with frequency and percentage for binary data.
Results: Among 3034 patients who delivered in the tertiary centre, the prevalence of gestational diabetes mellitus was found to be 104 (3.42%) (2.57-4.26 at 99% Confidence Interval). The majority of women were of maternal age >30 years in 69 (66.34%). Out of which 48 (46.15%) women had family history of diabetes mellitus. Thirty-eight (36.53%) patients required a caesarean section. The most common obstetric complication was polyhydramnios in 35 (35.57%).
Conclusions: The prevalence of gestational diabetes was lower when compared to other studies done in similar settings. The majority of women were of higher maternal age, had family history of diabetes mellitus and were also obese.
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Affiliation(s)
- Sumi Singh
- Nepal Medical College and Teaching Hospital, Jorpati, Kathmandu, Nepal
- Correspondence: Dr Sumi Singh, Nepal Medical College and Teaching Hospital, Jorpati Attarkhel, Kathmandu, Nepal. , Phone: +977-9860130690
| | - Manisha Yadav
- Nepal Medical College and Teaching Hospital, Jorpati, Kathmandu, Nepal
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Shankar Singh R, Bhadra Arna A, Dong H, Yadav M, Aggarwal A, Wu Y. Structure-function analysis of DEAD-box helicase DDX43. Methods 2022; 204:286-299. [DOI: 10.1016/j.ymeth.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 01/21/2023] Open
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Yadav M, Malla N. Editorial: Immune Responses in Sexually Transmitted Infections Caused by Parasites and DNA Viruses: New Insights. Front Cell Infect Microbiol 2022; 12:838799. [PMID: 35155285 PMCID: PMC8828637 DOI: 10.3389/fcimb.2022.838799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Manisha Yadav
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- *Correspondence: Manisha Yadav, ;
| | - Nancy Malla
- Department of Medical Parasitology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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Tripathi G, Rooge S, Yadav M, Mathew B, Sharma N, Bindal V, Hemati H, Singh Maras J, Gupta E. Baseline Plasma Metabotype Correlates With Direct-Acting Antiviral Therapy Nonresponse for HCV in HIV–HCV Coinfected Patients. Front Mol Biosci 2022; 8:748014. [PMID: 35083276 PMCID: PMC8784690 DOI: 10.3389/fmolb.2021.748014] [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: 07/29/2021] [Accepted: 12/15/2021] [Indexed: 11/22/2022] Open
Abstract
Introduction: With the advent of direct-acting antiviral (DAA) therapy for HCV, the cure is achieved at similar rates among HIV–HCV coinfected patients as in HCV mono-infected patients. The present study evaluates host plasma metabolites as putative indicators in predicting the treatment response in baseline HIV–HCV patients. Methods: Non-cirrhotic HIV–HCV (N = 43) coinfected patients were treated with sofosbuvir and daclatasvir for 12 weeks. Plasma metabolite profiling of pre- and post-therapy was analyzed in 20/43 patients. Of the 20 selected, 10 (50%) attained the sustained viral response [(SVR) (responders)] as defined by the absence of HCV RNA at 12 weeks after the treatment, and 10 (50%) did not attain the cure for HCV (nonresponders). Results: A total of 563 features were annotated (metabolomic/spectral databases). Before therapy, 39 metabolites differentiated (FC ±1.5, p < 0.05) nonresponders from responders. Of these, 20 upregulated and 19 downregulated were associated with tryptophan metabolism, nicotinamide metabolism, and others. Post therapy, 62 plasma metabolites (12 upregulated and 50 downregulated, FC±1.5, p < 0.05) differentiated nonresponders from responders and highlighted a significant increase in the steroid and histidine metabolism and significant decrease in tryptophan metabolism and ascorbate and pyruvate metabolism in the nonresponders. Based on random forest and multivariate linear regression analysis, the baseline level of N-acetylspermidine (FC > 2, AUC = 0.940, Bfactor = −0.267) and 2-acetolactate (FC > 2, AUC = 0.880, Bfactor = −0.713) significantly differentiated between nonresponders from responders in HIV–HCV coinfected patients and was able to predict the failure of treatment response. Conclusion: Increased baseline levels of N-acetylspermidine and 2-acetolactate levels are associated with the likeliness of failure to attain the cure for HCV in HIV–HCV coinfected patients.
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Affiliation(s)
- Gaurav Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Sheetalnath Rooge
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Manisha Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Babu Mathew
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Nupur Sharma
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Vasundhra Bindal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Hamed Hemati
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Jaswinder Singh Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
- *Correspondence: Ekta Gupta, ; Jaswinder Singh Maras,
| | - Ekta Gupta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
- *Correspondence: Ekta Gupta, ; Jaswinder Singh Maras,
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Yadav M, Eswari JS. Modern Paradigm Towards Potential Target Identification for Antiviral (SARS-nCoV-2) and Anticancer Lipopeptides: A Pharmacophore-Based Approach. Avicenna J Med Biotechnol 2022; 14:70-78. [PMID: 35509362 PMCID: PMC9017470 DOI: 10.18502/ajmb.v14i1.8172] [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: 03/15/2021] [Accepted: 07/28/2021] [Indexed: 11/24/2022] Open
Abstract
Background: Lipopeptides are potential microbial metabolites that are abandoned with broad spectrum biopharmaceutical properties ranging from antimicrobial, antiviral and anticancer, etc. Clinical studies are not much explored beyond the experimental methods to understand drug mechanisms on target proteins at the molecular level for large molecules. Due to the less available studies on potential target proteins of lipopeptide based drugs, their potential inhibitory role for more obvious treatment on disease have not been explored in the direction of lead optimization. However, Computational approaches need to be utilized to explore drug discovery aspects on lipopeptide based drugs, which are time saving and cost-effective techniques. Methods: Here a ligand-based drug discovery approach is coupled with reverse pharmacophore-mapping for the prediction of potential targets for antiviral (SARS-nCoV-2) and anticancer lipopeptides. Web-based servers PharmMapper and Swiss Target Prediction are used for the identification of target proteins for lipopeptides surfactin and iturin produced by Bacillus subtilis. Results: The studies have given the insight to treat the diseases with next-generation large molecule therapeutics. Results also indicate the affinity for Angiotensin-Converting Enzymes (ACE) and proteases as the potential viral targets for these categories of peptide therapeutics. A target protein for the Human Papilloma Virus (HPV) has also been mapped. Conclusion: The work will further help in exploring computer-aided drug designing of novel compounds with greater efficiency where the structure of the target proteins and lead compounds are known.
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Affiliation(s)
| | - J. Satya Eswari
- Corresponding author: J. Satya Eswari, Ph.D., Department of Biotechnology, National Institute of Technology Raipur, Chhattisgarh, 492010, India, E-mail:
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Yadav M, Pandey J, Chakraborty A, Hassan MI, Kundu JK, Roy A, Singh IK, Singh A. A Comprehensive Analysis of Calmodulin-Like Proteins of Glycine max Indicates Their Role in Calcium Signaling and Plant Defense Against Insect Attack. Front Plant Sci 2022; 13:817950. [PMID: 35371141 PMCID: PMC8965522 DOI: 10.3389/fpls.2022.817950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/25/2022] [Indexed: 05/09/2023]
Abstract
The calcium (Ca2+) signaling is a crucial event during plant-herbivore interaction, which involves a transient change in cytosolic Ca2+ concentration, which is sensed by Ca2+-sensors, and the received message is transduced to downstream target proteins leading to appropriate defense response. Calmodulin-like proteins (CMLs) are calcium-sensing plant-specific proteins. Although CMLs have been identified in a few plants, they remained uncharacterized in leguminous crop plants. Therefore, a wide-range analysis of CMLs of soybean was performed, which identified 41 true CMLs with greater than 50% similarity with Arabidopsis CMLs. The phylogenetic study revealed their evolutionary relatedness with known CMLs. Further, the identification of conserved motifs, gene structure analysis, and identification of cis-acting elements strongly supported their identity as members of this family and their involvement in stress responses. Only a few Glycine max CMLs (GmCMLs) exhibited differential expression in different tissue types, and rest of them had minimal expression. Additionally, differential expression patterns of GmCMLs were observed during Spodoptera litura-feeding, wounding, and signaling compound treatments, indicating their role in plant defense. The three-dimensional structure prediction, identification of interactive domains, and docking with Ca2+ ions of S. litura-inducible GmCMLs, indicated their identity as calcium sensors. This study on the characterization of GmCMLs provided insights into their roles in calcium signaling and plant defense during herbivory.
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Affiliation(s)
- Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Jyotsna Pandey
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Amrita Chakraborty
- EVA4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Jiban Kumar Kundu
- Plant Virus and Vector Interactions Group, Crop Research Institute, Prague, Czechia
| | - Amit Roy
- EVA4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
- *Correspondence: Amit Roy,
| | - Indrakant Kumar Singh
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- DBC-i4 Center, Deshbandhu College, University of Delhi, New Delhi, India
- Indrakant Kumar Singh,
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
- Archana Singh,
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Yadav M, Shivani, Ahamad A, Singh KK, Singh R, Misra A, Tandon P. ab-Initio and DFT study of HCN: Role of temperature for the formation of HCN molecule in the interstellar medium. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zwe YH, Yadav M, Zhen Ten MM, Srinivasan M, Jobichen C, Sivaraman J, Li D. Bacterial Antagonism of Chromobacterium haemolyticum and Characterization of its Putative Type VI Secretion System. Res Microbiol 2021; 173:103918. [PMID: 34906677 DOI: 10.1016/j.resmic.2021.103918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
This study reports the isolation of a new Chromobacterium haemolyticum strain named WI5 from a hydroponic farming facility. WI5 exhibited remarkable bacterial antagonistic properties, eliminating Salmonella, Escherichia coli, Listeria monocytogenes and Staphylococcus aureus (initial inoculum load ∼105 CFU/ml) in dual-species co-culture biofilms. Antagonism was strictly contact-dependent and highly influenced by nutrient availability. Next, we identified a complete suite of putative Type VI secretion system (T6SS) genes in the WI5 genome, annotated the gene locus architecture, and determined the crystal structure of hallmark T6SS tube protein Hcp1, which revealed a hexameric ring structure with an outer and inner diameter of 77 and 45Å, respectively. Structural comparison with homologs showed differences in the key loops connecting the β-strands in which the conserved residues are located, suggesting a role of these residues in the protein function. The T6SS is well-known to facilitate interbacterial competition, and the putative T6SS characterized herein might be responsible for the remarkable antagonism by C. haemolyticum WI5. Collectively, these findings shed light on the nature of bacterial antagonism and a putative key virulence determinant of C. haemolyticum, which might aid in further understanding its potential ecological role in natural habitats.
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Affiliation(s)
- Ye Htut Zwe
- Department of Food Science & Technology, 2 Science Drive 2, Faculty of Science, National University of Singapore, Singapore 117543
| | - Manisha Yadav
- Department of Biological Sciences, 14 Science Drive 4, Faculty of Science, National University of Singapore, Singapore 117543
| | - Michelle Mei Zhen Ten
- Department of Food Science & Technology, 2 Science Drive 2, Faculty of Science, National University of Singapore, Singapore 117543
| | - Mahalashmi Srinivasan
- Department of Biological Sciences, 14 Science Drive 4, Faculty of Science, National University of Singapore, Singapore 117543
| | - Chacko Jobichen
- Department of Biological Sciences, 14 Science Drive 4, Faculty of Science, National University of Singapore, Singapore 117543
| | - J Sivaraman
- Department of Biological Sciences, 14 Science Drive 4, Faculty of Science, National University of Singapore, Singapore 117543
| | - Dan Li
- Department of Food Science & Technology, 2 Science Drive 2, Faculty of Science, National University of Singapore, Singapore 117543.
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Tiwari M, Yadav M, Singh B, Pandey V, Nawaz K, Bhatia S. Evolutionary and functional analysis of two-component system in chickpea reveals CaRR13, a TypeB RR, as positive regulator of symbiosis. Plant Biotechnol J 2021; 19:2415-2427. [PMID: 34146435 PMCID: PMC8633487 DOI: 10.1111/pbi.13649] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 05/19/2023]
Abstract
The critical role of cytokinin in early nodulation in legumes is well known. In our study, exogenous cytokinin application to roots of the important crop legume, chickpea (Cicer arietinum L.), led to the formation of pseudo-nodules even in the absence of rhizobia. Hence, a genome-wide analysis of the cytokinin signalling, two-component system (TCS) genes, was conducted in chickpea, Medicago and Cajanus cajan. The integrated phylogenetic, evolutionary and expression analysis of the TCS genes was carried out, which revealed that histidine kinases (HKs) were highly conserved, whereas there was diversification leading to neofunctionalization at the level of response regulators (RRs) especially the TypeB RRs. Further, the functional role of the CaHKs in nodulation was established by complementation of the sln1Δ mutant of yeast and cre1 mutants of (Medicago) which led to restoration of the nodule-deficient phenotype. Additionally, the highest expressing TypeB RR of chickpea, CaRR13, was functionally characterized. Its localization in the nucleus and its Y1H assay-based interaction with the promoter of the early nodulation gene CaNSP2 indicated its role as a transcription factor regulating early nodulation. Overexpression, RNAi lines and complementation of cre1 mutants with CaRR13 revealed its critical involvement as an important signalling molecule regulating early events of nodule organogenesis in chickpea.
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Affiliation(s)
- Manish Tiwari
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Manisha Yadav
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Vimal Pandey
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Kashif Nawaz
- National Institute of Plant Genome ResearchNew DelhiIndia
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Rizvi RH, Vishnu R, Handa AK, Ramanan S, Yadav M, Mehdi A, Singh RK, Londhe S, Dhyani SK, Rizvi J, Anon P, Kumar R, Qaisar N. Mapping of Agroforestry Systems and <I>Salix</i> Species in Western Himalaya Agroclimatic Zone of India. CURR SCI INDIA 2021. [DOI: 10.18520/cs/v121/i10/1347-1351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Tiwari M, Pandey V, Singh B, Yadav M, Bhatia S. Evolutionary and expression dynamics of LRR-RLKs and functional establishment of KLAVIER homolog in shoot mediated regulation of AON in chickpea symbiosis. Genomics 2021; 113:4313-4326. [PMID: 34801685 DOI: 10.1016/j.ygeno.2021.11.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/10/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022]
Abstract
Chickpea shoot exogenously treated with cytokinin showed stunted phenotype of root, shoot and significantly reduced nodule numbers. Genome-wide identification of LRR-RLKs in chickpea and Medicago resulted in 200 and 371 genes respectively. Gene duplication analysis revealed that LRR-RLKs family expanded through segmental duplications in chickpea and tandem duplications in Medicago. Expression profiling of LRR-RLKs revealed their involvement in cytokinin signaling and plant organ development. Overexpression of KLAVIER ortholog of chickpea, Ca_LRR-RLK147, in roots revealed its localization in the membrane but showed no effect on root nodulation despite increased cle peptide levels. Two findings (i) drastic effect on nodule number by exogenous cytokinin treatment to only shoot and restoration to normal nodulation by treatment to both root and shoot tissue and (ii) no effect on nodule number by overexpression of Ca_LRR-RLK147 establishes the fact that despite presence of cle peptides in root, the function of Ca_LRR-RLK147 was shoot mediated during AON.
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Affiliation(s)
- Manish Tiwari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vimal Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Baljinder Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manisha Yadav
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Castillo CR, Alishahedani ME, Gough P, Chaudhary PP, Yadav M, Matriz J, Myles IA. Assessing the effects of common topical exposures on skin bacteria associated with atopic dermatitis. Skin Health Dis 2021; 1. [PMID: 34723253 PMCID: PMC8555759 DOI: 10.1002/ski2.41] [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] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Background While patients and families struggling with atopic dermatitis (AD) have documented concerns for a contributory role of skin care products in AD pathology, nearly all the skin microbiome studies to date have asked participants to avoid topical products (such as soaps or select medications) for the preceding days to weeks prior to sample collection. Thus, given the established role of the microbiome in AD, the interactions between topical exposures, dysbiosis and AD remains underrepresented in the academic literature. Objectives To address this knowledge gap, we expanded our previous evaluations to test the toxicological effects of a broader range of common chemicals, AD treatment lotions, creams and ointments using both health- and AD-associated strains of Roseomonas mucosa and Staphylococcus spp. Methods Use of in vitro culture techniques and mouse models were deployed to identify chemicals with dysbiotic or pre-biotic potential. A proof-of-concept study was subsequently performed in healthy volunteers to assess global microbiome shifts after exposure to select chemicals using dermatologic patch testing. Results Numerous chemicals possessed antibiotic properties, including many not marketed as anti-microbials. Through targeted combination of potentially beneficial chemicals, we identified combinations which promoted the growth of health-associated isolates over disease-associated strains in bacterial culture and enhanced microbe-specific outcomes in an established mouse model of AD; the most promising of which was the combination of citral and colophonium (often sold as lemon myrtle oil and pine tar). Additional studies would likely further optimize the combination of ingredients use. Similar results were seen in the proof-of-concept human studies. Conclusions Our results could offer a systematic, multiplex approach to identify which products carry dysbiotic potential and thus may guide formulation of new topicals to benefit patients with AD.
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Affiliation(s)
- C R Castillo
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - M E Alishahedani
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - P Gough
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - P P Chaudhary
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - M Yadav
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - J Matriz
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - I A Myles
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
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Singh M, Thakur M, Mishra M, Yadav M, Vibhuti R, Menon AM, Nagda G, Dwivedi VP, Dakal TC, Yadav V. Gene regulation of intracellular adhesion molecule-1 (ICAM-1): A molecule with multiple functions. Immunol Lett 2021; 240:123-136. [PMID: 34715236 DOI: 10.1016/j.imlet.2021.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]
Abstract
Intracellular adhesion molecule 1 (ICAM-1) is one of the most extensively studied inducible cell adhesion molecules which is responsible for several immune functions like T cell activation, extravasation, inflammation, etc. The molecule is constitutively expressed over the cell surface and is regulated up / down in response to inflammatory mediators like cellular stress, proinflammatory cytokines, viral infection. These stimuli modulate the expression of ICAM-1 primarily through regulating the ICAM-1 gene transcription. On account of the presence of various binding sites for NF-κB, AP-1, SP-1, and many other transcription factors, the architecture of the ICAM-1 promoter become complex. Transcription factors in union with other transcription factors, coactivators, and suppressors promote their assembly in a stereospecific manner on ICAM-1 promoter which mediates ICAM-1 regulation in response to different stimuli. Along with transcriptional regulation, epigenetic modifications also play a pivotal role in controlling ICAM-1 expression on different cell types. In this review, we summarize the regulation of ICAM-1 expression both at the transcriptional as well as post-transcriptional level with an emphasis on transcription factors and signaling pathways involved.
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Affiliation(s)
- Mona Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi-110067 India
| | - Mony Thakur
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana-123031 India
| | - Manish Mishra
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research- Institute of Microbial Technology, Chandigarh-160036 India
| | - Manisha Yadav
- Division of Cell Biology and Immunology, Council of Scientific and Industrial Research- Institute of Microbial Technology, Chandigarh-160036 India
| | - Rajkamal Vibhuti
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana-123031 India
| | - Athira M Menon
- Genome and computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan 313001 India
| | - Girima Nagda
- Department of Zoology, Mohanlal Sukhadia University, Udaipur, Rajasthan-313001 India
| | - Ved Prakash Dwivedi
- International Centre for Genetic Engineering and Biotechnology, ICGEB Campus, Aruna Asaf Ali Marg, New Delhi-110067 India
| | - Tikam Chand Dakal
- Genome and computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan 313001 India
| | - Vinod Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana-123031 India
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Yadav M, Srinivasan M, Tulsian NK, Liu YX, Lin Q, Rosenshine I, Sivaraman J. Binding specificity of type three secretion system effector NleH2 to multi-cargo chaperone CesT and their phosphorylation. Protein Sci 2021; 30:2433-2444. [PMID: 34662450 DOI: 10.1002/pro.4210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 11/06/2022]
Abstract
Gram-negative pathogens like Enteropathogenic Escherichia coli (EPEC) utilize the type three secretion system (T3SS) to translocate various effector proteins that are needed to "hijack" the host system for pathogenic survival. Specialized T3SS chaperones inside bacterial cells stabilize these effector proteins and facilitate their translocation. CesT is a unique multi-cargo chaperone that interacts with and translocates ~10 different effector proteins. Here, we report the specific interaction between CesT and its key effector, NleH2, and explore the potential role of NleH2 as a kinase for CesT phosphorylation. First, we identified the chaperone-binding domain (CBD; 19-97aa) of NleH2, and mapped the specific interaction sites for both CesT and NleH2. The N- and C-terminal residues of the CBD interact with the dimeric interface of CesT. Further, we compared the CesT binding to NleH2, to that of another key effector Tir and with the global carbon regulator CsrA. Notably, the effectors have the binding regions at the β-sheet core and dimer interface of CesT, whereas the CsrA regulator interacts predominantly through the C-terminal region, which is found ~17 Å away from the effectors-binding sites. Next, we showed that NleH2 remains an active kinase even as a complex with CesT and is responsible for its autophosphorylation as well as phosphorylation of CesT at Tyr153. Collectively, our findings enhance the understanding of the role of multi-cargo chaperone CesT in orchestrating effector translocation through T3SS.
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Affiliation(s)
- Manisha Yadav
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Nikhil K Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore
| | - Yu Xuan Liu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore
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