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Article ; Online: Molecular detection of monkeypox and related viruses: challenges and opportunities.

Ghate, Sudeep D / Suravajhala, Prashanth / Patil, Prakash / Vangala, Rajani Kanth / Shetty, Praveenkumar / Rao, R Shyama Prasad

Virus genes

2023 Volume 59, Issue 3, Page(s) 343–350

Abstract: ... disease by monkeypox virus (MPXV), has made global headlines. While transmissibility (R ...

Abstract	The recent widespread emergence of monkeypox (mpox), a rare and endemic zoonotic disease by monkeypox virus (MPXV), has made global headlines. While transmissibility (R
MeSH term(s)	Humans ; Mpox (monkeypox)/diagnosis ; Mpox (monkeypox)/pathology ; Monkeypox virus/genetics ; Polymerase Chain Reaction ; DNA, Viral/genetics ; Public Health
Chemical Substances	DNA, Viral
Language	English
Publishing date	2023-02-06
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	639496-6
ISSN	1572-994X ; 0920-8569
ISSN (online)	1572-994X
ISSN	0920-8569
DOI	10.1007/s11262-023-01975-3
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Zs.A 2397: Show issues

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Article ; Online: In silico identification of potential phytochemical inhibitors for mpox virus: molecular docking, MD simulation, and ADMET studies.

Ghate, Sudeep D / Pinto, Larina / Alva, Shivakiran / Srinivasa, Mahendra Gowdru / Vangala, Rajani Kanth / Naik, Prashantha / Revanasiddappa, B C / Rao, R Shyama Prasad

Molecular diversity

2024

Abstract: The mpox virus (MPXV), a member of the Poxviridae family, which recently appeared outside of the African continent has emerged as a global threat to public health. Given the scarcity of antiviral treatments for mpox disease, there is a pressing need to ... ...

Abstract	The mpox virus (MPXV), a member of the Poxviridae family, which recently appeared outside of the African continent has emerged as a global threat to public health. Given the scarcity of antiviral treatments for mpox disease, there is a pressing need to identify and develop new therapeutics. We investigated 5715 phytochemicals from 266 species available in IMMPAT database as potential inhibitors for six MPXV targets namely thymidylate kinase (A48R), DNA ligase (A50R), rifampicin resistance protein (D13L), palmytilated EEV membrane protein (F13L), viral core cysteine proteinase (I7L), and DNA polymerase (E9L) using molecular docking. The best-performing phytochemicals were also subjected to molecular dynamics (MD) simulations and in silico ADMET analysis. The top phytochemicals were forsythiaside for A48R, ruberythric acid for A50R, theasinensin F for D13L, theasinensin A for F13L, isocinchophyllamine for I7L, and terchebin for E9L. Interestingly, the binding energies of these potential phytochemical inhibitors were far lower than brincidofovir and tecovirimat, the standard drugs used against MPXV, hinting at better binding properties of the former. These findings may pave the way for developing new MPXV inhibitors based on natural product scaffolds. However, they must be further studied to establish their inhibitory efficacy and toxicity in in vitro and in vivo models.
Language	English
Publishing date	2024-03-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10797-2
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Zs.A 4946: Show issues

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Article ; Online: Extent of Virulence and Antibiotic Resistance Genes in Helicobacter pylori and Campylobacteria.

Rao, R Shyama Prasad / Ghate, Sudeep D / Pinto, Larina / Suravajhala, Prashanth / Patil, Prakash / Shetty, Praveenkumar / Ahsan, Nagib

Current microbiology

2024 Volume 81, Issue 6, Page(s) 154

Abstract: Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence ... ...

Abstract	Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. On average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. Large repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.
MeSH term(s)	Helicobacter pylori/genetics ; Helicobacter pylori/drug effects ; Helicobacter pylori/pathogenicity ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence/genetics ; Virulence Factors/genetics ; Bacterial Proteins/genetics ; Genome, Bacterial ; Helicobacter Infections/microbiology ; Humans
Chemical Substances	Anti-Bacterial Agents ; Virulence Factors ; Bacterial Proteins
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-024-03653-5
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Zs.A 1446: Show issues

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Article ; Online: Functional network analysis identifies multiple virulence and antibiotic resistance targets in Stenotrophomonas maltophilia.

Pinto, Larina / Shastry, Rajesh P / Alva, Shivakiran / Rao, R Shyama Prasad / Ghate, Sudeep D

Microbial pathogenesis

2023 Volume 183, Page(s) 106314

Abstract: Stenotrophomonas maltophilia, an emerging multidrug-resistant opportunistic bacterium in humans is of major concern for immunocompromised individuals for causing pneumonia and bloodborne infections. This bacterial pathogen is associated with a ... ...

Abstract	Stenotrophomonas maltophilia, an emerging multidrug-resistant opportunistic bacterium in humans is of major concern for immunocompromised individuals for causing pneumonia and bloodborne infections. This bacterial pathogen is associated with a considerable fatality/case ratio, with up to 100%, when presented as hemorrhagic fever. It is resistant to commonly used drugs as well as to antibiotic combinations. In-silico based functional network analysis is a key approach to get novel insights into virulence and resistance in pathogenic organisms. This study included the protein-protein interaction (PPI) network analysis of 150 specific genes identified for antibiotic resistance mechanism and virulence pathways. Eight proteins, namely, PilL, FliA, Smlt2260, Smlt2267, CheW, Smlt2318, CheZ, and FliM were identified as hub proteins. Further docking studies of 58 selected phytochemicals were performed against the identified hub proteins. Deoxytubulosine and corosolic acid were found to be potent inhibitors of hub proteins of pathogenic S. maltophilia based on protein-ligand interactive study. Further pharmacophore studies are warranted with these molecules to develop them as novel antibiotics against S. maltophilia.
MeSH term(s)	Humans ; Stenotrophomonas maltophilia/genetics ; Virulence/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Immunocompromised Host
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2023.106314
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Zs.A 2136: Show issues

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Article ; Online: Correction: Nutritional status of Indian adolescents (15-19 years) from National Family Health Surveys 3 and 4: Revised estimates using WHO 2007 Growth reference.

Bhargava, Madhavi / Bhargava, Anurag / Ghate, Sudeep D / Rao, R Shyama Prasad

PloS one

2020 Volume 15, Issue 9, Page(s) e0239923

Abstract: This corrects the article DOI: 10.1371/journal.pone.0234570.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pone.0234570.].
Language	English
Publishing date	2020-09-24
Publishing country	United States
Document type	Published Erratum
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0239923
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Article ; Online: Overexpression of a membrane transport system MSMEG_1381 and MSMEG_1382 confers multidrug resistance in Mycobacterium smegmatis.

Salini, S / Muralikrishnan, Balaji / Bhat, Sinchana G / Ghate, Sudeep D / Rao, R Shyama Prasad / Kumar, R Ajay / Kurthkoti, Krishna

Microbial pathogenesis

2023 Volume 185, Page(s) 106384

Abstract: Mycobacterium tuberculosis is a leading cause of human mortality worldwide, and the emergence of drug-resistant strains demands the discovery of new classes of antimycobacterial that can be employed in the therapeutic pipeline. Previously, a secondary ... ...

Abstract	Mycobacterium tuberculosis is a leading cause of human mortality worldwide, and the emergence of drug-resistant strains demands the discovery of new classes of antimycobacterial that can be employed in the therapeutic pipeline. Previously, a secondary metabolite, chrysomycin A, isolated from Streptomyces sp. OA161 displayed potent bactericidal activity against drug-resistant clinical isolates of M. tuberculosis and different species of mycobacteria. The antibiotic inhibits mycobacterial topoisomerase I and DNA gyrase, leading to bacterial death, but the mechanisms that could cause resistance to this antibiotic are currently unknown. To further understand the resistance mechanism, using M. smegmatis as a model, spontaneous resistance mutants were isolated and subjected to whole-genome sequencing. Mutation in a Tet
MeSH term(s)	Humans ; Mycobacterium smegmatis/genetics ; Mycobacterium smegmatis/metabolism ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; Mycobacterium tuberculosis/genetics ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Drug Resistance, Multiple, Bacterial/genetics ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism
Chemical Substances	Anti-Bacterial Agents ; Membrane Transport Proteins ; Bacterial Proteins
Language	English
Publishing date	2023-10-12
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2023.106384
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Article ; Online: Unveiling the role of hub proteins in controlling quorum sensing regulated virulence through analogues in Pseudomonas aeruginosa PAO1: A functional protein-protein network biology approach.

Bajire, Sukesh Kumar / Ghate, Sudeep D / Shetty, Shriya / Banerjee, Shukla / Rao, R Shyama Prasad / Shetty, Veena / Shastry, Rajesh P

Biochemical and biophysical research communications

2023 Volume 660, Page(s) 13–20

Abstract: The protein-protein interaction (PPI) network analysis of specific genes identified for biofilm production and virulence/secretion system mediated by quorum sensing. The PPI depicted 13 hub proteins (namely rhlR, lasR, pscU, vfr, exsA, lasI, gacA, toxA, ... ...

Abstract	The protein-protein interaction (PPI) network analysis of specific genes identified for biofilm production and virulence/secretion system mediated by quorum sensing. The PPI depicted 13 hub proteins (namely rhlR, lasR, pscU, vfr, exsA, lasI, gacA, toxA, pilJ, pscC, fleQ, algR, and chpA) out of 160 nodes involving 627 edges. The PPI network analysis based on topographical features depicted pcrD with the highest degree value and vfr gene with the greatest betweenness centrality and closeness centrality (BC and CC) values. Based on in silico results, curcumin used as an Acyl homo-serine lactone (AHL) mimicker in P. aeruginosa, was also found effective in suppressing the quorum sensing regulated virulence factors such as elastase and pyocyanin. Based on in vitro experiment, curcumin suppressed biofilm formation at 62 μg/ml concentration. Host-pathogen interaction experiment showed that curcumin was also proved to be efficient in saving C. elegans from paralysis and killing effects of P. aeruginosa PAO1.
MeSH term(s)	Animals ; Quorum Sensing/genetics ; Virulence/genetics ; Pseudomonas aeruginosa/metabolism ; Curcumin/pharmacology ; Curcumin/metabolism ; Caenorhabditis elegans/metabolism ; Biofilms ; Virulence Factors/metabolism ; Bacterial Proteins/metabolism ; Anti-Bacterial Agents/pharmacology ; Biology
Chemical Substances	Curcumin (IT942ZTH98) ; Virulence Factors ; Bacterial Proteins ; Anti-Bacterial Agents
Language	English
Publishing date	2023-04-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2023.03.079
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Article ; Online: Seasonal dynamics and polyphenism of butterfly communities in the coastal plains of central Western Ghats, India

Naik, Deepak / Rao, R Shyama Prasad / Kunte, Krushnamegh / Mustak, Mohammed S

J Biosci. 2022 Dec., v. 47, no. 4 p.79-79

2022

Abstract: Long-term socioeconomic progress requires a healthy environment/ecosystem, but anthropogenic activities cause environmental degradation and biodiversity loss. Constant ecological monitoring is, therefore, necessary to assess the state of biodiversity and ...

Abstract	Long-term socioeconomic progress requires a healthy environment/ecosystem, but anthropogenic activities cause environmental degradation and biodiversity loss. Constant ecological monitoring is, therefore, necessary to assess the state of biodiversity and ecological health. However, baseline data are lacking even for ecologically sensitive regions such as the Western Ghats. We looked at the seasonality and polyphenism of butterflies of the central Western Ghats to obtain baseline population patterns on these charismatic taxa. We recorded 43118 individuals (175 species) using fortnightly time-constrained counts for two consecutive years and found the peak abundance (49% of the total individuals) in the post-monsoon period (October to January). Seasonal abundance was correlated with the overall increase in species richness. Habitat differences were stronger than seasonality as samples clustered based on sites. Several species also displayed polyphenism with distinct distributions of wet and dry season forms. Seasonal equitability and indicator species analysis showed distinct inter-species differences in seasonality patterns. This work provides key baseline data on the seasonal dynamics of butterflies of the Western Ghats in the context of climate change and conservation. It will help monitor this ecologically sensitive region using butterflies.
Keywords	butterflies ; climate change ; dry season ; ecosystems ; environmental degradation ; environmental health ; habitats ; indicator species ; polyphenism ; species richness ; India
Language	English
Dates of publication	2022-12
Size	p. 79.
Publishing place	Springer India
Document type	Article ; Online
ZDB-ID	756157-x
ISSN	0973-7138 ; 0250-5991
ISSN (online)	0973-7138
ISSN	0250-5991
DOI	10.1007/s12038-022-00316-0
Database	NAL-Catalogue (AGRICOLA)

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Z 5290: Show issues

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Article: Ecological monitoring and indicator taxa: butterfly communities in heterogeneous landscapes of the Western Ghats and Malabar coast, India

Naik, Deepak / Rao, R. Shyama Prasad / Kunte, Krushnamegh / Mustak, Mohammed S.

Journal of insect conservation. 2022 Feb., v. 26, no. 1

2022

Abstract: As the pace of socioeconomic developments continues to accelerate, the environmental degradation and biodiversity loss become the norm. While it is crucial to constantly monitor and assess ecological impacts, baseline data are scanty for ecologically ... ...

Abstract	As the pace of socioeconomic developments continues to accelerate, the environmental degradation and biodiversity loss become the norm. While it is crucial to constantly monitor and assess ecological impacts, baseline data are scanty for ecologically sensitive regions and biodiversity hotspots such as the Western Ghats. With their great public appeal and ease to work with, butterflies are excellent communities to monitor the ecological health. To characterize the baseline patterns of butterfly communities, using time-constrained counts, we surveyed eight heterogeneous landscapes of the coastal plains of the Western Ghats. We recorded 43,118 individuals and 175 species, with large differences in their diversity and species-specific abundances among habitats. The coastal and semi-evergreen-forest habitats were at the two extremes with intermediate patterns in agricultural and other habitats that suffered diverse anthropogenic pressures. Using indicator value analysis, 22 habitat-specific and several shared indicator species were identified. Even some of the most abundant species showed distinct niches, and therefore can be used as indicator species to monitor community dynamics. Patterns of numerous habitat-specific host-plant butterfly species pairs that were identified were discussed in relation to butterfly abundance and conservation. IMPLICATIONS FOR INSECT CONSERVATION: This study has implications for insect conservation by providing important baseline data on butterfly taxa for future monitoring and assessment of this ecologically sensitive region.
Keywords	biodiversity ; butterflies ; coasts ; environmental degradation ; environmental health ; host plants ; indicator species ; India
Language	English
Dates of publication	2022-02
Size	p. 107-119.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	1395198-1
ISSN	1572-9753 ; 1366-638X
ISSN (online)	1572-9753
ISSN	1366-638X
DOI	10.1007/s10841-022-00368-5
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Article ; Online: Genes from oxidative phosphorylation complexes II-V and two dual-function subunits of complex I are transcribed in Viscum album despite absence of the entire mitochondrial holo-complex I.

Petersen, Gitte / Shyama Prasad Rao, R / Anderson, Benjamin / Zervas, Athanasios / Seberg, Ole / Rasmusson, Allan G / Max Møller, Ian

Mitochondrion

2021 Volume 62, Page(s) 1–12

Abstract: Mistletoes (Viscum) and close relatives are unique among flowering plants in having a drastically altered electron transport chain. Lack of complex I genes has previously been reported for the mitochondrial genome, and here we report an almost complete ... ...

Abstract	Mistletoes (Viscum) and close relatives are unique among flowering plants in having a drastically altered electron transport chain. Lack of complex I genes has previously been reported for the mitochondrial genome, and here we report an almost complete absence of nuclear-encoded complex I genes in the transcriptome of Viscum album. Compared to Arabidopsis with approximately 40 nuclear complex I genes, we recover only transcripts of two dual-function genes: gamma carbonic anhydrase and L-galactono-1,4-lactone dehydrogenase. The complement of genes belonging to complexes II-V of the oxidative phosphorylation pathway appears to be in accordance with other vascular plants. Additionally, transcripts encoding alternative NAD(P)H dehydrogenases and alternative oxidase were found. Despite sequence divergence, structural modeling suggests that the encoded proteins are structurally conserved. Complex I loss is a special feature in Viscum species and relatives, as all other parasitic flowering plants investigated to date seem to have a complete OXPHOS system. Hence, Viscum offers a unique system for specifically investigating molecular consequences of complex I absence, such as the role of complex I subunits involved in secondary functions.
MeSH term(s)	Electron Transport Complex I/physiology ; Gene Expression Regulation, Plant/physiology ; Mitochondria/metabolism ; Oxidative Phosphorylation ; Oxygen Consumption ; Plant Proteins ; Protein Subunits ; Viscum album/genetics ; Viscum album/metabolism
Chemical Substances	Plant Proteins ; Protein Subunits ; Electron Transport Complex I (EC 7.1.1.2)
Language	English
Publishing date	2021-11-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2056923-3
ISSN	1872-8278 ; 1567-7249
ISSN (online)	1872-8278
ISSN	1567-7249
DOI	10.1016/j.mito.2021.10.006
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