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Book ; Online ; E-Book: Fungal diseases in animals

Gupta, Arti / Pratap Singh, Nagendra

from infections to prevention

(Fungal biology)

2021

Author's details	Arti Gupta, Nagendra Pratap Singh, editors
Series title	Fungal biology
Keywords	Mycology ; Veterinary medicine ; Wildlife ; Fish ; Bacteriology ; Biochemistry
Subject code	579.135
Language	English
Size	1 Online-Ressource (XVI, 191 Seiten), Illustrationen
Edition	1st ed. 2021
Publisher	Springer
Publishing place	Cham
Publishing country	Switzerland
Document type	Book ; Online ; E-Book
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
HBZ-ID	HT021003199
ISBN	978-3-030-69507-1 ; 9783030695064 ; 9783030695088 ; 9783030695095 ; 3-030-69507-7 ; 3030695069 ; 3030695085 ; 3030695093
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Evaluating WHO prescribed sanitary inspection templates for assessing contamination risks in tubewells with handpump - case of 9 Indian districts.

Kulshrestha, Mukul / Singh, Nagendra Prasad

Archives of environmental & occupational health

2021 Volume 76, Issue 7, Page(s) 462–470

Abstract: WHO prescribes Sanitary Inspections in recommended formats for assessing contamination risks in Tubewells installed with handpump that often constitute primary drinking water sources in rural and remote areas. Sanitary inspections are easy alternatives ... ...

Abstract	WHO prescribes Sanitary Inspections in recommended formats for assessing contamination risks in Tubewells installed with handpump that often constitute primary drinking water sources in rural and remote areas. Sanitary inspections are easy alternatives to costlier and technically demanding laboratory water quality analysis. However, their efficacy remains uncertain despite decades of widespread usage. This study evaluates sanitary inspections by assessing contamination risk in 324 Tubewells with handpump across 9 districts in India. Results indicate that 62% of sampled sources were safe in lab analysis, despite sanitary inspections indicating varying risks. This implies that WHO prescribed inspections yield higher risks, and overestimated risk perception are likely to skew planning and policy, resulting in budgetary over-allocations and financial mismanagement in water-supplies. There is thus an urgent need to review and revise WHO prescribed sanitary inspection templates.
MeSH term(s)	Dietary Exposure/analysis ; Humans ; India ; Risk Assessment ; Rural Population ; Sanitary Surveys, Water Supply/standards ; Water Wells ; World Health Organization
Language	English
Publishing date	2021-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2245323-4
ISSN	2154-4700 ; 1933-8244 ; 0003-9896
ISSN (online)	2154-4700
ISSN	1933-8244 ; 0003-9896
DOI	10.1080/19338244.2021.1886033
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Article ; Online: miRNAs target databases: developmental methods and target identification techniques with functional annotations.

Singh, Nagendra Kumar

Cellular and molecular life sciences : CMLS

2017 Volume 74, Issue 12, Page(s) 2239–2261

Abstract: Purpose: microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by ... ...

Abstract	Purpose: microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases. In this paper, the different microRNA target databases and their functional annotations developed by various researchers have been reviewed. The concurrent research review aims at comprehending the significance of miRNA and presenting the existing status of annotated miRNA target resources built by researchers henceforth discovering the knowledge for diagnosis and prognosis. Methods and results: This review discusses the applications and developmental methodologies for constructing target database as well as the utility of user interface design. An integrated architecture is drawn and a graphically comparative study of present status of miRNA targets in diverse diseases and various biological processes is performed. These databases comprise of information such as miRNA target-associated disease, transcription factor binding sites (TFBSs) in miRNA genomic locations, polymorphism in miRNA target, A-to-I edited target, Gene Ontology (GO), genome annotations, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, target expression analysis, TF-miRNA and miRNA-mRNA interaction networks, drugs-targets interactions, etc. Conclusion: miRNA target databases contain diverse experimentally and computationally predicted target through various algorithms. The comparison of various miRNA target database has been performed on various parameters. The computationally predicted target databases suffer from false positive information as there is no common theory for prediction of miRNA targets. The review conclusion emphasizes the need of more intelligent computational improvement for the miRNA target identification, their functional annotations and datasbase development.
MeSH term(s)	Animals ; Computational Biology ; Databases, Genetic ; Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Models, Genetic ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2017-06
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-017-2469-1
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Article ; Online: microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations.

Singh, Nagendra Kumar

Interdisciplinary sciences, computational life sciences

2017 Volume 9, Issue 3, Page(s) 357–377

Abstract: microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base ... ...

Abstract	microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base pair with targeted mRNA along with Argonaut proteins complex, causes gene repression or endonucleolytic cleavage of mRNAs and results in many diseases and syndromes. After the discovery of miRNA lin-4 and let-7, subsequently large numbers of miRNAs were discovered by low-throughput and high-throughput experimental techniques along with computational process in various biological and metabolic processes. The miRNAs are important non-coding RNA for understanding the complex biological phenomena of organism because it controls the gene regulation. This paper reviews miRNA databases with structural and functional annotations developed by various researchers. These databases contain structural and functional information of animal, plant and virus miRNAs including miRNAs-associated diseases, stress resistance in plant, miRNAs take part in various biological processes, effect of miRNAs interaction on drugs and environment, effect of variance on miRNAs, miRNAs gene expression analysis, sequence of miRNAs, structure of miRNAs. This review focuses on the developmental methodology of miRNA databases such as computational tools and methods used for extraction of miRNAs annotation from different resources or through experiment. This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place.
Language	English
Publishing date	2017-09
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2493085-4
ISSN	1867-1462 ; 1913-2751
ISSN (online)	1867-1462
ISSN	1913-2751
DOI	10.1007/s12539-016-0166-7
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Article ; Online: Evolutionary fates of gene-body methylation and its divergent association with gene expression in pigeonpea.

Junaid, Alim / Singh, Nagendra Kumar / Gaikwad, Kishor

The plant genome

2022 Volume 15, Issue 3, Page(s) e20207

Abstract: Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene-body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM ...

Abstract	Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene-body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM features- slow evolution rate and increased length remained conserved. Genes with moderate CG body methylation showed highest expression where as highly-methylated genes showed lowest expression. Transposable element (TE)-related genes were methylated in multiple contexts and hence classified as C-methylated genes. A low expression among C-methylated genes was associated with transposons insertion in gene-body and upstream regulatory regions. The CG methylation patterns were found to be conserved in orthologs compared with non-CG methylation. By comparing methylation patterns between differentially methylated regions (DMRs) of the three genotypes, we found that variably methylated marks are less likely to target evolutionary conserved sequences. Finally, our analysis showed enrichment of nitrogen-related genes in GbM orthologs of legumes, which could be promising candidates for generating epialleles for crop improvement.
MeSH term(s)	Cajanus/genetics ; DNA Transposable Elements ; Gene Expression ; Methylation ; Nitrogen
Chemical Substances	DNA Transposable Elements ; Nitrogen (N762921K75)
Language	English
Publishing date	2022-07-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2375444-8
ISSN	1940-3372 ; 0011-183X
ISSN (online)	1940-3372
ISSN	0011-183X
DOI	10.1002/tpg2.20207
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Article: Evolutionary fates of gene‐body methylation and its divergent association with gene expression in pigeonpea

Junaid, Alim / Singh, Nagendra Kumar / Gaikwad, Kishor

The plant genome. 2022 Sept., v. 15, no. 3

2022

Abstract: Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene‐body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM ...

Abstract	Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene‐body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM features‐ slow evolution rate and increased length remained conserved. Genes with moderate CG body methylation showed highest expression where as highly‐methylated genes showed lowest expression. Transposable element (TE)‐related genes were methylated in multiple contexts and hence classified as C‐methylated genes. A low expression among C‐methylated genes was associated with transposons insertion in gene‐body and upstream regulatory regions. The CG methylation patterns were found to be conserved in orthologs compared with non‐CG methylation. By comparing methylation patterns between differentially methylated regions (DMRs) of the three genotypes, we found that variably methylated marks are less likely to target evolutionary conserved sequences. Finally, our analysis showed enrichment of nitrogen‐related genes in GbM orthologs of legumes, which could be promising candidates for generating epialleles for crop improvement.
Keywords	Cajanus cajan ; evolution ; gene expression ; genome ; methylation ; pigeon peas ; transposons
Language	English
Dates of publication	2022-09
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2375444-8
ISSN	1940-3372 ; 0011-183X
ISSN (online)	1940-3372
ISSN	0011-183X
DOI	10.1002/tpg2.20207
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Impact design of die parameters on Severe plastic deformation during Equal channel angular pressing

Singh Nagendra / Agrawal Manoj Kumar / Verma Sanjeev Kumar / Tiwari Ashish Kumar

E3S Web of Conferences, Vol 430, p

An overview

2023 Volume 01255

Abstract: Equal channel angular pressing causes less uniform deformation than simple shear, even though its not as obvious as with other metal forming procedures. Investigation is done into how internal and external factors affect the deformity inhomogeneity ... ...

Abstract	Equal channel angular pressing causes less uniform deformation than simple shear, even though its not as obvious as with other metal forming procedures. Investigation is done into how internal and external factors affect the deformity inhomogeneity through Equal .channel angular pressing. Finite element analysis of plastic deformity are integrated with die corner angle and the strain harden ability of metallic workpiece. The material characteristics are significantly influenced by the type of plastic shear deformation that occurs through Equal channel angular pressing and this is primarily impacted by the die geometry, the properties of the material and the process factors. Segmenting the workpiece into a front transient zone, end transient zone, outer less sheared zone and the remaining shear deforming zone allowed researchers to examine the uneven strain distribution throughout the workpiece. The deformed geometry for the non-hardening and it was assumed that rate-insensitive materials would be largely homogeneous. In materials that are strain-rate sensitive, gaps between the upper and lower channels developed, whereas strain-hardening materials experienced the corner gap. The strain hardening and implications of strain-rate sensitivity exponent had a considerable impact on the deformation inhomogeneity. Metals having an ultrafine grain microstructure can be created by severe plastic deformation. The FE models were used to affect the process and they all took as inputs the material properties, load variation, Different velocity and boundary conditioned. For the purpose of evaluating the impact of the channel angle on the AA5083 sample, The FE analysis produced the value of strain distribution. When the channel angle was 1200, there was less strain overall, but there was also less concentrated stress in the channel corner area.
Keywords	ecap ; strain hardening ; fem ; die corner angle ; plastic deformation homogeneity ; Environmental sciences ; GE1-350
Subject code	669
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic insight into variations associated with flowering-time and early-maturity in pigeonpea mutant TAT-10 and its wild type parent T21.

Singh, Anupam / Ramakrishna, Goriparthi / Singh, Nagendra Kumar / Abdin, Malik Zainul / Gaikwad, Kishor

International journal of biological macromolecules

2023 Volume 257, Issue Pt 2, Page(s) 128559

Abstract: Pigeonpea [Cajanus cajan (L.) Millspaugh] is an important grain legume crop with a broad range of 90 to 300 days for maturity. To identify the genomic variations associated with the early maturity, we conducted whole-genome resequencing of an early- ... ...

Abstract	Pigeonpea [Cajanus cajan (L.) Millspaugh] is an important grain legume crop with a broad range of 90 to 300 days for maturity. To identify the genomic variations associated with the early maturity, we conducted whole-genome resequencing of an early-maturing pigeonpea mutant TAT-10 and its wild type parent T21. A total of 135.67 and 146.34 million sequencing reads were generated for T21 and TAT-10, respectively. From this resequencing data, 1,397,178 and 1,419,904 SNPs, 276,741 and 292,347 InDels, and 87,583 and 92,903 SVs were identified in T21 and TAT-10, respectively. We identified 203 genes in the pigeonpea genome that are homologs of flowering-related genes in Arabidopsis and found 791 genomic variations unique to TAT-10 linked to 94 flowering-related genes. We identified three candidate genes for early maturity in TAT-10; Suppressor of FRI 4 (SUF4), Early Flowering In Short Days (EFS), and Probable Lysine-Specific Demethylase ELF6. The variations in ELF6 were predicted to be possibly damaging and the expression profiles of EFS and ELF6 also supported their probable role during early flowering in TAT-10. The present study has generated information on genomic variations associated with candidate genes for early maturity, which can be further studied and exploited for developing the early-maturing pigeonpea cultivars.
MeSH term(s)	Polymorphism, Single Nucleotide/genetics ; Genome, Plant/genetics ; Genes, Plant ; Quantitative Trait Loci ; Genomics ; Cajanus/genetics
Language	English
Publishing date	2023-12-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.128559
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Article: Immunoinformatics and reverse vaccinology approach in designing a novel highly immunogenic multivalent peptide-based vaccine against the human monkeypox virus.

Choudhury, Abhigyan / Chandra, Anshuman / Dawoud, Turki M / Nafidi, Hiba-Allah / Singh, Nagendra / Bourhia, Mohammed

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1295817

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2023-11-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1295817
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Article ; Online: The chickpea WIP2 gene underlying a major QTL contributes to lateral root development.

Dwivedi, Vikas / Pal, Lalita / Singh, Shilpi / Singh, Nagendra Pratap / Parida, Swarup Kumar / Chattopadhyay, Debasis

Journal of experimental botany

2023 Volume 75, Issue 2, Page(s) 642–657

Abstract: Lateral roots are a major component of root system architecture, and lateral root count (LRC) positively contributes to yield under drought in chickpea. To understand the genetic regulation of LRC, a biparental mapping population derived from two ... ...

Abstract	Lateral roots are a major component of root system architecture, and lateral root count (LRC) positively contributes to yield under drought in chickpea. To understand the genetic regulation of LRC, a biparental mapping population derived from two chickpea accessions having contrasting LRCs was genotyped by sequencing, and phenotyped to map four major quantitative trait loci (QTLs) contributing to 13-32% of the LRC trait variation. A single- nucleotide polymorphism tightly linked to the locus contributing to highest trait variation was located on the coding region of a gene (CaWIP2), orthologous to NO TRANSMITTING TRACT/WIP domain protein 2 (NTT/WIP2) gene of Arabidopsis thaliana. A polymorphic simple sequence repeat (SSR) in the CaWIP2 promoter showed differentiation between low versus high LRC parents and mapping individuals, suggesting its utility for marker-assisted selection. CaWIP2 promoter showed strong expression in chickpea apical root meristem and lateral root primordia. Expression of CaWIP2 under its native promoter in the Arabidopsis wip2wip4wip5 mutant rescued its rootless phenotype to produce more lateral roots than the wild-type plants, and led to formation of amyloplasts in the columella. CaWIP2 expression also induced the expression of genes that regulate lateral root emergence. Our study identified a gene-based marker for LRC which will be useful for developing drought-tolerant, high-yielding chickpea varieties.
MeSH term(s)	Humans ; Quantitative Trait Loci/genetics ; Chromosome Mapping ; Cicer/genetics ; Genotype ; Genetic Markers
Chemical Substances	Genetic Markers
Language	English
Publishing date	2023-04-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erad171
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