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Ahlawat S, Arora R, Sharma R, Chhabra P, Kumar A, Kaur M, Lal SB, Mishra DC, Farooqi MS, Srivastava S. Revelation of genes associated with energy generating metabolic pathways in the fighter type Aseel chicken of India through skeletal muscle transcriptome sequencing. Anim Biotechnol 2023; 34:4989-5000. [PMID: 37288785 DOI: 10.1080/10495398.2023.2219718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, comparative analysis of skeletal muscle transcriptome was carried out for four biological replicates of Aseel, a fighter type breed and Punjab Brown, a meat type breed of India. The profusely expressed genes in both breeds were related to muscle contraction and motor activity. Differential expression analysis identified 961 up-regulated and 979 down-regulated genes in Aseel at a threshold of log2 fold change ≥ ±2.0 (padj<0.05). Significantly enriched KEGG pathways in Aseel included metabolic pathways and oxidative phosphorylation, with higher expression of genes associated with fatty acid beta-oxidation, formation of ATP by chemiosmotic coupling, response to oxidative stress, and muscle contraction. The highly connected hub genes identified through gene network analysis in the Aseel gamecocks were HNF4A, APOA2, APOB, APOC3, AMBP, and ACOT13, which are primarily associated with energy generating metabolic pathways. The up-regulated genes in Punjab Brown chicken were found to be related to muscle growth and differentiation. There was enrichment of pathways such as focal adhesion, insulin signaling pathway and ECM receptor interaction in these birds. The results presented in this study help to improve our understanding of the molecular mechanisms associated with fighting ability and muscle growth in Aseel and Punjab Brown chicken, respectively.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Shashi Bhushan Lal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Md Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Arora R, Sharma R, Ahlawat S, Chhabra P, Kumar A, Kaur M, Vijh RK, Lal SB, Mishra DC, Farooqi MS, Srivastava S. Transcriptomics reveals key genes responsible for functional diversity in pectoralis major muscles of native black Kadaknath and broiler chicken. 3 Biotech 2023; 13:253. [PMID: 37396468 PMCID: PMC10310660 DOI: 10.1007/s13205-023-03682-0] [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: 03/16/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
RNA sequencing-based expression profiles from pectoralis major muscles of black meat (Kadaknath) and white meat (broiler) chicken were compared to identify differentially expressed genes. A total of 156 genes with log2 fold change ≥ ± 2.0 showed higher expression in Kadaknath and 68 genes were expressed at a lower level in comparison to broiler. Significantly enriched biological functions of up-regulated genes in Kadaknath were skeletal muscle cell differentiation, regulation of response to reactive oxygen, positive regulation of fat cell differentiation and melanosome. Significant ontology terms up-regulated in broiler included DNA replication origin binding, G-protein coupled receptor signaling pathway and chemokine activity. Highly inter-connected differentially expressed genes in Kadaknath (ATFs, C/EPDs) were observed to be important regulators of cellular adaptive functions, while in broiler, the hub genes were involved in cell cycle progression and DNA replication. The study is an attempt to get an insight into the transcript diversity of pectoralis major muscles of Kadaknath and broiler chicken. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03682-0.
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Affiliation(s)
- Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- Animal Biotechnology Division, G T Road By-Pass, P O Box 129, Karnal, Haryana 132001 India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - Shashi Bhushan Lal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Md. Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Sinha D, Sharma A, Mishra DC, Rai A, Lal SB, Kumar S, Farooqi MS, Chaturvedi KK. MetaConClust - Unsupervised Binning of Metagenomics Data using Consensus Clustering. Curr Genomics 2022; 23:137-146. [PMID: 36778980 PMCID: PMC9878838 DOI: 10.2174/1389202923666220413114659] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/18/2022] [Accepted: 02/21/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Binning of metagenomic reads is an active area of research, and many unsupervised machine learning-based techniques have been used for taxonomic independent binning of metagenomic reads. Objective: It is important to find the optimum number of the cluster as well as develop an efficient pipeline for deciphering the complexity of the microbial genome. Methods: Applying unsupervised clustering techniques for binning requires finding the optimal number of clusters beforehand and is observed to be a difficult task. This paper describes a novel method, MetaConClust, using coverage information for grouping of contigs and automatically finding the optimal number of clusters for binning of metagenomics data using a consensus-based clustering approach. The coverage of contigs in a metagenomics sample has been observed to be directly proportional to the abundance of species in the sample and is used for grouping of data in the first phase by MetaConClust. The Partitioning Around Medoid (PAM) method is used for clustering in the second phase for generating bins with the initial number of clusters determined automatically through a consensus-based method. Results: Finally, the quality of the obtained bins is tested using silhouette index, rand Index, recall, precision, and accuracy. Performance of MetaConClust is compared with recent methods and tools using benchmarked low complexity simulated and real metagenomic datasets and is found better for unsupervised and comparable for hybrid methods. Conclusion: This is suggestive of the proposition that the consensus-based clustering approach is a promising method for automatically finding the number of bins for metagenomics data.
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Affiliation(s)
- Dipro Sinha
- These authors contributed equally to this work
| | - Anu Sharma
- Address correspondence to this author at the Division of Agriculture Bioinformatics, ICAR-IASRI, New Delhi- 110012, India; E-mail:
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Kumar S, Bhati J, Saha A, Lal SB, Pandey PK, Mishra DC, Farooqi MS, Kumar A, Chaturvedi KK, Rai A. CerealESTDb: A Comprehensive Resource for Abiotic Stress-Responsive Annotated ESTs With Predicted Genes, Gene Ontology, and Metabolic Pathways in Major Cereal Crops. Front Genet 2022; 13:842868. [PMID: 35281847 PMCID: PMC8907976 DOI: 10.3389/fgene.2022.842868] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Cereals are the most important food crops and are considered key contributors to global food security. Loss due to abiotic stresses in cereal crops is limiting potential productivity in a significant manner. The primary reasons for abiotic stresses are abrupt temperature, variable rainfall, and declining nutrient status of the soil. Varietal development is the key to sustaining productivity under influence of multiple abiotic stresses and must be studied in context with genomics and molecular breeding. Recently, advances in a plethora of Next Generation Sequencing (NGS) based methods have accelerated the enormous genomic data generation associated with stress-induced transcripts such as microarray, RNAseq, Expressed Sequenced Tag (ESTs), etc. Many databases related to microarray and RNA-seq based transcripts have been developed and profusely utilized. However, an abundant amount of transcripts related to abiotic stresses in various cereal crops arising from EST technology are available but still remain underutilized in absence of a consolidated database. In this study, an attempt has been made with a primary goal to integrate, analyse, and characterise the available resources of ESTs responsive to abiotic stresses in major cereals. The developed CerealESTdb presents a customisable search in two different ways in the form of searchable content for easy access and potential use. This database comprises ESTs from four major cereal crops, namely rice (Oryza sativa L.), wheat (Triticum aestivum L.), sorghum (Sorghum bicolour L.), and maize (Zea mays L.), under a set of abiotic stresses. The current statistics of this cohesive database consists of 55,826 assembled EST sequences, 51,791 predicted genes models, and their 254,609 gene ontology terms including extensive information on 1,746 associated metabolic pathways. We anticipate that developed CerealESTdb will be helpful in deciphering the knowledge of complex biological phenomena under abiotic stresses to accelerate the molecular breeding programs towards the development of crop cultivars resilient to abiotic stresses. The CerealESTdb is publically available with the URL http://cabgrid.res.in/CerealESTDb.
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Venkatesh V, Rana SS, Kumar A, Aneja A, Lal SB. Hepatobiliary and Pancreatic: EUS-guided drainage of a ruptured amoebic liver abscess in a child. J Gastroenterol Hepatol 2020; 35:921. [PMID: 32144816 DOI: 10.1111/jgh.15014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 11/06/2019] [Revised: 02/07/2020] [Accepted: 02/15/2020] [Indexed: 12/09/2022]
Affiliation(s)
- V Venkatesh
- Division Of Paediatric Gastroenterology, Post Graduate Institute Of Medical Education and Research, Chandigarh, India
| | - S S Rana
- Department of Gastroenterology, Post Graduate Institute Of Medical Education and Research, Chandigarh, India
| | - A Kumar
- Division Of Paediatric Gastroenterology, Post Graduate Institute Of Medical Education and Research, Chandigarh, India
| | - A Aneja
- Division Of Paediatric Gastroenterology, Post Graduate Institute Of Medical Education and Research, Chandigarh, India
| | - S B Lal
- Division Of Paediatric Gastroenterology, Post Graduate Institute Of Medical Education and Research, Chandigarh, India
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Budhlakoti N, Mishra DC, Rai A, Lal SB, Chaturvedi KK, Kumar RR. A Comparative Study of Single-Trait and Multi-Trait Genomic Selection. J Comput Biol 2019; 26:1100-1112. [PMID: 30994361 DOI: 10.1089/cmb.2019.0032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In recent years of animal and plant breeding research, genomic selection (GS) became a choice for selection of appropriate candidate for breeding as it significantly contributes to enhance the genetic gain. Various studies related to GS have been carried out in the recent past. These studies were mostly confined to single trait. Although GS methods based on single trait have not performed very well in cases like pleiotropy, missing data and when the trait under study has low heritability. Gradually, some studies were carried out to explore the possibility of methods for GS based on multiple traits in the view of overcoming the above-mentioned problems in the method of single-trait GS (STGS). Currently, multi-trait-based GS methods are getting importance as it exploits the information of correlated structure among response. In this study, we have compared various methods related to STGS, such as stepwise regression, ridge regression, least absolute shrinkage and selection operator (LASSO), Bayesian, best linear unbiased prediction, and support vector machine, and multi-trait-based GS methods, such as multivariate regression with covariance estimation, conditional Gaussian graphical models, mixed model, and LASSO. In almost all cases, multi-trait-based methods are found to be more accurate. Based on the results of this study, it may be concluded that multi-trait-based methods have great potential to increase genetic gain as they utilize the correlation among the response variable as extra information, which contributes to estimate breeding value more precisely. This study is a comprehensive review of the methods of GS right from single trait to multiple traits and comparisons among these two classes.
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Affiliation(s)
- Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, India
| | | | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, India
| | - S B Lal
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, India
| | | | - Rajeev Ranjan Kumar
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, India
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Singh I, Deb R, Kumar S, Singh R, Andonissamy J, Smita S, Sengar GS, Kumar R, Ojha KK, Sahoo NR, Murali S, Chandran R, Nair RV, Lal SB, Mishra DC, Rai A. Deciphering foot-and-mouth disease (FMD) virus-host tropism. J Biomol Struct Dyn 2019; 37:4779-4789. [PMID: 30654708 DOI: 10.1080/07391102.2019.1567386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of Bos taurus, Gallus and Canis. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp 143RGD145 and at domain 676SIPLQ680 in alpha-integrin of B. taurus. Notably, in-silico site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and B. taurus integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, in-vitro analysis demonstrates the persistence of the putative tropism site 'SIPLQ' in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Indra Singh
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Rajib Deb
- ICAR-Central Institute for Research on Cattle , Meerut , India
| | - Sanjeev Kumar
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Rani Singh
- ICAR-Central Institute for Research on Cattle , Meerut , India
| | | | - Shuchi Smita
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | | | - Rajiv Kumar
- ICAR-Central Sheep and Wool Research Institute , Avikanagar , India
| | | | | | - S Murali
- ICAR-India National Bureau of Fish Genetic Resources , Lucknow , India
| | - Rejani Chandran
- ICAR-Central Institute of Fisheries Technology , Cochin , India
| | | | - S B Lal
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Dwijesh Chandra Mishra
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Anil Rai
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
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Kumar A, Farooqi MS, Mishra DC, Kumar S, Rai A, Chaturvedi KK, Lal SB, Sharma A. Prediction of miRNA and Identification of their Relationship Network Related to Late Blight Disease of Potato. Microrna 2017; 7:11-19. [PMID: 29237394 DOI: 10.2174/2211536607666171213123038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/12/2017] [Accepted: 12/04/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Late blight is a serious disease in potato caused by Phytophthora infestans. To date only few miRNA have been discovered which are related to late blight disease of potato during host pathogen interaction. Recent studies showed that miRNA, an important gene expression regulator, plays a very important role in host-pathogen interaction by silencing genes either by destructing or blocking of translation of mRNA. METHOD Homology search was performed between non-redundant mature miRNA sequences from miRBase database and Solanum tuberosum EST sequences from NCBI database. Screening of the potential miRNA was done after secondary structure prediction. The target related to late blight disease of respective miRNA was functionally annotated. To identify the relationship between the predicted and mature miRNAs, multiple sequence alignment and evolutionary relationships were established. RESULTS AND CONCLUSION 34 Candidate miRNA related to late blight disease of potato were identified which were associated to five target genes. These miRNAs were linked with Avr3a, INF1, INF2b genes which are elicitin like protein and triggers a hypersensitive response to host cell. Mapping of target sequences showed similarity with Solanum lycopersicum NRC1 gene of chr.1, which are reported as a casual protein required for Pto-mediated cell death and resistance in N. benthamiana. NRC1 are considered as a RX-CC_like domain-containing protein which shows similarity with coiledcoil domain of the potato virus X resistance protein (RX) in Solanum tuberosum. RX recognizes pathogen effector proteins and triggers a response that may be as severe as localized cell death thereby providing resistance against potato virus X.
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Affiliation(s)
- Animesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi 110012, India
| | - Dwijesh Chandra Mishra
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi 110012, India
| | - Sanjeev Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi 110012, India
| | - Krishna Kumar Chaturvedi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi 110012, India
| | - Shashi Bhushan Lal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi 110012, India
| | - Anu Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi 110012, India
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Abstract
Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: http://webapp.cabgrid.res.in/protein/
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Affiliation(s)
- Naveen Sharma
- Center for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- Center for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Krishna Kumar Chaturvedi
- Center for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Shashi Bhushan Lal
- Center for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Monendra Grover
- Center for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Anil Rai
- Center for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Pankaj Pandey
- Center for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
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Sharma A, Rai A, Lal SB. Workflow management systems for gene sequence analysis and evolutionary studies - A Review. Bioinformation 2013; 9:663-72. [PMID: 23930017 PMCID: PMC3732438 DOI: 10.6026/97320630009663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 02/23/2013] [Indexed: 11/23/2022] Open
Abstract
Post 'omic' era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.
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Affiliation(s)
- Anu Sharma
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi - 110012
| | - Anil Rai
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi - 110012
| | - SB Lal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi - 110012
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Lal SB, Pandey PK, Rai PK, Rai A, Sharma A, Chaturvedi KK. Design and development of portal for biological database in agriculture. Bioinformation 2013; 9:588-98. [PMID: 23888101 PMCID: PMC3717188 DOI: 10.6026/97320630009588] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 02/23/2013] [Accepted: 03/04/2013] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED The application of novel and modern techniques in genetic engineering and genomics has resulted in information explosion in genomics. Three major genome databases under International Nucleotide Sequence Database collaboration NCBI, DDBJ and EMBL have been providing a convenient platform for submission of sequences which they share among themselves. Many institutes in India under Indian Council of Agricultural Research have scientists working on biotechnology and bioinformatics research. The various studies conducted by them, generate massive data related to biological information of plants, animals, insects, microbes and fisheries. These scientists are dependent on NCBI, EMBL, DDBJ and other portals for their sequence submissions, analysis and other data mining tasks. Due to various limitations imposed on these sites and the poor connectivity problem prevents them to conduct their studies on these open domain databases. The valued information generated by them needs to be shared by the scientific communities to eliminate the duplication of efforts and expedite their knowledge extended towards new findings. A secured common submission portal system with user-friendly interfaces, integrated help and error checking facilities has been developed in such a way that the database at the backend consists of a union of the items available on the above mentioned databases. Standard database management concepts have been employed for their systematic storage management. Extensive hardware resources in the form of high performance computing facility are being installed for deployment of this portal. AVAILABILITY http://cabindb.iasri.res.in:8080/sequence_portal/
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Affiliation(s)
- Shashi Bhushan Lal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Pusa, New Delhi-110012, India
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Lal SB, Ramsey JJ, Monemdjou S, Weindruch R, Harper ME. Effects of caloric restriction on skeletal muscle mitochondrial proton leak in aging rats. J Gerontol A Biol Sci Med Sci 2001; 56:B116-22. [PMID: 11253148 DOI: 10.1093/gerona/56.3.b116] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Long-term caloric restriction (CR) retards aging processes and increases maximum life span. We investigated the influence of CR on mitochondrial proton leaks in rat skeletal muscle. Because CR lowers oxidative damage to mitochondrial membrane lipids and proteins, we hypothesized that leak would be lower in mitochondria from old CR rats than in age-matched controls. Three groups (n = 12) were studied: 4-month-old "young" control rats (body weight: 404 g +/- 7 SEM), 33-month-old CR rats (body weight: 262 g +/- 3), and 33-month-old control rats (body weight: 446 g +/- 5). CR rats received 67% of the energy intake of old control rats, with adequate intakes of all essential nutrients. Maximum leak-dependent O2 consumption (State 4) was 23% lower in CR rats than in age-matched controls, whereas protonmotive force values were similar, supporting our hypothesis. The overall kinetics of leak were similar between the two groups of old rats; in the young, kinetics indicated higher protonmotive force values. The latter indication is consistent with aging-induced alterations in proton leak kinetics that are independent of dietary intervention. There was no influence of age or diet on serum T4 level, whereas T3 was lower in young than in old control rats. These results support and extend the oxidative stress hypothesis of aging.
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Affiliation(s)
- S B Lal
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ontario, Canada
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Abstract
Ruminal acidosis was induced in six adult sheep by oral feeding of wheat grain at 90 g kg-1 body-weight. Ruminal fluid, blood, cerebrospinal fluid (CSF) and urine samples were collected before grain feeding (0 h) and thereafter at 12, 24, 48, 72, 96 and 120 hour intervals. Decrease in the rumen pH was associated with decreased pH in blood, CSF and urine and increased total lactic acid concentrations in rumen liquor, blood, CSF and urine. Significantly (P < 0.05) increased levels of sodium, inorganic phosphorus and decreased levels of potassium and calcium were observed in the serum of acidotic sheep. CSF analysis revealed decreased potassium and chloride levels and increased glucose concentration and total leucocyte count within 12 hours of the grain feeding. Pandy's test was positive in half of the surviving sheep at 12 hours and in all the sheep at 96 and 120 hours of observation. In urine, sodium and chloride levels decreased while potassium and inorganic phosphorus increased. The changes in the biochemical parameters started within 12 hours and lasted up to 48 to 120 hours of the observation period.
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Affiliation(s)
- R C Patra
- Division of Experimental Medicine and Surgery, Indian Veterinary Research Institute, Izatnagar
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Abstract
Experimental acidosis was induced in six goats aged between one and two years by administration of whole wheat grain at 100 g kg-1 bodyweight given intraruminally. Blood and cerebrospinal fluid (CSF) samples were collected from these goats before administration of wheat grain (0 hour) and thereafter at 12, 24, 48, 72, 96 and 120 hour intervals. These were analysed for serum enzyme activities and physicochemical characters of CSF. Significantly (P less than 0.05) higher activities of amylase (at 12 hours), lactate dehydrogenase (12 to 48 hours), creatine phosphokinase (12 to 48 hours), aspartate aminotransferase (12 to 24 hours), and gamma-glutamyl transferase (12 to 96 hours) were found in serum samples of acidotic goats. Changes in CSF included decrease of pH and chloride content and higher glucose values. No difference was seen in the physical character of CSF collected at different time intervals from acidotic goats.
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Affiliation(s)
- S B Lal
- Division of Experimental Medicine and Surgery, Indian Veterinary Research Institute, Izatnagar
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Singh G, Mallick KP, Lal SB. Bovine lameness associated with osteosclerosis. Mod Vet Pract 1981; 62:801-3. [PMID: 7341960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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