Hirak Barman

Hirak Barman
Central Institute of Freshwater Aquaculture | CIFA · Fish Genetics and Biotechnology

PhD

About

47
Publications
9,950
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861
Citations
Additional affiliations
July 1996 - present
Central Institute of Freshwater Aquaculture
Position
  • Principal Investigator

Publications

Publications (47)
Article
Full-text available
Background The physiological significance of a large family of heat-shock proteins (HSPs), comprised of the cytosolic HSP90A and the endoplasmic reticulum component of HSPB, is evident in prokaryotes and eukaryotes. The HSP90A is believed to play critical roles in diverse physiological functions of cell viability and chromosomal stability including...
Article
The promyelocytic leukemia zinc finger (Plzf) gene, being a transcriptional repressor, plays a crucial role in self-renewal and maintenance of spermatogonial stem cells (SSCs) across mammalian and non-mammalian species. It is now being considered as a candidate marker of proliferating SSC in teleost. The knowledge on its mechanism of expression is...
Article
Full-text available
Recent advances in high throughout DNA sequencing technologies have revolutionized for better understanding of structure-functional relationships of genes in identifying trait-associated transcriptomes and their regulated gene expressions. Subsequent breakthroughs in gene editing technologies such as zinc finger nucleases, transcriptional activator...
Article
Full-text available
Background The homeobox containing transcription factor Nanog plays crucial roles in embryonic development/proliferation and/or maintenance of spermatogonial stem cells (SSCs) via interacting with transcription factors such as Oct4 and Sox2 in mammals. However, knowledge of its exact mechanistic pathways remains unexploited. Very little is known ab...
Article
Full-text available
The NADH dehydrogenase is the first and largest enzyme complex in the mitochondrial oxygen respiration chain. In the present study, we intended to investigate the role of NADH dehydrogenase during hypoxia stress in the Murrel, Channa Striatus. We have cloned and characterized full length cDNA of NADH dehydrogenase (Ubiquinone) iron-sulfur protein 2...
Article
Full-text available
Advancements in the DNA sequencing technologies and computational biology have revolu- tionized genome/transcriptome sequencing of non- model fishes at an affordable cost. This has led to a paradigm shift with regard to our heightened under- standings of structure-functional relationships of genes at a global level, from model animals/fishes to non...
Article
Immune response mediated by toll-like receptor 22 (TLR22), only found in teleost/amphibians, is triggered by double-stranded RNA binding to its LRR (leucine-rich repeats) ecto-domain. Accumulated evidences suggested that missense mutations in TLR genes affect its function. However, information on mutation linked pathogen recognition for TLR22 was l...
Article
Glutamate dehydrogenase (GDH) plays a key role in the metabolism of free amino acids (FAA) in crustaceans and other metazoans. GDH has been widely implicated a central role in response to hyperosmotic condition. However, the response of GDH gene expression to salinity alterations has not yet been determined in Macrobrachium rosenbergii, a euryhalin...
Article
Full-text available
Channa striatus is a large-bodied fish of freshwater habitat capable of withstanding hypoxic conditions. Adaptive response to hypoxia is a complex physiological process. A laboratory-based rearing protocol for investigating long-term hypoxia stress tolerance in this species was established. Using suppression subtractive hybridization technique, we...
Article
Full-text available
Transgenesis is the revolutionary science of making a genetically modified organism. Interestingly, fish offer easier genetic manipulation compared to mammalian counterpart, as they bred easily and large number of eggs is laid by female (higher fecundity) and have independent embryonic biology. The primary goals for genetic manipulation of fish spe...
Article
The high-throughput sequencing technology provides a platform for revealing the expressed genes within a tissue at a specific time. The giant freshwater prawn, Macrobrachium rosenbergii, is an economically important species, which is surviving in a wide-range of salinity. In this study, to understand the physiological mechanism of adaptability with...
Article
The high-throughput sequencing technology provides a platform for revealing the expressed genes within a tissue at a specific time. The giant freshwater prawn, Macrobrachium rosenbergii, is an economically important species, which is surviving in a wide-range of salinity. In this study, to understand the physiological mechanism of adaptability with...
Article
Spermatogenesis is a highly co-ordinated and complex process. In vitro propagation of spermatogonial stem cells (SSCs) could provide an avenue in which to undertake in vivo studies of spermatogenesis. Very little information is known about the SSC biology of teleosts. In this study, collagenase-treated testicular cells of farmed catfish (Clarias ba...
Article
Full-text available
RbAp46/48, histone chaperone, is a family of evolutionarily conserved WD40 repeat-containing proteins, which are involved in various chromatin-metabolizing processes, but their in vivo functional relevance is yet unclear. In order to examine the biological role of pRbAp48 in chicken DT40 cells, we generated a tetracycline-inducible system for condi...
Article
Recent advances in gene editing techniques have not been exploited in farmed fishes. We established a gene targeting technique, using the CRISPR/Cas9 system in Labeo rohita, a farmed carp (known as rohu). We demonstrated that donor DNA was integrated via homologous recombination (HR) at the site of targeted double-stranded nicks created by CRISPR/C...
Article
Full-text available
The myostatin (MSTN) is a known negative growth regulator of skeletal muscle. The mutated myostatin showed a double-muscular phenotype having a positive significance for the farmed animals. Consequently, adequate information is not available in the teleosts, including farmed rohu carp, Labeo rohita . In the absence of experimental evidence, computa...
Article
Full-text available
Growth hormone (GH) is an important polypeptide necessary for normal growth as well as development in fishes. Even though, GH has been well characterized in several fishes, lack of information on the structure GH protein. Recent advances of computational tools are helpful for developing structure using protein sequences using either homology modell...
Article
Full-text available
We previously characterized the β-actin gene promoter of Indian domesticated rohu carp (Labeo rohita) and made a reporter construct via fusion to green fluorescence protein (GFP) cDNA. In this study, the same construct was used to breed transgenic rohu fish. About 20% of the transgenic offspring showed ubiquitous expression of the reporter GFP gene...
Article
Full-text available
The recent progress in DNA sequencing and computational algorithms dramatically heightened the quantum of SNP (single nucleotide polymorphisms) databases. The experimental study of mutation for particular gene of interests is laborious and time consuming. Therefore, in this study, we have used several computational algorithms for investigating stru...
Article
Full-text available
Promyelocytic leukemia zinc finger (Plzf), a transcriptional repressor, is involved in survival and maintenance of pluripotent stem cells including embryonic and spermatogonial stem cells in mammals. Its cDNA was characterized and expression in proliferating spermatogonial stem cells of rohu (Labeo rohita), a farmed carp, was documented. In teleost...
Article
Toll-like receptor 22 (TLR22) is present in teleost but not in mammals. Among Indian farmed carps, Catla catla is relatively more resistant than Labeo rohita to Argulus siamensis lice infection. TLR22 is believed to be associated with innate immunity against ectoparasite infection. To investigate the TLR22 mediated immunity against argulosis, we ha...
Article
We cloned the 5'-flanking region (1.2 kb) of a muscle-specific gene, encoding myosin light chain 2 polypeptide (mylz2) of a farmed carp, Labeo rohita (rohu). Sequence analysis using TRANSFAC-database search identified the consensus cis acting regulatory elements of TATA-box and E (CANNTG)-box, including the monocyte enhancer factor 2 motif, implyin...
Article
Full-text available
Mammalian Pou5f1 is a known transcriptional regulator involving maintenance of embryonic and spermatogonial stem cells. Little is known about teleost Pou2, an ortholog of mammalian Pou5f1. Evidences of discrepancy in expression pattern between fish species were documented. To better understand, we have cloned and characterized Pou2 gene of farmed r...
Article
Full-text available
The giant freshwater prawn, Macrobrachium rosenbergii, is an economically important species. It is a euryhaline shrimp, surviving in wide-range salinity conditions. A change in gene expression has been suggested as an important component for stress management. To better understand the osmoregulatory mechanisms mediated by the gill, a subtractive an...
Article
Expressed genes and polymorphisms were identified in lines of rohu Labeo rohita selected for resistance or susceptibility to Aeromonas hydrophila, an important bacterial pathogen causing aeromoniasis. All animals were grown in a common environment and RNA from ten individuals from each line pooled for Illumina mRNA-seq. De novo transcriptome assemb...
Article
The in vitro culture system for spermatogonial stem cells (SSCs) is a powerful tool for exploring molecular mechanisms of male gametogenesis and gene manipulation. Very little information is available for fish SSC biology. Our aim was to isolate highly pure SSCs from the testis of commercially important farmed carp, Labeo rohita. The minced testis...
Article
Genetic information linked to the testicular development of Labeo rohita (rohu) could contribute towards understanding and improving breeding efficiency. A rohu testis-enriched cDNA library was generated by the subtractive and suppressive hybridization technique to identify differentially expressed genes. Two-hundred and forty differentially screen...
Article
The promyelocytic leukemia zinc finger (Plzf) gene containing an evolutionary conserved BTB (bric-a-brac/tramtrack/broad complex) domain plays a key role in self-renewal of mammalian spermatogonial stem cells (SSCs) via recruiting transcriptional co-repressors. Little is known about the function of Plzf in vertebrate, especially in fish species. To...
Article
Amounts of soluble histones in cells are tightly regulated to ensure supplying them for the newly synthesized DNA and preventing the toxic effect of excess histones. Prior to incorporation into chromatin, newly synthesized histones H3 and H4 are highly acetylated in pre-deposition complex, wherein H4 is di-acetylated at Lys-5 and Lys-12 residues by...
Article
We previously reported that histone deacetylase-2 (HDAC2) controls the amount of IgM H-chain at the steps of transcription of its gene and alternative processing of its pre-mRNA in DT40 cells. Here, we showed not only that the HDAC2-deficiency caused repressions of gene expressions for HDAC7, EBF1, Pax5, Aiolos and Ikaros, and elevations of gene ex...
Article
Histone acetyltransferase 1 (HAT1) is implicated for diacetylation of Lys-5 and Lys-12 of newly synthesized histone H4, the biological significance of which remains unclear. To investigate the in vivo role of HAT1, we generated HAT1-deficient DT40 clone (HAT1(-/-)). HAT1(-/-) cells exhibited greatly reduced diacetylation levels of Lys-5 and Lys-12,...
Article
Full-text available
Asf1 (anti-silencing function 1), a well conserved protein from yeast to humans, acts as a histone chaperone and is predicted to participate in a variety of chromatin-mediated cellular processes. To investigate the physiological role of vertebrate Asf1 in vivo, we generated a conditional Asf1-deficient mutant from chicken DT40 cells. Induction of A...
Article
Alterations in the chromatin structure are essential for easy accesses to chromosomal DNA. Such architectural alterations can be achieved by four means: (i) variants of histone subtypes, (ii) chromatin remodeling, (iii) post-translational modification, and (iv) chromatin assembly. This chapter discusses mainly on the first, third and fourth mechani...
Article
Information on the genetic structure of cultivable fish species is essential for studying molecular systematics and optimising fisheries management and fish farming. The random amplified polymorphic DNA (RAPD) assay was evaluated for studying genetic relationships and diversities in four species of Indian major carps (Family Cyprinidae). Thirty-fou...

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Project (1)
Project
Spermatogonial stem cell Culture and purification. Identification and characterization of stem cell marker genes.