Papers by Chandra Mukhopadhyay
Toll-like receptors (TLRs) contribute to the host innate immunity by recognizing and binding to t... more Toll-like receptors (TLRs) contribute to the host innate immunity by recognizing and binding to the pathogen associated molecular patterns (PAMPs) through the receptor-specific extracellular leucine rich repeat (LRR) containing domain. The TLRs have been a subject of significant research endeavors in all the livestock species; however, a very little attention is paid towards indigenous fish TLRs. TLR9, expressed intra-cellularly by immune cells, recognizes unmethylated CpG sequences. Mammalian TLR9 has been reported to have experienced purifying selection; however, the evolutionary perspective of TLR9 of the indigenous major carps has never been studied. TLR9 partial cDNA (1155 nucleotides), reverse transcribed from total RNA isolated from spleen, was cloned into DH5α strain of E. coli and finally custom sequenced. Multiple sequence analysis of the translated amino-acid sequence indicated that it is conserved; with insertion of few amino acids in fish as compared to that of mammalia...
The Indian veterinary journal
Asian-Australasian Journal of Animal Sciences, 2015
In the present study, we used high-throughput sequencing, miRNA-seq, to discover and explore the ... more In the present study, we used high-throughput sequencing, miRNA-seq, to discover and explore the expression profiles of known and novel miRNAs in TLR ligand-stimulated vis-à-vis non-stimulated (i.e. Control) peripheral blood mononuclear cells (PBMCs) isolated from blood of healthy Murrah buffaloes. Six small RNA (sRNA) libraries were multiplexed in Ion Torrent PI chip and sequenced on Ion Proton System. The reads obtained were aligned to the Bos taurus genome (UMD3.1 assembly), which is phylogenetically closest species to buffalo (Bubalus bubalis). A total of 160 bovine miRNAs were biocomputationally identified in buffalo PBMCs and 130 putatively novel miRNAs (not enlisted in the bovine mirBase) were identified. All of these 290 miRNAs identified across the six treatment and control samples represent the repertoire of novel miRNAs for the buffalo species. The expression profiles of these miRNAs across the samples have been represented by sample dendrogram and heatmap plots. The uniquely expressed miRNAs in each treatment and control groups were identified. A few miRNAs were expressed at very high levels while the majority of them were moderately expressed. The miRNAs bta-miR-103 and-191 were found to be highly abundant and expressed in all the samples. Other abundantly expressed miRNAs include bta-miR-19b,-29b,-15a,-19a,-30d,-30b-5p and members of let family (let 7a-5p, let 7g & let 7f) in LPS and CpG treated PBMCS and bta-miR-191,-103 &-19b in Poly I:C stimulated PBMCs. Only one novel miRNA (bta-miR-11039) out of 130 identified putatively novel miR-NAs, was expressed in all the six samples and differentially expressed (>2-fold) miRNAs were identified. Six of the differentially expressed miRNAs across the groups (bta-miR-421, bta-let-7i, bta-miR-138, bta-miR-21-5p, bta-miR-222 and bta-miR-27b) were subsequently confirmed by TaqMan quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, the target genes of differentially expressed miRNAs were enriched for the roles in innate immunity and TLR signaling pathways. This maiden study on profiling and cataloguing of bubaline miRNAs expressed in TLR-ligand stimulated PBMCs will
Sub-clinical mastitis in buffalo is considered
as multi-factorial disease, which leads to huge ec... more Sub-clinical mastitis in buffalo is considered
as multi-factorial disease, which leads to huge economic
losses by reducing the quality and quantity of the milk. It
does not lead to any change in phenotypic expression, so
diagnosed through various tests as California Mastitis Test,
Somatic cell count, Electrical conductivity test. Although
bacteria are considered to be the main causative agent for
mastitis, beside this farm management practices are found to
be associated with the disease. In the present study, the
pathogens related to the occurrence of the disease were
examined via bacteriological culture of milk sample of the
animal. Prevalence of sub-clinical mastitis was found 20.4%,
out of this 7.8%, 9.8% and 2.8% were found effected with
latent mastitis, specific mastitis and nonspecific mastitis,
respectively. Left hind quarters were affected more with subclinical
mastitis (33.9%), followed by RH (24%),RF (22.4%)
and the least in LF (14.5%). The microorganisms isolated
from sub-clinical mastitis constituted Staphylococci (39%),
Streptococci (31%), Corynebacterium (25%) and E.coli (5%).
Farm management associated determinants (Type of feed,
type of floor, education of the owner, feeding after milking,
type of labor) were studied in association with sub-clinical
mastitis. Out of these education of the owner, type of labor
and feeding after milking were found to be significantly
associated with disease occurrence (p<0.05). While looking
at the animal determinants in association with sub-clinical
mastitis in the present investigation buffaloes with higher
parity showed more risk of developing sub-clinical mastitis.
So, the present investigation helps to understand the various
risk factors for the occurrence of sub-clinical mastitis in water
buffalo in Doaba region of Punjab.
The present work focuses on the in silico characterization of functional divergence of two ovine ... more The present work focuses on the in silico characterization of functional divergence of two ovine cathelicidin coding sequence (cds) variants (ie, Cath1 and Cath2) of Indian sheep. Overlapping partial cds of both the cathelicidin variants were cloned in pJet1.2/blunt vector and sequenced. Evolutionary analysis of the Cath2 and Cath1 indicated that the mammalian cathelicidins clustered separately from avian fowlicidins. The avian fowlicidins, which are very different from mammalian cathelicidins (Caths), clearly displayed signatures of purifying selection. The pairwise sequence alignments of translated amino acid sequences of these two sheep cathelicidins showed gaps in the antimicrobial domain of Cath1 variant; however, the amino terminal cathelin regions of both the Caths were conserved. Amino acid sequence analysis of full-length cathelicidins available at public database revealed that Cath1, Cath2, and Cath7 of different ruminant species (including our Cath1 and Cath2 variants) formed individual clads, suggesting that these types have evolved to target specific types of microbes. In silico analysis of Cath1 and Cath2 peptide sequences indicated that the C-terminal antimicrobial peptide domain of Cath2 is more immunogenic than that of the ovine Cath1 due to its higher positive antigenic index, making Cath1 a promising antigen for production of monoclonal antibodies. CITaTIon: Dhaliwal et al. In Silico characterization of functional Divergence of two cathelicidin variants in indian sheep.
Aromatase-P450 is an enzyme responsible for estrogen biosynthesis. It plays a major role in norma... more Aromatase-P450 is an enzyme responsible for estrogen biosynthesis. It plays a major role in normal spermatogenesis and it controls the sexual development and neuro-endocrine functions. Leptin, a 167 amino acid long protein-hormone, is the product of obese gene secreted by adipocytes. In the present study the expression of Leptin and Aromatase-P450 in the fresh ejaculates, using SYBR Green chemistry in real time PCR, from a total of 10 bulls- 4 buffalo and 6 crossbred cattle bulls were studied. The experimental animals were further categorized into acceptable (individual motility> 50%, post thaw motility> 45% in cattle and >40% in buffalo) or poor semen samples (individual motility< 50%, post thaw motility< 45% in cattle and < 40% in buffalo). The expression of Aromatase-P450 was found to be higher in acceptable semen ejaculates whereas for Leptin gene it was higher in poor quality semen for both the species. Sperm mitochondrial activity index (SMAI) was performed to determine association between the activity of sperm mitochondria, individual motility and with the expression of both the genes. Samples with high mass motility were showing high depositions of NBT dye and high expression of Aromatase-P450 gene but low expression of Leptin gene as compared to low mass motility. In conclusion, higher expression of aromatase and leptin genes in fresh ejaculates is directly and inversely proportional respectively, to higher sperm motility in both cattle and buffalo bulls.
Implementation of a successful cattle breeding program relies on selection of genetically superio... more Implementation of a successful cattle breeding program relies on selection of genetically superior and tested males against various andrological anomalies. In the present project, single stranded conformation polymorphism (SSCP) of holandric genes viz. ubiquitin specific protease, Y-linked (USPY) and RNA binding motif Y-linked (RBMY) was studied for identifying novel SNPs and associating the SNPs withspermatological attributes (sperm chromatin maturity, semen volume, initial motility) in cattle (10 HF crossbred) and buffalo (10 Murrah). The SSCP band patterns revealed species specific variation only in two primer-pairs (US2 and US3) of USPY gene. The maximum and minimum values of percent immature sperm were ranging between 0.392 to 2.586 in cattle and from 0.901 to 4.000 in buffalo. The percent immature spermatozoa in the ejaculates did not differ significantly either between species or between the categories (acceptable and unacceptable semen donors). The average immature sperm count was the least in buffalo ejaculates (1.383 ± 0.176). The correlation coefficient was found negative between the spermatological parameters (volume and initial motility) and the immature sperm yield in both cattle and buffalo ejaculates. It indicates that the immature sperm production might be negatively associated with semen volume and initial motility of the spermatozoa.
Stem cell research has appeared as a silver lining of hope over the dark cloud of some untreatabl... more Stem cell research has appeared as a silver lining of hope over the dark cloud of some untreatable diseases like cancer and certain neurological disorders. Embryonic stem cells, the tabula rasa, holds much promise in this regard owing to its totipotency, howbeit, it has whirled a severe tempest all over the world on the point of humanity. The present review article includes the chronology of stem cell research with special reference to the techniques that were evolved in due course of research, the controversy over the application of embryonic stem cells for therapeutics and present status of stem cell research under Indian context. India is being increasingly alluring the foreign companies to invest in this project since a huge prospect in stem cell marketing business is foreseen in this country.
American Journal of Bioinformatics, 2012
Interferon-tau (IFNt) contributes towards maternal recognition of pregnancy in ruminants (like, c... more Interferon-tau (IFNt) contributes towards maternal recognition of pregnancy in ruminants (like, cattle,
buffalo, goat, giraffe). IFNt has been extensively studied in most of the ruminants except for buffalo
Bubalus bubalis). The present study has been undertaken to predict the secondary structure of Interferon-tau
in buffalo. The available amino acid sequence of bubaline IFNt (sequence database of SwissProt) was
subjected to protein-BLAST to find similar sequences with high scores and low e-values. The ovine IFNt
sequence (PDB code: 1B5L) was selected for further computational analysis of the bubaline IFNt sequence
to predict the secondary and tertiary structure. The secondary structure of the modeled bubaline IFNt was
predicted using STRIDE. The 3D structure was generated using academic version of MODELER9v6. The
Probability Density Functions (PDF) was used to restrain Cα-Cα distances, main chain N-O distances as
well as main-chain and side-chain dihedral angles. The energy minimization and van der waal contacts were
taken care of using ACCELRYS DS Modeling 2.0. The residue profiles of the obtained three-dimensional
models were checked by VERIFY3D. The energetic architecture and the correctness of the generated model
revealed that the predicted secondary model was correct and acceptable. The predicted structure of the
bubaline IFNt constructed through homology modeling from ovine IFNt, can be used for functional
characterization of bubaline IFNt.
Subfertility problems are encountered frequently in the cattle and buffalo bulls commercially mai... more Subfertility problems are encountered frequently in the cattle and buffalo bulls commercially maintained for semen production in dairy farms and under field conditions for natural insemination. Reports are scarce on the incidence of subfertility in breeding bulls, especially in India. The objective of the present study was to assess the incidence of the male reproductive anomalies leading to disposal of bovine bulls at GADVASU dairy farm, Ludhiana, Punjab (India). Data on frequency of various subfertility and disposal pattern of bulls maintained at the dairy farm, GADVASU, were collected for 12 yrs (1999 to 2010) and compiled from different record registers. Percentage of bulls that produced freezable semen (out of reserved ones) was less in cattle (25.641%) as compared to that of buffalo (30.4%). Various subfertility traits like poor libido and unacceptable seminal profile were found to be the significant reasons (p<0.01) for culling of the breeding bulls. Inadequate sex drive and poor semen quality were the main contributing factors for bull disposal in cattle whereas poor semen freezability was most frequently observed in buffalo bulls. All the male reproductive traits were significantly different (p<0.05) for the periods of birth, except for semen volume, initial motility (IM), age at last semen collection (ALSC) and age at disposal. The ages at first and last semen collection as well as freezing (i.e. AFSC, ALSC and AFSF, ALSF, respectively) and age at disposal (AD) were higher in buffalo. The spermatological parameters and semen production period (SPP) were higher in cattle. The age at first semen donation and breeding period could be reduced by introducing the bulls to training at an early age. The results revealed an increasing trend in individual motility (IM) while semen volume, AFSC, AFSF, AD, FSPP, SPP, ALSC and ALSF showed a decreasing, however, not a definite trend, over the periods. The semen donation traits like, AFSF, of the cattle and buffalo bulls could be predicted from the AFSC, using prediction equation derived in the present study.
… AND GENOMIC TOOLS FOR ANALYSIS OF …
Indian Journal of …, 2010
Indian Journal of …, 2011
Indian Journal of …, 2008
The nuclear chromatin decondensation test (NCDT) detects the ability of the sperm chromatin to un... more The nuclear chromatin decondensation test (NCDT) detects the ability of the sperm chromatin to undergo decondensation following fertilization. The test does not have direct bearing with the fertilizing ability of the spermatozoa but only reflects the proportion of sperm that may swell following exposure to in vitro decondensing agents. The gross seminal parameters do not have any direct relationship on the ability of the sperm chromatin to effect decondensation whether in vivo or in vitro. The test can not be reliably used to assess the fertilizing potential of frozen thawed semen of bovines.
Indian Journal of …, 2008
Cryopreserved spermatozoa are prone to cryoinjury which induces membrane damage and render them i... more Cryopreserved spermatozoa are prone to cryoinjury which induces membrane damage and render them incapable to undergo acrosome reaction (AR). In the present study, cryopreserved semen samples obtained from 30 Karan Fries bulls were subjected to in vitro AR. The AR scores were correlated with the fertility rates (conception rates) following A.I. with frozen semen frozen semen. The AR scores and gross seminal parameters showed significant correlations except for semen volume. A prediction equation (R 2 = 37.3) was constructed from AR scores and was used to predict the conception rates of donor bulls. The predicted and observed conception rates did not show any significant difference for chi square test. The study indicates that in vitro acrosome reaction test may be complemented with the conventional semen analyses tests prior to using cryopreserved semen samples for AI purpose.
Veterinary World, 2011
Germ cells are endowed with unique properties like the ability to undergo meiosis and differentia... more Germ cells are endowed with unique properties like the ability to undergo meiosis and differentiate into gametes in order to perpetuate the genetic material. Spermatogonial stem cells (SSC) are considered as the best suited undifferentiated germ cells and are being consistently studied to reveal the basic physiology, genomics and transcriptomics of those cells. SSC provide an excellent model system to understand the differentiation, development and functioning of gonads and further use of these cells in transplantation-cell based therapies. In the present article, basic aspects of spermatogonial multiplication, regulation of stem cell renewal and differentiation would be discussed.
… -Australasian journal of …, 2010
The study had two objectives, namely, to estimate the andrological disorders leading to disposal ... more The study had two objectives, namely, to estimate the andrological disorders leading to disposal of Karan Fries (KF), Sahiwal cattle and Murrah buffalo bulls and to study the effect of various factors (species/breeds, season of birth and period of birth) on male reproductive parameters. Records on occurrence of subfertility problems and disposal pattern of bulls maintained at the National Dairy Research Institute herd were collected for 15 years (1991 to 2005). Percentage of bulls producing freezable semen was less in the crossbred cattle (58.46%) as compared to Sahiwal (81.69%) and Murrah bulls (81.05%). Various subfertility traits like poor libido and unacceptable seminal profile were found to be the significant reasons (p<0.01) for culling of the breeding bulls. Inadequate sex drive was the main contributing factor for bull disposal in Sahiwal (22.55%) and Murrah bulls (15.12%) whereas poor semen quality and freezability were most frequently observed in KF bulls (24.29 and 7.29 percent, respectively). Least squares analyses of different male reproductive parameters showed that species/breeds had significant effect (p<0.05) on all traits except for frozen semen production periods (FSPP). Periods of birth were significantly different (p<0.05) for all traits except for semen volume. Age at first semen collection (AFSC), age at first semen freezing (AFSF) and age at disposal (AD) were highest in Murrah, while frozen semen production period (FSPP) and semen production period (SPP) were highest in KF and lowest in Sahiwal. The age at first semen donation and breeding period could be reduced by introducing the bulls to training at an early age. These results revealed a declining trend in AFSC, AFSF, FSPP, SPP and AD, thereby indicating an improvement in reproductive performance over the years. The age at first semen donation in bovines can be reduced by introducing the young male calves to training at an early age, which could increase the dosage of semen obtained from each male. (
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Papers by Chandra Mukhopadhyay
as multi-factorial disease, which leads to huge economic
losses by reducing the quality and quantity of the milk. It
does not lead to any change in phenotypic expression, so
diagnosed through various tests as California Mastitis Test,
Somatic cell count, Electrical conductivity test. Although
bacteria are considered to be the main causative agent for
mastitis, beside this farm management practices are found to
be associated with the disease. In the present study, the
pathogens related to the occurrence of the disease were
examined via bacteriological culture of milk sample of the
animal. Prevalence of sub-clinical mastitis was found 20.4%,
out of this 7.8%, 9.8% and 2.8% were found effected with
latent mastitis, specific mastitis and nonspecific mastitis,
respectively. Left hind quarters were affected more with subclinical
mastitis (33.9%), followed by RH (24%),RF (22.4%)
and the least in LF (14.5%). The microorganisms isolated
from sub-clinical mastitis constituted Staphylococci (39%),
Streptococci (31%), Corynebacterium (25%) and E.coli (5%).
Farm management associated determinants (Type of feed,
type of floor, education of the owner, feeding after milking,
type of labor) were studied in association with sub-clinical
mastitis. Out of these education of the owner, type of labor
and feeding after milking were found to be significantly
associated with disease occurrence (p<0.05). While looking
at the animal determinants in association with sub-clinical
mastitis in the present investigation buffaloes with higher
parity showed more risk of developing sub-clinical mastitis.
So, the present investigation helps to understand the various
risk factors for the occurrence of sub-clinical mastitis in water
buffalo in Doaba region of Punjab.
buffalo, goat, giraffe). IFNt has been extensively studied in most of the ruminants except for buffalo
Bubalus bubalis). The present study has been undertaken to predict the secondary structure of Interferon-tau
in buffalo. The available amino acid sequence of bubaline IFNt (sequence database of SwissProt) was
subjected to protein-BLAST to find similar sequences with high scores and low e-values. The ovine IFNt
sequence (PDB code: 1B5L) was selected for further computational analysis of the bubaline IFNt sequence
to predict the secondary and tertiary structure. The secondary structure of the modeled bubaline IFNt was
predicted using STRIDE. The 3D structure was generated using academic version of MODELER9v6. The
Probability Density Functions (PDF) was used to restrain Cα-Cα distances, main chain N-O distances as
well as main-chain and side-chain dihedral angles. The energy minimization and van der waal contacts were
taken care of using ACCELRYS DS Modeling 2.0. The residue profiles of the obtained three-dimensional
models were checked by VERIFY3D. The energetic architecture and the correctness of the generated model
revealed that the predicted secondary model was correct and acceptable. The predicted structure of the
bubaline IFNt constructed through homology modeling from ovine IFNt, can be used for functional
characterization of bubaline IFNt.
as multi-factorial disease, which leads to huge economic
losses by reducing the quality and quantity of the milk. It
does not lead to any change in phenotypic expression, so
diagnosed through various tests as California Mastitis Test,
Somatic cell count, Electrical conductivity test. Although
bacteria are considered to be the main causative agent for
mastitis, beside this farm management practices are found to
be associated with the disease. In the present study, the
pathogens related to the occurrence of the disease were
examined via bacteriological culture of milk sample of the
animal. Prevalence of sub-clinical mastitis was found 20.4%,
out of this 7.8%, 9.8% and 2.8% were found effected with
latent mastitis, specific mastitis and nonspecific mastitis,
respectively. Left hind quarters were affected more with subclinical
mastitis (33.9%), followed by RH (24%),RF (22.4%)
and the least in LF (14.5%). The microorganisms isolated
from sub-clinical mastitis constituted Staphylococci (39%),
Streptococci (31%), Corynebacterium (25%) and E.coli (5%).
Farm management associated determinants (Type of feed,
type of floor, education of the owner, feeding after milking,
type of labor) were studied in association with sub-clinical
mastitis. Out of these education of the owner, type of labor
and feeding after milking were found to be significantly
associated with disease occurrence (p<0.05). While looking
at the animal determinants in association with sub-clinical
mastitis in the present investigation buffaloes with higher
parity showed more risk of developing sub-clinical mastitis.
So, the present investigation helps to understand the various
risk factors for the occurrence of sub-clinical mastitis in water
buffalo in Doaba region of Punjab.
buffalo, goat, giraffe). IFNt has been extensively studied in most of the ruminants except for buffalo
Bubalus bubalis). The present study has been undertaken to predict the secondary structure of Interferon-tau
in buffalo. The available amino acid sequence of bubaline IFNt (sequence database of SwissProt) was
subjected to protein-BLAST to find similar sequences with high scores and low e-values. The ovine IFNt
sequence (PDB code: 1B5L) was selected for further computational analysis of the bubaline IFNt sequence
to predict the secondary and tertiary structure. The secondary structure of the modeled bubaline IFNt was
predicted using STRIDE. The 3D structure was generated using academic version of MODELER9v6. The
Probability Density Functions (PDF) was used to restrain Cα-Cα distances, main chain N-O distances as
well as main-chain and side-chain dihedral angles. The energy minimization and van der waal contacts were
taken care of using ACCELRYS DS Modeling 2.0. The residue profiles of the obtained three-dimensional
models were checked by VERIFY3D. The energetic architecture and the correctness of the generated model
revealed that the predicted secondary model was correct and acceptable. The predicted structure of the
bubaline IFNt constructed through homology modeling from ovine IFNt, can be used for functional
characterization of bubaline IFNt.