Kafkas Universitesi Veteriner Fakultesi Dergisi, 2018
A copy number variation (CNV) is information of DNA segment containing deletion, duplication or i... more A copy number variation (CNV) is information of DNA segment containing deletion, duplication or insertion exist within diverse populations. This study detected 53 CNVs regions that overlapped with immune response, body size and parasitic resistance traits in Pakistani cattle breeds. This study characterized genetic diversity and provides lineage differentiated CNVs in these indigenous cattle breeds.
The bovine high density SNPs genotyping array has a wide range of applications including detectio... more The bovine high density SNPs genotyping array has a wide range of applications including detection of selection signatures, identification of copy number variants (CNVs), genome wide association studies, and dendrogram relationships. This array can also be used to improve the accuracy of genomic predictions for low heritable traits viz. reproductive traits. The effectiveness of this array for genomic selection mainly depends on polymorphism level. In this study, we used 136 individuals from ten different Pakistani cattle breeds, include Achi (18), Bhagnari (14), Cholistani (13), Dajal (10), Dhanni (10), Kankraj (12), Lohani (19), Red Sindhi (13), Sahiwal (14), and Tharparkar (13) using high density SNPs genotyping and this array contained approximately 777, 962 SNPs. The results of this study revealed that approximately 500, 939 SNPs were found polymorphic in these breeds. The results indicate that high density SNPs bead chip would offer an informative genotyping platform for quantitative trait loci (QTL) mapping in indigenous Pakistani cattle breeds.
Bioinformatics, an emerging powerful science gradually enfolds all sorts of sciences under its hu... more Bioinformatics, an emerging powerful science gradually enfolds all sorts of sciences under its huge banner; Forensic Sciences being one of them. With the passing time the productiveness, efficacy and virtue of Bioinformatics based tools is taking over the Forensic Sciences and research. Whether it be declaration via extracting the tiniest DNA from the tiniest microbial sample, DNA profiling, gender identification or the most advanced Automatic Fingerprint Recognition System, computational tools are aiding the Forensics in every possible way. Furthermore, Next Generation Sequencing technology along with the epigenetic studies gives rise to a vast research domain by simultaneously analyzing multiple loci that are of forensic interest in multiple genetic contexts. The paper evaluates then boosting influence of computation on this immensely significant field, especially in terms of law and order. A series of physical evidences are put up for the critical analysis that reveal pros and co...
Glyphosate is non-selective herbicide. Studies published in the last decade, point towards glypho... more Glyphosate is non-selective herbicide. Studies published in the last decade, point towards glyphosate toxicity. Shikimic acid pathway for the biosynthesis of folates and aromatic amino acids is inhibited by glyphosate. Glyphosate carcinogenicity is still considered to be a controversial issue. The World Health Organizations’ International Agency recently concluded that glyphosate is “probably carcinogenic to humans.” Some researchers believed that glyphosate is not linked with carcinogenicity.
International Journal of Agriculture and Biology, 2016
This study was designed to find single nucleotide polymorphism (SNPs) in coding and non-coding re... more This study was designed to find single nucleotide polymorphism (SNPs) in coding and non-coding region of PRKAA2 gene in Nili-Ravi and Kundi buffaloes. The PRKAA2 gene (AMPKα2) of 100 animals from both buffalo breeds were sequenced for SNPs identification. A total number of 43 inter and intra-generic SNPs were found. Out of which 17 SNPs were detected among buffalo breeds (intra-generic). All SNPs were intronic and may have a role in gene regulation and splicing patterns. These SNPs might be associated with commercially important production traits. This is the first study to identify novel SNPs that are linked to energy metabolism and production traits of buffalo.
The growth and follicles differentiation in ovary is controlled by the FecG gene of TGF-β superfa... more The growth and follicles differentiation in ovary is controlled by the FecG gene of TGF-β superfamily proteins. FecG (GDF9), FecB (BMPRIB) and FecX (BMP15) are three oocytederived genes of TGF-β superfamily, which have essential role in ovulation and follicular growth. This study was intended to identify the FecG mutation in 30 ewes of Lohi sheep. A fragment length of 139 bp of FecG gene at exon 2 was amplified with a forced PCR-RFLP primer pairs and products were digested with Ddel enzyme. The results revealed that there is no mutation at this locus, because Ddel enzyme could not recognize restriction site. In this study, we found wild type (++) alleles. The polymorphism analysis of Lohi sheep indicates that the reported mutation for litter size is not present in this breed. Therefore, it is important to identify other SNPs for FecG gene in Lohi sheep.
Abstract Text: Wagyu cattle are well known for producing beef with superior marbling. In general,... more Abstract Text: Wagyu cattle are well known for producing beef with superior marbling. In general, Wagyu cattle accumulate more intramuscular fat in carcass as compared to Angus cattle. Therefore, fibro/adipogenic progenitor cells derived from both breeds should present extremely valuable resources for unraveling molecular mechanisms involved in muscle adipogenesis. Using the digital gene expression tag profiling (DGETP) method we found that there are at least 8,038 genes expressed in bovine fibro/adipogenic progenitor cells. Among them, 7,357 genes were assigned to relevant GO (gene ontology) terms. By careful examination of our experimental data using cells from three Wagyu and three Angus, we discovered only 32 genes that were differentially expressed between these two breeds. Understanding these genes and their functions would help develop strategies to enhance marbling and reduce connective tissue in beef. Keywords: Transcriptome profiling Fibro/adipogenic progenitor cells Gene ...
DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. ... more DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak. In-silico functional analysis with PANTHER predicted putative deleterious functional impact of c.161 T>A; p. V54Q while alignment of bovine and human NTR-J domains revealed that p.Q19H, p.E20Q and p. E21X mutations occurred in helix 2 and p.V54Q missense mutation occurred in helix 3 respectively. The 124 bp insertion found in the yak DNAJA1 ortholog may have significant functional relevance warranting further investigation. Our r...
DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. ... more DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak. In-silico functional analysis with PANTHER predicted putative deleterious functional impact of c.161 T>A; p. V54Q while alignment of bovine and human NTR-J domains revealed that p.Q19H, p.E20Q and p. E21X mutations occurred in helix 2 and p.V54Q missense mutation occurred in helix 3 respectively. The 124 bp insertion found in the yak DNAJA1 ortholog may have significant functional relevance warranting further investigation. Our r...
The growth and follicles differentiation in ovary is controlled by the FecG gene of TGF-β superfa... more The growth and follicles differentiation in ovary is controlled by the FecG gene of TGF-β superfamily proteins. FecG (GDF9), FecB (BMPRIB) and FecX (BMP15) are three oocyte-derived genes of TGF-β superfamily, which have essential role in ovulation and follicular growth. This study was intended to identify the FecG mutation in 30 ewes of Lohi sheep. A fragment length of 139 bp of FecG gene at exon 2 was amplified with a forced PCR-RFLP primer pairs and products were digested with Ddel enzyme. The results revealed that there is no mutation at this locus, because Ddel enzyme could not recognize restriction site. In this study, we found wild type (++) alleles. The polymorphism analysis of Lohi sheep indicates that the reported mutation for litter size is not present in this breed. Therefore, it is important to identify other SNPs for FecG gene in Lohi sheep.
Kafkas Universitesi Veteriner Fakultesi Dergisi, 2018
A copy number variation (CNV) is information of DNA segment containing deletion, duplication or i... more A copy number variation (CNV) is information of DNA segment containing deletion, duplication or insertion exist within diverse populations. This study detected 53 CNVs regions that overlapped with immune response, body size and parasitic resistance traits in Pakistani cattle breeds. This study characterized genetic diversity and provides lineage differentiated CNVs in these indigenous cattle breeds.
The bovine high density SNPs genotyping array has a wide range of applications including detectio... more The bovine high density SNPs genotyping array has a wide range of applications including detection of selection signatures, identification of copy number variants (CNVs), genome wide association studies, and dendrogram relationships. This array can also be used to improve the accuracy of genomic predictions for low heritable traits viz. reproductive traits. The effectiveness of this array for genomic selection mainly depends on polymorphism level. In this study, we used 136 individuals from ten different Pakistani cattle breeds, include Achi (18), Bhagnari (14), Cholistani (13), Dajal (10), Dhanni (10), Kankraj (12), Lohani (19), Red Sindhi (13), Sahiwal (14), and Tharparkar (13) using high density SNPs genotyping and this array contained approximately 777, 962 SNPs. The results of this study revealed that approximately 500, 939 SNPs were found polymorphic in these breeds. The results indicate that high density SNPs bead chip would offer an informative genotyping platform for quantitative trait loci (QTL) mapping in indigenous Pakistani cattle breeds.
Bioinformatics, an emerging powerful science gradually enfolds all sorts of sciences under its hu... more Bioinformatics, an emerging powerful science gradually enfolds all sorts of sciences under its huge banner; Forensic Sciences being one of them. With the passing time the productiveness, efficacy and virtue of Bioinformatics based tools is taking over the Forensic Sciences and research. Whether it be declaration via extracting the tiniest DNA from the tiniest microbial sample, DNA profiling, gender identification or the most advanced Automatic Fingerprint Recognition System, computational tools are aiding the Forensics in every possible way. Furthermore, Next Generation Sequencing technology along with the epigenetic studies gives rise to a vast research domain by simultaneously analyzing multiple loci that are of forensic interest in multiple genetic contexts. The paper evaluates then boosting influence of computation on this immensely significant field, especially in terms of law and order. A series of physical evidences are put up for the critical analysis that reveal pros and co...
Glyphosate is non-selective herbicide. Studies published in the last decade, point towards glypho... more Glyphosate is non-selective herbicide. Studies published in the last decade, point towards glyphosate toxicity. Shikimic acid pathway for the biosynthesis of folates and aromatic amino acids is inhibited by glyphosate. Glyphosate carcinogenicity is still considered to be a controversial issue. The World Health Organizations’ International Agency recently concluded that glyphosate is “probably carcinogenic to humans.” Some researchers believed that glyphosate is not linked with carcinogenicity.
International Journal of Agriculture and Biology, 2016
This study was designed to find single nucleotide polymorphism (SNPs) in coding and non-coding re... more This study was designed to find single nucleotide polymorphism (SNPs) in coding and non-coding region of PRKAA2 gene in Nili-Ravi and Kundi buffaloes. The PRKAA2 gene (AMPKα2) of 100 animals from both buffalo breeds were sequenced for SNPs identification. A total number of 43 inter and intra-generic SNPs were found. Out of which 17 SNPs were detected among buffalo breeds (intra-generic). All SNPs were intronic and may have a role in gene regulation and splicing patterns. These SNPs might be associated with commercially important production traits. This is the first study to identify novel SNPs that are linked to energy metabolism and production traits of buffalo.
The growth and follicles differentiation in ovary is controlled by the FecG gene of TGF-β superfa... more The growth and follicles differentiation in ovary is controlled by the FecG gene of TGF-β superfamily proteins. FecG (GDF9), FecB (BMPRIB) and FecX (BMP15) are three oocytederived genes of TGF-β superfamily, which have essential role in ovulation and follicular growth. This study was intended to identify the FecG mutation in 30 ewes of Lohi sheep. A fragment length of 139 bp of FecG gene at exon 2 was amplified with a forced PCR-RFLP primer pairs and products were digested with Ddel enzyme. The results revealed that there is no mutation at this locus, because Ddel enzyme could not recognize restriction site. In this study, we found wild type (++) alleles. The polymorphism analysis of Lohi sheep indicates that the reported mutation for litter size is not present in this breed. Therefore, it is important to identify other SNPs for FecG gene in Lohi sheep.
Abstract Text: Wagyu cattle are well known for producing beef with superior marbling. In general,... more Abstract Text: Wagyu cattle are well known for producing beef with superior marbling. In general, Wagyu cattle accumulate more intramuscular fat in carcass as compared to Angus cattle. Therefore, fibro/adipogenic progenitor cells derived from both breeds should present extremely valuable resources for unraveling molecular mechanisms involved in muscle adipogenesis. Using the digital gene expression tag profiling (DGETP) method we found that there are at least 8,038 genes expressed in bovine fibro/adipogenic progenitor cells. Among them, 7,357 genes were assigned to relevant GO (gene ontology) terms. By careful examination of our experimental data using cells from three Wagyu and three Angus, we discovered only 32 genes that were differentially expressed between these two breeds. Understanding these genes and their functions would help develop strategies to enhance marbling and reduce connective tissue in beef. Keywords: Transcriptome profiling Fibro/adipogenic progenitor cells Gene ...
DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. ... more DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak. In-silico functional analysis with PANTHER predicted putative deleterious functional impact of c.161 T>A; p. V54Q while alignment of bovine and human NTR-J domains revealed that p.Q19H, p.E20Q and p. E21X mutations occurred in helix 2 and p.V54Q missense mutation occurred in helix 3 respectively. The 124 bp insertion found in the yak DNAJA1 ortholog may have significant functional relevance warranting further investigation. Our r...
DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. ... more DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak. In-silico functional analysis with PANTHER predicted putative deleterious functional impact of c.161 T>A; p. V54Q while alignment of bovine and human NTR-J domains revealed that p.Q19H, p.E20Q and p. E21X mutations occurred in helix 2 and p.V54Q missense mutation occurred in helix 3 respectively. The 124 bp insertion found in the yak DNAJA1 ortholog may have significant functional relevance warranting further investigation. Our r...
The growth and follicles differentiation in ovary is controlled by the FecG gene of TGF-β superfa... more The growth and follicles differentiation in ovary is controlled by the FecG gene of TGF-β superfamily proteins. FecG (GDF9), FecB (BMPRIB) and FecX (BMP15) are three oocyte-derived genes of TGF-β superfamily, which have essential role in ovulation and follicular growth. This study was intended to identify the FecG mutation in 30 ewes of Lohi sheep. A fragment length of 139 bp of FecG gene at exon 2 was amplified with a forced PCR-RFLP primer pairs and products were digested with Ddel enzyme. The results revealed that there is no mutation at this locus, because Ddel enzyme could not recognize restriction site. In this study, we found wild type (++) alleles. The polymorphism analysis of Lohi sheep indicates that the reported mutation for litter size is not present in this breed. Therefore, it is important to identify other SNPs for FecG gene in Lohi sheep.
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