scholarly journals ​Genetic Polymorphism within Exon 3 of HSP90AA1 Gene and its Association Studies in Sahiwal and Crossbred Cows

2021 ◽  
Author(s):  
J. Sai Prasanna ◽  
S.T. Viroji Rao ◽  
M. Gnana Prakash ◽  
Suresh Rathod ◽  
P. Kalyani
Keyword(s):  
Association Studies ◽  
Critical Role ◽  
Reproductive Traits ◽  
Single Strand Conformation Polymorphism ◽  
Superior Performance ◽  
Primary System ◽  
Heat Stress Response ◽  
Crossbred Cows ◽  
Lactation Length ◽  
Climate Resilience

Background: Heat shock proteins (HSPs) are molecular chaperones that play a critical role in recovering cells from stress and form a primary system for intra cellular self defense. They are highly conserved and play a crucial role in cellular thermo tolerance and heat stress response. Though there are many HSP genes, thermo tolerance is mainly correlated with HSP70 and HSP90 genes in Livestock species. Polymorphisms in these genes have shown an association with heat tolerance, milk production, fertility and disease susceptibility in livestock. They can be used as genetic markers for the selection of animals with better climate resilience, immune response and superior performance. Methods: The present study was carried out in Sahiwal (n=50) and Crossbred cows (n=50) with the objective to identify polymorphisms in HSP90AA1 gene. A 450 bp fragment of bovine HSP90AA1 gene covering exon3 was subjected to Polymerase Chain Reaction-Single-Strand Conformation Polymorphism (PCR-SSCP) technique to identify the polymorphism. PCR-SSCP patterns were correlated with the physiological, productive and reproductive traits in Sahiwal and crossbred cows using the univariate GLM model of SPSS 25. Result: The PCR-SSCP of exon 3 of HSP90AA1 gene yielded two conformational patterns AA and AB corresponding to two allelic variants A and B in both Sahiwal and crossbred cows. The allele frequencies of A and B were 0.78 and 0.22 and 0.84 and 0.16 in Sahiwal and crossbred cows, respectively. The association analysis of SSCP patterns revealed that genotype AA had higher lactation length in Sahiwal cows and higher total lactation milk yield and peak yield in crossbred cows.

scholarly journals Association between IGF-IR gene polymorphisms and productive and reproductive traits in Holstein cows

2005 ◽  
Vol 57 (6) ◽  
pp. 772-777 ◽  
Author(s):  
W. Schoenau ◽  
P.M. Porciuncula ◽  
G. Zamberlan ◽  
F.S. Mesquita ◽  
V. Vieira ◽  
...  
Keyword(s):  
Growth Factor ◽  
Gene Polymorphisms ◽  
Reproductive Traits ◽  
Single Strand Conformation Polymorphism ◽  
Calving Interval ◽  
Lactation Period ◽  
Chain Reaction ◽  
Factor I ◽  
Lactation Length ◽  
Conformation Polymorphism

The association between single-strand conformation polymorphism (SSCP) in the gene of insulin-like growth factor-I receptor (IGF-IR) and age at first calving (AFC), calving interval (CI), lactation length (LL), and milk yield (MY) was studied using 106 graded Holstein females. The polimerase chain reaction (PCR) with specific initiating oligonucleotides, resulted an amplified fragment of 335pb. The population genotypes frequencies were 82.1% and 17.9%, for AA and AB genotypes, respectively. The frequency of A allele was 0.91 and 0.09 of B allele. No association between the identified polymorphism and AFC, CI, and MY was observed. The LL was positively associated (P<0.05) with the absence of B allele. Animals carrying the AA genotype presented a longer lactation period.

scholarly journals Identification of Polymorphism within Exon 8 of Bovine HSP90AA1 Gene using PCR-SSCP Technique

2021 ◽  
Vol 12 (6) ◽  
pp. 611-616
Author(s):  
J. Sai Prasanna ◽  
◽  
S. T. Viroji Rao ◽  
M. Gnana Prakash ◽  
Suresh Rathod ◽  
...  
Keyword(s):  
Reproductive Traits ◽  
Experimental Period ◽  
Single Strand Conformation Polymorphism ◽  
Crossbred Cows ◽  
Self Defense ◽  
Service Period ◽  
Reproduction Traits ◽  
Sahiwal Cows ◽  
Stressed Cells ◽  
Shock Proteins

Heat shock proteins (HSPs) are a type of molecular chaperones that aid in the recovery of stressed cells and serve as a major system for intracellular self-defense. A study was conducted during the year 2018–19 at College of Veterinary Science Rajendranagar, Hyderabad, Telengana State, India to find polymorphisms in exon 8 of the bovine HSP90AA1 gene in Sahiwal (n=50) and crossbred (n=50) cows. Blood samples were collected from the experimental animals and genomic DNA was isolated. Physiological parameters like body temperature and respiration rate for each animal were taken during the experimental period and the heat tolerance coefficient was calculated. The data on production and reproduction traits were obtained from the history sheets of the animals. To detect the polymorphism, a 539 bp fragment of the HSP90AA1 gene covering exon 8 was subjected to the Polymerase Chain Reaction-Single-Strand Conformation Polymorphism (PCR-SSCP) technique.The PCR-SSCP of exon 8 of HSP90AA1 gene yielded two genotypic patterns AA and AB corresponding to two allelic variants with frequencies of 0.85, 0.15, 0.81 and 0.19 in Sahiwal and crossbred cows, respectively. The PCR-SSCP patterns obtained were correlated with the physiological, productive, and reproductive traits in both Sahiwal and crossbred cows. The association analysis of SSCP patterns of the exon 8 of HSP90AA1 gene revealed non-significant effect in Sahiwal cows, although the AB genotype had a significantly longer service period in crossbred cows.

scholarly journals Comparison of some important dairy traits of crossbred cows at Baghabarighat milk shed area of Bangladesh

2012 ◽  
Vol 41 (1) ◽  
pp. 13-18
Author(s):  
MS Hossen ◽  
SS Hossain ◽  
AKFH Bhuiyan ◽  
MA Hoque ◽  
MAS Talukder
Keyword(s):  
Birth Weight ◽  
Reproductive Traits ◽  
Reproductive Age ◽  
Calving Interval ◽  
Crossbred Cows ◽  
Lactation Length ◽  
Genetic Groups ◽  
Dairy Traits ◽  
Heat Period

Data on 3637 cows of seven genetic groups at Baghabarighat milk shed area during the period from 1991 to 2000 were analyzed. The genetic groups were Pabna Milking Cows (PMC), ½Sahiwal×½PMC (SL×PMC), ½Frisian×½PMC (FN×PMC), ½Australian Friesian Sahiwal×½PMC (AFS×PMC), ½Sahiwal×¼Friesian×¼PMC [SL(FN×PMC)], ½Friesian×¼Sahiwal×¼PMC [FN(SL×PMC)] and ½Friesian×¼Jersey×¼PMC [FN(JR×PMC)]. The purpose of this study was to compare the productive (birth weight, lactation length, lactation yield, fat% and SNF%) and reproductive (age at first service, service per conception, postpartum heat period and calving interval) traits of different crossbred cows. The highest birth weight of calves was obtained as 29.78 kg in AFS×PMC, lactation yield as 2225.52 liters in FN(JR×PMC), fat% as 4.48 in SL×PMC and SNF% as 8.10 in FN(SL×JR). The longest lactation length was observed as 305.18 days in AFS×PMC. The shortest age at first service was observed as 26.83 months in FN(PMC×SL), postpartum heat period as 133.23 days in PMC and calving interval as 414.90 days in PMC. The lowest service per conception was found to be 1.22 in PMC cows. The high genetic variability of birth weight, lactation yield, fat and SNF% indicated that there are good opportunities for genetic improvement of these traits through selection. From the results, it is evident that the level of production of different crossbred cows found to be higher but important reproductive traits were significantly better on PMC. Thus it may be concluded that for long term sustainable development and conservation program for PMC should be initiated alongside with that of crossbred in this particular study area.http://dx.doi.org/10.3329/bjas.v41i1.11970

scholarly journals Characterisation of exon 9 of solute carrier family 11 member A1 gene in Vechur cattle

2016 ◽  
Vol 32 (3) ◽  
pp. 251-260
Author(s):  
Anu Bosewell ◽  
Naicy Thomas ◽  
Thazhathu Aravindakshan
Keyword(s):  
Association Studies ◽  
Critical Role ◽  
Single Strand Conformation Polymorphism ◽  
Natural Resistance ◽  
Intracellular Pathogens ◽  
Solute Carrier Family ◽  
Slc11a1 Gene ◽  
Exon 9 ◽  
Solute Carrier ◽  
Hydroxyl Free Radicals

The solute carrier family 11 member A1 (SLC11A1) gene has been associated with natural resistance to intracellular pathogens such as Brucella, Salmonella, Leishmania and Mycobacterium in several species including bovine and plays a critical role in elimination of pathogens by generating hydroxyl free radicals. The objective of the present study was to investigate the polymorphism in exon 9 of SLC11A1 gene in Vechur cattle, one of the dwarf cattle of India which is known for its disease resistance. A 198 bp fragment containing exon 9 of the gene was amplified by polymerase chain reaction (PCR). The amplicons upon single strand conformation polymorphism (SSCP) analysis revealed two different banding patterns. A novel non synonymous SNP (g.46C>T) with predominance of CC genotype was also detected in Vechur cattle. These results suggest that there exists a considerable genetic variation at SLC11A1 locus and further association studies may help in development of a PCR based genotyping assay to select cattle with better immunity to intracellular pathogens.

scholarly journals RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes

2021 ◽  
Author(s):  
John T Walker ◽  
Diane C Saunders ◽  
Vivek Rai ◽  
Chunhua Dai ◽  
Peter Orchard ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Insulin Secretion ◽  
Association Studies ◽  
Critical Role ◽  
Regulatory Elements ◽  
Genome Wide Association Studies ◽  
Β Cells ◽  
Β Cell ◽  
Gene Regulatory

A hallmark of type 2 diabetes (T2D), a major cause of world-wide morbidity and mortality, is dysfunction of insulin-producing pancreatic islet β cells. T2D genome-wide association studies (GWAS) have identified hundreds of signals, mostly in the non-coding genome and overlapping β cell regulatory elements, but translating these into biological mechanisms has been challenging. To identify early disease-driving events, we performed single cell spatial proteomics, sorted cell transcriptomics, and assessed islet physiology on pancreatic tissue from short-duration T2D and control donors. Here, through integrative analyses of these diverse modalities, we show that multiple gene regulatory modules are associated with early-stage T2D β cell-intrinsic defects. One notable example is the transcription factor RFX6, which we show is a highly connected β cell hub gene that is reduced in T2D and governs a gene regulatory network associated with insulin secretion defects and T2D GWAS variants. We validated the critical role of RFX6 in β cells through direct perturbation in primary human islets followed by physiological and single nucleus multiome profiling, which showed reduced dynamic insulin secretion and large-scale changes in the β cell transcriptome and chromatin accessibility landscape. Understanding the molecular mechanisms of complex, systemic diseases necessitates integration of signals from multiple molecules, cells, organs, and individuals and thus we anticipate this approach will be a useful template to identify and validate key regulatory networks and master hub genes for other diseases or traits with GWAS data.

scholarly journals Chromatin architecture in addiction circuitry elucidates biological mechanisms underlying cigarette smoking and alcohol use traits.

2021 ◽  
Author(s):  
Nancy Y.A Sey ◽  
Benxia Hu ◽  
Marina Iskhakova ◽  
Huaigu Sun ◽  
Neda Shokrian ◽  
...  
Keyword(s):  
Risk Factors ◽  
Alcohol Use ◽  
Cigarette Smoking ◽  
Genetic Risk ◽  
Target Genes ◽  
Association Studies ◽  
Critical Role ◽  
Genetic Risk Factors ◽  
Genome Wide Association Studies ◽  
Risk Genes

Cigarette smoking and alcohol use are among the most prevalent substances used worldwide and account for a substantial proportion of preventable morbidity and mortality, underscoring the public health significance of understanding their etiology. Genome-wide association studies (GWAS) have successfully identified genetic variants associated with cigarette smoking and alcohol use traits. However, the vast majority of risk variants reside in non-coding regions of the genome, and their target genes and neurobiological mechanisms are unknown. Chromosomal conformation mappings can address this knowledge gap by charting the interaction profiles of risk-associated regulatory variants with target genes. To investigate the functional impact of common variants associated with cigarette smoking and alcohol use traits, we applied Hi-C coupled MAGMA (H-MAGMA) built upon cortical and midbrain dopaminergic neuronal Hi-C datasets to GWAS summary statistics of nicotine dependence, cigarettes per day, problematic alcohol use, and drinks per week. The identified risk genes mapped to key pathways associated with cigarette smoking and alcohol use traits, including drug metabolic processes and neuronal apoptosis. Risk genes were highly expressed in cortical glutamatergic, midbrain dopaminergic, GABAergic, and serotonergic neurons, suggesting them as relevant cell types in understanding the mechanisms by which genetic risk factors influence cigarette smoking and alcohol use. Lastly, we identified pleiotropic genes between cigarette smoking and alcohol use traits under the assumption that they may reveal substance-agnostic, shared neurobiological mechanisms of addiction. The number of pleiotropic genes was ~26-fold higher in dopaminergic neurons than in cortical neurons, emphasizing the critical role of ascending dopaminergic pathways in mediating general addiction phenotypes. Collectively, brain region- and neuronal subtype-specific 3D genome architecture refines neurobiological hypotheses for smoking, alcohol, and general addiction phenotypes by linking genetic risk factors to their target genes.

Analysing the importance of international knowledge, orientation, networking and commitment as entrepreneurial culture and market orientation in gaining competitive advantage and international performance

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Mohammad Falahat ◽  
Pedro Soto-Acosta ◽  
T. Ramayah
Keyword(s):  
Competitive Advantage ◽  
Market Orientation ◽  
Critical Role ◽  
Government Support ◽  
Superior Performance ◽  
Content Type ◽  
International Performance ◽  
Entrepreneurial Culture ◽  
International Knowledge ◽  
Depth Interviews

PurposeThis study argues that having an entrepreneurial culture and market orientation are critical for young enterprises to gain competitive advantage and superior international performance. We investigate how young entrepreneurial companies despite their limited resources and experience expand rapidly in foreign markets almost from their inception.Design/methodology/approachThis investigation uses a mixed-methods approach, combining in-depth interviews and survey data. In-depth interviews lead us to conceptualise a model highlighting the importance of international knowledge, international orientation, international networking and international commitment as entrepreneurial culture and market orientation for gaining competitive advantage and, in return, superior performance in the international market. Then, the derived conceptual model is empirically tested on a sample of Malaysian Small and Medium Enterprises (SMEs).FindingsResults show that entrepreneurial culture is positively associated with competitive advantage and international performance, while market orientation is positively related to competitive advantage but not to international performance. In addition, government support strengthens the positive effect of competitive advantage on international performance.Originality/valueThis study investigation analyses the importance of entrepreneurial culture and market orientation in contributing to competitive advantage and superior performance. In addition, this study examines the critical role of government support in the relationships between entrepreneurial culture and competitive advantage and between competitive advantage and international performance.

scholarly journals Lifetime productivity and repeatability estimation of selected traits of crossbred cows in Savar Dairy Farm

2018 ◽  
Vol 29 (2) ◽  
pp. 168-177
Author(s):  
MS Islam ◽  
A Akhtar ◽  
MA Hossain ◽  
MF Rahman ◽  
SS Hossain
Keyword(s):  
Milk Yield ◽  
Mixed Model ◽  
Dairy Farm ◽  
Cattle Breeding ◽  
Crossbred Cows ◽  
Lactation Length ◽  
Genetic Groups ◽  
Age At Puberty ◽  
Selected Traits ◽  
Productive Traits

The study was conducted on 244 crossbred cows of (Central Cattle Breeding and Diry Farm), Savar, Dhaka to evaluate the effect of different productive groups on their lifetime performance of various productive traits using twenty years data.  Data were accumulated from a prescribed data sheet maintained by Central Cattle Breeding Station, Savar, Dhaka. Genetic groups for this experiment were Local Friesian (LF), Local Jersey (LJ), Local Hariana X Friesian (LH x F), Local Friesian X Local Friesian (LF x LF) and Local Jersey X Local Jersey (LJ x LJ). The studied parameters were age at puberty, lactation length, lactation yield, total milking days, and total milk yield in lifetime. The data were analyzed using Least-Squares Mixed Model and Maximum Likelihood Computer Program (Harvey, 1990). Analysis showed that genetic groups had a significant effect on age at puberty, lactation length and lactation yield (P<0.01), total milking days and milk yield in lifetime (P<0.001). From the result it was found that earliest age at puberty were in L x F (749.27±99.01). Lactation length and standardized lactation yield were also higher in L x F (258.69±20.04 days and 1408.80±83.60 kg respectively). Total milking days and milk yield were observed higher in (LH x F) with mean of 1468.30±198.58 days and 7340.32±1813.28 kg, respectively. The repeatability estimates of lactation length for genetic groups LF, LJ, LH x F, LF x LF and LJ x LJ were 0.24±0.09, 0.04(-ve), 0.10±0.05, 0.07±0.05 and 0.49±0.22, respectively. The same for lactation yield was 0.17±0.08, 0.27± 0.02, 0.07±0.04, 0.17±0.08 and 0.03±0.05 respectively. From analysis it was revealed that in respect of productive performances the L x F genetic group was found superior compared to other groups but interns of total lifetime productivity, LH x F ranked the highest in the given environment. It is concluded that lifetime productivity needs to be considered as an appropriate guideline for selecting genetic groups for future productivity.Progressive Agriculture 29 (2): 168-177, 2018

scholarly journals Pangenome Graphs

2020 ◽  
Vol 21 (1) ◽  
pp. 139-162 ◽  
Author(s):  
Jordan M. Eizenga ◽  
Adam M. Novak ◽  
Jonas A. Sibbesen ◽  
Simon Heumos ◽  
Ali Ghaffaari ◽  
...  
Keyword(s):  
Graphical Models ◽  
Genome Assembly ◽  
Association Studies ◽  
Low Cost ◽  
Variant Calling ◽  
Superior Performance ◽  
Whole Genome ◽  
Coordinate Systems ◽  
Multiple Sequence ◽  
Additional Information

Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes. These approaches often use graphical models of the pangenome to support algorithms for sequence alignment, visualization, functional genomics, and association studies. The additional information provided to these methods by the pangenome allows them to achieve superior performance on a variety of bioinformatic tasks, including read alignment, variant calling, and genotyping. Pangenome graphs stand to become a ubiquitous tool in genomics. Although it is unclear whether they will replace linearreference genomes, their ability to harmoniously relate multiple sequence and coordinate systems will make them useful irrespective of which pangenomic models become most common in the future.

Notch2 Is Critical for CLL Development in the IRF4-/-Vh11 Mice

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 891-891 ◽  
Author(s):  
Vipul Shukla ◽  
Shibin Ma ◽  
Shantaram Joshi ◽  
Runqing Lu
Keyword(s):  
B Cells ◽  
Notch Signaling ◽  
Stromal Cells ◽  
Association Studies ◽  
Critical Role ◽  
Molecular Networks ◽  
Genome Wide Association Studies ◽  
Notch Receptors ◽  
Low Levels ◽  
B1 Cells

Abstract Chronic Lymphocytic Leukemia (CLL) is the most common adult leukemia in the western world. Despite considerable progress in our current understanding of CLL, the molecular events underlying the complex pathogenesis and clinical behavior of CLL have not been fully elucidated. IRF4 belongs to the IRF superfamily of transcription factors and plays critical roles at multiple stages of B cell development. Genome Wide Association Studies had linked Single Nucleotide Polymorphism (SNP) mediated IRF4 down regulation to the pathogenesis of human CLL (Di Bernardo et al. Nature Genetics, 2008). Moreover, low levels of IRF4 were found to correlate with poorer disease outcomes in human CLL (Chang et al. Blood, 2002). More recently, the studies from our group have established a causal relationship between low levels of IRF4 and development of CLL. We used Vh11 knock-in (Vh11) mice that express a prearranged immunoglobulin variable heavy chain (Vh11) leading to preferential generation of B1 cells (CLL precursors). Interestingly, we have shown that mice expressing the Vh11 transgene in the IRF4 deficient background (IRF4-/-Vh11) spontaneously develop CLL at complete penetrance (Shukla et al. Blood, 2013). Additionally, we have also shown that low levels of IRF4 dramatically accelerate CLL development in the New Zealand Black (NZB) mice (Ma et al. JBC, 2013). Although our studies have demonstrated a critical role for IRF4 in the pathogenesis of CLL, the molecular mechanism through which IRF4 controls CLL development remains unclear. In an attempt to identify the molecular networks regulated by IRF4 in CLL cells we performed gene expression profiling of CLL cells isolated from IRF4-/-Vh11 mice. Intriguingly, our analysis revealed that Notch signaling was hyperactive in the IRF4-/-Vh11 CLL cells compared to the IRF4+/+Vh11 B1 cells. This is particularly important because recent high depth sequencing studies have identified mutations in Notch1 protein leading to its stabilization and activation in ~10% of all CLL patients (Puente et al. Nature, 2011, Fabbri et al. JEM, 2011). Furthermore, the individuals carrying these mutations have an aggressive disease course and poor overall survival (Fabbri et al. JEM, 2011). Recently, studies by Simonetti et al have shown that the IRF4 deficient B cells express high levels of Notch receptors and display increased Notch activity (Simonetti et al. JEM, 2013). We also detected high levels of Notch2 but not Notch1 on the cell surface of IRF4-/-Vh11 CLL cells. To examine the contribution of Notch signaling in the pathogenesis of CLL, we crossed IRF4-/-Vh11 mice with Notch2 conditional mutant mice and with mice expressing cre recombinase in B cells (CD19cre). This approach allowed us to genetically delete Notch2 receptor specifically in B cells of IRF4-/-Vh11 mice (CD19creNotch2fl/flIRF4-/-Vh11). Surprisingly, CLL cells could still emerge from the majority of CD19creNotch2fl/flIRF4-/-Vh11 mice. However, further analysis revealed that those CLL cells expressed high levels of Notch2 on their surface and were apparently derived from IRF4-/-Vh11 B1 cells that escaped cre-mediated deletion. Importantly, our analysis also showed that the majority of B1 and B2 cells in the CD19creNotch2fl/flIRF4-/-Vh11 mice had lost the expression of Notch2, indicating that Notch2 is dispensable for their generation. We also performed a series of analysis to determine how Notch signaling affects B1 and CLL cells in vitro. We used a co-culture system to engage Notch receptors to their ligand (Delta like 1 or DL1) expressed on S17 stromal cells (S17-DL1). Co-culture of wild type B1 cells with S17-DL1 stromal cells led to enhanced proliferation and survival of B1 cells when compared with cells co-cultured on control vector transfected S17 stromal cells (S17-R1). Importantly, Notch2 receptor deficient B1 cells failed to respond to DL1 expressing S17 stromal cells. Similarly, IRF4-/-Vh11 CLL cells also showed enhanced survival on S17-DL1 stromal cells compared to S17-R1 stromal cells. In summary, our studies show that Notch2 is absolutely required for CLL development in the IRF4-/-Vh11 mice, thereby supporting a critical role for Notch signaling in the pathogenesis of CLL. Disclosures No relevant conflicts of interest to declare.

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