Kush Shrivastava

Single nucleotide polymorphism mining and nucleotide sequence analysis of Mx1 gene in exonic regions of Japanese quail

Aim: An attempt has been made to study the Myxovirus resistant (Mx1) gene polymorphism in Japanese quail. Materials and Methods: In the present, investigation four fragments viz. Fragment I of 185 bp (Exon 3 region), Fragment II of 148 bp (Exon 5 region), Fragment III of 161 bp (Exon 7 region), and Fragment IV of 176 bp (Exon 13 region) of Mx1 gene were amplified and screened for polymorphism by polymerase chain reaction-single-strand conformation polymorphism technique in 170 Japanese quail birds. Results: Out of the four fragments, one fragment (Fragment II) was found to be polymorphic. Remaining three fragments (Fragment I, III, and IV) were found to be monomorphic which was confirmed by custom sequencing. Overall nucleotide sequence analysis of Mx1 gene of Japanese quail showed 100% homology with common quail and more than 80% homology with reported sequence of chicken breeds. Conclusion: The Mx1 gene is mostly conserved in Japanese quail. There is an urgent need of comprehensive analysis of other regions of Mx1 gene along with its possible association with the traits of economic importance in Japanese quail.

Genotyping of major histocompatibility complex Class II DRB gene in Rohilkhandi goats by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing.

Aim: To study the major histocompatibility complex (MHC) Class II DRB1 gene polymorphism in Rohilkhandi goat using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and nucleotide sequencing techniques. Materials and Methods: DNA was isolated from 127 Rohilkhandi goats maintained at sheep and goat farm, Indian Veterinary Research Institute, Izatnagar, Bareilly. A 284 bp fragment of exon 2 of DRB1 gene was amplified and digested using BsaI and TaqI restriction enzymes. Population genetic parameters were calculated using Popgene v 1.32 and SAS 9.0. The genotypes were then sequenced using Sanger dideoxy chain termination method and were compared with related breeds/species using MEGA 6.0 and Megalign (DNASTAR) software. Results: TaqI locus showed three and BsaI locus showed two genotypes. Both the loci were found to be in Hardy–Weinberg equilibrium (HWE), however, population genetic parameters suggest that heterozygosity is still maintained in the population at both loci. Percent diversity and divergence matrix, as well as phylogenetic analysis revealed that the MHC Class II DRB1 gene of Rohilkhandi goats was found to be in close cluster with Garole and Scottish blackface sheep breeds as compared to other goat breeds included in the sequence comparison. Conclusion: The PCR-RFLP patterns showed population to be in HWE and absence of one genotype at one locus (BsaI), both the loci showed excess of one or the other homozygote genotype, however, effective number of alleles showed that allelic diversity is present in the population. Sequence comparison of DRB1 gene of Rohilkhandi goat with other sheep and goat breed assigned Rohilkhandi goat in divergence with Jamanupari and Angora goats.

Dataset for distribution of INGI/RIME and SLACS CRE transposable elements in Trypanosoma brucei genome

The current dataset is generated via bio-computational approach by surveying of INGI/RIME and SLACS CRE transposable elements (TEs) in latest update of Trypanosoma brucei genome. The distribution dataset (Supplementary File 1) shows the chromosome wise distribution of INGI/RIME and SLACS CRE transposable elements with the status of their -5′ and -3′ ends, genomic coverage and further elemental description about the completeness on the element. The 5′ upstream flanking sequence of 100 bp was then analyzed to find out possible regions that could act as insertion hotspots. The Fig. 1 represents the ten different motifs found in the 5′ flanking region of the INGI/RIME and SLACS CRE elements. The Supplementary File 2 describes the distribution of these ten motifs in different locations in Trypanosoma brucei genome. These new locations where motifs were found may provide useful information to track the future transposition events of INGI/RIME and SLACS CRE elements in different Trypanosoma species.

Exploring the molecular basis of resistance/ susceptibility to mixed natural infection of Haemonchus contortus in tropical Indian goat breed

The present investigation was carried out with the objective to identify putative candidate genes / Quantitative trait loci for resistance / susceptibility towards Haemonchus infestation in tropical goat breed (Rohilkhandi goat) of India. The mean faecal egg count (FEC) and packed cell volume (PCV) of the population were 142.78 ± 22.54 epg (eggs per gram) and 31.73% ± 0.49, respectively. Grouping of animals as per dot ELISA test showed 41.33% (n = 124) positive and 58.66% (n = 176) negative for Haemonchus infestation. The microsatellite loci DYA and ODRB1.2 were significantly associated (P ≤ 0.05) to parasite resistance. The locus DYA showed significant association with log FEC and dot ELISA and the locus ODRB1.2 showed significant association with log FEC, PCV and dot ELISA at P ≤ 0.05. Real time expression profiling revealed that the susceptible group (high FEC group) had 11.1-fold more expression of IFNγ mRNA (Th1 cytokine) and 0.11-fold lower expression of IL-10 mRNA (Th2 cytokine), which was found to be statistically significant (P ≤ 0.05).

Effect of Turmeric Supplementation on Production Performance of Adult Laying Birds

Since prehistoric times, plants and their extracts have been used worldwide for their medicinal properties with no adverse effect. Functional and nutraceutical foods are gaining popularity all over the globe due to their health enhancing potential. Turmeric, Latin name Curcuma longa of family Zingiberaceae, is a perennial plant having a short stem with large oblong leaves and bears ovate, pyriform or oblong rhizomes. Turmeric, a medicinal plant, is extensively used in Ayurveda, Unani and Siddha medicine as home remedy for various diseases (Ammon and Wahl, 1991). In traditional Indian medicine turmeric powder is used for the treatment of biliary disorders, anorexia, coryza, cough, diabetes, hepatic disorders, rheumatism and sinusitis (Srimal, 1997). According to Srinivasan (2007) This experiment was conducted to investigate the dietary effects of turmeric powder on production performances like feed intake, body weight, egg weight and egg production. A total of thirty, 32-wk-old, Jabalpur colour layers were divided into five groups six layers in each, and fed each one of five diets containing 0% turmeric powder (control), 1.5, 3.0, 4.5 and 6.0 g of turmeric powder/kg feed for treatment groups T1-T4, respectively, for 8 wks. No differences in feed intakes, egg weight and eggshell qualities were observed among the treatments, but production in the groups fed with diets containing turmeric powder was significantly higher than that in control (P < 0.05), the maximum increase (53.60%) in egg production was observed in groups T2 and T3 on day 56 of experiment. Significant body weight gain of 10.44% was observed in treatment group T3 fed diet containing turmeric powder supplementation 4.5g/kg feed. The cholesterol levels of egg yolk were significantly influenced by dietary turmeric supplementation. It was concluded that dietary turmeric supplementation was effective in improving laying performance and internal egg qualities. Turmeric powder can be also used as a feed additive for the production of valueenhanced eggs production with increased body weight hence reducing cost of feed for production per egg. K e y w o r d s

Genome wide occurrence and insertion preferences of INGI/RIME and SLACS CRE transposable elements in Trypanosoma brucei

ABSTRACT Retrotransposons play significant role in genome remodelling of T. brucei and about 5% of its genome consists of retrotransposons including INGI/RIME elements. INGI is one of the dispersed repetitive elements in T. brucei genome which is found distributed throughout all the chromosomes. SLACS (Spliced Leader Associated Conserved Sequence) however, is more conserved in its nature and lacks the typical poly-distributional pattern of LINE like transposons. We have found total 589 copies of these TEs with only 17.06 % (104 copies out of 589) copies with both ends intact thus showing a majority of truncated copies. Complete SLACS CRE were found only on chromosome 9, whereas, complete INGI/RIME were more ubiquitously distributed. The 50 – 70 bp upstream flanking sequence of these elements shows suitable nucleotide biophysical properties to favor transposition.