Riaz Ahmad Shah

Long non-coding RNAs: Mechanism of action and functional utility

Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs) are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA), small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs) are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological and pathological processes. LncRNAs are dysfunctional in a variety of human diseases varying from cancerous to non-cancerous diseases. Characterization of these lncRNA genes and their modes of action may allow their use for diagnosis, monitoring of progression and targeted therapies in various diseases. In this review, we summarize the functional perspectives as well as the mechanism of action of lncRNAs.

In vitro development of goat-sheep and goat-goat zona-free cloned embryos in different culture media.

The gradual decline in the genetic diversity of farm animals has threatened their survival and risk of their extinction has increased many fold in the recent past. Endangered species could be rescued using interspecies embryo production. The objective of this study was to investigate the effect of three different culture media on the development of Handmade cloned intraspecies (goat-goat) and interspecies (goat-sheep) embryo reconstructs. Research vitro cleave media (RVCL) yielded higher cleavage and morula-blastocyst development in intraspecies and interspecies nuclear transfer groups compared with G1.G2 and modified synthetic oviductal fluid (mSOFaaci). Cleavage frequency of intraspecies cloned embryos in RVCL, mSOFaaci, and G1.G2 did not differ significantly (87.12%, 82.45%, and 92.52%, respectively). However, the morula/blastocyst frequency in RVCL was greater in mSOFaaci and G1.G2 (51.18% vs. 38.28% vs. 36.50%, respectively). Cleavage and morula/blastocyst frequency in interspecies cloned embryos was greater in RVCL than in mSOFaaci and G1.G2 (76.14% and 42.3% vs. 65.9% and 38.3% vs. 58.56% and 33.1%, respectively). Goat oocytes were parthenogenetically activated and cultured in RVCL, mSOFaaci, and G1.G2 and kept as control. Cleavage and morula/blastocyst frequency in this group was greater in RVCL than in mSOFaaci and G1.G2 (89.66% and 65.26% vs. 85.44% and 48.05% vs. 86.58% and 42.06%, respectively). Conclusively, the results suggest that not only can the interspecies embryos of goat be produced using sheep oocytes as donor cytoplast but also the percentages can be improved by using RVCL media for culturing of the embryos.

LncRNAs and immunity: watchdogs for host pathogen interactions

Immune responses combat various infectious agents by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. The polygenic responses to these external stimuli are temporally and coordinately regulated. Specific lncRNAs are induced to modulate innate and adaptive immune responses which can function through various target interactions like RNA-DNA, RNA-RNA, and RNA-protein interaction and hence affect the immunogenic regulation at various stages of gene expression. LncRNA are found to be present in various immune cells like monocytes, macrophages, dendritic cells, neutrophils, T cells and B cells. They have been shown to be involved in many biological processes, including the regulation of the expression of genes, the dosage compensation and genomics imprinting, but the knowledge how lncRNAs are regulated and how they alter cell differentiation/function is still obscure. Further dysregulation of lncRNA has been seen in many diseases, but as yet very less research has been carried out to understand the role of lncRNAs in regulation during host-pathogens interactions. In this review, we summarize the functional developments and mechanism of action of lncRNAs, in immunity and defense of host against pathogens.

Open pulled straw vitrification and slow freezing of sheep IVF embryos using different cryoprotectants

The aim of the present study was to evaluate the post-thaw survival and hatching rates of sheep blastocysts using different cryoprotectants. In Experiment 1, Day 6 sheep embryos were cryopreserved by a slow freezing protocol using 10% ethylene glycol (EG), 10% dimethyl sulfoxide (DMSO) or a mixture of 5% EG and 5% DMSO. Hatching rates were higher in the 10% EG group than in the 10% DMSO or EG + DMSO groups (30% vs 18% and 20%, respectively). In Experiment 2, embryos were cryopreserved by open pulled straw (OPS) vitrification using either 33% EG, 33% DMSO or a mixture of 16.5% EG + 16.5% DMSO. Re-expansion and hatching rates in the EG + DMSO group (79.16% and 52.74%, respectively) were higher than those in the EG group (64.28% and 30.02%, respectively), whereas the outcomes for the DMSO group were the lowest (45.18% and 8.6%, respectively). In Experiment 3, embryos were cryopreserved by OPS vitrification using either 40% EG, 40% DMSO or a mixture of 20% EG + 20% DMSO. Re-expansion and hatching rates were highest in the EG group than in the EG + DMSO and DMSO groups (92.16% vs 76.30% and 55.84% re-expansion, respectively; and 65.78% vs 45.55% and 14.46% hatching, respectively). In conclusion, OPS vitrification was found to be more efficient for cryopreservation of in vitro-developed sheep embryos than traditional freezing.

Molecular characterization of RNA binding motif protein 3 (RBM3) gene from Pashmina goat.

Pashmina goat inhabits the high altitude cold arid desert of Ladakh, India. This goat is known for its finest and costliest under fiber. Though the under fiber may be a part of its complex thermoregulation mechanism, the genetics of its adaptability under cold conditions is not known. As an attempt to understand its adaptive genetics, and the role of RNA-binding proteins at the cellular response, this study was conducted to characterize the RBM3 gene in Pashmina goat and its expression during hypothermia. The ORF of Pashmina RBM3 gene was 273 bp. Phylogenetic analysis revealed that Pashmina RBM3 is closely related to Bos taurus RBM3. Pashmina RBM3 was characterized by comparative modeling studies. The final 3-D model contained two α-helices and four β-sheets. qRT-PCR data showed that Pashmina RBM3 gene expression was significantly higher (P < 0.05) at moderate (30 °C) hypothermic stress conditions as compared with deep (15 °C) hypothermia.

Advances in genome editing for improved animal breeding: A review

Since centuries, the traits for production and disease resistance are being targeted while improving the genetic merit of domestic animals, using conventional breeding programs such as inbreeding, outbreeding, or introduction of marker-assisted selection. The arrival of new scientific concepts, such as cloning and genome engineering, has added a new and promising research dimension to the existing animal breeding programs. Development of genome editing technologies such as transcription activator-like effector nuclease, zinc finger nuclease, and clustered regularly interspaced short palindromic repeats systems begun a fresh era of genome editing, through which any change in the genome, including specific DNA sequence or indels, can be made with unprecedented precision and specificity. Furthermore, it offers an opportunity of intensification in the frequency of desirable alleles in an animal population through gene-edited individuals more rapidly than conventional breeding. The specific research is evolving swiftly with a focus on improvement of economically important animal species or their traits all of which form an important subject of this review. It also discusses the hurdles to commercialization of these techniques despite several patent applications owing to the ambiguous legal status of genome-editing methods on account of their disputed classification. Nonetheless, barring ethical concerns gene-editing entailing economically important genes offers a tremendous potential for breeding animals with desirable traits.

Comparison between lignocaine hydrochloride and ropivacaine hydrochloride as lumbosacral epidural anaesthetic agents in goats undergoing laparoscopy assisted embryo transfer.

Abstract Goats (n=12) undergoing laparoscopy assisted embryo transfer were randomly allotted to two groups (I and II) and injected lignocaine hydrochloride (4mg/kg) or ropivacaine hydrochloride (1mg/kg) at the lumbosacral epidural space. The animals were held with raised hind quarters for the first three minutes following injection. Immediately after induction of regional anaesthesia, they were restrained in dorsal recumbency in the Trendelenburg position in a cradle. Laparoscopy was performed after creating pneumoperitoneum using filtered room air. The mean (± S.E) induction time in animals of group I was significantly shorter (5.33 ± 0.61 min) than those belonging to group II (12.66 ±1.99 min). Complete analgesia developed throughout the hind quarters and abdomen for 30 min and 60 min in group I and II animal’s respectively. Unlike animals of group I, group II goats continued to show moderate analgesia for 180 minutes. The motor activity returned after a lapse of 130.00 ± 12.64 min and 405.00 ± 46.31 min respectively. Occasional vocalization and struggling was noticed in two goats one from each group irrespective of the surgical manipulations during laparoscopy. The rectal temperature and respiration rates showed only non-significant increase, but the heart rate values were significantly higher (P < 0.5) up to 150 min in animals of both the groups when compared to their baseline values. From this study, it was concluded that both anaesthetic agents produced satisfactory regional anaesthesia in goats undergoing laparoscopy. However, considering the very long delay in regaining the hind limb motor activity, the use of ropivacaine may not be recommended for this purpose. Supplementation of sedative/tranquilizer with lumbosacral epidural anaesthesia needs evaluation.

Comparison of Two Doses of Ropivacaine Hydrochloride for Lumbosacral Epidural Anaesthesia in Goats Undergoing Laparoscopy Assisted Embryo Transfer

Goats (n = 12) undergoing laparoscopy assisted embryo transfer were randomly allotted to two groups (I and II) and injected same volume of ropivacaine hydrochloride at 1.0 mg/kg and 0.5 mg/kg body weight, respectively, at the lumbosacral epidural space. The hind quarters of all the animals were lifted up for the first 3.0 minutes following injection. Immediately after induction the animals were restrained in dorsal recumbency in Trendelenburg position in a cradle. Laparoscopy was performed after achieving pneumoperitoneum using filtered room air. Regional analgesia and changes in physiological parameters were recorded. The mean induction time in animals of group I (n = 6) was 12.666 ± 1.994 minutes. In these animals the analgesia extended up to the umbilical region and lasted for 60 minutes. Only two animals in group II were satisfactorily induced in 11.333 ± 2.333 minutes. In animals of group I, the time taken for regaining the full motor power was significantly long (405 ± 46.314 min) when compared to group II goats (95 ± 9.219 min). From this study it was concluded that ropivacaine did not produce adequate analgesia in most of the goats at 0.5 mg/kg. When used at 1.0 mg/kg, it produced satisfactory regional analgesia lasting for one hour but the prolonged motor loss precludes its use. Additional studies using ropivacaine hydrochloride at doses in between the two extremes used here may be undertaken before recommending it for lumbosacral anaesthesia in goats undergoing laparoscopy.

TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy

Membrane proteins plays significant role in living cells. Transmembrane proteins are estimated to constitute approximately 30% of proteins at genomic scale. It has been a difficult task to develop specific alignment tools for transmembrane proteins due to limited number of experimentally validated protein structures. Alignment tools based on homology modeling provide fairly good result by recapitulating 70–80% residues in reference alignment provided all input sequences should have known template structures. However, homology modeling tools took substantial amount of time, thus aligning large numbers of sequences becomes computationally demanding. Here we present TM-Aligner, a new tool for transmembrane protein sequence alignment. TM-Aligner is based on Wu-Manber and dynamic string matching algorithm which has significantly improved its accuracy and speed of multiple sequence alignment. We compared TM-Aligner with prevailing other popular tools and performed benchmarking using three separate reference sets, BaliBASE3.0 reference set7 of alpha-helical transmembrane proteins, structure based alignment of transmembrane proteins from Pfam database and structure alignment from GPCRDB. Benchmarking against reference datasets indicated that TM-Aligner is more advanced method having least turnaround time with significant improvements over the most accurate methods such as PROMALS, MAFFT, TM-Coffee, Kalign, ClustalW, Muscle and PRALINE. TM-Aligner is freely available through http://lms.snu.edu.in/TM-Aligner/.

Polymorphism in Exon-1 of MSTN Gene in Boer and Bakerwal Goats and its Association with Growth Traits

Majority of the goat population is nondescript that is capable of producing very less meat and milk. With shrinking resources and increasing demand of goat meat and milk, there is urgent need to genetically improve and manage these animals through modern scientific tools to enhance their productivity. Although, there is a need to utilize betweenbreed genetic differences for higher yields, greater emphasis is required on improvement of adapted indigenous breeds/types because of valuable adaptive traits they have developed International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 9 (2017) pp. 2629-2639 Journal homepage: http://www.ijcmas.com