Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach.

The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform. SNP markers were called using standard methodology. Genome-wide association study (GWAS) was undertaken in PLINK program to identify the informative SNP markers significantly associated with differential immune response. The results revealed significant SNPs associated with E2 antibody response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response against CSF vaccination were located on SSC10, SSC17, SSC9, SSC2, SSC3 and SSC6. The overlapping and flanking genes (500Kb upstream and downstream) of significant SNPs were CYB5R1, PCMTD2, WT1, IL9R, CD101, TMEM64, TLR6, PIGG, ADIPOR1, PRSS37, EIF3M, and DNAJC24. Functional enrichment and annotation analysis were undertaken for these genes in order to gain maximum insights into the association of these genes with immune system functionality in pigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly piglets while the identified informative SNPs may be used as suitable markers for determining variation in host immune response against CSF vaccination in pigs.

Oxymatrine Improves Oxidative Stress-Induced Senescence in HT22 Cells and Mice via the Activation of AMP-Activated Protein Kinase.

The accumulation of oxidative stress is one of the important factors causing cellular senescence. Oxymatrine (OM) is a natural quinolizidine alkaloid compound known for its antioxidant effects. This study aimed to investigate the anti-senescence potential of OM through oxidative stress-induced in vitro and in vivo models. By treating 600 µM of H2O2 to the HT22 mouse hippocampal neuronal cell line and by administering 150 mg/kg D-galactose to mice, we generated oxidative stress-induced senescence models. After providing 1, 2, and 4 µg/mL of OM to the HT22 mouse cell line and by administering 50 mg/kg OM to mice, we evaluated the enhancing effects. We evaluated different senescence markers, AMPK activity, and autophagy, along with DCFH-DA detection reaction and behavioral tests. In HT22 cells, OM showed a protective effect. OM, by reducing ROS and increasing p-AMPK expression, could potentially reduce oxidative stress-induced senescence. In the D-Gal-induced senescence mouse model, both the brain and heart tissues recovered AMPK activity, resulting in reduced levels of senescence. In neural tissue, to assess neurological recovery, including anxiety symptoms and exploration, we used a behavioral test. We also found that OM decreased the expression level of receptors for advanced glycation end products (RAGE). In heart tissue, we could observe the restoration of AMPK activity, which also increased the activity of autophagy. The results of our study suggest that OM ameliorates oxidative stress-induced senescence through its antioxidant action by restoring AMPK activity.

Multivariate analysis of morphometric traits of Malaimadu cattle-autochthonous draft cattle of south India.

Malaimadu cattle is a less explored indigenous cattle germplasm reared in the Western Ghats area of Tamil Nadu, south India. This study aimed to analyze the morphological structure of the Malaimadu cattle using a multivariate approach that explains and best represents body conformation. Sixteen body measurements were obtained from 156 adult female cattle from their native breeding tract. The Nearest Neighbor Method of Hierarchical Cluster analysis was used to group the morphometric traits into clusters. Pearson's coefficients of correlation (r) were estimated to determine the phenotypic correlations between different body measurements. Traits were analyzed using varimax rotated principal component analysis (PCA) with Kaiser normalization. Cluster analysis categorizes morphometric traits into two distinct clusters with the first cluster formed by traits related to horns and face, while the second cluster denotes general body conformation. Out of 120 phenotypic correlations, 55 were significant of which 51 were positive correlations. The estimated correlation coefficient ranges between - 0.50 (body length and face width) to 0.85 (chest girth and body weight). PCA extracted six components representing 70.19% of the total variance, while the first principal component comprises chest girth (CG), body weight (BW), height at wither (HW), and Paunch girth (PG) alone accounts for 23.70% thereby describing the general size and shape of the animal. The multivariate approach has proven to be effective in differentiating Malaimadu cattle from other indigenous breeds of south India with clear morphometric differences that help in identifying the pure phenotype for future propagation and also for devising breeding strategies.

A Review on Peripheral Tinnitus, Causes, and Treatments from the Perspective of Autophagy.

Tinnitus is the perception of phantom noise without any external auditory sources. The degeneration of the function or activity of the peripheral or central auditory nervous systems is one of the causes of tinnitus. This damage has numerous causes, such as loud noise, aging, and ototoxicity. All these sources excite the cells of the auditory pathway, producing reactive oxygen species that leads to the death of sensory neural hair cells. This causes involuntary movement of the tectorial membrane, resulting in the buzzing noise characteristic of tinnitus. Autophagy is an evolutionarily conserved catabolic scavenging activity inside a cell that has evolved as a cell survival mechanism. Numerous studies have demonstrated the effect of autophagy against oxidative stress, which is one of the reasons for cell excitation. This review compiles several studies that highlight the role of autophagy in protecting sensory neural hair cells against oxidative stress-induced damage. This could facilitate the development of strategies to treat tinnitus by activating autophagy.

Pan-tissue methylation aging clock: Recalibrated and a method to analyze and interpret the selected features.

The abundance of the biological data and the rapid evolution of the newer machine learning technologies have increased the epigenetics research in the last decade. This has enhanced the ability to measure the biological age of humans and different organisms via their omics data. DNA methylation array data are commonly used in the prediction of methylation age. Horvath clock has been adopted in various aging studies as a DNA methylation age predicting clock due to its higher accuracy and multi tissue prediction potential. In the current study, we have developed a pan tissue methylation-aging clock by using the publicly available illumina 450k and EPIC array methylation datasets. In doing that, we developed a highly accurate epigenetic clock, which predicts the age of multiple tissues with higher accuracy. We have also analyzed the selected probes for their biological relevance. Upon analyzing the selected features further, we found out evidences, which support the Antagonistic pleiotropy theory of aging.

Identification of genes affecting milk fat and fatty acid composition in Vrindavani crossbred cattle using 50 K SNP-Chip.

The aim of this study was to identify candidate genes associated with milk fat per cent and fatty acid (FA) composition in Vrindavani cattle using the Illumina 50 K single-nucleotide polymorphism (SNP) array. After quality control, a total of 41,427 informative and high-quality SNPs were used for a genome-wide association study (GWAS) for milk fat percentage and 16 different types of fatty acids. Lactation stage, parity, test day milk yield, and proportion of exotic inheritance were included as fixed effects in the GWAS model. A total of 67 genome-wide significant (P < 1.20 × 10-06) SNPs and 176 suggestive significant (P < 2.41 × 10-05) SNPs were identified. Out of these, 15 SNPs were associated with more than one trait. The strongest associations were found on BTA14 for milk fat percentage and on BTA2 and BTA16 for polyunsaturated fatty acids. Several significant SNPs were identified close to or within the genes ELOVL6, FABP4, PMP2, PLIN1, MFGE8, GHRL2, and LDLRAD3 which are known to be associated with fat percentage and FA composition in dairy cattle breeds. This study is a step forward to better characterize the molecular mechanisms of phenotypic variation in milk fatty acids in a taurine-indicine composite cattle breed reared in tropical environments.

Effect of Growth Factor-Loaded Acellular Dermal Matrix/MSCs on Regeneration of Chronic Tympanic Membrane Perforations in Rats.

The success rate of grafting using acellular dermal matrix (ADM) for chronic tympanic membrane was reported in previous studies to be lower than fascia or perichondrium. Combining mesenchymal stem cells (MSCs) and growth factor-loaded ADM for the regeneration of chronic TMP has not been reported so far. In this study, we hypothesized that combining growth factor-loaded ADM/MSCs could promote the recruitment of MSCs and assist in TMP regeneration. We evaluated the regeneration and compared the performance of four scaffolds in both in vitro and in vivo studies. MTT, qPCR, and immunoblotting were performed with MSCs. In vivo study was conducted in 4 groups (control; ADM only, ADM/MSC, ADM/MSC/bFGF, ADM/MSC/EGF) of rats and inferences were made by otoendoscopy and histological changes. Attachment of MSCs on ADM was observed by confocal microscopy. Proliferation rate increased with time in all treated cells. Regeneration-related gene expression in the treated groups was higher. Also, graft success rate was significantly higher in ADM/MSC/EGF group than other groups. Significant relationships were disclosed in neodrum thickness between each group. The results suggest, in future, combining EGF with ADM/MSCs could possibly be used as an outpatient treatment, without the need for surgery for eardrum regeneration.

Neuroprotective Effect of Valproic Acid on Salicylate-Induced Tinnitus.

High-dose salicylate induces temporary moderate hearing loss and the perception of a high-pitched tinnitus in humans and animals. Previous studies demonstrated that high doses of salicylate increase N-methyl-d-aspartate (NMDA) receptor levels, resulting in a rise in Ca2+ influx and induction of excitotoxicity. Glutamate excitotoxicity is associated with failure in the maintenance of calcium homeostasis, mitochondrial dysfunction, and production of reactive oxygen species (ROS). Valproic acid (VPA) is widely used for the management of bipolar disorder, epilepsy, and migraine headaches, and is known to regulate NMDA receptor activity. In this study, we examined the beneficial effects of VPA in a salicylate-induced tinnitus model in vitro and in vivo. Cells were pretreated with VPA followed by salicylate treatment. The expression levels of NMDA receptor subunit NR2B, phosphorylated cAMP response element-binding protein-an apoptosis marker, and intracellular levels of ROS were measured using several biochemical techniques. We observed increased expression of NR2B and its related genes TNFα and ARC, increased intracellular ROS levels, and induced expression of cleaved caspase-3. These salicylate-induced changes were attenuated in the neuronal cell line SH-SY5Y and rat cortical neurons after VPA pretreatment. Together, these results provide evidence of the beneficial effects of VPA in a salicylate-induced temporary hearing loss and tinnitus model.

Synthesis, characterization of acrylate polymer having chalcone moiety: evaluation of antimicrobial, anticancer and drug release study.

This article describes synthesis, characterization, antimicrobial, drug-releasing and anti-cancer activity of acrylate monomer and its polymer containing chalcone moiety. The synthesized polymers were characterized through IR, 1H NMR and UV-visible spectroscopy techniques. The molecular weight of the obtained polymer is found to be around 4000 g/mol. The synthesized polymers are thermally stable up to 260 °C. The monomer and its polymer show higher activity against gram-negative bacteria and these compounds show remarkable activity over breast cancer cells. The synthesized monomer and polymers showed higher anticancer activity. The inhibitory potential of monomers and polymers premeditated using optimized in vitro evaluation MTT assay and live cell images. The drug release potential was controlled through co-monomer, pH and temperature.

Selection and validation of differentially expressed metabolic and immune genes in weaned Ghurrah versus crossbred piglets.

In the present investigation, differentially expressed genes (DEGs) were studied using RNA sequencing (RNA-seq) technique in porcine peripheral blood mononuclear cells (PBMC) of weaned Ghurrah and crossbred piglets at 3-month age. Transcriptomic analysis was done using three different packages, namely, EBSeq, DESeq2, and edgeR, to identify the DEGs between Ghurrah and crossbred piglets. Total 7717 DEGs were commonly identified by all three packages, out of which 4151 genes found to be up-regulated, and 3566 genes were down-regulated. Functional annotation of these DEGs indicated metabolism as the most commonly enriched category followed by the immune response. Genes related to metabolism and growth were up-regulated in crossbred piglets as compared with Ghurrah piglets, whereas immunity-related genes were up-regulated in Ghurrah piglets elucidating the disease resistance nature of this indigenous breed over crossbred counterparts. Further, eight DEGs, namely, LRP-1, ADCY4, ERRFI1, LDHD, ARG1, OASL, MGARP, and S100A8, were validated by qRT-PCR in a separate set of biological samples and found to be in concordance with RNA-seq results. Finding in the present study provides insight into genes and their molecular mechanisms governing difference in growth performance between Ghurrah and crossbred pigs.

Signatures of Selection in Composite Vrindavani Cattle of India.

Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle. The constituent breeds were selected for higher milk production and adaptation to the tropical climate. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. A total of 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). The Vrindavani breed was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (F ST). We identified 11 common regions detected by more than one method harboring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B, and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.

Cross-sectional study on rotavirus A (RVA) infection and assessment of risk factors in pre- and post-weaning piglets in India.

Rotavirus A (RVA) infections are known to retard the piglets' growth and minimize the profit to the pig farming community. Between August 2014 and July 2017, in a cross-sectional study, we surveyed 13 organized pig farms located in the eight states of India representing northern, north-eastern and southern regions, to identify the risk factors associated with RVA infection in pre- and post-weaning piglets. Faecal samples (n = 411) comprising of non-diarrhoeic (n = 320) and diarrhoeic (n = 91) were collected and screened for RVA infection using VP6 gene-based RT-PCR. RVA positivity of 52.5% (168/320) in non-diarrhoeic and 59.3% (54/91) in diarrhoeic piglets was noticed. Further, 53.3% (120/225) and 54.8% (102/186) of the samples from pre- and post-weaned samples were positive for RVA, respectively. To note, no statistically significant association was noticed between RVA infection, health and weaning status. Additionally, a questionnaire-based survey was conducted to identify the risk factors for RVA infections in piglets. The analysis revealed that good ventilation (OR 0.2, 95% CI 0.15-0.39), use of deep well water (OR 0.2, 95% CI 0.13-0.43) and feeding of commercial feed (OR 0.3, 95% CI 0.18-0.41) were associated with reduced risk of RVA infection compared with poor ventilation, use of shallow well water and feeding of own milled feed, respectively. Contrarily, mixed farms (OR 2.1, 95% CI 1.26-3.37), use of heater or cooler (OR 5.9, 95% CI 3.74-9.30), sheds in different elevation (OR 2.5, 95% CI 1.20-5.01) and weekly and occasional use of disinfectant for surface cleaning (OR 1.8, 95% CI 1.12-2.96) were associated with higher RVA infection. Mitigating the risk factors might help in better health management of piglets and increase the economic return to pig farming community in the country.

Copy number variation in livestock: A mini review.

Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock.

Practical approach to syndromic pediatric retinal dystrophies.

PURPOSE OF REVIEW: The purpose of this review is to outline those systemic disorders that are associated with pediatric retinal dystrophy, summarize important retinal, and nonretinal clues that aid in syndromic diagnosis, provide an approach for ophthalmic and systematic systemic examination, describe the important systemic findings seen in pediatric syndromic retinal dystrophies and highlight the role of genetic testing. RECENT FINDINGS: With profound advances being made in the field of molecular genetics, a definitive molecular etiology is increasingly being made even in rare and unusual forms of retinal dystrophies. Early recognition and precise diagnosis of a syndromic association has major clinical implications. It not only ensures early and holistic care to the child but also provides an opportunity for the parents in better understanding the nature and course of the disorder. It greatly aids in genetic counseling. SUMMARY: Many syndromic retinal dystrophies may present initially to the ophthalmologist long before they present to the pediatrician with systemic symptoms. The intent of this article is to act as a resource in assisting the ophthalmologist to arrive at an early systemic diagnosis.

Wetting behavior of multi-walled carbon nanotube nanofluids.

Nanofluids-engineered colloidal suspensions in base liquids-have captivated the interest of researchers over the last two decades for various existing as well as emerging technological applications. The main impetus for the synthesis of such novel nanocomposite liquids is the potential to alter properties of the base liquid, such as its viscosity, thermal conductivity, and surface tension, and to introduce specific optical and magnetic properties. Numerous studies suggest trends and explanations for the effects associated with the addition of nanoparticles, and that deviation from the base liquid properties are dependent on nanoparticle concentration. However, there remains a certain ambiguity in the available literature. The wetting behavior and surface tension of nanofluids are particular examples where highly conflicting results exist. In this study, we used multi-walled carbon nanotubes (MWCNTs) functionalized by plasma treatment and dispersed in reverse osmosis water and 99% anhydrous ethanol. Our observations reveal that the surface tension and wetting behavior of the stable aqueous and ethanol-based nanofluids containing plasma functionalized MWCNTs are unaffected by the MWCNT loading up to 120 (0.012) and ∼210 (0.021) ppm (vol%), respectively. The ethanol-based MWCNT nanofluids allowed us to extend the study to higher loadings, and a linear increase of the surface tension past ∼200 ppm was observed. Conversely, nanofluids containing non-functionalized or surfactant-stabilized MWCNTs show drastically different contact angle values when compared to the base liquids even at very low concentrations (less than 100 ppm). We demonstrate that the stability of nanofluid and method of stabilization are crucial parameters in determining the wetting behavior of nanofluids.

Expression Profiling of Innate Immune Genes in Milk Somatic Cells During Subclinical Mastitis in Crossbred Dairy Cows.

Innate immune mechanism plays a key role in mammary defense, from recognition of pathogens to activation of nonspecific and specific immunity involved in elimination of pathogens. Expression profiles of innate immune response genes namely Toll like receptor 2 (TLR-2), Peptidoglycan recognition protein 1 (PGLYRP-1), Interleukin 8 receptor (IL-8 R), L-Selectin (SELL), and Osteopontin (OPN) in milk somatic cells of subclinical mastitis (SCM) affected crossbred cows were investigated under this study at transcript level using quantitative real time polymerase chain reaction (qRT-PCR). Dairy cows in mid lactation were screened for SCM using California Mastitis Test (CMT), Somatic Cell Count (SCC) and Electrical Conductivity test (EC). Based on results of SCM screening tests, crossbred cows were clustered into two groups with four Staphylococcus aureus infected SCM cows and four apparently healthy cows. The expressions levels of TLR-2, PGLYRP-1, IL-8 R, SELL, and OPN in milk somatic cells of SCM affected cows were significantly higher (p < 0.05) than healthy cows. These genes could be considered as candidate genes for innate immune response against S. aureus SCM infection.

Natural history of retinopathy in children and young people with type 1 diabetes.

PurposeTo describe the prevalence and natural history of retinopathy in a cohort of children and young people with type 1 diabetes attending a tertiary hospital diabetes clinic.MethodsWe analysed retinopathy screening data from 2008 to 2010 on all eligible children using the 'Twinkle' diabetes database and the regional retinal screening database.ResultsA total of 88% (149/169) of eligible children were screened in 2008, median age 14 years, 52% male. The prevalence of retinopathy was 19.5% (30/149). All children had background retinopathy grade R1. There was significant difference in median (range) duration of diabetes, 7.7 years (0.6-13.7) vs 5 years (0.2-12.5) (P<0.001) and median (range) HbA1C, 9.1% (7.2-14) vs 8.6% (5.6-13.1) (P=0.02), between the groups with and without retinopathy. At 2- years follow-up, 12/30 (40%) had unchanged retinopathy grade R1, 10/30 (33.3%) showed resolution of changes (R0), 1/30 progressed to maculopathy, and 7/30 had no follow-up data. Median (range) HbA1C in 2008 and 2010 for the groups with stable vs resolved changes was similar, 9.1% (7.2-14.0) and 9.2% (7-14.0) vs 9.5% (7.8-14.0) and 9.2% (8.7-14.0). Of the 119 without retinopathy in 2008, 27 (22.5%) had developed retinopathy within 2 years, including 1 with pre-proliferative retinopathy and 1 with maculopathy. There was no significant difference in HbA1c between those who progressed to retinopathy (8.7% (7.1-13.1)) (8.7% (7.1-13.1)), and those who did not (8.6% (6.3-12.2)).ConclusionsPrevalence of background retinopathy in our cohort was comparable to the previously published reports, with higher HbA1c and longer duration of diabetes being significant risk factors. On short-term follow-up, Grade 1 retinopathy is likely to resolve in a third of patients and remain unchanged in just over a third.

Organophosphate retinopathy.

Organophosphates have rarely been reported to cause various ocular sequelae including retinal degeneration. Retinal manifestations have been rarely reported and poorly characterized. We describe a case of a 76-year-old man with vision loss beginning in his 20s due to acute on chronic exposure to dimethoate, an organophosphate. He presented with bilateral geographic macular atrophy and midperipheral pigmentary clumping which we characterized by dilated fundoscopic examination, optical coherence tomography, and fundus autofluorescence.