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.

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.

Bazex Syndrome (Acrokeratosis Paraneoplastica): A Narrative Review of Pathogenesis, Clinical Manifestations, and Therapeutic Approaches

Acrokeratosis paraneoplastica, also known as Bazex syndrome, is a relatively understudied yet clinically important dermatological condition that is inextricably associated with squamous cell carcinoma, predominantly of the upper respiratory and gastrointestinal tracts. Manifesting as unique psoriasis-like cutaneous lesions, Bazex syndrome functions as an early warning signal for underlying malignancies, underscoring the urgent need for its timely diagnosis and intervention. Notwithstanding its clinical relevance, the molecular and cellular mechanisms underpinning its pathogenesis are not fully understood. To address these gaps, this comprehensive literature review undertook a meticulous search across reputable databases such as EMBASE, MEDLINE/PubMed, and Web of Science. Our analysis ventures into multiple putative pathogenic pathways, including shifts in Th2 immune responses, aberrant secretion of growth factors, and immunological reactions to tumor-specific antigens. We also detail the clinical phenotypes of Bazex syndrome and their chronological linkage with the corresponding malignancies. Finally, the review evaluates the therapeutic effectiveness of various approaches, including but not limited to targeted cancer treatments, PUVA therapy, and topical corticosteroids. This synthesis aims to arm healthcare providers with a nuanced understanding of Bazex syndrome, facilitating more accurate diagnosis and tailored treatment paradigms.

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.

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.

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.

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.

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.

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.

Molecular identification of Campylobacter jejuni and coli from chicken, calves and dogs to determine its potential threat on human being

Aim:

Campylobacter is an emerging zoonotic pathogen and one of the leading cause of foodborne infection worldwide and it has been isolated from a variety of animal species. The aim of this study was to identify Campylobacter jejuni and Campylobacter coli from dogs, calves, and poultry using polymerase chain reaction (PCR).

Methodology:

A total of 104 number of samples comprising cloacal swab from poultry (38), a rectal swab from dogs (40), and calves (26) were collected for the isolation of thermophilic Campylobacters using conventional culture method. PCR was used for identification of mapA gene for C.jejuni and ceuE for C.coli.

Results:

The overall presence of Campylobacter was found to be 67(64.42%) from the samples, out of which 6 isolates belongs to C. jejuni species, were 5(18.51%) from chicken and 1(4.17%) from dog was recorded and about 17 isolates belongs to C. coli species were 9(33.33%), 6 (25%), and 1(9.09%) from chicken, dog and calves was recorded.

Conclusion:

Results suggested that Campylobacter reservoirs chicken, calves and pet dogs can play a role as the source of infection to human beings and PCR can be an ideal tool for molecular confirmation at the species level.

Screening Isolates of Soybean mosaic virus for Infectivity in a Model Plant, Nicotiana benthamiana

Soybean mosaic virus (SMV), belonging to the genus Potyvirus of the family Potyviridae, has a relatively narrow host range almost exclusively confined to leguminous hosts. While disease management through genetic transformation can be an effective approach, soybean remains recalcitrant to routine genetic transformation. In this context, it is important to identify new hosts for SMV that can be used to develop effective transgenic resistance strategies. Transformation in Nicotiana benthamiana is simple and highly efficient; hence, here we demonstrate the infectivity of SMV strain SC7 in N. benthamiana plants. To identify an SMV strain infectious in N. benthamiana, we mechanically inoculated N. benthamiana plants with 37 isolates from 21 (SC1 to SC21) SMV strains. Plants inoculated with isolates of strain SC7 produced mosaic symptoms on leaves. However, N. benthamiana plants inoculated with the 20 other SMV strains showed no visible symptoms. Furthermore, soybean cv. Nannong 1138-2 inoculated with sap prepared from symptomatic N. benthamiana leaves showed typical SMV mosaic symptoms 2 weeks after inoculation. In addition, SMV was detected in symptomatic N. benthamiana and soybean leaves by RT-PCR, DAS-ELISA, and further identified by sequencing. Together, the results indicate that N. benthamiana plants could support multiplication of SMV strain SC7. The findings of this study would be useful for the investigation of SMV resistance using the model plant N. benthamiana.

Cloning and expression analysis of a stress-induced GmIMT1 gene in soybean (Glycine max)

Here, we aimed to clone and identify the GmIMT1 gene related to the salt stress response in soybean. The full-length cDNA sequence of the GmIMT1 gene was amplified in soybean using degenerate primers of Mesembrythmum crystallium. To understand the stress response, the GmIMT1 gene was cloned and sequenced. Then, the expression vectors of the gene were constructed, and introduced into the model plant Arabidopsis thaliana through Agrobacterium mediated transformation, and the salt tolerance was analyzed in the transgenic plants. In addition, the expression patterns of GmIMT1 gene in soybean were analyzed. The expression was examined in different organs (roots, leaves, flower seeds, and stem) and under different stress conditions (drought, high salt, low temperature, salicylic acid, ethane, abscisic acid, and methyl jasmonate) by real-time fluorescent quantitative polymerase chain reaction analysis. The results showed that the root, leaves, and stems exhibited high level of GmIMT1 gene expression, whereas there was no expression in the seeds. In addition, the GmIMT1 gene expression was upregulated under all stress conditions. Overall, the results clearly indicate that GmIMT1 might be involved in multiple plant response pathways to the different environmental conditions. Furthermore transgenic plants exhibited higher salt-tolerance compared to wild type plants.

Growth response of Casuarina equisetifolia Forst. rooted stem cuttings to Frankia in nursery and field conditions

Casuarina equisetifolia Forst. is a tree crop that provides fuel wood, land reclamation, dune stabilization, and scaffolding for construction, shelter belts, and pulp and paper production. C. equisetifolia fixes atmospheric nitrogen through a symbiotic relationship with Frankia, a soil bacterium of the actinobacteria group. The roots of C. equisetifolia produce root nodules where the bacteria fix atmospheric nitrogen, which is an essential nutrient for all plant metabolic activities. However, rooted stem cuttings of elite clones of C. equisetifolia by vegetative propagation is being planted by the farmers of Pondicherry as costeffective method. As the vegetative propagation method uses inert material (vermiculite) for rooting there is no chance for Frankia association. Therefore after planting of these stocks the farmers are applying 150 kg of di-ammonium phosphate (DAP)/acre/year. To overcome this fertilizer usage, the Frankia-inoculated rooted stem cuttings were propagated under nursery conditions and transplanted in the nutrient-deficient soils of Karaikal, Pondicherry (India), in this study. Under nursery experiments the growth and biomass of C. equisetifolia rooted stem cuttings inoculated with Frankia showed 3 times higher growth and biomass than uninoculated control. These stocks were transplanted and monitored for their growth and survival for 1 year in the nutrient-deficient farm land. The results showed that the rooted stem cuttings of C. equisetifolia significantly improved growth in height (8.8 m), stem girth (9.6 cm) and tissue nitrogen content (3.3 mg g-1) than uninoculated controls. The soil nutrient status was also improved due to inoculation of Frankia.

Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants

Metabolic networks reconstructed from sequenced genomes or transcriptomes can help visualize and analyze large-scale experimental data, predict metabolic phenotypes, discover enzymes, engineer metabolic pathways, and study metabolic pathway evolution. We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: a comprehensive, all-plant reference pathway database, PlantCyc, and a reference enzyme sequence database, RESD, for annotating metabolic functions of protein sequences. PlantCyc (version 3.0) includes 714 metabolic pathways and 2,619 reactions from over 300 species. RESD (version 1.0) contains 14,187 literature-supported enzyme sequences from across all kingdoms. We used RESD, PlantCyc, and MetaCyc (an all-species reference metabolic pathway database), in conjunction with the pathway prediction software Pathway Tools, to reconstruct a metabolic pathway database, PoplarCyc, from the recently sequenced genome of Populus trichocarpa. PoplarCyc (version 1.0) contains 321 pathways with 1,807 assigned enzymes. Comparing PoplarCyc (version 1.0) with AraCyc (version 6.0, Arabidopsis [Arabidopsis thaliana]) showed comparable numbers of pathways distributed across all domains of metabolism in both databases, except for a higher number of AraCyc pathways in secondary metabolism and a 1.5-fold increase in carbohydrate metabolic enzymes in PoplarCyc. Here, we introduce these new resources and demonstrate the feasibility of using them to identify candidate enzymes for specific pathways and to analyze metabolite profiling data through concrete examples. These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site (http://plantcyc.org).

Synthesis, characterization and photocatalytic activity of nanotitania loaded W-MCM-41

Nanocrystalline titanium oxide (TiO(2)) is a promising material as a photocatalyst for photodecomposition of hazardous organic pollutants under illumination, because it is cheap, safe, environmentally benign, and chemically stable. However, the control of particle size and monodispersity of TiO(2) is a challenging task. The use of MCM-41, an inorganic template of uniform pore size (2-10 nm), can overcome this difficulty and produce stable nanoparticles of uniform size and shape. In an attempt to extend light absorption of the TiO(2)-based photocatalyst towards the visible light range and eliminate the rapid recombination of excited electrons/holes during photoreaction, a new photocatalyst (25%TiO(2)-loaded W-MCM-41) powder was prepared. W-MCM-41, with different ratios of Si to W (Si/W = 25, 50, 75), was synthesized by a hydrothermal method and loaded with 25 wt% TiO(2) utilizing a sol-gel method. In order to compare the photocatalytic activity of our sample, titania-loaded plain MCM-41 was also prepared. These materials were characterized by various physiochemical techniques such as UV-visible absorption spectroscopy, x-ray diffraction, nitrogen adsorption-desorption isotherm measurement, Fourier transform infrared (FT-IR) spectroscopy, and transmission electron microscopy. The photocatalytic activity of the prepared samples was evaluated using methyl orange as a model organic compound. It was found that the photodegradation ability of 25% TiO(2)-loaded W-MCM-41 was highly related to the amount of W atoms present in the sample; the optimum atomic ratio of Si to W was 25. It has been confirmed that the recombination rate of electrons/holes in 25%TiO(2)/W-MCM-41 declined due to the existence of W atoms in the sample.

Ocular myasis and associated mucopurulent conjuctivitis acquired occupationally: A case study

Ocular myasis and associated mucopurulent conjunctivitis in human eyes is a rare phenomenon. However, if the sheep bot fly abounds and poor hygienic environment prevails, the Oestrous ovis deposits its larvae in the conjunctival eye sac of human. The present paper reports a case study of ocular myasis among sheep farm workers caused by Oestrous ovis. The ocular myasis and the associated mucopurulent conjunctivitis are occupationally acquired in these cases. This study also suggests the treatment of patients and the recovery of the larvae.