Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle - elucidating genetic variation.

Cattle contribute to the nutritional needs and economy of a place. The performance and fitness of cattle depend on the response and adaptation to local climatic conditions. Genomic and genetic studies are important for advancing cattle breeding, and availability of relevant reference genomes is essential. In the present study, the genome of a Vechur calf was sequenced on both short-read Illumina and long-read Nanopore sequencing platforms. The hybrid de novo assembly approach was deployed to obtain an average contig length of 1.97 Mbp and an N50 of 4.94 Mbp. By using a short-read genome sequence of the corresponding sire and dam, a haplotype-resolved genome was also assembled. In comparison to the taurine reference genome, we found 28,982 autosomal structural variants and 16,926,990 SNVs, with 883,544 SNVs homozygous in the trio samples. Many of these SNPs have been reported to be associated with various QTLs including growth, milk yield, and milk fat content, which are crucial determinants of cattle production. Furthermore, population genotype data analysis indicated that the present sample belongs to an Indian cattle breed forming a unique cluster of Bos indicus. Subsequent FST analysis revealed differentiation of the Vechur cattle genome at multiple loci, especially those regions related to whole body growth and cell division, especially IGF1, HMGA2, RRM2, and CD68 loci, suggesting a possible role of these genes in its small stature and better disease resistance capabilities in comparison with the local crossbreeds. This provides an opportunity to select and engineer cattle breeds optimized for local conditions.

Tinospora cordifolia ameliorated titanium dioxide nanoparticle-induced toxicity via regulating oxidative stress-activated MAPK and NRF2/Keap1 signaling pathways in Nile tilapia (Oreochromis niloticus).

Titanium dioxide nanoparticle (TNP) has been suggested for use in fish farms to prevent or alleviate bacterial diseases owing to its bactericidal property. Unfortunately, the interaction of TNP with cells impaired the host defenses of fish resulting in increased mortality during bacterial challenges. The present study evaluated the efficacy of the ethanolic extract of Tinospora cordifolia (TCE) as a dietary supplement in ameliorating TNP induced toxicity in Nile tilapia (Oreochromis niloticus). The fishes were exposed to environmentally relevant concentration (10 mg/L) of TNP for 14 days and the effect of TCE supplemented feed at 3 different doses (5, 10, and 15 g/kg) was studied. TCE signally increased the weight gain, specific growth rate, and decreased feed conversion ratio in fish. TCE significantly (P < 0.05) ameliorated the toxic effects caused by TNP by increasing the antioxidant (CAT, SOD, GPx) activity and decreasing the levels of serum enzymes (ALT, AST, ALP, ACP), macromolecular oxidation, excessive ROS production, and pro-inflammatory cytokines (IL-1ß, IL-6, IL-8, INF-γ, TNF-α, PGE-2). TNP bioaccumulation and histopathological alterations in gill, liver, and kidney were also significantly alleviated by TCE supplementation. TCE perceptibly regulated the expression of heat shock proteins (HSP60, -70), MAPKs (pERK1/2, pp38), antioxidant (NRF2, Keap1, HO-1), apoptotic (p53, PDRG1), and anti-apoptotic (AKT, Bcl2) proteins in fish. Regarding disease resistance, the TCE co-treated groups showed reduced cumulative mortality and higher relative percent survival with A. hydrophila. Our results suggest that TNP-induced apoptosis is mediated by the MAPK/NRF2/Keap1 pathway and underlines the therapeutic potential of TCE in aqua-farming.

An Immunopathological Evaluation of the Porcine Cholecyst Matrix as a Muscle Repair Graft in a Male Rat Abdominal Wall Defect Model.

With the increasing use of animal-based biomaterials for regenerative medical applications, the need for their safety assessment is paramount. A porcine cholecyst-derived scaffold (CDS), intended as a muscle repair graft, prepared by a nondetergent/enzymatic method was engrafted in a rat abdominal wall defect model. Host tissue-scaffold interface samples were collected 2, 8, and 16 weeks postimplantation and evaluated by histopathology, immunohistochemistry, and electron microscopy. The nature of the tissue reaction was compared with those induced by a jejunum-derived scaffold (JDS) prepared by the same method and a commercial-grade small intestinal submucosa (CSIS) scaffold. A study of the immunopathological response in major lymphoid tissues and immunophenotyping for M1 and M2 macrophages was performed at the host tissue-scaffold interface. Further, "irritancy scores" for CDS and JDS were determined using CSIS as the reference material. Both CDS and JDS appeared to be potential biomaterials for muscle grafts, but the former stimulated a skeletal muscle tissue remodeling response predominated by M2 macrophages. The data support the notion that biomaterials with similar biocompatibility, based on local tissue response on implantation, may cause differential immunogenicity. Additionally, CDS compared to JDS and CSIS was found to be less immunotoxic.

Comparative cytomorphometric analysis of oral mucosal cells in normal, tobacco users, oral leukoplakia and oral squamous cell carcinoma.

BACKGROUND: Squamous cell carcinoma (SCC) is the third most common cause of oral morbidity in India despite the numerous advances made in the treatment protocol. AIM: To compare the cytomorphometric changes of oral mucosal cells in normal subjects (Group I) with that of tobacco users without any lesion (Group II), tobacco users with oral leukoplakia (Group III), and tobacco users with oral SCC (Group IV) through a semi-automated image analysis system. MATERIALS AND METHODS: Oral mucosal cells collected from study subjects (n = 100) stained using rapid Papanicolaou stain. Photomicrograph of 50 nonoverlapping cells captured at 50× magnification with a digital image capture system. Cytomorphometric analysis of cells in the captured images was performed with Image-Pro image analysis software. Image analysis was performed to obtain cell diameter (CD), cytoplasmic area (CyA), nuclear diameter (ND), nuclear area (NA), and nuclear-to-cytoplasmic ratio. These values were statistically compared among the groups using one-way analysis of variance (ANOVA) and Mann-Whitney U test. RESULTS: The ND, NA, and nuclear-to-cytoplasmic ratio values were found to be increased in the samples collected from leukoplakia and oral SCC. The CD and CyA decreased compared to the normal mucosa in oral SCC samples. CONCLUSION: The cytomorphometric changes observed in samples from oral SCC and oral leukoplakia were consistent with the current diagnostic features. Hence, the semi-automated cytomorphometric analysis of oral mucosal cells can be used as an objective adjunct diagnostic tool in the diagnosis of these lesions.

Porcine cholecyst-derived scaffold promotes full-thickness wound healing in rabbit.

Graft-assisted healing is an important strategy for treating full-thickness skin wounds. This study evaluated the properties of porcine cholecyst-derived scaffold and its use for treating full-thickness skin wound in rabbit. The physical properties of cholecyst-derived scaffold were congenial for skin-graft application. Compared to a commercially available skin-graft substitute made of porcine small intestinal submucosa, the cholecyst-derived scaffold was rich in natural biomolecules like elastin and glycosaminoglycans. When used as a xenograft, it promoted healing with excess cell proliferation at early phases and acceptable collagen deposition in the later remodelling phases.