Keratin as an effective coating material for in vitro stem cell culture, induced differentiation and wound healing assays

The utilization of stem cells in tissue engineering holds great promise as efficient tools for tissue regeneration and in treating numerous musculoskeletal diseases. However, several limiting factors, such as precise delivery and control of differentiation of these stem cells as well as mimicking the microenvironment required to modulate stem cell behaviour in-vivo, have given rise to an urgent need for the development of new biomaterials which could be tailored to enhance cell renewal and/or direct cell fates. Keratin-rich biological materials offer several advantages, such as biocompatibility, tailorable mechanical properties, huge bioavailability, non-toxicity, non-immunogenic, and intrinsic tissue repair and/or regeneration capabilities, which makes them highly valued. In the present work, we report the preparation of keratin-based bio-materials from goat hair waste and its effectiveness as a coating material for in vitro culture and induced differentiation of mesenchymal stem cells (MSC's) and primary goat fibroblast cells. Since no known keratinase enzymes are expressed as such in human and/or animal systems, these keratin biomaterials could be used to slow the rate of degradation and deliver keratin-loaded stem cell scaffolds to induce their directed differentiation in vivo. The generated keratin materials have been characterized for surface morphology, protein structures, size and other properties using SDS-PAGE, LC/MS-MS, SEM, FTIR etc. Also, in vitro cell culture assays such as cell adhesion, viability using MTT, live dead assays, differentiation assays and in vitro scratch/wound healing assays were performed. Our results provide important data supporting tissue engineering applications of these keratinous biomaterials by combining the unique biological characteristics of goat hair-derived keratin material with the regenerative power of stem cells and their combinatorial use in applications such as disease treatment and injury repair as well as their use in the preparation of wound healing products, such as dressings and bandages, for management of clinical care in animals.

Climate plays a dominant role over land management in governing soil carbon dynamics in North Western Himalayas

The soil carbon (C) dynamics is strongly influenced by climate and land-use patterns in the Himalayas. Therefore, soils under five prominent land use [e.g., maize (Zea mays), horticulture, natural forest, grassland, and wasteland] were sampled down up to 30 cm depth under two climatic conditions viz., temperate and subtropical to assess the impacts of climate and landuse on soil C dynamics. Results demonstrated that irrespective of land use, temperate soil contains 30.66% higher C than subtropical soils. Temperate soils under natural forests had the higher total organic carbon (TOC, 21.90 g kg^-1), Walkley-Black carbon (WBC, 16.42 g kg^-1), contents, and stocks (TOC, 66.92 Mg ha^-1 and WBC, 50.24 Mg ha^-1), and total soil organic matter (TSOM, 3.78%) concentration as compared to other land uses like maize, horticulture, grassland, and wasteland. Under both climatic conditions, maize land use had the lowest TOC 9.63, 6.55 g kg^-1 and WBC 7.22, 4.91 g kg^-1 at 0-15 and 15-30 cm soil depth, respectively. Horticulture land use had 62.58 and 62.61% higher TOC and WBC over maize-based land use under subtropical and temperate climatic conditions at 0-30 cm soil depth, respectively. However, soils of maize land use under temperate conditions had ∼2 times more TOC than in subtropical conditions. The study inferred that the C-losses is more in the subtropical soil than in temperate soils. Hence, the subtropical region needs more rigorous adoption of C conservation farming practices than the temperate climatic setting. Although, the adoption of C storing and conserving practices is crucial under both climatic settings to arrest land degradation. Horticultural land uses along with conservation effective soil management practices may be encouraged to restore more soil C and to improve the livelihood security of the hill populace in the North Western Himalayas.

Comparison of various models for the estimation of heritability and breeding values

The exploration of additive genetic variance for the selection of animals is the central paradigm in quantitative genetics and it is important to use appropriate animal models considering important factors. This study compares various factor effects for heritability and breeding values estimations on data collected on the Corriedale. Overall, the heritability estimates were the highest for birthweight (BW). Both the additive genetic variance and the heritability values were reduced upon adding more random effects. Year-effect as random reduced the heritability except for BW. The highest average accuracy for breeding values for birth, weaning, 6, 9, and 12-month-weights for were 0.656, 0.567, 0.519, 0.486, and 0.515. These were observed for models having sex or sex and parity as fixed effects. It is concluded that fixed and random factors have a significant impact on genetic-factors and breeding-value accuracies and should be considered during selection programs and make the selection program more effective.

Scavenger receptor B1 facilitates the endocytosis of Escherichia coli via TLR4 signaling in mammary gland infection

SCARB1 belongs to class B of Scavenger receptors (SRs) that are known to be involved in binding and endocytosis of various pathogens. SRs have emerging role in regulating innate immunity and host-pathogen interactions by acting in co-ordination with Toll-like receptors.Query Little is known about the function of SCARB1 in milk-derived mammary epithelial cells (MECs). This study reports the role of SCARB1 in infection and its potential association in TLR4 signaling on bacterial challenge in Goat mammary epithelial cells (GMECs). The novelty in the establishment of MEC culture lies in the method that aims to enhance the viability of the cells with intact characteristics upto a higher passage number. We represent MEC culture to be used as a potential infection model for deeper understanding of animal physiology especially around the mammary gland. On E.coli challenge the expression of SCARB1 was significant in induced GMECs at 6 h. Endoribonuclease-esiRNA based silencing of SCARB1 affects the expression of TLR4 and its pathways i.e. MyD88 and TRIF pathways on infection. Knockdown also affected the endocytosis of E.coli in GMECs demonstrating that E.coli uses SCARB1 function to gain entry in cells. Furthermore, we predict 3 unique protein structures of uncharacterized SCARB1 (Capra hircus) protein. Overall, we highlight SCARB1 as a main participant in host defence and its function in antibacterial advances to check mammary gland infections. Video Abstract.

Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry

Salmonella, one of the major infectious diseases in poultry, causes considerable economic losses in terms of mortality and morbidity, especially in countries that lack effective vaccination programs. Besides being resistant to diseases, indigenous chicken breeds are also a potential source of animal protein in developing countries. For understanding the disease resistance, an indigenous chicken line Kashmir faverolla, and commercial broiler were selected. RNA-seq was performed after challenging the chicken with Salmonella Typhimurium. Comparative differential expression results showed that following infection, a total of 3153 genes and 1787 genes were differentially expressed in the liver and spleen, respectively. The genes that were differentially expressed included interleukins, cytokines, NOS2, Avβ-defensins, toll-like receptors, and other immune-related gene families. Most of the genes and signaling pathways involved in the innate and adaptive immune responses against bacterial infection were significantly enriched in the Kashmir faverolla. Pathway analysis revealed that most of the enriched pathways were MAPK signaling pathway, NOD-like receptor signaling pathway, TLR signaling pathway, PPAR signaling pathway, endocytosis, etc. Surprisingly some immune-related genes like TLRs were upregulated in the susceptible chicken breed. On postmortem examination, the resistant birds showed small lesions in the liver compared to large necrotic lesions in susceptible birds. The pathological manifestations and RNA sequencing results suggest a balancing link between resistance and infection tolerance in Kashmir faverolla. Here we also developed an online Poultry Infection Database (https://skuastk.org/pif/index.html), the first publicly available gene expression resource for disease resistance in chickens. The available database not only shows the data for gene expression in chicken tissues but also provides quick search, visualization and download capacity.

Genome wide expression analysis of circular RNAs in mammary epithelial cells of cattle revealed difference in milk synthesis

Milk is an excellent source of nutrients for humans. Therefore, in order to enhance the quality and production of milk in cattle, it is interesting to examine the underlying mechanisms. A number of new investigations and research have found that, circRNA; a specific class of non-coding RNAs, is linked with the development of mammary gland and lactation. In the present study, genome wide identification and expression of the circRNAs in mammary epithelial cells of two distinct cattle breeds viz Jersey and Kashmiri at peak lactation was conducted. We reported 1554 and 1286 circRNA in Jersey and Kashmiri cattle, respectively, with 21 circRNAs being differentially expressed in the two breeds. The developmental genes of the established differentially expressed circRNAs were found to be largely enriched in antioxidant activity, progesterone, estradiol, lipid, growth hormone, and drug response. Certain pathways like MAPK, IP3K and immune response pathways were found significantly enriched in KEGG analysis. These results add to our understanding of the controlling mechanisms connected with the lactation process, as well as the function of circRNAs in bovine milk synthesis. Additionally, the comparative analysis of differentially expressed circRNAs showed significant conservation across different species.

Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation

Pashmina goats produce the world's finest and the most costly animal fiber (Pashmina) with an average fineness of 11-13 microns and have more evolved mechanisms than any known goat breed around the globe. Despite the repute of Pashmina goat for producing the finest and most sought-after animal fiber, meager information is available in the public domain about Pashmina genomics and transcriptomics. Here we present a 2.94 GB genome sequence from a male Changthangi white Pashmina goat. We generated 294.8 GB (>100X coverage) of the whole-genome sequence using the Illumina HiSeq 2500 sequencer. All cleaned reads were mapped to the goat reference genome (2,922,813,246 bp) which covers 97.84% of the genome. The Unaligned reads were used for de novo assembly resulting in a total of 882 MB non-reference contigs. De novo assembly analysis presented in this study provides important insight into the adaptation of Pashmina goats to cold stress and helps enhance our understanding of this complex phenomenon. A comparison of the Pashmina goat genome with a wild goat genome revealed a total of 2,823 high impact single nucleotide variations and small insertions and deletions, which may be associated with the evolution of Pashmina goats. The Pashmina goat genome sequence provided in this study may improve our understanding of complex traits found in Pashmina goats, such as annual fiber cycling, defense mechanism against hypoxic, survival secret in extremely cold conditions, and adaptation to a sparse diet. In addition, the genes identified from de novo assembly could be utilized in differentiating Pashmina fiber from other fibers to avoid falsification at marketing practices.

Comparative milk proteome analysis of Kashmiri and Jersey cattle identifies differential expression of key proteins involved in immune system regulation and milk quality

Background

Exploration of the bioactive components of bovine milk has gained global interest due to their potential applications in human nutrition and health promotion. Despite advances in proteomics profiling, limited studies have been carried out to fully characterize the bovine milk proteome. This study explored the milk proteome of Jersey and Kashmiri cattle at day 90 of lactation using high-resolution mass spectrometry based quantitative proteomics nano-scale LC-MS/Q-TOF technique. Data are available via ProteomeXchange with identifier PXD017412.

Results

Proteins from whey were fractionated by precipitation into high and low abundant proteins. A total of 81 high-abundant and 99 low-abundant proteins were significantly differentially expressed between Kashmiri and Jersey cattle, clearly differentiating the two breeds at the proteome level. Among the top differentiating proteins, the Kashmiri cattle milk proteome was characterised by increased concentrations of immune-related proteins (apelin, acid glycoprotein, CD14 antigen), neonatal developmental protein (probetacellulin), xenobiotic metabolising enzyme (flavin monooxygenase 3 (FMO3), GLYCAM1 and HSP90AA1 (chaperone) while the Jersey milk proteome presented higher concentrations of enzyme modulators (SERPINA1, RAC1, serine peptidase inhibitor) and hydrolases (LTF, LPL, CYM, PNLIPRP2). Pathway analysis in Kashmiri cattle revealed enrichment of key pathways involved in the regulation of mammary gland development like Wnt signalling pathway, EGF receptor signalling pathway and FGF signalling pathway while a pathway (T-cell activation pathway) associated with immune system regulation was significantly enriched in Jersey cattle. Most importantly, the high-abundant FMO3 enzyme with an observed 17-fold higher expression in Kashmiri cattle milk seems to be a characteristic feature of the breed. The presence of this (FMO3) bioactive peptide/enzyme in Kashmiri cattle could be economically advantageous for milk products from Kashmiri cattle.

Conclusion

In conclusion, this is the first study to provide insights not only into the milk proteome differences between Kashmiri and Jersey cattle but also provides potential directions for application of specific milk proteins from Kashmiri cattle in special milk preparations like infant formula.

Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat

The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to identify and characterize intricate interactions between genes that cause complex coat color variation in Changthangi Pashmina goats, producer of finest and costly commercial animal fiber. We systematically identified differentially expressed mRNAs and lncRNAs from black, brown and white Pashmina goat skin samples by using RNA-sequencing technique. A pairwise comparison of black, white and brown skin samples yielded 2479 significantly dysregulated genes (2422 mRNA and 57 lncRNAs). Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, developmental pigmentation, melanosome transport activities GO terms. Our analysis suggested the potential role of lncRNAs on color coding mRNAs in cis and trans configuration. We have also developed online data repository as a component of the study to provide a central location for data access, visualization and interpretation accessible through http://pcd.skuastk.org/.

Comparative transcriptome analysis of mammary epithelial cells at different stages of lactation reveals wide differences in gene expression and pathways regulating milk synthesis between Jersey and Kashmiri cattle

Jersey and Kashmiri cattle are important dairy breeds that contribute significantly to the total milk production of the Indian northern state of Jammu and Kashmir. The Kashmiri cattle germplasm has been extensively diluted through crossbreeding with Jersey cattle with the goal of enhancing its milk production ability. However, crossbred animals are prone to diseases resulting to unsustainable milk production. This study aimed to provide a comprehensive transcriptome profile of mammary gland epithelial cells at different stages of lactation and to find key differences in genes and pathways regulating milk traits between Jersey and Kashmiri cattle. Mammary epithelial cells (MEC) isolated from milk obtained from six lactating cows (three Jersey and three Kashmiri cattle) on day 15 (D15), D90 and D250 in milk, representing early, mid and late lactation, respectively were used. RNA isolated from MEC was subjected to next-generation RNA sequencing and bioinformatics processing. Casein and whey protein genes were found to be highly expressed throughout the lactation stages in both breeds. Largest differences in differentially expressed genes (DEG) were between D15 vs D90 (1,805 genes) in Kashmiri cattle and, D15 vs D250 (3,392 genes) in Jersey cattle. A total of 1,103, 1,356 and 1,397 genes were differentially expressed between Kashmiri and Jersey cattle on D15, D90 and D250, respectively. Antioxidant genes like RPLPO and RPS28 were highly expressed in Kashmiri cattle. Differentially expressed genes in both Kashmiri and Jersey were enriched for multicellular organismal process, receptor activity, catalytic activity, signal transducer activity, macromolecular complex and developmental process gene ontology terms. Whereas, biological regulation, endopeptidase activity and response to stimulus were enriched in Kashmiri cattle and, reproduction and immune system process were enriched in Jersey cattle. Most of the pathways responsible for regulation of milk production like JAK-STAT, p38 MAPK pathway, PI3 kinase pathway were enriched by DEG in Jersey cattle only. Although Kashmiri has poor milk production efficiency, the present study suggests possible physicochemical and antioxidant properties of Kashmiri cattle milk that needs to be further explored.

SSR based genetic diversity of pigmented and aromatic rice (Oryza sativa L.) genotypes of the western Himalayan region of India

A set of 24 of SSR markers were used to estimate the genetic diversity in 16 rice genotypes found in Western Himalayas of Kashmir and Himachal Pradesh, India. The level of polymorphism among the genotypes of rice was evaluated from the number of alleles and PIC value for each of the 24 SSR loci. A total of 68 alleles were detected across the 16 genotypes through the use of these 24 SSR markers The number of alleles per locus generated varied from 2 (RM 338, RM 452, RM 171) to 6 (RM 585, RM 249, RM 481, RM 162). The PIC values varied from 0.36 (RM 1) to 0.86 (RM 249) with an average of 0.62 per locus. Based on information generated, the genotypes got separated in six different clusters. Cluster 1 comprised of 4 genotypes viz; Zag 1, Zag 13, Pusa sugandh 3, and Zag 14, separated from each other at a similarity value of 0.40. Cluster second comprised of 3 landraces viz; Zag 2. Zag 4 and Zag10 separated from each other at a similarity value of 0.45. Cluster third comprised of 3 genotypes viz; Grey rice, Mushk budji and Kamad separated from each other at a similarity value of 0.46. Cluster fourth had 2 landraces viz; Kawa kreed and Loual anzul, and was not sub clustered. Fifth cluster had 3 genotypes viz; Zag 12, Purple rice and Jhelum separated from each other at a similarity value of 0.28. Cluster 6 comprised of a single popular variety i.e. Shalimar rice 1 with independent lineage.

Comparison of slow freezing and vitrification on ovine immature oocytes

BACKGROUND

Immature oocytes are more sensitive to cold injury than mature oocytes.

OBJECTIVE

The study was to evaluate the post thaw normal oocytes, cleavage and blastocyst rates of ovine cumulus oocyte complexes (COC's) using different cryoprotectants by slow freezing and Open pulled straw (OPS) vitrification.

METHODS

In five replicates, abattoir derived COC's were collected and distributed into three groups. In Experiment 1, COC's were cryopreserved by a slow freezing protocol using 10% concentration of ethylene glycol (EG), 10% dimethyl sulphoxide (DMSO) or 5% EG and 5% DMSO mixture. In Experiment 2 and 3 embryos were cryopreserved by OPS vitrification using either 33% or 40% (EG, DMSO or an equal mixture of EG and DMSO mixture. Normal oocytes post thaw were in vitro matured and parthenogenetically activated.

RESULTS

Although, there was no difference in the number of post thaw normal oocytes between the groups, cleavage and blastocyst rates were higher in 10% slow freezing group than any of the vitrified groups.

CONCLUSION

The study demonstrates better cryopreservation of ovine COC's by controlled slow freezing than OPS vitrification.

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.

Novel polymorphisms in the bovine beta-lactoglobulin gene and their effects on beta-lactoglobulin protein concentration in milk

The aim of our study was to detect new polymorphisms in the bovine beta-lactoglobulin (beta-LG) gene with significant effects on beta-LG protein concentration. Genomic DNA samples from 22 proven bulls were screened for polymorphisms in the coding and promoter regions of the beta-LG gene. In total, 50 polymorphisms were detected. Two single nucleotide polymorphisms (SNPs) (g.1772G>A and g.3054C>T) lead to amino acid changes and are the causal genetic polymorphisms of beta-LG protein variants A and B. Forty-two polymorphisms were in complete linkage disequilibrium (LD) with beta-LG protein variants A and B. Any of these 42 polymorphisms can be involved in the differential expression of the respective A and B alleles of the beta-LG gene. The eight polymorphisms not in complete LD with beta-LG protein variants A and B and the two polymorphisms causing the amino acid changes were genotyped in a set of 208 cows: 106 animals homozygous for beta-LG protein variant A and 102 animals homozygous for beta-LG protein variant B. Of these eight polymorphisms, six SNPs segregated only within the cows homozygous for beta-LG protein variant A and two SNPs segregated only within the cows homozygous for beta-LG protein variant B. One of the eight polymorphisms had a significant effect on beta-LG protein concentration. This SNP, g.-731G>A, segregated only within the 106 cows homozygous for beta-LG protein variant A. Within these cows, adjusted relative beta-LG protein concentration was reduced by 1.22% (w/w) in animals homozygous g.-731AA compared with animals homozygous g.-731GG.

Genetic variation within and among three Indian breeds of goat using heterologous microsatellite markers

The parameters of genetic variation, genetic distances and time of divergence in three Indian goat breeds were studied using 16 cattle microsatellite markers. The mean number of alleles and mean allele size (bp) per microsatellite marker in goats were 5.37 +/- 0.78 and 143.9 +/- 33.75 bp respectively. The average values of heterozygosity and polymorphism information content were 0.54 +/- 0.2 and 0.48 +/- 0.20, respectively. Five of the eight genetic distance methods were highly correlated, revealing a closer relationship between Jamnapari and Barbari goats. A phylogenetic tree constructed from inter-individual distances revealed that the individuals clustered according to the breed to which they belonged, and the Jamnapari and Barbari goats formed a cluster. The divergence times between Sirohi and Jamnapari, and Sirohi and Barbari were approximately 2000 years, while its value between Barbari and Jamnapari goats was approximately 1370 years.

DNA amplification assay for rapid detection of bovine tubercle bacilli in semen

Tubercle bacilli shed in the semen can be a potential hazard for unlimited number of cows through artificial insemination. We have evaluated the efficacy of a DNA amplification technique by polymerase chain reaction (PCR) for the detection of tubercle bacilli in fresh and frozen semen using spiked samples. The test was based on insertion sequence IS 1081 and could detect as low as 10-100 bacterial cells per ml of spiked semen. The specificity of the test was 100%. The method was applied to semen samples from known and suspected tuberculous bulls. Each of 20 semen samples (fresh and frozen diluted) from one of the three breeding bulls included in the study was found positive while the remaining 40 samples from the other two bulls failed to generate any detectable signal. PCR products were confirmed with Southern blot hybridization to an alpha 32P labeled-PCR product of the target sequence from the IS 1081 element of the Mycobacterium tuberculosis complex.