Development of selection strategies for genetic improvement in production traits of Mecheri sheep based on a Bayesian multi trait evaluation.

The progression of genetic selection techniques to enhance farm animal performance traits is guided by the present level of genetic variation and maternal impact in each trait, as well as the genetic association between traits. This study was conducted on a population of Mecheri sheep maintained from 1980 to 2018 at Mecheri Sheep Research Station, Pottaneri, India, to determine variance and covariance components, as well as genetic parameters for various production performance traits. A total of 2616 lambs, produced by 1044 dams and 226 sires, were examined in the study and the production traits of Mecheri sheep assessed include birth weight (BW), weaning weight (WW), six-month weight (SMW), nine-month weight (NMW), and yearling weight (YW). The Bayesian approach, using the Gibbs sampler, analyzed six animal models with different combinations of additive direct and maternal additive effects. Direct genetics, maternal genetics, and residual effects models were the major contributors to total phenotypic variation for all the production traits studied. Direct heritability estimates of birth weight, WW, SMW, NMW, and YW were 0.25, 0.20, 0.12, 0.14, and 0.13, respectively. The maternal heritability estimated for BW, WW, SMW, NMW, and YW were 0.17, 0.10, 0.12, 0.14, and 0.14, respectively. The maternal effects had a major impact on the pre-weaning production traits. The genetic correlations estimated between different pairs of production traits studied ranged from 0.19 to 0.93. The body weight at birth exhibited a higher genetic relationship with weaning weight than post-weaning growth characteristics, and the genetic correlation between weaning weight and post-weaning attributes was moderate to high (0.52 to 0.72). Based on the additive genetic variance in weaning weight and the correlation estimates of weaning weight with post-weaning traits, weaning weight was proposed as a selection criterion for improving growth traits in Mecheri sheep.

In Vitro Characterization of chIFITMs of Aseel and Kadaknath Chicken Breeds against Newcastle Disease Virus Infection.

Newcastle disease (ND) is highly contagious and usually causes severe illness that affects Aves all over the world, including domestic poultry. Depending on the virus's virulence, it can impact the nervous, respiratory, and digestive systems and cause up to 100% mortality. The chIFITM genes are activated in response to viral infection. The current study was conducted to quantify the mRNA of chIFITM genes in vitro in response to ND viral infection. It also examined its ability to inhibit ND virus replication in chicken embryo fibroblast (CEF) cells of the Aseel and Kadaknath breeds. Results from the study showed that the expression of all chIFITM genes was significantly upregulated throughout the period in the infected CEF cells of both breeds compared to uninfected CEF cells. In CEF cells of the Kadaknath breed, elevated levels of expression of the chIFITM3 gene dramatically reduced ND viral growth, and the viral load was 60% lower than in CEF cells of the Aseel breed. The expression level of the chIFITMs in Kadaknath ranged from 2.39 to 11.68 log2 folds higher than that of control CEFs and was consistently (p < 0.01) higher than Aseel CEFs. Similar to this, theIFN-γ gene expresses strongly quickly and peaks at 13.9 log2 fold at 48 hpi. Based on these cellular experiments, the Kadaknath breed exhibits the potential for greater disease tolerance than Aseel. However, to gain a comprehensive understanding of disease resistance mechanisms in chickens, further research involving in vivo investigations is crucial.

Genetic Parameters of Growth Traits and Quantitative Genetic Metrics for Selection and Conservation of Mecheri Sheep of Tamil Nadu.

Determining the genetic and non-genetic sources of variation in a breed is vital for the formulation of strategies for its conservation and improvement. The present study was aimed at estimating the (co)variance components and genetic parameters of Mecheri sheep by fitting six different animal models in the restricted maximum likelihood method, with a preliminary investigation on the performance of animals for non-genetic sources of variation. A total of 2616 lambs were studied, and varying levels of significance were found for the effects of period, season, parity of dam, and birth type on different body-weight traits. Direct heritability estimates derived from the best animal model for body weight at birth, three months, six months, nine months, and twelve months were 0.21, 0.24, 0.10, 0.15, and 0.09, respectively, and the maternal heritability of the corresponding traits was 0.12, 0.05, 0.04, 0.04, and 0.04, respectively. The genetic correlations between the body-weight traits were all positive and moderate-to-strong, except for the correlation between birth weight and the other body-weight traits. The significance of non-genetic factors studied in this work demanded a correction to improve the accuracy of the direct selection of lambs for body-weight traits. The estimated genetic parameters identified the weaning weight as a selection criterion for the improvement in body weight of Mecheri lambs at different ages. Inbred individuals accounted for approximately 13% of the total population in the Mecheri sheep population studied. There were 877 founders in the population, and the actual effective population size was 128.48. The population's mean generation interval was 3.26. The mean inbreeding values ranged from 0.005 to 0.010 across generations. The population's average relatedness ranged from 0.001 to 0.014 across generations. Individual inbreeding was found to be 0.45 per cent for the entire population and 3.4 per cent for the inbred population.

Exposure to high thermal conditions for a long time induces apoptosis and decreases total RNA concentration in peripheral blood mononuclear cells among Indian Zebu-Jersey crossbreds.

Background and Aim: Global warming has grave consequences on livestock production systems and profound negative effects on animal production. This study aimed to carry out an in vitro thermal stress stimulation (TSS) of bovine peripheral blood mononuclear cells (PBMCs) using different thermal assault conditions (TACs), including normal to extreme temperatures and varying durations of thermal exposure (DTE) to understand how PBMCs of Indian Zebu-Jersey crossbreds respond to various levels and durations of heat shock. Materials and Methods: Ten milliliters of blood were collected from 70 Indian Zebu-Jersey crossbreds under aseptic conditions and were sampled for isolating PBMCs. Peripheral blood mononuclear cells were divided into seven groups, each comprising 10 PBMC samples isolated from 10 different animals. Aliquots of 500 µL of PBMCs were stressed by exposure to different TACs (37, 40, and 45°C) for DTEs of 3 or 6 h. Subsequently, the cells were harvested. The control unstressed samples (500 µL aliquots of PBMCs) were exposed to no TAC (0°C) and zero DTE (0 h). Total RNA from all the treatment groups of PBMCs were isolated and quantitated. Results: We found a very strong association between TACs and RNA levels. In addition, PBMCs viability was negatively affected by heat shock. This led to an exponential reduction in PBMC count as TACs toughened. Only 3.59 × 105 ± 0.34 cells/mL were viable after exposure to 45°C for a 6 h DTE. This cell viability was lower than that measured in controls subjected to no stress and zero time DTE (2.56 × 107 ± 0.22 cells/mL). We also observed a reduction in the concentration of RNA isolated from thermally stressed PBMCs. Conclusion: In vitro TSS of PBMCs provided biological information on the response of cellular systems to heat shock after exposure to TACs. This will help to mitigate and manage the effects of thermal stress in bovine species. The association between the reduction in PBMC count after in vitro TSS and the expression of heat shock protein 70 gene will be investigated in the future to further understand how Indian Zebu-Jersey crossbreds respond to in vitro thermal conditions. This will be used to determine the in vivo response of Indian Jersey crossbreds to different environmental thermal conditions and will further enable the in vivo understanding of thermotolerance potentials of bovine species for better adaptation, survival, and production performance.

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin.

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

Solid-State Phase Transformation and Self-Assembly of Amorphous Nanoparticles into Higher-Order Mineral Structures.

Materials science has been informed by nonclassical pathways to crystallization, based on biological processes, about the fabrication of damage-tolerant composite materials. Various biomineralizing taxa, such as stony corals, deposit metastable, magnesium-rich, amorphous calcium carbonate nanoparticles that further assemble and transform into higher-order mineral structures. Here, we examine a similar process in abiogenic conditions using synthetic, amorphous calcium magnesium carbonate nanoparticles. Applying a combination of high-resolution imaging and in situ solid-state nuclear magnetic resonance spectroscopy, we reveal the underlying mechanism of the solid-state phase transformation of these amorphous nanoparticles into crystals under aqueous conditions. These amorphous nanoparticles are covered by a hydration shell of bound water molecules. Fast chemical exchanges occur: the hydrogens present within the nanoparticles exchange with the hydrogens from the surface-bound H2O molecules which, in turn, exchange with the hydrogens of the free H2O molecule of the surrounding aqueous medium. This cascade of chemical exchanges is associated with an enhanced mobility of the ions/molecules that compose the nanoparticles which, in turn, allow for their rearrangement into crystalline domains via solid-state transformation. Concurrently, the starting amorphous nanoparticles aggregate and form ordered mineral structures through crystal growth by particle attachment. Sphere-like aggregates and spindle-shaped structures were, respectively, formed from relatively high or low weights per volume of the same starting amorphous nanoparticles. These results offer promising prospects for exerting control over such a nonclassical pathway to crystallization to design mineral structures that could not be achieved through classical ion-by-ion growth.

Single-nucleotide polymorphism-based genetic diversity analysis of the Kilakarsal and Vembur sheep breeds.

AIM: The present study was thus undertaken to analyze the genetic diversity of Kilakarsal and Vembur sheep breeds using single-nucleotide polymorphism (SNP) markers within Toll-like receptor (TLR) 3, 5, 6, 9, and 10 genes. MATERIALS AND METHODS: Competitive allele-specific polymerase chain reaction (PCR)-based end-point genotyping was performed using real-time PCR to type the SNPs. Allele discrimination module implemented in real-time PCR was utilized to call the genotypes based on fluorescence intensity recorded for each of the two alleles. Basic diversity indices, namely, gene frequencies, observed heterozygosity, expected heterozygosity, and inbreeding coefficient (FIS), and testing for Hardy-Weinberg equilibrium (HWE) were estimated using package for elementary analysis of SNP data software program. RESULTS: Of the 25 SNPs, 22 were found to be polymorphic, whereas two SNPs, namely, TLR3_1081_AC and TLR9_2036_CT, were monomorphic in both Kilakarsal and Vembur sheep populations. The SNP TLR10_1180_AG was monomorphic in Kilakarsal but polymorphic in Vembur sheep. The observed heterozygosities were estimated as 0.289 and 0.309 in Kilakarsal and Vembur sheep, respectively, whereas the expected heterozygosity values were 0.305 and 0.309 in the two breeds, respectively. The overall mean FIS was 0.107 ranging from -0.005 to 0.241 in Kilakarsal sheep and -0.047 ranging from -0.005 to 0.255 in Vembur sheep. In Kilakarsal sheep, the test for HWE revealed TLR9_1308_GC SNP locus with significant deviation (p<0.05) due to heterozygosity deficit. In Vembur sheep, TLR10_82_CT and TLR10_292_CG loci showed significant deviation (p<0.05) due to heterozygosity excess. Other SNP loci did not deviate from HWE (p>0.05) revealing that the population was in HWE proportions. CONCLUSIONS: The SNP markers within five TLR genes (TLR3, TLR5, TLR6, TLR9, and TLR10) utilized for genotyping in this study were highly polymorphic in Kilakarsal and Vembur breeds of sheep. This study on the genetic diversity analysis of the Kilakarsal and Vembur sheep breeds revealed considerable genetic variation within the breeds and it can be utilized to improve desirable traits.

Biological control of aragonite formation in stony corals.

Little is known about how stony corals build their calcareous skeletons. There are two prevailing hypotheses: that it is a physicochemically dominated process and that it is a biologically mediated one. Using a combination of ultrahigh-resolution three-dimensional imaging and two-dimensional solid-state nuclear magnetic resonance (NMR) spectroscopy, we show that mineral deposition is biologically driven. Randomly arranged, amorphous nanoparticles are initially deposited in microenvironments enriched in organic material; they then aggregate and form ordered aragonitic structures through crystal growth by particle attachment. Our NMR results are consistent with heterogeneous nucleation of the solid mineral phase driven by coral acid-rich proteins. Such a mechanism suggests that stony corals may be able to sustain calcification even under lower pH conditions that do not favor the inorganic precipitation of aragonite.

IDEAL-A fast single scan method for X pulse width calibration.

In line with the recent development of the rapid single scan technique to calibrate proton flip angle, a new method that allows calibration of X-nucleus pulse width in a single scan is presented. The method involves observation of the anti-phase coherence of a proton coupled to a hetero-nuclear X-spin with nutation pulses applied at the X-spin resonance frequency in a gated decoupling experiment. The X-spin nutation causes the well-known illusions of decoupling, enabling estimation of rf amplitude level and the method is, thus, dubbed as IDEAL.

Spectral unraveling by space-selective Hadamard spectroscopy.

Spectral unraveling by space-selective Hadamard spectroscopy (SUSHY) enables recording of NMR spectra of multiple samples loaded in multiple sample tubes in a modified spinner turbine and a regular 5mm liquids NMR probe equipped with a tri-axis pulsed field gradient coil. The individual spectrum from each sample is extracted by adding and subtracting data that are simultaneously obtained from all the tubes based on the principles of spatially resolved Hadamard spectroscopy. The well-known Hadamard spectroscopy has been applied for spatial selection and the method utilizes standard configuration of NMR instrument hardware. The SUSHY method can be easily incorporated in multi-dimensional multi-tube NMR experiments. This method combines the excitation multiplexing, natural advantage of FTNMR, and sample multiplexing and offers high-throughput by reducing the total experimental time by up to a factor of four in a 4-tube mode.

NMR analyses of the activation of the Arp2/3 complex by neuronal Wiskott-Aldrich syndrome protein.

The VCA domain of the neuronal Wiskott-Aldrich syndrome protein (N-WASP) is a potent activator of the Arp2/3 complex, a 240 kDa heteroheptameric actin-nucleating assembly. We used site-directed spin labeling of N-WASP peptides in conjunction with methyl-TROSY spectra of the intact, selectively labeled Arp2/3 complex to identify regions of the VCA that are proximal to the ARPC3 subunit of the assembly. We also cross-linked CA peptides to the Arp3, Arp2, ARPC1, and ARPC3 subunits. The combined data suggest that the extreme C-terminus of the A region and the C-terminus of the C region of N-WASP are proximal to ARPC3. These results have implications for the mechanism of Arp2/3 complex activation by VCA peptides. This study also demonstrates the utility of NMR spectroscopy for studying ligand binding events in large, asymmetric, macromolecular assemblies.