Deciphering genetic diversity in conserved cattle bulls to achieve sustainable development goals.

The primary objective of Sustainable Development Goal target 2.5 established by the United Nations is to ensure the preservation of genetic diversity in domesticated animals. The ICAR-National Bureau of Animal Genetic Resources in India has been actively engaged in the conservation of cattle and buffalo bull semen for long-term storage. This present study aimed to assess the genetic diversity present in the conserved cattle bull semen, which would aid in determining the most suitable strategy for future conservation management. A total of 192 bull semen belonging to 19 cattle breeds were selected to evaluate genetic diversity using 17 pairs of FAO recommended microsatellite primers. Total 267 alleles were detected across all the samples which indicates substantial amount of allelic variation is being maintained in conserved bulls. Further, all cattle bulls semen conserved showed higher observed heterozygosity than expected heterozygosity which indicates excess genetic diversity in all the populations. The FST, F IT and FIS value across the loci and population is 0.146 ± 0.009, 0.054 ± 0.038, and - 0.105 ± 0.035, respectively, which suggests lack of inbreeding in conserved cattle bull semen. This study has established genetic diversity in conserved cattle semen samples to achieve sustainable development goals. In addition, it provides compelling evidence that the current approach for conserving cattle bull semen is heading in the correct direction.

Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations.

The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as RYR2, SYNE2, BOLA, HF1, and the novel transcript ENSBGRG00000011079 were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters viz., effective population size, inbreeding, and observed and expected heterozygosity.

Comparative analysis of various methods for estimating expected genetic gain of production and reproduction traits in Murrah buffaloes.

The present study was conducted to assess the expected genetic gain for first lactation production and reproduction traits in Murrah buffaloes, in addition to optimization of progenies/sire. Data for period 1971-2020 were used from National Dairy Research Institute. Performance traits considered were 305 days milk yield (305DMY), average daily milk yield (ADMY), peak yield (PY), lactation length (LL), calving to first insemination interval (CFI), days open (DO), and calving interval (CI). Expected ΔG was estimated and compared by three different methods; method I involved heritability and selection differential; method II involved selection intensity, phenotypic standard deviation, and heritability; method III involved estimation of ΔG through four paths of inheritance. Initially, eleven progenies/sire were utilized for assessing expected ΔG by method III, and expected ΔG was found as 34.33, 0.12, 0.12 kg, 2.63, 1.51, 2.74, and 2.80 days/year for 305DMY, ADMY, PY, LL, CFI, DO, and CI, respectively. Additionally, there was a significant increase in expected ΔG on increasing progenies/sire from 6 to 11 while subsequent increase upto 16 had little effect on expected ΔG. These findings will be helpful in formulating breeding strategies worldwide in small buffalo herds to obtain sustainable ΔG in production and reproduction traits.

Comparative gene expression profile in circulating PBMCs of Bos indicus and crossbred cattle to understand disease tolerance mechanism.

The present investigation was performed to compare the global gene expression profile in peripheral blood mononuclear cells (PBMCs) of Bos indicus and crossbred (Bos taurus × B. indicus) cattle. Previously, several studies revealed the disease tolerance potential of B. indicus cattle but underlying genetic mechanism is still not fully explored. The PBMCs model was used for this investigation as it plays crucial role in the immune system regulation. Transcriptomic analysis revealed total 6767 significantly differentially expressed transcripts (fold change (absolute) >2.0, p < .05). In addition, 4149 transcripts were upregulated, 2618 transcripts were downregulated and fold change (absolute) of differentially expressed transcript varied from -223.32 to 213.63. Functional annotation analysis of differentially expressed genes confirmed their role in various molecular pathways viz. innate immune response, antigen processing and presentation, MHC protein complex, defense response to bacterium, regulation of immune response, positive regulation of JAK-STAT cascade, cytoskeletal protein binding, etc. Protein-protein interaction network analysis provided understanding of inter-relationship of immune genes with differentially expressed genes. In conclusion, this study could provide comprehensive information about the dysregulated genes and biological pathways in PBMCs which might be responsible for disease tolerance in B. indicus cattle.

Differentially expressed microRNAs in biochemically characterized FrieswalTM crossbred bull semen.

In addition to the transmission of paternal genome, spermatozoa also carry coding as well as noncoding microRNAs (miRNAs) into the female oocyte during the process of biological fertilization. Based on RNA deep sequencing, a total 28 number of differentially expressed miRNAs were cataloged in categorized FrieswalTM crossbred (Holstein Friesian X Sahiwal) bull semen on the basis of conception rate (CR) in field progeny testing program. Validation of selected miRNAs viz. bta-mir-182, bta-let-7b, bta-mir-34c and bta-mir-20a revealed that, superior bull semen having comparatively (p < .05) lower level of all the miRNAs in contrast to inferior bull semen. Additionally, it was illustrated that, bta-mir-20a and bta-mir-34c miRNAs are negatively (p < .01) correlated with seminal plasma catalase (CAT) activity and glutathione peroxidase (GPx) level. Interactome studies identified that bta-mir-140, bta-mir-342, bta-mir-1306 and bta-mir-217 can target few of the important solute carrier (SLC) proteins viz. SLC30A3, SLC39A9, SLC31A1 and SLC38A2, respectively. Interestingly, it was noticed that all the SLCs were significantly (p < .05) expressed at higher level in superior quality bull semen and they are negatively correlated (p < .01) with their corresponding miRNAs as mentioned. This study may reflect the role of miRNAs in regulating few of the candidate genes and thus may influence the bull semen quality traits.

Eco-evolutionary impact of ultraviolet radiation (UVR) exposure on microorganisms, with a special focus on our skin microbiome.

Sunlight is pivotal for our survival, and daily UV exposure has impacted the evolutionary course of all forms of life, from microorganisms to humans. Deciphering the role of UVR in regulating the microbial dynamics of environmental and host-associated microbes is crucial. UVR may be responsible for affecting skin pathology by influencing the skin microbiome, both qualitatively and quantitatively, as evident in low-dose narrow-band UVB phototherapy. Some findings have suggested that the skin microbiome has immunomodulatory roles when exposed to UVR; however, its involvement in UV screening or protection has yet to be fully explored. Furthermore, numerous skin disorders are associated not only with an altered skin microbiome but also with an altered gut microbiome. Hence, the skin-gut axis needs to be in physiological homeostasis and immunological harmony. The purpose of this review is to examine the impact of natural UVR on human immunomodulatory mechanisms and the associated cutaneous microbiome, with an emphasis on interactions among UVR, skin homeostasis, vitamin D, and the related skin-gut axis. With the 'nature as an inspiration' approach, ongoing research is trying to decipher photoprotective secrets in several microbial-based natural compounds to be used as sunscreens or other topical formulations. In addition, various probiotics have also been shown to have significant antioxidant, antiwrinkle, and antiaging effects that ameliorate UV-induced cellular and molecular damage, as highlighted in the review. These cosmetics, nutricosmetics, and probiotaceuticals will undoubtedly be next-generation solutions against photoaging and maintaining skin health.

Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak.

Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima's D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.

Bacteriophage therapeutics to confront multidrug-resistant Acinetobacter baumannii - a global health menace.

We have already entered the post-antibiotic era as the outbreaks of numerous multidrug-resistant strains in the community as well as hospital-acquired infections are ringing alarm bells in the health sector. Acinetobacter baumannii is one such pathogen that has been considered a worldwide threat as it acquires multidrug resistance. It is one of the most challenging hospital-acquired pathogens as World Health Organization has listed carbapenem-resistant A. baumannii as a critical priority pathogen with limited therapeutic options. There is an urgent need to develop novel strategies against such pathogens to tackle the global crisis. Bacteriophages (phages), especially the lytic ones have re-emerged as a potential therapeutic approach. This review encompasses vast majority of phages against A. baumannii strains with special references related to single phage or monophage therapy, use of phage cocktails, combination therapy with antibiotics, use of phage-derived enzymes like endolysins and depolymerases to combat the pathogen and explore their therapeutic aspects. The concurrent ecological as well as evolutionary interplay between the phages and host bacteria demands in depth-research and knowledge, so as to utilize the maximum potential of the bacteriophage therapy.

Microbial, environmental and anthropogenic factors influencing the indoor microbiome of the built environment.

A built environment is a human-made environment providing surroundings for human occupancy, activities, and settlement. It is supposed to safeguard humans from all undesirable and harmful pollutants; however, indoor concentrations of some pollutants are much greater than that of the outdoors. Bioaerosols infiltrate from the outdoors in addition to many indoor sources of bioaerosols including the use of various chemicals as well as activities like cooking, smoking, cleaning, or even normal movement. They are also associated with a number of serious health concerns. Various ecological factors associated with the generation, the persistence as well as the dispersal of these microbial components of indoor bioaerosols, are discussed in this review, that have not been considered all together till now. The factors like microbial taxa, environmental factors, and anthropogenic activities (human occupancy, activities, and impact of urbanization) are addressed in the review. Effects of both indoor environmental factors like architectural design, lighting, ventilation, temperature, humidity, indoor/outdoor ratio, particulate matter, indoor chemistry as well as outdoor environmental factors like geography, seasons, and meteorology on the microbial concentrations have been discussed. Efforts are underway to design selective pressures for microbes to create a healthy symbiotic built microbiome as the "right" indoor microbiome is a "healthy" indoor microbiome.

Comparison of Mental Health Status of Married and Unmarried Girls of Late Adolescent Age in an Urban Slum of Delhi.

INTRODUCTION: Late adolescence age (16-19 years) is organized around central task of achieving an identity. In India, age at marriage for girls has been legally declared as 18 years, but many girls are married much before this age. Early marriage for girls can have profound psychological and emotional impacts. AIMS AND OBJECTIVES: The aim was to study the impact of marriage on mental health of married girls of late adolescent age and to compare them with unmarried girls of the same age. MATERIALS AND METHODS: A comparison study was conducted among girls of late adolescent age in an urban slum of North East Delhi. Background information was collected through oral questionnaire method. The mental health of the study participants was assessed using validated tool "General Health Questionnaire-12" and "Symptom Checklist-90." RESULTS: Education and economic status of participants and parents were significantly associated with early marriage. Majority of married girls were found to be associated with risk of developing mental health disorders.

Maternal and severe anaemia in delivering women is associated with risk of preterm and low birth weight: A cross sectional study from Jharkhand, India.

BACKGROUND AND OBJECTIVES: Haemoglobin content is the well accepted indicator for anaemia assessment. The high prevalence of anaemia, maternal health care issues and adverse delivery outcome in Jharkhand, we investigated whether delivering women with anaemia would present a modifiable risk of preterm (PTB) and low birth weight (LBW). METHODS: A facility-based cross-sectional study involving pregnant women, with screening for pregnancy endpoints and haemoglobin assay, were conducted. Anaemia was classified according to World Health Organization's definition of anaemia in pregnancy. Confounding variables were adjusted in a logistic model. The adjusted odds ratios (AORs) with 95% confidence intervals (CIs) were used for analyzing the association among maternal anaemia, PTB and LBW. RESULTS: We observed a high prevalence of anaemia (78.45%) in delivering women, whereas high prevalence of preterm birth (34.75%) and LBW (32.81%) in delivering women overall. In the adjusted analysis, overall anaemia in pregnancy was strongly associated with preterm birth (OR, 3.42; 95% CI, 1.98-5.88; P ≤ .0001) as compared to LBW (OR, 1.12; 95% CI, 0.65-1.61; P = .0003). The risk of PTB and LBW were dependent on the stratification of the anaemia group, as the strongest association was observed in severe (OR, 4.86) followed by mild (OR, 3.66) and moderate (OR, 3.18) anaemia in PTB; whereas risk of LBW was found in severe (OR, 2.5) followed by moderate (OR, 1.11) and mild (OR, 0.57) anaemia. The risk of PTB and LBW across six pregnancy haemoglobin groups were compared, haemoglobin of 10-10.9 g/dl (OR, 1.25) and ≤ 8 g/dl (OR, 1.03) have shown association with PTB and LBW, respectively. However, high haemoglobin concentration was not associated with either PTB or LBW. CONCLUSIONS: Anaemia in delivering women was associated with an elevated risk of PTB and LBW and the risk increased with the severity of anaemia in pregnant women.

Risk assessment of low arsenic exposure using biomarkers of oxidative and genotoxic stress in a piscine model.

The high level exposure to arsenic induces marked oxidative and genotoxic stress. However, information on the potential of low level arsenic exposure in this context is still scanty. In the present study, the extent of oxidative stress and genetic toxicity induced by low arsenic exposure was explored in freshwater fish Channa punctatus. Fish were exposed to low levels of arsenic (10 and 50 µg L-1) as well as to its high level (500 µg L-1) using sodium arsenite in aquaria water for 14 consecutive days. The TBARS assay for lipid peroxidation exhibited the increased occurrence of oxidative damage in the erythrocytes of fish at both the lower and higher levels of arsenic exposure. The level of reduced glutathione was also elevated in all the three arsenic exposed groups of fish compared to control. In contrast, significant decline was observed in the levels of three major antioxidant enzymes namely, superoxide dismutase, catalase and glutathione peroxidase, upon exposure to higher as well as lower levels of arsenic. Significant increases in micronucleus induction were found in the erythrocytes of fish even at the low levels of arsenic exposure. The study further revealed the occurrence of DNA fragmentation in the erythrocytes of fish at low arsenic exposures as well. The low level exposure to arsenic (using sodium arsenite), therefore, appeared to be capable of inducing noticeable oxidative stress as well as potential genotoxic effect in Channa punctatus. Moreover, the ability of arsenic to induce oxidative stress invariably appeared correlated with its genotoxic potential.

Genome-Wide Analysis to Identify HLA Factors Potentially Associated With Severe Dengue.

The pathogenesis of dengue hemorrhagic fever (DHF), following dengue virus (DENV) infection, is a complex and poorly understood phenomenon. In view of the clinical need of identifying patients with higher likelihood of developing this severe outcome, we undertook a comparative genome-wide association analysis of epitope variants from sequences available in the ViPR database that have been reported to be differentially related to dengue fever and DHF. Having enumerated the incriminated epitope variants, we determined the corresponding HLA alleles in the context of which DENV infection could potentially precipitate DHF. Our analysis considered the development of DHF in three different perspectives: (a) as a consequence of primary DENV infection, (b) following secondary DENV infection with a heterologous serotype, (c) as a result of DENV infection following infection with related flaviviruses like Zika virus, Japanese Encephalitis virus, West Nile virus, etc. Subject to experimental validation, these viral and host markers would be valuable in triaging DENV-infected patients for closer supervision owing to the relatively higher risk of poor prognostic outcome and also for the judicious allocation of scarce institutional resources during large outbreaks.

Role of IL-1ß, IL-6 and TNF-α cytokines and TNF-α promoter variability in Plasmodium vivax infection during pregnancy in endemic population of Jharkhand, India.

BACKGROUND: The combinatorial effects of Plasmodium infection, perturbation of inflammatory responses and the dichotomic role of TNF promoter polymorphism has potential clinical and physiological relevance during pregnancy. OBJECTIVE AND METHODS: This coordinated orchestration instigated us to investigate the circulating level of inflammatory cytokines (IL-1ß, TNF-α and IL-6) employing ELISA in a stratified group of samples and the plausible genetic association of TNF-α -308 G/A using PCR-RFLP/sequencing during Plasmodium vivax infection in pregnancy. RESULTS: We observed significantly elevated concentrations of IL-1ß were observed, followed by IL-6 and TNF-α in women with malaria (WWM) and in malaria in pregnancy (MIP). Further, elevated IL-1ß, followed by TNF-α and IL-6 were detected in the non-infected pregnancy group. The differential dynamics of inflammatory cytokine concentration during each trimester of pregnancy with and without P. vivax infection were detected. For the first time, a high level of IL-6 was observed in the first trimester of MIP and high IL-1ß in healthy pregnancies. In the second trimester, however, we observed a high level of IL-1ß in the MIP group compared to a sustained high level of IL-1ß in the healthy pregnancy group. In the third trimester, high IL-1ß was sustained in the MIP group and healthy pregnancies acquired a high TNF-α level. The genotypic distribution for the TNF-α promoter -308 G/A position was observed to be nonsignificant and mildly associated during MIP (OR = 1.4) and in WWM (OR = 1.2). Moreover, based on genotypic distribution, we observed a well-correlated and significantly elevated TNF-α concentration in the mutant homozygote genotype (AA; p = 0.001) followed by heterozygotes (GA; p = 0.0001) and ancestral genotypes (GG; p = 0.0001) in both MIP and WWM subjects. CONCLUSION: The observation of elevated IL-1ß and IL-6 in MIP and TNF-α in WWM may be regarded as a prognostic inflammatory marker of infection and pregnancy. Most particularly, the TNF-α concentration and its polymorphic variability in the promoter region may indicate genetic susceptibility and mildly influence the risk for P. vivax infection during pregnancy and in women with malaria.

An effective method to identify various factors for denoising wrist pulse signal using wavelet denoising algorithm.

BACKGROUND: WPS is a non-invasive method to investigate human health. During signal acquisition, noises are also recorded along with WPS. OBJECTIVE: Clean WPS with high peak signal to noise ratio is a prerequisite before use in disease diagnosis. Wavelet Transform is a commonly used method in the filtration process. Apart from its extensive use, the appropriate factors for wavelet denoising algorithm is not yet clear in WPS application. The presented work gives an effective approach to select various factors for wavelet denoise algorithm. With the appropriate selection of wavelet and factors, it is possible to reduce noise in WPS. METHODS: In this work, all the factors of wavelet denoising are varied successively. Various evaluation parameters such as MSE, PSNR, PRD and Fit Coefficient are used to find out the performance of the wavelet denoised algorithm at every one step. RESULTS: The results obtained from computerized WPS illustrates that the presented approach can successfully select the mother wavelet and other factors for wavelet denoise algorithm. The selection of db9 as mother wavelet with sure threshold function and single rescaling function using UWT has been a better option for our database. CONCLUSION: The empirical results proves that the methodology discussed here could be effective in denoising WPS of any morphological pattern.

iNOS polymorphism modulates iNOS/NO expression via impaired antioxidant and ROS content in P. vivax and P. falciparum infection.

Nitric oxide (NO) has dicotomic influence on modulating host-parasite interplay, synchronizing physiological orchestrations and diagnostic potential; instigated us to investigate the plausible association and genetic regulation among NO level, components of oxidative stress, iNOS polymorphisms and risk of malaria. Here, we experimentally elucidate that iNOS promoter polymorphisms are associated with risk of malaria; employing mutation specific genotyping, functional interplay using western blot and RT-PCR, quantitative estimation of NO, total antioxidant content (TAC) and reactive oxygen species (ROS). Genotyping revealed significantly associated risk of P. vivax (adjusted OR = 1.92 and 1.72) and P. falciparum (adjusted OR = 1.68 and 1.75) infection with SNP at iNOS-954G/C and iNOS-1173C/T positions, respectively; though vivax showed higher risk of infection. Intriguingly, mutation and infection specific differential upregulation of iNOS expression/NO level was observed and found to be significantly associated with mutant genotypes. Moreover, P. vivax showed pronounced iNOS protein (2.4 fold) and mRNA (2.5 fold) expression relative to healthy subjects. Furthermore, TAC and ROS were significantly decreased in infection; and differentially decreased in mutant genotypes. Our findings endorse polymorphic regulation of iNOS expression, altered oxidant-antioxidant components and evidences of risk association as the hallmark of malaria pathogenesis. iNOS/NO may serve as potential diagnostic marker in assessing clinical malaria.

Genome wide host gene expression analysis in mice experimentally infected with Pasteurella multocida.

Pasteurella multocida causes acute septicemic and respiratory diseases, including haemorrhagic septicaemia, in cattle and buffalo with case fatality of 100%. In the present study, mice were infected with P. multocida (1.6 × 103 cfu, intraperitoneal) to evaluate host gene expression profile at early and late stages of infection using high throughput microarray transcriptome analyses. Several differentially expressed genes (DEGs) at both the time points were identified in P.multocida infected spleen, liver and lungs. Functional annotation of these DEGs showed enrichment of key pathways such as TLR, NF-κB, MAPK, TNF, JAK-STAT and NOD like receptor signaling pathways. Several DEGs overlapped across different KEGG pathways indicating a crosstalk between them. The predicted protein-protein interaction among these DEGs suggested, that the recognition of P. multocida LPS or outer membrane components by TLR4 and CD14, results in intracellular signaling via MyD88, IRAKs and/or TRAF6 leading to activation of NFκB and MAPK pathways and associated cytokines.

Global gene expression profile of peripheral blood mononuclear cells challenged with Theileria annulata in crossbred and indigenous cattle.

Bovine tropical theileriosis is an important haemoprotozoan disease associated with high rates of morbidity and mortality particularly in exotic and crossbred cattle. It is one of the major constraints of the livestock development programmes in India and Southeast Asia. Indigenous cattle (Bos indicus) are reported to be comparatively less affected than exotic and crossbred cattle. However, genetic basis of resistance to tropical theileriosis in indigenous cattle is not well documented. Recent studies incited an idea that differentially expressed genes in exotic and indigenous cattle play significant role in breed specific resistance to tropical theileriosis. The present study was designed to determine the global gene expression profile in peripheral blood mononuclear cells derived from indigenous (Tharparkar) and cross-bred cattle following in vitro infection of T. annulata (Parbhani strain). Two separate microarray experiments were carried out each for cross-bred and Tharparkar cattle. The cross-bred cattle showed 1082 differentially expressed genes (DEGs). Out of total DEGs, 597 genes were down-regulated and 485 were up-regulated. Their fold change varied from 2283.93 to -4816.02. Tharparkar cattle showed 875 differentially expressed genes including 451 down-regulated and 424 up-regulated. The fold change varied from 94.93 to -19.20. A subset of genes was validated by qRT-PCR and results were correlated well with microarray data indicating that microarray results provided an accurate report of transcript level. Functional annotation study of DEGs confirmed their involvement in various pathways including response to oxidative stress, immune system regulation, cell proliferation, cytoskeletal changes, kinases activity and apoptosis. Gene network analysis of these DEGs plays an important role to understand the interaction among genes. It is therefore, hypothesized that the different susceptibility to tropical theileriosis exhibited by indigenous and crossbred cattle is due to breed-specific differences in the dealing of infected cells with other immune cells, which ultimately influence the immune response responded against T. annulata infection.