Whole-transcriptome sequencing analysis to identify key circRNAs, miRNAs, and mRNAs in the development of yak testes.

BACKGROUND: The Testis is an important reproductive organ in male mammals and the site for spermatogenesis, androgen synthesis, and secretion. Non-coding RNAs (ncRNAs) play an important regulatory role in various biological processes. However, the regulatory role of ncRNAs in the development of yak testes and spermatogenesis remains largely unclear. RESULT: In this study, we compared the expression profiles of circular RNAs (circRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) in yak testicular tissue samples collected at 6 months (Y6M), 18 months (Y18M), and 4 years (Y4Y). Using RNA sequencing (RNA-Seq), we observed a significant difference in the expression patterns of ncRNAs in the samples collected at different testicular development stages. Twenty-two differentially expressed (DE) circRNAs, 69 DE miRNAs, and 64 DE mRNAs were detected in Y6M, Y18M, and Y4Y testicular samples, respectively. The results of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the source genes of DE circRNAs, predicted target genes of DE miRNAs, and DE mRNAs were specifically associated with signaling pathways and GO terms that were related to sperm synthesis, sperm vitality, and testicular development, such as cell cycle, Wnt signaling pathway, MAPK signaling pathway, GnRH signaling pathway, and spermatogenesis. The analysis of the circRNA-miRNA-mRNA network revealed that some DE ncRNAs, including miR-574, miR-449a, CDC42, and CYP11A1, among others, may be involved in testicular spermatogenesis. Concurrently, various circRNA-miRNA interaction pairs were observed. CONCLUSION: Our findings provide a database of circRNAs, miRNAs, and mRNAs expression profiles in testicular tissue of yaks at different developmental stages and a detailed understanding of the regulatory network of ncRNAs in yak testicular development and provide data that can help elucidate the molecular mechanisms underlying yak testicular development.

Dynamic changes in cellular atlases and communication patterns within yak ovaries across diverse reproductive states unveiled by single-cell analysis.

Yaks (Bos grunniens) exhibit exceptional adaptation to the challenging high-altitude environment of the Qinghai-Tibetan plateau, making them the sole bovine species capable of thriving in such exreme conditions. Investigating the cellular and molecular characteristics of yak ovaries across different reproductive states is crucial for gaining insight into their ovarian functions. Herein, the cellular atlases of yak ovaries in different reproductive states were depicted by single-cell RNA-sequencing (scRNA-seq). The cellular atlases of the ovaries were established by identifying specific gene expression patterns of various cell types, including granulosa cells, theca cells, stromal cells, smooth muscle cells, endothelial cells, glial cell, macrophages, natural killer cells, and proliferating cells. The cellular compositions of the ovaries vary among different reproductive states. Furthermore, the granulosa cells comprise six cell subtypes, while theca cells consist of eight cell subtypes. The granulosa cells and theca cells exhibit distinct biological functions throughout different reproductive states. The two cell types were aligned along their respective pseudotime trajectories. Moreover, a cell-to-cell communication network was constructed among distinct cell types within the ovary, spanning the three reproductive states. Notably, during the estrus period, the granulosa cells demonstrated more prominent interactions with other cell types compared to the remaining reproductive states.

Study of volatile flavor derived from lipids degeneration in yak Milk based on Semiquantitative Lipidomics.

Milk lipids greatly affect the volatile flavor of milk, and the relationship between lipids and volatile flavor in yak milk was explored in this study. The volatile flavor compounds (VFCs), lipids profile, fatty acids in yak ordinary milk and colostrum were detected with HP/SPME-GC-MS, the semiquantitative lipidomics based on LC-MS/MS, GC-MS, respectively. The VFCs differences in yak milk were closely related to 1-((1 s,3ar,4r,7 s,7as)-4-hydroxy-7-isopropyl-4-methyloctahloctahydro-1h-inden-1-Yl)-ethanone,2,6,6-trimethyl-2,4-cycloheptadien-1-one, pentanal, 2-phenylethyl propionate, octanoic acid methyl ester, diphosphoric acid diisooctyl ester, (Z)-3,4,4-trimethyl-5-oxo-2-hexenoic acid and acetic acid. The volatile flavor in yak milk was well correlated with milk lipids, and TG(4:0_12:3_18:1), TG(6:0_8:0_18:1), TG(4:0_12:3_18:1), TG(12:0_18:2_18:3) and TG(16:0e_18:1_22:5) were the crucial lipid molecules affecting volatile flavor. The degeneration of above lipids by hydrolysis produced some fatty acids and alcohol, then these compounds were further derived into other VFCs especially above crucial 8 molecules. This study provided a theoretical basis for improving the volatile flavor by controlling lipids in yak milk.

The Combined Analysis of GC-IMS and GC-MS Reveals the Differences in Volatile Flavor Compounds between Yak and Cattle-Yak Meat.

In order to investigate the composition and differences in volatile organic compounds (VOCs) in yak and cattle-yak meat and determine the key metabolites and metabolic pathways related to flavor formation. In this study, the VOCs and non-volatile metabolites in Longissimus dorsi muscle of two groups of samples were detected and analyzed by gas chromatography-ion migration spectrometry (GC-IMS) and gas chromatography-mass spectrometry (GC-MS). The results showed that 31 VOCs were identified by GC-IMS, including 5 alcohols, 5 ketones, 5 esters, 3 aldehydes, 2 furans, 2 hydrocarbons, 1 amine, 1 acid, 1 thiazole, 1 pyrazine, and 5 others. Most of them were alcohols, ketones, esters, and aldehydes. A total of 75 non-volatile metabolites with significant differences were obtained by GC-MS screening, among which amino acid contents such as serine, glycine, phenylalanine, and aspartic acid were significantly up-regulated in cattle-yak, and glutamic acid and tyrosine were significantly up-regulated in yak. The non-volatile differential metabolites in the two groups were significantly enriched in the metabolic pathways of arginine biosynthesis and oxidative phosphorylation. By combining GC-IMS and GC-MS, this study comprehensively and intuitively reflected the differences in VOCs between yak and cattle-yak meat, and clarified the metabolomic reasons for the differences in VOCs, so as to provide a theoretical basis for meat quality improvement.

Potential COVID-19 remedies from repurposed drugs and herbal small RNAs.

To date, SARS-CoV-2 has caused millions of deaths, but the choice of treatment is limited. We previously established a platform for identifying Food and Drug Administration (FDA)-approved repurposed drugs for avian influenza A virus infections that could be used for coronavirus disease 2019 (COVID-19) treatment. In this study, we analyzed blood samples from two cohorts of 63 COVID-19 patients, including 19 patients with severe disease. Among the 39 FDA-approved drugs we identified for COVID-19 therapy in both cohorts, 23 drugs were confirmed by literature mining data, including 14 drugs already under COVID-19 clinical trials and 9 drugs reported for COVID-19 treatments, suggesting the remaining 16 FDA-approved drugs may be candidates for COVID-19 therapy. Additionally, we previously reported that herbal small RNAs (sRNAs) could be effective components in traditional Chinese medicine (TCM) for treating COVID-19. Based on the abundance of sRNAs, we screened the 245 TCMs in the Bencao (herbal) sRNA Atlas that we had previously established, and we found that the top 12 TCMs for COVID-19 treatment was consistent across both cohorts. We validated the efficiency of the top 30 sRNAs from each of the top 3 TCMs for COVID-19 treatment in poly(I:C)-stimulated human non-small cell lung cancer cells (A549 cells). In conclusion, our study recommends potential COVID-19 remedies using FDA-approved repurposed drugs and herbal sRNAs from TCMs.

Comprehensive analysis of differentially expressed mRNAs, circRNAs, and miRNAs and their ceRNA network in the testis of cattle-yak, yak, and cattle.

Cattle-yak is a hybrid offspring resulting from the crossbreeding of yak and cattle, and it exhibits substantial heterosis in production performance. However, male sterility in cattle-yak remains a concern. Reports suggest that noncoding RNAs are involved in the regulation of spermatogenesis. Therefore, in this study, we comprehensively compared testicular transcription profiles among cattle, yak, and cattle-yak. Numerous differentially expressed genes (DEGs), differentially expressed circRNAs (DECs), and differentially expressed miRNAs (DEMs) were identified in the intersection of two comparison groups, namely cattle versus cattle-yak and yak versus cattle-yak, with the number of DEGs, DECs, and DEMs being 4968, 360, and 59, respectively. The DEGs in cattle-yaks, cattle, and yaks were mainly associated with spermatogenesis, male gamete generation, and sexual reproduction. Concurrently, GO and KEGG analyses indicated that DEC host genes and DEM source genes were involved in the regulation of spermatogenesis. The construction of a potential competing endogenous RNA network revealed that some differentially expressed noncoding RNAs may be involved in regulating the expression of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, and miR-15b, as well as previously unreported miR-6123 and miR-1306, along with various miRNA-circRNA interaction pairs. This study serves as a valuable reference for further investigations into the mechanisms underlying male sterility in cattle-yaks.

Chinese herbal medicine Shufeng Jiedu capsule for mild to moderate COVID-19: a multicenter, randomized, double-blind, placebo-controlled phase II trial.

Background: The COVID-19 pandemic has had a profound global impact, although the majority of recently infected cases have presented with mild to moderate symptoms. Previous clinical studies have demonstrated that Shufeng Jiedu (SFJD) capsule, a Chinese herbal patent medicine, effectively alleviates symptoms associated with the common cold, H1N1 influenza, and COVID-19. This study aimed to assess the efficacy and safety of SFJD capsules in managing symptoms of mild to moderate COVID-19 infection. Methods: A randomized, double-blind, placebo-controlled trial was conducted from May to December 2022 at two hospitals in China. Mild and moderate COVID-19-infected patients presenting respiratory symptoms within 3 days from onset were randomly assigned to either the SFJD or placebo groups in a 1:1 ratio. Individuals received SFJD capsules or a placebo three times daily for five consecutive days. Participants were followed up for more than 14 days after their RT-PCR nucleoid acid test for SARS-CoV-2 turned negative. The primary outcome measure was time to alleviate COVID-19 symptoms from baseline until the end of follow-up. Results: A total of 478 participants were screened; ultimately, 407 completed the trial after randomization (SFJD, n = 203; placebo, n = 204). No statistically significant difference in baseline parameters was observed between the two groups. The median time to alleviate all symptoms was 7 days in the SFJD group compared to 8 days in the placebo group (p = 0.037). Notably, the SFJD group significantly attenuated fever/chills (p = 0.04) and headache (p = 0.016) compared to the placebo group. Furthermore, the median time taken to reach normal body temperature within 24 h was reduced by 7 hours in the SFJD group compared to the placebo group (p = 0.033). No deaths or instances of serious or critical conditions occurred during this trial period; moreover, no serious adverse events were reported. Conclusion: The trial was conducted in a unique controlled hospital setting, and the 5-day treatment with SFJD capsules resulted in a 1-day reduction in overall symptoms, particularly headache and fever/chills, among COVID-19-infected participants with mild or moderate symptoms. Compared to placebo, SFJD capsules were found to be safe with fewer side effects. SFJD capsules could potentially serve as an effective treatment for alleviating mild to moderate symptoms of COVID-19. Clinical Trial Registration: https://www.isrctn.com/, identifier ISRCTN14236594.

Complete characterization of the yak testicular development using accurate full-length transcriptome sequencing.

Alternative splicing is a prevalent phenomenon in testicular tissues. Due to the low assembly accuracy of short-read RNA sequencing technology in analyzing post-transcriptional regulatory events, full-length (FL) transcript sequencing is highly demanded to accurately determine FL splicing variants. In this study, we performed FL transcriptome sequencing of testicular tissues from 0.5, 1.5, 2.5, and 4-year-old yaks and 4-year-old cattle-yaks using Oxford Nanopore Technologies. The obtained sequencing data were predicted to have 47,185 open reading frames (ORFs), including 26,630 complete ORFs, detected 7645 fusion transcripts, 15,355 alternative splicing events, 25,798 simple sequence repeats, 7628 transcription factors, and 35,503 long non-coding RNAs. A total of 40,038 novel transcripts were obtained from the sequencing data, and the proportion was almost close to the number of known transcripts identified. Structural analysis and functional annotation of these novel transcripts resulted in the successful annotation of 9568 transcripts, with the highest and lowest annotation numbers in the Nr and KOG databases, respectively. Weighted gene co-expression network analysis revealed the key regulatory pathways and hub genes at various stages of yak testicular development. Our findings enhance our comprehension of transcriptome complexity, contribute to genome annotation refinement, and provide foundational data for further investigations into male sterility in cattle-yaks.

Effect of second booster vaccination on clinical outcomes of Omicron-variant breakthrough infection: A propensity score matching cohort study.

Objective: To further explore the effect of vaccination regimen and frequency on clinical outcomes of breakthrough infections caused by the Omicron variant, as well as the durability of vaccine effectiveness. Methods: A retrospective, propensity score matching, real-world cohort study was conducted. Vaccination frequency was categorized into regular vaccination, first booster, and second booster. Results: A total of 7428 cases were included, with 3910 (53 %) being male. The median age was 39 years. BA.2 than BA.5/5.2 infection presented with more pulmonary symptoms and fewer influenza-like symptoms. Among the 3516 cases of BA.5/5.2 breakthrough infections, patients who received the second booster than the first booster or regular vaccination had higher first IgM and IgG titers and first cycle thredhold values for N gene on admission, a lower percentage of fever, lower peak body temperatures, and a higher percentage of asymptomatic cases. Patients who received the first booster vaccinated with homologous mRNA or heterologous inactivated plus mRNA vaccines than homologous inactivated vaccines had higher first IgM and IgG titers, a higher percentage of asymptomatic cases, and a lower percentage of fever. Moreover, significantly different first IgG titers were observed among patients receiving the second booster vaccinated with any of the three regimens. There was no statistical difference between booster regimens of homologous mRNA vaccines and heterologous inactivated plus mRNA vaccines. Patients in Month 7- than Month 0-6 after the first booster had lower first IgM and IgG titers and first cycle thredhold values, a lower percentage of asymptomatic cases, and a higher percentage of fever; and a higher percentage of pneumonia after the second booster. Conclusions: Repeated booster vaccinations every six months, with priority given to heterologous mRNA vaccine booster regimens in countries previously primarily using inactivated vaccines, may provide protection for adult patients with Omicron-variant breakthrough infections and improve clinical outcomes.

Do microbial-gut-muscle mediated by SCFAs, microbial-gut-brain axis mediated by insulin simultaneously regulate yak IMF deposition?

Ruminant rumen plays an important role in the digestibility of cellulose, hemicellulose, starch and fat. In this study, the yaks under graze and stall feeding were chosen as the models of different rumen bacteria and intramuscular fat (IMF). The characteristics of IMF deposition, serum indexes in yaks were detected; the bacteria, metabolites in rumen was explored by 16S rRNA sequencing technology, untargeted metabolomics based on liquid chromatography-mass spectrometer and gas chromatography, respectively; the transcriptome of longissimus thoracis was identified by RNA-Sequencing analysis. Based on above results, a hypothesis that yak IMF deposition is regulated by the combined action of microbiome-gut-brain and muscle axis was proposed. The short-chain fatty acids (SCFAs) and neurotransmitters precursors like acetylcholine produced in yak rumen promoted insulin secretion via central nervous system. These insulin resulted in the high expression of SREBF1 gene by gut-brain axis; SCFAs can directly arrive to muscular tissue via blood circulation system, then activated the expression of PPARγ gene by gut-muscle axis. The expression of lipogenesis gene SCD, FABP3, CPT1, FASN and ACC2 was accordingly up-regulated. This study firstly introduce the theory of microbiome-gut-brain/muscle axis into the study of ruminant, and comprehensively expounded the regulatory mechanism of yak IMF deposition.

Analysis of multiple organ function damage in patients with severe COVID-19 pneumonia.

Background: This study aims to analyze the changes and significance of organ function indices in patients with severe Coronavirus Disease 2019 (COVID-19) pneumonia for prediction of major organ damages and guiding treatment schemes. Methods: 63 patients with severe COVID-19 pneumonia were selected as the severe group and 73 patients with mild syndromes were selected as the mild group. SAS9.4 software was used for statistical analysis of the data. Results: Levels of ALT, AST, cTnI, Cr, PT, APTT and Ddimer of the severe group were significantly higher while PLT was lower than those of the mild group. The data of all quantitative variables were converted into categorical variables. Significantly higher levels of AST, ALB, D-dimer and higher proportion of bilateral lung involvement were observed from the severe group comparing to those in the mild group, while the difference in the other indices between the two groups was insignificant in statistical perspective. Conclusions: There are significant differences in the levels of multiple organ function indices between the severe group and the mild group of patients with COVID-19 pneumonia infection. Through examining the relevant indices, conditions of patients' multiple organ function damage could be predicted and used as guidance of treatment.

Transcriptome Studies Reveal the N6-Methyladenosine Differences in Testis of Yaks at Juvenile and Sexual Maturity Stages.

Studying the mechanism of spermatogenesis is key to exploring the reproductive characteristics of male yaks. Although N6-methyladenosine (m6A) RNA modification has been reported to regulate spermatogenesis and reproductive function in mammals, the molecular mechanism of m6A in yak testis development and spermatogenesis remains largely unknown. Therefore, we collected testicular tissue from juvenile and adult yaks and found that the m6A level significantly increased after sexual maturity in yaks. In MeRIP-seq, 1702 hypermethylated peaks and 724 hypomethylated peaks were identified. The hypermethylated differentially methylated RNAs (DMRs) (CIB2, AK1, FOXJ2, PKDREJ, SLC9A3, and TOPAZ1) mainly regulated spermatogenesis. Functional enrichment analysis showed that DMRs were significantly enriched in the adherens junction, gap junction, and Wnt, PI3K, and mTOR signaling pathways, regulating cell development, spermatogenesis, and testicular endocrine function. The functional analysis of differentially expressed genes showed that they were involved in the biological processes of mitosis, meiosis, and flagellated sperm motility during the sexual maturity of yak testis. We also screened the key regulatory factors of testis development and spermatogenesis by combined analysis, which included BRCA1, CREBBP, STAT3, and SMAD4. This study indexed the m6A characteristics of yak testicles at different developmental stages, providing basic data for further research of m6A modification regulating yak testicular development.

Single-cell RNA sequencing and UPHLC-MS/MS targeted metabolomics offer new insights into the etiological basis for male cattle-yak sterility.

The variety of species can be efficiently increased by interspecific hybridization. However, because the males in the hybrid progeny are usually sterile, this heterosis cannot be employed when other cattle and yaks are hybridized. While some system-level studies have sought to explore the etiological basis for male cattle-yak sterility, no systematic cellular analyses of this phenomenon have yet been performed. Here, single-cell RNA sequencing and UPHLC-MS/MS targeted metabolomics methods were used to study the differences in testicular tissue between 4-year-old male yak and 4-year-old male cattle-yak, providing new and comprehensive insights into the causes of male cattle-yak sterility. Cattle-yak testes samples detected 6 somatic cell types and one mixed germ cell type. Comparisons of these cell types revealed the more significant differences in Sertoli cells (SCs) and [Leydig cells and myoid cells (LCs_MCs)] between yak and cattle-yak samples compared to other somatic cell clusters. Even though the LCs and MCs from yaks and cattle-yaks were derived from the differentiation of the same progenitor cells, a high degree of overlap between LCs and MCs was observed in yak samples. Still, only a small overlap between LCs and MCs was observed in cattle-yak samples. Functional enrichment analyses revealed that genes down-regulated in cattle-yak SCs were primarily enriched in biological activity, whereas up-regulated genes in these cells were enriched for apoptotic activity. Furthermore, the genes of up-regulated in LCs_MCs of cattle-yak were significantly enriched in enzyme inhibitor and molecular function inhibitor activity. On the other hand, the genes of down-regulated in these cells were enriched for signal receptor binding, molecular function regulation, positive regulation of biological processes, and regulation of cell communication activity. The most significant annotated differences between yak and cattle-yak LCs_MCs were associated with cell-to-cell communication. While yak LCs_MCs regulated spermatogenic cells at spermatogonia, spermatocyte, and spermatid levels, no such relationships were found between cattle-yak LCs_MCs and germ cells. This may suggest that the somatic niche in male cattle-yak testes is a microenvironment that is ultimately not favorable for spermatogenesis.

Efficacy and safety of SIM0417 (SSD8432) plus ritonavir for COVID-19 treatment: a randomised, double-blind, placebo-controlled, phase 1b trial.

Background: SIM0417 (SSD8432) is an orally administered coronavirus main proteinase (3CLpro) inhibitor with potential anti-SARS-CoV-2 activity. This study aimed to evaluate the efficacy and safety of SIM0417 plus ritonavir (a pharmacokinetic enhancer) in adults with COVID-19. Methods: This was a randomised, double-blind, placebo-controlled, phase 1b study in China. Adults with asymptomatic infection, mild or moderate COVID-19 were randomly assigned (3:3:2) to receive either 750 mg SIM0417 plus 100 mg ritonavir, 300 mg SIM0417 plus 100 mg ritonavir or placebo every 12 h for 10 doses. The main efficacy endpoints included SARS-CoV-2 viral load, proportion of participants with positive SARS-CoV-2 nucleic acid test and time to alleviation of COVID-19 symptoms. This trial is registered with ClinicalTrials.gov, NCT05369676. Findings: Between May 12 and August 29, 2022, 32 participants were enrolled and randomised to high dose group (n = 12), low dose group (n = 12) or placebo (n = 8). The viral load change from baseline in high dose group was statistically lower compared with placebo, with a maximum mean difference of -2.16 ± 0.761 log10 copies/mL (p = 0.0124) on Day 4. The proportion of positive SARS-CoV-2 in both active groups were lower than the placebo. The median time to sustained alleviation of COVID-19 symptoms was 2.0 days in high dose group versus 6.0 days in the placebo group (HR = 3.08, 95% CI 0.968-9.818). SIM0417 plus ritonavir were well tolerated with all adverse events in grade 1. Interpretation: SIM0417 plus ritonavir was generally well tolerated. The efficacy of SIM0417 showed a monotonic dose-response relationship, and the 750 mg SIM0417 plus 100 mg ritonavir was selected as the recommended clinical dose. Funding: The study was funded by Jiangsu Simcere Pharmaceutical Co., Ltd.

Single-Cell RNA Sequencing Reveals Atlas of Yak Testis Cells.

Spermatogenesis is a complex process that involves proliferation and differentiation of diploid male germ cells into haploid flagellated sperm and requires intricate interactions between testicular somatic cells and germ cells. The cellular heterogeneity of this process presents a challenge in analyzing the different cell types at various developmental stages. Single-cell RNA sequencing (scRNA-seq) provides a useful tool for exploring cellular heterogeneity. In this study, we performed a comprehensive and unbiased single-cell transcriptomic study of spermatogenesis in sexually mature 4-year-old yak using 10× Genomics scRNA-seq. Our scRNA-seq analysis identified six somatic cell types and various germ cells, including spermatogonial stem cells, spermatogonia, early-spermatocytes, late-spermatocytes, and spermatids in yak testis. Pseudo-timing analysis showed that Leydig and myoid cells originated from common progenitor cells in yaks. Moreover, functional enrichment analysis demonstrated that the top expressed genes in yak testicular somatic cells were significantly enriched in the cAMP signaling pathway, PI3K-Akt signaling pathway, MAPK signaling pathway, and ECM receptor interactions. Throughout the spermatogenesis process, genes related to spermatogenesis, cell differentiation, DNA binding, and ATP binding were expressed. Using immunohistochemical techniques, we identified candidate marker genes for spermatogonial stem cells and Sertoli cells. Our research provides new insights into yak spermatogenesis and the development of various types of cells in the testis, and presents more reliable marker proteins for in vitro culture and identification of yak spermatogonial stem cells in the later stage.

Comparative Analysis of Epididymis Cauda of Yak before and after Sexual Maturity.

Epididymis development is the basis of male reproduction and is a crucial site where sperm maturation occurs. In order to further understand the epididymal development of yak and how to regulate sperm maturation, we conducted a multi-omics analysis. We detected 2274 differential genes, 222 differential proteins and 117 co-expression genes in the cauda epididymis of yak before and after sexual maturity by RNA-seq and proteomics techniques, which included TGFBI, COL1A1, COL1A2, COL3A1, COL12A1, SULT2B1, KRT19, and NPC2. These high abundance genes are mainly related to cell growth, differentiation, adhesion and sperm maturation, and are mainly enriched via extracellular matrix receptor interaction, protein differentiation and absorption, and lysosome and estrogen signaling pathways. The abnormal expression of these genes may lead to the retardation of epididymal cauda development and abnormal sperm function in yak. In conclusion, through single and combined analysis, we provided a theoretical basis for the development of the yak epididymal cauda, sperm maturation, and screening of key genes involved in the regulation of male yak reproduction.

The Effect of the Feeding System on Fat Deposition in Yak Subcutaneous Fat.

Fat deposition is very important to the growth and reproduction of yaks. In this study, the effect of the feeding system on fat deposition in yaks was explored by transcriptomics and lipidomics. The thickness of the subcutaneous fat in yaks under stall (SF) and graze feeding (GF) was evaluated. The transcriptomes and lipidomes of the subcutaneous fat in yaks under different feeding systems were detected by RNA-sequencing (RNA-Seq) and non-targeted lipidomics based on ultrahigh-phase liquid chromatography tandem mass spectrometry (UHPLC-MS), respectively. The differences in lipid metabolism were explored, and the function of differentially expressed genes (DEGs) was evaluated by gene ontology (GO) and Kyoto encyclopedia of genes and genome (KEGG) analysis. Compared with GF yaks, SF yaks possessed stronger fat deposition capacity. The abundance of 12 triglycerides (TGs), 3 phosphatidylethanolamines (PEs), 3 diglycerides (DGs), 2 sphingomyelins (SMs) and 1 phosphatidylcholine (PC) in the subcutaneous fat of SF and GF yaks was significantly different. Under the mediation of the cGMP-PKG signaling pathway, the blood volume of SF and GF yaks may be different, which resulted in the different concentrations of precursors for fat deposition, including non-esterified fatty acid (NEFA), glucose (GLU), TG and cholesterol (CH). The metabolism of C16:0, C16:1, C17:0, C18:0, C18:1, C18:2 and C18:3 in yak subcutaneous fat was mainly realized under the regulation of the INSIG1, ACACA, FASN, ELOVL6 and SCD genes, and TG synthesis was regulated by the AGPAT2 and DGAT2 genes. This study will provide a theoretical basis for yak genetic breeding and healthy feeding.

The Study of Yak Colostrum Nutritional Content Based on Foodomics.

The utilization of yak milk is still in a primary stage, and the nutrition composition of yak colostrum is not systematically characterized at present. In this study, the lipids, fatty acids, amino acids and their derivatives, metabolites in yak colostrum, and mature milk were detected by the non-targeted lipidomics based on (ultra high performance liquid chromatography tandem quadrupole mass spectrometer) UHPLC-MS, the targeted metabolome based on gas chromatography-mass spectrometer (GC-MS), the targeted metabolome analysis based on UHPLC-MS, and the non-targeted metabolome based on ultra high performance liquid chromatography tandem quadrupole time of flight mass spectrometer (UHPLC-TOF-MS), respectively. Meanwhile, the nutrition composition of yak colostrum was compared with the data of cow mature milk in the literatures. The results showed that the nutritive value of yak colostrum was higher by contrast with yak and cow mature milk from the perspective of the fatty acid composition and the content of Σpolyunsaturated fatty acids (PUFAs), Σn-3PUFAs; the content of essential amino acid (EAA) and the ratio of EAA/total amino acid (TAA) in yak colostrum were higher than the value in yak mature milk; and the content of functional active lipids including phosphatidylcholines (PC), phosphatidylglycerol (PG), phosphatidylserine (PS), lyso-phosphatidylcholine (LPC), lyso-phosphatidylglycerol (LPG), lyso-phosphatidylinositol (LPI), sphingomyelin (SM), ganglioside M3 (GM3), ganglioside T3 (GT3), and hexaglycosylceramide (Hex1Cer) in yak colostrum, was higher than the value of yak mature milk. Moreover, the differences of nutritive value between yak colostrum and mature milk were generated by the fat, amino acids and carbohydrate metabolism that were regulated by the ovarian hormone and referencesrenin-angiotensin-aldosterone system in yaks. These research results can provide a theoretical basis for the commercial product development of yak colostrum.

Analysis of Chromatin Openness in Testicle Tissue of Yak and Cattle-Yak.

Cattle-yak, a crossbreed of yak and cattle, which can exhibit obvious heterosis and can adapt to the harsh environmental conditions of the Qinghai Tibet Plateau (QTP). However, F1 cattle-yak were found to be sterile because they were unable to produce sperm, which adversely restricted the fixation of heterosis. Many prior attempts have been made to decipher the mechanism underlying the spermatogenesis stagnation of cattle-yak. However, the open chromatin region (OCR) map of yak and cattle-yak testes has not been generated yet. Here, we have analyzed the OCRs landscape of testicular tissues of cattle-yak and yaks by performing ATAC-seq technology. The OCRs of cattle-yak and yak testes displayed similar genome distribution and showed priority in intergenic regions, introns and promoters. The pathway enrichment analysis indicated that the differential OCRs-related genes were involved in spermatogenesis, involving the cell cycle, as well as Hippo, mTOR, MAPK, Notch, and Wnt signaling pathways. The integration of ATAC-seq and mRNA-seq indicated that the majority of the gene expression levels were positively correlated with chromatin openness. At the same time, we have identified a number of transcription factors (TFs) related to spermatogenesis and the differential expression of these TFs may contribute to the spermatogenesis stagnation of the cattle-yak. Overall, the findings of this study provide valuable information for advancing the research related to yak crossbreeding improvement and sperm production stagnation of cattle-yak.

Whole-Genome Resequencing Highlights the Unique Characteristics of Kecai Yaks.

Kecai yaks are regarded as an important genetic resource in China owing to their high fecundity and flavorful meat. However, the genetic characteristics of Kecai yaks have not been effectively characterized to date, and the relationship between Kecai yaks and other yak breeds remains to be fully characterized. In this paper, the resequencing of the Kecai yak genome is performed leading to the identification of 11,491,383 high-quality single nucleotide polymorphisms (SNPs). Through principal component, phylogenetic, and population genetic structure analyses based on these SNPs, Kecai yaks were confirmed to represent an independent population of yaks within China. In this study, marker and functional enrichment analysis of genes related to positive selection in Kecai yak was carried out, and the results show that such selection in Kecai yaks is associated with the adaptation to alpine environments and the deposition of muscle fat. Overall, these results offer a theoretical foundation for the future utilization of Kecai yak genetic resources.