Yak genome database: a multi-omics analysis platform.

BACKGROUND: The yak (Bos grunniens) is a large ruminant species that lives in high-altitude regions and exhibits excellent adaptation to the plateau environments. To further understand the genetic characteristics and adaptive mechanisms of yak, we have developed a multi-omics database of yak including genome, transcriptome, proteome, and DNA methylation data. DESCRIPTION: The Yak Genome Database ( http://yakgenomics.com/ ) integrates the research results of genome, transcriptome, proteome, and DNA methylation, and provides an integrated platform for researchers to share and exchange omics data. The database contains 26,518 genes, 62 transcriptomes, 144,309 proteome spectra, and 22,478 methylation sites of yak. The genome module provides access to yak genome sequences, gene annotations and variant information. The transcriptome module offers transcriptome data from various tissues of yak and cattle strains at different developmental stages. The proteome module presents protein profiles from diverse yak organs. Additionally, the DNA methylation module shows the DNA methylation information at each base of the whole genome. Functions of data downloading and browsing, functional gene exploration, and experimental practice were available for the database. CONCLUSION: This comprehensive database provides a valuable resource for further investigations on development, molecular mechanisms underlying high-altitude adaptation, and molecular breeding of yak.

Oligodendrocytes in central nervous system diseases: the effect of cytokine regulation.

Cytokines including tumor necrosis factor, interleukins, interferons, and chemokines are abundantly produced in various diseases. As pleiotropic factors, cytokines are involved in nearly every aspect of cellular functions such as migration, survival, proliferation, and differentiation. Oligodendrocytes are the myelin-forming cells in the central nervous system and play critical roles in the conduction of action potentials, supply of metabolic components for axons, and other functions. Emerging evidence suggests that both oligodendrocytes and oligodendrocyte precursor cells are vulnerable to cytokines released under pathological conditions. This review mainly summarizes the effects of cytokines on oligodendrocyte lineage cells in central nervous system diseases. A comprehensive understanding of the effects of cytokines on oligodendrocyte lineage cells contributes to our understanding of central nervous system diseases and offers insights into treatment strategies.

Targeting optimal power consumption: Optimizing operational parameters for orchard furrowing and fertilizing machine.

In response to the problem of excessive power consumption during the furrowing operation of orchard furrowing fertilizer machines, an optimization experiment of furrowing operation parameters for orchard furrowing fertilizer machine was conducted based on discrete element simulations. This research focused on the impact of furrowing device operation parameters on furrowing power consumption under full machine operating conditions. Firstly, a kinematics analysis of the soil granules during cutting was done. The mathematical model of soil granules through three movement processes of rising, detachment, and falling was established to determine the main factors affecting the power consumption of furrowing. Secondly, in assessing the furrowing power consumption, the stability coefficient of the furrowing depth, and the percentage of soil cover, alongside the key parameters of furrowing depth, forward propulsion velocity, and furrowing blade rotation speed, a comprehensive quadratic orthogonal rotation regression experiment was meticulously conducted. It was established that test metrics and test parameters regress. Finally, the test parameters were comprehensively optimized after analyzing each factor's impact on the test metrics. The orchard furrowing fertilizer machine's optimal operating parameters were determined, and the verification test was performed. According to the field test findings, the forward propulsion velocity was 785 m/h, and the furrowing blade rotation speed was 190 r/min when the furrowing depth was 275 mm. At this point, the furrowing power consumption was 2.39 kW, the soil cover percentage was 69.06%, and the furrowing depth stability coefficient was 95.08%. These results were in line with the requirements of orchard furrowing operation. The findings of the study can be utilized as a guide for structural changes to orchard furrowing equipment and the management of furrowing operation parameters.

The myelination-associated G protein-coupled receptor 37 is regulated by Zfp488, Nkx2.2, and Sox10 during oligodendrocyte differentiation.

Oligodendrocyte differentiation and myelination in the central nervous system are controlled and coordinated by a complex gene regulatory network that contains several transcription factors, including Zfp488 and Nkx2.2. Despite the proven role in oligodendrocyte differentiation little is known about the exact mode of Zfp488 and Nkx2.2 action, including their target genes. Here, we used overexpression of Zfp488 and Nkx2.2 in differentiating CG4 cells to identify aspects of the oligodendroglial expression profile that depend on these transcription factors. Although both transcription factors are primarily described as repressors, the detected changes argue for an additional function as activators. Among the genes activated by both Zfp488 and Nkx2.2 was the G protein-coupled receptor Gpr37 that is important during myelination. In agreement with a positive effect on Gpr37 expression, downregulation of the G protein-coupled receptor was observed in Zfp488- and in Nkx2.2-deficient oligodendrocytes in the mouse. We also identified several potential regulatory regions of the Gpr37 gene. Although Zfp488 and Nkx2.2 both bind to one of the regulatory regions downstream of the Gpr37 gene in vivo, none of the regulatory regions was activated by either transcription factor alone. Increased activation by Zfp488 or Nkx2.2 was only observed in the presence of Sox10, a transcription factor continuously present in oligodendroglial cells. Our results argue that both Zfp488 and Nkx2.2 also act as transcriptional activators during oligodendrocyte differentiation and cooperate with Sox10 to allow the expression of Gpr37 as a modulator of the myelination process.

First-principle study on the photoelectric properties of monolayer h-BN under different strain types.

CONTEXT: Two-dimensional materials are a new and promising research field in materials science. This is mainly attributed to their unique photoelectric and chemical properties. In addition to possessing unique optoelectronic and chemical properties, two-dimensional materials also have important application prospects in the field of field-effect devices. Based on density functional theory, the effects of uniaxial strain and equibiaxial strain on the mechanical properties, electronic structure, and optical properties of monolayer h-BN were studied using first principles. The results indicate that compressive strain has a significant impact on the stability of monolayer h-BN. The band gap width of monolayer h-BN decreases with increasing strain, and the optical properties of monolayer h-BN exhibit a relative trend under tensile and compressive strains. The influence of biaxial strain on the mechanical properties, electronic structure, and optical properties of monolayer h-BN is greater than that of uniaxial strain. METHODS: All the calculations were done by the VASP software based on density functional theory. The interaction between atomic nuclei and electrons is described by the projected added wave pseudopotential (PAW), using the generalized gradient approximation (GGA) to exchange the Perdew-Burke-Ernzerhof (PBE) of the functional. To avoid interlayer interactions, a 15-Å vacuum layer was set up. The Brillouin zone selects the Monkhorst-Pack method to generate 9 × 9 × 1 of k-point grid, the cut off energy is set to 500 eV, the energy convergence standard of the system is 1 × 10-5 eV, and the interaction force between atoms is 0.01 eV/Å.

Role of Gltp in Maturation of Oligodendrocytes Under the Regulation of Nkx2.2.

Myelin, a lipid-enriched multi-layer membrane structure, allows for rapid long-distance saltatory conduction of neuronal impulses. Although glycolipids are the predominant types of lipids in the myelin bilayer, the role of glycolipid transfer protein (GLTP), which selectively mediates the transfer of various glycolipids between phospholipid bilayer, in myelin development and maintenance remains unknown at present. In this study, we identified Gltp as the key lipid metabolism gene in myelin-forming oligodendrocytes (OLs) through integrated omics analysis across independent transcriptomic and single-cell sequencing studies. Gene expression analysis revealed that Gltp is selectively expressed in the differentiated OLs. Functional study demonstrated that its expression is essential for the differentiation of OLs, and promotes the outgrowth of OL membrane. Moreover, we found that the expression of Gltp is regulated by OL-lineage transcriptional factors, such as NKX2.2, OLIG2, SOX10, and MYRF. These findings provide important insights into the unrecognized functions of Gltp in OL differentiation and maturation.

Preparation and Antibacterial Properties of a Composite Fiber Membrane Material Loaded with Cationic Antibacterial Agent by Electrospinning.

Microbial infections due to bacteria, viruses, and molds are a serious threat to both human life and the health of other organisms. To develop inexpensive, easy-to-prepare, efficient, and portable nano-antibacterial materials, as well as to explore the antibacterial prospects of cationic antibacterial agents, in this work, six different membrane materials were prepared by the electrostatic spinning method and characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and Fourier transform infrared (FT-IR). The materials were tested for antimicrobial properties using a modified AATCC100-200 test method. Under the most suitable spinning conditions, the doping amount of the cationic antimicrobial agent, CTAB, had the greatest influence on the antimicrobial performance. The antimicrobial performance of PCL/PEO/CS/CTAB0.4 was the highest among the prepared materials, with 83.7% effectiveness against S. aureus and 99.9% against E. coli. The antimicrobial performance was found to be stable. In our study, we determined the most suitable spinning ratio to prepare an inexpensive and efficient cationic antimicrobial agent. Biodegradable, high-antimicrobial-activity antimicrobial materials can be applied as films, and this new nanofiber material has shown great potential in wound dressings and as a mask material due to its remarkable antimicrobial efficiency.

Genome-wide comparison of DNA methylation patterns between yak and three cattle strains and their potential association with mRNA transcription.

Yak has evolved specific adaptative mechanisms to high-altitude environment. Up to date, only a few studies reported the DNA methylation in yak. In the present study, genome-wide DNA methylome and transcriptome profiles in lung, mammary, and biceps brachii muscle tissues were compared between yak and three cattle breeds (Tibetan cattle, Sanjiang cattle, and Holstein cattle). The association between differentially expressed genes (DEGs) and differentially methylated regions (DMRs) was analyzed, and the biological functions of DEGs potentially driven by DMRs were explored by KEGG enrichment analysis. Finally, we found that yak-specific DMRs-driven DEGs were mainly involved in neuromodulation, respiration, lung development, blood pressure regulation, cardiovascular protection, energy metabolism, DNA repair, and immune functions. The higher levels of the key genes associated with these functions were observed in yak than in cattle, suggesting that DNA methylation might regulate these genes. Overall, the present study contributes basic data at the DNA methylation level to further understand the physiological metabolism in yak.

Genome-wide identification of SNPs associated with body weight in yak.

BACKGROUND: The yak is the most important livestock in the Qinghai-Tibet Plateau, and body weight directly affects the economic values of yak. Up to date, the genome-wide profiling of single-nucleotide polymorphisms (SNPs) associating with body weight has not been reported in yak. In the present study, the SNPs in 480 yaks from three breeds were analyzed using the commercial high-density (600 K) yak SNP chips. RESULTS: The results identified 12 and 4 SNPs potentially associated with body weight in male and female yaks, respectively. Among them, 9 and 2 SNPs showed significant difference in yak body weight between different genotypes at each locus in male and female yaks, respectively. Further exploration found 33 coding genes within the 100 kbp upstream or downstream to the SNP loci, which might be potentially affected by the variation of SNPs. Among them, G protein-coupled receptor kinase 4 (GRK4) might be potentially affected by the SNP AX-174555047, which has been reported to affect the functioning of two body-weight associated hormones (parathyroid hormone, PTH, and adrenomedullin, ADM). Determination of PTH and ADM levels in yak revealed positive relationship between PTH level and body weight, negative relationship between ADM level and body weight along with the variation of AX-174555047 mutation. CONCLUSIONS: These results suggested that the SNP AX-174555047 might potentially affect body weight through mediating GRK4 expression and then PTH and ADM functioning. Thus, the SNP AX-174555047 might be used as a biomarker for molecular breeding of yak. More investigations are required to validate this point.

Dynamic alterations in yak (Bos grunniens) rumen microbiome in response to seasonal variations in diet.

Rumen microorganisms play important roles in the healthy growth of yaks. This study investigated changes in yak rumen microbiome during natural grazing at the warm seasons and supplementary feeding at cold seasons. High-throughput sequencing of 16S rRNA and metagenome analysis were conducted to investigate the structures and functions of yak rumen microbial communities. The results indicated that Bacteroidetes and Firmicutes were the most abundant phyla. In addition, Bacteroidetes might play a more important role than Firmicutes during the supplementary feeding stage (spring and winter), but less during natural grazing stage (summer and autumn). KEGG analysis showed that the amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, starch and sucrose metabolism, and fructose and mannose metabolism were the main pathways in the microbial community, which were significantly different between seasons. The carbohydrate-active enzymes (CAZyme) annotation revealed that cellulose was an important carbon source for microorganisms in yak rumen. Glycoside hydrolases (GHs) were the most abundant class of CAZymes, followed by glycosyl transferases (GTs), which were important to digestion of oil, cellulose, and hemicellulose in food. These results contribute to the understanding of microbial components and functions in yak rumen.

Comparison of rumen bacterial communities between yaks (Bos grunniens) and Qaidam cattle (Bos taurus) fed a low protein diet with different energy levels.

The yak (Bos grunniens), an indigenous bovine on the Qinghai-Tibetan plateau (QTP), is reported to digest low quality forage to a greater extent and to require less protein and energy for maintenance than the introduced Qaidam cattle (Bos taurus). Ruminal bacteria play a major role in feed degradation, and therefore, we hypothesized that ruminal bacteria composition would differ between yaks and cattle, and confer an advantage to yaks for poor quality diets. To test our hypothesis, we determined the ruminal bacteria profiles, rumen fermentation parameters, and enzyme activities in these bovine species consuming a low-protein diet differing in energy level. Six castrated yaks (155 ± 5.8 kg) and 6 castrated Qaidam cattle (154 ± 8.0 kg) were used in two concurrent 4 × 4 Latin square designs with 2 additional animals of each species in each period. The animals were offered a low-protein diet of 70.4 g/kg dry matter (DM) and one of four metabolizable energy levels, namely 6.62, 8.02, 9.42, and 10.80 MJ/kg. Ruminal pH, concentrations of ammonia-N and total volatile fatty acids (VFAs), the molar proportion of acetate, and the ratio of acetate to propionate (A:P) were greater (P < 0.05), whereas the molar proportion of propionate was lesser (P = 0.043) in yaks than in cattle. With increasing dietary energy level, ruminal pH, the molar proportion of acetate and the ratio of A:P decreased linearly (P < 0.05), whereas, the concentration of total VFAs, molar proportions of propionate, butyrate, iso-butyrate, and iso-valerate and concentration of ammonia-N increased linearly (P < 0.05). The relative abundance (RA) of Firmicutes increased linearly (P < 0.01), whereas, the RA of Bacteroidetes decreased linearly (P < 0.001) with increasing energy level in both bovine species. The RAs of Prevotella and Rikenellaceae_RC9_gut_group decreased linearly (P < 0.05) with increasing energy level in both yaks and cattle. The RAs of fibrolytic (e.g., Rikenellaceae_RC9_gut_group), and H2-incorporating (e.g., Quinella) bacteria were greater (P < 0.05) in yaks than in cattle. We concluded that the two bovines differ in ruminal bacterial profiles and rumen fermentation parameters, and confer an advantage to yaks over cattle in consuming a low protein diet with differing energy level.

Carbazoles in Oils, and Their Application in Identifying Oil Filling Pathways in Eocene Syn-Rift Fault Blocks in the Dongpu Depression, Bohai Bay Basin, East China.

Carbazoles and dimethyl carbazoles (DMCs) are important nitrogen heterocyclic aromatic compounds in oils and sedimentary rock extracts. Based on both migration fractionation effects and differences in the thermal stability of their isomers, carbazoles can be used to trace oil migration orientations and filling pathways. Molecular biomarker compositions indicate that all oils and oil-bearing sand extracts in the Eocene fault-blocked reservoirs of the Huzhuangji area (Western Slope Belt) of the Dongpu Depression (Bohai Bay Basin, East China) belong to a single oil population. In this study, four geochemical indicators relating to carbazoles, namely (a) 1,8-/2,7-dimethyl carbazoles (1,8-/2,7-DMC); (b) 1,8-/2,5-dimethyl carbazoles (1,8-/2,5-DMC); (c) 1,8-/N-exposed dimethyl carbazoles (1,8-/N-exposed DMC); and (d) G1 N-shielded %, were applied to trace oil migration orientations and filling pathways. The results show that these parameter values gradually increase toward the Hu-5 fault block at the structural high. The measured values from the subsurface are consistent with the results calculated from the molecular adsorption modeling. Therefore, it is concluded that the relative parameters of dimethyl carbazoles are practical molecular indicators for tracing oil migration orientations and filling pathways in syn-rift fault-blocked reservoirs.

Differences in proteomic profiles between yak and three cattle strains provide insights into molecular mechanisms underlying high-altitude adaptation.

Yaks display unique properties of the lung and heart, enabling their adaptation to high-altitude environments, but the underlying molecular mechanisms are still largely unknown. In the present study, the proteome differences in lung and heart tissues were compared between yak (Bos grunniens) and three cattle strains (Bos taurus, Holstein, Sanjiang and Tibetan cattle) using the sequential window acquisition of all theoretical mass spectra/data-independent acquisition (SWATH/DIA) proteomic method. In total, 51,755 peptides and 7215 proteins were identified. In the lung tissue, there were 162, 310 and 118 differential abundance proteins (DAPs) in Tibetan, Holstein and Sanjiang cattle compared to yak respectively. In the heart tissue, there were 71, 57 and 78 DAPs in Tibetan, Holstein and Sanjiang cattle compared to yak respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the DAPs were enriched for the retinol metabolism and toll-like receptor categories in lung tissue. The changes in these two pathways may regulate hypoxia-induced factor and immune function in yaks. Moreover, DAPs in heart tissues were enriched for cardiac muscle contraction, Huntington's disease, chemical carcinogenesis and drug metabolism-cytochrome P450. Further exploration indicated that yaks may alter cardiac function through regulation of type 2 ryanodine receptor (RyR2) and Ca2+ -release channels. The present results are useful to further develop an understanding of the mechanisms underlying adaptation of animals to high-altitude conditions.

Effect of Supplementary Levels of Rumen-Protected Lysine and Methionine on Growth Performance, Carcass Traits, and Meat Quality in Feedlot Yaks (Bos grunniens).

Yak, a unique bovine species on the Qinghai-Tibetan Plateau, has provided pastoralists with the basic materials of production and life for thousands of years. Existing literature showed that yak meat is of high nutritional value for humans whereas the growth performance is relatively low. As it has been demonstrated, lysine and methionine are the two key limiting amino acids in ruminants. Therefore, this study was conducted to investigate the effect of supplementary levels of rumen-protected lysine (RPL) and methionine (RPM) on growth performance, carcass traits, and meat quality in feedlot yaks. Thirty-two male yaks, with initial body weight (IBW) of 237.5 ± 13.99 kg were randomly assigned to four dietary treatments (n = 8), including control group (CON; basal diet without adding rumen-protected amino acid (RPAA)), low RPAA supplementation group (Group Low; basal diet supplemented with RPL (30.0 g/animal/day) and RPM (7.5 g/animal/day)), medium RPAA supplementation group (Group Medium; basal diet supplemented with RPL (50.0 g/animal/day) and RPM (12.5 g/animal/day)), and high RPAA supplementation group (Group High; basal diet supplemented with RPL (70.0 g/animal/day) and RPM (17.5 g/animal/day)). The average daily gain was increased linearly (p < 0.001) and quadratically (p < 0.01) while feed to gain ratio was decreased linearly (p < 0.001) and quadratically (p < 0.001) with the increasing RPAA supplementation, and the average daily gain was higher while feed to gain ratio was lower in RPAA than CON (p < 0.001). Meat color L* values and b* were decreased linearly (p < 0.01) with the increase of RPAA supplementation, and b* was lower in RPAA than CON (p < 0.05). Meat color a* value was increased linearly (p < 0.05) with the increasing RPAA supplementation, and a* was higher in RPAA than CON (p < 0.05). The 24 h drip loss and shear force were decreased quadratically (p < 0.01) with the increasing RPAA supplementation, and drip loss and shear force values were lower in RPAA than CON (p < 0.05). The glycine concentration in longissimus dorsi (LD) increased linearly (p < 0.05) with the increasing RPAA supplementation. These results demonstrated that both the growth performance and meat quality characteristics were improved in feedlot yaks as an effect of the dietary supplementation with RPL and RPM, and the medium supplementary level is recommended, since it showed the most promising results.

Genome-Wide DNA Methylation and Hydroxymethylation Changes Revealed Epigenetic Regulation of Neuromodulation and Myelination in Yak Hypothalamus.

Both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are important epigenetic modifications in neurodevelopment. However, there is little research examining the genome-wide patterns of 5mC and 5hmC in brain regions of animals under natural high-altitude conditions. We used oxidative reduced representation bisulfite sequencing (oxRRBS) to determine the 5mC and 5hmC sites in the brain, brainstem, cerebellum, and hypothalamus of yak and cattle. We reported the first map of genome-wide DNA methylation and hydroxymethylation in the brain, brainstem, cerebellum, and hypothalamus of yak (living at high altitudes) and cattle. Overall, we found striking differences in 5mC and 5hmC between the hypothalamus and other brain regions in both yak and cattle. Genome-wide profiling revealed that 5mC level decreased and 5hmC level increased in the hypothalamus than in other regions. Furthermore, we identified differentially methylated regions (DMRs) and differentially hydroxymethylated regions (DhMRs), most of which overlapped with each other. Interestingly, transcriptome results for these brain regions also showed distinctive gene levels in the hypothalamus. Finally, differentially expressed genes (DEGs) regulated by DMRs and DhMRs may play important roles in neuromodulation and myelination. Overall, our results suggested that mediation of 5mC and 5hmC on epigenetic regulation may broadly impact the development of hypothalamus and its biological functions.

Rumen Bacterial Community of Grazing Lactating Yaks (Poephagus grunniens) Supplemented with Concentrate Feed and/or Rumen-Protected Lysine and Methionine.

Traditionally, yaks graze only natural pasture all year round without supplements. Forage intake of lactating yaks is below energy and protein requirements, even in the summer, and suckling yaks lose a substantial amount of significant body weight. Today, to mitigate the loss in body weight, supplementary feed is being offered to lactating yaks. However, the effects of supplementary feed on ruminal bacterial communities in lactating yaks is unknown. In the current study, we examined the effect of supplementary feed on ruminal microbiota, using 16S rRNA sequencing, and on volatile fatty acids (VFAs). Twenty-four lactating yaks of similar body weight (218 ± 19.5 kg) and grazing natural pasture were divided randomly into four groups and received different supplements: (1) rumen-protected amino acids (RPA); (2) concentrate feed (C); (3) RPA plus C (RPA+C); and (4) no supplements (control-CON). The concentrations of total VFAs, acetate, and butyrate were greater (p < 0.05) when supplemented with concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA). Bacteroidetes (B) and Firmicutes (F) were the dominant ruminal bacterial phyla in all groups. The ratio of relative abundance of F:B in RPA+C was greater than in the RPA group, while there was no difference between CON and RPC (interaction, p = 0.026). At the genus level, the relative abundances of Absconditabacteriales_SR1, Bacteroidales-RF16-group, Bacteroidales_BS11_gut_group, Prevotellaceae, and Rikenellaceae_RC9_gut_group were lesser (p < 0.05) with supplementary concentrate feed (C and RPA+C) than without concentrate feed (CON and RPA), whereas Butyrivibrio_2 and Pseudobutyrivibrio were greater (p < 0.05) with supplementary rumen-protected amino acids (RPA and RPA+C) than without rumen-protected amino acids (CON and C). These results demonstrate that supplementary feed: (1) alters the composition of rumen microbiota and concentrations of ruminal VFAs in lactating yaks; and (2) can be used to manipulate the composition of rumen microbiota.

Methyltrimethyltridecylchromans in Mature Oils from Saline Lacustrine Settings in the Dongpu Depression, Bohai Bay Basin, East China.

The measured composition and distribution of methyltrimethyltridecylchroman (MTTC) compounds in the crude oils from Wenliu (salt-rich zone) and Machang (salt-free zone) areas of the Dongpu Depression were correlated with redox conditions and paleosalinity. The oil samples derived from the mesosaline environment were found with all alkylated MTTC series present. In addition, the dimethyl MTTCs developed more favorably in the oils derived from a relatively reducing and hypersaline environment (Wenliu) compared to those from the fresh lacustrine settings (Machang), while the trimethyl MTTCs developed more favorably in the fresh water environment (Machang). Determination of the oil maturity in the "oil window" by a series of aromatic maturity indicators suggests that MTTC compounds are not only present in immature or low-mature oils but also distributed in mature oils. Therefore, the "low-mature" oil found with abundant MTTC compounds, especially derived from the saline lacustrine settings, should be assessed with caution.

Whole-Transcriptome Analysis of Yak and Cattle Heart Tissues Reveals Regulatory Pathways Associated With High-Altitude Adaptation.

BACKGROUND: The yak (Bos grunniens) is an important livestock species that can survive the extremely cold, harsh, and oxygen-poor conditions of the Qinghai-Tibetan Plateau and provide meat, milk, and transportation for the Tibetans living there. However, the regulatory network that drive this hypoxic adaptation remain elusive. RESULTS: The heart tissues from LeiRoqi (LWQY) yak and their related cattle (Bos Taurus) breeds, which are two native cattle breeds located in high altitude (HAC) and low altitude (LAC) regions, respectively, were collected for RNA sequencing. A total of 178 co-differentially expressed protein-coding transcripts (co-DETs) were discovered in each of the LAC-vs-LWQY and LAC-vs-HAC comparison groups, including NFATC2, NFATC1, ENPP2, ACSL4, BAD, and many other genes whose functions were reported to be associated with the immune-system, endocrine-system, and lipid metabolism. Two and 230 lncRNA transcripts were differentially expressed in the LAC-vs-LWQY and LAC-vs-HAC comparisons' respectively, but no lncRNA transcripts that were co-differentially expressed. Among the 58 miRNAs that were co-differentially expressed, 18 were up-regulated and 40 were down-regulated. In addition, 640 (501 up-regulated and 139 down-regulated) and 152 (152 up-regulated and one down-regulated) circRNAs showed differential expression in LAC-vs-LWQY and LAC-vs-HAC comparison groups, respectively, and 53 up-regulated co-differentially expressed circRNAs were shared. Multiple co-DETs, which are the targets of miRNAs/lncRNAs, are significantly enriched in high-altitude adaptation related processes, such as, T cell receptor signaling, VEGF signaling, and cAMP signaling. A competing endogenous RNA (ceRNA) network was constructed by integrating the competing relationships among co-differentially expressed mRNAs, miRNAs, lncRNAs and circRNAs. Furthermore, the hypoxic adaptation related ceRNA network was constructed, and the six mRNAs (MAPKAPK3, PXN, NFATC2, ATP7A, DIAPH1, and F2R), the eight miRNAs (including miR-195), and 15 circRNAs (including novel-circ-017096 and novel-circ-018073) are proposed as novel and promising candidates for regulation of hypoxic adaptation in the heart. CONCLUSION: In conclusion, the data recorded in the present study provides new insights into the molecular network of high-altitude adaptation along with more detailed information of protein-coding transcripts and non-coding transcripts involved in this physiological process, the detailed mechanisms behind how these transcripts "crosstalk" with each other during the plateau adaptation are worthy of future research efforts.

Hydrocarbon Kitchen Evolution in the Early Cretaceous Bayingebi 2 Formation in the Chagan Depression, Yingen-Ejinaqi Basin, North Central China.

The Chagan Depression is an important oil and gas exploration tectonic unit in the Yingen-Ejinaqi Basin, north central China. It has been revealed that the Chagan Depression has abundant oil and gas resources, but the study of hydrocarbon kitchens has not been carried out. The Early Cretaceous Bayingebi 2 Formation has the most important source rocks in the Chagan Depression. In this paper, the Bayingebi 2 Formation was selected to study the hydrocarbon kitchen evolution. The thermal maturity evolution of the source rocks and the locations and geological time of the development of hydrocarbon kitchens were revealed. The results show that the maturity of source rocks in the Bayingebi 2 Formation has reached the maximum during the middle depositional period of the Yingen Formation, and the hydrocarbon generation has ceased since the Late Cretaceous. The source rocks of the Bayingebi 2 Formation in the Chagan Depression have two hydrocarbon kitchens, namely, the western subdepression and the eastern subdepression hydrocarbon kitchens. The western subdepression hydrocarbon kitchen was formed in the Suhongtu 1 Formation depositional period and ended in the Yingen Formation depositional period. The location of the hydrocarbon kitchen was relatively stable and developed in the central and southern parts. However, the eastern subdepression hydrocarbon kitchen developed only during the Yingen Formation depositional period and was located in the north subsag of the Hantamiao sag zone. Finally, the evolution of the hydrocarbon kitchen reveals that oil and gas exploration still needs to be carried out around the western subdepression hydrocarbon kitchen and it may be considered to abandon the exploration in the eastern subdepression.

Comparison of Rumen Fermentation Parameters and Microbiota of Yaks From Different Altitude Regions in Tibet, China.

Rumen microbiota are closely linked to feed utilization and environmental adaptability of ruminants. At present, little is known about the influence of different extreme environments on the rumen microbiota of yaks. In this study, 30 ruminal fluid samples from 30 healthy female yaks (average 280 kg of BW) in 5-8 years of life were collected from three regions in Tibet, China, and compared by gas chromatography and high-throughput sequencing. Results showed that propionic acid, butyric acid, and total volatile fatty acids were significantly (p < 0.05) higher, while microbial abundance and diversity were significantly (p < 0.05) lower, in the Nagqu (4,500 m altitude) compared with the Xigatse (4,800 m altitude) and Lhasa (3,800 m altitude) regions. Principal coordinate analysis revealed significant (p < 0.05) differences in rumen microbial composition of yaks from different regions. Specifically, Bacteroidetes and Firmicutes were identified by linear discriminant analysis effect size (LDA > 3) as being the signature phyla for Xigatse and Nagqu regions, respectively. In addition, the relative abundance of Rikenellaceae_RC9_gut_group, Quinella, Prevotellaceae_UCG-003, Lachnospiraceae_NK3A20_group, Papillibacter, Ruminococcaceae_UCG-010, Prevotellaceae_NK3B31_group, and Ruminococcaceae_UCG-005 correlated with altitude and rumen fermentation parameters (p < 0.05). Finally, the predicted function of rumen microbiota was found to differ between regions (p < 0.05). In summary, our results reveal that regions located at different altitudes influence microbiota composition and fermentation function of yaks' rumen. The present findings can provide mechanistic insights on yak adaptation to high altitudes and improve the feeding efficiency of these animals in extreme regions.