A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses.

Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.

Construction of transcriptome atlas of white yak hair follicle during anagen and catagen using single-cell RNA sequencing.

BACKGROUND: As the direct organ of villus, hair follicles have obvious seasonal cycles. The hair follicle cycle is orchestrated by multiple cell types that together direct cell renewal and differentiation. But the regulation property of hair follicle cells from anagen to catagen in yak is still unknown. RESULTS: In this study, single-cell RNA sequencing was performed on 24,124 single cells of the scapular skin from white yak. Based on tSNE cluster analysis, the cell types of IFE-DC, epidermal cell lines, fibroblasts, keratinocytes, IRS, DS, INFU, and other cells in yak hair follicles during anagen and catagen were successfully identified, and the gene expression profiles were described. The GO enrichment analysis indicated the different cells characteristic genes to be mainly enriched in the epidermal development, epithelial cell differentiation and wound healing pathways. The pseudotime trajectory analysis described the differentiation trajectory of the epidermal lineage and dermal lineage of the hair follicle during anagen and catagen. Moreover, the dynamic changes of the genes like LHX2, KRT25, and KRT71 were found to be highly expressed in HS and IRS, but not in the IFE-DC, INFU, and keratinocyte during differentiation. CONCLUSIONS: Our results analyzed the time-varying process of gene expression in the dermal cell lineage and epidermal cell lineage of hair follicles during anagen and catagen during fate differentiation was expounded at the single cell level, revealing the law of fate specialization of different types of cells. In addition, based on the enrichment analysis, the transcriptional regulatory factors involved in the different cell fates were also revealed. These results will help to enhance our understanding of yak hair follicle cycle and promote the development and utilization of yak villus.

The seasonal development dynamics of the yak hair cycle transcriptome.

BACKGROUND: Mammalian hair play an important role in mammals' ability to adapt to changing climatic environments. The seasonal circulation of yak hair helps them adapt to high altitude but the regulation mechanisms of the proliferation and differentiation of hair follicles (HFs) cells during development are still unknown. Here, using time series data for transcriptome and hormone contents, we systematically analyzed the mechanism regulating the periodic expression of hair development in the yak and reviewed how different combinations of genetic pathways regulate HFs development and cycling. RESULTS: This study used high-throughput RNA sequencing to provide a detailed description of global gene expression in 15 samples from five developmental time points during the yak hair cycle. According to clustering analysis, we found that these 15 samples could be significantly grouped into three phases, which represent different developmental periods in the hair cycle. A total of 2316 genes were identified in these three consecutive developmental periods and their expression patterns could be divided into 9 clusters. In the anagen, genes involved in activating hair follicle growth are highly expressed, such as the WNT pathway, FGF pathway, and some genes related to hair follicle differentiation. In the catagen, genes that inhibit differentiation and promote hair follicle cell apoptosis are highly expressed, such as BMP4, and Wise. In the telogen, genes that inhibit hair follicle activity are highly expressed, such as DKK1 and BMP1. Through co-expression analysis, we revealed a number of modular hub genes highly associated with hormones, such as SLF2, BOP1 and DPP8. They may play unique roles in hormonal regulation of events associated with the hair cycle. CONCLUSIONS: Our results revealed the expression pattern and molecular mechanisms of the seasonal hair cycle in the yak. The findings will be valuable in further understanding the alpine adaptation mechanism in the yak, which is important in order to make full use of yak hair resources and promote the economic development of pastoral plateau areas.

Study on Single Nucleotide Polymorphism of LAP3 Gene and Its Correlation with Dairy Quality Traits of Gannan Yak.

This study explored the polymorphism of the leucine aminopeptidase (LAP3) gene and its relationship with milk quality characteristics in Gannan yak. A cohort of 162 Gannan yak was genotyped utilizing the Illumina Yak cGPS 7K BeadChip, and the identified single nucleotide polymorphisms (SNPs) were evaluated for their association with milk protein, casein, lactose, and fat concentrations. The results showed that four SNPs (g.4494G > A, g.5919A > G, g.8033G > C, and g.15,615A > G) in the LAP3 gene exhibited polymorphism with information content values of 0.267, 0.267, 0.293, and 0.114, respectively. All four SNPs were in Hardy-Weinberg equilibrium (p > 0.05). The g.4494G > A and g.5919A > G SNPs were significantly associated with protein content (p < 0.05), with homozygous genotypes showing significantly higher protein content than heterozygous genotypes (p < 0.05). The g.8033G > C SNP was significantly associated with casein content, protein content, non-fat solids, and acidity (p < 0.05), with the CC genotype having significantly higher casein, protein, and non-fat solids content than the GG and GC genotypes (p < 0.05). The g.15,615A > G SNP was significantly associated with average fat globule diameter (p < 0.05). In general, the mutations within the LAP3 gene demonstrated a positive impact on milk quality traits in Gannan yak, with mutated genotypes correlating with enhanced milk quality. These results indicate that the LAP3 gene could be a significant or candidate gene affecting milk quality traits in Gannan yak and offer potential genetic markers for molecular breeding programs in this species.

Interpretation of the Yak Skin Single-Cell Transcriptome Landscape.

The morphogenesis of hair follicle structure is accompanied by the differentiation of skin tissue. Mammalian coats are produced by hair follicles. The formation of hair follicles requires signal transmission between the epidermis and dermis. However, knowledge of the transcriptional regulatory mechanism is still lacking. We used single-cell RNA sequencing to obtain 26,573 single cells from the scapular skin of yaks at hair follicle telogen and anagen stages. With the help of known reference marker genes, 11 main cell types were identified. In addition, we further analyzed the DP cell and dermal fibroblast lineages, drew a single-cell map of the DP cell and dermal fibroblast lineages, and elaborated the key genes, signals, and functions involved in cell fate decision making. The results of this study provide a very valuable resource for the analysis of the heterogeneity of DP cells and dermal fibroblasts in the skin and provide a powerful theoretical reference for further exploring the diversity of hair follicle cell types and hair follicle morphogenesis.

Understanding Mammalian Hair Follicle Ecosystems by Single-Cell RNA Sequencing.

Single-cell sequencing technology can fully reflect the heterogeneity of cell populations at the single cell level, making it possible for us to re-recognize various tissues and organs. At present, the sequencing study of hair follicles is transiting from the traditional ordinary transcriptome level to the single cell level, which will provide diverse insights into the function of hair follicle cells. This review focuses on research advances in the hair follicle microenvironment obtained from scRNA-seq studies of major cell types in hair follicle development, with a special emphasis on the discovery of new subpopulations of hair follicles by single-cell techniques. We also discuss the problems and current solutions in scRNA-seq observation and look forward to its prospects.

No significant association between Fc receptor-like 3 gene polymorphisms and human leukocyte antigen-B27 positive ankylosing spondylitis in Han Chinese population.

Ankylosing spondylitis (AS) is a rheumatoid arthritis, which is a common autoimmune disease with a complex genetic etiology. Although HLA-B27 has been identified to be associated with AS, a number of other genes may also be involved in the disease. Fc receptor-like 3 (FCRL3) gene has been shown to be associated with rheumatoid arthritis in Japanese population. Here we aim to explore the association FCRL3 gene and susceptibility to human leukocyte antigen (HLA)-B27-positive AS in Han Chinese population. Among 169 AS patients, the frequencies of C and T (rs7522061) in FCRL3 gene were 38.7 and 61.3%, respectively; in 184 controls (HLA-B27-positive), the frequencies of C and T were 38.6 and 61.4%, respectively. The frequencies of alleles and genotype are not of statistically significant difference in two groups (chi(2) = 0.000, P = 0.983; chi(2) = 0.099, P = 0.952, respectively), but the distribution of HLA-B27 subtypes are statistically significant difference between cases and controls (chi(2) = 8.214, P = 0.042). Our data reveal that the FCRL3 gene does not appear associated with susceptibility to HLA-B27-positive AS in Han Chinese population.

Publisher Correction: Reservoir characteristics and logging evaluation of gas - bearing mudstone in the south of North China Plain.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Reservoir characteristics and logging evaluation of gas-bearing mudstone in the south of North China Plain.

Mudstone is very similar to shale except it lacks sheet bedding. Shale gas is widely concerned and successfully exploited commercially in the world, while gas-bearing mudstone is rarely paid attention. To evaluate the reservoir characteristics and exploitation potential of gas-bearing mudstone, a total of 127 mudstone samples from the Shanxi formation were tested by X-ray diffraction (XRD), scanning electron microscope (SEM), gas content, etc., and the qualitative identification and quantitative evaluation of gas-bearing mudstone reservoirs were performed on four wells using the logging curve overlay method and reservoir parameter calculation equations. The results showed that: (1) the average total gas content of core measurement is 1.81 m3/t, and the total content of brittle minerals is 44.2%, which confirms that mudstones can also have good gas content and fracturing performance; (2) logging evaluation the average thickness of gas-bearing mudstone is 55.7 m, the average total gas content is 1.6 m3/t, and the average brittleness index is 38.1%, which indicates that the mudstone of Shanxi formation in the study area is generally gas-bearing and widely distributed. All the results reveal that gas-bearing mudstone with block bedding has the same exploitation potential as shale with sheet bedding,which deserves more attention.

High-altitude well log evaluation of a permafrost gas hydrate reservoir in the Muli area of Qinghai, China.

The Muli area is the only permafrost region on the Chinese mainland wherein gas hydrates have been discovered. The gas hydrates are present in the fractures and pore spaces of the host rocks with a lamellar or micro-disseminated structure. By combining conventional and image logs, we describe the thickness of the permafrost layer and the well log responses of the gas hydrate reservoir, and calculate the porosity and gas hydrate saturation. We then analyze the advantages and disadvantages of different logging methods for evaluating gas hydrate reservoirs. Our results indicate that (1) gas hydrates are present below the permafrost in the Muli area, (2) gas hydrates predominantly occur in rock fractures, (3) the apparent resistivity is sensitive to gas hydrates present in pore spaces, and both apparent resistivity and acoustic logs are sensitive to gas hydrates present in fractures, (4) a density log is more appropriate for calculating porosity, and (5) gas hydrate saturation can be effectively calculated by the Archie equation, the modified Archie equation, and the Indonesian equation.

Lithology and mineralogy recognition from geochemical logging tool data using multivariate statistical analysis.

The availability of a deep well that penetrates deep into the Ultra High Pressure (UHP) metamorphic rocks is unusual and consequently offers a unique chance to study the metamorphic rocks. One such borehole is located in the southern part of Donghai County in the Sulu UHP metamorphic belt of Eastern China, from the Chinese Continental Scientific Drilling Main hole. This study reports the results obtained from the analysis of oxide log data. A geochemical logging tool provides in situ, gamma ray spectroscopy measurements of major and trace elements in the borehole. Dry weight percent oxide concentration logs obtained for this study were SiO2, K2O, TiO2, H2O, CO2, Na2O, Fe2O3, FeO, CaO, MnO, MgO, P2O5 and Al2O3. Cross plot and Principal Component Analysis methods were applied for lithology characterization and mineralogy description respectively. Cross plot analysis allows lithological variations to be characterized. Principal Component Analysis shows that the oxide logs can be summarized by two components related to the feldspar and hydrous minerals. This study has shown that geochemical logging tool data is accurate and adequate to be tremendously useful in UHP metamorphic rocks analysis.

Use of spectral gamma ray as a lithology guide for fault rocks: A case study from the Wenchuan Earthquake Fault Scientific Drilling project Borehole 4 (WFSD-4).

The main purpose of the Wenchuan Earthquake Fault Scientific drilling project (WFSD) was to produce an in-depth borehole into the Yingxiu-Beichuan (YBF) and Anxian-Guanxian faults in order to gain a much better understanding of the physical and chemical properties as well as the mechanical faulting involved. Five boreholes, namely WFSD-1, WFSD-2, WFSD-3P, WFSD-3 and WFSD-4, were drilled during the project entirety. This study, therefore, presents first-hand WFSD-4 data on the lithology (original rocks) and fault rocks that have been obtained from the WFSD project. In an attempt to determine the physical properties and the clay minerals of the lithology and fault rocks, this study analyzed the spectral gamma ray logs (Total gamma ray, Potassium, Thorium and Uranium) recorded in WFSD-4 borehole on the Northern segment of the YBF. The obtained results are presented as cross-plots and statistical multi log analysis. Both lithology and fault rocks show a variability of spectral gamma ray (SGR) logs responses and clay minerals. This study has shown the capabilities of the SGR logs for well-logging of earthquake faults and proves that SGR logs together with others logs in combination with drill hole core description is a useful method of lithology and fault rocks characterization.

A fast forward algorithm for real-time geosteering of azimuthal gamma-ray logging.

Geosteering is an effective method to increase the reservoir drilling rate in horizontal wells. Based on the features of an azimuthal gamma-ray logging tool and strata spatial location, a fast forward calculation method of azimuthal gamma-ray logging is deduced by using the natural gamma ray distribution equation in formation. The response characteristics of azimuthal gamma-ray logging while drilling in the layered formation models with different thickness and position are simulated and summarized by using the method. The result indicates that the method calculates quickly, and when the tool nears a boundary, the method can be used to identify the boundary and determine the distance from the logging tool to the boundary in time. Additionally, the formation parameters of the algorithm in the field can be determined after a simple method is proposed based on the information of an offset well. Therefore, the forward method can be used for geosteering in the field. A field example validates that the forward method can be used to determine the distance from the azimuthal gamma-ray logging tool to the boundary for geosteering in real-time.

Crosswell electromagnetic modeling from impulsive source: Optimization strategy for dispersion suppression in convolutional perfectly matched layer.

This study applied the finite-difference time-domain (FDTD) method to forward modeling of the low-frequency crosswell electromagnetic (EM) method. Specifically, we implemented impulse sources and convolutional perfectly matched layer (CPML). In the process to strengthen CPML, we observed that some dispersion was induced by the real stretch κ, together with an angular variation of the phase velocity of the transverse electric plane wave; the conclusion was that this dispersion was positively related to the real stretch and was little affected by grid interval. To suppress the dispersion in the CPML, we first derived the analytical solution for the radiation field of the magneto-dipole impulse source in the time domain. Then, a numerical simulation of CPML absorption with high-frequency pulses qualitatively amplified the dispersion laws through wave field snapshots. A numerical simulation using low-frequency pulses suggested an optimal parameter strategy for CPML from the established criteria. Based on its physical nature, the CPML method of simply warping space-time was predicted to be a promising approach to achieve ideal absorption, although it was still difficult to entirely remove the dispersion.

The protective antibodies induced by a novel epitope of human TNF-alpha could suppress the development of collagen-induced arthritis.

Tumor necrosis factor alpha (TNF-alpha) is a major inflammatory mediator that exhibits actions leading to tissue destruction and hampering recovery from damage. At present, two antibodies against human TNF-alpha (hTNF-alpha) are available, which are widely used for the clinic treatment of certain inflammatory diseases. This work was undertaken to identify a novel functional epitope of hTNF-alpha. We performed screening peptide library against anti-hTNF-alpha antibodies, ELISA and competitive ELISA to obtain the epitope of hTNF-alpha. The key residues of the epitope were identified by means of combinatorial alanine scanning and site-specific mutagenesis. The N terminus (80-91 aa) of hTNF-alpha proved to be a novel epitope (YG1). The two amino acids of YG1, proline and valine, were identified as the key residues, which were important for hTNF-alpha biological function. Furthermore, the function of the epitope was addressed on an animal model of collagen-induced arthritis (CIA). CIA could be suppressed in an animal model by prevaccination with the derivative peptides of YG1. The antibodies of YG1 could also inhibit the cytotoxicity of hTNF-alpha. These results demonstrate that YG1 is a novel epitope associated with the biological function of hTNF-alpha and the antibodies against YG1 can inhibit the development of CIA in animal model, so it would be a potential target of new therapeutic antibodies.

[Immunogenicity of a synthetic peptide vaccine from glucosyltransferase].

OBJECTIVE: To measure the immunogenicity of a synthetic peptide of glucosyltransferase (GTF) for designing synthetic peptide-based vaccine of dental caries. METHODS: A fusion 27-mer peptide, containing the conserved regions within catalytic and glucan-binding domains of GTF, was synthesized. Serum antibodies to the synthetic peptide were determined by ELISA method. Inhibitions of both GTF activity and S. mutans adherence were detected for the functions of antisera. RESULTS: The sequence of fusion peptide vaccine was ANDVDNSNPVVQAEQLYFRANGVQVKG. The spleen weights of immunized mice were heavier than the control ones. Specific antibodies were effectually elicited. The immune sera not only inhibited GTF enzymatic activity but also inhibited the vitro adherence of S. mutans. CONCLUSIONS: The peptide vaccine which involves antibody-mediated inhibition of the catalytic and the glucan-binding activities of GTF may be valuable for controlling the dental caries.

[A pilot study of repair of periodontal bone defects with carbonated phosphate bone cement modified with synthesized peptides in dogs].

OBJECTIVE: To explore the possibility of repairing periodontal defects with carbonated calcium phosphate bone cement (CCPBC) modified with synthesized peptides. METHODS: Periodontal bone defects in 4 dogs were surgically created and then restored directly with hydroxyapatite (HA), Perioglass, CCPBC and CCPBC modified with peptides. The results were compared at different levels. RESULTS: Bone replacement materials were lost in HA and Perioglass groups. In the HA group defects were restored with connective tissue. Perioglass group had only a little new bone around materials by alveolar bone. CCPBC could firmly stay in bone defects to maintain the space of bone defects even without membrane use. CCPBC modified with peptides was superior to HA, Perioglass, and CCPBC, surrounded by a great deal of new bone. CONCLUSION: Under limitation of this study, CCPBC modified with peptides has some osteoinuctive activity and may have good prospect for the clinical application in periodontal defect repair.