Estimation of Genetic Parameters for Early Growth Traits in Luzhong Mutton Sheep.

In this study, six different animal models were fitted, and the constrained maximum likelihood method was used to assess the genetic parameters and genetic trends of early growth traits in Luzhong mutton sheep. The experimental data of this study included the newborn weight (BWT, N = 2464), weaning weight (WWT, N = 2923), weight at 6 months of age (6WT, N = 2428), average daily weight gain from birth to weaning (ADG1, N = 2424), and average daily weight gain from weaning to 6 months of age (ADG2, N = 1836) in Luzhong mutton sheep (2015~2019). The best model for the genetic parameters of the five traits in Luzhong mutton sheep was identified as Model 4 using the Akaike information criterion (AIC) and likelihood ratio test (LRT) methods, in which the estimated values of direct heritability for the BWT, WWT, 6WT, ADG1, and ADG2 were 0.156 ± 0.057, 0.547 ± 0.031, 0.653 ± 0.031, 0.531 ± 0.035, and 0.052 ± 0.046, respectively, and the values for maternal heritability were 0.201 ± 0.100, 0.280 ± 0.047, 0.197 ± 0.053, 0.275 ± 0.052, and 0.081 ± 0.092, respectively. The genetic correlation between the ADG2 and WWT was negative, and the genetic and phenotypic correlations among the remaining traits were positive. In this study, maternal effects had a more significant influence on early growth traits in Luzhong mutton sheep. In conclusion, to effectively improve the accuracy of genetic parameter estimation, maternal effects must be fully considered to ensure more accurate and better breeding planning.

Isobutyramide and Slow-Release Urea as Substitutes for Soybean Meal in the Finishing Diet of Beef Cattle.

Two experiments were conducted to investigate the effects of isobutyramide (IBA) and slow-release urea (SRU) as substitutes for soybean meal (SBM) in the finishing diet of beef cattle. The completely randomized design in vitro experiment with five treatments, i.e., control, 0.9% SRU group, 0.6% SRU + 0.3% IBA group (SRU-I), 0.3% SRU + 0.6% IBA group (IBA-S), 0.9% IBA group was conducted. The results showed that the IBA-S and IBA increased (p ≤ 0.05) substrate disappearance of dry matter (DM), neutral detergent fiber (NDF), acid detergent fiber (ADF), total gas, and total volatile fatty acids (TVFA). The SRU group had the highest (p < 0.01) crude protein disappearance and ammonia nitrogen concentration, but the IBA contrarily decreased (p < 0.01) them compared with the control. Inclusion of IBA increased isobutyrate concentrations (p = 0.01) with the highest value for the IBA group. Then, an 84-day replicate 4 × 4 Latin square design with 8 Angus steers and four treatments, i.e., control, SRU, SRU-I, IBA-S was performed. The results showed that the treatments did not affect DM intake (p > 0.05) but tended (p = 0.09) to increase average daily gain. The inclusion of IBA increased (p < 0.05) the apparent digestibility of DM, organic matter, NDF, ADF, TVFA, and microbial crude protein with the highest values for the IBA-S group. The IBA-contained groups also increased (p ≤ 0.01) isobutyrate concentration, activities of carboxymethyl cellulase and xylanase, and the relative abundance of Butyrivibrio fibrisolvens with the highest values for the IBA-S group. The SRU had no effect on animal growth and nutrient apparent digestibility. In conclusion, IBA was developed as a new substitute for SBM in the finishing diet of beef cattle, and the optimal strategy was the isonitrogenous substitution of SBM with 0.3% SRU and 0.6% IBA of the diet.

Genome-Wide DNA Methylation Analysis and Functional Validation of Litter Size Traits in Jining Grey Goats.

DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (SERPINB2: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, CFAP43: chr26_27046601_27046800, LRP1B. chr2_79720201_79720400, EPHA6: chr1_40088601_40088800, TTC29: chr17_59385801_59386000, PDE11A: chr2_117418601_117418800 and PGF: chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size.

MiR-23b and miR-133 Cotarget TGFß2/NOTCH1 in Sheep Dermal Fibroblasts, Affecting Hair Follicle Development.

Wool is produced and controlled by hair follicles (HFs). However, little is known about the mechanisms involved in HF development and regulation. Sheep dermal fibroblasts (SDFs) play a key role in the initial stage of HF development. Analyzing the molecular mechanism that regulates early HF development in superfine wool sheep is of great importance for better understanding the HF morphogenesis process and for the breeding of fine wool sheep. Here, we show that two microRNAs (miRNAs) affect the development of HFs by targeting two genes that are expressed by SDFs. Meanwhile, the overexpression and inhibition of oar-miR-23b and oar-miR-133 in SDFs cells and cell proliferation, apoptosis, and migration were further detected using a CCK-8 assay, an Annexin V-FITC assay, a Transwell assay, and flow cytometry. We found that oar-miR-23b, oar-miR-133, and their cotarget genes TGFß2 and NOTCH1 were differentially expressed during the six stages of HF development in superfine wool sheep. Oar-miR-23b and oar-miR-133 inhibited the proliferation and migration of SDFs and promoted the apoptosis of SDFs through TGFß2 and NOTCH1. oar-miR-23b and oar-miR-133 inhibited the proliferation and migration of SDFs by jointly targeting TGFß2 and NOTCH1, thereby inhibiting the development of superfine wool HFs. Our research provides a molecular marker that can be used to guide the breeding of ultrafine wool sheep.

scRNA-seq and proteomics reveal the distinction of M2-like macrophages between primary and recurrent malignant glioma and its critical role in the recurrence.

AIMS: Tumor-associated macrophages (TAMs) in the immune microenvironment play an important role in the increased drug resistance and recurrence of malignant glioma, but the mechanism remains incompletely inventoried. The focus of this study was to investigate the distinctions of M2-like TAMs in the immune microenvironment between primary and recurrent malignant glioma and its influence in the recurrence. METHODS: We employed single-cell RNA sequencing to construct a single-cell atlas for a total of 23,010 individual cells from 6 patients with primary or recurrent malignant glioma and identified 5 cell types, including TAMs and malignant cells. Immunohistochemical techniques and proteomics analysis were performed to investigate the role of intercellular interaction between malignant cells and TAMs in the recurrence of malignant glioma. RESULTS: Six subgroups of TAMs were annotated and M2-like TAMs were found to increase in recurrent malignant glioma significantly. A pseudotime trajectory and a dynamic gene expression profiling during the recurrence of malignant glioma were reconstructed. Up-regulation of several cancer pathways and intercellular interaction-related genes are associated with the recurrence of malignant glioma. Moreover, the M2-like TAMs can activate the PI3K/Akt/HIF-1α/CA9 pathway in the malignant glioma cells via SPP1-CD44-mediated intercellular interaction. Interestingly, high expression of CA9 can trigger the immunosuppressive response in the malignant glioma, thus promoting the degree of malignancy and drug resistance. CONCLUSION: Our study uncovers the distinction of M2-like TAMs between primary and recurrent glioma, which offers unparalleled insights into the immune microenvironment of primary and recurrent malignant glioma.

Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors.

BACKGROUND: Human primary hepatocytes (PHCs) are considered to be the best cell source for cell-based therapies for the treatment of end-stage liver disease and acute liver failure. To obtain sufficient and high-quality functional human hepatocytes, we have established a strategy to dedifferentiate human PHCs into expandable hepatocyte-derived liver progenitor-like cells (HepLPCs) through in vitro chemical reprogramming. However, the reduced proliferative capacity of HepLPCs after long-term culture still limits their utility. Therefore, in this study, we attempted to explore the potential mechanism related to the proliferative ability of HepLPCs in vitro culture. RESULTS: In this study, analysis of assay for transposase accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) were performed for PHCs, proliferative HepLPCs (pro-HepLPCs) and late-passage HepLPCs (lp-HepLPCs). Genome-wide transcriptional and chromatin accessibility changes during the conversion and long-term culture of HepLPCs were studied. We found that lp-HepLPCs exhibited an aged phenotype characterized by the activation of inflammatory factors. Epigenetic changes were found to be consistent with our gene expression findings, with promoter and distal regions of many inflammatory-related genes showing increased accessibility in the lp-HepLPCs. FOSL2, a member of the AP-1 family, was found to be highly enriched in the distal regions with increased accessibility in lp-HepLPCs. Its depletion attenuated the expression of aging- and senescence-associated secretory phenotype (SASP)-related genes and resulted in a partial improvement of the aging phenotype in lp-HepLPCs. CONCLUSIONS: FOSL2 may drive the aging of HepLPCs by regulating inflammatory factors and its depletion may attenuate this phenotypic shift. This study provides a novel and promising approach for the long-term in vitro culture of HepLPCs.

Integrated analysis of miRNAs and mRNA profiling reveals the potential roles of miRNAs in sheep hair follicle development.

BACKGROUND: Merino sheep exhibit high wool production and excellent wool quality. The fleece of Merino sheep is predominantly composed of wool fibers grown from hair follicles (HFs). The HF is a complex biological system involved in a dynamic process governed by gene regulation, and gene expression is regulated by microRNAs (miRNAs). miRNA inhibits posttranscriptional gene expression by specifically binding to target messenger RNA (mRNA) and plays an important role in regulating gene expression, the cell cycle and biological development sequences. The purpose of this study was to examine mRNA and miRNA binding to identify key miRNAs and target genes related to HF development. This will provide new and important insights into fundamental mechanisms that regulate cellular activity and cell fate decisions within and outside of the skin. RESULTS: We analyzed miRNA data in skin tissues collected from 18 Merino sheep on four embryonic days (E65, E85, E105 and E135) and two postnatal days (D7 and D30) and identified 87 differentially expressed miRNAs (DE-miRNAs). These six stages were further divided into two longer developmental stages based on heatmap cluster analysis, and the results showed that DE-mRNAs in Stage A were closely related to HF morphogenesis. A coanalysis of Stage A DE-mRNAs and DE-miRNAs revealed that 9 DE-miRNAs and 17 DE-mRNAs presented targeting relationships in Stage A. We found that miR-23b and miR-133 could target and regulate ACVR1B and WNT10A. In dermal fibroblasts, the overexpression of miR-133 significantly reduced the mRNA and protein expression levels of ACVR1B. The overexpression of miR-23b significantly reduced the mRNA and protein expression levels of WNT10A. CONCLUSION: This study provides a new reference for understanding the molecular basis of HF development and lays a foundation for further improving sheep HF breeding. miRNAs and target genes related to hair follicular development were found, which provided a theoretical basis for molecular breeding for the culture of fine-wool sheep.

Effect of the FA2H Gene on cashmere fineness of Jiangnan cashmere goats based on transcriptome sequencing.

BACKGROUND: Cashmere goats are a heterogeneous hairy mammal. The fineness of cashmere can affect its economic value. Therefore, in this study, we used transcriptome sequencing techniques to analyze the gene expression profiles of the skin tissues of cashmere goats with different cashmere fineness. The selected candidate genes were functionally verified with the secondary hair follicle hair papillary cells of cashmere goats. RESULTS: We identified 479 DEGs, of which 238 mRNAs were up-regulated in the fine velvet group and 241 mRNA were down-regulated. Based on functional annotation and protein interaction network analysis, we found some genes that may affect the fineness of cashmere, including SOX18, SOX4, WNT5A, IGFBP4, KAP8, KRT36, and FA2H. Using qRT-PCR, Western blot, CCK-8 cell viability detection, EDU cell proliferation detection, and flow cytometry, we found that overexpression of the FA2H gene could promote the proliferation of secondary hair follicle DPCs in cashmere goats. At the same time, we proved that FA2H could regulate the expression levels of the FGF5 and BMP2 genes in DPCs. CONCLUSION: The results of this study provide a useful reference for the genetics and breeding of Jiangnan cashmere goats and goat genome annotation, and provide an experimental basis for improving cashmere quality of the cashmere goat.

Gene network analysis reveals candidate genes related with the hair follicle development in sheep.

BACKGROUND: Merino sheep are the most famous fine wool sheep in the world. They have high wool production and excellent wool quality and have attracted worldwide attention. The fleece of the Merino sheep is composed predominantly of wool fibers grown from secondary wool follicles. Therefore, it is necessary to study the development of hair follicles to understand the mechanism of wool production. The hair follicle is a complex biological system involved in a dynamic process governed by gene regulation. The hair follicle development process is very complex and poorly understood. The purpose of our research is to identify candidate genes related to hair follicle development, provide a theoretical molecular breeding basis for the cultivation of fine wool sheep, and provide a reference for the problems of hair loss and alopecia areata that affect human beings. RESULTS: We analyzed mRNAs data in skin tissues of 18 Merino sheep at four embryonic days (E65, E85, E105 and E135) and two postnatal days (P7 and P30). G1 to G6 represent hair follicles developmental at six stages (i.e. E65 to P30). We identified 7879 differentially expressed genes (DEGs) and 12623 novel DEGs, revealed different expression patterns of these DEGs at six stages of hair follicle development, and demonstrated their complex interactions. DEGs with stage-specific expression were significantly enriched in epidermal differentiation and development, hair follicle development and hair follicle morphogenesis and were enriched in many pathways related to hair follicle development. The key genes (LAMA5, WNT10A, KRT25, SOSTDC1, ZDHHC21, FZD1, BMP7, LRP4, TGFß2, TMEM79, SOX10, ITGB4, KRT14, ITGA6, and GLI2) affecting hair follicle morphogenesis were identified by network analysis. CONCLUSION: This study provides a new reference for the molecular basis of hair follicle development and lays a foundation for further improving sheep hair follicle breeding. Candidate genes related to hair follicular development were found, which provided a theoretical basis for molecular breeding for the culture of fine wool sheep. These results are a valuable resource for biological investigations of fleece evolution in animals.

CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency.

Polycomb group (PcG) proteins are essential for post-implantation development by depositing repressive histone modifications at promoters, mainly CpG islands (CGIs), of developmental regulator genes. However, promoter PcG marks are erased after fertilization and de novo established in peri-implantation embryos, coinciding with the transition from naive to primed pluripotency. Nevertheless, the molecular basis for this establishment remains unknown. In this study, we show that the expression of the long KDM2B isoform (KDM2BLF), which contains the demethylase domain, is specifically induced at peri-implantation and that its H3K36me2 demethylase activity is required for PcG enrichment at CGIs. Moreover, KDM2BLF interacts with BRG1/BRM-associated factor (BAF) and stabilizes BAF occupancy at CGIs for subsequent gain of accessibility, which precedes PcG enrichment. Consistently, KDM2BLF inactivation results in significantly delayed post-implantation development. In summary, our data unveil dynamic chromatin configuration of CGIs during exit from naive pluripotency and provide a conceptual framework for the spatiotemporal establishment of PcG functions.

Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN.

Key transcription factors (TFs) play critical roles in zygotic genome activation (ZGA) during early embryogenesis, whereas genome-wide occupancies of only a few factors have been profiled during ZGA due to the limitation of cell numbers or the lack of high-quality antibodies. Here, we present FitCUT&RUN, a modified CUT&RUN method, in which an Fc fragment of immunoglobulin G is used for tagging, to profile TF occupancy in an antibody-free manner and demonstrate its reliability and robustness using as few as 5000 K562 cells. We applied FitCUT&RUN to zebrafish undergoing embryogenesis to generate reliable occupancy profiles of three known activators of zebrafish ZGA: Nanog, Pou5f3, and Sox19b. By profiling the time-series occupancy of Nanog during zebrafish ZGA, we observed a clear trend toward a gradual increase in Nanog occupancy and found that Nanog occupancy prior to the major phase of ZGA is important for the activation of some early transcribed genes.

Gallic acid as a key substance to inhibit proliferation and adipogenesis in bovine subcutaneous adipocyte.

Gallic acid (GA) is a widespread naturally occurring phenolic acid and one of the main active monomers that forms polyphenols such as tannins. In recent years, GA has been found as a potential regulator in lipid metabolism. However, effects and possible mechanisms of GA on cell growth and lipid metabolism of bovine subcutaneous adipocytes remain unknown. In this study, we investigated whether GA could affect proliferation and adipogenesis of subcutaneous adipocyte in beef cattle. We found that GA possesses inhibitive effects on proliferation and adipogenesis of bovine subcutaneous adipocyte via activating the metabolic master factor AMP-activated protein kinase alpha (AMPKα) to promote programmed cell death and lipolysis. The findings prove GA is a key substance to inhibit proliferation and adipogenesis of bovine subcutaneous adipocyte in vitro. Further in vivo study needs conducted to verify the reductive effects of GA on subcutaneous fat in beef cattle.

Protective effect of resveratrol against hydrogen peroxide-induced oxidative stress in bovine skeletal muscle cells.

The objective of this study was to investigate the protective effects and the underlying mechanisms of resveratrol (RES) against hydrogen peroxide (H2O2)-induced oxidative stress in bovine skeletal muscle cells (BMCs). Pretreatment of BMCs with RES prior to H2O2 exposure increased cell viability, attenuated reactive oxygen species, and stabilized the redox state. H2O2 exposure activated sirtuin type 1 (SIRT1) and nuclear factor E2-related factor 2 (NRF2)-mediated signaling pathways. Pretreatment with RES did not alter SIRT1-regulated genes but inhibited the upregulation of NRF2, whereas enhanced heme oxygenase 1 (HO-1) expression. Pretreatment with RES prior to H2O2 exposure failed to suppress NRF2 expression when NRF2 was knocked down by RNA interference. However, HO-1 expression still could be induced by RES. These results suggest that RES has benifical effects against oxidative stress. NRF2-mediated pathway play an important role, and HO-1 upregulation is the key process in RES regulation. RES may be used as a therapeutic agent for meat quality improvement in beef cattle.

Rare-earth nanoparticles induce depression, anxiety-like behavior, and memory impairment in mice.

Rare-earth nanoparticles have been widely studied for disease diagnosis, in vivo optical imaging, biosensing, and drug delivery. However, the effects of rare-earth nanoparticles on a central nervous system remain unclear. Here, we report that the continuous exposure to rare-earth nanoparticles in mice can cause behavioral alterations including cognitive deficits, anxiety, and depression-like behavior. Using an open-field test and a morris water maze, we showed that long-term exposure to rare-earth nanoparticles may lead to significant depression, anxiety-like behavior, and memory impairment. The histopathological investigation on the neurotoxicological effects of nanoparticles indicated a significant decrease in cell viability after seven days' nanoparticle exposure. Western blotting analysis suggested that the changes of ATP-citrate lyase (ACLY) and O-linked N-acetylglucosamine transferase (OGT, a unique glycosyltransferase enzyme) played important roles in neurobehavioral disorders in mice. These findings provide a pathway to understand the cytotoxicity of rare-earth nanoparticles for medial applications and offer insights into the risk of these nanoparticles in biological systems.

Regulation of microRNA-33, SREBP and ABCA1 genes in a mouse model of high cholesterol.

MicroRNAs are short non-coding RNAs that regulate gene expression. Several microRNAs, useful for coronary artery disease assessment, have previously been identified. MicroRNA-33 is located within SREBP introns and controls cholesterol homeostasis. In order to find the possibility of microRNA-33 as a potential biomarker in high cholesterol disease, we developed a mouse model for coronary heart disease by feeding mice with a high-fat diet. The expression differences of microRNA-33, SREBP and ABCA1 genes in the liver, muscle, and lipid tissues were compared between a high-cholesterol group and control group in mice. The results showed that ABCA1 was up-regulated by high cholesterol conditions in liver, muscle and lipid tissues. SREBP1C was up-regulated by high cholesterol conditions in the liver and lipid tissues and down-regulated by high cholesterol conditions in the muscle tissue. MicroRNA-33 and SREBP2 were down-regulated by high cholesterol conditions in the liver and muscle tissues and up-regulated by high cholesterol conditions in the lipid tissue. Our study suggests that antisense therapeutic targeting of microRNA-33 may be a potential biomarker for cardiovascular disease.

NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.

BACKGROUND: Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public data sets. RESULTS: The NUCOME is a database focused on filtering qualified nucleosome organization referenced landscapes covering various cell types in human and mouse based on QC metrics. The filtering strategy guarantees the quality of nucleosome organization referenced landscapes and exempts users from redundant data set selection and processing. The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci. CONCLUSIONS: The NUCOME provides valuable data resources for integrative analyses focus on nucleosome organization. The NUCOME is freely available at http://compbio-zhanglab.org/NUCOME .

Interaction between valproic acid and carbapenems: decreased plasma concentration of valproic acid and liver injury.

BACKGROUND: Several case reports and retrospective studies have indicated that carbapenems decrease the plasma concentration of valproic acid (VPA). This retrospective study examines the effect of carbapenems on VPA levels, and explores whether the drug-drug interaction can influence the liver function of patients. METHODS: The data of 141 patients were collected from the Department of Neurosurgery at Shanxi Bethune Hospital from January 2018 to December 2019. We compared the VPA levels between the VPA monotherapy group and VPA + carbapenem group to evaluate the influence of carbapenem antibiotics on the plasma concentration of VPA. We also compared the liver injury rate of the VPA monotherapy group, VPA + meropenem group, and VPA + imipenem group to evaluate the influence of concomitant use of VPA with carbapenem antibiotics on liver function. RESULTS: The VPA serum concentration in the VPA + meropenem group was 22.32±21.77 µg/mL, which was markedly lower than that in the VPA monotherapy group (i.e., without carbapenems) (65.17±21.49 µg/mL) (P<0.01). The rate of liver injury was significantly different between the VPA monotherapy, VPA + meropenem, and VPA + imipenem groups (χ2=30.13, P<0.01). Further comparisons showed that the liver injury rate of the VPA + meropenem group (35.42%) was higher than that of the VPA + imipenem (3.7%) and VPA monotherapy (1.52%) groups (P<0.01). Although no significant differences in liver injury rate were observed between the VPA + imipenem (3.7%) and VPA monotherapy (1.52%) groups, the alanine aminotransferase (ALT) value of the VPA + imipenem group after co-administration (65.22±48.01 U/L) was notably higher than before (40.48±24.97 U/L) (P<0.01). CONCLUSIONS: In this study, the interaction between VPA and carbapenems resulted in decreased plasma concentrations of VPA as well as possible liver injury. Clinicians should be aware of this potential interaction, and closely monitor VPA concentrations and liver function. Different carbapenems combined with VPA showed different effects on both VPA concentration and liver function, indicating that the mechanisms of these two effects might be related.

GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization.

BACKGROUND: Germline cells are important carriers of genetic and epigenetic information transmitted across generations in mammals. During the mammalian germline cell development cycle (i.e., the germline cycle), cell potency changes cyclically, accompanied by dynamic transcriptional changes and epigenetic reprogramming. Recently, to understand these dynamic and regulatory mechanisms, multiomic analyses, including transcriptomic and epigenomic analyses of DNA methylation, chromatin accessibility and histone modifications of germline cells, have been performed for different stages in human and mouse germline cycles. However, the long time span of the germline cycle and material scarcity of germline cells have largely limited the understanding of these dynamic characteristic changes. A tool that integrates the existing multiomics data and visualizes the overall continuous dynamic trends in the germline cycle can partially overcome such limitations. RESULTS: Here, we present GLEANER, a web server for GermLine cycle Expression ANalysis and Epigenetics Roadmap visualization. GLEANER provides a comprehensive collection of the transcriptome, DNA methylome, chromatin accessibility, and H3K4me3, H3K27me3, and H3K9me3 histone modification characteristics in human and mouse germline cycles. For each input gene, GLEANER shows the integrative analysis results of its transcriptional and epigenetic features, the genes with correlated transcriptional changes, and the overall continuous dynamic trends in the germline cycle. We further used two case studies to demonstrate the detailed functionality of GLEANER and highlighted that it can provide valuable clues to the epigenetic regulation mechanisms in the genetic and epigenetic information transmitted during the germline cycle. CONCLUSIONS: To the best of our knowledge, GLEANER is the first web server dedicated to the analysis and visualization of multiomics data related to the mammalian germline cycle. GLEANER is freely available at http://compbio-zhanglab.org/GLEANER .

Caffeic acid modulates methane production and rumen fermentation in an opposite way with high-forage or high-concentrate substrate in vitro.

BACKGROUND: Plant secondary metabolites, including tannins, saponins and phenolic acids, possess potential methane (CH4 ) inhibition bioactivity. Caffeic acid (CA), as one of the typical phenolic acids, serves as a promising rumen CH4 inhibitor, but the underlying mechanisms and investigations with typical formulated rations are still not well documented. Therefore, a batch culture study was conducted to investigate the effects of CA on methanogenesis, rumen fermentation and growth of ruminal microorganisms when high-forage or high-concentrate substrates are fermented. RESULTS: After 48 h incubations, adding CA up to 40 g kg-1 dry matter linearly reduced (P < 0.05) the disappearance of dry matter, neutral detergent fiber (NDFD), total gas, methanogenesis, total volatile fatty acid and 16S rDNA copy numbers of Ruminococcus albus and Butyrivibrio fibrisolvens, and increased 16S rDNA copy numbers of methanogens for the high-forage treatment. For the high-concentrate treatment, CA exerted opposite effects (P < 0.05) on the above variables, except that CA did not affect (P > 0.05)16S rDNA copy numbers of methanogens or R. albus. CONCLUSION: Caffeic acid inhibited in vitro methanogenesis and rumen fermentation with high-forage substrate incubation. Contrarily, CA benefited in vitro fermentation and enhanced methanogenesis with high-concentrate substrate incubation. It suggests that CA modulates methanogenesis and rumen fermentation mainly by affecting the growth of cellulolytic bacteria in vitro. © 2020 Society of Chemical Industry.

Immunohistochemical Analysis of PGC-1α and ERRα Expression Reveals Their Clinical Significance in Human Ovarian Cancer.

PURPOSE: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) and estrogen-related receptor alpha (ERRα) play a vital role in various human cancers. The purpose of this study was to investigate whether the PGC-1α/ERRα axis could serve as an effective prognostic marker in ovarian cancer (OC). PATIENTS AND METHODS: We investigated the expression of both PGC-1α and ERRα in 42 ovarian cancer and 31 noncancerous ovarian samples by immunohistochemistry (IHC). The relationship between the expression of PGC-1α and ERRα in OC and the clinical characteristics of patients was evaluated. In addition, data from the Human Protein Atlas (HPA) database were collected to validate the prognostic significance of PGC-1α and ERRα mRNA expression in OC. RESULTS: PGC-1α and ERRα showed notably higher expression in OC tissues than in noncancerous tissues (P=0.0059, P=0.002). Moreover, in patients with OC, high ERRα and PGC-1α/ERRα expression significantly correlated with tumor differentiation (P=0.027; P=0.04), lymph node status (P=0.023; P=0.021), CA125 (P=0.036; P=0.021), and HE4 (P=0.021; P=0.05), while high PGC-1α expression was only significantly associated with tumor differentiation (P=0.029). The combined analysis of high PGC-1α and ERRα expression revealed a tendency towards poor cancer-specific survival (P=0.1276). CONCLUSION: PGC-1α and ERRα are overexpressed in OC and might be significant prognostic factors for this cancer.