Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones

Background Sex hormones play important roles in the estrus return of post-weaning sows.Previous studies have demonstrated a complex and bi-directional regulation between sex hormones and gut microbiota.However,the extent to which the gut microbiota affects estrus return of post-weaning sows is largely unknown.Results In this study,we first screened 207 fecal samples from well-phenotyped sows by 16S rRNA gene sequencing and identified significant associations between microbes and estrus return of post-weaning sows.Using metagenomic sequencing data from 85 fecal samples,we identified 37 bacterial species that were significantly associated with estrus return.Normally returning sows were characterized by increased abundances of L.reuteri and P.copri and decreased abundances of B.fragilis,S.suis,and B.pseudolongum.The changes in gut microbial composition significantly altered the functional capacity of steroid hormone biosynthesis in the gut microbiome.The results were confirmed in a validation cohort.Significant changes in sex steroid hormones and related compounds were found between normal and non-return sows via metabolome analysis.An integrated analysis of differential bacterial species,metagenome,and fecal metabolome provided evidence that normal return-associated bacterial species L.reuteri and Prevotella spp.participated in the degradation of pregnenolone,progesterone,and testosterone,thereby promoting estrogen biosynthesis.Furthermore,the microbial metabolites related to sow energy and nutrient supply or metabolic disorders also showed relationships with sow estrus return.Conclusions An integrated analysis of differentially abundant bacterial species,metagenome,and fecal metabolome revealed the involvement of L.reuteri and Prevotella spp.in sow estrus return.These findings provide deep insight into the role of gut microbiota in the estrus return of post-weaning sows and the complex cross-talk between gut microbiota and sex hormones,suggesting that the manipulation of the gut microbiota could be an effective strategy to improve sow estrus return after weaning.

Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.

成人腭大孔解剖与腭穹隆形态相关性的CBCT影像研究

目的 研究成人腭大孔(greater palatine foramen,GPF)解剖位置及其与腭穹窿高低的相关性,为涉及上腭区域的临床操作提供理论依据。方法 从昆明医科大学附属口腔医院影像科收集2020年1~6月符合纳入标准的180名成人患者的CBCT图像,评估双侧360例腭大孔相对于上颌磨牙的位置以及距上颌腭中缝线和釉牙骨质界的距离,并分析不同腭穹窿高低与腭大孔分布的关联。结果 腭大孔在第2磨牙腭侧、第3磨牙近中腭侧、第3磨牙腭侧的分布率分别是21.39%、21.11%和57.50%。男性和女性腭大孔与腭中缝(midsagittal suture,MMS)的距离(GPF-MMS)分别为(16.31±1.18) mm和(15.82±1.32) mm,腭大孔至对应磨牙釉牙骨质界(enamelo-cemental junction,CEJ)的距离(GPF-M)为(17.11±2.50) mm和(15.79±2.57) mm,均显示男性大于女性(P <0.05)。GPF-MMS在高腭组中略低于低腭组(P <0.05);然而,GPF-M在高腭组中明显高于低腭组(P <0.05)。结论 成人腭大孔位置与其性别和腭穹隆高低有关。

Mimotope peptide modified pompon mum-like magnetic microparticles for precise recognition,capture and biotransformation analysis of rituximab in biological fluids

Due to low immobilized ligand density,limited binding capacity,and severe interference from serum proteins,developing ideal peptide-based biomaterials for precise recognition and in vivo analysis of biopharmaceuticals remains a huge challenge.In this study,mimotope peptide modified pompon mum-like biomimetic magnetic microparticles(MMPs,3.8μm)that mimic the specific functionalities of CD20 on malignant B cells were developed for the first time.Benefit from the numerous ligand binding sites(Ni^(2+))on the pompon mum-like MMPs,these novel materials achieved≥10 times higher peptide ligand densities(>2300 mg/g)and antibody binding capacities(1380 mg/g)compared to previous reported biomaterials.Leveraging the high specificity of the mimotope peptide,rituximab can be precisely recognized and enriched from cell culture media or serum samples.We also established an LC-MS/MS method using the MMPs for tracking rituximab biotransformation in patient serum.Intriguingly,deamidation of Asn55 and Asn33,as well as oxidation of Met81 and Met34 were observed at the key complementarity determining regions of rituximab,which could potentially influence antibody function and require careful monitoring.Overall,these versatile biomimetic MMPs demonstrate superior recognition and enrichment capabilities for target antibodies,offering interesting possibilities for biotransformation analysis of biopharmaceuticals in patient serum.

Unravelling the genetic basis for skeletal muscle mitochondrial DNA copy number variations in pigs

Dear Editor,Mitochondria are the center of cellular energy generation and free radical metabolism,with important functions in regulating intracellular calcium levels,cell apoptosis,cell cycle and epigenetic modifications.Mitochondrial DNA copy number(mtDNA-CN)is an indicator of mitochondrial biogenesis and has been associated with several diseases,such as cardiovascular disease,depression,chronic kidney disease and aging in humans(Clyde,2022).

Correction:Fundamental and practical approaches for single-cell ATAC-seq analysis

Correction:aBIOTECH(2022)3:212–223 https://doi.org/10.1007/s42994-022-00082-5 The copyright holder for this article was incorrectly given as’Agricultural Information Institute,Chinese Academy of Agricultural Sciences’but should have been’The Authors’.This article was originally published with the incorrect licence;it should have been:Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,which permits use,sharing,adaptation,distribution and reproduction in any medium or format,as long as you give appropriate credit to the original author(s)and the source,provide a link to the Creative Commons licence,and indicate if changes were made.The images or other third party material in this article are included in the article’s Creative Commons licence,unless indicated otherwise in a credit line to the material.

Polyhalogenated carbazoles induce hepatic metabolic disorders in mice via alteration in gut microbiota

Polyhalogenated carbazoles(PHCZs)have been widely accepted as emerging pollutants,whereas their ecological and health risks remain uncertain.Herein,female and male Sprague-Dawley(SD)mice were treated with four typical PHCZs to investigate their negative consequences,along with alternations in gutmicrobiota to indicate underlyingmechanisms.In female mice,the relative liver weight ratio increased after four PHCZs exposure;2-bromocarbazole(2-BCZ)increased urine glucose level;3-bromocarbazole(3-BCZ)decreased the glucose and total cholesterol levels;3,6-dichlorocarbazole(3,6-DCCZ)decreased glucose level.The only disturbed biochemical index in male mice was the promoted alkaline phosphatase(ALP)level by 3,6-DCCZ.We also found that the differential blood biochemical indices were correlated with gut microbiota.3-BCZ and 3,6-DCCZ altered Bacteroidetes and Proteobacteria phyla in female and male mice,which were correlated with metabolic disorders.Our findings demonstrated the correlation between PHCZs induced potential hepatotoxicity andmetabolic disordersmay be due to their dioxin-like potentials and endocrine disrupting activities,and the gender differences might result from their estrogenic activities.Overall,data presented here can help to evaluate the ecological and health risks of PHCZs and reveal the underlying mechanisms.

Rational construction of high-active CO_(3)O_(4) electrocatalysts for oxygen evolution reaction

Rational construction of high-efficiency electrocatalysts for oxygen evolution reaction(OER)is critical for renewable-energy technologies,but it is highly challenging to rationally regulate their surface structures to improve the OER performance.Herein,we proposed a“model-etching”strategy to investigate chemical etching of CO_(3)O_(4).The cubic CO_(3)O_(4)nanocrystals enclosed by well-defined facets are synthesized as model crystals,whose uniform surface structures allow us to study the etching mechanism at atomic level.Etching kinetics study together with DFT calculations discloses that{111}facets,the highly active facets for OER,serve as etch-stop facets in the etching reaction and H_(2)SO_(4)molecules play a special role in creating surface Co2^(+),the active center of OER.These results direct us to rationally optimize the surface structures of CO_(3)O_(4) to develop highly active OER electrocatalysts.The favorable performance of overpotential(η)and the Tafel slope decrease even to 268 mV@10 mA·cm−2 and 74 mV·dec−1,respectively.In general,our study shows that chemical etching of model crystals could help us rationally construct high-efficiency electrocatalysts.

新区域主义下跨市空间规划与多层级治理研究——以珠三角为例

经济一体化背景下,政府管理的'破碎化'和区域交通、生态、环境等公共问题逐渐制约大都市区增长,带来区域层面多层次政府协作发展的需求。然而,我国目前缺乏类似跨市层面的规划组织机构,尤其是在正式区域制度尚不完善的环境中,多层级政府间如何通过正式和非正式并存的协调制度以实现更好的都市区空间治理,成为城市区域规划和政策制定的重要方向。珠三角在区域规划、跨市规划与基础设施合作等取得一定的成效。论文首先分析了区域管治和新区域主义的理论基础,进而总结珠三角城际轨道、广东省绿道网络、粤港澳优质生活圈等跨市规划和设施建设的管治模式,最后尝试分析影响区域规划进程的原因。研究指出,区域公共问题、共同利益和'激励一规制'引导机制驱动多元政府形成合作框架,而地方保护主义和缺乏有效的市场参与增加了跨市协调的成本,进而影响区域规划的进程。

微流控芯片在遗传性耳聋基因热点突变检测分析中的应用

目的探索将微流控芯片用于遗传性耳聋基因热点突变的分型检测。方法将专门设计加工的微流控芯片与KASP扩增整合,借助激光共聚焦荧光扫描仪实现遗传性耳聋常见4个相关基因的23个热点突变分型检测,采集276例(听障组:成都市2019年出生并诊断为听力损失的131例新生儿;对照组:成都市2020年出生且听力筛查结果为双耳通过的145例新生儿)新生儿的足跟血斑样品验证其结果准确性和临床应用可行性。结果微流控芯片通过聚类分析对全部质控品均实现准确分型,其最低检测限可达1 mg/L。276例新生儿血斑样品的微流控芯片分型结果全部通过复核确认。听障组131例新生儿,检出66例阳性携带者,阳性携带率50.4%;对照组145例新生儿,检出40例阳性携带者,阳性携带率27.6%。其中携带率最高的突变热点为GJB2基因c.109G>A,在听障组和对照组中阳性携带率分别为46.6%(61/131)和23.4%(34/145)。结论微流控芯片可用于遗传性耳聋相关热点突变的分型检测,具有准确性高、防污染能力强、操作简单、用时短等优势,能更好地满足新生儿耳聋基因筛查等遗传性耳聋基因检测需求。

Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs

The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted Ch IP-Seq and RNA-Seq in fetal(prenatal days 74–75) and adult(postnatal days 132–150) tissues(brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages(which could indicate safe harbor locus for exogenous gene insertion) and tissue-and developmental stage-specific peaks(which regulate gene pathways matching tissue-and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results(http://segtp.jxau.edu.cn/pencode/?genome=sus Scr11).

Fundamental and practical approaches for single-cell ATAC-seq analysis

Assays for transposase-accessible chromatin through high-throughput sequencing(ATAC-seq)are effective tools in the study of genome-wide chromatin accessibility landscapes.With the rapid development of single-cell technology,open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches.The application of scATAC-seq has become as popular as that of scRNA-seq.However,owing to the nature of scATAC-seq data,which are sparse and noisy,processing the data requires different methodologies and empirical experience.This review presents a practical guide for processing scATAC-seq data,from quality evaluation to downstream analysis,for various applications.In addition to the epigenomic profiling from scATAC-seq,we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage.We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.