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Predicting Lactobacillus delbrueckii subsp. bulgaricusStreptococcus thermophilus interactions based on a highly accurate semi-supervised learning method

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Science China Life Sciences 2024年

作者： Shujuan Yang Mei Bai Weichi Liu Weicheng Li Zhi Zhong Lai-Yu Kwok Gaifang Dong Zhihong Sun key laboratory of Dairy biotechnology and Engineering Ministry of Education Inner Mongolia Agricultural University key laboratory of Dairy Products Processing Ministry of Agriculture and Rural Affairs Inner Mongolia Agricultural University Inner Mongolia key laboratory of Dairy biotechnology and Engineering Inner Mongolia Agricultural University Collaborative Innovative Center for Lactic Acid Bacteria and Fermented Dairy Products Ministry of Education Inner Mongolia Agricultural University College of Computer and Information Engineering Inner Mongolia Agricultural University Inner Mongolia Autonomous Region key laboratory of Big Data Research and Application of agriculture and animal Husbandry

Lactobacillus delbrueckii subsp. bulgaricus(L. bulgaricus) and Streptococcus thermophilus(S. thermophilus) are commonly used starters in milk fermentation. Fermentation experiments revealed that L. bulgaricus-S. thermophilus interactions(LbSt I) substantially impact dairy product quality and production. Traditional biological humidity experiments are time-consuming and labor-intensive in screening interaction combinations, an artificial intelligence-based method for screening interactive starter combinations is necessary. However,in the current research on artificial intelligence based interaction prediction in the field of bioinformatics, most successful models adopt supervised learning methods, and there is a lack of research on interaction prediction with only a small number of labeled ***, this study aimed to develop a semi-supervised learning framework for predicting LbSt I using genomic data from 362 isolates(181per species). The framework consisted of a two-part model: a co-clustering prediction model(based on the Kyoto Encyclopedia of Genes and Genomes(KEGG) dataset) and a Laplacian regularized least squares prediction model(based on K-mer analysis and gene composition of all isolates datasets). To enhance accuracy, we integrated the separate outcomes produced by each component of the two-part model to generate the ultimate LbSt I prediction results, which were verified through milk fermentation experiments. Validation through milk fermentation experiments confirmed a high precision rate of 85%(17/20; validated with 20 randomly selected combinations of expected interacting isolates). Our data suggest that the biosynthetic pathways of cysteine, riboflavin, teichoic acid, and exopolysaccharides, as well as the ATP-binding cassette transport systems, contribute to the mutualistic relationship between these starter bacteria during milk fermentation. However, this finding requires further experimental verification. The presented model and data are valua

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Gut microbiota: a potential target for hyperuricemia and gout

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Food Science and Human Wellness 2024年

作者： Feiyan Zhao Shuying Yang Laiyu Kwok Hongbin Li Heping Zhang Zhihong Sun Inner Mongolia key laboratory of Dairy biotechnology and Engineering key laboratory of Dairy Products Processing， ministry of agriculture and Rural Affairs key laboratory of Dairy biotechnology and Engineering， ministry of Education， Inner Mongolia Agricultural University Department of Rheumatology and Immunology， The Affiliated Hospital of Inner Mongolia Medical University， Inner Mongolia key laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases

Modern lifestyle and diet have increased the incidence rate of uric acid (UA) metabolism-related diseases like hyperuricemia (HUA) and gout， posing heavy economic burden to individual patients and their families and the society. Uric acid metabolism is a complex physiological process involving the kidney， intestine， and other organs. A number of factors together regulate UA metabolism， including genetics， diet， hormones， and the gut microbiota. This review summaries the gut microbiota features in subjects with HUA and gout， and the therapeutic effects of implementing microecological therapies (probiotics， prebiotics， or fecal microbiota transplant) that target modulate the gut microbiota and its downstream metabolism on the disease. Current evidence shows that these strategies are safe and promising in alleviate inflammation， reduce UA， and restoring a healthy gut microbiota in subjects with UA metabolism-related diseases. However， most clinical data are generated by animal studies. Therefore， we propose that vigorous human intervention trials should be conducted in the future to evaluate the therapeutic effects of microecological therapies in managing HUA and gout.

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Mannanase improves the growth performance of broilers by alleviating inflammation of the intestinal epithelium and improving intestinal microbiota

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动物营养学报 2024年第1期16卷 376-394页

作者： Xiaodan Zhang Huiping Xu Lu Gong Jiao Wang Jianyang Fu Zengpeng Lv Liangjuan Zhou Xuejun Li Qiong Liu Pingyu Xia Yuming Guo State key laboratory of animal Nutrition and Feeding College of Animal Science and Technology China Agricultural University Beijing 100193 China Beijing Strowin biotechnology Co. Ltd. Beijing 100094 China

This experiment aimed to discuss and reveal the effect and mechanism of mannanase on intestinal inflammation in broilers triggered by a soybean meal diet. In this experiment, 384 Arbor Acres broilers at 1 d old were randomly divided into 3 treatment groups. The broilers were fed a corn-soybean meal basal diet, a low-energy diet (metabolizable energy reduced by 50 kcal/kg), and a low-energy diet supplemented with 100 mg/kg mannanase for 42 d. The low-energy diet increased feed conversion ratio from 0 to 42 d, reduced ileal villus height and villus height-to-crypt depth ratio and upregulated the expression of nuclear factor kappa B ( NF-κB ) in the ileum ( P P P CLDN1 ) and zonula occludens-1 ( ZO-1 ) in the jejunum at 21 d, downregulated the expression of ilealNF-κB , and increased the content of isobutyric acid in the cecum of broilers ( P Lactobacillus reuteri in the ileum of broilers. The addition of mannanase increased the relative abundance ofLactobacillus-KC45b andLactobacillus johnsonii in broilers. Furthermore, a low-energy diet reduced the relative abundance ofButyricicoccus in the intestine of broilers and inhibited oxidative phosphorylation and phosphoinositol metabolism. Mannanase increased the relative abundance ofOdoribacter , promoted energy metabolism and N-glycan biosynthesis, and increased the activities of GH3 and GH18. It is concluded that mannanase could improve the growth performance of broilers by reducing the expression ofNF-κB in the ileum, increasing the production of SCFA in the cecum, suppressing intestinal inflammation, balancing the intestinal microbiota, reducing damage to the intestinal barrier, and improving the efficiency of nutrient utilization to alleviate the adverse effects caused by the decrease in dietary energy *** The PDF

关键词： Broiler Low-energy diet Mannanase Intestinal inflammatory response Intestinal microbiota Metagenome

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Genome-Wide Association Study of Cooked Rice Textural Attributes and Starch Physicochemical Properties in indica Rice

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Rice science 2024年第3期31卷 300-316,I0018-I0041页

作者： DENG Bowen ZHANG Yanni ZHANG Fan WANG Wensheng XU Jianlong ZHANG Yu BAO Jinsong Institute of Nuclear Agricultural Sciences Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang ProvinceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China Hainan Institute Zhejiang UniversitySanya 572025China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China

Rice cooking and eating qualities(CEQ)are mainly determined by cooked rice textural parameters and starch physicochemical ***,the genetic bases of grain texture and starch properties in rice have not been fully *** conducted a genome-wide association study for apparent amylose content(AAC),starch pasting viscosities,and cooked rice textural parameters using 279 indica rice accessions from the 3000 Rice Genome *** identified 26 QTLs in the whole population and detected single nucleotide polymorphisms(SNPs)with the lowest P-value at the Waxy(Wx)locus for all traits except pasting temperature and ***,we detected significant SNPs at the SUBSTANDARD STARCH GRAIN6(SSG6)locus for AAC,setback(SB),hardness,adhesiveness,chewiness(CHEW),gumminess(GUM),and *** subsequently divided the population using a SNP adjacent to the Waxy locus,and identified 23 QTLs and 12 QTLs in two sub-panels,WxT and WxA,*** these sub-panels,SSG6 was also identified to be associated with pasting parameters,including peak viscosity,hot paste viscosity,cold paste viscosity,and consistency ***,a candidate gene encoding monosaccharide transporter 5(OsMST5)was identified to be associated with AAC,breakdown,SB,CHEW,and *** total,39 QTLs were co-localized with known genes or previously reported *** identified genes and QTLs provide valuable information for genetic manipulation to improve rice CEQ.

关键词： cooking and eating quality genome-wide association study rice Waxy gene

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Correlation of gut microorganisms and non-volatile flavor substances provides new insights for breeding Scylla paramamosain

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Journal of Oceanology and Limnology 2024年第4期42卷 1336-1347页

作者： Gao GAO Xing LI Kangxiang QIN Yun HU Xiaosong JIANG Chenxi CHE Yuntao LI Changkao MU Chunlin WANG Huan WANG School of Marine Science Ningbo UniversityNingbo 315211China key laboratory of Applied Marine biotechnology Ministry of EducationNingbo UniversityNingbo 315211China

The farming of Scylla paramamosain with specific flavors has a higher commercial value,and the flavors are related to the integrated farming environment and non-volatile flavor substances,while the survival environment is one of the important ways to source gut microorganisms in the *** this study,the levels of dominant taxa in the gut flora of *** from Mong Cai,Vietnam(VN),Taishan City,Guangdong Province(TS)of China,and Ninghai County,Ningbo City(NB)Zhejiang Province of China converged with those of *** from Sanmen County,Ningbo City(CK 1,CK 2,and CK 3)at 28 d of *** top 15 genera with the highest abundance of VN,TS,and NB gut flora were the same as CK 1,CK 2,and CK 3,but with different percentages,and gradually converged to CK 1,CK 2,and CK 3,respectively,at 28 d of *** between intestinal flora and non-volatile flavor substances in the hepatopancreas at the percentage level of relative abundance of bacterial genera found that above 28 d of domestication,Muribaculaceae,Psychrilyobacter,Clostridia_vadinBB 60_group,Halarcobacter Carboxylicivirga,Sediminispirochaeta may be the most important genera affecting flavor amino acids of ***,Carboxylicivirga,Halarcobacter,Photobacterium,ZOR 0006,Psychrilyobacter,and Pseudomonas may be the most important genera affecting flavor amino acids of ***,Carboxylicivirga,Halarcobacter,Photobacterium,ZOR 0006,Vibrio,and Sphingomonas may be the most important genera affecting flavor amino acids of *** results show that the intestinal flora structure of crabs from different areas were domesticated in the same area for at least 28 d before they converged to that of the domesticated crab,and the most important genera affecting the flavor amino acids of TS,VN,and NB were also *** results of this study provide a reference and basis for the technique of directional cultivation of the flavor quality of the crab.

关键词： survival environment Scylla paramamosain intestinal flora structure non-volatile flavor substance directional breeding

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Decreased eggshell strength caused by impairment of uterine calcium transport coincide with higher bone minerals and quality in aged laying hens

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Journal of animal Science and biotechnology 2024年第3期15卷 1258-1277页

作者： Yu Fu Jianmin Zhou Martine Schroyen Haijun Zhang Shugeng Wu Guanghai Qi Jing Wang key laboratory of Feed biotechnology Ministry of Agriculture and Rural AffairsInstitute of Feed ResearchChinese Academy of Agricultural SciencesBeijing 100081China Precision Livestock and Nutrition laboratory Gembloux Agro‑Bio TechTERRA Teaching and Research CentreUniversity of LiegeGembloux B‑5030Belgium

Background Deteriorations in eggshell and bone quality are major challenges in aged laying *** study compared the differences of eggshell quality,bone parameters and their correlations as well as uterine physiologi-cal characteristics and the bone remodeling processes of hens laying eggs of different eggshell breaking strength to explore the mechanism of eggshell and bone quality reduction and their interaction.A total of 24074-week-old Hy-line Brown laying hens were selected and allocated to a high(HBS,44.83±1.31 N)or low(LBS,24.43±0.57 N)eggshell breaking strength *** A decreased thickness,weight and weight ratio of eggshells were observed in the LBS,accompanied with ultrastructural deterioration and total Ca *** quality was negatively correlated with eggshell quality,marked with enhanced structures and increased components in the *** the LBS,the mammillary knobs and effective layer grew *** the initiation stage of eggshell calcification,a total of 130 differentially expressed genes(DEGs,122 upregulated and 8 downregulated)were identified in the uterus of hens in the LBS relative to those in the *** DEGs were relevant to apoptosis due to the cellular Ca *** values of p62 protein level,caspase-8 activity,Bax protein expression and lower values of Bcl protein expression and Bcl/Bax ratio were seen in the *** assay and hematoxylin-eosin staining showed a significant increase in TUNEL-positive cells and tissue damages in the uterus of the *** few DEGs were identified at the growth stage,similar uterine tissue damages were also observed in the *** expressions of runt-related transcription factor 2 and osteocal-cin were upregulated in humeri of the *** diameter and more structural damages of endocortical bones and decreased ash were observed in femurs of the *** The lower eggshell breaking strength may be attributed to a declined Ca transport due to uterine tissue damages,which

关键词： Bone parameter Calcium transport Eggshell quality Laying hen Tissue damage

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Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet

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Journal of animal Science and biotechnology 2024年第4期15卷 1494-1511页

作者： Guangliang Gao Rui Liu Silu Hu Mengnan He Jiaman Zhang Dengfeng Gao Jing Li Jiwei Hu Jiwen Wang Qigui Wang Mingzhou Li Long Jin Livestock and Poultry Multi‑Omics key laboratory of ministry of agriculture and Rural Affairs College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China Chongqing Engineering Research Center of Goose Genetic Improvement Institute of Poultry ScienceChongqing Academy of Animal SciencesRongchang DistrictChongqing 402460China

Background Goose, descendants of migratory ancestors, have undergone extensive selective breeding, resulting in their remarkable ability to accumulate fat in the liver and exhibit a high tolerance for significant energy intake. As a result, goose offers an excellent model for studying obesity, metabolic disorders, and liver diseases in mammals. Although the impact of the three-dimensional arrangement of chromatin within the cell nucleus on gene expression and transcriptional regulation is widely acknowledged, the precise functions of chromatin architecture reorganization during fat deposition in goose liver tissues still need to be fully *** In this study, geese exhibited more pronounced changes in the liver index and triglyceride(TG) content following the consumption of the high-fat diet(HFD) than mice without significant signs of inflammation. Additionally, we performed comprehensive analyses on 10 goose liver tissues(5 HFD, 5 normal), including generating highresolution maps of chromatin architecture, conducting whole-genome gene expression profiling, and identifying H3K27ac peaks in the livers of geese and mice subjected to the HFD. Our results unveiled a multiscale restructuring of chromatin architecture, encompassing Compartment A/B, topologically associated domains, and interactions between promoters and enhancers. The dynamism of the three-dimensional genome architecture, prompted by the HFD, assumed a pivotal role in the transcriptional regulation of crucial genes. Furthermore, we identified genes that regulate chromatin conformation changes, contributing to the metabolic adaptation process of lipid deposition and hepatic fat changes in geese in response to excessive energy intake. Moreover, we conducted a cross-species analysis comparing geese and mice exposed to the HFD, revealing unique characteristics specific to the goose liver compared to a mouse. These chromatin conformation changes help elucidate the observed characteristics of fat

关键词： Compartment A/B Goose fatty liver Promoter-enhancer interactions Regulation of gene expression

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Revealing the role of CCoAOMT1: fine-tuning bHLH transcription factors for optimal anther development

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Science China(Life Sciences) 2024年第3期67卷 565-578页

作者： Zesen Lai Jianzheng Wang Ying Fu Menghan Wang Hong Ma Shiqing Peng Fang Chang State key laboratory of Genetic Engineering Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity SciencesInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai 200438China School of Tropical agriculture and Forestry Agriculture-Rural Affairs and Rural RevitalizationHainan UniversityHaikou 570228China key laboratory of Biology and Genetic Resources of Tropical Crops Ministry of AgricultureInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikou 571101China Department of Biology Huck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPA 16802USA

The tapetum,a crucial innermost layer encompassing male reproductive cells within the anther wall,plays a pivotal role in normal pollen *** transcription factors (TFs) bHLH010/089/091 redundantly facilitate the rapid nuclear accumulation of DYSFUNCTIONAL TAPETUM 1,a gatekeeper TF in the ***,the regulatory mechanisms governing the activity of bHLH010/089/091 remain *** this study,we reveal that caffeoyl coenzyme A O-methyltransferase 1 (CCoAOMT1) is a negative regulator affecting the nuclear localization and function of bHLH010 and bHLH089,probably through their K259 *** findings underscore that CCoAOMT1 promotes the nuclear export and degradation of bHLH010 and ***,elevated CCoAOMT1 expression resulted in defective pollen development,mirroring the phenotype observed in bhlh010 bhlh089 ***,our investigation revealed that the K259A mutation in the bHLH089 protein disrupted its translocation from the nucleus to the cytosol and impeded its degradation induced by ***,transgenic plants with the probHLH089::bHLH089^(K259A)construct failed to rescue proper pollen development or gene expression in bhlh010 bhlh089 ***,these findings emphasize the need to maintain balanced TF homeostasis for male *** firmly establish CCoAOMT1 as a pivotal regulator that is instrumental in achieving equilibrium between the induction of the tapetum transcriptional network and ensuring appropriate anther development.

关键词： anther development nuclear localization bHLH O-methyltransferase transcription factor homeostasis

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Advances in the study of auxin early response genes:Aux/IAA,GH3,and SAUR

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The Crop Journal 2024年第4期12卷 964-978页

作者： Dongfang Bao Senqiu Chang Xiaodong Li Yanhua Qi key laboratory of Herbage&Endemic Crop Biology of ministry of Education Inner Mongolia Key Laboratory of Herbage&Endemic Crop BiotechnologySchool of Life SciencesInner Mongolia UniversityHohhot 010000Inner MongoliaChina

Auxin plays a crucial role in all aspects of plant growth and *** can induce the rapid and efficient expression of some genes,which are named auxin early response genes(AERGs),mainly including the three families:auxin/indole-3-acetic acid(Aux/IAA),Gretchen Hagen 3(GH3),and small auxin-up RNA(SAUR).Aux/IAA encodes the Aux/IAA protein,which is a negative regulator of auxin ***/IAA and auxin response factor(ARF)form a heterodimer and participate in a variety of physiological processes through classical or non-classical auxin signaling *** GH3 encodes auxin amide synthetase,which catalyzes the binding of auxin to acyl-containing small molecule substrates(such as amino acids and jasmonic acid),and regulates plant growth and stresses by regulating auxin *** is a class of small auxin up-regulated *** response to auxin is complex,and the process may occur at the transcriptional,post-transcriptional and protein *** the development of multi-omics,significant progress has been made in the study of Aux/IAA,GH3,and SAUR genes,but there are still many *** review offers insight into the characteristics of Aux/IAA,GH3,and SAUR gene families,and their roles in roots,hypocotyls,leaves,leaf inclinations,flowers,seed development,stress response,and phytohormone crosstalk,and provides clues for future research on phytohormone signaling and the molecular design breeding of crops.

关键词： Auxin Aux/IAA GH3 SAUR Stress

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Application of CRISPR/Cas12i.3 for targeted mutagenesis in broomcorn millet(Panicum miliaceum L.)

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Journal of Integrative Plant Biology 2024年第8期66卷 1544-1547页

作者： Yuhe Bai Shengnan Liu Yan Bai Zhisong Xu Hainan Zhao Haiming Zhao Jinsheng Lai Ya Liu Weibin Song State key laboratory of Maize Bio-breeding Key Laboratory of Genome Editing Research and ApplicationMinistry of Agriculture and Rural AffairsDepartment of Plant Genetics and BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China National Agricultural Technology Extension&Service Center Beijing 100125China Beijing key laboratory of Maize DNA Fingerprinting and Molecular Breeding Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China

As the global human population continues to grow and is predicted to reach 10 billion by 2050,the demand for food volume and quality raises a tremendous challenge(OECD/FAO,2017).The worldwide arable land area is decre... 详细信息

关键词： arable continue raise

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