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RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages

Virologica Sinica 2024年第1期39卷 156-168页

作者： Changqiao You Shuai Jiang Yunyun Ding Shunxing Ye Xiaoxiao Zou Hongming Zhang Zeqi Li Fenglin Chen Yongliang Li Xingyi Ge Xinhong Guo college of Biology Hunan UniversityChangsha410082China college of Bioscience and biotechnology Hunan Agricultural UniversityChangsha410128China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations.In this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 lineages.Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages.Through genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2.Subsequently,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores.Post-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on identification.They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://virusbarcodedatabase.top/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis.Moreover,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.

关键词： RNA barcode segments SARS-CoV-2 variants and related lineages HCoVs Genetic tests Complete genome sequences

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A pipeline to characterize p53 effectors by integrative cistrome and transcriptome analysis in a genetically-defined organoid model

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Genes & Diseases 2024年第2期11卷 512-515页

作者： June-Ha Shin Hwa-Ryeon Kim Jae-Seok Roe Department of Biochemistry College of Life Science and BiotechnologyYonsei UniversitySeoul 120-749Republic of Korea

Tumor-protein 53(p53)is a transcription factor(TF)encoded by TP53(Trp53 in mice)and is a master regulator of tumor-suppressive programs'.Importantly,TP53 is the most frequently mutated gene in human cancer,and its loss of function contributes to tumor development,exemplified by variable p53 mutations detected in 50%-75%of pancreatic cancers.2 From these perceptions,a number of targets transcribed by p53 that confer tumor suppression have been identified.Nevertheless,our understanding of how p53 prevents normal cells from initiating tumorigenesis is still incomplete.To complement this limitation,herein,we established a new approach to identify underlying effectors transcribed by p53 in normal physiology.

关键词： incomplete initiating herein

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Mechanism of action, benefits, and research gap in fermented soybean meal utilization as a high-quality protein source for livestock and poultry

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Animal Nutrition 2024年第1期16卷 130-146页

作者： Modinat T.Lambo Haokai Ma Haosheng Zhang Peng Song Hongxiang Mao Guowen Cui Baisheng Dai Yang Li Yonggen Zhang college of Animal Science and Technology Northeast Agricultural University Wilmar (Shanghai) biotechnology Research and Development Center Co. Ltd college of Electrical Engineering and Information Northeast Agricultural University

Animal nutritionists have incessantly worked towards providing livestock with high-quality plant protein feed resources.Soybean meal (SBM) has been an essential and predominantly adopted vegetable protein source in livestock feeding for a long time;however,several SBM antinutrients could potentially impair the animal's performance and growth,limiting its use.Several processing methods have been employed to remove SBM antinutrients,including fermentation with fungal or bacterial microorganisms.According to the literature,fermentation,a traditional food processing method,could improve SBM's nutritional and functional properties,making it more suitable and beneficial to livestock.The current interest in health-promoting functional feed,which can enhance the growth of animals,improve their immune system,and promote physiological benefits more than conventional feed,coupled with the ban on the use of antimicrobial growth promoters,has caused a renewed interest in the use of fermented SBM (FSBM) in livestock diets.This review details the mechanism of SBM fermentation and its impacts on animal health and discusses the recent trend in the application and emerging advantages to livestock while shedding light on the research gap that needs to be critically addressed in future studies.FSBM appears to be a multifunctional high-quality plant protein source for animals.Besides removing soybean antinutrients,beneficial bioactive peptides and digestive enzymes are produced during fermentation,providing probiotics,antioxidants,and immunomodulatory effects.Critical aspects regarding FSBM feeding to animals remain uncharted,such as the duration of fermentation,the influence of feeding on digestive tissue development,choice of microbial strain,and possible environmental impact.

关键词： Soybean meal Protein feed Fermentation Microorganism Livestock

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P-induced electron transfer interaction for enhanced selective hydrogenation rearrangement of furfural to cyclopentanone

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Journal of Energy Chemistry 2024年第5期92卷 43-51页

作者： Weichen Wang Hongke Zhang Yidan Wang Fangyuan Zhou Zhiyu Xiang Wanbin Zhu Hongliang Wang Center of Biomass Engineering College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China

Optimizing the intrinsic activity of non-noble metal by precisely tailoring electronic structure offers an appealing way to construct cost-effective catalysts for selective biomass valorization.Herein,we reported a P-doping bifunctional catalyst(Ni-P/mSiO_(2))that achieved 96.6%yield for the hydrogenation rearrangement of furfural to cyclopentanone at mild conditions(1 MPaH_(2),150°C).The turnover frequency of Ni-P/mSiO_(2)was 411.9 h^(-1),which was 3.2-fold than that of Ni/mSiO_(2)(127.2 h^(-1)).Detailed characterizations and differential charge density calculations revealed that the electron-deficient Niδ+species were generated by the electron transfer from Ni to P,which promoted the ring rearrangement reaction.Density functional theory calculations illustrated that the presence of P atoms endowed furfural tilted adsorb on the Ni surface by the C=O group and facilitated the desorption of cyclopentanone.This work unraveled the connection between the localized electronic structures and the catalytic properties,so as to provide a promising reference for designing advanced catalysts for biomass valorization.

关键词： Furfural Hydrogenation rearrangement P-doping Electron transfer Biomass valorization

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Effects of different doses of glucose and fructose on central metabolic pathways and intercellular wireless communication networks in humans

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Food Science and Human Wellness 2024年第4期13卷 1906-1916页

作者： Dingqiang Lu Yujiao Liu Miao Zhao Shuai Yuan Danyang Liu Xinqian Wang Yixuan Liu Yifei Zhang Ming Li Yufeng Lü Guangchang Pang Ruijuan Ren college of biotechnology&Food Science Tianjin University of CommerceTianjin Key Laboratory of Food BiotechnologyTianjin 300314China Tianjin Institute for Food Safety Inspection Technology Tianjin 300134China

Fructose and glucose are often widely used in food processing and may contribute to many metabolic diseases.To observe the effects of different doses of glucose and fructose on human metabolism and cellular communication,volunteers were given low,medium,and high doses of glucose and fructose.Serum cytokines,glucose,lactate,nicotinamide adenine dinucleotide(NADH)and metabolic enzymes were assayed,and central carbon metabolic pathway networks and cytokine communication networks were constructed.The results showed that the glucose and fructose groups basically maintained the trend of decreasing catabolism and increasing anabolism with increasing dose.Compared with glucose,low-dose fructose decreased catabolism and increased anabolism,significantly enhanced the expression of the inflammatory cytokine interferon-γ(IFN-γ),macrophage-derived chemokine(MDC),induced protein-10(IP-10),and eotaxin,and significantly reduced the activity of isocitrate dehydrogenase(ICDH)and pyruvate dehydrogenase complexes(PDHC).Both medium and high doses of fructose increase catabolism and anabolism,and there are more cytokines and enzymes with significant changes.Furthermore,multiple cytokines and enzymes show strong relevance to metabolic regulation by altering the transcription and expression of enzymes in central carbon metabolic pathways.Therefore,excessive intake of fructose should be reduced to avoid excessive inflammatory responses,allergic reactions and autoimmune diseases.

关键词： Fructose Glucose Central carbon metabolic pathway Metabolic enzymes Cytokine network

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A sustainable process to 100%bio-based nylons integrated chemical and biological conversion of lignocellulose

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Green Energy & Environment 2024年第2期9卷 390-402页

作者： Ruijia Hu Ming Li Tao Shen Xin Wang Zhuohua Sun Xinning Bao Kequan Chen Kai Guo Lei Ji Hanjie Ying Pingkai Ouyang Chenjie Zhu college of biotechnology and Pharmaceutical Engineering Nanjing Tech UniversityNanjingChina National Engineering Research Center for biotechnology Nanjing Tech UniversityNanjingChina Beijing Key Laboratory of Lignocellulosic Chemistry Beijing Forestry UniversityBeijingChina

Considerable progress has been made in recent years to the development of sustainable polymers from bio-based feedstocks.In this study,100%bio-based nylons were prepared via an integrated chemical and biological process from lignocellulose.These novel nylons were obtained by the melt polymerization of 3-propyladipic acid derived from lignin and 1,5-pentenediamine/1,4-butanediamine derived from carbohydrate sugar.Central to the concept is a three-step noble metal free catalytic chemical funnelling sequence(Raney Ni mediated reductive catalytic fractionation-reductive funnelling-oxidative funnelling),which allowed for obtaining a single component 3-propyladipic acid from lignin with high efficiency.The structural and thermodynamic properties of the obtained nylons have been systematically investigated,and thus obtained transparent bio-based nylons exhibited higher Mw(>32,000)and excellent thermal stability(Td5%>265℃).Considering their moderate Tg and good melt strength,these transparent bio-based nylons could serve as promising functional additives or temperature-responsive materials.

关键词： Lignocellulose Lignin Reductive catalytic fractionation Bio-based nylon

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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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Animal Nutrition 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 Strowin biotechnology Co. Ltd.

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 at1 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 from0 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 < 0.05). It also reduced cecal short-chain fatty acids(SCFA), such as acetic acid(P < 0.05). Compared with low-energy diets, the addition of mannanase increased body weight at 42 d, promoted the digestibility of nutrients, and maintained the morphology and integrity of the intestinal epithelium of broilers(P < 0.05). In addition, mannanase upregulated the expression of claudin-1(CLDN1) and zonula occludens-1(ZO-1) in the jejunum at 21 d,downregulated the expression of ileal NF-κB, and increased the content of isobutyric acid in the cecum of broilers(P < 0.05). The results for the ileal microbiota showed that a low-energy diet led to a decrease in the relative abundance of Lactobacillus reuteri in the ileum of broilers. The addition of mannanase increased the relative abundance of Lactobacillus-KC45b and Lactobacillus johnsonii in broilers. Furthermore, a low-energy diet reduced the relative abundance of Butyricicoccus in the intestine of broilers and inhibited oxidative phosphorylation and phosphoinositol metabolism. Mannanase increased the relative abundance of Odoribacter, 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 of NF-κB in the ileum, increasing the production of SCFA in the cecum, suppressing intestina

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

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Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens

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Journal of Animal Science and biotechnology 2024年第3期15卷 1086-1100页

作者： Yanli Liu Zhuqing Zheng Chaohui Wang Yumeng Wang Xi Sun Zhouzheng Ren Xin Yang Xiaojun Yang college of Animal Science and Technology Northwest A&F UniversityYangling 712100China Institute of Agricultural biotechnology Jingchu University of TechnologyJingmen 448000China

Background Fatty liver disease causes huge economic losses in the poultry industry due to its high occurrence and lethality rate.Three-dimensional(3D)chromatin architecture takes part in disease processing by regulating tran-scriptional reprogramming.The study is carried out to investigate the alterations of hepatic 3D genome and H3K27ac profiling in early fatty liver(FLS)and reveal their effect on hepatic transcriptional reprogramming in laying hens.Results Results show that FLS model is constructed with obvious phenotypes including hepatic visible lipid deposi-tion as well as higher total triglyceride and cholesterol in serum.A/B compartment switching,topologically associat-ing domain(TAD)and chromatin loop changes are identified by high-throughput/resolution chromosome conforma-tion capture(HiC)technology.Targeted genes of these alternations in hepatic 3D genome organization significantly enrich pathways related to lipid metabolism and hepatic damage.H3K27ac differential peaks and differential expres-sion genes(DEGs)identified through RNA-seq analysis are also enriched in these pathways.Notably,certain DEGs are found to correspond with changes in 3D chromatin structure and H3K27ac binding in their promoters.DNA motif analysis reveals that candidate transcription factors are implicated in regulating transcriptional reprogram-ming.Furthermore,disturbed folate metabolism is observed,as evidenced by lower folate levels and altered enzyme expression.Conclusion Our findings establish a link between transcriptional reprogramming changes and 3D chromatin struc-ture variations during early FLS formation,which provides candidate transcription factors and folate as targets for FLS prevention or treatment.

关键词： 3D chromatin architecture Fatty liver disease Folate H3K27ac profiling Transcription reprogramming

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A signaling cascade mediating fruit trait development via phosphorylation-modulated nuclear accumulation of JAZ repressor

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Journal of Integrative Plant Biology 2024年第6期66卷 1106-1125页

作者： Wei Wang Jinyao Ouyang Yating Li Changsheng Zhai Bing He Huahan Si Kunsong Chen Jocelyn K.C.Rose Wensuo Jia college of Horticulture China Agricultural University college of Agriculture and biotechnology Zhejiang UniversityZijingang Campus Plant Biology Section School of Integrative Plant Science Cornell University Institute of Horticulture Crops Xinjiang Academy of Agricultural Sciences

It is generally accepted that jasmonate-ZIM domain(JAZ) repressors act to mediate jasmonate(JA) signaling via CORONATINE-INSENSITIVE1(COI1)-mediated degradation. Here, we report a cryptic signaling cascade where a JAZ repressor,FvJAZ12, mediates multiple signaling inputs via phosphorylation-modulated subcellular translocation rather than the COI1-mediated degradation mechanism in strawberry(Fragaria vesca).FvJAZ12 acts to regulate flavor metabolism and defense response, and was found to be the target of Fv MPK6, a mitogen-activated protein kinase that is capable of responding to multiple signal stimuli. FvMPK6 phosphorylates FvJAZ12 at the amino acid residues S179 and T183 adjacent to the PY residues, thereby attenuating its nuclear accumulation and relieving its repression for FvMYC2, which acts to control the expression of lipoxygenase 3(FvLOX3), an important gene involved in JA biosynthesis and a diverse array of cellular metabolisms. Our data reveal a previously unreported mechanism for JA signaling and decipher a signaling cascade that links multiple signaling inputs with fruit trait development.

关键词： defense response JAZ repressor phosphorylation strawberry subcellular translocation

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Characterization,expression dynamics,and potential function of OPA1 for regulation of mitochondrial morphology during spermiogenesis in Phascolosoma esculenta

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Journal of Oceanology and Limnology 2024年第1期42卷 187-200页

作者： Xinming GAO Binbin FENG Chen DU Congcong HOU Shan JIN Daojun TANG Junquan ZHU Key Laboratory of Applied Marine biotechnology by the Ministry of Education and Key Laboratory of Marine biotechnology of Zhejiang Province School of Marine SciencesNingbo UniversityNingbo 315211China college of Ecology Lishui UniversityLishui 323000China

Mitochondria undergo morphological changes during spermatogenesis in some animals.The mechanism and role of mitochondrial morphology regulation,however,remain somewhat unclear.In this study,we analyzed the molecular characteristics,expression dynamics and subcellular localization of optic atrophy protein 1(OPA1),a mitochondrial fusion and cristae maintenance-related protein,to reveal the possible regulatory mechanisms underlying mitochondrial morphology in Phascolosoma esculenta spermiogenesis.The full-length cDNA of the P.esculenta opa1 gene(Pe-opa1)is 3743 bp in length and encodes 975 amino acids.The Pe-OPA1 protein is highly conservative and includes a transmembrane domain,a GTPase domain,two helical bundle domains,and a lipid-interacting stalk.Gene and protein expression was higher in the coelomic fluid(a site of spermatid development)of male P.esculenta and increased first and then decreased from March to December.Moreover,their expression during the breeding stage was significantly higher than during the non-breeding stage,suggesting that Pe-OPA1 is involved in P.esculenta reproduction.The Pe-OPA1 protein was more abundant in components consisting of many spermatids than in components without,indicating that Pe-OPA1 mainly plays a role in the spermatid in coelomic fluid.Moreover,Pe-OPA1 was mainly detected in the spermatid mitochondria.Immunofluorescence experiments showed that the Pe-OPA1 are constitutively expressed and co-localized with mitochondria during spermiogenesis,suggesting its involvement in P.esculenta spermiogenesis.These results provide evidence for Pe-OPA1's involvement in the regulation of mitochondrial morphology during spermiogenesis.

关键词： optic atrophy protein 1(OPA1) spermiogenesis Phascolosoma esculenta mitochondrial dynamics spermatid

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