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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 *** research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related *** 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 *** 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 *** genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying ***,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 ***-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on *** were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://***/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism ***,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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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 ***,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 *** 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 *** 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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Preparation of Regenerated Silk Fibroin Hybrid Fibers with Hydrogen Peroxide Sensing Properties by Wet Spinning

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Journal of Renewable Materials 2024年第6期12卷 1043-1055页

作者： Song Lu Jianjun Guo Richard Ansah Herman Xinyi Wu Lin Ma Guohua Wu college of biotechnology Jiangsu University of Science and TechnologyZhenjiang212100China college of Agriculture Anshun UniversityAnshun561000China

Silk is widely used in the production of high-quality *** the same time,the amount of silk textiles no longer in use and discarded is increasing,resulting in significant waste and *** issue is of great concern in many countries where silk is *** peroxide as a naturally occurring compound is an important indicator of detection in both biology and the *** study aims to develop a composite fiber with hydrogen peroxide-sensing properties using discarded silk *** achieve this goal,firstly,polydopamine(PDA)was used to encapsulate the ZnFe_(2)O_(4) NPs to achieve the improvement of dispersion,and then regenerated silk fibroin(RSF)and PDA@ZnFe_(2)O_(4)/RSF hybrid fibers are prepared by wet *** has shown that PDA@ZnFe_(2)O_(4)/RSF demonstrates exceptional sensitivity,selectivity,and stability in detecting hydrogen peroxide,while maintaining high mechanical ***,the complete hybridization of PDA@ZnFe_(2)O_(4) with silk fibroin not only results in the combination of the durability of silk fibroin and PDA@ZnFe_(2)O_(4)’s rigidity,ensuring a reliable service life,but also makes PDA@ZnFe_(2)O_(4)/RSF exhibit excellent catalytic activity and ***,the composite fiber exhibits exceptional mechanical properties and reliable hydrogen peroxide sensing capabilities,making it a promising material for biological and medical applications.

关键词： Regenerated silk fibroin modified zinc ferrite nanoparticles composite fiber hydrogen peroxide sensor wet spinning

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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 ***,our understanding of how p53 prevents normal cells from initiating tumorigenesis is still *** 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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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 *** 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 *** cytokines,glucose,lactate,nicotinamide adenine dinucleotide(NADH)and metabolic enzymes were assayed,and central carbon metabolic pathway networks and cytokine communication networks were *** results showed that the glucose and fructose groups basically maintained the trend of decreasing catabolism and increasing anabolism with increasing *** 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 ***,multiple cytokines and enzymes show strong relevance to metabolic regulation by altering the transcription and expression of enzymes in central carbon metabolic ***,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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Carrimycin inhibits coronavirus replication by decreasing the efficiency of programmed–1 ribosomal frameshifting through directly binding to the RNA pseudoknot of viral frameshift-stimulatory element

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Acta Pharmaceutica Sinica B 2024年第6期14卷 2567-2580页

作者： Hongying Li Jianrui Li Jiayu Li Hu Li Xuekai Wang Jing Jiang Lei Lei Han Sun Mei Tang Biao Dong Weiqing He Shuyi Si Bin Hong Yinghong Li Danqing Song Zonggen Peng Yongsheng Che Jian-Dong Jiang CAMS Key Laboratory of Antiviral Drug Research Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Beijing Key Laboratory of Antimicrobial Agents Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Key Laboratory of biotechnology of Antibiotics the National Health and Family Planning Commission(NHFPC)Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China

The pandemic of SARS-CoV-2 worldwide with successive emerging variants urgently calls for small-molecule oral drugs with broad-spectrum antiviral ***,we show that carrimycin,a new macrolide antibiotic in the clinic and an antiviral candidate for SARS-CoV-2 in phase III trials,decreases the efficiency of programmed–1 ribosomal frameshifting of coronaviruses and thus impedes viral replication in a broad-spectrum *** binds directly to the coronaviral frameshift-stimulatory element(FSE)RNA pseudoknot,interrupting the viral protein translation switch from ORF1a to ORF1b and thereby reducing the level of the core components of the viral replication and transcription *** carrimycin with known viral replicase inhibitors yielded a synergistic inhibitory effect on *** the FSE mechanism is essential in all coronaviruses,carrimycin could be a new broad-spectrum antiviral drug for human coronaviruses by directly targeting the conserved coronaviral FSE *** finding may open a new direction in antiviral drug discovery for coronavirus variants.

关键词： Carrimycin Coronavirus Broad-spectrum antiviral activity Programmed-1 ribosomal frameshifting RNA pseudoknot Antiviral agent RNA target Synergistic inhibitory effect

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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 *** this study,100%bio-based nylons were prepared via an integrated chemical and biological process from *** 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 *** 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 *** 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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Magnesium-incorporated biocomposite scaffolds:A novel frontier in bone tissue engineering

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Journal of Magnesium and Alloys 2024年第6期12卷 2231-2248页

作者： Abinaya Shanmugavadivu Sundaravadhanan Lekhavadhani Sushma Babu Nivetha Suresh Nagarajan Selvamurugan Department of biotechnology School of BioengineeringCollege of Engineering and TechnologySRM Institute of Science and TechnologyKattankulathur603203Tamil NaduIndia

Nonunion represents a crucial challenge in orthopedic medicine,demanding innovative solutions beyond the scope of traditional bone grafting *** the various strategies available,magnesium(Mg)implants have been recognized for their biocompatibility and ***,their susceptibility to rapid corrosion and degradation has garnered notable research interest in bone tissue engineering(BTE),particularly in the development of Mg-incorporated biocomposite *** scaffolds gradually release Mg2+,which enhances immunomodulation,osteogenesis,and angiogenesis,thus facilitating effective bone *** review presents myriad fabrication techniques used to create Mg-incorporated biocomposite scaffolds,including electrospinning,three-dimensional printing,and sol-gel *** these advancements,the application of Mg-incorporated biocomposite scaffolds faces challenges such as controlling the degradation rate of Mg and ensuring mechanical *** limitations highlight the necessity for ongoing research aimed at refining fabrication techniques to better regulate the physicochemical and osteogenic properties of *** review provides insights into the potential of Mg-incorporated biocomposite scaffolds for BTE and the challenges that need to be addressed for their successful translation into clinical applications.

关键词： Magnesium Bone tissue engineering Immunomodulation Osteogenesis Angiogenesis

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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 *** mechanism and role of mitochondrial morphology regulation,however,remain somewhat *** 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 *** full-length cDNA of the *** opa1 gene(Pe-opa1)is 3743 bp in length and encodes 975 amino *** Pe-OPA1 protein is highly conservative and includes a transmembrane domain,a GTPase domain,two helical bundle domains,and a lipid-interacting *** and protein expression was higher in the coelomic fluid(a site of spermatid development)of male *** and increased first and then decreased from March to ***,their expression during the breeding stage was significantly higher than during the non-breeding stage,suggesting that Pe-OPA1 is involved in *** *** 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 ***,Pe-OPA1 was mainly detected in the spermatid *** experiments showed that the Pe-OPA1 are constitutively expressed and co-localized with mitochondria during spermiogenesis,suggesting its involvement in *** *** 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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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 *** 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 *** processing methods have been employed to remove SBM antinutrients,including fermentation with fungal or bacterial *** to the literature,fermentation,a traditional food processing method,could improve SBM's nutritional and functional properties,making it more suitable and beneficial to *** 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 *** 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 *** appears to be a multifunctional high-quality plant protein source for *** removing soybean antinutrients,beneficial bioactive peptides and digestive enzymes are produced during fermentation,providing probiotics,antioxidants,and immunomodulatory *** 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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