Drug–target affinity (DTA) prediction is a critical step in virtual screening and significantly accelerates drug development. However, existing deep learning-based methods relying on single-modal representations (e.g., text or graphs) struggle to fully capture the complex interactions between drugs and targets. This study proposes CM-DTA, a cross-modal feature fusion model that integrates drug textual representations and molecular graphs with target protein amino acid sequences and structural graphs, enhancing feature diversity and expressiveness. The model employs the multi-perceptive neighborhood self-attention aggregation strategy to capture first- and second-order neighborhood information, overcoming limitations in graph isomorphism networks (GIN) for structural representation. The experimental results on the Davis and KIBA datasets show that CM-DTA significantly improves the performance of drug–target affinity prediction, achieving higher accuracy and better prediction metrics compared to state-of-the-art (SOTA) models.
随着全球环境污染加剧、气候持续变化和人口不断增长,如何保障安全、营养和可持续的食品供给面临巨大挑战.这些挑战对未来食品供给方式和功能提出了新的要求.采用合成生物学技术,创建适用于食品工业的细胞工厂,将可再生原料转化为重要食品组分、功能性食品添加剂和营养化学品是解决食品领域所面临问题的重要途径.本文首先介绍了合成生物学对食品制造领域创新和突破的重要性.其次,以基于合成生物学制造植物蛋白肉所需关键组分、黄酮类植物天然提取物和母乳寡糖这三种典型食品为例,探讨了目前食品合成生物学的任务与挑战.最后,对我国合成生物学与食品制造领域的发展趋势进行了总结和展望.通过加强食品合成生物学等具有重大意义的食品生物技术的开发和应用,开展新食品资源开发和高值利用、多样化食品生产方式变革、功能性食品添加剂和营养化学品制造,并率先实现产业化,将抢占世界科技的前沿和产业高地,造福人类.
The poor gel properties of fish gelatin limit its commercial application.Enzyme-catalyzed modification of fish gelatin has great advantages such as environmental friendliness,safety and high efficiency.However,there are few gelatin-modified enzymes reported at present,and most of them are covalent cross-linking enzymes,which easily make gelatin form thermal irreversible gel.In this study,two proline hydroxylases that increase the non-covalent action of collagen were cloned and expressed in prokaryotic cells.After purification,the fish gelatin was catalyzed respectively using two proline hydroxylases.The results show that the two enzymes have the effect of improving the gel strength and texture characteristics of fish gelatin.In addition,the surface display technology of Corynebacterium crenatum was studied.The two enzymes were displayed on the surface of C.crenatum,and an immobilized enzyme system with C.crenatum as the carrier was prepared for studying the modification effect of two immobilized enzyme systems on fish gelatin.This study has enriched the catalytic enzyme system of fish gel and provided a new idea for the catalytic modification of fish gelatin.
Objective:To prepare anti-ET antibody for rapid detection of ET using the colloidal gold method.Methods:After identified by mass spectrometry and ultraviolet spectrum,the synthetic ET antigen was used to immunize Balb/C mice.ET hybridoma cell lines with high specificity were obtained by hybridoma technique.After purification by Protein G column,the antibody with appropriate sensitivity was selected and applied to ET colloidal gold reagent.The sensitivity and specificity of the antibody were identified by drug cross interference experiment and clinical experiment.Results:The antibody produced by 10F9 cell line was suitable for ET colloidal gold immunochromatography reagent.The ET reagent was used to detect 12 kinds of e-liquid additives and 48 kinds of commonly used drugs without cross-reaction.The cutoff of ET reagent in urine and e-liquid were both 500 ng/mL,the sensitivity was 100％,and the specificity was 99.5％.Conclusions:The monoclonal antibody(mAb)against ET was successfully prepared and applied to the colloidal gold immunochromatographic reagent.
Programmed cell death(PCD)is a collective term for the intrinsically regulated death of cells.Different forms of cell death are caused by their own programmed regulation during the growth and development of organisms and stress responses to the environment and diseases.PCD includes apoptosis,pyroptosis,necroptosis,autophagy and ferroptosis.It is not only essential for the growth and development of organisms,but also plays an important role in intervening in the process of pathogens invasion.Staphylococcus aureus can regulate various forms of PCD such as apoptosis,pyroptosis,necroptosis and autophagy in host cells,thereby affecting bacterial infection.This article reviews the crosstalk between Staphylococcus aureus infection and PCD to further understand the relationship between Staphylococcus aureus and cell death,in order to provide new ideas for the diagnosis and treatment of clinical Staphylococcus aureus infection.
Cyanobacteria have long been used as model organisms in basic biological research on topics such as photosynthesis,chloroplast origins and plant evolution.Additionally,due to their fast growth,simple culture techniques and convenient genetic manipulation,cyanobacteria have gained increasing attention in photosynthetic bio-manufacturing.One strategy for studying cyanobacteria is to first obtain mutants with specific phenotypes,and then further analyze their functional mutations and related mechanisms.Moreover,in the development of photosynthetic biomanufacturing technologies,enhancing the physiological tolerance of chassis cells is of significant importance for the large-scale application of cyanobacteria photosynthetic cell factories.Evolutionary engineering offers significant advantages in the acquisition of mutants and the optimization of complex physiological tolerance phenotypes,as it does not require knowledge of the microbial genetic background and metabolic network.This paper reviews the progress of evolutionary engineering in the analysis of cyanobacteria physiological metabolism mechanisms and the optimization of physiological tolerance in cyanobacteria photosynthetic biomanufacturing chassis,and meanwhile it also discusses the challenges and future directions of evolutionary engineering in cyanobacteria applications.
Objective:To compare and analyze the difference in performance and application value of five common machine learning algorithms in type 2 diabetes mellitus(T2DM)risk prediction models.Methods:Public diabetes datasets such as the Pima Indians diabetes dataset(PIDD)were utilized to model five common algorithms,namely,logistic regression(LR),support vector machine(SVM),decision tree(DT),naive Bayes(NB)and k-nearest neighbor(KNN).Different training set proportions were set and random repeated sampling was performed.Accuracy and stability were used as the main criteria to compare different models.Results:Through the comparative study of the five models,it is found that their outcomes were closely related to the sample size.It is recommended that the proportion of training sets in model training should be in the range of 0.8 to 0.85,and certain missing values can be tolerated.In addition,the prediction effect of the model is closely related to the sampling of datasets,and LR,SVM and NB methods have better prediction effect.Conclusions:Different prediction models have significantly different performances,with the LR model having the best performance and clear advantages over the other models.The study's findings can be used as a guide when choosing the fundamental algorithm of a clinical T2DM risk prediction model.
Objective:To investigate the effect of TGF-β1 on laminin γ2(LAMC2)expression in mouse normal hepatocyte lines AML12,and the role of LAMC2 on the differentiation of AML12 cells.Methods:Lentiviral vector of LAMC2(Lent-LAMC2)was transfected with AML12 cells,Lenti-NC was used as the control group,the transfection efficiency was detected by Western blot,and the role of LAMC2 on the AML12 differentiation was detected by qPCR analysis.The AML12 cells were stimulated with TGF-β1(5 ng/mL)from 6 h to 24 h,and the mRNA expression of TGF-β1 and LAMC2 was detected by real-time PCR(qPCR).AML12 cells were stimulated with TGF-β1 or TGF-β1+TGF-β inhibitor(SB431542)for 24 h,and the mRNA of LAMC2 was detected by qPCR analysis.Finally,small interfering RNA(siRNA)was used to inhibit the expression of LAMC2 in AML12 cells,and the differentiation of AML12 cells was detected by Western blot followed by stimulation of TGF-β1 at dose of 5 ng/mL.Results:Compared with the Lenti-NC vector group,the protein level of LAMC2 was significantly increased in the LAMC2 overexpressed cells,the expressions of α-SMA and Col1a1 mRNA were up-regulated(all P＜0.05),and ALB expressions were significantly down-regulated(P＜0.05).With the prolongation of the AML12 cell time of TGF-β1,the mRNA expression of LAMC2 gradually increased,which was positively correlated with the stimulation time of TGF-β1(P＜0.05).The transcription level of LAMC2 in TGF-β1+SB431542 group was significantly lower than that in TGF-β1 group(P＜0.05).Importantly,compared with the siNC group,the siLAMC2 group can effectively block the effect of TGF-β1 on the upregulation of expression in AML12 cells α-SMA and Col1a1.Conclusion:Laminin γ2 overexpression induces mesenchymal-like cell changes in AML12 cells.TGF-β1 promotes the expression of LAMC2 in AML12 cells,and LAMC2 specific siRNAs block the fibrogenic effect of TGF-β1 on AML12 cells.
Mesenchymal stem cells(MSCs)are adult multipotent stem cells possessing the advantages of rich and wide sources,low immunogenicity,homing to the tissue of injury,paracrine activity,immunomodulation capacity,and easiness to be engineered.With the above-mentioned advantages,MSCs may have great application value in the treatment of cancer.Despite the controversial roles of MSC in cancer therapy,engineering MSCs with homing capacity to tumor tissues show great antitumor potential for delivering anticancer agents,suicide genes,and oncolytic viruses to tumors.Current clinical trial utilizing engineered MSCs in GBM treatment was shown to exert anti-GBM activity.Therefore,the following review elaborates on the characteristics of MSCs as well as the effects of engineering MSCs on tumor cells and their microenvironments,in order to provide new insights into MSCs'value in translational medicine and tumor treatment.
The nanobodies existing in the sera of camels and sharks have different structural characteristics and molecular weight from traditional monoclonal antibodies,as well as such characteristics as high specificity,high physicochemical stability and tissue permeability,which show great application potential and are considered to be promising therapeutic proteins in the development of biomedicine.Microorganisms are used to produce expression nanobodies without post-translational modification,which can be produced in large quantities and significantly reduce production costs.At present,the conventional expression systems for producing nanobodies are mainly Escherichia coli,Pichia pastoris,and mammalian cell lines,as well as fungi,plant cells,insect cells and lactobacillus expression systems.E.coli has the advantages of fast growth,high yield,easy culture and cost effectiveness.Pichia pastoris has high expression efficiency,can be cultured in high density,and uses methanol as the only carbon source to reduce pollution.Mammalian cells can adapt to serum-free suspension culture.On this basis,the research progress of characteristics,advantages and applications of different expression systems is reviewed,the urgent problems of each system are analyzed,and the production,research and development of therapeutic nanobody drugs and clinical disease treatment applications are summarized,in order to provide reference for the selection of appropriate expression systems for the production of therapeutic nanobodies and their applications in clinical treatment.
Surface plasmon resonance(SPR)biosensors are a new type of biosensor technology based on the principle of SPR.They have numerous advantages including non-labeling,strong specificity,high sensitivity,and real-time dynamic detection,especially for the field of biological molecule interaction,drug-screening,etc.Many countries are stepping up their layout of intellectual property rights(IPRs)for SPR biosensor technology.The number of China's intellectual property applications has increased significantly in recent years.Based on the IncoPat patent database,this study conducts an in-depth analysis on the overall development trend,intellectual property layout,popular technologies of SPR biosensors,and the identification of key IPRs.The results show that the SPR biosensor technology in China is becoming an increasingly active area of research,and China is ranked among the world's leading countries in terms of the number of patent applications in this regard.However,several problems still exist,such as a small number of original IPRs,limited conversion rate of IPRs,and low market share of products.In view of the broad market prospects of SPR biosensor technologies,future development strategies of SPR biosensor technologies in China are proposed.
Tomato transcription factor SlNAC1 has been reported to regulate several biotic and abiotic stress responses,but its upstream regulatory transcription factors remain unknown,which limits our understanding of its molecular mechanism of stress responses.We constructed series of 5'-deleted SINAC1 promoters(2 039 bp,1 508 bp,1 373 bp and 777 bp upstream of start codon)-driven GUS transgenic Nicotiana benthamiana and analyzed quantitatively their GUS activity under cold,heat and ABA treatment conditions in order to identify cold-,heat-,and ABA-responsive cis elements.Our results show that the GUS activity of 2 039 bp promoter-driven transgenic Nicotiana benthamiana increased much higher than that of any other transgenic Nicotiana benthamiana and wild-type Nicotiana benthamiana after cold and heat treatment,while the GUS activity of 1 508 bp promoter-driven transgenic Nicotiana benthamiana increased much higher than that of any other transgenic Nicotiana benthamiana and wild-type Nicotiana benthamiana after ABA treatment.These results indicate that both cold-responsive and heat-responsive cis elements were located in the region from-2 039 bp to-1 508 bp,and ABA-responsive cis element(s)was(were)located in the region from-1 508 bp to-777 bp.According to cis elements'prediction of SINAC1 promoter,there were only one cold/heat/drought/salt-responsive cis element DRE/CRT in the region from-2 039 bp to-1 508 bp and only one ABA-responsive cis element ABRE in the region from-1 508 bp to-777 bp.Therefore,these two cis elements will be used as candidates for subsequent site-directed mutagenesis validation and screening of the upstream regulatory transcription factor of SlNAC1.
Promoter is the most important element of initiation gene transcription and its function is closely related to the gene expression level.The promoter engineering aims to study the functional modification and directed evolution of promoters,which can expand and deepen the application of Saccharomyces cerevisiae promoters in synthetic biology.Based on the structural characteristics of S.cerevisiae promoters,this review focuses on the strategies and applications of S.cerevisiae promoter engineering,including regulatory sequence knockout,random mutation of traditional promoters,saturated mutation,promoter hybridization,synthesis of minimum promoter skeleton,and modification of transcription factor binding sites.In addition,the latest progress of CRISPR/dCas9 and artificial intelligence tools in the field of S.cerevisiae promoter engineering is introduced.The future development prospects of promoter engineering in the field of synthetic biology are also discussed.
As a class of polymer polyester widely existing in microbial cells,Polyhydroxyalkanoate(PHA)has complete biodegradability and excellent biocompatibility,and is considered to be one of the most environmentally friendly bio-based polymer materials.In recent years,the utilization of synthetic biotechnology in genetically modified PHA-producing bacteria,coupled with the escalating demand for eco-friendly materials such as PHA in social and economic development,has led to significant advancements in PHA fermentation technology.However,the extraction cost has emerged as a pivotal factor impeding the commercial application of PHA.This article comprehensively summarizes the technologies and principles underlying various PHA extraction processes,encompassing physical,chemical and biological methods.Furthermore,it conducts a comparative analysis of the advantages and disadvantages associated with each extraction process,with the aim of providing valuable information and references for further cost reduction and efficiency enhancement in PHA extraction.Building upon the current state of PHA extraction process development,this article also presents prospects for the development of PHA extraction.Presently,PHA extraction processes typically combine multiple extraction methods to overcome the limitations of individual techniques;however,process conditions still necessitate optimization.The application of a novel PHA recovery biological system constructed using synthetic biotechnology holds great promise as the most effective strategy for reducing the cost of PHA extraction in the future.
目的:由于强化流加培养工艺(intensified fed batch of ultra-high seeding density,uHSD-IFB)的接种密度与运行密度较高,传统低密度培养工艺的流加策略往往不能提供充足的营养物质用于该过程的细胞维持与产物表达,最终导致过程产率低、经济性下降;通过优化流加培养基以及补料方案,成功建立CHO细胞强化流加培养过程,从而提高目的蛋白产量.方法:以一株表达单克隆抗体的CHO-K1细胞株为研究对象,通过代谢动力学与化学计量学分析,设计出以葡萄糖为控制模型的两阶段动态反馈流加策略,并结合实验设计(design of experiment,DoE)筛选并优化流加培养基中关键微量元素的营养浓度.结果:优化设计后的uHSD-IFB过程有效缓解了 uHSD-IFB过程营养物质的耗竭与代谢副产物累积之间的矛盾,实现了超高接种密度培养工艺的细胞生长与产物合成的目的;累积产量相较于优化前提高了 95％,日体积产量提高了约97％.结论:该补料策略有助于快速建立高细胞密度、高产物表达的高接种密度强化流加培养过程.
代谢物在细胞生命周期中具有重要作用,包括为细胞生命活动提供能量及合成原料、参与生物信号转导等.已有研究表明,活性代谢物可通过体内自发化学反应共价修饰蛋白,调控蛋白质结构和功能,进而影响细胞生命活动的各个环节.近年来,发展迅速的蛋白质组学技术能够捕获这类非酶促修饰的靶蛋白,继而阐明代谢物对靶蛋白功能的调控机制.由活性代谢物产生的非酶促共价修饰,分为可逆和不可逆两种类型.详细介绍代谢物衍生的非酶促翻译后修饰的形成机理,并列举蛋白质组学技术如何鉴定这类修饰进而揭示代谢调控机制的经典研究案例.
金属酶由金属辅因子和蛋白骨架构成.金属辅因子提供催化活性,是金属酶发挥功能的关键,而蛋白骨架为金属辅因子提供附着位点,同时提供手性环境.天然金属酶种类较多,可催化羟基化、环氧化等反应,其辅因子主要以金属离子或金属配体的形式存在,所含金属元素以Fe、Cu、Zn居多,部分天然金属酶也含Mn等金属元素.然而,由于天然金属酶难以催化非天然底物,且部分金属酶体外催化效率低、自身稳定性较差,无法得以广泛应用.近年来研究发现,通过对起催化功能的金属辅因子和提供酶促反应微环境的蛋白骨架进行理性设计构建人工金属酶(artificial metalloenzymes,ArMs),可提高金属酶的催化效率或使其能够催化多种天然和非天然反应.此外,利用纳米技术修饰人工金属酶可以提高金属酶的稳定性和可调控性,为人工金属酶的优化提供了新思路.总结近年来人工金属酶领域取得的成果,着重介绍构建人工金属酶策略方面的研究进展,包括金属辅因子的改造、蛋白骨架的设计、基于纳米技术的修饰等,并展望了设计改造人工金属酶所面临的机遇和挑战,以期为人工金属酶的设计和应用提供参考.
以类胡萝卜素为主的四萜类化合物普遍具有抗氧化、抗炎、抗癌等特性,因此被广泛应用于医疗、食品等领域.传统的从天然产物中提取和化学合成四萜类化合物的方法存在颇多局限,如成本较高、产物活性和纯度较差等.随着基因编辑等技术的发展,微生物合成的方法逐渐被应用于合成高价值产品.介绍生物合成类胡萝卜素的主要途径,综述近年来不同类型底盘菌种的类胡萝卜素合成研究进展,总结当前研究中使用的主要优化策略.对比不同菌种合成类胡萝卜素的策略和产量,指出进一步提高目标产物滴度的研究方向,以期为微生物合成类胡萝卜素的相关研究提供更多参考.
蓝细菌是重要的光合自养微生物,可利用太阳能将二氧化碳转化成高附加产值化学品,且具有营养需求低、生长迅速以及遗传背景简单等优势.伪枝藻素是一种脂溶性芳香族生物碱色素,由少数蓝细菌在胁迫环境下形成,具有很强的紫外吸收、抗炎以及抑制癌细胞增殖的活性,在日化和医药健康领域具有巨大的开发潜力和应用前景.目前,伪枝藻素的合成和调控机制在蓝细菌念珠藻Nostoc punctiforme PCC 73102等中已得到初步解析,但由于天然宿主在遗传改造和工程应用层面存在多重瓶颈,仍无法实现稳定、高效、绿色的生产.随着合成生物学和代谢工程技术的发展,有望通过异源合成及调控实现伪枝藻素的高效生产.总结伪枝藻素的结构、化学性质、功能应用、生物合成途径、调控机制和环境胁迫影响等相关研究进展,并对其未来发展前景进行展望.
目的:通过基因工程技术制备表面展示具有促进膜融合作用的水泡性口炎病毒糖蛋白G(vesicular stomatitis virus glycoprotein,VSVG)的外泌体 VSVG-Exos,利用核酸探针介导 DNA 杂交链式反应在其膜表面修饰靶向树突状细胞间黏附分子-3-结合非整合素DC-SIGN的核酸适配体,构建功能化外泌体,通过重编程肿瘤细胞与树突细胞之间的靶向识别过程增强相互作用.方法:以小鼠乳腺癌细胞4T1和小鼠树突状细胞DC2.4为研究对象,通过共聚焦成像和流式细胞术等实验证明VSVG-Exos以膜融合方式特异性结合4T1细胞,以及DC-SIGN适配体具有特异性靶向DC2.4细胞的能力.结果:功能化外泌体可以重编程修饰4T1细胞,增强与DC2.4细胞之间的靶向识别效应.结论:功能化外泌体有效地输送具有特定功能的分子到肿瘤细胞表面,对其进行重编程修饰,提高免疫细胞精准定位和高效攻击肿瘤细胞的能力,为靶向清除肿瘤细胞提供了新的思路和策略.
