Recent advancements in DNA and RNA bioengineering have paved the way for developing stimuli-responsive nanostructures with remarkable potential across various applications.These nanostructures,crafted through sophisti...Recent advancements in DNA and RNA bioengineering have paved the way for developing stimuli-responsive nanostructures with remarkable potential across various applications.These nanostructures,crafted through sophisticated bioengineering techniques,can dynamically and precisely respond to both physiological and physical stimuli,including nucleic acids(DNA/RNA),adenosine triphosphate,proteins,ions,small molecules,pH,light,and temperature.They offer high sensitivity and specificity,making them ideal for applications such as biomarker detection,gene therapy,and controlled targeted drug delivery.In this review,we summarize the bioengineering methods used to assemble versatile stimuli-responsive DNA/RNA nanostructures and discuss their emerging applications in structural biology and biomedicine,including biosensing,targeted drug delivery,and therapeutics.Finally,we highlight the challenges and opportunities in the rational design of these intelligent bioengineered nanostructures.展开更多
目的探讨灰度共生矩阵和灰度梯度共生矩阵统计学纹理特征在CT图像上甲状腺结节良恶性鉴别的可行性。方法回顾性收集甲状腺结节经手术病理证实的CT图像134例,手动提取含结节的单侧甲状腺感兴趣区(region of interest,ROI)。计算ROI的统...目的探讨灰度共生矩阵和灰度梯度共生矩阵统计学纹理特征在CT图像上甲状腺结节良恶性鉴别的可行性。方法回顾性收集甲状腺结节经手术病理证实的CT图像134例,手动提取含结节的单侧甲状腺感兴趣区(region of interest,ROI)。计算ROI的统计学纹理特征并归一化到[0,1],支持向量机作为分类器,并结合留一交叉验证法来评价实验效果。结果统计学纹理特征在甲状腺结节良恶性鉴别中的准确率为0.76,敏感度0.60,特异性0.86和受试者操作曲线下面积为0.81。结论基于灰度共生矩阵和灰度梯度共生矩阵的统计法纹理特征,在甲状腺CT图像上对于结节的良恶性鉴别具有较好的分类效果。展开更多
BACKGROUND The healthcare burden of inflammatory bowel disease(IBD)is rising globally and there are limited non-invasive biomarkers for accurate and early diagnosis.AIM To understand the important role that intestinal...BACKGROUND The healthcare burden of inflammatory bowel disease(IBD)is rising globally and there are limited non-invasive biomarkers for accurate and early diagnosis.AIM To understand the important role that intestinal microbiota play in IBD pathogenesis and identify anti-microbial antibody signatures that benefit clinical management of IBD patients.METHODS We performed serological profiling of 100 Crohn’s disease(CD)patients,100 ulcerative colitis(UC)patients and 100 healthy controls against 1173 bacterial and 397 viral proteins from 50 bacteria and 33 viruses on protein microarrays.The study subjects were randomly divided into discovery(n=150)and validation(n=150)sets.Statistical analysis was performed using R packages.RESULTS Anti-bacterial antibody responses showed greater differential prevalence among the three subject groups than anti-viral antibody responses.We identified novel antibodies against the antigens of Bacteroidetes vulgatus(BVU_0562)and Streptococcus pneumoniae(SP_1992)showing higher prevalence in CD patients relative to healthy controls.We also identified antibodies against the antigen of Streptococcus pyogenes(SPy_2009)showing higher prevalence in healthy controls relative to UC patients.Using these novel antibodies,we built biomarker panels with area under the curve(AUC)of 0.81,0.87,and 0.82 distinguishing CD vs control,UC vs control,and CD vs UC,respectively.Subgroup analysis revealed that penetrating CD behavior,colonic CD location,CD patients with a history of surgery,and extensive UC exhibited highest antibody prevalence among all patients.We demonstrated that autoantibodies and anti-microbial antibodies in CD patients had minimal correlation.CONCLUSION We have identified antibody signatures for CD and UC using a comprehensive analysis of antimicrobial antibody response in IBD.These antibodies and the source microorganisms of their target antigens improve our understanding of the role of specific microorganisms in IBD pathogenesis and,after future validation,should aid early and accurate diagnosis of IBD.展开更多
Polymer electrolytes(PEs)have been long recognized as the key materials to enable energy-dense batteries and render flexible energy devices practically viable,owing to their chemical and mechanical reliability.However...Polymer electrolytes(PEs)have been long recognized as the key materials to enable energy-dense batteries and render flexible energy devices practically viable,owing to their chemical and mechanical reliability.However,much of their promise is yet to be realized.The roomtemperature ion conductivity of existing PEs still falls short of the implementation criterion of 10^(-4) S cm^(-1) on the promise of acceptable mechanical properties,thereby precluding their practical application.The twin but inversely related duties of polymers,that is,functioning as both an ion-conducting medium and a structural backbone,underlie this issue but are less elucidated systematically.The polyacrylate(PA)family is among promising polymer matrices on account of ester polarity,electrode compatibility,chemical tunability,and mechanical durability.The extensive applicability of PA in plasticized gels,dry solids,and emerging composites makes PA-based PEs representative to illustrate the trade-off between ion conduction and mechanical strength.We herein seek to outline the stated long-standing conflict exemplified by PA-based PEs,focusing on crucial strategies toward balancing and reconciling the two mutually exclusive properties,with the intention of offering designing guidelines for next-generation PEs.展开更多
As one of the transition metals, vanadium（V）（V（V）） in trace amounts represents an essential element for normal cell growth, but becomes toxic when its concentration is above 1 mg/L. V（V） can alter cellular dif...As one of the transition metals, vanadium（V）（V（V）） in trace amounts represents an essential element for normal cell growth, but becomes toxic when its concentration is above 1 mg/L. V（V） can alter cellular differentiation, gene expression, and other biochemical and metabolic phenomena. A feasible method to detoxify V（V） is to reduce it to V（IV）, which precipitates and can be readily removed from the water. The bioreduction of V（V） in a contaminated groundwater was investigated using autohydrogentrophic bacteria and hydrogen gas as the electron donor. Compared with the previous organic donors,H2 shows the advantages as an ideal electron donor, including nontoxicity and less production of excess biomass. V（V） was 95.5% removed by biochemical reduction when autohydrogentrophic bacteria and hydrogen were both present, and the reduced V（IV）precipitated, leading to total-V removal. Reduction kinetics could be described by a first-order model and were sensitive to p H and temperature, with the optimum ranges of p H 7.5–8.0 and 35–40°C, respectively. Phylogenetic analysis by clone library showed that the dominant species in the experiments with V（V） bioreduction belonged to theβ-Proteobacteria. Previously known V（V）-reducing species were absent, suggesting that V（V）reduction was carried out by novel species. Their selective enrichment during V（V）bioreduction suggests that Rhodocyclus, a denitrifying bacterium, and Clostridium, a fermenter known to carry out metal reduction, were responsible for V（V） bioreduction.展开更多
This study assessed the effects of changes in organic carbon content on soil bacterial community composition and diversity in the Antarctic Fildes Peninsula.16 S rRNA gene sequencing was performed to investigate bacte...This study assessed the effects of changes in organic carbon content on soil bacterial community composition and diversity in the Antarctic Fildes Peninsula.16 S rRNA gene sequencing was performed to investigate bacterial community composition.Firstly,we found that organic carbon(OrC)and nutrients showed an increasing trend in the lake area.Secondly,soil geochemistry changes affected microbial composition in the soil.Specifically,we found 3416 operational taxonomical units(OTUs)in 300 genera in five main phyla:Proteobacteria,Actinobacteria,Acidobacteria,Chloroflexi,and Bacteroidetes.Although the diversity was similar among the four sites,the composition was different.Among them,Hungateii content changed very significantly,from 16.67% to 33.33%.Canonical correspondence analysis showed that most measured geochemical factors were relevant in structuring microbiomes,and organic carbon concentration showed the highest correlation,followed by NO3^--N.Hungateii was significantly correlated with the content of organic carbon.Our finding suggested organic carbon played an important role in soil bacterial communities of the Antarctic coastal lake region.展开更多
One major consequence of global warming in the Antarctic region is increased ice-free zones.Subsequent colonization of these ice-free areas by penguins alters their biogeochemistry,with one prominent example being ele...One major consequence of global warming in the Antarctic region is increased ice-free zones.Subsequent colonization of these ice-free areas by penguins alters their biogeochemistry,with one prominent example being elevation of inorganic phosphate concentrations around feces depositions.The complex soil biochemistry in the region makes it difficult to define the causal factors of these changes using common research approaches.Here,we addressed the effects of phosphate alone on microbiome structure and dynamics over time by adding external phosphate to selected soils in the Antarctic region.We then analyzed the soil bacterial community composition and diversity using 16S rRNA amplicon sequencing and compared these data with phosphate levels.Parallel geochemical analysis revealed changes in nine soil geochemical factors upon phosphate addition,all of which were relevant to microbiome structure,with soil pH showing the highest correlation.Links between geochemical factors and composition were identified,as were interactions between bacterial taxa.Additionally,Sphingobacteriia,Sphingobacteriales and Chitinophagaceae were found to be more abundant in phosphate-treated soils.Co-occurrence network analysis revealed significantly increased levels of associations in all major network properties over time after phosphate supplementation.Therefore,we conclude phosphate addition has diverse effects on Antarctic soil microbiomes.展开更多
Large language model(LLM)-based chatbots like Chat Generative Pre-trained Transformer(ChatGPT),equipped with broad biological knowledge[1],have demonstrated an impressive capability for bioinformatics coding[2].When g...Large language model(LLM)-based chatbots like Chat Generative Pre-trained Transformer(ChatGPT),equipped with broad biological knowledge[1],have demonstrated an impressive capability for bioinformatics coding[2].When given well-crafted instructions,these chatbots hold the potential to significantly augment bioinformatics education and research[3,4].However,opportunities entail both rewards and risks.This commentary explores the challenges of using chatbots in bioinformatics and proposes strategies to manage the associated risks while maximizing the benefits.展开更多
The year 2023 marked a significant surge in the exploration of applying large language model chatbots,notably Chat Generative Pre-trained Transformer(ChatGPT),across various disciplines.We surveyed the application of ...The year 2023 marked a significant surge in the exploration of applying large language model chatbots,notably Chat Generative Pre-trained Transformer(ChatGPT),across various disciplines.We surveyed the application of ChatGPT in bioinformatics and biomedical informatics throughout the year,covering omics,genetics,biomedical text mining,drug discovery,biomedical image understanding,bioinformatics programming,and bioinformatics education.Our survey delineates the current strengths and limitations of this chatbot in bioinformatics and offers insights into potential avenues for future developments.展开更多
This perspective provides an overview of the techniques that have been developed for the conjugation of DNA to colloidal quantum dots （QDs）, or semiconductor nanocrystals. Methods described include： ligand exchange...This perspective provides an overview of the techniques that have been developed for the conjugation of DNA to colloidal quantum dots （QDs）, or semiconductor nanocrystals. Methods described include： ligand exchange at the QD surface, covalent conjugation of DNA to the QD surface ligands, and one-step DNA functionalization on core QDs or during core/shell QD synthesis in aqueous solution, with an emphasis on tile most recent progress in our lab. We will also discuss emerging trends in DNA-functionalized QDs for potential applications.展开更多
A long-term pilot-scale H_(2)-based membrane biofilm reactor(MBfR)was tested for removal of nitrate from actual groundwater.A key feature of this secondgeneration pilot MBfR is that it employed lower cost polyester ho...A long-term pilot-scale H_(2)-based membrane biofilm reactor(MBfR)was tested for removal of nitrate from actual groundwater.A key feature of this secondgeneration pilot MBfR is that it employed lower cost polyester hollow fibers and still achieved high loading rate.The steady-state maximum nitrate surface loading at which the effluent nitrate and nitrite concentrations were below the Maximum Contaminant Level(MCL)was at least 5.9 g·N·(m^(2)·d)^(–1),which corresponds to a maximum volumetric loading of at least 7.7 kg·N·(m^(3)·d)^(–1).The steady-state maximum nitrate surface area loading was higher than the highest nitrate surface loading reported in the firstgeneration MBfRs using composite fibers(2.6 g·N·(m^(2)·d)^(–1)).This work also evaluated the H_(2)-utilization efficiency in MBfR.The measured H_(2)supply rate was only slightly higher than the stoichiometric H_(2)-utilization rate.Thus,H_(2)utilization was controlled by diffusion and was close to 100%efficiency,as long as biofilm accumulated on the polyester-fiber surface and the fibers had no leaks.展开更多
Many plant disease resistance(R)genes function specifically in reaction to the presence of cognate effectors from a pathogen.Xanthomonas oryzae pathovar oryzae(Xoo)uses transcription activator-like effectors(TALes)to ...Many plant disease resistance(R)genes function specifically in reaction to the presence of cognate effectors from a pathogen.Xanthomonas oryzae pathovar oryzae(Xoo)uses transcription activator-like effectors(TALes)to target specific rice genes for expression,thereby promoting host susceptibility to bacterial blight.Here,we report the molecular characterization of Xa7,the cognate R gene to the TALes AvrXa7 and PthXo3,which target the rice major susceptibility gene SWEET14.Xa7 was mapped to a unique 74-kb region.Gene expression analysis of the region revealed a candidate gene that contained a putative AvrXa7 effector binding element(EBE)in its promoter and encoded a 113-amino-acid peptide of unknown function.Genome editing at the Xa7 locus rendered the plants susceptible to avrXa7-carrying Xoo strains.Both AvrXa7 and PthXo3 activated a GUS reporter gene fused with the EBE-containing Xa7 promoter in Nicotiana benthamiana.The EBE of Xa7 is a close mimic of the EBE of SWEET14 for TALe-induced disease susceptibility.Ectopic expression of Xa7 triggers cell death in N.benthamiana.Xa7 is prevalent in indica rice accessions from 3000 rice genomes.Xa7 appears to be an adaptation that protects against pathogen exploitation of SWEET14 and disease susceptibility.展开更多
Quinoline （C9H7N） commonly occurs in wastewaters from the chemical, pharmaceutical, and dyeing industries. As quinoline is biodegraded, nitrogen is released as ammonium. Total-N removal requires that the ammonium-N ...Quinoline （C9H7N） commonly occurs in wastewaters from the chemical, pharmaceutical, and dyeing industries. As quinoline is biodegraded, nitrogen is released as ammonium. Total-N removal requires that the ammonium-N be nitrified and then denitrified. The objective of this study was to couple quinoline biodegradation with total-N removal. In a proof-of-concept step, activated sludge was sequenced from aerobic to anoxic stages. The ammonium nitrogen released from quinoline biodegradation in the aerobic stage was nitrified to nitrate in parallel. Anoxic biodegradation of the aerobic effluent then brought about nitrogen and COD removals through denitrification. Then, simultaneous quinoline biodegradation and total-N removal were demonstrated in a novel airlift internal loop biofilm reactor （AILBR） having aerobic and anoxic zones. Experimental results showed that the AILBR could achieve complete removal of quinoline, 91% COD removal, and 85% total-N removal when glucose added as a supplemental electron donor once nitrate was formed.展开更多
Nanopores have been studied as a unique DNA sequencing technology that can quickly read long stretched DNA sequences. A DNA molecule could pass through a nanopore in a speed of microsecond per base and even faster. Wi...Nanopores have been studied as a unique DNA sequencing technology that can quickly read long stretched DNA sequences. A DNA molecule could pass through a nanopore in a speed of microsecond per base and even faster. With this speed, a human genome can potentially be sequenced by one nanopore in 〈1 h. In contrast to next- generation DNA sequencing （NGS）, the nanopore sequencing is enzyme free without need of sample amplification due to its single-molecule nature. The nanopore sequencing has been envisioned as a new generation of DNA sequencing technology in the post-NGS era. This progress focuses on status quo of the nanopore DNA sequencing and discusses the opportunities and challenges in this rapidly growing field.展开更多
The differentiation status of neuroblastoma （NB） strongly correlates with its clinical outcomes; however, the molecular mechanisms driving maintenance of sternness and differentiation remain poorly understood. Here,...The differentiation status of neuroblastoma （NB） strongly correlates with its clinical outcomes; however, the molecular mechanisms driving maintenance of sternness and differentiation remain poorly understood. Here, we show that plant homeodomain finger-containing protein 20 （PHF20） functions as a critical epigenetic regulator in sustaining stem cell-like phenotype of NB by using CRISPR/Casg-based targeted knockout （KO） for high-throughput screening of gene function in NB cell differentiation. The expression of PHF20 in NB was significantly associated with high aggressiveness of the tumor and poor outcomes for NB patients. Deletion of PHF20 inhibited NB cell proliferation, invasive migration, and stem ceU-Uke traits. Mechanistically, PHF20 interacts with poly（ADP-ribose） polymerase 1 （PARP1） and directly binds to promoter regions of octamer-binding transcription factor 4 （OCT4） and sex determining region Y-box 2 （SOX2） to modulate a histone mark associated with active transcription, trimethylation of lysine 4 on histone H3 protein subunit （H3K4me3）. Overexpression of OCT4 and SOX2 restored growth and progression of PHF20 KO tumor cells. Consistently, OCT4 and SOX2 protein levels in clinical NB specimens were positively correlated with PHF20 expression. Our results establish PHF20 as a key driver of NB stem cell-like properties and aggressive behaviors, with implications for prognosis and therapy.展开更多
The impressive conversational and programming abilities of ChatGPT make it an attractive tool for facilitating the education of bioinformatics data analysis for beginners.In this study,we proposed an iterative model t...The impressive conversational and programming abilities of ChatGPT make it an attractive tool for facilitating the education of bioinformatics data analysis for beginners.In this study,we proposed an iterative model to fine-tune instructions for guiding a chatbot in generating code for bioinformatics data analysis tasks.We demonstrated the feasibility of the model by applying it to various bioinformatics topics.Additionally,we discussed practical considerations and limitations regarding the use of the model in chatbot-aided bioinformatics education.展开更多
Cyanobacterium offers a promising chassis for phototrophic production of renewable chemicals. Although engineered cyanobacteria can achieve similar product carbon yields as heterotrophic microbial hosts, their product...Cyanobacterium offers a promising chassis for phototrophic production of renewable chemicals. Although engineered cyanobacteria can achieve similar product carbon yields as heterotrophic microbial hosts, their production rate and titer under photoautotrophic conditions are 10 to 100 folds lower than those in fast growing E. colt. Cyanobacterial factories face three indomitable bottlenecks. First, photosynthesis has limited ATP and NADPH generation rates. Second, CO2 fixation by ribulose-l,5-bisphosphate carboxylase/oxygenase （RuBisCO） has poor efficiency. Third, CO2 mass transfer and light supply are deficient within large photobioreac- tors. On the other hand, cyanobacteria may employ organic substrates to promote phototrophic cell growth, Nz fixation, and metabolite synthesis. The photo-fermenta- tions show enhanced photosynthesis, while CO2 loss from organic substrate degradation can be reused by the Calvin cycle. In addition, the plasticity of cyanobacterial path- ways （e.g., oxidative pentose phosphate pathway and the TCA cycle） has been recently revealed to facilitate the catabolism. The use of cyanobacteria as ＂green E. colt＂ could be a promising route to develop robust photobiorefineries.展开更多
文摘Recent advancements in DNA and RNA bioengineering have paved the way for developing stimuli-responsive nanostructures with remarkable potential across various applications.These nanostructures,crafted through sophisticated bioengineering techniques,can dynamically and precisely respond to both physiological and physical stimuli,including nucleic acids(DNA/RNA),adenosine triphosphate,proteins,ions,small molecules,pH,light,and temperature.They offer high sensitivity and specificity,making them ideal for applications such as biomarker detection,gene therapy,and controlled targeted drug delivery.In this review,we summarize the bioengineering methods used to assemble versatile stimuli-responsive DNA/RNA nanostructures and discuss their emerging applications in structural biology and biomedicine,including biosensing,targeted drug delivery,and therapeutics.Finally,we highlight the challenges and opportunities in the rational design of these intelligent bioengineered nanostructures.
文摘目的探讨灰度共生矩阵和灰度梯度共生矩阵统计学纹理特征在CT图像上甲状腺结节良恶性鉴别的可行性。方法回顾性收集甲状腺结节经手术病理证实的CT图像134例,手动提取含结节的单侧甲状腺感兴趣区(region of interest,ROI)。计算ROI的统计学纹理特征并归一化到[0,1],支持向量机作为分类器,并结合留一交叉验证法来评价实验效果。结果统计学纹理特征在甲状腺结节良恶性鉴别中的准确率为0.76,敏感度0.60,特异性0.86和受试者操作曲线下面积为0.81。结论基于灰度共生矩阵和灰度梯度共生矩阵的统计法纹理特征,在甲状腺CT图像上对于结节的良恶性鉴别具有较好的分类效果。
文摘BACKGROUND The healthcare burden of inflammatory bowel disease(IBD)is rising globally and there are limited non-invasive biomarkers for accurate and early diagnosis.AIM To understand the important role that intestinal microbiota play in IBD pathogenesis and identify anti-microbial antibody signatures that benefit clinical management of IBD patients.METHODS We performed serological profiling of 100 Crohn’s disease(CD)patients,100 ulcerative colitis(UC)patients and 100 healthy controls against 1173 bacterial and 397 viral proteins from 50 bacteria and 33 viruses on protein microarrays.The study subjects were randomly divided into discovery(n=150)and validation(n=150)sets.Statistical analysis was performed using R packages.RESULTS Anti-bacterial antibody responses showed greater differential prevalence among the three subject groups than anti-viral antibody responses.We identified novel antibodies against the antigens of Bacteroidetes vulgatus(BVU_0562)and Streptococcus pneumoniae(SP_1992)showing higher prevalence in CD patients relative to healthy controls.We also identified antibodies against the antigen of Streptococcus pyogenes(SPy_2009)showing higher prevalence in healthy controls relative to UC patients.Using these novel antibodies,we built biomarker panels with area under the curve(AUC)of 0.81,0.87,and 0.82 distinguishing CD vs control,UC vs control,and CD vs UC,respectively.Subgroup analysis revealed that penetrating CD behavior,colonic CD location,CD patients with a history of surgery,and extensive UC exhibited highest antibody prevalence among all patients.We demonstrated that autoantibodies and anti-microbial antibodies in CD patients had minimal correlation.CONCLUSION We have identified antibody signatures for CD and UC using a comprehensive analysis of antimicrobial antibody response in IBD.These antibodies and the source microorganisms of their target antigens improve our understanding of the role of specific microorganisms in IBD pathogenesis and,after future validation,should aid early and accurate diagnosis of IBD.
基金National Natural Science Foundation of China,Grant/Award Numbers:21975271,22139001Shandong Energy Institute,Grant/Award Number:SEI I202127+3 种基金Youth Innovation Promotion Association of CAS,Grant/Award Number:2019214Key Scientific and Technological Innovation Project of Shandong,Grant/Award Number:2020CXGC010401Major basic research projects of Shandong Natural Science Foundation,Grant/Award Number:ZR2020ZD07Strategic Priority Research Program of Chinese Academy of Sciences,Grant/Award Number:XDA22010600。
文摘Polymer electrolytes(PEs)have been long recognized as the key materials to enable energy-dense batteries and render flexible energy devices practically viable,owing to their chemical and mechanical reliability.However,much of their promise is yet to be realized.The roomtemperature ion conductivity of existing PEs still falls short of the implementation criterion of 10^(-4) S cm^(-1) on the promise of acceptable mechanical properties,thereby precluding their practical application.The twin but inversely related duties of polymers,that is,functioning as both an ion-conducting medium and a structural backbone,underlie this issue but are less elucidated systematically.The polyacrylate(PA)family is among promising polymer matrices on account of ester polarity,electrode compatibility,chemical tunability,and mechanical durability.The extensive applicability of PA in plasticized gels,dry solids,and emerging composites makes PA-based PEs representative to illustrate the trade-off between ion conduction and mechanical strength.We herein seek to outline the stated long-standing conflict exemplified by PA-based PEs,focusing on crucial strategies toward balancing and reconciling the two mutually exclusive properties,with the intention of offering designing guidelines for next-generation PEs.
基金supported by the National Natural Science Foundation of China (No. 51378368)
文摘As one of the transition metals, vanadium（V）（V（V）） in trace amounts represents an essential element for normal cell growth, but becomes toxic when its concentration is above 1 mg/L. V（V） can alter cellular differentiation, gene expression, and other biochemical and metabolic phenomena. A feasible method to detoxify V（V） is to reduce it to V（IV）, which precipitates and can be readily removed from the water. The bioreduction of V（V） in a contaminated groundwater was investigated using autohydrogentrophic bacteria and hydrogen gas as the electron donor. Compared with the previous organic donors,H2 shows the advantages as an ideal electron donor, including nontoxicity and less production of excess biomass. V（V） was 95.5% removed by biochemical reduction when autohydrogentrophic bacteria and hydrogen were both present, and the reduced V（IV）precipitated, leading to total-V removal. Reduction kinetics could be described by a first-order model and were sensitive to p H and temperature, with the optimum ranges of p H 7.5–8.0 and 35–40°C, respectively. Phylogenetic analysis by clone library showed that the dominant species in the experiments with V（V） bioreduction belonged to theβ-Proteobacteria. Previously known V（V）-reducing species were absent, suggesting that V（V）reduction was carried out by novel species. Their selective enrichment during V（V）bioreduction suggests that Rhodocyclus, a denitrifying bacterium, and Clostridium, a fermenter known to carry out metal reduction, were responsible for V（V） bioreduction.
基金supported by the National Natural Science Foundation of China (No. 41776198)the Basic Scientific Fund for National Public Research Institutes of China (No. GY0219Q10)the Development Fund of Marine Bioactive Substances, SOA (No. MBSMAT-201701)
文摘This study assessed the effects of changes in organic carbon content on soil bacterial community composition and diversity in the Antarctic Fildes Peninsula.16 S rRNA gene sequencing was performed to investigate bacterial community composition.Firstly,we found that organic carbon(OrC)and nutrients showed an increasing trend in the lake area.Secondly,soil geochemistry changes affected microbial composition in the soil.Specifically,we found 3416 operational taxonomical units(OTUs)in 300 genera in five main phyla:Proteobacteria,Actinobacteria,Acidobacteria,Chloroflexi,and Bacteroidetes.Although the diversity was similar among the four sites,the composition was different.Among them,Hungateii content changed very significantly,from 16.67% to 33.33%.Canonical correspondence analysis showed that most measured geochemical factors were relevant in structuring microbiomes,and organic carbon concentration showed the highest correlation,followed by NO3^--N.Hungateii was significantly correlated with the content of organic carbon.Our finding suggested organic carbon played an important role in soil bacterial communities of the Antarctic coastal lake region.
基金funded by the National Key R&D Program of China(Grant no.2018YFC1406700)the National Natural Science Foundation of China(Grant no.41776198)the Basic Scientific Fund for National Public Research Institutes of China(Grant no.GY0219Q10)。
文摘One major consequence of global warming in the Antarctic region is increased ice-free zones.Subsequent colonization of these ice-free areas by penguins alters their biogeochemistry,with one prominent example being elevation of inorganic phosphate concentrations around feces depositions.The complex soil biochemistry in the region makes it difficult to define the causal factors of these changes using common research approaches.Here,we addressed the effects of phosphate alone on microbiome structure and dynamics over time by adding external phosphate to selected soils in the Antarctic region.We then analyzed the soil bacterial community composition and diversity using 16S rRNA amplicon sequencing and compared these data with phosphate levels.Parallel geochemical analysis revealed changes in nine soil geochemical factors upon phosphate addition,all of which were relevant to microbiome structure,with soil pH showing the highest correlation.Links between geochemical factors and composition were identified,as were interactions between bacterial taxa.Additionally,Sphingobacteriia,Sphingobacteriales and Chitinophagaceae were found to be more abundant in phosphate-treated soils.Co-occurrence network analysis revealed significantly increased levels of associations in all major network properties over time after phosphate supplementation.Therefore,we conclude phosphate addition has diverse effects on Antarctic soil microbiomes.
基金supported by grants from the National Institute of General Medical Sciences(NIGMS,Grants Nos.P20 GM103434 and U54 GM-104942)to Gangqing Huthe National Library of Medicine(NLM,Grant No.R01LM013438)to Li Liu+1 种基金the National Institute of Diabetes and Digestive and Kidney Diseases(NIDDK,Grant No.T32 DK137525)to Li Liuthe NLM(Grant No.R01LM013392)to Dong Xu.
文摘Large language model(LLM)-based chatbots like Chat Generative Pre-trained Transformer(ChatGPT),equipped with broad biological knowledge[1],have demonstrated an impressive capability for bioinformatics coding[2].When given well-crafted instructions,these chatbots hold the potential to significantly augment bioinformatics education and research[3,4].However,opportunities entail both rewards and risks.This commentary explores the challenges of using chatbots in bioinformatics and proposes strategies to manage the associated risks while maximizing the benefits.
基金National Institute of General Medical Sciences,Grant/Award Numbers:P20 GM103434,U54 GM104942U.S.National Library of Medicine,Grant/Award Numbers:R01LM013392,R01LM013438+1 种基金National Science Foundation,Grant/Award Number:2125872National Institute of Diabetes and Digestive and Kidney Diseases,Grant/Award Number:T32 DK137525。
文摘The year 2023 marked a significant surge in the exploration of applying large language model chatbots,notably Chat Generative Pre-trained Transformer(ChatGPT),across various disciplines.We surveyed the application of ChatGPT in bioinformatics and biomedical informatics throughout the year,covering omics,genetics,biomedical text mining,drug discovery,biomedical image understanding,bioinformatics programming,and bioinformatics education.Our survey delineates the current strengths and limitations of this chatbot in bioinformatics and offers insights into potential avenues for future developments.
基金The authors acknowledge the grant support from the Office of Naval Research （ONR） to YL and ZD, and the National Science Foundation （NSF） to HY and YL We also thank Dr. Jeanette Nangreave for assistance in proofreading the manuscript.
文摘This perspective provides an overview of the techniques that have been developed for the conjugation of DNA to colloidal quantum dots （QDs）, or semiconductor nanocrystals. Methods described include： ligand exchange at the QD surface, covalent conjugation of DNA to the QD surface ligands, and one-step DNA functionalization on core QDs or during core/shell QD synthesis in aqueous solution, with an emphasis on tile most recent progress in our lab. We will also discuss emerging trends in DNA-functionalized QDs for potential applications.
文摘A long-term pilot-scale H_(2)-based membrane biofilm reactor(MBfR)was tested for removal of nitrate from actual groundwater.A key feature of this secondgeneration pilot MBfR is that it employed lower cost polyester hollow fibers and still achieved high loading rate.The steady-state maximum nitrate surface loading at which the effluent nitrate and nitrite concentrations were below the Maximum Contaminant Level(MCL)was at least 5.9 g·N·(m^(2)·d)^(–1),which corresponds to a maximum volumetric loading of at least 7.7 kg·N·(m^(3)·d)^(–1).The steady-state maximum nitrate surface area loading was higher than the highest nitrate surface loading reported in the firstgeneration MBfRs using composite fibers(2.6 g·N·(m^(2)·d)^(–1)).This work also evaluated the H_(2)-utilization efficiency in MBfR.The measured H_(2)supply rate was only slightly higher than the stoichiometric H_(2)-utilization rate.Thus,H_(2)utilization was controlled by diffusion and was close to 100%efficiency,as long as biofilm accumulated on the polyester-fiber surface and the fibers had no leaks.
基金supported by the United States Department of Agriculture National Institute of Agriculture and Food(2017-67013-26521 to B.Y.)the National Science Foundation(1238189 to F.F.W.,V.P.B.,and B.Y.,1741090 to F.F.W.)subawards to University of Missouri and University of Florida from the Heinrich Heine University Düsseldorf funded by the Bill&Melinda Gates Foundation[OPP1155704](B.Y.and F.F.W.).
文摘Many plant disease resistance(R)genes function specifically in reaction to the presence of cognate effectors from a pathogen.Xanthomonas oryzae pathovar oryzae(Xoo)uses transcription activator-like effectors(TALes)to target specific rice genes for expression,thereby promoting host susceptibility to bacterial blight.Here,we report the molecular characterization of Xa7,the cognate R gene to the TALes AvrXa7 and PthXo3,which target the rice major susceptibility gene SWEET14.Xa7 was mapped to a unique 74-kb region.Gene expression analysis of the region revealed a candidate gene that contained a putative AvrXa7 effector binding element(EBE)in its promoter and encoded a 113-amino-acid peptide of unknown function.Genome editing at the Xa7 locus rendered the plants susceptible to avrXa7-carrying Xoo strains.Both AvrXa7 and PthXo3 activated a GUS reporter gene fused with the EBE-containing Xa7 promoter in Nicotiana benthamiana.The EBE of Xa7 is a close mimic of the EBE of SWEET14 for TALe-induced disease susceptibility.Ectopic expression of Xa7 triggers cell death in N.benthamiana.Xa7 is prevalent in indica rice accessions from 3000 rice genomes.Xa7 appears to be an adaptation that protects against pathogen exploitation of SWEET14 and disease susceptibility.
文摘Quinoline （C9H7N） commonly occurs in wastewaters from the chemical, pharmaceutical, and dyeing industries. As quinoline is biodegraded, nitrogen is released as ammonium. Total-N removal requires that the ammonium-N be nitrified and then denitrified. The objective of this study was to couple quinoline biodegradation with total-N removal. In a proof-of-concept step, activated sludge was sequenced from aerobic to anoxic stages. The ammonium nitrogen released from quinoline biodegradation in the aerobic stage was nitrified to nitrate in parallel. Anoxic biodegradation of the aerobic effluent then brought about nitrogen and COD removals through denitrification. Then, simultaneous quinoline biodegradation and total-N removal were demonstrated in a novel airlift internal loop biofilm reactor （AILBR） having aerobic and anoxic zones. Experimental results showed that the AILBR could achieve complete removal of quinoline, 91% COD removal, and 85% total-N removal when glucose added as a supplemental electron donor once nitrate was formed.
基金supported by the National Natural Science Foundation of China (21372183)the Hubei Province Natural Science Foundation (2013CFB328)+1 种基金the Key Laboratory of Analytical Chemistry for Biology and Medicine (Wuhan University), Ministry of Education (ACBM2014001)the Start-Up-Fund grant provided by Wuhan University of Science and Technology
文摘Nanopores have been studied as a unique DNA sequencing technology that can quickly read long stretched DNA sequences. A DNA molecule could pass through a nanopore in a speed of microsecond per base and even faster. With this speed, a human genome can potentially be sequenced by one nanopore in 〈1 h. In contrast to next- generation DNA sequencing （NGS）, the nanopore sequencing is enzyme free without need of sample amplification due to its single-molecule nature. The nanopore sequencing has been envisioned as a new generation of DNA sequencing technology in the post-NGS era. This progress focuses on status quo of the nanopore DNA sequencing and discusses the opportunities and challenges in this rapidly growing field.
基金This work was supported by grants from the National Natural Science Foundation of China （81572766 and 31771630）, the National Key Research and Development Program of China （2017YFA0103800）, Guangdong Innovative and Entrepreneurial Research Team Program （2016ZT06S029）, Guangdong Natural Science Foundation （2016A030313215 and 2016A030313238）, SYSU Young Teachers Training Program （16YKZD14） and grants （CA101795 and IU54CA210181） from U.S. National Cancer Institute, National Institutes of Health （NIH）, DOD （W81XWH-16- 1-0417）, and CPRIT （DP150099, RP170537, and RP150611）.
文摘The differentiation status of neuroblastoma （NB） strongly correlates with its clinical outcomes; however, the molecular mechanisms driving maintenance of sternness and differentiation remain poorly understood. Here, we show that plant homeodomain finger-containing protein 20 （PHF20） functions as a critical epigenetic regulator in sustaining stem cell-like phenotype of NB by using CRISPR/Casg-based targeted knockout （KO） for high-throughput screening of gene function in NB cell differentiation. The expression of PHF20 in NB was significantly associated with high aggressiveness of the tumor and poor outcomes for NB patients. Deletion of PHF20 inhibited NB cell proliferation, invasive migration, and stem ceU-Uke traits. Mechanistically, PHF20 interacts with poly（ADP-ribose） polymerase 1 （PARP1） and directly binds to promoter regions of octamer-binding transcription factor 4 （OCT4） and sex determining region Y-box 2 （SOX2） to modulate a histone mark associated with active transcription, trimethylation of lysine 4 on histone H3 protein subunit （H3K4me3）. Overexpression of OCT4 and SOX2 restored growth and progression of PHF20 KO tumor cells. Consistently, OCT4 and SOX2 protein levels in clinical NB specimens were positively correlated with PHF20 expression. Our results establish PHF20 as a key driver of NB stem cell-like properties and aggressive behaviors, with implications for prognosis and therapy.
基金NIH-NIGMS grants P20 GM103434,U54 GM-104942,and 1P20 GM121322 to GHNIH-NLM grant R01LM013438 to LL.
文摘The impressive conversational and programming abilities of ChatGPT make it an attractive tool for facilitating the education of bioinformatics data analysis for beginners.In this study,we proposed an iterative model to fine-tune instructions for guiding a chatbot in generating code for bioinformatics data analysis tasks.We demonstrated the feasibility of the model by applying it to various bioinformatics topics.Additionally,we discussed practical considerations and limitations regarding the use of the model in chatbot-aided bioinformatics education.
文摘Cyanobacterium offers a promising chassis for phototrophic production of renewable chemicals. Although engineered cyanobacteria can achieve similar product carbon yields as heterotrophic microbial hosts, their production rate and titer under photoautotrophic conditions are 10 to 100 folds lower than those in fast growing E. colt. Cyanobacterial factories face three indomitable bottlenecks. First, photosynthesis has limited ATP and NADPH generation rates. Second, CO2 fixation by ribulose-l,5-bisphosphate carboxylase/oxygenase （RuBisCO） has poor efficiency. Third, CO2 mass transfer and light supply are deficient within large photobioreac- tors. On the other hand, cyanobacteria may employ organic substrates to promote phototrophic cell growth, Nz fixation, and metabolite synthesis. The photo-fermenta- tions show enhanced photosynthesis, while CO2 loss from organic substrate degradation can be reused by the Calvin cycle. In addition, the plasticity of cyanobacterial path- ways （e.g., oxidative pentose phosphate pathway and the TCA cycle） has been recently revealed to facilitate the catabolism. The use of cyanobacteria as ＂green E. colt＂ could be a promising route to develop robust photobiorefineries.
