Hibiscus Linn.,an angiosperm genus belonging to Malvaceae,Malvales,is mainly distributed in tropic and subtropic regions.Numerous species within the Hibiscus genus exhibit large and visually appealing flowers that are...Hibiscus Linn.,an angiosperm genus belonging to Malvaceae,Malvales,is mainly distributed in tropic and subtropic regions.Numerous species within the Hibiscus genus exhibit large and visually appealing flowers that are highly prized for their ornamental beauty and enjoy widespread admiration.For instance,H.syriacus serves as the national flower of South Korea,H.rosa-sinensis is favored as the floral emblem of Malaysia,and Chengdu city has earned the moniker"City of H.mutabilis"owing to its substantial cultivation.展开更多
Remodeling plant intracellular nucleotide-binding leucine-rich repeat immune receptors(NLRs)to engineer synthetic disease-resistance genes has emerged as a promising approach to achieving broad-spectrum disease resist...Remodeling plant intracellular nucleotide-binding leucine-rich repeat immune receptors(NLRs)to engineer synthetic disease-resistance genes has emerged as a promising approach to achieving broad-spectrum disease resistance.But strategies for expanding NLR recognition spectra[[1],[2],[3],[4],[5]]are often limited by the rapid evolution of pathogens and pests.In our recent study,we developed an innovative strategy to engineer broad-spectrum,durable and complete disease resistance in plants by remodeling autoactive NLRs into protease-activated switches[6].展开更多
Dear Editor,Influenza viruses cause significant mortality and morbidity in humans.Vaccination is currently the most effective way to combat the virus(Perofsky and Nelson,2020).Unfortunately,the influenza virus frequen...Dear Editor,Influenza viruses cause significant mortality and morbidity in humans.Vaccination is currently the most effective way to combat the virus(Perofsky and Nelson,2020).Unfortunately,the influenza virus frequently changes its antigenicity through rapid mutations,leading to decreased vaccine efficacy or even failure.To improve vaccine effectiveness,it is necessary to monitor antigenic variation and update vaccine strains when significant antigenic variation occurs(Perofsky and Nelson,2020;Malik et al.,2024).展开更多
During the final proofing stage of the paper,the wrong version of Fig.2 was accidently used when replacing it with a high-resolution version.The star and circle marks were missing in the published version.
Combined with elastic network model(ENM),the perturbation response scanning(PRS)has emerged as a robust technique for pinpointing allosteric interactions within proteins.Here,we proposed the PRS analysis of drug-targe...Combined with elastic network model(ENM),the perturbation response scanning(PRS)has emerged as a robust technique for pinpointing allosteric interactions within proteins.Here,we proposed the PRS analysis of drug-target networks(DTNs),which could provide a promising avenue in network medicine.We demonstrated the utility of the method by introducing a deep learning and network perturbation-based framework,for drug repurposing of multiple sclerosis(MS).First,the MS comorbidity network was constructed by performing a random walk with restart algorithm based on shared genes between MS and other diseases as seed nodes.Then,based on topological analysis and functional annotation,the neurotransmission module was identified as the“therapeutic module”of MS.Further,perturbation scores of drugs on the module were calculated by constructing the DTN and introducing the PRS analysis,giving a list of repurposable drugs for MS.Mechanism of action analysis both at pathway and structural levels screened dihydroergocristine as a candidate drug of MS by targeting a serotonin receptor of se-rotonin 2B receptor(HTR2B).Finally,we established a cuprizone-induced chronic mouse model to evaluate the alteration of HTR2B in mouse brain regions and observed that HTR2B was significantly reduced in the cuprizone-induced mouse cortex.These findings proved that the network perturbation modeling is a promising avenue for drug repurposing of MS.As a useful systematic method,our approach can also be used to discover the new molecular mechanism and provide effective candidate drugs for other complex diseases.展开更多
Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,199...Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).展开更多
Objective:To investigate the antibacterial activity and phytochemical screening of the aqueous.methanol and petroleum ether leaf extracts of Merremia emarginata(M.emarginata).Methods:The antibavterial activity of leaf...Objective:To investigate the antibacterial activity and phytochemical screening of the aqueous.methanol and petroleum ether leaf extracts of Merremia emarginata(M.emarginata).Methods:The antibavterial activity of leaf extracts of M.emarginata were evaluated by agar well diffusion method against four selected bacterial species.Results:The presence of tannins,flavonoids,amino acids,starch,glycosides and carbohydrates in the different leaf extracts was established.The methanol extract was more effective against Baciilus cereus and Eseherkhia coli,whereas aqueous extract was more effective against Staphylococcus aureus and Pseudomonas aeruginosa.Condusions:The results in the present study suggest that M.emarginata leaf can be used in treating diseases caused by the tested organisms.展开更多
Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, ...Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.展开更多
Cyanophages are double-stranded DNA viruses that infect cyanobacteria, and they can be found in both freshwater and marine environments. They have a complex pattem of host ranges and play important roles in controllin...Cyanophages are double-stranded DNA viruses that infect cyanobacteria, and they can be found in both freshwater and marine environments. They have a complex pattem of host ranges and play important roles in controlling cyanobacteria population. Unlike marine cyanophages, for which there have been a number of recent investigations, very little attention has been paid to freshwater cyanophages. This review summarizes the taxonomy and morphology, host range, distribution, seasonal dynamics, and complete genomes of freshwater cyanophages, as well as diagnostic markers that can be used to identify them.展开更多
Vacuolar H^＋-translocating pyrophosphatase （V-PPase） is a key enzyme related to plant growth as well as abiotic stress tolerance. In this work, wheat V-PPase genes TaVP1, TaVP2 and TaVP3 were identified. TaVP1 and ...Vacuolar H^＋-translocating pyrophosphatase （V-PPase） is a key enzyme related to plant growth as well as abiotic stress tolerance. In this work, wheat V-PPase genes TaVP1, TaVP2 and TaVP3 were identified. TaVP1 and TaVP2 are more similar to each other than to TaVP3. Their deduced polypeptide sequences preserve the topological structure and essential residues of V-PPases. Phylogenetic studies suggested that monocot plants, at least monocot grasses, have three VP paralogs. TaVP3 transcripts were only detected in developing seeds, and no TaVP2 transcripts were found in germinating seeds. TaVP2 was mainly expressed in shoot tissues and down-regulated in leaves under dehydration. Its expression was up-regulated in roots under high salinity. TaVP1 was relatively more ubiquitously and evenly expressed than TaVP2. Its expression level in roots was highest among the tissues examined, and was inducible by salinity stress. These results indicated that the V-PPase gene paralogs in wheat are differentially regulated spatially and in response to dehydration and salinity stresses.展开更多
Plant height is one of the most important agronomic traits that directly determines plant architecture,and compact or dwarf plants can allow for increased planting density and land utilization as well as increased lod...Plant height is one of the most important agronomic traits that directly determines plant architecture,and compact or dwarf plants can allow for increased planting density and land utilization as well as increased lodging resistance and economic yield.At least four dwarf/semidwarf genes have been identified in different melon varieties,but none of them have been cloned,and little is known about the molecular mechanisms underlying internode elongation in melon.Here,we report map-based cloning and functional characterization of the first semidwarf gene short internode(Cmsi)in melon,which encodes an ERECTA-like receptor kinase regulating internode elongation.Spatial-temporal expression analyses revealed that CmSI exhibited high expression in the vascular bundle of the main stem during internode elongation.The expression level of CmSI was positively correlated with stem length in the different melon varieties examined.Ectopic expression of CmSI in Arabidopsis and cucumber suggested CmSI as a positive regulator of internode elongation in both species.Phytohormone quantitation and transcriptome analysis showed that the auxin content and the expression levels of a number of genes involved in the auxin signaling pathway were altered in the semidwarf mutant,including several well-known auxin transporters,such as members of the ABCB family and PINFORMED genes.A melon polar auxin transport protein CmPIN2 was identified by protein–protein interaction assay as physically interacting with CmSI to modulate auxin signaling.Thus,CmSI functions in an auxin-dependent regulatory pathway to control internode elongation in melon.Our findings revealed that the ERECTA family gene CmSI regulates stem elongation in melon through auxin signaling,which can directly affect polar auxin transport.展开更多
Dear Editor,East Lake,located in the middle and lower reaches of the Yangtze River,is a major source of drinking water for local residents.However,the large increase of population density and the rapid development of ...Dear Editor,East Lake,located in the middle and lower reaches of the Yangtze River,is a major source of drinking water for local residents.However,the large increase of population density and the rapid development of industry has resulted in heavy eutrophication of East Lake over the past few decades.Microcystis aeruginosa is a well-known展开更多
Aim： To compare the results of bladder tumor associated antigen （BTA TRAK）, nuclear matrix protein 22 （NMP 22） and voided urine cytology （VUC） in detecting bladder cancer. Methods： A total of 135 elderly male ...Aim： To compare the results of bladder tumor associated antigen （BTA TRAK）, nuclear matrix protein 22 （NMP 22） and voided urine cytology （VUC） in detecting bladder cancer. Methods： A total of 135 elderly male and 50 healthy volunteers enrolled in this study were classified into three groups： （i） 93 patients with bladder cancer; （ii） 42 patients with urinary benign conditions; and （iii） 50 healthy volunteers. BTA TRAK and NMP 22 kits were used to detect bladder cancer. Voided urine cytology was used to compare the sensitivity and specificity of the screening tests. Results： The sensitivity and specificity of cytology, BTA TRAK and NMP 22 were 24% and 97%, 51% and 73%, 78% and 73%, respectively. The level of NMP 22 increased with tumor grading. The BTA TRAK kit has the lowest sensitivity among the screening tests. The NMP 22 with the best sensitivity can be an adjunct to cytology for evaluating bladder cancer. Conclusion： The NMP 22 test has a better correlation with the grading of the bladder cancer than BTA TRAK. As cytology units are typically not available in hospitals or in outpatient clinics, NMP 22 might be a promising tool for screening bladder cancer.展开更多
The virus receptors are key for the viral infection of host cells.Identification of the virus receptors is still challenging at present.Our previous study has shown that human virus receptor proteins have some unique ...The virus receptors are key for the viral infection of host cells.Identification of the virus receptors is still challenging at present.Our previous study has shown that human virus receptor proteins have some unique features including high N-glycosylation level,high number of interaction partners and high expression level.Here,a random-forest model was built to identify human virus receptorome from human cell membrane proteins with an accepted accuracy based on the combination of the unique features of human virus receptors and protein sequences.A total of 1424 human cell membrane proteins were predicted to constitute the receptorome of the human-infecting virome.In addition,the combination of the random-forest model with protein–protein interactions between human and viruses predicted in previous studies enabled further prediction of the receptors for 693 human-infecting viruses,such as the enterovirus,norovirus and West Nile virus.Finally,the candidate alternative receptors of the SARS-Co V-2 were also predicted in this study.As far as we know,this study is the first attempt to predict the receptorome for the human-infecting virome and would greatly facilitate the identification of the receptors for viruses.展开更多
We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is feature...We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is featured by fusing multiple individual predictors, each of which is established based on one special feature derived from the protein sequence. The ensemble pre-dictor thus formed is superior to the individual ones, as demonstrated by achieving higher correlation coefficient and lower root mean square deviation between the predicted and observed results when examined by the jack-knife cross-validation on a benchmark dataset constructed recently. As a user-friendly web- server, Pred-PFR is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/Folding Rate/.展开更多
Cyanobacteria and eukaryotic algae are abundant in freshwater and marine environments,and are fundamentally important in global biogeochemical cycles and for primary productivity.Under certain conditions,such as an ex...Cyanobacteria and eukaryotic algae are abundant in freshwater and marine environments,and are fundamentally important in global biogeochemical cycles and for primary productivity.Under certain conditions,such as an excess of nutrients due to human activities through fertilizers or sewage,展开更多
Aim： To determine the incidence of adenocarcinoma of the prostate for patients undergoing radical cystoprostatectomy for bladder cancer in Taiwan. Methods： A total of 248 patients in Taiwan who were histologically c...Aim： To determine the incidence of adenocarcinoma of the prostate for patients undergoing radical cystoprostatectomy for bladder cancer in Taiwan. Methods： A total of 248 patients in Taiwan who were histologically confirmed for transitional cell carcinoma of the bladder underwent cystoprostatectomy. Histopathologic evaluation of the prostate specimens sectioned at 5 mm intervals was performed. Results： Of the 248 patients, 10 （4.03%） were found to have prostate cancer. Of the 10 cases of unsuspected prostate cancer, eight proved to be at stage T1 or T2, and two at T3 and T4, respectively. This rate of incidentally found prostate cancer amongst our bladder cancer patients appeared to be lower than that found in bladder cancer patients in similar studies in USA. Conclusion： Although the incidence of incidental prostate cancer in patients in Taiwan with bladder cancer is not high compared with that in Western countries, we suggest that digital rectal examination and prostate-specific antigen （PSA） are important screening tools for men with bladder cancer, especially for those aged 60 years and older in Taiwan.展开更多
The coronavirus 3C-like(3CL)protease,a cysteine protease,plays an important role in viral infection and immune escape.However,there is still a lack of effective tools for determining the cleavage sites of the 3CL prot...The coronavirus 3C-like(3CL)protease,a cysteine protease,plays an important role in viral infection and immune escape.However,there is still a lack of effective tools for determining the cleavage sites of the 3CL protease.This study systematically investigated the diversity of the cleavage sites of the coronavirus 3CL protease on the viral polyprotein,and found that the cleavage motif were highly conserved for viruses in the genera of Alphacoronavirus,Betacoronavirus and Gammacoronavirus.Strong residue preferences were observed at the neighboring positions of the cleavage sites.A random forest(RF)model was built to predict the cleavage sites of the coronavirus 3CL protease based on the representation of residues in cleavage motifs by amino acid indexes,and the model achieved an AUC of 0.96 in cross-validations.The RF model was further tested on an independent test dataset which were composed of cleavage sites on 99 proteins from multiple coronavirus hosts.It achieved an AUC of 0.95 and predicted correctly 80%of the cleavage sites.Then,1,352 human proteins were predicted to be cleaved by the 3CL protease by the RF model.These proteins were enriched in several GO terms related to the cytoskeleton,such as the microtubule,actin and tubulin.Finally,a webserver named 3CLP was built to predict the cleavage sites of the coronavirus 3CL protease based on the RF model.Overall,the study provides an effective tool for identifying cleavage sites of the 3CL protease and provides insights into the molecular mechanism underlying the pathogenicity of coronaviruses.展开更多
BACKGROUND Radiation induces rapid bone loss and enhances bone resorption and adipogenesis, leading to an increased risk of bone fracture. There is still a lack of effective preventive or therapeutic method for irradi...BACKGROUND Radiation induces rapid bone loss and enhances bone resorption and adipogenesis, leading to an increased risk of bone fracture. There is still a lack of effective preventive or therapeutic method for irradiation-induced bone injury.Receptor activator of nuclear factor κB ligand(RANKL) provides the crucial signal to induce osteoclast differentiation and plays an important role in bone resorption. However, the mechanisms of radiation-induced osteoporosis are not fully understood.AIM To investigate the role of CR6-interacting factor-1(Crif1) in osteoclastogenesis after radiation and its possible mechanism.METHODS C57 BL/6 mice were exposed to Co-60 gamma rays and received 5 Gy of wholebody sublethal irradiation at a rate of 0.69 Gy/min. For in vitro study, mouse bone marrow mesenchymal stem/stromal cells(BM-MSCs) were irradiated with Co-60 at a single dose of 9 Gy. For osteoclast induction, monocyte-macrophage RAW264.7 cells were cocultured with mouse BM-MSCs for 7 d. Clus Pro and Inter Pro Surf were used to investigate the interaction interface in Crif1 and protein kinase cyclic adenosine monophosphate(c AMP)-activited catalytic subunit alpha complex. Virtual screening using 462608 compounds from the Life Chemicals database around His120 of Crif1 was carried out using the program Autodock_vina. A tetrazolium salt(WST-8) assay was carried out to study the toxicity of compounds to different cells, including human BM-MSCs, mouse BMMSCs, and Vero cells.RESULTS Crif1 expression increased in bone marrow cells after radiation in mice.Overexpression of Crif1 in mouse BM-MSCs and radiation exposure could increase RANKL secretion and promote osteoclastogenesis in vitro. Deletion of Crif1 in BM-MSCs could reduce both adipogenesis and RANKL expression,resulting in the inhibition of osteoclastogenesis. Deletion of Crif1 in RAW264.7 cells did not affect the receptor activator of nuclear factor κB expression or osteoclast differentiation. Following treatment with protein kinase A(PKA)agonist(forskolin) and inhibitor(H-89) in mouse BM-MSCs, Crif1 induced RANKL secretion via the c AMP/PKA pathway. Moreover, we identified the Crif1-protein kinase cyclic adenosine monophosphate-activited catalytic subunit alpha interaction interface by in silico studies and shortlisted interface inhibitors through virtual screening on Crif1. Five compounds dramatically suppressed RANKL secretion and adipogenesis by inhibiting the c AMP/PKA pathway.CONCLUSION Crif1 promotes RANKL expression via the c AMP/PKA pathway, which induces osteoclastogenesis by binding to receptor activator of nuclear factor κB on monocytes-macrophages in the mouse model. These results suggest a role for Crif1 in modulating osteoclastogenesis and provide insights into potential therapeutic strategies targeting the balance between osteogenesis and adipogenesis for radiation-induced bone injury.展开更多
文摘Hibiscus Linn.,an angiosperm genus belonging to Malvaceae,Malvales,is mainly distributed in tropic and subtropic regions.Numerous species within the Hibiscus genus exhibit large and visually appealing flowers that are highly prized for their ornamental beauty and enjoy widespread admiration.For instance,H.syriacus serves as the national flower of South Korea,H.rosa-sinensis is favored as the floral emblem of Malaysia,and Chengdu city has earned the moniker"City of H.mutabilis"owing to its substantial cultivation.
基金supported by the Biological Breeding-National Science and Technology Major Project(2024ZD04077).
文摘Remodeling plant intracellular nucleotide-binding leucine-rich repeat immune receptors(NLRs)to engineer synthetic disease-resistance genes has emerged as a promising approach to achieving broad-spectrum disease resistance.But strategies for expanding NLR recognition spectra[[1],[2],[3],[4],[5]]are often limited by the rapid evolution of pathogens and pests.In our recent study,we developed an innovative strategy to engineer broad-spectrum,durable and complete disease resistance in plants by remodeling autoactive NLRs into protease-activated switches[6].
基金upported by the Major Project of Guangzhou National Laboratory(GZNL2024A01002)National Key Plan for Scientific Research and Development of China(2022YFC2303802)+1 种基金National Natural Science Foundation of China(32170651&32370700)Hunan Provincial Natural Science Foundation of China(2024JJ2015).
文摘Dear Editor,Influenza viruses cause significant mortality and morbidity in humans.Vaccination is currently the most effective way to combat the virus(Perofsky and Nelson,2020).Unfortunately,the influenza virus frequently changes its antigenicity through rapid mutations,leading to decreased vaccine efficacy or even failure.To improve vaccine effectiveness,it is necessary to monitor antigenic variation and update vaccine strains when significant antigenic variation occurs(Perofsky and Nelson,2020;Malik et al.,2024).
文摘During the final proofing stage of the paper,the wrong version of Fig.2 was accidently used when replacing it with a high-resolution version.The star and circle marks were missing in the published version.
基金supported by the National Natural Science Foundation of China(Grant Nos.:32271292,31872723,32200778,and 22377089)the Jiangsu Students Innovation and Entrepre-neurship Training Program,China(Program No.:202210285081Z)+6 种基金the Project of MOE Key Laboratory of Geriatric Diseases and Immunology,China(Project No.:JYN202404)Proj-ect Funded by the Priority Academic Program Development(PAPD)of Jiangsu Higher Education Institutions,Natural Science Foundation of Jiangsu Province,China(Project No.:BK20220494)Suzhou Medical and Health Technology Innovation Project,China(Grant No.:SKY2022107)the Clinical Research Center of Neuro-logical Disease in The Second Affiliated Hospital of Soochow University,China(Grant No.:ND2022A04)State Key Laboratory of Drug Research(Grant No.:SKLDR-2023-KF-05)Jiangsu Shuang-chuang Program for Doctor,Young Science Talents Promotion Project of Jiangsu Science and Technology Association(Program No.:TJ-2023-019)Young Science Talents Promotion Project of Suzhou Science and Technology Association,Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases,and startup funding(Grant Nos.:NH21500221,NH21500122,and NH21500123)to Qifei Cong.
文摘Combined with elastic network model(ENM),the perturbation response scanning(PRS)has emerged as a robust technique for pinpointing allosteric interactions within proteins.Here,we proposed the PRS analysis of drug-target networks(DTNs),which could provide a promising avenue in network medicine.We demonstrated the utility of the method by introducing a deep learning and network perturbation-based framework,for drug repurposing of multiple sclerosis(MS).First,the MS comorbidity network was constructed by performing a random walk with restart algorithm based on shared genes between MS and other diseases as seed nodes.Then,based on topological analysis and functional annotation,the neurotransmission module was identified as the“therapeutic module”of MS.Further,perturbation scores of drugs on the module were calculated by constructing the DTN and introducing the PRS analysis,giving a list of repurposable drugs for MS.Mechanism of action analysis both at pathway and structural levels screened dihydroergocristine as a candidate drug of MS by targeting a serotonin receptor of se-rotonin 2B receptor(HTR2B).Finally,we established a cuprizone-induced chronic mouse model to evaluate the alteration of HTR2B in mouse brain regions and observed that HTR2B was significantly reduced in the cuprizone-induced mouse cortex.These findings proved that the network perturbation modeling is a promising avenue for drug repurposing of MS.As a useful systematic method,our approach can also be used to discover the new molecular mechanism and provide effective candidate drugs for other complex diseases.
基金supported by the National Natural Science Foundation of China(32270217,31970205,31770211)Metasequoia funding of Nanjing Forestry University to YY。
文摘Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).
文摘Objective:To investigate the antibacterial activity and phytochemical screening of the aqueous.methanol and petroleum ether leaf extracts of Merremia emarginata(M.emarginata).Methods:The antibavterial activity of leaf extracts of M.emarginata were evaluated by agar well diffusion method against four selected bacterial species.Results:The presence of tannins,flavonoids,amino acids,starch,glycosides and carbohydrates in the different leaf extracts was established.The methanol extract was more effective against Baciilus cereus and Eseherkhia coli,whereas aqueous extract was more effective against Staphylococcus aureus and Pseudomonas aeruginosa.Condusions:The results in the present study suggest that M.emarginata leaf can be used in treating diseases caused by the tested organisms.
基金support from the National Institute of Environmental Health Sciences (USA) training grant to the NCSU Bioinformatics Research Centersupported by National Institutes of Health (USA) grant no.GM070806
文摘Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.
文摘Cyanophages are double-stranded DNA viruses that infect cyanobacteria, and they can be found in both freshwater and marine environments. They have a complex pattem of host ranges and play important roles in controlling cyanobacteria population. Unlike marine cyanophages, for which there have been a number of recent investigations, very little attention has been paid to freshwater cyanophages. This review summarizes the taxonomy and morphology, host range, distribution, seasonal dynamics, and complete genomes of freshwater cyanophages, as well as diagnostic markers that can be used to identify them.
基金supported by Outstanding Youth Fund of NNSFC (30025030)2000's Trans-Century Talent Development Program of Ministry of Education, China+2 种基金GCP Project SP2-1Transgenic program 2008ZX08009-002‘111’ Project B08025
文摘Vacuolar H^＋-translocating pyrophosphatase （V-PPase） is a key enzyme related to plant growth as well as abiotic stress tolerance. In this work, wheat V-PPase genes TaVP1, TaVP2 and TaVP3 were identified. TaVP1 and TaVP2 are more similar to each other than to TaVP3. Their deduced polypeptide sequences preserve the topological structure and essential residues of V-PPases. Phylogenetic studies suggested that monocot plants, at least monocot grasses, have three VP paralogs. TaVP3 transcripts were only detected in developing seeds, and no TaVP2 transcripts were found in germinating seeds. TaVP2 was mainly expressed in shoot tissues and down-regulated in leaves under dehydration. Its expression was up-regulated in roots under high salinity. TaVP1 was relatively more ubiquitously and evenly expressed than TaVP2. Its expression level in roots was highest among the tissues examined, and was inducible by salinity stress. These results indicated that the V-PPase gene paralogs in wheat are differentially regulated spatially and in response to dehydration and salinity stresses.
基金supported by grants from the National Natural Science Foundation of China(31872133)the Project for Scientific and Technological Activities of Overseas Students of Henan Province,the Zhongyuan Youth Talent Support Program(ZYQR201912161)the Program for Science&Technology Innovation Talents in Universities of Henan Province(20HASTIT035).
文摘Plant height is one of the most important agronomic traits that directly determines plant architecture,and compact or dwarf plants can allow for increased planting density and land utilization as well as increased lodging resistance and economic yield.At least four dwarf/semidwarf genes have been identified in different melon varieties,but none of them have been cloned,and little is known about the molecular mechanisms underlying internode elongation in melon.Here,we report map-based cloning and functional characterization of the first semidwarf gene short internode(Cmsi)in melon,which encodes an ERECTA-like receptor kinase regulating internode elongation.Spatial-temporal expression analyses revealed that CmSI exhibited high expression in the vascular bundle of the main stem during internode elongation.The expression level of CmSI was positively correlated with stem length in the different melon varieties examined.Ectopic expression of CmSI in Arabidopsis and cucumber suggested CmSI as a positive regulator of internode elongation in both species.Phytohormone quantitation and transcriptome analysis showed that the auxin content and the expression levels of a number of genes involved in the auxin signaling pathway were altered in the semidwarf mutant,including several well-known auxin transporters,such as members of the ABCB family and PINFORMED genes.A melon polar auxin transport protein CmPIN2 was identified by protein–protein interaction assay as physically interacting with CmSI to modulate auxin signaling.Thus,CmSI functions in an auxin-dependent regulatory pathway to control internode elongation in melon.Our findings revealed that the ERECTA family gene CmSI regulates stem elongation in melon through auxin signaling,which can directly affect polar auxin transport.
基金support from the Knowledge Innovation Program of the Chinese Academy of Sciences(KSCX2-YW-Z-0954,KSCX2-EW-Z-3)
文摘Dear Editor,East Lake,located in the middle and lower reaches of the Yangtze River,is a major source of drinking water for local residents.However,the large increase of population density and the rapid development of industry has resulted in heavy eutrophication of East Lake over the past few decades.Microcystis aeruginosa is a well-known
文摘Aim： To compare the results of bladder tumor associated antigen （BTA TRAK）, nuclear matrix protein 22 （NMP 22） and voided urine cytology （VUC） in detecting bladder cancer. Methods： A total of 135 elderly male and 50 healthy volunteers enrolled in this study were classified into three groups： （i） 93 patients with bladder cancer; （ii） 42 patients with urinary benign conditions; and （iii） 50 healthy volunteers. BTA TRAK and NMP 22 kits were used to detect bladder cancer. Voided urine cytology was used to compare the sensitivity and specificity of the screening tests. Results： The sensitivity and specificity of cytology, BTA TRAK and NMP 22 were 24% and 97%, 51% and 73%, 78% and 73%, respectively. The level of NMP 22 increased with tumor grading. The BTA TRAK kit has the lowest sensitivity among the screening tests. The NMP 22 with the best sensitivity can be an adjunct to cytology for evaluating bladder cancer. Conclusion： The NMP 22 test has a better correlation with the grading of the bladder cancer than BTA TRAK. As cytology units are typically not available in hospitals or in outpatient clinics, NMP 22 might be a promising tool for screening bladder cancer.
基金supported by the National Key Plan for Scientific Research and Development of China(2016YFD0500300)Hunan Provincial Natural Science Foundation of China(2018JJ3039)+1 种基金the Chinese Academy of Medical Sciences(2016-I2M-1-005)the special project for COVID-19 of Guangzhou Regenerative Medicine and Health Guangdong Laboratory(2020GZR110406001)
文摘The virus receptors are key for the viral infection of host cells.Identification of the virus receptors is still challenging at present.Our previous study has shown that human virus receptor proteins have some unique features including high N-glycosylation level,high number of interaction partners and high expression level.Here,a random-forest model was built to identify human virus receptorome from human cell membrane proteins with an accepted accuracy based on the combination of the unique features of human virus receptors and protein sequences.A total of 1424 human cell membrane proteins were predicted to constitute the receptorome of the human-infecting virome.In addition,the combination of the random-forest model with protein–protein interactions between human and viruses predicted in previous studies enabled further prediction of the receptors for 693 human-infecting viruses,such as the enterovirus,norovirus and West Nile virus.Finally,the candidate alternative receptors of the SARS-Co V-2 were also predicted in this study.As far as we know,this study is the first attempt to predict the receptorome for the human-infecting virome and would greatly facilitate the identification of the receptors for viruses.
文摘We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is featured by fusing multiple individual predictors, each of which is established based on one special feature derived from the protein sequence. The ensemble pre-dictor thus formed is superior to the individual ones, as demonstrated by achieving higher correlation coefficient and lower root mean square deviation between the predicted and observed results when examined by the jack-knife cross-validation on a benchmark dataset constructed recently. As a user-friendly web- server, Pred-PFR is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/Folding Rate/.
文摘Cyanobacteria and eukaryotic algae are abundant in freshwater and marine environments,and are fundamentally important in global biogeochemical cycles and for primary productivity.Under certain conditions,such as an excess of nutrients due to human activities through fertilizers or sewage,
文摘Aim： To determine the incidence of adenocarcinoma of the prostate for patients undergoing radical cystoprostatectomy for bladder cancer in Taiwan. Methods： A total of 248 patients in Taiwan who were histologically confirmed for transitional cell carcinoma of the bladder underwent cystoprostatectomy. Histopathologic evaluation of the prostate specimens sectioned at 5 mm intervals was performed. Results： Of the 248 patients, 10 （4.03%） were found to have prostate cancer. Of the 10 cases of unsuspected prostate cancer, eight proved to be at stage T1 or T2, and two at T3 and T4, respectively. This rate of incidentally found prostate cancer amongst our bladder cancer patients appeared to be lower than that found in bladder cancer patients in similar studies in USA. Conclusion： Although the incidence of incidental prostate cancer in patients in Taiwan with bladder cancer is not high compared with that in Western countries, we suggest that digital rectal examination and prostate-specific antigen （PSA） are important screening tools for men with bladder cancer, especially for those aged 60 years and older in Taiwan.
基金supported by the National Key Plan for Scientific Research and Development of China(2016YFD0500300)National Natural Science Foundation of China(32170651)Hunan Provincial Natural Science Foundation of China(2020JJ3006)。
文摘The coronavirus 3C-like(3CL)protease,a cysteine protease,plays an important role in viral infection and immune escape.However,there is still a lack of effective tools for determining the cleavage sites of the 3CL protease.This study systematically investigated the diversity of the cleavage sites of the coronavirus 3CL protease on the viral polyprotein,and found that the cleavage motif were highly conserved for viruses in the genera of Alphacoronavirus,Betacoronavirus and Gammacoronavirus.Strong residue preferences were observed at the neighboring positions of the cleavage sites.A random forest(RF)model was built to predict the cleavage sites of the coronavirus 3CL protease based on the representation of residues in cleavage motifs by amino acid indexes,and the model achieved an AUC of 0.96 in cross-validations.The RF model was further tested on an independent test dataset which were composed of cleavage sites on 99 proteins from multiple coronavirus hosts.It achieved an AUC of 0.95 and predicted correctly 80%of the cleavage sites.Then,1,352 human proteins were predicted to be cleaved by the 3CL protease by the RF model.These proteins were enriched in several GO terms related to the cytoskeleton,such as the microtubule,actin and tubulin.Finally,a webserver named 3CLP was built to predict the cleavage sites of the coronavirus 3CL protease based on the RF model.Overall,the study provides an effective tool for identifying cleavage sites of the 3CL protease and provides insights into the molecular mechanism underlying the pathogenicity of coronaviruses.
基金National Natural Science Foundation of China,No.81502754 and No.31571352Interdisciplinary and International Cooperation Projects of The Second Affiliated Hospital,Third Military Medical University,No.2016YXKJC0。
文摘BACKGROUND Radiation induces rapid bone loss and enhances bone resorption and adipogenesis, leading to an increased risk of bone fracture. There is still a lack of effective preventive or therapeutic method for irradiation-induced bone injury.Receptor activator of nuclear factor κB ligand(RANKL) provides the crucial signal to induce osteoclast differentiation and plays an important role in bone resorption. However, the mechanisms of radiation-induced osteoporosis are not fully understood.AIM To investigate the role of CR6-interacting factor-1(Crif1) in osteoclastogenesis after radiation and its possible mechanism.METHODS C57 BL/6 mice were exposed to Co-60 gamma rays and received 5 Gy of wholebody sublethal irradiation at a rate of 0.69 Gy/min. For in vitro study, mouse bone marrow mesenchymal stem/stromal cells(BM-MSCs) were irradiated with Co-60 at a single dose of 9 Gy. For osteoclast induction, monocyte-macrophage RAW264.7 cells were cocultured with mouse BM-MSCs for 7 d. Clus Pro and Inter Pro Surf were used to investigate the interaction interface in Crif1 and protein kinase cyclic adenosine monophosphate(c AMP)-activited catalytic subunit alpha complex. Virtual screening using 462608 compounds from the Life Chemicals database around His120 of Crif1 was carried out using the program Autodock_vina. A tetrazolium salt(WST-8) assay was carried out to study the toxicity of compounds to different cells, including human BM-MSCs, mouse BMMSCs, and Vero cells.RESULTS Crif1 expression increased in bone marrow cells after radiation in mice.Overexpression of Crif1 in mouse BM-MSCs and radiation exposure could increase RANKL secretion and promote osteoclastogenesis in vitro. Deletion of Crif1 in BM-MSCs could reduce both adipogenesis and RANKL expression,resulting in the inhibition of osteoclastogenesis. Deletion of Crif1 in RAW264.7 cells did not affect the receptor activator of nuclear factor κB expression or osteoclast differentiation. Following treatment with protein kinase A(PKA)agonist(forskolin) and inhibitor(H-89) in mouse BM-MSCs, Crif1 induced RANKL secretion via the c AMP/PKA pathway. Moreover, we identified the Crif1-protein kinase cyclic adenosine monophosphate-activited catalytic subunit alpha interaction interface by in silico studies and shortlisted interface inhibitors through virtual screening on Crif1. Five compounds dramatically suppressed RANKL secretion and adipogenesis by inhibiting the c AMP/PKA pathway.CONCLUSION Crif1 promotes RANKL expression via the c AMP/PKA pathway, which induces osteoclastogenesis by binding to receptor activator of nuclear factor κB on monocytes-macrophages in the mouse model. These results suggest a role for Crif1 in modulating osteoclastogenesis and provide insights into potential therapeutic strategies targeting the balance between osteogenesis and adipogenesis for radiation-induced bone injury.
