Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity an...Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.展开更多
Polyploidy,or whole-genome duplication,is an important evolutionary process that has shaped the genomes and traits of many plants,including numerous important crops.The Brassica genus,which includes diverse vegetables...Polyploidy,or whole-genome duplication,is an important evolutionary process that has shaped the genomes and traits of many plants,including numerous important crops.The Brassica genus,which includes diverse vegetables and oilseeds,is a key model system for studying how polyploidy affects plant diversification and domestication.This review summarizes the current understanding of how multiple rounds of ancient and more recent polyploidization events laid the foundation for the wide diversity seen in Brassica.We discuss the key outcomes through which polyploidy facilitates the accumulation of genetic variation,including genomic buffering that enables mutation retention.Furthermore,we explore the significant roles of interspecies and interploidy introgression in introducing external genetic novelty.We highlight homoeologous exchange(HE)as a critical mechanism unique to allopolyploids,driving substantial genomic rearrangements including presence-absence variations and gene dosage alterations that directly contribute to significant phenotypic innovation and adaptation in Brassica.Together,these polyploidy-associated processes have led to the extensive range of genomic variations that shaped great morphological diversification in the domestication of Brassica.By integrating insights from genomics,genetics,and evolutionary biology,this review shows how polyploidy has been central to Brassica's success and agricultural value.We also suggest future research areas to better understand polyploid evolution and improve crop breeding.展开更多
Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we...Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground truth.Gene expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription factors.Parallel to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides.Based on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization.To explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics.The results demonstrated the utility of our computational approach for predicting candidate genes in crop species.Our findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.展开更多
Previous phytochemical investigation of the leaves and seeds of Pittosporum angustifolium Lodd.led to the isolation and structural elucidation of polyphenols and triterpene saponins.Evaluation for cytotoxicity of isol...Previous phytochemical investigation of the leaves and seeds of Pittosporum angustifolium Lodd.led to the isolation and structural elucidation of polyphenols and triterpene saponins.Evaluation for cytotoxicity of isolated saponins revealed that the predominant structural feature for a cytotoxic activity are acyl substituents at the oleanane aglycon backbone.The present work reports the results of a screening of 10 selected acylated saponins for their potential to inhibit the human DNA-topoisomerase I,giving rise to IC50 values in a range of 2.8-46.5 lM.To clarify the mode of observed cytotoxic action and,moreover,to distinguish from a pure surfactant effect which is commonly accompanied with saponins,these results indicate an involvement of the topoisomerase I and its role as a possible target structure for a cytotoxic activity.In addition,computational predictions of the fitting of saponins to the topoisomerase I-DNA complex,indicate a similar binding mode to that of clinically used topoisomerase I inhibitors.Graphical Abstract Ten acylated triterpene saponins from Pittosporum angustifolium were investigated for their potential to inhibit the human DNA-topoisomerase I and computational predictions of the fitting of saponins to the topoisomerase I-DNA complex were carried out.展开更多
Objective:To assess the virus infection in mosquitoes during different seasons and correlated with various climatic factors.Methods:The field collected vectors were screened for Japanese encephalitis(JE) virus after d...Objective:To assess the virus infection in mosquitoes during different seasons and correlated with various climatic factors.Methods:The field collected vectors were screened for Japanese encephalitis(JE) virus after dessication using ELISA method.Most of the positive pools were recorded from Culex tritaeniorhynchus(Cx.tritaeniorhynchus) and Culex.gelidus(Cx.gelidus) during JE transmission season(winter) and some positive pools were also reported during non JE transmission periods(i.e.summer and rainy seasons).Results:The minimum infection rates(MIR) of 1.75 from Cx.tritaeniorhynchus and 0.17 from Cx.gelidus has been reported in the year 2002 at the beginning of the study and the values were found nil at the end of the study(2006) from the study areas of Kurnool district.Conclusions:From this study it is noted that MTR of Cx.gelidus and Cx.tritaeniorhynchus were modulated by various meteorological parameters.The mosquito vector abundance increases after the monsoon period(winter) and lowest in dry season(summer). Similarly,MIR fluctuated between seasons with higher MIR recorded after monsoon period and lower in the rest of season.Impact of these metrological parameters in JE virus infected mosquitoes is discussed in this paper.展开更多
Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid)...Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid),M (glycoprotein),and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require elucidation.In this work we collected all full length S segment sequences and generated a phylogenetic tree based on the alignment of these 62 samples.We then analyzed the alignment using entries from AAIndex,the Amino Acid Index database,to identify amino acid mutations that performed significant changes in charge,pka,hydropathy and side chain volume.Finally,we mapped these changes back to the tree and alignment to identify correlated mutations or sites that characterized a specific lineage.Based on this analysis we are able to propose a number of sites that appear to be important for virus function and which would be good candidates for experimental mutational analysis studies.展开更多
This research focused on the modification of the functional groups of oseltamivir as neuraminidase inhibitor against influenza A virus subtype H1N1.Interactions of three of the best ligands were evaluated in the hydra...This research focused on the modification of the functional groups of oseltamivir as neuraminidase inhibitor against influenza A virus subtype H1N1.Interactions of three of the best ligands were evaluated in the hydrated state using molecular dynamics simulation at two different temperatures.The docking result showed that AD3BF2 D ligand（N-[（1S,6R）-5-amino-5-{[（2R,3S,4S）-3,4-dihydroxy-4-（hydroxymethyl） tetrahydrofuran-2-yl]oxy}-4-formylcyclohex-3-en-1-yl]acetamide-3-（1-ethylpropoxy）-1-cyclohexene-1-carboxylate） had better binding energy values than standard oseltamivir.AD3BF2 D had several interactions,including hydrogen bonds,with the residues in the catalytic site of neuraminidase as identified by molecular dynamics simulation.The results showed that AD3BF2 D ligand can be used as a good candidate for neuraminidase inhibitor to cope with influenza A virus subtype H1N1.展开更多
MicroRNAs(miRNAs)are a class of small non-coding RNAs that play important roles in post-transcriptional regulation of gene expression[1].A large number of miRNAs have been found to be involved in a broad spectrum of b...MicroRNAs(miRNAs)are a class of small non-coding RNAs that play important roles in post-transcriptional regulation of gene expression[1].A large number of miRNAs have been found to be involved in a broad spectrum of biological functions such as regulation of innate and adaptive immunity,cell differentiation and development as well as展开更多
High throughput gene expression analysis is swiftly becoming the focal point for deciphering molecular mechanisms underlying various dif-ferent biological questions. Testament to this is the fact that vast volumes of ...High throughput gene expression analysis is swiftly becoming the focal point for deciphering molecular mechanisms underlying various dif-ferent biological questions. Testament to this is the fact that vast volumes of expression profiles are being generated rapidly by scientists worldwide and subsequently stored in publicly available data repositories such as ArrayEx-press and the Gene Expression Omnibus (GEO). Such wealth of biological data has motivated biologists to compare expression profiles gen-erated from biologically-related microarray ex-periments in order to unravel biological mecha-nisms underlying various states of diseases. However, without the availability of appropriate software and tools, they are compelled to use manual or labour-intensive methods of com-parisons. A scrutiny of current literature makes it apparent that there is a soaring need for such bioinformatics tools that cater for the multiple analyses of expression profiles. In order to contribute towards this need, we have developed an efficient software pipeline for the analysis of multiple gene expression data-sets, called Micropath, which implements three principal functions;1) it searches for common genes amongst n number of datasets using a number crunching method of comparison as well as applying the principle of permutations and combinations in the form of a search strat-egy, 2) it extracts gene expression patterns both graphically and statistically, and 3) it streams co-expressed genes to all molecular pathways belonging to KEGG in a live fashion. We sub-jected MicroPath to several expression datasets generated from our tolerance-related in-house microarray experiments as well as published data and identified a set of 31 candidate genes that were found to be co-expressed across all interesting datasets. Pathway analysis revealed their putative roles in regulating immune toler-ance. MicroPath is freely available to download from: www.1066technologies.co.uk/micropath.展开更多
Immunotherapy is currently one of the most promising treatment options for malignant melanoma[1].To uncover new immunological targets for future treatment approaches,single-cell transcriptomic and epigenomic analyses ...Immunotherapy is currently one of the most promising treatment options for malignant melanoma[1].To uncover new immunological targets for future treatment approaches,single-cell transcriptomic and epigenomic analyses were performed on human primary melanoma(MM)and melanocytic nevus(Nev)samples(Figure 1A).展开更多
The editors regret there was an error in“Shotgun metagenome library construction and sequencing”section.“The raw sequences can be found in BGID(CRA000815)”should be corrected to“The raw metagenome sequencing data...The editors regret there was an error in“Shotgun metagenome library construction and sequencing”section.“The raw sequences can be found in BGID(CRA000815)”should be corrected to“The raw metagenome sequencing data have been deposited in the Genome Sequence Archive at Beijing Institute of Genomics,Chinese Academy of Sciences(GSA:CRA000815),and are publicly accessible at https://bigd.big.ac.cn/gsa/”.The correct section is shown below.The editors would like to apologize for any inconvenience caused.展开更多
Many economically important perennial species bear recalcitrant seeds, including tea, coffee, cocoa, mango,citrus, rubber, oil palm and coconut. Orthodox seeds can be dried almost completely without losing viability, ...Many economically important perennial species bear recalcitrant seeds, including tea, coffee, cocoa, mango,citrus, rubber, oil palm and coconut. Orthodox seeds can be dried almost completely without losing viability, but so-called recalcitrant seeds have a very limited storage life and die upon drying below a higher critical moisture content than orthodox seeds. As a result, the development of longterm storage methods for recalcitrant seeds is compromised.Lowering this critical moisture content would be very valuable since dry seed storage is the safest, most convenient and cheapest method for conserving plant genetic resources.Therefore, we have attempted to induce desiccation tolerance(DT) in the desiccation sensitive seeds of Citrus limon. We show that DT can be induced by paclobutrazol(an inhibitor of gibberellin biosynthesis) and we studied its associated transcriptome to delineate the molecular mechanisms underlying this induction of DT. Paclobutrazol not only interfered with gibberellin related gene expression but also caused extensive changes in expression of genes involved in the biosynthesis and signaling of other hormones. Paclobutrazol induced a transcriptomic switch encompassing suppression of biotic-and induction of abiotic responses.We hypothesize that this is the main driver of the induction of DT by paclobutrazol in C. limon seeds.展开更多
Traditional Chinese medicine （TCM） clinical practice. So far, the methods commonly preparations are widely used for healthcare and used for quality evaluation of TCM preparations mainly focused on chemical ingredien...Traditional Chinese medicine （TCM） clinical practice. So far, the methods commonly preparations are widely used for healthcare and used for quality evaluation of TCM preparations mainly focused on chemical ingredients. The biological ingredient analysis of TCM preparations is also important because TCM preparations usually contain both plant and animal ingredients, which often include some mis-identified herbal materials, adulterants or even some biological contaminants. For biological ingredient analysis, the efficiency of DNA extraction is an important factor which might affect the accuracy and reliability of identification. The component complexity in TCM preparations is high, and DNA might be destroyed or degraded in different degrees after a series of processing procedures. Therefore, it is necessary to establish an effective protocol for DNA extraction from TCM preparations. In this study, we chose a classical TCM preparation, Liuwei Dihuang Wan （LDW）, as an example to develop a TCM-specific DNA extraction method. An optimized cetyl trimethyl ammonium bromide （CTAB） method （TCM-CTAB） and three commonly-used extraction kits were tested for extraction of DNA from LDW samples. Experimental results indicated that DNA with the highest purity and concentration was obtained by using TCM-CTAB. To further evaluate the different extraction methods, amplification of the second internal transcribed spacer （ITS2） and the chloroplast genome trnL intron was carried out.展开更多
The functional impact of several long intergenic non-coding RNAs (lincRNAs) has been characterized in previous studies. However, it is difficult to identify lincRNAs on a large-scale and to ascertain their functions o...The functional impact of several long intergenic non-coding RNAs (lincRNAs) has been characterized in previous studies. However, it is difficult to identify lincRNAs on a large-scale and to ascertain their functions or predict their structures in laboratory experiments because of the diversity, lack of knowledge and specificity of expression of lincRNAs. Furthermore, although there are a few well-characterized examples of lincRNAs associated with cancers, these are just the tip of the iceberg owing to the complexity of cancer. Here, by combining RNA-Seq data from several kinds of human cell lines with chromatin-state maps and human expressed sequence tags, we successfully identified more than 3000 human lincRNAs, most of which were new ones. Subsequently, we predicted the functions of 105 lincRNAs based on a coding-non-coding gene co-expression network. Finally, we propose a genetic mediator and key regulator model to unveil the subtle relationships between lincRNAs and lung cancer. Twelve lincRNAs may be principal players in lung tumorigenesis. The present study combines large-scale identification and functional prediction of human lincRNAs, and is a pioneering work in characterizing cancer-associated lincRNAs by bioinformatics.展开更多
Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination pot...Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that shortterm antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ～3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.展开更多
Despite recent encouragement to follow the FAIR principles,the day-to-day research practices have not changed substantially.Due to new developments and the increasing pressure to apply best practices,initiatives to im...Despite recent encouragement to follow the FAIR principles,the day-to-day research practices have not changed substantially.Due to new developments and the increasing pressure to apply best practices,initiatives to improve the efficiency and reproducibility of scientific workflows are becoming more prevalent.In this article,we discuss the importance of well-annotated tools and the specific requirements to ensure reproducible research with FAIR outputs.We detail how Galaxy,an open-source workflow management system with a web-based interface,has implemented the concepts that are put forward by the Canonical Workflow Framework for Research(CWFR),whilst minimising changes to the practices of scientific communities.Although we showcase concrete applications from two different domains,this approach is generalisable to any domain and particularly useful in interdisciplinary research and science-based applications.展开更多
With the current fast accumulation of microbial community samples and related metagenomic sequencing data, data integration and analysis system is urgently needed for in-depth analysis of large number of metagenomic s...With the current fast accumulation of microbial community samples and related metagenomic sequencing data, data integration and analysis system is urgently needed for in-depth analysis of large number of metagenomic samples （also referred to as ＂microbial communities＂） of interest. Although several existing databases have collected a large number of metagenomie samples, they mostly serve as data repositories with crude annotations, and offer limited functionality for analysis. Moreover, the few available tools for comparative analysis in the literature could only support the comparison of a few pre-defined set of metagenomic samples. To facilitate comprehensive comparative analysis on large amount of diverse microbial community samples, we have designed a Meta-Mesh system for a variety of analyses including quantitative analysis of similarities among microbial communities and computation of the correlation between the meta-information of these samples. We have used Meta-Mesh for systematically and efficiently analyses on diverse sets of human associate-habitat microbial community samples. Results have shown that Meta-Mesh could serve well as an efficient data analysis platform for discovery of clusters, biomarker and other valuable biological information from a large pool of human microbial samples.展开更多
Mammals and other complex organisms can transcribe an abundance of long non-coding RNAs(lncRNAs)that fulfill a wide variety of regulatory roles in many biological processes.These roles,including as scaffolds and as gu...Mammals and other complex organisms can transcribe an abundance of long non-coding RNAs(lncRNAs)that fulfill a wide variety of regulatory roles in many biological processes.These roles,including as scaffolds and as guides for protein-coding genes,mainly depend on the structure and expression level of lncRNAs.In this review,we focus on the current methods for analyzing lncRNA structure and expression,which is basic but necessary information for in-depth,large-scale analysis of lncRNA functions.展开更多
基金The lab of AK obtained support from the Interdisciplinary Center for Clinical Research(IZKF)Jena(MSPProject ID:MSP09)+2 种基金DG and MJA B were supported by the Circular Vision project,which has received funding from the European Union's Horizon 2020 research and innovation program(Grant agreement No.899417)the Ministerio de Ciencia e Innovoción,Spain(Grant No.PID2020-119715GB-I00/AEI/10.13039/501100011033)the Instituto de Salud CarlosⅢ,Infrastructure of Precision Medicine associated with Science and Technology(IMPaCT)of the Strategic Action in Health(iDATAMP)(to MJAB)。
文摘Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.
基金supported by the National Key Research and Development Program of China(Grant No.2021YFF1000104)the Agricultural Science and Technology Innovation Program(ASTIP),Beijing Municipal Science and Technology Project(Grant No.Z231100003723009)+4 种基金the Central Public-interest Scientific Institution Basal Research Fund(Grant No.Y2023PT16)TKI project(Grant No.KV1605-004)support from the China Scholarship Councilthe NPO bursary funding from Wageningen universitythe scholarship from Institute of vegetables and flowers,CAAS.
文摘Polyploidy,or whole-genome duplication,is an important evolutionary process that has shaped the genomes and traits of many plants,including numerous important crops.The Brassica genus,which includes diverse vegetables and oilseeds,is a key model system for studying how polyploidy affects plant diversification and domestication.This review summarizes the current understanding of how multiple rounds of ancient and more recent polyploidization events laid the foundation for the wide diversity seen in Brassica.We discuss the key outcomes through which polyploidy facilitates the accumulation of genetic variation,including genomic buffering that enables mutation retention.Furthermore,we explore the significant roles of interspecies and interploidy introgression in introducing external genetic novelty.We highlight homoeologous exchange(HE)as a critical mechanism unique to allopolyploids,driving substantial genomic rearrangements including presence-absence variations and gene dosage alterations that directly contribute to significant phenotypic innovation and adaptation in Brassica.Together,these polyploidy-associated processes have led to the extensive range of genomic variations that shaped great morphological diversification in the domestication of Brassica.By integrating insights from genomics,genetics,and evolutionary biology,this review shows how polyploidy has been central to Brassica's success and agricultural value.We also suggest future research areas to better understand polyploid evolution and improve crop breeding.
基金supported by the National Key Research and Development Program of China (Grant No.2022YFF1003003)the Central Public-interest Scientific Institution Basal Research Fund (Grant No.Y2023PT16)+1 种基金the Agricultural Science and Technology Innovation Program (ASTIP)supported by China Scholarship Council (Grant No.202103250097)。
文摘Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground truth.Gene expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription factors.Parallel to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides.Based on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization.To explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics.The results demonstrated the utility of our computational approach for predicting candidate genes in crop species.Our findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.
文摘Previous phytochemical investigation of the leaves and seeds of Pittosporum angustifolium Lodd.led to the isolation and structural elucidation of polyphenols and triterpene saponins.Evaluation for cytotoxicity of isolated saponins revealed that the predominant structural feature for a cytotoxic activity are acyl substituents at the oleanane aglycon backbone.The present work reports the results of a screening of 10 selected acylated saponins for their potential to inhibit the human DNA-topoisomerase I,giving rise to IC50 values in a range of 2.8-46.5 lM.To clarify the mode of observed cytotoxic action and,moreover,to distinguish from a pure surfactant effect which is commonly accompanied with saponins,these results indicate an involvement of the topoisomerase I and its role as a possible target structure for a cytotoxic activity.In addition,computational predictions of the fitting of saponins to the topoisomerase I-DNA complex,indicate a similar binding mode to that of clinically used topoisomerase I inhibitors.Graphical Abstract Ten acylated triterpene saponins from Pittosporum angustifolium were investigated for their potential to inhibit the human DNA-topoisomerase I and computational predictions of the fitting of saponins to the topoisomerase I-DNA complex were carried out.
基金Indian Council of Madical Research,Government of India for sponsoring and funding the project
文摘Objective:To assess the virus infection in mosquitoes during different seasons and correlated with various climatic factors.Methods:The field collected vectors were screened for Japanese encephalitis(JE) virus after dessication using ELISA method.Most of the positive pools were recorded from Culex tritaeniorhynchus(Cx.tritaeniorhynchus) and Culex.gelidus(Cx.gelidus) during JE transmission season(winter) and some positive pools were also reported during non JE transmission periods(i.e.summer and rainy seasons).Results:The minimum infection rates(MIR) of 1.75 from Cx.tritaeniorhynchus and 0.17 from Cx.gelidus has been reported in the year 2002 at the beginning of the study and the values were found nil at the end of the study(2006) from the study areas of Kurnool district.Conclusions:From this study it is noted that MTR of Cx.gelidus and Cx.tritaeniorhynchus were modulated by various meteorological parameters.The mosquito vector abundance increases after the monsoon period(winter) and lowest in dry season(summer). Similarly,MIR fluctuated between seasons with higher MIR recorded after monsoon period and lower in the rest of season.Impact of these metrological parameters in JE virus infected mosquitoes is discussed in this paper.
文摘Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid),M (glycoprotein),and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require elucidation.In this work we collected all full length S segment sequences and generated a phylogenetic tree based on the alignment of these 62 samples.We then analyzed the alignment using entries from AAIndex,the Amino Acid Index database,to identify amino acid mutations that performed significant changes in charge,pka,hydropathy and side chain volume.Finally,we mapped these changes back to the tree and alignment to identify correlated mutations or sites that characterized a specific lineage.Based on this analysis we are able to propose a number of sites that appear to be important for virus function and which would be good candidates for experimental mutational analysis studies.
文摘This research focused on the modification of the functional groups of oseltamivir as neuraminidase inhibitor against influenza A virus subtype H1N1.Interactions of three of the best ligands were evaluated in the hydrated state using molecular dynamics simulation at two different temperatures.The docking result showed that AD3BF2 D ligand（N-[（1S,6R）-5-amino-5-{[（2R,3S,4S）-3,4-dihydroxy-4-（hydroxymethyl） tetrahydrofuran-2-yl]oxy}-4-formylcyclohex-3-en-1-yl]acetamide-3-（1-ethylpropoxy）-1-cyclohexene-1-carboxylate） had better binding energy values than standard oseltamivir.AD3BF2 D had several interactions,including hydrogen bonds,with the residues in the catalytic site of neuraminidase as identified by molecular dynamics simulation.The results showed that AD3BF2 D ligand can be used as a good candidate for neuraminidase inhibitor to cope with influenza A virus subtype H1N1.
文摘MicroRNAs(miRNAs)are a class of small non-coding RNAs that play important roles in post-transcriptional regulation of gene expression[1].A large number of miRNAs have been found to be involved in a broad spectrum of biological functions such as regulation of innate and adaptive immunity,cell differentiation and development as well as
文摘High throughput gene expression analysis is swiftly becoming the focal point for deciphering molecular mechanisms underlying various dif-ferent biological questions. Testament to this is the fact that vast volumes of expression profiles are being generated rapidly by scientists worldwide and subsequently stored in publicly available data repositories such as ArrayEx-press and the Gene Expression Omnibus (GEO). Such wealth of biological data has motivated biologists to compare expression profiles gen-erated from biologically-related microarray ex-periments in order to unravel biological mecha-nisms underlying various states of diseases. However, without the availability of appropriate software and tools, they are compelled to use manual or labour-intensive methods of com-parisons. A scrutiny of current literature makes it apparent that there is a soaring need for such bioinformatics tools that cater for the multiple analyses of expression profiles. In order to contribute towards this need, we have developed an efficient software pipeline for the analysis of multiple gene expression data-sets, called Micropath, which implements three principal functions;1) it searches for common genes amongst n number of datasets using a number crunching method of comparison as well as applying the principle of permutations and combinations in the form of a search strat-egy, 2) it extracts gene expression patterns both graphically and statistically, and 3) it streams co-expressed genes to all molecular pathways belonging to KEGG in a live fashion. We sub-jected MicroPath to several expression datasets generated from our tolerance-related in-house microarray experiments as well as published data and identified a set of 31 candidate genes that were found to be co-expressed across all interesting datasets. Pathway analysis revealed their putative roles in regulating immune toler-ance. MicroPath is freely available to download from: www.1066technologies.co.uk/micropath.
基金supported by the Deutsche Forschungsgemeinschaft(DFG)(German Research Foundation,grant numbers:KU 1320/10-1 and HO 6586/1-1,and SFB1430,project 424228829)the Sachsische Aufbaubank(grant number:10071450).
文摘Immunotherapy is currently one of the most promising treatment options for malignant melanoma[1].To uncover new immunological targets for future treatment approaches,single-cell transcriptomic and epigenomic analyses were performed on human primary melanoma(MM)and melanocytic nevus(Nev)samples(Figure 1A).
文摘The editors regret there was an error in“Shotgun metagenome library construction and sequencing”section.“The raw sequences can be found in BGID(CRA000815)”should be corrected to“The raw metagenome sequencing data have been deposited in the Genome Sequence Archive at Beijing Institute of Genomics,Chinese Academy of Sciences(GSA:CRA000815),and are publicly accessible at https://bigd.big.ac.cn/gsa/”.The correct section is shown below.The editors would like to apologize for any inconvenience caused.
基金financial support from CNPq-National Council for Scientific and Technological Development Brazil(246220/2012-0)
文摘Many economically important perennial species bear recalcitrant seeds, including tea, coffee, cocoa, mango,citrus, rubber, oil palm and coconut. Orthodox seeds can be dried almost completely without losing viability, but so-called recalcitrant seeds have a very limited storage life and die upon drying below a higher critical moisture content than orthodox seeds. As a result, the development of longterm storage methods for recalcitrant seeds is compromised.Lowering this critical moisture content would be very valuable since dry seed storage is the safest, most convenient and cheapest method for conserving plant genetic resources.Therefore, we have attempted to induce desiccation tolerance(DT) in the desiccation sensitive seeds of Citrus limon. We show that DT can be induced by paclobutrazol(an inhibitor of gibberellin biosynthesis) and we studied its associated transcriptome to delineate the molecular mechanisms underlying this induction of DT. Paclobutrazol not only interfered with gibberellin related gene expression but also caused extensive changes in expression of genes involved in the biosynthesis and signaling of other hormones. Paclobutrazol induced a transcriptomic switch encompassing suppression of biotic-and induction of abiotic responses.We hypothesize that this is the main driver of the induction of DT by paclobutrazol in C. limon seeds.
基金supported by the grants from the National Natural Science Foundation of China (Grant Nos. 30870572, 61303161 and 61103167)National High-tech R&D Program (863 Program)funded by Ministry of Science and Technology of China (Grant Nos. 2012AA02A707 and 2014AA021502)
文摘Traditional Chinese medicine （TCM） clinical practice. So far, the methods commonly preparations are widely used for healthcare and used for quality evaluation of TCM preparations mainly focused on chemical ingredients. The biological ingredient analysis of TCM preparations is also important because TCM preparations usually contain both plant and animal ingredients, which often include some mis-identified herbal materials, adulterants or even some biological contaminants. For biological ingredient analysis, the efficiency of DNA extraction is an important factor which might affect the accuracy and reliability of identification. The component complexity in TCM preparations is high, and DNA might be destroyed or degraded in different degrees after a series of processing procedures. Therefore, it is necessary to establish an effective protocol for DNA extraction from TCM preparations. In this study, we chose a classical TCM preparation, Liuwei Dihuang Wan （LDW）, as an example to develop a TCM-specific DNA extraction method. An optimized cetyl trimethyl ammonium bromide （CTAB） method （TCM-CTAB） and three commonly-used extraction kits were tested for extraction of DNA from LDW samples. Experimental results indicated that DNA with the highest purity and concentration was obtained by using TCM-CTAB. To further evaluate the different extraction methods, amplification of the second internal transcribed spacer （ITS2） and the chloroplast genome trnL intron was carried out.
基金supported by Beijing Natural Science Foundation(5122029)
文摘The functional impact of several long intergenic non-coding RNAs (lincRNAs) has been characterized in previous studies. However, it is difficult to identify lincRNAs on a large-scale and to ascertain their functions or predict their structures in laboratory experiments because of the diversity, lack of knowledge and specificity of expression of lincRNAs. Furthermore, although there are a few well-characterized examples of lincRNAs associated with cancers, these are just the tip of the iceberg owing to the complexity of cancer. Here, by combining RNA-Seq data from several kinds of human cell lines with chromatin-state maps and human expressed sequence tags, we successfully identified more than 3000 human lincRNAs, most of which were new ones. Subsequently, we predicted the functions of 105 lincRNAs based on a coding-non-coding gene co-expression network. Finally, we propose a genetic mediator and key regulator model to unveil the subtle relationships between lincRNAs and lung cancer. Twelve lincRNAs may be principal players in lung tumorigenesis. The present study combines large-scale identification and functional prediction of human lincRNAs, and is a pioneering work in characterizing cancer-associated lincRNAs by bioinformatics.
基金supported by the Lundbeck Foundatation and EU FP7-Health Program Evotar (Grant No. 282004)approved (Grant No. REG-026-2014) by the Regional Ethics Committee and Danish National Medicine Agency+2 种基金the Centre for Genomic Sciences (CGS) of The University of Hong Kong (HKU) for their supportthe project providing the ARG annotation pipeline of the shotgun metagenomics analysisThe raw sequences were deposited in BIGD (CRA000815)
文摘Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that shortterm antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ～3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.
基金supported by the European Union's Horizon 2020 programme(No.857652,EOSCNordic,and No.101017501,RELIANCE)supported by BMBF grants 031 A538A/A538C(de.NBI-RBC),NFDI7/1-42077441(DataPLANT)and 031L0101C(de.NBI-epi)+2 种基金supported by Research Foundation-Flanders(FWO)for ELIXIR Belgium(I002819N)the European Union's Horizon 2020 programme(No.824087,EOSC-Life)partially supported by the Research Council of Norway's grant 270068 for ELIXIR Norway.
文摘Despite recent encouragement to follow the FAIR principles,the day-to-day research practices have not changed substantially.Due to new developments and the increasing pressure to apply best practices,initiatives to improve the efficiency and reproducibility of scientific workflows are becoming more prevalent.In this article,we discuss the importance of well-annotated tools and the specific requirements to ensure reproducible research with FAIR outputs.We detail how Galaxy,an open-source workflow management system with a web-based interface,has implemented the concepts that are put forward by the Canonical Workflow Framework for Research(CWFR),whilst minimising changes to the practices of scientific communities.Although we showcase concrete applications from two different domains,this approach is generalisable to any domain and particularly useful in interdisciplinary research and science-based applications.
基金This work is supported in part by Chinese Academy of Sciences＇ e-Science grant （NO. 1NFO-115-D01-Z006）, Ministry of Science and Technology＇s high-tech （863） grant （NO. 2009AA02Z310 and NO. 2014AA21502）, National Science Foundation of China Grant （NO. 61103167, NO. 31271410 and NO. 61303161）, and The Open Fund of Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Chinese Academy of Sciences （NO. KLMEES201304）.
文摘With the current fast accumulation of microbial community samples and related metagenomic sequencing data, data integration and analysis system is urgently needed for in-depth analysis of large number of metagenomic samples （also referred to as ＂microbial communities＂） of interest. Although several existing databases have collected a large number of metagenomie samples, they mostly serve as data repositories with crude annotations, and offer limited functionality for analysis. Moreover, the few available tools for comparative analysis in the literature could only support the comparison of a few pre-defined set of metagenomic samples. To facilitate comprehensive comparative analysis on large amount of diverse microbial community samples, we have designed a Meta-Mesh system for a variety of analyses including quantitative analysis of similarities among microbial communities and computation of the correlation between the meta-information of these samples. We have used Meta-Mesh for systematically and efficiently analyses on diverse sets of human associate-habitat microbial community samples. Results have shown that Meta-Mesh could serve well as an efficient data analysis platform for discovery of clusters, biomarker and other valuable biological information from a large pool of human microbial samples.
基金supported by the National High Technology Research and Development Program of China(2012AA020402)National Natural Science Foundation of China(11074084,30970558)
文摘Mammals and other complex organisms can transcribe an abundance of long non-coding RNAs(lncRNAs)that fulfill a wide variety of regulatory roles in many biological processes.These roles,including as scaffolds and as guides for protein-coding genes,mainly depend on the structure and expression level of lncRNAs.In this review,we focus on the current methods for analyzing lncRNA structure and expression,which is basic but necessary information for in-depth,large-scale analysis of lncRNA functions.
