Dynamic nitrification and denitrification processes are affected by changes in soil redox conditions,and they play a vital role in regulating soil N_(2)O emissions in rice-based cultivation.It is imperative to underst...Dynamic nitrification and denitrification processes are affected by changes in soil redox conditions,and they play a vital role in regulating soil N_(2)O emissions in rice-based cultivation.It is imperative to understand the influences of different upland crop planting systems on soil N_(2)O emissions.In this study,we focused on two representative rotation systems in Central China:rapeseed–rice(RR)and wheat–rice(WR).We examined the biotic and abiotic processes underlying the impacts of these upland plantings on soil N_(2)O emissions.The results revealed that during the rapeseed-cultivated seasons in the RR rotation system,the average N_(2)O emissions were 1.24±0.20 and 0.81±0.11 kg N ha^(–1)for the first and second seasons,respectively.These values were comparable to the N_(2)O emissions observed during the first and second wheat-cultivated seasons in the WR rotation system(0.98±0.25 and 0.70±0.04 kg N ha^(–1),respectively).This suggests that upland cultivation has minimal impacts on soil N_(2)O emissions in the two rotation systems.Strong positive correlations were found between N_(2)O fluxes and soil ammonium(NH_(4)^(+)),nitrate(NO_(3)^(–)),microbial biomass nitrogen(MBN),and the ratio of soil dissolved organic carbon(DOC)to NO_(3)^(–)in both RR and WR rotation systems.Moreover,the presence of the AOA-amoA and nirK genes were positively associated with soil N_(2)O fluxes in the RR and WR systems,respectively.This implies that these genes may have different potential roles in facilitating microbial N_(2)O production in various upland plantation models.By using a structural equation model,we found that soil moisture,mineral N,MBN,and the AOA-amoA gene accounted for over 50%of the effects on N_(2)O emissions in the RR rotation system.In the WR rotation system,soil moisture,mineral N,MBN,and the AOA-amoA and nirK genes had a combined impact of over 70%on N_(2)O emissions.These findings demonstrate the interactive effects of functional genes and soil factors,including soil physical characteristics,available carbon and nitrogen,and their ratio,on soil N_(2)O emissions during upland cultivation seasons under rice-upland rotations.展开更多
The long-term impact of fulvic acid(FA)on partial nitritation(PN)systemwas initially examined in this study.The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulatio...The long-term impact of fulvic acid(FA)on partial nitritation(PN)systemwas initially examined in this study.The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulation rate(NAR nearly 100%)and ammonium removal rate(ARR 56.85%),while FA over 50 mg/L decreased ARR from 56.85%to 0.7%.Sludge characteristics analysis found that appropriate FA(<50 mg/L)exposure promoted the settling performance and granulation of PN sludge by removing Bacteroidetes and accumulating Chloroflexi.The analysis of metagenomics suggested that the presence of limited FA(0-50 mg/L)stimulated the generation of NADH,which favors the denitrification and nitrite reduction.The negative impact of FA on the PN system could be divided into two stages.Initially,limited FA(50-120 mg/L)was decomposed by Anaerolineae to stimulate the growth and propagation of heterotrophic bacteria(Thauera).Increasing heterotrophs competed with AOB(Nitrosomonas)for dissolved oxygen,causing AOB to be eliminated and ARR to declined.Subsequently,when FA dosage was over 120 mg/L,Anaerolineae were inhibited and heterotrophic bacteria reduced,resulting in the abundance of AOB recovered.Nevertheless,the ammonium transformation pathway was suppressed because genes amoABC and hao were obviously reduced,leading to the deterioration of reactor performance.Overall,these results provide theoretical guidance for the practical application of PN for the treatment of FA-containing sewage.展开更多
A field experiment involving cry1Ab transgenic rice(GM) and its parental non-cry1Ab rice(M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes ...A field experiment involving cry1Ab transgenic rice(GM) and its parental non-cry1Ab rice(M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes which drive the conversion of nitrogen in paddy soil were analyzed during the growth period of rice in the fifth year of the experiment, using 16 S rRNAbased Illumina Mi Seq and real-time PCR on the amoA, nirS and nirK genes. The results showed no differences in the alpha diversity indexes of the bacterial communities, including Chao1, Shannon and Simpson, between the fields cultivated with line GM and cultivar M at any of the growth stages of rice. However, the bacterial communities in the paddy soil with line GM were separated from those of paddy soil with cultivar M at each of the growth stages of rice, based on the unweighted Uni Frac NMDS or PCoA. In addition, the analyses of ADONIS and ANOSIM, based on the unweighted Uni Frac distance, indicated that the above separations between line GM and cultivar M were statistically significant(P<0.05) during the growth season of rice. The increases in the relative abundances of Acidobacteria or Bacteroidetes, in the paddy soils with line GM or cultivar M, respectively, led to the differences in the bacterial communities between them. At the same time, functional gene prediction based on Illumina Mi Seq data suggested that the abundance of many functional genes increased in the paddy soil with line GM at the maturity stage of rice, such as genes related to the metabolism of starch, amino acids and nitrogen. Otherwise, the copies of bacterial amo A gene, archaeal amo A gene and denitrifying bacterial nir K gene significantly increased(P<0.05 or 0.01) in the paddy soil with line GM. In summary, the release of cry1Ab transgenic rice had effects on either the composition of bacterial communities or the abundance of microbial functional genes in the paddy soil.展开更多
High concentrations of ammonium nitrogen released from tannery sludge during storage in open air may cause nitrogen pollution to soil and groundwater.To study the transformation mechanism of NH_(4)^(+)-N by nitrifying...High concentrations of ammonium nitrogen released from tannery sludge during storage in open air may cause nitrogen pollution to soil and groundwater.To study the transformation mechanism of NH_(4)^(+)-N by nitrifying functional bacteria in tannery sludge contaminated soils,a series of contaminated soil culture experiments were conducted in this study.The contents of ammonium nitrogen(as NH_(4)^(+)-N),nitrite nitrogen(as NO_(2)^(−)-N)and nitrate nitrogen(as NO_(3)^(−)-N)were analyzed during the culture period under different conditions of pollution load,soil particle and redox environment.Sigmodial equation was used to interpret the change of NO_(3)^(−)-N with time in contaminated soils.The abundance variations of nitrifying functional genes(amoA and nxrA)were also detected using the real-time quantitative fluorescence PCR method.The results show that the nitrification of NH_(4)^(+)-N was aggravated in the contaminated silt soil and fine sand under the condition of lower pollution load,finer particle size and more oxidizing environment.The sigmodial equation well fitted the dynamic accumulation curve of the NO_(3)^(−)-N content in the tannery sludge contaminated soils.The Cr(III)content increased with increasing pollution load,which inhibited the reproduction and activity of nitrifying bacteria in the soils,especially in coarse-grained soil.The accumulation of NO_(2)^(−)-N contents became more obvious with the increase of pollution load in the fine sand,and only 41.5%of the NH_(4)^(+)-N was transformed to NO_(3)^(−)-N.The redox environment was the main factor affecting nitrification process in the soil.Compared to the aerobic soil environment,the transformation of NH_(4)^(+)-N was significantly inhibited under anaerobic incubation condition,and the NO_(3)^(−)-N contents decreased by 37.2%,61.9%and 91.9%under low,medium and high pollution loads,respectively.Nitrification was stronger in the silt soil since its copy number of amoA and nxrA genes was two times larger than that of fine sand.Moreover,the copy numbers of amoA and nxrA genes in the silt soil under the aerobic environment were 2.7 times and 2.2 times larger than those in the anaerobic environment.The abundance changes of the amoA and nxrA functional genes have a positive correlation with the nitrification intensity in the tannery sludge-contaminated soil.展开更多
Biological desilication process is an effective way to remove silicate from rutile so that high purity rutile could be obtained. However, little is known about the molecular mechanism of this process. In this work, a ...Biological desilication process is an effective way to remove silicate from rutile so that high purity rutile could be obtained. However, little is known about the molecular mechanism of this process. In this work, a newly developed rutile bio-desilication reactor was applied to enrich rutile from rough rutile concentrate obtained from Nanzhao rutile mine and a comprehensive high through-put functional gene array(Geo Chip 4.0) was used to analyze the functional gene diversity, structure and metabolic potential of microbial communities in the biological desilication reactor. The results show that TiO2 grade of the rutile concentrate could increase from 78.21% to above 90% and the recovery rate could reach to 96% or more in 8-12 d. The results also show that almost all the key functional genes involved in the geochemical cycling process, totally 4324 and 4983 functional microorganism genes, are detected in the liquid and ore surface, respectively. There are totally 712 and 831 functional genes involved in nitrogen cycling for liquid and ore surface samples, respectively. The relative abundance of functional genes involved in the phosphorus and sulfur cycling is higher in the ore surface than liquid. These results indicate that nitrogen, phosphorus and sulfur cycling are also present in the desiliconization process of rutile. Acetogenesis genes are detected in the liquid and ore surface, which indicates that the desiliconizing process mainly depends on the function of acetic acid and other organic acids. Four silicon transporting genes are also detected in the sample, which proves that the bacteria have the potential to transfer silicon in the molecule level. It is shown that bio-desilication is an effective and environmental-friendly way for enrichment of rough rutile concentrate and presents an overview of functional diversity and structure of desilication microbial communities, which also provides insights into our understanding of metabolic potential in biological desilication reactor ecosystems.展开更多
Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herb...Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herbaceous plants,with notable applications in species such as Arabidopsis(Yin et al.,2024),soybean(Zhang et al.,2024),rice(Zhang et al.,2020),and Chinese cabbage(Li et al.,2021).However,its application in fruit trees is limited.This is primarily due to their long growth cycles and lack of rapid,efficient,and stable transgenic systems,which severely hinders foundational research involving plant genetic transformation(Mei et al.,2024).Furthermore,for subtropical fruit trees,the presence of recalcitrant seeds adds an extra layer of difficulty to genetic transformation(Umarani et al.,2015),as most methods rely on seed germination as a basis for transformation.展开更多
Inflammatory bowel disease(IBD)is an incurable disease of the digestive system;however,the therapeutic methods for IBD remain limited.The pathogenesis of IBD was systematically discussed and compared in this paper,pri...Inflammatory bowel disease(IBD)is an incurable disease of the digestive system;however,the therapeutic methods for IBD remain limited.The pathogenesis of IBD was systematically discussed and compared in this paper,primarily comprising Crohn’s disease and ulcerative colitis.This paper focused on six common aspects:(1)Dysregulated immune responses;(2)Gene function changes;(3)Intestinal microbes disorder and imbalance;(4)Microbial infections;(5)Associations between IBD and other inflammatory diseases;and(6)Other factors.In addition,the pathogenesis differences between these two forms of IBD were unraveled and clearly distinguished.These unique aspects of pathogenesis provide crucial insights for the precise treatment of both Crohn’s disease and ulcerative colitis.This paper illustrates the root causes and beneficial factors of resistance to IBD,which provides novel insights on early prevention,development of new therapeutic agents,and treatment options of this disease.展开更多
A rhizobox system constructed with crude oil- contaminated soil was vegetated with alfalfa （Medicago sativa L.） to evaluate the rhizosphere effects on the soil microbial population and functional structure, and to e...A rhizobox system constructed with crude oil- contaminated soil was vegetated with alfalfa （Medicago sativa L.） to evaluate the rhizosphere effects on the soil microbial population and functional structure, and to explore the potential mechanisms by which plants enhance the removal of crude oil in soil. During the 80-day experiment, 31.6% of oil was removed from the adjacent rhizosphere （AR）; this value was 27% and 53% higher than the percentage of oil removed from the far rhizosphere （FR） and from the non-rhizosphere （NR）, respectively. The populations of heterotrophic bacteria and hydrocarbon- degrading bacteria were higher in the AR and FR than in the NR. However, the removal rate of crude oil was positively correlated with the proportion of hydrocarbon- degrading bacteria in the rhizosphere. In total, 796, 731, and 379 functional genes were detected by microarray in the AR, FR, and NR, respectively. Higher proportions of functional genes related to carbon degradation and organic remediation, were found in rhizosphere soil compared with NR soil, suggesting that the rhizosphere selectively increased the abundance of these specific functional genes. The increase in water-holding capacity and decrease in pH as well as salinity of the soil all followed the order of AR 〉 FR 〉 NR. Canonical component analysis showed that salinity was the most important environmental factor influencing the microbial functional structure in the rhizosphere and that salinity was negatively correlated with the abundance of carbon and organic degradation genes.展开更多
Peatlands on the southwestern plateau of China are important carbon sinks for high-altitude terrestrial ecosystems in Asia.However,the specific microecological mechanism responsible for alterations in carbon processes...Peatlands on the southwestern plateau of China are important carbon sinks for high-altitude terrestrial ecosystems in Asia.However,the specific microecological mechanism responsible for alterations in carbon processes in this region due to the simultaneous impacts of global warming and drought has not been fully elucidated.Investigating this mechanism will improve our understanding of carbon cycle feedback in peatland ecosystems,as it is affected by changes in hydrology and temperature,especially in vulnerable habitats.This study examined the influence of soil carbon decomposition functional microorganisms on soil respiration and temperature sensitivity(expressed as Q_(10))in high-elevation peatlands using field investigations,simulated warming experiments,and metagenomic sequencing.We found that hydrothermal conditions had a significant effect on soil respiration,leading to an increase in cumulative soil respiration as soil moisture and temperature increased.Soil moisture affected soil respiration and soil organic carbon mainly through soil microorganisms,with a predominance of carbon-decomposing genes.We found that genes regulating the decomposition of plant-derived carbon such as cellulose and lignin were the critical factor influencing Q_(10)in peatlands.Genes involved in cellulose and lignin decomposition showed a significant positive correlation with Q_(10)(P<0.05),while genes involved in hemicellulose decomposition showed a significant negative correlation with Q_(10)(P<0.05).Specifically,genes such as ACO,xylF,and hpaE,which are involved in lignin decomposition,and glgB,which is responsible for cellulose decomposition,showed significant positive correlations(P<0.05)with Q_(10).Conversely,the gene uxaC,involved in the decomposition of hemicellulose,showed a significant negative correlation(P<0.05)with Q_(10).Finally,we analyzed the relevant carbon metabolic pathways and found that although they were affected by water,they were not significantly related to Q_(10).In short,this research highlights the importance of microorganisms with genes for decomposing plant-derived carbon in influencing carbon emissions in plateau peatlands during periods of warming.展开更多
Ion channels are crucial in the generation and modulation of excitability in the nervous system and have been implicated in human epilepsy. Forty-one epilepsyassociated ion channel genes and their mutations are system...Ion channels are crucial in the generation and modulation of excitability in the nervous system and have been implicated in human epilepsy. Forty-one epilepsyassociated ion channel genes and their mutations are systematically reviewed. In this paper, we analyzed the genotypes, functional alterations（funotypes）, and phenotypes of these mutations. Eleven genes featured loss-offunction mutations and six had gain-of-function mutations.Nine genes displayed diversified funotypes, among which a distinct funotype-phenotype correlation was found in SCN1A. These data suggest that the funotype is an essential consideration in evaluating the pathogenicity of mutations and a distinct funotype or funotype-phenotype correlation helps to define the pathogenic potential of a gene.展开更多
Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription ...Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription factor gene families, was recently suggested to play important roles in plant development and stress response. In rice, the results of analyses of expression pattern and ectopic overexpressor lines also support this viewpoint, and the evidences implicate rice WRKY proteins in transcriptional reprogramming during biotic or abiotic stresses, senescence, sugar metabolites, and morphological architecture. In this paper, we review the advance in study of rice WRKY gene family and also propose unified nomenclature for rice WRKY factors to eliminate confusion.展开更多
The nuclear factor Y(NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelo...The nuclear factor Y(NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelon, a valued and nutritious fruit, remain largely unknown and their functions have not been characterized. In the present study, 22 ClNF-Y genes in watermelon, 29 CsNF-Y genes in cucumber, and 24CmNF-Y genes in melon were identified based on the whole-genome investigation and their protein properties, gene location, gene structure, motif composition, conserved domain, and evolutionary relationship were investigated. ClNF-YB9 from watermelon and its homologs in cucumber and melon were expressed specifically in seeds. Its expression remained low in the early stages of watermelon seed development,increased at 20 days after pollination(DAP), and peaked at 45–50 DAP. Moreover, the knockout mutant Clnf-yb9 exhibited abnormal leafy cotyledon phenotype, implying its critical role during seed formation.Finally, protein interaction assays showed that ClNF-YB9 interacts with all ClNF-YCs and the ClNF-YB9-YC4 heterodimer was able to recruit a ClNF-YA7 subunit to assemble a complete NF-Y complex, which may function in seed development. This study revealed the structure and evolutionary relationships of the NF-Y gene family in Cucurbitaceae and the novel function of ClNF-YB9 in regulating seed development in watermelon.展开更多
Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） fro...Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） from the Philippines. IR24 was highly susceptible to all the strains, and six common wild rice accessions resisted all the nine strains, with a resistance frequency of 67%. The accessions Yulin and Wanning were only susceptible to PXO280 and PXO71, respectively. The accession Gaozhou was susceptible to the three strains PXO79, PXO99 and PXO339, whereas resistant to the other six strains. It could be concluded that there is at least one resistance gene in each common wild rice accession. The functional markers of the genes xa5, xa13, Xa21 and Xa27 were used to detect the presence of these resistance genes in the nine tested wild rice accessions, and it was found that four wild rice accessions contained heterozygous xa13. Among the nine common wild rice accessions, five were homozygous for Xa27 and three homozygous for xa27, and the accession Laibin contained neither xa27 nor Xa27. In addition, there were no xa5 and Xa21 in all of these accessions.展开更多
The Human Genome Project was launched at the end of the 1980s.Since then,the cloning and identification of functional genes has been a major focus of research across the world.In China too,the potentially profound imp...The Human Genome Project was launched at the end of the 1980s.Since then,the cloning and identification of functional genes has been a major focus of research across the world.In China too,the potentially profound impact of such studies on the life sciences and on human health was realized,and relevant studies were initiated in the 1990s.To advance China's involvement in the Human Genome Project,in the mid-1990s,Committee of Experts in Biology from National High Technology Research and Development Program of China(863 Program) proposed the "two 1%" goal.This goal envisaged China contributing 1% of the total sequencing work,and cloning and identifying 1% of the total human functional genes.Over the past 20 years,tremendous achievement has been accomplished by Chinese scientists.It is well known that scientists in China finished the 1% of sequencing work of the Human Genome Project,whereas,there is no comprehensive report about "whether China had finished cloning and identifying 1% of human functional genes".In the present study,the GenBank database at the National Center of Biotechnology Information,the PubMed search tool,and the patent database of the State Intellectual Property Office,China,were used to retrieve entries based on two screening standards:(i) Were the newly cloned and identified genes first reported by Chinese scientists?(ii) Were the Chinese scientists awarded the gene sequence patent? Entries were retrieved from the databases up to the cut-off date of 30 June 2011 and the obtained data were analyzed further.The results showed that 589 new human functional genes were first reported by Chinese scientists and 159 gene sequences were patented(http:gene.fudan.sh.cn/introduction/database/chinagene/chinagene.html).This study systematically summarizes China's contributions to human functional genomics research and answers the question "has China finished cloning and identifying 1% of human functional genes?" in the affirmative.展开更多
Synthetic biology is one of the rapid developing scientific fields in recent years. Through synthetic biology,we have a better understanding of the natural synthesis process of natural products, which provides a favor...Synthetic biology is one of the rapid developing scientific fields in recent years. Through synthetic biology,we have a better understanding of the natural synthesis process of natural products, which provides a favorable method to research the diversity of natural products, and also provides new tools for us to create new approach for producing natural products, we can synthesize compounds with different structures by artificial combination of different synthesis modules.展开更多
Studies on the cold-responsive genes and cold signaling of woody species drop far behind in comparison to herbaceous plants.Due to similar lignified structure,perennial characteristic,and enhanced tolerance,it seems m...Studies on the cold-responsive genes and cold signaling of woody species drop far behind in comparison to herbaceous plants.Due to similar lignified structure,perennial characteristic,and enhanced tolerance,it seems much easier to find strongly antifreeze genes and obtain effective results in transgenic woody plants.In this study,Ammopiptanthus mongolicus,an evergreen,broadleaf and cold-resist leguminous shrub growing in the desert of Inner Mongolia,was used as a material for low-temperature induced gene isolation.Through differential expression analysis induced by low-temperature,thirteen up-regulated cDNAs were identified.One of them,AmEBP1,(accession number:DQ519359)confers enhanced cold-tolerance to both transgenic E.coli and transgenic Arabidopsis.Results suggest that AmEBP1 can stimulate the synthesis of ribosome and the dephosphyration of the α-subunit of initiation factor 2(eIF2α),and subsequently promote the translation process.By which the transgenic plants obtained increased cold-resistant ability.展开更多
Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by Plasmodiophora brassicae infection.Breeding of clubroot resistant cultivars bas...Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by Plasmodiophora brassicae infection.Breeding of clubroot resistant cultivars based on mapping and cloning of resistant genes is commonly regarded as the most cost-effective and efficient way to fight against this disease.The traditional way of R gene functional validation requires stable transformation that is both time-and labor-consuming.In this study,a rapid and efficient hairy-root transgenic protocol mediated by Agrobacterium rhizogenes was developed.The transformation positive rate was over 80%in Brassica napus showed by GUS reporter gene and this transformation only took 1/6 of the time compared with stable transformation.The system was applicable to different B.napus varieties and other cruciferous crops including Brassica rapa and Brassica oleracea.In particular,two known CR genes,CRA3.7.1 and CRA8.2.4 were used respectively,as example to show that the system works well for CR gene study combined with subsequent P.brassicae infection in B.napus.Most importantly,it works both in over-expression that led to disease resistance,as well as in RNAi which led to disease susceptible phenotype.Therefore,this system can be used in batch-wise identification of CR genes,and also offered the possibility of manipulating key genes within the P.brassicae genome that could improve our knowledge on host-pathogen interaction.展开更多
Low temperature is one of the main environmental stress factors influenc- ing plant growth and development and crop yield. Cold tolerance genes and progress of their application in genetic engineering of plant for col...Low temperature is one of the main environmental stress factors influenc- ing plant growth and development and crop yield. Cold tolerance genes and progress of their application in genetic engineering of plant for cold tolerance were reviewed comprehensively and systematically from the aspect of genes that are in- volved in biosynthesis of osmotic substances, genes coding fatty acid desaturation enzymes, antifreeze protein genes, genes coding antioxidant enzymes and so on, aiming at laying the foundation for genetic improvement of cold tolerance and breeding of plants.展开更多
Microplastics (MPs), fluoride (FR), and fungicide mancozeb (MZ) are common contaminants in soil. However, there is no information about the combined impacts of MPs, FR, and MZ on tomato plant growth features in the li...Microplastics (MPs), fluoride (FR), and fungicide mancozeb (MZ) are common contaminants in soil. However, there is no information about the combined impacts of MPs, FR, and MZ on tomato plant growth features in the literature. This study aimed to investigate the effects of combined application of MPs, FR, and MZ (both analytical grade and commercial) on the growth and development of tomato plants and metagenomics of rhizosphere soil. A pot experiment was set up in an artificial greenhouse with two sets of treatments. One set was the combined application of MPs, FR, and analytical grade MZ (B2) and a control without the application of MPs, FR, and MZ (W2), and the other set was the combined application of MPs, FR, and commercial MZ (B3) and a control without the application of MPs, FR, and MZ (W3). No detrimental effects of MPs, FR, and MZ were detected on the growth parameters of tomato plants, including the number of leaves and chlorophyll concentration. However, tomato roots showed knot and nodulation-type structures, and metabolomic profiling revealed that combined exposure to MPs, FR, and MZ profoundly reprogrammed the primary metabolism in tomato roots, with marked alterations in carbohydrate and amino acid pathways. Metagenome whole genome sequencing showed that the B2 and B3 treatments profoundly affected soil microbial community composition, diversity, gene abundances, and functional gene variations compared to W2 and W3. Proteobacteria became the dominating phylum in B2 and B3, causing a significant shift in the microbiome. Its abundance soared to 66.7% in B2 and 75.4% in B3, compared to only 35.9% in W2 and 28.9% in W3. On the other hand, Actinobacteria decreased significantly from 55.6% in W2 and 63.8% in W3 to 18.1% in B2 and 9.6% in B3. This study highlights the microbial shifts due to combined application of MPs, FR, and MZ, providing evidence for understanding their environmental risks.展开更多
Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and th...Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and their influencing factors in hot springs remain largely unclear.Therefore,this study investigated the microbial functional genes and their potential for controlling biogeochemical cycles(C,N,S,and P) in the hot Springs of Tengchong,China,using the Geochip method,a functional gene microarray technology.The examined hot springs have very different microbial functional genes.A total of 22 736 gene probe signals were identified,belonging to 567 functional genes and associated with 15 ecological functions,mainly involving stress response,carbon cycle,nitrogen cycle,sulfur cycle,phosphorus cycle and energy processes.The amyA,narG,dsrA and ppx genes were most abundant in carbon,nitrogen,sulfur and phosphorus cycles,respectively,and were significantly correlated with pH,temperature and SO_(4)^(2-).The diversity and abundance of detected gene probes were negatively correlated with temperature.The α-diversity(i.e.,Shannon index) was high at low temperature and low pH.Molecular functional interactions revealed by the gene connectivity levels were negatively correlated with temperature,pH and SO_(4)^(2-).These results suggested that the abundance,diversity and interactions of microbial functional genes were significantly influenced by geochemical parameters.-In addition,some genera possessed functional genes related to carbon,nitrogen,sulfur,and phosphorus cycles and can synergistically control the biogeochemical cycles of carbon,nitrogen,sulfur and phosphorus.These findings provide new insights into the functional potentials of microorganisms to participate in biogeochemical cycles and their responses to environmental factors in hot springs.展开更多
基金the National Key Research and Development Program of China(2017YFD0800102)the Hubei Provincial Key Research and Development Program,China(2021BCA156)。
文摘Dynamic nitrification and denitrification processes are affected by changes in soil redox conditions,and they play a vital role in regulating soil N_(2)O emissions in rice-based cultivation.It is imperative to understand the influences of different upland crop planting systems on soil N_(2)O emissions.In this study,we focused on two representative rotation systems in Central China:rapeseed–rice(RR)and wheat–rice(WR).We examined the biotic and abiotic processes underlying the impacts of these upland plantings on soil N_(2)O emissions.The results revealed that during the rapeseed-cultivated seasons in the RR rotation system,the average N_(2)O emissions were 1.24±0.20 and 0.81±0.11 kg N ha^(–1)for the first and second seasons,respectively.These values were comparable to the N_(2)O emissions observed during the first and second wheat-cultivated seasons in the WR rotation system(0.98±0.25 and 0.70±0.04 kg N ha^(–1),respectively).This suggests that upland cultivation has minimal impacts on soil N_(2)O emissions in the two rotation systems.Strong positive correlations were found between N_(2)O fluxes and soil ammonium(NH_(4)^(+)),nitrate(NO_(3)^(–)),microbial biomass nitrogen(MBN),and the ratio of soil dissolved organic carbon(DOC)to NO_(3)^(–)in both RR and WR rotation systems.Moreover,the presence of the AOA-amoA and nirK genes were positively associated with soil N_(2)O fluxes in the RR and WR systems,respectively.This implies that these genes may have different potential roles in facilitating microbial N_(2)O production in various upland plantation models.By using a structural equation model,we found that soil moisture,mineral N,MBN,and the AOA-amoA gene accounted for over 50%of the effects on N_(2)O emissions in the RR rotation system.In the WR rotation system,soil moisture,mineral N,MBN,and the AOA-amoA and nirK genes had a combined impact of over 70%on N_(2)O emissions.These findings demonstrate the interactive effects of functional genes and soil factors,including soil physical characteristics,available carbon and nitrogen,and their ratio,on soil N_(2)O emissions during upland cultivation seasons under rice-upland rotations.
基金supported by the Key Research&Developmental Program of Shandong Province(Nos.2021CXGC011202,2020CXGC011404)the Beijing Natural Science Foundation(No.8192004)the Beijing Major Science and Technology Projects(No.Z181100005318001)
文摘The long-term impact of fulvic acid(FA)on partial nitritation(PN)systemwas initially examined in this study.The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulation rate(NAR nearly 100%)and ammonium removal rate(ARR 56.85%),while FA over 50 mg/L decreased ARR from 56.85%to 0.7%.Sludge characteristics analysis found that appropriate FA(<50 mg/L)exposure promoted the settling performance and granulation of PN sludge by removing Bacteroidetes and accumulating Chloroflexi.The analysis of metagenomics suggested that the presence of limited FA(0-50 mg/L)stimulated the generation of NADH,which favors the denitrification and nitrite reduction.The negative impact of FA on the PN system could be divided into two stages.Initially,limited FA(50-120 mg/L)was decomposed by Anaerolineae to stimulate the growth and propagation of heterotrophic bacteria(Thauera).Increasing heterotrophs competed with AOB(Nitrosomonas)for dissolved oxygen,causing AOB to be eliminated and ARR to declined.Subsequently,when FA dosage was over 120 mg/L,Anaerolineae were inhibited and heterotrophic bacteria reduced,resulting in the abundance of AOB recovered.Nevertheless,the ammonium transformation pathway was suppressed because genes amoABC and hao were obviously reduced,leading to the deterioration of reactor performance.Overall,these results provide theoretical guidance for the practical application of PN for the treatment of FA-containing sewage.
基金the National Science and Technology Major Project of the Ministry of Science and Technology of China (2016ZX08001-001)。
文摘A field experiment involving cry1Ab transgenic rice(GM) and its parental non-cry1Ab rice(M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes which drive the conversion of nitrogen in paddy soil were analyzed during the growth period of rice in the fifth year of the experiment, using 16 S rRNAbased Illumina Mi Seq and real-time PCR on the amoA, nirS and nirK genes. The results showed no differences in the alpha diversity indexes of the bacterial communities, including Chao1, Shannon and Simpson, between the fields cultivated with line GM and cultivar M at any of the growth stages of rice. However, the bacterial communities in the paddy soil with line GM were separated from those of paddy soil with cultivar M at each of the growth stages of rice, based on the unweighted Uni Frac NMDS or PCoA. In addition, the analyses of ADONIS and ANOSIM, based on the unweighted Uni Frac distance, indicated that the above separations between line GM and cultivar M were statistically significant(P<0.05) during the growth season of rice. The increases in the relative abundances of Acidobacteria or Bacteroidetes, in the paddy soils with line GM or cultivar M, respectively, led to the differences in the bacterial communities between them. At the same time, functional gene prediction based on Illumina Mi Seq data suggested that the abundance of many functional genes increased in the paddy soil with line GM at the maturity stage of rice, such as genes related to the metabolism of starch, amino acids and nitrogen. Otherwise, the copies of bacterial amo A gene, archaeal amo A gene and denitrifying bacterial nir K gene significantly increased(P<0.05 or 0.01) in the paddy soil with line GM. In summary, the release of cry1Ab transgenic rice had effects on either the composition of bacterial communities or the abundance of microbial functional genes in the paddy soil.
基金supported jointly by Natural Science Foundation of Hebei Province(D2020504003)National Key Research and Development Program of China(No.2019YFC1805300).
文摘High concentrations of ammonium nitrogen released from tannery sludge during storage in open air may cause nitrogen pollution to soil and groundwater.To study the transformation mechanism of NH_(4)^(+)-N by nitrifying functional bacteria in tannery sludge contaminated soils,a series of contaminated soil culture experiments were conducted in this study.The contents of ammonium nitrogen(as NH_(4)^(+)-N),nitrite nitrogen(as NO_(2)^(−)-N)and nitrate nitrogen(as NO_(3)^(−)-N)were analyzed during the culture period under different conditions of pollution load,soil particle and redox environment.Sigmodial equation was used to interpret the change of NO_(3)^(−)-N with time in contaminated soils.The abundance variations of nitrifying functional genes(amoA and nxrA)were also detected using the real-time quantitative fluorescence PCR method.The results show that the nitrification of NH_(4)^(+)-N was aggravated in the contaminated silt soil and fine sand under the condition of lower pollution load,finer particle size and more oxidizing environment.The sigmodial equation well fitted the dynamic accumulation curve of the NO_(3)^(−)-N content in the tannery sludge contaminated soils.The Cr(III)content increased with increasing pollution load,which inhibited the reproduction and activity of nitrifying bacteria in the soils,especially in coarse-grained soil.The accumulation of NO_(2)^(−)-N contents became more obvious with the increase of pollution load in the fine sand,and only 41.5%of the NH_(4)^(+)-N was transformed to NO_(3)^(−)-N.The redox environment was the main factor affecting nitrification process in the soil.Compared to the aerobic soil environment,the transformation of NH_(4)^(+)-N was significantly inhibited under anaerobic incubation condition,and the NO_(3)^(−)-N contents decreased by 37.2%,61.9%and 91.9%under low,medium and high pollution loads,respectively.Nitrification was stronger in the silt soil since its copy number of amoA and nxrA genes was two times larger than that of fine sand.Moreover,the copy numbers of amoA and nxrA genes in the silt soil under the aerobic environment were 2.7 times and 2.2 times larger than those in the anaerobic environment.The abundance changes of the amoA and nxrA functional genes have a positive correlation with the nitrification intensity in the tannery sludge-contaminated soil.
基金Project(2011-622-40) supported by the Mineral Exploration Foundation of Henan Province,ChinaProject(51104189) supported by the National Natural Science Foundation of ChinaProject(2013M531814) supported by the Postdoctoral Science Foundation of China
文摘Biological desilication process is an effective way to remove silicate from rutile so that high purity rutile could be obtained. However, little is known about the molecular mechanism of this process. In this work, a newly developed rutile bio-desilication reactor was applied to enrich rutile from rough rutile concentrate obtained from Nanzhao rutile mine and a comprehensive high through-put functional gene array(Geo Chip 4.0) was used to analyze the functional gene diversity, structure and metabolic potential of microbial communities in the biological desilication reactor. The results show that TiO2 grade of the rutile concentrate could increase from 78.21% to above 90% and the recovery rate could reach to 96% or more in 8-12 d. The results also show that almost all the key functional genes involved in the geochemical cycling process, totally 4324 and 4983 functional microorganism genes, are detected in the liquid and ore surface, respectively. There are totally 712 and 831 functional genes involved in nitrogen cycling for liquid and ore surface samples, respectively. The relative abundance of functional genes involved in the phosphorus and sulfur cycling is higher in the ore surface than liquid. These results indicate that nitrogen, phosphorus and sulfur cycling are also present in the desiliconization process of rutile. Acetogenesis genes are detected in the liquid and ore surface, which indicates that the desiliconizing process mainly depends on the function of acetic acid and other organic acids. Four silicon transporting genes are also detected in the sample, which proves that the bacteria have the potential to transfer silicon in the molecule level. It is shown that bio-desilication is an effective and environmental-friendly way for enrichment of rough rutile concentrate and presents an overview of functional diversity and structure of desilication microbial communities, which also provides insights into our understanding of metabolic potential in biological desilication reactor ecosystems.
基金funded by the Key-Area Research and Development Program of Guangdong Province(Grant No.2022B0202070002)the Guangxi Science and Technology Major Program(Grant No.GuikeAA23023007-2)+1 种基金the Guangdong Province Modern Agricultural Industry Technology System Innovation Team Construction Project(2024CXTD19)Guangdong Basic and Applied Basic Research Foundation(Grant No.2023A1515010303)。
文摘Agrobacterium tumefaciens-mediated transformation has been widely adopted for plant genetic engineering and the study of gene function(Krenek et al.,2015).This method is prevalent in the genetic transformation of herbaceous plants,with notable applications in species such as Arabidopsis(Yin et al.,2024),soybean(Zhang et al.,2024),rice(Zhang et al.,2020),and Chinese cabbage(Li et al.,2021).However,its application in fruit trees is limited.This is primarily due to their long growth cycles and lack of rapid,efficient,and stable transgenic systems,which severely hinders foundational research involving plant genetic transformation(Mei et al.,2024).Furthermore,for subtropical fruit trees,the presence of recalcitrant seeds adds an extra layer of difficulty to genetic transformation(Umarani et al.,2015),as most methods rely on seed germination as a basis for transformation.
基金Supported by Tianjin Municipal Science and Technology Commission Grant,No.24ZXRKSY00010Program for Innovative Research Team in Peking Union Medical College,CAMS Initiative for Innovative Medicine,No.2023-I2M-2-008.
文摘Inflammatory bowel disease(IBD)is an incurable disease of the digestive system;however,the therapeutic methods for IBD remain limited.The pathogenesis of IBD was systematically discussed and compared in this paper,primarily comprising Crohn’s disease and ulcerative colitis.This paper focused on six common aspects:(1)Dysregulated immune responses;(2)Gene function changes;(3)Intestinal microbes disorder and imbalance;(4)Microbial infections;(5)Associations between IBD and other inflammatory diseases;and(6)Other factors.In addition,the pathogenesis differences between these two forms of IBD were unraveled and clearly distinguished.These unique aspects of pathogenesis provide crucial insights for the precise treatment of both Crohn’s disease and ulcerative colitis.This paper illustrates the root causes and beneficial factors of resistance to IBD,which provides novel insights on early prevention,development of new therapeutic agents,and treatment options of this disease.
文摘A rhizobox system constructed with crude oil- contaminated soil was vegetated with alfalfa （Medicago sativa L.） to evaluate the rhizosphere effects on the soil microbial population and functional structure, and to explore the potential mechanisms by which plants enhance the removal of crude oil in soil. During the 80-day experiment, 31.6% of oil was removed from the adjacent rhizosphere （AR）; this value was 27% and 53% higher than the percentage of oil removed from the far rhizosphere （FR） and from the non-rhizosphere （NR）, respectively. The populations of heterotrophic bacteria and hydrocarbon- degrading bacteria were higher in the AR and FR than in the NR. However, the removal rate of crude oil was positively correlated with the proportion of hydrocarbon- degrading bacteria in the rhizosphere. In total, 796, 731, and 379 functional genes were detected by microarray in the AR, FR, and NR, respectively. Higher proportions of functional genes related to carbon degradation and organic remediation, were found in rhizosphere soil compared with NR soil, suggesting that the rhizosphere selectively increased the abundance of these specific functional genes. The increase in water-holding capacity and decrease in pH as well as salinity of the soil all followed the order of AR 〉 FR 〉 NR. Canonical component analysis showed that salinity was the most important environmental factor influencing the microbial functional structure in the rhizosphere and that salinity was negatively correlated with the abundance of carbon and organic degradation genes.
基金financial support from the Natural Science Foundation of Sichuan Province,China(No.2023NSFSC0143)the National Natural Science Foundation of China(No.31800458)the Transportation Science and Technology Project of Sichuan Province,China(No.2019-ZL-19)。
文摘Peatlands on the southwestern plateau of China are important carbon sinks for high-altitude terrestrial ecosystems in Asia.However,the specific microecological mechanism responsible for alterations in carbon processes in this region due to the simultaneous impacts of global warming and drought has not been fully elucidated.Investigating this mechanism will improve our understanding of carbon cycle feedback in peatland ecosystems,as it is affected by changes in hydrology and temperature,especially in vulnerable habitats.This study examined the influence of soil carbon decomposition functional microorganisms on soil respiration and temperature sensitivity(expressed as Q_(10))in high-elevation peatlands using field investigations,simulated warming experiments,and metagenomic sequencing.We found that hydrothermal conditions had a significant effect on soil respiration,leading to an increase in cumulative soil respiration as soil moisture and temperature increased.Soil moisture affected soil respiration and soil organic carbon mainly through soil microorganisms,with a predominance of carbon-decomposing genes.We found that genes regulating the decomposition of plant-derived carbon such as cellulose and lignin were the critical factor influencing Q_(10)in peatlands.Genes involved in cellulose and lignin decomposition showed a significant positive correlation with Q_(10)(P<0.05),while genes involved in hemicellulose decomposition showed a significant negative correlation with Q_(10)(P<0.05).Specifically,genes such as ACO,xylF,and hpaE,which are involved in lignin decomposition,and glgB,which is responsible for cellulose decomposition,showed significant positive correlations(P<0.05)with Q_(10).Conversely,the gene uxaC,involved in the decomposition of hemicellulose,showed a significant negative correlation(P<0.05)with Q_(10).Finally,we analyzed the relevant carbon metabolic pathways and found that although they were affected by water,they were not significantly related to Q_(10).In short,this research highlights the importance of microorganisms with genes for decomposing plant-derived carbon in influencing carbon emissions in plateau peatlands during periods of warming.
基金supported by the National Natural Science Foundation of China (81571273,81571274,81501124,81271434,and 81301107)Omics-based precision medicine of epilepsy being entrusted by Key Research Project of the Ministry of Science and Technology of China (2016YFC0904400)+5 种基金the Natural Science Foundation of Guangdong Province,China (2014A030313489)Science and Technology Planning Projects of Guangdong Province,China (2012B031800404 and 2013B051000084)the Department of Education of Guangdong Province,China (2013CXZDA022,2013KJCX0156,and 2012KJCX009)the Foundation for High-level Talents in Higher Education of Guangdong Province,China (2013-167)Yangcheng Scholar Research Projects of Guangzhou Municipal College (12A016S and 12A017G)Science and Technology Projects of Guangzhou,Guangdong Province,China (2014J4100069,201508020011,201604020161,and 201607010002)
文摘Ion channels are crucial in the generation and modulation of excitability in the nervous system and have been implicated in human epilepsy. Forty-one epilepsyassociated ion channel genes and their mutations are systematically reviewed. In this paper, we analyzed the genotypes, functional alterations（funotypes）, and phenotypes of these mutations. Eleven genes featured loss-offunction mutations and six had gain-of-function mutations.Nine genes displayed diversified funotypes, among which a distinct funotype-phenotype correlation was found in SCN1A. These data suggest that the funotype is an essential consideration in evaluating the pathogenicity of mutations and a distinct funotype or funotype-phenotype correlation helps to define the pathogenic potential of a gene.
基金supported by the Science Foundation of the Chinese Academy of Sciences (Grant No.KSCX2-YW-N-007)the National Natural Science Foundation of China (Grant No.30370803)+1 种基金the Ministry of Science and Technology of China (Grant No.2005DKA21006)‘Hundred Talents’ Program of the Chinese Academy of Sciences
文摘Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription factor gene families, was recently suggested to play important roles in plant development and stress response. In rice, the results of analyses of expression pattern and ectopic overexpressor lines also support this viewpoint, and the evidences implicate rice WRKY proteins in transcriptional reprogramming during biotic or abiotic stresses, senescence, sugar metabolites, and morphological architecture. In this paper, we review the advance in study of rice WRKY gene family and also propose unified nomenclature for rice WRKY factors to eliminate confusion.
基金supported by the National Youth Talent Program (A279021801)Key-Area R&D Program of Guangdong province (2022B0202060001)+4 种基金Key R&D Program of Shaanxi Province (2023-YBNY-008)the Science and Technology Innovation Team of Shaanxi (2021TD-32)the Natural Science Foundation of Shaanxi Province (2021JM-089, 2022JM-112 and 2022JQ-162)the Key R&D Project from Yangling Seed Industry Innovation Center (K3031322016)the Fundamental Research Fund from Northwest A&F University (2452022111)。
文摘The nuclear factor Y(NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelon, a valued and nutritious fruit, remain largely unknown and their functions have not been characterized. In the present study, 22 ClNF-Y genes in watermelon, 29 CsNF-Y genes in cucumber, and 24CmNF-Y genes in melon were identified based on the whole-genome investigation and their protein properties, gene location, gene structure, motif composition, conserved domain, and evolutionary relationship were investigated. ClNF-YB9 from watermelon and its homologs in cucumber and melon were expressed specifically in seeds. Its expression remained low in the early stages of watermelon seed development,increased at 20 days after pollination(DAP), and peaked at 45–50 DAP. Moreover, the knockout mutant Clnf-yb9 exhibited abnormal leafy cotyledon phenotype, implying its critical role during seed formation.Finally, protein interaction assays showed that ClNF-YB9 interacts with all ClNF-YCs and the ClNF-YB9-YC4 heterodimer was able to recruit a ClNF-YA7 subunit to assemble a complete NF-Y complex, which may function in seed development. This study revealed the structure and evolutionary relationships of the NF-Y gene family in Cucurbitaceae and the novel function of ClNF-YB9 in regulating seed development in watermelon.
基金supported by the Project of the National Ministry of Science and Technology,China (Grant No.2006AA10Z1C8)the Knowledge Innovative Program of the Chinese Academy of Sciences (Grant Nos.KSCX-YW-N-009-02 and KSCX1-YW-03)+1 种基金the National Basic Research Program of China (Grant No.2009CB126004)the Natural Science Foundation of Hainan Province,China (Grant No.309019)
文摘Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） from the Philippines. IR24 was highly susceptible to all the strains, and six common wild rice accessions resisted all the nine strains, with a resistance frequency of 67%. The accessions Yulin and Wanning were only susceptible to PXO280 and PXO71, respectively. The accession Gaozhou was susceptible to the three strains PXO79, PXO99 and PXO339, whereas resistant to the other six strains. It could be concluded that there is at least one resistance gene in each common wild rice accession. The functional markers of the genes xa5, xa13, Xa21 and Xa27 were used to detect the presence of these resistance genes in the nine tested wild rice accessions, and it was found that four wild rice accessions contained heterozygous xa13. Among the nine common wild rice accessions, five were homozygous for Xa27 and three homozygous for xa27, and the accession Laibin contained neither xa27 nor Xa27. In addition, there were no xa5 and Xa21 in all of these accessions.
基金supported by the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (Grant No. 30024001)the National Basic Research Program of China (Grant No. 2004CB518605)+1 种基金the Major National Science and Technology Program of China (Grant No. 2008ZX10002-020)the National High Technology Research and Development Program of China (Grant Nos. 2006AA020501 and 2001AA221081)
文摘The Human Genome Project was launched at the end of the 1980s.Since then,the cloning and identification of functional genes has been a major focus of research across the world.In China too,the potentially profound impact of such studies on the life sciences and on human health was realized,and relevant studies were initiated in the 1990s.To advance China's involvement in the Human Genome Project,in the mid-1990s,Committee of Experts in Biology from National High Technology Research and Development Program of China(863 Program) proposed the "two 1%" goal.This goal envisaged China contributing 1% of the total sequencing work,and cloning and identifying 1% of the total human functional genes.Over the past 20 years,tremendous achievement has been accomplished by Chinese scientists.It is well known that scientists in China finished the 1% of sequencing work of the Human Genome Project,whereas,there is no comprehensive report about "whether China had finished cloning and identifying 1% of human functional genes".In the present study,the GenBank database at the National Center of Biotechnology Information,the PubMed search tool,and the patent database of the State Intellectual Property Office,China,were used to retrieve entries based on two screening standards:(i) Were the newly cloned and identified genes first reported by Chinese scientists?(ii) Were the Chinese scientists awarded the gene sequence patent? Entries were retrieved from the databases up to the cut-off date of 30 June 2011 and the obtained data were analyzed further.The results showed that 589 new human functional genes were first reported by Chinese scientists and 159 gene sequences were patented(http:gene.fudan.sh.cn/introduction/database/chinagene/chinagene.html).This study systematically summarizes China's contributions to human functional genomics research and answers the question "has China finished cloning and identifying 1% of human functional genes?" in the affirmative.
文摘Synthetic biology is one of the rapid developing scientific fields in recent years. Through synthetic biology,we have a better understanding of the natural synthesis process of natural products, which provides a favorable method to research the diversity of natural products, and also provides new tools for us to create new approach for producing natural products, we can synthesize compounds with different structures by artificial combination of different synthesis modules.
文摘Studies on the cold-responsive genes and cold signaling of woody species drop far behind in comparison to herbaceous plants.Due to similar lignified structure,perennial characteristic,and enhanced tolerance,it seems much easier to find strongly antifreeze genes and obtain effective results in transgenic woody plants.In this study,Ammopiptanthus mongolicus,an evergreen,broadleaf and cold-resist leguminous shrub growing in the desert of Inner Mongolia,was used as a material for low-temperature induced gene isolation.Through differential expression analysis induced by low-temperature,thirteen up-regulated cDNAs were identified.One of them,AmEBP1,(accession number:DQ519359)confers enhanced cold-tolerance to both transgenic E.coli and transgenic Arabidopsis.Results suggest that AmEBP1 can stimulate the synthesis of ribosome and the dephosphyration of the α-subunit of initiation factor 2(eIF2α),and subsequently promote the translation process.By which the transgenic plants obtained increased cold-resistant ability.
基金supported by grants from the Wuhan Science and Technology Major Project on Key techniques of biological breeding and Breeding of new varieties(Grant No.2022021302024851)the special project for sustainable development agenda of innovation demonstration zone(Grant No.202204AC100001-A04)the National Key R&D Program of China(Grant No.2022YFD1200400)。
文摘Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by Plasmodiophora brassicae infection.Breeding of clubroot resistant cultivars based on mapping and cloning of resistant genes is commonly regarded as the most cost-effective and efficient way to fight against this disease.The traditional way of R gene functional validation requires stable transformation that is both time-and labor-consuming.In this study,a rapid and efficient hairy-root transgenic protocol mediated by Agrobacterium rhizogenes was developed.The transformation positive rate was over 80%in Brassica napus showed by GUS reporter gene and this transformation only took 1/6 of the time compared with stable transformation.The system was applicable to different B.napus varieties and other cruciferous crops including Brassica rapa and Brassica oleracea.In particular,two known CR genes,CRA3.7.1 and CRA8.2.4 were used respectively,as example to show that the system works well for CR gene study combined with subsequent P.brassicae infection in B.napus.Most importantly,it works both in over-expression that led to disease resistance,as well as in RNAi which led to disease susceptible phenotype.Therefore,this system can be used in batch-wise identification of CR genes,and also offered the possibility of manipulating key genes within the P.brassicae genome that could improve our knowledge on host-pathogen interaction.
基金Supported by National Natural Science Foundation of China(30871512,31000701)Startup Foundation for Advanced Talents of Henan Academy of Agricultural Sciences(2060503)~~
文摘Low temperature is one of the main environmental stress factors influenc- ing plant growth and development and crop yield. Cold tolerance genes and progress of their application in genetic engineering of plant for cold tolerance were reviewed comprehensively and systematically from the aspect of genes that are in- volved in biosynthesis of osmotic substances, genes coding fatty acid desaturation enzymes, antifreeze protein genes, genes coding antioxidant enzymes and so on, aiming at laying the foundation for genetic improvement of cold tolerance and breeding of plants.
基金the Department of Science and Technology(DST)-India for providing a departmental grant to the Department of Biochemistry,Central University of Punjab,Bathinda,India,in the form of a DST-Fund for Improvement of S&T Infrastructure(FIST)grant。
文摘Microplastics (MPs), fluoride (FR), and fungicide mancozeb (MZ) are common contaminants in soil. However, there is no information about the combined impacts of MPs, FR, and MZ on tomato plant growth features in the literature. This study aimed to investigate the effects of combined application of MPs, FR, and MZ (both analytical grade and commercial) on the growth and development of tomato plants and metagenomics of rhizosphere soil. A pot experiment was set up in an artificial greenhouse with two sets of treatments. One set was the combined application of MPs, FR, and analytical grade MZ (B2) and a control without the application of MPs, FR, and MZ (W2), and the other set was the combined application of MPs, FR, and commercial MZ (B3) and a control without the application of MPs, FR, and MZ (W3). No detrimental effects of MPs, FR, and MZ were detected on the growth parameters of tomato plants, including the number of leaves and chlorophyll concentration. However, tomato roots showed knot and nodulation-type structures, and metabolomic profiling revealed that combined exposure to MPs, FR, and MZ profoundly reprogrammed the primary metabolism in tomato roots, with marked alterations in carbohydrate and amino acid pathways. Metagenome whole genome sequencing showed that the B2 and B3 treatments profoundly affected soil microbial community composition, diversity, gene abundances, and functional gene variations compared to W2 and W3. Proteobacteria became the dominating phylum in B2 and B3, causing a significant shift in the microbiome. Its abundance soared to 66.7% in B2 and 75.4% in B3, compared to only 35.9% in W2 and 28.9% in W3. On the other hand, Actinobacteria decreased significantly from 55.6% in W2 and 63.8% in W3 to 18.1% in B2 and 9.6% in B3. This study highlights the microbial shifts due to combined application of MPs, FR, and MZ, providing evidence for understanding their environmental risks.
基金supported by grants from the National Natural Science Foundation of China(Nos.42172339,91951205)。
文摘Microorganisms actively participate in biogeochemical cycling processes and play a crucial role in maintaining the dynamic balance of hot spring ecosystems.However,the distribution of microbial functional genes and their influencing factors in hot springs remain largely unclear.Therefore,this study investigated the microbial functional genes and their potential for controlling biogeochemical cycles(C,N,S,and P) in the hot Springs of Tengchong,China,using the Geochip method,a functional gene microarray technology.The examined hot springs have very different microbial functional genes.A total of 22 736 gene probe signals were identified,belonging to 567 functional genes and associated with 15 ecological functions,mainly involving stress response,carbon cycle,nitrogen cycle,sulfur cycle,phosphorus cycle and energy processes.The amyA,narG,dsrA and ppx genes were most abundant in carbon,nitrogen,sulfur and phosphorus cycles,respectively,and were significantly correlated with pH,temperature and SO_(4)^(2-).The diversity and abundance of detected gene probes were negatively correlated with temperature.The α-diversity(i.e.,Shannon index) was high at low temperature and low pH.Molecular functional interactions revealed by the gene connectivity levels were negatively correlated with temperature,pH and SO_(4)^(2-).These results suggested that the abundance,diversity and interactions of microbial functional genes were significantly influenced by geochemical parameters.-In addition,some genera possessed functional genes related to carbon,nitrogen,sulfur,and phosphorus cycles and can synergistically control the biogeochemical cycles of carbon,nitrogen,sulfur and phosphorus.These findings provide new insights into the functional potentials of microorganisms to participate in biogeochemical cycles and their responses to environmental factors in hot springs.
