如果人类基因仅有3万个,这意味着什么

已经证实在人类基因组中可能只有不到3万个蛋白编码基因,这是Venter等人发表在<SCIENCE>上的纪念碑式的工作的关键结果之一.基因数量仅增加1/3便可以从简单的线虫纲动物(Caenorhbditis elegans,约有2万个基因)进化到人类,这当然会引起争论,而且将会在新世纪的开端不容置疑地引发出科学的、哲理的、道德的和宗教的问题.

Structure and functional heterogeneity of soil microbial communities in different farmland types on the Loess Plateau

Background,aim,and scope Soil microbes are important drivers of nutrient transformation and energy f low.Reclaiming forest land for agricultural use may have profound effects on soil properties and microbial communities.However,the response of soil microbial communities to soil reclamation in the dryland agroecosystem is less understood.Therefore,it is necessary to investigate the changes of soil microbial communities driven by land use conversion to promote nutrient cycling in reclaimed farmland.Materials and methods Based on the metagenomic technique,we evaluated the microbial composition and function of the newly created farmland(NF)after reclamation with two types of traditional farmland(slope farmland(SF),checkdam farmland(CF))on the Loess Plateau,and explored the response of nutrient cycling function to dominant genera and soil properties.Results The results showed that Proteobacteria,Actinobacteria,and Acidobacteria were prevalent in the three types of farmlands.Compared with SF and CF,NF increased the relative abundance of Actinobacteria and Nocardioides,as well as genes related to amino acid metabolism and carbohydrate metabolism.The relative abundance of functional genes related to carbon and nitrogen cycling in the NF was higher than that in the traditional farmland(SF and CF).The relative abundance of nutrient cycling functional genes was positively correlated with dominant genera in the three types of farmlands.Except for pH,soil physicochemical factors were negatively correlated with genes related to amino acid metabolism and carbon cycle.Discussion Previous studies have shown that the nutrient conditions of the soil may intensify the competition between the eutrophic and oligotrophic microbial populations.After long-term cultivation and fertilization,the soil properties of traditional farmland were significantly different from those of NF,leading to the differentiation of dominant microbial groups.Microbes usually have functional redundancy to cope with changing environments.Soil microbes in traditional farmland may contain more genes related to replication and repair,cell growth and death,and environmental adaptation in response to disturbances caused by agricultural practices.On the contrary,the NF was less disturbed by agricultural activities,and the soil properties were more similar to forest land,so the carbon and nitrogen cycle function genes were more abundant.The nutrient cycling function was affected by the abundance of microbial dominant groups and soil properties,which may be related to the availability of soil nutrients and agricultural disturbance in different farmlands.Aspects of soil microbial-driven nutrient cycling in agriculture could be regulated in sustainable method.Conclusions The change from forest land to farmland kept more carbon and nitrogen cycling function in the newly created farmland,while long-term agricultural activities have drastically changed the functional structure of traditional farmland,resulting in the nutrient cycling function more concentrated to meet the needs of crop growth.Recommendations and perspectives Hence,it is necessary to apply sustainable agricultural method to regulate microbial-driven nutrient cycling.The insights are meaningful for sustainable agricultural development and land management in arid areas.

Induced Expression of Cytochrome P450 CYP305 B1V1 Gene in Different Tissues of Wild Mulberry Silkworm(Bombyx mandarina)

[ Objective] The aim of this study was to investigate effects of various inducers on the expression of cytochrome P450 CYP305 B1 V1 Gene in different tissues of wild mulberry silkworm. [ Method] Referring to the mRNA sequence of CYP305 B1 V1 Gene published in GenBank for wild mulberry silkworm, one pair of primers was designed, and the expression of cytochrome P450 CYP305 B1 V1 Gene in different tissues of wild mulberry silkworm treated by NaF, rutin, cypermethrin and ecdysone was also analyzed by the semi - quantitative RT - PCR. Furthermore, homology comparison and phylogenetic analysis for amino acid sequences of this gene were studied. [ Result] Rutin, cypermethrin and NaF had effects on the expression of P450 CYP305 B1 V1 Gene in different tissues of wild mulberry silkworm, while ecdysone had no significant effect. Homology comparison for amino acids indicated that the amino acid sequence of this gene was the most similar to that of CYP305 B1 gene in Bombyx mori with 100% amino acid identity, and highly similar to those of Tribolium casmneum CYP305A1, Apis mellifera CYP305A1, Drosophi- la melanogaster CYP305A1, Anopheles gambiae CYP305A2and Culex pipiens quinquefasciatus CYP2LI. [ Conclusion] CYP305 B1 V1 Gene of wild mulberry silkworm is likely to mainly take part in the metabolism of exogenous compounds, which is of great significance for revealing the function of cytochrome P450 and the metabolic mechanism of different drugs.

How to Analyze the Function of Control Genes in Batches

Functional analysis of control genes is playing an important role in animal development.The research is mainly focused on developing a method of estimating the gene's effect or function in the development of animals.In this article,the gene's expression and control are described by models of quantitative genetics,which include the genetic models about the genes with no interaction and interaction effect.On this basis,a method analyzing the functions of control genes in batches is advanced,the method includes three steps as follows: Firstly,describe the gene's expression and control with multiple regression models in statistic method in different conditions.Secondly,collect the material of gene's polymorphism related to the gene's expression and control.Because,gene's polymorphism or the codominant molecular marker electropherogram in a gene locus present 3 states,and can be expressed with -1,0 and 1 respectively.The author thinks it can be regarded as levels in orthogonal layout.Discard the materials of gene's polymorphism not fitting the orthogonal layout,and use the materials of gene's polymorphism fitting the orthogonal layout as the data to estimate the gene's effects.Thirdly,analyze the gene's effect or function with equations as follows:suppose that a quantitative trait is controlled by N gene loci,in each locus there are two alleles,the alleles' effects are A GM1 ?a GM1 ;A GM2 ? a GM2 ;...;A GMi ?a GMi ;...;A GMN ;a GMN units respectively.When the genotype in a locus is heterozygous A GMi a GMi ,the interaction coefficient of alleles in a locus is K units.If there is no interaction among different gene loci,the author thinks,the gene's effects and gene's type can be estimated by using such equation: P GM =2∑Ni=1(A i-a i+K i)+∑Ni=1(A i-a i)M GMi -∑Ni=1K GMi M GMi 2 If there are interactions among different gene loci,and the effect of the x th gene's state combined with the y th gene's state in the k th gene group is defined as Y xyr ,and let gene group electropherogram states be r (where r∈ ),the author thinks,the gene group's effects can be estimated by the equation: Y xyr = K PCxy0 +K PCxy r+K PCxy' r 2+K PCxy'' 3+K PCxy(3') r 4+K PCxy(4') r 5+K PCxy(5') r 6+K PCxy(6') r 7+K PCxy(7') r 8 If there are interactions among more genes,the analogous method can also be used. In this way,be using the gene's codominent marker materials fitting the orthogonal layout,the gene's expression and control can be researched by the method of multiple regression,the gene's relative effect can be estimated,the overdominant gene's overdominant coefficient can be assessed,the gene's type can be identified,the interaction gene group's relative effect and the interaction gene's relation can be estimated as well,and furthermore,the gene's relation can be expressed in equations.For the sake of understanding the method used in this paper,the rout to prove it is given as well.Finally,the author thinks,this method is very useful to research the gene's function in molecular developmental biology.

Functional genomic approach to the study of biodiversitywithin Trichoderma

Trichoderma is a fungal genus of great and demonstrable biotechnological value, but its genome is poorly surveyed compared with other model microorganisms. Due to their ubiquity and rapid substrate colonization, Trichoderma species have been widely used as biocontrol organisms for agriculture, and their enzyme systems are widely used in industry. Therefore, there is a clear interest to explore beyond the phenotype to exploit the underlying genetic systems using functional genomics tools. The great diversity of species within the Trichoderma genus, the absence of optimized systems for its exploration, and the great variety of genes expressed under a wide range of ambient conditions are the main challenges to consider when starting a comprehensive functional genomics study. An initial project started by three Spanish groups has been extended into the project TRICHOEST, funded by the EU (FP5, QLRT-2001-02032) to target the transcriptome analysis of selected Trichoderma strains with biocontrol potential, in conditions related to antagonism, nutrient stress and plant interactions. Once specific conditions were defined, cDNA libraries were produced and used for EST sequencing. Nine strains from seven Trichoderma species have been considered in this study and an important amount of gene sequence data has been generated, analyzed and used to compare the gene expression in different strains. In parallel to sequencing, genomic expression studies were carried out by means of macro-arrays to identify genes expressed in specific conditions. In silico analysis of DNA sequencing data together with macro-array expression results have lead to a selection based on the potential use of the gene sequences. The selected clone sequences were completed and cloned in appropriate vectors to initiate functional analysis by means of expression studies in homologous and heterologous systems.

Construction of Two Gateway-compatible Destination Vectors for Tomato Functional Genomics under Abiotic Stress

[Objective] This research aimed at constructing two gateway-compatible plant expression vectors for functional genomics of abiotic stress in tomato.[Method] pK2GW7I was generated from the plant expression vector pK2GW7,0 by replacing the CaMV 35S promoter with abiotic-stress inducible plant promoter pRD29A,which was derived from the promoter of Arabidopsis gene RD29A.pKGW121 was generated by replacing the CaMV 35S of the plant expression vector pRD410 with the gateway recombinant cassette(attR1-cmR-ccdB-attR2)from pK2GW7,0.Constitutive and root-specific promoters were tested on pKGW121.[Result] Two gateway-compatible destination vectors,pK2GW7I and pKGW121,were successfully constructed;practicability test proved that pKGW121 was applicable for promoter analysis.[Conclusion] With the incorporation of gateway cloning technology or abiotic-stress inducible promoter,pKGW121 and pK2GW7I will be promising in large-scale investigation of tomato functional genes associated with various abiotic stresses.A high-throughput workflow for the construction of plant transformation vector was proposed and validated.

Research on Oxalate Oxidase and Its Genes in Plants

This paper introduces the discovery,composition and structure of oxalate oxidase,as well as illustrates the biological functions of this enzyme.With a comprehensive introduction upon previous researches upon gene cloning and heredity transformation of this enzyme,it indicates that heredity transformation can increase the content of oxalate oxidase within the plants and also enhance their resistance.The paper also points out the problems such as lack of gene resources and difficulty in the transformation of heterologous genes,and the focus in later researches should be laid upon the exploration of plant resources relative to this enzyme and selection of resistant species.

Role ofthe IncRNA-p53 regulatory network in cancer

Advances in functional genomics have led to discovery of a large group of previous uncharacterized long non-coding RNAs （IncRNAs）. Emerging evidence indicates that IncRNAs may serve as master gene regulators through various mechanisms. Dysregulation of IncRNAs is often associated with a variety of human diseases including cancer. Of significant interest, recent studies suggest that IncRNAs participate in the p53 tumor suppressor regulatory network. In this review, we discuss how IncRNAs serve as p53 regulators or p53 effectors. Further characterization of these p53-associated IncRNAs in cancer will provide a better understanding of lncRNA- mediated gene regulation in the p53 pathway. As a result, IncRNAs may prove to be valuable biomarkers for cancer diagnosis or poten- tial targets for cancer therapy.

Recent advances in biosynthesis of bioactive compounds in traditional Chinese medicinal plants

Plants synthesize and accumulate large amount of specialized （or secondary） metabolites also known as natural products, which provide a rich source for modem pharmacy. In China, plants have been used in traditional medicine for thousands of years. Recent development of molecular biology, genomics and functional genomics as well as high-throughput analytical chemical technologies has greatly promoted the research on medicinal plants. In this article, we review recent advances in the elucidation of biosynthesis of specialized metabolites in medicinal plants, including phenylpropanoids, terpenoids and alkaloids. Th- ese natural products may share a common upstream path- way to form a limited numbers of common precursors, but are characteristic in distinct modifications leading to highly variable structures. Although this review is focused on traditional Chinese medicine, other plants with a great medicinal interest or potential are also discussed. Under- standing of their biosynthesis processes is critical for producing these highly value molecules at large scale and low cost in microbes and will benefit to not only human health but also plant resource conservation.

Virus-induced gene silencing and its application in plant functional genomics

Virus-induced gene silencing is regarded as a powerful and efficient tool for the analysis of gene function in plants because it is simple, rapid and transformation-free. It has been used to perform both forward and reverse genetics to identify plant functional genes. Many viruses have been developed into virus-induced gene silencing vectors and gene functions involved in development, biotic and abiotic stresses, metabolism, and cellular signaling have been reported. In this review, we discuss the development and application of virus-induced gene silencing in plant functional genomics.

Genomic data mining for functional annotation of human long noncoding RNAs

Life may have begun in an RNA world,which is supported by increasing evidence of the vital role that RNAs perform in biological systems.In the human genome,most genes actually do not encode proteins;they are noncoding RNA genes.The largest class of noncoding genes is known as long noncoding RNAs(lncRNAs),which are transcripts greater in length than 200 nucleotides,but with no protein-coding capacity.While some lncRNAs have been demonstrated to be key regulators of gene expression and 3D genome organization,most lncRNAs are still uncharacterized.We thus propose several data mining and machine learning approaches for the functional annotation of human lncRNAs by leveraging the vast amount of data from genetic and genomic studies.Recent results from our studies and those of other groups indicate that genomic data mining can give insights into lncRNA functions and provide valuable information for experimental studies of candidate lncRNAs associated with human disease.

Literature and patent analysis of the cloning and identification of human functional genes in China

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.

Functional genomic analysis of Hawaii marine metagenomes

Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysis on seven samples of metagenomic data from different depth seawater in Hawaii. The results of gene prediction and function annotation indicate that there are large amounts of potential novel genes of which functions remain unknown at present. Based on the gene annotation, codon usage bias is studied on ribosomal protein-related genes and shows an evident influence by the marine extreme environment. Furthermore, focusing on the marine environmental differences such as light intensity, dissolved oxygen, temperature and pressure among various depths, comparative analysis is carried out on related genes and metabolic pathways. Thus, the understanding as well as new insights into the correlation between marine environment and microbes are proposed at molecular level. Therefore, the studies herein afford a clue to reveal the special living strategies of microbial community from sea surface to deep sea.

Zebrafish:A Renewed Model System For Functional Genomics

In the post genome era, a major goal in molecular biology is to determine the function of the many thousands of genes present in the vertebrate genome. The zebrafish （ Danio redo） provides an almost ideal genetic model to identify the biological roles of these novel genes, in part because their embryos are transparent and develop rapidly, The zebrafish has many advantages over mouse for genome-wide mutagenesis studies, allowing for easier, cheaper and faster functional characterization of novel genes in the vertebrate genome. Many molecular research tools such as chemical mutagenesis, transgenesis , gene trapping, gene knockdown,

Review:Advances in methodology of DNA methylation assay

DNA methylation is one of the most signaficant epigenetic events which greatly influence gene activation, gene imprinting, chromatin stability, and so on. The level of methylation in genome and certain regions should be in a normal range, because any variation would cause physiological dysfunction. In account of essential roles of DNA methylation in the living system, the detection of methylation in both overall genome and specific positions has drawn great interest. So far many biological and chemical methods have been developed to detect DNA methylation. Herein, we summerize some novel methods mainly based on chemical modification and analytic methods in DNA detection.