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.

生物信息学在动物遗传育种中的应用

随着计算机网络技术的发展,生命科学以及信息科学两个领域之间的关联更加密切,这促进了生物信息学的良好发展,并在一定程度上使得现代医药产业和生物工程都得到了进一步的发展。当前我国在生物信息学中的研究进展较为可观,其中在生命科学中研究所得的核酸与蛋白质两大分子的结构序列,极大地丰富了生物信息学数据库结构和种类。但是在生物信息学在实际应用中,仍然有很大的发展空间,需要与各类科学技术进行结合,以完善我们当前所获取和存储的生命序列信息,并以此促进我们的农业、生物工程、动物遗传育种等方面的应用发展。本文详细研究了当前生物信息学在动物遗传育种中的应用策略,推进动物遗传育种研究的进一步发展。

The Influence of Plant Diversity and Functional Composition on Ecosystem Stability of Four Stipa Communities in the Inner Mongolia Plateau

The main purpose of this study was to examine the effects of plant species diversity and functional composition (the identity of the plant functional groups) on ecosystem stability of Stipa, communities in the Inner Mongolia Plateau. The research work was based on a 12-year study (from 1984 to 1995) of species abundance, diversity, and primary productivity of four Stipa communities, i.e. S. baicalensis Roshev., S. grandis P. Smirn., S, krylovii Roshev., and S. klemenzii Roshev. respectively. The Shnnon-Wiener index was used as a measurement of plant diversity, while functional composition was used to differentiate the functional groups that were included in the communities. The plant species of four Stipa communities were classified into functional groups based on the differences in life forms and ecological groups, which influence their performance in resource requirements, seasonality of growth, tolerance to water stress, and life history. Plant species were classified into five functional groups based on their differences in life form, shrubs and half shrubs, perennial bunch grasses, perennial rhizome grasses, forbs, annuals and biennials. Based on their differences in water requirement these species were classified into four functional groups: xerads, intermediate xerads, intermediate mesophytes, and mesophytes. The results showed: 1) Plant species diversity stabilized ecosystem processes. Shannon-Wiener index were 2.401 4, 2.172 0, 1.624 8, 0.354 3 from S. baicalensis community to S. grandis, S. krylovii and S. klemenzii community, respectively. The dynamics of the aboveground net primary productivity (ANPP) for a 12-year's period showed a reverse pattern, the coefficients of variation of the four communities were 21.94%, 20.63%, 29.21% and 39.72% respectively. 2) The Life form functional group component of diversity was a greater determinant of the ecosystem processes than the species component of diversity. The effects of perennial bunch grasses, perennial rhizome grasses and forbs on community stability were highly significant. 3) The ecological group component of diversity was also a great determinant of the ecosystem processes. The effects of xerads, intermediate xerads, and mesophytes on community stability were also very strong.

Research Progress on MEF2B Gene in Human and Animals

Myocyte enhancer factor 2B （MEF2B） gene belongs to myocyte enhancer factor 2 （MEF2） gene family. They are all widely expressed in muscle and nerve tissues of human and animals. MEF2B plays an important role in the growth of muscle, development and differentiation of nerve system and liver fibrosis. This re- view mainly focused on the structural characteristics, tissue distribution, biological functions and research progress of MEF2B gene in human and animals.

Leptin: a multifunctional hormone

Leptin is the protein product encoded by the obese (ob)gene. It is a circulating hormone produced primarily by the adipose tissue. ob/ob mice with mutations of the gene encoding leptin become morbidly obese, infertile, hyperphagic, hypothermic,and diabetic. Since the cloning of leptin in 1994, our knowledge in body weight regulation and the role played by leptin has increased substantially. We now know that leptin signals through its receptor, OB-R, which is a member of the cytokine receptor superfamily. Leptin serves as an adiposity signal to inform the brain the adipose tissue mass in a negative feedback loop regulating food intake and energy expenditure. Leptin also plays important roles in angiogenesis, immune function, fertility and bone formation. Humans with mutations in the gene encoding leptin are also morbidly obese and respond to leptin treatment,demonstrating that enhancing or inhibiting leptin’s activities in vivo may have potential therapeutic benefits.

The evolution and functional diversification of animal microRNA genes

microRNAs （miRNAs） are an abundant class of-22 nucleotide （nt） regulatory RNAs that are pervasive in higher eukaryotic genomes. In order to fully understand their prominence in genomes, it is necessary to elucidate the molecular mechanisms that can diversify miRNA activities. In this review, we describe some of the many strategies that allow novel miRNA functions to emerge, with particular emphasis on how miRNA genes evolve in animals. These mechanisms include changes in their sequence, processing, or expression pattern; acquisition of miRNA^＊ functionality or antisense processing; and de novo gene birth. The facility and versatility of miRNAs to evolve and change likely underlies how they have become dominant constituents of higher genomes.

Responses of biomass to the addition of water, nitrogen and phosphorus in Keerqin sandy grassland, Inner Mongolia, China

The effects of water, nitrogen and phosphorus on productivity of sandy grassland were investigated with a fully factorial experi- ment to find out the main factors limiting natural restoration of grassland productivity in the southeastern Keerqin sandy land. In total, eight treatments were designed as water addition （W）, nitrogen fertilizer addition （N）, phosphorus fertilizer addition （P）, water ＋ nitrogen fertilizer addition （WN）, water ＋ phosphorus fertilizer addition （WP）, nitrogen fertilizer ＋ phosphorus fertilizer addition （NP）, water ＋ nitrogen fertilizer ＋ phosphorus fertilizer addition （WNP） and control （CK）. Each treatment was replicated six times and randomly assigned to 48 plots （4 m × 4 m） that were separated by a 2-m buffer. Results show that restoration of productivity is only limited by nitrogen factor for sandy grassland of Keerqin sandy land and not limited by water and phosphorus. Relative to CK plots, the biomass and the aboveground net primary productivity （ANPP） of all the plots added with nitrogen fertilizer were significantly enhanced （P 〈 0.05） in 2005 growing season. Grass root mass is dominant in underground biomass. The present study possibly underestimates net primary productivity of grassland in northern China, due to limitation of underground biomass measurements.

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.

Biomass Allocation Patterns of Alpine Grassland Species and Functional Groups along a Precipitation Gradient on the Northern Tibetan Plateau

Variations in the fractions of biomass allocated to functional components are widely considered as plant responses to resource availability for grassland plants. Observations indicated shoots isometrically relates to roots at the community level but allometrically at the species level in Tibetan alpine grasslands. These differences may result from the specific complementarity of functional groups between functional components, such as leaf, root, stem and reproductive organ. To test the component complementary responses to regional moisture variation, we conducted a multi-site transect survey to measure plant individual size and component biomass fractions of common species belonging to the functional groups： forbs, grasses, legumes and sedges on the Northern Tibetan Plateau in peak growing season in 2010. Along the mean annual precipitation （MAP） gradient, we sampled 7o species, in which 2o are in alpine meadows, 20 in alpine steppes, 15 in alpine desert-steppes and 15 in alpine deserts, respectively. Our results showed that the size of alpine plants is small with individual biomass mostly lower than 1.0 g. Plants keep relative conservative component individual responses moisture functional fractions across alpine grasslands at the level. However, the complementary between functional components to variations specifically differ among groups. These results indicate that functional group diversity may be an effective tool for scaling biomass allocation patterns from individual up to community level. Therefore, it is necessary andvaluable to perform intensive and systematic studies on identification and differentiation the influences of compositional changes in functional groups on ecosystem primary services and processes.

Experimental genomics:The application of DNA microarrays in cellular and molecular biology studies

The genome sequence information in combination with DNA microarrays promises to revolutionize the way of cellu-lar and molecular biological research by allowing complex mixtures of RNA and DNA to interrogated in a parallel and quantita-tive fashion. DNA microarrays can be used to measure levels of gene expression for tens of thousands of gene simultane-ously and take advantage of all available sequence information for experimental design and data interpretation in pursuit of biological understanding. Recent progress in experimental genomics allows DNA microarrays not simply to provide a cata-logue of all the genes and information about their function, but to understand how the components work together to comprise functioning cells and organisms. This brief review gives a survey of DNA microarrays technology and its applications in ge-nome and gene function analysis, gene expression studies, biological signal and defense system, cell cycle regulation, mechanism of transcriptional regulation, proteomics, and the functionality of food component.

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.

Microbial roles equivalent to geological agents of high temperature and pressure in deep Earth

Microbes not only show sensitive responses to environmental changes but also play important roles in geochemical and geophysical systems. It is well known that microbes have caused major changes in surface environments and biogeochemical cycles through Earth history. Microbial processes can also induce the synthesis of certain minerals under Earth-surface conditions that previously were believed to form only under high temperatures and pressures in the deep Earth. For example, microbes can promote the conversion of smectite to illite, synthesis of authigenic plagioclase, precipitation of dolomite, and biotransformation of geolipids. These effects of microbes are due to their large surface/volume ratios, enzyme production, and abundant functional groups. Microbial catalyzation of chemical reactions proceeds through reaction-specific enzymes, a decrease in Gibbs' s free energy, and/or break through the dynamics reaction thresholds via their metabolisms and physiology. Microbes can lower the surface free energy of mineral nuclei via biophysical adsorption due to their large surface/volume ratios and abundant functional groups. The mineral precipitation and transformation processes induced by microbes are functionally equivalent to geological processes operating at high temperatures and pressures in the deep Earth, suggesting that microbial processes can serve as analogs to deep abiotic processes that are difficult to observe.

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.

Ecogenotoxicology in earthworms： A review

Pollutant dynamics and bioavailability greatly differ in soil and aquatic systems. Therefore, specific approaches and models are needed to assess the impact of soil contamination to terrestrial ecosystems. Earthworms among other soil invertebrates have received more attention because of their ecological importance. They represent a dominant part of the soil biomass and are soil engineers regulating important soil processes, notably fertilization. The release in soils of pollutants known for their persistence and/or their toxicity is a concern. Exposure of terrestrial species to pollutants that may alter genomic function has become an increasing topic of research in the last decade. Indeed, genome disturbances due to genetic and epigenetic mechanisms may impair growth, as well as reproduction and population dynamics in the long term. Despite their importance in gene expres- sion, epigenetic mechanisms are not yet understood in soil invertebrates. Until now, pollutant-induced changes in genome expression in natural biota are still being studied through structural alteration of DNA. The first biomarker relating to genotoxicant exposure in earthworms from multi-contaminated soils reported is DNA adducts measurements. It has been replaced by DNA breakage measured by the Comet assay, now more commonly used. Functional genomic changes are now being explored owing to molecular ＂omic＂ technologies. Approaches, objectives and results are overviewed herein. The focus is on studies dealing with genotoxicity and populational effects established from environmentally-relevant experiments and in situ studies [Current Zoology 60 （2）： 255-272, 2014].

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.

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.