土壤活性有机质组分的分类方法及其研究进展

土壤活性有机质对农田管理措施和气候变化的响应敏感且快速,是表征土壤质量变化的重要指标,成为土壤生态学及环境土壤学交叉领域的研究热点。本文系统归纳了土壤活性有机质的物理组分(轻组有机质、颗粒有机质、大团聚体有机质、酸碱提取有机质和溶解有机质),化学组分(酸水解有机质和易氧化有机质),生物学组分(微生物生物量碳和氮、潜在可矿化碳和氮)和联合分组组分(游离态团聚体有机质、物理保护有机质和游离活性有机质)的分类方法,分析了不同组分的来源、典型数量(占土壤总有机质的比例)、性质和意义,评述了相关组分的研究进程、作用和影响因素,探讨了土壤活性有机质分组方法的整合应用及其研究进展,提出了补充和验证土壤活性有机质数量测定的不确定性和难比较性的可能技术途径,以期为科学解析土壤活性有机质在土壤质量变化研究中的作用提供理论依据和技术参考。

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.

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.

Cytological and Molecular Identification of Alien Chromatin in Giant Spike Wheat Germplasm

Alien chromosomes of twelve giant spike wheat germplasm lines were identified by C-banding, genomic in situ hybridization (GISH), sequence characterized amplified region (SCAR), and random amplified polymorphic DNA (RAPD). All lines showed a chromosome number of 2n = 42, five of them carried both a pair of wheat-rye (Triticum aestivum-Secale cereal) 1BL/1RS translocation chromosomes and a pair of Agropyron intermedium (Ai) chromosomes, three carried a pair of Ai chromosomes only, three others carried a pair of 1BL/1RS chromosomes only, and one carried neither 1BL/1BS nor Ai chromosome. Further identification revealed that the identical Ai chromosome in these germplasm lines substituted the chromosome 2D of common wheat (T aestivum L.), designated as 2Ai. The genetic implication and further utilization of 2Ai in wheat improvement were also discussed.

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.

A hybrid neural network system for prediction and recognition of promoter regions in human genome

This paper proposes a high specificity and sensitivity algorithm called PromPredictor for recognizing promoter regions in the human genome. PromPredictor extracts compositional features and CpG islands information from genomic sequence,feeding these features as input for a hybrid neural network system (HNN) and then applies the HNN for prediction. It combines a novel promoter recognition model, coding theory, feature selection and dimensionality reduction with machine learning algorithm.Evaluation on Human chromosome 22 was ～66% in sensitivity and ～48% in specificity. Comparison with two other systems revealed that our method had superior sensitivity and specificity in predicting promoter regions. PromPredictor is written in MATLAB and requires Matlab to run. PromPredictor is freely available at http://www.whtelecom.com/Prompredictor.htm.

Prediction of pyrolysis kinetic parameters from biomass constituents based on simplex-lattice mixture design

The aim of this study is to determine the effect of the main chemical components ofbiomass： cellulose, hemicel- lulose and lignin, on chemical kinetics ofbiomass pyrolysis. The experiments were designed based on a simplex- lattice mixture design. The pyrolysis was observed by using a thermogravimetric analyzer. The curves obtained from the employed analytical method fit the experimental data （R2 〉 0.9）. This indicated that this method has the potential to determine the kinetic parameters such as the activation energy （E~）, frequency factor （A） and re- action order （n） for each point of the experimental design. The results obtained from the simplex-lattice mixture design indicated that cellulose had a significant effect on Ea and A, and the interaction between cellulose and lignin had an important effect on the reaction order, n. The proposed models were then proved to be useful for predicting pyrolysis behavior in real biomass and so could be used as a simple approximation for predicting the overall trend of chemical reaction kinetics.

Emerging Trends for Microbiome Analysis： From Single-Cell Functional Imaging to Microbiome Big Data

Method development has always been and will continue to be a core driving force of microbiome science, In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms： ① a shift from dissecting microbiota structure by sequencing to tracking microbiota state, function, and intercellular interaction via imaging; ② a shift from interrogating a consortium or population of cells to probing individual cells; and ③a shift from microbiome data analysis to microbiome data science. Some of the recent methoddevelopment efforts by Chinese microbiome scientists and their international collaborators that underlie these technological trends are highlighted here. It is our belief that the China Microbiome Initiative has the opportunity to deliver outstanding ＂Made-in-China＂ tools to the international research community, by building an ambitious, competitive, and collaborative program at the forefront of method development for microbiome science.

Paleoclimate Study of Mountain Ecosystems by Multiple Group Biological Analysis

Methodological problems of climatic reconstruction for different periods of Holocene are discussed on the basis of a multiple group biological analysis on peat-sapropel sediments. The possibility of biological analysis is exemplified by the paleoclimatic reconstruction for Carpathian and Altai Mountain ranges. For the ＂Skolevsky Beskidy＂ national park of Carpaty the paleoclimatic scenarios have been drown up aiming at the more precise definition of climatic conditions for the period of mass mountain slope terracing. The stability of terrace systems of various designs in the current climatic conditions has been assessed. It is shown that during periods of humid climate the terraces, whose designs have been focused on drainage, were built. In periods of dry and warm climate the terrace systems capable of accumulating water were built. Both these types of terrace systems are destroyed in nowadays. Only those terrace systems are stable which were adjusted by their builders to contrast variations of precipitation. For Western Altais the paleoclimatic scenario has been done to forecast the safety of the Bronze Age kurgans （burial earth mounds） with permafrost inside the construction. In the Altay region during the Holocene it has revealed two periods of sharp cooling, the peaks of which occurred in the intervals 4500- 4300 and 2500-2300 years pronounced climatic drying ago, and two periods of 4900-4700 and 130-70 years ago. Depletion of the algae composition in the layer corresponding to the last period of drying climate indicates a very sharp change in the parameters of moisture and turning the lake into a dry swamp. Periods of cold weather may have contributed to the formation of special ritual traditions of the Sakan tribes that require the frozen ground to bury the dead. The later climate fluctuations identified have not affected the safety of permafrost in burial mounds constructed in the V-III cc BC.

The regional nature of nitrate-dominant haze pollution during autumn over the Pearl River Delta area

China has experienced severe haze and visibility degradation problems in recent years because of rapid urbanization and industrialization.In this study,daily atmospheric fine-aerosol samples were concurrently collected at three sites over the Pearl River Delta(PRD)region during 1–29 October 2014.PM2.5 samples were analyzed for organic carbon and elemental carbon using a thermal/optical carbon analyzer.Major water-soluble inorganic ions including F−,Cl−,NO3−,SO42−,Na+,NH4+,K+,Mg2+,and Ca2+were analyzed by ion chromatography.The results show that the temporal variations of PM2.5 concentration at the three sites were highly parallel,with particle pollution events simultaneously observed during 13–19 October(EP1)and 23–27 October(EP2),suggesting that pollution events in the PRD region are usually regional.This can most likely be attributed to the significant influences of synoptic conditions,which regionally facilitate or block diffusion of air pollutants.The chemical compositions of PM2.5 at the three sites were also found to be similar,dominated by organics and sulfates.The results indicate that accumulation of traffic emissions seems to play important roles in particle pollution for the PRD region,leading in this case to elevated nitrate contributions during both EP1 and EP2 at the three sites.Moreover,the authors found that locally emitted aerosols from biomass burning only markedly influenced the air condition at one site,Nanhai,during EP1,while regionally transported biomass burning aerosols from eastern and northern Guangdong Province influenced all three sampling sites when the PRD was dominated by polluted air from these directions during EP2.

The Biology of Chilo Iridescent Virus

Chilo iridescent virus (CIV) is the type species for genus Iridovirus, and belongs to the family Iridoviridae. Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure. The virions contain a single linear ds DNA molecule that is circularly permuted and terminally redundant. The genome of CIV has been entirely sequenced. The CIV virion consists of an unusual three-layer structure containing an outer proteinaceous capsid, an intermediate lipid membrane, and a core DNA-protein complex containing the genome. CIV has a broad host spectrum and has, in general, a limited mortality effect on its hosts. Up to now there have been several studies about CIV describing its structure, ecology, and molecular biology. In this review study we present all these studies together to describe the CIV.

Variations in Laboratory-Scale Actinomycete Communities Exposed to Cadmium as Assessed by Denaturing Gradient Gel Electrophoresis Profiles

The actinomycete populations and functions in cadmium （Cd） contaminated soil were investigated by the cultivation- independent molecular methods. The genomic DNA was extracted and purified from soil adulterated with various con- centrations of Cd in the laboratory. The partial 16S rDNA genes were amplified by polymerase chain reaction （PCR） using specific primers bound to evolutionarily conserved regions within these actinomycete genes. The diversity in PCR- amplified products, as measured by denaturing gradient gel electrophoresis （EGGE）, was used as a genetic fingerprint of the population. Principle component analysis and Shannon-Weaver diversity index （H） analyses were used to analyze the DGGE results. Results showed that the two principal components accounted for only a low level of the total variance. The value H in contaminated soil was lower than that in the control at later stages of cultivation, whereas at earlier stages it was higher. Among the six sampling time points, the first, fifth and sixth weeks had the highest values of H. Significantly negative correlations between bioavallable Cd concentration and H values existed in the samples from weeks 2 （R = 0.929, P 〈 0.05） and 4 （R = 0.909, P 〈 0.05）. These results may shed light on the effect of Cd on the soil environment and the chemical behavior and toxicity of Cd to actinomycetes.

Development of Bioinfo-Portal Tool for the Analysis of Genomic and Proteomic Data

The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them For the biologist, running bioinformatics analyses involve a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally we have designed a system, Bioinfo-Portal, to provide a flexible and usable web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using an adobe flex tool. Bioinfo-Portal can also act as a front end to provide a unified view of already-existing collections of bioinformatics resources. Users can analyze genomic and proteomic data by using the tools that has been integrated in the portal （tools for alignments, dotplots, motif detection, domain analysis, profile searching and tertiary structure prediction）. The sequences that user obtained from portal＇s nucleotide and protein databases are easily analyzed by the portal tools on the same interface in no time. User can also take benefit from the animations.

Mineral weathering and element cycling in soil-microorganism-plant system

Soil is an essential part of the critical zone,and soil-microbe-plant system serves as a key link among lithosphere,biosphere,atmosphere and hydrosphere.As one of the habitats with the richest biodiversity,soil plays a critical role in element biogeochemistry on the earth surface(weathered crust).Here we review the soil biological processes that are relevant to mineral weathering,element cycling,and transformation,with an emphasis on rock weathering mediated by soil microbes,plant root and the rhizosphere.

Lifeomics leads the age of grand discoveries

When our knowledge of a field accumulates to a certain level,we are bound to see the rise of one or more great scientists.They will make a series of grand discoveries/breakthroughs and push the discipline into an 'age of grand discoveries'.Mathematics,geography,physics and chemistry have all experienced their ages of grand discoveries;and in life sciences,the age of grand discoveries has appeared countless times since the 16th century.Thanks to the ever-changing development of molecular biology over the past 50 years,contemporary life science is once again approaching its breaking point and the trigger for this is most likely to be 'lifeomics'.At the end of the 20th century,genomics wrote out the 'script of life';proteomics decoded the script;and RNAomics,glycomics and metabolomics came into bloom.These 'omics',with their unique epistemology and methodology,quickly became the thrust of life sciences,pushing the discipline to new high.Lifeomics,which encompasses all omics,has taken shape and is now signalling the dawn of a new era,the age of grand discoveries.

Overview of available methods for diverse RNA-Seq data analyses

RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.

Impact of the next-generation sequencing data depth on various biological result inferences

Next-generation sequencing(NGS) technologies have revolutionized the field of genomics and provided unprecedented opportunities for high-throughput analysis at the levels of genomics,transcriptomics and epigenetics.However,the cost of NGS is still prohibitive for many laboratories.It is imperative to address the trade-off between the sequencing depth and cost.In this review,we will discuss the effects of sequencing depth on the detection of genes,quantification of gene expression and discovering of gene structural variants.This will provide readers information on choosing appropriate sequencing depth that best meet the needs of their particular project.

Secretory/releasing proteome-based identification of plasma biomarkers in HBV-associated hepatocellular carcinoma

For successful therapy, hepatocellular carcinoma (HCC) must be detected at an early stage. Herein, we used a proteomic approach to analyze the secretory/releasing proteome of HCC tissues to identify plasma biomarkers. Serum-free conditioned media (CM) were collected from primary cultures of cancerous tissues and surrounding noncancerous tissues. Proteomic analysis of the CM proteins permitted the identification of 1365 proteins. The enriched molecular functions and biological processes of the CM proteins, such as hydrolase activity and catabolic processes, were consistent with the liver being the most important metabolic organ. Moreover, 19% of the proteins were characterized as extracellular or membrane-bound. For validation, secretory proteins involved in transforming growth factor-β signaling pathways were validated in plasma samples. Alphafetoprotein (AFP), metalloproteinase (MMP)1, osteopontin (OPN), and pregnancy-specific beta-1-glycoprotein (PSG)9 were significantly increased in HCC patients. The overall performance of MMP1 and OPN in the diagnosis of HCC remained greater than that of AFP. In addition, this study represents the first report of MMP1 as a biomarker with a higher sensitivity and specificity than AFP. Thus, this study provides a valuable resource of the HCC secretome with the potential to investigate serological biomarkers. MMP1 and OPN could be used as novel biomarkers for the early detection of HCC and to improve the sensitivity of biomarkers compared with AFP.

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.

Tetrahymena Gene Expression Database (TGED):A resource of microarray data and co-expression analyses for Tetrahymena

Tetrahymena thermophila is a model eukaryotic organism. Functional genomic analyses in Tetrahymena present rich opportunities to address fundamental questions of cell and molecular biology. The Tetrahymena Gene Expression Database (TGED; available at http://tged.ihb.ac.cn) is the first expression database of a ciliated protozoan. It covers three major physiological and developmental states: growth, starvation, and conjugation, and can be accessed through a user-friendly web interface. The gene expression profiles and candidate co-expressed genes for each gene can be retrieved using Gene ID or Gene description searches. Descriptions of standardized methods of sample preparation and the opportunity to add new Tetrahymena microarray data will be of great interest to the Tetrahymena research community. TGED is intended to be a resource for all members of the scientific research community who are interested in Tetrahymena and other ciliates.