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.

牛传染性鼻气管炎病毒gB蛋白研究进展

牛传染性鼻气管炎病毒能引起牛多系统感染,是导致养牛业重大经济损失的一种重要病原。该病毒是有囊膜的双股DNA病毒,病毒囊膜蛋白在病毒致病中发挥了重要作用,其中gB蛋白对病毒的吸附、侵入、复制和细胞间扩散是必需的,可刺激机体产生大量的中和抗体。对gB蛋白的研究不仅是理解病毒分子生物学功能特征的需要,而且在临床诊断和疾病预防中也具有重要意义。文章就gB蛋白的结构特征、生物学功能以及在免疫学和诊断方面的研究做了综述,并对上述方面进行了展望。

Plant F-Box Protein and Its Biological Function

F-box protein is an expanding family member of eukaryotic protein characterized by an F-box motif which has specificity of substrate recognition in the ubiquitin-mediated proteolysis.These proteins have been proved to be critical for many physiological processes,such as cell-cycle transition,signal transduction,gene transcription,male sterility,programmed cell death （PCD） and so on.This paper mainly introduces the biological functions of the known F-box proteins and the analysis of F-box gene phylogeny.

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 IAP family: endogenous caspase inhibitors with multiple biological activities

IAPs (inhibitors of apoptosis) are a family of proteins containing one or more characteristic BIR domains. These proteins have multiple biological activities that include binding and inhibiting caspases, regulating cell cycle progression, and modulating receptor-mediated signal transduction. Our recent studies found the IAP family members XIAP and c-IAP1 are ubiquitinated and degraded in proteasomes in response to apoptotic stimuli in T cells, and their degradation appears to be important for T cells to commit to death. In addition to three BIR domains, each of these IAPs also contains a RING finger domain.We found this region confers ubiquitin protease ligase (E3) activity to IAPs, and is responsible for the auto-ubiquitination and degradation of IAPs after an apoptotic stimulus. Given the factthat IAPs can bind a variety of proteins, such as caspases and TRAFs, it will be of interest to characterize potential substrates of the E3 activity of IAPs and the effects of ubiquitination byIAPs on signal transduction, cell cycle, and apoptosis.

Is kinase activity essential for biological functions of BRI1？

Brassinosteroids （BRs） are a major group of plant hormones that regulate plant growth and development. BRI1, a protein localized to the plasma membrane, functions as a BR receptor and it has been proposed that its kinase activity has an essential role in BR-regulated plant growth and development. Here we report the isolation and molecular characterization of a new allele of bril, bril-301, which shows moderate morphological phenotypes and a reduced response to BRs under normal growth conditions. Sequence analysis identified a two-base alteration from GG to AT, resulting in a conversion of 989G to 9891 in the BRI1 kinase domain. An in vitro assay of kinase activity showed that bril-301 has no detectable autophosphorylation activity or phosphorylation activity towards the BRI1 substrates TTL and BAK1. Furthermore, our results suggest that bril-301, even with extremely impaired kinase activity, still retains partial function in regulating plant growth and development, which raises the question of whether BRI1 kinase activity is essential for BR-mediated growth and development in higher plants.

Significance of regenerating islet-derived type Ⅳ gene expression in gastroenterological cancers

The regenerating islet-derived members （Reg）, a group of small secretory proteins, which are involved in cell proliferation or differentiation in digestive organs, are upregulated in several gastrointestinal cancers, functioning as trophic or antiapoptotic factors. Regenerat- ing islet-derived type Ⅳ （RegⅣ）, a member of the Reg gene family, has been reported to be overexpressed in gastroenterological cancers. RegIV overexpression in tumor cells has been associated with carcinogen- esis, cell growth, survival and resistance to apoptosis. Cancer tissue expressing RegIV is generally associated with more malignant characteristics than that with- out such expression, and RegⅣ is considered a novel prognostic factor as well as diagnostic marker in some gastroenterological cancers. We previously investigated the expression levels of RegⅣ mRNA of 202 surgical colorectal cancer specimens with quantitative real-time reverse-transcriptase polymerase chain reaction and reported that a higher level of RegⅣ gene expression was a significant independent predictor of colorec- tal cancer. The biologic functions of RegⅣ protein in cancer tissue, associated with carcinogenesis, anti- apoptosis and invasiveness, are being elucidated by molecular investigations using transfection techniques or neutralizing antibodies of RegIV, and the feasibility of antibody therapy targeting RegIV is being assessed. These studies may lead to novel therapeutic strate- gies for gastroenterological cancers expressing RegⅣ. This review article summarizes the current information related to biological functions as well as clinical impor- tance of RegⅣ gene to clarify the significance of Reg~ expression in gastroenterological cancers.

Physiological diversity of orchids

The Orchidaceae is a diverse and wide spread family of flowering plants that are of great value in ornamental, medical, conservation, and evolutionary research. The broad diversity in morphology,growth form, life history, and habitat mean that the members of Orchidaceae exhibit various physiological properties. Epiphytic orchids are often characterized by succulent leaves with thick cell walls,cuticles, and sunken stomata, whereas terrestrial orchids possess rhizomes, corms, or tubers. Most orchids have a long juvenile period, slow growth rate, and low photosynthetic capacity. This reduced photosynthetic potential can be largely explained by CO_2 diffusional conductance and leaf internal structure. The amount of light required for plant survival depends upon nutritional mode, growth form,and habitat. Most orchids can adapt to their light environments through morphological and physiological adjustments but are sensitive to sudden changes in irradiance. Orchids that originate from warm regions are susceptible to chilling temperatures, whereas alpine members are vulnerable to high temperatures.For epiphytic orchids, rapid water uptake by the velamen radicum, water storage in their pseudobulbs and leaves, slow water loss, and Crassulacean Acid Metabolism contribute to plant-water balance and tolerance to drought stress. The presence of the velamen radicum and mycorrhizal fungi may compensate for the lack of root hairs, helping with quick absorbance of nutrients from the atmosphere.Under cultivation conditions, the form and concentration of nitrogen affect orchid growth and flowering.However, the limitations of nitrogen and phosphorous on epiphytic orchids in the wild, which require these plants to depend on mycorrhizal fungi for nutrients throughout the entire life cycle, are not clearly understood. Because they lack endosperm, seed germination depends upon obtaining nutrients via mycorrhizal fungi. Adult plants of some autotrophic orchids also gain carbon, nitrogen, phosphorus, and other elements from their mycorrhizal partners. Future studies should examine the mechanisms that determine slow growth and flower induction, the physiological causes of variations in flowering behavior and floral lifespan, the effects of nutrients and atmospheric-nitrogen deposition, and practical applications of mycorrhizal fungi in orchid cultivation.

Functional imaging and endoscopy

The emergence of endoscopy for the diagnosis of gastrointestinal diseases and the treatment of gastrointestinal diseases has brought great changes.The mere observation of anatomy with the imaging mode using modern endoscopy has played a significant role in this regard.However,increasing numbers of endoscopies have exposed additional deficiencies and defects such as anatomically similar diseases.Endoscopy can be used to examine lesions that are difficult to identify and diagnose.Early disease detection requires that substantive changes in biological function should be observed,but in the absence of marked morphological changes,endoscopic detection and diagnosis are difficult.Disease detection requires not only anatomic but also functional imaging to achieve a comprehensive interpretation and understanding.Therefore,we must ask if endoscopic examination can be integrated with both anatomic imaging and functional imaging.In recent years,as molecular biology and medical imaging technology have further developed,more functional imaging methods have emerged.This paper is a review of the literature related to endoscopic optical imaging methods in the hopes of initiating integration of functional imaging and anatomical imaging to yield a new and more effective type of endoscopy.

High-resolution 3D Structures Reveal the Biological Functions of Reoviruses

Viruses in the family Reoviridae are non-enveloped particles comprising a segmented double-stranded RNA genome surrounded by a two-layered or multi-layered icosahedral protein capsid.These viruses are classified into two sub-families based on their particle structural organization.Recent studies have focused on high-resolution three-dimensional structures of reovirus particles by using cryo-electron microscopy (cryo-EM) to approach the resolutions seen in X-ray crystallographic structures.The results of cryo-EM image reconstructions allow tracing of most of the protein side chains,and thus permit integration of structural and functional information into a coherent mechanism for reovirus assembly and entry.

Understanding biological functions through molecular networks

The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.

Correlation of serum leptin levels with anthropometric and metabolic parameters and biochemical liver function in Chinese patients with chronic hepatitis C virus infection

AIM: To determine serum leptin levels and investigate their correlations with anthropometric and metabolic parameters and biochemical liver function in patients with chronic hepatitis C virus (HCV) infection and their potential clinical implications.METHODS: Forty-two chronic HCV-infected patients without anti-viral treatment were enrolled in this study, 30 patients had chronic hepatitis C, 10 had cirrhosis, and 2 had hepatocellular carcinoma (HCC). Thirty age- and sex-matched healthy individuals served as controls. Serum leptin levels were determined by ELISA. The biochemical liver function and serum lipids were determined at the same time. The height and body weight of patients and controls were measured, and body mass index (BMI) and body fat were calculated simultaneously. The correlations of serum leptin levels with anthropometric and metabolic parameters and biochemical liver function were assessed statistically.RESULTS: The mean of serum leptin levels in patients with chronic hepatitis C, HCV-associated cirrhosis, HCVassociated HCC and control groups was (6.13±3.94),(5.25±4.21), (4.17±0.28), and (3.59±3.44) ng/mL, respectively. The serum leptin level in patients with chronic hepatitis C was significantly higher than that in controls. The serum leptin levels between cirrhotic patients and controls and between male and female cirrhotic patients had no significant difference. Serum leptin levels were positively-correlated with body fat, BMI, and apolipoprotein B (Apo B) in patients with chronic HCV infection. The serum alanine aminotransferase (ALT) levels were closelycorrelated with BMI in patients with chronic hepatitis C. CONCLUSION: HCV infection interferes with fat and lipid metabolism in patients with chronic HCV infection and leptin may play a role in hepatosteatosis.

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.

MULTIVARIATE ANALYSIS OF RELATIONSHIPS BETWEEN IODINE BIOLOGICAL EXPOSURE AND SUBCLINICAL THYROID DYSFUNCTIONS

Objective To assess the relationships between iodine biological exposure and subclinical thyroid dysfunctions. Methods The cross-sectional survey was performed to obtain the epidemiologic data of population in three communities with different iodine biological exposure： mild iodine deficiency [median urinary iodine concentration （MUI） of 50-99 μg/L], more than adequate iodine intake （MUI of 200-299 μg/L）, and excessive iodine intake （MUI over 300 μg/L）. Univariate and multivariate analysis （logistic regression analysis） were used to analyze the risk factors of subclinical hypothyroidism and subclinical hyperthyroidism. Logistic regression analysis with sex and age controlled suggested that more than adequate iodine intake （OR = 3.172, P = 0.0004） and excessive iodine intake （OR = 6.391, P = 0.0001） increased the risk of subclinical hypothyroidism, while excessive iodine intake decreased the risk of subclinical hyperthyroidism （OR = 0.218, P= 0.0001）. Logistic regression analysis including interaction of iodine intake and antibodies [tryroid peroxidase antibody （TPOAb） and thyroglobulin antibody （TgAb）] suggested that excessive iodine intake was an independent risk factor of subclinical hypothyroidism （OR = 6.360, P= 0.0001）, but independent protect factor of subclinical hyperthyroidism （OR = 0.193, P= 0.0001）. More than adequate iodine intake and it＇s interaction with TgAb increased the risk of subclinical hypothyroidism independently, in addition, it decreased the risk of subclinical hyperthyroidism at the present of TPOAb. Conclusion Both excessive iodine intake and more than adequate iodine intake could increase risk of subclinical hypothyroidism, supplement of iodine should be controlled to ensure MUI within the safe range.

Rheological and Structural Properties of Sea Cucumber Stichopus japonicus During Heat Treatment

Changes in tissue structure, rheological properties and water content of raw and heated sea cucumber meat were studied. Sea cucumber Stichopus japonicus was heated at 25℃, 70℃ and 100℃ water for 5 min. The structural changes were observed using a light microscope and the rheological parameters （rupture strength, adhesive strength and deformation） determined using a texture meter. Microscopic photograph revealed that the structural change of heated meat was greater than that of raw meat. The rupture strength, adhesive strength and deformation of raw meat were smaller than those of the heated meat. Meanwhile, rheological parameters showed positive correlation with heating temperature. These changes are mainly caused by thermal denaturation and gelatinization of collagen during heating. These changes were also evidenced in observations using a light microscope and differential scanning calorimetry.

BIOMECHANICAL STUDY ON UNILATERAL SINGLE-PLANE EXTERNAL FIXER

Six tibias removed from 30-40 years old males, who died in an accident for in less than 12 hours, were osteotomized at one-third supra-medium segment. They were fixed by an unilateral adjustable external fixer (UAEF), to be used as a model of external fixation of tibial fracture (MEFTF). The compression. tension, torsion, antero-posterior and lateral bending strength, and the strength for vertically extracting the pins from the tibia were determined in the MEFTF. Within a certain range of load, the correlation of strain to stress was basically a linear relationship. These data provide a theoretical basis of biomechanics for the improvement of UAEF and for early exercises of fracture patients, such as extend-bending of the joint.raising the limb and walking with a walking stick.

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.

New Representation of Maxwell Relation

A new representation of the Maxwell relation for phase transformation is given, which is expressed in simpler form and has more direct physical meaning than the original Maxwell relation. It is shown that the physical conjecture for the so-called "lock-up" condition suggested by Jensen (1999) is correct, but the equation for the "lock-up" condition suggested by Jensen (1999) is not. Numerical examples also demonstrate that the application of the new representation of Maxwell relation gives exactly the same solutions as the ones with application of the original Maxwell relation and, however, application of the "lock-up" condition gives no real solutions.

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.