黄土高原半干旱偏旱区草粮轮作田土壤水分恢复效应模拟

采用实地调查和EPIC模型相结合的方法,模拟研究了黄土高原半干旱偏旱区不同草粮轮作模式的土壤水分恢复效应.结果表明：多年生苜蓿地和苜蓿翻耕后种植粮食作物农田0～10 m土层土壤湿度调查值与模拟值间的相关系数均超过0.9（P<0.01）,相对均方根误差在0.05～0.16,相对误差均低于10%;模拟与实测的土壤湿度剖面分布变化趋势一致.在黄土高原半干旱偏旱区,苜蓿地深层土壤干层恢复难度较大,在种植苜蓿期间应避免8～10 m土层土壤湿度降到5.7%以下.苜蓿地适宜种植年限为4～6 a,最长不应超过8 a.苜蓿翻耕后适宜采用马铃薯→马铃薯→春小麦轮作模式进行土壤水分恢复,32～33 a后可以再次种植苜蓿.     

The use of race, ethnicity and ancestry in human genetic research

Post-Human Genome Project progress has enabled a new wave of population genetic research, and intensified controversy over the use of race/ethnicity in this work. At the same time, the development of methods for inferring genetic ancestry offers more empirical means of assigning group labels. Here, we provide a systematic analysis of the use of race/ethnicity and ancestry in current genetic research. We base our analysis on key published recommendations for the use and reporting of race/ethnicity which advise that researchers: explain why the terms/categories were used and how they were measured, carefully define them, and apply them consistently. We studied 170 population genetic research articles from high impact journals, published 2008-2009. A comparative perspective was obtained by aligning study metrics with similar research from articles published 2001-2004. Our analysis indicates a marked improvement in compliance with some of the recommendations/guidelines for the use of race/ethnicity over time, while showing that important shortfalls still remain: no article using 'race', 'ethnicity' or 'ancestry' defined or discussed the meaning of these concepts in context; a third of articles still do not provide a rationale for their use, with those using 'ancestry' being the least likely to do so. Further, no article discussed potential socio-ethical implications of the reported research. As such, there remains a clear imperative for highlighting the importance of consistent and comprehensive reporting on human populations to the genetics/genomics community globally, to generate explicit guidelines for the uses of ancestry and genetic ancestry, and importantly, to ensure that guidelines are followed.     

Household obesity prevention: Take Action--a group-randomized trial

The purpose of the present study was to evaluate an intervention to prevent weight gain among households (HHs) in the community. Ninety HHs were randomized to intervention or control group for 1 year. Intervention consisted of six face-to-face group sessions, placement of a television (TV) locking device on all home TVs, and home-based intervention activities. Measures were collected in person at baseline and 1 year. Weight, height, eating behaviors, physical activity (PA), and TV viewing were measured among HH members ages ≥ 12 years. Follow-up rate at 1 year was 96%. No significant intervention effects were observed for change in HH BMI-z score. Intervention HHs significantly reduced TV viewing, snacks/sweets intake, and dollars per person spent eating out, and increased (adults only) PA and self-weighing frequency compared with control HHs. A 1 year obesity prevention intervention targeting entire HHs was effective in reducing TV viewing, snack/sweets intake and eating out purchases. Innovative methods are needed to strengthen the home food environment intervention component. Longer intervention durations also need to be evaluated.     

A Partial Least Squares based algorithm for parsimonious variable selection

Background

We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases.

Results

We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances.

Conclusions

Several biologically relevant special cases of the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies.     

Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition

The Pyrococcus horikoshii OT3 genome contains a gene (PH0601 or nikR) encoding a protein (PhNikR) that shares 33.8% amino acid sequence identity with Escherichia coli nickel responsive repressor NikR (EcNikR), including many residues that are functionally important in the E.coli ortholog. We succeeded in crystallization and structural characterization of PhNikR in the apo form and two nickel bound forms that exhibit different conformations, open and closed. Moreover, we have identified a putative "low-affinity" nickel-binding pocket in the closed form. This binding site has unusual nickel coordination and exhibits high sensitivity to phosphate in the crystal structure. Analysis of the PhNikR structures and structure-based mutational studies with EcNikR reveals a plausible mechanism of nickel-dependent promoter recognition by the NikR family of proteins.     

Crystal structure of a purine/pyrimidine phosphoribosyltransferase-related protein from Thermus thermophilus HB8

Adenine phosphoribosyltransferase (APRTase) is a widely distributed enzyme involved in the salvage of adenine to form an adenine nucleotide. We crystallized and determined the X-ray crystallographic structure of a purine/pyrimidine phosphoribosyltransferase-related protein from the thermophilic bacterium, Thermus thermophilus HB8. The crystal space group was C2 with unit cell dimensions of a = 167.42 A, b = 61.41 A, c = 102.39 A, beta = 94.0 degrees . Initial phases were determined to 2.6 A using the multiple wavelength anomalous dispersion method and selenomethionine substituted protein (Se-MAD), and refined using a 1.9 A "native" data set. The asymmetric unit contains two pairs of identical dimers, each related by noncrystallographic two-fold symmetry. The fifth monomer forms a similar dimer across a crystallographic two-fold axis. These dimers appear to be the biological unit with both monomers contributing to an unusual highly charged arginine-rich bridge region separating the two active sites. Comparison with distantly related APRTases reveal similarities and differences of the active site.     

Nature, nurture and neurology: gene-environment interactions in neurodegenerative disease. FEBS Anniversary Prize Lecture delivered on 27 June 2004 at the 29th FEBS Congress in Warsaw

Neurodegenerative disorders, such as Huntington's, Alzheimer's, and Parkinson's diseases, affect millions of people worldwide and currently there are few effective treatments and no cures for these diseases. Transgenic mice expressing human transgenes for huntingtin, amyloid precursor protein, and other genes associated with familial forms of neurodegenerative disease in humans provide remarkable tools for studying neurodegeneration because they mimic many of the pathological and behavioural features of the human conditions. One of the recurring themes revealed by these various transgenic models is that different diseases may share similar molecular and cellular mechanisms of pathogenesis. Cellular mechanisms known to be disrupted at early stages in multiple neurodegenerative disorders include gene expression, protein interactions (manifesting as pathological protein aggregation and disrupted signaling), synaptic function and plasticity. Recent work in mouse models of Huntington's disease has shown that enriching the environment of transgenic animals delays the onset and slows the progression of Huntington's disease-associated motor and cognitive symptoms. Environmental enrichment is known to induce various molecular and cellular changes in specific brain regions of wild-type animals, including altered gene expression profiles, enhanced neurogenesis and synaptic plasticity. The promising effects of environmental stimulation, demonstrated recently in models of neurodegenerative disease, suggest that therapy based on the principles of environmental enrichment might benefit disease sufferers and provide insight into possible mechanisms of neurodegeneration and subsequent identification of novel therapeutic targets. Here, we review the studies of environmental enrichment relevant to some major neurodegenerative diseases and discuss their research and clinical implications.     

Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate

2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus protein (TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger alpha/beta domain and a smaller beta-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 angstroms. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.     

Expression analysis of the novel gene collagen triple helix repeat containing-1 (Cthrc1)

We recently identified collagen triple helix repeat containing-1 (Cthrc1) as a novel gene induced in adventitial fibroblasts after arterial injury. Cthrc1 is a 30 kDa secreted protein that has the ability to inhibit collagen matrix synthesis. Cthrc1 is also glycosylated and retains a signal sequence consistent with the presence of Cthrc1 in the extracellular space. In injured arteries and skin wounds, we have found Cthrc1 expression to be associated with myofibroblasts and sites of collagen matrix deposition. Furthermore, we demonstrated that Cthrc1 inhibits collagen matrix deposition in vitro. Using in situ hybridization and immunohistochemistry, we characterized the expression domains of Cthrc1 during murine embryonic development and in postnatal tissues. In mouse embryos, Cthrc1 was expressed in the visceral endoderm, notochord, neural tube, developing kidney, and heart. Abundant expression of Cthrc1 was observed in the developing skeleton, i.e., in cartilage primordia, in growth plate cartilage with exclusion of the hypertrophic zone, in the bone matrix and periostium. Bones from adults showed expression of Cthrc1 only in the bone matrix and periostium while the articular cartilage lacked expression. Cthrc1 is typically expressed at epithelial-mesenchymal interfaces that include the epidermis and dermis, basal corneal epithelium, airway epithelium, esophagus epithelium, choroid plexus epithelium, and meninges. In the adult kidney, collecting ducts and distal tubuli expressed Cthrc1. Collectively, the sites of Cthrc1 expression overlap considerably with those reported for TGF-beta family members and interstitial collagens. The present study provides useful information towards the understanding of potential Cthrc1 functions.