A mapping of an ensemble of mitochondrial sequences for various organisms into 3D space based on the word composition

To visualize a bird's-eye view of an ensemble of mitochondrial genome sequences for various species, we recently developed a novel method of mapping a biological sequence ensemble into Three-Dimensional (3D) vector space. First, we represented a biological sequence of a species s by a word-composition vector x(s), where its length ∣x(s)∣represents the sequence length, and its unit vector x(s)/∣x(s)∣represents the relative composition of the K-tuple words through the sequence and the size of the dimension, N=4(K), is the number of all possible words with the length of K. Second, we mapped the vector x(s) to the 3D position vector y(s), based on the two following simple principles: (1) ∣y(s)∣=∣x(s)∣and (2) the angle between y(s) and y(t) maximally correlates with the angle between x(s) and x(t). The mitochondrial genome sequences for 311 species, including 177 Animalia, 85 Fungi and 49 Green plants, were mapped into 3D space by using K=7. The mapping was successful because the angles between vectors before and after the mapping highly correlated with each other (correlation coefficients were 0.92-0.97). Interestingly, the Animalia kingdom is distributed along a single arc belt (just like the Milky Way on a Celestial Globe), and the Fungi and Green plant kingdoms are distributed in a similar arc belt. These two arc belts intersect at their respective middle regions and form a cross structure just like a jet aircraft fuselage and its wings. This new mapping method will allow researchers to intuitively interpret the visual information presented in the maps in a highly effective manner.     

Dissecting of the FHB resistance QTL on the short arm of wheat chromosome 2D using a comparative genomic approach: from QTL to candidate gene

Colinearity in gene content and order between rice and closely related cereal crops has been a powerful tool for gene identification. Using a comparative genomic approach, we have identified the rice genomic region syntenous to the region of the short arm of wheat chromosome 2D, on which quantitative trait loci (QTLs) for Fusarium head blight (FHB) resistance and for controlling accumulation of the mycotoxin deoxynivalenol (DON) are closely located. Utilizing markers known to reside near the FHB resistance QTL and data from several wheat genetic maps, we have limited the syntenous region to 6.8 Mb of the short arm of rice chromosome 4. From the 6.8-Mb sequence of rice chromosome 4, we found three putative rice genes that could have a role in detoxification of mycotoxins. DNA sequences of these putative rice genes were used in BLAST searches to identify wheat expressed sequence tags (ESTs) exhibiting significant similarity. Combined data from expression analysis and gene mapping of wheat homologues and results of analysis of DON accumulation using doubled haploid populations revealed that a putative gene for multidrug resistance-associated protein (MRP) is a possible candidate for the FHB resistance and/or DON accumulation controlling QTLs on wheat chromosome 2DS and can be used as a molecular marker to eliminate the susceptible allele when the Chinese wheat variety Sumai 3 is used as a resistance source. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A novel giant gene CSMD3 encoding a protein with CUB and sushi multiple domains: a candidate gene for benign adult familial myoclonic epilepsy on human chromosome 8q23.3-q24.1

We identified a novel giant gene encoding a transmembrane protein with CUB and sushi multiple domains on the human chromosome 8q23.3-q24.1 in which benign adult familial myoclonic epilepsy type 1 (BAFME1/FAME, OMIM:601068) has been mapped. This giant gene consists of 73 exons and spans over 1.2Mb on the genomic DNA region. It showed significant homology to two genes, CSMD1 gene on 8p23 and CSMD2 gene on 1p34, at reduced amino acid sequence level and hence we designated as CSMD3. The CSMD3 gene was expressed mainly in adult and fetal brains. We performed mutation analysis on the CSMD3 gene for seven patients with BAFME1/FAME, but no mutation was found in the coding sequence of the CSMD3 gene. Comparative genomic analysis revealed a conserved family of CSMD genes in the mouse and fugu genomes. Possible functions of the CSMD gene family are discussed.     

B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes

The crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 A resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram-positive and Gram-negative bacteria. The deduced amino acid sequence reveals the presence of an N-terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys-containing motif of hitherto unknown structure. As the wild-type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112-residue-long C-terminal domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology.     

Theoretical 3D model of histamine N-methyltransferase: insights into the effects of a genetic polymorphism on enzymatic activity and thermal stability

Histamine N-methyltransferase (HNMT) catalyzes the N-methylation of histamine in mammals. The experimentally determined HNMT three-dimensional (3D) structure is not available. However, there is a common genetic polymorphism for human HNMT (Thr105Ile) that reduces enzymatic activity and is a risk factor for asthma. To obtain insights into mechanisms responsible for the effects of that polymorphism on enzymatic activity and thermal stability, we predicted the 3D structure of HNMT using the threading method and molecular dynamics simulations in water. Herein, we report a theoretical 3D model of human HNMT which reveals that polymorphic residue Thr105Ile is located in the turn between a beta strand and an alpha helix on the protein surface away from the active site of HNMT. Ile105 energetically destabilizes folded HNMT because of its low Chou-Fasman score for forming a turn conformation and the exposure of its hydrophobic side chain to aqueous solution. It thus promotes the formation of misfolded proteins that are prone to the clearance by proteasomes. This information explains, for the first time, how genetic polymorphisms can cause enhanced protein degradation and why the thermal stability of allozyme Ile105 is lower than that of Thr105. It also supports the hypothesis that the experimental observation of a significantly lower level of HNMT enzymatic activity for allozyme Ile105 than that with Thr105 is due to a decreased concentration of allozyme Ile105, but not an alternation of the active-site topology of HNMT caused by the difference at residue 105.     

LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value

Searching for protein structure-function relationships using three-dimensional (3D) structural coordinates represents a fundamental approach for determining the function of proteins with unknown functions. Since protein structure databases are rapidly growing in size, the development of a fast search method to find similar protein substructures by comparison of protein 3D structures is essential. In this article, we present a novel protein 3D structure search method to find all substructures with root mean square deviations (RMSDs) to the query structure that are lower than a given threshold value. Our new algorithm runs in O(m + N/m(0.5)) time, after O(N log N) preprocessing, where N is the database size and m is the query length. The new method is 1.8-41.6 times faster than the practically best known O(N) algorithm, according to computational experiments using a huge database (i.e., >20,000,000 C-alpha coordinates).     

Microcirculation in the murine liver: a computational fluid dynamic model based on 3D reconstruction from in vivo microscopy

The liver is organized in hexagonal functional units – termed lobules – characterized by a rather peculiar blood microcirculation, due to the presence of a tangled network of capillaries – termed sinusoids. A better understanding of the hemodynamics that governs liver microcirculation is relevant to clinical and biological studies aimed at improving our management of liver diseases and transplantation.Herein, we built a CFD model of a 3D sinusoidal network, based on in vivo images of a physiological mouse liver obtained with a 2-photon microscope. The CFD model was developed with Fluent 16.0 (ANSYS Inc., Canonsburg, PA), particular care was taken in imposing the correct boundary conditions representing a physiological state. To account for the remaining branches of the sinusoids, a lumped parameter model was used to prescribe the correct pressure at each outlet. The effect of an adhered cell on local hemodynamics is also investigated for different occlusion degrees.The model here proposed accurately reproduces the fluid dynamics in a portion of the sinusoidal network in mouse liver. Mean velocities and mass flow rates are in agreement with literature values from in vivo measurements. Our approach provides details on local phenomena, hardly described by other computational studies, either focused on the macroscopic hepatic vasculature or based on homogeneous porous medium model.     

Allergome: the characterization of allergens based on a 2D gel electrophoresis approach

Type I hypersensitivity reactions are in constant progression in industrialized countries. The physiopathologic mechanism of these diseases implicates the production of specific immunoglobulin (Ig)E to allergenic molecules, their binding to the Fcε receptor on the surface of mast cells and basophils, and the release of inflammatory mediators when allergens are introduced into the body and crosslink with the IgE bound to the cell surface. An allergen is defined as a molecule that induces the production of, and binds to, IgE. The identification of the allergenic molecules is an important goal to improve diagnosis and treatment of allergy. This characterization aims to extract proteins from the allergenic source, to analyze IgE specificity by immunoblotting and to identify the proteins that bind IgE.     

基于文献计量的公园绿地可达性分析

公园绿地是城市生态系统和绿色基础设施的重要组成部分。可达性作为衡量城市公园绿地空间布局合理性的重要指标,是近年相关学科研究的热点。为全面了解国际期刊上有关公园绿地可达性研究的发展脉络和前沿动态,本文采用科学知识图谱和文献计量法,以"公园可达性"、"绿地可达性"等为主题,提取到了Web of Science核心数据库国际期刊收录的262篇相关文献,并基于关键词、作者、期刊分布和文献引用等情况,利用CiteSpace工具进行了可视化数据统计分析。结果表明：（1）随着时间的演进,文献数量呈现出跨越式增长,研究方法和内容日趋丰富,涵盖了风景园林、城乡规划、地理学、社会学、医学等相关学科;（2）研究热点不断发生变化,呈现出由前期着重探讨公园绿地可达性概念、内涵转向中后期着重关注公共健康、环境正义话题的变化趋势;（3）研究视角日趋丰富和不断深化,饮食、肥胖、体力活动、公共健康等一系列相关的话题已成为公园绿地可达性研究的热点。对国际期刊上公园绿地可达性研究的梳理总结可为我国公园绿地的规划研究和建设实践提供启示。     

Sporadic Creutzfeldt–Jakob disease subtype‐specific alterations of the brain proteome: Impact on Rab3a recycling

Sporadic Creutzfeldt–Jakob disease (sCJD) is characterized by wide clinical and pathological variability, which is mainly influenced by the conformation of the misfolded prion protein, and by the methionine and valine polymorphism at codon 129 of the prion protein gene. This heterogeneity likely implies differences in the molecular cascade that leads to the development of certain disease phenotypes. In this study, we investigated the proteome of the frontal cortex of patients with the two most common sCJD subtypes (MM1 and VV2) using 2D‐DIGE and MS. Analysis of 2D maps revealed that 46 proteins are differentially expressed in the sCJD. Common differential expression was detected for seven proteins, four showed opposite direction of differential expression, and the remaining ones displayed subtype‐specific alteration. The highest number of differentially expressed proteins was associated with signal transduction and neuronal activity. Moreover, functional groups of proteins involved in cell cycle and death, as well as in structure and motility included subtype‐specific expressed proteins exclusively. The expression of Rab GDP dissociation inhibitor alpha, which regulates Rab3a‐mediated neurotransmitter release, was affected in both sCJD subtypes that were analyzed. Therefore, we also investigated as to whether Rab3a recycling is altered. Indeed, we found an accumulation of the membrane‐associated form, thus the active one, which suggests that dysfunction of the Rab3a‐mediated exocytosis might be implicated in sCJD pathology.     

重力对锥形血管中血流压力的影响——基于考虑体位改变的三维流固耦合数学模型

重力是体位改变过程中最基本的生物力学刺激因素．血流压力是表征心血管功能状态的一个基本指标．目前,体位改变影响心血管系统的确切内部机制尚不清楚．为此,采用在流体和固体方程中分别引入体力项的方法,建立一个基于血流动力学概念的三维流固耦合数学模型,用以研究体位改变,确切量化重力对血流压力的影响．通过数值计算,得到以下结果．水平卧位条件下：a．单一血管中血流压力由无重力影响的轴对称二维分布变为重力影响下的三维不对称分布;b．随着进出口压差由小变大,重力对压力分布和极值的影响由大变小,当压差值分别达到10 665.6 Pa(80 mmHg)和2 666.4 Pa(20 mmHg)时,重力的影响就不再随进出口压差增大而变化;对三维单一流体,重力影响的总体趋势类似．对正、倒直立位,压力均为二维轴对称分布,其重力影响强度约为水平卧位的2倍以上．结果表明：基于血流动力学概念,引入体力项,建立三维流固耦合模型为研究体位改变提供了一种新思路,重力对单一血管中血流压力分布和大小的影响因体位不同而不同,并与进出口压差密切相关,提示,若血管进出口压差较小,忽略重力影响,不考虑体位改变,以二维轴对称模型来研究血管中血流状态,须谨慎解释所得结果．     

基于微粒群-马尔科夫复合模型的生态空间预测模拟——以长株潭城市群为例

生态空间具有重要的生态功能,对生态空间进行科学预测模拟可为保护国土空间生态安全提供决策依据。利用Arc GIS及MATLAB软件,在生态空间风险评价的基础上构建了微粒群-马尔科夫复合模型,并以长株潭城市群为研究区,基于2013年土地利用现状数据,对2020年的生态空间进行了预测模拟,最后在此基础上提出了生态空间重构的基本思路。结果表明:1)微粒群-马尔科夫复合模型(PSO-Markov)构建的基本步骤为:第一步:粒子的选择与设计,以2000 m×2000 m的正方形单元作为基本粒子。第二步:粒子的初始化设定,根据生态空间风险由低到高的原则进行选择。第三步:适应度函数的建立,用生态空间的风险值来确定生态空间的空间格局。第四步:空间位置的更新,根据自身的历史最优值及粒子群的全局最优值进行速度和位置更新。2)微粒群-马尔科夫复合模型(PSO-Markov)是一种土地利用格局预测的新途径,生态空间的数量规模可以通过改进后的马尔科夫模型进行预测,生态空间的格局可以通过微粒群模型进行预测。3)微粒群-马尔科夫复合模型具有4个特点:第一、数量预测较为合理。第二、搜索范围大、较好地考虑到局部对全局的影响。第三、受问题维数变化影响小,在求解多目标问题时具有明显优势。第四、收敛时间短、运算速度快、易于实现。4)2020年,长株潭城市群的生态空间总体数量减少,其中林地和未利用地面积变化最明显,空间变化主要集中分布在西南部地区。生态空间总面积减小的主要原因是建设用地的扩张。因此,要控制城市群的人口密度,优化城市群生产—生活—生态的数量结构及空间布局,尤其要合理规划与利用城市建设用地,充分发挥水体与未利用地的生态价值,重点保护好生态源地、廊道及关键结点,构建结构合理、功能齐全的生态网络系统,提高系统的生态服务价值功能,要在规划的指导下合理调整城市群的城乡局部空间结构,保护生态环境,提高生境质量和景观多样性。这是今后一段时期面临的主要任务。     

A framework for querying a database for structural information on 3D images of macromolecules: A web-based query-by-content prototype on the BioImage macromolecular server

Nowadays we are experiencing a remarkable growth in the number of databases that have become accessible over the Web. However, in a certain number of cases, for example, in the case of BioImage, this information is not of a textual nature, thus posing new challenges in the design of tools to handle these data. In this work, we concentrate on the development of new mechanisms aimed at "querying" these databases of complex data sets by their intrinsic content, rather than by their textual annotations only. We concentrate our efforts on a subset of BioImage containing 3D images (volumes) of biological macromolecules, implementing a first prototype of a "query-by-content" system. In the context of databases of complex data types the term query-by-content makes reference to those data modeling techniques in which user-defined functions aim at "understanding" (to some extent) the informational content of the data sets. In these systems the matching criteria introduced by the user are related to intrinsic features concerning the 3D images themselves, hence, complementing traditional queries by textual key words only. Efficient computational algorithms are required in order to "extract" structural information of the 3D images prior to storing them in the database. Also, easy-to-use interfaces should be implemented in order to obtain feedback from the expert. Our query-by-content prototype is used to construct a concrete query, making use of basic structural features, which are then evaluated over a set of three-dimensional images of biological macromolecules. This experimental implementation can be accessed via the Web at the BioImage server in Madrid, at http://www.bioimage.org/qbc/index.html.     

Open questions on the 3D structures of collagen containing vertebrate mineralized tissues: A perspective

Our current understanding of the structures of vertebrate mineralized tissues is largely based on light microscopy/histology and projections of 3D structures onto 2D planes using electron microscopy. We know little about the fine details of these structures in 3D at the length scales of their basic building blocks, the inherent variations of structure within a tissue and the cell-extracellular tissue interfaces. This limits progress in understanding tissue formation, relating structure to mechanical and metabolic functions, and obtaining deeper insights into pathologies and the evolution of these tissues. In this perspective we identify and discuss a series of open questions pertaining to collagen containing vertebrate mineralized tissues that can be addressed using appropriate 3D structural determination methods. By so doing we hope to encourage more research into the 3D structures of mineralized vertebrate tissues.     

基于遥感的城市绿色空间演化过程的温度效应研究——以福州主城区为例

以福州主城区绿色空间为研究对象,基于遥感手段,研究绿色空间的复杂演化对地表温度扰动的影响。研究发现:(1)1993—2016年,福州主城区下垫面绿色空间损失和扩张面积分别为46.50km²和4.73km²,面积差达到41.77km²。(2)不同温度区的分布格局发生了较大变化,冷岛区面积大幅减少,热岛区面积显著增加。从各温度等级内的土地利用分布来看,低温区内分布较多湿地和水体,次低温区以林/草地为主。(3)城市热岛重心与城市重心的迁移方向有关;而城市冷岛重心与城市绿色空间的分布关系密切。(4)不同绿色空间演化过程引起的降温效应大小依次为:绿色空间扩张>绿色空间不变>绿色空间交换>绿色空间损失。绿色空间扩张带来的平均降温幅度约为5.0℃,而绿色空间损失引起的平均增温约为7.0℃。不同的演化过程下,通过增加等面积的绿色空间,并不能抵消先前绿色空间损失带来的升温。因此,科学合理的绿色空间规划对于有效缓解城市热岛至关重要。     

Hoverflies (Diptera: Syrphidae) benefit from a cultivation of the bioenergy crop Silphium perfoliatum L. (Asteraceae) depending on larval feeding type,landscape composition and crop management

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Determination of n-3 HUFA content in Atlantic salmon flesh based on the lipid content, morphometric measurements and blood fatty acid composition: A modeling approach

Fish are the most important source of n-3 highly unsaturated fatty acids (HUFA) in the human diet and, with declining wild stocks, an increasing proportion is being provided by aquaculture. Paradoxically, aquaculture fish diets have traditionally incorporated fish oil and meal derived from wild fisheries. Continued aquaculture development requires fish oil to be replaced with vegetable oils, the only sustainable alternative. However, vegetable oils lack n-3 HUFA and so flesh from fish reared on these diets can also have reduced n-3 HUFA and thus reduced nutritional quality. This accepted, the flesh n-3 HUFA content should be an economically important trait, however to be included in the breeding goal the trait must be measurable. In the present study, we investigated whether the flesh n-3 HUFA content of salmon can be estimated in a non-fatal way. We showed that a general regression model based on flesh lipid content, morphometric and blood fatty acid measurements could estimate and predict flesh n-3 HUFA content. This would allow a choice from a range of selection methods, including mass selection or within-family selection, if this important flesh quality trait is to be included in future salmon breeding programmes.