Key genes and functional coexpression modules involved in the pathogenesis of systemic lupus erythematosus

We performed a systematic review of genome‐wide gene expression datasets to identify key genes and functional modules involved in the pathogenesis of systemic lupus erythematosus (SLE) at a systems level. Genome‐wide gene expression datasets involving SLE patients were searched in Gene Expression Omnibus and ArrayExpress databases. Robust rank aggregation (RRA) analysis was used to integrate those public datasets and identify key genes associated with SLE. The weighted gene coexpression network analysis (WGCNA) was adapted to identify functional modules involved in SLE pathogenesis, and the gene ontology enrichment analysis was utilized to explore their functions. The aberrant expressions of several randomly selected key genes were further validated in SLE patients through quantitative real‐time polymerase chain reaction. Fifteen genome‐wide gene expression datasets were finally included, which involved a total of 1,778 SLE patients and 408 healthy controls. A large number of significantly upregulated or downregulated genes were identified through RRA analysis, and some of those genes were novel SLE gene signatures and their molecular roles in etiology of SLE remained vague. WGCNA further successfully identified six main functional modules involved in the pathogenesis of SLE. The most important functional module involved in SLE included 182 genes and mainly enriched in biological processes, including defense response to virus, interferon signaling pathway, and cytokine‐mediated signaling pathway. This study identifies a number of key genes and functional coexpression modules involved in SLE, which provides deepening insights into the molecular mechanism of SLE at a systems level and also provides some promising therapeutic targets.     

喜旱莲子草在增温背景下的密度制约与生长权衡

研究植株个体与种群数量的关系对探究植物的适应策略、理解植物入侵机理有重要意义。但多数研究着眼于常温处理下植株响应密度变化的生长权衡,对增温处理下植株的密度制约调节机理和常温与增温处理下响应密度变化的调节规律是否发生变化认识不足。以喜旱莲子草（Alternanthera philoxeroides）为研究对象,采用密度（1、5、9株/盆,37、186、335株/m²）和温度（常温、增温）双因素实验设计,探究了全球变暖背景下,密度制约与喜旱莲子草的关系、地上与地下部分的密度制约调节规律。结果表明：（1）地上构件特征与温度呈显著正相关关系（P<0.05）,地上构件特征和比叶面积表现出明显密度依赖性（P<0.05）。温度与种群密度及其交互作用对地下指标无显著影响（P>0.05）。（2）无论增温与否,随密度压力增加,根生物量分配比率增大,各构件平均生物量、茎生物量分配比率降低。叶生物量分配比率在各密度下维持恒定。（3）用生物量-密度异速指数γ衡量种群密度调控强弱。常温处理下,γ_leaf（-1.685） < γ_above-ground（-1.612） < γ_stem（-1.605） < γ _individual（-1.558） < γ_root（-1.524）,受密度制约调控强度的大小依次为：叶>地上>茎>个体>根。增温处理下,γ_stem（-2.075） < γ_above-ground（-2.038） < γ_individual（-1.982） < γ_leaf（-1.933） < γ_root（-1.800）,受密度制约调控强度的大小依次为：茎 > 地上 > 个体 > 叶 > 根。喜旱莲子草种群地上构件受密度的调节作用强于地下构件。由此可见,无论增温与否,喜旱莲子草种群地下资源的竞争能力随密度增加而增强,地上资源竞争能力随密度增加而减弱,喜旱莲子草地上部分调节强于地下部分,常温处理下,叶受密度制约作用更强,增温处理下,茎受密度制约最强。根受密度制约最弱。地上资源的竞争占主导地位。     

Cellulosomal carbohydrate-binding module from Clostridium josui binds to crystalline and non-crystalline cellulose,and soluble polysaccharides

To understand the lignocellulose degradation activity of the Clostridium josui cellulosome, a carbohydrate-binding module of the scaffoldin CjCBM3 was characterized. CjCBM3 shows binding to crystalline cellulose, non-crystalline cellulose and soluble polysaccharides. The binding isotherm of CjCBM3 to acid-swollen cellulose is best fitted by the Langmuir two-site model, suggesting that there are two CjCBM3 binding sites on acid-swollen cellulose with different affinities. The second site shows lower affinity and larger binding capacity, suggesting that the cellulosome is directly targeted to the cellulose surface with high affinity, where larger amounts of the cellulosome bind to cellulose with low affinity.     

FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks

The characterization of the interacting behaviors of complex biological systems is a primary objective in protein–protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected protein–protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in diseases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.     

Recognition of cellooligosaccharides by a family 28 carbohydrate-binding module

The crystal structures of a carbohydrate-binding module (CBM) family 28 domain of endoglucanase Cel5A from Clostridium josui have been determined in ligand-free and complex forms with cellobiose, cellotetraose, and cellopentaose as the first complex structures of this family. In the cleft of a β-sandwich fold, the ligands are recognized by stacking interactions and hydrogen bonds. Conformations of the bound cellooligosaccharides are similar to those in crystals and solution but clearly different from the cellulose structure. Interestingly, the glucan chain bound on CBM28 is in the opposite direction of that bound to CBM17, although these families share significant structural similarity.     

昆虫飞行模拟监控系统设计

本文根据昆虫飞行的特点,模拟昆虫飞行的实验装置,由飞行磨、单片机及微型计算机组成,编辑设计飞行监控软件,该程序分为三个模块：系统监控程序模块;时钟程序模块和信号处理程序模块。利用微机适时采集飞行数据,记录和分析监测结果,模拟昆虫的飞行速度和持续时间。     

Blood Group Antigen Recognition by a Solute-Binding Protein from a Serotype 3 Strain of Streptococcus pneumoniae

Streptococcus pneumoniae is a common bacterial pathogen that is well known for its ability to cause acute respiratory disease (pneumonia), ear infections, and other serious illnesses. This Gram-positive bacterium relies on its carbohydrate-metabolizing capabilities for full virulence in its host; however, the range of glycan targets that it can attack is presently not fully appreciated. S. pneumoniae is known to have a fucose utilization operon that in the TIGR4 strain plays a role in its virulence. Here we identify a second type of fucose utilization operon that is present in a subset of S. pneumoniae strains, including the serotype 3 strain SP3-BS71. This operon contains a transporter with a solute-binding protein, FcsSBP (fucose solute-binding protein), that interacts tightly (K_a ∼ 1 × 10⁶ M^− 1) and specifically with soluble A- and B-antigen trisaccharides but displays no selectivity between these two sugars. The structure of the FcsSBP in complex with the A-trisaccharide antigen, determined to 2.35 Å, reveals its mode of binding to the reducing end of this sugar, thus highlighting this protein's requirement for soluble blood group antigen ligands. Overall, this report exposes a heretofore unknown capability of certain S. pneumoniae strains to transport and potentially metabolize the histo-blood group antigen carbohydrates of its host.     

Rhogocytes in gastropod larvae: developmental transformation from protonephridial terminal cells

Rhogocytes, terminal cells of protonephridia, and podocytes of metanephridial systems share an architectural feature that creates an apparent sieving device. The sieve serves to ultrafilter body fluid during the excretion and osmoregulation process carried out by nephridial systems, but its function in rhogocytes is unclear. Rhogocytes are molluscan hemocoelic cells that appear to have various functions related to metabolism of metal ions, including synthesis of hemocyanin in some gastropods and metal detoxification in pteriomorph bivalves. A hypothesis that proposed developmental and possibly evolutionary conversion between protonephridial terminal cells and rhogocytes has never been further explored; indeed, information on the occurrence of rhogocytes in molluscan developmental stages is meager. We used transmission electron microscopy to show that rhogocytes are present within larvae of eight species of gastropods sampled from the three major gastropod clades with a feeding larval stage in the life history. In larvae of a heterobranch gastropod, a rhogocyte was located next to each terminal cell of a pair of protonephridia that flanked the foregut, whereas all six species of caenogastropod larvae and a neritimorph larva that we examined had rhogocytes, but no protonephridia, in this location. We did not find ring‐shaped profiles of hemocyanin decamers within rhogocytes of larvae or pre‐hatch embryos. Rhogocytes in newly released larvae of Nerita melanotragus contained orderly bundles of cylinders, but the diameter of the cylinders was only 70% of the diameter typical of hemocyanin multidecamers. By examining embryos of the caenogastropod Nassarius mendicus at four successive developmental time points that bracketed the occurrence of larval hatching, we found that terminal cells from non‐functional protonephridia in pre‐hatch embryos transformed into rhogocytes around the time of hatching. This empirical evidence of ontogenetic transformation of protonephridial terminal cells into rhogocytes might be interpreted as developmental recapitulation of an evolutionary transition that occurred early in molluscan history.     

A novel fibronectin type III module binding motif identified on C-terminus of Leptospira immunoglobulin-like protein, LigB

Infection by pathogenic strains of Leptospira hinges on the pathogen’s ability to adhere to host cells via extracellular matrix such as fibronectin (Fn). Previously, the immunoglobulin-like domains of Leptospira Lig proteins were recognized as adhesins binding to N-terminal domain (NTD) and gelatin binding domain (GBD) of Fn. In this study, we identified another Fn-binding motif on the C-terminus of the Leptospira adhesin LigB (LigBCtv), residues 1708-1712 containing sequence LIPAD with a β-strand and nascent helical structure. This motif binds to 15th type III modules (15F₃) (K_D = 10.70 μM), and association (k_on = 600 M⁻¹ s⁻¹) and dissociation (k_off = 0.0129 s⁻¹) rate constants represents a slow binding kinetics in this interaction. Moreover, pretreatment of MDCK cells with LigB_1706-1716 blocked the binding of Leptospira by 39%, demonstrating a significant role of LigB_1706-1716 in cellular adhesion. These data indicate that the LIPAD residues (LigB_1708-1712) of the Leptospira interrogans LigB protein bind 15F₃ of Fn at a novel binding site, and this interaction contributes to adhesion to host cells.     

Inverse PCR-based site-directed mutagenesis of nucleotide sequences coding for carbohydrate-binding fragments of legume lectins

A new method of site-directed mutagenesis was developed to allow manipulation with extended plasmid-cloned gene fragments irrespective of their position and the presence of restriction sites. The method was used to obtain chimeric constructs encoding a Pisum sativum lectin with the native carbohydrate-binding region replaced by its counterpart from other legumes. The method can be used in plasmid construction to clone a coding gene fragment under the control of a promoter in a certain reading frame.