用激光共聚焦扫描技术研究昆虫触角叶的雌雄异构性

【目的】本研究探讨用激光共聚焦扫描显微镜对昆虫触角叶内结构的扫描技术。【方法】选取鳞翅目斜纹夜蛾Spodoptera litura, 蜚蠊目美洲大蠊Periplaneta americana和鞘翅目松墨天牛Monochamus alternatus, 仔细解剖得到昆虫完整脑组织, 经过Lucifer yellow染色、戊二醛固定、梯度酒精脱水和透明等一系列处理后, 用激光共聚焦扫描显微镜对昆虫触角叶结构进行分层扫描。【结果】结果显示: 经该方法处理后在激发光488 nm下能清晰扫描出昆虫触角内典型结构神经纤维球, 并且可清晰看到这3种昆虫雄性触角叶结构内的扩大型神经纤维球复合体(macroglomerular complex, MGC), 而在相应雌性昆虫体内都没有此复合体。另外通过5 μm分层扫描得到斜纹夜蛾、美洲大蠊和松墨天牛的触角叶平均厚度分别为130, 235和115 μm, 神经纤维球数量分别为35, 59和39个。【结论】激光共聚焦扫描技术是获得昆虫触角叶内部结构的一个可行方法。     

Lipoproteomics II: mapping of proteins in high-density lipoprotein using two-dimensional gel electrophoresis and mass spectrometry

High-density lipoprotein (HDL) is the most abundant lipoprotein particle in the plasma and a negative risk factor of atherosclerosis. By using a proteomic approach it is possible to obtain detailed information about its protein content and protein modifications that may give new information about the physiological roles of HDL. In this study the two subfractions; HDL(2) and HDL(3), were isolated by two-step discontinuous density-gradient ultracentrifugation and the proteins were separated with two-dimensional gel electrophoresis and identified with peptide mass fingerprinting, using matrix-assisted laser desorption/ionisation time of flight mass spectrometry. Identified proteins in HDL were: the dominating apo A-I as six isoforms, four of them with a glycosylation pattern and one of them with retained propeptide, apolipoprotein (apo) A-II, apo A-IV, apo C-I, apo C-II, apo C-III (two isoforms), apo E (five isoforms), the recently discovered apo M (two isoforms), serum amyloid A (two isoforms) and serum amyloid A-IV (six isoforms). Furthermore, alpha-1-antitrypsin was identified in HDL for the first time. Additionally, salivary alpha-amylase was identified as two isoforms in HDL(2), and apo L and a glycosylated apo A-II were identified in HDL(3). Besides confirming the presence of different apolipoproteins, this study indicates new patterns of glycosylated apo A-I and apo A-II. Furthermore, the study reveals new proteins in HDL; alpha-1-antitrypsin and salivary alpha-amylase. Further investigations about these proteins may give new insight into the functional role of HDL in coronary artery diseases.     

Comparison of Commercially Available Target Enrichment Methods for Next-Generation Sequencing

Isolating high-priority segments of genomes greatly enhances the efficiency of next-generation sequencing (NGS) by allowing researchers to focus on their regions of interest. For the 2010–11 DNA Sequencing Research Group (DSRG) study, we compared outcomes from two leading companies, Agilent Technologies (Santa Clara, CA, USA) and Roche NimbleGen (Madison, WI, USA), which offer custom-targeted genomic enrichment methods. Both companies were provided with the same genomic sample and challenged to capture identical genomic locations for DNA NGS. The target region totaled 3.5 Mb and included 31 individual genes and a 2-Mb contiguous interval. Each company was asked to design its best assay, perform the capture in replicates, and return the captured material to the DSRG-participating laboratories. Sequencing was performed in two different laboratories on Genome Analyzer IIx systems (Illumina, San Diego, CA, USA). Sequencing data were analyzed for sensitivity, specificity, and coverage of the desired regions. The success of the enrichment was highly dependent on the design of the capture probes. Overall, coverage variability was higher for the Agilent samples. As variant discovery is the ultimate goal for a typical targeted sequencing project, we compared samples for their ability to sequence single-nucleotide polymorphisms (SNPs) as a test of the ability to capture both chromosomes from the sample. In the targeted regions, we detected 2546 SNPs with the NimbleGen samples and 2071 with Agilent''s. When limited to the regions that both companies included as baits, the number of SNPs was ∼1000 for each, with Agilent and NimbleGen finding a small number of unique SNPs not found by the other.     

He-Ne激光和增强UV-B辐射对小麦幼苗核蛋白的影响

采用低剂量(5 mW.mm-2)He-Ne激光辐照经增强UV-B辐射处理(10.08 KJ.m-2.d-1)后的‘ML7113’小麦幼苗,待小麦幼苗长7 d后,对各处理组小麦幼苗的核蛋白进行提取,通过紫外吸收法测定各个处理组幼苗核蛋白的含量。采用SDS聚丙烯酰胺凝胶电泳法(SDS-PAGE)进行电泳。结果显示:小麦幼苗经UV-B辐射后核蛋白含量明显增高;单独激光处理后,小麦幼苗核蛋白含量低于对照组;经He-Ne激光和增强UV-B辐射复合处理后,小麦幼苗核蛋白含量低于UV-B辐射处理组,而高于对照组,推测一定剂量的He-Ne激光在一定程度上抑制了增强UV-B辐射的促进作用。     

BaitsTools: Software for hybridization capture bait design

Nucleic acid hybridization capture is a principal technology in molecular ecology and genomics. Bait design, however, is a nontrivial task and few resources currently exist to automate the process. Here, I present baitstools , an open‐source, user‐friendly software package to facilitate the design of nucleic acid baits for hybridization capture.     

Stigmatellin Y – An anti-biofilm compound from Bacillus subtilis BR4 possibly interferes in PQS–PqsR mediated quorum sensing system in Pseudomonas aeruginosa

Hitherto this is the first report pertaining to production of biofilm inhibitory compound(s) (BIC) from Bacillus subtilis BR4 against Pseudomonas aeruginosa (ATCC 27853) coupled with production optimization. In order to achieve this, combinations of media components were formulated by employing statistical tools such as Plackett–Burman analysis and central composite rotatable design (CCRD). It was evident that at 35 ml L^?1 glycerol and 3.8 g L^?1 casamino acid, anti-biofilm activity and production of extracellular protein significantly increased by 1.5-fold and 1.2-fold, respectively. These results corroborate that the combination of glycerol and casamino acid plays a key role in the production of BIC. Further, metabolic profiling of BIC was carried out using liquid chromatography/tandem mass spectrometry (LC–MS/MS) based on m/z value. The presence of Stigmatellin Y was predicted with monoisotopic neutral mass of 484.2825 Da. In support of optimization study, higher production of BIC was confirmed in the optimized-media-grown BR4 (OPT-BR4) than in the ideal-media-grown BR4 (ID-BR4) by LC–MS/MS analysis. PqsR in P. aeruginosa is a potential target for anti-virulent therapy. Molecular docking study has revealed that Stigmatellin Y interacts with PqsR in the similar orientation like a cognate signal (PQS) and synthetic inhibitor. In addition, Stigmatellin Y was found to exhibit interaction with four more amino acid residues of PqsR to establish strong affinity. Stigmatellin Y thus might play a role of competitor for PQS to distract PQS–PqsR mediated communication in P. aeruginosa. The present investigation thus paves new avenues to develop anti-Pseudomonas virulent therapy.     

Allosteric signaling in the biotin repressor occurs via local folding coupled to global dampening of protein dynamics

The biotin repressor is an allosterically regulated, site-specific DNA-binding protein. Binding of the small ligand bio-5′-AMP activates repressor dimerization, which is a prerequisite to DNA binding. Multiple disorder-to-order transitions, some of which are known to be important for the functional allosteric response, occur in the vicinity of the ligand-binding site concomitant with effector binding to the repressor monomer. In this work, the extent to which these local changes are coupled to additional changes in the structure/dynamics of the repressor was investigated using hydrogen/deuterium exchange coupled to mass spectrometry. Measurements were performed on the apo-protein and on complexes of the protein bound to four different effectors that elicit a range of thermodynamic responses in the repressor. Global exchange measurements indicate that binding of any effector to the intact protein is accompanied by protection from exchange. Mass spectrometric analysis of pepsin-cleavage products generated from the exchanged complexes reveals that the protection is distributed throughout the protein. Furthermore, the magnitude of the level of protection in each peptide from hydrogen/deuterium exchange correlates with the magnitude of the functional allosteric response elicited by a ligand. These results indicate that local structural changes in the binding site that occur concomitant with effector binding nucleate global dampening of dynamics. Moreover, the magnitude of dampening of repressor dynamics tracks with the magnitude of the functional response to effector binding.     

Environmental landscape determinants of maximum forest canopy height of boreal forests

Aims Canopy height is a key driver of forest biodiversity and carbon cycling. Accurate estimates of canopy height are needed for assessing mechanisms relating to ecological patterns and processes of tree height limitations. At global scales forest canopy height patterns are largely controlled by climate, while local variation at fine scales is due to differences in disturbance history and local patterns in environmental conditions. The relative effect of local environmental drivers on canopy height is poorly understood partly due to gaps in data on canopy height and methods for examining limiting factors. Here, we used airborne laser scanning (ALS) data on vegetation structure of boreal forests to examine the effects of environmental factors on potential maximum forest canopy height.