RegStatGel: proteomic software for identifying differentially expressed proteins based on 2D gel images

Image analysis of two-dimensional gel electrophoresis is a key step in proteomic workflow for identifying proteins that change under different experimental conditions. Since there are usually large amount of proteins and variations shown in the gel images, the use of software for analysis of 2D gel images is inevitable. We developed open-source software with graphical user interface for differential analysis of 2D gel images. The user-friendly software, RegStatGel, contains fully automated as well as interactive procedures. It was developed and has been tested under Matlab 7.01. AVAILABILITY: The database is available for free at http://www.mediafire.com/FengLi/2DGelsoftware.     

无创性颈动脉瞬时减速度波强测定评价左心室舒张功能的研究

目的：探讨无创检测心功能的指标—颈动脉瞬时减速度波强（W2）评价左心室舒张功能的价值。方法：测量40例高血压病患者和43例健康对照者的左、右侧颈总动脉W2,组织多普勒测定二尖瓣环运动速度和血清脑利钠肽前体（N-terminal probrain natriuretic peptide,NT-proBNP）,分析W2与各参数间的相关性。结果：①高血压组W2低于对照组,以左侧明显（1126±996vs1690±1126 mmHg.m/s3,P〈0.01）;②高血压组与对照组比较：E/Em（二尖瓣舒张早期峰值速度/二尖瓣环舒张早期纵向运动峰值速度）增大（9.37±3.32vs7.39±1.83,P〈0.01）,NT-proB-NP升高（94.6±48.5vs45.2±13.8,P〈0.01）;③相关性分析：W2与E/Em负相关（r=-0.46,P〈0.05）,与NT-proBNP负相关（r=-0.21,P〈0.05）。结论：无创性评价血流动力学的新技术指标W2是反映早期左室舒张功能受损的敏感指标。     

Trachymolgus purpureus sp. n., an armored snout mite (Acari, Bdellidae) from the Ozark highlands: morphology, development, and key to Trachymolgus Berlese

Trachymolgus purpureus Fisher & Dowling sp. n. is described from the Ozark highlands of North America. A diversity of imaging techniques are used to illustrate the species including low-temperature scanning electron microscopy (LT-SEM), stereomicrography, compound light micrography, and digitally created line drawings. Developmental stages (larva, nymphs, and adult) and morphology are illustrated and discussed, and terminological corrections are suggested. Trachymolgus recki Gomelauri, 1961 is regarded as being described from tritonymphs. A key to Trachymolgus is presented.     

间歇性充气加压疗法对下肢深静脉血栓患者血液流变学的影响

目的:观察间歇性充气加压疗法(intermittent pneumatic compression,IPC)对下肢深静脉血栓形成(deep vein thrombosis of lower limbs,DVT)患者的治疗效果,并从血液流变学方面探讨间歇性充气加压的作用机理.方法:2003年3月-2010年9月我科收治的243例下肢深静脉血栓患者,将其中42例IPC治疗病例定为B组实验组,145例单纯药物治疗病例中选取60例定为A组对照组.观察两组患者血液流变学指标和小腿肿胀消退情况的对比.结果:两组患者全血粘度、红细胞聚集指数、红细胞电泳时间、红细胞变形性,在治疗第1天较入院时无差异,组间无差异(P＞0.05),第3天较入院时有差异(P＜0.05),组间第3天有差异(P＜0.05),两组患者下肢肿胀度均明显消退,但B组肿胀消退速度明显快于对照组(P＜0.05).结论:间歇性充气加压治疗仪可有效改变血液流变学状态,改善血液高凝状态,有效缓解肢体肿胀症状,缩短住院时间.且不增加治疗难度,使用简单,治疗依从性好.     

Genetic parsimony: a factor in the evolution of complexity, order and emergence

Two conjectures, drawn from Gregory Chaitin's Algorithmic Information Theory, are examined with respect to the relationship between an algorithm and its product; in particular his finding that, where an algorithm is minimal, its length provides a measure of the complexity of the product. Algorithmic complexity is considered from the perspective of the relationship between genotype and phenotype, which Chaitin suggests is analogous to other algorithm-product systems. The first conjecture is that the genome is a minimal set of algorithms for the phenotype. Evidence is presented for a factor, here termed 'genetic parsimony', which is thought to have helped minimize the growth of genome size during evolution. Species that depend on rapid replication, such as prokaryotes which are generally r -selected are more likely to have small genomes, while the K -strategists accumulate introns and have large genomes. The second conjecture is that genome size could provide a measure of organism complexity. A surrogate index for coding DNA is in agreement with an established phenotypic index (number of cell types), in exhibiting an evolutionary trend of increasing organism complexity over time. Evidence for genetic parsimony indicates that simplicity in coding has been selected, and is responsible for phenotypic order. It is proposed that order evolved because order in the phenotype can be encoded more economically than disorder. Thus order arises due to selection for genetic parsimony, as does the evolution of other 'emergent' properties.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 295–308.     

Elucidation of the stator organization in the V-ATPase of Neurospora crassa

V-ATPases are membrane protein complexes that pump protons in the lumen of various subcellular compartments at the expense of ATP. Proton pumping is done by a rotary mechanism that requires a static connection between the membrane pumping domain (V(0)) and the extrinsic catalytic head (V(1)). This static connection is composed of several known subunits of the V-ATPase, but their location and topological relationships are still a matter of controversy. Here, we propose a model for the V-ATPase of Neurospora crassa on the basis of single-particle analysis by electron microscopy. Comparison of the resulting map to that of the A-ATPase from Thermus thermophilus allows the positioning of two subunits in the static connecting region that are unique to eukaryotic V-ATPases (C and H). These two subunits seem to be located on opposite sides of a semicircular arrangement of the peripheral connecting elements, suggesting a role in stabilizing the stator in V-ATPases.     

A three-dimensional cryo-electron microscopy structure of the bacteriophage phiKZ head

The three-dimensional structure of the Pseudomonas aeruginosa bacteriophage phiKZ head has been determined by cryo-electron microscopy and image reconstruction to 18A resolution. The head has icosahedral symmetry measuring 1455 A in diameter along 5-fold axes and a unique portal vertex to which is attached an approximately 1800 A-long contractile tail. The 65 kDa major capsid protein, gp120, is organized into a surface lattice of hexamers, with T = 27 triangulation. The shape and size of the hexamers is similar to the hexameric building blocks of the bacteriophages T4, phi29, P22, and HK97. Pentameric vertices of the capsid are occupied by complexes composed of several special vertex proteins. The double-stranded genomic DNA is packaged into a highly condensed series of layers, separated by 24 A, that follow the contour of the inner wall of the capsid.     

Refining the structure of the Halobacterium salinarum flagellar filament using the iterative helical real space reconstruction method: insights into polymorphism

The eubacterial flagellar filament is an external, self-assembling, helical polymer approximately 220 A in diameter constructed from a highly conserved monomer, flagellin, which polymerizes externally at the distal end. The archaeal filament is only approximately 100 A in diameter, assembles at the proximal end and is constructed from different, glycosylated flagellins. Although the phenomenology of swimming is similar to that of eubacteria, the symmetry of the archebacterial filament is entirely different. Here, we extend our previous study on the flagellar coiled filament structure of strain R1M1 of Halobacterium salinarum. We use strain M175 of H.salinarum, which forms poly-flagellar bundles at high yield which, under conditions of relatively low ionic-strength (0.8 M versus 5 M) and low pH ( approximately 2.5 versus approximately 6.8), form straight filaments. We demonstrated previously that a single-particle approach to helical reconstruction has many advantages over conventional Fourier-Bessel methods when dealing with variable helical symmetry and heterogeneity. We show here that when this method is applied to the ordered helical structure of the archebacterial uncoiled flagellar filament, significant extensions in resolution can be obtained readily when compared to applying traditional helical techniques. The filament population can be separated into classes of different morphologies, which may represent polymorphic states. Using cryo-negatively stained images, a resolution of approximately 10-15 A has been achieved. Single alpha-helices can be fit into the reconstruction, supporting the proposed similarity of the structure to that of type IV bacterial pili.     

Application of Image Analysis Techniques in Activated Sludge Wastewater Treatment Processes

Image analytical techniques have been extensively developed to evaluate complex microbial aggregates such as sludge flocs and biofilms. This review covers the latest contributions concerning the application of image analysis to the activated sludge systems with respect to the most frequently used morphological parameters and relations between them and traditional wastewater treatment parameters. Recent developments have indicated that image analysis can be successfully used for the quantification of flocs and filamentous bacteria in the operating wastewater treatment plants, which enables prediction of bulking events and pinpoint flocs formation.