Homologs of eukaryotic Ras superfamily proteins in prokaryotes and their novel phylogenetic correlation with their eukaryotic analogs

Ras superfamily proteins are key regulators in a wide variety of cellular processes. Previously, they were considered to be specific to eukaryotes, and MglA, a group of obviously different prokaryotic proteins, were recognized as their only prokaryotic an

A critical reassessment of the role of mitochondria in tumorigenesis

Background Mitochondrial DNA (mtDNA) is being analyzed by an increasing number of laboratories in order to investigate its potential role as an active marker of tumorigenesis in various types of cancer. Here we question the conclusions drawn in most of these investigations, especially those published in high-rank cancer research journals, under the evidence that a significant number of these medical mtDNA studies are based on obviously flawed sequencing results. Methods and Findings In our analyses, we take a phylogenetic approach and employ thorough database searches, which together have proven successful for detecting erroneous sequences in the fields of human population genetics and forensics. Apart from conceptual problems concerning the interpretation of mtDNA variation in tumorigenesis, in most cases, blocks of seemingly somatic mutations clearly point to contamination or sample mix-up and, therefore, have nothing to do with tumorigenesis. Conclusion The role of mitochondria in tumorigenesis remains unclarified. Our findings of laboratory errors in many contributions would represent only the tip of the iceberg since most published studies do not provide the raw sequence data for inspection, thus hindering a posteriori evaluation of the results. There is no precedent for such a concatenation of errors and misconceptions affecting a whole subfield of medical research.

Implications of local lifecycle analyses and low carbon fuel standard design on gasohol transportation fuels

State and regional policies, such as low carbon fuel standards (LCFSs), increasingly mandate that transportation fuels be examined according to their greenhouse gas (GHG) emissions. We investigate whether such policies benefit from determining fuel carbon intensities (FCIs) locally to account for variations in fuel production and to stimulate improvements in FCI. In this study, we examine the FCI of transportation fuels on a lifecycle basis within a specific state, Minnesota, and compare the results to FCIs using national averages. Using data compiled from 18 refineries over an 11-year period, we find that ethanol production is highly variable, resulting in a 42% difference between carbon intensities. Historical data suggests that lower FCIs are possible through incremental improvements in refining efficiency and the use of biomass for processing heat. Stochastic modeling of the corn ethanol FCI shows that gains in certainty due to knowledge of specific refinery inputs are overwhelmed by uncertainty in parameters external to the refiner, including impacts of fertilization and land use change. The LCA results are incorporated into multiple policy scenarios to demonstrate the effect of policy configurations on the use of alternative fuels. These results provide a contrast between volumetric mandates and LCFSs. © 2011 Elsevier Ltd.

3D FE Analyses of Buried Pipeline with Elbows Subjected to Lateral Loading

This study investigates the interaction between soil and pipeline in sand subjected to lateral ground displacements with emphasis on the peak force exerted to a bended elbow-pipe. A series of three-dimensional (3D) finite-element (FE) analyses were performed in both opening and closing modes of the elbow section for different initial pipe bending angles. To model the mechanical behavior of sands, two soil models were adopted: Mohr-Coulomb and Nor-Sand soil model. Investigations also included the effects of pipe embedment depth and soil density. Results show that the opening mode exhibits higher ultimate forces and greater localized deformations than the closing mode. Nondimensional charts that account for pipeline location, bending angle, and soil density are developed. Soil-spring pipeline analyses of an elbow-pipe were performed using modified F-δ soil-spring models based on the 3D FE results and were compared to the findings of conventional spring model analyses using the standard two-dimensional soil-spring model. Results show that the pipe strain does not change in the closing mode case. However, in the opening mode case, the pipe strain computed by the modified analysis is larger than that by the conventional analysis and the difference is more pronounced when the pipe stiffness is stiffer. © 2011 American Society of Civil Engineers.

High Altitude Adaptation and Phylogenetic Analysis of Tibetan Horse Based on the Mitochondrial Genome

研究测定了西藏那曲(4,500 m)、云南中甸(3,300 m)、云南德钦(3,300 m)地区3匹藏马线粒体全基因组序列.3个地区的藏马线粒体基因组全长以及结构均与韩国济州岛的马类似,但比瑞典马线粒体基因组短.藏马基因组在DNA序列上的两两相似性达99.3%.通过对线粒体蛋白编码区的分析发现,NADH6基因的蛋白序列在三匹藏马中均表现快速进化的现象.这表明NADH6基因在藏马高原适应进化过程中扮演着重要角色.此外,利用7匹藏马的D-loop区域序列以及与其亲缘关系较近的马的序列首次构建的藏马的系统发育树显示,那曲藏马与中甸、德钦藏马属于不同的分支,且存在较大的遗传多样性,表明藏马可能为多地区起源.

XMolecular Cloning and Sequence Analyses of cDNAs Encoding Seven C2type Lectin2like Protein Subunits from Daboia russellii siamensis

按照Promega 公司的mRNA 提取试剂盒操作手册, 从圆斑蝰蛇( Daboia russellii siamensis ) 的毒腺中提 取mRNA ; 利用RT2PCR 的方法进行体外扩增, 获得C - 型凝集素蛋白的基因, 克隆到pMD182T 载体中。随机挑 选14 个阳性克隆进行核酸测序, 获得7 个编码不同蛇毒C - 型凝集素样蛋白亚基的cDNA , 分别命名为DRS2L1 、 DRS2L2 、DRS2L3 、DRS2L4 、DRS2L5 、DRS2L6 和DRS2L7 。由基因序列推导出的氨基酸序列表明, 克隆到的7 个蛇 毒C - 型凝集素样蛋白的亚基中均有糖识别结构域存在。BLAST 分析显示, 仅有DRS2L1 的蛋白序列与目前已知 的蛇毒C - 型凝集素样蛋白的α亚基相似。序列同源性比较并结合半胱氨酸位点分析, 推测DRS2L1 和DRS2L2 可能分别是圆斑蝰蛇毒Ⅹ因子激活剂的轻链LC2 和LC1 。DRS2L3 和DRS2L4 可能是高分子量的蛇毒C - 型凝集 素样蛋白的β亚基, 而DRS2L5 和DRS2L6 可能是低分子量的蛇毒C - 型凝集素样蛋白的β亚基。DRS2L7 可能是 类似于血小板膜糖蛋白Ib 结合蛋白的β亚基。

THE PHYLOGENETIC-RELATIONSHIPS AND CLASSIFICATION OF THE DOUCS AND SNUB-NOSED LANGURS OF CHINA AND VIETNAM

The taxonomy of the douc and snub-nosed langurs has changed several times during the 20th century. The controversy over the systematic position of these animals has been due in part to difficulties in studying them: both the doucs and the snub-nosed langurs are rare in the wild and are generally poorly represented in institutional collections. This review is based on a detailed examination of relatively large numbers of specimens of most of the species of langurs concerned. An attempt was made to draw upon as many types of information as were available in order to make an assessment of the phyletic relationships between the langur species under discussion. Toward this end, quantitative and qualitative features of the skeleton, specific features of visceral anatomy and characteristics of the pelage were utilized. The final data matrix comprised 178 characters. The matrix was analyzed using the program Hennig86. The results of the analysis support the following conclusions: (1) that the douc and snub-nosed langurs are generically distinct and should be referred to as species of Pygathrix and Rhinopithecus, respectively; (2) that the Tonkin snub-nosed langur be placed in its own subgenus as Rhinopithecus (Presbytiscus) avunculus and that the Chinese snub-nosed langur thus be placed in the subgenus Rhinopithecus (Rhinopithecus); (3) that four extant species of Rhinopithecus be recognized: R. (Rhinopithecus) roxellana Milne Edwards, 1870; R. (Rhinopithecus) bieti Milne Edwards, 1897; R. (Rhinopithecus) brelichi Thomas, 1903, and R. (Presbytiscus) avunculus Dollman, 1912; (4) that the Chinese snub-nosed langurs fall into northern and southern subgroups divided by the Yangtze river; (5) that R. lantianensis Hu and Qi, 1978, is a valid fossil species, and (6) the precise affinities and taxonomic status of the fossil species R. tingianus Matthew and Granger, 1923, are unclear because the type specimen is a subadult.

Meiothermus rosaceus sp nov isolated from Tengchong hot spring in Yunnan, China

A rosy-pigmented Gram-negative, thermophilic bacterium with an optimum growth temperature of about 55degreesC was isolated from Tengchong hot springs in Yunnan province, China. Its growth scarcely occurred below 40degreesC or above 70degreesC. Phylogenetic and secondary structural analyses of 16S rRNA and DNA-DNA hybridization showed that the organism represented a new species of the genus Meiothermus. This new species could be distinguished easily from other species of the genus Meiothermus by the following phenotypic characteristics: rosy pigment, expanded body, sucrose and maltose were not utilized, gelatin and starch were not hydrolyzed. On the basis of the above data, the name Meiothermus rosaceus sp. nov. was proposed for the species represented by the strain RH9901(T)(CCTCC-AB200291). (C) 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

On-going generation of multiple forms of HIV-1 intersubtype recombinants in the Yunnan Province of China

Objectives: To investigate the molecular epidemiology of HIV in China's Yunnan Province, where the initial HIV-1 outbreak among injecting drug users (IDU) occurred in 1989, and to analyse the genesis and interrelationship of the epidemic with that in surrounding areas. Design: A molecular epidemiological investigation was conducted among IDU in three prefectures in Yunnan Province, including Wenshan (east), Honghe (southeast) and Dehong (west). Methods: Thirty-nine specimens were collected from consenting IDU in 2000-2001. The nucleotide sequences of 2.6 kb gag-RT and 340 base pair (bp) env (C2/V3) regions were determined. Phylogenetic tree and recombination breakpoint analyses were performed. Results: The circulating recombinant form (CRF), CRF08_BC, predominated in east Yunnan near Guangxi Province (89% in Wenshan and 81% in Honghe), whereas it was not detected in Dehong(0/14) in the west. In contrast, 71% (10/14) of the Dehong isolates were unique recombinant forms (URF), mostly between subtypes B' (Thailand variant of subtype B) and C, with distinct profiles of recombination breakpoints. The subtype B' accounts for the remaining 29% (4/14) of Dehong isolates. Interestingly, two Honghe isolates (2/16) shared some of the precise B'/C recombination breakpoints with CRF07_BC. Conclusion: New recombinant strains are arising continually in west Yunnan near the Myanmar border. Some appeared to be secondary recombinants derived from CRF07_BC that had further recombined with other strains. The uneven distribution of subtypes, CRF and URF, suggests the presence of independent transmission networks and clusters among IDU in Yunnan. (C) 2002 Lippincott Williams Wilkins.

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

The Phylogenetic Relationships of the Chinese and Vietnamese Waterfall frogs of the genus Amolops

Ranid frogs of the genus Amolops occur in Southeast Asia and are typically found near waterfalls. Their phylogenetic relationships have not been resolved. We include 2,213 aligned nucleotide sites of the 12S, 16S and tRNA(val) gene regions of the mitochondrial DNA genome from 43 individuals of Chinese and Vietnamese Amotops, Huia, Hylarana, Meristogenys, Odorrana and Rana. The outgroup species were from the genera Chaparana, Limnonectes, Nanorana, and Paa. The data were analyzed within the framework of a refutationist philosophy using maximum parsimony. Four clades of waterfall frogs were resolved. Meristogenys was not resolved as the sister group to either Huia nor Amolops. The hypothesis Of evolutionary relationships placed Amolops chapaensis and Huia nasica in the genus Odorrana.

Seismic analyses of shallow tunnels by dynamic centrifuge tests and finite elements

The increments of internal forces induced in a tunnel lining during earthquakes can be assessed with several procedures at different levels of complexity. However, the substantial lack of well-documented case histories still represents a difficulty in order to validate any of the methods proposed in literature. To bridge this gap, centrifuge model tests were carried out on a circular aluminium tunnel located at two different depths in dense and loose dry sand. Each model has been instrumented for measuring soil motion and internal loads in the lining and tested under several dynamic input signals. The tests performed represented an experimental benchmark to calibrate dynamic analyses with different approaches to account for soil-tunnel kinematic interaction. © 2009 IOS Press.

Multiply conditioned analyses of stratification in highly swirling methane/air flames

The effects of stratification on a series of highly swirling turbulent flames under globally lean conditions (φg=0.75) are investigated using a new high-spatial resolution multi-scalar dataset. This dataset features two key properties: high spatial resolution which approaches the 60 micron optical limit of the measurement system, and a wavelet oversampling methodology which significantly reduces the influence of noise. Furthermore, the very large number of realizations (30,000) acquired in the stratified cases permits statistically significant results to be obtained even after aggressive conditioning is applied. Data are doubly conditioned on equivalence ratio and the degree of stratification across the flame in each instantaneous realization. The influence of stoichiometry is limited by conditioning on the equivalence ratio at the location of peak CO mass fraction, which is shown to be a good surrogate for the location of peak heat release rate, while the stratification is quantified using a linear gradient in equivalence ratio across the instantaneous flame front. This advanced conditioning enables robust comparisons with the baseline lean premixed flame. Species mass fractions of both carbon monoxide and hydrogen are increased in temperature space under stratified conditions. Stratification is also shown to significantly increase thermal gradients, yet the derived three-dimensional flame surface density is shown to be relatively insensitive to stratification. Whilst the presence of instantaneous stratification broadens the curvature distribution relative to the premixed case, the degree of broadening is not significantly influenced by the range of global stratification ratios examined in this study. © 2012 The Combustion Institute.