Methods for mapping of interaction networks involving membrane proteins

Nearly one-third of all genes in various organisms encode membrane-associated proteins that participate in numerous protein-protein interactions important to the processes of life. However, membrane protein interactions pose significant challenges due to the need to solubilize membranes without disrupting protein-protein interactions. Traditionally, analysis of isolated protein complexes by high-resolution 2D gel electrophoresis has been the main method used to obtain an overall picture of proteome constituents and interactions. However, this method is time consuming, labor intensive, detects only abundant proteins and is limited with respect to the coverage required to elucidate large interaction networks. In this review, we discuss the application of various methods to elucidate interactions involving membrane proteins. These techniques include methods for the direct isolation of single complexes or interactors as well as methods for characterization of entire subcellular and cellular interactomes.     

Robustness of an odds-ratio test in a stratified group sequential trial with a binary outcome measure

Many clinical trials compare two or more treatment groups by using a binary outcome measure. For example, the goal could be to determine whether the frequency of pain episodes is significantly reduced in the treatment group (arm A) as compared to the control group (arm B). However, for ethical or regulatory reasons, group sequential designs are commonly employed. Then, based on a binomial distribution, the stopping boundaries for the interim analyses are constructed for assessing the difference in the response probabilities between the two groups. This is easily accomplished by using any of the standard procedures, e.g., those discussed by Jennison and Turnbull (2000), and using one of the most commonly used software packages, East (2000). Several factors are known to often affect the primary outcome of interest, but their true distributions are not known in advance. In addition, these factors may cause heterogeneous treatment responses among individuals in a group, and their exact effect size may be unknown. To limit the effect of such factors on the comparison of the two arms, stratified randomization is used in the actual conduct of the trial. Then, a stratified analysis based on the odds ratio proposed in Jennison and Turnbull (2000, pages 251-252) and consistent with the stratified design is undertaken. However, the stopping rules used for the interim analyses are those obtained for determining the differences in response rates in a design that was not stratified. The purpose of this paper is to assess the robustness of such an approach on the performance of the odds ratio test when the underlying distribution and effect size of the factors that influence the outcome may vary. The simulation studies indicate that, in general, the stratified approach offers consistently better results than does the unstratified approach, as long as the difference in the weighted average of the response probabilities across strata between the two groups remains closer to the hypothesized values, irrespective of the differences in the (allocation) distributions and heterogeneous response rate. However, if the response probabilities deviate significantly from the hypothesized values so that the difference in the weighted average is less than the hypothesized value, then the proposed study could be significantly underpowered.     

Integrating cooperative breeding into theoretical concepts of cooperation

In cooperative breeding systems, some individuals help to raise offspring that are not their own. While early explanations for such altruistic behaviour were predominantly based on kin selection, recent evidence suggests that direct benefits may be important in the maintenance of cooperation. To date, however, discussions of cooperative breeding have made little reference to more general theories of cooperation between unrelated individuals (while these theories rarely address cooperative breeding). Here, we attempt to integrate the two fields. We identify four key questions that can be used to categorise different mechanisms for the maintenance of cooperative behaviour: (1) whether or not individuals invest in others; (2) whether or not this initial investment elicits a return investment by the beneficiary; (3) whether the interaction is direct, i.e. between two partners, or indirect (involving third parties) and (4) whether only actions that increase the fitness of the partner or also fitness reducing actions (punishment) are involved in the interaction. Asking these questions with regards to concepts in the literature on cooperative breeding, we found that (a) it is often straightforward to relate these concepts to general mechanisms of cooperation, but that (b) a single term (such as 'pay-to-stay', 'group augmentation' or 'prestige') may sometimes subsume two or more distinct mechanisms, and that (c) at least some mechanisms that are thought to be important in cooperative breeding systems have remained largely unexplored in the theoretical literature on the evolution of cooperation. Future theoretical models should incorporate asymmetries in power and pay off structure caused for instance by dominance hierarchies or partner choice, and the use of N-player games. The key challenges for both theoreticians and empiricists will be to integrate the hitherto disparate fields and to disentangle the parallel effects of kin and non-kin based mechanisms of cooperation.     

Subspecies-specific distribution of intervening sequences in the Bacillus subtilis prophage ribonucleotide reductase genes

A collection of 212 gram-positive bacilli isolated from natural habitats was screened for the presence of intervening sequences (introns and intein-coding sequences) in the SPbeta prophage-related ribonucleotide reductase genes bnrdE and bnrdF. Three novel configurations were identified on the basis of the presence of (i) intervening sequences in bnrdE and bnrdF, and (ii) an ORF in the bnrdE-bnrdF spacer. Analysis of the cell wall genetic determinants as well as of the incorporation of radio-labelled glycerol into cell wall allowed newly and previously identified B. subtilis strains with different configurations of bnrdE/bnrdF intervening sequences to be assigned to one of two subspecies. Strains apparently belonging to the subsp. subtilis contain three intervening sequences many of which are associated with the putative homing endonuclease activity. Strains of the subsp. spizizenii contain only one or two ORF-less group I introns. Introns occupying bnrdF are confined to the subspecies subtilis.     

Proteomic analysis of tilapia Oreochromis niloticus Streptococcus agalactiae strains with different genotypes and serotypes

Nine tilapia Oreochromis niloticus group B streptococcus (GBS) strains differing in serotype and genotype were selected and paired. Two‐dimensional difference gel electrophoresis (2D DIGE) and matrix‐assisted laser‐desorption ionization time‐of‐flight‐mass spectrometry (MALDI‐TOF‐MS) were used to analyse the protein profiles of the strain pairs. Forty‐three proteins corresponding to 66 spots were identified, of which 35 proteins were found in the seven selected strain pairs that represented pairs differing in genotype and serotype. Among the 35 proteins, numbers of differentially expressed proteins in strains of different serotypes were greater than found in strains of different genotypes, suggesting that serotype plays a more essential role than genotype in the differential protein expression among GBS strains. No distinct pattern was found with respect to genotype and the protein expression profile of GBS strains. Several proteins were identified as surface‐associated cytoplasmic proteins that possessed the typical immunity‐eliciting characteristics of surface proteins. The identified proteins were found to be involved in 16 biological processes and seven Kyoto encyclopaedia of genes and genomes (KEGG) pathways. The data, for the first time, identified differentially expressed proteins in O. niloticus GBS strains of different serotypes, which play a major role in immunogenicity of O. niloticus GBS than does genotype, offering further information for design of a vaccine against O. niloticus GBS.     

Fossil juvenile coelacanths from the Devonian of South Africa shed light on the order of character acquisition in actinistians

A new coelacanth genus from the Famennian (Upper Devonian) of South Africa is described, principally from presumed juveniles. S erenichthys kowiensis gen. et sp. nov. uniquely shares with Diplocercides a ventral expansion of the elbow‐like lachrymojugal, as well as a symmetrical diphycercal tail supported by expanded neural and haemal spines and radials. Serenichthys is distinguished from Diplocercides by a number of derived characters, including possession of longer anterior parietals, a more crescent‐shaped postorbital with a more anteriorly positioned infraorbital canal, and a far smaller squamosal, which is well separated from the skull roof. By contrast, Serenichthys appears to lacks a second dorsal fin lobe, a derived feature present in Diplocercides. Most specimens of Serenichthys are between 3 and 6 cm in length. They have large eyes, and dermal bones of the skull ornamented with long wavy ridges, similar to the dermal ornament of other Devonian coelacanths such as Gavinia. Larger isolated operculae also collected from the Waterloo Farm locality and attributed to Serenichthys indicate that with growth the ridges on the dermal bones transformed into elongate tubercles, reminiscent of those of Diplocercides and Carboniferous taxa. Phylogenetic analysis resolves Serenichthys as the sister group of Holopterygius and all known post‐Devonian coelacanths. The clade including the unusual leaf‐shaped coelacanths, the Devonian Holopterygius and Carboniferous Allenypterus, branches from the coelacanth lineage immediately crownward of Serenichthys. The presence of abundant juveniles within an estuarine setting strongly parallels the discovery of similarly sized juveniles of Rhabdoderma exiguus together with eggs and yolk‐sack larvae in the Upper Carboniferous Mazon Creek biota. It is therefore argued that Serenichthys, like Rhabdoderma, was using the sheltered estuarine environment as a nursery. © 2015 The Linnean Society of London     

Wing morphometrics as a possible tool for the diagnosis of the Ceratitis fasciventris,C. anonae,C. rosa complex (Diptera,Tephritidae)

Previous attempts to resolve the Ceratitis FAR complex (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa, Diptera, Tephritidae) showed contrasting results and revealed the occurrence of five microsatellite genotypic clusters (A, F1, F2, R1, R2). In this paper we explore the potential of wing morphometrics for the diagnosis of FAR morphospecies and genotypic clusters. We considered a set of 227 specimens previously morphologically identified and genotyped at 16 microsatellite loci. Seventeen wing landmarks and 6 wing band areas were used for morphometric analyses. Permutational multivariate analysis of variance detected significant differences both across morphospecies and genotypic clusters (for both males and females). Unconstrained and constrained ordinations did not properly resolve groups corresponding to morphospecies or genotypic clusters. However, posterior group membership probabilities (PGMPs) of the Discriminant Analysis of Principal Components (DAPC) allowed the consistent identification of a relevant proportion of specimens (but with performances differing across morphospecies and genotypic clusters). This study suggests that wing morphometrics and PGMPs might represent a possible tool for the diagnosis of species within the FAR complex. Here, we propose a tentative diagnostic method and provide a first reference library of morphometric measures that might be used for the identification of additional and unidentified FAR specimens.     

Mitogenome rearrangement in the cold-water scleractinian coral Lophelia pertusa (Cnidaria, Anthozoa) involves a long-term evolving group I intron

Group I introns are genetic insertion elements that invade host genomes in a wide range of organisms. In metazoans, however, group I introns are extremely rare, so far only identified within mitogenomes of hexacorals and some sponges. We sequenced the complete mitogenome of the cold-water scleractinian coral Lophelia pertusa, the dominating deep sea reef-building coral species in the North Atlantic Ocean. The mitogenome (16,150 bp) has the same gene content but organized in a unique gene order compared to that of other known scleractinian corals. A complex group I intron (6460 bp) inserted in the ND5 gene (position 717) was found to host seven essential mitochondrial protein genes and one ribosomal RNA gene. Phylogenetic analysis supports a vertical inheritance pattern of the ND5-717 intron among hexacoral mitogenomes with no examples of intron loss. Structural assessments of the Lophelia intron revealed an unusual organization that lacks the universally conserved ωG at the 3′ end, as well as a highly compact RNA core structure with overlapping ribozyme and protein coding capacities. Based on phylogenetic and structural analyses we reconstructed the evolutionary history of ND5-717, from its ancestral protist origin, through intron loss in some early metazoan lineages, and into a compulsory feature with functional implications in hexacorals.     

团体咨询改善小学生社会技能的实验研究

目的:通过实验研究表明团体咨询对改善小学生社会技能方面有重要作用。方法:某小学四年级一个班作为实验组,共41人(其中男生23人,女生18人)。采用前后测设计。对实验组进行十二次团体心理咨询,采用社会技能等级评定表进行前后测,以前后测结果的对照及受欢迎程度的改变值和喜欢他人程度的改变值作为效果指标。结果:在受欢迎程度上,前后测得分在受欢迎组、被拒绝组、低接纳组和女生中差异显著,被拒绝组学生团体咨询效果要优于受欢迎组的;在喜欢他人程度的改变上,低接纳组学生的团体咨询效果要优于高接纳组的;在受欢迎程度的改变上,女生的团体咨询效果要优于男生。结论:团体心理咨询对小学生社会技能的干预有效;采取班级团体心理咨询的方式,团体咨询的效果在人际关系不良的学生及女生中表现得更为明显。     

贺兰山保护区冬季岩羊集群特征的初步分析

Group size and composition of blue sheep （Pseudois nayaur) were studied in the Helan Mountains, Ningxia Autonomous Region from November to December 2003. We scanned mountain slopes with binoculars and observed with 20 - 60 x spotting-scope. A total of 310 herds of blue sheep and 1 336 individuals were observed during the study period. Blue sheep were frequently seen in small herds of 2 to 8 individuals, which represent 94.8% of total herds observed. Herds consisting of 9 individuals or more represented 5.2%. The largest herd we observed numbered 51 individuals. Mean group size was 4.2 individuals. Blue sheep herds can be divided into three types: male herds （composed solely of males), female herds (consisting of females with or without juveniles of both sexes), and mixed herds （including adult males, females, and subadults). Among the 310 herds, female herds were counted 150 times (48.4%}, mixed herds 154 times (49.7%), and male berds 6 times (1.9%) . Of 1 336 blue sheep classified by sex and age, adults, subadults and juveniles composed 64.1%, 20.8%, and 15.1% respectively. The female: male ratio of adults was 1:0.73. The ratio of adult females to juveniles was 1:0.56, which is higher than the ratio recorded in spring （ 1:0.43) or summer （ 1:0.44). The results showed that the Helan Mountains State Nature Reserve has succeed in protecting blue sheep.