ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line resources are available for revealing globular domains in sequences, there has hitherto been no comprehensive collection of small functional sites/motifs comparable to the globular domain resources, yet these are as important for the function of multidomain proteins. Short linear peptide motifs are used for cell compartment targeting, protein-protein interaction, regulation by phosphorylation, acetylation, glycosylation and a host of other post-translational modifications. ELM, the Eukaryotic Linear Motif server at http://elm.eu.org/, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryotic proteins, aiming to fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate because the usual significance assessments are inappropriate. Therefore the server is implemented with several logical filters to eliminate false positives. Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more.     

反义锁核酸阻断耐甲氧西林金黄色葡萄球菌agr群体感应系统

目的:利用反义策略,设计、筛选针对agrA mRNA的反义锁核酸,阻断agr群体感应系统,降低MRSA毒力因子的表达,减小细菌生存压力,为抗耐药菌感染提供一种新策略。方法:应用Primer Premier 5.0和RNA structure 4.5两种软件,设计、筛选2条针对agrA mRNA的反义寡核苷酸序列,对其进行锁核酸修饰,并与透膜肽(KFF)3K共价连接,将这两条反义序列导入细菌体内。体外与MRSA共培养,观察细菌生存情况。实时定量PCR检测其对agrA及agr群体感受系统的效应分子RNAⅢ和下游毒力基因hla的转录水平的影响,Western blot检测其是否能抑制α-溶血素的表达。结果:两条反义锁核酸序列PLNA34和PLNA522在体外均无抗菌活性,但都能不同程度的抑制agrA,RNAⅢ和hla的转录水平;相比较而言,PLNA34的抑制效果更佳,并能明显抑制α-溶血素的分泌表达。结论:agrA可作为抗MRSA感染的新靶点,为新型抗MRSA药物的研发提供了理论基础。     

Reproductive system and fitness of Vriesea friburgensis,a self‐sterile bromeliad species

Reproductive biology and plant fertility are directly related to many aspects of plant evolution and conservation biology. Vriesea friburgensis is an epiphytic and terrestrial bromeliad endemic to the Brazilian Atlantic rainforest. Hand‐pollination experiments were used to examine the reproductive system in a wild population of V. friburgensis. Plant fertility was assigned considering flower production, fruit and seed set, seed germination, and pollen viability. Self‐sterility observed from spontaneous selfing and manual self‐pollination treatments may be the consequence of late‐acting self‐incompatibility. Hand‐pollination results indicated no pollen limitation in the population studied. Floral biology features such as a few daily open flowers, nectar production, and sugar concentration corroborate hummingbirds as effective pollinators, although bees were also documented as pollinators. Components of fitness such as high flower, fruit, and seed production together with high seed and pollen viability indicate that this wild population is viable. From a conservation point of view, we highlight that this self‐sterile species depends on pollinator services to maintain its population fitness and viability through cross‐pollination. Currently, pollinators are not limited in this population of V. friburgensis. Conversely, the maintenance and continuous conservation of this community is essential for preserving this plant–pollinator mutualism.     

Sports genetics: the PPARA gene and athletes’ high ability in endurance sports. A systematic review and meta-analysis

A meta-analysis was performed with the aim of re-evaluating the role of the peroxisome proliferator activated receptor alpha (PPARA) gene intron 7 G/C polymorphism (rs4253778) in athletes’ high ability in endurance sports. Design: A meta-analysis of case control studies assessing the association between the G/C polymorphisms of the PPARA gene and endurance sports was conducted. The Cochrane Review Manager software was used to compare the genotype and allele frequencies between endurance athletes and controls to determine whether a genetic variant is more common in athletes than in the general population. Five studies, encompassing 760 endurance athletes and 1792 controls, fulfilled our inclusion criteria. The pooled odds ratio (and confidence intervals, CIs) for the G allele compared to the C allele was 1.65 (95% CI 1.39-1.96). The pooled OR for the GG genotype compared to the GC genotype was 1.79 (95% CI 1.44-2.22), and for the GG genotype compared to the CC genotype 2.37 (95% CI 1.40-3.99). There was no evidence of heterogeneity (I² =0%) or of publication bias. Athletes with high ability in endurance sports had a higher frequency of the GG genotype and G allele.     

Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information

Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in the PDB with respect to the great amount of interaction data coming from high-throughput experiments (two-hybrid or affinity purification of protein complexes and mass spectrometry). Nevertheless, we can rely on computational techniques for the extraction of high-quality and information-rich data from the known structures and for their spreading in the protein sequence space. We describe here the ongoing research projects in our group: we analyse the protein complexes stored in the PDB and, for each complex involving one domain belonging to a family of interaction domains for which some interaction data are available, we can calculate its probability of interaction with any protein sequence. We analyse the structures of proteins encoding a function specified in a PROSITE pattern, which exhibits relatively low selectivity and specificity, and build extended patterns. To this aim, we consider residues that are well-conserved in the structure, even if their conservation cannot easily be recognized in the sequence alignment of the proteins holding the function. We also analyse protein surface regions and, through the annotation of the solvent-exposed residues, we annotate protein surface patches via a structural comparison performed with stringent parameters and independently of the residue order in the sequence. Local surface comparison may also help in identifying new sequence patterns, which could not be highlighted with other sequence-based methods.     

Reduction of chromosome number in Eleocharis subarticulata (Cyperaceae) by multiple translocations

Eleocharis subarticulata is recorded as the third species of Cyperaceae with a reduced chromosome number ( n  = 3), following reports on Rhynchospora tenuis ( n  = 2) and Fimbristylis umbellaris ( n  = 3). For Eleocharis, the numbers recorded to date vary from 2 n  = 10 to 2 n  = c. 196, with x  = 5 as the possible basic number. The karyotype of E. subarticulata was studied using conventional staining (mitosis and meiosis), C-CMA₃/DAPI banding, and FISH with 45S rDNA and telomere probes. The chromosomes showed no primary constrictions, as expected in the holocentric chromosomes of Cyperaceae. The meiotic behaviour was abnormal, with a single multivalent ring of six chromosomes at metaphase I, resulting from multiple translocations. At anaphase I six chromatids migrated to each pole, evidencing the inverted meiosis, and these groups were also visible at metaphase II. The C-CMA₃/DAPI banding technique showed only four terminal GC-rich blocks. FISH with 45S rDNA probes revealed four terminal signals, probably associated with GC-rich blocks. The telomeric probe located terminal signals in all the chromosomes, besides a hybridization site in the middle of the large pair. The occurrence of ectopic telomeric sites has not been described previously for plants with holokinetic karyotypes and with reduced chromosome numbers. These data reinforce the hypothesis of the reduction in chromosome number by multiple translocations.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 149 , 457–464.     

STUDIES ON THE FORMATION AND STATE OF DETERMINATION OF THE TRUNK ORGANIZER IN THE NEWT, CYNOPS PYRRHOGASTER

Mesoderm formation in the presumptive trunk organizer was analyzed in gastrulae of Cynops pyrrhogaster. The presumptive trunk organizer showed little or no mesodermal differentiation in the beginning gastrula (0 h embryo). But as soon as the presumptive trunk organizer came into contact with the newly invaginated cranial archenteron roof, it rapidly formed mesoderm. This suggests that this differentiation was brought about by an inductive effect of the underlying cranial archenteron roof. For investigation of this possibility, the presumptive trunk organizer of 0 h embryos (Tr-0) and the newly invaginated cranial archenteron roof (presumptive pharyngeal endoderm and prechordal plate) of successive stages were cultured in isolation and by the sandwich technique. The newly invaginated presumptive pharyngeal endoderm and prechordal plate had no effect on mesoderm formation of the presumptive trunk organizer, and mesodermal differentiation of the combinations was similar to that of the Tr-0 alone. On the other hand, results showed that the prechordal plate, which came into contact with the still uninvaginated presumptive trunk organizer, stimulated dorsalisation of the weakly mesodermized trunk organizer. Based on these results, the stepwise process of mesoderm formation in the trunk organizer is discussed.     

The presence of Compsocerops (Brachyopoidea: Chigutisauridae) (Late Triassic) in southern Brazil with comments on chigutisaurid palaeobiogeography

Abstract: Chigutisauridae is the longest‐lived trematosaurian clade (from early Triassic to early Cretaceous). They were reported in Argentina, Australia, India and South Africa. This contribution reports a putative chigutisaurid specimen in the Carnian of southern Brazil (Santa Maria Formation, Paraná Basin). The material comprises two skull fragments, a mandibular fragment, a clavicular blade and a humerus. Ontogenetic features point to an early development stage of the specimen. The presence of a long, straight and pointed tabular horn, which runs parallel to the skull midline towards its tip, and a distinctive projection in the posterior border of the postparietal indicates a close relationship of the Brazilian chigutisaurid with the Indian Compsocerops cosgriffi. Three distinctive and combined characters suggest that the Brazilian chigutisaurid is a distinctive specimen: the presence of an alar process of the jugal in the ventral margin of the orbit; jugal does not extend well beyond the anterior margin of the orbit; and tabular does not contact the parietal. These characters could justify the erection of a new taxon; however, they might reflect its immature ontogenetic stage as well. Accordingly, we attribute this new specimen to Compsocerops sp. Argentinean and Indian occurrences are dated as Norian, so the presence of a Carnian chigutisaurid in southern Brazil indicates that western Gondwana chigutisaurids have first occupied the Paraná Basin and later migrated towards west (to Argentina) and east (India). However, the presence of ghost chigutisaurid taxa cannot be dismissed, because their long temporal range contrasts with their still short (in comparison with other temnospondyl groups) geographic distribution. Hence, they might have been more geographically widespread than their fossil record suggests.