Structural fragment clustering reveals novel structural and functional motifs in <Emphasis Type="Italic">α</Emphasis>-helical transmembrane proteins

Background  

A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology.     

Dispersal limitation inferred from an experimental translocation of Lomatium (Apiaceae) species outside their geographic ranges

Determining limitations on poleward range expansion is important for predicting how climate change will alter the distribution of species. For most species, it is not known what factors set their distributional limits and the role dispersal limitation might play if range‐limiting factors were altered. We conducted a transplant study of three related and co‐occurring Lomatium species at their northern range limits to test competing hypotheses of range limitation. We added seeds to experimental plots inside and outside the species’ geographic range (a regional treatment) in a replicated design with vegetation intact and vegetation reduced (a disturbance treatment) and with herbivore access and herbivore exclusion (an herbivory treatment). Germination and reemergence were measured through two growing seasons, along with community‐level variables. A fully‐crossed linear mixed model revealed that Lomatium survivorship outside the current range was as good or better than survivorship within the range, at least when the vegetative community remained intact. This suggests that the species are dispersal limited. Germination often was improved in the presence of an intact vegetative community, but this potentially facilitative effect was absent in second‐year reemergence. Plots exposed to herbivory had slightly, but significantly, reduced germination, though reemergence did not differ between herbivore treatments. Lomatium dissectum, a rare species, had significantly lower survivorship than its congeners, suggesting that range shifts in rare taxa may be particularly difficult. Seed additions beyond species’ range limits may be a strategy for overcoming dispersal limitation and assisting species in poleward migrations.     

Reduction of isoflurane MAC with buprenorphine and morphine in rats

Preoperative analgesics are being increasingly used to provide analgesia in the intraoperative and postoperative period. Opioids reduce anaesthetic requirements, although the effect varies with the different drug and species. The aim of this work was to determine whether buprenorphine reduces the minimum alveolar concentration (MAC) of isoflurane in a dose-related fashion, and whether this effect is similar to morphine when clinical doses of both drugs are used in the rat. Thirty-six male Wistar rats were anaesthetized with isoflurane, and MAC was determined before and after the administration of either buprenorphine or morphine. MAC of isoflurane was determined from alveolar gas samples when a standard noxious stimulus, in the form of a tail clamp, was applied. The duration and degree of reduction of the MAC of isoflurane were recorded. Basic cardiovascular and respiratory measurements were also recorded. Buprenorphine (10, 30 and 100 microg/kg) and morphine (1, 3 and 10 mg/kg) reduced in a dose-dependent fashion the MAC of isoflurane by 15%, 30% and 50%, respectively. Buprenorphine resulted in less cardiovascular and respiratory depression and had a longer-lasting action than morphine. In conclusion, buprenorphine has a dose-related isoflurane sparing effect in the rat similar to that caused by morphine at clinical doses of both drugs.     

Revealing Molecular Mechanisms by Integrating High-Dimensional Functional Screens with Protein Interaction Data

Functional genomics screens using multi-parametric assays are powerful approaches for identifying genes involved in particular cellular processes. However, they suffer from problems like noise, and often provide little insight into molecular mechanisms. A bottleneck for addressing these issues is the lack of computational methods for the systematic integration of multi-parametric phenotypic datasets with molecular interactions. Here, we present Integrative Multi Profile Analysis of Cellular Traits (IMPACT). The main goal of IMPACT is to identify the most consistent phenotypic profile among interacting genes. This approach utilizes two types of external information: sets of related genes (IMPACT-sets) and network information (IMPACT-modules). Based on the notion that interacting genes are more likely to be involved in similar functions than non-interacting genes, this data is used as a prior to inform the filtering of phenotypic profiles that are similar among interacting genes. IMPACT-sets selects the most frequent profile among a set of related genes. IMPACT-modules identifies sub-networks containing genes with similar phenotype profiles. The statistical significance of these selections is subsequently quantified via permutations of the data. IMPACT (1) handles multiple profiles per gene, (2) rescues genes with weak phenotypes and (3) accounts for multiple biases e.g. caused by the network topology. Application to a genome-wide RNAi screen on endocytosis showed that IMPACT improved the recovery of known endocytosis-related genes, decreased off-target effects, and detected consistent phenotypes. Those findings were confirmed by rescreening 468 genes. Additionally we validated an unexpected influence of the IGF-receptor on EGF-endocytosis. IMPACT facilitates the selection of high-quality phenotypic profiles using different types of independent information, thereby supporting the molecular interpretation of functional screens.     

Geographic patterns of genetic diversity from the native range of <Emphasis Type="Italic">Cactoblastis cactorum</Emphasis> (Berg) support the documented history of invasion and multiple introductions for invasive populations

Spread of the invasive cactus-feeding moth Cactoblastis cactorum has been well documented since its export from Argentina to Australia as a biocontrol agent, and records suggest that all non-native populations are derived from a single collection in the moth’s native range. The subsequent global spread of the moth has been complex, and previous research has suggested multiple introductions into North America. There exists the possibility of additional emigrations from the native range in nursery stock during the late twentieth century. Here, we present mitochondrial gene sequence data (COI) from South America (native range) and North America (invasive range) to test the hypothesis that the rapid invasive spread in North America is enhanced by unique genetic combinations from isolated portions of the native range. We found that haplotype richness in the native range of C. cactorum is high and that there was 90% lower richness in Florida than in Argentina. All Florida C. cactorum haplotypes are represented in a single, well-defined clade, which includes collections from the reported region of original export from Argentina. Thus, our data are consistent with the documented history suggesting a single exportation of C. cactorum from the eastern region of the native range. Additionally, the presence of geographic structure in three distinct haplotypes within the same clade across Florida supports the hypothesis of multiple introductions into Florida from a location outside the native range. Because the common haplotypes in Florida are also known to occur in the neighboring Caribbean Islands, the islands are a likely source for independent North American colonization events. Our data show that rapid and successful invasion within North America cannot be attributed to unique genetic combinations. This suggests that successful invasion of the southeastern US is more likely the product of a fortuitous introduction into favorable abiotic conditions and/or defense responses of specific Opuntia hosts, rapid adaptation, or a release from native enemies.     

Human sperm physiology: estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ) influence sperm metabolism and may be involved in the pathophysiology of varicocele-associated male infertility

The mechanisms by which varicocele affects fertility remain undetermined. Estrogens play a key role in the human male reproduction and human sperm expresses the estrogen receptors (ERs) and aromatase. In this study, by Western blotting we evidenced the ERs content concomitantly in healthy sperm and in oligoastenoteratozoospermic (OAT) samples without and with varicocele. In varicocele a strong reduction of the ERβ was observed, while the ERα was almost absent. Besides, transmission electron microscopy (TEM) confirmed the reduction of ERs expression in "varicocele" sperm, indicating that varicocele has a detrimental effect on sperm structure at molecular level. To further define the estrogen significance in male gamete and the pathophysiology of varicocele we investigated both the expression of ERα and ERβ in normal and pathologic sperm samples as well as we evaluated estradiol (E2) action on lipid and glucose sperm metabolism. Responses to E2 treatments on cholesterol efflux, protein tyrosine phosphorylations, motility, and acrosin activity in varicocele sperm were reduced or absent. The evaluation of the triglycerides content, lipase and acyl-CoA dehydrogenase activities, suggest that E2 exerts a lipolytic effect on human sperm metabolism. Concerning glucose metabolism, it appears that E2 induces G6PDH activity concomitantly to the insulin secretion. In "varicocele" sperm, the E2 did not induce energy expenditure. OAT sperm had E2-responsiveness but in a lesser extent with respect healthy sperm. This study discovered a novel role for E2/ERs in human sperm physiology, since they modulate sperm metabolism and new detrimental effects related to the pathophysiology of the varicocele condition.     

Mitogen-activated protein kinases and asthma

Mitogen-activated protein kinases (MAPKs) are evolutionary conserved enzymes which play a key role in signal transduction mediated by cytokines, growth factors, neurotransmitters and various types of environmental stresses. In the airways, these extracellular stimuli elicit complex inflammatory and structural changes leading to the typical features of asthma including T cell activation, eosinophil and mast cell infiltration, as well as bronchial hyperresponsiveness and airway remodelling. Because MAPKs represent an important point of convergence for several different signalling pathways, they affect multiple aspects of normal airway function and also significantly contribute to asthma pathophysiology. Therefore, this review focuses on the crucial involvement of MAPKs in asthma pathogenesis, thus also discussing their emerging role as molecular targets for anti-asthma drugs.