A Predictive Model of Intein Insertion Site for Use in the Engineering of Molecular Switches

Inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. Successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. By analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant correlation with the location of the intein insertion sites, and therefore may be useful in predicting insertion sites in other proteins that provide native-like intein function. Three of these properties, the distance to the active site and dimer interface site, the SVM score of the splice site cassette, and the sequence conservation of the site showed statistically significant correlation and strong predictive power, with area under the curve (AUC) values of 0.79, 0.76, and 0.73 respectively, while the distance to secondary structure/loop junction showed significance but with less predictive power (AUC of 0.54). In a case study of 20 insertion sites in the XynB xylanase, two features of native insertion sites showed correlation with the splice sites and demonstrated predictive value in selecting non-native splice sites. Structural modeling of intein insertions at two sites highlighted the role that the insertion site location could play on the ability of the intein to modulate activity of the host protein. These findings can be used to enrich the selection of insertion sites capable of supporting intein splicing and hosting an intein switch

Life-History Evolution on Tropidurinae Lizards: Influence of Lineage, Body Size and Climate

The study of life history variation is central to the evolutionary theory. In many ectothermic lineages, including lizards, life history traits are plastic and relate to several sources of variation including body size, which is both a factor and a life history trait likely to modulate reproductive parameters. Larger species within a lineage, for example tend to be more fecund and have larger clutch size, but clutch size may also be influenced by climate, independently of body size. Thus, the study of climatic effects on lizard fecundity is mandatory on the current scenario of global climatic change. We asked how body and clutch size have responded to climate through time in a group of tropical lizards, the Tropidurinae, and how these two variables relate to each other. We used both traditional and phylogenetic comparative methods. Body and clutch size are variable within Tropidurinae, and both traits are influenced by phylogenetic position. Across the lineage, species which evolved larger size produce more eggs and neither trait is influenced by temperature components. A climatic component of precipitation, however, relates to larger female body size, and therefore seems to exert an indirect relationship on clutch size. This effect of precipitation on body size is likely a correlate of primary production. A decrease in fecundity is expected for Tropidurinae species on continental landmasses, which are predicted to undergo a decrease in summer rainfall

Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation

Association between single nucleotide polymorphisms in the mu opioid receptor gene (OPRM1) and self-reported responses to alcohol in American Indians

Abstract Background Variation in response to the hedonic and adverse effects of a substance is in part an inherited factor that may influence its use, abuse and dependence. The mu opioid receptor is the primary site of action for opiates and individuals with polymorphisms in this receptor appear to have variation in the CNS effects of opiates. Several studies have suggested that this receptor may also mediate some of the effects of non-opioid drugs, such as alcohol. The purpose of this study was to investigate associations between 13 single nucleotide polymorphisms in the mu opioid receptor gene (OPRM1) with self-reported responses to alcohol, an endophenotype associated with the development of alcohol dependence, in American Indians living on eight contiguous reservations. Methods Each participant gave a blood sample and completed a structured diagnostic interview. Additionally, response to alcohol was indexed using the expectation version of the subjective high assessment scale (SHAS-E). SNPs were genotyped in 251 participants and data analyses were conducted using SOLAR. Results The estimated heritability (h2) for the SHAS-E phenotypes ranged from 0.01 to 0.28. Endorsing the expectation of a more intense response on one or more of the following items from the SHAS-E: buzzed, clumsy, dizzy, drunk, effects, high, nausea, sleepy, talkative, terrible, and/or uncomfortable after imbibing 2–3 drinks was significantly associated with having at least one minor allele for at least one of 7 SNPs (p < 0.01) in the OPRM1 receptor gene. Conclusion These studies provide data to suggest that the minor allele, for most of the polymorphisms in the OPRM1 receptor gene investigated, was found to be associated with a more intense, and/or more adverse, response to alcohol, traits that are significantly correlated with lowered quantity of alcohol consumption and less susceptibility to dependence in this Indian population. These data further suggest that making conclusions on the role of the mu opiod receptor gene in the development of alcohol dependence may be limited if only one polymorphism in the gene is evaluated in isolation

Enhancing Specific Health Literacy with a Digital Evidence-Based Patient Decision Aid for Hypertension: A Randomized Controlled Trial

Kai Wehkamp,1&ndash; 3,* Felicia Beatrice Kiefer,4,* Friedemann Geiger,1,5 Fueloep Scheibler,1 Jens Ulrich Rueffer,6 Norbert Donner-Banzhoff,7 Cornelia Betsch4 1Department of Pediatrics/Project SHARE TO CARE, University Hospital Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany; 2Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany; 3Department of Medical Management, MSH Medical School Hamburg, Hamburg, Germany; 4Center for Empirical Research in Economics and Behavioral Sciences, University of Erfurt, Erfurt, Th&uuml;ringen, Germany; 5Department of Psychology, MSH Medical School Hamburg, Hamburg, Germany; 6Take Part Media &amp; Science GmbH, Cologne, Nordrhein-Westfalen, Germany; 7Department of General Practice/Family Medicine, University of Marburg, Marburg, Hessen, Germany*These authors contributed equally to this workCorrespondence: Kai WehkampDepartment of Internal Medicine I, Project SHARE TO CARE, University Hospital Schleswig-Holstein (UKSH), Arnold-Heller-Stra&szlig;e 3, Kiel, 24105, GermanyTel +49 (0)431-500-0Email [email protected]: Health literacy is an important competency to make informed, shared decisions in line with patient&rsquo;s preferences. On the other hand, lower health literacy is associated with poorer health outcomes. Evidence-based patient decision aids (EbPDA) are validated instruments to support informed medical decisions and empower patients for relevant involvement in their care. This study aimed to investigate the effect of a digital EbPDA for hypertension on health literacy.Methods: In a randomized controlled trial, 124 participants were presented with a web-based scenario related to a newly diagnosed condition of arterial hypertension. The intervention group was provided with an online decision aid, while the control group was prompted to search for related information without support. Specific health literacy for hypertension was operationalized based on the European survey for health literacy (HLS-EU-Q47).Results: The intervention group showed a statistically significant increase in subjectively perceived overall specific health literacy regarding hypertension (p=0.02, Cohen&rsquo;s d=0.44). The effect was also statistically significant for the subcategories understanding, appraising, and applying health-related information (all p&lt; 0.05). At least equal results could be shown for participants with a lower level of education compared to participants with a high level.Conclusion: The findings suggest that digital EbPDAs can be an effective and easily scalable instrument to improve populations&rsquo; specific health literacy. A possible advantage of the measure could be that patients are addressed concerning important and pressing personal decisions, fostering awareness of the individual&rsquo;s need for health literacy to reflect one&rsquo;s options and preferences. EbPDAs may also be a promising approach to target vulnerable populations, as the investigated EbPDA seems to perform equally in less versus more educated individuals. For future research, it may be interesting to investigate whether EbPDAs have effects on general health literacy that go beyond the disease specifically addressed.Keywords: shared decision-making, decision aids, health literacy, equity, preference