Application of Mu in vitro transposition for high-precision mapping of protein–protein interfaces on a yeast two-hybrid platform

High-precision mapping of regions involved in protein–protein interfaces of interacting protein partners is an essential component on a path to understand various cellular functions. Transposon-based systems, particularly those involving in vitro reactions, offer exhaustive insertion mutant libraries and high-throughput platforms for many types of genetic analyses. We present here a genetic strategy to accurately map interacting protein regions at amino acid precision that is based on transposition-assisted construction, sampling, and analysis of a comprehensive insertion mutant library. The methodology integrates random pentapeptide mutagenesis of proteins, yeast two-hybrid screening, and high-resolution genetic footprinting. This straightforward strategy is general, and it provides a rapid and easy means to identify critical contact regions in proteins without the requirement of prior structural knowledge.     

A statistical score for assessing the quality of multiple sequence alignments

Background  

Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc. Although the automatic construction of a multiple sequence alignment for a set of remotely related sequences cause a very challenging and error-prone task, many downstream analyses still rely heavily on the accuracy of the alignments.     

Haemoconcentration via diuresis in short-term hypoxia: a possible role for cardiac natriuretic peptide in rainbow trout

Rainbow trout, exposed to acute hypoxia (decrease of oxygen level from full to 30% air saturation for 1 h, stable 30% air saturation for 2 h), showed more than twofold increase in urine flow rate. Hypoxic diuresis was associated with a sustained increase in dorsal aortic cardiac peptide (sCP) level, and the diuresis could be completely inhibited by a bolus injection of sCP antiserum. These results suggest that hypoxic haemoconcentration, which is partially achieved via increased urine flow rate in vertebrates, is caused by cardiac peptides. The results further suggest that cardiac peptide receptors in hypoxic fish gills modulate the postbranchial systemic level of sCP.     

Divergent selection on,but no genetic conflict over,female and male timing and rate of reproduction in a human population

The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution.     

In vitro maturation supplements affect developmental competence of bovine cumulus-oocyte complexes and embryo quality after vitrification

Oocyte quality affects subsequent embryo development and quality. We examined the impact of bovine oocyte in vitro maturation (IVM) conditions on subsequent embryo yield, quality and cryosurvival. Cumulus–oocyte complexes (COCs) were sampled for cytological and gene expression analysis after IVM in TCM199 supplemented with 10% fetal bovine serum (FBS), 4 mg/ml of fatty-acid-free bovine serum albumin (FAFBSA), 4 mg/ml of polyvinylpyrrolidone (PVP), FAFBSA with epidermal growth factor (EGF, 100 ng/ml) and insulin-like growth factor 1 (IGF-I, 100 ng/ml) (FAFBSAGF), PVP with EGF and IGF-I (PVPGF) or PVP with single strength BME and MEM amino acids (PVPAA). The remaining COCs were fertilized. On day 7 (IVF = day 0) quality 1 blastocysts were vitrified or analyzed for glucose transporter 1 (Glut-1) expression levels. The remaining blastocysts (days 7–9) were evaluated for morphology and total cell counts. After warming, survival and hatching rates were evaluated followed by total cell counts and Glut-1 expression levels. Only PVPGF IVM resulted in embryo production rates comparable to those recorded with FBS IVM. Growth factors with FAFBSA and amino acids with PVP reduced embryo production rates whereas the effect of the growth factors with PVP was negligible. Insulin-like growth factor 2 binding protein 3 (IGF2BP3) and beta cell translocation gene 4 (BTG4) were revealed as potential candidates for oocyte developmental competence, and secreted protein, acidic and rich in cysteine (SPARC) for cumulus cell expansion. There were no differences among treatments in hatching rates of vitrified embryos after warming. However, total cell numbers and Glut-1 expression levels at 72 h were affected.     

Increased Mortality Exposure within the Family Rather than Individual Mortality Experiences Triggers Faster Life-History Strategies in Historic Human Populations

Life History Theory predicts that extrinsic mortality risk is one of the most important factors shaping (human) life histories. Evidence from contemporary populations suggests that individuals confronted with high mortality environments show characteristic traits of fast life-history strategies: they marry and reproduce earlier, have shorter birth intervals and invest less in their offspring. However, little is known of the impact of mortality experiences on the speed of life histories in historical human populations with generally higher mortality risk, and on male life histories in particular. Furthermore, it remains unknown whether individual-level mortality experiences within the family have a greater effect on life-history decisions or family membership explains life-history variation.In a comparative approach using event history analyses, we study the impact of family versus individual-level effects of mortality exposure on two central life-history parameters, ages at first marriage and first birth, in three historical human populations (Germany, Finland, Canada). Mortality experience is measured as the confrontation with sibling deaths within the natal family up to an individual''s age of 15.Results show that the speed of life histories is not adjusted according to individual-level mortality experiences but is due to family-level effects. The general finding of lower ages at marriage/reproduction after exposure to higher mortality in the family holds for both females and males. This study provides evidence for the importance of the family environment for reproductive timing while individual-level mortality experiences seem to play only a minor role in reproductive life history decisions in humans.     

Browsing‐mediated shrub canopy changes drive composition and species richness in forest‐tundra ecosystems

Changes in climate and in browsing pressure are expected to alter the abundance of tundra shrubs thereby influencing the composition and species richness of plant communities. We investigated the associations between browsing, tundra shrub canopies and their understory vegetation by utilizing a long‐term (10–13 seasons) experiment controlling reindeer and ptarmigan herbivory in the subarctic forest tundra ecotone in northwestern Fennoscandia. In this area, there has also been a consistent increase in the yearly thermal sum and precipitation during the study period. The cover of shrubs increased 2.8–7.8 fold in exclosures and these contrasted with browsed control areas creating a sharp gradient of canopy cover of tundra shrubs across a variety of vegetation types. Browsing exclusions caused significant shifts in more productive vegetation types, whereas little or no shift occurred in low‐productive tundra communities. The increased deciduous shrub cover was associated with significant losses of understory plant species and shifts in functional composition, the latter being clearest in the most productive plant community types. The total cover of understory vegetation decreased along with increasing shrub cover, while the cover of litter showed the opposite response. The cover of cryptogams decreased along with increasing shrub cover, while the cover of forbs was favoured by a shrub cover. Increasing shrub cover decreased species richness of understory vegetation, which was mainly due to the decrease in the cryptogam species. The effects were consistent across different types of forest tundra vegetation indicating that shrub increase may have broad impacts on arctic vegetation diversity. Deciduous shrub cover is strongly regulated by reindeer browsing pressure and altered browsing pressure may result in a profound shrub expansion over the next one or two decades. Results suggest that the impact of an increase in shrubs on tundra plant richness is strong and browsing pressure effectively counteracts the effects of climate warming‐driven shrub expansion and hence maintains species richness.     

Bile acid-cysteamine conjugates: structural properties, gelation, and toxicity evaluation

Design, synthesis, and characterization of six novel bile acid-cysteamine conjugates together with investigation of their structural studies, gelation properties, and preliminary toxicity evaluation, are reported. Solid state properties of selected compounds were studied by means of X-ray diffraction and (13)C CPMAS NMR spectroscopy. N-(2-thioethyl)-3α,7α,12α-trihydroxy-5β-cholan-24-amide was shown to exhibit (pseudo)polymorphism, and a single crystal structure of its non-stoichiometric hydrate is reported herein. Cholyl and dehydrocholyl derivatives bearing three functionalities in their steroidal backbone were shown to undergo self-assembly leading to gelation in certain organic solvents. Preliminary morphology studies of the formed gels by scanning electron microscopy (SEM) were performed. The standard model mouse fibroblast cell line together with the MTT and NR tests were utilized for evaluating the toxicity of the prepared compounds. Lithocholyl, ursodeoxycholyl, and dehydrocholyl derivatives turned out to be relatively non-toxic in the conditions studied.     

Rat prostate gland--a good model for demonstration of ornithine decarboxylase by immunohistochemistry

Summary Ornithine decarboxylase was localized immunohistochemically in paraffin sections of prostate glands of the rat using Sternberger's PAP technique. Two types of immunoreactive cells were detected in the gland epithelium: strongly positive ones and weakly positive ones. Unreactive cells were also present. The functional role of the enzyme in the secretory process of the glands is discussed in the light of these findings.