Ecosystem size predicts eco‐morphological variability in a postglacial diversification

Identifying the processes by which new phenotypes and species emerge has been a long‐standing effort in evolutionary biology. Young adaptive radiations provide a model to study patterns of morphological and ecological diversification in environmental context. Here, we use the recent radiation (ca. 12k years old) of the freshwater fish Arctic charr (Salvelinus alpinus) to identify abiotic and biotic environmental factors associated with adaptive morphological variation. Arctic charr are exceptionally diverse, and in postglacial lakes there is strong evidence of repeated parallel evolution of similar morphologies associated with foraging. We measured head depth (a trait reflecting general eco‐morphology and foraging ecology) of 1,091 individuals across 30 lake populations to test whether fish morphological variation was associated with lake bathymetry and/or ecological parameters. Across populations, we found a significant relationship between the variation in head depth of the charr and abiotic environmental characteristics: positively with ecosystem size (i.e., lake volume, surface area, depth) and negatively with the amount of littoral zone. In addition, extremely robust‐headed phenotypes tended to be associated with larger and deeper lakes. We identified no influence of co‐existing biotic community on Arctic charr trophic morphology. This study evidences the role of the extrinsic environment as a facilitator of rapid eco‐morphological diversification.     

Plant community composition and species richness in the High Arctic tundra: From the present to the future

Arctic plant communities are altered by climate changes. The magnitude of these alterations depends on whether species distributions are determined by macroclimatic conditions, by factors related to local topography, or by biotic interactions. Our current understanding of the relative importance of these conditions is limited due to the scarcity of studies, especially in the High Arctic. We investigated variations in vascular plant community composition and species richness based on 288 plots distributed on three sites along a coast‐inland gradient in Northeast Greenland using a stratified random design. We used an information theoretic approach to determine whether variations in species richness were best explained by macroclimate, by factors related to local topography (including soil water) or by plant‐plant interactions. Latent variable models were used to explain patterns in plant community composition. Species richness was mainly determined by variations in soil water content, which explained 35% of the variation, and to a minor degree by other variables related to topography. Species richness was not directly related to macroclimate. Latent variable models showed that 23.0% of the variation in community composition was explained by variables related to topography, while distance to the inland ice explained an additional 6.4 %. This indicates that some species are associated with environmental conditions found in only some parts of the coast–inland gradient. Inclusion of macroclimatic variation increased the model's explanatory power by 4.2%. Our results suggest that the main impact of climate changes in the High Arctic will be mediated by their influence on local soil water conditions. Increasing temperatures are likely to cause higher evaporation rates and alter the distribution of late‐melting snow patches. This will have little impact on landscape‐scale diversity if plants are able to redistribute locally to remain in areas with sufficient soil water.     

Reactive oxidant and p42/44 MAP kinase signaling is necessary for mechanical strain-induced proliferation in pulmonary epithelial cells.

Mechanical strain is necessary for normal lung growth and development. Individuals with respiratory failure are supported with mechanical ventilation, leading to altered lung growth and injury. Understanding signaling pathways initiated by mechanical strain in lung epithelial cells will help guide development of strategies aimed at optimizing strain-induced lung growth while mitigating ventilator-induced lung injury. To study strain-induced proliferative signaling, focusing on the role of reactive oxidant species (ROS) and p42/44 mitogen-activated protein (MAP) kinase, human pulmonary epithelial H441 and MLE15 cells were exposed to equibiaxial cyclic mechanical strain. ROS were increased within 15 min of strain. N-acetylcysteine inactivated strain-induced ROS and inhibited p42/44 MAP kinase phosphorylation and strain-induced proliferation. PD98059 and UO126, p42/44 MAP kinase inhibitors, blocked strain-induced proliferation. To verify the specificity of p42/44 MAP kinase inhibition, cells were transfected with dominant-negative mitogen-activated protein kinase kinase-1 plasmid DNA. Transfected cells did not proliferate in response to mechanical strain. To determine whether strain-induced tyrosine kinase activity is necessary for strain-induced ROS-p42/44 MAP kinase signaling, genistein, a tyrosine kinase inhibitor, was used. Genistein did not block strain-induced ROS production or p42/44 MAP kinase phosphorylation. Gadolinium, a mechanosensitive calcium channel blocker, blocked strain-induced ROS production and p42/44 MAP kinase phosphorylation but not strain-induced tyrosine phosphorylation. These data support ROS production and p42/44 MAP kinase phosphorylation being involved in a common strain-induced signaling pathway, necessary for strain-induced proliferation in pulmonary epithelial cells, with a parallel strain-induced tyrosine kinase pathway.     

A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types

The study of induced pluripotency is complicated by the need for infection with high-titer retroviral vectors, which results in genetically heterogeneous cell populations. We generated genetically homogeneous 'secondary' somatic cells that carry the reprogramming factors as defined doxycycline (dox)-inducible transgenes. These cells were produced by infecting fibroblasts with dox-inducible lentiviruses, reprogramming by dox addition, selecting induced pluripotent stem cells and producing chimeric mice. Cells derived from these chimeras reprogram upon dox exposure without the need for viral infection with efficiencies 25- to 50-fold greater than those observed using direct infection and drug selection for pluripotency marker reactivation. We demonstrate that (i) various induction levels of the reprogramming factors can induce pluripotency, (ii) the duration of transgene activity directly correlates with reprogramming efficiency, (iii) cells from many somatic tissues can be reprogrammed and (iv) different cell types require different induction levels. This system facilitates the characterization of reprogramming and provides a tool for genetic or chemical screens to enhance reprogramming.     

Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge

Background  

Many common disorders have multiple genetic components which convey increased susceptibility. SNPs have been used to identify genetic components which are associated with a disease. Unfortunately, many studies using these methods suffer from low reproducibility due to lack of power.     

BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

Background

Recently in a number of studies, it has been demonstrated that the innate immune system doesn't merely acts as the first line of defense but provides critical signals for the development of specific adaptive immune response. Innate immune system employs a set of receptors called pattern recognition receptors (PRRs) that recognize evolutionarily conserved patterns from pathogens called pathogen associated molecular patterns (PAMPs). In order to assist scientific community, a database PRRDB has been developed that provides extensive information about pattern recognition receptors and their ligands.

Results

The current version of database contains around 500 patterns recognizing receptors from 77 distinct organisms ranging from insects to human. This includes 177 Toll-like receptors, 124 are Scavenger receptors and 67 are Nucleotide Binding Site-Leucine repeats rich receptors. The database also provides information about 266 ligands that includes carbohydrates, proteins, nucleic acids, glycolipids, glycoproteins, lipopeptides. A number of web tools have been integrated in PRRDB in order to provide following services: i) searching on any field; ii) database browsing; and iii) BLAST search against the pattern-recognition receptors. PRRDB also provides external links to standard databases like Swiss-Prot and Pubmed.

Conclusion

PRRDB is a unique database of its kind, which provides comprehensive information about innate immunity. This database will be very useful in designing effective adjuvant for subunit vaccine and in understanding role of innate immunity. The database is available from the URL's in the Availabiltiy and requirements section.     

Mortality rates in subjects with fetal alcohol spectrum disorders and their siblings

BACKGROUND: Our objective was to estimate the mortality rate in subjects with fetal alcohol spectrum disorders (FASD) and their siblings whose FASD status was unknown. METHODS: We used the state FASD Registry to link subjects with FASD to a North Dakota birth certificate. We were able to link 304 of 486 cases (63%). We used the birth certificates to identify the mother and children born to the mother (siblings). We then searched for death certificates for both the FASD cases and their siblings. We then calculated the annual and age‐adjusted mortality rates for the siblings of the Registry cases and compared them with mortality rates from North Dakota. RESULTS: The FASD case mortality rate was 2.4%, with a 4.5% mortality rate for their sibings, accounting for 14% of all deaths when compared to the North Dakota residents matched by age and year of death. The sibling deaths accounted for 21.5% of all cause mortality matched by age and year of death. The age‐standardized mortality ratios were 4.9 for the FASD cases and 2.6 for their siblings whose FASD status was unknown. CONCLUSIONS: Mortality rates for FASD cases and their siblings were increased and represent a substantial proportion of all cause mortality in North Dakota. Prevention of FASD may be a useful strategy to decrease mortality. Birth Defects Research (Part A), 2008. © 2008 Wiley‐Liss, Inc.