Epac1 and cAMP-dependent protein kinase holoenzyme have similar cAMP affinity, but their cAMP domains have distinct structural features and cyclic nucleotide recognition

The cAMP-dependent protein kinase (PKA I and II) and the cAMP-stimulated GDP exchange factors (Epac1 and -2) are major cAMP effectors. The cAMP affinity of the PKA holoenzyme has not been determined previously. We found that cAMP bound to PKA I with a K(d) value (2.9 microM) similar to that of Epac1. In contrast, the free regulatory subunit of PKA type I (RI) had K(d) values in the low nanomolar range. The cAMP sites of RI therefore appear engineered to respond to physiological cAMP concentrations only when in the holoenzyme form, whereas Epac can respond in its free form. Epac is phylogenetically younger than PKA, and its functional cAMP site has presumably evolved from site B of PKA. A striking feature is the replacement of a conserved Glu in PKA by Gln (Epac1) or Lys (Epac2). We found that such a switch (E326Q) in site B of human RIalpha led to a 280-fold decreased cAMP affinity. A similar single switch early in Epac evolution could therefore have decreased the high cAMP affinity of the free regulatory subunit sufficiently to allow Epac to respond to physiologically relevant cAMP levels. Molecular dynamics simulations and cAMP analog mapping indicated that the E326Q switch led to flipping of Tyr-373, which normally stacks with the adenine ring of cAMP. Combined molecular dynamics simulation, GRID analysis, and cAMP analog mapping of wild-type and mutated BI and Epac1 revealed additional differences, independent of the Glu/Gln switch, between the binding sites, regarding space (roominess), hydrophobicity/polarity, and side chain flexibility. This helped explain the specificity of current cAMP analogs and, more importantly, lays a foundation for the generation of even more discriminative analogs.     

Bacterial Communities of Two Ubiquitous Great Barrier Reef Corals Reveals Both Site- and Species-Specificity of Common Bacterial Associates

Background

Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral.

Methodology/Principal Findings

Denaturing Gradient Gel Electrophoresis (DGGE) of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by “White Syndrome” (WS) underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome.

Conclusions/Significance

This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine invertebrate associates. Finally, the results did not support the contention that a single bacterial pathogen may be the causative agent of WS Acroporids on the GBR.     

Modeling the Time Evolution of the Nanoparticle-Protein Corona in a Body Fluid

Background

Nanoparticles in contact with biological fluids interact with proteins and other biomolecules, thus forming a dynamic corona whose composition varies over time due to continuous protein association and dissociation events. Eventually equilibrium is reached, at which point the continued exchange will not affect the composition of the corona.

Results

We developed a simple and effective dynamic model of the nanoparticle protein corona in a body fluid, namely human plasma. The model predicts the time evolution and equilibrium composition of the corona based on affinities, stoichiometries and rate constants. An application to the interaction of human serum albumin, high density lipoprotein (HDL) and fibrinogen with 70 nm N-iso-propylacrylamide/N-tert-butylacrylamide copolymer nanoparticles is presented, including novel experimental data for HDL.

Conclusions

The simple model presented here can easily be modified to mimic the interaction of the nanoparticle protein corona with a novel biological fluid or compartment once new data will be available, thus opening novel applications in nanotoxicity and nanomedicine.     

Recruitment in species-rich grasslands: the effects of functional traits and propagule pressure

Aims The assembly of plant communities is a complex process which combines impacts from the species pool, dispersal and propagule pressure, niche requirements of colonizing species and the niche structure of the community. Recent theory development has incorporated all these aspects, e.g. in 'stochastic niche theory'. We investigated recruitment into a species-rich grassland community, using an experimental approach where we manipulated the trait composition of the community and examined the success of colonizing species entering with various propagule pressure. Specifically, we examined two predictions: (i) colonization success increases with increasing difference between traits of the colonizing species and the trait profile of the community and (ii) colonization success increases with increasing propagule pressure.Methods The examined communities were species-rich semi-natural grasslands located in southern Sweden. After a careful documentation of the composition of the plant communities at the experimental sites, we manipulated the trait profile of species-rich grassland plots based on the plant functional trait specific leaf area (SLA), which is correlated with several key life history functions. In addition to SLA, seed mass was also used to describe the trait profile of grassland plots. Seeds of 12 plant species from the regional species pool, varying in SLA and seed mass, were sown into plots using four different levels of propagule pressure. Recruitment was examined after 1 year. We also planted juvenile 'plug plants' of the same species which allowed us to examine survivorship and growth beyond the seedling stage.Important findings Overall we found very limited evidence for relationships between the traits of the colonizing species and the trait profile of the community and for recruitment after sowing these relationships were contrary to the prediction. Survival of plug plants after two seasons of growth was high irrespective of the trait profile of the community, but growth of plug plants was affected by the trait profile of the surrounding community. For four of the species there was a positive effect of increased propagule pressure on colonization. The results suggest that species assembly in species-rich grasslands is not strongly dependent on the niche structure of the community. However, the finding that colonization of only a third of the species responded positively to increased propagule pressure indicates that there might be niche-related effects that were not captured by our treatments. Overall, our results indicate that the factors determining colonization in this community are species specific. Some species are able to colonize irrespective of niche relationships, provided that the propagule pressure is sufficiently high to overcome stochastic mortality after seed arrival. For other species, however, we cannot exclude that niche assembly occurred, but we failed to identify the relevant niche factor.     

Small worms, big appetites: ratios of different functional morphs in relation to interspecific competition in trematode parasites

Animals living in colonies or collectives composed of highly-related individuals often produce morphs that are physically and behaviourally specialised to perform specific tasks. Because such morphs are often sterile, their production represents a fitness cost for the colony and there should be an optimal ratio of the numbers of sterile specialists and reproductive members that may be adjustable to environmental conditions. Trematode parasites undergo asexual multiplication within their snail intermediate host, resulting in large numbers of clonal stages known as rediae or sporocysts, depending on the trematode species. In areas with high prevalences of infection, the host can be infected by multiple species, which can lead to intense competition for limited resources. Here, we describe the existence of specialised ‘mini-rediae’ in the trematode Philophthalmus sp. that are morphologically and functionally specialised for interspecific competition. Mini-rediae were observed feeding on the sporocysts of a co-occurring trematode species - Maritrema novaezealandensis. In addition, in larger snails - which are less likely to have M. novaezealandensis infections - Philophthalmus sp. produces relatively fewer mini-rediae than expected. Our findings support results from a prior study which demonstrated the existence of morphs that perform specialised functions in antagonistic interspecific interactions in trematodes, and additionally shows that the number of these morphs in each host is associated with the likelihood of encountering other species within the same host. Trematodes may thus provide interesting models for studying morphological specialisation in colonial organisms.     

Intra-host competition between co-infecting digeneans within a bivalve second intermediate host: Dominance by priority-effect or taking advantage of others?

We experimentally investigated the interactions between two parasites known to manipulate their host's phenotype, the trematodes Acanthoparyphium sp. and Curtuteria australis, which infect the cockle Austrovenus stutchburyi. The larval stages of both species encyst within the tissue of the bivalve's muscular foot, with a preference for the tip of the foot. As more individuals accumulate at that site, they impair the burrowing behaviour of cockles and increase the probability of the parasites' transmission to a bird definitive host. However, individuals at the foot tip are also vulnerable to non-host predators in the form of foot-cropping fish which selectively bite off the foot tip of exposed cockles. Parasites encysted at the foot base are safe from such predators although they do not contribute to altering host behaviour, but nevertheless benefit from host manipulation as all parasites within the cockle are transmitted if it is ingested by a bird. Experimental infection revealed that Acanthoparyphium sp. and C. australis have different encystment patterns within the host, with proportionally fewer Acanthoparyphium metacercariae encysting at the foot tip than C. australis. This indicates that Acanthoparyphium may benefit indirectly from C. australis and incur a lower risk of non-host predation. However, in co-infections, not only did C. australis have higher infectivity than Acanthoparyphium, it also severely affected the latter's infection success. The asymmetrical strategies and interactions between the two species suggest that the advantages obtained from exploiting the host manipulation efforts of another parasite might be offset by traits such as reduced competitiveness in co-infections.     

Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields

Thermophilic anaerobic noncellulolytic Thermoanaerobacter species are of great biotechnological importance in cellulosic ethanol production due to their ability to produce high ethanol yields by simultaneous fermentation of hexose and pentose. Understanding the genome structure of these species is critical to improving and implementing these bacteria for possible biotechnological use in consolidated bioprocessing schemes (CBP) for cellulosic ethanol production. Here we describe a comparative genome analysis of two ethanologenic bacteria, Thermoanaerobacter sp. X514 and Thermoanaerobacter pseudethanolicus 39E. Compared to 39E, X514 has several unique key characteristics important to cellulosic biotechnology, including additional alcohol dehydrogenases and xylose transporters, modifications to pentose metabolism, and a complete vitamin B₁₂ biosynthesis pathway. Experimental results from growth, metabolic flux, and microarray gene expression analyses support genome sequencing-based predictions which help to explain the distinct differences in ethanol production between these strains. The availability of whole-genome sequence and comparative genomic analyses will aid in engineering and optimizing Thermoanaerobacter strains for viable CBP strategies.     

Survival of Escherichia coli O157:H7 on cattle hides

The objective of this study was to determine the time period that Escherichia coli O157:H7 survives on the hides of cattle. Extensive research has been conducted and is ongoing to identify and develop novel preharvest intervention strategies to reduce the presence of E. coli O157:H7 on live cattle and subsequent transfer to processed carcasses. If a reduction of E. coli O157:H7 levels in feces can be achieved through preharvest intervention, it is not known how long it would take for such reductions to be seen on the hide. In the study presented herein, three trials were conducted to follow E. coli O157:H7 hide prevalence over time. For each trial, 36 animals were housed in individual stanchions to minimize or prevent hide contamination events. Through prevalence determination and isolate genotyping with pulsed-field gel electrophoresis, survival of E. coli O157:H7 on the hides of live cattle was determined to be short lived, with an approximate duration of 9 days or less. The results of this study suggest that any preharvest interventions that are to be administered at the end of the finishing period will achieve maximum effect in reducing E. coli O157:H7 levels on cattle hides if given 9 days before the cattle are presented for processing. However, it should be noted that interventions reducing pathogen shedding would also contribute to decreasing hide contamination through lowering the contamination load of the processing plant lairage environment, regardless of the time of application.     

Toward preclinical predictive drug testing for metabolism and hepatotoxicity by using in vitro models derived from human embryonic stem cells and human cell lines - a report on the Vitrocellomics EU-project

Drug-induced liver injury is a common reason for drug attrition in late clinical phases, and even for post-launch withdrawals. As a consequence, there is a broad consensus in the pharmaceutical industry, and within regulatory authorities, that a significant improvement of the current in vitro test methodologies for accurate assessment and prediction of such adverse effects is needed. For this purpose, appropriate in vivo-like hepatic in vitro models are necessary, in addition to novel sources of human hepatocytes. In this report, we describe recent and ongoing research toward the use of human embryonic stem cell (hESC)-derived hepatic cells, in conjunction with new and improved test methods, for evaluating drug metabolism and hepatotoxicity. Recent progress on the directed differentiation of human embryonic stem cells to the functional hepatic phenotype is reported, as well as the development and adaptation of bioreactors and toxicity assay technologies for the testing of hepatic cells. The aim of achieving a testing platform for metabolism and hepatotoxicity assessment, based on hESC-derived hepatic cells, has advanced markedly in the last 2-3 years. However, great challenges still remain, before such new test systems could be routinely used by the industry. In particular, we give an overview of results from the Vitrocellomics project (EU Framework 6) and discuss these in relation to the current state-of-the-art and the remaining difficulties, with suggestions on how to proceed before such in vitro systems can be implemented in industrial discovery and development settings and in regulatory acceptance.     

Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States

Spatial variation in the epidemiological patterns of successive waves of pandemic influenza virus in humans has been documented throughout the 20th century but never understood at a molecular level. However, the unprecedented intensity of sampling and whole-genome sequencing of the H1N1/09 pandemic virus now makes such an approach possible. To determine whether the spring and fall waves of the H1N1/09 influenza pandemic were associated with different epidemiological patterns, we undertook a large-scale phylogeographic analysis of viruses sampled from three localities in the United States. Analysis of genomic and epidemiological data reveals distinct spatial heterogeneities associated with the first pandemic wave, March to July 2009, in Houston, TX, Milwaukee, WI, and New York State. In Houston, no specific H1N1/09 viral lineage dominated during the spring of 2009, a period when little epidemiological activity was observed in Texas. In contrast, major pandemic outbreaks occurred at this time in Milwaukee and New York State, each dominated by a different viral lineage and resulting from strong founder effects. During the second pandemic wave, beginning in August 2009, all three U.S. localities were dominated by a single viral lineage, that which had been dominant in New York during wave 1. Hence, during this second phase of the pandemic, extensive viral migration and mixing diffused the spatially defined population structure that had characterized wave 1, amplifying the one viral lineage that had dominated early on in one of the world's largest international travel centers.