Carry‐over effects of winter habitat vary with age and sex in yellow warblers Setophaga petechia

We use stable isotope data to investigate the role of winter habitat use in altering the breeding phenology of yellow warblers Setophaga petechia. We first confirm that δ¹³C and δ¹⁵N isotopic signatures vary with winter habitat use in this species. We then examine the relationship between winter habitat use, breeding phenology and productivity within four age‐sex‐classes, since life history theory would predict that carry‐over effects should vary with age and gender. The δ¹³C signatures of yellow warblers using riparian habitats over winter were more depleted than the signatures of those using agricultural or scrub habitat. Individuals on the Pacific coast of Mexico were also more δ¹⁵N enriched than those on the southern Gulf of Mexico. δ¹³C and δ¹⁵N signatures were only correlated with earlier clutch initiation and subsequent higher productivity in first‐breeding‐season females. We estimate that shifts in δ¹³C equivalent to a shift from scrub to riparian winter habitat would be associated with the production of 0.8 more fledglings by yearling females. Pre‐breeding events that influence the timing of breeding could also influence the reproductive performance of older males and females, but we found little evidence that winter habitat use influenced breeding season phenology in these birds.     

A flexible docking approach for prediction of T cell receptor–peptide–MHC complexes

T cell receptors (TCRs) are immune proteins that specifically bind to antigenic molecules, which are often foreign peptides presented by major histocompatibility complex proteins (pMHCs), playing a key role in the cellular immune response. To advance our understanding and modeling of this dynamic immunological event, we assembled a protein–protein docking benchmark consisting of 20 structures of crystallized TCR/pMHC complexes for which unbound structures exist for both TCR and pMHC. We used our benchmark to compare predictive performance using several flexible and rigid backbone TCR/pMHC docking protocols. Our flexible TCR docking algorithm, TCRFlexDock, improved predictive success over the fixed backbone protocol, leading to near‐native predictions for 80% of the TCR/pMHC cases among the top 10 models, and 100% of the cases in the top 30 models. We then applied TCRFlexDock to predict the two distinct docking modes recently described for a single TCR bound to two different antigens, and tested several protein modeling scoring functions for prediction of TCR/pMHC binding affinities. This algorithm and benchmark should enable future efforts to predict, and design of uncharacterized TCR/pMHC complexes.     

A novel mechanism of ligand binding and release in the odorant binding protein 20 from the malaria mosquito Anopheles gambiae

Anopheles gambiae mosquitoes that transmit malaria are attracted to humans by the odor molecules that emanate from skin and sweat. Odorant binding proteins (OBPs) are the first component of the olfactory apparatus to interact with odorant molecules, and so present potential targets for preventing transmission of malaria by disrupting the normal olfactory responses of the insect. AgamOBP20 is one of a limited subset of OBPs that it is preferentially expressed in female mosquitoes and its expression is regulated by blood feeding and by the day/night light cycles that correlate with blood‐feeding behavior. Analysis of AgamOBP20 in solution reveals that the apo‐protein exhibits significant conformational heterogeneity but the binding of odorant molecules results in a significant conformational change, which is accompanied by a reduction in the conformational flexibility present in the protein. Crystal structures of the free and bound states reveal a novel pathway for entrance and exit of odorant molecules into the central‐binding pocket, and that the conformational changes associated with ligand binding are a result of rigid body domain motions in α‐helices 1, 4, and 5, which act as lids to the binding pocket. These structures provide new insights into the specific residues involved in the conformational adaptation to different odorants and have important implications in the selection and development of reagents targeted at disrupting normal OBP function.     

Examining post‐translational modification‐mediated protein–protein interactions using a chemical proteomics approach

Post‐translational modifications (PTM) of proteins can control complex and dynamic cellular processes via regulating interactions between key proteins. To understand these regulatory mechanisms, it is critical that we can profile the PTM‐dependent protein–protein interactions. However, identifying these interactions can be very difficult using available approaches, as PTMs can be dynamic and often mediate relatively weak protein–protein interactions. We have recently developed CLASPI (cross‐linking‐assisted and stable isotope labeling in cell culture‐based protein identification), a chemical proteomics approach to examine protein–protein interactions mediated by methylation in human cell lysates. Here, we report three extensions of the CLASPI approach. First, we show that CLASPI can be used to analyze methylation‐dependent protein–protein interactions in lysates of fission yeast, a genetically tractable model organism. For these studies, we examined trimethylated histone H3 lysine‐9 (H3K9Me₃)‐dependent protein–protein interactions. Second, we demonstrate that CLASPI can be used to examine phosphorylation‐dependent protein–protein interactions. In particular, we profile proteins recognizing phosphorylated histone H3 threonine‐3 (H3T3‐Phos), a mitotic histone “mark” appearing exclusively during cell division. Our approach identified survivin, the only known H3T3‐Phos‐binding protein, as well as other proteins, such as MCAK and KIF2A, that are likely to be involved in weak but selective interactions with this histone phosphorylation “mark”. Finally, we demonstrate that the CLASPI approach can be used to study the interplay between histone H3T3‐Phos and trimethylation on the adjacent residue lysine 4 (H3K4Me₃). Together, our findings indicate the CLASPI approach can be broadly applied to profile protein–protein interactions mediated by PTMs.     

Process model comparison and transferability across bioreactor scales and modes of operation for a mammalian cell bioprocess

A Monod kinetic model, logistic equation model, and statistical regression model were developed for a Chinese hamster ovary cell bioprocess operated under three different modes of operation (batch, bolus fed‐batch, and continuous fed‐batch) and grown on two different bioreactor scales (3 L bench‐top and 15 L pilot‐scale). The Monod kinetic model was developed for all modes of operation under study and predicted cell density, glucose glutamine, lactate, and ammonia concentrations well for the bioprocess. However, it was computationally demanding due to the large number of parameters necessary to produce a good model fit. The transferability of the Monod kinetic model structure and parameter set across bioreactor scales and modes of operation was investigated and a parameter sensitivity analysis performed. The experimentally determined parameters had the greatest influence on model performance. They changed with scale and mode of operation, but were easily calculated. The remaining parameters, which were fitted using a differential evolutionary algorithm, were not as crucial. Logistic equation and statistical regression models were investigated as alternatives to the Monod kinetic model. They were less computationally intensive to develop due to the absence of a large parameter set. However, modeling of the nutrient and metabolite concentrations proved to be troublesome due to the logistic equation model structure and the inability of both models to incorporate a feed. The complexity, computational load, and effort required for model development has to be balanced with the necessary level of model sophistication when choosing which model type to develop for a particular application. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013     

A distinctive fungal community inhabiting cryoconite holes on glaciers in Svalbard

Cryoconite holes on glacier surfaces are ice-cold hot spots of microbial diversity and activity but still little is known about their fungal inhabitants. We provide the first report of distinctive fungal communities in cryoconite debris from three valley glaciers at Kongsfjorden, Svalbard. Multivariate analysis of terminal-restriction fragment length polymorphism (T-RFLP) profiles of rRNA ITS amplicons revealed that quite distinct fungal communities were found in cryoconite holes compared with soils from adjacent moraine and tundra sites, and that communities on glaciers with contrasting ice-surface hydrology also differed. Most of the fungi cultured from cryoconite sediment were basidiomycetous yeasts or filamentous Ascomycota (Helotiales/Pleosporales). The latter included aeroaquatic fungi, such as Articulospora and Varicosporium, implying a role for these important freshwater decomposers in the carbon dynamics of cryoconite holes. Matching of the dominant peaks from T-RFLP analysis to predicted peaks of cultured isolates confirmed the abundance of these aeroaquatic fungi but also revealed that most of the dominant T-RFLP peaks did not match any cultured isolates. Considering the prevalence and endangerment of glacial environments worldwide, these findings would suggest that their potential as reservoirs of fungal diversity should not be overlooked.     

Community-wide plasmid gene mobilization and selection

Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host''s chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.