Whether rising atmospheric carbon dioxide (CO2) concentrations will cause forests to grow faster and store more carbon is an open question. Using free air CO2 release in combination with a canopy crane, we found an immediate and sustained enhancement of carbon flux through 35-meter-tall temperate forest trees when exposed to elevated CO2. However, there was no overall stimulation in stem growth and leaf litter production after 4 years. Photosynthetic capacity was not reduced, leaf chemistry changes were minor, and tree species differed in their responses. Although growing vigorously, these trees did not accrete more biomass carbon in stems in response to elevated CO2, thus challenging projections of growth responses derived from tests with smaller trees.

Flexible polypeptides such as unfolded proteins may access an astronomical number of conformations. The most advanced simulations of such states usually comprise tens of thousands of individual structures. In principle, a comparison of parameters predicted from such ensembles to experimental data provides a measure of their quality. In practice, analyses that go beyond the comparison of unbiased average data have been impossible to carry out on the entirety of such very large ensembles and have, therefore, been restricted to much smaller subensembles and/or nondeterministic algorithms. Here, we show that such very large ensembles, on the order of 10(4) to 10(5) conformations, can be analyzed in full by a maximum entropy fit to experimental average data. Maximizing the entropy of the population weights of individual conformations under experimental χ(2) constraints is a convex optimization problem, which can be solved in a very efficient and robust manner to a unique global solution even for very large ensembles. Since the population weights can be determined reliably, the reweighted full ensemble presents the best model of the combined information from simulation and experiment. Furthermore, since the reduction of entropy due to the experimental constraints is well-defined, its value provides a robust measure of the information content of the experimental data relative to the simulated ensemble and an indication for the density of the sampling of conformational space. The method is applied to the reweighting of a 35,000 frame molecular dynamics trajectory of the nonapeptide EGAAWAASS by extensive NMR (3)J coupling and RDC data. The analysis shows that RDCs provide significantly more information than (3)J couplings and that a discontinuity in the RDC pattern at the central tryptophan is caused by a cluster of helical conformations. Reweighting factors are moderate and consistent with errors in MD force fields of less than 3kT. The required reweighting is larger for an ensemble derived from a statistical coil model, consistent with its coarser nature. We call the method COPER, for convex optimization for ensemble reweighting. Similar advantages of large-scale efficiency and robustness can be obtained for other ensemble analysis methods with convex targets and constraints, such as constrained χ(2) minimization and the maximum occurrence method.

Acid-sensing ion channels (ASICs) are H +-activated neuronal Na + channels. They are involved in fear behavior, learning, neurodegeneration after ischemic stroke and in pain sensation. ASIC activation has so far been studied only with fast pH changes, although the pH changes associated with many roles of ASICs are slow. It is currently not known whether slow pH changes can open ASICs at all. Here, we investigated to which extent slow pH changes can activate ASIC1a channels and induce action potential signaling. To this end, ASIC1a current amplitudes and charge transport in transfected Chinese hamster ovary cells, and ASIC-mediated action potential signaling in cultured cortical neurons were measured in response to defined pH ramps of 1-40 s duration from pH 7.4 to pH 6.6 or 6.0. A kinetic model of the ASIC1a current was developed and integrated into the Hodgkin-Huxley action potential model. Interestingly, whereas the ASIC1a current amplitude decreased with slower pH ramps, action potential firing was higher upon intermediate than fast acidification in cortical neurons. Indeed, fast pH changes (<4 s) induced short action potential bursts, while pH changes of intermediate speed (4-10 s) induced longer bursts. Slower pH changes (>10 s) did in many experiments not generate action potentials. Computer simulations corroborated these observations. We provide here the first description of ASIC function in response to defined slow pH changes. Our study shows that ASIC1a currents, and neuronal activity induced by ASIC1a currents, strongly depend on the speed of pH changes. Importantly, with pH changes that take >10 s to complete, ASIC1a activation is inefficient. Therefore, it is likely that currently unknown modulatory mechanisms allow ASIC activity in situations such as ischemia and inflammation.

Whether screening the metabolic activity of immune cells facilitates discovery of molecular pathology remains unknown. Here we prospectively screened the extracellular acidification rate (ECAR) as a measure of glycolysis and the oxygen consumption rate (OCR) as a measure of mitochondrial respiration in B cells from patients with primary antibody deficiency (PAD). The highest OCR values were detected in three study participants with persistent polyclonal B cell lymphocytosis (PPBL). Exome sequencing identified germline mutations in SDHA, which encodes succinate dehydrogenase subunit A, in all three patients with PPBL. SDHA gain-of-function led to accumulation of fumarate in PPBL B cells, which engaged the KEAP1-Nrf2 system to drive the transcription of genes encoding inflammatory cytokines. In a single patient trial, blocking the activity of the cytokine IL-6 in vivo prevented systemic inflammation and ameliorated clinical disease. Overall, our study has identified pathological mitochondrial retrograde signaling as a disease modifier in PAD. 3 Primary immunodeficiency disorders (PIDs) are rare genetic syndromes arising from defects in the immune system 1. The majority of PID patients display primary antibody deficiency (PAD) that can develop due to B cell intrinsic defects 2. The causes and genetic background of PADs are complex and pathogenic mutations have been identified only in a minority of cases 3, 4, 5. PADs present with a spectrum of clinical problems, ranging from infections to autoinflammation, autoimmunity, lymphoproliferation and enteropathy. Non-infectious complications are typically unaffected by immunoglobulin replacement therapy and contribute to excess mortality 6. The spectrum of clinical presentation is broad even in patients harboring the same pathogenic mutations, pointing to disease modifiers shaping clinical features 6. Cellular metabolism governs immune cell function 7, 8, 9. Specifically, various facets of glycolysis and glutaminolysis impact the function of B cells 10, 11, 12, 13. Glutaminolysis can contribute to ATP production, and glutamine-derived α-ketoglutarate (α-KG) serves as an anaplerotic source of tricarboxylic acid (TCA) cycle metabolites 14. Mitochondrial oxidative phosphorylation (OxPhos) produces most of the ATP required for anabolic processes in immune cells 15. Non-bioenergetic features of mitochondria also regulate immune cell function. Production of mitochondrial reactive oxygen species (mROS) has been linked to the activation of the transcription factor NFAT in CD4 + T cells and to inhibition of the B cell antigen receptor (BCR) signaling in B cells 16, 17. In T cells, mitochondrial function and epigenetic remodeling are interlinked via pyruvate oxidation and conversion of pyruvate-derived citrate to acetyl-CoA, which is required for histone acetylation 18, 19. Metabolites of the TCA cycle can also directly activate (a-KG), or inhibit (fumarate, succinate) dioxygenases involved in histone and DNA demethylation, thus modulating transcriptional activity. This process of m...

Acid-sensing ion channels (ASICs) act as pH sensors in neurons. ASICs contribute to pain sensation, learning, fear behavior and to neuronal death after ischemic stroke. Extracellular acidification induces a transient activation and subsequent desensitization of these Na +-selective channels. ASICs are trimeric channels made of identical or homologous subunits. We have previously shown that mutation of the highly conserved Gly212 residue of human ASIC1a to Asp affects the channel function. Gly212 is located in the proximity of a predicted Cl − binding site at a subunit interface. Here, we have measured the function of a series of Gly212 mutants. We show that substitution of Gly212 affects the ASIC1a pH dependence and current decay kinetics. Intriguingly, the mutations to the acidic residues Asp and Glu have opposing effects on the pH dependence and the current decay kinetics. Analysis of molecular dynamics simulation trajectories started with the coordinates of the closed conformation indicates that the immediate environment of residue 212 in G212E, which shifts the pH dependence to more alkaline values, adopts a conformation closer to the open state. The G212D and G212E mutants have a different pattern of intersubunit salt bridges, that, in the case of G212E, leads to an approaching of neighboring subunits. Based on the comparison of crystal structures, the conformational changes in this zone appear to be smaller during the open-desensitized transition. Nevertheless, MD simulations highlight differences between mutants, suggesting that the changed function upon substitution of residue 212 is due to differences in intra-and intersubunit interactions in its proximity.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.

Limited thymic recovery after extracorporeal photopheresis in a low-bodyweight patient with acute graft-versus-host disease of the skin.