Global assessment of experimental climate warming on tundra vegetation: heterogeneity over space and time

Understanding the sensitivity of tundra vegetation to climate warming is critical to forecasting future biodiversity and vegetation feedbacks to climate. In situ warming experiments accelerate climate change on a small scale to forecast responses of local plant communities. Limitations of this approach include the apparent site-specificity of results and uncertainty about the power of short-term studies to anticipate longer term change. We address these issues with a synthesis of 61 experimental warming studies, of up to 20 years duration, in tundra sites worldwide. The response of plant groups to warming often differed with ambient summer temperature, soil moisture and experimental duration. Shrubs increased with warming only where ambient temperature was high, whereas graminoids increased primarily in the coldest study sites. Linear increases in effect size over time were frequently observed. There was little indication of saturating or accelerating effects, as would be predicted if negative or positive vegetation feedbacks were common. These results indicate that tundra vegetation exhibits strong regional variation in response to warming, and that in vulnerable regions, cumulative effects of long-term warming on tundra vegetation - and associated ecosystem consequences - have the potential to be much greater than we have observed to date.     

Populous: a tool for building OWL ontologies from templates

BACKGROUND: Ontologies are being developed for the life sciences to standardise the way we describe and interpret the wealth of data currently being generated. As more ontology based applications begin to emerge, tools are required that enable domain experts to contribute their knowledge to the growing pool of ontologies. There are many barriers that prevent domain experts engaging in the ontology development process and novel tools are needed to break down these barriers to engage a wider community of scientists. RESULTS: We present Populous, a tool for gathering content with which to construct an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontologies. Populated tables are mapped to patterns that can then be used to automatically generate the ontology's content. These forms can be exported as spreadsheets, providing an interface that is much more familiar to many biologists. CONCLUSIONS: Populous's contribution is in the knowledge gathering stage of ontology development; it separates knowledge gathering from the conceptualisation and axiomatisation, as well as separating the user from the standard ontology authoring environments. Populous is by no means a replacement for standard ontology editing tools, but instead provides a useful platform for engaging a wider community of scientists in the mass production of ontology content.     

Thermodynamic Efficiency Limit of Molecular Donor‐Acceptor Solar Cells and its Application to Diindenoperylene/C60‐Based Planar Heterojunction Devices

In organic photovoltaic (PV) cells, the well‐established donor‐acceptor (D/A) concept enabling photo‐induced charge transfer between two partners with suitable energy level alignment has proven extremely successful. Nevertheless, the introduction of such a heterojunction is accompanied with additional energy losses as compared to an inorganic homojunction cell, owing to the presence of a charge‐transfer (CT) state at the D/A interface. Based on the principle of detailed balance, a modified Shockley‐Queisser theory is developed including the essential effects of interfacial CT states, that allows for a quantitative assessment of the thermodynamic efficiency limits of molecular D/A solar cells. Key parameters, apart from the optical gap of the absorber material, entering the model are the energy (E_CT) and relative absorption strength (α_CT) of the CT state. It is demonstrated how the open‐circuit voltage (V_OC) and thus the power conversion efficiency are affected by different parameter values. Furthermore, it is shown that temperature dependent device characteristics can serve to determine the CT energy, and thus the upper limit of V_OC for a given D/A combination, as well as to quantify non‐radiative recombination losses. The model is applied to diindenoperylene (DIP)‐based photovoltaic devices, with open‐circuit voltages between 0.9 and 1.4 V, depending on the partner, that have recently been reported.     

Investigating the macropinocytic proteome of Dictyostelium amoebae by high-resolution mass spectrometry

The cellular slime mold Dictyostelium discoideum is a soil-living eukaryote, which feeds on microorganisms engulfed by phagocytosis. Axenic laboratory strains have been produced that are able to use liquid growth medium internalized by macropinocytosis as the source of food. To better define the macropinocytosis process, we established the inventory of proteins associated with this pathway using mass spectrometry-based proteomics. Using a magnetic purification procedure and high-performance LC-MS/MS proteome analysis, a list of 2108 non-redundant proteins was established, of which 24% featured membrane-spanning domains. Bioinformatics analyses indicated that the most abundant proteins were linked to signaling, vesicular trafficking and the cytoskeleton. The present repertoire validates our purification method and paves the way for a future proteomics approach to study the dynamics of macropinocytosis.     

Systematic Identification of Rhythmic Genes Reveals camk1gb as a New Element in the Circadian Clockwork

A wide variety of biochemical, physiological, and molecular processes are known to have daily rhythms driven by an endogenous circadian clock. While extensive research has greatly improved our understanding of the molecular mechanisms that constitute the circadian clock, the links between this clock and dependent processes have remained elusive. To address this gap in our knowledge, we have used RNA sequencing (RNA–seq) and DNA microarrays to systematically identify clock-controlled genes in the zebrafish pineal gland. In addition to a comprehensive view of the expression pattern of known clock components within this master clock tissue, this approach has revealed novel potential elements of the circadian timing system. We have implicated one rhythmically expressed gene, camk1gb, in connecting the clock with downstream physiology of the pineal gland. Remarkably, knockdown of camk1gb disrupts locomotor activity in the whole larva, even though it is predominantly expressed within the pineal gland. Therefore, it appears that camk1gb plays a role in linking the pineal master clock with the periphery.     

Lysosomal dysfunction in Parkinson disease: ATP13A2 gets into the groove

Mutations in ATP13A2 (PARK9) cause an autosomal recessive form of early-onset parkinsonism with pyramidal degeneration and dementia called Kufor-Rakeb Syndrome (KRS). The ATP13A2 gene encodes a transmembrane lysosomal P5-type ATPase (ATP13A2) whose physiological function in mammalian cells, and hence its potential role in Parkinson disease (PD), remains elusive. In this context, we have recently shown that KRS-linked mutations in ATP13A2 leads to several lysosomal alterations in ATP13A2 KRS patient-derived fibroblasts, including impaired lysosomal acidification, decreased proteolytic processing of lysosomal enzymes, reduced degradation of lysosomal substrates and diminished lysosomal-mediated clearance of autophagosomes (AP). Similar alterations are observed in stable ATP13A2-knockdown dopaminergic cell lines, which are associated with cell death. Restoration of ATP13A2 levels in ATP13A2-mutant/depleted cells is able to restore lysosomal function and attenuate cell death. Relevant to PD, we have determined that ATP13A2 levels are decreased in dopaminergic nigral neurons from sporadic PD patients. Interestingly in these patients, the main signal of ATP13A2 is detected in the Lewy bodies. Our results unravel an instrumental role of ATP13A2 in lysosomal function and in cell viability. Altogether, our results validate ATP13A2 as a likely therapeutic target against PD degeneration.     

alpha B-crystallin is a cytoplasmic interaction partner of the kidney-specific cadherin-16

The Ca^2 +-dependent membrane-spanning classical cadherins bind directly to cytosolic catenins. This cadherin-catenin interaction is known to be critical for the fundamental role of cadherins in cell-cell adhesion. The small subfamily of the 7D-cadherins, however, cannot interact with catenins due to their highly truncated cytoplasmic tail. Thus far, no cytoplasmic interaction partner for the 7D-cadherins has been described. With the use of the cytoplasmic domain of the Ksp (kidney-specific)-cadherin, which belongs to the family of 7D-cadherins, as bait in affinity chromatography with human kidney lysates, the small heat-shock protein αB-crystallin was identified by matrix-assisted laser desorption/ionization-time-of-flight analysis as a cytosolic binding partner of Ksp-cadherin. This interaction was verified by co-immunoprecipitation analysis. With the use of overlapping peptides representing the entire αB-crystallin molecule, the N-terminal part of αB-crystallin, which does not possess chaperone activity, was identified as responsible for the binding to Ksp-cadherin. This interaction was found to be specific since only the cytoplasmic domain of Ksp-cadherin, but not LI (liver-intestine)-cadherin (another member of the 7D-cadherin family), interacted with αB-crystallin. In the human kidney, both αB-crystallin and Ksp-cadherin co-localize to cells of the collecting duct. They also co-localize with the actin cytoskeleton and co-precipitate with the latter. These findings suggest that the interaction of Ksp-cadherin with αB-crystallin is important for the connection of Ksp-cadherin to the cytoskeleton and thus for maintaining tissue integrity in the kidney.     

Sensitive biochemical aggregate detection reveals aggregation onset before symptom development in cellular and murine models of Huntington's disease

A CAG-repeat gene expansion translated into a pathogenic polyglutamine stretch at the N-terminus of huntingtin triggers Huntington's Disease. Mutated huntingtin is predicted to adopt toxic properties mainly if aggregation-prone N-terminal fragments are released by proteolysis. Huntingtin-aggregates are indeed a major hallmark of this disorder and could represent useful markers of disease-onset or progression. We designed a simple method for qualitative and quantitative characterization of aggregates. For this, we analyzed samples from in vitro and in vivo Huntington's Disease models by agarose gel electrophoresis and showed that in the brain of transgenic mice huntingtin-aggregates became larger as a function of disease progression. This appears to be a property of cytoplasmic but not nuclear aggregates. In cell cultures, treatment with Congo Red inhibited aggregate growth but not total load. Finally, we showed that in primary striatal neurons and in brains of R6/2 and Hdh Q150 mice, the presence of aggregates preceded initiation of any other functional deficits. This observation argues for a pathogenic role of huntingtin-aggregation in Huntington's Disease. Our results emphasize that thorough analysis of huntingtin metabolism and aggregation is now feasible, thus significantly improving the power of studies assessing therapies designed to lower huntingtin levels or to interfere with its aggregation.