GOTax: investigating biological processes and biochemical activities along the taxonomic tree

GOTax, a novel web-based platform that integrates protein annotation with protein family classification and taxonomy, allows for an extensive assessment of functional similarity between proteins and for comparing and analyzing the distribution of protein families and protein functions over different taxonomic groups

Compact low power infrared tube furnace for in situ X-ray powder diffraction.

We describe the development and implementation of a compact, low power, infrared heated tube furnace for in situ powder X-ray diffraction experiments. Our silicon carbide (SiC) based furnace design exhibits outstanding thermal performance in terms of accuracy control and temperature ramping rates while simultaneously being easy to use, robust to abuse and, due to its small size and low power, producing minimal impact on surrounding equipment. Temperatures in air in excess of 1100 °C can be controlled at an accuracy of better than 1%, with temperature ramping rates up to 100 °C/s. The complete "add-in" device, minus power supply, fits in a cylindrical volume approximately 15 cm long and 6 cm in diameter and resides as close as 1 cm from other sensitive components of our experimental synchrotron endstation without adverse effects

Applications of semantic similarity measures

There has been much interest in uncovering protein-protein interactions and their underlying domain-domain interactions. Many experimental techniques have been developed, for example yeast-two-hybrid screening and tandem affinity purification. Since it is time consuming and expensive to perform exhaustive experimental screens, in silico methods are used for predicting interactions. However, all experimental and computational methods have considerable false positive and false negative rates. Therefore, it is necessary to validate experimentally determined and predicted interactions. One possibility for the validation of interactions is the comparison of the functions of the proteins or domains. Gene Ontology (GO) is widely accepted as a standard vocabulary for functional terms, and is used for annotating proteins and protein families with biological processes and their molecular functions. This annotation can be used for a functional comparison of interacting proteins or domains using semantic similarity measures. Another application of semantic similarity measures is the prioritization of disease genes. It is know that functionally similar proteins are often involved in the same or similar diseases. Therefore, functional similarity is used for predicting disease associations of proteins. In the first part of my talk, I will introduce some semantic and functional similarity measures that can be used for comparison of GO terms and proteins or protein families. Then, I will show their application for determining a confidence threshold for domain-domain interaction predictions. Additionally, I will present FunSimMat (http://www.funsimmat.de/), a comprehensive resource of functional similarity values available on the web. In the last part, I will introduce the problem of comparing diseases, and a first attempt to apply functional similarity measures based on GO to this problem

Role of RNA-binding proteins Rbfox1l and Rbfox2 in neuronal development and behavior in zebrafish

Rbfox proteins are RNA-binding proteins that play a significant role in the alternative splicing of neuronal transcripts in the central nervous system (CNS). Rbfox proteins are required for proper brain development and function. In humans, RBFOX1 has been implicated in a variety of neurological disorders, including autism, anxiety, epilepsy, and schizophrenia. Rbfox2 is involved in cerebellar development in mammals. The zebrafish is used as a model system for studies in neurobiology given their neuroanatomical conservation with mammals, and remarkable capability to regenerate parts of their CNS. Rbfox1l (Rbfox1-like) and Rbfox2 have been identified in neurons of the adult zebrafish brain. Rbfox1l was found in a restricted population of dorsal telencephalic neurons, and Rbfox2 was found broadly throughout the brain. Both genes have been found in Purkinje cells of the cerebellum. Utilizing antibody staining on zebrafish brain tissue sections, we will analyze expression of Rbfox1l and Rbfox2 at larval stages and stages leading up to adulthood. Furthermore, we will use rbfox1l and rbfox2 mutant zebrafish (in collaboration with Ohio State University) to better understand the role of rbfox1l in behavior and determine whether rbfox2 is necessary for the regeneration of the cerebellum. Understanding the role of the Rbfox proteins in neural development, regeneration, and behavior may lead to a substantial advancement in the research field and health care

Role of RNA-binding proteins Rbfox1l and Rbfox2 in neuronal development and behavior in zebrafish

Rbfox proteins are RNA-binding proteins that play a significant role in the alternative splicing of neuronal transcripts in the central nervous system (CNS). Rbfox proteins are required for proper brain development and function. In humans, RBFOX1 has been implicated in a variety of neurological disorders, including autism, anxiety, epilepsy, and schizophrenia. Rbfox2 is involved in cerebellar development in mammals. The zebrafish is used as a model system for studies in neurobiology given their neuroanatomical conservation with mammals, and remarkable capability to regenerate parts of their CNS. Rbfox1l (Rbfox1-like) and Rbfox2 have been identified in neurons of the adult zebrafish brain. Rbfox1l was found in a restricted population of dorsal telencephalic neurons, and Rbfox2 was found broadly throughout the brain. Both genes have been found in Purkinje cells of the cerebellum. Utilizing antibody staining on zebrafish brain tissue sections, we will analyze expression of Rbfox1l and Rbfox2 at larval stages and stages leading up to adulthood. Furthermore, we will use rbfox1l and rbfox2 mutant zebrafish (in collaboration with Ohio State University) to better understand the role of rbfox1l in behavior and determine whether rbfox2 is necessary for the regeneration of the cerebellum. Understanding the role of the Rbfox proteins in neural development, regeneration, and behavior may lead to a substantial advancement in the research field and health care

Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus

Structural analysis of the inhibitor Telaprevir (VX-950) of the hepatitis C virus (HCV) protease NS3-4A shows that mutations at V36 and/or T54 result in impaired interaction with VX-950, explaining the development of viral breakthrough variants

Macro- and microscopic properties of strontium doped indium oxide

Solid state synthesis and physical mechanisms of electrical conductivity variation in polycrystalline, strontium doped indium oxide In2O3:(SrO)x were investigated for materials with different doping levels at different temperatures (T=20-300 C) and ambient atmosphere content including humidity and low pressure. Gas sensing ability of these compounds as well as the sample resistance appeared to increase by 4 and 8 orders of the magnitude, respectively, with the doping level increase from zero up to x=10%. The conductance variation due to doping is explained by two mechanisms: acceptor-like electrical activity of Sr as a point defect and appearance of an additional phase of SrIn2O4. An unusual property of high level (x=10%) doped samples is a possibility of extraordinarily large and fast oxygen exchange with ambient atmosphere at not very high temperatures (100-200 C). This peculiarity is explained by friable structure of crystallite surface. Friable structure provides relatively fast transition of samples from high to low resistive state at the expense of high conductance of the near surface layer of the grains. Microscopic study of the electro-diffusion process at the surface of oxygen deficient samples allowed estimation of the diffusion coefficient of oxygen vacancies in the friable surface layer at room temperature as 3x10^(-13) cm^2/s, which is by one order of the magnitude smaller than that known for amorphous indium oxide films.Comment: 19 pages, 7 figures, 39 reference

Metastable Corundum-Type In2O3: Phase Stability, Reduction Properties, and Catalytic Characterization

The phase stability, reduction, and catalytic properties of corundum-type rhombohedral In2O3 have been comparatively studied with respect to its thermodynamically more stable cubic In2O3 counterpart. Phase stability and transformation were observed to be strongly dependent on the gas environment and the reduction potential of the gas phase. As such, reduction in hydrogen caused both the efficient transformation into the cubic polymorph as well as the formation of metallic In especially at high reduction temperatures between 573 and 673 K. In contrast, reduction in CO suppresses the transformation into cubic In2O3 but leads to a larger quantity of In metal at comparable reduction temperatures. This difference is also directly reflected in temperature-dependent conductivity measurements. Catalytic characterization of rh-In2O3 reveals activity in both routes of the water-gas shift equilibrium, which gives rise to a diminished CO2-selectivity of 60% in methanol steam reforming. This is in strong contrast to its cubic counterpart where CO2 selectivities of close to 100% due to the suppressed inverse water-gas shift reaction, have been obtained. Most importantly, rh-In2O3 in fact is structurally stable during catalytic characterization and no unwanted phase transformations are triggered. Thus, the results directly reveal the application-relevant physicochemical properties of rh-In2O3 that might encourage subsequent studies on other less-common In2O3 polymorphs.(VLID)2581066Accepted versio