Publication Date: 2008 Nov 20 PMID: 19020613br/Authors: Biver, S. - Belge, H. - Bourgeois, S. - Van Vooren, P. - Nowik, M. - Scohy, S. - Houillier, P. - Szpirer, J. - Szpirer, C. - Wagner, C. A. - Devuyst, O. - Marini, A. M.br/Journal: Naturebr/br/The kidney has an important role in the regulation of acid-base homeostasis. Renal ammonium production and excretion are essential for net acid excretion under basal conditions and during metabolic acidosis. Ammonium is secreted into the urine by the collecting duct, a distal nephron segment where ammonium transport is believed to occur by non-ionic NH(3) diffusion coupled to H(+) secretion. Here we show that this process is largely dependent on the Rhesus factor Rhcg. Mice lacking Rhcg have abnormal urinary acidification due to impaired ammonium excretion on acid loading-a feature of distal renal tubular acidosis. In vitro microperfused collecting ducts of Rhcg(-/-) acid-loaded mice show reduced apical permeability to NH(3) and impaired transepithelial NH(3) transport. Furthermore, Rhcg is localized in epididymal epithelial cells and is required for normal fertility and epididymal fluid pH. We anticipate a critical role for Rhcg in ammonium handling and pH homeostasis both in the kidney and the male reproductive tract.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19020613title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Nov 19 PMID: 19020035br/Authors: Ben-Zvi, A. - Manor, O. - Schachner, M. - Yaron, A. - Tessier-Lavigne, M. - Behar, O.br/Journal: J Neuroscibr/br/Extensive neuronal cell death during development is believed to be due to a limiting supply of neurotrophic factors. In vitro studies suggest that axon guidance molecules directly regulate neuronal survival, raising the possibility that they play a direct role in neuronal cell death in vivo. However, guidance errors may also influence survival indirectly due to loss of target-derived neurotrophic support. The role of guidance molecules in neuronal death in vivo has thus been difficult to decipher. Semaphorin3A, a repulsive guidance cue for sensory neurons, can induce sensory neuron death in vitro. Null mice studies of the Semaphorin3A coreceptors showed that guidance activity is mediated by PlexinA4, but PlexinA3 partially compensates in PlexinA4(-/-) mice. Here we demonstrate that both Plexins contribute to Sema3A-induced cell death in vitro, albeit in a different hierarchy. PlexinA3 is absolutely required, while PlexinA4 makes a smaller contribution to cell death. We found that PlexinA3(-/-) mice, which, unlike PlexinA4(-/-) mice, do not exhibit sensory axon patterning defects, show reduced neuronal apoptosis and an increased number of DRG neurons. Semaphorin3A involvement in neuronal death in vivo was demonstrated by a sensitization experiment using the proapoptotic effector Bax. Our results identify Plexins as mediators of Semaphorin-induced cell death in vitro, and provide the first evidence implicating Semaphorin/Plexin signaling in neuronal survival independent of its role in axon guidance. The results also support the idea that naturally occurring neuronal cell death reflects not only competition for target-derived trophic factors, but also the action of proapoptotic signaling via a Semaphorin/Plexin pathway.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19020035title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Nov 19 PMID: 19020030br/Authors: Ma, X. M. - Kiraly, D. D. - Gaier, E. D. - Wang, Y. - Kim, E. J. - Levine, E. S. - Eipper, B. A. - Mains, R. E.br/Journal: J Neuroscibr/br/Rho GTPases activated by GDP/GTP exchange factors (GEFs) play key roles in the developing and adult nervous system. Kalirin-7 (Kal7), the predominant adult splice form of the multifunctional Kalirin RhoGEF, includes a PDZ [postsynaptic density-95 (PSD-95)/Discs large (Dlg)/zona occludens-1 (ZO-1)] binding domain and localizes to the postsynaptic side of excitatory synapses. In vitro studies demonstrated that overexpression of Kal7 increased dendritic spine density, whereas reduced expression of endogenous Kal7 decreased spine density. To evaluate the role of Kal7 in vivo, mice lacking the terminal exon unique to Kal7 were created. Mice lacking both copies of the Kal7 exon (Kal7(KO)) grew and reproduced normally. Golgi impregnation and electron microscopy revealed decreased hippocampal spine density in Kal7(KO) mice. Behaviorally, Kal7(KO) mice showed decreased anxiety-like behavior in the elevated zero maze and impaired acquisition of a passive avoidance task, but normal behavior in open field, object recognition, and radial arm maze tasks. Kal7(KO) mice were deficient in hippocampal long-term potentiation. Western blot analysis confirmed the absence of Kal7 and revealed compensatory increases in larger Kalirin isoforms. PSDs purified from the cortices of Kal7(KO) mice showed a deficit in Cdk5, a kinase known to phosphorylate Kal7 and play an essential role in synaptic function. The early stages of excitatory synaptic development proceeded normally in cortical neurons prepared from Kal7(KO) mice, with decreased excitatory synapses apparent only after 21 d in vitro. Expression of exogenous Kal7 in Kal7(KO) neurons rescued this deficit. Kal7 plays an essential role in synaptic structure and function, affecting a subset of cognitive processes.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19020030title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Nov 19 PMID: 19020024br/Authors: Nakamura, K. - Nemani, V. M. - Wallender, E. K. - Kaehlcke, K. - Ott, M. - Edwards, R. H.br/Journal: J Neuroscibr/br/The aggregation of abnormally folded proteins is a defining feature of neurodegenerative disease, but it has not previously been possible to assess the conformation of these proteins in a physiologically relevant context, before they form morphologically recognizable aggregates. We now describe FRET-based reporters for the conformation of alpha-synuclein, a protein central to the pathogenesis of Parkinson's disease (PD). Characterization in vitro shows that alpha-synuclein adopts a relatively closed conformation in solution that converts to open on membrane binding. In living cells, the closed conformation predominates. In neurons, however, cell bodies contain a much larger proportion of the open conformation than synaptic boutons. To account for these differences, we also used the reporters to characterize the interaction with native membranes. We find that the conformation of alpha-synuclein responds selectively to mitochondria, indicating a direct link between alpha-synuclein and an organelle strongly implicated in the pathogenesis of PD.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19020024title=Entrez+PubmedCiteULike/a

Motivation: Regulatory proteases modulate proteomic dynamics with a spectrum of specificities against substrate proteins. Predictions of the substrate sites in a proteome for the proteases would facilitate understanding the biological functions of the proteases. High-throughput experiments could generate suitable datasets for machine learning to grasp complex relationships between the substrate sequences and the enzymatic specificities. But the capability in predicting protease substrate sites by integrating the machine learning algorithms with the experimental methodology has yet to be demonstrated.

Results: Factor Xa, a key regulatory protease in the blood coagulation system, was used as model system, for which effective substrate site predictors were developed and benchmarked. The predictors were derived from bootstrap aggregation (machine learning) algorithms trained with data obtained from multilevel substrate phage display experiments. The experimental sampling and computational learning on substrate specificities can be generalized to proteases for which the active forms are available for the in vitro experiments.

Availability: http://asqa.iis.sinica.edu.tw/fXaWeb/

Contact: hsu@iis.sinica.edu.tw; yangas@gate.sinica.edu.tw

Supplementary information: Supplementary data are available at Bioinformatics online.

Motivation: Cell lines are used extensively in biomedical research, but the nomenclature describing cell lines has not been standardized. The problems are both linguistic and experimental. Many ambiguous cell line names appear in the published literature. Users of the same cell line may refer to it in different ways, and cell lines may mutate or become contaminated without the knowledge of the user. As a first step towards rationalizing this nomenclature, we created a cell line knowledgebase (CLKB) with a well-structured collection of names and descriptive data for cell lines cultured in vitro. The objectives of this work are: (i) to assist users in extracting useful information from biomedical text and (ii) to highlight the importance of standardizing cell line names in biomedical research. This CLKB contains a broad collection of cell line names compiled from ATCC, Hyper CLDB and MeSH. In addition to names, the knowledgebase specifies relationships between cell lines. We analyze the use of cell line names in biomedical text. Issues include ambiguous names, polymorphisms in the use of names and the fact that some cell line names are also common English words. Linguistic patterns associated with the occurrence of cell line names are analyzed. Applying these patterns to find additional cell line names in the literature identifies only a small number of additional names. Annotation of microarray gene expression studies is used as a test case. The CLKB facilitates data exploration and comparison of different cell lines in support of clinical and experimental research.

Availability: The web ontology file for this cell line collection can be downloaded at http://www.stateslab.org/data/celllineOntology/cellline.zip.

Contact: dstates@umich.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Summary: Oscillations in mRNA and protein of circadian clock components can be continuously monitored in vitro using synchronized cell lines. These rhythms can be highly variable due to culture conditions and are non-stationary due to baseline trends, damping and drift in period length. We present a technique for characterizing the modal frequencies of oscillation using continuous wavelet decomposition to non-parametrically model changes in amplitude and period while removing baseline effects and noise.

Availability: The method has been implemented as the package waveclock for the free statistical software program R and is available for download from http://cran.r-project.org/

Contact: thomas.price@iop.kcl.ac.uk

Supplementary information: Supplementary figures are available at Bioinformatics online.