Pripper: prediction of caspase cleavage sites from whole proteomes

Background  

Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments.     

Zasp/Cypher internal ZM-motif containing fragments are sufficient to co-localize with alpha-actinin--analysis of patient mutations

Z-band alternatively spliced PDZ-containing protein (ZASP/Cypher) has an important role in maintaining Z-disc stability in striated and cardiac muscle. ZASP/Cypher interacts through its PDZ domain with the major Z-disc actin cross-linker, alpha-actinin. ZASP/Cypher also has a conserved sequence called the ZM-motif, and it is found in two alternatively spliced exons 4 and 6. We have shown earlier that the ZM-motif containing internal regions of two related proteins ALP and CLP36 interact with alpha-actinin rod region, and that the ZM-motif is important in targeting ALP to the alpha-actinin containing structures in cell. Here, we show that the ZASP/Cypher internal fragments containing either ZM exon 4 or 6 co-localized with alpha-actinin in cultured myoblasts and nonmuscle cells. Fragments of 130 residues around the ZM-consensus were sufficient for localization, which is similar to our previous results of ALP. Moreover, ZASP/Cypher protein interacted directly with the alpha-actinin rod and competed with ALP in binding to the rod. During the inhibition of stress fiber assembly ZASP/Cypher and alpha-actinin co-localization could be partially disturbed, suggesting that ZASP/Cypher is bound to alpha-actinin mainly when alpha-actinin is localizing in stress fibers. Many point mutations found in cardiomyopathy patients are located in the internal region of ZASP/Cypher. However, we found no evidence that human patient mutations in the internal domain would affect the ZASP/Cypher co-localization with alpha-actinin, or that the mutations would destabilize the ZASP/Cypher protein.     

Immunoreactivity to cell surface syndecans in cytoplasm and nucleus: tubulin-dependent rearrangements

Syndecans are transmembrane proteoglycans implicated in the regulation of cell growth and differentiation, by interacting with growth factors. Although syndecans play a major role in regulating cell morphology, little is known about their subcellular distribution and in vivo association with the cytoskeleton. To address this question, we investigated the subcellular distribution and dynamic rearrangement of syndecans-1, -2, and -4, using confocal laser microscopy. Furthermore, we monitored the spatial relation of syndecans to tubulin in both mitotic and interphase cells. Initially, the reactivity to syndecans was confined to the cytoplasm, staining of the cell membranes appearing later. Syndecan-1 also seems to translocate to the nucleus in a time-dependent manner. The mitotic spindle shows unexpectedly more syndecans than that found in interphase cells. After vinblastine treatment, both syndecan-1 and tubulin were recovered as paracrystalline occlusion bodies, and the nuclear reactivity to syndecan-1 disappeared, suggesting tubulin-mediated nuclear transport of this proteoglycan. Plasma membrane staining reappeared in the postmitotic cells. Nuclear translocation predominantly affected syndecan-1, whereas syndecan-2 and -4 remained in cytoplasm and cell membrane. This is the first report on regulated nuclear translocation and the presence of syndecan-1 in the mitotic spindle, where it may stabilize the mitotic machinery. The syndecan-1/tubulin complex may also act as a vehicle for the transport of protein growth factors to the cell nucleus.     

Towards a unified paradigm for sequence‐based identification of fungi

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database ( http://unite.ut.ee ) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third‐party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released ( http://unite.ut.ee/repository.php ) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web‐based sequence management system in UNITE.     

Heterotrimeric G proteins of the Gq/11 family are crucial for the induction of maternal behavior in mice

Heterotrimeric G proteins of the G(q/11) family transduce signals from a variety of neurotransmitter receptors and have therefore been implicated in several functions of the central nervous system. To investigate the potential role of G(q/11) signaling in behavior, we generated mice which lack the alpha-subunits of the two main members of the G(q/11) family, Galpha(q) and Galpha(11), selectively in the forebrain. We show here that forebrain Galpha(q/11)-deficient females do not display any maternal behavior such as nest building, pup retrieving, crouching, or nursing. However, olfaction, motor behavior and mammary gland function are normal in forebrain Galpha(q/11)-deficient females. We used c-fos immunohistochemistry to investigate pup-induced neuronal activation in different forebrain regions and found a significant reduction in the medial preoptic area, the bed nucleus of stria terminalis, and the lateral septum both in postpartum females and in virgin females after foster pup exposure. Pituitary function, especially prolactin release, was normal in forebrain Galpha(q/11)-deficient females, and activation of oxytocin receptor-positive neurons in the hypothalamus did not differ between genotypes. Our findings show that G(q/11) signaling is indispensable to the neuronal circuit that connects the perception of pup-related stimuli to the initiation of maternal behavior and that this defect cannot be attributed to either reduced systemic prolactin levels or impaired activation of oxytocin receptor-positive neurons of the hypothalamus.     

Quantification of 1H NMR spectra of human cerebrospinal fluid: a protocol based on constrained total-line-shape analysis

A protocol for quantitative ¹H NMR analysis of human cerebrospinal fluid (hCSF) was built up and assessed as based on Constrained Total-Line-Shape (CTLS) fitting. In this method, linear constraints were applied to spectral structures. The ¹H NMR spectra of 45 human CSF samples were measured and quantified using the CTLS method. The quantification strategies based on total-line-shape fitting are discussed. The metabolic model for CTLS includes 31 metabolites covering 85% of the total spectral intensity, excluding the protein contribution. Prior to data analysis, the data was divided into patients with no Alzheimer’s disease (AD), but with a normal AD marker profile (the peptide β-amyloid₄₂ and tau protein) present in CSF, and into controls that do not have an AD marker profile in CSF. Unexpectedly large variations in metabolite concentrations within the two patient groups were detected, but an analysis of variance revealed a significant (P = 0.027) difference only in the concentration of creatinine which was higher in patients that had a normal AD marker profile. Multivariate classification tools such as self-organizing maps (SOM) failed in separation of the two classes.     

A novel glucoamylase preparation for grain mash saccharification

Summary The capacity to saccharify barley grain mash of Hormoconis resinae glucoamylase P produced by a heterologous host, Trichoderma reesei, was compared with that of Aspergillus niger glucoamylase. The results showed that the glucoamylase P secreted by T. reesei produces more fermentable sugars from mash and thus makes a higher ethanol yield possible in fermentation.