Mitogen-inducible gene 6 is an endogenous inhibitor of HGF/Met-induced cell migration and neurite growth

Hepatocyte growth factor (HGF)/Met signaling controls cell migration, growth and differentiation in several embryonic organs and is implicated in human cancer. The physiologic mechanisms that attenuate Met signaling are not well understood. Here we report a mechanism by which mitogen-inducible gene 6 (Mig6; also called Gene 33 and receptor-associated late transducer) negatively regulates HGF/Met-induced cell migration. The effect is observed by Mig6 overexpression and is reversed by Mig6 small interfering RNA knock-down experiments; this indicates that endogenous Mig6 is part of a mechanism that inhibits Met signaling. Mig6 functions in cells of hepatic origin and in neurons, which suggests a role for Mig6 in different cell lineages. Mechanistically, Mig6 requires an intact Cdc42/Rac interactive binding site to exert its inhibitory action, which suggests that Mig6 acts, at least in part, distally from Met, possibly by inhibiting Rho-like GTPases. Because Mig6 also is induced by HGF stimulation, our results suggest that Mig6 is part of a negative feedback loop that attenuates Met functions in different contexts and cell types.     

Safety and regulation of yeasts used for biocontrol or biopreservation in the food or feed chain

Yeasts have been important components of spontaneous fermentations in food and beverage processing for millennia. More recently, the potential of utilising antagonistic yeasts, e.g. Pichia anomala and Candida spp., for post-harvest biological control of spoilage fungi during storage of plant-derived produce (‘biopreservation’) has been clearly demonstrated. Although some yeast species are among the safest microorganisms known, several have been reported in opportunistic infections in humans, including P. anomala and bakers’ yeast, Saccharomyces cerevisiae. More research is needed about the dominant pathogenicity and virulence factors in opportunistic yeasts, and whether increased utilisation of biopreservative yeasts in general could contribute to an increased prevalence of yeast infections. The regulatory situation for yeasts used in post-harvest biocontrol is complex and the few products that have reached the market are mainly registered as biological pesticides. The qualified presumption of safety (QPS) approach to safety assessments of microorganisms intentionally added to food or feed, recently launched by the European Food Safety Authority, can lead to more efficient evaluations of new products containing microbial species with a sufficient body of knowledge or long-term experience on their safety. P. anomala is one of several yeast species that have been given QPS status, although the status is restricted to use of this yeast for enzyme and metabolite production purposes. With regard to authorisation of new biopreservative yeasts, we recommend that the possibility to regulate microorganisms for food biopreservation as food additives be considered.     

OMERO: flexible, model-driven data management for experimental biology

Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.     

Estimation of cell numbers of methanotrophic bacteria in boreal peatlands based on analysis of specific phospholipid fatty acids

Abstract: Concentrations of two phospholipid fatty acids (PLFAs) specific for methane-oxidizing bacteria (16:1 ω8 and 18:1 ω8), were used to estimate the biomass and cell numbers of this group of bacteria in two Sphagnum-dominated boreal peatlands. Concentration ranges of 16:1 ω8 and 18:1 ω8 were 0.0–73 and 1.0–486 pmol g⁻¹ of wet peat, respectively. Concentrations in the peat of each fatty acid were positively correlated with the potential methane oxidation activity ( V _max), which was used as an independent estimate of methanotrophic biomass. This correlation suggests that the two PLFAs are good biomarkers for the population of methanotrophic bacteria in peatlands. Concentrations of the two PLFAs were transformed to cell numbers using conversion factors for the cell content of PLFAs, average cell volume and percentage of cellular dry matter. The total cell number of methanotrophic bacteria in peat samples from a range of sites and depths ranged between 0.3 and 51 × 10⁶ cells g⁻¹ of wet peat, with similar proportions of type I and type II methanotrophic bacteria in most samples. Within particular peat profiles, numbers of methanotrophic bacteria were highest around the level of the water table, implying that the supplies of methane and oxygen largely determine the biomass distribution of methanotrophic bacteria in this type of peatlands.     

OLS Dialog: An open-source front end to the Ontology Lookup Service

Background  

With the growing amount of biomedical data available in public databases it has become increasingly important to annotate data in a consistent way in order to allow easy access to this rich source of information. Annotating the data using controlled vocabulary terms and ontologies makes it much easier to compare and analyze data from different sources. However, finding the correct controlled vocabulary terms can sometimes be a difficult task for the end user annotating these data.     

A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins

Structural similarity among proteins is reflected in the distribution of hydropathicity along the amino acids in the protein sequence. Similarities in the hydropathy distributions are obvious for homologous proteins within a protein family. They also were observed for proteins with related structures, even when sequence similarities were undetectable. Here we present a novel method that employs the hydropathy distribution in proteins for identification of (sub)families in a set of (homologous) proteins. We represent proteins as points in a generalized hydropathy space, represented by vectors of specifically defined features. The features are derived from hydropathy of the individual amino acids. Projection of this space onto principal axes reveals groups of proteins with related hydropathy distributions. The groups identified correspond well to families of structurally and functionally related proteins. We found that this method accurately identifies protein families in a set of proteins, or subfamilies in a set of homologous proteins. Our results show that protein families can be identified by the analysis of hydropathy distribution, without the need for sequence alignment.     

The shrubland vegetation in western Shewa,Ethiopia and its possible recovery

Shrubland vegetation and environmental data in western Shewa, Ethiopia have been analysed. Vegetation data include cover-abundance values of vascular plant species; environmental data comprise physical and chemical properties of the soil, altitude, slope, grazing and browsing pressure. The vegetation data were subj ected to hierarchical and non-hierarchical classification and ordination with correspondence analysis. The classification resulted in seven different vegetation types, ranging from grassland with scattered shrubs to degenerated forest. Ordination of the data and biplot analysis showed that the vegetation is influenced by anthropogenic factors and altitudinal variation. Sand content is related to a low level of anthropogenic influence whereas silt content is related to a high level. This is explained by historical events rather than by the present situation. Total nitrogen, organic carbon, altitude and slope are positively correlated and these variables are negatively related to anthropogenic influences. The shrubland vegetation may have expanded from lower altitudes and drier sites as forests gradually disappeared. The recovery of an economically more rewarding vegetation type may be achieved through pro viding alternative sources of fuel and construction and through prohibiting cultivation and grazing in the shrublands on the hillsides. Regeneration can be accelerated by actively introducing seedlings of tree species that do not need a heavy canopy cover for establishment and growth.     

NSAID-induced gut inflammation and vasoconstriction: Causes and potential reversal with beta-CGRP - A hypothesis

Traditional non-steroidal anti-inflammatory drugs, cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) inhibitors control inflammation. While these drugs are formulated to reduce one of the cardinal signs of inflammation by reducing prostaglandin levels at the site of inflammation, COX-1 inhibitors induce inflammation in the stomach as well as the small bowel. The COX-2 inhibitors, a large portion of the non-steroidal anti-inflammatory drug market, provide a gastro-intestinally safer class of drugs. However, COX-2 inhibitors induce vasoconstriction via actions in renal and cardiovascular tissues. Since COX-2 inhibitors also have anticancer potential, it is worthwhile to design drug formulations that will not cause hypertension or cardiovascular damage. An attempt has thus been made in this article to formulate a hypothesis to circumvent the COX inhibitors induced inflammation and vasoconstriction through COX independent activation of calcitonin gene-related peptide (CGRP), a potent vasodilator neuropeptide found throughout the vascular and sensory nervous system.     

Meiotic regulation of the CDK activator RINGO/Speedy by ubiquitin-proteasome-mediated processing and degradation

Xenopus RINGO/Speedy (XRINGO) is a potent inducer of oocyte meiotic maturation that can directly activate Cdk1 and Cdk2. Here, we show that endogenous XRINGO protein accumulates transiently during meiosis I entry and then is downregulated. This tight regulation of XRINGO expression is the consequence of two interconnected mechanisms: processing and degradation. XRINGO processing involves recognition of at least three distinct phosphorylated recognition motifs by the SCF(betaTrCP) ubiquitin ligase, followed by proteasome-mediated limited degradation, resulting in an amino-terminal XRINGO fragment. XRINGO processing is directly stimulated by several kinases, including protein kinase A and glycogen synthase kinase-3beta, and may contribute to the maintenance of G2 arrest. On the other hand, XRINGO degradation after meiosis I is mediated by the ubiquitin ligase Siah-2, which probably requires phosphorylation of XRINGO on Ser 243 and may be important for the omission of S phase at the meiosis-I-meiosis-II transition in Xenopus oocytes.     

Chick growth and survival in northern lapwings Vanellus vanellus indicate that secondary females do the best of a bad job

The polygyny threshold model predicts that monogamous and secondary females on average settle at the same time and have similar reproductive success. This is not generally found. Incorporating varying female competitive strength into the model, changes the predictions to state that secondary females should breed later and show a reduced success compared to that of monogamous and primary females. We examined if this was the case by investigating growth and survival in chicks of northern lapwings Vanellus vanellus from mothers of monogamous, primary and secondary mating status. Chicks where monitored from hatching to the age of 15–18 d. Growth and survival in secondary chicks was lower than in monogamous and primary chicks. Primary chicks survived significantly better than secondary chicks. Survival of monogamous chicks was comparable to primary chicks and close to significantly higher than in secondary chicks (p = 0.086). Among surviving chicks, daily weight gain in monogamous chicks was significantly higher than in secondary chicks. Growth rates of primary chicks were comparable to monogamous chicks and tended to be higher than in secondary chicks (p = 0.11). Monogamous and primary females both bred significantly earlier than secondary females, and chick survival and body‐mass growth decreased significantly with hatching date. Given the premium on early breeding in lapwings, secondary females appeared to do the best of a bad job, and their later onset of breeding could have been caused by poorer condition and/or lower breeding experience. Additional costs might also have accrued from sharing breeding resources with primary females that presumably were stronger competitors.