An alternate pathway for recruiting template RNA to the brome mosaic virus RNA replication complex

The multidomain RNA replication protein 1a of brome mosaic virus (BMV), a positive-strand RNA virus in the alphavirus-like superfamily, plays key roles in assembly and function of the viral RNA replication complex. 1a, which encodes RNA capping and helicase-like domains, localizes to endoplasmic reticulum membranes, recruits BMV 2a polymerase and viral RNA templates, and forms membrane-bound, capsid-like spherules in which RNA replication occurs. cis-acting signals necessary and sufficient for RNA recruitment by 1a have been mapped in BMV genomic RNA2 and RNA3. Both signals comprise an extended stem-loop whose apex matches the conserved sequence and structure of the TPsiC stem-loop in tRNAs (box B). Mutations show that this box B motif is crucial to 1a responsiveness of wild-type RNA2 and RNA3. We report here that, unexpectedly, some chimeric mRNAs expressing the 2a polymerase open reading frame from RNA2 were recruited by 1a to the replication complex and served as templates for negative-strand RNA synthesis, despite lacking the normally essential, box B-containing 5' signal. Further studies showed that this template recruitment required high-efficiency translation of the RNA templates. Moreover, multiple small frameshifting insertion or deletion mutations throughout the N-terminal region of the open reading frame inhibited this template recruitment, while an in-frame insertion did not. Providing 2a in trans did not restore template recruitment of RNAs with frameshift mutations. Only those deletions in the N-terminal region of 2a that abolished 2a interaction with 1a abolished template recruitment of the RNA. These and other results indicate that this alternate pathway for 1a-dependent RNA recruitment involves 1a interaction with the translating mRNA via the 1a-interactive N-terminal region of the nascent 2a polypeptide. Interaction with nascent 2a also may be involved in 1a recruitment of 2a polymerase to membranes.     

Transparent mediation-based access to multiple yeast data sources using an ontology driven interface

BACKGROUND: Saccharomyces cerevisiae is recognized as a model system representing a simple eukaryote whose genome can be easily manipulated. Information solicited by scientists on its biological entities (Proteins, Genes, RNAs...) is scattered within several data sources like SGD, Yeastract, CYGD-MIPS, BioGrid, PhosphoGrid, etc. Because of the heterogeneity of these sources, querying them separately and then manually combining the returned results is a complex and time-consuming task for biologists most of whom are not bioinformatics expert. It also reduces and limits the use that can be made on the available data. RESULTS: To provide transparent and simultaneous access to yeast sources, we have developed YeastMed: an XML and mediator-based system. In this paper, we present our approach in developing this system which takes advantage of SB-KOM to perform the query transformation needed and a set of Data Services to reach the integrated data sources. The system is composed of a set of modules that depend heavily on XML and Semantic Web technologies. User queries are expressed in terms of a domain ontology through a simple form-based web interface. CONCLUSIONS: YeastMed is the first mediation-based system specific for integrating yeast data sources. It was conceived mainly to help biologists to find simultaneously relevant data from multiple data sources. It has a biologist-friendly interface easy to use. The system is available at http://www.khaos.uma.es/yeastmed/.     

Inhibitor effect of products of metabolism on growth of Clostridium acetobutylicum

Summary The growth of Clostridium acetobutylicum was studied by three ways. 1. In batch fermentation, referred to as the control. 2. Fermentation in dialysis which permits elimination of all the products of metabolism: acids, solvents and gases. In order to test the toxic effect of acids, cultures were dialysed against 2 g l^-1 acetic acid or 2 g l^-1 butyric acid. 3. To test the toxic effect of gases only, batch fermentations were carried out under vacuum or with a continuous bubbling of nitrogen. The first method resulted in a productivity of 1.2 g l^-1 dry cell weight and a maximal specific growth rate of 0.2 h^-1; the second, 20 g l^-1 dry cell weight and a constant maximum specific growth rate (μ=0.39 h^-1) between 14 and 20 h. The toxic effect of acetic and butyric acids, starts at low concentrations and about 4 g l^-1 of both acids results in a decrease of 50% of maximal specific growth rate. The third series of experiments showed that gases produced by the bacteria have a high toxic effect, comparable to that of 5 g l^-1 of acid.     

Brief communication: The size of the human frontal sinuses in adults presenting complete persistence of the metopic suture

The notion of absence of the frontal sinuses in human individuals presenting a persistence of the metopic suture is considered as classical in many treatises of reference; however, precise studies are very rare and even controversial. The purpose of this study was thus to provide original data to confirm or refute this classical affirmation with the perspective of some original insights into biological significance of the frontal sinuses and the factors influencing their exceptional polymorphism. The material consisted of 143 dry skulls of adult individuals (European Homo sapiens), distributed in two groups: 80 skulls presenting a complete frontal closure with total disappearance of the metopic suture, and 63 skulls presenting a complete persistence of the metopic suture. Each skull was radiographed in oblique projection using the occipitomental view. A simple morphological quantification of the sinus size was defined with four categories: (1) aplasia, (2) hypoplasia, (3) medium size, (4) hyperplasia. Statistically significant difference in frontal sinusal size was found between both groups of skulls. Absent and small sinuses were considerably more frequent in skulls with persistence of the metopic suture (57.9 vs. 11.9%): small frontal sinuses (hypoplasia) were much more frequent (50.8 vs. 9.4%), although the frequency of absence of frontal sinuses (aplasia) was only slightly higher (7.1 vs. 2.5%). Am J Phys Anthropol 154:621–627, 2014. © 2014 Wiley Periodicals, Inc.     

Morphometric variations of the skull in the Gray Wolf (<Emphasis Type=Italic>Canis lupus</Emphasis>) in Iran

The Gray Wolf is a wide ranging carnivore in Iran, absent only in the central deserts and Dasht-e Lut. This study was carried out to verify whether, despite their high mobility, individual wolves belonging to different populations show morphological variations in the skull. We collected 48 skulls from various regions of Iran and measured 24 variables on the cranium. These primary variables were then used to generate six indices to examine any variations in the shape of the skulls collected in different regions of the country. Although the largest skulls collected for this study originated in the mountainous regions of the northwest, northeast, and west, principle component analysis (PCA) did not result in a meaningful difference in the size and shape of wolf skulls in different regions of Iran. Our results confirm that the minor morphological variations of the skull in wolves of Iran are not an evidence for the separation of wolf populations in different regions or the existence of various subspecies in the country. This uniformity can be explained by the strong gene flow among populations as well as high mobility of the wolf that facilitates movement of individuals between populations.