PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)

MOTIVATION: A plugin for the Java-based PathVisio pathway editor has been developed to help users draw diagrams of bioregulatory networks according to the Molecular Interaction Map (MIM) notation. Together with the core PathVisio application, this plugin presents a simple to use and cross-platform application for the construction of complex MIM diagrams with the ability to annotate diagram elements with comments, literature references and links to external databases. This tool extends the capabilities of the PathVisio pathway editor by providing both MIM-specific glyphs and support for a MIM-specific markup language file format for exchange with other MIM-compatible tools and diagram validation. AVAILABILITY: The PathVisio-MIM plugin is freely available and works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X and Linux. Information about MIM notation and the MIMML format is available at http://discover.nci.nih.gov/mim. The plugin, along with diagram examples, instructions and Java source code, may be downloaded at http://discover.nci.nih.gov/mim/mim_pathvisio.html.     

Evolutionary history of the OmpR/IIIA family of signal transduction two component systems in Lactobacillaceae and Leuconostocaceae

Background  

Two component systems (TCS) are signal transduction pathways which typically consist of a sensor histidine kinase (HK) and a response regulator (RR). In this study, we have analyzed the evolution of TCS of the OmpR/IIIA family in Lactobacillaceae and Leuconostocaceae, two families belonging to the group of lactic acid bacteria (LAB). LAB colonize nutrient-rich environments such as foodstuffs, plant materials and the gastrointestinal tract of animals thus driving the study of this group of both basic and applied interest.     

Right time - right location - right move: TRPs find motors for common functions

TRP channels are localized at specialized sub-cellular compartments like filopodial tips, ciliary structures, growth cones and spines that have importance in the context of several sensory functions. Several motor proteins largely regulate these localizations. Recent studies indicate that both physical and genetic interactions exist between TRP channels with actin and microtubule-based motor proteins. These two groups of proteins share specialized and fine regulation underlying physiological functions. Indeed, mutations causing loss of these interactions and regulations result in development of pathophysiological disorders and syndromes. In this review we analyze the recent progress made in cell-biological, biochemical, electrophysiological and genetic studies and summarize the multi-dimensional crosstalk between TRP channels with different motor proteins.     

Reproductive pattern in agrarian and immigrant receptor populations: a survey of El Ejido (SE Spain)

This paper deals with the fertility pattern of the El Ejido population, an agricultural Spanish community characterised by the rapid development of its modern agrarian economy. Consequently, the arrival of immigrants has sharply increased throughout the second half of the twentieth century, with important demographic consequences as well as reproductive changes. The analyses of the age-specific fertility rate (fx) and the total fertility rate (TFR) were used in order to describe the reproductive pattern of this population in 2000. The main characteristics were the following: a) Regarding the temporal change, an important decrease of fx has been observed in all age groups for the last twenty years, as a consequence of progressive birth control. However, the reproductive pattern has kept almost invariable and has been characterised by a maximum fertility at age group of 25-29 years old. b) Regarding the general Spanish fertility, the comparison of fx in both populations suggests a younger maternity in the agricultural population than in the national, the maximum fertility delayed to the 30-34 age group. c) Moreover, the El Ejido population showed a clear higher offspring per woman (TFR = 1.42) than the national (TFR = 1.24), according to the agrarian character of the El Ejido population. d) Finally, this greater reproductive level of El Ejido is also due to the arrival of women at fertile age, who come mainly from Africa, and above all from Morocco.     

Kaposi's sarcoma-associated herpesvirus glycoprotein K8.1 is dispensable for virus entry

Kaposi's sarcoma-associated herpesvirus (KSHV) is considered the etiologic agent of Kaposi's sarcoma and several lymphoproliferative disorders. Recently, the KSHV genome was cloned into a bacterial artificial chromosome and used to construct a recombinant KSHV carrying a deletion of the viral interferon regulatory factor gene (F. C. Zhou, Y. J. Zhang, J. H. Deng, X. P. Wang, H. Y. Pan, E. Hettler, and S. J. Gao, J. Virol. 76:6185-6196, 2002). The K8.1 glycoprotein is a structural component of the KSHV particle and is thought to facilitate virus entry by binding to heparan sulfate moieties on cell surfaces. To further address the role of K8.1 in virus infectivity, a K8.1-null recombinant virus (BAC36DeltaK8.1) was constructed by deletion of most of the K8.1 open reading frame and insertion of a kanamycin resistance gene cassette within the K8.1 gene. Southern blotting and diagnostic PCR confirmed the presence of the engineered K8.1 gene deletion. Transfection of the wild-type genome (BAC36) and mutant genome (BAC36DeltaK8.1) DNAs into 293 cells in the presence or absence of the complementing plasmid (pCDNAK8.1A), transiently expressing the K8.1A gene, produced infectious virions in the supernatants of transfected cells. These results demonstrated that the K8.1 glycoprotein is not required for KSHV entry into 293 cells.     

Causes of neonatal mortality in Spain (1975-98): influence of sex, rural-urban residence and age at death

Neonatal mortality during the first week of life, corresponding to the years 1975-1998, was studied in Spain. The first week of life is the time in which the highest number of deaths occur. The temporal decrease of the neonatal mortality rate (NMR) was modelled according to log10(NMR+1)= 2.784 - 0.023 per year. This decline cannot be explained by an increase in the mean birth weight (MBW=23440.835 - 10.107 g per year). From the most frequent of the causes of death to the least were: congenital anomalies, preterm born or low birth weight, respiratory problems, pregnancy difficulties, hypoxaemia/asphyxia, delivery difficulties and infectious diseases. This sequence changed when the specific age at death was considered. The NMR descended evenly for both sexes for the causes indicated above, except for preterm born or low birth weight, in which the male mortality decrease was greater since its rate was more elevated at the beginning of the period studied. For all the causes listed, NMR was more elevated both in urban areas and for males. Early neonatal mortality (first 24 hours) was higher for pregnancy difficulties, preterm born or low birth weight, congenital anomalies and hypoxaemia/asphyxia.     

An electrically coupled network of skeletal muscle in zebrafish distributes synaptic current

Fast and slow skeletal muscle types are readily distinguished in larval zebrafish on the basis of differences in location and orientation. Additionally, both muscle types are compact, rendering them amenable to in vivo patch clamp study of synaptic function. Slow muscle mediates rhythmic swimming, but it does so purely through synaptic drive, as these cells are unable to generate action potentials. Our patch clamp recordings from muscle pairs of zebrafish reveal a network of electrical coupling in slow muscle that allows sharing of synaptic current within and between segmental boundaries of the tail. The synaptic current exhibits slow kinetics (tau(decay) approximately 4 ms), which further facilitates passage through the low pass filter, a consequence of the electrically coupled network. In contrast to slow muscle, fast skeletal muscle generates action potentials to mediate the initial rapid component of the escape response. The combination of very weak electrical coupling and synaptic kinetics (tau(decay) <1 ms) too fast for the network low pass filter minimizes intercellular sharing of synaptic current in fast muscle. These differences between muscle types provide insights into the physiological role(s) of electrical coupling in skeletal muscle. First, intrasegmental coupling among slow muscle cells allows effective transfer of synaptic currents within tail segments, thereby minimizing differences in synaptic depolarization. Second, a fixed intersegmental delay in synaptic current transit, resulting from the low pass filter properties of the slow muscle network, helps coordinate the rostral-caudal wave of contraction.     

Costs of twins in free-ranging white-bellied spider monkeys (Ateles belzebuth belzebuth) at Tinigua National Park, Colombia

A female spider monkey (Ateles belzebuth belzebuth) that gave birth to twins was studied during 13 months, and her activity budget and diet were compared to those of females with single offspring and females with no offspring to assess selective pressures that could influence litter size. We recorded qualitative information on the development and social interactions of the twins and three other single infants. Emi, the female that had the twins, had the highest proportion of resting time and the lowest proportion of feeding and moving time compared to other adult females and males. Emi also had the lowest average daily travel distance and relied more heavily on flowers and leaves than other group members who included a higher proportion of fruits in their diets. These results suggest that twins are energetically costly to spider monkeys because of the direct energy allocated into raising and carrying the twins and, also, because these costs have direct effects in the ability of a mother to obtain high-quality resources (e.g., fruits). The twins had a slower rate of physical and social development as well as a smaller body size compared to same-aged singletons by the end of the study. Thus, the extended periods of maternal care and the costs associated with rearing and carrying offspring are some of the factors that influence the evolution and maintenance of a litter size of one in most anthropoid primates.