Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes

The timing and order of divergences within the genus Rattus have, to date, been quite speculative. In order to address these important issues we sequenced six new whole mitochondrial genomes from wild-caught specimens from four species, Rattus exulans, Rattus praetor, Rattus rattus and Rattus tanezumi. The only rat whole mitochondrial genomes available previously were all from Rattus norvegicus specimens. Our phylogenetic and dating analyses place the deepest divergence within Rattus at approximately 3.5 million years ago (Mya). This divergence separates the New Guinean endemic R. praetor lineage from the Asian lineages. Within the Asian/Island Southeast Asian clade R. norvegicus diverged earliest at approximately 2.9Mya. R. exulans and the ancestor of the sister species R. rattus and R. tanezumi subsequently diverged at approximately 2.2Mya, with R. rattus and R. tanezumi separating as recently as approximately 0.4Mya. Our results give both a better resolved species divergence order and diversification dates within Rattus than previous studies.     

Hosts are more important than destinations: What genetic variation in Microctonus aethiopoides (Hymenoptera: Braconidae) means for foreign exploration for natural enemies

Nucleotide sequence data were generated from the gene regions COI, 16S, and arginine kinase to assess genetic variation within the Palearctic parasitoid, Microctonus aethiopoides, reared from Sitona discoideus, S. hispidulus, and Hypera postica collected from two proximate locations in Mediterranean France. Partitioned Bayesian phylogenetic analyses of the molecular data provided strong support for the presence of at least two M. aethiopoides biotypes, one associated with Hypera species and the other with Sitona species. These new results combined with previously published data from 14 countries show that M. aethiopoides genetic variation is much more strongly correlated with host taxon than with sampling location. This contrasts with earlier perceptions that M. aethiopoides exhibits significant geographic variation, and helps to explain the widely varying biological control outcomes that have been obtained following the introductions of M. aethiopoides to Australia, New Zealand, and North America. The results strongly suggest that success rates and environmental safety in biological control would both be improved by ensuring that parasitoids collected in the native range are reared from the same host species as the one being targeted for control in the region of introduction. The results also provided insights both on the evolution of M. aethiopoides' host range, and on its evolutionary transition between solitary and gregarious larval development.     

The triple-120 meter shuttle test: a sport-specific test for assessing anaerobic endurance fitness in rugby league players

The aim of this study was to design a simple field test to measure the anaerobic endurance fitness of rugby league players, which is an important fitness quality in the game of rugby league. Twelve amateur football players with a mean (+/-SD) age of 21.5 years (+/-2.2) volunteered to participate in the study. The subjects completed 1 trial of the Wingate 60-second (W60) cycle test and 2 trials of the new Triple-120 meter shuttle (T120S) test. All trials were completed 4 days apart. The validity of the T120S was determined by comparing physiological responses (heart rate and blood lactate) and rating of perceived exertion to the all-out W60 cycle test. The results indicate there is a significant relationship between maximum heart rate (r = 0.63 and 0.71) for the 2 trials of the T120S and the W60 cycle test. There was no significant relationship between the 2 trials and the W60 cycle test for post 3 minute lactate (r = 0.112 and 0.101) and rating of perceived exertion (r = 0.94 and 0.161). However, the T120S test elicited greater mean values for these measures than the W60 cycle test. The results indicate that the T120S is a valid test of anaerobic endurance and represents a sports specific test of this quality that may provide useful information for players and coaches involved in the sport of rugby league.     

Development of DNA aptamers for cytochemical detection of acetylcholine

This report describes a novel approach to the detection of acetylcholine using DNA aptamers. Aptamers were developed by eight rounds of acetylcholine affinity column chromatography and polymerase chain reaction (PCR) amplification. Sequences from rounds 5 and 8 were screened by colorimetric enzyme-based microtiter plate assays and found to bind acetylcholine and related compounds, but not unrelated compounds. One of the highest affinity aptamers, designated ACh 6R, was further tested in aptamer-peroxidase and aptamer-fluorescence staining protocols. Using Neuro-2a murine neuroblastoma cells induced to differentiate in the presence of 1 μM all-trans-retinoic acid for 5–7 d, ACh 6R detected cholinergic cells by both the peroxidase and fluorescence methods. Unrelated DNA aptamers did not stain the cells using either method. Fixation with cold 2% paraformaldehyde was compared to cold alkaline allyl alcohol plus glutaraldehyde for immobilization of acetylcholine in situ and appeared to enable detection of greater numbers of cholinergic cells, although differences in levels of differentiation may have been a factor as well. Acetylcholine generally appeared to be distributed throughout the differentiated Neuro-2a cell bodies. However, in some cells, punctate staining along neurite outgrowths and near the termini of cellular processes suggested detection of acetylcholine in discrete vesicles.     

The plastidial MEP pathway: unified nomenclature and resources

In plants, the plastid-localized 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway provides the precursors for the synthesis of isoprenoid hormones, monoterpenes, carotenoids and the side chain of chlorophylls, tocopherols and prenylquinones. As a result of the fast progress in the elucidation and characterization of the pathway (mainly by genetic approaches in Escherichia coli and Arabidopsis thaliana), different names have been used in the literature to designate the orthologous bacterial and plant genes and the corresponding null and partial loss-of-function mutants. This has led to a confusing variety of naming conventions in this field. Here, we propose a reorganization of the various naming systems with the aim of facilitating the dissemination and sharing of genetic resources and tools central to plant isoprenoid research.     

Optimal design of thermally stable proteins

MOTIVATION: For many biotechnological purposes, it is desirable to redesign proteins to be more structurally and functionally stable at higher temperatures. For example, chemical reactions are intrinsically faster at higher temperatures, so using enzymes that are stable at higher temperatures would lead to more efficient industrial processes. We describe an innovative and computationally efficient method called Improved Configurational Entropy (ICE), which can be used to redesign a protein to be more thermally stable (i.e. stable at high temperatures). This can be accomplished by systematically modifying the amino acid sequence via local structural entropy (LSE) minimization. The minimization problem is modeled as a shortest path problem in an acyclic graph with nonnegative weights and is solved efficiently using Dijkstra's method.     

Roads as barriers to animal movement in fragmented landscapes

Roads can act as barriers to animal movement through mortality during crossing attempts or behavioral avoidance. This barrier effect has negative demographic and genetic consequences that can ultimately result in local or regional extinction. Here we use radio-telemetry data on three terrestrial vertebrates (eastern massasauga Sistrurus catenatus , eastern box turtle Terrapene carolina and ornate box turtle Terrapene ornata ) to test whether roads acted as barriers to movement. Specifically, we test whether individuals avoided crossing roads by comparing the number of observed crossings with the number of road crossings predicted by randomizations of individual movement paths. All species crossed roads significantly less often than predicted by chance, indicating strong road avoidance. Results of this study showing behavioral avoidance and previous studies on road mortality indicate that roads are strong barriers to these species. High mortality during crossing attempts would select for road avoidance, reducing the number of individuals killed on roads over time but leading to genetically partitioned subpopulations due to a lack of gene flow. In species that are long-lived and late-maturing, negative genetic effects might not be observable over short time-scales, thus placing populations at high risk of extinction because of a failure to detect an incrementally worsening problem. Formulating successful management strategies for many species in decline will require integrating data on road mortality, animal behavior and population genetics in order to understand more clearly the barrier effect of roads.     

Classifying aquatic macrophytes as indicators of eutrophication in European lakes

Aquatic macrophytes are one of the biological quality elements in the Water Framework Directive (WFD) for which status assessments must be defined. We tested two methods to classify macrophyte species and their response to eutrophication pressure: one based on percentiles of occurrence along a phosphorous gradient and another based on trophic ranking of species using Canonical Correspondence Analyses in the ranking procedure. The methods were tested at Europe-wide, regional and national scale as well as by alkalinity category, using 1,147 lakes from 12 European states. The grouping of species as sensitive, tolerant or indifferent to eutrophication was evaluated for some taxa, such as the sensitive Chara spp. and the large isoetids, by analysing the (non-linear) response curve along a phosphorous gradient. These thresholds revealed in these response curves can be used to set boundaries among different ecological status classes. In total 48 taxa out of 114 taxa were classified identically regardless of dataset or classification method. These taxa can be considered the most consistent and reliable indicators of sensitivity or tolerance to eutrophication at European scale. Although the general response of well known indicator species seems to hold, there are many species that were evaluated differently according to the database selection and classification methods. This hampers a Europe-wide comparison of classified species lists as used for the status assessment within the WFD implementation process.     

Meiotic genes and proteins in cereals

We review the current status of our understanding and knowledge of the genes and proteins controlling meiosis in five major cereals, rye, wheat, barley, rice and maize. For each crop, we describe the genetic and genomic infrastructure available to investigators, before considering the inventory of genes and proteins that have roles to play in this process. Emphasis is given throughout as to how translational genomic and proteomic approaches have enabled us to circumvent some of the intractable features of this important group of plants.     

Solution properties of conventional gum arabic and a matured gum arabic (Acacia (sen) SUPER GUM)

Dilute solution properties of two specially matured gum arabic samples (EM1 and EM2) were compared to the conventional gum (EM0) using static light scattering. The apparent molar mass (M(w,app) and radius of gyration (R(g,app)) for the three samples showed unusual concentration dependence. These data were satisfactorily interpreted by a simple association model that takes into account the repulsive interaction among clusters, which allowed us to obtain the true molar mass (Mw(0)) and radius of gyration (Rg(0)). A common power law relation was observed between Mw(0) and Rg(0) , giving a somewhat higher exponent than expected for linear and branched polymers in a good solvent. Mw(0) and Rg(0) obtained for the three gums do not differ significantly from each other. However, the data showed clearly a constant increase of the association from EM0 to EM2 with increasing concentration. This is in accordance with the previously observed improved functional properties for the matured products.