quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation.

quantiNemo is an individual-based, genetically explicit stochastic simulation program. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNemo is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc. quantiNemo is coded in C++ using an object-oriented approach and runs on any computer platform. Availability: Executables for several platforms, user's manual, and source code are freely available under the GNU General Public License at http://www2.unil.ch/popgen/softwares/quantinemo.

Systems Genetics of Metabolism: The Use of the BXD Murine Reference Panel for Multiscalar Integration of Traits.

Metabolic homeostasis is achieved by complex molecular and cellular networks that differ significantly among individuals and are difficult to model with genetically engineered lines of mice optimized to study single gene function. Here, we systematically acquired metabolic phenotypes by using the EUMODIC EMPReSS protocols across a large panel of isogenic but diverse strains of mice (BXD type) to study the genetic control of metabolism. We generated and analyzed 140 classical phenotypes and deposited these in an open-access web service for systems genetics (www.genenetwork.org). Heritability, influence of sex, and genetic modifiers of traits were examined singly and jointly by using quantitative-trait locus (QTL) and expression QTL-mapping methods. Traits and networks were linked to loci encompassing both known variants and novel candidate genes, including alkaline phosphatase (ALPL), here linked to hypophosphatasia. The assembled and curated phenotypes provide key resources and exemplars that can be used to dissect complex metabolic traits and disorders.

Revision to the SUDAS Traffic Signal Design Guide, TR-546, 2009

Changes in technology have an impact on standard practice, materials, and equipment. The traffic signal industry is constantly producing more energy-efficient and durable equipment, better communications, and more sophisticated detection and monitoring capabilities. Accordingly, this project provides an update to the traffic signal content within the Statewide Urban Design and Specifications (SUDAS) Design Manual and Standard Specifications. This work was completed through a technical advisory committee with a variety of participants representing contractors, the Iowa Department of Transportation, cities, consultants, vendors, and university research and support staff.

Improved Methods for Determining Wind Loads on Highway Sign and Traffic-Signal Structures, TR-559, 2007

The main objective of the proposed study is to use Computational Fluid Dynamics (CFD) tools to determine the wind loads by accurate numerical simulations of air flow characteristics around large highway sign structures under severe wind speeds conditions. Fully three-dimensional Reynolds- Averaged Navier-Stokes (RANS) simulations are used to estimate the total force on different panels, as well as the actual pressure distribution on the front and back faces of the panels. In particular, the present study investigates the effects of aspect ratio and sign spacing for regular panels, the effect of sign depth for the dynamic message signs that are now being used on Iowa highways, the effect induced by the presence of back-to-back signs, the effect of the presence of add-on exit signs, and the effect of the presence of trucks underneath the signs potentially creating “wind tunnel” effect.

Is the macromolecule signal tissue-specific in healthy human brain? A (1)H MRS study at 7 Tesla in the occipital lobe.

PURPOSE: The macromolecule signal plays a key role in the precision and the accuracy of the metabolite quantification in short-TE (1) H MR spectroscopy. Macromolecules have been reported at 1.5 Tesla (T) to depend on the cerebral studied region and to be age specific. As metabolite concentrations vary locally, information about the profile of the macromolecule signal in different tissues may be of crucial importance. METHODS: The aim of this study was to investigate, at 7T for healthy subjects, the neurochemical profile differences provided by macromolecule signal measured in two different tissues in the occipital lobe, predominantly composed of white matter tissue or of grey matter tissue. RESULTS: White matter-rich macromolecule signal was relatively lower than the gray matter-rich macromolecule signal from 1.5 to 1.8 ppm and from 2.3 to 2.5 ppm with mean difference over these regions of 7% and 12% (relative to the reference peak at 0.9 ppm), respectively. The neurochemical profiles, when using either of the two macromolecule signals, were similar for 11 reliably quantified metabolites (CRLB < 20%) with relatively small concentration differences (< 0.3 μmol/g), except Glu (± 0.8 μmol/g). CONCLUSION: Given the small quantification differences, we conclude that a general macromolecule baseline provides a sufficiently accurate neurochemical profile in occipital lobe at 7T in healthy human brain.

Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology.

BACKGROUND: The model plant Arabidopsis thaliana (Arabidopsis) shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, the potential of Arabidopsis for molecular genetic analysis of this natural variation has increased dramatically in recent years. SCOPE: Advanced genomics has accelerated molecular phylogenetic analysis and gene identification by quantitative trait loci (QTL) mapping and/or association mapping in Arabidopsis. In particular, QTL mapping utilizing natural accessions is now becoming a major strategy of gene isolation, offering an alternative to artificial mutant lines. Furthermore, the genomic information is used by researchers to uncover the signature of natural selection acting on the genes that contribute to phenotypic variation. The evolutionary significance of such genes has been evaluated in traits such as disease resistance and flowering time. However, although molecular hallmarks of selection have been found for the genes in question, a corresponding ecological scenario of adaptive evolution has been difficult to prove. Ecological strategies, including reciprocal transplant experiments and competition experiments, and utilizing near-isogenic lines of alleles of interest will be a powerful tool to measure the relative fitness of phenotypic and/or allelic variants. CONCLUSIONS: As the plant model organism, Arabidopsis provides a wealth of molecular background information for evolutionary genetics. Because genetic diversity between and within Arabidopsis populations is much higher than anticipated, combining this background information with ecological approaches might well establish Arabidopsis as a model organism for plant evolutionary ecology.

Effects of parental larval diet on egg size and offspring traits in Drosophila.

If a mother's nutritional status predicts the nutritional environment of the offspring, it would be adaptive for mothers experiencing nutritional stress to prime their offspring for a better tolerance to poor nutrition. We report that in Drosophila melanogaster, parents raised on poor larval food laid 3-6% heavier eggs than parents raised on standard food, despite being 30 per cent smaller. Their offspring developed 14 h (4%) faster on the poor food than offspring of well-fed parents. However, they were slightly smaller as adults. Thus, the effects of parental diet on offspring performance under malnutrition apparently involve both adaptive plasticity and maladaptive effects of parental stress.

Root traits of common bean genotypes used in breeding programs for disease resistance

The objective of this work was to assess root traits of 19 common bean genotypes, used in breeding programs for disease resistance. Genotypes DOR 364 and G 19833 were used as deep and shallow basal root checks, respectively. The number of whorls and basal roots were assessed on five-day old seedlings grown in germination paper. Growth pouch studies were conducted to evaluate basal root gravitropism and lateral root length from primary roots, in seven-day old seedlings. The following root gravitropic traits were estimated: basal growth angle, shallow basal root length (localized in the top 2 cm), and relative shallow basal root growth. Number of whorls varied from 1.47 to 3.07, and number of basal roots ranged from 5.67 (genotype TO) to 12.07 (cultivar Jalo MG-65). Cultivars BRS MG Talismã, Carioca, BRS Pioneiro, and Diamante Negro exhibited shallow basal roots, while genotypes Vi-10-2-1, TU, AB 136, and México 54 showed deep basal roots. Cultivar Jalo MG-65 showed more lateral roots from the primary root than the other genotypes. Genotypes used on common bean breeding programs for disease resistance have great variability on basal and primary root traits.

Elevation gradient of successful plant traits for colonizing alpine summits under climate change

Upward migration of plant species due to climate change has become evident in several European mountain ranges. It is still, however, unclear whether certain plant traits increase the probability that a species will colonize mountain summits or vanish, and whether these traits differ with elevation. Here, we used data from a repeat survey of the occurrence of plant species on 120 summits, ranging from 2449 to 3418 m asl, in south-eastern Switzerland to identify plant traits that increase the probability of colonization or extinction in the 20th century. Species numbers increased across all plant traits considered. With some traits, however, numbers increased proportionally more. The most successful colonizers seemed to prefer warmer temperatures and well-developed soils. They produced achene fruits and/or seeds with pappus appendages. Conversely, cushion plants and species with capsule fruits were less efficient as colonizers. Observed changes in traits along the elevation gradient mainly corresponded to the natural distribution of traits. Extinctions did not seem to be clearly related to any trait. Our study showed that plant traits varied along both temporal and elevational gradients. While seeds with pappus seemed to be advantageous for colonization, most of the trait changes also mirrored previous gradients of traits along elevation and hence illustrated the general upward migration of plant species. An understanding of the trait characteristics of colonizing species is crucial for predicting future changes in mountain vegetation under climate change.

recueil de traités de médecine

Contient : Avicenne, Canon livre 2, paragraphes 1-2 (hébreu) Josué ibn Vivas de Lorca, גרם המעלות

Mechanism of hcnA mRNA recognition in the Gac/Rsm signal transduction pathway of Pseudomonas fluorescens.

In the plant-beneficial bacterium Pseudomonas fluorescens CHA0, the expression of antifungal exoproducts is controlled by the GacS/GacA two-component system. Two RNA binding proteins (RsmA, RsmE) ensure effective translational repression of exoproduct mRNAs. At high cell population densities, GacA induces three small RNAs (RsmX, RsmY, RsmZ) which sequester both RsmA and RsmE, thereby relieving translational repression. Here we systematically analyse the features that allow the RNA binding proteins to interact strongly with the 5' untranslated leader mRNA of the P. fluorescens hcnA gene (encoding hydrogen cyanide synthase subunit A). We obtained evidence for three major RsmA/RsmE recognition elements in the hcnA leader, based on directed mutagenesis, RsmE footprints and toeprints, and in vivo expression data. Two recognition elements were found in two stem-loop structures whose existence in the 5' leader region was confirmed by lead(II) cleavage analysis. The third recognition element, which overlapped the hcnA Shine-Dalgarno sequence, was postulated to adopt either an open conformation, which would favour ribosome binding, or a stem-loop structure, which may form upon interaction with RsmA/RsmE and would inhibit access of ribosomes. Effective control of hcnA expression by the Gac/Rsm system appears to result from the combination of the three appropriately spaced recognition elements.