Effect of analytical conditions in wavelength dispersive electron microprobe analysis on the measurement of strontium-to-calcium (Sr/Ca) ratios in otoliths of anadromous salmonids

The use of strontium-to-calcium (Sr/Ca) ratios in otoliths is becoming a standard method to describe life history type and the chronology of migrations between freshwater and seawater habitats in teleosts (e.g. Kalish, 1990; Radtke et al., 1990; Secor, 1992; Rieman et al., 1994; Radtke, 1995; Limburg, 1995; Tzeng et al. 1997; Volk et al., 2000; Zimmerman, 2000; Zimmerman and Reeves, 2000, 2002). This method provides critical information concerning the relationship and ecology of species exhibiting phenotypic variation in migratory behavior (Kalish, 1990; Secor, 1999). Methods and procedures, however, vary among laboratories because a standard method or protocol for measurement of Sr in otoliths does not exist. In this note, we examine the variations in analytical conditions in an effort to increase precision of Sr/Ca measurements. From these findings we argue that precision can be maximized with higher beam current (although there is specimen damage) than previously recommended by Gunn et al. (1992).

MicroRNA regulation and the variability of human cortical gene expression

Understanding the driving forces of gene expression variation within human populations will provide important insights into the molecular basis of human phenotypic variation. In the genome, the gene expression variability differs among genes, and at prese

Factors affecting leaf morphology: a case study of Ranunculus natans C. A. Mey. (Ranunculaceae) in the arid zone of northwest China

In order to examine the role of environmental factors affecting foliar morphology, we performed a case study of leaf morphological variation of Ranunculus natans found in the arid zone of northwest China. We found that foliar phenotypic variation differed significantly between populations. We described substantial positive correlations between altitude and leaf area (LA) as well as leaf perimeter (LP), and also between longitude and number of teeth, along with dissection index (DI). The pH, conductivity, and salinity of the environment caused a significant decrease in both LA and LP. Ranked in terms of their impacts on leaf morphology, the six selected factors were: altitude > pH > conductivity > salinity > longitude > latitude. We found that foliar morphological variations are functional responses to water-quantity factors (e.g., altitude and longitude at regional scales) and water-availability relation factors (e.g., pH, conductivity, and salinity at local scales), rather than to temperature-relation factors (latitude). Therefore, altitude and longitude, along with pH, conductivity, and salinity, are the main factors that significantly influence foliar morphology in the arid zone of China. We found that main factors played major roles in plant phenotypic plasticity in a complex ecosystem, although different combinations and interactions of environmental and geographical factors in each local environment may obscure the general trends in trait changes along environmental gradients.

Identification of quantitative trait loci for growth-related traits in the Pacific abalone Haliotis discus hannai Ino

The locations and effects of quantitative trait loci (QTL) were estimated for nine characters for growth-related traits in the Pacific abalone (Haliotis discus hannai Ino) using a randomly amplified polymorphic DNA (RAPD), amplification fragment length polymorphism (AFLP) and SSR genetic linkage map. Twenty-eight putatively significant QTLs (LOD > 2.4) were detected for nine traits (shell length, shell width, total weight, shell weight, weight of soft part, muscle weight, gonad and digestive gland weight, mantle weight and gill weight). The percentage of phenotypic variation explained by a single QTL ranged from 8.0% to 35.9%. The significant correlations (P < 0.001) were found among all the growth-related traits, and Pearson's correlation coefficients were more than 0.81. For the female map, the QTL for growth were concentrated on groups 1 and 4 linkage maps. On the male map, the QTL that influenced growth-related traits gathered on the groups 1 and 9 linkage maps. Genetic linkage map construction and QTL analysis for growth-related traits are the basis for the marker-assisted selection and will eventually improve production and quality of the Pacific abalone.

The Framingham Heart Study 100K SNP genome-wide association study resource: overview of 17 phenotype working group reports

BACKGROUND:The Framingham Heart Study (FHS), founded in 1948 to examine the epidemiology of cardiovascular disease, is among the most comprehensively characterized multi-generational studies in the world. Many collected phenotypes have substantial genetic contributors; yet most genetic determinants remain to be identified. Using single nucleotide polymorphisms (SNPs) from a 100K genome-wide scan, we examine the associations of common polymorphisms with phenotypic variation in this community-based cohort and provide a full-disclosure, web-based resource of results for future replication studies.METHODS:Adult participants (n = 1345) of the largest 310 pedigrees in the FHS, many biologically related, were genotyped with the 100K Affymetrix GeneChip. These genotypes were used to assess their contribution to 987 phenotypes collected in FHS over 56 years of follow up, including: cardiovascular risk factors and biomarkers; subclinical and clinical cardiovascular disease; cancer and longevity traits; and traits in pulmonary, sleep, neurology, renal, and bone domains. We conducted genome-wide variance components linkage and population-based and family-based association tests.RESULTS:The participants were white of European descent and from the FHS Original and Offspring Cohorts (examination 1 Offspring mean age 32 +/- 9 years, 54% women). This overview summarizes the methods, selected findings and limitations of the results presented in the accompanying series of 17 manuscripts. The presented association results are based on 70,897 autosomal SNPs meeting the following criteria: minor allele frequency [greater than or equal to] 10%, genotype call rate [greater than or equal to] 80%, Hardy-Weinberg equilibrium p-value [greater than or equal to] 0.001, and satisfying Mendelian consistency. Linkage analyses are based on 11,200 SNPs and short-tandem repeats. Results of phenotype-genotype linkages and associations for all autosomal SNPs are posted on the NCBI dbGaP website at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007.CONCLUSION:We have created a full-disclosure resource of results, posted on the dbGaP website, from a genome-wide association study in the FHS. Because we used three analytical approaches to examine the association and linkage of 987 phenotypes with thousands of SNPs, our results must be considered hypothesis-generating and need to be replicated. Results from the FHS 100K project with NCBI web posting provides a resource for investigators to identify high priority findings for replication.

Phenotypical characterization in "Plasmopara halstedii" (sunflower downy mildew) isolates of several races

Phenotypic variation (morphological and pathogenic characters), and genetic variability were studied in 50 isolates of seven Plasmopara halstedii (sunflower downy mildew) races 100, 300, 304, 314, 710, 704 and 714. There were significant morphological, aggressiveness, and genetic differences for pathogen isolates. However, there was no relationship between morphology of zoosporangia and sporangiophores and pathogenic and genetic characteristics for the races used in our study. Also, our results provided evidence that no relation between pathogenic traits and multilocus haplotypes may be established in P. halstedii. The hypothesis explaining the absence of relationships among phenotypic and genetic characteristics is discussed.

Diverse pathogenicity of Burkholderia cepacia complex strains in the Caenorhabditis elegans host model

A fast screening method was developed to assess the pathogenicity of a diverse collection of environmental and clinical Burkholderia cepacia complex isolates in the nematode Caenorhabditis elegans. The method was validated by comparison with the standard slow-killing assay. We observed that the pathogenicity of B. cepacia complex isolates in C. elegans was strain-dependent but species-independent. The wide range of observed pathogenic phenotypes agrees with the high degree of phenotypic variation among species of the B. cepacia complex and suggests that the taxonomic classification of a given strain within the complex cannot predict pathogenicity.

Arsenic uptake and metabolism in arsenic resistant and nonresistant plant species

Elevation of arsenic levels in soils causes considerable concern with respect to plant uptake and subsequent entry into wildlife and human food chains, Arsenic speciation in the environment is complex, existing in both inorganic and organic forms, with interconversion between species regulated by biotic and abiotic processes. To understand and manage the risks posed by soil arsenic it is essential to know how arsenic is taken up by the roots and metabolized within plants. Some plant species exhibit phenotypic variation in response to arsenic species, which helps us to understand the toxicity of arsenic and the way in which plants have evolved arsenic resistances. This knowledge, for example, could be used produce plant cultivars that are more arsenic resistant or that have reduced arsenic uptake. This review synthesizes current knowledge on arsenic uptake, metabolism and toxicity for arsenic resistant and nonresistant plants, including the recently discovered phenomenon of arsenic hyperaccumulation in certain fern species. The reasons why plants accumulate and metabolize arsenic are considered in an evolutionary context. © New Phytologist.

LaGomiCs - Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order

The order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action “A Collaborative European Network on Rabbit Genome Biology—RGB-Net” and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration.

Chromosomal structure: a selectable trait for evolution

Dissertation presented to obtain the Ph.D degree in Evolutionary Biology

Nutritional plasticity and evolutionary divergence in the Drosophila ovary

The environment can modify developmental trajectories and generate a range of distinct phenotypes without altering an organism’s genome, a widespread phenomenon called developmental plasticity. The past decades have seen a resurgent interest in understanding how developmental plasticity contributes to evolutionary processes, as it can produce phenotypic variation among individuals and facilitate diversification among populations that inhabit distinct ecological niches. To better understand the importance of plastic responses for evolutionary change, we need to explore how the environment alters development to produce phenotypic variation and then compare this to how genetic variation influences these same developmental processes.(...)

Variability in the Stability and Productivity of Transfected Genes in Chinese Hamster Ovary (CHO) cells

In the field of biologics production, productivity and stability of the transfected gene of interest are two very important attributes that dictate if a production process is viable. To further understand and improve these two traits, we would need to further our understanding of the factors affecting them. These would include integration site of the gene, gene copy number, cell phenotypic variation and cell environment. As these factors play different parts in the development process, they lead to variable productivity and stability of the transfected gene between clones, the well-known phenomenon of “clonal variation”. A study of this phenomenon and how the various factors contribute to it will thus shed light on strategies to improve productivity and stability in the production cell line. Of the four factors, the site of gene integration appears to be one of the most important. Hence, it is proposed that work is done on studying how different integration sites affect the productivity and stability of transfected genes in the development process. For the study to be more industrially relevant, it is proposed that the Chinese Hamster Ovary dhfr-deficient cell line, CHO-DG44, is used as the model system.

Genetic analysis of heat tolerance at anthesis in rice

Genetic analysis of heat tolerance will help breeders produce rice (Oryza sativa L.) varieties adapted to future climates. An F6 population of 181 recombinant inbred lines of Bala (tolerant) × Azucena (susceptible) was screened for heat tolerance at anthesis by measuring spikelet fertility at 30°C (control) and 38°C (high temperature) in experiments conducted in the Philippines and the United Kingdom. The parents varied significantly for absolute spikelet fertility under control (79–87%) and at high temperature (2.9–47.1%), and for relative spikelet fertility (high temperature/control) at high temperature (3.7–54.9%). There was no correlation between spikelet fertility in control and high-temperature conditions and no common quantitative trait loci (QTLs) were identified. Two QTLs for spikelet fertility under control conditions were identified on chromosomes 2 and 4. Eight QTLs for spikelet fertility under high-temperature conditions were identified on chromosomes 1, 2, 3, 8, 10, and 11. The most significant heat-responsive QTL, contributed by Bala and explaining up to 18% of the phenotypic variation, was identified on chromosome 1 (38.35 mega base pairs on the rice physical genome map). This QTL was also found to influence plant height, explaining 36.6% of the phenotypic variation. A comparison with other studies of abiotic (drought, cold, salinity) stresses showed QTLs at similar positions on chromosomes 1, 3, 8, and 10, suggesting common underlying stress-responsive regions of the genome.

Auriculo-condylar syndrome: mapping of a first locus and evidence for genetic heterogeneity

Auriculo-condylar syndrome (ACS), an autosomal dominant disorder of first and second pharyngeal arches, is characterized by malformed ears (`question mark ears`), prominent cheeks, microstomia, abnormal temporomandibular joint, and mandibular condyle hypoplasia. Penetrance seems to be complete, but there is high inter-and intra-familial phenotypic variation, with no evidence of genetic heterogeneity. We herein describe a new multigeneration family with 11 affected individuals (F1), in whom we confirm intra-familial clinical variability. Facial asymmetry, a clinical feature not highlighted in other ACS reports, was highly prevalent among the patients reported here. The gene responsible for ACS is still unknown and its identification will certainly contribute to the understanding of human craniofacial development. No chromosomal rearrangements have been associated with ACS, thus mapping and positional cloning is the best approach to identify this disease gene. To map the ACS gene, we conducted linkage analysis in two large ACS families, F1 and F2 (F2; reported elsewhere). Through segregation analysis, we first excluded three known loci associated with disorders of first and second pharyngeal arches (Treacher Collins syndrome, oculo-auriculo-vertebral spectrum, and Townes-Brocks syndrome). Next, we performed a wide genome search and we observed evidence of linkage to 1p21.1-q23.3 in F2 (LOD max 3.01 at theta = 0). Interestingly, this locus was not linked to the phenotype segregating in F1. Therefore, our results led to the mapping of a first locus of ACS (ACS1) and also showed evidence for genetic heterogeneity, suggesting that there are at least two loci responsible for this phenotype.

Underutilized Annona Species from the Brazilian Cerrado and Amazon Rainforest: A Study on Fatty Acids Profile and Yield of Seed Oils

Annona (Annonaceae) is an important source of fruits in the Brazilian Cerrado and the Amazon Rainforest. Some Annona species are widely commercialized as fresh fruit or as frozen pulp. Seeds are accustomedly discarded. Our main goal was to analyze fatty acids profile from seeds of A. crassiflora and A. coriacea from Cerrado, A. montana from Amazon Forest, and three cultivars (A. cherimola cv. Madeira, A. cherimola x A. squamosa cv. Pink`s Mammonth and A. cherimola x A. squamosa cv. Gefner). The total oil yield ranged between 20 and 42% by weight of dry mass. The A cherimola x A. squamosa cv. Gefner has significantly higher total lipid yield than all other samples. 100 g of fruit of this species present 6-8 g of seeds. Considering the fruit production of Chile (over 221 ton of fruits/year), more than 1300 ton of seed/year could be obtained, which could provide at least 200 ton of seed oil. Oleic acid was predominant for most samples, but for A. montana linoleic acid was the most abundant FA. Phenotypic variation on FAME profile was observed. These new data are an urgent requirement for supporting conservation programs, mainly for Cerrado areas in Brazil.