PubMed Health⌕ Search

Biomedical subjects

Joanne Russell

Publications and source records attributed to Joanne Russell.

7 recordsLinked to original sources

Creating an infrastructure for training in the responsible conduct of research: the University of Pittsburgh's experience.

In response to public concerns about the consequences of research misconduct, academic institutions have become increasingly cognizant of the need to implement comprehensive, effective training in the responsible conduct of research (RCR) for faculty, staff, students, and external collaborators. The ability to meet this imperative is challenging as universities confront declining financial resources and increasing complexity of the research enterprise. The authors describe the University of Pittsburgh's design, implementation, and evaluation of a Web-based, institution-wide RCR training program called Research and Practice Fundamentals (RPF). This project, established in 2000, was embedded in the philosophy, organizational structure, and technology developed through the Integrated Advanced Information Management Systems grant from the National Library of Medicine. Utilizing a centralized, comprehensive approach, the RPF system provides an efficient mechanism for deploying content to a large, diverse cohort of learners and supports the needs of research administrators by providing access to information about who has successfully completed the training. During its first 3 years of operation, the RPF served over 17,000 users and issued more than 38,000 training certificates. The 18 modules that are currently available address issues required by regulatory mandates and other content areas important to the research community. RPF users report high levels of satisfaction with content and ease of using the system. Future efforts must explore methods to integrate non-RCR education and training into a centralized, cohesive structure. The University of Pittsburgh's experience with the RPF demonstrates the importance of developing an infrastructure for training that is comprehensive, scalable, reliable, centralized, affordable, and sustainable.

Academic Medical Centers↗

Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress.

More than 2,000 genome-wide barley single nucleotide polymorphisms (SNPs) were developed by resequencing unigene fragments from eight diverse accessions. The average genome-wide SNP frequency observed in 877 unigenes was 1 SNP per 200 bp. However, SNP frequency was highly variable with the least number of SNP and SNP haplotypes observed within European cultivated germplasm reflecting effects of breeding history on genetic diversity. More than 300 SNP loci were mapped genetically in three experimental mapping populations which allowed the construction of an integrated SNP map incorporating a large number of RFLP, AFLP and SSR markers (1,237 loci in total). The genes used for SNP discovery were selected based on their transcriptional response to a variety of abiotic stresses. A set of known barley abiotic stress QTL was positioned on the linkage map, while the available sequence and gene expression information facilitated the identification of genes potentially associated with these traits. Comparison of the sequenced SNP loci to the rice genome sequence identified several regions of highly conserved gene order providing a framework for marker saturation in barley genomic regions of interest. The integration of genome-wide SNP and expression data with available genetic and phenotypic information will facilitate the identification of gene function in barley and other non-model organisms.

Expressed Sequence Tags↗

Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare.

In human genetics a detailed knowledge of linkage disequilibrium (LD) is considered a prerequisite for effective population-based, high-resolution gene mapping and cloning. Similar opportunities exist for plants; however, differences in breeding system and population history need to be considered. Here we report a detailed study of localized LD in different populations of an inbreeding crop species. We measured LD between and within four gene loci within the region surrounding the hardness locus in three different gene pools of barley (Hordeum vulgare). We demonstrate that LD extends to at least 212 kb in elite barley cultivars but is rapidly eroded in related inbreeding ancestral populations. Our results indicate that haplotype-based sequence analysis in multiple populations will provide new opportunities to adjust the resolution of association studies in inbreeding crop species.

Chromosomes, Plant↗

Single-feature polymorphism discovery in the barley transcriptome.

A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.

Gene Expression Profiling↗

Isolation of high molecular weight DNA suitable for BAC library construction from woody perennial soft-fruit species.

We have developed a novel nuclei extraction method that allows for the extraction of high molecular weight DNA from leaves of woody perennial soft-fruit species that contain high levels of carbohydrates and polyphenolics. The method utilizes a modified buffer system including 4% (w/v) polyvinylpyrrolidone (PVP)-10 and a combination of nylon filters and Percoll gradients to purify nuclei extracts prior to embedding in agarose plugs. The effectiveness of the method was demonstrated on leaves of red raspberry (Rubus idaeus) and blackcurrant (Ribes nigrum), two soft-fruit species that have shown to be recalcitrant to standard genomic DNA extraction methods. Extracted DNA was readily digested by restriction enzymes and, as shown for raspberry, suitable for bacterial artificial chromosome (BAC) library construction.

Chromosomes, Artificial, Bacterial↗

A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome.

Direct estimates of sequence diversity provides an abundant source of DNA polymorphisms based on single nucleotide polymorphisms (SNPs). The frequency and distribution of nucleotide diversity within 23 genes associated with grain germination in barley were determined in a sample of accessions representing European cultivars, landraces, and wild barley accessions from throughout the fertile crescent. The overall nucleotide diversity ranged from 0.0021 to 0.0189 with a single nucleotide change being detected every 78 bp and insertion-deletion events being observed every 680 bp. Within the cultivated (H. vulgare) genepool, a small number of haplotypes were detected, the total number of haplotypes observed in H. spontaneum was almost double that detected in H. vulgare (46 and 26, respectively). Distinct haplotypes were observed in the H. spontaneum and landrace genepools, which are highly divergent from H. vulgare. A comparison of SNP-based haplotype data with EST-derived SSRs and genomic SSRs revealed a similar trend of decreasing variability in the cultivated genepool. However, the number of unique alleles identified in the cultivated sample was much greater with genomic SSRs (18%) compared with only 2.1% for SNPs and 3.8% for EST-derived SSRs. The potential utility of SNPs and EST-derived SSRs for association mapping in barley is discussed.

Base Sequence↗

A microarray-based high throughput molecular marker genotyping method: the tagged microarray marker (TAM) approach.

A microarray-based method has been developed for scoring thousands of DNAs for a co-dominant molecular marker on a glass slide. The approach was developed to detect insertional polymorphism of transposons and works well with single nucleotide polymorphism (SNP) markers. Biotin- terminated allele-specific PCR products are spotted unpurified onto streptavidin-coated glass slides and visualised by hybridisation of fluorescent detector oligonucleotides to tags attached to the allele- specific PCR primers. Two tagged primer oligonucleotides are used per locus and each tag is detected by hybridisation to a concatameric DNA probe labelled with multiple fluorochromes.

Biotinylation↗