The landscape of transcription errors in eukaryotic cells.

Accurate transcription is required for the faithful expression of genetic information. To understand the molecular mechanisms that control the fidelity of transcription, we used novel sequencing technology to provide the first comprehensive analysis of the fidelity of transcription in eukaryotic cells. Our results demonstrate that transcription errors can occur in any gene, at any location, and affect every aspect of protein structure and function. In addition, we show that multiple proteins safeguard the fidelity of transcription and provide evidence suggesting that errors that evade these layers of RNA quality control profoundly affect the physiology of living cells. Together, these observations demonstrate that there is an inherent limit to the faithful expression of the genome and suggest that the impact of mutagenesis on cellular health and fitness is substantially greater than currently appreciated.

Put the healthy item first: Order of ingredient listing influences consumer selection.

This study examined effects of an order form intervention on choice of healthy ingredients among college students ordering submarine sandwiches (subs). Over eight weekly sub-nights, college students submitted 9765 orders. The order form format was manipulated in one condition making the healthier selections more salient. Main outcome measures were selection of ingredients. Multi-level logistic regression, chi square, and analysis of variance were used to examine the effect of experimental conditions on selection of ingredients. The health-salient form increased selection of healthier and decreased selection of unhealthy ingredients. The manipulation increased fiber, decreased sodium, but did not impact calorie/fat levels of the subs served.

Direct comparison of fatty acid ratios in single cellular lipid droplets as determined by comparative Raman spectroscopy and gas chromatography.

Cellular lipid droplets are the least studied and least understood cellular organelles in eukaryotic and prokaryotic cells. Despite a significant body of research studying the physiology of lipid droplets it has not yet been possible to fully determine the composition of individual cellular lipid droplets. In this paper we use Raman spectroscopy on single cellular lipid droplets and least-squares fitting of pure fatty acid spectra to determine the composition of individual lipid droplets in cells after treatment with different ratios of oleic and palmitic acid. We validate the results of the Raman spectroscopy-based single lipid droplet analysis with results obtained by gas chromatography analysis of millions of cells, and find that our approach can accurately predict the relative amount of a specific fatty acid in the lipid droplet. Based on these results we show that the fatty acid composition in individual lipid droplets is on average similar to that of all lipid droplets found in the sample. Furthermore, we expand this approach to the investigation of the lipid composition in single cellular peroxisomes. We determine the location of cellular peroxisomes based on two-photon excitation fluorescence (TPEF) imaging of peroxisomes labeled with the green fluorescent protein, and successive Raman spectroscopy of peroxisomes. We find that in some cases peroxisomes can produce a detectable CARS signal, and that the peroxisomal Raman spectra exhibit an oleic acid-like signature.

Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum.

BACKGROUND: Genomic resources within the phylum Arthropoda are largely limited to the true insects but are beginning to include unexplored subphyla, such as the Crustacea and Chelicerata. Investigations of these understudied taxa uncover high frequencies of orphan genes, which lack detectable sequence homology to genes in pre-existing databases. The ticks (Acari: Chelicerata) are one such understudied taxon for which genomic resources are urgently needed. Ticks are obligate blood-feeders that vector major diseases of humans, domesticated animals, and wildlife. In analyzing a transcriptome of the lone star tick Amblyomma americanum, one of the most abundant disease vectors in the United States, we find a high representation of unannotated sequences. We apply a general framework for quantifying the origin and true representation of unannotated sequences in a dataset and for evaluating the biological significance of orphan genes. RESULTS: Expressed sequence tags (ESTs) were derived from different life stages and populations of A. americanum and combined with ESTs available from GenBank to produce 14,310 ESTs, over twice the number previously available. The vast majority (71%) has no sequence homology to proteins archived in UniProtKB. We show that poor sequence or assembly quality is not a major contributor to this high representation by orphan genes. Moreover, most unannotated sequences are functional: a microarray experiment demonstrates that 59% of functional ESTs are unannotated. Lastly, we attempt to further annotate our EST dataset using genomic datasets from other members of the Acari, including Ixodes scapularis, four other tick species and the mite Tetranychus urticae. We find low homology with these species, consistent with significant divergence within this subclass. CONCLUSIONS: We conclude that the abundance of orphan genes in A. americanum likely results from 1) taxonomic isolation stemming from divergence within the tick lineage and limited genomic resources for ticks and 2) lineage-specific genes needing functional genomic studies to evaluate their association with the unique biology of ticks. The EST sequences described here will contribute substantially to the development of tick genomics. Moreover, the framework provided for the evaluation of orphan genes can guide analyses of future transcriptome sequencing projects.

Involving youth with disabilities in the development and evaluation of a new advocacy training: Project TEAM.

PURPOSE: This paper describes a participatory research process in which six youth with disabilities (Youth Panel) participated in the development and evaluation of a manualized advocacy training, Project TEAM (Teens making Environment and Activity Modifications). Project TEAM teaches youth with disabilities how to identify environmental barriers, generate solutions, and request accommodations. METHOD: The Youth Panel conducted their evaluation after the university researcher implemented Project TEAM with three groups of trainees. The Youth Panel designed and administered a survey and focus group to evaluate enjoyment and usefulness of Project TEAM with support from an advocate/researcher. Members of the Youth Panel analyzed survey response frequencies. The advocate/researcher conducted a content analysis of the open-ended responses. RESULTS: Sixteen of 21 Project TEAM trainees participated in the evaluation. The evaluation results suggest that the trainees found the interactive and individualized aspects of the Project TEAM most enjoyable and useful. Some instructional materials were difficult for trainees with cognitive disabilities to understand. CONCLUSIONS: The Youth Panel's involvement in the development of Project TEAM may explain the relatively positive experiences reported by trainees. Project TEAM should continue to provide trainees with the opportunity to apply concepts in real-life situations. Project TEAM requires revisions to ensure it is enjoyable and useful for youth with a variety of disabilities. IMPLICATIONS FOR REHABILITATION: • Group process strategies, picture-based data collection materials, peer teamwork, and mentorship from adults with disabilities can enable youth with disabilities to engage in research. • Collaborating with youth with disabilities in the development of new rehabilitation approaches may enhance the relevance of interventions for other youth with disabilities. • Youth with cognitive disabilities participating in advocacy and environment-focused interventions may prefer interactive and experiential learning activities over passive teaching approaches such as powerpoints and videos.