Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing

<p>Abstract</p> <p>Background</p> <p>Understanding animal development and physiology at a molecular-biological level has been advanced by the ability to determine at high resolution the repertoire of mRNA molecules by whole transcriptome resequencing. This includes the ability to detect and quantify rare abundance transcripts and isoform-specific mRNA variants produced from a gene.</p> <p>The sex hierarchy consists of a pre-mRNA splicing cascade that directs the production of sex-specific transcription factors that specify nearly all sexual dimorphism. We have used deep RNA sequencing to gain insight into how the Drosophila sex hierarchy generates somatic sex differences, by examining gene and transcript isoform expression differences between the sexes in adult head tissues.</p> <p>Results</p> <p>Here we find 1,381 genes that differ in overall expression levels and 1,370 isoform-specific transcripts that differ between males and females. Additionally, we find 512 genes not regulated downstream of <it>transformer </it>that are significantly more highly expressed in males than females. These 512 genes are enriched on the × chromosome and reside adjacent to dosage compensation complex entry sites, which taken together suggests that their residence on the × chromosome might be sufficient to confer male-biased expression. There are no transcription unit structural features, from a set of features, that are robustly significantly different in the genes with significant sex differences in the ratio of isoform-specific transcripts, as compared to random isoform-specific transcripts, suggesting that there is no single molecular mechanism that generates isoform-specific transcript differences between the sexes, even though the sex hierarchy is known to include three pre-mRNA splicing factors.</p> <p>Conclusions</p> <p>We identify thousands of genes that show sex-specific differences in overall gene expression levels, and identify hundreds of additional genes that have differences in the abundance of isoform-specific transcripts. No transcription unit structural feature was robustly enriched in the sex-differentially expressed transcript isoforms. Additionally, we found that many genes with male-biased expression were enriched on the × chromosome and reside adjacent to dosage compensation entry sites, suggesting that differences in sex chromosome composition contributes to dimorphism in gene expression. Taken together, this study provides new insight into the molecular underpinnings of sexual differentiation.</p

Evolution of Sex-Specific Traits through Changes in HOX-Dependent doublesex Expression

Analysis in Drosophila suggests that evolutionary changes in the spatial regulation of the transcription factor doublesex play a key role in the origin, diversification, and loss of sex-specific structures

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Mycoremediation of petroleum contaminated soils: progress, prospects and perspectives

Mycoremediation, an aspect of bioremediation, has been investigated for some decades. However, there seems to be little progress on its commercial application to petroleum-contaminated soils despite some promising outcomes. In this review, mycoremediation is examined to identify development, limitations and perspectives for its optimal utilization on petroleum-contaminated soils. Mycoremediation agents and substrates that have been used for the treatment of petroleum contaminated soils have been identified, application methods discussed, recent advances highlighted and limitations for its applications accentuated. Possible solutions to the challenges in applying mycoremediation to petroleum-contaminated soils have also been discussed. From this review, we conclude that for optimal utilization of mycoremediation of petroleum-contaminated soils, ideal environmental, edaphic and climatic factors of a typical contaminated site must be incorporated into the approach from first principles. Development of application procedures that can easily translate laboratory results to field applications is also required

After The Flood: A Follow Up on the Trophic State of Lake Blackshear, Georgia

Proceedings of the 2003 Georgia Water Resources Conference, held April 23-24, 2003, at the University of Georgia.Chlorophyll a based trophic state conditions during the summer in Lake Blackshear in 2001 were compared to pre-flood conditions of 1992. Median values were similar in the transition zone but lower in the middle and lower portions of the reservoir. It is not possible to determine whether lower chlorophyll a values in 2001 represent a change in lake productivity following the flooding event or simply reflect low flows during severe drought. Phytoplankton growth in the lake did not achieve the potential level predicted by nutrient concentrations or lake transparency

The occurrence and light induced formation of ortho-quinonoid lignin structures in white spruce refiner mechanical pulp

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