CLUSTERING A SERIES OF REPLICATED POLYPLOID GENE EXPRESSION EXPERIMENTS IN MAIZE

Ploidy level is defined as the number of individual sets of chromosomes contained in a single cell. Many important crop plants, such as potato, soybean and wheat are polyploid. Although it is widely known that polyploidy is a frequent evolutionary event, it is not fully understand why polyploids have been so successful. In this work cluster analysis is employed to study gene expression changes in a maize inbred line (B73) across a range of polyploidy levels. The B73 ploidy series includes monoploid, diploid, triploid and tetraploid plants and consists of biological and technical replicates as measured by microarray technology. An improved version of CORE (iCORE; improved Clustering of Repeat Expression) is presented to differentiate highly negatively correlated genes while taking advantage of the additional information that is provided by replication. The error information from the replicate experiments is utilized to cluster gene expression for both simulated and real ploidy-series data. Simulation results indicate that iCORE leads to an improvement in accuracy over both CORE and hierarchical clustering based on average gene expression only. When applied to the maize ploidy series, the iCORE results provide information that may aid in understanding of the effect of gene dose on gene expression in a ploidy series

Leiomyosarcoma Arising in the Pancreatic Duct: A Case Report and Review of the Current Literature

Context. Leiomyosarcomas are rare malignant smooth muscle tumors that may arise in any organ or tissue that contains smooth muscle, commonly within the gastrointestinal tract. They are most often found in the stomach, large and small intestines, and retroperitoneum. Primary pancreatic leiomyosarcoma is extremely rare, and to the best of our knowledge only 30 cases have been reported in the world literature since 1951. Our case represents the first to have a clear origin from the main pancreatic duct. Case Report. This case was diagnosed in a large, tertiary care center in Tampa, Florida. Pertinent information was obtained from chart review and interdepartmental collaboration. A mass in the tail of the pancreas was identified with large pleomorphic and spindle-shaped cells. Immunohistochemistry for vimentin, smooth muscle actin, and desmin was positive. All remaining immunohistochemical markers performed were negative. The tumor clearly originated from the pancreatic duct wall, filled and expanded the duct lumen, and was covered with a layer of benign biliary epithelium. Conclusion. Leiomyosarcoma of the pancreas is an extremely rare malignancy with few reported cases in the literature. The prognosis is poor, and treatment consists of alleviating symptoms and pain management. To our knowledge, this represents the first reported case demonstrating clear origin of a leiomyosarcoma from the pancreatic duct

Targeting of P-Element Reporters to Heterochromatic Domains by Transposable Element 1360 in Drosophila melanogaster

Heterochromatin is a common DNA packaging form employed by eukaryotes to constitutively silence transposable elements. Determining which sequences to package as heterochromatin is vital for an organism. Here, we use Drosophila melanogaster to study heterochromatin formation, exploiting position-effect variegation, a process whereby a transgene is silenced stochastically if inserted in proximity to heterochromatin, leading to a variegating phenotype. Previous studies identified the transposable element 1360 as a target for heterochromatin formation. We use transgene reporters with either one or four copies of 1360 to determine if increasing local repeat density can alter the fraction of the genome supporting heterochromatin formation. We find that including 1360 in the reporter increases the frequency with which variegating phenotypes are observed. This increase is due to a greater recovery of insertions at the telomere-associated sequences (∼50% of variegating inserts). In contrast to variegating insertions elsewhere, the phenotype of telomere-associated sequence insertions is largely independent of the presence of 1360 in the reporter. We find that variegating and fully expressed transgenes are located in different types of chromatin and that variegating reporters in the telomere-associated sequences differ from those in pericentric heterochromatin. Indeed, chromatin marks at the transgene insertion site can be used to predict the eye phenotype. Our analysis reveals that increasing the local repeat density (via the transgene reporter) does not enlarge the fraction of the genome supporting heterochromatin formation. Rather, additional copies of 1360 appear to target the reporter to the telomere-associated sequences with greater efficiency, thus leading to an increased recovery of variegating insertions

Gattini 2010: Cutting Edge Science at the Bottom of the World

The high altitude Antarctic sites of Dome A and the South Pole offer intriguing locations for future large scale optical astronomical Observatories. The Gattini project was created to measure the optical sky brightness, large area cloud cover and aurora of the winter-time sky above such high altitude Antarctic sites. The Gattini-DomeA camera was installed on the PLATO instrument module as part of the Chinese-led traverse to the highest point on the Antarctic plateau in January 2008. This single automated wide field camera contains a suite of Bessel photometric filters (B, V, R) and a long-pass red filter for the detection and monitoring of OH emission. We have in hand one complete winter-time dataset (2009) from the camera that was recently returned in April 2010. The Gattini-South Pole UV camera is a wide-field optical camera that in 2011 will measure for the first time the UV properties of the winter-time sky above the South Pole dark sector. This unique dataset will consist of frequent images taken in both broadband U and B filters in addition to high resolution (R similar to 5000) long slit spectroscopy over a narrow bandwidth of the central field. The camera is a proof of concept for the 2m-class Antarctic Cosmic Web Imager telescope, a dedicated experiment to directly detect and map the redshifted lyman alpha fluorescence or Cosmic Web emission we believe possible due to the unique geographical qualities of the site. We present the current status of both projects

Sex-specific Aging in Animals: Perspective and Future Directions

Sex differences in aging occur in many animal species, and they include sex differences in lifespan, in the onset and progression of age-associated decline, and in physiological and molecular markers of aging. Sex differences in aging vary greatly across the animal kingdom. For example, there are species with longer-lived females, species where males live longer, and species lacking sex differences in lifespan. The underlying causes of sex differences in aging remain mostly unknown. Currently, we do not understand the molecular drivers of sex differences in aging, or whether they are related to the accepted hallmarks or pillars of aging or linked to other well-characterized processes. In particular, understanding the role of sex-determination mechanisms and sex differences in aging is relatively understudied. Here, we take a comparative, interdisciplinary approach to explore various hypotheses about how sex differences in aging arise. We discuss genomic, morphological, and environmental differences between the sexes and how these relate to sex differences in aging. Finally, we present some suggestions for future research in this area and provide recommendations for promising experimental designs

Sex-specific aging in animals: Perspective and future directions

Sex differences in aging occur in many animal species, and they include sex differences in lifespan, in the onset and progression of age‐associated decline, and in physiological and molecular markers of aging. Sex differences in aging vary greatly across the animal kingdom. For example, there are species with longer‐lived females, species where males live longer, and species lacking sex differences in lifespan. The underlying causes of sex differences in aging remain mostly unknown. Currently, we do not understand the molecular drivers of sex differences in aging, or whether they are related to the accepted hallmarks or pillars of aging or linked to other well‐characterized processes. In particular, understanding the role of sex‐determination mechanisms and sex differences in aging is relatively understudied. Here, we take a comparative, interdisciplinary approach to explore various hypotheses about how sex differences in aging arise. We discuss genomic, morphological, and environmental differences between the sexes and how these relate to sex differences in aging. Finally, we present some suggestions for future research in this area and provide recommendations for promising experimental designs

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function

Gene Fusion Characterization of Rare Aggressive Prostate Cancer Variants ‐ Adenosquamous Carcinoma, Pleomorphic Giant Cell Carcinoma, and Sarcomatoid Carcinoma: An Analysis of 19 Cases

Aims We evaluated the molecular underpinnings of rare aggressive prostate cancer variants adenosquamous, pleomorphic giant cell, and sarcomatoid carcinomas. Methods and Results We retrieved 19 tumors with one or more variant(s) and performed ERG immunohistochemistry, a next‐generation sequencing assay targeting recurrent gene fusions, and fluorescence in situ hybridization (FISH) for ERG and BRAF. Divergent differentiation included: sarcomatoid (n=10), adenosquamous (n=7), and pleomorphic giant cell carcinoma (n=7). Five patients had more than one variant. Four had variants only in metastases. ERG rearrangement was detected in 9 (47%, 7 via sequencing, showing TMPRSS2‐ERG and one GRHL2‐ERG fusion, and 2 via FISH, showing rearrangement via deletion). Of these, ERG immunohistochemistry was positive in the adenocarcinoma for 8/9 (89%) but only 5/9 (56%, typically decreased) in the variant. One patient had false‐positive ERG immunohistochemistry in the sarcomatoid component despite negative FISH. Two (11%) harbored BRAF fusions (FAM131A‐BRAF and SND1‐BRAF). Conclusions ERG gene fusions are present in these rare prostate cancer variants with a close frequency to conventional prostate cancer (9/19, 47%). ERG immunohistochemistry usually detects rearrangement in the adenocarcinoma but is less sensitive for the variant histology with weak to negative staining. Adenosquamous and sarcomatoid variants particularly can occur together. Molecular assessment may be an additional tool in select cases to confirm prostatic origin of unusual tumors. The presence of 2 BRAF gene rearrangements suggests that this gene fusion may be enriched in this setting, as RAF kinase fusions have been previously reported in 1‐2% of prostate cancers