PlanTEnrichment: A How-to Guide on Rapid Identification of Transposable Elements Associated with Regions of Interest in Select Plant Genomes.

Transposable elements (TEs) are repeat elements that can relocate or create novel copies of themselves in the genome and contribute to genomic complexity and expansion, via events such as chromosome recombination or regulation of gene expression. However, given the large number of such repeats across the genome, identifying repeats of interest can be a challenge in even well-annotated genomes, especially in more complex, TE-rich plant genomes. Here, we describe a protocol for PlanTEnrichment, a database we created comprising information on 11 plant genomes to analyze stress-associated TEs using publicly available data. By selecting a genome and providing a list of genes or genomic regions whose TE associations the user wants to identify, the user can rapidly obtain TE subfamilies found near the provided regions, as well as their superfamily and class, and the enrichment values of the repeats. The results also provide the locations of individual repeat instances found, alongside the input regions or genes they are associated with, and a bar graph of the top ten most significant repeat subfamilies identified. PlanTEnrichment is freely available at http://tools.ibg.deu.edu.tr/plantenrichment/ and can be used by researchers with rudimentary or no proficiency in computational analysis of TE elements, allowing for expedience in the identification of TEs of interest and helping further our understanding of the potential contributions of TEs in plant genomes.

Differential Occupancy and Regulatory Interactions of KDM6A in Bladder Cell Lines.

Epigenetic deregulation is a critical theme which needs further investigation in bladder cancer research. One of the most highly mutated genes in bladder cancer is KDM6A, which functions as an H3K27 demethylase and is one of the MLL3/4 complexes. To decipher the role of KDM6A in normal versus tumor settings, we identified the genomic landscape of KDM6A in normal, immortalized, and cancerous bladder cells. Our results showed differential KDM6A occupancy in the genes involved in cell differentiation, chromatin organization, and Notch signaling depending on the cell type and the mutation status of KDM6A. Transcription factor motif analysis revealed HES1 to be enriched at KDM6A peaks identified in the T24 bladder cancer cell line; moreover, it has a truncating mutation in KDM6A and lacks a demethylase domain. Our co-immunoprecipitation experiments revealed TLE co-repressors and HES1 as potential truncated and wild-type KDM6A interactors. With the aid of structural modeling, we explored how truncated KDM6A could interact with TLE and HES1, as well as RUNX and HHEX transcription factors. These structures provide a solid means of studying the functions of KDM6A independently of its demethylase activity. Collectively, our work provides important contributions to the understanding of KDM6A malfunction in bladder cancer.

Development of a medical module for disaster information systems.

This study aims to improve a medical module which provides a real-time medical information flow about pre-hospital processes that gives health care in disasters; transferring, storing and processing the records that are in electronic media and over internet as a part of disaster information systems. In this study which is handled within the frame of providing information flow among professionals in a disaster case, to supply the coordination of healthcare team and transferring complete information to specified people at real time, Microsoft Access database and SQL query language were used to inform database applications. System was prepared on Microsoft .Net platform using C# language. Disaster information system-medical module was designed to be used in disaster area, field hospital, nearby hospitals, temporary inhabiting areas like tent city, vehicles that are used for dispatch, and providing information flow between medical officials and data centres. For fast recording of the disaster victim data, accessing to database which was used by health care professionals was provided (or granted) among analysing process steps and creating minimal datasets. Database fields were created in the manner of giving opportunity to enter new data and search old data which is recorded before disaster. Web application which provides access such as data entry to the database and searching towards the designed interfaces according to the login credentials access level. In this study, homepage and users' interfaces which were built on database in consequence of system analyses were provided with www.afmedinfo.com web site to the user access. With this study, a recommendation was made about how to use disaster-based information systems in the field of health. Awareness has been developed about the fact that disaster information system should not be perceived only as an early warning system. Contents and the differences of the health care practices of disaster information systems were revealed. A web application was developed supplying a link between the user and the database to make date entry and data query practices by the help of the developed interfaces.