The how and why of lncRNA function: An innate immune perspective.

Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen

Herreshoff Marine Museum: Historical Analysis

These methods that Herreshoff utilized can be classified as early stages of the LEAN manufacturing concept which is used today in a majority of America’s leading manufacturers. Herreshoff made sure that his entire inventory was used and nothing was wasted. By reducing/eliminating waste, Nat preserved the value of his products and increased the efficiency of operation

International Space Station Utilization: Tracking Investigations from Objectives to Results

Since the first module was assembled on the International Space Station (ISS), on-orbit investigations have been underway across all scientific disciplines. The facilities dedicated to research on ISS have supported over 1100 investigations from over 900 scientists representing over 60 countries. Relatively few of these investigations are tracked through the traditional NASA grants monitoring process and with ISS National Laboratory use growing, the ISS Program Scientist s Office has been tasked with tracking all ISS investigations from objectives to results. Detailed information regarding each investigation is now collected once, at the first point it is proposed for flight, and is kept in an online database that serves as a single source of information on the core objectives of each investigation. Different fields are used to provide the appropriate level of detail for research planning, astronaut training, and public communications. http://www.nasa.gov/iss-science/. With each successive year, publications of ISS scientific results, which are used to measure success of the research program, have shown steady increases in all scientific research areas on the ISS. Accurately identifying, collecting, and assessing the research results publications is a challenge and a priority for the ISS research program, and we will discuss the approaches that the ISS Program Science Office employs to meet this challenge. We will also address the online resources available to support outreach and communication of ISS research to the public. Keywords: International Space Station, Database, Tracking, Method

CRISPR/Cas-based screening of long non-coding RNAs (lncRNAs) in macrophages with an NF-κB reporter.

The innate immune system protects against infections by initiating an inducible inflammatory response. NF-κB is one of the critical transcription factors controlling this complex response, but some aspects of its regulation remain unclear. For example, although long non-coding RNAs (lncRNAs) have been shown to critically regulate gene expression, only a fraction of these have been functionally characterized, and the extent to which lncRNAs control NF-κB expression is unknown. Here, we describe the generation of a GFP-based NF-κB reporter system in immortalized murine bone marrow-derived macrophages (iBMDM). Activation of this reporter, using Toll-like receptor ligands, resulted in GFP expression, which could be monitored by flow cytometry. We also established a CRISPR/Cas9 gene deletion system in this NF-κB reporter line, enabling us to screen for genes that regulate NF-κB signaling. Our deletion-based approach identified two long intergenic non-coding(linc)RNAs, lincRNA-Cox2 and lincRNA-AK170409, that control NF-κB signaling. We demonstrate a potential novel role for lincRNA-Cox2 in promoting IκBα degradation in the cytoplasm. For lincRNA-AK170409, we provide evidence that this nuclearly-localized lincRNA regulates a number of inflammation-related genes. In conclusion, we have established an NF-κB-GFP iBMDM reporter cell line and a line that stably expresses Cas9. Our approach enabled the identification of lincRNA-Cox2 and lincRNA-AK170409 as NF-κB regulators, and this tool will be useful for identifying additional genes involved in regulating this transcription factor critical for immune function

Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24.

Off-target binding of hydrophobic drugs can lead to unwanted side effects, either through specific or non-specific binding to unintended membrane protein targets. However, distinguishing the binding of drugs to membrane proteins from that of detergents, lipids and cofactors is challenging. Here, we use high-resolution mass spectrometry to study the effects of HIV protease inhibitors on the human zinc metalloprotease ZMPSTE24. This intramembrane protease plays a major role in converting prelamin A to mature lamin A. We monitored the proteolysis of farnesylated prelamin A peptide by ZMPSTE24 and unexpectedly found retention of the C-terminal peptide product with the enzyme. We also resolved binding of zinc, lipids and HIV protease inhibitors and showed that drug binding blocked prelamin A peptide cleavage and conferred stability to ZMPSTE24. Our results not only have relevance for the progeria-like side effects of certain HIV protease inhibitor drugs, but also highlight new approaches for documenting off-target drug binding

The Seven Words of the Virgin: Identifying Change in the Discourse Context of the Concept of Virginity in Early Modern English

No abstract available

A common ground for virtual humans: using an ontology in a natural language oriented virtual human architecture

When dealing with large, distributed systems that use state-of-the-art components, individual components are usually developed in parallel. As development continues, the decoupling invariably leads to a mismatch between how these components internally represent concepts and how they communicate these representations to other components: representations can get out of synch, contain localized errors, or become manageable only by a small group of experts for each module. In this paper, we describe the use of an ontology as part of a complex distributed virtual human architecture in order to enable better communication between modules while improving the overall flexibility needed to change or extend the system. We focus on the natural language understanding capabilities of this architecture and the relationship between language and concepts within the entire system in general and the ontology in particular. 1

A Website to help the International Students Experience (WISE)

Our VCU campus has been steadily expanding its international student population and has become an increasingly global university community. We have identified together with GEO, the need to build tangible resources that can support faculty and staff to more effectively educate our international student population. The creation of online content to be added to GEO’s current webpage seems to best fit the existing need. Our project outlines a blueprint for this online content by means of identifying data and resources that should be included as well as determining cost, sustainability and feasibility plans. Ultimately, the goal is to pave the way for centralized online content that can connect faculty and staff with important resources to optimize the academic experience and success of international students at VCU

Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions.

BackgroundCTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation.ResultsHere we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of the BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells.ConclusionsWe discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells