1,720,991 research outputs found
Transcriptional Analysis Of Deinococcus Radiodurans Reveals Novel Small Rnas That Are Differentially Expressed Under Ionizing Radiation
Get PDFSmall noncoding RNAs (sRNAs) are posttranscriptional regulators that have been identified in multiple species and shown to play essential roles in responsive mechanisms to environmental stresses. The natural ability of specific bacteria to resist high levels of radiation has been of high interest to mechanistic studies of DNA repair and biomolecular protection. Deinococcus radiodurans is a model extremophile for radiation studies that can survive doses of ionizing radiation of >12,000 Gy, 3,000 times higher than for most vertebrates. Few studies have investigated posttranscriptional regulatory mechanisms of this organism that could be relevant in its general gene regulatory patterns. In this study, we identified 199 potential sRNA candidates in D. radiodurans by whole-transcriptome deep sequencing analysis and confirmed the expression of 41 sRNAs by Northern blotting and reverse transcriptase PCR (RT-PCR). A total of 8 confirmed sRNAs showed differential expression during recovery after acute ionizing radiation (15 kGy). We have also found and confirmed 7 sRNAs in Deinococcus geothermalis, a closely related radioresistant species. The identification of several novel sRNAs in Deinococcus bacteria raises important questions about the evolution and nature of global gene regulation in radioresistance.Welch Foundation F-1756Defense Threat Reduction Agency Young Investigator Program HDTRA1-12-0016Air Force Office of Scientific Research Young Investigator Program FA9550-13-1-0160Chemical EngineeringChemistryBiochemistr
Discovery Of Ethanol-Responsive Small Rnas In Zymomonas Mobilis
Get PDFZymomonas mobilis is a bacterium that can produce ethanol by fermentation. Due to its unique metabolism and efficient ethanol production, Z. mobilis has attracted special interest for biofuel energy applications; an important area of study is the regulation of those specific metabolic pathways. Small RNAs (sRNAs) have been studied as molecules that function as transcriptional regulators in response to cellular stresses. While sRNAs have been discovered in various organisms by computational prediction and experimental approaches, their discovery in Z. mobilis has not yet been reported. In this study, we have applied transcriptome analysis and computational predictions to facilitate identification and validation of 15 novel sRNAs in Z. mobilis. We furthermore characterized their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4, and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed, respectively. Importantly, when we tested the effect of ethanol stress on the expression of sRNAs in Z. mobilis, Zms2, Zms6, and Zms18 showed differential expression under 5% ethanol stress conditions. These data suggest that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses.NSF CBET-1254754Welch Foundation F-1756Cellular and Molecular BiologyChemical Engineerin
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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Modeling the Csr System and BarA/UvrY Two Component System (TCS) in response to stress
Get PDFThe Carbon Storage Regulatory System (Csr) in Escherichia coli is a model posttranscriptional regulatory network that includes four components: CsrA protein, CsrB and CsrC
noncoding RNAs, and CsrD protein. This system is important to study as it has a wide reach in
controlling other regulatory networks throughout E. coli and is necessary for stress responses. The
Carbon Storage Regulatory System responds to external stimuli through the BarA/UvrY Two
Component System (TCS). The BarA/UvrY TCS is composed of a histidine kinase, BarA and a
response regulator, UvrY, and are primarily connected to the Csr system, as the two proteins serve
as a transcriptional activator of CsrB and CsrC. The goal for this project is to understand and
computationally model how the Csr and TCS system interact in response to extracellular
metabolites. Results of the computational model developed show that incorporating the TCS
system allows for quicker response times and could potentially account for the differences in Csr
system component concentrations observed in literature. Experimental validation of model with in
vivo results is required to verify the accuracy of the model. This project is one of the first that
works on computationally linking the external metabolite stimuli to the Csr system and could pave
the way for advances in the engineering of bacterial genetic circuitry.Chemical Engineerin
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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Advances in applications of modern biotechnology methods in methanogens
Get PDFtextMethanogens are autotrophic Archaea that produce methane as a product of their anaerobic metabolism. They are the largest producers of global methane, contributing over 60% of the total methane budget each year. Methane is an extremely potent greenhouse gas, with emissions providing the second-largest contribution to historical global temperature increases after carbon dioxide. Methanogens have become extremely important industrially as because they are used in the production of biofuels, as well as in treating industrial waste for industrial processes. This report will focus on those successful genetic methods and modifications that have been developed for methanogens and how they have started to contribute to understanding methanogen biochemistry.Chemical Engineerin
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