Positive and Negative Regulatory Elements in the HIV-1 5'UTR Control Specific Recognition by Gag

Biological Sciences (The Ohio State University Denman Undergraduate Research Forum)The 5ʹ untranslated region (5ʹUTR) of the human immunodeficiency virus type 1 (HIV-1) genomic RNA (gRNA) contains a structured RNA element (termed Psi) that is specifically recognized by the HIV-1 Gag polyprotein, ensuring that two strands of gRNA are packaged into newly assembled virions. However, the mechanism by which Gag recognizes gRNA over other cellular RNAs and spliced viral RNAs is not well understood. A recent study suggested that a negative regulatory element upstream of Psi reduces high-affinity Gag binding, and a positive regulatory element downstream of Psi counteracts the upstream element and restores high-affinity binding. The aim of this study is to determine how these elements affect the specificity and mode of Gag binding. Using a fluorescence anisotropy-based salt-titration binding assay, the electrostatic and nonelectrostatic (i.e., specific) components of binding were measured. We have previously shown that Gag interacts with a 109-nucleotide (nt) Psi RNA construct that lacks the putative regulatory elements with high specificity and relatively few electrostatic interactions. Using a 356-nt RNA construct that includes the negative regulatory element in addition to Psi, we observed a loss in Gag binding specificity and an increase in electrostatic interactions. Interestingly, a 400-nt construct that contains the positive and negative elements flanking Psi restored highly specific binding and reduced the electrostatic interactions made with the RNA. Furthermore, a construct wherein the 40-nt positive regulatory element was appended to Psi, demonstrated the same specificity as Psi alone. Taken together, these data are consistent with a mechanism whereby the negative and positive regulatory elements flanking Psi modulate Gag binding mode and specificity.Undergraduate Education Summer Research FellowshipArts & Sciences Undergraduate Research ScholarshipSOLAR Research GrantNo embargoAcademic Major: Biochemistr

Evaluating data capture methods for the establishment of diagnostic reference levels in CT scanning

Objective: Concerns about the radiation dose associated with CT scanning have led to a call for establishment of diagnostic reference levels. Self-complete surveys have been used extensively to gather this information, however, departmental Radiological Information System's/Picture Archive Communication Systems (RIS/PACS) also hold this information. We compared dosimetry derived from survey with those using RIS/PACSs.Methods: Technical data were collected from a large metropolitan tertiary hospital in WA using both data collection methods for a range of adult CT scanning examinations. Radiation dose was calculated from both datasets and the results evaluated for several indexes of inter-rater agreement.Results: Radiation dose calculated using self-report survey data differed both systematically and proportionally from that calculated using RIS/PACS data. Differences were not consistent across CT examination type and thus not amenable to simple correction. The disparity was greater and more variable for organ dose than effective dose due to reliance of survey data on “generic” anatomical start and stop limits compared with actual data available on RIS/PACS.Conclusions: The bias observed in our study indicates that care should be taken when interpreting the results of studies measuring radiation dose using self-complete surveys. The availability of electronic databases that include information required for the evaluation and monitoring of CT radiation dose provides the opportunity to capture better quality data in a cost-effective manner. We recommend that national and local databases are established that routinely capture these data so as to facilitate the development and monitoring of radiation dose associated with CT scanning

REDD+ on the rocks? Conflict over forest and politics of justice in Vietnam

In Vietnam, villagers involved in a REDD+ (reduced emissions from deforestation and forest degradation) pilot protect areas with rocks which have barely a tree on them. The apparent paradox indicates how actual practices differ from general ideas about REDD+ due to ongoing conflict over forest, and how contestations over the meaning of justice are a core element in negotiations over REDD+. We explore these politics of justice by examining how the actors involved in the REDD+ pilot negotiate the particular subjects, dimensions, and authority of justice considered relevant, and show how politics of justice are implicit to practical decisions in project implementation. Contestations over the meaning of justice are an important element in the practices and processes constituting REDD+ at global, national and local levels, challenging uniform definitions of forest justice and how forests ought to be managed

Codified methods to analyse the failures of water pipelines: A Review

Pipelines used for the transportation of water and other services are very important lifelines in modern society. The important role that they play in our present economy is reflected by thousands of kilometres of service laid in urban centres worldwide. As many of these pipelines have been laid few decades earlier, in most cases, their condition has been deteriorated mainly by electro-chemical and (or) micro-biological corrosion. There are several codes of practice available at present to analyse the condition of such deteriorated pipes. This paper identifies and reviews all such relevant standards applicable to corroded water mains with the use of some case studies. Three dimensional finite element analyses are also conducted to investigate the capabilities of simulating the failures of corroded pipelines and thus to ascertain the validity of codified methods. By careful assessment of the current codes of practice in use, it is possible to understand where these codes are lacking and which codes can rightly predict the realistic water pipe failures observed in the past

Flux-area operator and black hole entropy

We show that, for space-times with inner boundaries, there exists a natural area operator different from the standard one used in loop quantum gravity. This new flux-area operator has equidistant eigenvalues. We discuss the consequences of substituting the standard area operator in the Ashtekar-Baez-Corichi-Krasnov definition of black hole entropy by the new one. Our choice simplifies the definition of the entropy and allows us to consider only those areas that coincide with the one defined by the value of the level of the Chern-Simons theory describing the horizon degrees of freedom. We give a prescription to count the number of relevant horizon states by using spin components and obtain exact expressions for the black hole entropy. Finally we derive its asymptotic behavior, discuss several issues related to the compatibility of our results with the Bekenstein-Hawking area law and the relation with Schwarzschild quasi-normal modes.Comment: 25 page

Controlling spontaneous chirality in achiral materials : liquid crystal oligomers and the heliconical twist-bend nematic phase

Peer reviewedPublisher PD

Strange Decays of Nonstrange Baryons

The strong decays of excited nonstrange baryons into the final states Lambda K, Sigma K, and for the first time into Lambda(1405) K, Lambda(1520) K, Sigma(1385) K, Lambda K*, and Sigma K*, are examined in a relativized quark pair creation model. The wave functions and parameters of the model are fixed by previous calculations of N pi and N pi pi, etc., decays. Our results show that it should be possible to discover several new negative parity excited baryons and confirm the discovery of several others by analyzing these final states in kaon production experiments. We also establish clear predictions for the relative strengths of certain states to decay to Lambda(1405) K and Lambda(1520) K, which can be tested to determine if a three-quark model of the Lambda(1405) K is valid. Our results compare favorably with the results of partial wave analyses of the limited existing data for the Lambda K and Sigma K channels. We do not find large Sigma K decay amplitudes for a substantial group of predicted and weakly established negative-parity states, in contrast to the only previous work to consider decays of these states into the strange final states Lambda K and Sigma K.Comment: 25 pages, 8 figures, RevTe

Hierarchy of Conservation Laws of Diffusion--Convection Equations

We introduce notions of equivalence of conservation laws with respect to Lie symmetry groups for fixed systems of differential equations and with respect to equivalence groups or sets of admissible transformations for classes of such systems. We also revise the notion of linear dependence of conservation laws and define the notion of local dependence of potentials. To construct conservation laws, we develop and apply the most direct method which is effective to use in the case of two independent variables. Admitting possibility of dependence of conserved vectors on a number of potentials, we generalize the iteration procedure proposed by Bluman and Doran-Wu for finding nonlocal (potential) conservation laws. As an example, we completely classify potential conservation laws (including arbitrary order local ones) of diffusion--convection equations with respect to the equivalence group and construct an exhaustive list of locally inequivalent potential systems corresponding to these equations.Comment: 24 page