Identification of functional cis-regulatory elements by sequential enrichment from a randomized synthetic DNA library

BACKGROUND: The identification of endogenous cis-regulatory DNA elements (CREs) responsive to endogenous and environmental cues is important for studying gene regulation and for biotechnological applications but is labor and time intensive. Alternatively, by taking a synthetic biology approach small specific DNA binding sites tailored to the needs of the scientist can be generated and rapidly identified. RESULTS: Here we report a novel approach to identify stimulus-responsive synthetic CREs (SynCREs) from an unbiased random synthetic element (SynE) library. Functional SynCREs were isolated by screening the SynE libray for elements mediating transcriptional activity in plant protoplasts. Responsive elements were chromatin immunoprecipitated by targeting the active Ser-5 phosphorylated RNA polymerase II CTD (Pol II ChIP). Using sequential enrichment, deep sequencing and a bioinformatics pipeline, candidate responsive SynCREs were identified within a pool of constitutively active DNA elements and further validated. These included bonafide biotic/abiotic stress-responsive motifs along with novel SynCREs. We tested several SynCREs in Arabidopsis and confirmed their response to biotic stimuli. CONCLUSIONS: Successful isolation of synthetic stress-responsive elements from our screen illustrates the power of the described methodology. This approach can be applied to any transfectable eukaryotic system since it exploits a universal feature of the eukaryotic Pol II

MONEY ILLUSION, GORMAN AND LAU

Any demand equation satisfying Lau’s (1982) Fundamental Theorem of Exact Aggregation and 0° homogeneity in prices and income will have a Gorman (1981) functional form for each income term. This property does not depend on symmetry or adding up. The implications of this result are illustrated by an extensive example.Demand, exact aggregation, functional form, homogeneity

Development of an Additively Manufactured Capacitive Humidity Sensor for the International Space Station

The ability to measure humidity on the International Space Station and other long-duration spaceflight missions is a crucial part of the onboard systems. For example, the Environmental Control and Life Support System (ECLSS) needs to know the amount of humidity in the air to make decisions about whether it should spend power to run the dehumidifier systems to attempt to reclaim that water. Other issues can arise if the humidity reaches too high of levels and condensation builds up on electrical components. With that in mind, it is vital that the spacecraft keeps spare sensors on board or has the ability to manufacture new sensors on demand. An additively manufactured sensor would be additionally beneficial because it would save space onboard that would normally be taken up by spares, save money from costly resupply missions, and allow the sensor to be constantly updated with the most effective design. This Technical Memorandum outlines a development process carried out to design, manufacture, and test an additively manufactured humidity sensor

Moral reasoning and homosexuality: the acceptability of arguments about lesbian and gay issues

In the political arena, lesbian and gay issues have typically been contested on grounds of human rights, but with variable success. Using a moral developmental framework, the purpose of this study was to explore preferences for different types of moral arguments when thinking about moral dilemmas around lesbian and gay issues. The analysis presented here comprised data collected from 545 students at UK universities, who completed a questionnaire, part of which comprised a moral dilemma task. Findings of the study showed that respondents do not apply moral reasoning consistently, and do not (clearly) favour human rights reasoning when thinking about lesbian and gay issues. Respondents tended to favour reasoning supporting existing social structures and frameworks, therefore this study highlights the importance of structural change in effecting widespread attitude change in relation to lesbian and gay rights issues. The implications of the findings for moral education are also discussed.</p

Elasticity of Semiflexible Biopolymer Networks

We develop a model for gels and entangled solutions of semiflexible biopolymers such as F-actin. Such networks play a crucial structural role in the cytoskeleton of cells. We show that the rheologic properties of these networks can result from nonclassical rubber elasticity. This model can explain a number of elastic properties of such networks {\em in vitro}, including the concentration dependence of the storage modulus and yield strain.Comment: Uses RevTeX, full postscript with figures available at http://www.umich.edu/~fcm/preprints/agel/agel.htm

Trace-gas metabolic versatility of the facultative methanotroph Methylocella silvestris

The climate-active gas methane is generated both by biological processes and by thermogenic decomposition of fossil organic material, which forms methane and short-chain alkanes, principally ethane, propane and butane1, 2. In addition to natural sources, environments are exposed to anthropogenic inputs of all these gases from oil and gas extraction and distribution. The gases provide carbon and/or energy for a diverse range of microorganisms that can metabolize them in both anoxic3 and oxic zones. Aerobic methanotrophs, which can assimilate methane, have been considered to be entirely distinct from utilizers of short-chain alkanes, and studies of environments exposed to mixtures of methane and multi-carbon alkanes have assumed that disparate groups of microorganisms are responsible for the metabolism of these gases. Here we describe the mechanism by which a single bacterial strain, Methylocella silvestris, can use methane or propane as a carbon and energy source, documenting a methanotroph that can utilize a short-chain alkane as an alternative to methane. Furthermore, during growth on a mixture of these gases, efficient consumption of both gases occurred at the same time. Two soluble di-iron centre monooxygenase (SDIMO) gene clusters were identified and were found to be differentially expressed during bacterial growth on these gases, although both were required for efficient propane utilization. This report of a methanotroph expressing an additional SDIMO that seems to be uniquely involved in short-chain alkane metabolism suggests that such metabolic flexibility may be important in many environments where methane and short-chain alkanes co-occur

Detection of Asynchronous Message Passing Errors Using Static Analysis

Concurrent programming is hard and prone to subtle errors. In this paper we present a static analysis that is able to detect some commonly occurring kinds of message passing errors in languages with dynamic process creation and communication based on asynchronous message passing. Our analysis is completely automatic, fast, and strikes a proper balance between soundness and completeness: it is effective in detecting errors and avoids false alarms by computing a close approximation of the interprocess communication topology of programs. We have integrated our analysis in dialyzer, a widely used tool for detecting software defects in Erlang programs, and demonstrate its effectiveness on libraries and applications of considerable size. Despite the fact that these applications have been developed over a long period of time and are reasonably well-tested, our analysis has managed to detect a significant number of previously unknown message passing errors in their code

Force-Extension Relation and Plateau Modulus for Wormlike Chains

We derive the linear force-extension relation for a wormlike chain of arbitrary stiffness including entropy elasticity, bending and thermodynamic buckling. From this we infer the plateau modulus $G^0$ of an isotropic entangled solution of wormlike chains. The entanglement length $L_e$ is expressed in terms of the characteristic network parameters for three different scaling regimes in the entangled phase. The entanglement transition and the concentration dependence of $G^0$ are analyzed. Finally we compare our findings with experimental data.Comment: 5 pages, 1 eps-figure, to appear in PR