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

Sciduction: Combining Induction, Deduction, and Structure for Verification and Synthesis

Even with impressive advances in automated formal methods, certain problems in system verification and synthesis remain challenging. Examples include the verification of quantitative properties of software involving constraints on timing and energy consumption, and the automatic synthesis of systems from specifications. The major challenges include environment modeling, incompleteness in specifications, and the complexity of underlying decision problems. This position paper proposes sciduction, an approach to tackle these challenges by integrating inductive inference, deductive reasoning, and structure hypotheses. Deductive reasoning, which leads from general rules or concepts to conclusions about specific problem instances, includes techniques such as logical inference and constraint solving. Inductive inference, which generalizes from specific instances to yield a concept, includes algorithmic learning from examples. Structure hypotheses are used to define the class of artifacts, such as invariants or program fragments, generated during verification or synthesis. Sciduction constrains inductive and deductive reasoning using structure hypotheses, and actively combines inductive and deductive reasoning: for instance, deductive techniques generate examples for learning, and inductive reasoning is used to guide the deductive engines. We illustrate this approach with three applications: (i) timing analysis of software; (ii) synthesis of loop-free programs, and (iii) controller synthesis for hybrid systems. Some future applications are also discussed

Systems, methods and apparatus for modeling, specifying and deploying policies in autonomous and autonomic systems using agent-oriented software engineering

Systems, methods and apparatus are provided through which in some embodiments, an agent-oriented specification modeled with MaCMAS, is analyzed, flaws in the agent-oriented specification modeled with MaCMAS are corrected, and an implementation is derived from the corrected agent-oriented specification. Described herein are systems, method and apparatus that produce fully (mathematically) tractable development of agent-oriented specification(s) modeled with methodology fragment for analyzing complex multiagent systems (MaCMAS) and policies for autonomic systems from requirements through to code generation. The systems, method and apparatus described herein are illustrated through an example showing how user formulated policies can be translated into a formal mode which can then be converted to code. The requirements-based programming systems, method and apparatus described herein may provide faster, higher quality development and maintenance of autonomic systems based on user formulation of policies

A Fault Tolerant System for an Integrated Avionics Sensor Configuration

An aircraft sensor fault tolerant system methodology for the Transport Systems Research Vehicle in a Microwave Landing System (MLS) environment is described. The fault tolerant system provides reliable estimates in the presence of possible failures both in ground-based navigation aids, and in on-board flight control and inertial sensors. Sensor failures are identified by utilizing the analytic relationships between the various sensors arising from the aircraft point mass equations of motion. The estimation and failure detection performance of the software implementation (called FINDS) of the developed system was analyzed on a nonlinear digital simulation of the research aircraft. Simulation results showing the detection performance of FINDS, using a dual redundant sensor compliment, are presented for bias, hardover, null, ramp, increased noise and scale factor failures. In general, the results show that FINDS can distinguish between normal operating sensor errors and failures while providing an excellent detection speed for bias failures in the MLS, indicated airspeed, attitude and radar altimeter sensors