Phages 933W, BAA2326, 434, and λ are evolutionarily-related temperate lambdoid phages that infect... more Phages 933W, BAA2326, 434, and λ are evolutionarily-related temperate lambdoid phages that infect Escherichia coli. Although these are highly-similar phages, BAA2326 and 933W naturally encode Shiga toxin 2 (Stx +), but phage 434 and λ do not (Stx´). Previous reports suggest that the 933W Stx + prophage forms less stable lysogens in E. coli than does the Stx´prophages λ, P22, and 434. The higher spontaneous induction frequency of the Stx + prophage may be correlated with both virulence and dispersion of the Stx2-encoding phage. Here, we examined the hypothesis that lysogen instability is a common feature of Stx + prophages. We found in both the absence and presence of prophage inducers (DNA damaging agents, salts), the Stx + prophages induce at higher frequencies than do Stx´prophages. The observed instability of Stx + prophages does not appear to be the result of any differences in phage development properties between Stx + and Stx´phages. Our results indicate that differential stability of Stx + and Stx´prophages results from both RecA-dependent and RecA-independent effects on the intracellular concentration of the respective cI repressors.
In a λ(imm434) lysogen, two proteins are expressed from the integrated prophage. Both are encoded... more In a λ(imm434) lysogen, two proteins are expressed from the integrated prophage. Both are encoded by the same mRNA whose transcription initiates at the P(RM) promoter. One protein is the 434 repressor, needed for the establishment and maintenance of lysogeny. The other is Hex which is translated from an open reading frame that apparently partially overlaps the 434 repressor coding region. In the wild type host, disruption of the gene encoding Hex destabilizes λ(imm434) lysogens. However, the hex mutation has no effect on lysogen stability in a recA(-) host. These observations suggest that Hex functions by modulating the ability of RecA to stimulate 434 repressor autocleavage. We tested this hypothesis by identifying and purifying Hex to determine if this protein inhibited RecA‑stimulated autocleavage of 434 repressor in vitro. Our results show that in vitro a fragment of Hex prevents RecA-stimulated autocleavage of 434 repressor, as well as the repressors of the closely related phag...
We present a static analysis that approximates the relational semantics of imperative programs by... more We present a static analysis that approximates the relational semantics of imperative programs by systems of low-degree polynomial equalities. Our method is based on Abstract Interpretation in a lattice of polynomial pseudo ideals-finite-dimensional vector spaces of degree-bounded polynomials that are closed under degree-bounded products. For a fixed degree bound, the sizes of bases of pseudo ideals and the lengths of chains in the lattice of pseudo ideals are bounded by polynomials in the number of program variables. Despite the approximate nature of our analysis, for several programs taken from the literature on non-linear polynomial invariant generation our method produces results that are as precise as those produced by methods based on polynomial ideals and Gröbner bases.
Water is a major route for infection of humans by exotoxin-producing bacteria, including Shiga to... more Water is a major route for infection of humans by exotoxin-producing bacteria, including Shiga toxin-producing Escherichia coli (STEC). While STEC has the potential to be present in nearly every type of water source, its distribution is sporadic, and an understanding of factors that govern its emergence and persistence within water is lacking. In this study, we examined the influence of microbe content on STEC persistence in freshwater. We found that depletion of microbes in the water leads to a considerable increase in the persistence of STEC, an effect that can be mitigated by adding grazing protists to the water. STEC strains appear to be more resistant to the impact of grazing protists than E. coli strains that lack the Shiga toxin (stx) gene. Our results demonstrate that the microcosm can dramatically influence the persistence of STEC in aquatic ecosystems and that the overall impact by microbes on STEC strains is fundamentally different from that of non-STEC strains of bacteria. Overall, these results provide insight into why STEC and possibly other exotoxin-producing bacterial pathogens display such variability in abundance, distribution, and persistence in aquatic ecosystems.
We present two algorithms to prove termination of programs by synthesizing linear ranking functio... more We present two algorithms to prove termination of programs by synthesizing linear ranking functions. The first uses an invariant generator based on iterative forward propagation with widening and extracts ranking functions from the generated invariants by manipulating polyhedral cones. It is capable of finding subtle ranking functions which are linear combinations of many program variables, but is limited to programs with few variables. The second, more heuristic, algorithm targets the class of structured programs with single-variable ranking functions. Its invariant generator uses a heuristic extrapolation operator to avoid iterative forward propagation over program loops. For the programs we have considered, this approach converges faster and the invariants it discovers are sufficiently strong to imply the existence of ranking functions.
Nominal Isabelle is a definitional extension of the Isabelle/HOL theorem prover. It provides a pr... more Nominal Isabelle is a definitional extension of the Isabelle/HOL theorem prover. It provides a proving infrastructure for reasoning about programming language calculi involving named bound variables (as opposed to de-Bruijn indices). In this paper we present an extension of Nominal Isabelle for dealing with general bindings, that means term constructors where multiple variables are bound at once. Such general bindings are ubiquitous in programming language research and only very poorly supported with single binders, such as lambda-abstractions. Our extension includes new definitions of alpha-equivalence and establishes automatically the reasoning infrastructure for alphaequated terms. We also prove strong induction principles that have the usual variable convention already built in.
The Stanford Temporal Prover, STEP, combines deductive methods with algorithmic techniques to ver... more The Stanford Temporal Prover, STEP, combines deductive methods with algorithmic techniques to verify linear-time temporal logic specifications of reactive and real-time systems. STeP uses verification rules, verification diagrams, automatically generated invariants, model checking, and a collection of decision procedures to verify finite-and infinite-state systems. System Description: The Stanford Temporal Prover, STEP, supports the computer-aided formal verification of reactive, real-time (and, in particular, concurrent) systems based on temporal specifications. Reactive systems maintain an ongoing interaction with their environment; their specifications are typically expressed as constraints on their behavior over time. STeP is not restricted to finite-state systems, but combines algorithmic and deductive methods to allow the verification of a broad class of systems, including parameterized (Ncomponent) circuit designs, parameterized (N-process) programs, and programs with infinite data domains. The deductive methods of STeP verify temporal properties of systems by means of verification rules and verification diagrams. Verification rules are used to reduce temporal properties of systems to first-order verification conditions [8]. Verification diagrams [7, 3] provide a visual language for guiding, organizing, and displaying proofs. Verification diagrams allow the user to construct proofs hierarchically, starting from a high-level, intuitive proof sketch and proceeding incrementally, as necessary, through layers of greater detail. Deductive verification almost always relies on finding, for a given program and specification, suitably strong auxiliary invariants and intermediate assertions. STeP implements a variety of techniques for automatic invariant generation. These methods include local, linear and polyhedral invariant generation, which perform an approximate, abstract propagation through the system [2]. Verification conditions can then be established using the automatically generated auxiliary invariants as background properties.
Journal of The American College of Cardiology, 2010
Background: Adverse events from oral anticoagulation are increasingly recognized, however few stu... more Background: Adverse events from oral anticoagulation are increasingly recognized, however few studies evaluate this problem in patients with congenital heart disease (CHD). Our purpose was to evaluate predictors of attaining target international normalized ratios (INR) and of adverse events for patients with CHD on warfarin.
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Papers by Michael Colon