Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments

In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We present a new technique for characterizing the kinetics of loop formation in vitro, as observed using the tethered particle method, and apply it to experimental data on looping induced by lambda repressor. Our method uses a modified (diffusive) hidden Markov analysis that directly incorporates the Brownian motion of the observed tethered bead. We compare looping lifetimes found with our method (which we find are consistent over a range of sampling frequencies) to those obtained via the traditional threshold-crossing analysis (which can vary depending on how the raw data are filtered in the time domain). Our method does not involve any time filtering and can detect sudden changes in looping behavior. For example, we show how our method can identify transitions between long-lived, kinetically distinct states that would otherwise be difficult to discern

Proving Temporal Properties of Z Specifications Using Abstraction

This paper presents a systematic approach to proving temporal properties of arbitrary Z specifications. The approach involves (i) transforming the Z specification to an abstract temporal structure (or state transition system), (ii) applying a model checker to the temporal structure, (iii) determining whether the temporal structure is too abstract based on the model checking result and (iv) refining the temporal structure where necessary. The approach is based on existing work from the model checking literature, adapting it to Z

Diffusive Hidden Markov Model Characterization of DNA Looping Dynamics in Tethered Particle Experiments

In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such “DNA looping” interactions. We present a new technique for characterizing the kinetics of loop formation in vitro, as observed using the tethered particle method, and apply it to experimental data on looping induced by lambda repressor. Our method uses a modified (“diffusive”) hidden Markov analysis that directly incorporates the Brownian motion of the observed tethered bead. We compare looping lifetimes found with our method (which we find are consistent over a range of sampling frequencies) to those obtained via the traditional threshold-crossing analysis (which can vary depending on how the raw data are filtered in the time domain). Our method does not involve any time filtering and can detect sudden changes in looping behavior. For example, we show how our method can identify transitions between long-lived, kinetically distinct states that would otherwise be difficult to discern

Sprinter: A didactic linter for structured programming

Code linters are tools for detecting improper uses of programming constructs and violations of style issues. Despite that professional linters are available for numerous languages, they are not targeted to introductory programming, given their prescriptive nature that does not take into consideration a didactic viewpoint of learning programming fundamentals. We present Sprinter, a didactic code linter for structured programming supporting Java whose novelty aspects are twofold: (a) providing formative feedback on code with comprehensive explanatory messages (rather then prescriptive); (b) capability of detecting some control-flow issues to a deeper extent than professional linters. We review Sprinter features against popular tools, namely IntelliJ IDEA and Sonarlint.info:eu-repo/semantics/publishedVersio

Single Molecule investigations of DNA Looping Using the Tethered Particle Method and Translocation by Acto-Myosin Using Polarized Total Internal Reflection Fluorescence Microscopy

Single molecule biophysics aims to understand biological processes by studying them at the single molecule level in real time. The proteins and nucleic acids under investigation typically exist in an aqueous environment within approximately ten degrees of room temperature. These seemingly benign conditions are actually quite chaotic at the nanoscale, where single bio-molecules perform their function. As a result, sensitive experiments and statistical analyses are required to separate the weak single molecule signal from its background. Protein-DNA interactions were investigated by monitoring DNA looping events in tethered particle experiments. A new analysis technique, called the Diffusive hidden Markov method, was developed to extract kinetic rate constants from experimental data without any filtering of the raw data; a common step that improves the signal to noise ratio, but at the expense of lower time resolution. In the second system, translocation of the molecular motor myosin along its actin filament track was studied using polarized total internal reflection (polTIRF) microscopy, a technique that determines the orientation and wobble of a single fluorophore attached to the bio-molecule of interest. The range of resolvable angles was increased 4-fold to include a hemisphere of possible orientations. As a result, the handedness of actin filament twirling as it translocated along a myosin-coated surface was determined to be left-handed. The maximum time resolution of a polTIRF setup was increased 50-fold, in part by recording the arrival times and polarization state of single photons using a modified time-correlated single photon counting device. A new analysis, the Multiple Intensity Change Point algorithm, was developed to detect changes in molecular orientation and wobble using the raw time-stamped data with no user-defined bins or thresholds. The analysis objectively identified changes in the orientation of a bifunctional-rhodamine labeled calmodulin that was attached to a myosin V molecule translocating along an actin filament. Long intervals corresponding to stable positions between tilting motions of the lever arm during each step were routinely observed. Substeps in the cycle that preceded these long dwells were measured, but only occasionally most likely because of the low number of photons detected during these rapid events

A Method, Based on Plans, for Understanding How a Loop Implements a Computation

This report describes research done at the Artificial Intelligence Laboratory of the Massachusetts Institute of Technology. Support for the laboratory's artificial intelligence research is provided in part by the Advanced Research Projects Agency of the Department of Defense under Office of Naval Research contract N00014-75-C-0643.The plan method analyzes the structure of a program. The plan which results from applying the method represents this structure by specifying how the parts of the program interact. This paper demonstrates the utility of the plan method by showing how a plan for a loop can be used to help prove the correctness of a loop. The plan does this by providing a convenient description of what the loop does. This paper also shows how a plan for a loop can be developed based on the code for the loop without the assistance of any commentary. This is possible primarily because most loops are built up in stereotyped ways according to a few fundamental plan types. An experiment is presented which supports the claim that a small number of plan types cover a large percentage of actual cases.MIT Artificial Intelligence Laboratory Department of Defense Advanced Research Projects Agenc

Semi-unification

Semi-unifiability is a generalization of both unification and matching. It is used to check nontermination of rewrite rules. In this paper an inference system is presented that decides semi-unifiability of two terms s and t and computes a semi-unifier. In contrast to an algorithm by Kapur, Musser et al, this inference system comes very close to the one for ordinary unification

Automatic autoprojection of recursive equations with global variables and abstract data types

AbstractSelf-applicable partial evaluation has been implemented for half a decade now, but many problems remain open. This paper addresses and solves the problems of automating call unfolding, having an open-ended set of operators, and processing global variables updated by side effects. The problems of computation duplication and termination of residual programs are addressed and solved: residual programs never duplicate computations of the source program; residual programs do not terminate more often than source programs.This paper describes the automatic autoprojector (self-applicable partial evaluator) Similix; it handles programs with user-defined primitive abstract data type operators which may process global variables. Abstract data types make it possible to hide actual representations of data and prevent specializing operators over these representations. The formally sound treatment of global variables makes Similix fit well in an applicative order programming environment.We present a new method for automatic call unfolding which is simpler, faster, and sometimes more effective than existing methods: it requires neither recursion analysis of the source program, nor call graph analysis of the residual program.To avoid duplicating computations and preserve termination properties, we introduce an abstract interpretation of the source program, abstract occurence counting analysis, which is performed during preprocessing. We express it formally and simplify it