Inferring the dynamics of underdamped stochastic systems

Many complex systems, ranging from migrating cells to animal groups, exhibit stochastic dynamics described by the underdamped Langevin equation. Inferring such an equation of motion from experimental data can provide profound insight into the physical laws governing the system. Here, we derive a principled framework to infer the dynamics of underdamped stochastic systems from realistic experimental trajectories, sampled at discrete times and subject to measurement errors. This framework yields an operational method, Underdamped Langevin Inference (ULI), which performs well on experimental trajectories of single migrating cells and in complex high-dimensional systems, including flocks with Viscek-like alignment interactions. Our method is robust to experimental measurement errors, and includes a self-consistent estimate of the inference error

DNA photodamage recognition by RNA polymerase II.

During gene transcription, RNA polymerase (Pol) II encounters obstacles, including lesions in the DNA template. Here, we review a recent structure–function analysis of Pol II transcribing DNA with a bulky photo-lesion in the template strand. The study provided the molecular basis for recognition of a damaged DNA by Pol II, which is the first step in transcription-coupled DNA repair (TCR). The results have general implications for damage recognition and the TCR mechanism.http://dx.doi.org

Learning dynamical models of single and collective cell migration: a review

Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualizing the emergent behavior of cells. We first review how this inference problem has been addressed in freely migrating cells on two-dimensional substrates and in structured, confining systems. Moreover, we discuss how data-driven methods can be connected with molecular mechanisms, either by integrating mechanistic bottom-up biophysical models, or by performing inference on subcellular degrees of freedom. Finally, we provide an overview of applications of data-driven modelling in developing frameworks for cell-to-cell variability in behaviours, and for learning the collective dynamics of multicellular systems. Specifically, we review inference and machine learning approaches to recover cell-cell interactions and collective dynamical modes, and how these can be integrated into physical active matter models of collective migration

Monitoring of Cell Layer Integrity with a Current-Driven Organic Electrochemical Transistor

The integrity of CaCo-2 cell barriers is investigated by organic electrochemical transistors (OECTs) in a current-driven configuration. Ion transport through cellular barriers via the paracellular pathway is modulated by tight junctions between adjacent cells. Rupturing its integrity by H2O2 is monitored by the change of the output voltage in the transfer characteristics. It is demonstrated that by operating the OECT in a current-driven configuration, the sensitive and temporal resolution for monitoring the cell barrier integrity is strongly enhanced as compared to the OECT transient response measurement. As a result, current-driven OECTs are useful tools to assess dynamic and critical changes in tight junctions, relevant for clinical applications as drug targeting and screening

CPD damage recognition by transcribing RNA polymerase II.

Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light–induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5′-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II

CLINICAL EVALUATION OF A SPECIFIC BENZODIAZEPINE ANTAGONIST (RO 15-1788): Studies in Elderly Patients after Regional Anaesthesia under Benzodiazepine Sedation

The efficacy, usefulness and side effects of RO 15-1788 (RO), a specific benzodiazepine (BZD) antagonist, have been evaluated. Sixty-two patients (ASA l-lll, mean age 72±9 yr) scheduled for urological surgery under regional anaesthesia and BZD sedation received placebo or RO in a randomized, double-blind fashion at the end of the procedure, folio wing sedation with midazolam. When compared with placebo, RO improved alertness and collaboration for 15 min, and suppressed anterograde amnesia for 60 min. No major side effect was noted, although five patients became anxious after administration of RO. Two cases of a paradoxical reaction to midazolam were treated successfully by R

Mechanism of transcriptional stalling at cisplatin-damaged DNA.

The anticancer drug cisplatin forms 1,2-d(GpG) DNA intrastrand cross-links (cisplatin lesions) that stall RNA polymerase II (Pol II) and trigger transcription-coupled DNA repair. Here we present a structure-function analysis of Pol II stalling at a cisplatin lesion in the DNA template. Pol II stalling results from a translocation barrier that prevents delivery of the lesion to the active site. AMP misincorporation occurs at the barrier and also at an abasic site, suggesting that it arises from nontemplated synthesis according to an 'A-rule' known for DNA polymerases. Pol II can bypass a cisplatin lesion that is artificially placed beyond the translocation barrier, even in the presence of a GdotA mismatch. Thus, the barrier prevents transcriptional mutagenesis. The stalling mechanism differs from that of Pol II stalling at a photolesion, which involves delivery of the lesion to the active site and lesion-templated misincorporation that blocks transcription