Doaa Taha

Grain boundary properties and collective dynamics of inversion domains in binary two-dimensional materials

Understanding and controlling the properties and dynamics of topological defects is a lasting challenge in the study of two-dimensional materials, and is crucial to achieve high-quality films required for technological applications. Here grain boundary structures, energies, and dynamics of binary two-dimensional materials are investigated through the development of a phase field crystal model that is parametrized to match the ordering, symmetry, energy, and length scales of hexagonal boron nitride. Our studies reveal some new dislocation core structures for various symmetrically and asymmetrically tilted grain boundaries, in addition to those obtained in previous experiments and first-principles calculations. We also identify a defect-mediated growth dynamics for inversion domains governed by the collective atomic migration and defect core transformation at grain boundaries and junctions, a process that is related to inversion symmetry breaking in binary lattice.

R1 motif is the major actin-binding domain of TRIOBP-4.

TRIOBP is an actin-bundling protein. Mutations of TRIOBP are associated with human deafness DFNB28. In vitro, TRIOBP isoform 4 (TRIOBP-4) forms dense F-actin bundles resembling the inner ear hair cell rootlet structure. Deletion of TRIOBP isoforms 4 and 5 leads to hearing loss in mice due to the absence of stereocilia rootlets. The mechanism of actin bundle formation by TRIOBP is not fully understood. The amino acid sequences of TRIOBP isoforms 4 and 5 contain two repeated motifs, referred to here as R1 and R2. To examine the potential role of R1 and R2 motifs in F-actin binding, we generated TRIOBP-4 mutant proteins deleted for R1 and/or R2, and then assessed their actin-binding activity and bundle formation in vitro using actin cosedimentation assays, and fluorescence and electron microscopy. Cellular distributions of the TRIOBP-4 mutants were examined by confocal microscopy. We showed that deletion of both R1 and R2 motifs completely disrupted the actin binding/bundling activities of TRIOBP-4 and impaired its localization to cellular actin cytoskeleton structures. By contrast, TRIOBP-4, lacking only R2 motif, retained its F-actin bundling ability and remained localized to actin filaments in cells, similar to full length TRIOBP-4. On the contrary, the R1 motif-deleted TRIOBP-4 mutant, which mainly consists of the R2 motif, formed thin F-actin bundles in vitro but failed to colocalize to actin filaments in cells. These results indicate that R1 motif is the major actin-binding domain of TRIOBP-4, and the binding of R2 motif with actin filaments is nonspecific.

Neuroprotection Is Technology, Not Science

All human clinical trials of neuroprotection after brain ischemia and reperfusion injury have failed. Brain ischemia is currently conceptualized as an “ischemic cascade” and therapy is directed to treating one or another element of this cascade. This approach conflates the science of cell injury with the development of neuroprotective technologies. Here we review a theory that describes the generic nonlinear dynamics of acute cell injury. This approach clearly demarcates the science of cell injury from any possible downstream technological applications. We begin with a discussion that contrasts the qualitative, descriptive approach of biology to the quantitative, mathematical approach used in physics. Next we discuss ideas from quantitative biology that underlie the theory. After briefly reviewing the autonomous theory, we present, for the first time, a non-autonomous theory that describes multiple injuries over time and can simulate pre- or post-conditioning or post-injury pharmacologics. The non-autonomous theory provides a foundation for three-dimensional spatial models that can simulate complex tissue injuries such as stroke. The cumulative theoretical formulations suggest new technologies. We outline possible prognosticative and neuroprotective technologies that would operate with engineering precision and function on a patient-by-patient basis, hence personalized medicine. Thus, we contend that a generic, mathematical approach to acute cell injury will accomplish what highly detailed descriptive biology has so far failed to accomplish: successful neuroprotective technology.

Inductive and Deductive Approaches to Acute Cell Injury.

Many clinically relevant forms of acute injury, such as stroke, traumatic brain injury, and myocardial infarction, have resisted treatments to prevent cell death following injury. The clinical failures can be linked to the currently used inductive models based on biological specifics of the injury system. Here we contrast the application of inductive and deductive models of acute cell injury. Using brain ischemia as a case study, we discuss limitations in inductive inferences, including the inability to unambiguously assign cell death causality and the lack of a systematic quantitative framework. These limitations follow from an overemphasis on qualitative molecular pathways specific to the injured system. Our recently developed nonlinear dynamical theory of cell injury provides a generic, systematic approach to cell injury in which attractor states and system parameters are used to quantitatively characterize acute injury systems. The theoretical, empirical, and therapeutic implications of shifting to a deductive framework are discussed. We illustrate how a deductive mathematical framework offers tangible advantages over qualitative inductive models for the development of therapeutics of acutely injured biological systems.

Abstraction and Idealization in Biomedicine: The Nonautonomous Theory of Acute Cell Injury

Neuroprotection seeks to halt cell death after brain ischemia and has been shown to be possible in laboratory studies. However, neuroprotection has not been successfully translated into clinical practice, despite voluminous research and controlled clinical trials. We suggested these failures may be due, at least in part, to the lack of a general theory of cell injury to guide research into specific injuries. The nonlinear dynamical theory of acute cell injury was introduced to ameliorate this situation. Here we present a revised nonautonomous nonlinear theory of acute cell injury and show how to interpret its solutions in terms of acute biomedical injuries. The theory solutions demonstrate the complexity of possible outcomes following an idealized acute injury and indicate that a “one size fits all” therapy is unlikely to be successful. This conclusion is offset by the fact that the theory can (1) determine if a cell has the possibility to survive given a specific acute injury, and (2) calculate the degree of therapy needed to cause survival. To appreciate these conclusions, it is necessary to idealize and abstract complex physical systems to identify the fundamental mechanism governing the injury dynamics. The path of abstraction and idealization in biomedical research opens the possibility for medical treatments that may achieve engineering levels of precision.