20 research outputs found
Persistence and stability of generalized ribosome flow models with time-varying transition rates
In this paper the qualitative dynamical properties of so-called generalized
ribosome flow models are studied. Ribosome flow models known from the
literature are generalized by allowing an arbitrary directed network structure
between the compartments and secondly, by assuming a general time-varying rate
function describing the compartmental transitions. Persistence of the dynamics
is shown using the chemical reaction network (CRN) representation of the
system. We show the stability of different compartmental structures including
strongly connected ones with an entropy-like logarithmic Lyapunov function. The
L1 contractivity of solutions is also studied in the case of periodic reaction
rates having the same period. It is also shown that different Lyapunov
functions may be assigned to the same model depending on the factorization of
the reaction rates.Comment: 28 pages, 8 figure
Protocol for evaluating mitochondrial morphology changes in response to CCCP-induced stress through open-source image processing software
Summary: Mitochondrial morphology is an indicator of cellular health and function; however, its quantification and categorization into different subclasses is a complicated process. Here, we present a protocol for mitochondrial morphology quantification in the presence and absence of carbonyl cyanide m-chlorophenyl hydrazone stress. We describe steps for the preparation of cells for immunofluorescence microscopy, staining, and morphology quantification. The quantification protocol generates an aspect ratio that helps to categorize mitochondria into two clear subclasses.For complete details on the use and execution of this protocol, please refer to Nag et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics
CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks
Summary: Chemical reaction network theory is widely used in
modeling and analyzing complex biochemical systems such as
metabolic networks and cell signalling pathways. Being able to
produce all the biologically and chemically important
qualitative dynamical features, chemical reaction networks
(CRNs) have attracted significant attention in the systems
biology community. It is well-known that the reliable inference
of CRN models generally requires thorough identifiability and
distinguishability analysis together with carefully selected
prior modeling assumptions. Here, we present a software toolbox
CRNreals that supports the distinguishability and
identifiability analysis of CRN models using recently published
optimization-based procedures.
Availability and implementation: The CRNreals toolbox and the
associated documentation are available at
http://www.iim.csic.es/~gingproc/CRNreals/. The toolbox runs
under the popular MATLAB computational environment and supports
several free and commercial linear programming and mixed integer
linear programming solvers
A toolbox for model-based fault detection and isolation
info:eu-repo/semantics/publishe
PGAM5 is an MFN2 phosphatase that plays an essential role in the regulation of mitochondrial dynamics
Summary: Mitochondrial morphology is regulated by the post-translational modifications of the dynamin family GTPase proteins including mitofusin 1 (MFN1), MFN2, and dynamin-related protein 1 (DRP1). Mitochondrial phosphatase phosphoglycerate mutase 5 (PGAM5) is emerging as a regulator of these post-translational modifications; however, its precise role in the regulation of mitochondrial morphology is unknown. We show that PGAM5 interacts with MFN2 and DRP1 in a stress-sensitive manner. PGAM5 regulates MFN2 phosphorylation and consequently protects it from ubiquitination and degradation. Further, phosphorylation and dephosphorylation modification of MFN2 regulates its fusion ability. Phosphorylation enhances fission and degradation, whereas dephosphorylation enhances fusion. PGAM5 dephosphorylates MFN2 to promote mitochondrial network formation. Further, using a Drosophila genetic model, we demonstrate that the MFN2 homolog Marf and dPGAM5 are in the same biological pathway. Our results identify MFN2 dephosphorylation as a regulator of mitochondrial fusion and PGAM5 as an MFN2 phosphatase
Variscan Preflysch (Devonian-Early Carboniferous) Environments. ISBN: 963 671 244 1 CM
TECTONOSTRATIGRAPHIC TERRANE AND PALEOENVIRONMENT MAPS OF THE CIRCUM-PANNONIAN REGIO