Biology subjects

Fares, M. A.

Publications and source records attributed to Fares, M. A..

3 recordsLinked to original sources

bioRxiv2023

Unlocking the Power of R: A High-Accuracy Method for Measuring DAB Staining on Immunohistochemical Slides

The current research aimed to establish a method for measuring the percentage of diaminobenzidine (DAB) staining on immunohistochemical slides with high accuracy and efficiency. The R programming language was utilized in this endeavor. A total of 50 slides were collected from various types of tissue, and were stained using an anti-cytokeratin antibody and the DAB detection method. These slides were then scanned using a high-resolution scanner, and the resulting images were analyzed using R, a custom script was specifically developed to segment the tissue and DAB-positive areas, and calculate the percentage of DAB staining on the slide. The results were then compared to manual measurements of DAB staining performed by a trained technician. The R-based method was found to be highly accurate, with a mean absolute error of only 0.76 % compared to manual measurements, this study provides evidence that the use of R for DAB quantification is a fast and reliable alternative to manual methods, enabling the analysis of large numbers of slides in a short period of time. It offers a valuable tool for researchers and technicians in the field of histopathology, enabling them to quickly and accurately analyze DAB staining on immunohistochemical slides, which is essential for the diagnosis and treatment of various diseases.

bioinformatics↗

bioRxiv2019

Molecular chaperones accelerate the evolution of their protein clients in yeast

Protein stability is a major constraint on protein evolution. Molecular chaperones, also known as heat-shock proteins, can relax this constraint and promote protein evolution by diminishing the deleterious effect of mutations on protein stability and folding. This effect, however, has only been stablished for a few chaperones. Here, we use a comprehensive chaperone-protein interaction network to study the effect of all yeast chaperones on the evolution of their protein substrates, that is, their clients. In particular, we analyze how yeast chaperones affect the evolutionary rates of their clients at two very different evolutionary time scales. We first study the effect of chaperone-mediated folding on protein evolution over the evolutionary divergence of Saccharomyces cerevisiae and S. paradoxus. We then test whether yeast chaperones have left a similar signature on the patterns of standing genetic variation found in modern wild and domesticated strains of S. cerevisiae. We find that genes encoding chaperone clients have diverged faster than genes encoding nonclient proteins when controlling for their number of protein-protein interactions. We also find that genes encoding client proteins have accumulated more intra-specific genetic diversity than those encoding nonclient proteins. In a number of multivariate analyses, controlling by other well-known factors that affect protein evolution, we find that chaperone dependence explains the largest fraction of the observed variance in the rate of evolution at both evolutionary time scales. Chaperones affecting rates of protein evolution mostly belong to two major chaperone families: Hsp70s and Hsp90s. Our analyses show that protein chaperones, by virtue of their ability to buffer destabilizing mutations and their role in modulating protein genotype-phenotype maps, have a considerable accelerating effect on protein evolution.

evolutionary biology↗

bioRxiv2017

Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria

Bacteria interact with their environment through the secretion of a specific set of proteins (known as secretome) through various secretion systems. Molecular modifications of these secretion systems may lead to the emergence of new bacterial-environment interactions, although this remains unexplored. In this study we investigate the possible link between molecular and functional changes in secretion proteins and the ecological diversity of bacteria. We studied functional modifications in secretion proteins by identifying events of functional evolutionary divergence--that is, changes at the molecular level that have driven changes of proteins function. We present data supporting that these functional diversifications occurred in essential secretion proteins in bacteria. In particular, functional divergence of the two most important secretion proteins SecA and SecY in pathogenic bacteria suggests that molecular changes at these proteins are responsible for their adaptations to the host. Functional divergence has mainly occurred at protein domains involved in ATP hydrolysis in SecA and membrane pore formation in SecY. This divergence is stronger in pathogenic bacteria for protein copies resulting from the duplication of SecA/SecY, known as SecA2/SecY2. In concert with these results, we find that the secretome of bacteria with the strongest functional divergence is enriched for proteins specialized in the interaction with specific environments. We unravel evolutionary signatures that link mutations at secretion proteins to the ecological diversification of bacteria.

microbiology↗