Related papers: Frequency-Rank Correlations of Rhodopsin Mutations…
Retinitis pigmentosa (RP) is a group of inherited degenerative eye diseases characterized by mutations in the genetic structure of the photoreceptors that leads to the premature death of both rod and cone photoreceptors. Defects in…
Proteins appear to be the most dramatic natural example of self-organized network criticality (SONC), a concept that explains many otherwise apparently exponentially unlikely phenomena. Adaptive plasticity is a term which has become much…
Retinitis pigmentosa (RP), one of the leading causes of vision loss and blindness globally, is a progressive retinal disease involving the degradation of photoreceptors (7) and/or retinal pigment epithelial cells (14). Affecting…
Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein conformational functionality is often dominated by long-range…
Rhodopsin is a G-protein coupled receptor found in retinal rod cells, where it mediates monocrhromatic vision in dim light. It is one of the most studied proteins with thousands of reviewed entries in Uniprot. It has seven transmembrane…
We focus here on the scaling properties of small interspecies differences between red cone opsin transmembrane proteins, using a hydropathic elastic roughening tool previously applied to the rhodopsin rod transmembrane proteins. This tool…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
The retinal pigment epithelium (RPE) is a key site of pathogenesis for many retina diseases. The formation of drusen in the retina is characteristic of retinal degeneration. We investigate morphological changes in the RPE in the presence of…
The characterization of plasticity, robustness, and evolvability, an important issue in biology, is studied in terms of phenotypic fluctuations. By numerically evolving gene regulatory networks, the proportionality between the phenotypic…
regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal…
Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins.…
Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its deregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs),…
Noisy data and the similarity in the ocular appearances caused by different ophthalmic pathologies pose significant challenges for an automated expert system to accurately detect retinal diseases. In addition, the lack of knowledge…
The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such…
The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of…
Sub-resolution porosity (SRP) is an ubiquitous, yet often ignored, feature in Digital Rock Physics. It embodies the trade-off between image resolution and field-of-view, and it is a direct result of choosing an imaging resolution that is…
Recent clinical research describes a subset of glioblastoma patients that exhibit REP prior to start of radiation therapy. Current literature has thus far described this population using clinicopathologic features. To our knowledge, this…
We analyze protein-protein interaction networks for six different species under the framework of random matrix theory. Nearest neighbor spacing distribution of the eigenvalues of adjacency matrices of the largest connected part of these…
In a recent paper (hep-ph/0608271) we describe a new approach to rapidity gap survival (RGS) in the production of high-mass systems (H = dijet, Higgs, etc.) in exclusive double-gap diffractive pp scattering, pp -> p + H + p. It is based on…
In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…