Biomedical subjects

Mark Geanacopoulos

Publications and source records attributed to Mark Geanacopoulos.

6 recordsLinked to original sources

PubMed2005

Glomerular disease workshop.

Recent observations regarding intrinsic glomerular cell biology, particularly in the podocyte, have provided exciting new insights into potential pathogenic mechanisms of human glomerular disease. Although both immune and nonimmune mechanisms of glomerular injury have been studied previously, experimental models of disease and recent techniques that provide tools for molecular profiling show great promise for identifying glomerular disease biomarkers. Despite these recent advances, additional work in both basic and clinical studies of glomerular disease is needed to advance the field. Standardization of animal models of distinct forms of glomerular disease would likely facilitate the search for biomarkers. Several factors limit current efforts to implement clinical trials of glomerular disease. Identification of disease biomarkers, development of disease-specific end points, and organization of collaborative clinical groups are critical for ultimately designing and implementing appropriately powered trials of glomerular disease.

Animals↗

PubMed2005

Gal repressor-operator-HU ternary complex: pathway of repressosome formation.

DNA transaction reactions require formation of nucleoprotein complexes that involve multifaceted DNA-protein and protein-protein interactions. Genetic and biochemical studies suggested that the higher order Gal repressosome structure, which governs the transcription of two tandem galpromoters in Escherichia coli, involves sequence-specific binding of GalR repressor dimers to two operators, O(E) and O(I), located 113 bp apart, binding of GalR to the sequence-nonspecific DNA binding protein HU, interaction of HU with an architecturally critical DNA site between the two operators, and interaction between two DNA-bound GalR dimers generating a loop of the intervening DNA segment. In this paper, we demonstrate and determine the thermodynamic parameters of several of these interactions, GalR dimer-O(E), GalR tetramerization, HU-GalR, and HU-GalR-O(E) interactions, by analytical ultracentrifugation, fluorescence anisotropy, and fluorescence resonance energy transfer. The physiological significance of several of these interactions was confirmed by the finding that a mutant HU, which is unable to form the repressosome in vivo and in vitro, failed to show the HU-GalR interaction. The results help to construct a pathway of Gal repressosome assembly.

Base Sequence↗

PubMed2005

An introduction to RNA-mediated gene silencing.

Careful analysis of cases where introduction of additional copies of endogenous genes caused coordinate silencing of both the transgene and the endogenous gene laid the ground work for the discovery of RNA-mediated silencing. Silencing begins with the expression and recognition of double-stranded RNA, which is cleaved into short RNAs that recognize, by complementarity, sequences that are targets for down regulation. An RNA target can be regarded (post-transcriptional gene silencing), but the small RNAs can also direct the sequence-specific modification of DNA and chromatin. RNA-mediated gene silencing in eukaryotes may have originated as surveillance mechanism to protect the organism from transposable elements and viruses and then evolved to specify chromosomal modifications and to regulate expression of a significant fraction of endogenous genes by microRNAs. This review seeks to furnish the student and non-expert with some idea of how RNA-mediated silencing was discovered and a broad overview of the present state of knowledge.

Animals↗

PubMed2004

The determinants of lifespan in the nematode Caenorhabditis elegans: a short primer.

Transparent, easily-maintained, amenable to genetic manipulation, and living for only a few weeks, the nematode Caenorhabditis elegans is a leading animal model for the study of the determinants of lifespan. The original genetic screen for increased longevity identified a mutant, age-1, with a defect in one component of a signal transduction pathway. This pathway functioned as a genetic switch and governed the decision whether to enter a specialized larval form, dauer, that enables the worm to withstand the scarcity of food or other stressful conditions. These age-1 worms had an increased tendency to become dauers, but if they did not adopt the dauer developmental pathway, they lived longer than wild type worms. age-1 and other longevity mutants with dauer phenotypes are vigorous, indicating that they do not suffer from a significant energy deficit, and stress resistant. Mutation of genes encoding mitochondrial components was found to be another means of extending the lifespan of the worm, although the associated phenotypes suggest a deficiency of available energy. While there are now many documented genetic manipulations which can extend the worm's lifespan, it has been difficult to come to definite conclusions as to the mechanism(s) by which lifespan is extended. The most carefully studied mutant strains have complex changes in gene expression and metabolism making it difficult to ascertain what changes are critical. The free radical theory of aging is the dominant biochemical theory of aging, and the phenotypes of the well-characterized longevity mutants worm can be accommodated to it. However discrete interventions to lower reactive oxygen species, or mitigate their effects, have not produced consistent easily-interpretable results in terms of lifespan extension. It has become clear that the insulin-dependent signalling mechanism that regulates lifespan in the worm functions in the context of a complex endocrine system and the hormonal control of aging is an emerging focus of research in worms and higher organisms.

Aging↗

PubMed2002

Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding.

The assembly of the Gal repressosome, a higher order nucleoprotein complex that represses transcription of the gal operon in Escherichia coli, involves the formation of a DNA loop encompassing the promoter segment. GalR dimers bound to two spatially separated operators, O(E) and O(I), specifically interact with the histone-like protein HU and close the loop in supercoiled DNA. We isolated and characterized a GalR mutant containing an amino acid substitution (R282L) that can repress transcription in the absence of HU and supercoiled DNA both in vivo and in vitro. Repression involves the same DNA looping; deletion of either O(E) or O(I) makes the mutant GalR ineffective in repression. This and other results suggest that the R282L substitution increases the normal affinity between two DNA-bound GalR dimers, allowing looping. We conclude that GalR dimers interact directly and do not use HU as an adaptor in loop closure; HU and DNA supercoiling act in concert to stabilize the GalR tetramer. The stronger GalR-GalR interaction also made the gal transcription non-inducible, suggesting that the inducer binding acts by modulating tetramerization.

DNA, Bacterial↗

PubMed2002

Genetic analysis of GalR tetramerization in DNA looping during repressosome assembly.

The Gal repressosome is a nucleoprotein complex consisting of 2 GalR dimers, 1 HU, and 1 DNA loop, which represses the transcription of the gal operon. We have adopted a structure-based genetic approach to complement ongoing physical studies of the complex. Homology-based and subsequent alanine-scanning mutageneses suggest that five residues in the DNA-distal subdomain of GalR dimer are important for repressosome formation. A further analysis of these and intragenic suppressors of looping-defective GalR mutants as well as gain-of-function mutants that permit repressosome assembly in the absence of HU show that GalR dimers contact each other in the repressosome in a partially stacked configuration.

Alanine↗