A transformational-grammar approach to the study of the regulation of gene expression

An important problem in biology is the lack of a set of common principles unifying biological knowledge. We propose generative grammar for constructing an integrative paradigm for the understanding of genome organization and the regulation of gene expression. Linguistic terms in molecular biology are defined. A genetic syntactic structure is defined as being equivalent to a sentence. The hypotheses for the grammar of genome structure are: (i) the "grammaticality" of the linguistic approach studies the "regulability" of genome structures; (ii) the "regulability" of genetic structures is independent from their specific biochemical meaning and (iii) the dynamics of regulation is implicit in the genome structure. A general structure is presented for the grammar; the application of phase-structure rules is justified by the existence of lexical categories. Transformational rules are utilized to represent loops of regulation. Negative inducible, positive repressible, positive inducible and negative repressible alternative mechanisms of regulation are represented, by four transformational rules, and the application of these rules is established by two principles. Finally, this approach is compared to other linguistic applications in molecular biology.     

Hypoxia and the regulation of gene expression

The optimal delivery of oxygen to tissues is essential both to ensure adequate energy provision and to avoid the toxic effects of higher oxygen concentrations. For this to occur, organisms must be able to sense oxygen and respond to changes in oxygen tension by altering gene expression. The analysis of the regulation of erythropoiesis has provided important insights into the mechanisms of oxygen-regulated gene expression. These mechanisms have a role in the regulation of many genes, in many cell types and appear to be of relevance to many common pathologies in which disturbances of oxygen supply are central.     

Whole-body integration of gene expression and single-cell morphology

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Hormonal regulation of gene expression

The involvement of plant hormones in the regulation of gene expression is well-recognized. Current research using molecular approaches has resulted in the isolation and characterization of a number of hormone-responsive genes and cDNAs. These genes are proving to be valuable molecular probes to study the mode of action of plant hormones. This review will briefly describe some recent molecular data from selected hormone-responsive plant systems. Results of these studies indicate potential complexity in the regulation of these genes. These results and future challenges are discussed.     

Comparative studies of gene expression and the evolution of gene regulation

The hypothesis that differences in gene regulation have an important role in speciation and adaptation is more than 40 years old. With the advent of new sequencing technologies, we are able to characterize and study gene expression levels and associated regulatory mechanisms in a large number of individuals and species at an unprecedented resolution and scale. We have thus gained new insights into the evolutionary pressures that shape gene expression levels and have developed an appreciation for the relative importance of evolutionary changes in different regulatory genetic and epigenetic mechanisms. The current challenge is to link gene regulatory changes to adaptive evolution of complex phenotypes. Here we mainly focus on comparative studies in primates and how they are complemented by studies in model organisms.     

Nutritional regulation of gene expression

Summary The human genome has now been mapped with a complete sequence to follow shortly. The race is on to apply the vast amount of information contained in the billions of base-pairs. Concurrently, there is an increased demand from the public for perceived natural products. The nutritional supplement and pharmaceutical industries are broadening their product lines to meet this ever-increasing demand. As the genetic basis of disease becomes more evident, it is clear that the two industries will be forced to turn their attention to nutrients affecting gene expression. Such nutritional regulators of gene expression, or genomeceuticals (Brudnak, 2001), have enormous potential for therapeutic and prophylactic applications in both industries by affecting the integrity and expression of genes. However, there are caveats to this application, which if unheeded, may have disastrous results. This paper explores the idea behind the burgeoning area of genomeceuticals as well as some potential pit-falls that this novel area harbors. Representative examples are presented with a subsequent discussion focusing on the specifics of the application. Calculations based on: mw of GlcNAc · HCl=215.64, mw GlcNAc=179.18. Given: an infusion rate of 15 μM/Kg/min, 15 μM of GlcNAc=2.68 mg, and GHCl (glucosamine hydrochloride) is 83% GlcNAc.     

Temporal regulation of gene expression

Molecular biology gives a static--not a dynamic--vision of the mechanisms regulating gene expression. Genetics already gave to time a limited place in the explanation of living phenomena. Such a static vision is supported by the techniques--such as X-ray crystallography--used by the biologists. However time is an important parameter in the control of gene expression during the cellular response to external signals, during life and aging of organisms or even in the succession of living forms which takes place in evolution. Models are slowly moving, due to the eruption of new technologies giving access to the fast events which occur inside living cells. A new dynamic vision is progressively replacing the old one. The consequences of these changes on the form of the future biology remain still unknown.     

Translational regulation of gene expression

A report on the Cold Spring Harbor Laboratory meeting 'Translational Control', Cold Spring Harbor, USA, 7-12 September 2004.