A life-long quest to understand and treat genetic blood disorders

This year's Lasker-Koshland Special Achievement Award in Medical Science is conferred on Sir David Weatherall for his 50 years of dedication to biomedical research, his groundbreaking discoveries about genetic blood diseases, and his life-long passion for bringing improved medical care to the developing world.     

A genetic push to understand motion detection

Two articles in this issue of Neuron (Eichner et?al. and Clark et?al.) attack the problem of explaining how neuronal hardware in Drosophila implements the Reichardt motion detector, one of the most famous computational models in neuroscience, which has proven intractable up to now.     

Mutants as tools to understand cellular and molecular drought tolerance mechanisms

The use of mutants: a most promising way to detect genes involved in development or in response to environmental stress. The model species Arabidopsis, particularly amenable to dissect the genetics and molecular mechanisms underlying physiological responses, also offers the advantage of a wide variety of mutants. As far as drought tolerance is concerned, hormonal mutants, impaired in hormone biosynthesis — deficient mutants — or in the signal transduction pathway—responsive mutants—provide a valuable tool to analyse the role of phytohormone interaction in the plant drought behaviour as well as to differentiate the mutant phenotypes with new criteria.These two categories of mutants (in particular the abscisic acid, ABA, mutants) were shown to be affected in developmental processes during seed maturation-in the desiccation phase- and/or in response to environmental stress (drought, ...) in vegetative tissues. The present report will focus on this last aspect: alterations in drought responses in vegetative tissues (adaptive strategies and drought tolerance mechanisms) essentially in Arabidopsis hormonal mutants (ABA-deficient and ABA-insensitive, GA-deficient, auxin and ethylene-insensitive).Some of the results are discussed with regard to the predicted functions of genes affected by the mutations.     

A proposal for using the ensemble approach to understand genetic regulatory networks

Understanding the genetic regulatory network comprising genes, RNA, proteins and the network connections and dynamical control rules among them, is a major task of contemporary systems biology. I focus here on the use of the ensemble approach to find one or more well-defined ensembles of model networks whose statistical features match those of real cells and organisms. Such ensembles should help explain and predict features of real cells and organisms. More precisely, an ensemble of model networks is defined by constraints on the "wiring diagram" of regulatory interactions, and the "rules" governing the dynamical behavior of regulated components of the network. The ensemble consists of all networks consistent with those constraints. Here I discuss ensembles of random Boolean networks, scale free Boolean networks, "medusa" Boolean networks, continuous variable networks, and others. For each ensemble, M statistical features, such as the size distribution of avalanches in gene activity changes unleashed by transiently altering the activity of a single gene, the distribution in distances between gene activities on different cell types, and others, are measured. This creates an M-dimensional space, where each ensemble corresponds to a cluster of points or distributions. Using current and future experimental techniques, such as gene arrays, these M properties are to be measured for real cells and organisms, again yielding a cluster of points or distributions in the M-dimensional space. The procedure then finds ensembles close to those of real cells and organisms, and hill climbs to attempt to match the observed M features. Thus obtains one or more ensembles that should predict and explain many features of the regulatory networks in cells and organisms.     

The quest for the mechanisms of life

The genomic revolution, manifested by the sequencing of the complete genome of many organisms, along with technological advances, such as DNA microarrays and developments in high-throughput analysis of proteins, metabolites, and isotopic tracer distribution patterns, challenged the conventional ways in which questions are approached in the biological sciences: (a) rather than examining a small number of genes and/or reactions at any one time;, we can now analyze gene expression and protein activity in the context of systems of interacting genes and gene products; (b) comprehensive analysis of biological systems requires the integration of all cellular fingerprints: genome sequence, maps of gene expression, protein expression, metabolic output, and in vivo enzymatic activity; and (c) collecting, managing, and analyzing comparable data from various cellular profiles requires expertise from several fields that transcend traditional discipline boundaries. While researchers in systems biology have still to address difficult challenges in both experimental and computational arenas, they possess, for the first time, the opportunity to unravel the mechanisms of life. The enormous impact of these discoveries in diverse areas, such as metabolic engineering, strain selection, drug screening and development, bioprocess development, disease prognosis and diagnosis, gene and other medical therapies, is an obvious motivation for pursuing integrated analyses of cellular systems.     

The genetic and molecular mechanisms of motor neuron disease

Significant progress has been made in the identification of genes and chromosomal loci associated with several types of motor neuron disease. Of particular interest is recent work on the pathogenic mechanisms underlying these diseases, especially studies in in vitro model systems and in transgenic and gene-targeted mice.     

Developmental mechanisms and experimental models to understand forebrain malformative diseases

The development of the central nervous system can be divided into a number of phases, each of which can be subject of genetic or epigenetic alterations that may originate particular developmental disorders. In recent years, much progress has been made in elucidating the molecular and cellular mechanisms by which the vertebrate forebrain develops. Therefore, our understanding of major developmental brain disorders such as cortical malformations and neuronal migration disorders has significantly increased. In this review, we will describe the major stages in forebrain morphogenesis and regionalization, with special emphasis on developmental molecular mechanisms derailing telencephalic development with subsequent damage to cortical function. Because animal models, mainly mouse, have been fundamental for this progress, we will also describe some characteristic mouse models that have been capital to explore these molecular mechanisms of malformative diseases of the human brain. Although most of the genes involved in the regulation of basic developmental processes are conserved among vertebrates, the extrapolation of mouse data to corresponding gene expression and function in humans needs careful individual analysis in each functional system.     

Caveolae--from ultrastructure to molecular mechanisms

Almost 50 years after the first sighting of small pits that covered the surface of mammalian cells, investigators are now getting to grips with the detailed workings of these enigmatic structures that we now know as caveolae.     

Hereditary catalepsy: genetic and molecular mechanisms of catalepsy in mice

The results of experiments on the inheritance and neurobiological mechanism of high predisposition to tonic immobility (catalepsy) in CBA mice are discussed. Genetic analysis has demonstrated a monogenic inheritance of the predisposition to catalepsy. A set of polymorphic microsatellite markers has been used to demonstrate that the predisposition to catalepsy is linked to the distal fragment of mouse chromosome 13, which contains the gene of the 5-HT1A-serotonin receptor. Pharmacological and biochemical evidence for the association between hereditary catalepsy and 5-HT1A-receptor dysfunction are presented. The use of CBA mice for studying the mechanisms of depression and the effects of antidepressants is discussed.     

Spontaneous modulation of a dynamic balance between bacterial genomic stability and mutability: roles and molecular mechanisms of the genetic switch

Bacteria need a high degree of genetic stability to maintain their species identities over long evolutionary times while retaining some mutability to adapt to the changing environment.It is a long unanswered question that how bacteria reconcile these seemingly contradictory biological properties.We hypothesized that certain mechanisms must maintain a dynamic balance between genetic stability and mutability for the survival and evolution of bacterial species.To identify such mechanisms,we analyzed bacterial genomes,focusing on the Salmonella mismatch repair(MMR)system.We found that the MMR gene mutL functions as a genetic switch through a slipped-strand mispairing mechanism,modulating and maintaining a dynamic balance between genetic stability and mutability during bacterial evolution.This mechanism allows bacteria to maintain their phylogenetic status,while also adapting to changing environments by acquiring novel traits.In this review,we outline the history of research into this genetic switch,from its discovery to the latest findings,and discuss its potential roles in the genomic evolution of bacteria.     

The quest for molecular quasi-species in ligand-activity space and its application to directed enzyme evolution

We propose that the proper evolving unit in enzyme evolution is not a single “fittest molecule”, but a cluster of related variants denoted a “quasi-species”. A distribution of variants provides genetic variability and thereby reduces the risk of inbreeding and evolutionary dead-ends. Different matrices of substrates or activity modulators will lead to different selection criteria and divergent evolutionary trajectories. We provide examples from our directed evolution of glutathione transferases illustrating the interplay between libraries of enzyme variants and ligand matrices in the identification of quasi-species. The ligand matrix is shown to be crucial to the outcome of the search for novel activities. In this sense the experimental system resembles the biological environment in governing the evolution of enzymes.