701 research outputs found
Facilitated diffusion of DNA-binding proteins
The diffusion-controlled limit of reaction times for site-specific
DNA-binding proteins is derived from first principles. We follow the generally
accepted concept that a protein propagates via two competitive modes, a
three-dimensional diffusion in space and a one-dimensional sliding along the
DNA. However, our theoretical treatment of the problem is new. The accuracy of
our analytical model is verified by numerical simulations. The results confirm
that the unspecific binding of protein to DNA, combined with sliding, is
capable to reduce the reaction times significantly.Comment: 4 pages, 2 figures Nov 22 2005 - accepted for PR
Effects of Noise on Ecological Invasion Processes: Bacteriophage-mediated Competition in Bacteria
Pathogen-mediated competition, through which an invasive species carrying and
transmitting a pathogen can be a superior competitor to a more vulnerable
resident species, is one of the principle driving forces influencing
biodiversity in nature. Using an experimental system of bacteriophage-mediated
competition in bacterial populations and a deterministic model, we have shown
in [Joo et al 2005] that the competitive advantage conferred by the phage
depends only on the relative phage pathology and is independent of the initial
phage concentration and other phage and host parameters such as the
infection-causing contact rate, the spontaneous and infection-induced lysis
rates, and the phage burst size. Here we investigate the effects of stochastic
fluctuations on bacterial invasion facilitated by bacteriophage, and examine
the validity of the deterministic approach. We use both numerical and
analytical methods of stochastic processes to identify the source of noise and
assess its magnitude. We show that the conclusions obtained from the
deterministic model are robust against stochastic fluctuations, yet deviations
become prominently large when the phage are more pathological to the invading
bacterial strain.Comment: 39 pages, 7 figure
Forces During Bacteriophage DNA Packaging and Ejection
The conjunction of insights from structural biology, solution biochemistry,
genetics and single molecule biophysics has provided a renewed impetus for the
construction of quantitative models of biological processes. One area that has
been a beneficiary of these experimental techniques is the study of viruses. In
this paper we describe how the insights obtained from such experiments can be
utilized to construct physical models of processes in the viral life cycle. We
focus on dsDNA bacteriophages and show that the bending elasticity of DNA and
its electrostatics in solution can be combined to determine the forces
experienced during packaging and ejection of the viral genome. Furthermore, we
quantitatively analyze the effect of fluid viscosity and capsid expansion on
the forces experienced during packaging. Finally, we present a model for DNA
ejection from bacteriophages based on the hypothesis that the energy stored in
the tightly packed genome within the capsid leads to its forceful ejection. The
predictions of our model can be tested through experiments in vitro where DNA
ejection is inhibited by the application of external osmotic pressure
Hormonal Signal Amplification Mediates Environmental Conditions during Development and Controls an Irreversible Commitment to Adulthood
Many animals can choose between different developmental fates to maximize fitness. Despite the complexity of environmental cues and life history, different developmental fates are executed in a robust fashion. The nematode Caenorhabditis elegans serves as a powerful model to examine this phenomenon because it can adopt one of two developmental fates (adulthood or diapause) depending on environmental conditions. The steroid hormone dafachronic acid (DA) directs development to adulthood by regulating the transcriptional activity of the nuclear hormone receptor DAF-12. The known role of DA suggests that it may be the molecular mediator of environmental condition effects on the developmental fate decision, although the mechanism is yet unknown. We used a combination of physiological and molecular biology techniques to demonstrate that commitment to reproductive adult development occurs when DA levels, produced in the neuroendocrine XXX cells, exceed a threshold. Furthermore, imaging and cell ablation experiments demonstrate that the XXX cells act as a source of DA, which, upon commitment to adult development, is amplified and propagated in the epidermis in a DAF-12 dependent manner. This positive feedback loop increases DA levels and drives adult programs in the gonad and epidermis, thus conferring the irreversibility of the decision. We show that the positive feedback loop canalizes development by ensuring that sufficient amounts of DA are dispersed throughout the body and serves as a robust fate-locking mechanism to enforce an organism-wide binary decision, despite noisy and complex environmental cues. These mechanisms are not only relevant to C. elegans but may be extended to other hormonal-based decision-making mechanisms in insects and mammals
Formation of regulatory modules by local sequence duplication
Turnover of regulatory sequence and function is an important part of
molecular evolution. But what are the modes of sequence evolution leading to
rapid formation and loss of regulatory sites? Here, we show that a large
fraction of neighboring transcription factor binding sites in the fly genome
have formed from a common sequence origin by local duplications. This mode of
evolution is found to produce regulatory information: duplications can seed new
sites in the neighborhood of existing sites. Duplicate seeds evolve
subsequently by point mutations, often towards binding a different factor than
their ancestral neighbor sites. These results are based on a statistical
analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome,
and a comparison set of intergenic regulatory sequence in Saccharomyces
cerevisiae. In fly regulatory modules, pairs of binding sites show
significantly enhanced sequence similarity up to distances of about 50 bp. We
analyze these data in terms of an evolutionary model with two distinct modes of
site formation: (i) evolution from independent sequence origin and (ii)
divergent evolution following duplication of a common ancestor sequence. Our
results suggest that pervasive formation of binding sites by local sequence
duplications distinguishes the complex regulatory architecture of higher
eukaryotes from the simpler architecture of unicellular organisms
From DNA sequence to application: possibilities and complications
The development of sophisticated genetic tools during the past 15 years have facilitated a tremendous increase of fundamental and application-oriented knowledge of lactic acid bacteria (LAB) and their bacteriophages. This knowledge relates both to the assignments of open reading frames (ORF’s) and the function of non-coding DNA sequences. Comparison of the complete nucleotide sequences of several LAB bacteriophages has revealed that their chromosomes have a fixed, modular structure, each module having a set of genes involved in a specific phase of the bacteriophage life cycle. LAB bacteriophage genes and DNA sequences have been used for the construction of temperature-inducible gene expression systems, gene-integration systems, and bacteriophage defence systems.
The function of several LAB open reading frames and transcriptional units have been identified and characterized in detail. Many of these could find practical applications, such as induced lysis of LAB to enhance cheese ripening and re-routing of carbon fluxes for the production of a specific amino acid enantiomer. More knowledge has also become available concerning the function and structure of non-coding DNA positioned at or in the vicinity of promoters. In several cases the mRNA produced from this DNA contains a transcriptional terminator-antiterminator pair, in which the antiterminator can be stabilized either by uncharged tRNA or by interaction with a regulatory protein, thus preventing formation of the terminator so that mRNA elongation can proceed. Evidence has accumulated showing that also in LAB carbon catabolite repression in LAB is mediated by specific DNA elements in the vicinity of promoters governing the transcription of catabolic operons.
Although some biological barriers have yet to be solved, the vast body of scientific information presently available allows the construction of tailor-made genetically modified LAB. Today, it appears that societal constraints rather than biological hurdles impede the use of genetically modified LAB.
Piecewise-Linear Models of Genetic Regulatory Networks: Theory and Example
International audienceThe experimental study of genetic regulatory networks has made tremendous progress in recent years resulting in a huge amount of data on the molecular interactions in model organisms. It is therefore not possible anymore to intuitively understand how the genes and interactions together influence the behavior of the system. In order to answer such questions, a rigorous modeling and analysis approach is necessary. In this chapter, we present a family of such models and analysis methods enabling us to better understand the dynam-ics of genetic regulatory networks. We apply such methods to the network that underlies the nutritional stress response of the bacterium E. coli. The functioning and development of living organisms is controlled by large and complex networks of genes, proteins, small molecules, and their interactions, so-called genetic regulatory networks. The study of these networks has recently taken a qualitative leap through the use of modern genomic techniques that allow for the simultaneous measurement of the expression levels of all genes of an organism. This has resulted in an ever growing description of the interactions in the studied genetic regulatory networks. However, it is necessary to go beyond the simple description of the interactions in order to understand the behavior of these networks and their relation with the actual functioning of the organism. Since the networks under study are usually very large, an intuitive approach for their understanding is out of ques-tion. In order to support this work, mathematical and computer tools are necessary: the unambiguous description of the phenomena that mathematical models provide allows for a detailed analysis of the behaviors at play, though they might not exactly represent the exact behavior of the networks. In this chapter, we will be mostly interested in the modeling of the genetic reg-ulatory networks by means of differential equations. This classical approach allows precise numerical predictions of deterministic dynamic properties of genetic regu-latory networks to be made. However, for most networks of biological interest the application of differential equations is far from straightforward. First, the biochemi-cal reaction mechanisms underlying the interactions are usually not or incompletel
Genetic Labeling of Neuronal Subsets through Enhancer Trapping in Mice
The ability to label, visualize, and manipulate subsets of neurons is critical for elucidating the structure and function of individual cell types in the brain. Enhancer trapping has proved extremely useful for the genetic manipulation of selective cell types in Drosophila. We have developed an enhancer trap strategy in mammals by generating transgenic mice with lentiviral vectors carrying single-copy enhancer-detector probes encoding either the marker gene lacZ or Cre recombinase. This transgenic strategy allowed us to genetically identify a wide variety of neuronal subpopulations in distinct brain regions. Enhancer detection by lentiviral transgenesis could thus provide a complementary method for generating transgenic mouse libraries for the genetic labeling and manipulation of neuronal subsets
Effect of promoter architecture on the cell-to-cell variability in gene expression
According to recent experimental evidence, the architecture of a promoter,
defined as the number, strength and regulatory role of the operators that
control the promoter, plays a major role in determining the level of
cell-to-cell variability in gene expression. These quantitative experiments
call for a corresponding modeling effort that addresses the question of how
changes in promoter architecture affect noise in gene expression in a
systematic rather than case-by-case fashion. In this article, we make such a
systematic investigation, based on a simple microscopic model of gene
regulation that incorporates stochastic effects. In particular, we show how
operator strength and operator multiplicity affect this variability. We examine
different modes of transcription factor binding to complex promoters
(cooperative, independent, simultaneous) and how each of these affects the
level of variability in transcription product from cell-to-cell. We propose
that direct comparison between in vivo single-cell experiments and theoretical
predictions for the moments of the probability distribution of mRNA number per
cell can discriminate between different kinetic models of gene regulation.Comment: 35 pages, 6 figures, Submitte
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