The role of microRNA in the delayed negative feedback regulation of gene expression

Oscillatory gene expression plays an important role in somite segmentation during the early developmental stages of vertebrates. Recent experimental studies have shown that microRNA can regulate gene expression by stimulating degradation of mRNA and/or repression of translation. In this communication, we incorporate miRNA into a previous mathematical model of gene expression with delayed negative feedback and demonstrate how this modified model can elucidate the possible effect of miRNA on the oscillatory gene expression. Our finding suggests that miRNA maybe a destabilizing or stabilizing factor in the dynamics of gene expression depending on the severity of its effect on mRNA degradation. Our finding provides testable hypothesis for experimental biologists to further investigate miRNA's increasing functional roles in regulating cellular processes and development.     

Polyethylene glycol-mediated direct gene transfer in Nicotiana spp.

Direct gene transfer to protoplasts is a widespread experimental procedure. In this review, it is discussed in relation to the fate and expression of transforming DNA and its genetic transmission upon integration, and expression (in)stability during successive meiotic generations. The results suggest that the major differences between Nicotiana plumbaginifolia and N. tabacum were not in DNA uptake but rather in the specific fate of the transforming DNA. Differences between integrative transformation versus transient gene expression are discussed. Transient gene expression experiments with cotransformed independent constructs enable accurate assays of gene activity modulation, including both activation and repression. The study of the time of integration of foreign DNA using haploid mesophyll protoplasts showed that foreign DNA integration took place during the first two division cycles of the protoplasts. Most of the transfomants inherited the foreign genes as a monogenic trait: N. plumbaginifolia exhibited a higher proportion of multiple insertions compared with N. tabacum . Furthermore, gene integration occurs as a random process. Compared to 'simple' transformation, cotransformation with independent constructs showed a higher level of rearrangement of the inserted DNA. Foreign gene transmission, followed through different generations, indicated that inactivation of the inserted gene could happen through a variety of processes. These results open up a series of questions concerning the applied aspects of direct gene transfer to plants.     

Quantitative in vivo microscopy: the return from the 'omics'

The confluence of recent advances in microscopy instrumentation and image analysis, coupled with the widespread use of GFP-like proteins as reporters of gene expression, has opened the door to high-throughput in vivo studies that can provide the morphological and temporal context to the biochemical pathways regulating cell function. We are now able to quantify the concentration and three-dimensional distribution of multiple spectrally resolved GFP-tagged proteins. Using automatic segmentation and tracking we can then measure the dynamics of the processes in which these elements are involved. In this way, parallel studies are feasible where multiple cell colonies treated with drugs or gene expression repressors can be monitored and analyzed to study the dynamics of relevant biological processes.     

Mutual interaction in network motifs robustly sharpens gene expression in developmental processes

The gene regulatory network of a developmental process contains many mutually repressive interactions between two genes. They are often regulated by or regulate an additional factor, which constitute prominent network motifs, called regulated and regulating mutual loops. Our database analysis on the gene regulatory network for Drosophila melanogaster indicates that those with mutual repression are working specifically for the segmentation process. To clarify their biological roles, we mathematically study the response of the regulated mutual loop with mutual repression to input stimuli. We show that the mutual repression increases the response sensitivity without affecting the threshold input level to activate the target gene expression, as long as the network output is unique for a given input level. This high sensitivity of the motif can contribute to sharpening the spatial domain pattern without changing its position, assuring a robust developmental process. We also study transient dynamics that shows shift of domain boundary, agreeing with experimental observations. Importance of mutual repression is addressed by comparing with other types of regulations.     

Inositol and phosphatidylinositol mediated mediated glucose derepression, gene expression and invertase secretion in yeasts

Glucose Repression [1,2] Saccharomyces cerevisiae and other yeasts can growwell on different kinds of carbon sources. However,glucose and fructose are the best carbon sources for theirgrowth. When the medium contains glucose or fructose,the biosynthesis of enzyme catalyzing degradation of othercarbon sources will be greatly reduced or stopped. Thisphenomenon is called glucose repression. Although much progress has been made in this field,the exact mechanisms of glucose repression in yeastsa…     

Stochastic Models of Gene Expression with Delayed Degradation

In many biochemical reactions occurring in living cells, number of various molecules might be low which results in significant stochastic fluctuations. In addition, most reactions are not instantaneous, there exist natural time delays in the evolution of cell states. It is a challenge to develop a systematic and rigorous treatment of stochastic dynamics with time delays and to investigate combined effects of stochasticity and delays in concrete models.We propose a new methodology to deal with time delays in biological systems and apply it to simple models of gene expression with delayed degradation. We show that time delay of protein degradation does not cause oscillations as it was recently argued. It follows from our rigorous analysis that one should look for different mechanisms responsible for oscillations observed in biological experiments.We develop a systematic analytical treatment of stochastic models of time delays. Specifically we take into account that some reactions, for example degradation, are consuming, that is: once molecules start to degrade they cannot be part in other degradation processes.We introduce an auxiliary stochastic process and calculate analytically the variance and the autocorrelation function of the number of protein molecules in stationary states in basic models of delayed protein degradation.     

Are time delays always destabilizing? Revisiting the role of time delays and the Allee effect

One of the main challenges in ecology is to determine the cause of population fluctuations. Both theoretical and empirical studies suggest that delayed density dependence instigates cyclic behavior in many populations; however, underlying mechanisms through which this occurs are often difficult to determine and may vary within species. In this paper, we consider single species population dynamics affected by the Allee effect coupled with discrete time delay. We use two different mathematical formulations of the Allee effect and analyze (both analytically and numerically) the role of time delay in different feedback mechanisms such as competition and cooperation. The bifurcation value of the delay (that results in the Hopf bifurcation) as a function of the strength of the Allee effect is obtained analytically. Interestingly, depending on the chosen delayed mechanism, even a large time delay may not necessarily lead to instability. We also show that, in case the time delay affects positive feedback (such as cooperation), the population dynamics can lead to self-organized formation of intermediate quasi-stationary states. Finally, we discuss ecological implications of our findings.     

Integrative modelling of gene expression and cell metabolism

The goal of modelling biochemical networks is to understand the system's behaviour (dynamics and control) of these networks in terms of the properties of the individual molecules. Most modelling approaches have dealt with either gene expression or cell metabolism. In light of the widespread use of robotic technologies in laboratories and improved computational power, it is now time to incorporate information from all biochemical levels--gene expression, protein interactions and metabolism--into integrated models. Here, we review the literature on modelling gene expression with cell metabolism. At the end we describe some analytic methods to deal with these systems.     

Oscillations and multiple steady states in a cyclic gene model with repression

In this paper we study the cyclic gene model with repression considered by H. T. Banks and J. M. Mahaffy. Roughly, the model describes a biochemical feedback loop consisting of an integer number G of single gene reaction sequences in series. The model leads to a system of functional differential equations. We show that there is a qualitative difference in the dynamics between even and odd G if the feedback repression is sufficiently large. For even G, multiple stable steady states can coexist while for odd G, periodic orbits exist.This research was supported in part by the Air Force Office of Scientific Research under Contract #AFOSR-84-0376 and by the US Army Research Office under Contract #DAAG29-84-K-0082     

The effect of long time delays in predator-prey systems

Past studies have indicated that a time delay longer than the natural period of a system will generally cause instability; however here it is shown that including long maturational time delays in a general predator-prey model need not have this effect. In each of the three cases studied (a predator delay, a prey delay, and both), local stability can persevere despite the presence of arbitrarily long time delays. This perseverence depends upon an interaction between delayed and undelayed features of the model. Delayed processes always act to destabilize the model. For example, prey self-regulation, usually a source of stability, becomes destabilizing if subject to a long delay. However, the effect of such a delay is offset by undelayed regulatory processes, such as a stabilizing functional reponse. In addition, the adverse effects of delayed predator recruitment can be reduced by the nonreproductive component of the numerical reponse, a feature not usually involved in determining stability. Finally, it is shown that long time delays are not necessarily more disruptive than short delays; it cannot be assumed that lengthening a time delay progessively reduces stability.     

Temporal control of colicin E1 induction.

The expression of the gene encoding colicin E1, cea, was studied in Escherichia coli by using cea-lacZ gene fusions. Expression of the fusions showed the same characteristics as those of the wild-type cea gene: induction by treatments that damage DNA and regulation by the SOS response, sensitivity to catabolite repression, and a low basal level of expression, despite the presence of the fusion in a multicopy plasmid. Induction of expression by DNA-damaging treatments was found to differ from other genes involved in the SOS response (exemplified by recA), in that higher levels of DNA damage were required and expression occurred only after a pronounced delay. The delay in expression following an inducing treatment was more pronounced under conditions of catabolite repression, indicating that the cyclic AMP-cyclic AMP receptor protein complex may play a role in induction. These observations also suggest a biological rationale for the control of cea expression by the SOS response and the cyclic AMP-cyclic AMP receptor protein catabolite repression system.     

Chromatin loops in gene regulation

The control of gene expression involves regulatory elements that can be very far from the genes they control. Several recent technological advances have allowed the direct detection of chromatin loops that juxtapose distant genomic sites in the nucleus. Here we review recent studies from various model organisms that have provided new insights into the functions of chromatin loops and the mechanisms that form them. We discuss the widespread impact of chromatin loops on gene activation, repression, genomic imprinting and the function of enhancers and insulators.