Faculty Bibliography

What is systems biology? What can biologists gain from an attempt to algebraize the questions in systems biology? Starting with plausible biological theses, can one algebraically model them and then manipulate them to suggest meaningful hypotheses? Using these hypotheses, can one measure and mine suitable experimental data to validate or refute these hypotheses? Through these intertwined processes of measuring, mining, modeling and manipulating biological systems, can one generate the set of theses and hypotheses upon which systems biology will be founded? This review provides one algorithmic-algebraist's somewhat idiosyncratic response to these and other related questions, but also aims to persuade young algebraists to examine the possible role they and algebra can play to enrich this subject.

A series of papers, all under the title of Algorithmic Algebraic Model Checking (AAMC), has sought to combine techniques from algorithmic algebra, model checking and dynamical systems to examine how a biochemical hybrid dynamical system can be made amenable to temporal analysis, even when the initial conditions and unknown parameters may only be treated as symbolic variables. This paper examines how to specialize this framework to metabolic control analysis (MCA) involving many reactions operating at many dissimilar time-scales. In the earlier AAMC papers, it has been shown that the dynamics of various biochemical semi-algebraic hybrid automata could be unraveled using powerful techniques from computational real algebraic geometry. More specifically, the resulting algebraic model checking techniques were found to be suitable for biochemical networks modeled using general mass action (GMA) based ODEs. This paper scrutinizes how the special properties of metabolic networks - a subclass of the biochemical networks previously handled - can be exploited to gain improvement in computational efficiency. The paper introduces a general framework for performing symbolic temporal reasoning over metabolic network hybrid automata that handles both GMA-based equilibrium estimation and flux balance analysis (FBA). While algebraic polynomial equations over ?[x 1,..., x n] can be symbolically solved using Gröbner bases or Wu-Ritt characteristic sets, the FBA-based estimation can be performed symbolically by rephrasing the algebraic optimization problem as a quantifier elimination problem. Effectively, an approximate hybrid automaton that simulates the metabolic network is derived, and is thus amenable to manipulation by the algebraic model checking techniques previously described in the AAMC papers.

Recent research progress using X-ray cryo-crystallography with the photon beams from third-generation synchrotron sources has resulted in recognition that this intense radiation commonly damages protein samples even when they are held at 100 K. Other structural biologists examining thin protein crystals or single particle specimens encounter similar radiation damage problems during electron diffraction and imaging, but have developed some effective countermeasures. The aim of this concise review is to examine whether analogous approaches can be utilized to alleviate the X-ray radiation damage problem in synchrotron macromolecular crystallography. The critical discussion of this question is preceded by presentation of background material on modern technical procedures with electron beam instruments using 300-400 kV accelerating voltage, low-dose exposures for data recording, and protection of protein specimens by cryogenic cooling; these practical approaches to dealing with electron radiation damage currently permit best resolution levels of 6 A (0.6 nm) for single particle specimens, and of 1.9 A for two-dimensional membrane protein crystals. Final determination of the potential effectiveness and practical value of using such new or unconventional ideas will necessitate showing, by experimental testing, that these produce significantly improved protection of three-dimensional protein crystals during synchrotron X-ray diffraction.

Nervous systems have evolved two basic mechanisms for increasing the conduction speed of the electrical impulse. The first is through axon gigantism: using axons several times larger in diameter than the norm for other large axons, as for example in the well-known case of the squid giant axon. The second is through encasing axons in helical or concentrically wrapped multilamellar sheets of insulating plasma membrane--the myelin sheath. Each mechanism, alone or in combination, is employed in nervous systems of many taxa, both vertebrate and invertebrate. Myelin is a unique way to increase conduction speeds along axons of relatively small caliber. It seems to have arisen independently in evolution several times in vertebrates, annelids and crustacea. Myelinated nerves, regardless of their source, have in common a multilamellar membrane wrapping, and long myelinated segments interspersed with 'nodal' loci where the myelin terminates and the nerve impulse propagates along the axon by 'saltatory' conduction. For all of the differences in detail among the morphologies and biochemistries of the sheath in the different myelinated animal classes, the function is remarkably universal.

The unparalleled complexity of intercellular connections in the nervous system presents requirements for high levels of both specificity and diversity for the proteins that mediate cell adhesion. Here we describe recent advances toward understanding the molecular mechanisms that underlie adhesive binding, specificity, and diversity for several well-characterized families of adhesion molecules in the nervous system. Although many families of adhesion proteins, including cadherins and immunoglobulin superfamily members, are utilized in neural and nonneural contexts, nervous system-specific diversification mechanisms, such as precisely regulated alternative splicing, provide an important means to enable their function in the complex context of the nervous system.

Here we review how prior experience with stress alters the response to a subsequent homotypic or heterotypic stressor, focusing on the catecholaminergic systems in the adrenal medulla and the locus coeruleus (LC). The changes in response to homotypic stress differ depending on the stressor applied. With immobilization stress (IMO), transcriptional responses in the adrenal medulla to a single exposure are pronounced and several of the transcription factors and signaling kinases induced or activated are reviewed and compared to the longer term alterations with repeated stress, consistent with persistent activation of gene expression of catecholamine (CA) biosynthetic enzymes. In the LC, transcriptional and post-transcriptional activation of gene expression are shown to be important. Repeated IMO stress triggers further activation of a number of signalling pathways. Neither adrenal medulla nor LC display habituation to long term repeated stress. In contrast, gene expression for CA biosynthetic enzymes habituates to prolonged cold stress in the adrenal medulla and LC, but displays an exaggerated response with exposure to a novel or heterotypic stressor such as IMO. Some of the transcriptional pathways displaying sensitization are described.

Although processes leading up to the point of synapse formation are fairly well understood, the precise sequence of events in which the membranes of two separate cells "lock in" to form a mature synaptic junctional complex is poorly understood. A careful study of the molecules operating at the synapse indicates that their roles are more multifarious than once imagined. In this review we posit that the synapse is a functional organelle with poorly defined boundaries and a complex biochemistry. The role of adhesion molecules, including the integration of their signaling and adhesive properties in the context of synaptic activity is discussed.

Tyrosine hydroxylase is the rate-limiting enzyme in catecholamine biosynthesis, and its N-terminus plays a critical role in the intracellular stability of the enzyme. In the present study, we investigated the mechanism by which the N-terminus of human tyrosine hydroxylase type 1 (hTH1) affects the stability. The results obtained by using N-terminus-deleted hTH1 mutants identified the sequence up to Ala(23) as mediating the stability. The down-regulation of 14-3-3eta proteins in PC12D cells exogenously expressing hTH1, enhanced the stability of the wild-type enzyme and that of the mutant lacking the N-terminus up to Ala(23). However, the stability of the mutant was reduced compared to the wild-type enzyme. The stability of the mutant with the N-terminus deleted up to Glu(43) was not affected by the down-regulation of 14-3-3eta. These results suggest that the 14-3-3eta protein regulates hTH1 stability by acting on the N-terminus.

The catecholamines play key roles in orchestrating the response to stress. While this is crucial to handle emergency situations, stress becomes maladaptive when prolonged or repeated, increasing allosteric load and susceptibility to a wide range of serious diseases. The time frame of the regulation of gene expression, especially as it relates to catecholamine (CA) biosynthetic enzymes are compared in three crucial catecholaminergic locations, the adrenal medulla, sympathetic ganglia and locus coeruleus in male animals. The adrenal medulla displays very rapid response to stress and gene profiling reveals a wide repertoire of target genes, many of them activated by single and not by repeated stress. In contrast to the adrenal medulla, the sympathetic ganglia are especially responsive to activation of the HPA axis, and ACTH may have a direct effect. The locus coeruleus, origin of most of the noradrenergic neurons innervating much of the brain, displays activation of additional signalling pathways and transcription factor with repeated compared to single exposure to stress. Most of the studies have been performed in males. However, there is considerable evidence that females respond differently to stress. Estradiol can regulate TH, DBH and GTPCH gene expression, as well as to modulate its response to other second messenger such as cAMP. Prior treatment with estradiol was found to alter the response of CA biosynthetic enzymes to stress. This emphasizes the tissue and sex specific features of the mechanistic underpinning of the adaptation or maladaptation of the catecholaminergic systems to stress and provides the basis for specific interventions. Key words: Adrenal medulla - Catecholamine biosynthesis - Estrogen - Sympathetic ganglia - Locus coeruleus - Stress - Transcription factors.

Recent studies have demonstrated that the LIM homeodomain transcription factor Islet1 (Isl1) marks pluripotent cardiovascular progenitor cells and is required for proliferation, survival, and migration of recently defined second heart field progenitors. Factors that are upstream of Isl1 in cardiovascular progenitors have not yet been defined. Here we demonstrate that beta-catenin is required for Isl1 expression in cardiac progenitors, directly regulating the Isl1 promoter. Ablation of beta-catenin in Isl1-expressing progenitors disrupts multiple aspects of cardiogenesis, resulting in embryonic lethality at E13. beta-Catenin is also required upstream of a number of genes required for pharyngeal arch, outflow tract, and/or atrial septal morphogenesis, including Tbx2, Tbx3, Wnt11, Shh, and Pitx2. Our findings demonstrate that beta-catenin signaling regulates proliferation and survival of cardiac progenitors.