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Systems Biology Reviews: 2003
(38 References)
Adams, P. D., R. W. Grosse-Kunstleve, et al. (2003). "Computational aspects of high-throughput crystallographic macromolecular structure determination." Methods Biochem Anal 44: 75-87.
Aebersold, R. and M. Mann (2003). "Mass spectrometry-based proteomics." Nature 422(6928): 198-207.
Recent successes illustrate the role of mass spectrometry-based proteomics as an indispensable tool for molecular and cellular biology and for the emerging field of systems biology. These include the study of protein-protein interactions via affinity-based isolations on a small and proteome-wide scale, the mapping of numerous organelles, the concurrent description of the malaria parasite genome and proteome, and the generation of quantitative protein profiles from diverse species. The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.
Armitage, J. P., C. J. Dorman, et al. (2003). "Thinking and decision making, bacterial style: Bacterial Neural Networks, Obernai, France, 7th-12th June 2002." Mol Microbiol 47(2): 583-93.
Bacteria exhibit a bewildering range of behavioural responses and permutations of metabolic pathways for maximum exploitation of their environment. These are based on sensory perception of external and internal signals through batteries of surface and cytoplasmic receptors, evaluation of complex information flows and rapid decision making. Appreciation of the diversity of bacterial behaviour and adaptation capacities requires the study of a broad range of organisms and at this meeting we sampled more than 30 species with new findings which included the nature of gaseous receptors, advances in chemotaxis, subversion of host defences by pathogens, adaptation to high salt, community life and its obvious benefits, cell to cell communications and even the nature of bacterial circadian rhythms. With around 80 bacterial genomes now completed, and many more almost there, it was appropriate to complete the meeting with an introduction to Systems Biology and prospects for simulating the virtual cell. The versatility and seemingly 'intelligent' behaviour of bacteria will continue to fascinate, and this meeting on Bacterial Neural Networks fully reflected the excitement of this field.
Baker, N. A. and J. A. McCammon (2003). "Electrostatic interactions." Methods Biochem Anal 44: 427-40.
Bauer, A. and B. Kuster (2003). "Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes." Eur J Biochem 270(4): 570-8.
Multi-protein complexes are emerging as important entities of biological activity inside cells that serve to create functional diversity by contextual combination of gene products and, at the same time, organize the large number of different proteins into functional units. Many a time, when studying protein complexes rather than individual proteins, the biological insight gained has been fundamental, particularly in cases in which proteins with no previous functional annotation could be placed into a functional context derived from their 'molecular environment'. In this minireview, we summarize the current state of the art for the retrieval of multiprotein complexes by affinity purification and their analysis by mass spectrometry. The advances in technology made over the past few years now enable the study of protein complexes on a proteomic scale and it can be anticipated that the knowledge gathered from such projects will fuel drug target discovery and validation pipelines and that the technology is also going to prove valuable in the emerging field of systems biology.
Chanda, S. K. and J. S. Caldwell (2003). "Fulfilling the promise: drug discovery in the post-genomic era." Drug Discov Today 8(4): 168-74.
The genomic era has brought with it a basic change in experimentation, enabling researchers to look more comprehensively at biological systems. The sequencing of the human genome coupled with advances in automation and parallelization technologies have afforded a fundamental transformation in the drug target discovery paradigm, towards systematic whole genome and proteome analyses. In conjunction with novel proteomic techniques, genome-wide annotation of function in cellular models is possible. Overlaying data derived from whole genome sequence, expression and functional analysis will facilitate the identification of causal genes in disease and significantly streamline the target validation process. Moreover, several parallel technological advances in small molecule screening have resulted in the development of expeditious and powerful platforms for elucidating inhibitors of protein or pathway function. Conversely, high-throughput and automated systems are currently being used to identify targets of orphan small molecules. The consolidation of these emerging functional genomics and drug discovery technologies promises to reap the fruits of the genomic revolution.
Davidov, E., J. Holland, et al. (2003). "Advancing drug discovery through systems biology." Drug Discov Today 8(4): 175-83.
Pharmaceutical companies are facing an urgent need to both increase their lead compound and clinical candidate portfolios and satisfy market demands for continued innovation and revenue growth. Here, we outline an emerging approach that attempts to facilitate and alleviate many of the current drug discovery issues and problems. This is, in part, achieved through the systematic integration of technologies, which results in a superior output of data and information, thereby enhancing our understanding of biological function, chemico-biological interactions and, ultimately, drug discovery. Systems biology is one new discipline that is positioned to significantly impact this process.
den Aantrekker, E. D., R. M. Boom, et al. (2003). "Quantifying recontamination through factory environments--a review." Int J Food Microbiol 80(2): 117-30.
Recontamination of food products can be the origin of foodborne illnesses and should therefore be included in quantitative microbial risk assessment (MRA) studies. In order to do this, recontamination should be quantified using predictive models. This paper gives an overview of the relevant modelling approaches that are available in the literature to quantify recontamination via factory environment. Different recontamination routes are described: recontamination via air, via processing equipment or via hand contact. Unfortunately, not many available models are directly applicable to the food industry; most models are developed for aquatic or environmental systems. Finally, a general systematic approach is proposed for modelling contamination from surfaces via air, hands or liquid into the product and ranges for the parameters are given.
Gielo-Perczak, K. and W. Karwowski (2003). "Ecological models of human performance based on affordance, emotion and intuition." Ergonomics 46(1-3): 310-26.
This paper proposes a complementary approach to Rasmussen's taxonomy of the human skill-, rule-, and knowledge-based performance models by combining the ecological concept of affordances with the neural concepts of human emotion and intuition. The classical cognitive engineering framework is extended through the neuro-ecological approach, including personal human attributes important in exercising control over the work environment. The proposed affordance-, emotion-, and intuition-based models correspond to the three types of human performance, namely: learning, adaptive and tuning control, respectively. The new framework is not a predictive model of the operator behaviour, but rather it describes the processes of neuro-ecological control of the human environment.
Hofmann, H. A. (2003). "Functional genomics of neural and behavioral plasticity." J Neurobiol 54(1): 272-82.
How does the environment, particularly the social environment, influence brain and behavior and what are the underlying physiologic, molecular, and genetic mechanisms? Adaptations of brain and behavior to changes in the social or physical environment are common in the animal world, either as short-term (i.e., modulatory) or as long-term modifications (e.g., via gene expression changes) in behavioral or physiologic properties. The study of the mechanisms and constraints underlying these dynamic changes requires model systems that offer plastic phenotypes as well as a sufficient level of quantifiable behavioral complexity while being accessible at the physiological and molecular level. In this article, I explore how the new field of functional genomics can contribute to an understanding of the complex relationship between genome and environment that results in highly plastic phenotypes. This approach will lead to the discovery of genes under environmental control and provide the basis for the study of the interrelationship between an individual's gene expression profile and its social phenotype in a given environmental context.
Hood, L. and D. Galas (2003). "The digital code of DNA." Nature 421(6921): 444-8.
The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. Two features of DNA structure account for much of its remarkable impact on science: its digital nature and its complementarity, whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information--the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes.
Ibanez, A., C. Blanco, et al. (2003). "Genetics of pathological gambling." J Gambl Stud 19(1): 11-22.
Pathological gambling (PG) is an impulse control disorder and a model 'behavioral' addiction. Familial factors have been observed in clinical studies of pathological gamblers, and twin studies have demonstrated a genetic influence contributing to the development of PG. Serotonergic, noradrenergic, and dopaminergic dysfunction have been reported as biological factors contributing to the pathophysiology of PG. Molecular genetic techniques have been used to investigate the role of genetic factors in PG. Molecular genetic research has identified specific allele variants of candidate genes corresponding to these neurotransmitter systems to be associated with PG. Associations have been reported between pathological gamblers and allele variants of polymorphisms at dopamine receptor genes, the serotonin transporter gene, and the monoamine-oxidase A gene. Although preliminary data suggest that some of these differences are gender-specific, more research needs to be performed to substantiate gender-specific genetic contributions to the development of pathological gambling. The review of the current findings on genetics of PG suggests that liability to PG is in part mediated by genetic factors. Additional studies are needed to replicate and extend these findings, as well as to better understand the influence of specific allelic variants to differences in biological and behavioral functioning.
Lefranc, M. P. (2003). "IMGT databases, web resources and tools for immunoglobulin and T cell receptor sequence analysis, http://imgt.cines.fr." Leukemia 17(1): 260-6.
IMGT, the international ImMunoGeneTics database((R)) (http://imgt.cines.fr), is a high-quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complex (MHC) of human and other vertebrates, created in 1989, by LIGM, at the Universite Montpellier II, CNRS, Montpellier, France. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT includes several databases (IMGT/LIGM-DB, IMGT/3Dstructure-DB, IMGT/HLA-DB), Web resources ('IMGT Marie-Paule page') and interactive tools (IMGT/V-QUEST, IMGT/JunctionAnalysis). IMGT expertly annotated data and tools described in this paper are particularly useful for the analysis of the IG and TR rearrangements in leukemia, lymphoma and myeloma, and in translocations involving the antigen receptor loci. IMGT is freely available at http://imgt.cines.fr.
Locke, M. (2003). "Surface membranes, Golgi complexes, and vacuolar systems." Annu Rev Entomol 48: 1-27.
In the absence of fossils, the cells of vertebrates are often described in lieu of a general animal eukaryote model, neglecting work on insects. However, a common ancestor is nearly a billion years in the past, making some vertebrate generalizations inappropriate for insects. For example, insect cells are adept at the cell remodeling needed for molting and metamorphosis, they have plasma membrane reticular systems and vacuolar ferritin, and their Golgi complexes continue to work during mitosis. This review stresses the ways that insect cells differ from those of vertebrates, summarizing the structure of surface membranes and vacuolar systems, especially of the epidermis and fat body, as a prerequisite for the molecular studies needed to understand cell function. The objective is to provide a structural base from which molecular biology can emerge from biochemical description into a useful analysis of function.
Lord, E. M. (2003). "Adhesion and guidance in compatible pollination." J Exp Bot 54(380): 47-54.
The mechanisms of compatible pollination are less studied than those of incompatible pollination and yet most of the angiosperms show self-compatibility. From the release of pollen from anthers to the penetration of the micropyle by the pollen tube tip, there are numerous steps where the interaction between pollen and the pistil can be regulated. Recent studies have documented some diverse ways in which pollen tubes carrying sperm cells are guided to the ovules through the pistil extracellular matrices of the transmitting tract. What is still missing is an understanding of pollen tube cell biology in vivo. A recent finding supports the role of the synergids in the crucial guidance cue for the pollen tube tip at the micropyle, but experimental evidence for other 'guidepost' cells in the pistil is still lacking. The fact that the pollen tube must first travel through the matrices of the stigma and style before it can respond to the cue from the ovule makes it likely that there is a hierarchy of signalling events in pollen-pistil interactions starting at the stigma and ending at the micropyle. On the pistil side, several model systems have been used in the discovery of molecules implicated in either physical or chemical guidance. In lily, which has a hollow style, adhesion molecules (pectin and SCA) are implicated in guidance. SCA alone is also capable of inducing pollen chemotropism in an in vitro assay, suggesting that this peptide plays a dual role in lily pollination: chemotactic in the stigma and haptotactic (adhesion mediated) in the style.
Mackay, D. and E. Webster (2003). "A perspective on environmental models and QSARs." SAR QSAR Environ Res 14(1): 7-16.
A general review is presented of the roles of QSARs and mass balance models as tools for assessing the environmental fate and effects of chemicals of commerce. It is argued that all such chemicals must be assessed using a consistent and transparent methodology that uses chemical property data derived from QSARs, or experimental determinations when possible and applies evaluative or region-specific environmental models. These data and models enable an assessment to be made of the key chemical features of persistence, bioaccumulation, potential for long-range transport and toxicity. The other key feature is quantity used or discharged to the environment. A taxonomy of environmental models is presented in which it is suggested that rather than develop a single comprehensive model, the aim should be to establish a set of coordinated and consistent models treating evaluative and real environmental systems at a variety of scales from local to global and including food web models, organism-specific models and human exposure and pharmacokinetic models. The concentrations derived from these models can then be compared with levels judged to be of toxic significance. A brief account is given of perceived QSAR needs in terms of partitioning, reactivity, transport and toxicity data to support these models.
Markley, J. L., E. L. Ulrich, et al. (2003). "Macromolecular structure determination by NMR spectroscopy." Methods Biochem Anal 44: 89-113.
Miller, E. S., E. Kutter, et al. (2003). "Bacteriophage T4 genome." Microbiol Mol Biol Rev 67(1): 86-156, table of contents.
Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.
Mueller, U. and S. Huebner (2003). "Economic aspects of amino acids production." Adv Biochem Eng Biotechnol 79: 137-70.
Amino acids represent basic elements of proteins, which as a main source of nutrition themselves serve as a major reserve for maintaining essential functions of humans as well as animals. Taking the recent state of scientific knowledge into account, the industrial sector of amino acids is a priori "suitable" to a specific kind of an ecologically sound way of production, which is based on biotechnology. The following article may point out characteristics of this particular industrial sector and illustrates the applicability of the latest economic methods, founded on development of the discipline of bionics in order to describe economic aspects of amino acids markets. The several biochemical and technological fields of application of amino acids lead to specific market structures in high developed and permanently evolving systems. The Harvard tradition of industrial economics explains how market structures mould the behaviour of the participants and influences market results beyond that. A global increase in intensity of competition confirms the notion that the supply-side is characterised by asymmetric information in contrast to Kantzenbachs concept of "narrow oligopoly" with symmetrical shared knowledge about market information. Departing from this point, certain strategies of companies in this market form shall be derived. The importance of Research and Development increases rapidly and leads to innovative manufacturing methods which replace more polluting manufacturing processes like acid hydrolysis. In addition to these modifications within the production processes the article deals furthermore with the pricing based on product life cycle concept and introduces specific applications of tools like activity based costing and target costing to the field of amino acid production. The authors come to the conclusion that based on a good transferability of latest findings in bionics and ecological compatibility competitors in amino acids manufacturing are well advised to exercise concepts of the management of complex systems in order to choose the right strategy towards gaining market leadership.
Nam, N. H. and K. Parang (2003). "Current targets for anticancer drug discovery." Curr Drug Targets 4(2): 159-79.
The call for the discovery of less toxic, more selective, and more effective agents to treat cancer has become more urgent. Inhibition of angiogenesis continues to be one of the main streams in the current cancer drug discovery activity. Insights into tumor angiogenesis biology have led to the identification of a number of molecules, which are important for the progression of these processes. Of particular interest is a group of growth factors including fibroblast growth factor, platelet-derived growth factor, and vascular endothelial growth factor. These growth factors and their corresponding receptor tyrosine kinases have become important targets for inhibition of the proliferation of endothelial cells, the main component of blood vessels. The validated targets for inhibition of angiogenesis also include a family of matrix metalloproteinases and cell adhesion molecules. In the closely related area, protein kinases have emerged as one of the most important targets for drug discovery. Besides growth factor receptor tyrosine kinases, numerous other protein kinases implicated in malignancies have been identified including non-receptor kinases such as Bcl-Abl and Src kinases. In addition, the cell cycle regulators (cyclin-dependent kinases, p21 gene) and apoptosis modulators (Bcl-2 oncoprotein, p53 tumor suppressor gene, survivin protein, etc) have also attracted renewed interest as potential targets for anticancer drug discovery. Other molecular targets include protein farnesyltransferase (FTase), histone deacetylase (HDAC), and telomerase, which have essential roles in cellular signal transduction pathways (FTase, HDAC) and cell life-span (telomerase). This review presents a comprehensive summary and discussion on the most important targets currently attracting a great deal of interest in contemporary anticancer drug design and discovery. Recent advances complementing these targets are also highlighted.
Nguyen, A. and M. B. Yaffe (2003). "Proteomics and systems biology approaches to signal transduction in sepsis." Crit Care Med 31(1 Suppl): S1-6.
Sepsis and resulting multiple system organ failure are the leading causes of mortality in intensive care units. Although it is generally appreciated that rampant, deregulated inflammatory pathways play a major role in sepsis, a comprehensive understanding based on the integrated response of multiple signal transduction pathways has remained elusive. Here we review the main signal transduction pathways involved in the progression from inflammation to sepsis and discuss emerging genomic, proteomic, and systems biology approaches to decipher how these signaling pathways converge to cause the septic state. We propose that an integrative approach involving functional proteomics will provide a quantitative and mechanistic description that unifies inflammatory signaling networks in sepsis and will identify critical regulatory nodes for therapeutic manipulation. These types of systems biology-based approaches may lead to more effective therapies than those currently available.
Ostenfeld, T. and C. N. Svendsen (2003). "Recent advances in stem cell neurobiology." Adv Tech Stand Neurosurg 28: 3-89.
1. Neural stem cells can be cultured from the CNS of different mammalian species at many stages of development. They have an extensive capacity for self-renewal and will proliferate ex vivo in response to mitogenic growth factors or following genetic modification with immortalising oncogenes. Neural stem cells are multipotent since their differentiating progeny will give rise to the principal cellular phenotypes comprising the mature CNS: neurons, astrocytes and oligodendrocytes. 2. Neural stem cells can also be derived from more primitive embryonic stem (ES) cells cultured from the blastocyst. ES cells are considered to be pluripotent since they can give rise to the full cellular spectrum and will, therefore, contribute to all three of the embryonic germ layers: endoderm, mesoderm and ectoderm. However, pluripotent cells have also been derived from germ cells and teratocarcinomas (embryonal carcinomas) and their progeny may also give rise to the multiple cellular phenotypes contributing to the CNS. In a recent development, ES cells have also been isolated and grown from human blastocysts, thus raising the possibility of growing autologous stem cells when combined with nuclear transfer technology. 3. There is now an emerging recognition that the adult mammalian brain, including that of primates and humans, harbours stem cell populations suggesting the existence of a previously unrecognised neural plasticity to the mature CNS, and thereby raising the possibility of promoting endogenous neural reconstruction. 4. Such reports have fuelled expectations for the clinical exploitation of neural stem cells in cell replacement or recruitment strategies for the treatment of a variety of human neurological conditions including Parkinson's disease (PD), Huntington's disease, multiple sclerosis and ischaemic brain injury. Owing to their migratory capacity within the CNS, neural stem cells may also find potential clinical application as cellular vectors for widespread gene delivery and the expression of therapeutic proteins. In this regard, they may be eminently suitable for the correction of genetically-determined CNS disorders and in the management of certain tumors responsive to cytokines. Since large numbers of stem cells can be generated efficiently in culture, they may obviate some of the technical and ethical limitations associated with the use of fresh (primary) embryonic neural tissue in current transplantation strategies. 5. While considerable recent progress has been made in terms of developing new techniques allowing for the long-term culture of human stem cells, the successful clinical application of these cells is presently limited by our understanding of both (i) the intrinsic and extrinsic regulators of stem cell proliferation and (ii) those factors controlling cell lineage determination and differentiation. Although such cells may also provide accessible model systems for studying neural development, progress in the field has been further limited by the lack of suitable markers needed for the identification and selection of cells within proliferating heterogeneous populations of precursor cells. There is a further need to distinguish between the committed fate (defined during normal development) and the potential specification (implying flexibility of fate through manipulation of its environment) of stem cells undergoing differentiation. 6. With these challenges lying ahead, it is the opinion of the authors that stem-cell therapy is likely to remain within the experimental arena for the foreseeable future. In this regard, few (if any) of the in vivo studies employing neural stem cell grafts have shown convincingly that behavioural recovery can be achieved in the various model paradigms. Moreover, issues relating to the quality control of cultured cells and their safety following transplantation have only begun to be addressed. 7. While on the one hand cell biotechnologists have been quick to realise the potential commercial value, human stem cell research and its clinical applications has been the subject of intense ethical and legislative considerations. The present chapter aims to review some recent aspects of stem cell research applicable to developmental neurobiology and the potential applications in clinical neuroscience.
Patterson, S. D. and R. H. Aebersold (2003). "Proteomics: the first decade and beyond." Nat Genet 33 Suppl: 311-23.
Proteomics is the systematic study of the many and diverse properties of proteins in a parallel manner with the aim of providing detailed descriptions of the structure, function and control of biological systems in health and disease. Advances in methods and technologies have catalyzed an expansion of the scope of biological studies from the reductionist biochemical analysis of single proteins to proteome-wide measurements. Proteomics and other complementary analysis methods are essential components of the emerging 'systems biology' approach that seeks to comprehensively describe biological systems through integration of diverse types of data and, in the future, to ultimately allow computational simulations of complex biological systems.
Plevy, S. and L. Mayer (2003). "Meeting summary: Signal transduction pathways in immune and inflammatory cells. November 30-December 3, 2000, Amelia Island, Florida, U.S.A." Inflamm Bowel Dis 9(1): 28-33.
Throughout this symposium, recurrent themes were highlighted that may provide important clues to the pathogenesis of mucosal inflammation and IBD. First, the mucosal immune system is unique: Studies describing signaling paradigms in peripheral immunocytes should be re-explored in the gut where the rules that govern cell signaling may not be the same. Paradigms are a point of departure to characterize similarities and differences in mucosal immunity. A good example is a differential requirement for costimulation through CD2 in lamina propria T cells compared with peripheral T cells. Furthermore, a new definition of T-cell "costimulation" is beginning to emerge. Costimulatory molecules may function to overcome physical barriers by allowing cognate interactions between other molecules or by targeting signaling complexes to membrane microdomains. This concept also relates to another recurrent theme: Interactions between signaling pathways and the cytoskeleton are functionally important. Finally, we were introduced to the novel concept of metabolic parameters as a readout for signal transduction in the immune system. In the recent past, cell signaling has been viewed as a linear exercise, connecting a cell surface receptor to a series of intermediate molecules to a program of gene expression. However, signal transduction is in fact a three-dimensional exercise in cell biology. The future challenge, as pointed out in the keynote address, is to integrate reductionist models into reality and describe networks of signal transduction pathways in complex biosystems. "Threshold" responses were emphasized, with a small incremental increase or decrease in enzymatic activity leading to an on-off phenomenon referred to as a "molecular switch." In IBD, minute genetically determined differences in enzymatic activity may be critical. This point emphasizes the power of a genetic approach in IBD. Without strong genetic evidence, it is unlikely that fuctional assays will clarify the importance of small differences in enzymatic activity that may have dramatic biologic consequences. This symposium identified recently described signal transduction molecules that may be attractive therapeutic targets in IBD. Characterization of signaling molecules such as SLP-76, SLAM, SAP, and Fyb in the mucosal immune system will be an important area of future research. Ultimately, well-developed scientific hypotheses need to be tested in human beings. This paradigm was perhaps best illustrated by PPARgamma, where reductionist models and mouse experiments have recently lead to small trials suggesting proof of concept in human IBD. This meeting also emphasized a renewed interest in innate immunity in IBD and inflammation research. The role of enteric flora in initiating and perpetuating inflammation in animal models of IBD suggests at some level the importance of the innate immune response. The role of TLRs and bacterial interactions were discussed, as was NF-kappaB as the prominent transcription factor target of innate immune activation. Numerous bridges between innate and adaptive immunity were highlighted, including IL-10, IL-12, IL-18, and IFN-gamma. Their production during an innate immune response can profoundly affect functional T-cell responses in humans. In conclusion, the challenge of understanding signal transduction in IBD is one of integrating well-characterized inflammatory pathways into a complex biologic system that is inhabited by diverse cell types that communicate, and is characterized by interactions with a complex microbial environment. Making sense of this complexity is a daunting task that will require a multifactorial approach utilizing reductionist systems, mouse models, genetic studies, and ultimately human clinical trials.
Ressom, H., R. Reynolds, et al. (2003). "Increasing the efficiency of fuzzy logic-based gene expression data analysis." Physiol Genomics 13(2): 107-17.
DNA microarray technology can accommodate a multifaceted analysis of the expression of genes in an organism. The wealth of spatiotemporal data generated by this technology allows researchers to potentially reverse engineer a particular genetic network. "Fuzzy logic" has been proposed as a method to analyze the relationships between genes and help decipher a genetic network. This method can identify interacting genes that fit a known "fuzzy" model of gene interaction by testing all combinations of gene expression profiles. This paper introduces improvements made over previous fuzzy gene regulatory models in terms of computation time and robustness to noise. Improvement in computation time is achieved by using a cluster analysis as a preprocessing method to reduce the total number of gene combinations analyzed. This approach speeds up the algorithm by a factor of 50% with minimal effect on the results. The model's sensitivity to noise is reduced by implementing appropriate methods of "fuzzy rule aggregation" and "conjunction" that produce reliable results in the face of minor changes in model input.
Rodriguez, J. M., M. I. Martinez, et al. (2003). "Heterologous production of bacteriocins by lactic acid bacteria." Int J Food Microbiol 80(2): 101-16.
Over the last two decades, bacteriocins produced by lactic acid bacteria (LAB) have been the subject of considerable research and industrial interest due to their potential as food biopreservatives. The development of heterologous expression systems for such antimicrobial compounds may offer a number of advantages over native systems, such as facilitating the control of bacteriocin gene expression or achieving higher production levels. In addition, the heterologous production by food-grade LAB offers an attractive method for overcoming some of the adverse situations that may affect the effectiveness of some bacteriocins in food systems. Construction of multibacteriocinogenic strains or acquisition of antimicrobial properties by industrial strains are further objectives that can be achieved through the use of heterologous gene expression systems. The development of new biotechnological tools and recent advances in LAB genetics account for the escalating number of studies dealing with heterologous production of bacteriocins by such hosts. This paper reviews the literature published on the subject and compares the different experimental strategies that have been used up to the present for this purpose.
Sapolsky, R. M. (2003). "Gene therapy for psychiatric disorders." Am J Psychiatry 160(2): 208-20.
There has been tremendous progress in developing techniques for manipulating genetic material, and the birth of gene therapy as a discipline has been one consequence of this. Most considerations of gene therapy in the nervous system have focused on attempts to transfer novel genes in for the purpose of protecting neurons from neurological insults. In this review, the author considers the progress in that field and the possible application of related gene therapy approaches to the far more difficult task of buffering against a psychiatric disorder. As an emphasis, the author reviews how the biology of psychiatric disorders is so often one of vulnerability to particular environments. Because of this context dependency, it would be likely that many possible gene therapeutic interventions would need to be context dependent as well. Thus, the author considers the plausibility of developing gene vector therapies that use conditional expression systems, in particular ones whose expression would be induced by the same environmental perturbations that exacerbate psychiatric symptoms themselves. In particular, the author considers the role of stress as a predisposing factor in certain psychiatric disorders and the ways in which stress signals can be harnessed as inducers of conditional expression systems in gene therapy.
Sato, Y., A. Kadota, et al. (2003). "Chloroplast movement: dissection of events downstream of photo- and mechano-perception." J Plant Res 116(1): 1-5.
The study of chloroplast photorelocation movement is progressing rapidly now that mutants for chloroplast movement have become available in Arabidopsis thaliana. However, mechanistic approaches in cell biology still stand to elucidate the mechanisms and regulations of such movement. The fern Adiantum capillus-veneris and the moss Physcomitrella patens are particularly suitable materials for analyzing the kinetics of intracellular chloroplast movement. In these plants, chloroplast movement is induced by red light as well as blue light, mediated by phytochrome and blue light receptor, respectively. In this paper, we review the unique force-generating system for chloroplast motility in P. patens. In addition to light-induced chloroplast movement, we also summarize mechanically induced chloroplast movement in these plants and the motility systems involved. Finally, the different dependency of mechano- and photo-relocation movement on external Ca(2+) is discussed.
Schaffner, P. and M. M. Dard (2003). "Structure and function of RGD peptides involved in bone biology." Cell Mol Life Sci 60(1): 119-32.
This review focuses on recent papers that describe the involvement of the RGD sequence in bone biology and incorporate the use of synthetic RGD peptides to develop new drugs or control the bioactivity of materials used for bone regeneration. Because in vivo bone function is completely dependent on angiogenesis and vessels, the present publication is focused on physiology, pathophysiology and therapeutics of RGD peptides dedicated to bone cells and endothelial systems. It appears that alphavbeta3, alphavbeta5 and alphaIIbbeta3 are the integrins most reported to be involved in bone function and RGD sequence binding. The specificity of RGD peptides depends on backbone conformation, orientations of the charged side chains of Arg and Asp residues, and hydrophobic moieties flanking the Asp residue. Despite of recent progress in integrins and RGD peptide structures and function, future work should focus on integrin selectivity of RGD-based agents, model structure and activity-selectivity relationships.
Steeg, P. S., D. Palmieri, et al. (2003). "Histidine kinases and histidine phosphorylated proteins in mammalian cell biology, signal transduction and cancer." Cancer Lett 190(1): 1-12.
Intensive investigation of protein tyrosine, serine and threonine phosphorylation has lead to advances in signal transduction research and cancer treatment. This feature summarizes research on mammalian proteins exhibiting histidine phosphorylation. Histidine kinases are well known in prokaryotic and lower eukaryotic systems where they form the 'two-component' signal transduction system. The relative invisibility of histidine phosphorylation in mammalian cells may result from technical obstacles such as its acid lability, which precludes detection in electrophoretic systems, amino acid sequencing, etc. Emerging data have identified mammalian histidine kinases for the kinase suppressor of ras, a scaffold molecule for the Map kinase pathway, as well as histone H4, aldolase C and the beta-subunit of heterotrimeric G proteins. Additional mammalian proteins of interest to signal transduction and cancer research exhibit histidine phosphorylation, including P-selectin, annexin I and the 20S proteasome. Other candidate histidine phosphorylated proteins are identified. These data suggest the existence of another series of phosphorylation patterns in signal transduction.
Strange, K. (2003). "From genes to integrative physiology: ion channel and transporter biology in Caenorhabditis elegans." Physiol Rev 83(2): 377-415.
The stunning progress in molecular biology that has occurred over the last 50 years drove a powerful reductionist approach to the study of physiology. That same progress now forms the foundation for the next revolution in physiological research. This revolution will be focused on integrative physiology, which seeks to understand multicomponent processes and the underlying pathways of information flow from an organism's "parts" to increasingly complex levels of organization. Genetically tractable and genomically defined nonmammalian model organisms such as the nematode Caenorhabditis elegans provide powerful experimental advantages for elucidating gene function and the molecular workings of complex systems. This review has two main goals. The first goal is to describe the experimental utility of C. elegans for investigating basic physiological problems. A detailed overview of C. elegans biology and the experimental tools, resources, and strategies available for its study is provided. The second goal of this review is to describe how forward and reverse genetic approaches and direct behavioral and physiological measurements in C. elegans have generated novel insights into the integrative physiology of ion channels and transporters. Where appropriate, I describe how insights from C. elegans have provided new understanding of the physiology of membrane transport processes in mammals.
Tate, J. (2003). "Molecular visualization." Methods Biochem Anal 44: 135-58.
Valencia, A. and F. Pazos (2003). "Prediction of protein-protein interactions from evolutionary information." Methods Biochem Anal 44: 411-26.
van Blitterswijk, W. J., A. H. van der Luit, et al. (2003). "Ceramide: second messenger or modulator of membrane structure and dynamics?" Biochem J 369(Pt 2): 199-211.
The physiological role of ceramide formation in response to cell stimulation remains controversial. Here, we emphasize that ceramide is not a priori an apoptotic signalling molecule. Recent work points out that the conversion of sphingomyelin into ceramide can play a membrane structural (physical) role, with consequences for membrane microdomain function, membrane vesiculation, fusion/fission and vesicular trafficking. These processes contribute to cellular signalling. At the Golgi, ceramide takes part in a metabolic flux towards sphingomyelin, diacylglycerol and glycosphingolipids, which drives lipid raft formation and vesicular transport towards the plasma membrane. At the cell surface, receptor clustering in lipid rafts and the formation of endosomes can be facilitated by transient ceramide formation. Also, signalling towards mitochondria may involve glycosphingolipid-containing vesicles. Ceramide may affect the permeability of the mitochondrial outer membrane and the release of cytochrome c. In the effector phase of apoptosis, the breakdown of plasma membrane sphingomyelin to ceramide is a consequence of lipid scrambling, and may regulate apoptotic body formation. Thus ceramide formation serves many different functions at distinct locations in the cell. Given the limited capacity for spontaneous intracellular diffusion or membrane flip-flop of natural ceramide species, the topology and membrane sidedness of ceramide generation are crucial determinants of its impact on cell biology.
Volkmann, N. and D. Hanein (2003). "Electron microscopy." Methods Biochem Anal 44: 115-33.
Weiss, J. N., Z. Qu, et al. (2003). "Understanding biological complexity: lessons from the past." Faseb J 17(1): 1-6.
Advances in molecular biology now permit complex biological systems to be tracked at an exquisite level of detail. The information flow is so great, however, that using intuition alone to draw connections is unrealistic. Thus, the need to integrate mathematical biology with experimental biology is greater than ever. To achieve this integration, obstacles that have traditionally prevented effective communication between theoreticians and experimentalists must be overcome, so that experimentalists learn the language of mathematics and dynamical modeling and theorists learn the language of biology. Fifty years ago Alan Hodgkin and Andrew Huxley published their quantitative model of the nerve action potential; in the same year, Alan Turing published his work on pattern formation in activator-inhibitor systems. These classic studies illustrate two ends of the spectrum in mathematical biology: the detailed model approach and the minimal model approach. When combined, they are highly synergistic in analyzing the mechanisms underlying the behavior of complex biological systems. Their effective integration will be essential for unraveling the physical basis of the mysteries of life.
Wimmer, E. A. (2003). "Innovations: applications of insect transgenesis." Nat Rev Genet 4(3): 225-32.
The recent establishment of broadly applicable genetic transformation systems will allow the analysis of gene function in diverse insect species. This will increase our understanding of developmental and evolutionary biology. Furthermore, insect transgenesis will provide new strategies for insect pest management and methods to impair the transmission of pathogens by human disease vectors. However, these powerful techniques must be applied with great care to avoid harm to our environment.
Yu, D. Y., E. N. Su, et al. (2003). "Isolated preparations of ocular vasculature and their applications in ophthalmic research." Prog Retin Eye Res 22(2): 135-69.
The purpose of this review is to outline the techniques and applications for isolated ocular vascular preparations and their significance to ophthalmic research. Various isolated ocular vascular preparations have been utilized in studies of ocular vascular biology, physiology and pharmacology, including work in both normal and diseased conditions. However, there is still significant potential for further studies to improve our understanding of the ocular circulation and its regulation. Experience has shown that there is no single preparation capable of addressing all of the questions that must be answered if a complete understanding of mechanisms of vascular regulation in the eye is to be achieved. Rather, it is necessary to select the appropriate preparation and techniques to address each individual question in the most appropriate manner. In this review, particular emphasis is placed on the applications for isolated ocular preparations and the relevance of such studies to our understanding of the pathogenesis of eye diseases involving the vasculature. Examples are given where therapeutic approaches in diabetes and glaucoma are assessed in terms of their impact on the vasoactive properties of the ocular vasculature.A significant heterogeneity is present in the different parts of the ocular vasculature, not only in the structural and functional properties of vessel itself, but also in terms of the tissue environment and innervation. A single vasoactive agent may also have different effects when applied to the inside or the outside of the same region of a vessel. The vasoactive response of the vascular system as a whole is what determines the rate of blood flow through the system, but this is regulated by a multitude of factors in different regions of the vascular network. Isolating individual components of the ocular vasculature is readily achievable for the extraocular vessels such as the ophthalmic or ophthalmocilliary arteries, which can be studied in myograph type systems measuring the mechanical vasoactive force generated by the vessel. Retinal vessels from very large animals can also be studied in this way, but the small diameter of the retinal vessels in most species requires a perfusion rather than myograph based technique. Perfusion based studies of vessel diameter in response to vasoactive stimuli can be applied to individual retinal arteries and their branches. Perfusion of more complex elements of the ocular vasculature such as isolated segments of the retina or ciliary body, or whole isolated perfused eyes may use the perfusate pressure as the determinant of vasoactive state. However, when several components of the ocular vasculature are being perfused simultaneously it may be difficult to separate out the contribution from the different vascular elements.The advantage of isolated preparations is that systemic influences can be eliminated, and vascular components can be studied that are inaccessible in vivo. The disadvantage is that no matter how well controlled the in vitro environment may be, it will always be a relatively poor mimic of the in vivo conditions. However, such in vitro work has certainly improved our understanding of the vasoactive properties of different regions of the ocular vasculature in both health and disease.