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TGFbeta and Wnt pathway cross-talk.

Transforming growth factor-betas (TGFbeta) and Wnts represent two distinct families of secreted molecules each of which utilizes different signaling pathways to elicit their biological effects. These factors regulate numerous developmental events and mutations in components of both pathways have been described in human cancers including colorectal carcinomas. Several studies have demonstrated that TGFbeta and Wnt ligands can cooperate to regulate differentiation and cell fate determination by controlling gene expression patterns. In addition, their cooperation in promoting tumorigenesis in mice has been described. Here, we focus on reviewing our current understanding of the molecular mechanisms that may mediate these cooperative effects.

Cell Differentiation↗

Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology.

Mycobacterium vanbaalenii PYR-1 was the first bacterium isolated by virtue of its ability to metabolize the high-molecular-weight polycyclic aromatic hydrocarbon (PAH) pyrene. We used metabolic, genomic, and proteomic approaches in this investigation to construct a complete and integrated pyrene degradation pathway for M. vanbaalenii PYR-1. Genome sequence analyses identified genes involved in the pyrene degradation pathway that we have proposed for this bacterium. To identify proteins involved in the degradation, we conducted a proteome analysis of cells exposed to pyrene using one-dimensional gel electrophoresis in combination with liquid chromatography-tandem mass spectrometry. Database searching performed with the M. vanbaalenii PYR-1 genome resulted in identification of 1,028 proteins with a protein false discovery rate of <1%. Based on both genomic and proteomic data, we identified 27 enzymes necessary for constructing a complete pathway for pyrene degradation. Our analyses indicate that this bacterium degrades pyrene to central intermediates through o-phthalate and the beta-ketoadipate pathway. Proteomic analysis also revealed that 18 enzymes in the pathway were upregulated more than twofold, as indicated by peptide counting when the organism was grown with pyrene; three copies of the terminal subunits of ring-hydroxylating oxygenase (NidAB2, MvanDraft_0817/0818, and PhtAaAb), dihydrodiol dehydrogenase (MvanDraft_0815), and ring cleavage dioxygenase (MvanDraft_3242) were detected only in pyrene-grown cells. The results presented here provide a comprehensive picture of pyrene metabolism in M. vanbaalenii PYR-1 and a useful framework for understanding cellular processes involved in PAH degradation.

Bacterial Proteins↗

Recent advances in molecular biology and physiology of the prostaglandin E2-biosynthetic pathway.

Prostanoids represent a group of lipid mediators that are produced from arachidonic acid via the cyclooxygenase pathway. Once formed, the prostanoids are released from the cells and act on their cognate receptors on cell surfaces to exert their biological actions. Of these, prostaglandin E(2) (PGE(2)) is the most common prostanoid, being produced by a wide variety of cells and tissues and has a broad range of bioactivity. Recent advance in this field has led to identification and characterization of a number of enzymes that play roles in the biosynthesis of PGE(2), namely phospholipase A(2), cyclooxygenase and terminal PGE synthase. Each of these three reactions can be rate-limiting and involves multiple enzymes/isozymes that can act in different phases of cell activation and exhibit distinct functional coupling. In this review, we will overview a recent understanding of the molecular biology, regulatory mechanisms, and physiological functions of these enzymes.

Animals↗

A novel endocytic recycling signal distinguishes biological responses of Trk neurotrophin receptors.

Endocytic trafficking of signaling receptors to alternate intracellular pathways has been shown to lead to diverse biological consequences. In this study, we report that two neurotrophin receptors (tropomyosin-related kinase TrkA and TrkB) traverse divergent endocytic pathways after binding to their respective ligands (nerve growth factor and brain-derived neurotrophic factor). We provide evidence that TrkA receptors in neurosecretory cells and neurons predominantly recycle back to the cell surface in a ligand-dependent manner. We have identified a specific sequence in the TrkA juxtamembrane region, which is distinct from that in TrkB receptors, and is both necessary and sufficient for rapid recycling of internalized receptors. Conversely, TrkB receptors are predominantly sorted to the degradative pathway. Transplantation of the TrkA recycling sequence into TrkB receptors reroutes the TrkB receptor to the recycling pathway. Finally, we link these divergent trafficking pathways to alternate biological responses. On prolonged neurotrophin treatment, TrkA receptors produce prolonged activation of phosphatidylinositol 3-kinase/Akt signaling as well as survival responses, compared with TrkB receptors. These results indicate that TrkA receptors, which predominantly recycle in signal-dependent manner, have unique biological properties dictated by its specific endocytic trafficking itinerary.

Amino Acid Sequence↗

Afferent connections and spinal projections of the pressor region in the rostral ventrolateral medulla of the cat.

Following microinjection of wheat germ agglutinin conjugated to horseradish peroxidase (WGA-HRP) into the pressor region of the rostral ventrolateral medulla of the cat, the medulla, pons and hypothalamus were examined for retrogradely labelled cell bodies, while the thoracolumbar segments of the spinal cord were examined for anterogradely labelled axons. Dense groups of labelled cells were found in the following areas: (1) the nucleus of the solitary tract, particularly the medial, ventrolateral and commissural subnuclei; (2) the ambiguous complex and immediately surrounding area; (3) the Kölliker-Fuse nucleus in the pons; (4) the paraventricular nucleus and lateral hypothalamic area. In the spinal cord, labelled axons formed a band extending throughout the dorsolateral and ventrolateral funiculi at thoracic segments, while terminal labelling was observed in the intermediolateral nucleus and to a lesser extent the central autonomic area, but not in other parts of the grey matter. The findings are discussed in relation to the role of the rostral ventrolateral medulla in cardiovascular regulation, particularly the baroreceptor reflex.

Afferent Pathways↗

Alternate FGF2-ERK1/2 signaling pathways in retinal photoreceptor and glial cells in vitro.

Basic fibroblast growth factor (FGF2) stimulates photoreceptor survival in vivo and in vitro, but the molecular signaling mechanism(s) involved are unknown. Immunohistochemical and immunoblotting analyses of pure photoreceptors, inner retinal neurons, and Müller glial cells (MGC) in vitro revealed differential expression of the high affinity FGF receptors (FGFR1-4), as well as many cytoplasmic signaling intermediates known to mediate the extracellular signal-regulated kinase (ERK1/2) pathway. FGF2-induced tyrosine phosphorylation in vitro exhibited distinct profiles for each culture type, and FGF2-induced ERK1/2 activation was observed for all three preparations. Whereas U0126, a specific inhibitor of ERK kinase (MEK), completely abolished FGF2-induced ERK1/2 tyrosine phosphorylation and survival in cultured photoreceptors, persistent ERK1/2 phosphorylation was observed in cultured inner retinal cells and MGC. Furthermore U0126 treatment entirely blocked nerve growth factor-induced ERK1/2 activation in MGC, as well as FGF2-induced ERK1/2 activation in cerebral glial cells. Taken together, these data indicate that FGF2-induced ERK1/2 activation is entirely mediated by MEK within photoreceptors, which is responsible for FGF2-stimulated photoreceptor survival. In contrast, inner retina/glia possess alternative, cell type, and growth factor-specific MEK-independent ERK1/2 activation pathways. Hence signaling and biological effects elicited by FGF2 within retina are mediated by cell type-specific pathways.

Animals↗

Advanced computing for systems biology.

Systems biology is based on computational modelling and simulation of large networks of interacting components. Models may be intended to capture processes, mechanisms, components and interactions at different levels of fidelity. Input data are often large and geographically disperse, and may require the computation to be moved to the data, not vice versa. In addition, complex system-level problems require collaboration across institutions and disciplines. Grid computing can offer robust, scaleable solutions for distributed data, compute and expertise. We illustrate some of the range of computational and data requirements in systems biology with three case studies: one requiring large computation but small data (orthologue mapping in comparative genomics), a second involving complex terabyte data (the Visible Cell project) and a third that is both computationally and data-intensive (simulations at multiple temporal and spatial scales). Authentication, authorisation and audit systems are currently not well scalable and may present bottlenecks for distributed collaboration particularly where outcomes may be commercialised. Challenges remain in providing lightweight standards to facilitate the penetration of robust, scalable grid-type computing into diverse user communities to meet the evolving demands of systems biology.

Animals↗

Metabolomics of a superorganism.

The human can be thought of as a human-microbe hybrid, and the health of this superorganism will be affected by intrinsic properties such as human genetics, diurnal cycles, and age and by extrinsic factors such as lifestyle choices (food and drink, drug intake) and the acquisition of a stable "healthy" gut microflora (the so-called microbiome). Alterations in this superorganism will be manifest in the metabolite complement within its serum and urine samples. The unraveling of this metabolic compartmentalization in this complex ecosystem will certainly be a challenge for systems biology and necessary for defining human health at the molecular level. Within the systems biology framework, functional analyses at the level of gene expression (transcriptomics), protein translation (proteomics), and, more recently, the metabolite network (metabolomics) have become increasingly popular. Metabolomics experiments aim to quantify all metabolites in a cellular system (cell or tissue) under defined states and at different time points so that the dynamics of any biotic, abiotic, or genetic perturbation can be accurately assessed. This article provides an overview of metabolomics and discusses how data are generated and analyzed within a systems biology framework. The role of metabolomics in nutrigenomics is also discussed, as are the concepts of the human being a superorganism and the complexities required to be overcome to understand human health and disease.

Animals↗

The primary projections of the lateral-line nerves of the Florida gar, Lepisosteus platyrhincus.

Gars, like most other ray-finned fishes, possess lines of superficial and canal neuromasts that form highly ordered spatial arrays on the head and trunk. These neuromasts are innervated by three pairs of cranial nerves: anterior, middle and posterior lateral-line nerves. Application of horseradish peroxidase to the roots of these nerves indicates that the afferent fibers of each nerve terminate throughout the rostrocaudal extent of the ipsilateral octavolateralis column, composed of medial and caudal octavolateralis nuclei, as well as rostrally in the eminentia granularis of the cerebellum. The afferents of each nerve terminate within different regions of these nuclei, thus preserving a rostrocaudal somatotopy of the peripheral receptors. The individual rami of these nerves innervate peripheral receptors in a dorsoventral sequence; however, application of horseradish peroxidase to these rami indicates an almost total overlap of the terminal fields of adjacent rami and, thus, little or no preservation of dorsoventral somatotopy of the peripheral receptors. Similarly, the terminal fields of fibers that innervate canal and superficial neuromasts overlap extensively, and there is no evidence for separate maps of canal and superficial neuromasts. Furthermore, the position of the terminal fields of superficial neuromasts is not consistent with a hypothesis that these receptors may have evolved into electroreceptors in some teleosts. However, these experiments do indicate that superficial neuromasts, like canal neuromasts, are innervated by efferent fibers of rostral and caudal efferent nuclei, but there is no evidence of a diencephalic efferent nucleus as occurs in teleosts.

Afferent Pathways↗

Revealing hidden relationships among yeast genes involved in chromosome segregation using systematic synthetic lethal and synthetic dosage lethal screens.

The vast accumulation of knowledge from genome sequencing projects and studies with model organisms has presented a remarkable challenge to biologists: to understand the functions of thousands of highly conserved genes and how they work together to regulate fundamental cellular processes. This challenge is compounded by the inescapable reality that most genes are 'buffered' by other genes that contribute to the same biological processes, limiting the impact of phenotypic studies with single mutants. In budding yeast, functional genomic methods have been developed for the systematic application of established genetic techniques. In particular, the Synthetic Genetic Array (SGA) method allows genome-wide synthetic lethal (SL) and synthetic dosage lethal (SDL) screens thus enabling an unbiased survey of genetic interactions. We have used genes encoding components of the yeast kinetochore as a biological testbed for assaying the utility of SGA-based SL and SDL screens for revealing new pathways and genes involved in chromosome segregation. We identified 211 nonessential deletion mutants that were unable to tolerate either overexpression or loss of function of kinetochore genes. Our study uncovered a wealth of relationships between gene products that functionally interact with the kinetochore, and also highlighted the value of performing genome-wide screens with both hypomorphic and hypermorphic alleles of query genes. Here, we will highlight our recent kinetochore SGA genomic screens, in the broader context of applying complementary genetic screening approaches in the systematic exploration of biological pathways or functional complexes.

Cell Division↗

[Influence of Smad4-independent pathway of transforming growth factor beta1 on the biological activity of pancreatic cancer cells].

OBJECTIVE: To study effects of the expression of transforming growth factor (TGF)-beta1 on the growth of Smad4-null pancreatic cancer cells. METHODS: TGF-beta1 eukaryotic expression vector was transfected into pancreatic cancer cell line BxPC3. Effects of the expressison of TGF-beta1 was studied by growth curve analysis and flow cytometry. Cell motility was monitored by wound-healing assay. Western blot was used to estimate the expression level of p21(WAF/CLIP1), a cyclin-dependent kinase inhibitor. RESULTS: Transfection of TGF-beta1 changed the morphology of BxPC3 into spindle shaped cells. The growth rate of BxPC3 began to decrease after the fourth day of TGF-beta1 transfection, compared with the control groups. Flow cytometry showed that the percentages of cells in the S phase were (27.53 +/- 0.02)%, (26.32 +/- 0.01)% and (17.01 +/- 0.03)% in naïve BxPC3, vector-control group and TGF-beta1 transfection group respectively. Lesser cells entered the S phase after TGF-beta1 transfection (P < 0.01), but no difference was seen between the BxPC3 and vector groups (P > 0.05). The expression of p21(WAF/CLIP1) increased upon the expression of TGF-beta1. CONCLUSION: The Smad4-independent pathway of TGF-beta1 not only induces epithelial-mesenchymal transition in pancreatic cancer BxPC3, but also inhibits its growth through the up-regulation of p21(WAF/CLIP1).

Cell Line, Tumor↗

The vitamin D3 pathway in human skin and its role for regulation of biological processes.

The skin is the only tissue yet known in which the complete ultraviolet-B (UV-B)-induced pathway from 7-dehydrocholesterol to hormonally active calcitriol (1alpha,25-dihydroxyvitamin D(3)) occurs under physiological conditions. Epidermal synthesis of calcitriol could be of fundamental relevance because calcitriol regulates important cellular functions in keratinocytes and immunocompetent cells. Because of their antiproliferative and prodifferentiating effects, calcitriol and other vitamin D analogs are highly efficient in the treatment of psoriasis vulgaris. The known antipsoriatic effect of UV-B light could, at least in part, be mediated via UV-B-induced synthesis of calcitriol. In addition, mounting evidence indicates that cutaneous vitamin D(3) synthesis is of high importance for the prevention of a broad variety of diseases, including various malignancies. New but controversially discussed sun-protection guidelines were established for the prevention of internal cancers. A better understanding of the metabolism of vitamin D in the skin opens new perspectives for therapeutic applications of vitamin D analogs.

Cholecalciferol↗

Periodontal inflammation: from gingivitis to systemic disease?

There has been a resurgence of interest in recent years in the systemic effects of oral infections such as periodontal diseases. The study of the various means by which periodontal infections and inflammation may influence a variety of systemic conditions is collectively referred to as periodontal medicine. The periodontium responds to tooth-borne biofilm (dental plaque) by the process of inflammation. Dental biofilms release a variety of biologically active products, such as bacterial lipopolysaccharides (endotoxins), chemotactic peptides, protein toxins, and organic acids. These molecules stimulate the host to produce a variety of responses, among them the production and release of potent agents known as cytokines. These include interleukin-1 beta, interleukin-8, prostaglandins, and tumor necrosis factor-alpha. There is a spectrum of periodontal response to these molecules, from mild gingivitis to severe destructive periodontitis. These and other host products and responses may influence a variety of important disease pathways, including atherosclerosis, mucosal inflammation, and premature parturition. The purpose of this article is to review the possible biological pathways by which periodontal diseases may influence these disease processes.

Animals↗

Non-cell autonomous RNA silencing.

In plants and in some animals, the effects of post-transcriptional RNA silencing can extend beyond its sites of initiation, owing to the movement of signal molecules. Although the mechanisms and channels involved are different, plant and animal silencing signals must have RNA components that account for the nucleotide sequence-specificity of their effects. Studies carried out in plants and Caenorhabditis elegans have revealed that non-cell autonomous silencing is operated through specialized, remarkably sophisticated pathways and serves important biological functions, including antiviral immunity and, perhaps, developmental patterning. Recent intriguing observations suggest that systemic RNA silencing pathways may also exist in higher vertebrates.

Animals↗

Identifying active transcription factors and kinases from expression data using pathway queries.

MOTIVATION: Although progress has been made identifying regulatory relationships from expression data in general, only few methods have focused on detecting biological mechanisms like active pathways using a single measurement. This is of particular importance when only few measurements are available, e.g. if special cell types or conditions are under investigation. Here we present a method to test user specified hypotheses (pathway queries) on expression data where prior knowledge is given in the form of networks and functional annotations. Based on this method, we develop a scoring function to identify active transcription factors or kinases, thus making a first step toward explaining the measured expression data. RESULTS: We apply the algorithm to the Rosetta Yeast Compendium dataset, finding that in many cases the results are in concordance with biological knowledge. We were able to confirm that transcription factors and to a lesser degree, kinases identified by our method play an important role in the biological processes affected by the respective knockouts. Furthermore, we show that correlation of inferred activities can provide evidence for a physical interaction or cooperation of transcription factors where correlation of plain expression data fails to do so.

Algorithms↗

Different signal transduction pathways are involved during human sperm capacitation induced by biological and pharmacological agents.

Human sperm capacitation involves complex signal transduction mechanisms during which double phosphorylation of the threonine-glutamine-tyrosine motif (P-Thr-Glu-Tyr-P) occurs in some sperm proteins. The objective of this study was to investigate the regulation of this process. Fetal cord serum ultrafiltrate (FCSu), follicular fluid ultrafiltrate (FFu), progesterone and a combination of N(6),2'-O-dibutyryl cAMP (dbcAMP; cell permeant analogue of cAMP) and 3-isobutyl-1-methylxanthine (IBMX; phosphodiesterase inhibitor) were used as inducers of capacitation alone or in combination with inhibitors of protein kinase A (H89), protein kinase C (chelerythrine), protein tyrosine kinase (tyrphostin A47, PP2) and of dual specificity kinase (MEK-like kinases; PD98059). The level of P-Thr-Glu-Tyr-P in sperm proteins of 80 and 105 kDa during capacitation induced by FCSu, FFu and progesterone was regulated by a similar signal transduction pathway and involved receptor type protein tyrosine kinase and dual specificity kinase (MEK or MEK-like) but not protein kinase A or C. However, the level of P-Thr-Glu-Tyr-P in these sperm proteins during capacitation induced by dbcAMP+IBMX was mainly mediated through protein kinase A and C and receptor type protein tyrosine kinase, but not by dual specificity kinase. In conclusion, human sperm capacitation induced by some biological and pharmacological agents is regulated through very different signal transduction pathways.

1-Methyl-3-isobutylxanthine↗

Amphotericin B: a biological response modifier in targeting against the salvage pathways.

Dipyridamole, a nucleoside transport inhibitor which blocks the rescue effect of exogenous nucleosides, is a compound of interest for use in combination with antimetabolites of de novo purine and pyrimidine biosynthesis. This study has provided evidence that the dipyridamole inhibitory effect on nucleoside incorporation varied markedly during the course of cell growth in culture. Human colon cancer HT-29 cells in lag and log phases were highly sensitive to the blocking action of dipyridamole on thymidine incorporation with IC50 values of 0.06 and 0.07 microM respectively. In contrast, stationary phase cells were comparatively insensitive to dipyridamole with an IC50 of 46 microM. Amphotericin B restored the sensitivity of stationary phase cells to dipyridamole, lowering the IC50 value for thymidine incorporation to 0.03 microM. A similar pattern was observed for cytidine incorporation. Amphotericin B also enhanced the growth inhibitory action of dipyridamole in stationary phase cells. The combination of amphotericin B and dipyridamole should be potentially useful in cancer chemotherapy.

Amphotericin B↗

Systems biology of the human red blood cell.

While the potential possibilities of systems biology appear to hold great promise, there are still many challenges to overcome, notably lack of complete characterization of biological components and their interactions and ways to measure these changes experimentally. The comparative simplicity of the human red cell sidesteps much of these challenges. Detailed models of human red cell metabolism have been developed for the last quarter century and continued development of these models has resulted in the ability to make functional phenotype predictions, in silico. Additionally, existing experimental proteomic and metabolomic technologies now provide the capability to perform individualized characterization of erythrocytes. While an experimentally testable systems biology model of most human cells is presently out of reach, it may be achievable with the red cell.

Computational Biology↗