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At least 1,207 records · Page 67Linked to original sources
PubMed2005

Hormonal influences on cancer progression and prognosis.

Cell differentiation, proliferation, apoptosis, and cell motility are induced and regulated by a host of growth factors, vitamins, and hormones. The mode of function of these modifiers of biological response, the signaling pathways that they activate, and the interacting pathways that can influence the biological outcome have been the focus of attention. Especially recognized and discussed in this review is the deregulation of their function, leading to abnormalities in cell proliferation, alteration of intercellular adhesive cohesion, remodeling of the extracellular matrix, and invasive behavior and metastatic deposition that are so characteristic of tumor development and progression, which strongly underscores the concept of molecular progression of cancer constructed on the basis of the relationship between genetic changes and the biological events associated with cancer progression. The molecular changes associated with hormone- and vitamin-driven responses and the deregulation of the expression and function of their target genes seem to correlate with specific biological events linked with cancer invasion and progression, and these findings could lead to the establishment of new markers of progression and to the development of new strategies for patient management. The scope of this work has been restricted by design and is dictated by the field of interest of the author's laboratory, but it is hoped that this field would be regarded adequately to reflect the wide genre of scientific interest in this field of human disease.

Animals↗
PubMed2006

Time-dependent sensitivity analysis of biological networks: coupled MAPK and PI3K signal transduction pathways.

Sensitivity analysis has been widely used in the studies of complicated chemical reaction and biological networks, for example, in combustion studies and metabolic control analysis of pathways. In the latter cases, the responses of system properties at steady states with respect to changes of parameters, such as initial concentrations and rate constants, are often expressed as sensitivities. Besides steady-state sensitivities, time-dependent sensitivities should be useful; however, the explicit use of them in analyzing complicated biological systems has so far been limited. Using the coupled mitogen activated protein kinase (MAPK)-phophatidylinoisitol 3'-kinase (PI3K) system of the Ras pathways, known to be involved in about 30% of human cancers, as an example, we show that time-dependent sensitivities are useful for the studies of complex biological systems. They provide, for example, the following information: (a) multiple time scales existing in a complex system involving cross-talks and feedback loops; (b) the signs and strengths of responses to perturbations (as system complication increases, the signs of global responses are not always easily determined; for example, response may change sign more than once as time evolves); (c) beyond concentration dynamics, sensitivities revealing further details about the intricate dynamics and the effects of the cross-talks; (d) ranking of vulnerability of nodes of a biological network using integrated sensitivity-a first step toward the identification of drug targets; (e) reduced sensitivity serving as a measure of the stability or robustness of pathways. Our results indicate that the role of the PI3K branch in the coupled pathways is to enhance the robustness of the MAPK pathway. More importantly, they demonstrate that time-dependent sensitivity analysis can be a valuable tool in system biology.

Mitogen-Activated Protein Kinases↗
PubMed2002

Bioinformatics of large-scale protein interaction networks.

We survey recent techniques for construction and prediction of large-scale protein interaction networks, focusing on computational processing steps. Special emphasis is placed on critical assessment of data completeness and reliability of the various approaches. Once built, protein interaction networks can be used for functional annotation or to generate higher-level biological hypotheses on pathways.

Bacterial Proteins↗
PubMed2003

Biological stratification of human neuroblastoma by complex "B" pathway ganglioside expression.

Ganglioside metabolism has been linked to the clinical and biological behavior of human neuroblastoma. This study investigated the importance of differences in complex "b" ganglioside (GD1b, GT1b, and GQ1b; designated CbG) expression in this tumor. Gangliosides of 74 neuroblastomas were analyzed by high-performance TLC. Associations of CbG expression with known prognostic markers and with event-free survival (EFS) were evaluated. Higher CbG expression characterized nonprogressive versus progressive tumors (median 41% versus 18% of total gangliosides; P = 0.001) and completely accounted for the observed higher overall "b" pathway ganglioside expression (median 81% versus 68%; P = 0.003). In contrast, expression of the structurally simpler "b" pathway gangliosides (GD2 and GD3) did not differ (median 31% versus 35%; P = 0.4). Absolute CbG content differed even more (median 93 versus 29 nmol/g among nonprogressive versus progressive tumors; P = 0.02) and was most striking in the case of GQ1b content (8-fold higher in nonprogressive tumors). High CbG (> or =35% of total gangliosides) expression was strongly predictive of a favorable outcome in: (a) the entire study population (90% versus 60% EFS at 25 months; P = 0.001); and (b) among patients assigned a low-risk status by a either single genetic or biochemical tumor marker (MYCN, DNA, NSE, or ferritin), or by both unamplified MYCN and aneuploid DNA (22-28% difference in EFS at 25 months). These data suggest that high tumor CbG content may substratify "good prognosis" neuroblastoma patients, identifying patients at very low risk of relapse or death, and that the biological roles of CbG in neuroblastoma will be of importance to define.

Carbohydrate Sequence↗
PubMed2003

Biomimetic modelling.

Biomimetics is seen as a path from biology to engineering. The only path from engineering to biology in current use is the application of engineering concepts and models to biological systems. However, there is another pathway: the verification of biological mechanisms by manufacture, leading to an iterative process between biology and engineering in which the new understanding that the engineering implementation of a biological system can bring is fed back into biology, allowing a more complete and certain understanding and the possibility of further revelations for application in engineering. This is a pathway as yet unformalized, and one that offers the possibility that engineers can also be scientists.

Biomimetics↗
PubMed1998

Generation of biologically active IL-1 beta by matrix metalloproteinases: a novel caspase-1-independent pathway of IL-1 beta processing.

Biologic activity of IL-1 beta requires processing of the inactive precursor, a function generally ascribed to IL-1 beta-converting enzyme (caspase-1). However, alternative mechanisms of IL-1 beta activation have been postulated in local inflammatory reactions. Expression of IL-1 beta and matrix metalloproteinases (MMPs) frequently occurs simultaneously at sites of inflammation. We describe here that stromelysin-1 (MMP-3), as well as the gelatinases A (MMP-2) and B (MMP-9), processes recombinant human IL-1 beta precursor (pIL-1 beta) into biologically active forms. Detection of both pIL-1 beta processing and biologic IL-1 beta activity demonstrated different processing capacities of the respective MMPs. Conversion of pIL-1 beta by stromelysin-1 required coincubation for at least 1 h, and biologic activity faded after 8 h to 24 h. Gelatinase A was less effective in processing pIL-1 beta, requiring at least 24 h of coincubation. In contrast, gelatinase B processed pIL-1 beta within minutes, resulting in immunoreactive products as well as biologic activity stable for 72 h. In addition, prolonged incubation of mature IL-1 beta with stromelysin-1, and to a lesser extent also with gelatinases, but not with interstitial collagenase, resulted in the degradation of mature IL-1 beta. None of the MMPs processed the second isoform of IL-1, IL-1 alpha. The present study indicates a biphasic regulation of IL-1 beta activity by MMPs: a caspase-1-independent pathway of IL-1 beta activation and inhibition of IL-1 beta activity by degrading the mature cytokine. The balance of the respective MMPs and pIL-1 beta might regulate the long term appearance of IL-1 beta activity at sites of acute or chronic inflammation.

Animals↗
PubMed2003

Energetics of protein transport across biological membranes. a study of the thylakoid DeltapH-dependent/cpTat pathway.

Among the pathways for protein translocation across biological membranes, the DeltapH-dependent/Tat system is unusual in its sole reliance upon the transmembrane pH gradient to drive protein transport. The free energy cost of protein translocation via the chloro-plast DeltapH-dependent/Tat pathway was measured by conducting in vitro transport assays with isolated thylakoids while concurrently monitoring energetic parameters. These experiments revealed a substrate-specific energetic barrier to cpTat-mediated transport as well as direct utilization of protons from the gradient, consistent with a H+/protein antiporter mechanism. The magnitude of proton flux was assayed by four independent approaches and averaged 7.9 x 10(4) protons released from the gradient per transported protein. This corresponds to a DeltaG transport of 6.9 x 10(5) kJ.mol protein translocated(-1), representing the utilization of an energetic equivalent of 10(4) molecules of ATP. At this cost, we estimate that the DeltapH-dependent/cpTat pathway utilizes approximately 3% of the total energy output of the chloroplast.

Adenosine Triphosphate↗
PubMed1999

Receptors of the glial cell line-derived neurotrophic factor family of neurotrophic factors signal cell survival through the phosphatidylinositol 3-kinase pathway in spinal cord motoneurons.

The members of the glial cell line-derived neurotrophic factor (GDNF) family of neurotrophic factors (GDNF, neurturin, persephin, and artemin) are able to promote in vivo and in vitro survival of different neuronal populations, including spinal cord motoneurons. These factors signal via multicomponent receptors that consist of the Ret receptor tyrosine kinase plus a member of the GDNF family receptor alpha (GRFalpha) family of glycosylphosphatidylinositol-linked coreceptors. Activation of the receptor induces Ret phosphorylation that leads the survival-promoting effects. Ret phosphorylation causes the activation of several intracellular pathways, but the biological effects caused by the activation of each of these pathways are still unknown. In the present work, we describe the ability of the GDNF family members to promote chicken motoneuron survival in culture. We show the presence of Ret and GFRalpha-1, GFRalpha-2, and GFRalpha-4 in chicken motoneurons using in situ hybridization and reverse transcription-PCR techniques. By Western blot analysis and kinase assays, we demonstrate the ability of these factors to induce the phosphatidylinositol 3 kinase (PI 3-kinase) and the extracellular regulated kinase (ERK)-mitogen-activated protein (MAP) kinase pathways activation. To characterize the involvement of these pathways in the survival effect, we used the PI 3-kinase inhibitor LY 294002 and the MAP kinase and ERK kinase (MEK) inhibitor PD 98059. We demonstrate that LY 294002, but not PD 98059, prevents GDNF-, neurturin-, and persephin-induced motoneuron survival, suggesting that PI 3-kinase intracellular pathway is responsible in mediating the neurotrophic effect.

Animals↗
PubMed2003

Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis.

Huge advances in plant biology are possible now that we have the complete genome sequences of several flowering plants. Now, genomes can be comprehensively compared and map-based cloning can be performed more easily. Association study is emerging as a powerful method for the functional identification of genes and molecular genetics has begun to reveal the basis of plant diversity. Taking the flowering pathways as an example, we discuss the potential of several approaches to comparative biology.

Arabidopsis↗
PubMed1984

Transmembrane delivery of polypeptide hormones bypassing the intrinsic cell surface receptors: a conjugate of insulin with alpha 2-macroglobulin (alpha 2M) recognizing both insulin and alpha 2M receptors and its biological activity in relation to endocytic pathways.

125I-labeled insulin has been cross-linked to alpha 2-macroglobulin (alpha 2M) via a disulfide bond. The resulting insulin-alpha 2M conjugate carried 2.2 insulin moieties per mole of alpha 2M and was able to deliver insulin into rat hepatoma cells H35 and HTC. The insulin delivery was mediated predominantly through alpha 2M receptors and 2 h after binding it was found in the lyposomal fractions in the form of conjugate. When the conjugate was applied to rat hepatoma cells it stimulated activity of tyrosine aminotransferase (TAT) with a potency one-half that of native insulin. Hepatoma cells which were treated with conjugate in the presence of bacitracin were also stimulated for TAT activity. Since bacitracin completely inhibited the alpha 2M binding to its receptors, but inhibited conjugate binding by only 80%, this stimulation must have resulted from the remaining binding of conjugate. These results indicate that the insulin-alpha 2M conjugate was biologically active if it bound to insulin receptors, but that the conjugate bound and internalized through alpha 2M receptors did not act as a mediator for TAT activation. Our results using Percoll density gradients indicate a difference in intracellular processing between insulin, alpha 2M and the conjugate. Mechanisms of action of the conjugate are discussed in relation to the receptor-mediated endocytic pathways.

Animals↗
PubMed2005

Probability current in protein electron transfer reactions: a Green function pathway model.

In a biological electron transfer reaction problem we have found distinct electron probability current representations of macromolecular currents, amino acid and interamino acid currents, atomic and interatomic currents. We present a general interatomic current approach to obtain the electron probability current from donor to acceptor sites, and vice versa. Symmetric (or antisymmetric) renormalizable interatomic currents provide exact (or approximate) effective tunneling matrix element between donor and acceptor states. The electron probability currents allow us to investigate stationary tunneling pathways through protein bridge medium, from molecular to subatomic resolution at any level of electronic description of the biological structure. Analytical comparison among interatomic pathway models is presented and we found equivalent interatomic current representations with distinct dependence on the tunneling energy from the weak to strong coupling between protein bridge and the donoracceptor sites.

Electron Transport↗
PubMed2005

Synthesis and trafficking of alkaloid biosynthetic enzymes.

The biosynthesis of plant natural products involves a large number of enzymes that create and elaborate a bewildering array of chemical structures, which are generally involved in ecophysiological interactions. Alkaloids are one of the largest groups of natural products and are generally produced through an assortment of intricate pathways. The application of molecular biochemical approaches to investigate the cell biology of alkaloid pathways has revealed a paradigm for the complex, yet highly ordered, organization of biosynthetic enzymes at both the cellular and subcellular levels. Many different cell types have been implicated in alkaloid formation and storage, in one case suggesting the intercellular transport of enzymes. The localization of enzymes to numerous cellular compartments shows the importance of protein targeting in the assembly of alkaloid pathways. Recent studies have also pointed to the possible interaction of biosynthetic enzymes in multi-enzyme complexes. These processes must be considered to be integral components of the mechanisms that regulate alkaloid biosynthesis and perhaps other natural product pathways.

Alkaloids↗
PubMed2006

Distribution and interrelationship of ubiquitin proteasome pathway component activities and ubiquitin pools in various porcine tissues.

The ubiquitin-proteasome pathway fulfills major biological functions, but its physiologic tissue distribution and the interrelationship between pathway component activities and ubiquitin pools are unknown. Therefore, we analyzed free and conjugated ubiquitin, ubiquitin-protein ligation rates (UbPL) and chymotryptic- and tryptic-like proteasome peptidase activities in porcine skeletal muscle, heart, lung, liver, spleen and kidney (n=5 each). There were considerable differences between tissues (p<0.05 for all parameters). Lung and spleen showed high levels of free and conjugated ubiquitin and high UbPL. Proteasome activities were highest in kidney and heart. There were linear relationships between tryptic-like and chymotryptic-like proteasome peptidase activities (r(2) = 0.624, p<0.001) and between free and conjugated ubiquitin tissue levels (r(2) = 0.623, p<0.001). Tissue levels of free and conjugated ubiquitin correlated linear with UbPL (p<0.005), but they were not correlated with proteasome peptidase activities. The results suggest that tissue ubiquitin pools are tightly regulated and indicate a constant proportion of conjugated ubiquitin. They further support the hypothesis that ubiquitin-protein ligase systems, and probably deubiquitylating enzymes, are key regulators of ubiquitin homeostasis. The detected differences are suggestive of tissue-specific roles of ubiquitin-proteasome pathway components. Besides the known importance of the ubiquitin proteasome pathway in heart, kidney and the immune system, the results suggest the lung as another organ in which ubiquitin proteasome pathway components may also significantly contribute to disease processes.

Animals↗
PubMed2004

Cytokine therapy for craniosynostosis.

The birth prevalence of craniosynostosis (premature suture fusion) is 300-500 per 1,000,000 live births. Surgical management involves the release of the synostosed suture. In many cases, however, the suturectomy site rapidly reossifies, further restricts the growing brain and alters craniofacial growth. This resynostosis requires additional surgery, which increases patient morbidity and mortality. New findings in bone biology and molecular pathways involved with suture fusion, combined with novel tissue engineering techniques, may allow the design of targeted and complementary therapies to decrease complications inherent in high-risk surgical procedures. This paper selectively reviews recent advances in i) identifying genetic mutations and the aetiopathogenesis of a number of craniosynostotic conditions; ii) cranial suture biology and molecular biochemical pathways involved in suture fusion; and iii) the design, development and application of various vehicles and tissue engineered constructs to deliver cytokines and genes to cranial sutures. Such biologically based therapies may be used as surgical adjuncts to rescue fusing sutures or help manage postoperative resynostosis.

Child↗
PubMed2003

Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate.

Onto-Tools is a set of four seamlessly integrated databases: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Onto-Express is able to automatically translate lists of genes found to be differentially regulated in a given condition into functional profiles characterizing the impact of the condition studied upon various biological processes and pathways. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. Once the initial exploratory analysis identified a number of relevant biological processes, specific mechanisms of interactions can be hypothesized for the conditions studied. Currently, many commercial arrays are available for the investigation of specific mechanisms. Each such array is characterized by a biological bias determined by the extent to which the genes present on the array represent specific pathways. Onto-Compare is a tool that allows efficient comparisons of any sets of commercial or custom arrays. Using Onto-Compare, a researcher can determine quickly which array, or set of arrays, covers best the hypotheses studied. In many situations, no commercial arrays are available for specific biological mechanisms. Onto-Design is a tool that allows the user to select genes that represent given functional categories. Onto-Translate allows the user to translate easily lists of accession numbers, UniGene clusters and Affymetrix probes into one another. All tools above are seamlessly integrated. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html.

Databases, Nucleic Acid↗
PubMed1998

Fibroblast growth factor 2 uses PLC-gamma1 for cell proliferation and PI3-kinase for alteration of cell shape and cell proliferation in corneal endothelial cells.

PURPOSE: Fibroblast growth factor 2 (FGF-2) induces endothelial-mesenchymal modulation in corneal endothelial cells, including stimulation of cell proliferation and cell shape change and induction of fibrillar collagen. In the present study, we investigated whether FGF-2 uses distinct signaling pathways for individual biological activities. METHODS: Specific metabolic inhibitors were used to block cell proliferation, while reversion of cellular morphology (modulated with FGF-2) was determined using specific antibodies and inhibitors. Immunocytochemical analysis was performed to identify any changes observed in the cytoskeleton in relation to cell shape. Association of cytoskeleton molecules with phosphatidylinositol 3-kinase was determined using co-precipitation. Cell proliferation was assayed using a colorimetric method for determining the number of viable cells. RESULTS: The fibroblastic morphology induced by FGF-2 reverted to a polygonal shape in cells treated with anti-FGF-2 antibody, anti-phosphatidylinositol 3-kinase antibody, LY294002, and genistein, while anti-phospholipase C gamma1 antibody did not to reverse the modulated cell morphology. Cell proliferation mediated by FGF-2 was blocked by metabolic inhibitors (genistein, LY294002 and wortmannin); genistein inhibited FGF-mediated cell proliferation in a dose-response manner and had a maximum inhibition of 80% at 100 microM, while inhibitors of phosphatidylinositol 3-kinase had less inhibitory effect than did genistein. When cytoskeleton proteins were examined, the characteristic punctated staining profiles of vinculin observed in normal cells were maintained in fibroblastic corneal endothelial cells treated with FGF-2. The inhibitors that cause reversion of cell shape also demonstrated the punctated staining potential. Likewise, the staining profiles of alpha-actinin and smooth muscle alpha-actin were not altered, regardless of cell shape. Filamentous actin and alpha-actinin were co-localized to the cytoskeleton and phosphatidylinositol 3-kinase was associated with the cytoskeleton, regardless of cell shape. CONCLUSIONS: These findings indicate that FGF-2 uses distinct and/or dual signaling pathways for individual biological activities.

Androstadienes↗