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Results for “Pathway informed transformer”

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PubMed2002

The role of hydrogen peroxide in endothelial proliferative responses.

Hydrogen peroxide (H2O2) is a recently recognized second messenger regulating proliferation in mammalian cells. Endothelial cells possess NADPH oxidases, which produce the H202 precursor superoxide (.O2-) in response to receptor-mediated signaling. Multiple physiologic agents have been shown to stimulate endothelial cells to produce .O2-/H2O2, including growth factors, such as vascular endothelial growth factor and transforming growth factor-beta1, and alterations in biomechanical forces, such as shear stress and cyclic strain. Downstream effects of these stimuli can often be inhibited by scavenging H2O2. Low concentrations of H2O2 stimulate proliferation or enhanced survival in a wide variety of cell types. Also, low concentrations of H2O2 stimulate endothelial migration as well as tube formation in an in vitro model of angiogenesis. Although low concentrations of H2O2 have been shown to be involved in numerous signal transduction pathways and to independently stimulate mitogenesis, there has been little information presented on precisely how mammalian cells respond biochemically to these low concentrations of H2O2. Recently a functional proteomics approach has been utilized to identify proteins responsive to low concentrations of H2O2 in human endothelial cells.

Animals↗

PubMed1983

Fructose, fructose 1-phosphate, and glyceraldehyde breakdown in carbohydrate metabolism.

Recent investigations showed that all enzymes that are involved in the catabolism of fructose via fructose 1-phosphate (F-1-p) are present in the bovine lens. The present studies were performed to provide information regarding the extent to which fructose, F-1-p and glyceraldehyde (GA) are actually catabolized via this pathway, and how they increase the lactate, alpha-glycerophosphate and glycerol concentrations. Incubation was performed with a homogenate of bovine lens equator. F-1-p, and particularly fructose + ATP, considerably increased lactate and alpha-glycerophosphate concentrations, while the glycerol concentration remained unchanged compared to controls. Lactate formation through GA was not observed; while small amounts of glycerol and alpha-glycerophosphate are formed, it seems that the major part is transformed to glycerate. The results show that the further breakdown of lenticular fructose occurs via F-1-p and that the phosphorylated C3 fragments (dihydroxyacetone phosphate) are transferred to the energy metabolism, which is not the case with GA.

Animals↗

PubMed2003

The mitogen-activated protein kinase signaling module as a therapeutic target in hematologic malignancies.

Important insights into the cellular and molecular biology of cancer in general and of hematologic malignancies in particular have been gained in the past two decades. The genes, and their protein products, involved in the transformation of cells from normal to neoplastic, as well as in the progression of neoplastic cells to a more aggressive, therapy-resistant phenotype, are being elucidated in great detail. However, most hematologic malignancies, particularly adult acute leukemias, remain associated with high mortality rates and new therapeutic approaches are urgently needed. The challenge is therefore to carefully and efficiently translate the information gained into effective therapeutic strategies. The clinical success achieved by tyrosine kinase inhibitors, such as ST1571 in chronic myelogenous leukemia, has stimulated interest for kinase-based signaling pathways as therapeutic targets in hematologic malignancies. The mitogen-activated protein kinase (MAPK) pathway is a common point of convergence of many different mitogenic and anti-apoptotic signal transduction pathways in hematopoietic, as well as epithelial, cancer cells and can now be clinically targeted by highly selective small molecule inhibitors. The mounting preclinical evidence of anti-leukemic activity of MAPK inhibitors, alone or in combination with pro-apoptotic small molecules or with conventional chemotherapeutic agents provides rationale that MAPK inhibition-based treatment strategies could soon enrich our therapeutic armamentarium against human leukemias.

Antineoplastic Agents↗

PubMed1991

A population perspective on multistage carcinogenesis.

The concept of multistage carcinogenesis is one of the central dogmas of cancer research today. Recent laboratory work suggests that many specific genetic changes are associated with carcinogenesis. At the same time, there is increasing evidence that cell proliferation kinetics are important in carcinogenesis. In 1971, Knudson proposed his now celebrated two-mutation model for embryonal tumors. In fact, a two-mutation model that explicitly considers cell kinetics is the most parsimonious model consistent with the incidence of both childhood and adult cancer in human populations. This model has been known to be consistent, as well, with other epidemiologic and experimental data. But can such a model be reconciled with the laboratory evidence suggesting that many genetic alterations are required for malignant transformation? In this paper, I examine multistage carcinogenesis from the population perspective. Can cancer incidence data in populations provide some insight into the number and nature of stages involved in malignant transformation? I focus attention on carcinoma of the colon because of the considerable amount of information that is now available on the genetics of these tumors. Also, as is the case with retinoblastoma, colon cancer occurs in sporadic and dominantly inherited forms. A comparison of the incidence of these two forms of colon cancer suggests that mutation at the familial adenomatous polyposis (FAP) locus is not necessary for colon cancer, and that inheritance of the gene for FAP is not equivalent to inheriting one of the essential steps on the pathway to colon cancer. Thus, colon cancer does not follow the retinoblastoma paradigm. The incidence of colon cancer in the general population and among polyposis subjects is consistent with two or three mutations on the pathway to malignancy. A three-mutation model is more consistent with the genetic alterations observed in colon carcinogenesis. I present and discuss a working model for colon cancer.

Adenomatous Polyposis Coli↗

PubMed2005

The genetics of ray pattern variation in Caenorhabditis briggsae.

BACKGROUND: How does intraspecific variation relate to macroevolutionary change in morphology? This question can be addressed in species in which derived characters are present but not fixed. In rhabditid nematodes, the arrangement of the nine bilateral pairs of peripheral sense organs (rays) in tails of males is often the most highly divergent character between species. The development of ray pattern involves inputs from hometic gene expression patterns, TGFbeta signalling, Wnt signalling, and other genetic pathways. In Caenorhabditis briggsae, strain-specific variation in ray pattern has provided an entree into the evolution of ray pattern. Some strains were fixed for a derived pattern. Other strains were more plastic and exhibited derived and ancestral patterns at equal frequencies. RESULTS: Recombinant inbred lines (RILs) constructed from crosses between the variant C. briggsae AF16 and HK104 strains exhibited a wide range of phenotypes including some that were more extreme than either parental strain. Transgressive segregation was significantly associated with allelic variation in the C. briggsae homolog of abdominal B, Cb-egl-5. At least two genes that affected different elements of ray pattern, ray position and ray fusion, were linked to a second gene, mip-1. Consistent with this, the segregation of ray position and ray fusion phenotypes were only partially correlated in the RILs. CONCLUSIONS: The evolution of ray pattern has involved allelic variation at multiple loci. Some of these loci impact the specification of ray identities and simultaneously affect multiple ray pattern elements. Others impact individual characters and are not constrained by covariance with other ray pattern elements. Among the genetic pathways that may be involved in ray pattern evolution is specification of anteroposterior positional information by homeotic genes.

Alleles↗

PubMed2006

Regulating p73 isoforms in human tumours.

Although mutations in the TP73 gene are extremely rare in human tumours, altered expression is common. In some tumours, most notably leukaemias and lymphomas, expression of TP73 is reduced, suggesting a tumour suppressor role. In contrast, TP73 is over-expressed in many other tumour types, implying that it has oncogenic functions in human tumourigenesis. These conflicting scenarios can be reconciled by the observations that the TP73 gene produces p53-like isoforms (TAp73) and anti-p53 isoforms (DeltaTAp73). Thus, loss of TAp73 or over-expression of DeltaTAp73 should each promote oncogenic transformation, and the balance of expression of the opposing isoforms is the crucial factor. The mechanisms that regulate expression of TP73 isoforms are therefore of great interest. Recent data provide evidence for interacting roles of ZEB1, p300, and a polymorphic 73 bp deletion in intron 1 of the human TP73 gene in this process. Importantly, alterations to the proposed regulatory pathway for controlling TP73 isoform expression in colorectal cancer are associated with adverse clinico-pathological characteristics. Because p73 is also associated with tumour chemosensitivity, these new findings should provide prognostic information and have the potential to guide future therapeutic decisions.

DNA-Binding Proteins↗

PubMed1996

What's new in ras genes? Physiological role of ras genes in signal transduction and significance of ras gene activation in tumorigenesis.

Ras gene mutations have been found with variable prevalence in different tumor types. While during the past decade a lot of information has been accumulated on the frequency of ras oncogene activation in tumors, the last two years brought considerable progress in elucidating molecular mechanisms of signal transduction for which cellular ras proteins are key elements. They transmit signals from upstream tyrosine kinases to downstream serine/threonine kinases ultimately leading to changes of gene expression cytoskeletal architecture, cell-to-cell interactions and metabolism. These signalling pathways are of interest for the physiological regulation of proliferation and differentiation in normal, as well as in cancer tissue. Mutational activation of cellular ras genes to transforming oncogenes is thought to promote cell growth even in the absence of extracellular stimuli, and may thereby contribute to the initiation and/or progression of tumors.

Animals↗

PubMed2005

cGMP signaling in vertebrate retinal photoreceptor cells.

The visual transduction pathway in vertebrate photoreceptors transforms a light stimulus entering the photoreceptor outer segments into an electrical response at the synapses of rod and cone photoreceptor cells. This process is mediated by complex biochemical pathways that precisely regulate cGMP levels, thereby controlling the extent, duration, and adaptation of the photoreceptor to the light stimulus. This review first summarizes the major mechanisms of regulating cytoplasmic cGMP levels (synthesis, degradation, buffering, and efflux) as well as the primary targets of action of cGMP (cyclic nucleotide-gated ion channels, cGMP-dependent protein kinase, and cGMPregulated phosphodiesterases). This information is applied to our current understanding of how these processes operate in the signal-transducing outer segment of rod and cone photoreceptors to carry out visual excitation, recovery, and adaptation in response to light stimulation.

Animals↗

PubMed1998

How do tissues respond to damage at the cellular level? The role of cytokines in irradiated tissues.

The capacity of ionizing radiation to affect tissue function, control tumor growth and elicit pathological sequelae has been attributed in great part to its effects on cellular DNA, which, as the transmitter of genetic information, can both register damage and perpetuate it. Nonetheless, multicellular organisms function as the result of the cooperation of many cell types. What then occurs when individual cells are damaged by ionizing radiation? Is tissue response a sum of cellular effects such as cell death and DNA damage? Or does the tissue respond as a coherent unit to the damage of its parts? In this paper, data in support of the latter model that indicate a role for cytokines, in particular transforming growth factor beta1, as critical components of extracellular signaling pathways that mediate tissue response to radiation will be reviewed. The key to manipulating the consequences of radiation exposure lies in understanding the complex interplay of events initiated at the cellular level, but acting on the tissue.

Animals↗

PubMed1998

The organization of the cortical motor system: new concepts.

A series of recent anatomical and functional data has radically changed our view on the organization of the motor cortex in primates. In the present article we present this view and discuss its fundamental principles. The basic principles are the following: (a) the motor cortex, defined as the agranular frontal cortex, is formed by a mosaic of separate areas, each of which contains an independent body movement representation, (b) each motor area plays a specific role in motor control, based on the specificity of its cortical afferents and descending projections, (c) in analogy to the motor cortex, the posterior parietal cortex is formed by a multiplicity of areas, each of which is involved in the analysis of particular aspects of sensory information. There are no such things as multipurpose areas for space or body schema and (d) the parieto-frontal connections form a series of segregated anatomical circuits devoted to specific sensorimotor transformations. These circuits transform sensory information into action. They represent the basic functional units of the motor system. Although these conclusions mostly derive from monkey experiments, anatomical and brain-imaging evidence suggest that the organization of human motor cortex is based on the same principles. Possible homologies between the motor cortices of humans and non-human primates are discussed.

Animals↗

PubMed2001

Nonandrogenic mediators of prostatic growth.

Prostate growth and development are primarily under the control of androgens; however, other factors can also influence prostatic growth through alternative pathways. This article discusses some of the major nonandrogenic mediators of prostate growth. Information on the pathways by which these factors exert their effects is also reviewed.

APUD Cells↗

PubMedDate not supplied

Signal integration during development: mechanisms of EGFR and Notch pathway function and cross-talk.

Metazoan development relies on a highly regulated network of interactions between conserved signal transduction pathways to coordinate all aspects of cell fate specification, differentiation, and growth. In this review, we discuss the intricate interplay between the epidermal growth factor receptor (EGFR; Drosophila EGFR/DER) and the Notch signaling pathways as a paradigm for signal integration during development. First, we describe the current state of understanding of the molecular architecture of the EGFR and Notch signaling pathways that has resulted from synergistic studies in vertebrate, invertebrate, and cultured cell model systems. Then, focusing specifically on the Drosophila eye, we discuss how cooperative, sequential, and antagonistic relationships between these pathways mediate the spatially and temporally regulated processes that generate this sensory organ. The common themes underlying the coordination of the EGFR and Notch pathways appear to be broadly conserved and should, therefore, be directly applicable to elucidating mechanisms of information integration and signaling specificity in vertebrate systems.

Amyloid Precursor Protein Secretases↗

PubMed2006

Fatty acid production in Schizochytrium sp.: Involvement of a polyunsaturated fatty acid synthase and a type I fatty acid synthase.

Schizochytrium sp. is a marine microalga that has been developed as a commercial source for docosahexaenoic acid (DHA, C22:6 (omega-3), enriched biomass, and oil. Previous work suggested that the DHA, as well as docosapentaenoic acid (DPA, C22:5 omega-6), that accumulate in Schizochytrium are products of a multi-subunit polyunsaturated fatty acid (PUFA) synthase (1). Here we show data to support this view and also provide information on other aspects of fatty acid synthesis in this organism. Three genes encoding subunits of the PUFA synthase were isolated from genomic DNA and expressed in E. coli along with an essential accessory gene encoding a phosphopantetheinyl transferase (PPTase). The resulting transformants accumulated both DHA and DPA. The ratio of DHA to DPA was approximately the same as that observed in Schizochytrium. Treatment of Schizochytrium cells with certain levels of cerulenin resulted in inhibition of 14C acetate incorporation into short chain fatty acids without affecting labeling of PUFAs, indicating distinct biosynthetic pathways. A single large gene encoding the presumed short chain fatty acid synthase (FAS) was cloned and sequenced. Based on sequence homology and domain organization, the Schizochytrium FAS resembles a fusion of fungal FAS beta and alpha subunits.

Amino Acid Sequence↗

PubMed2005

Amino acid catalyzed neogenesis of carbohydrates: a plausible ancient transformation.

Hexose sugars play a fundamental role in vital biochemical processes and their biosynthesis is achieved through enzyme-catalyzed pathways. Herein we disclose the ability of amino acids to catalyze the asymmetric neogenesis of carbohydrates by sequential cross-aldol reactions. The amino acids mediate the asymmetric de novo synthesis of natural L- and D-hexoses and their analogues with excellent stereoselectivity in organic solvents. In some cases, the four new stereocenters are assembled with almost absolute stereocontrol. The unique feature of these results is that, when an amino acid is employed as the catalyst, a single reaction sequence can convert a protected glycol aldehyde into a hexose in one step. For example, proline and its derivatives catalyze the asymmetric neogenesis of allose with >99 % ee in one chemical manipulation. Furthermore, all amino acids tested catalyzed the asymmetric formation of natural sugars under prebiotic conditions, with alanine being the smallest catalyst. The inherent simplicity of this catalytic process suggests that a catalytic prebiotic "gluconeogenesis" may occur, in which amino acids transfer their stereochemical information to sugars. In addition, the amino acid catalyzed stereoselective sequential cross-aldol reactions were performed as a two-step procedure with different aldehydes as acceptors and nucleophiles. The employment of two different amino acids as catalysts for the iterative direct aldol reactions enabled the asymmetric synthesis of deoxysugars with >99 % ee. In addition, the direct amino acid catalyzed C(2)+C(2)+C(2) methodology is a new entry for the short, highly enantioselective de novo synthesis of carbohydrate derivatives, isotope-labeled sugars, and polyketide natural products. The one-pot asymmetric de novo syntheses of deoxy and polyketide carbohydrates involved a novel dynamic kinetic asymmetric transformation (DYKAT) mediated by an amino acid.

Amino Acids↗

PubMed2004

The prefrontal cortex and working memory: physiology and brain imaging.

Sustained activity has been recorded in the prefrontal cortex during working memory tasks. First, we compare the anatomical distribution of this activity in humans and monkeys. Then, we show that it reflects many factors, maintenance of the items presented, preparation for the response, transformation of the items during the delay, task rules and task goals. Finally, we point out that sustained activity has also been recorded in other areas, such as the parietal cortex. We suggest that the key to prefrontal cortex lies not in the maintenance of sensory information but in the prospective use of that information for behaviour.

Animals↗

PubMed2006

Neural-endocrine-immune complex in the central modulation of tumorigenesis: facts, assumptions, and hypotheses.

For the precise coordination of systemic functions, the nervous system uses a variety of peripherally and centrally localized receptors, which transmit information from internal and external environments to the central nervous system. Tight interconnections between the immune, nervous, and endocrine systems provide a base for monitoring and consequent modulation of immune system functions by the brain and vice versa. The immune system plays an important role in tumorigenesis. On the basis of rich interconnections between the immune, nervous and endocrine systems, the possibility that the brain may be informed about tumorigenesis is discussed in this review article. Moreover, the eventual modulation of tumorigenesis by central nervous system is also considered. Prospective consequences of the interactions between tumor and brain for diagnosis and therapy of cancer are emphasized.

Animals↗

PubMed2005

Transforming growth factor-beta1 and disorders of the lung.

The transforming growth factor (TGF) superfamily encompasses about 30 members in mammals. The effect of TGF-beta subfamily members is exerted and regulated via selective pathways of synthesis and signaling that involve activation of latent TGF-beta, specific and high-affinity binding to cell membrane serine/threonine kinase receptors, activation of intracellular cascades that include Smad molecules and mitogen-activated protein kinases, and regulated termination of the effect by diverse mechanisms including protein degradation and transcriptional activation. Several comprehensive reviews on TGF-beta biology in general and on the role of this cytokine in other diseases have been published recently. In recent years an unexpected role of TGF-beta on lung homeostasis has been revealed. Here, we discuss the contribution of TGF-beta to the pathogenesis of asthma and chronic obstructive pulmonary disease, two common illnesses of the lung, as well as of lymphangioleiomyomatosis, a rare disease in women. The information we collate and integrate places TGF-beta at a pivotal point within complex networks that control lung physiology as well as the physiopathology of these lung diseases.

Animals↗

PubMed2004

Aerobic degradation of polychlorinated biphenyls.

The microbial degradation of polychlorinated biphenyls (PCBs) has been extensively studied in recent years. The genetic organization of biphenyl catabolic genes has been elucidated in various groups of microorganisms, their structures have been analyzed with respect to their evolutionary relationships, and new information on mobile elements has become available. Key enzymes, specifically biphenyl 2,3-dioxygenases, have been intensively characterized, structure/sequence relationships have been determined and enzymes optimized for PCB transformation. However, due to the complex metabolic network responsible for PCB degradation, optimizing degradation by single bacterial species is necessarily limited. As PCBs are usually not mineralized by biphenyl-degrading organisms, and cometabolism can result in the formation of toxic metabolites, the degradation of chlorobenzoates has received special attention. A broad set of bacterial strategies to degrade chlorobenzoates has recently been elucidated, including new pathways for the degradation of chlorocatechols as central intermediates of various chloroaromatic catabolic pathways. To optimize PCB degradation in the environment beyond these metabolic limitations, enhancing degradation in the rhizosphere has been suggested, in addition to the application of surfactants to overcome bioavailability barriers. However, further research is necessary to understand the complex interactions between soil/sediment, pollutant, surfactant and microorganisms in different environments.

Aerobiosis↗