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Results for “Biologic pathways”

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PubMed1998

Direct selection cloning vectors adapted to the genetic analysis of gram-negative bacteria and their plasmids.

A range of specific and unusual biological pathways are found in Gram-negative bacteria. It is possible to express the genes involved in these processes in Escherichia coli, however, some genes prove lethal when cloned into high copy number vectors in common usage. Conversely, various genetic functions remain silent in E. coli and require to be transferred into their original host for expression and subsequent analysis. To facilitate the cloning and the characterisation of bacterial genes, we have constructed CcdB 'positive-selection' vectors that possess one or more of the following properties: (i) low or medium copy number; (ii) narrow or broad replication host range; (iii) conjugational mobilisation. In this communication, we illustrate the use of these new cloning tools and analyse the CcdB toxicity in different bacterial species.

Bacterial Proteins↗

PubMed2003

Identification of gene expression profiles in rat ears with cDNA microarrays.

The physiological processes of hearing implicate thousands of molecules acting in harmony; however, their identities are only partially understood. We used cDNA microarrays containing 1,176 genes to identify >150 genes expressed in rat middle and inner ear tissue. Expressed genes covered several gene families and biological pathways, many of which have previously not been described. Transcription factor genes that were expressed included inhibitors of DNA binding protein (Id). These were localized to the spiral ganglion, organ of Corti and stria vascularis, and they are possibly involved in neurogenesis and angiogenesis. Transcriptional factors that were highly expressed included Gax (homeobox) and I-kappaB, which inhibit cellular proliferation. Their presence suggests that inhibitory programs for cell proliferation are enforced in the ear. Ion channel genes that were expressed included voltage-dependent L-type calcium channels (LTCC) and proton-gated cation channels (PGCC). Genes involved in neurotransmitter production and release included glutamic acid decarboxylase (GAD1). Genes involved in postsynaptic inhibition included neuropeptide Y5 receptors (NPY5) and GAD1. Due to the existence of receptors and/or enzymes involved in their biochemical synthesis, neurotransmitters associated with these might include serotonin, glutamide, acetylcholine, gamma-aminobutyric acid (GABA), neurotensin, and dopamine.

Animals↗

PubMed2000

Common gene variants, mortality and extreme longevity in humans.

Genetic factors influence variation in human life span. The fast technological advancements in genome research and the methodology for statistical analysis of complex traits provided new tools to unravel these genetic influences. Most of the genetic epidemiology and quantitative genetics is focused on the dissection of the genetic component of specific diseases rather than of human life span. Nevertheless, common variants of 22 genes have been tested for their contribution to mortality in the general population and extreme longevity in one or more studies. These studies provide indications as to the nature of biological pathways that might play a role in human ageing. Perhaps even more important at this time is the fact that they give valuable insights in the strengths and weaknesses of current strategies to identify gene variants affecting human life span and point at more powerful approaches.

Apolipoproteins E↗

PubMed2001

Molecular biology of nervous system tumors.

Many genetic alterations that contribute to CNS tumorigenesis and progression have been identified. One goal of such studies is to identify loci that would serve as diagnostic prognostic markers or both. A significant advance is the observation that chromosome 1p loss identified anaplastic oligodendroglioma and a subset of high-grade glioma patients who responded to chemotherapy and had longer survival times. Combined 1p and 19q loss was a predictor of prolonged survival of patients having pure oligodendrogliomas. Such markers eventually may be used to identify patients upfront who would benefit from treatment, while sparing patients who would not benefit. Although many molecular participants involved in the biologic pathways that promote proliferation, angiogenesis, and invasion have been elucidated, there are still many gaps in clinicians' knowledge. It is expected that the use of the human genome project information and databases such as SAGEmap, in combination with techniques such as cDNA arrays and proteomics, will facilitate greatly the identification of novel genes that contribute to CNS tumors. cDNA arrays and tissue arrays will permit the construction of CNS-specific screening tools that will permit the identification of tumor-specific mutations and alterations so that patient-specific therapies can be designed.

Cell Division↗

PubMed2003

RNA cargoes associating with FMRP reveal deficits in cellular functioning in Fmr1 null mice.

The Fragile X mental retardation-1 (Fmr1) gene encodes a multifunctional protein, FMRP, with intrinsic RNA binding activity. We have developed an approach, antibody-positioned RNA amplification (APRA), to identify the RNA cargoes associated with the in vivo configured FMRP messenger ribonucleoprotein (mRNP) complex. Using APRA as a primary screen, putative FMRP RNA cargoes were assayed for their ability to bind directly to FMRP using traditional methods of assessing RNA-protein interactions, including UV-crosslinking and filter binding assays. Approximately 60% of the APRA-defined mRNAs directly associate with FMRP. By examining a subset of these mRNAs and their encoded proteins in brain tissue from Fmr1 knockout mice, we have observed that some of these cargoes as well as the proteins they encode show discrete changes in abundance and/or differential subcellular distribution. These data are consistent with spatially selective regulation of multiple biological pathways by FMRP.

Animals↗

PubMed2000

The role of apolipoprotein E in Alzheimer's disease: pharmacogenomic target selection.

The association of inheritance of different apolipoprotein E (APOE, gene; apoE, protein) alleles with the risk and rate of onset of Alzheimer's disease (AD) is now well established and widely confirmed. While there are now a collection of hypotheses concerning the specific relationship of APOE polymorphisms to various phenotypic manifestations of AD, no single compelling theory has been tested and universally accepted. The only clear fact emerging during the past 6 years is that differences in APOE genotype affect the average rate of disease onset as a predictable function of the inheritance of this polymorphic gene. Methods now exist to enable experimental designs to study the metabolic effects of inheriting different APOE alleles, addressing what differences that may be present for many years, perhaps over the entire lifetime, can lead to earlier or later manifestations of the disease and are therapeutically tractable. This review summarizes part of an experimental approach to identify biological pathways influenced by the different APOE polymorphisms that are relevant to the pathogenesis of AD.

Alleles↗

PubMed1997

Bioinformatics: from genome data to biological knowledge.

Recently, molecular biologists have sequenced about a dozen bacterial genomes and the first eukaryotic genome. We can now obtain answers to detailed questions about the complete set of genes of an organism. Bioinformatics methods are increasingly used for attaching biological knowledge to long lists of genes, assigning genes to biological pathways, comparing the gene sets of different species, identifying specificity factors, and describing sets of highly conserved proteins common to all domains of life. Substantial progress has recently been made in the availability of primary and added-value databases, in the development of algorithms and of network information services for genome analysis. The pharmaceutical industry has greatly benefited from the accumulation of sequence data through the identification of targets and candidates for the development of drugs, vaccines, diagnostic markers and therapeutic proteins.

Databases, Factual↗

PubMed2002

Effects of combination anti-vascular endothelial growth factor receptor and anti-epidermal growth factor receptor therapies on the growth of gastric cancer in a nude mouse model.

We hypothesised that the combination of anti-angiogenic and anti-epidermal growth factor (EFG)-receptor (R) therapies would more effectively inhibit gastric cancer growth than single-agent therapy. TMK-1 gastric cancer cells were injected into the gastric wall of nude mice to generate tumours. After 4 days, mice were randomly assigned to the following groups: control, DC101 ([vascular endothelial growth factor (VEGF)-receptor (R)-2 antibody], C225 (EGF-R antibody), or a combination of DC101 and C225. The combination therapy significantly inhibited gastric tumour growth compared with the control group, whereas the decrease in tumour growth in mice treated with DC101 or C225 alone did not reach statistical significance. All mice administered DC101 demonstrated decreased tumour vascularity and increased endothelial cell apoptosis. C225 alone did not affect angiogenesis, but inhibited tumour cell proliferation. The combination therapy led to a further decrease in tumour cell proliferation. The combination of anti-VEGF-R and anti-EGF-R therapies was effective in inhibiting gastric cancer growth. These findings support the hypothesis that inhibiting multiple biological pathways that mediate tumour growth may be an effective therapeutic strategy.

Animals↗

PubMed2001

Structure of CD40 ligand in complex with the Fab fragment of a neutralizing humanized antibody.

BACKGROUND: CD40 ligand (CD40L or CD154), a member of the tumor necrosis factor (TNF) family, plays a critical role in both humoral and cellular immune responses and has been implicated in biological pathways involving epithelial cells, fibroblasts, and platelets. Such a pathway is T cell-mediated B cell activation, a process that occurs through the interaction of CD40L with CD40 receptor expressed on B cells. It results in various B cell responses, including immunoglobulin isotype switching and B cell differentiation and proliferation. These responses can be inhibited by the monoclonal antibody 5c8, which binds with high affinity to CD40L. RESULTS: To understand the structural basis of the inhibition, we determined the crystal structure of the complex of the extracellular domain of CD40L and the Fab fragment of humanized 5c8 antibody. The structure shows that the complex has the shape of a three-bladed propeller with three Fab fragments bound symmetrically to a CD40L homotrimer. To further study the nature of the antibody-antigen interface, we assessed the ability of 23 site-directed mutants of CD40L to bind to 5c8 and CD40 and analyzed the results in the context of the crystal structure. Finally, we observed via confocal microscopy that 5c8 binding to CD40L on the cell surface results in the formation of patches of clustered complexes. CONCLUSIONS: The structure reveals that 5c8 neutralizes CD40L function by sterically blocking CD40 binding. The antigenic epitope is localized in a region of the surface that is likely to be structurally perturbed as a result of genetic mutations that cause hyper-IgM syndrome. The symmetric trimeric arrangement of the Fab fragments in the complex results in a geometry that facilitates the formation of large clusters of complexes on the cell surface.

Amino Acid Sequence↗

PubMed1998

Small-molecule-based strategies for controlling gene expression.

A central goal in chemical biology is to gain control over biological pathways using small molecules, and the mRNA-synthesizing machinery is a particular important target. New advances in our understanding of transcriptional regulation suggests strategies to manipulate these pathways using small molecules.

Animals↗

PubMed2003

Mouse models as tools for dissecting disorders of lipoprotein metabolism.

The overexpression of proteins as transgenes or by adenovirus-mediated gene transfer as well as the disruption of genes by homologous DNA recombination in the mouse provide powerful tools to dissect the role of individual proteins in complex biological pathways. These and similar techniques have been widely used to characterize the function of most of the players involved in lipoprotein metabolism. These models are expected to greatly advance the finding of new therapeutic strategies for the treatment of disorders of lipoprotein metabolism.

Animals↗

PubMedDate not supplied

Genetics of primary generalized osteoarthritis.

Osteoarthritis (OA) is a common joint disease with complex etiology, including biomechanical, biochemical, and genetic components. The genetics of primary idiopathic OA is likely complex as multiple susceptibility loci have been identified from genome-wide scans. The future lies in finer mapping of these chromosomal regions, association studies, and candidate gene analysis and identification, which should collectively give rise to an improved understanding of the genetic mutations and biological pathways which increase the risk of developing this common joint disorder.

Chromosome Mapping↗

PubMed2002

[Target-volume selection and delineation in the cervico-maxillo-facial region: beyond the concepts of the ICRU].

Improvement in irradiation techniques, which allows dose distributions sculpting around volumes of very complex shapes, has revealed the limitations in selection and delineation of target volumes. The use of functional imaging (PET, fMRI) in addition to anatomic imaging, will probably bring an extra level of complexity to this issue. In particular, the use of specific markers to visualize biological pathways known to influence response to ionizing radiation (e.g. hypoxia, proliferation) could lead to the delineation of sub-target volumes for delivering an extra boost dose. Such concept of Image-Guided Radiation Therapy still need to be tested in experimental models and in well defined clinical situations before its use in a routine clinical set-up.

Head and Neck Neoplasms↗

PubMed2001

Recent developments in computational proteomics.

The mapping of the human genome was completed earlier this year and efforts are underway to understand the role of gene products (i.e. proteins) in biological pathways and human disease and to exploit their functional roles to derive protein therapeutics and protein-based drugs. A key component to the next revolution in the 'post-genomic' era will be the increasingly widespread use of protein structure in rational experimental design. Improvements in quality, availability and utility of large-scale three- and four-dimensional protein structural information are enabling a revolution in rational design, having particular impact on drug discovery and optimization. New computational methodologies now yield modeled structures that are, in many cases, quantitatively comparable with crystal structures, at a fraction of the cost.

Journal Article↗

PubMed2003

Genetics of osteoarthritis and potential for drug development.

Genome-wide linkage scans for the mapping of osteoarthritis susceptibility loci have come to the fore in recent years, driven by the failure of candidate gene association studies. Four scans have been published, with several strong linkages reported. These do not encompass the major cartilage structural genes that many consider the most likely susceptibility loci. This has increased the probability that the biological pathways responsible for susceptibility are modifiable by drug treatment, which one would not reasonably expect for a structural protein. This in itself has stimulated the interest of several pharmaceutical companies. Such interest will be to the benefit of patients, but will require candid co-operation between academics and industry if the delay in transferring research findings from the laboratory to the clinic is to be minimised.

Drug Delivery Systems↗

PubMed2003

Effects of gender, anthropometric variables, and aging on the evolution of hip strength in men and women aged over 65.

Although gender differences in fall rates may partly explain the higher prevalence of fractures in elderly women than men, male bones may also be intrinsically stronger or suffer less structural degradation with age than those of women. We used hip structural analysis (HSA) to study gender differences in hip geometry and bone mineral density (BMD) as they evolved over time in elderly white men and women with the aim of identifying candidate biological pathways leading to heightened risk of hip fracture. We recruited 443 women and 439 men aged 67-79 years from a diet and cancer prospective population-based cohort study to a study of hip bone loss. Hip BMD was measured on two occasions 2-5 years apart by dual-energy X-ray absorptiometry and HSA software used to derive BMD and structural parameters at the narrow neck (NN), the intertrochanter (IT), and the shaft (S) regions. Structural indices calculated in each region were cross-sectional area (CSA)-amount of bone surface area in the cross section after excluding soft tissue space; section modulus (Z)-an index of bending resistance, subperiosteal width, endocortical width, cortical thickness; and cortical buckling ratio (CBR)-a measure of cortical instability. Compared to men, women had lower values of BMD, CSA, Z, subperiosteal width, endocortical width, and cortical thickness in all regions, except S endocortical width, after adjusting for weight, height, and age (P < 0.0001). CBR was higher in women than in men (P < 0.0001) in all regions. Longitudinal analysis of rates of change revealed faster rates of BMD decline in women than in men at the Hologic total hip, Hologic femoral neck, and IT regions (P < 0.029). Women had faster rates of subperiosteal and endosteal expansion than men at the NN (P < 0.011) and IT (P < 0.049) and faster increase in Z at the NN (P = 0.029). At the IT region, cortical thinning was faster in women than in men (P = 0.037) and CBR increased at a faster rate in women (P = 0.011). In conclusion, Z is lower in women than in men and expansion of the proximal femur occurs in both sexes, being faster in women than in men. Z does not decline at the same rate as BMD, implying that part of the effect of aging on BMD is due to expansion of the bony envelope without loss of bone mineral content. Faster expansion in the female femoral neck may in turn lead to greater fragility if wider diameter and thinner cortices become locally unstable.

Age Distribution↗

PubMed1997

Social network in relation to plasma fibrinogen.

Consistent findings about the inverse association of social network level with coronary heart disease mortality and morbidity suggest the importance of investigating biological pathways of association. Differences in plasma fibrinogen level were investigated among middle-aged men with weak and strong structural and functional social network ties. Men with low scores in the adequacy of social participation variable (structural) had higher mean values of plasma fibrinogen than those with high scores. The difference remained after adjustment for age, smoking and cardiovascular health status and after possible modifying factors were taken into account, but did not remain significant after allowing for physical fitness. Men with high scores in overall support (functional) had higher plasma fibrinogen levels compared to the men with low scores. This difference persisted after age and cardiovascular health status were taken into account but was explained by smoking. The data suggest that smoking and cardiorespiratory fitness are important mediating or modifying factors between structural and functional aspects of social network ties and plasma fibrinogen.

Cardiovascular Diseases↗

PubMedDate not supplied

How does stress affect you? An overview of stress, immunity, depression and disease.

OBJECTIVE: Stress is a term that has become synonymous with modern life. This review aims to appraise the evidence linking stress with disease with particular reference to the major causes of morbidity and mortality in the Western World, cardiovascular disease, cancer, and depression. Changes in immune parameters in stressful situations were reviewed as a possible pathophysiological mechanism for such effects. METHOD: A Medline search was carried out for the period 1996-2000 to identify recent findings in this field using the terms "stress", "disease", "immune system". Relevant references that were found in all identified publications were also followed up. RESULTS: There is evidence to link stress with the onset of major depression and with a poorer prognosis in cardiovascular disease and cancer. Few small studies suggest that stress management strategies may help to improve survival. Chronic stress appears to result in suppression of the immune response, whereas immune activation and suppression have been associated with acute stress. Inflammatory cytokines, soluble mediators of the immune response, can result in symptoms of depression. CONCLUSION: Further prospective epidemiologically based studies are needed to clarify the role of stress on disease onset, course, and prognosis. Stress management strategies, aimed at prolonging survival in patients with cardiovascular disease, cancer, and possibly other chronic illnesses, are an exciting area of further research. Immune system changes may account for the relationship between stress and disease. We propose the "stress, cytokine, depression" model as a biological pathway to explain the link between stressful life events and depression.

Coronary Disease↗