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Relevant Genes (relevant + gene)
Selected AbstractsGene Transfer in Human Vestibular Epithelia and the Prospects for Inner Ear Gene Therapy,,THE LARYNGOSCOPE, Issue 5 2008Bradley W. Kesser MD Abstract Transfer of exogenous genetic material into the mammalian inner ear using viral vectors has been characterized over the last decade. A number of different viral vectors have been shown to transfect the varying cell types of the nonprimate mammalian inner ear. Several routes of delivery have been identified for introduction of vectors into the inner ear while minimizing injury to existing structures and at the same time ensuring widespread distribution of the agent throughout the cochlea and the rest of the inner ear. These studies raise the possibility that gene transfer may be developed as a potential strategy for treating inner ear dysfunction in humans. Furthermore, a recent report showing successful transfection of excised human vestibular epithelia offers proof of principle that viralgene transfer is a viable strategy for introduction andexpression of exogenous genetic material to restore function to the inner ear. Human vestibular epithelia were harvested from patients undergoing labyrinthectomy, either for intractable Ménière's disease or vestibular schwannoma resection, and cultured for as long as 5 days. In those experiments, recombinant, multiply-deleted, replication-deficient adenoviral vectors were used to transfect and express a reporter gene as well as the functionally relevant gene, wild-type KCNQ4, a potassium channel gene that when mutated causes the autosomal dominant HL DFNA2. Here, we review the current state of viral-mediated gene transfer in the inner ear and discuss different viral vectors, routes of delivery, and potential applications of gene therapy. Emphasis is placed on experiments demonstrating viral transfection of human inner ear tissue and implications of these findings and for the future of gene therapy in the human inner ear. [source] The lim domain only protein 7 is important in zebrafish heart developmentDEVELOPMENTAL DYNAMICS, Issue 12 2008Elisabeth B. Ott Abstract The LIM domain only protein 7 (LMO7), a member of the PDZ and LIM domain-containing protein family is a candidate gene with possible roles in embryonic development and breast cancer progression. LMO7 has been linked to actin cytoskeleton organization through nectin/afadin and to cell,cell adhesion by means of E-cadherin/catenin. In addition, LMO7 has been shown to regulate transcription of the nuclear membrane protein Emerin and other muscle relevant genes. In this study, we used in situ hybridization to investigate LMO7 expression during embryonic development in three widely used vertebrate model species: the zebrafish, the chicken and the mouse. Our temporal and spatial gene expression analysis revealed both common and distinct patterns between these species. In mouse and chicken embryos we found expression in the outflow tract, the inflow tract, the pro-epicardial organ and the second heart field, structures highly important in the developing heart. Furthermore, gene knockdown experiments in zebrafish embryos resulted in severe defects in heart development with effects on the conduction system and on heart localization. In summary, we present here the first developmental study of LMO7. We reveal the temporal and spatial expression patterns of this important gene during mouse, chicken and fish development and our findings suggest essential functions for LMO7 during vertebrate heart development. Developmental Dynamics 237:3940,3952, 2008. © 2008 Wiley-Liss, Inc. [source] INDIRECT GENETIC EFFECTS INFLUENCE ANTIPREDATOR BEHAVIOR IN GUPPIES: ESTIMATES OF THE COEFFICIENT OF INTERACTION PSI AND THE INHERITANCE OF RECIPROCITYEVOLUTION, Issue 7 2009Bronwyn H. Bleakley How and why cooperation evolves, particularly among nonrelatives, remains a major paradox for evolutionary biologists and behavioral ecologists. Although much attention has focused on fitness consequences associated with cooperating, relatively little is known about the second component of evolutionary change, the inheritance of cooperation or reciprocity. The genetics of behaviors that can only be expressed in the context of interactions are particularly difficult to describe because the relevant genes reside in multiple social partners. Indirect genetic effects (IGEs) describe the influence of genes carried in social partners on the phenotype of a focal individual and thus provide a novel approach to quantifying the genetics underlying interactions such as reciprocal cooperation. We used inbred lines of guppies and a novel application of IGE theory to describe the dual genetic control of predator inspection and social behavior, both classic models of reciprocity. We identified effects of focal strain, social group strain, and interactions between focal and group strains on variation in focal behavior. We measured ,, the coefficient of the interaction, which describes the degree to which an individual's phenotype is influenced by the phenotype of its social partners. The genetic identity of social partners substantially influences inspection behavior, measures of threat assessment, and schooling and does so in positively reinforcing manner. We therefore demonstrate strong IGEs for antipredator behavior that represent the genetic variation necessary for the evolution of reciprocity. [source] Interferons as pathogenic effectors in autoimmunityIMMUNOLOGICAL REVIEWS, Issue 1 2005Roberto Baccala Summary:, Interferons (IFNs) type-1 (IFN ,/,) and type-II (IFN-,) are the most pleiotropic molecules in the intricate cytokine network. This dominance arises from three crucial factors: (i) initiation of IFN-,/, and IFN-, production at the inception of most innate immune responses, which primes for the ensuing adaptive immune responses, primarily through the sine qua non upregulation of major histocompatibility complex and costimulatory molecules; (ii) magnification of their production and signaling by cross-talk between themselves, and synergistic or antagonistic effects on other cytokines; and (iii) direct or indirect initiation of transcription of hundreds of immunologically relevant genes. Considering that aberrant immune responses against self-molecules seem to depend on the same constituents and pathways as those against exogenous antigens, it follows that IFNs are also major effectors in the pathogenesis of autoimmunity. Here, we review the diverse biological effects of IFNs on the immune system, discuss findings pertaining to the nature of exogenous and endogenous stimuli that might induce IFN production through the engagement of Toll-like receptors, and summarize the detrimental and, in some instances, beneficial effects of IFNs in systemic and organ-specific autoimmune diseases. [source] Molecular characterization of the response to chemotherapy in conventional osteosarcomas: Predictive value of HSD17B10 and IFITM2INTERNATIONAL JOURNAL OF CANCER, Issue 4 2009Sébastien Salas Abstract The therapy regimen of high-grade osteosarcoma includes chemotherapy followed by surgical resection and postoperative chemotherapy. The degree of necrosis following definitive surgery remains the only reliable prognostic factor and is used to guide the choice of postoperative chemotherapy. The aim of this study was to find molecular markers able to classify patients with an osteosarcoma as good or poor responders to chemotherapy before beginning treatment. Gene expression screening of 20 nonmetastatic high-grade osteosarcoma patients was performed using cDNA microarray. Expression of selected relevant genes was validated using QRT-PCR. Immunohistochemistry on tissue microarrays sections of 73 biopsies was performed to investigate protein expression. Fluorescent in situ hybridization was performed for RPL8 gene. We have found that HSD17B10 gene expression was up-regulated in poor responders and that immunohistochemistry expression of HSD17B10 on biopsy before treatment was correlatedto response to chemotherapy. Other results include correlationof IFITM2, IFITM3, and RPL8 gene expression to chemotherapy response. A statistical correlation was found between polysomy 8 or gain of RPL8 and good response to chemotherapy. These data suggest that HSD17B10, RPL8, IFITM2, and IFITM3 genes are involved in the response to the chemotherapy and that HSD17B10 may be a therapeutic target. RPL8 and IFITM2 may be useful in the assessment at diagnosis and for stratifying patients taking part in randomized trials. © 2009 UICC [source] Embryonic reversions and lineage infidelities in tumour cells: genome-based models and role of genetic instabilityINTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY, Issue 2 2005Leon P. Bignold Summary Reversions to ,embryonic precursor'-type cells and infidelities of tumour cell lineage (including metaplasias) have been recognized as aspects of various tumour types since the 19th century. Since then, evidence of these phenomena has been obtained from numerous clinical, biochemical, immunological and molecular biological studies. In particular, microarray studies have suggested that ,aberrant' expressions of relevant genes are common. An unexplained aspect of the results of these studies is that, in many tumour types, the embryonic reversion or lineage infidelity only occurs in a proportion of cases. As a parallel development during the molecular biological investigation of tumours over the last several decades, genetic instability has been found much more marked, at least in some preparations of tumour cells, than that identified by means of previous karyotypic investigations of tumours. This study reviews examples of embryonic reversion and lineage infidelity phenomena, which have derived from the various lines of investigation of cancer over the last 150 or so years. Four categories of circumstances of the occurrence of embryonic reversions or lineage infidelities have been identified , (i) as part of the defining phenotype of the tumour, and hence being presumably integral to the tumour type, (ii) present ab initio in only some cases of the tumour type, and presumably being regularly associated with, but incidental to, the essential features of the tumour type, (iii) occurring later in the course of the disease and thus being possibly a manifestation of in vivo genetic instability and ,tumour progression' and (iv) arising probably by genetic instability, during the processes, especially cell culture, associated with ex vivo investigations. Genomic models are described which might account for the origin of these phenomena in each of these circumstances. [source] Properties of cell penetrating peptides (CPPs)IUBMB LIFE, Issue 1 2006Alexandre Kerkis Abstract Different approaches have been developed for the introduction of macromolecules, proteins and DNA into target cells. Viral (retroviruses, lentiviruses, etc.) and nonviral (liposomes, bioballistics etc.) vectors as well as lipid particles have been tested as DNA delivery systems. However, all of them share several undesirable effects that are difficult to overcome, such as unwanted immunoresponse and limited cell targeting. The discovery of the cell penetrating peptides (CPPs) showing properties of macromolecules carriers and enhancers of viral vectors, opened new opportunities for the delivery of biologically active cargos, including therapeutically relevant genes into various cells and tissues. This review summarizes recent data about the best characterized CPPs as well as those sharing cell-penetrating and cargo delivery properties despite differing in the primary sequence. The putative mechanisms of CPPs penetration into cells and interaction with intracellular structures such as chromosomes, cytoskeleton and centrioles are addressed. We further discuss recent developments in overcoming the lack of cells specificity, one of the main obstacles for CPPs application in gene therapy. In particular, we review a newly discovered affinity of CPPs to actively proliferating cells. IUBMB Life, 58: 7 - 13, 2006 [source] Stable genetic polymorphism in heterogeneous environments: balance between asymmetrical dispersal and selection in the acorn barnacleJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2006D. VÉLIZ Abstract Elucidating the processes responsible for maintaining polymorphism at ecologically relevant genes is intimately related to understanding the interplay between selection imposed by habitat heterogeneity and a species' capacity for dispersal in the face of environmental constraints. In this paper, we used a model-based approach to solve equilibria of balanced polymorphism, given values of fitness and larval dispersal among different habitats in the acorn barnacle Semibalanus balanoides from the Gulf of St Lawrence. Our results showed that allele frequencies observed at both MPI* and GPI* loci represented stable equilibria, given empirical estimates of fitness values, and that considerably more larvae dispersed from one region (north) to the other (south) than vice versa. Dispersal conditions were predicted to be similar for the maintenance of polymorphism at both loci. Moreover, the values of asymmetrical dispersal required by the model to reach stable equilibria were compatible with empirical estimates of larval dispersal and oceanic circulation documented in this system. Overall, this study illustrated the usefulness of a modified and computable version of Bulmer's model (1972) in order to test hypotheses of balanced polymorphism resulting from interactions between spatial selection and asymmetrical dispersal. [source] The transcriptional response to alkaline pH in Saccharomyces cerevisiae: evidence for calcium-mediated signallingMOLECULAR MICROBIOLOGY, Issue 5 2002Raquel Serrano Summary The short-time transcriptional response of yeast cells to a mild increase in external pH (7.6) has been investigated using DNA microarrays. A total of 150 genes increased their mRNA level at least twofold within 45 min. Alkalinization resulted in the repression of 232 genes. The response of four upregulated genes, ENA1 (encoding a Na+ -ATPase also induced by saline stress) and PHO84, PHO89 and PHO12 (encoding genes upregulated by phosphate starvation), was characterized further. The alkaline response of ENA1 was not affected by mutation of relevant genes involved in osmotic or oxidative signalling, but was decreased in calcineurin and rim101 mutants. Mapping of the ENA1 promoter revealed two pH-responsive regions. The response of the upstream region was fully abolished by the drug FK506 or mutation of CRZ1 (a transcription factor activated by calcium/calcineurin), whereas the response of the downstream region was essentially calcium independent. PHO84 and PHO12 responses were unaffected in crz1 cells, but required the presence of Pho2 and Pho4. In contrast, part of the alkali-induced expression of PHO89 was maintained in pho4 or pho2 cells, but was fully abolished in a crz1 strain or in the presence of FK506. Heterologous promoters carrying the minimal calcineurin-dependent response elements found in ENA1 or FKS2 were able to drive alkaline pH-induced expression. These results demonstrate that the transcriptional response to alkaline pH involves different signalling mechanisms, and that calcium signalling is a relevant component of this response. [source] Identification of target genes and pathways associated with chicken microRNA miR-143ANIMAL GENETICS, Issue 4 2010N. Trakooljul Summary MicroRNA (miRNA) is a family of small regulatory RNAs that post-transcriptionally regulate many biological functions including growth and development. Recently, the expression of chicken miRNA miR-143 was identified by using a deep sequencing approach. In other vertebrate species, miR-143 functions as a regulator of adipocyte differentiation and as a tumour suppressor. However, little is known about the biological function(s) of miR-143 in chickens. To study the functions of chicken miR-143, DNA microarray analysis and a dual luciferase reporter assay were employed to identify genes directly targeted by miR-143 as well as other biologically relevant genes. Microarray analysis indicated that 124 genes were differentially expressed upon in vitro anti- miR-143 treatment in embryonic chick splenocytes (P -value cutoff <0.01). Many of these genes are associated with cell proliferation, apoptosis and tumourigenesis. Six of the up-regulated genes possess at least one potential miR-143 binding site in their 3,UTRs, of these the binding sites of PYCR2, PSTPIP1 and PDCD5 were validated by an in vitro luciferase reporter assay. In addition, several potential targets with important biological functions were identified by the miRanda algorithm and experimentally confirmed. These targets include KLF5, MAP3K7, TARDBP and UBE2E3, which have conserved miR-143 binding sites across multiple vertebrate species. Potential chicken specific miR-143 target sites were also validated for LPIN1, PCK2, PYCR2, METTL14, SLC2A2 and TNFSF10. Overall, the current study suggests that miR-143 is ubiquitously expressed among tissues and is likely to be involved in the regulation of cell proliferation and apoptosis. [source] Ligands for retinoic acid receptors are elevated in osteoarthritis and may contribute to pathologic processes in the osteoarthritic jointARTHRITIS & RHEUMATISM, Issue 6 2009Mark R. Davies Objective Vitamin A derivatives, including all- trans -retinoic acid (ATRA), have a well-established role during skeletal development and limb formation and have been shown to have profound effects on chondrocyte phenotype. The aim of this study was to elucidate the effects of retinoids and components of the retinoid metabolic pathway on chondrocyte phenotype in the tibiofemoral joints of patients with osteoarthritis (OA), to show that the retinoids can have multiple effects relevant to the OA disease process. Methods Human explant tissue and a chondrocyte-like cell line were treated with ATRA, and the responses of 4 key markers of chondrocyte phenotype were analyzed. In addition, the effects of ATRA on a number of novel genes associated with OA were assessed using a low-density microarray containing 80 disease marker genes. Results Vitamin A metabolite levels were elevated in synovial fluid, serum, and cartilage from patients with OA. Expression profiling of a retinoic acid receptor , coactivator protein, P/CAF, demonstrated elevated expression in patients with OA, suggesting the potential for increased signaling via the retinoid receptors in the disease. ATRA increased the levels of matrix metalloproteinase 13 and aggrecanase activity in human cartilage explants and in a human chondrocyte cell line. Furthermore, ATRA altered the expression of a wide range of relevant genes, including the types I, II, IX, and XI collagen genes, toward a nonchondrogenic and OA-like phenotype. Conclusion These results suggest that retinoid signaling could have a central role in OA, and that components of the pathway may provide potential disease biomarkers or targets for therapeutic intervention. [source] MutationView/KMcancerDB: A database for cancer gene mutationsCANCER SCIENCE, Issue 3 2007Nobuyoshi Shimizu It is known that cancers are caused by accumulated mutations in various genes and consequent functional alterations of proteins that are important for maintenance of normal cellular functions. The changes in nucleotide sequences and expression patterns of cancer-related genes are being extensively studied to better understand the mechanisms of tumorigenesis and to develop methods for DNA protein diagnosis and drug discovery. At present, a number of computer databases for molecular information on cancer-related genes are available publicly through the internet. These databases deal with familial cancer and sporadic cancer at the levels of germline mutation or somatic mutation, genomic or chromosomal abnormalities, and changes in the expression levels of relevant genes. Previously, we constructed a human gene mutation database named MutationView (http://mutview.dmb.med.keio.ac.jp/) and have accumulated mutation data for ,300 genes that are involved mainly in monogenic diseases. Forty-two genes are cancer-related and therefore a separate cancer database named KMcancerDB was constructed. MutationView/KMcancerDB utilizes a graphic display function for both queries and search results much more often than other existing databases, making the system quite user friendly. MutationView/KMcancerDB provides a highly sophisticated search function for all genes through a single internet URL. In the present paper, we briefly review various useful databases for cancer-related genes, and describe MutationView/KMcancerDB in more detail. (Cancer Sci 2007; 98: 259,267) [source] HYPOXIA-INDUCED ERYTHROPOIETIN PRODUCTION: A PARADIGM FOR OXYGEN-REGULATED GENE EXPRESSIONCLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, Issue 10 2006Christian Stockmann SUMMARY 1The mechanisms controlling the expression of the gene encoding for the hormone erythropoietin (EPO) are exemplary for oxygen-regulated gene expression. In humans and other mammals, hypoxia modulates EPO levels by increasing expression of the EPO gene. An association between polycythaemia and people living at high altitudes was first reported more than 100 years ago. 2Since the identification of EPO as the humoral regulator of red blood cell production and the cloning of the EPO gene, considerable progress has been made in understanding the regulation of EPO gene expression. This has finally led to the identification of a widespread cellular oxygen-sensing mechanism. Central to this mechanism is the transcription factor complex hypoxia-inducible factor (HIF)-1. 3The abundance and activity of HIF-1, a heterodimer of an ,- and ,-subunit, is predominantly regulated by oxygen-dependent post-translational hydroxylation of the ,-subunit. Non-heme ferrous iron containing hydroxylases use dioxygen and 2-oxoglutarate to specifically target proline and an asparagine residue in HIF-1,. As such, the three prolyl hydroxylases (prolyl hydroxylase domain-containing protein (PHD) 1, PHD2 and PHD3) and the asparagyl hydroxylase (factor inhibiting HIF (FIH)-1) act as cellular oxygen sensors. In addition to erythropoiesis, HIF-1 regulates a broad range of physiologically relevant genes involved in angiogenesis, apoptosis, vasomotor control and energy metabolism. Therefore, the HIF system is implicated in the pathophysiology of many human diseases. 4In addition to the tight regulation by oxygen tension, temporal and tissue-specific signals limit expression of the EPO gene primarily to the fetal liver and the adult kidney. [source] | |||||||||||||