Search results for "bioinformatics"

Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR

2015

Metastasis is respoMetastasis is responsible for most cancer-related deaths, and, among common tumor types, melanoma is one with great potential to metastasize. Here we study the contribution of epigenetic changes to the dissemination process by analyzing the changes that occur at the DNA methylation level between primary cancer cells and metastases. We found a hypomethylation event that reactivates a cryptic transcript of the Rab GTPase activating protein TBC1D16 (TBC1D16-47 kDa; referred to hereafter as TBC1D16-47KD) to be a characteristic feature of the metastatic cascade. This short isoform of TBC1D16 exacerbates melanoma growth and metastasis both in vitro and in vivo. By combining imm…

Analyzing Oligomerization of Individual Transmembrane Helices and of Entire Membrane Proteins in E. coli: A Hitchhiker’s Guide to GALLEX

2012

Genetic systems, which allow monitoring interactions of individual transmembrane α-helices within the cytoplasmic membrane of the bacterium Escherichia coli, are now widely used to probe the structural biology and energetics of helix-helix interactions and the consequences of mutations. In contrast to other systems, the GALLEX system allows studying homo- as well as heterooligomerization of individual transmembrane α-helices, and even enables estimation of the energetics of helix-helix interactions within a biological membrane. Given that many polytopic membrane proteins form oligomers within membranes, the GALLEX system represents a unique and powerful approach to monitor formation and sta…

Improving the Techniques for Human Hepatocyte Transplantation: Report from a Consensus Meeting in London

2012

On September 6 and 7, 2009 a meeting was held in London to identify and discuss what are perceived to be current roadblocks to effective hepatocyte transplantation as it is currently practiced in the clinics and, where possible, to offer suggestions to overcome the blocks and improve the outcomes for this cellular therapy. Present were representatives of most of the active clinical hepatocyte transplant programs along with other scientists who have contributed substantial basic research to this field. Over the 2-day sessions based on the experience of the participants, numerous roadblocks or challenges were identified, including the source of cells for the transplants and problems with tra…

RATIONALE FOR THE USE OF ANTIOXIDANT VITAMINS IN CLINICAL ORGAN TRANSPLANTATION

1996

From Bench to Bedside—The Bad Berka Experience With First-in-Human Studies

2019

Precision oncology is being driven by rapid advances in novel diagnostics and therapeutic interventions, with treatments targeted to the needs of individual patients on the basis of genetic, biomarker, phenotypic, or psychosocial characteristics that distinguish a given patient from other patients with similar clinical presentations. Inherent in the theranostics paradigm is the assumption that diagnostic test results can precisely determine whether an individual is likely to benefit from a specific treatment. As part and integral in the current era of precision oncology, theranostics in the context of nuclear medicine aims to identify the appropriate molecular targets in neoplasms (diagnost…

Tris(cyclo-hexyl-ammonium) cis-di-chlorido-bis-(oxalato-κ(2) O (1),O (2))stann-ate(IV) chloride monohydrate.

2013

The crystal structure of the title compound, (C6H14N)3[Sn(C2O4)2Cl2]Cl·H2O, contains three cyclohexylammonium cations, one stannate(IV) dianion, one isolated chloride anion and one lattice water molecule. The cyclohexylammonium cations adopt chair conformations. In the complex anion, two bidentate oxalate ligands and two chloride anions incispositions coordinate octahedrally to the central SnIVatom. The cohesion of the molecular entities is ensured by the formation of N—H...O, O—H...O, O—H...Cl and N—H...Cl interactions involving cations, anions and the lattice water molecule, giving rise to a layer-like arrangement parallel to (010).

A helicopter perspective on TB biomarkers: pathway and process based analysis of gene expression data provides new insight into TB pathogenesis.

2013

Biomarker host genetic signatures are considered key tools for improved early diagnosis of tuberculosis (TB) disease (development). The analysis of gene expression changes based on a limited number of genes or single study designs, however, may not be sufficient for the identification of universal diagnostic biomarker profiles. Here we propose that biological pathway and process based analyses from multiple data sets may be more relevant for identification of key pathways in TB pathogenesis, and may reveal novel candidate diagnostic TB biomarkers. A number of independent genome-wide gene expression studies have recently been performed to study expression of biomarkers for TB disease. We hav…

Zebrafish xenografts as a tool for in vivo studies on human cancer

2012

The zebrafish has become a powerful vertebrate model for genetic studies of embryonic development and organogenesis and increasingly for studies in cancer biology. Zebrafish facilitate the performance of reverse and forward genetic approaches, including mutagenesis and small molecule screens. Moreover, several studies report the feasibility of xenotransplanting human cells into zebrafish embryos and adult fish. This model provides a unique opportunity to monitor tumor-induced angiogenesis, invasiveness, and response to a range of treatments in vivo and in real time. Despite the high conservation of gene function between fish and humans, concern remains that potential differences in zebrafis…

JSSPrediction: a Framework to Predict Protein Secondary Structures Using Integration

2006

Identifying protein secondary structures is a difficult task. Recently, a lot of software tools for protein secondary structure prediction have been produced and made available on-line, mostly with good performances. However, prediction tools work correctly for families of proteins, such that users have to know which predictor to use for a given unknown protein. We propose a framework to improve secondary structure prediction by integrating results obtained from a set of available predictors. Our contribution consists in the definition of a two phase approach: (i) select a set of predictors which have good performances with the unknown protein family, and (ii) integrate the prediction resul…

Urinary MicroRNA Profiling Predicts the Development of Microalbuminuria in Patients with Type 1 Diabetes

2015

Microalbuminuria provides the earliest clinical marker of diabetic nephropathy among patients with Type 1 diabetes, yet it lacks sensitivity and specificity for early histological manifestations of disease. In recent years microRNAs have emerged as potential mediators in the pathogenesis of diabetes complications, suggesting a possible role in the diagnosis of early stage disease. We used quantiative polymerase chain reaction (qPCR) to evaluate the expression profile of 723 unique microRNAs in the normoalbuminuric urine of patients who did not develop nephropathy (n = 10) relative to patients who subsequently developed microalbuminuria (n = 17). Eighteen microRNAs were strongly associated w…