Expression data collected using a custom Affymetrix array (Adenoma Biomarker Gene Chip) designed to differentiate neoplastic colorectal from non-neoplastic
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE24713 | GEO | 2010/11/13
SECONDARY ACCESSION(S): PRJNA132335
REPOSITORIES: GEO
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Project description:This array was designed to verify a number of previously identified markers for colo-rectal adenoma. It contains probesets from the Affymetrix Hu133, HuGene and other novel probesets not included on other arrays. 68 samples of colon tissues were analysed, covering the classes normal, adenoma and carcinoma.
2010-11-13 | E-GEOD-24713 | biostudies-arrayexpress
Project description:We designed a custom expression 8x15 k microarray for Cottus fishes based on transcriptome sequencing. It is a known fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. Please refer to the accompanying publication (Czypionka et al. 2011."Transcriptome changes after genome wide admixture in invasive sculpins" Molecular Ecology; no doi yet) for more information.
2012-03-27 | GSE36800 | GEO
Project description:Despite the success of cross-sectional imaging in evaluating hepatopancreatobiliary system malignancies, several non-malignant disease processes may closely mimic malignancy. Differentiating these benign diseases from malignancy may be difficult, or even impossible, even in the hands of experienced imagers. In this manuscript, we present benign mimics involving the hepatopancreatobiliary system and try to increase awareness of these potential pitfalls.
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Project description:Advances in aerosol technology over the past 10 years have enabled the generation and design of ultrafine nanoscale materials for many applications. A key new method is flame spray pyrolysis (FSP), which produces particles by pyrolyzing a precursor solution in the gas phase. FSP is a highly versatile technique for fast, single-step, scalable synthesis of nanoscale materials. New innovations in particle synthesis using FSP technology, including variations in precursor chemistry, have enabled flexible, dry synthesis of loosely agglomerated, highly crystalline ultrafine powders (porosity ? 90%) of binary, ternary, and mixed-binary-and-ternary oxides. FSP can fulfill much of the increasing demand, especially in biological applications, for particles with specific material composition, high purity, and high crystallinity. In this Account, we describe a strategy for creating nanoparticle libraries (pure or Fedoped ZnO or TiO?) utilizing FSP and using these libraries to test hypotheses related to the particles' toxicity. Our innovation lies in the overall integration of the knowledge we have developed in the last 5 years in (1) synthesizing nanomaterials to address specific hypotheses, (2) demonstrating the electronic properties that cause the material toxicity, (3) understanding the reaction mechanisms causing the toxicity, and (4) extracting from in vitro testing and in vivo testing in terrestrial and marine organisms the essential properties of safe nanomaterials. On the basis of this acquired knowledge, we further describe how the dissolved metal ion from these materials (Zn²? in this Account) can effectively bind with different cell constituents, causing toxicity. We use Fe-S protein clusters as an example of the complex chemical reactions taking place after free metal ions migrate into the cells. As a second example, TiO? is an active material in the UV range that exhibits photocatalytic behavior. The induction of electron-hole (e?/h?) pairs followed by free radical production is a key mechanism for biological injury. We show that decreasing the bandgap energy increases the phototoxicity in the presence of near-visible light. We present in detail the mechanism of electron transfer in biotic and abiotic systems during light exposure. Through this example we show that FSP is a versatile technique for efficiently designing a homologous library, meaning a library based on a parent oxide doped with different amounts of dopant, and investigating the properties of the resulting compounds. Finally, we describe the future outlook and state-of-the-art of an innovative two-flame system. A double-flame reactor enables independent control over each flame, the nozzle distances and the flame angles for efficient mixing of the particle streams. In addition, it allows for different flame compositions, flame sizes, and multicomponent mixing (a grain-grain heterojunction) during the reaction process.
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| S-EPMC10983830 | biostudies-literature
Project description:We designed a custom expression 8x15 k microarray for Cottus fishes based on transcriptome sequencing. It is a known fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. Please refer to the accompanying publication (Czypionka et al. 2011."Transcriptome changes after genome wide admixture in invasive sculpins" Molecular Ecology; no doi yet) for more information. Labeled cRNA was prepared from 3 Cottus fish. These 3 fish were representative of species (C.rhenanus, C.perifretum, invasive hybrid species) used in another experiment. An calibration pool was prepared from equimolar amounts of this cRNA. Increasing amounts of labeled cRNA (75 ng, 150 ng, 300 ng, 600 ng, 1200 ng, 2400 ng, 4800 ng), corresponding to (1/8, 1/4, 1/2, 1, 2, 4 and 8 times the recommended amount of 600 ng) were hybridized to 7 microarrays (one microarray per dilution-step). The change in observed signal intensity in relation to the change in amount of labeled cRNA was used to infer the target-binding behavior of the individual probes. This information was extracted, to be used for a normalization procedure in another experiment with the same microarray (see Czypionka et al. 2011."Transcriptome changes after genome wide admixture in invasive sculpins" Molecular Ecology; no doi yet)
2012-03-26 | E-GEOD-36800 | biostudies-arrayexpress
Project description:The main challenge in the management of indeterminate incidentally discovered adrenal tumours is to differentiate benign from malignant lesions. In the absence of clear signs of invasion or metastases, imaging techniques do not always precisely define the nature of the mass. The present pilot study aimed to determine whether radiomics may predict malignancy in adrenocortical tumours. CT images in unenhanced, arterial, and venous phases from 19 patients who had undergone resection of adrenocortical tumours and a cohort who had undergone surveillance for at least 5 years for incidentalomas were reviewed. A volume of interest was drawn for each lesion using dedicated software, and, for each phase, first-order (histogram) and second-order (grey-level colour matrix and run-length matrix) radiological features were extracted. Data were revised by an unsupervised machine learning approach using the K-means clustering technique. Of operated patients, nine had non-functional adenoma and 10 carcinoma. There were 11 patients in the surveillance group. Two first-order features in unenhanced CT and one in arterial CT, and 14 second-order parameters in unenhanced and venous CT and 10 second-order features in arterial CT, were able to differentiate adrenocortical carcinoma from adenoma (P < 0.050). After excluding two malignant outliers, the unsupervised machine learning approach correctly predicted malignancy in seven of eight adrenocortical carcinomas in all phases. Radiomics with CT texture analysis was able to discriminate malignant from benign adrenocortical tumours, even by an unsupervised machine learning approach, in nearly all patients.
| S-EPMC7937424 | biostudies-literature
Project description:Site-directed mutagenesis in higher plants remains a significant technical challenge for basic research and molecular breeding. Here, we demonstrate targeted-gene inactivation for an endogenous gene in Arabidopsis using zinc finger nucleases (ZFNs). Engineered ZFNs for a stress-response regulator, the ABA-INSENSITIVE4 (ABI4) gene, cleaved their recognition sequences specifically in vitro, and ZFN genes driven by a heat-shock promoter were introduced into the Arabidopsis genome. After heat-shock induction, gene mutations with deletion and substitution in the ABI4 gene generated via ZFN-mediated cleavage were observed in somatic cells at frequencies as high as 3%. The homozygote mutant line zfn_abi4-1-1 for ABI4 exhibited the expected mutant phenotypes, i.e., ABA and glucose insensitivity. In addition, ZFN-mediated mutagenesis was applied to the DNA repair-deficient mutant plant, atku80. We found that lack of AtKu80, which plays a role in end-protection of dsDNA breaks, increased error-prone rejoining frequency by 2.6-fold, with increased end-degradation. These data demonstrate that an approach using ZFNs can be used for the efficient production of mutant plants for precision reverse genetics.
| S-EPMC2900650 | biostudies-literature
Project description:BackgroundSomatic genetic testing is rapidly becoming the standard of care in many adult and pediatric cancers. Previously, the standard approach was single-gene or focused multigene testing, but many centers have moved towards broad-based next-generation sequencing (NGS) panels. Here, we report the laboratory validation and clinical utility of a large cohort of clinical NGS somatic sequencing results in diagnosis, prognosis, and treatment of a wide range of pediatric cancers.MethodsSubjects were accrued retrospectively at a single pediatric quaternary-care hospital. Sequence analyses were performed on 367 pediatric cancer samples using custom-designed NGS panels over a 15-month period. Cases were profiled for mutations, copy number variations, and fusions identified through sequencing, and their clinical impact on diagnosis, prognosis, and therapy was assessed.ResultsNGS panel testing was incorporated meaningfully into clinical care in 88.7% of leukemia/lymphomas, 90.6% of central nervous system (CNS) tumors, and 62.6% of non-CNS solid tumors included in this cohort. A change in diagnosis as a result of testing occurred in 3.3% of cases. Additionally, 19.4% of all patients had variants requiring further evaluation for potential germline alteration.ConclusionsUse of somatic NGS panel testing resulted in a significant impact on clinical care, including diagnosis, prognosis, and treatment planning in 78.7% of pediatric patients tested in our institution. Somatic NGS tumor testing should be implemented as part of the routine diagnostic workup of newly diagnosed and relapsed pediatric cancer patients.
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Project description:Multiple genetic disorders can be associated with excessive signalling by mutant G-protein-coupled receptors (GPCRs) that are either constitutively active or have lost sites where phosphorylation by GPCR kinases is necessary for desensitisation by cognate arrestins. Phosphorylation-independent arrestin1 can compensate for defects in phosphorylation of the GPCR rhodopsin in retinal rod cells, facilitating recovery, improving light responsiveness, and promoting photoreceptor survival. These proof-of-principle experiments show that, based on mechanistic understanding of the inner workings of a protein, one can modify its functional characteristics to generate custom-designed mutants that improve the balance of signalling in congenital and acquired disorders. Manipulations of arrestin elements responsible for scaffolding mitogen-activated protein kinase cascades and binding other signalling proteins involved in life-or-death decisions in the cell are likely to yield mutants that affect cell survival and proliferation in the desired direction. Although this approach is still in its infancy, targeted redesign of individual functions of many proteins offers a promise of a completely new therapeutic toolbox with huge potential.
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