Proteomics Analysis of Ovarian Cancer Cell Lines and Tissues Reveals Drug Resistance-associated Proteins

Background: Carboplatin and paclitaxel form the cornerstone of chemotherapy for epithelial ovarian cancer, however, drug resistance to these agents continues to present challenges. Despite extensive research, the mechanisms underlying this resistance remain unclear. Materials and Methods: A 2D-gel proteomics method was used to analyze protein expression levels of three human ovarian cancer cell lines and five biopsy samples. Representative proteins identified were validated via western immunoblotting. Ingenuity pathway analysis revealed metabolomic pathway changes. Results: A total of 189 proteins were identified with restricted criteria. Combined treatment targeting the proteasome-ubiquitin pathway resulted in re-sensitisation of drug-resistant cells. In addition, examination of five surgical biopsies of ovarian tissues revealed α-enolase (ENOA), elongation factor Tu, mitochondrial (EFTU), glyceraldehyde-3-phosphate dehydrogenase (G3P), stress-70 protein, mitochondrial (GRP75), apolipoprotein A-1 (APOA1), peroxiredoxin (PRDX2) and annexin A (ANXA) as candidate biomarkers of drug-resistant disease. Conclusion: Proteomics combined with pathway analysis provided information for an effective combined treatment approach overcoming drug resistance. Analysis of cell lines and tissues revealed potential prognostic biomarkers for ovarian cancer

Proteins identification of wheat-rye translocation lines by MALDI-TOF-TOF mass spectrometry and ESI-QTOF/MS

OBJECTIVE: To examine the relationship between Timed Up and Go (TUG) performance, verbal executive function (EF) performance, and quality-of-life (QOL) measures in Parkinson's disease (PD). DESIGN: Cross-sectional. SETTING: Sixteen movement disorder centers from across the United States. PARTICIPANTS: Patients with PD (N=1964). INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: TUG test, immediate and delayed 5-word recall, verbal fluency, PD QOL Questionnaire. RESULTS: TUG performance and verbal EF performance were significantly associated with, and predictors of, QOL measures, having the greatest association and predictability with the mobility domain of the QOL measures. CONCLUSIONS: The TUG test and verbal EF tests have QOL correlates, making the combined evaluation of mobility, cognitive, and QOL decline a potential examination tool to evaluate the sequelae of PD

Temporomandibular Joint Disorder Complaints in Tinnitus: Further Hints for a Putative Tinnitus Subtype

OBJECTIVE: Tinnitus is considered to be highly heterogeneous with respect to its etiology, its comorbidities and the response to specific interventions. Subtyping is recommended, but it remains to be determined which criteria are useful, since it has not yet been clearly demonstrated whether and to which extent etiologic factors, comorbid states and interventional response are related to each other and are thus applicable for subtyping tinnitus. Analyzing the Tinnitus Research Initiative Database we differentiated patients according to presence or absence of comorbid temporomandibular joint (TMJ) disorder complaints and compared the two groups with respect to etiologic factors. METHODS: 1204 Tinnitus patients from the Tinnitus Research Initiative (TRI) Database with and without subjective TMJ complaints were compared with respect to demographic, tinnitus and audiological characteristics, questionnaires, and numeric ratings. Data were analysed according to a predefined statistical analysis plan. RESULTS: Tinnitus patients with TMJ complaints (22% of the whole group) were significantly younger, had a lower age at tinnitus onset, and were more frequently female. They could modulate or mask their tinnitus more frequently by somatic maneuvers and by music or sound stimulation. Groups did not significantly differ for tinnitus duration, type of onset (gradual/abrupt), onset related events (whiplash etc.), character (pulsatile or not), hyperacusis, hearing impairment, tinnitus distress, depression, quality of life and subjective ratings (loudness etc.). CONCLUSION: Replicating previous work in tinnitus patients with TMJ complaints, classical risk factors for tinnitus like older age and male gender are less relevant in tinnitus patients with TMJ complaints. By demonstrating group differences for modulation of tinnitus by movements and sounds our data further support the notion that tinnitus with TMJ complaints represents a subgroup of tinnitus with clinical features that are highly relevant for specific therapeutic management

Comparing Psoriatic Arthritis Low-field Magnetic Resonance Imaging, Ultrasound, and Clinical Outcomes: Data from the TICOPA Trial

Objective: The Tight Control of inflammation in Psoriatic arthritis (TICOPA; isrctn.com: ISRCTN30147736) trial compared standard care (StdC) and tight control (TC) in early psoriatic arthritis (PsA), demonstrating better outcomes for TC. This substudy evaluated the performance metrics of modern imaging outcomes and compared them to the clinical data. Methods: Non-contrast 0.2T magnetic resonance imaging (MRI; single hand) was assessed using the Outcomes in Rheumatology (OMERACT) PsA MRI Scoring System (PsAMRIS) with an additional global inflammation score. Ultrasound (US; same hand) was scored for greyscale, power Doppler, and erosions at the metacarpophalangeal (MCP) and proximal interphalangeal (PIP) joints and scores summated. Results: Seventy-eight patients had paired (baseline and 48 weeks) US data and 61 paired MRI data; 50 had matched clinical, MR, and US data. Significant within-group changes were seen for the inflammatory PsAMRIS components at MCP level: MRI global inflammation [median difference (range), standardized response mean (SRM)]: 3.25 (−5.0 to 12.0), 0.68; 1.0 (−4.5 to 17.5), 0.45 for TC and StdC, respectively. Similar within-group differences were obtained for US: 1.0 (−13.0 to 23.0), 0.45; 3.0 (−6.0 to 21.0), 0.77 for TC and StdC, respectively. No differences were seen between treatment groups. Significant correlations were found between baseline and change MRI and US scores. A significant correlation was found between baseline PsA disease activity scores and MRI global inflammation scores (Spearman ρ for MCP, PIP: 0.46, 0.63, respectively). No differences in erosion progression were observed. Conclusion: The PsAMRIS and US inflammation scores demonstrated good responsiveness. No between-group differences were demonstrated, but this substudy was likely underpowered to determine differences between the 2 treatment strategies

An optoelectronic framework enabled by low-dimensional phase-change films.

Accepted author version. The definitive version was published in: Nature 511, 206–211 (10 July 2014) doi:10.1038/nature13487The development of materials whose refractive index can be optically transformed as desired, such as chalcogenide-based phase-change materials, has revolutionized the media and data storage industries by providing inexpensive, high-speed, portable and reliable platforms able to store vast quantities of data. Phase-change materials switch between two solid states--amorphous and crystalline--in response to a stimulus, such as heat, with an associated change in the physical properties of the material, including optical absorption, electrical conductance and Young's modulus. The initial applications of these materials (particularly the germanium antimony tellurium alloy Ge2Sb2Te5) exploited the reversible change in their optical properties in rewritable optical data storage technologies. More recently, the change in their electrical conductivity has also been extensively studied in the development of non-volatile phase-change memories. Here we show that by combining the optical and electronic property modulation of such materials, display and data visualization applications that go beyond data storage can be created. Using extremely thin phase-change materials and transparent conductors, we demonstrate electrically induced stable colour changes in both reflective and semi-transparent modes. Further, we show how a pixelated approach can be used in displays on both rigid and flexible films. This optoelectronic framework using low-dimensional phase-change materials has many likely applications, such as ultrafast, entirely solid-state displays with nanometre-scale pixels, semi-transparent 'smart' glasses, 'smart' contact lenses and artificial retina devices.Engineering and Physical Sciences Research Council (EPSRC)OUP John Fell Fun

Expression of phosphorylated raf kinase inhibitor protein (pRKIP) is a predictor of lung cancer survival

<p>Abstract</p> <p>Background</p> <p>Raf-1 kinase inhibitor protein (RKIP) has been reported to negatively regulate signal kinases of major survival pathways. RKIP activity is modulated in part by phosphorylation on Serine 153 by protein kinase C, which leads to dissociation of RKIP from Raf-1. RKIP expression is low in many human cancers and represents an indicator of poor prognosis and/or induction of metastasis. The prognostic power has typically been based on total RKIP expression and has not considered the significance of phospho-RKIP.</p> <p>Methods</p> <p>The present study examined the expression levels of both RKIP and phospho-RKIP in human lung cancer tissue microarray proteomics technology.</p> <p>Results</p> <p>Total RKIP and phospho-RKIP expression levels were similar in normal and cancerous tissues. phospho-RKIP levels slightly decreased in metastatic lesions. However, the expression levels of phospho-RKIP, in contrast to total RKIP, displayed significant predictive power for outcome with normal expression of phospho-RKIP predicting a more favorable survival compared to lower levels (P = 0.0118); this was even more pronounced in more senior individuals and in those with early stage lung cancer.</p> <p>Conclusions</p> <p>This study examines for the first time, the expression profile of RKIP and phospho-RKIP in lung cancer. Significantly, we found that phospho-RKIP was a predictive indicator of survival.</p

Gene set analysis exploiting the topology of a pathway

<p>Abstract</p> <p>Background</p> <p>Recently, a great effort in microarray data analysis is directed towards the study of the so-called gene sets. A gene set is defined by genes that are, somehow, functionally related. For example, genes appearing in a known biological pathway naturally define a gene set. The gene sets are usually identified from a priori biological knowledge. Nowadays, many bioinformatics resources store such kind of knowledge (see, for example, the Kyoto Encyclopedia of Genes and Genomes, among others). Although pathways maps carry important information about the structure of correlation among genes that should not be neglected, the currently available multivariate methods for gene set analysis do not fully exploit it.</p> <p>Results</p> <p>We propose a novel gene set analysis specifically designed for gene sets defined by pathways. Such analysis, based on graphical models, explicitly incorporates the dependence structure among genes highlighted by the topology of pathways. The analysis is designed to be used for overall surveillance of changes in a pathway in different experimental conditions. In fact, under different circumstances, not only the expression of the genes in a pathway, but also the strength of their relations may change. The methods resulting from the proposal allow both to test for variations in the strength of the links, and to properly account for heteroschedasticity in the usual tests for differential expression.</p> <p>Conclusions</p> <p>The use of graphical models allows a deeper look at the components of the pathway that can be tested separately and compared marginally. In this way it is possible to test single components of the pathway and highlight only those involved in its deregulation.</p

Mining Biological Pathways Using WikiPathways Web Services

WikiPathways is a platform for creating, updating, and sharing biological pathways [1]. Pathways can be edited and downloaded using the wiki-style website. Here we present a SOAP web service that provides programmatic access to WikiPathways that is complementary to the website. We describe the functionality that this web service offers and discuss several use cases in detail. Exposing WikiPathways through a web service opens up new ways of utilizing pathway information and assisting the community curation process

Search for the Flavor-Changing Neutral Current Decay D0→μ+μ−D^0 \to \mu^+\mu^- with the HERA-B Detector

We report on a search for the flavor-changing neutral current decay $D^0 \to \mu^+\mu^-$ using $50 \times 10^6$ events recorded with a dimuon trigger in interactions of 920 GeV protons with nuclei by the HERA-B experiment. We find no evidence for such decays and set a 90% confidence level upper limit on the branching fraction $Br(D^0 \to \mu^+\mu^-) <2.0 \times 10^{-6}$.Comment: 17 pages, 4 figures (of which 1 double), paper to be submitted to Physics Letters