1,190 research outputs found
Unusual oxygen binding behavior of a 24-meric crustacean hemocyanin
No full textHemocyanins from Crustacea usually are found as 1 × 6 or 2 × 6-meric assemblies. An exception is the hemocyanin isolated from thalassinidean shrimps where the main component is a 24-meric structure. Our analysis of oxygen binding data of the thalassinidean shrimp Upogebia pusilla based on a three-state MWC-model revealed that despite the 24-meric structure the functional properties can be described very well based on the hexamer as allosteric unit. In contrast to the hemocyanins from other thalassinidean shrimps the oxygen affinity of hemocyanin from U. pusilla is increased upon addition of l-lactate. A particular feature of this hemocyanin seems to be that l-lactate already enhances oxygen affinity under resting conditions which possibly compensates the rather low intrinsic affinity observed in absence of l-lactate. The fast rate of oxygen dissociation might indicate that in this hemocyanin a higher cooperativity is less important than a fast response of saturation level to changes in oxygen concentration. © 2010 Elsevier Inc. All rights reserved
The novel mTOR inhibitor RAD001 (Everolimus) induces antiproliferative effects in human pancreatic neuroendocrine tumor cells
No full textBackground/Aim: Tumors exhibiting constitutively activated PI(3) K/Akt/mTOR signaling are hypersensitive to mTOR inhibitors such as RAD001 (everolimus) which is presently being investigated in clinical phase II trials in various tumor entities, including neuroendocrine tumors (NETs). However, no preclinical data about the effects of RAD001 on NET cells have been published. In this study, we aimed to evaluate the effects of RAD001 on BON cells, a human pancreatic NET cell line that exhibits constitutively activated PI(3) K/Akt/mTOR signaling. Methods: BON cells were treated with different concentrations of RAD001 to analyze its effect on cell growth using proliferation assays. Apoptosis was examined by Western blot analysis of caspase-3/PARP cleavage and by FACS analysis of DNA fragmentation. Results: RAD001 potently inhibited BON cell growth in a dose-dependent manner which was dependent on the serum concentration in the medium. RAD001-induced growth inhibition involved G0/G1-phase arrest as well as induction of apoptosis. Conclusion: In summary, our data demonstrate antiproliferative and apoptotic effects of RAD001 in NET cells in vitro supporting its clinical use in current phase II trials in NET patients. Copyright (c) 2007 S. Karger AG, Basel
Medicinal Plants Used in Meric Town from Turkey
No full text3rd Mediterranean Symposium on Medicinal and Aromatic Plants (MESMAP) -- APR 13-16, 2017 -- Girne, CYPRUSBackground: There are a few studies on medical plants used in the Trakya region of Turkey ( Havsa, Lalapasa, Uzunkopru, Ipsala, Enez, Kirklareli). However, there has been no research study performed investigating the preparation and medicinal uses of wild plants in Meric town. Aim: The aim of this study is to determine the parts of locally growing medicinal plants used by local people in Meric town and the purpose of their use. Methods: In this study, 16 villages in Meric town (Edirne province, Turkey) were visited, and interviews were performed with 38 persons in total. Results: As result of the study, 24 plant taxa in 19 families were recorded as medicinal plants used by local people. Conclusion: These traditional medicinal plants have been mostly used for the treatment of diabetes, stomach ailments, hemorrhoids, rheumatism and asthma.Trakya University [TUBAP 2013/22]The author would like to thank to all the villagers of Meric town who collaborated in the realization of this study. This study was supported by The Scientific Research Fund of Trakya University (Project no. TUBAP 2013/22)
WATER AND SEDIMENT QUALITY ASSESSMENT OF THE LIFEBLOOD OF THRACE REGION (TURKEY): MERIC RIVER BASIN
No full textMeric River, which is the longest river in Balkans, is one of the most important aquatic ecosystems in Thrace Region of Turkey. But as many aquatic ecosystems, Meric River Basin is known to be exposed to an intensive organic and inorganic pollution by means of agricultural and industrial pressure on the system. The aim of this study was to determine the water and sediment quality of Meric River Basin by using some statistical techniques. For this purpose, water and sediment samples were collected in spring (rainy) season of 2017 from 24 stations selected on the basin. Total of 19 water quality parameters (temperature, dissolved oxygen, % oxygen saturation, pH, EC, TDS, salinity, turbidity, nitrate, nitrite, ammonium, phosphate, sulphate, floride, chloride, ORP, COD, BOD and fecal coliform) were investigated in water samples and also total of 9 inorganic pollution parameters (Cd, Pb, As, B, Cu, Zn, Cr, Ni and Se) were investigated in water and sediment samples. Cluster Analysis (CA) and Factor Analysis (FA) were applied to the results in order to evaluate the detected data effectively. According to detected data, pollution levels of the investigated rivers and lakes as follows; Ergene River > Meric River > Tunca River > Lakes of Meric Delta in general. It was also determined that organic contamination levels in water and toxic element levels in sediment of the Meric River Basin have reached to critical levels and the system is under effect of agricultural and industrial pressure.Trakya University, Turkey; Trakya University, Commission of Scientific Research Projects [2016/247]The author would like to thank for the financial and technical supports supplied by Trakya University, Turkey. This investigation has been supported by the project numbered as 2016/247 accepted by Trakya University, Commission of Scientific Research Projects
The molecular heterogeneity of hemocyanin: structural and functional properties of the 4x6-meric protein of Crustacea.
No full textThe structural properties of the hemocyanin isolated from the Mediterranean mud shrimp, Upogebia pusilla (Decapoda: Thalassinidea), were investigated. Our intent was to make use of the U. pusilla case to perform a structural comparison between crustacean and chelicerate 4 x 6-meric hemocyanins. The thalassinidean hemocyanin appears similar in size but different in structural organization compared to the chelicerate 4 x 6-mer. Ultracentrifiage analyses on the purified protein revealed a sedimentation coefficient of 39S, typical of 4 x 6 hemocyanins. Electron micrographs are in agreement with a model in which four 2 x 6-meric building blocks are arranged in a tetrahedron-like quaternary structure and not in the quasi-square-planar orientation characteristic of the chelicerate protein. Size-exclusion chromatography-fast protein chromatography analysis showed elevated instability of the protein in absence of divalent ions or at pH values higher than 8.0. This analysis also shows that the dissociation of the U. pusilla 4 x 6-meric hemocyanin into hexamers occurs without any intermediate 2 x 6-meric state, in contrast with the dissociation profile of the chelicerate protein exhibiting several dissociation intermediates. The oxygen-binding properties of U. pusilla hemocyanin were studied to disclose possible effects by the typical allosteric effectors that modulate the functional properties of crustacean hemocyanin. A marked Bohr and lactate effect, but no significant influence of urate, on the oxygen affinity of U. pusilla hernocyanin were found
Ribociclib plus letrozole in early breast cancer: A presurgical, window-of-opportunity study
No full textAbstractObjectivesCyclin D–cyclin-dependent kinase (CDK) 4/6–inhibitor of CDK4/6–retinoblastoma (Rb) pathway hyperactivation is associated with hormone receptor-positive (HR+) breast cancer (BC). This study assessed the biological activity of ribociclib (LEE011; CDK4/6 inhibitor) plus letrozole compared with single-agent letrozole in the presurgical setting.Materials and methodsPostmenopausal women (N = 14) with resectable, HR+, human epidermal growth factor receptor 2-negative (HER2–) early BC were randomized 1:1:1 to receive 2.5 mg/day letrozole alone (Arm 1), or with 400 or 600 mg/day ribociclib (Arm 2 or 3). Circulating tumor DNA and tumor biopsies were collected at baseline and, following 14 days of treatment, prior to or during surgery. The primary objective was to assess antiproliferative response per Ki67 levels in Arms 2 and 3 compared with Arm 1. Additional assessments included safety, pharmacokinetics, and genetic profiling.ResultsMean decreases in the Ki67-positive cell fraction from baseline were: Arm 1 69% (range 38–100%; n = 2), Arm 2 96% (range 78–100%; n = 6), Arm 3 92% (range 75–100%; n = 3). Decreased phosphorylated Rb levels and CDK4, CDK6, CCND2, CCND3, and CCNE1 gene expression were observed following ribociclib treatment. Ribociclib and letrozole pharmacokinetic parameters were consistent with single-agent data. The ribociclib plus letrozole combination was well tolerated, with no Grade 3/4 adverse events over the treatment.ConclusionThe results suggest absence of a drug–drug interaction between ribociclib and letrozole and indicate ribociclib plus letrozole may reduce Ki67 expression in HR+, HER2– BC (NCT01919229)
Pathway modeling: from gene expression to pathway dynamics
No full textBiological pathways represent a critical level of biological organization and understanding of biochemical pathways is identified as key to future advances in biological sciences (Schaefer, 2004). The overall goal of this thesis is to develop a pathway based approach that integrates different aspects of biological pathways, specifically the structure and the dynamics of a pathway in order to characterize cells’ behavior. Our objectives are to asses structural and functional cross-species comparison of pathways (Chapter 2), to formulate a reliable pathway activity metric based on gene expression data (Chapter 3), to demonstrate that our pathway activity formulation can predict the underlying dynamics (Chapter 4) and finally to demonstrate that the pathway activity formulation can identify cell’s response to a stimulant (Chapter 5). Chapter 3-5 present how a significant pathway can be identified. Then, cross-species comparison of pathways (Chapter 2) can be used. Note that we could have Chapter 2 and Shapter 5 swapped for a more fluent flow. Neverthless, we present the chapters in this order for a better read. In Chapter 2, we propose an improvement of the reaction alignment method, emerged as the most successful pathway comparison method, by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. In Chapter 3, we explore an extension of the pathway activity methodology which entails singular value decomposition (SVD) of the expression data of the genes constituting a given pathway. We show that pathway analysis enhances our ability to detect relevant changes in pathway activity using synthetic data. In addition, we illustrate that pathway activity formulation should be coupled with a significance analysis to distinguish significant information from random deviations.In Chapter 4, we perform an unsupervised pathway level analysis, based on the formulation presented in Chapter 3, on a rich time series of transcriptional profiling in rat liver. The over-represented five specific patterns of pathway activity levels, which cannot be explained by random events, exhibit circadian rhythms. The identification of the circadian signatures at the pathway level identify pathways related to energy metabolism, amino acid metabolism, lipid metabolism and DNA replication and protein synthesis, which are biologically relevant in rat liver. In Chapter 5, we demonstrate that our pathway activity formulation enables us to detect relevant changes in pathways due to in utero di-butyl-phthalate (DBP) exposure. Our findings suggest that the pathways that produce precursors to cholesterol synthesis exhibit more significant change compared to the rest of the affected pathways. In addition, pathway activity levels of certain biological functions accompany testosterone decrease, which is the critical event for male reproductive developmental effects of DBP, such as steroid hormone metabolism and biosynthesis of steroids.Ph.D.Includes bibliographical referencesIncludes vitaby Ayse Meric Ovaci
Abstract P3-07-04: EphA2: An emerging target in triple-negative breast cancer
No full textAbstract
Purpose: Breast tumors classified as 'triple negative' (TNBC) lack defining markers ER/PR/HER2 and do not have clinically-approved targeted therapy. This heterogeneous classification of breast cancers, while immediately responsive to standard chemotherapy, commonly develop resistance and have a poor five-year survival rate. As such, the identification of new therapeutic targets are warranted. As part of our drug discovery platform, we have identified EphA2, as a synthetic-lethal gene that enhances the therapeutic action of FDA-approved, anti-inflammatory compounds. Thus we sought to ascertain the relevance of EphA2-targeted therapy in TNBC, through the evaluation of the marker in preclinical and clinical specimens.
Methods: Sixty-one human and murine breast cancer cell lines or patient-derived xenografts were collated. Protein lysates were created from cells in vitro or from respective tumors established from cells implanted into NSG mice. Forty-nine tumors established (minimum 500mm3) and were surgically removed, fixed in formalin and paraffin embedded. A TMA was constructed with tumor specimens represented twice on the array and reflected all molecular subtypes including; ER-positive (n=5), PR-positive (n=3), HER2-positive (n=9) and TNBC (n=31). Immunostaining for EphA2 was performed with the rabbit monoclonal antibody EphA2 (D4A2) XP (Cell Signaling, #6997) using manufacturer's instructions. Immunostaining was evaluated using the H-score method (score between 0-300), with positive staining for EphA2 reflecting a score of 100 or greater. Analysis of breast cancer lysates by western blot was analyzed by absolute and relative quantitation methods; gene expression data was assessed through Oncomine or using the BreastMark algorithm (http://glados.ucd.ie/BreastMark/). This algorithm integrates gene expression and survival data from 26 datasets on 12 different microarray platforms corresponding to ˜17,000 genes in up to 4,738 samples.
Results: In an integrated gene expression platform (BreastMark), we observed that elevated EphA2 expression was associated with poor prognosis in a cohort of TNBC patient tumor samples. Western blot analysis of EphA2 protein on breast cancer cell lines, identified a greater percentage of TNBC cells expressing EphA2 compared to non-TNBC cell lines. EphA2 immunostaining was observed in the majority of tumor tissues. When present on cancer cells, EphA2 localized to the cell surface; while displaying ubiquitous localization within stromal populations. Cell surface expression of EphA2 on cancer cells was largely restricted to TNBC tumors (11/31 tumors, 35.5%) compared to other molecular subtypes (1/13 non-TNBC tumors, 7.7%; p = 0.0294). Expression of EphA2 in stromal cell populations was similar between groups (TNBC = 22/31, non-TNBC = 11/13; p = 0.1711).
Conclusions: Our analysis determined that EphA2 was specifically expressed on cancer cells derived from tumors with a 'triple-negative' molecular subtype. Collectively our data suggests that EphA2 is an emerging target in TNBC and that therapies directed against EphA2 may provide a significant benefit for a majority of patients that express this marker.
Citation Format: Eckhardt BL, Torres AM, Woodward WA, Krishnamurthy S, Meric-Bernstam F, Ueno NT. EphA2: An emerging target in triple-negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-07-04.</jats:p
A comparative ecotoxicity investigation on fungicides using marine and freshwater species.
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