138 research outputs found
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
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
DRINKING WATER QUALITY ASSESSMENT IN VILLAGES LOCATED IN MERIC RIVER BASIN (EDIRNE, TURKEY)
No full textThis study was carried out to determine the drinking water quality of Ipsala, Kesan, Uzunkopru and Meric Districts, which are located in the Meric River Basin in Edirne Province of Turkey. Water samples were collected from 51 villages in autumn season of 2017. Some physical and chemical water quality parameters including dissolved oxygen, oxygen saturation, pH, electrical conductivity (EC), total dissolved solids (TDS), salinity, turbidity, nitrite (NO2), nitrate (NO3), phosphate (PO4) and cyanide (CN) were determined and the results were assessed according to national and international quality criteria. Pearson Correlation Index (PCI) and Principle Component Analysis (PCA) were applied to experimental data in order to determine the significant relations among the investigated parameters and effective factors on groundwater quality of the region. Geographic Information System (GIS) was also used in order to make a visual explanation by presenting distribution maps of investigated parameters. According to data observed, although the investigated parameter levels in drinking water of villages did not exceeded the limit values for drinking, the region has Class I - II water quality in terms of cyanide, nitrite and nitrate parameters; Class II - III in terms of electrical conductivity parameter; and Class III - IV in terms of phosphate parameter in general.Trakya University, Turkey; [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
A novel mechanism of iron-core formation by Pyrococcus furiosus archaeoferritin, a member of an uncharacterized branch of the ferritin-like superfamily
No full textStorage of iron in a nontoxic and bioavailable form is essential for many forms of life. Three subfamilies of the ferritin-like superfamily, namely, ferritin, bacterioferritin, and Dps (DNA-binding proteins from starved cells), are able to store iron. Although the function of these iron-storage proteins is constitutive to many organisms to sustain life, the genome of some organisms appears not to encode any of these proteins. In an attempt to identify new iron-storage systems, we have found and characterized a new member of the ferritin-like superfamily of proteins, which unlike the multimeric storage system of ferritin, bacterioferritin, and Dps is monomeric in the absence of iron. Monomers catalyze oxidation of Fe(II) and they store the Fe(III) product as they assemble to form structures comparable to those of 24-meric ferritin. We propose that this mechanism is an alternative method of iron storage by the ferritin-like superfamily of proteins in organisms that lack the regular preassociated 24-meric/12-meric ferritins.BT/BiotechnologyApplied Science
Inverse Reinforcement Learning (IRL) in Presence of Risk and Uncertainty Related Cognitive Biases: To what extent can IRL learn rewards from expert demonstrations with loss and risk aversion?
No full textA key issue in Reinforcement Learning (RL) research is the difficulty of defining rewards. Inverse Reinforcement Learning (IRL) is a technique that addresses this challenge by learning the rewards from expert demonstrations. In a realistic setting, expert demonstrations are collected from humans, and it is important to acknowledge that these demonstrations can deviate from rationality due to systematic biases known as cognitive biases. One group of cognitive biases, known as risk-sensitive cognitive biases, pertains to individuals' attitudes and behaviors towards risk and uncertainty. This paper investigates the extent to which IRL can learn from demonstrations that contain risk-sensitive cognitive biases such as loss aversion and risk aversion. Modelling biases using concepts from Prospect Theory and System 1 and 2 model and using Maximum Entropy IRL algorithm, this paper concludes that IRL can recreate similar solutions to experts but inferring the underlying motivations and the interactions between them is an intricate problem that requires novel approaches.CSE3000 Research ProjectComputer Science and Engineerin
Iron-Storage Mechanism of Ferritin
No full textStorage of Fe(III) is a common mechanism by which the cellular machinery controls the availability of Fe(II) and Fe(III) for biosynthesis of iron-containing cofactors of enzymes which are involved in several essential biological processes, including oxidative phosphorylation. The conserved 24-meric iron-storage protein ferritin has been identified in many organisms to control the availability of Fe(II) by oxidizing the excess Fe(II) and storing the Fe(III) oxidation product in a soluble and nontoxic form. A conserved diiron center, the ferroxidase center, is responsible for catalytic oxidation of Fe(II), the ferroxidase reaction. The mechanism by which ferritin stores the Fe(III) is not fully understood, and the current models in the literature suggest different mechanisms for the functioning of ferritins from different Domains of life. Moreover, a structural gene for a 24-meric ferritin has not been found in some organisms including Pyrococcus abyssi or Pyrococcus horikoshii. Below we first outline methods which can be used to measure ferroxidase activity of different proteins. As an example we measure the ferroxidase activity of two proteins, human H ferritin and ceruloplasmin, and that of a synthetic peptide. Subsequently, using these techniques we study the mechanism of iron oxidation of a ferritin from hyperthermophilic archaeal anaerobe Pyrococcus furiosus. We then employ new experimental approaches using isotopically labeled 57Fe(II) to compare the iron-storage mechanism of P. furiosus ferritin with that of eukaryotic human H ferritin. We demonstrate that, conflicting with the current models in the literature these proteins employ a common mechanism to store the Fe(III) oxidation product. We suggest that this mechanism is general from archaea to eukaryotes. Finally, we carry out the in-vitro biochemical characterization of a new member of the ferritin superfamily of proteins that unlike the 24-meric ferritin is monomeric in the absence of iron. We name this protein archaeoferritin and we show that monomers oxidize Fe(II) and reversibly assemble to form Fe(III)-storing oligomeric structures comparable to that of ferritin.BiotechnologyApplied Science
Author response
No full textThe presynaptic active zone proteins UNC-13/Munc13s are essential for synaptic vesicle (SV) exocytosis by directly interacting with SV fusion apparatus. An open question is how their association with active zones, hence their position to Ca(2+) entry sites, regulates SV release. The N-termini of major UNC-13/Munc13 isoforms contain a non-calcium binding C2A domain that mediates protein homo- or hetero-meric interactions. Here, we show that the C2A domain of Caenorhabditis elegans UNC-13 regulates release probability of evoked release and its precise active zone localization. Kinetics analysis of SV release supports that the proximity of UNC-13 to Ca(2+) entry sites, mediated by the C2A-domain containing N-terminus, is critical for accelerating neurotransmitter release. Additionally, the C2A domain is specifically required for spontaneous release. These data reveal multiple roles of UNC-13 C2A domain, and suggest that spontaneous release and the fast phase of evoked release may involve a common pool of SVs at the active zone. DOI: http://dx.doi.org/10.7554/eLife.01180.001
Evaluation of Turkish rice varieties (Oryza sativa L.) for reproductive stage cold environmental conditions tolerancein Africa
No full textLow-temperature-induced crop loss is one of a major threat in rice production; introduction of cold tolerant trait from cultivars that are well adapted to cooler climates is considered a vital strategy to mitigate the crop loss. In this study, twenty genotypes obtained from Trakya Agricutural Research Institute, in Turkey were evaluated for their reproductive stage cold tolerance in order to identify best performers for African cold-prone rice growing ecologies. The genotypes were first screened in temperature regulated screen house at AfricaRice research station in Tanzania, then field evaluated in Madagascar at the elevation of 1650 meter above sea level in rainfed lowland ecology. The genotypes showed range of reactions for the cold stress from highly susceptible to highly tolerant level. The susceptible genotypes showed consistent delay in flowering date up to 20 days, height reduction up to 40% and spikelet sterility up to 100% and consequently yield loss up to 100%. Nevertheless, in the field trial six genotypes; namely: Meric, Surek-95, Serhat-92, Duragan, Negis and Halilbey were identified to have superior performance compared to the local cold tolerant checks, with the yield potential of more than 5 t/ha. These candidate genotypes can be used to expand rice production in cold prone areas and contribute to food security in Africa. © 2020 Parlar Scientific Publications. All rights reserved
- …
