Turkish-Greek relations within the European Union framework

Turko-Greek relations have been strained by a number of conflicting issues such as Cyprus, Continental Shelf, Territorial Waters, the Öcalan affair, and the S-300 Missiles crisis on Cyprus. Until the December 1999 Helsinki Summit, Greece was one of the strong opponents of Turkey's membership in the European Union (EU). However, at the Helsinki Summit of 1999, Greece dropped her negative position permitting Turkey to be declared by the EU as a candidate country. This shift in foreign policy had a direct impact on both Turkey-Greece and Turkey-EU relations. It also represents a major step forward on bilateral relations. The research question tries to explore how did Greek-Turkish relations, disputes in the Aegean and Cyprus entanglement shape Turkey-EU relations and after the Helsinki Summit in 1999 and also with Greek-Turkish rapprochement, how do we expect Greek-Turkish relations to influence Turkey-EU relations. The focus of the thesis will cover a time period between the Athens Treaty of 1961 and December 2005, when Turkey reached the negotiation phase in her EU accession

Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies

It isn't over ‘till it’s over: A continuing concern of the SARS-CoV-2 variants, and miRNAs targeting the S protein as a probable absolute cure

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak which still continues to affect the general population, has mutated day by day and new variants have emerged. More than 40 variants, usually caused by mutations in the spike (S) protein, have been recorded. Observation of S protein mutations in the development of t herapeutic agents will increase success rates. As we identify the three-dimensional (3D) conformation of viruses, it is more and more possible to work on models for understanding molecular interactions. Development of agents for arrays and 3D sequencing of proteins paves the way for potential therapeutic studies against variants. MicroRNAs (miRNAs) seemingly act as a potentially important group of biomolecules in combating uncontrolled cytokine release. Besides antiviral response, miRNAs promise to be  powerful therapeutic agents against infections. Studies have shown that miRNAs are able to inhibit the genome directly by miRNA-based treatments as they are sprecific to the SARS-CoV-2 genome. In order to expose this potential, in silico studies before continuing with lab studies are helpful. In our bioinformatics analysis, we proposed to compare the S protein similarities of Delta and Omicron, two of the most common variants, and to detect miRNAs targeting the S protein. The S proteins and coding sequences were compared between the two variants, and differences were determined. Within our analysis, 105 and 109 miRNAs for the Delta and Omicron variants, respectively, were detected. We believe that our study will be a potential guide for deciding on the miRNAs that may most likely have an effect on the management of the infection caused by both variants

The impact of BNT162b2 mRNA vaccine on adaptive and innate immune responses

The mRNA-based BNT162b2 protects against severe disease and mortality caused by SARS-CoV-2 via induction of specific antibody and T-cell responses. Much less is known about its broad effects on immune responses against other pathogens. Here, we investigated the adaptive immune responses induced by BNT162b2 vaccination against various SARS-CoV-2 variants and its effects on the responsiveness of immune cells upon stimulation with heterologous stimuli. BNT162b2 vaccination induced effective humoral and cellular immunity against SARS-CoV-2 that started to wane after six months. We also observed long-term transcriptional changes in immune cells after vaccination. Additionally, vaccination with BNT162b2 modulated innate immune responses as measured by inflammatory cytokine production after stimulation - higher IL-1/IL-6 release and decreased IFN-α production. Altogether, these data expand our knowledge regarding the overall immunological effects of this new class of vaccines and underline the need for additional studies to elucidate their effects on both innate and adaptive immune responses.</p

A Prospective Study of Etiology of Childhood Acute Bacterial Meningitis, Turkey

Vaccines to prevent bacterial meningitis in this region must provide reliable protection against serogroup W-135

Population dynamics and induced resistance in biological control by Lysobacter enzymogenes strain C3

The spatial and temporal pattern of colonization by Lysobacter enzymogenes strain C3 was investigated on tall fescue at the scale of individual leaf segments and whole leaves. A high degree of nonuniformity in colonization by C3 was found along the length of the grass leaves when populations of C3 was examined at the leaf segment scale. The aggregation of C3 populations on leaf surfaces became more evident as population levels started to decline. When C3 populations were examined at the whole leaf scale, a uniform pattern of colonization was predominant over the course of the experiment while C3 population sizes were highly variable among leaves. The relationship of C3 population sizes to germination of B. sorokiniana conidia was also determined. Inhibition of Bipolaris conidial germination was inversely related to the C3 population numbers on the same leaf when Bipolaris conidia were deposited onto treated leaves shortly after C3 application. However, there was no dose-response relationship when pathogen inoculation was delayed by at least 1 day. In this study, induced resistance was found to be another mechanism of action by C3 in addition to chitinolysis. Induced resistance elicited by C3 resulted in arrested germination of B. sorokiniana conidia on the phylloplane, in addition to reduced development of leaf spot. When applied to tall fescue leaves, heat-killed cells, which retained no direct antifungal activity, were effective in inducing the pathogen-inhibitory effect. Application of live or heat-killed cells of C3 to tall fescue leaves resulted in localized resistance expressed within 1 day of the elicitor treatment. Treatment of roots resulted in systemic resistance expressed in the foliage following a delay of over 5 days. Induced resistance by C3 was not pathogen or host specific. It was effective against B. sorokiniana in wheat and against R. solani in tall fescue. In tall fescue, treatments with C3 were associated with significant increases in peroxidase activity over the control, supporting the hypothesis that C3 can elicit a host response. Similar results were found with certain PGPR strains and the chemical inducer Benzothiadiazole (BTH)

Induced Resistance as a Mechanism of Biological Control by \u3ci\u3eLysobacter enzymogenes\u3c/i\u3e Strain C3

Induced resistance was found to be a mechanism for biological control of leaf spot, caused by Bipolaris sorokiniana, in tall fescue (Festuca arundinacea) using the bacterium Lysobacter enzymogenes strain C3. Resistance elicited by C3 suppressed germination of B. sorokiniana conidia on the phylloplane in addition to reducing the severity of leaf spot. The pathogen-inhibitory effect could be separated from antibiosis by using heat-inactivated cells of C3 that retained no antifungal activity. Application of live or heat-killed cells to tall fescue leaves resulted only in localized resistance confined to the treated leaf, whereas treatment of roots resulted in systemic resistance expressed in the foliage. The effects of foliar and root applications of C3 were long lasting, as evidenced by suppression of conidial germination and leaf spot development even when pathogen inoculation was delayed 15 days after bacterial treatment. When C3 population levels and germination of pathogen conidia was examined on leaf segments, germination percentage was reduced on all segments from C3-treated leaves compared with segments from nontreated leaves, but no dose–response relationship typical of antagonism was found. Induced resistance by C3 was not host or pathogen specific; foliar application of heat-killed C3 cells controlled B. sorokiniana on wheat and also was effective in reducing the severity of brown patch, caused by Rhizoctonia solani, on tall fescue. Treatments of tall fescue foliage or roots with C3 resulted in significantly elevated peroxidase activity compared with the control