Search

Cognitive decline has been reported as a common consequence of COVID-19, and studies have suggested a link between COVID-19 infection and Alzheimer’s disease (AD). However, the molecular mechanisms underlying this association remain unclear. To shed light on this link, we conducted an integrated genomic analysis using a novel Robust Rank Aggregation method to identify common transcriptional signatures of the frontal cortex, a critical area for cognitive function, between individuals with AD and COVID-19. We then performed various analyses, including the KEGG pathway, GO ontology, protein-protein interaction, hub gene, gene-miRNA, and gene-transcription factor interaction analyses to identify molecular components of biological pathways that are associated with AD in the brain also show similar changes in severe COVID-19. Our findings revealed the molecular mechanisms underpinning the association between COVID-19 infection and AD development and identified several genes, miRNAs, and TFs that may be targeted for therapeutic purposes. However, further research is needed to investigate the diagnostic and therapeutic applications of these findings.

Dietary restriction (DR) without malnutrition is associated with longevity in various organisms. However, it has also been shown that reduced calorie intake is often ineffective in extending life span. Selecting optimal dietary regimens for DR studies is complicated, as the same regimen may lead to different outcomes depending on genotype and environmental factors. Recent studies suggested that interventions such as moderate protein restriction with or without adequate nutrition (e.g., particular amino acids or carbohydrates) may have additional beneficial effects mediated by certain metabolic and hormonal factors implicated in the biology of aging, regardless of total calorie intake. In particular, it was shown that restriction of a single amino acid, methionine, can mimic the effects of DR and extend life span in various model organisms. We discuss the beneficial effects of a methionine-restricted diet, the molecular pathways involved, and the use of this regimen in longevity interventions.

Boron is an essential micronutrient for plants and animals; however, it can be toxic when present at high concentrations. The purpose of this study was to understand the mechanisms of boron tolerance in the Turkish barley (Hordeum vulgare) Anadolu cultivar. For this purpose, 2-dimensional electrophoresis (2-DE) was used to screen differentially expressed proteins for both control and boron-stressed Anadolu barley genotypes. Seven proteins were revealed by 2-DE: 1) ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo large chain), 2) TLP5, a thaumatin-like protein, 3) PR5, a basic pathogenesis-related protein, 4) a RNase S-like protein, 5) a PSI type III chlorophyll a/b-binding protein, 6) a light-harvesting complex I LHC I, and 7) the vacuolar proton-translocating ATPase subunit E protein. These were found to be upregulated in response to boron treatment. Even though the protein encoded by the V-ATPase subunit E gene was overexpressed, its transcript level was downregulated by boron treatment. Heterologous expression of the barley V-ATPase subunit E gene in yeast provided boron resistance to yeast cells. These results indicated that the V-ATPase subunit E gene was functional and conferred tolerance to toxic boron levels in yeast and might play a role in the overall boron tolerance of barley. © TÜBITAK., Bor, bitkiler ve hayvanlar için gerekli olan mikrolementlerdendir. Ancak yüksek konsantrasyonlarda toksik etki göstermektedir. Bu çalışmada bora dayanıklı Anadolu arpa (Hordeum vulgare) genotipindeki bor tolerans mekanizmasının anlaşılması amaçlanmıştır. Kontrol ve bor stresi uygulanmış ve Anadolu genotipi arasındaki farklı seviyede ekspres olan proteinleri taramak için 2 boyutlu elektroforez tekniği uygulanmıştır. İki boyutlu elektroforez deneyi sonucu ekspresyon seviyesi artan yedi protein bulunmuştur: ribuloz 1,5-bifosfat karboksilaz/oksijenaz büyük zincir, thaumatin benzeri protein TLP5, patojenaz benzeri protein PR5, RNaz S benzeri protein, PSI tipi III a/bbağlayıcı protein, ışık toplayan kompleks protein I LHC I ve vakuol proton translokasyon ATPaz alt birim E. V-ATPaz alt birim E geni tarafından kodlanan proteinin seviyesinin bor uygulaması ile artmasına rağmen, genin transkript seviyesi azalmıştır. Arpa V-ATPaz alt birim E geninin maya hücrelerinde ifadenlenmesi maya hücrelerine bora karşı dayanıklılık sağlamıştır. Bu sonuçlar, V-ATPaz alt birim E geninin mayada fonksiyonel olduğunu ve maya hücrelerine, toksik bor seviyelerine karşı dayanıklılık sağladığını ve de arpada bor toleransında bir rolü olabileceğini göstermektedir., TUBITAK 104T213; TUBITAK TBAG-2354; IYTE-BAP20

Boron is an essential micronutrient for plants and animals; however, it can be toxic when present at high concentrations. The purpose of this study was to understand the mechanisms of boron tolerance in the Turkish barley (Hordeum vulgare) Anadolu cultivar. For this purpose, 2-dimensional electrophoresis (2-DE) was used to screen differentially expressed proteins for both control and boron-stressed Anadolu barley genotypes. Seven proteins were revealed by 2-DE: 1) ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo large chain), 2) TLP5, a thaumatin-like protein, 3) PR5, a basic pathogenesis-related protein, 4) a RNase S-like protein, 5) a PSI type III chlorophyll a/b-binding protein, 6) a light-harvesting complex I LHC I, and 7) the vacuolar proton-translocating ATPase subunit E protein. These were found to be upregulated in response to boron treatment. Even though the protein encoded by the V-ATPase subunit E gene was overexpressed, its transcript level was downregulated by boron treatment. Heterologous expression of the barley V-ATPase subunit E gene in yeast provided boron resistance to yeast cells. These results indicated that the V-ATPase subunit E gene was functional and conferred tolerance to toxic boron levels in yeast and might play a role in the overall boron tolerance of barley.

Büyük hidroelektrik santrallerin yatırım maliyetlerinin yüksek olması büyük debi veya düşülere ihtiyaç duyması ayrıca çevreci kabul edilmemeye başlaması yeni yatırımların küçük hidroelektrik santrallere doğru kaymasına neden olmuştur [1]. Ülkemizde büyük hidroelektrik santrallerin kurulacağı yeni yerlerin olmayışı veya verimli toprakların ve tarihi yapıların su altında kalması nedeniyle küçük hidroelektrik santraller, günümüzde en önemli yenilenebilir enerji kaynağı olarak görülmektedir. Bu çalışmanın özgün tarafı, çapraz akış türbinlerinde debi ayarının ilk defa bir sürgülü vana kullanılarak yapılmasıdır. Bu amaçla, ilk olarak; çapraz akış (Banki) türbini temel alınarak yeni bir çapraz akış türbin geliştirme ve kontrol sistemi tasarımı yapılmıştır. Çalışmanın ikinci aşamasında; tamamen yerli kaynaklar kullanılarak Türkiye Elektro Mekanik Sanayi (TEMSAN) A.Ş.'ye tasarlanan ve çizimleri yapılan türbin imal ettirilmiştir. Üçüncü aşamada ise; türbinin test edilebilmesi için bir deney düzeneği tasarımı yapılarak GYTE'de düzeneğin kurulumu gerçekleştirilmiştir. Dördüncü aşamada; Banki türbininin çalışma koşullarının belirlenmesi amacı ile Yüzey Cevap Yöntemi (YCY) uygulanarak optimizasyon çalışmaları yapılmıştır. Çalışma şartları belirlendikten sonra, beşinci aşamada; türbin performansı deneyleri, altıncı aşamada; ise sürgülü vana performansı deneyleri yapılmıştır. Deneylerde debi kontrolü sürgülü vana ile yapılarak türbinin, düşük debilerde yüksek verimde çalışması sağlanmıştır. Yedinci aşamada; Deneylerden elde edilen sonuçlar, hesaplamalı akışkanlar dinamiği analizleri ile mukayese edilmiştir. Sekizinci ve son aşamada ise; sistemden çekilen güç değişimlerinde sürgülü vananın rolü üzerine, Matlab-Simulink programı kullanılarak modelleme çalışmaları yapılmıştır. Çalışmanın sonucunda ise, ilk kez bir sürgülü vana kullanılarak Çapraz Akış Türbininin debi ayarının yapılabildiği ve sürgülü vana kullanımı ile tasarım debisinden daha düşük debilerde verimde % 5'e varan iyileştirmeler elde edildiği görülmüştür. Ayrıca hesaplamalı akışkanlar dinamiği analizleri (HAD) ile mukayese edildiğinde nitelik bakımından benzer sonuçlar elde edilmiştir. Micro hydroelectric power plants have been considered as the most important renewable energy sources since larger plants are no more environmentally accepted and finding suitable sites are difficult. Due to the fact that in our country there is no appropriate places to construct big hydroelectric power plants or possibility of flooding historical places and fertile land, micro hydroelectric power plant would be one of the most important renewable energy resources. Analysis of turbines yields that cross flow turbine is one of the suitable types considering resources of our country. The reason behind their rare use is their lower efficiency at variable flow rates. In this study, first of all, responding to our country?s demand and conditions, a cross flow turbine was designed. In the development-phase, turbine theory and experience of other researchers have been utilized. The turbine has been manufactured by Turkish Electro Mechanics Industry (TEMSAN), the only public institution of Turkey in its area and using completely domestic sources. In the second phase an experimental setup was designed and installed at Gebze Institute of Technology for testing the turbines of similar capacities. And then in the fourth phase Surface Response Method was applied to specify the operating range of the Banki Turbine. Turbine performance was tested, after constructing a hydroelectric laboratory with needed experimental setup and performance of the sliding valve which was a major contribution of this study was tested as a fifth and sixth phase, respectively. In the seventh phase, results were verified by computational fluid dynamics analyses. In the final phase, using Matlab-Simulink modelling and simulation were performed on the role of sliding valve for different power outputs. Our results showed that as the first time it is possible to make flow rate control of Cros Flow Turbine by using sliding valve. It is also shown that using the sliding valve increased the efficiency up to 5% under flow rates of designed flow rate. The computational fluid dynamic analysis also showed similar results to our experimental data. 128

Thesis (Master)--Izmir Institute of Technology, Biotechnology, Izmir, 2008, Includes bibliographical references (leaves: 24-28), Text in English; Abstract: Turkish and English, ix, 33 leaves, Boron, is an essential microelement that plays a role in plant and animal development. However, an excess amount of boron is toxic for both types of organisms.The yeast Saccharomyces cerevisiae is an ideal model organism for describing the mechanism and regulation of metal ion transport in eukaryotes. We screened a yeast genomic DNA library to find genes that confer boron resistance to wild-type cells.Thirty transformants were isolated that were able to grow in the presence of a toxic amount of boron and all of them contained the multidrug efflux transporter gene ATR1 (YML116w) in the expression cassette. Our subsequent analysis revealed that ATR1 deletion mutants (.atr1) were sensitive to boron treatment and hyper-accumulated boron inside cells, whereas wild-type cells overexpressing the ATR1 gene were resistant to boron and hypoaccumulated boron in cells. We also analysed the global gene expression pattern in response to boron treatment and found that expression of ATR1 is upregulated along with many other transporter and amino acid biosynthesis genes. Our data suggest that the ATR1 gene functions as a boron efflux pump and is reqired for boron tolerance in yeast cells.

IV ÖZET Bu çalışmada, sıcaklık ve hız faktörlerinin, deneysel, teorik ve sayısal olarak, dönen dairesel disk akışına etkileri incelenmiştir. Dönen disk akışı ile ilgili olarak yapılmış olan çoğu çalışmada düzlemsel disk kullanılmıştır. Birkaç çalışma da gözenekli disk üzerine yapılmıştır. Bu çalışmada ise ilk defa konik geometriye sahip bir disk kullanılmıştır. Yüksek devirlere çıkabilecek bir sistem tasarlanmakta olduğundan, dönen milin eksensel simetrisi oldukça önem arz etmektedir. Yatak sürtünmesini en aza indirmek, yüksek daimi hızlara ulaşabilmek ve ısıl izolasyona katkı sağlayabilmek için dönen mil, havalı iki radyal yatak ve alttan bir havalı eksensel yatak ile desteklenmiştir. Düzenek, kararlılığını sağlamak için alttan zemine, yandan duvara çelik dübellerle sabitlenmiştir. Merkezkaç gerilmeler yapılan sonlu elemanlar analizi ile belirlenmiştir. Yüksek hızlara ulaşabilmek için sürtünme katsayısı en düşük olan yatak (havalı yatak) kullanılmıştır. Diskin 3000 d/d'ye çıkabilmesi ve bu değer civarlarındaki hızlarda kendi haline bırakıldığında 30 dakikanın üzerinde bir zaman zarfında durgun hale gelmesi, havalı yatak kullanımının ne denli önemli olduğunun göstergesidir. Hazırlanan deney düzeneğinde diskin tahrik edilmesi dremel, ısıtılması oksijen kaynağı ile yapılmıştır. Bu tip yüksek devirli ve sıcak koşullara maruz sistemlerde, hava yastıklı yatak kullanımının uygun olduğu görülmüştür. Ayrıca, dönen parçanın mümkünse bir defada aynı tezgâhtan eksensel simetrik olarak üretilmesinin balans açısından önemli olduğu gözlemlenmiştir. Teorik ve bu çalışmada yapılan sayısal hesaplarda ortaya çıkan, disk ucundan dışarıya doğru akışkan üflemesi olarak gözlemlenen pompalama etkisi, deneylerde, bu bölgedeki sıcaklığın, dönen sıcak diskin açısal hızıyla artan bir davranış arz etmesine yol açmıştır. Üst ve alt yüzeyler arasındaki sıcaklık farkının akış alanına etkilerini gözlemlemek ise, disk içindeki hızlı ısı transferi nedeniyle sağlıklı bir biçimde gerçekleştirilememiştir. SUMMARY Rotating disc flow and heat transfer problem is a classical fluid mechanics problem of theoretical and practical importance. Heat transfer from a rotating part is important in various rotating machinery. Disk drives in computers and gas turbine rotors may be shown as examples. In this study, effects of temperature and velocity on the rotating disc flow were experimentally, theoretically, and numerically investigated. Most of the studies on rotating disc focus on planar geometry. Some studies involving porous disk exist, as well. This study, on the other hand, uses a disc with conical shape as a first. Axial symmetricity of the rotating disc is crucial, simply because it is intended to design a high rpm system. In order to minimize the bearing frictions, to achieve high steady speeds, and to contribute on the thermal insulation, the rotating shaft was supported by two radial and one axial air-bearings. The whole assembly was fixed to the ground and side wall using steel pegs, to get a stiff structure. Centrifugal stresses were estimated using a finite element analysis. In order to achieve high speeds, bearing with least friction (air-bearing) was chosen. When left free at 3000 rpm, continuation of the rotation for more than 30 minutes proves how important the use of air-bearings was. In the experimental setup, dremel and oxygen-acetylene welding were used to rotate and heat the disk, respectively. It has been concluded that, use of air cushioned bearing in this kind of high rpm and hot surface systems was suitable. Added to this, if it is possible, for the sake of axial symmetry, manufacturing of the rotating part cut from a whole at once should be achieved for balance. The pumping effect that was observed as outward blowing of the fluid at the tip of the disk in theoretical and numerical calculations done in this study caused a temperature increase at that region as the angular velocity increases. Because of the fast heat conduction through the disk material, it was not possible to conduct a sound investigation on how the temperature difference between the upper and lower surfaces of the disk affects the flow field. 65