Dissecting out the mechanisms of hypoxia-dependent responses in rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic inflammatory disease with a significant impact on patients’ quality of life. One of the well-described features in RA is hypoxia. It has been shown that both RA synovial fluid and synovial tissue are characterised by insufficient amount of oxygen. Abnormality in hypoxia-inducible factor (HIF) expression is a marker of decreased oxygen tension in RA and in other pathological conditions. HIFs, together with the proteins which regulate their stabilisation and transactivation, namely prolyl hydroxylase domain (PHD) enzymes and factor inhibiting HIF-1 (FIH-1), were the main focus of this thesis. The first aim of the study was to investigate the specific roles of HIF isoforms in RA fibroblast-like synoviocytes (FLS), which are the key cells in RA pathogenesis. Expression of HIF-1α, HIF-2α and a panel of genes involved in angiogenesis (ANGPTL-4, ephrin-A3, VEGF), glycolysis (GLUT-1, ENO-1), pH regulation (CA9) and apoptosis (BNIP-3) were significantly increased by hypoxia. Successful silencing of both HIFs using short interfering RNA (siRNA) was achieved in RA FLS, and was followed by examination of the HIF-dependence of the candidate genes. The majority of these genes were found to be HIF-1α- dependent, whereas only ANGPTL-4 and VEGF were regulated by both HIF-1α and HIF-2α. Subsequently, the mRNA and protein expression of PHDs and FIH-1 in RA FLS, their response to hypoxic conditions and their HIF-dependence were examined. Specific knockdown of the hydroxylases was performed and the effects on HIFs and genes of interest were assessed. The most significant changes were noticed after silencing PHD-2, which led to HIF-α stabilisation and upregulation of HIF-dependent genes. In addition, PHD-2 depletion increased a number of pro-angiogenic genes and also contributed to new tubule formation in a functional angiogenesis assay. Comparison of RA, osteoarthritis (OA) FLS and normal human dermal fibroblasts (NHDF) revealed that PHD-2 has similar functions in promoting neovascularisation in arthritic cells (RA and OA), but not in non-arthritic cells (NHDF). Finally, the last chapter describes preliminary data on the expression of the least investigated HIF-3α subunit and its negative splice variant, HIF-3α4, in RA FLS. This research contributes to a better understanding of the upstream and downstream regulation of HIF signalling in RA, showing that PHD-2 has a key role in regulating hypoxic responses via HIFs in RA FLS. Because this pathway controls the expression of so many genes relevant to the disease, it may be an important target for RA therapy. One of the most critical challenges would be to target the correct HIF/PHDs molecule in the right tissue/cell, ensuring that it will not affect angiogenesis in healthy tissues

A molecular epidemiological study of black queen cell virus in honeybees (Apis mellifera) of Turkey: the first genetic characterization and phylogenetic analysis of field viruses

Black queen cell virus (BQCV) is one of the most common honeybee pathogens causing queen brood deaths. The 63 apiaries were sampled between 2007 and 2013 from four different ecogeographic regions in Turkey to estimate BQCV molecular structural characteristics. The BQCV positivity was 47.6%. The 25 local Black queen cell viruses (TrBQCVs) were molecularly characterized and investigated for their genetic relationship with previous records. The identity of the helicase gene among the TrBQCVs was 92-98%, whereas the similarity ranged from 37 to 85% in comparison with the intercontinental records. The identity of the partial capsid gene among the TrBQCVs was 91-100%, and the similarity rate varied from 86 to 97, 88-96, 90-97 and 89-99% in comparison with the Asian, African, American and European counterparts, respectively. The four nonsynonymous substitutions on the partial capsid protein suggest a predicted genotype that is specific among TrBQCVs

Zinc oxide nanoclusters and their potential application as CH4 and CO2 gas sensors: Insight from DFT and TD-DFT

We have investigated the adsorption of CH4 and CO2 gases on zinc oxide nanoclusters (ZnO NCs) using density functional theory (DFT). It was found that the CH4 tends to be physically adsorbed on the surface of all the ZnO NCs with adsorption energy in the range −11 to −14 kcal/mol. Even though, the CO2 is favorably chemisorbed on the Zn12O12 and Zn15O15 NCs, with adsorption energy about −38 kcal/mol at B3LYP/6-311G(d,p) level of theory. When the CH4 and CO2 gases are adsorbed on the ZnO NCs, their electrical conductivities are decreased, and thus the studied ZnO NCs do not generate an electrical signal in the presence of CH4 and CO2 gases. Interestingly, both pure and gas adsorbed Zn22O22 NC exhibited more favorable electronic and reactive properties than other NCs. Comparison of the structural, electronic, and optical data predicted by DFT/B3LYP and TD-DFT/CAM-B3LYP calculations with those experimentally obtained show good agreement. © 2022 Wiley Periodicals LLC

Electronic Transport and Non-linear Optical Properties of Hexathiopentacene (HTP) Nanorings: A DFT Study

The electronic structure and structural and optoelectronic properties of hexathiopentacene (HTP) nanorings have been carried out by density functional theory (DFT) and time-dependent DFT (TD-DFT). Herein, the binding energy per atom, ionization potential, electron affinity, chemical hardness, highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap, refractive index, charge distributions, absorbance spectra and non-linear optical properties have been measured. The calculations on these nanorings show that the HOMO–LUMO gaps range from 1.87 eV to 1.28 eV, which corresponds to the bandgap of known photovoltaic semiconductors, while the absorbance spectrum increases from 674 nm (1.84 eV) to 874 nm (1.42 eV), which indicates that the HTP nanorings absorb more light as the nanoring size is increased. From the binding energy, the stability of the HTP nanorings is higher than that of the HTP structure. Our results show that an increase in the size may play a significant role in improving the design of optoelectronic devices based upon these HTP nanorings. © 2020, The Minerals, Metals & Materials Society

Isolation of aerobic bacteria from the lungs of chickens showing respiratory disorders and confirmation of Pasteurella multocida by polymerase chain reaction (PCR)

In this study, lung samples of chickens slaughtered at an abattoir in Elazig province were tested for the presence of Pasteurella multocida and other aerobic bacteria. The identity of P. multocida was proved by mouse pathogenicity test and polymerase chain reaction (PCR). A total of 2000 chickens were examined at post-mortem, and 250 samples with pneumonia were collected. All lungs were collected from 10 different commercially reared chicken flocks showing respiratory disorders. Blood agar supplemented with 7% sheep blood was used for isolation of the agents. Of the examined chicken lung samples 16 (6.4%) P. multocida were isolated and identified. In addition, mouse pathogenicity test was carried out on P. multocida suspected isolates. Twelve (75%) of isolates were all positive. All P. multocida-suspicious isolates were positive in PCR. However, toxigenic P. multocida were not detected using PCR primers derived from toxA gene. This study showed that P. multocida is not widespread among the chicken population in Elazig

The electronic structure, transport and structural properties of nitrogen-decorated graphdiyne nanomaterials

We focus on a theoretical investigation using the DFT and LC-SCC-DFTB for investigating the structural, optical and reactivity properties and electronic structure of pristine graphdiyne (GDY) and nitrogen (N)-doped hexagonal carbon rings of GDY nanomaterials. Our calculations show that the energy gap (E-g) of the GDY is 1.00 eV which is excellent agreement with the DFTB. By increasing the content of N, the E-g changes in the wide range of 0.15-0.98 eV. The absorbance maxima are at 1.91 eV (647 nm) for the GDY, 1.46 eV (845 nm) for the N-GDY, 2.15 eV (576 nm) and 1.21 eV (1020 nm). The decrease in the value of the E-g with temperature for the GDY and 3 N GDY is observed due to variations of the bond energy which reflects the E-g. However, an increase in the value of the E-g with temperature is found linearly for the N-GDY because the Fermi energy level is pushed higher from -3.722 to -4.027 eV. The dipole moment increases when increasing the content of N and temperature. Obtained results herein suggest the GDY and N-doped GDY nanomaterials can be used as very promising advancements for potentially useful optoelectronic novel applications. (C) 2020 Elsevier B.V. All rights reserved

Enhancement of electronic, photophysical and optical properties of 5,5 '-Dibromo-2,2 '-bithiophene molecule: new aspect to molecular design

WOS: 000474358100002The aims of this study were to enhance electronic, photophysical and optical properties of molecular semiconductors. For this purpose, the isomers of the B-doped molecule (5,5'-Dibromo-2,2'-bithiophene) have been investigated by density functional theory (DFT) based on B3LYP/6-311++G** level of theory. The isomers were first calculated using kick algorithm. The most stable isomers of the B-doped molecule are presented depending on the binding energy, fragmentation energy, ionization potential, electron affinity, chemical hardness, refractive index, radial distribution function and HOMO-LUMO energy gap based on DFT. Ultraviolet-visible (UV-vis) spectra have been also researched by time-dependent (TD) DFT calculations. The value of a band gap for isomer with the lowest total energy decreases from 4.20 to 3.47 eV while the maximum peaks of the absorbance and emission increase from 292 to 324 nm and 392 to 440 nm with boron doped into 5,5'-Dibromo-2,2'-bithiophene. Obtained results reveal that the B-doped molecule has more desirable optoelectronic properties than the pure molecule. (C) 2019 Association of Polish Electrical Engineers (SEP). Published by Elsevier B.V. All right

Size‑dependent adsorption performance of ZnO nanoclusters for drug delivery applications

We have investigated the size-dependent adsorption performance of ZnO nanoclusters (NCs) as drug delivery carriers for the first time. Our results show that the adsorption energy of the favipiravir drug on the ZnO NCs is predicted in the range of - 26.69 and - 34.27 kcal/mol. The adsorption energy (- 34.27 kcal/mol) between (ZnO)(18) NC and the favipiravir is energetically desirable and more favorable than the other interactions. The size of ZnO NCs and the position of the favipiravir on the ZnO NCs cause a decrease in the energy gap, which makes the charge-transfer process easier. The bonds between O-Zn, N-Zn, and F-Zn atoms exhibit dual covalent and ionic natures. The non-covalent interaction analysis shows that the strongest H-bonds are observed near NH2 within the favipiravir molecule. Finally, the acquired results show that the interaction of ZnO NCs with the favipiravir anticancer drug can have the potential as drug delivery carriers

Electronic structures and bonding of graphdiyne and its BN analogs: Transition from quasi-planar to planar sheets

We demonstrate a possible structural transition from graphdiyne (GDY) to boron nitride (BN)-diyne (C90-18n(BN)9nH18; n = 0-5) sheets using the density functional theory (DFT). The aim of this study is to investigate the effects of substitution of carbon atoms by B and N atoms on structural, electronic and reactivity properties. We found that a structural transition from quasi-planar to planar occurs at n = 2. The stability decreases with increasing the number of B/N. Moreover, the pristine BNdiyne is only less stable than pristine GDY by about 0.92 eV/atom. Our calculations also show that the energy gap (Eg) of the GDY and its BN structural analog models changes in the wide range of 0.45–5.52 eV as the number of B and N atoms increases in the system. The Eg of the BNdiyne (n = 5) is found to be 5.52 eV, indicating electrically an insulating behavior, however, it is 0.45 eV for the BNdiyne (n = 4) which is higher conductivity than that of pristine GDY. Molecular dynamics simulations show that temperature induces a decrease in the Eg due to variations of the bond energy and deformation in the structures under heat treatment. The ELF analysis also confirms that the B–N bonds in new GDY-like BN sheets potentially exhibit covalent characteristics. Our results herein show that new BNdiyne sheets can be used in promising applications from chemical nanosensors to solar cell applications. © 2020 Elsevier B.V

Neonicotinoid Analysis in Sunflower (Helianthus annuus) Honey Samples Collected around Tekirdag in Turkey

In recent years, the widespread use of neonicotinoids in agricultural areas has caused environmental pollution due to its lower toxicity to mammals. Honey bees, which are considered as biological indicators of environmental pollution, can carry these pollutants to the hives. Forager bees returning from sunflower crops that have been treated with neonicotinoids treated sunflower fields cause residue accumulation in the hives, which reason colony-level adverse effects. This study analyses neonicotinoid residues in sunflower (Helianthus annuus) honey sampled by beekeepers from Tekirdag province. Honey samples have been subjected to liquid-liquid extraction methods before liquid chromatography-mass spectrometry (LC-MS/MS). The method validation was carried out to fulfill all the necessary requirements of procedures SANCO/12571/2013. Accuracy was in the range of 93.63-108.56%, for recovery in the range of 63.04-103.19%, and for precision in the range 6.03-12.77%. Detection and quantification limits were determined according to the maximum residue limits of each analyte. No neonicotinoid residues were found above the maximum residue limit in the sunflower honey samples analysed.Scientific Research Project Coordination Unit of Tekirdag Namik Kemal University [NKUBAP.00.23, AR.14.05]AcknowledgmentsThis work was supported by the Scientific Research Project Coordination Unit of Tekirdag Namik Kemal University, Tekirdag (project number: NKUBAP.00.23.AR.14.05)