Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis

: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes several proteins that inhibit host interferon responses. Among these, ORF6 antagonizes interferon signaling by disrupting nucleocytoplasmic trafficking through interactions with the nuclear pore complex components Nup98-Rae1. However, the roles and contributions of ORF6 during physiological infection remain unexplored. We assessed the role of ORF6 during infection using recombinant viruses carrying a deletion or loss-of-function (LoF) mutation in ORF6. ORF6 plays key roles in interferon antagonism and viral pathogenesis by interfering with nuclear import and specifically the translocation of IRF and STAT transcription factors. Additionally, ORF6 inhibits cellular mRNA export, resulting in the remodeling of the host cell proteome, and regulates viral protein expression. Interestingly, the ORF6:D61L mutation that emerged in the Omicron BA.2 and BA.4 variants exhibits reduced interactions with Nup98-Rae1 and consequently impairs immune evasion. Our findings highlight the role of ORF6 in antagonizing innate immunity and emphasize the importance of studying the immune evasion strategies of SARS-CoV-2

The assesment of empirical potential evapotranspiration methods: A case study of Konya closed basin

WOS:000505778200004Evapotranspirasyon, hidrolojik çevrimde kritik bir rol oynar. Ancak havza ve tarla ölçeğinde miktarının tahmini zordur. Bilim insanları, bu konuyu incelemek amacıyla yaygın erişilebilir ölçülmüş değişkenlere dayanan tahminler sağlayan ampirik denklemler geliştirmişlerdir. Blaney-Criddle, Jensen-Haise, Makkink, Turc, Priestley-Taylor ve Hargreaves-Samani adlı altı ampirik yöntemin performansları, Konya Kapalı Havzası'ndaki beş istasyondan alınan günlük meteorolojik veriler kullanılarak FAO-56 Penman-Monteith yöntemi ile karşılaştırılmış ve tartışılmıştır. Turc, Hargreaves-Samani ve Priestley-Taylor yöntemlerinin FAO-56 Penman-Monteith’e alternatif olarak ön plana çıktığı sonucuna varılmıştır. Ayrıca, sulama sezonu dikkate alındığında Turc, altı yöntemden en iyisi olmuştur. Sadece günlük sıcaklık verisine ihtiyaç duyan Hargreaves-Samani yönteminin bölge özelindeki performansının yadsınamayacak derecede başarılı olduğu vurgulanması gereken bir diğer noktadır.Evapotranspiration plays a critical role in hydrologic cycle. However, it is difficult to estimate its quantification at basin and arable land scales. Scientists have developed array of empirical equations that provide estimates of it based on more readily measured quantities in order to analyze this issue. The performance of six empirical methods namely Blaney-Criddle, Jensen-Haise, Makkink, Turc, Priestley-Taylor and Hargreaves-Samani were discussed comparing with FAO-56 Penman-Monteith method using daily meteorological data obtained from five stations in Konya Closed Basin. The results showed that Turc, Hargreaves-Samani ve Priestley-Taylor methods have come into prominence as an alternative to FAO-56 PM. Furthermore, Turc was best among the six methods when the irrigation season was considered. Another point to be emphasized is that the performance of Hargreaves-Samani method, which only needs daily temperature data, was undeniably successful in this region

Gazlı Amortisörlerde Kullanılan Mil Malzemelerine Uygulanan Farklı Yüzey İşlemlerinin Aşınma Performansına Etkisi

Gazlı amortisörler, birçok uygulamada yük ve ağırlık ihtiva eden kapakları eş kuvvet ile dengelemek ve kullanım alanında hız kontrolü sağlamak, damperlemek hatta yükü kaldırmak gibi roller oynamaktadırlar. En bilinenleri, arabaların bagaj ve motor kapakları, mobilya kapakları, makina kapakları, ameliyat masaları, çeşitli&nbsp;endüstriyel uygulamalar, vb.’dir. Çalışma ömrünü belirleyen sızdırmazlığı sağlayan elemanlar üzerindeki&nbsp;tribolojik mekanizmada sürtünme ve aşınma rol oynamaktadır. Mil malzemesi&nbsp;ile sızdırmazlık elemanı arasındaki&nbsp;olaylar dizisinde mil malzemesinin yüzey pürüzlülüğü, sızdırmazlık parçası olan keçe ve O-ringlerin malzeme özellikleri etkendir. Mil malzemesinin pürüzlülüğünü iyileştirmek ve aşınmaya karşı direncini&nbsp;arttırmak için farklı prosesler ile yüzey özellikleri&nbsp;iyileştirilebilmektedir. Bu çalışmada, aynı çaplarda ve aynı özelliklerde hazırlanmış olan gazlı amortisörlerde nitrürasyon uygulanmış C35, krom kaplanmış C45 ve krom kaplanmış SS316 olmak üzere 3 farklı milin ve farklı özelliklerdeki&nbsp;keçelerin amortisör ömrüne olan etkisi&nbsp;tribolojik olarak araştırılmıştır. Yapılan testlerde yüzey pürüzlülükleri, sertlikleri, aşınma dirençleri, sürtünme kuvvetleri, ömür testlerindeki gaz kayıpları ölçülmüş ve yorumlanmıştır. Sonuç olarak en iyi amortisör ömrüne, düşük pürüzlülükteki mil ve PU keçe ile ulaşılmıştır.Gas springs play roles in many applications, such as balancing the covers containing load and weight with equal force and providing speed control in the area of use, damping and even lifting the load. Best known applications are luggage and engine covers of cars, furniture covers, machine covers, surgical tables and different industrial applications, etc. Friction and abrasion play a role in the tribological mechanism on the sealing elements that determines the working life. The events between the rod material and the sealing element are affected by the surface roughness of the rod material, and material properties of the sealings and O-rings. To improve the roughness of the rod material and increase its resistance to wear, surface properties can be improved by different processes. In this study, the effect of the rod material and surface properties was investigated tribologically on the life of the gas springs. Three different rods were prepared with the same specifications and with the same diameter, as nitrided C35, chromium plated C45 and chromium plated SS316. Surface roughness, hardness, wear resistances, friction forces and gas losses in the life-cycle tests were measured and interpreted. As a result, the best gas spring life is achieved with lowroughness rod and with PU seal.</p

Estimation of potential evapotranspiration in the Karaman province

Dünyada tarım arazilerinin sulama planlamaları, terleme yoluyla bitki su tüketimleri ve buharlaşmamiktarlarını göz önünde bulunduran su bütçesi hesaplamalarıyla yapılmaktadır. Bitki kaplı alanlardameydana gelen söz konusu buharlaşma ve terleme olaylarının toplamı, hidrolojik çevrimin ölçülmesi enzor bileşeni olan evapotranspirasyonu meydana getirmektedir. Evapotranspirasyonun, belli referans bitkiörtüleri, su alma ve büyüme koşulları varsayımlarındaki potansiyel değerleri, pek çok araştırmacı tarafındangeliştirilen ampirik yöntemler ile tahmin edilebilmektedir. Bunların en başında gelen FAO56 PenmanMonteith (FAO56 PM), güçlü teorik alt yapısı ve tahminlerinin güvenilirliği bakımından, tüm dünyada enyaygın olarak kullanılan referans potansiyel evapotranspirasyon (PET) tahmin yöntemi haline gelmiştir.Güvenilir tahminlerine karşın, FAO56 PM’nin, PET tahminlerinde çok fazla meteorolojik gözlem verisineihtiyaç duyması ve karmaşık hesaplama adımları, daha az gözlem verisi gerektiren tahmin yöntemlerinikullanmamızı zaruri kılabilmektedir. Bu çalışmada, Konya Kapalı Havzası’nda yer alan ve önemli tarımsalfaaliyetler gerçekleştiren Karaman ili potansiyel evapotranspirasyon miktarları FAO56 PM ile günlük, Turc(TC), Makkink (MK), Priestley Taylor (PT), Jensen Haise (JH), Hargreaves Samani (HS), Blaney Criddle (BC),Thornthwaite (TH) gibi FAO56 PM’ye kıyasla daha az ölçülmüş veri ihtiyacı olan ve kullanımı nispetendaha basit yedi farklı ampirik yöntemle ise aylık zaman adımlarında hesaplanmıştır. FAO56 PM günlüktahminlerinin toplanmasıyla elde edilen aylık PET değerleri, diğer PET tahmin yöntemleriyle elde edilenaylık değerlerle karşılaştırılmıştır. Sonuç olarak, çalışmaya dâhil edilen yedi PET tahmin yönteminden, Turc,FAO56 PM ile 0.97’lik korelasyon (R2) ve 16.94 mm’lik (aylık) ortalama hata karelerinin karekökü (RMSE)değerleri ile en uyumlu sonucu vermiştir. Turc metodu uygun bir kalibrasyon yapılması durumundaKaraman ili özelinde önerilebilir bulunmuş ve geri kalan yöntemlerin uygulanabilirliği tartışılmıştır.Irrigation scheduling is performed with the water budget calculations considering the plant water consumption by transpiration and evaporation, at the farmlands around the world. Sum of these transpiration and evaporation events which takes place at the plant covered areas, composes evapotranspiration which is the hardest components of the hydrological cycle to measure. The potential values of evapotranspiration, under assumptions as certain reference plant cover, watering and growing conditions, can be estimated with empirical methods developed by many researches. At the top of them, FAO56 Penman-Monteith (FAO56 PM) is widely used reference potential evapotranspiration estimation (PET) method worldwide through its strong theoretical background and reliability of estimation.Despite of its reliable estimation, complicated calculation steps and requirement of various observed meteorological data impel us to use more practical PET estimation methods which require more easily findable meteorological data. In this study, the potential amounts of evapotranspiration, occuring in the Karaman province located in the Konya Closed Basin where advanced agricultural activities are carried out, were calculated by FAO56 PM method with daily time steps and by Turc (TC), Makkink (MK), Priestley Taylor (PT), Jensen Haise (JH), Hargreaves Samani (HS), Blaney Criddle (BC), Thornthwaite (TH) methods with monthly time steps. The monthly PET values were obtained by summing of daily estimations of FAO56 PM and then compared with the monthly PET values estimated by other empirical methods. As a conclusion, among seven PET estimation methods, Turc yielded most compatible results in comparison with FAO56 PM by 0.97 correlation coefficient value (R2) and 16.97 mm (monthly) root mean square error (RMSE) value. Turc was recommended with convenient calibration and remained methods were discussed

Genetic Uniformity of a Specific Region in SARS-CoV-2 Genome and In-Silico Target-Oriented Repurposing of N-Acetyl-D-Glucosamine

Causative agent of the viral pneumonia outbreak in the World identified as SARS-CoV2 leads to a severe respiratory illness like SARS and MERS. The pathogen spreading has turned into a pandemic dissemination and increased the mortality rate. Therefore, useful information is urgently necessary for effective control of the disease. Our study shows the existence of unvarying sequence with no mutation, including ORF1ab regions in 134 high-quality filtered genome sequences of SARS-CoV2 downloaded from the GISAID database. We have detected this sequence stability by using MAUVE analysis andpairwisealignment with GlobalNeedleman Wunschalgorithm for each two different sequences, reciprocally. They also confirmed all these results were also with theClustalW analysis. The first 6500bpincluding ORF1ab region is an unvarying sequence. According to the highest TM-score of predicted protein structure analysis, the results showed it is very similar to spike protein of feline infectious peritonitis virus strain UU4 (PDB 6JX7) depending on amino acid sequences encoded by this unvarying region, and N-acetyl-D-glucosamine is the ligand of this protein. These results have confirmed that N-acetyl-D-glucosamine could play an important role in controlling of SARS-CoV-2. Also, our molecular docking analysis data supports a strong protein-ligand interaction of N-acetyl-D-glucosamine with spike receptor-binding domain bound with ACE2 (PDB 6M0J) and RNA-binding domain of nucleocapsid phosphoprotein (PDB 6WKP) from SARS CoV-2. Therefore, binding of N-acetyl-D-glucosamine to these proteins could inhibit SARS CoV-2’s replication. In the present work, we have suggested providing a repurposing compound for furtherin vitroandin vivostudies and new insights for ongoing clinical treatments as a new strategy to control of SARS-CoV-2 infections

Süt sığırlarında mortellaro hastalığının patomorfolojik bulguları

Mortellaro disease is an infection caused by mostly spirochete bacteria in dairy cows, sheep, and goats. The aim of the present study was to define to Mortellaro disease pathomorphologically and immunohistochemically and investigate whether cell-cell adhesion connections are lost in cell proliferation. Tissue samples were collected from underfoots of Holstein (n: 6) and Swiss Brown (n: 15) dairy cattle. The sections were stained with hematoxylin-eosin (H&E) and Warthin-Starry (WS) for isolation of spirochetes histopathologically and with P-catenin and PCNA primary antibodies immunohistochemically. Histopathologically, number of the cells in the stratum spinosum layer increased excessively, and it gave finger-like extensions to the dermis. Black stained spirochetes were detected among enlarged keratinocytes and inflammatory cells in WS staining. beta-catenin was strongly positive in the cell membranes of epithelial cells in all slides. PCNA also gave positive reaction moderately (n: 18) and strongly (n: 3) in nuclei of epithelial cells. It was observed that P-catenin cell-cell adhesion connections did not impair in the disease, so this is thought to positively affect the prognosis of the disease. The high expression of PCNA showed that the mitotic activity was high and explained the formation of wart-like. As a result, while the disease does not have a poor prognosis, the disease has a negative economic impact, and the economical results of this disease might be much greater than the treatment costs. It is still seen in our country and causes in loss of yield for the economy of country

Intercomparison of the expected change in the temperature and the precipitation retrieved from CMIP6 and CMIP5 climate projections: A Mediterranean hot spot case, Turkey

WOS:000643527900003The performances of a large number of Global Circulation Models (GCMs) belonging to the latest release the Coupled Model Intercomparison Project phase 6 (CMIP6) in comparison with its predecessor CMIP5 are evaluated for monthly precipitation and temperature over Turkey (i.e. climate change hotspot). The ensemble of best top four models from both CMIP simulations is also used to investigate the future climate change under medium and high emissions for short, medium, and long terms. Results show CMIP6 products outperform CMIP5 in terms of accuracy statistics, particularly for precipitation. Overall, CMIP6 indicate less intermodel variability, implying the climate signal obtained via CMIP6 is improved relative to CMIP5. The CMIP6 reduce the error in precipitation and temperature 11% and 6%, respectively while increasing the correlation 13% for precipitation. Correlation is not changed for temperature. The substantial success of CMIP6 mainly manifests itself in the winter precipitation and autumn temperature. A slightly warmer (up to 0.35 ?C) climate from the CMIP6 is projected while precipitation change in mean precipitation decline is about 2.5% smaller for CMIP6. However, precipitation changes in maximum decline and increase are more noticeable for CMIP6, addressing the better resolving for future climate variability. The summer warming (up to 6.5 ?C) and drying (up to -40%) towards autumn spread across the country. The increased precipitation projection in the winter and spring over the east of the Black Sea Region and north-east of Anatolia may further increase the flood risks in the area.The authors would like to thank the World Climate Research Programme and its Working Group on Coupled Modelling, coordinated and promoted CMIP5 and CMIP6. The authors also thank the climate modelling groups for producing and making publicly available their model outputs, the Earth System Grid Federation (ESGF) for archiving the data and providing access, and the multiple funding agencies who support CMIP5, CMIP6, and ESGF. Authors also thanks to Turkish GDM for providing access to monthly temperature and precipitation data throughout the country

GENETIC UNIFORMITY OF A SPECIFIC REGION IN SARS-CoV-2 GENOME AND REPURPOSING OF N-ACETYL-D-GLUCOSAMINE

The causative agent of the viral pneumonia outbreak in the world identified as SARS-CoV-2 leads to a severe respiratory illness like SARS and MERS. The pathogen spreading has turned into a pandemic dissemination and increased the mortality rate. Therefore, any useful information is essential for effective control of the disease. Our findings show the existence of unvarying sequence with no mutation in ORF1ab regions from 134 high-quality filtered genome sequences of SARS-CoV-2 downloaded from the GISAID database. We have detected this sequence region by using MAUVE analysis and pairwise alignment using Global Needleman Wunsch algorithm. All these results were also confirmed with the Clustal W analysis. The first 6500 bp of the consensus genome including ORF1ab region is an unvarying sequence in SARS-CoV-2 genome. Unvarying sequence in SARS-CoV-2 genome has been very similar to another spike protein, which belongs to feline infectious peritonitis virus strain UU4 (PDB 6JX7), depending on amino acid sequences encoded, and N-acetyl-D-glucosamine is the ligand of this protein according to the highest TM-score of predicted protein structure analysis. These results have confirmed that N-acetyl-D-glucosamine could play an important effect on pathogenicity of SARS-CoV-2. Also, our molecular docking analysis data supports a strong protein-ligand interaction of N-acetyl-D-glucosamine with spike receptor-binding domain bound with ACE2 (PDB 6M0J) and RNA-binding domain of nucleocapsid phosphoprotein (PDB 6WKP) from SARS-CoV-2. Therefore, binding of N-acetyl-D-glucosamine to these proteins could inhibit SARS-CoV-2’s replication. In the present work, we have suggested providing a repurposing compound for further in vitro and in vivo studies and new insights for ongoing clinical treatments as a new strategy to control of SARS-CoV-2 infections