Fusarium species isolated from wheat samples showing root and crown rot symptoms in Southeast Anatolia

Wheat is one of the most largely grown cereals in Turkey and it is very important for meet calorie requirements of humans and animals. However, due to numerous fungal diseases suffered, the wheat supply is threatened. Fusarium spp., known as the big portion of plant parasitic fungi, causes some quality and quantity problems on wheat production. This large genus has over one hundred sub-species, therefore, it is so difficult to diagnose in species level. Using certain molecular and microscopic approaches, this study aimed at determining the Fusarium spp., causing root and crown rot on wheat in Southeast Anatolia. Molecularly, using polymerase chain reaction (PCR) experiment with some species-specific primers and sequencing of some part of ribosomal RNA region after amplification by PCR were used to differentiate the species. Additionally, colony and different spore characteristics of cultures were used to diagnose some Fusarium species microscopically. At the end of the study, 143 Fusarium isolates including 19 species were obtained from wheat producing areas in Diyarbakır, Şanlıurfa, Mardin, and Adıyaman provinces. Although the most frequently isolated species was F. proliferatum at the rate of 17.4%, F. pseudograminearum and F. culmorum, which were the most important crown rot pathogens, were isolated at 13% of the total isolated Fusarium isolates

Geographic variations for cone and seed characteristics of oriental spruce (picea orientalis)

Bu çalışmanın amacı Doğu Ladini (Picea orientalis) kozalak ve tohum özelliklerindeki coğrafi farklılıkların belirlenmesi amaçlanmıştır. Materyal olarak Doğu Ladini’nin Artvin ve Posof (Ardahan)’daki doğal yayılış alanı içinde 33 noktadan 3 veya 5 anaçtan açık tozlaşma ürünü kozalaklar toplanmıştır. Kozalak ve tohum özelliklerine ait karakterler (kozalak boyu, kozalak eni, elde edilen tohumların 1000 tane ağırlığı, tohum eni, tohum boyu ve tohum kanat uzunluğu) ölçülmüştür. Araştırma alanının coğrafik özelliklerine göre bu veriler değerlendirilmiştir. Kozalakların elde edildiği ağaçların bulunduğu yerin GPS yardımıyla koordinatları, denizden yüksekliği ve bakıları tespit edilmiştir. Elde edilen istatistik analizlerine tabi tutulmuştur. Yapılan korelasyon analizi sonucunda tohum toplanan alanların yükseltisi ile bazı kozalak değerleri (kozalak eni ve kozalak boyu) arasında negatif bir korelasyon olduğu belirlenmiştir. Yükselti arttıkça kozalak eni ve kozalak boyu değerleri azalmaktadır. Ayrıca denizden uzaklık ile kozalak eni, tohum eni ve 1000 tane ağırlığı arasında yine negatif bir korelasyon olduğu tespit edilmiştir (p<0.05).The aim of this study is to investigate the geographic variations of some cone and seed characteristics of oriental spruce (Picea orientalis). Fort this purpose, the cones were collected from 33 sampling plots within the species natural distribution in Artvin and Posof (Ardahan). Cone length and diameter, 1000-seed weight, seed length and diameter, height of seed wing and number of seeds in a cone were determined. Geographical features such as altitude, aspect, and distance to the Black Sea, longitude and latitude of the sample plots were recorded. According to the analysis of correlation, the negative correlations were defined between the altitude of sampling points and cone length and diameter. In addition to this, there were negative correlations between the distance to the Black Sea and cone diameter, seed diameter and 1000-seed weight (p<0.05)

Artvin yöresi potansiyel erozyon sahaları ile ağaçlandırma ve erozyon kontrol çalışmalarına genel bir bakış

Artvin-Çoruh Vadisi boyunca toprak erozyonu ciddi şekilde devam etmektedir. Vadi boyunca içerilere doğru gidildikçe iklim karasala dönüşmekte ve giderek kuraklaşmaktadır. Arazi yapısının çok dik, engebeli ve eğimli olmasından dolayı büyük ölçüde erozyona maruz kalan bu alanlarda toprak ve bitki örtüsü arasındaki ekolojik dengenin devam ettirilmesi zorunludur. Bunun için potansiyel ağaçlandırma ve erozyon kontrol alanlarının tespiti yanlış arazi kullanımının önüne geçilmesinde ve erozyonun önlenmesinde önemli bir adım olacaktır. Çalışmamıza göre Artvin ilinde orman sınırları içinde kalan 153915 ha ve orman sınırları dışında kalan 55990 ha alanda ağaçlandırma ve erozyon kontrol çalışması yapılması gerekmektedir. 1992-2003 yılları arasında yılda ortalama 380.8 ha ağaçlandırma ve 1009.2 ha erozyon kontrol çalışması planlanmış, bunların sırasıyla % 35.4 ve % 104.5’i gerçekleştirilmiştirThe soil erosion has been going on seriously in the Çoruh River Valley. Climate changes to dry terrestrial climate from marine as one moves to inland through the valley. It is necessary to maintain ecological balance between soil and vegetation in this region where the terrain is very steep and rugged, and subject to significant soil erosion. Therefore, determination of the potential afforestation and erosion control areas would be the first step towards stopping inappropriate land use practices and erosion. According to our results 153915 ha area in forest boundary and 55990 ha area out of forest boundary are subject to afforestation and erosion control efforts in Artvin province. Between 1992 and 2003 380.8 ha afforestation and 1009.2 ha erosion control are planned per year, and 35.4 % and 104.5 % are realized, respectivel

Effects of some pretreatments on germination of bladder-senna (Colutea armena Boiss. and Huet.) and smoke-tree (Cotinus coggygria Scop.) seeds

This study was carried out to determine effects of pre-treatments including floating in hot water (100,C) followed by continual cooling for 24 hr in the same water, floating in tap water for 24 hr, submersion in concentrate (98%)sulphuric acid (H2SO4) and cold stratification for different durations (20, 40 and 60 days) and their combinations on seed germination and to investigate how to overcome dormancy of seeds of Colutea armena Boiss. and Huet. and Cotinus coggygria Scop. The seeds were sown in polyethylene pots in the greenhouse and on seedbeds under open field conditions. The statistical design was a randomized complete block design with three replications. The highest germination percentage (77.19%), the best germination rate (16 days) and the highest growth rate (69.01%) were obtained from Colutea armena seeds that were submersed in sulphuric acid for 30 min and sown in the greenhouse. The pre-treatment of submersion in sulphuric acid for 20 min with cold stratification for 60 days gave the highest germination percentage (82.77%) and the highest growth rate (79.37%) in the greenhouse for Cotinus coggygria seeds. On the other hand, the best germination rate (9 days) was obtained from smoketree seeds that were cold stratified 60 days and sown under open field conditions, It can be stated that there is an affirmative effect of the greenhouse condition on germination percentage and growth rate values of the seeds used in this study

Buğdayda Sorun Olan Septorya Yaprak Lekesi (Zymoseptoria tritici) Patojeni'nde Fungal Efektör Adayı Bazı SSP (Small Secreted Protein) Genlerinin Fonksiyonel Analizi

TÜBİTAK TOVAG Proje15.12.2017Septorya yaprak leke hastalığı etmeni Zymoseptoria tritici ülkemizde buğdayın en önemliyaprak hastalıklarından birisidir. Askomiset, hemibiotrof bir fungus olan fungusun tam genom sekans analizleri tamamlanmış ve erişime açılmıştır. Fungusun genomundaki genlerin fonksiyonlarının ve bitkiyi hastalandırma sürecinde görev alan efektör genlerinin belirlenmesi fungusa karşı mücadele stratejilerinin geliştirilmesinde büyük önem arz etmektedir.Bu proje buğday yaprak lekesi etmeni Z. tritici genomunda yer alan bazı küçük, hücre arasına salınan proteinleri kodlayan, fungal efektör adayı genlerin (Small Secreted Protein- SSP) gen silme tekniği ile fungusun genomundan silinip, fungusun biyolojik ve patolojik özelliklerine etkilerinin belirlenmesi amacıyla gerçekleştirilmiştir. Hedef SSP genlerine ait nükleotid dizileri kullanılarak oluşturulan gen silme kasetleri ve Agrobacterium temelli transformasyon tekniği kullanılarak patojenin genomundan hedeflenen genlerin tamamı silinebilmiştir.Silinen SSP genlerinden biri (Zt-3) fungusun temel biyolojik özelliklerinden biri olan mayaformunda gelişim özelliğini önemli oranda etkilemiştir. Zt-3 geni silinmiş izolat sadece makro piknidiospor üretebilmiştir. Çalışılan genlerin fungusun hastalandırma yeteneği üzerinde etkili olup olmadığı, geni silinmiş izolatlar ile yapılan patojenisite testleri ile araştırılmıştır. Herhangi bir etki bulunamamıştır. Çalışma sonunda Z. tritici gen fonksiyonu çalışmalarında gen silme tekniği ülkemizde ilk defa kullanılmış ve optimize edilmiştir. Yapılan çalışma bu tekniğin fungal genlerin fonksiyonlarının belirlenmesinde başarılı ve etkin bir şekilde kullanılabileceğini ortaya koymuştur.Septoria leaf blotch is one of the most important leaf diseases of wheat in Turkey.Ascomycet and hemibiotrophic fungus was sequenced as whole genome andrelease in public. It is very important to find out functions of the fungal genes andeffector proteins having roles in pathogenicity to develop new managementstrategies against fungus.This project was carried out to knock out of some Small Secreted Proteins (SSP)genes and examine the effects of gene deletion process on biological andpathogenic characteristics of it. Target SSP genes were successfully deletedusing gene deletion cassettes produced using nucleotide sequences of SSPgenes and Agrobacterium mediated transformation.One of deleted SSP genes (Zt-3) effected to development of yeast form of thefungus in important scale. Mutant isolate could only produce macropicniospores.It was investigated for the selected SSP genes whether gene deletion causedany difference on fungal pathogenicity using plant tests. Results showed therewas no effects of deletion of these genes.At the end of the study, gene deletion technique was firstly optimized and used ingene function studies on Z. tritici. This study showed that this technology can beused properly and effectively on gene function studies of the fungi

Tümör mikroçevresinde CD8’in yüksek ekspresyonu, yüksek dereceli seröz over kanserinde PD-1 ekspresyonu ve hasta sağkalımı ile ilişkilidir

Objective: The current study assesss programmed death-1 (PD-1) receptor expression and CD3, CD4, and CD8 tumor-infiltrating lymphocytes (TILs) in high-grade serous ovarian cancer (HGSOC) and to associate our results with neoadjuvant chemotherapy history and disease prognosis. Materials and Methods: We included cases diagnosed with primary HGSOC with biopsy or surgical resection materials in this study. The immunoreactivity of CD3, CD4, CD8, and PD1 was assessed immunohistochemically in tumor tissue. We analyzed TILs in two predetermined groups of high and low TIL. The relationships between clinical characteristics, PD-1, and TIL were assessed. by the χ(2) test or Fisher’s Exact test. We used Kaplan-Meier survival analysis and Cox proportional hazards regression model to the connection between survival and the amounts of TIL, and PD1. Results: Univariate analysis demonstrated that optimal debulking (p<0.001), early International Federation of Gynecology and Obstetrics stage (p=0.046), and higher scores of stromal CD8+ TIL expression (p=0.028) in tumor cells were all substantially correlated with longer disease-free survival (DFS), whereas the remaining variables analyzed, including PD-1 positivity, stromal CD3+, and CD4+ TILs, and intraepithelial CD3+, CD4+, and CD8+ TILs, were not correlated with DFS. Also, univariate analysis revealed that optimal debulking (p=0.010), and higher scores of stromal CD8+ TIL expression (p=0.021) in tumor cells were all substantially correlated with longer overall survival (OS). Conclusion: Higher scores of stromal CD8+ TILs are substantially correlated with DFS and OS in univariate analyses, whereas scores of stromal CD3+ and CD4+ TILs, and intraepithelial CD3+, CD4+, and CD8+ TILs are not correlated with DFS and OS in both univariate and multivariate analyses. Also, we found a significant association between PD-1 positivity and the scores of stromal CD3+ TILs and intraepithelial CD8+ TILs. However, no remarkable relationship was revealed between PD-1 positivity and the survival of HGSOC cases.Amaç: Çalışmamızın amacı, yüksek dereceli seröz over kanserinde (HGSOC) programlanmış ölüm-1 (PD-1) reseptör ekspresyonunu ve CD3, CD4 ve CD8 tümör infiltre edici lenfositleri (TIL) değerlendirmek ve bulgularımızın neoadjuvan kemoterapi öyküsü ve hastalık prognozu ile ilişkisini incelemektir. Gereç ve Yöntemler: Biyopsi veya cerrahi rezeksiyon materyalleri ile primer HGSOC tanısı alan olgular çalışmaya dahil edildi. CD3, CD4, CD8 ve PD1’in immünoreaktivitesi, tümör dokusunda immünohistokimyasal olarak değerlendirildi. TIL, önceden tanımlanmış iki grup olan düşük ve yüksek TIL grubunda analiz edildi. Klinik özellikler, PD-1 ve TIL arasındaki ilişkiler χ(2) testi veya Fisher’s Exact test ile değerlendirildi. TIL, PD1 ve hayatta kalma arasındaki ilişki için Kaplan-Meier hayatta kalma analizi ve Cox oransal hazard regresyon modeli kullanıldı. Bulgular: Tek değişkenli analiz, tümör hücrelerinde optimal debulking (p<0,001), erken Uluslararası Jinekoloji ve Obstetrik Federasyonu evresi (p=0,046) ve daha yüksek stromal CD8+ TIL ekspresyonu skorlarının (p=0,028) tümünün daha uzun hastalıksız sağkalım (DFS) ile önemli ölçüde ilişkili olduğunu gösterdi; oysa ki kalan değişkenler, PD-1 pozitifliği, stromal CD3+ ve CD4+ TIL’ler ve intraepitelyal CD3+, CD4+ ve CD8+ TIL’ler dahil olmak üzere, analiz edildiğinde DFS ile korele değildi. Ayrıca, tek değişkenli analiz, tümör hücrelerinde optimal debulking (p=0,010) ve daha yüksek stromal CD8+ TIL ekspresyonu skorlarının (p=0,021) tümünün daha uzun genel sağkalım (OS) ile önemli ölçüde ilişkili olduğunu ortaya koydu. Sonuç: Daha yüksek stromal CD8+ TIL skorları, tek değişkenli analizde DFS ve OS ile anlamlı şekilde ilişkiliyken, stromal CD3+ ve CD4+ TIL’lerin ve intraepitelyal CD3+, CD4+ ve CD8+ TIL’lerin skorları, hem tek değişkenli hem de çok değişkenli analizlerde DFS ve OS ile ilişkili değildi. Ayrıca, PD-1 pozitifliği ile stromal CD3+ TIL’lerin ve intraepitelyal CD8+ TIL’lerin skorları arasında anlamlı bir ilişki bulundu. Ancak, PD-1 pozitifliği ile HGSOC hastalarının sağkalımı arasında anlamlı bir ilişki gözlenmedi

Survival outcomes of patients with oligometastatic non-small cell lung cancer who were treated with radical therapy: A multicenter analysis

Background/aim: Oligometastatic disease for nonsmall cell lung cancer (NSCLC) patients is generally thought to represent a better prognosis with a quieter biology, limited number of disease sites and long-term disease control. In this study, we aimed to determine the efficacy of radical treatment options for patients with oligometastatic NSCLC. Materials and methods: This retrospective trial included totally 134 patients with oligometastatic NSCLC. The presence of oncodriver mutation, tumor stages and nodal status, the number of metastases and involved metastatic site, treatment of primary tumor and oligometastasis, response rate, overall survival (OS) and progression-free survival (PFS) were evaluated. Results: Of 134 patients 66.4% were defined as adenocarcinoma, 26.1% were squamous cell carcinoma and 7.5% of patients were in other histology. Based on the treatment of primary tumor, in 36 patients (26.9%) curative surgery has undergone, in addition, 19 (14.2%) patients were received chemotherapy, 73 (54.5%) were treated with chemoradiotherapy, while immunotherapy and targeted therapy were used in 1 (0.7%) and 2 (1.4%), respectively. The preferred treatment for oligometastatic lesions were SBRT in 72.4% of patients, surgery in 10.5%, and both SBRT and surgery in 17.1% of patients. At the median follow up of 31.3 months (range: 9.5–48.5), the median PFS and OS times were 17 and 24.4 months, respectively. Moreover, OS-2 after progression was also 7.2 months. Conclusion: Based on our real-life experience, we demonstrated a significant correlation between good response to first treatment and survival in oligometastatic disease, we also understand that local ablative treatment modalities prolong and also delay both OS and PFS in oligometastatic NSCLC patients OS-2

Clinicopathological and survival characteristics of mismatch repair status and PD-1 expression in serous ovarian cancer

Objective: To evaluate the clinicopathological characteristics of mismatch repair (MMR) deficiency and its clinical outcomes by performing immunohistochemistry (IHC) for MMR genes in the serous ovarian cancer (SOC) tumour sections.Study Design: A retrospective case-control study. Place and Duration of the Study: Gynecology Department of Kanuni Sultan Suleyman Training and Research Hospital, and Department of Medical Oncology of Medipol University, between March 2001 and January 2020. Methodology: IHC was carried out for MLH1, MSH2, MSH6, and PMS2 on full-section slides from 127 SOCs to evaluate the MMR status. MMR-negative and MMR-low groups together were defined as MMR deficient and called microsatellite instability-high (MSI-H). The MSI status and expression of programmed cell death-1 (PD-1) were compared in SOCs with different MMR statuses. Results: A significantly higher frequency of MMR-deficient SOCs was diagnosed at early stages compared with the patients in the MSS group (38.6% and 20.6%, respectively, p=0.022). The frequency of cases with PD-1 expression was significantly higher in the MSI-H group (76.2%) than in the MSS counterparts (58.8%, p=0.028). Patients in the MSI-H group had significantly longer DFS (25.6 months) and OS (not reached) than those in the MSS group (16 months and 48.9 months, p=0.039 and p=0.026, respectively).Conclusion: MSI-H SOCs were diagnosed at an earlier stage as compared to MMR proficient cases. The presence of PD-1 expres-sion was significantly higher in cases presenting MMR deficiency compared with MMR-proficient cases. MSI status was significantly associated with DFS and OS

Germination of Anatolian Black Pine (Pinus nigra subsp. pallasiana) Seeds from the Lakes Region of Turkey: Geographic Variation and Effect of Storage

Effects of 10-year storage on germination of seeds in 191 Anatolian Black Pine trees from 23 populations in the Lakes Region of Turkey were investigated. Germination tests were conducted with both fresh (in year 1999) and stored (in year 2009) seeds and variation in germination was related to geographic features of the populations. Significant reductions in germination rate (from 79.93% to 30.68%) and germination percentage (from 95.99% to 58.41%) were observed after 10-year storage. Germination characteristics seem to be associated with humidity of population locations. Seeds from more inland (i.e., continental) populations germinated slower but attained higher germination percentage for both seed sets. Germination percentage of stored seeds is highest at elevations with high humidity. Greater attention should be given to environmental conditions of seed sources in storing Anatolian Black Pine seeds in the Lakes Region of Turkey as it is a very important tool in ensuring continuous seedling production and genetic conservation

The prevalence of drug-drug interactions and reported therapy related side-effects in oncology out-patients

Objective: The use of multiple medications in cancer patients is unavoidable; thus, adverse drug-drug interactions are frequent. This study aims to assess the prevalence of potential drug interactions in oncology patients visiting the outpatient chemotherapy unit. Method: Demographic and health-related information of patients visiting an outpatient chemotherapy unit was recorded using a pre-prepared form. A comprehensive list of all concurrently used medications was compiled and checked for interactions with the Micromedex online drug interaction tool.Results: A total of 179 adult patients were included. We recorded an average of 9.3 drugs per patient with 79 patients using more than 10 drugs. A total of 1671 drugs including 303 chemotherapeutic agents were assessed for drug-drug interactions. A total of 374 interactions, of which 203 were significant, were recorded in 118 (65.9%) patients with an average of 3.2 interactions per patient. Only 46 major interactions were recorded for anticancer agents. Cyclophosphamide (n=13) and cisplatin (n=12) were involved in most interactions. The number of interactions correlated with the number of drugs used (p=.001) and the presence of comorbidities (p=.002). The presence of comorbidities increased the risk of interaction by 1.21 (p=.04). Recorded side effects were not correlated to drug interactions. Conclusion: Medication review in cancer patients is essential in establishing all medications used by patients. Routine assessment in terms of potential drug interactions and evaluation of these interactions by a qualified pharmacist may help in optimizing patient outcomes