The Effect of 5-Fu and Ruxolitinib on Mitochondrial Apoptosis in Glioblastoma U87 Cell Line

DergiPark: 819208tmsjAims: The aim of this study is to carry out the effect of 5-Fluorouracil alone or combined with Ruxolitinib on both apoptosis and JAK/STAT pathway in U87 glioblastoma cells. Methods: We used U87 glioblastoma cell lines as the human brain cancer cells. We treated the cells with 5-Fluorouracil (3.125 ?M-400 ?M) alone and with a combination of Ruxolitinib (100 ?M or 400 ?M of Ruxolitinib with 3.125-25 ?M 5-Fluorouracil), and performed the MTT test for calculating IC50 value. Molecular fluorescence staining was performed with Hoechst and acridine orange/ethidium bromide probes. The alteration in mitochondrial apoptosis and JAK/STAT pathways to drug treatment was analyzed by the qRT-PCR assay. Results: Decrease in cell viability was more prominent in U87 cells treated with a combination of 5-Fluorouracil and Ruxolitinib compared to those treated with 5-Fluoro- uracil alone. In gene expression analysis, apoptosis signals were observed in cells treated with 5-Fluorouracil alone and 5-Fluo- rouracil+Ruxolitinib treatment. Conclusion: Treatment with 5-Fluorouracil alone and 5-Fluorouracil+Ruxolitinib combination increased apoptosis in U87 glioblastoma cells. However, it is difficult to mention an evident difference between treatments. Therefore, further studies are needed

An Investigation on the Anticancer Effect of Spider Web in Human Cervical Cell Line

DergiPark: 539659tmsjAims: The aim of this study is to investigate the anti-cancer and anti-proliferative effect of spider web extract, and mitochondrial apoptosis signaling response via gene expression levels belonging to caspase-3 depended apoptosis in both healthy Astrocyte and cancerous HeLa cell lines. Methods: We used HeLa and C8-D1A Astrocyte type I clone cell lines as the human cervical cancer and healthy cell line, respectively. We treated the cells with spider web extract and performed MTT assay. IC50 was calculated by probit analysis. Molecular fluorescence staining and TALI cytometer measurements were also applied. The response of the mitochondrial apoptosis pathway to spider web extract treatment was analyzed by the qRT-PCR assay. Results: The spider web extract administered in different concentrations to the HeLa cell line reduced cell viability at a statistically significant level after 24 hours of application. In the astrocyte cell line, the spider web extract did not cause statistically significant cell death. In the analysis of gene expressions, a strong mitochondrial apoptosis signaling was observed. Conclusion: While spider web extract does not cause any cytotoxic effects on healthy cell lines, it causes a strong fatal effect in cancer cell line. In addition, IC50 dose of the spider web extract is satisfying compared to many other natural products in the market which have anti-cancer effects. Spider web extract causes a programmed cell death by following death signaling pathway

The effect of abscisic acid application on root-shoot length and some antioxidant enzyme activities of two different tomato seedlings

In this study, we determined the changes in root-shoot length, chlorophyll and carotenoid contents, and some antioxidant enzyme activities in leaf tissues of two different tomato (Lycopersicon esculentum Mill. cv. Aspendos and Donna) seedlings exposed to exogenous abscisic acid (ABA) 7 day intervals for a period of 28 days. Tomato seedlings were grown under controlled conditions using at seedling industry. When the seedlings had first true leaves, ABA was sprayed at 1, 10, 50 and 100 µM on upper and lower epidermis of plants. While 1 and 10 µM ABA exposure caused increases, 50 and 100 µM ABA exposure caused decreases in root and stem length of both tomato cultivars compared to control. Treatment with all ABA concentrations significantly increased the activities of superoxide dismutase (SOD, E.C. 1.15.1.1), catalase (CAT, E.C. 1.11.1.6) and peroxidase (POD, E.C. 1.11.1.7) enzymes. Root-shoot length and pigment content were positively affected by ABA application for 14 and 21 days but 28 days application caused reductions in both parameters. Results of this study revealed that application of ABA at 1 or 10 µM for 14-21 day have shown beneficial role for tomato seedlings. Additionally, we thought that these seedlings which have higher chlorophyll content and SOD, POD and CAT activity compared to controls, were more resistant against various environmental stresses

Genetic relationships among Eurasian Puccinellia distans genotypes

Puccinellia distans (Jacq.) Parl. is a common grass species found throughout the world. It can grow in arid and saline environments as well as under toxic boron concentrations. In this work we performed sequence related amplified polymorphism (SRAP) marker analysis on 20 wild P. distans genotypes to understand the genetic relationships among different genotypes and subspecies. We tested 119 SRAP primer pairs and found that 43 were polymorphic. The molecular data were then analyzed to determine the genetic relationships and population structure of the genotypes. We were able to trace the origin of genotypes that were carried to distant locations or gathered for research purposes. We also found that geographical distance between genotypes was not an important determinant of genetic relationships as even distantly located Puccinellia genotypes were closely related. As P. distans is known to be tolerant to salinity stress and toxic mineral concentrations, the findings of this work can be used as a starting point for selection of genotypes that should be tested under such conditions.Scientific and Technological Research Council of Turkey (113Z930

Genetic diversity and population structure of faba bean (Vicia faba) from Turkey

Faba bean (Vicia faba L.) is an important food and feed legume because of the nutritional value of its seed protein and starch content, good biomass, and high efficiency nitrogen fixation.This study analyzed the molecular genetic diversity and population structure of 101 Turkish faba bean accessions using simple sequence repeat (SSR) markers.A total of 32 SSR markers yielded 281 loci of which 277 (98.6%) were polymorphic.Mean dissimilarity between genotypes was 0.355, a relatively high value which was expected given faba bean’s large genome and limited breeding history.According to the results, faba bean individuals grouped into three main clusters based on both distance matrix (neighbor-joining algorithm) and model-based (population structure) clustering analyses.Clustering was not correlated with seed size or origin within Turkey.Six cultivars were included in the analysis and showed high genetic diversity compared with the landraces, as expected, given the fact that at least some of the cultivars were bred by hybridization.A total of 47 individuals were selected for the core collection to represent the diversity of Turkish faba bean germplasm.This core set encompasses material adapted to all growing regions and should be a priority for morphological characterization. © 2016, American Society for Horticultural Science.All rights reserved.Republic of Turkey's Ministry of Science, Industry and Technology (0424.STZ.2013-2

Determination of genetic diversity in watermelon [Citrullus lanatus (Thunb.) Matsum & Nakai] germplasm

The genetic diversity and relatedness of 90 watermelon (Citrullus lanatus var. lanthus and Citrullus. lanatus var. citroides) accessions were molecularly characterized using 30 sequence-related amplified polymorphism (SRAP) marker combinations. The accessions were collected from Turkey (59 accessions) and other regions of the world by the United States Department of Agriculture (USDA) and the molecular data were analysed using UPGMA (Unweighted Pair Group Method Analysis). The SRAP combinations were highly polymorphic (97%) with 87 polymorphic bands determined among 201 amplified fragments (43%). The UPGMA analysis characterized five major clusters (A, B, C, D and E). While minimum genetic similarity among groups A, B and C was high (83%), group E was the most distant with 63% genetic similarity. Principal component analysis (PCA) was performed and used to produce a two-dimensional plot from which two main groups could be distinguished. Based on the analyses, genetic diversity of watermelons was very low and Turkish watermelons were not distinct from other countries' accessions. These results could be used for generation of a core collection of watermelon by elimination of redundant accessions and for watermelon breeding by helping to identify useful, genetically distinct lines. In addition, the study indicated that SRAP markers are useful for analysing genetic diversity in crops like watermelon which have low variability

Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing

Opium poppy (Papaver somniferum L.) is an important pharmaceutical crop with very few genetic marker resources. To expand these resources, we sequenced genomic DNA using pyrosequencing technology and examined the DNA sequences for simple sequence repeats (SSRs). A total of 1,244,412 sequence reads were obtained covering 474 Mb. Approximately half of the reads (52 %) were assembled into 166,724 contigs representing 105 Mb of the opium poppy genome. A total of 23,283 non-redundant SSRs were identified in 18,944 contigs (11.3 % of total contigs). Trinucleotide and tetranucleotide repeats were the most abundant SSR repeats, accounting for 49.0 and 27.9 % of all SSRs, respectively. The AAG/TTC repeat was the most abundant trinucleotide repeat, representing 19.7 % of trinucleotide repeats. Other SSR repeat types were AT-rich. A total of 23,126 primer pairs (98.7 % of total SSRs) were designed to amplify SSRs. Fifty-three genomic SSR markers were tested in 37 opium poppy accessions and seven Papaver species for determination of polymorphism and transferability. Intraspecific polymorphism information content (PIC) values of the genomic SSR markers were intermediate, with an average 0.17, while the interspecific average PIC value was slightly higher, 0.19. All markers showed at least 88 % transferability among related species. This study increases sequence coverage of the opium poppy genome by sevenfold and the number of opium poppy-specific SSR markers by sixfold. This is the first report of the development of genomic SSR markers in opium poppy, and the genomic SSR markers developed in this study will be useful in diversity, identification, mapping and breeding studies in opium poppy.Scientific and Technological Research Council of Turkey (TUBITAK-109O797

Molecular diversity and identification of alleles for Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm

Cotton is an important crop in the textile, food and pharmaceutical industries. In the present study, a panel of 108 elite cotton (Gossypium hirsutum L.) lines was genotyped with 177 genome-wide SSR markers to assess genetic diversity, linkage disequilibrium, population structure and association analyses. A total of 967 loci were assayed and the lines fell into four main groups with a mean genetic distance of 39%. The linkage disequilibrium (LD) decay rate was estimated to be 20–30 cm (r2 ≤ 0.5). Association analyses were performed with both general linear model and mixed linear model methods to identify SSR marker loci linked to Verticillium wilt resistance. Verticillium wilt is a fungal disease that causes huge yield losses in cotton production throughout the world. A total of 26 marker loci distributed on 14 chromosomes were associated with resistance at p ≤ 0.05. Eight of the 26 associated marker loci were highly significant (p < 0.01). The phenotypic variation explained (r2) by individual markers ranged from 3.2% to 8.2%. Three of the 26 marker loci (JESPR153, JESPR274 and CIR218) were consistent with previous studies. Our results should be useful in improving Verticillium wilt resistance in cotton breeding lines.GDARP (General Directorate of Agricultural Research and Policies, Ministry of Food, Agriculture and Livestock Republic of Turkey) (TAGEM-11/AR-GE/17

Ruksolitinib ile Engellenen Glioblastoma İnvazyonunda AnjiyomiR’lerin Ekspresyon Profili

Amaç: MikroRNA’lar (miR), insan genomunda gen ifadesinin düzenlenmesinde önemli rolü olan düzenleyicilerdir. Son yıllarda anjiyogenezde rol oynayan spesifik bir miR grubu tanımlanmış (anjiyo-miR) ve bazı anjiyo-miR’lerin gliomalarda etkin rol oynadıkları ortaya konmuştur. Bu çalışmada, glioblastoma hücrelerindeki anjiyo-miR’lerin ifade değerlerindeki değişiklikleri ve bu değişikliklerin invazyon ve tümör büyümesi ile ilişkisini araştırdık. Gereç ve Yöntem: Bu çalışmada, insan glioblastoma hücre hattı U-87 MG kullanılarak glioblastoma tümör sferoidleri elde edildi. Matrigel yöntemi ile tümör sferoidlerine 48 saat süresince 50 nM, 100 nM and 200 nM ruksolitinib uygulandı. Kırk sekiz saat tedaviden sonra glioblastoma tümör sferoidlerinde tümör hacmi ve invazyon oluşumu relatif yüzde tümör gelişimi ve relatif yüzde invazyon alanı ölçüldü. Aynı zamanda, niceliksel gerçek zamanlı polimeraz zincir reaksiyonu (qRT-PZR) analizi yapıldı ve miR ifade değerleri belirlendi. Farklı şekillerde ifade edilen miRNA’ların modelini görüntülemek için normalize edilen miRNA ifade değerleri kullanılarak heatmap ve volcano plot analizleri ile seçilen en önemli (importance features) miRNA’lar gösterildi. Bulgular: Tümör sferoidlerine 50 nM, 100 nM ve 200 nM ruksolitinib uygulamasının tümör hacmi ve invazyon üzerine etkisi değerlendirildiğinde, uygulanan her dozda anlamlı fark saptandı. Ancak 200 nM ruksolitinib dozunda tümör yayılımını engelleyici etkisinin en yüksek olduğu gözlendi. 200 nM ruksolitinib uygulaması ile qRT-PZR testi ile elde edilen miR ifade değerleri incelendiğinde 10 miR’nin ifade değerlerinin arttığı, 4 tanesinin ifade değerlerinin ise azaldığı belirlendi. Sonuç: Sonuç olarak anjiyo-miR ifade değerleri gliomaların prognostik sürecini daha iyi anlamamızı sağlayabilmeleri açısından önemlidirler. Çoklu susturma özellikleri sayesinde glioblastomalar için yeni terapötik hedefler ve prognostik biyobelirteçler olarak kullanılabilmesi açısından ileri çalışmalarla kliniğe katkı sağlayabilirle

Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant

Quantitative trait loci (QTL) for domestication-related traits were identified in an interspecific F2 population of eggplant (Solanum linnaeanum × S. melongena). Although 62 quantitative trait loci (QTL) were identified in two locations, most of the dramatic phenotypic differences in fruit weight, shape, color, and plant prickliness that distinguish cultivated eggplant from its wild relative could be attributed to six loci with major effects. Comparison of the genomic locations of the eggplant fruit weight, fruit shape, and color QTL with the positions of similar loci in tomato, potato, and pepper revealed that 40% of the different loci have putative orthologous counterparts in at least one of these other crop species. Overall, the results suggest that domestication of the Solanaceae has been driven by mutations in a very limited number of target loci with major phenotypic effects, that selection pressures were exerted on the same loci despite the crops' independent domestications on different continents, and that the morphological diversity of these four crops can be explained by divergent mutations at these loci.U.S. Department of Agriculture National Research Initiative Cooperative Grants Program (no. 96-35300-3646); The Binational Agricultural Research and Development Fund (no. US 2427-94); The National Science Foundation (No. 9872617) to S.D.T