Molecular analysis of historical wine grape variety candidates found in Urla

Urla had been an important center of viticulture and wine making due to its suitable ecology for vineyards. It is also known that there are some grape varieties endemic to this area. However, for various reasons, the viticulture in Urla started to diminish in the beginning of the twentieth century, almost getting to the point of extinction in the mid-century. As the interest for wines and wine grapes rose in the 1990s, vineyards have started to be rebuilt in this area. However, mostly foreign varieties are grown in these vineyards; the local cultivars are non-existent now, except for some small vineyards. Rebuilding of vineyards and wineries would be very valuable for both economic and touristic development of Urla. Detecting and registering local grape cultivars and producing high-quality chateau wines from these grapes would create a greater added value. Five grapevines that might represent different red wine grape varieties have been found in Urla. Although these vines might represent historical local grape cultivars, they might also be some examples of grape varieties that are already known. In this study the vines that were found in Urla were compared to the black grape cultivars collected from the Aegean Region, and to the major Turkish and the world red wine grape varieties, using molecular methods. For the molecular analyses, SSR (Simple Sequence Repeat) markers were utilized first. 14 grapevine varieties that show close relationship to the vines found in Urla were further analyzed with AFLP (Amplified Fragment Length Polymorphism) markers. UPGMA graph and genetic similarity coefficient values of the AFLP analysis indicated that Urla karası 4 and Urla karası 5 belong to grapevine accessions certainly different from the analyzed samples. However, in order to determine whether or not the vines found in Urla represent economically valuable novel red wine grape varieties, these should be further propagated and their wine qualitys were analysed

Autophagy: a cellular stres and a cell death mechanism (Otofaji: bir hücresel stres yanıtı ve ölüm mekanizması)

Autophagy is a physiological phenomenon responsible for the degradation of long-lived proteins, organelles and cytoplasmic fragments. It allows cellular recycling following lysosomal degradation and helps the cell to survive various stress conditions including starvation, growth factor and oxidative stress. Paradoxically, under certain conditions autophagy may kill the cell through a caspase-independent, non-apoptotic type of cell death (Type II cell death or autophagic cell death). Several lines of evidence point out to a direct connection between classical apoptosis and autophagy. Molecular mechanisms of apoptosis-autophagy connection start to be unraveled. The cross-talk between autophagy and apoptosis seems quite complex but certainly is critical for the development of novel diagnosis, follow-up and treatment modalities in health problems such as cancer, infections and neurodegenerative diseases

Эксплуатационные показатели качества транспортной телекоммуникационной первичной сети Украины

Приведены статистические данные о количестве, причинах и характере повреждений подземных волоконно-оптических линий связи, которые являются основой транспортной телекоммуникационной первичной сети на примере Донецкой и Луганской областей за период с 2001 по 2010 годы. Сравнение значений этих характеристик со значениями аналогичных параметров за 2001—2005 гг. позволяет разработать рекомендации по повышению надежности телекоммуникационных сетей.В роботі наведено статистичні дані про кількість, причини та характер пошкоджень підземних волоконно-оптичних ліній зв’язку, які є основою транспортної телекомунікаційної первинної мережі, на прикладі Донецької та Луганської областей за період з 2001 по 2010 рр. Порівняння значень цих характеристик із значеннями аналогічних характеристик за 2001—2005 рр. дозволяє розробити рекомендації по підвищенню надійності телекомунікаціїйних мереж.The paper presents statistical data on the number, nature and causes of the damage to underground fiber-optic communication lines, on which the transport telecommunication primary network is based, using an example of Donetsk and Lugansk regions for the period between 2001 and 2010. Comparison of these characteristics with the values of similar parameters over 2001—2005 allows to develop recommendations for the improvement of the reliability of telecommunication networks

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

p53 binds enhancers to regulate key target genes. Here, we globally mapped p53-regulated enhancers by looking at enhancer RNA (eRNA) production. Intriguingly, while many p53-induced enhancers contained p53-binding sites, most did not. As long non-coding RNAs(lncRNAs) are prominent regulators of chromatin dynamics, we hypothesized that p53-induced lncRNAs contribute to the activation of enhancers by p53. Among p53-induced lncRNAs, we identified LED and demonstrate that its suppression attenuates p53 function. Chromatin-binding and eRNA expression analyses show that LED associates with and activates strong enhancers. One prominent target of LED was located at an enhancer region within CDKN1A gene, a potent p53-responsive cell cycle inhibitor. LED knockdown reduces CDKN1A enhancer induction and activity, and cell cycle arrest following p53 activation. Finally, promoter-associated hypermethylation analysis shows silencing of LED in human tumours. Thus, our study identifies a new layer of complexity in the p53 pathway and suggests its dysregulation in cancer

MIR376A is a regulator of starvation-induced autophagy

Background: Autophagy is a vesicular trafficking process responsible for the degradation of long-lived, misfolded or abnormal proteins, as well as damaged or surplus organelles. Abnormalities of the autophagic activity may result in the accumulation of protein aggregates, organelle dysfunction, and autophagy disorders were associated with various diseases. Hence, mechanisms of autophagy regulation are under exploration. Methods: Over-expression of hsa-miR-376a1 (shortly MIR376A) was performed to evaluate its effects on autophagy. Autophagy-related targets of the miRNA were predicted using Microcosm Targets and MIRanda bioinformatics tools and experimentally validated. Endogenous miRNA was blocked using antagomirs and the effects on target expression and autophagy were analyzed. Luciferase tests were performed to confirm that 3’ UTR sequences in target genes were functional. Differential expression of MIR376A and the related MIR376B was compared using TaqMan quantitative PCR. Results: Here, we demonstrated that, a microRNA (miRNA) from the DlkI/Gtl2 gene cluster, MIR376A, played an important role in autophagy regulation. We showed that, amino acid and serum starvation-induced autophagy was blocked by MIR376A overexpression in MCF-7 and Huh-7 cells. MIR376A shared the same seed sequence and had overlapping targets with MIR376B, and similarly blocked the expression of key autophagy proteins ATG4C and BECN1 (Beclin 1). Indeed, 3’ UTR sequences in the mRNA of these autophagy proteins were responsive to MIR376A in luciferase assays. Antagomir tests showed that, endogenous MIR376A was participating to the control of ATG4C and BECN1 transcript and protein levels. Moreover, blockage of endogenous MIR376A accelerated starvation-induced autophagic activity. Interestingly, MIR376A and MIR376B levels were increased with different kinetics in response to starvation stress and tissue-specific level differences were also observed, pointing out to an overlapping but miRNA-specific biological role. Conclusions: Our findings underline the importance of miRNAs encoded by the DlkI/Gtl2 gene cluster in stress-response control mechanisms, and introduce MIR376A as a new regulator of autophagy

A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation

Estrogen receptor α (ERα) is an enhancer activating transcription factor, a key driver of breast cancer and a main target for cancer therapy. ERα-mediated gene regulation requires proper chromatin-conformation to facilitate interactions between ERα-bound enhancers and their target promoters. A major determinant of chromatin structure is the CCCTC-binding factor (CTCF), that dimerizes and together with cohesin stabilizes chromatin loops and forms the boundaries of topologically associated domains. However, whether CTCF-binding elements (CBEs) are essential for ERα-driven cell proliferation is unknown. To address this question in a global manner, we implemented a CRISPR-based functional genetic screen targeting CBEs located in the vicinity of ERα-bound enhancers. We identified four functional CBEs and demonstrated the role of one of them in inducing chromatin conformation changes in favor of activation of PREX1, a key ERα target gene in breast cancer. Indeed, high PREX1 expression is a bona-fide marker of ERα-dependency in cell lines, and is associated with good outcome after anti-hormonal treatment. Altogether, our data show that distinct CTCF-mediated chromatin structures are required for ERα- driven breast cancer cell proliferation

CUEDC1 is a primary target of ERα essential for the growth of breast cancer cells

Breast cancer is the most prevalent type of malignancy in women with ∼1.7 million new cases diagnosed annually, of which the majority express ERα (ESR1), a ligand-dependent transcription factor. Genome-wide chromatin binding maps suggest that ERα may control the expression of thousands of genes, posing a great challenge in identifying functional targets. Recently, we developed a CRISPR-Cas9 functional genetic screening approach to identify enhancers required for ERα-positive breast cancer cell proliferation. We validated several candidates, including CUTE, a putative ERα-responsive enhancer located in the first intron of CUEDC1 (CUE-domain containing protein). Here, we show that CUTE controls CUEDC1 expression, and that this interaction is essential for ERα-mediated cell proliferation. Moreover, ectopic expression of CUEDC1, but not a CUE-domain mutant, rescues the defects in CUTE activity. Finally, CUEDC1 expression correlates positively with ERα in breast cancer. Thus, CUEDC1 is a functional target gene of ERα and is required for breast cancer cell proliferation

LncRNA-OIS1 regulates DPP4 activation to modulate senescence induced by RAS

Oncogene-induced senescence (OIS), provoked in response to oncogenic activation, is considered an important tumor suppressor mechanism. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt without a protein-coding capacity. Functional studies showed that deregulated lncRNA expression promote tumorigenesis and metastasis and that lncRNAs may exhibit tumor-suppressive and oncogenic function. Here, we first identified lncRNAs that were differentially expressed between senescent and non-senescent human fibroblast cells. Using RNA interference, we performed a loss-function screen targeting the differentially expressed lncRNAs, and identified lncRNA-OIS1 (lncRNA#32, AC008063.3 or ENSG00000233397) as a lncRNA required for OIS. Knockdown of lncRNA-OIS1 triggered bypass of senescence, higher proliferation rate, lower abundance of the cell-cycle inhibitor CDKN1A and high expression of cell-cycle-associated genes. Subcellular inspection of lncRNA-OIS1 indicated nuclear and cytosolic localization in both normal culture conditions as well as following oncogene induction. Interestingly, silencing lncRNA-OIS1 diminished the senescent-associated induction of a nearby gene (Dipeptidyl Peptidase 4, DPP4) with established role

A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis

Background: Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiveness. Although thousands of YAP/TEAD4 binding-sites are annotated, their functional importance is unknown. Here, we aim at further identification of enhancer elements that are required for YAP functions. Results: We first apply genome-wide ChIP profiling of YAP to systematically identify enhancers that are bound by YAP/TEAD4. Next, we implement a genetic approach to uncover functions of YAP/TEAD4-associated enhancers, demonstrate its robustness, and use it to reveal a network of enhancers required for YAP-mediated proliferation. We focus on EnhancerTRAM2, as its target gene TRAM2 shows the strongest expression-correlation with YAP activity in nearly all tumor types. Interestingly, TRAM2 phenocopi