Turkish journal of biology = Turk biyoloji dergisi最新文献_第10页

Linkage of nanosecond protein motion with enzymatic methyl transfer by nicotinamide N-methyltransferase. 纳秒级蛋白质运动与烟酰胺n -甲基转移酶酶促甲基转移的联系。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-06-23 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2101-54

Yahui Jing, Yiting Cheng, Fangya Li, Yuping Li, Fan Liu, Jianyu Zhang

引用次数: 0

Reconstitution of Pol II (G) responsive form of the human Mediator complex. 人中介体复合物Pol II (G)反应形式的重构。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-06-23 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2009-12

Murat Alper Cevher

引用次数: 1

Crosstalk between autophagy and DNA repair systems. 自噬和DNA修复系统之间的串扰。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-06-23 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2103-51

Sinem Demirbağ-Sarikaya, Hatice Çakir, Devrim Gözüaçik, Yunus Akkoç

引用次数: 2

Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels. 不同微环境和异质性水平下癌症测序管道的详细评估。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-04-20 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2008-8

Batuhan Kısakol, Şahin Sarıhan, Mehmet Arif Ergün, Mehmet Baysan

{"title":"Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels.","authors":"Batuhan Kısakol, Şahin Sarıhan, Mehmet Arif Ergün, Mehmet Baysan","doi":"10.3906/biy-2008-8","DOIUrl":"https://doi.org/10.3906/biy-2008-8","url":null,"abstract":"The importance of next generation sequencing (NGS) rises in cancer research as accessing this key technology becomes easier for researchers. The sequence data created by NGS technologies must be processed by various bioinformatics algorithms within a pipeline in order to convert raw data to meaningful information. Mapping and variant calling are the two main steps of these analysis pipelines, and many algorithms are available for these steps. Therefore, detailed benchmarking of these algorithms in different scenarios is crucial for the efficient utilization of sequencing technologies. In this study, we compared the performance of twelve pipelines (three mapping and four variant discovery algorithms) with recommended settings to capture single nucleotide variants. We observed significant discrepancy in variant calls among tested pipelines for different heterogeneity levels in real and simulated samples with overall high specificity and low sensitivity. Additional to the individual evaluation of pipelines, we also constructed and tested the performance of pipeline combinations. In these analyses, we observed that certain pipelines complement each other much better than others and display superior performance than individual pipelines. This suggests that adhering to a single pipeline is not optimal for cancer sequencing analysis and sample heterogeneity should be considered in algorithm optimization.","PeriodicalId":23375,"journal":{"name":"Turkish journal of biology = Turk biyoloji dergisi","volume":"45 2","pages":"114-126"},"PeriodicalIF":0.0,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38914103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeting the tumor stroma: integrative analysis reveal GATA2 and TORYAIP1 as novel prognostic targets in breast and ovarian cancer. 靶向肿瘤基质:综合分析揭示GATA2和TORYAIP1是乳腺癌和卵巢癌新的预后靶点。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-04-20 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2010-39

Ömer Faruk Erceylan, Ayşe Savaş, Esra Göv

{"title":"Targeting the tumor stroma: integrative analysis reveal GATA2 and TORYAIP1 as novel prognostic targets in breast and ovarian cancer.","authors":"Ömer Faruk Erceylan, Ayşe Savaş, Esra Göv","doi":"10.3906/biy-2010-39","DOIUrl":"https://doi.org/10.3906/biy-2010-39","url":null,"abstract":"Tumor stroma interaction is known to take a crucial role in cancer growth and progression. In the present study, it was performed gene expression analysis of stroma samples with ovarian and breast cancer through an integrative analysis framework to identify common critical biomolecules at multiomics levels. Gene expression datasets were statistically analyzed to identify common differentially expressed genes (DEGs) by comparing tumor stroma and normal stroma samples. The integrative analyses of DEGs indicated that there were 59 common core genes, which might be feasible to be potential marks for cancer stroma targeted strategies. Reporter molecules (i.e. receptor, transcription factors and miRNAs) were determined through a statistical test employing the hypergeometric probability density function. Afterward, the tumor microenvironment protein-protein interaction and the generic network were reconstructed by using identified reporter molecules and common core DEGs. Through a systems medicine approach, it was determined that hub biomolecules, AR, GATA2, miR-124, TOR1AIP1, ESR1, EGFR, STAT1, miR-192, GATA3, COL1A1, in tumor microenvironment generic network. These molecules were also identified as prognostic signatures in breast and ovarian tumor samples via survival analysis. According to literature searching, GATA2 and TORYAIP1 might represent potential biomarkers and candidate drug targets for the stroma targeted cancer therapy applications.","PeriodicalId":23375,"journal":{"name":"Turkish journal of biology = Turk biyoloji dergisi","volume":"45 2","pages":"127-137"},"PeriodicalIF":0.0,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38914104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells. 与硒缺乏依赖的氧化应激相关的转录组谱在肝癌细胞中确定潜在的诊断和治疗靶点。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-04-20 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2009-56

Damla Gözen, Deniz Cansen Kahraman, Kübra Narci, Huma Shehwana, Özlen Konu, Rengül Çetin-Atalay

{"title":"Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells.","authors":"Damla Gözen, Deniz Cansen Kahraman, Kübra Narci, Huma Shehwana, Özlen Konu, Rengül Çetin-Atalay","doi":"10.3906/biy-2009-56","DOIUrl":"https://doi.org/10.3906/biy-2009-56","url":null,"abstract":"Hepatocellular carcinoma (HCC) is one of the most common cancer types with high mortality rates and displays increased resistance to various stress conditions such as oxidative stress. Conventional therapies have low efficacies due to resistance and off-target effects in HCC. Here we aimed to analyze oxidative stress-related gene expression profiles of HCC cells and identify genes that could be crucial for novel diagnostic and therapeutic strategies. To identify important genes that cause resistance to reactive oxygen species (ROS), a model of oxidative stress upon selenium (Se) deficiency was utilized. The results of transcriptome-wide gene expression data were analyzed in which the differentially expressed genes (DEGs) were identified between HCC cell lines that are either resistant or sensitive to Se-deficiency-dependent oxidative stress. These DEGs were further investigated for their importance in oxidative stress resistance by network analysis methods, and 27 genes were defined to have key roles; 16 of which were previously shown to have impact on liver cancer patient survival. These genes might have Se-deficiency-dependent roles in hepatocarcinogenesis and could be further exploited for their potentials as novel targets for diagnostic and therapeutic approaches.","PeriodicalId":23375,"journal":{"name":"Turkish journal of biology = Turk biyoloji dergisi","volume":"45 2","pages":"149-161"},"PeriodicalIF":0.0,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38915085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Arid4b physically interacts with Tfap2c in mouse embryonic stem cells. 在小鼠胚胎干细胞中，Arid4b与Tfap2c发生物理相互作用。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-04-20 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2010-67

Ezgi Gül Keskin, Jialiang Huang, Nihal Terzi Çizmecioğlu

{"title":"Arid4b physically interacts with Tfap2c in mouse embryonic stem cells.","authors":"Ezgi Gül Keskin, Jialiang Huang, Nihal Terzi Çizmecioğlu","doi":"10.3906/biy-2010-67","DOIUrl":"10.3906/biy-2010-67","url":null,"abstract":"Precise regulation of gene expression is required for embryonic stem cell (ESC) differentiation. Transcription factor (TF) networks coordinate the balance of pluripotency and differentiation in response to extracellular and intracellular signals. Chromatin factors work alongside TFs to achieve timely regulation of gene expression for differentiation process. Our previous studies showed that a member of the Sin3a corepressor complex, Arid4b, is critical for proper mouse ESC differentiation into mesoderm and endoderm. We found elevated histone 3 lysine 27 acetylation (H3K27Ac) in a subset of genomic loci in meso/endoderm directed arid4bΔ cells, coincident with their derepression. We reasoned that Sin3a complex may be required for the suppression of these genes during differentiation. To identify TFs that might cooperate with Arid4b for this function, we found consensus TF binding sequences enriched in H3K27Ac elevated regions in arid4bΔ cells. Of these candidate TFs, we validated expression of Bach1, Ddit3, Prrx2, Znf354c and Tfap2c in mESCs. We then demonstrated a physical interaction between Arid4b and Tfap2c in mESCs using endogenous coimmunoprecipitation and proximity ligation assay experiments. Our results point to a role of Arid4b in the Sin3a complex in repression of a subset of Tfap2c-regulated genes during meso/endoderm differentiation.","PeriodicalId":23375,"journal":{"name":"Turkish journal of biology = Turk biyoloji dergisi","volume":"45 2","pages":"162-170"},"PeriodicalIF":0.0,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38915086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Negative regulation of diminutive cancer regulator through differentiation and microRNA pathway components in Drosophila cells. 果蝇细胞通过分化和microRNA通路组分对小型癌症调节剂的负调控。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-04-20 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2012-4

Sumira Malik

引用次数: 1

Compensatory expression regulation of highly homologous proteins HNRNPA1 and HNRNPA2. 高度同源蛋白HNRNPA1和HNRNPA2的代偿表达调控。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-04-20 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2010-29

Yan Chang, Xiaofeng Lu, Jiaying Qiu

{"title":"Compensatory expression regulation of highly homologous proteins HNRNPA1 and HNRNPA2.","authors":"Yan Chang, Xiaofeng Lu, Jiaying Qiu","doi":"10.3906/biy-2010-29","DOIUrl":"https://doi.org/10.3906/biy-2010-29","url":null,"abstract":"Heterogeneous nuclear ribonucleoprotein (HNRNP) A1 and A2 are the most abundant HNRNPs with nearly identical functions, and play important roles in regulating gene expression at multiple levels (i.e. transcription, posttranscription, and translation). However, the expression and regulation mechanism of HNRNPA1 and A2 themselves remain unclear. In this study, the amino acid sequences of HNRNPA1 and HNRNPA2 were compared and found to have 78% and 86% homology in key functional domains. Transfection of HEK293 cells with small interfering RNA and overexpression vectors of HNRNPA1 and HNRNPA2 demonstrated that HNRNPA1 and HNRNPA2 paralogs regulate each other's expression in a compensatory manner at both the RNA and protein levels. Multiprimer reverse transcription-polymerase chain reaction showed that HNRNPA1 and HNRNPA2 did not affect splicing of the HNRNPA2 and HNRNPA1 gene. Using luciferase reporting system, we found that compensatory degradation was mediated by the 3'UTR of the two genes rather than by the promoter. Moreover, treatment with cycloheximide inhibited the compensatory regulation. Our results indicate a novel regulation mechanism of HNRNPA1 and A2 expression. Through compensatory regulation, the expression levels of HNRNPA1 and HNRNPA2 are strictly controlled within a certain range to maintain normal cellular activities under different physiological conditions.","PeriodicalId":23375,"journal":{"name":"Turkish journal of biology = Turk biyoloji dergisi","volume":"45 2","pages":"187-195"},"PeriodicalIF":0.0,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38915088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Helicobacter-stimulated IL-10-producing B cells suppress differentiation of lipopolysaccharide/Helicobacter felis-activated stimulatory dendritic cells. 幽门螺杆菌刺激产生il -10的B细胞抑制脂多糖/幽门螺杆菌激活的刺激树突状细胞的分化。

Turkish journal of biology = Turk biyoloji dergisi Pub Date : 2021-04-20 eCollection Date: 2021-01-01 DOI: 10.3906/biy-2012-11

Doğuş Altunöz, Ayça Sayi Yazgan

{"title":"Helicobacter-stimulated IL-10-producing B cells suppress differentiation of lipopolysaccharide/Helicobacter felis-activated stimulatory dendritic cells.","authors":"Doğuş Altunöz, Ayça Sayi Yazgan","doi":"10.3906/biy-2012-11","DOIUrl":"https://doi.org/10.3906/biy-2012-11","url":null,"abstract":"Regulatory B cells (Bregs) produce antiinflammatory cytokines and inhibits proinflammatory response. Recently, immunosuppressive roles of Bregs in the effector functions of dendritic cells (DCs) were demonstrated. However, cross talk between Bregs and DCs in Helicobacter infection remains unknown. Here, we showed that direct stimulation of bone marrow-derived DCs (BM-DCs) with Helicobacter felis (H. felis) antigen upregulates their CD86 surface expression and causes the production of interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), interleukin-12 (IL-12), and interleukin-10 (IL-10). Furthermore, prestimulation of DCs with supernatants derived from both Helicobacter-stimulated IL-10- B (Hf stim -IL-10- B) or IL-10+ B (Hf stim -IL-10+) cells suppresses the secretion of TNF-α and IL-6, but does not affect the expression of CD86 and secretion of IL-12 by lipopolysaccharide (LPS) or H. felis-activated BM-DCs. Remarkably, soluble factors secreted by Hf stim -IL-10- B cells, but not by Hf stim -IL-10+ B cells, suppress the secretion of IL-10 by BM-DCs upon subsequent LPS stimulation. In contrast, prestimulation with BM-DCs with supernatants of Hf stim -IL-10+ B cells before H. felis antigen stimulation induces significantly their IL-10 production. Collectively, our data indicated that prestimulation with soluble factors secreted by Hf stim -IL-10+ B cells, DCs exhibit a tolerogenic phenotype in response to LPS or Helicobacter antigen by secreting high levels of IL-10, but decreased levels of IL-6 and TNF-α.","PeriodicalId":23375,"journal":{"name":"Turkish journal of biology = Turk biyoloji dergisi","volume":"45 2","pages":"214-224"},"PeriodicalIF":0.0,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38915090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2