Journal of Biological Research-Thessaloniki最新文献

{"title":"Evaluating the effect of <i>TLR4</i>-overexpressing on the transcriptome profile in ovine peripheral blood mononuclear cells.","authors":"Xiaofei Guo,&nbsp;Jinlong Zhang,&nbsp;Yao Li,&nbsp;Jing Yang,&nbsp;Yihai Li,&nbsp;Chunxiao Dong,&nbsp;Guoshi Liu,&nbsp;Zhengxing Lian,&nbsp;Xiaosheng Zhang","doi":"10.1186/s40709-020-00124-3","DOIUrl":"https://doi.org/10.1186/s40709-020-00124-3","url":null,"abstract":"<p><strong>Background: </strong>Toll-like receptor 4 (TLR4) plays an important role in the elimination of Gram-negative bacteria infections and the initiation of antiinflammatory response. Using the technology of pronuclear microinjection, genetically modified (GM) sheep with <i>TLR4</i> overexpression were generated. Previous studies have shown that these GM sheep exhibited a higher inflammatory response to Gram-negative bacteria infection than wild type (WT) sheep. In order to evaluate the gene expression of GM sheep and study the co-expressed and downstream genes for <i>TLR4</i>, peripheral blood mononuclear cells (PBMC) from <i>TLR4</i>-overexpressing (Tg) and wild type (WT) sheep were selected to discover the transcriptomic differences using RNA-Seq.</p><p><strong>Result: </strong>An average of 18,754 and 19,530 known genes were identified in the Tg and WT libraries, respectively. A total of 338 known genes and 85 novel transcripts were found to be differentially expressed in the two libraries (<i>p</i> < 0.01). A differentially expressed genes (DEGs) enrichment analysis showed that the GO terms of inflammatory response, cell recognition, etc. were significantly (FDR < 0.05) enriched. Furthermore, the above DEGs were significantly (FDR < 0.05) enriched in the sole KEGG pathway of the Phagosome. Real-time PCR showed the <i>OLR1</i>, <i>TLR4</i> and <i>CD14</i> genes to be differentially expressed in the two groups, which validated the DEGs data.</p><p><strong>Conclusions: </strong>The RNA-Seq results revealed that the overexpressed <i>TLR4</i> in our experiment strengthened the ovine innate immune response by increasing the phagocytosis in PBMC.</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00124-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38235191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach.","authors":"Umair Ilyas,&nbsp;Shahiq Uz Zaman,&nbsp;Reem Altaf,&nbsp;Humaira Nadeem,&nbsp;Syed Aun Muhammad","doi":"10.1186/s40709-020-00121-6","DOIUrl":"https://doi.org/10.1186/s40709-020-00121-6","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1186/s40709-020-00118-1.].</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00121-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38139423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aberrant methylation-mediated downregulation of lncRNA <i>CCND2 AS1</i> promotes cell proliferation in cervical cancer.","authors":"Chengcheng Zhao,&nbsp;Jian Liu,&nbsp;Huazhang Wu,&nbsp;Jiaojiao Hu,&nbsp;Jianquan Chen,&nbsp;Jie Chen,&nbsp;Fengchang Qiao","doi":"10.1186/s40709-020-00122-5","DOIUrl":"https://doi.org/10.1186/s40709-020-00122-5","url":null,"abstract":"<p><strong>Background: </strong>Long non-coding RNA (lncRNA) plays an important role in tumorigenesis. The lncRNA <i>CCND2 AS1</i> has been shown to be involved in the growth of several tumors; however, its role in cervical cancer has not been elucidated. This study aimed to explore the expression, function, and underlying mechanism of action of <i>CCND2 AS1</i> in cervical cancer. Expression of <i>CCND2 AS1</i> was examined in cervical cancer and adjacent normal cervical tissues by quantitative real-time polymerase chain reaction (qRT-PCR) and by bioinformatic analysis of data from the Gene Expression Profiling Interactive Analysis (GEPIA) database. The function of <i>CCND2 AS1</i> was investigated by overexpressing or silencing <i>CCND2 AS1</i> in HeLa and SiHa cervical cancer cells followed by in vitro and in vivo analyses. Methylation-specific PCR (MSP) and bisulfite genomic sequencing (BGS) were used to detect <i>CCND2 AS1</i> promoter methylation status in cervical cancer cells.</p><p><strong>Results: </strong><i>CCND2 AS1</i> expression was lower in cervical cancer compared with normal cervical tissues, and the level was significantly correlated with the patient age and tumor size. <i>CCND2 AS1</i> overexpression inhibited the proliferation and cell cycle progression of HeLa cells in vitro and/or in vivo, whereas <i>CCND2 AS1</i> silencing had the opposite effects. <i>CCND2 AS1</i> expression was elevated after treatment of cervical cancer cells with the DNA methyltransferase inhibitor 5'-azacytidine (5'-Aza), and this was mediated, at least in part, via reduced CpG methylation at the <i>CCND2 AS1</i> promoter.</p><p><strong>Conclusion: </strong><i>CCND2 AS1</i> expression is downregulated in cervical cancer, potentially through increased <i>CCND2 AS1</i> promoter methylation, and the upregulation of <i>CCND2 AS1</i> expression inhibited tumor growth. These data suggest that <i>CCND2 AS1</i> could be a diagnostic marker and potential therapeutic target for cervical cancer.</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00122-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38109834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>bolA</i> gene involved in curli amyloids and fimbriae production in <i>E. coli</i>: exploring pathways to inhibit biofilm and amyloid formation.","authors":"Mohd W Azam,&nbsp;Azna Zuberi,&nbsp;Asad U Khan","doi":"10.1186/s40709-020-00120-7","DOIUrl":"https://doi.org/10.1186/s40709-020-00120-7","url":null,"abstract":"<p><strong>Background: </strong>Biofilm formation is a complex phenomenon of bacterial cells, involved in several human infections. Its formation is regulated and controlled by several protein factors. The BolA-like proteins (<i>bolA</i> gene) are conserved in both prokaryotes and eukaryotes. The BolA protein is a transcription factor involved in bacterial cell motility and biofilm formation. This study was initiated to elucidate the role of the <i>bolA</i> gene in the curli biogenesis and amyloid production as well as to observe changes in the expression of <i>fimH</i>, a fimbriae gene.</p><p><strong>Methods: </strong>Knockdown mutants of <i>Escherichia coli</i> MG1655 <i>bolA</i> gene <i>(bolA</i>-<i>KD)</i> were generated using CRISPR interference. The results obtained, were validated through gene expression using RT-PCR, microscopic analysis and different biofilm and amyloid assays.</p><p><strong>Results: </strong>The <i>bolA</i> knockdown mutants showed a decrement in curli amyloid fibers, in fimbriae production and biofilm formation. We have also observed a reduction in EPS formation, eDNA production and extracellular protein content. Gene expression data showed that <i>bolA</i> downregulation caused the suppression of <i>csgA</i> and <i>csgD</i> of curli that led to the reduction in curli fiber and the amyloid formation and also the suppression of <i>fimH</i>, leading to the loss of fimbriae.</p><p><strong>Conclusions: </strong>Curli fibers and fimbriae are found to be involved in biofilm formation leading to the pathogenicity of the bacterial cell. BolA is a conserved protein and is found to play a significant role in curli and fimbriae formation in <i>E. coli.</i> This study further proved that CRISPRi mediated suppression of the <i>bol</i>A gene leads to inhibition of biofilm formation through curli and fimbriae inhibition. Hence, it may be proposed as a possible target for intervention of biofilm mediated infections.</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00120-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38073554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The occurrence of cancer in vertebrates: a mini review.","authors":"Christos V Kitsoulis,&nbsp;Athanasios D Baxevanis,&nbsp;Theodore J Abatzopoulos","doi":"10.1186/s40709-020-00119-0","DOIUrl":"https://doi.org/10.1186/s40709-020-00119-0","url":null,"abstract":"<p><p>Neoplasia is a multilevel condition caused by irregularities over the genome, which can lead to a fatal result. To fully understand this phenomenon, an evolutionary challenge has risen during the last decades, away from human limits, driving the scientific quest into the wild life. The study of wild vertebrate populations in their natural habitats has shown that cancer is rather prominent. Thus, the diversity of vertebrates reported with some form of neoplasia is quite scattered through a variety of habitats. However, some species constitute exceptions by exhibiting cancer-protective features, driven by certain loci in their DNA. It is obvious that from an evolutionary standpoint, the incidence of cancer in different taxa is nowadays studied by seeking for patterns and their roots. The main purpose of the evolutionary approach is no other than to answer a fundamental question: Could cancer be ultimately regarded as another evolutionary force conducive to the formation or shaping-up of species?</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00119-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38040666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach.","authors":"Umair Ilyas,&nbsp;Shaiq Uz Zaman,&nbsp;Reem Altaf,&nbsp;Humaira Nadeem,&nbsp;Syed Aun Muhammad","doi":"10.1186/s40709-020-00118-1","DOIUrl":"https://doi.org/10.1186/s40709-020-00118-1","url":null,"abstract":"<p><strong>Background: </strong>Colorectal cancer is known to be the most common type of cancer worldwide with high disease-related mortality. It is the third most common cancer in men and women and is the second major cause of death globally due to cancer. It is a complicated and fatal disease comprising of a group of molecular heterogeneous disorders.</p><p><strong>Results: </strong>This study identifies the potential biomarkers of CRC through differentially expressed analysis, system biology, and proteomic analysis. Ten publicly available microarray datasets were analyzed and seven potential biomarkers were identified from the list of differentially expressed genes having a <i>p</i> value < 0.05. The expression profiling and the functional enrichment analysis revealed the role of these genes in cell communication, signal transduction, and immune response. The protein-protein interaction showed the functional association of the source genes (CTNNB1, NNMT, PTCH1, CALD1, CXCL14, CXCL8, and TNFAIP3) with the target proteins, such as AXIN, MAPK, IL6, STAT, APC, GSK3B, and SHH.</p><p><strong>Conclusion: </strong>The integrated pathway analysis indicated the role of these genes in important physiological responses, such as cell cycle regulation, WNT, hedgehog, MAPK, and calcium signaling pathways during colorectal cancer. These pathways are involved in cell proliferation, chemotaxis, cellular growth, differentiation, tissue patterning, and cytokine production. The study shows the regulatory role of these genes in colorectal cancer and the pathways that can be effected after the dysregulation of these genes.</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00118-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38032072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TRAF3 can interact with GMEB1 and modulate its anti-apoptotic function.","authors":"George Kotsaris,&nbsp;Despoina Kerselidou,&nbsp;Dimitrios Koutsoubaris,&nbsp;Elena Constantinou,&nbsp;George Malamas,&nbsp;Dimitrios A Garyfallos,&nbsp;Eudoxia G Ηatzivassiliou","doi":"10.1186/s40709-020-00117-2","DOIUrl":"https://doi.org/10.1186/s40709-020-00117-2","url":null,"abstract":"<p><strong>Background: </strong>Members of Tumor Necrosis Factor (TNF) Receptor-Associated Factors (TRAFs) family interact with the cytoplasmic tails of TNF receptor family members to mediate signal transduction processes. TRAF3 has a major immunomodulatory function and TRAF3 deficiency has been linked to malignancies, such as multiple myeloma and lymphoid defects. In order to characterize the molecular mechanisms of TRAF3 signaling, the yeast two-hybrid system was used to identify proteins that interact with TRAF3.</p><p><strong>Results: </strong>The yeast two-hybrid screen of a human B cell cDNA library with TRAF3 as bait, identified Glucocorticoid Modulatory Element-Binding Protein 1 (GMEB1) as a TRAF3-interacting protein. Previous studies indicated that GMEB1 functions as a potent inhibitor of caspase activation and apoptosis. The interaction of TRAF3 and GMEB1 proteins was confirmed in mammalian cells lines, using immunoprecipitation assays. The RING and TRAF-C domains of TRAF3 were not essential for this interaction. The overexpression of TRAF3 protein enhanced the anti-apoptotic function of GMEB1 in HeLa cells. On the other hand, downregulation of TRAF3 by RNA interference decreased significantly the ability of GMEB1 to inhibit apoptosis. In addition, LMP1(1-231), a truncated form of the EBV oncoprotein LMP1, that can interact and oligomerize with TRAF3, was also able to cooperate with GMEB1, in order to inhibit apoptosis.</p><p><strong>Conclusions: </strong>Our protein-interaction experiments demonstrated that TRAF3 can interact with GMEB1, which is an inhibitor of apoptosis. In addition, cell viability assays showed that overexpression of TRAF3 enhanced the anti-apoptotic activity of GMEB1, supporting a regulatory role of TRAF3 in GMEB1-mediated inhibition of apoptosis. Better understanding of the molecular mechanism of TRAF3 function will improve diagnostics and targeted therapeutic approaches for TRAF3-associated disorders.</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00117-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38023411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A potential prognostic model based on miRNA expression profile in The Cancer Genome Atlas for bladder cancer patients.","authors":"Yan Liu,&nbsp;Dong Yan Zhu,&nbsp;Hong Jian Xing,&nbsp;Yi Hou,&nbsp;Yan Sun","doi":"10.1186/s40709-020-00116-3","DOIUrl":"https://doi.org/10.1186/s40709-020-00116-3","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to construct prognostic model by screening prognostic miRNA signature of bladder cancer.</p><p><strong>Methods: </strong>The miRNA expression profile data of bladder cancer (BC) in The Cancer Genome Atlas (TCGA) were obtained and randomly divided into the training set and the validation set. Differentially expressed miRNAs (DEMs) between BC and normal control samples in the training set were firstly identified, and DEMs related to prognosis were screened by Cox Regression analysis. Then, the MiR Score system was constructed using X-Tile based cutoff points and verified in the validation set. The prognostic clinical factors are selected out by univariate and multivariate Cox Regression analysis. Finally, the mRNAs related to prognosis were screened and the biological pathway analysis was carried out.</p><p><strong>Results: </strong>We identified the 7-miRNA signature was significantly associated with the patient's Overall Survival (OS). A prognostic model was constructed based on the prognostic 7-miRNA signature, and possessed a relative satisfying predicted ability both in the training set and validation set. In addition, univariate and multivariate Cox Regression analysis showed that age, lymphovascular invasion and MiR Score were considered as independent prognostic factors in BC patients. Furthermore, based on MiR Score prognostic model, several differentially expressed genes (DEGs), such as <i>WISP3</i> and <i>UNC5C</i>, as well as their related biological pathway(s), including cell-cell adhesion and neuroactive ligand-receptor interaction, were considered to be related to BC prognosis.</p><p><strong>Conclusion: </strong>The prognostic model which was constructed based on the prognostic 7-miRNA signature presented a high predictive ability for BC.</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00116-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37992931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From the call to prayer to the silences of the museum","authors":"Eleni Kallimopoulou, Kostis Kornetis, P. Poulos","doi":"10.4324/9780429201561-17","DOIUrl":"https://doi.org/10.4324/9780429201561-17","url":null,"abstract":"","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84202790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A review on Zika virus outbreak, epidemiology, transmission and infection dynamics.","authors":"Syeda Sidra Kazmi,&nbsp;Waqar Ali,&nbsp;Nousheen Bibi,&nbsp;Faisal Nouroz","doi":"10.1186/s40709-020-00115-4","DOIUrl":"https://doi.org/10.1186/s40709-020-00115-4","url":null,"abstract":"<p><p>Zika virus (ZIKV) is a newly emergent relative of the Flaviviridae family and linked to dengue (DENV) and Chikungunya (CHIVKV). ZIKV is one of the rising pathogens promptly surpassing geographical borders. ZIKV infection was characterized by mild disease with fever, headache, rash, arthralgia and conjunctivitis, with exceptional reports of an association with Guillain-Barre syndrome (GBS) and microcephaly. However, since the end of 2015, an increase in the number of GBS associated cases and an astonishing number of microcephaly in fetus and new-borns in Brazil have been related to ZIKV infection, raising serious worldwide public health concerns. ZIKV is transmitted by the bite of infected female mosquitoes of <i>Aedes</i> species. Clarifying such worrisome relationships is, thus, a current unavoidable goal. Here, we extensively described the current understanding of the effects of ZIKV on heath, clinical manifestation, diagnosis and treatment options based on modern, alternative and complementary medicines regarding the disease.</p>","PeriodicalId":50251,"journal":{"name":"Journal of Biological Research-Thessaloniki","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2020-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40709-020-00115-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37726359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}