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https://www.readbyqxmd.com/read/28101227/downregulation-of-mir-23b-in-plasma-is-associated-with-poor-prognosis-in-patients-with-colorectal-cancer
#1
Chang-Hua Kou, Tian Zhou, Xi-Lin Han, Hui-Jie Zhuang, Hai-Xin Qian
MicroRNAs (miRNAs) are short, non-coding RNA molecules that act as regulators of gene expression. Circulating blood miRNAs have potential as cancer biomarkers. The main objective of the present study was to assess the effect of miRNA-23b (miR-23b) expression in plasma on the diagnosis and prognosis of colorectal cancer (CRC). Reverse transcription-quantitative polymerase chain reaction (PCR) was used to measure miR-23b expression levels, and methylation-specific PCR was used to test the promoter methylation status...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28100049/cell-free-translation-is-more-variable-than-transcription
#2
Fabio Chizzolini, Michele Forlin, Noël Yeh Martín, Giuliano Berloffa, Dario Cecchi, Sheref S Mansy
Although RNA synthesis can be reliably controlled with different T7 transcriptional promoters during cell-free gene expression with the PURE system, protein synthesis remains largely unaffected. To better control protein levels, a series of ribosome binding sites (RBS) was investigated. While RBS strength did strongly affect protein synthesis, the RBS sequence could explain less than half of the variability of the data. Protein expression was found to depend on other factors besides the strength of the RBS, including GC content...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28099529/a-possible-role-of-the-full-length-nascent-protein-in-post-translational-ribosome-recycling
#3
Debasis Das, Dibyendu Samanta, Arpita Bhattacharya, Arunima Basu, Anindita Das, Jaydip Ghosh, Abhijit Chakrabarti, Chanchal Das Gupta
Each cycle of translation initiation in bacterial cell requires free 50S and 30S ribosomal subunits originating from the post-translational dissociation of 70S ribosome from the previous cycle. Literature shows stable dissociation of 70S from model post-termination complexes by the concerted action of Ribosome Recycling Factor (RRF) and Elongation Factor G (EF-G) that interact with the rRNA bridge B2a/B2b joining 50S to 30S. In such experimental models, the role of full-length nascent protein was never considered seriously...
2017: PloS One
https://www.readbyqxmd.com/read/28099151/clinical-impact-of-serum-survivin-positivity-and-tissue-expression-of-ebv-encoded-rna-in-diffuse-large-b-cell-lymphoma-patients-treated-with-rituximab-chop
#4
Jung Yong Hong, Kyung Ju Ryu, Chaehwa Park, Mineui Hong, Young Hyeh Ko, Won Seog Kim, Seok Jin Kim
Survivin is an inhibitor of apoptosis and is upregulated by Epstein-Barr virus (EBV) latent genes. Given the frequent association of EBV with lymphoid malignancies, survivin is expected to have prognostic value in diffuse large B-cell lymphoma (DLBCL). Thus, we measured the pretreatment serum level of survivin in DLBCL patients and analyzed its association with survival outcome and EBV status, as represented by EBV-encoded RNA (EBER) in DLBCL. Pretreatment serum survivin level was measured in patients registered in a prospective cohort study (n = 210), and serum survivin-positivity was defined as any detectable level of survivin...
January 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28098872/trim29-promotes-progression-of-thyroid-carcinoma-via-activating-p13k-akt-signaling-pathway
#5
Jinkai Xu, Zongyu Li, Qinghua Su, Jun Zhao, Jiancang Ma
Thyroid cancer (TC) is a common malignancy of the endocrine system. Abnormal expression of tripartite motif-containing 29 (TRIM29) has been reported to promote tumorigenesis and predict poor prognosis in several human malignancies. The aim of this study was to assess the involvement of TRIM29 in the significance and prognosis of TC. Fifty-six tumor samples and their clinicopathological para-meters were obtained from TC patients; the expression level of TRIM29 was detected by RT-qPCR and western blotting. TRIM29 expression was knocked down by small interfering RNA (siRNA) among TT, TPC-1, and K1 cells to investigate the biological role of TRIM29 in TC cells...
January 13, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28097161/effects-of-extremely-low-frequency-electromagnetic-field-on-expression-levels-of-some-antioxidant-genes-in-human-mcf-7-cells
#6
Hamideh Mahmoudinasab, Fatemeh Sanie-Jahromi, Mostafa Saadat
In the past three decades, study on the biological effects of extremely low-frequency electromagnetic fields (ELF-EMFs) has been of interest to scientists. Although the exact mechanism of its effect is not fully understood, free radical processes has been proposed as a possible mechanism. This study was designed to evaluate the effect of 50-Hz EMFs on the mRNA levels of seven antioxidant genes (CAT, SOD1, SOD2, GSTO1, GSTM3, MSGT1, and MSGT3) in human MCF-7 cells. The EMF exposure patterns were: 1) 5 min field-on/5 min filed-off, 2) 15 min field-on/15 min field-off, 3) 30 min field-on continuously...
June 2016: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28096075/hpprna-a-snakemake-based-handy-parameter-free-pipeline-for-rna-seq-analysis-of-numerous-samples
#7
Dapeng Wang
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for an easy-to-learn workflow to cope with the increased demands from a large number of laboratories across the world. We report a one-in-all solution called hppRNA, composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection, written by a series of individual Perl and R scripts, counting on well-established and preinstalled software, irrespective of single-end or paired-end, unstranded or stranded sequencing method...
January 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28093281/kindlin-2-in-pancreatic-stellate-cells-promotes-the-progression-of-pancreatic-cancer
#8
Naoki Yoshida, Atsushi Masamune, Shin Hamada, Kazuhiro Kikuta, Tetsuya Takikawa, Fuyuhiko Motoi, Michiaki Unno, Tooru Shimosegawa
Pancreatic stellate cells (PSCs) play a pivotal role in pancreatic fibrosis associated with pancreatic ductal adenocarcinoma (PDAC). Kindlin-2 is a focal adhesion protein that regulates the activation of integrins. This study aimed to clarify the role of kindlin-2 in PSCs in pancreatic cancer. Kindlin-2 expression in 79 resected pancreatic cancer tissues was examined by immunohistochemical staining. Kindlin-2-knockdown immortalized human PSCs were established using small interfering RNA. Pancreatic cancer cells were treated with conditioned media of PSCs, and the cell proliferation and migration were examined...
January 13, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28089386/detection-of-urinary-cell-free-mir-210-as-a-potential-tool-of-liquid-biopsy-for-clear-cell-renal-cell-carcinoma
#9
Guorong Li, An Zhao, Michel Péoch, Michèle Cottier, Nicolas Mottet
BACKGROUND: Recent findings show that cell-free miRNAs are stable in biological fluid. Urine provides an alternative to blood serum or plasma as a potential source of tumor biomarkers. MiR-210 is proven to be overexpressed in patients with a clear cell renal cell carcinoma (ccRCC). The purpose of this pilot study was to examine the urinary cell-free miR-210 as a potential tool of liquid biopsy for ccRCC. METHODS: Overall, 75 patients with a ccRCC and 45 control subjects without a cancer were included in this study...
January 12, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28088733/long-non-coding-rna-uc001kfo-promotes-hepatocellular-carcinoma-proliferation-and-metastasis-by-targeting-%C3%AE-sma
#10
Yanfeng Pan, Tao Qin, Shenglu Yin, Xianqiang Zhang, Xiaojuan Gao, Lifen Mu
Several long non-coding RNAs (lncRNAs) have been investigated and found to be correlated with the behaviours and prognosis of hepatocellular carcinoma (HCC); Specifically, we revealed that the lncRNA UC001kfo was differentially expressed in HCC tissues compared with normal liver tissues using lncRNA microarrays, but its functional role in cancers, including HCC, has not yet been elucidated. The present study found that the expression of UC001kfo was upregulated in HCC tissues and cell lines in comparison with tumour-adjacent tissues and normal hepatocytes, respectively...
January 12, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28087619/genome-wide-transcription-profiling-of-aerobic-and-anaerobic-escherichia-coli-biofilm-and-planktonic-cultures
#11
Bihter Bayramoglu, David Toubiana, Osnat Gillor
Many studies have described the response of the facultative anaerobe, Escherichia coli, to anaerobic conditions, yet they all investigated free-living (planktonic) cells because attempts to cultivate anaerobic E. coli biofilm were mostly unsuccessful. We challenged these findings and cultivated E. coli strain MG1655 biofilm under both aerobic and anaerobic conditions, characterizing the mature biofilm architecture and global gene expression profile. We used RNA sequencing technology to compare stationary phase planktonic cells with mature biofilm, cultured with and without oxygen...
January 12, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28086949/nek2-promotes-aerobic-glycolysis-in-multiple-myeloma-through-regulating-splicing-of-pyruvate-kinase
#12
Zhimin Gu, Jiliang Xia, Hongwei Xu, Ivana Frech, Guido Tricot, Fenghuang Zhan
BACKGROUND: Aerobic glycolysis, a hallmark of cancer, is characterized by increased metabolism of glucose and production of lactate in normaxia. Recently, pyruvate kinase M2 (PKM2) has been identified as a key player for regulating aerobic glycolysis and promoting tumor cell proliferation and survival. METHODS: Tandem affinity purification followed up by mass spectrometry (TAP-MS) and co-immunoprecipitation (Co-IP) were used to study the interaction between NIMA (never in mitosis gene A)-related kinase 2 (NEK2) and heterogeneous nuclear ribonucleoproteins (hnRNP) A1/2...
January 13, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28069892/post-translational-regulation-of-the-dicing-activities-of-arabidopsis-dicer-like-3-and-4-by-inorganic-phosphate-and-the-redox-state
#13
Atsushi Seta, Midori Tabara, Yuki Nishibori, Akihiro Hiraguri, Naoko Ohkama-Ohtsu, Tadashi Yokoyama, Satoshi Hara, Keisuke Yoshida, Toru Hisabori, Akihito Fukudome, Hisashi Koiwa, Hiromitsu Moriyama, Nobuhiro Takahashi, Toshiyuki Fukuhara
In Arabidopsis thaliana, small interfering RNAs (siRNAs) generated by two Dicer isoforms, DCL3 and DCL4, function in distinct epigenetic processes, i.e. RNA-directed DNA methylation and post-transcriptional gene silencing, respectively. Plants often respond to their environment by producing a distinct set of small RNAs; however, the mechanism for controlling the production of different siRNAs from the same dsRNA substrate remains unclear. We established a simple biochemical method to visualize the dsRNA-cleaving activities of DCL3 and DCL4 in cell-free extracts prepared from Arabidopsis seedlings...
January 9, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28069036/tpx2-expression-is-associated-with-poor-survival-in-gastric-cancer
#14
Chiharu Tomii, Mikito Inokuchi, Yoko Takagi, Toshiaki Ishikawa, Sho Otsuki, Hiroyuki Uetake, Kazuyuki Kojima, Tatsuyuki Kawano
BACKGROUND: Targeting protein for Xenopus kinesin-like protein 2 (TPX2) is a microtubule-associated protein required for microtubule formation in human cells. Several studies have demonstrated that TPX2 is overexpressed in multiple tumor types and promotes tumor growth and metastasis. However, there have been few reports regarding its role in gastric cancer. In this study, we evaluated TPX2 expression and investigated its correlations with gastric cancer clinicopathological features and prognosis...
January 9, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28068897/neotenic-phenomenon-in-gene-expression-in-the-skin-of-foxn1-deficient-nude-mice-a-projection-for-regenerative-skin-wound-healing
#15
Anna Kur-Piotrowska, Marta Kopcewicz, Leslie P Kozak, Pawel Sachadyn, Anna Grabowska, Barbara Gawronska-Kozak
BACKGROUND: Mouse fetuses up to 16 day of embryonic development and nude (Foxn1- deficient) mice are examples of animals that undergo regenerative (scar-free) skin healing. The expression of transcription factor Foxn1 in the epidermis of mouse fetuses begins at embryonic day 16.5 which coincides with the transition point from scar-free to scar-forming skin wound healing. In the present study, we tested the hypothesis that Foxn1 expression in the skin is an essential condition to establish the adult skin phenotype and that Foxn1 inactivity in nude mice keeps skin in the immature stage resembling the phenomena of neoteny...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068069/re-engineering-extracellular-vesicles-as-smart-nanoscale-therapeutics
#16
James P K Armstrong, Margaret N Holme, Molly M Stevens
In the past decade, extracellular vesicles (EVs) have emerged as a key cell-free strategy for the treatment of a range of pathologies, including cancer, myocardial infarction, and inflammatory diseases. Indeed, the field is rapidly transitioning from promising in vitro reports toward in vivo animal models and early clinical studies. These investigations exploit the high physicochemical stability and biocompatibility of EVs as well as their innate capacity to communicate with cells via signal transduction and membrane fusion...
January 9, 2017: ACS Nano
https://www.readbyqxmd.com/read/28061446/%C3%AE-40p53-is-involved-in-the-inactivation-of-autophagy-and-contributes-to-inhibition-of-cell-death-in-hct116-%C3%AE-40p53-cells
#17
Yunjin Zang, Ying Shi, Kai Liu, Luxin Qiao, Xianghua Guo, Dexi Chen
Δ40p53 is an isoform of wild-type p53 (wtp53). Here, we assessed whether Δ40p53 has the same functions as wild-type p53 in the regulation of cell death and autophagy. First, we used HCT116 (p53+/+) and H1299 (p53-free) cells to produce two cell lines (HCT116-Δ40p53 and H1299-Δ40p53) that express exogenous Δ40p53 but not wtp53. By using these cell lines, we determined that Δ40p53 inhibited starvation-induced autophagy, as does wtp53. This inhibition arises from both Δ40p53 and wtp53 having 3'-5' exonuclease activity, which reduces the levels of double-stranded RNA (dsRNA) and then inhibits PKR/eIF2α-induced autophagy in cells exposed to starvation...
January 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060897/visualization-of-x4-and-r5-tropic-hiv-1-viruses-expressing-fluorescent-proteins-in-human-endometrial-cells-application-to-tropism-study
#18
Rachel Terrasse, Meriam Memmi, Sabine Palle, Leo Heyndrickx, Guido Vanham, Bruno Pozzetto, Thomas Bourlet
Worldwide most HIV infections occur through heterosexual transmission, involving complex interactions of cell-free and cell-associated particles with cells of the female genital tract mucosa. The ability of HIV-1 to "infect" epithelial cells remains poorly understood. To address this question, replicative-competent chimeric constructs expressing fluorescent proteins and harboring the envelope of X4- or R5-tropic HIV-1 strains were used to "infect" endometrial HEC1-A cells. The virus-cell interactions were visualized using confocal microscopy (CM) at various times post infection...
2017: PloS One
https://www.readbyqxmd.com/read/28060411/scarless-cas9-assisted-recombineering-no-scar-in-escherichia-coli-an-easy-to-use-system-for-genome-editing
#19
Christopher R Reisch, Kristala L J Prather
The discovery and development of genome editing systems that leverage the site-specific DNA endonuclease system CRISPR/Cas9 has fundamentally changed the ease and speed of genome editing in many organisms. In eukaryotes, the CRISPR/Cas9 system utilizes a "guide" RNA to enable the Cas9 nuclease to make a double-strand break at a particular genome locus, which is repaired by non-homologous end joining (NHEJ) repair enzymes, often generating random mutations in the process. A specific alteration of the target genome can also be generated by supplying a DNA template in vivo with a desired mutation, which is incorporated by homology-directed repair...
January 5, 2017: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/28053879/lysozyme-association-with-circulating-rna-extracellular-vesicles-and-chronic-stress
#20
Sarah K Abey, Yuana Yuana, Paule V Joseph, Natnael D Kenea, Nicolaas H Fourie, LeeAnne B Sherwin, Gregory E Gonye, Paul A Smyser, Erin S Stempinski, Christina M Boulineaux, Kristen R Weaver, Christopher K E Bleck, Wendy A Henderson
BACKGROUND: Stress has demonstrated effects on inflammation though underlying cell-cell communication mechanisms remain unclear. We hypothesize that circulating RNAs and extracellular vesicles (EVs) in patients with chronic stress contain signals with functional roles in cell repair. METHODS: Blood transcriptome from patients with Irritable Bowel Syndrome versus controls were compared to identify signaling pathways and effectors. Plasma EVs were isolated (size-exclusion chromatography) and characterized for effectors' presence (immunogold labelling-electron microscopy)...
June 2017: BBA Clinical
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