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https://www.readbyqxmd.com/read/27922078/malat1-and-hotair-long-non-coding-rnas-play-opposite-role-in-estrogen-mediated-transcriptional-regulation-in-prostate-cancer-cells
#1
Aurora Aiello, Lorenza Bacci, Agnese Re, Cristian Ripoli, Francesco Pierconti, Francesco Pinto, Riccardo Masetti, Claudio Grassi, Carlo Gaetano, Pier Francesco Bassi, Alfredo Pontecorvi, Simona Nanni, Antonella Farsetti
In the complex network of nuclear hormone receptors, the long non-coding RNAs (lncRNAs) are emerging as critical determinants of hormone action. Here we investigated the involvement of selected cancer-associated lncRNAs in Estrogen Receptor (ER) signaling. Prior studies by Chromatin Immunoprecipitation (ChIP) Sequencing showed that in prostate cancer cells ERs form a complex with the endothelial nitric oxide synthase (eNOS) and that in turn these complexes associate with chromatin in an estrogen-dependent fashion...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922070/deep-sequencing-of-the-16s-ribosomal-rna-of-the-neonatal-oral-microbiome-a-comparison-of-breast-fed-and-formula-fed-infants
#2
S S Al-Shehri, E L Sweeney, D M Cowley, H G Liley, P D Ranasinghe, B G Charles, P N Shaw, D Vagenas, J A Duley, C L Knox
In utero and upon delivery, neonates are exposed to a wide array of microorganisms from various sources, including maternal bacteria. Prior studies have proposed that the mode of feeding shapes the gut microbiota and, subsequently the child's health. However, the effect of the mode of feeding and its influence on the development of the neonatal oral microbiota in early infancy has not yet been reported. The aim of this study was to compare the oral microbiota of healthy infants that were exclusively breast-fed or formula-fed using 16S-rRNA gene sequencing...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921398/effects-of-rhizobacteria-paenibacillus-polymyxa-apec136-and-bacillus-subtilis-apec170-on-biocontrol-of-postharvest-pathogens-of-apple-fruits
#3
Young Soo Kim, Kotnala Balaraju, Yongho Jeon
In this study, plant growth-promoting rhizobacteria (PGPR) were evaluated as potential biocontrol agents against postharvest pathogens of apple fruits. In vitro bioassays revealed that, out of 30 isolates screened, isolates APEC136 and APEC170 had the most significant inhibitory effects against the mycelial growth of several fungal pathogens. Analysis of 16S ribosomal RNA (rRNA) sequences identified the two effective isolates as Paenibacillus polymyxa and Bacillus subtilis, respectively. The two strains showed greater growth in brain-heart infusion broth than in other growth media...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27920979/transcript-profiling-in-the-milk-of-dairy-ewes-fed-extruded-linseed
#4
Tommaso Giordani, Alberto Vangelisti, Giuseppe Conte, Andrea Serra, Lucia Natali, Annamaria Ranieri, Marcello Mele, Andrea Cavallini
The identification of genes regulating milk secretion by mammary glands is a key-step for exploiting changes in milk composition induced by different diet regimens. Linseed supplementation is a reliable feeding strategy to enhance polyunsaturated fatty acid content in milk fat from sheep, increasing milk quality and nutraceutical value. To investigate the molecular bases of diet induced differences in milk composition, we collected milk from dairy ewes at 90 day of lactation and after 3 weeks of diet supplementation with extruded linseed...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27920554/next-generation-sequence-detects-arap3-as-a-novel-oncogene-in-papillary-thyroid-carcinoma
#5
Qing-Xuan Wang, En-Dong Chen, Ye-Feng Cai, Yi-Li Zhou, Zhou-Ci Zheng, Ying-Hao Wang, Yi-Xiang Jin, Wen-Xu Jin, Xiao-Hua Zhang, Ou-Chen Wang
PURPOSE: Thyroid cancer is the most frequent malignancies of the endocrine system, and it has became the fastest growing type of cancer worldwide. Much still remains unknown about the molecular mechanisms of thyroid cancer. Studies have found that some certain relationship between ARAP3 and human cancer. However, the role of ARAP3 in thyroid cancer has not been well explained. This study aimed to investigate the role of ARAP3 gene in papillary thyroid carcinoma. METHODS: Whole exon sequence and whole genome sequence of primary papillary thyroid carcinoma (PTC) samples and matched adjacent normal thyroid tissue samples were performed and then bioinformatics analysis was carried out...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27920295/a-novel-transcriptional-regulator-related-to-thiamine-phosphate-synthase-controls-thiamine-metabolism-genes-in-archaea
#6
Dmitry A Rodionov, Semen A Leyn, Xiaoqing Li, Irina A Rodionova
: Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamin biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages from the Crenarchaeota phylum, as well as in the Halobacteria and Thermococci classes of the Euryarchaeota ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain that is similar to the archaeal thiamin phosphate synthase ThiN...
December 5, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27920199/the-active-bacterial-assemblages-of-the-upper-gi-tract-in-individuals-with-and-without-helicobacter-infection
#7
Christian Schulz, Kerstin Schütte, Nadine Koch, Ramiro Vilchez-Vargas, Melissa L Wos-Oxley, Andrew P A Oxley, Marius Vital, Peter Malfertheiner, Dietmar H Pieper
OBJECTIVE: Patients infected with Helicobacter pylori develop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whether H. pylori influences the bacterial communities of gastroduodenal niches. DESIGN: Saliva, gastric and duodenal aspirates as well as gastric and duodenal biopsies were collected during oesophagogastroduodenoscopy from 24 patients (m:9, f:15, mean age 52...
December 5, 2016: Gut
https://www.readbyqxmd.com/read/27920176/laboratory-diagnosis-of-chikungunya-virus-infections-and-commercial-sources-for-diagnostic-assays
#8
Barbara W Johnson, Brandy J Russell, Christin H Goodman
Detection of chikungunya virus (CHIKV) or viral RNA is the primary laboratory test used to diagnose infection in serum collected <6 days after onset of illness. Two real-time reverse transcription-polymerase chain reaction (RT-PCR) kits are available commercially, but validity data are limited. There are 2 commercial sources of inactivated positive-control CHIKV RNA to be used with purchased primers. The Centers for Disease Control and Prevention provides viral RNA-positive controls and primer and probe nucleotide sequences for real-time RT-PCR testing...
December 15, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27919963/expression-levels-of-piwi-interacting-rna-pir-823-are-deregulated-in-tumor-tissue-blood-serum-and-urine-of-patients-with-renal-cell-carcinoma
#9
Robert Iliev, Michal Fedorko, Tana Machackova, Hana Mlcochova, Marek Svoboda, Dalibor Pacik, Jan Dolezel, Michal Stanik, Ondrej Slaby
BACKGROUND: Renal cell carcinoma (RCC) is the most common neoplasm of adult kidney accounting for about 3% of adult malignancies. P-Element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a new class of naturally occurring, short non-coding RNAs involved in silencing of transposable elements and in sequence-specific chromatin modifications. There were preliminary data published indicating that piR-823 expression is deregulated in circulating tumor cells and tumor tissue in gastric and kidney cancer, respectively...
December 2016: Anticancer Research
https://www.readbyqxmd.com/read/27919705/the-complete-mitochondrial-genome-of-thitarodes-sejilaensis-lepidoptera-hepialidae-a-host-insect-of-ophiocordyceps-sinensis-and-its-implication-in-taxonomic-revision-of-hepialusadopted-in-china
#10
Zhiwen Zou, Qiang Min, Shiyu Cheng, Tianrong Xin, Bin Xia
The mitochondrial genome is widely used for phylogenetic analyses and evolutionary biology. The complete mitochondrial genome of Thitarodes sejilaensis (Lepidoptera: Hepialidae) was sequenced and analyzed in this study. This mitogenome is a typical circular molecule of 15,290bp, with the gene content, orientation and order identical to other insects in the family Hepialidae. The genome nucleotide composition is heavily biased towards As and Ts, accounting for 80.87% of total nucleotide content. The major strand shows a positive AT-skew and negative GC-skew...
December 2, 2016: Gene
https://www.readbyqxmd.com/read/27919263/derivation-of-chicken-induced-pluripotent-stem-cells-tolerant-to-newcastle-disease-virus-induced-lysis-through-multiple-rounds-of-infection
#11
Leonardo Susta, Ying He, Jessica M Hutcheson, Yangqing Lu, Franklin D West, Steven L Stice, Ping Yu, Zaid Abdo, Claudio L Afonso
BACKGROUND: Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a devastating disease of poultry and wild birds. ND is prevented by rigorous biocontainment and vaccination. One potential approach to prevent spread of the virus is production of birds that show innate resistance to NDV-caused disease. Induced pluripotent stem cell (iPSC) technology allows adult cells to be reprogrammed into an embryonic stem cell-like state capable of contributing to live offspring and passing on unique traits in a number of species...
December 5, 2016: Virology Journal
https://www.readbyqxmd.com/read/27919066/designed-proteins-induce-the-formation-of-nanocage-containing-extracellular-vesicles
#12
Jörg Votteler, Cassandra Ogohara, Sue Yi, Yang Hsia, Una Nattermann, David M Belnap, Neil P King, Wesley I Sundquist
Complex biological processes are often performed by self-organizing nanostructures comprising multiple classes of macromolecules, such as ribosomes (proteins and RNA) or enveloped viruses (proteins, nucleic acids and lipids). Approaches have been developed for designing self-assembling structures consisting of either nucleic acids or proteins, but strategies for engineering hybrid biological materials are only beginning to emerge. Here we describe the design of self-assembling protein nanocages that direct their own release from human cells inside small vesicles in a manner that resembles some viruses...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27918597/seqplots-interactive-software-for-exploratory-data-analyses-pattern-discovery-and-visualization-in-genomics
#13
Przemyslaw Stempor, Julie Ahringer
Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps...
2016: Wellcome Open Res
https://www.readbyqxmd.com/read/27918539/rapidly-evolving-homing-crispr-barcodes
#14
Reza Kalhor, Prashant Mali, George M Church
We present an approach for engineering evolving DNA barcodes in living cells. A homing guide RNA (hgRNA) scaffold directs the Cas9-hgRNA complex to the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cell populations and show that they can be used to record lineage history and that the barcode RNA can be amplified in situ, a prerequisite for in situ sequencing...
December 5, 2016: Nature Methods
https://www.readbyqxmd.com/read/27918112/validation-of-adam10-metalloprotease-as-a-bacillus-thuringiensis-cry3aa-toxin-functional-receptor-in-colorado-potato-beetle-leptinotarsa-decemlineata
#15
V M Ruiz-Arroyo, I García-Robles, C Ochoa-Campuzano, G A Goig, E Zaitseva, G Baaken, A C Martínez-Ramírez, C Rausell, M D Real
Bacillus thuringiensis parasporal crystal proteins (Cry proteins) are insecticidal pore-forming toxins that bind to specific receptor molecules on the brush border membrane of susceptible insect midgut cells to exert their toxic action. In the Colorado potato beetle (CPB), a coleopteran pest, we previously proposed that interaction of Cry3Aa toxin with a CPB ADAM10 metalloprotease is an essential part of the mode of action of this toxin. Here, we annotated the gene sequence encoding an ADAM10 metalloprotease protein (CPB-ADAM10) in the CPB genome sequencing project, and using RNA interference gene silencing we demonstrated that CPB-ADAM10 is a Cry3Aa toxin functional receptor in CPB...
December 5, 2016: Insect Molecular Biology
https://www.readbyqxmd.com/read/27917920/transcriptome-and-long-noncoding-rna-sequencing-of-three-extracellular-vesicle-subtypes-released-from-the-human-colon-cancer-lim1863-cell-line
#16
Maoshan Chen, Rong Xu, Hong Ji, David W Greening, Alin Rai, Keiichi Izumikawa, Hideaki Ishikawa, Nobuhiro Takahashi, Richard J Simpson
Previously we reported that LIM1863 colorectal cancer (CRC) cells secrete three distinct extracellular vesicle subtypes - two subpopulations of exosomes (apical EpCAM-Exos and basolateral A33-Exos) and shed microvesicles (sMVs) - with distinct protein and miRNA signatures. Here, we extend our omics approach to understand the fundamental role of LIM1863-derived EVs by performing a comprehensive analysis of their mRNAs and long non-coding RNAs (lncRNAs) using RNA-Seq. We show that 2,389 mRNAs, 317 pseudogene transcripts, 1,028 lncRNAs and 206 short non-coding RNAs selectively distributed to (i...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917860/interrogating-the-degradation-pathways-of-unstable-mrnas-with-xrn1-resistant-sequences
#17
Volker Boehm, Jennifer V Gerbracht, Marie-Charlotte Marx, Niels H Gehring
The turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5'-3' mRNA decay...
December 5, 2016: Nature Communications
https://www.readbyqxmd.com/read/27917784/suppression-of-bromodomain-containing-protein-4-by-shrna-a-new-approach-for-cancer-treatment
#18
Turan Kaya, Berke Kahraman, Nurgeldi Bazarov, Alperen S Toker, Ayse Celik, Sadik Cigdem, Esra Gunduz
PURPOSE: MYC is a transcription factor coding gene that is believed to control 15% of the genes in the entire human genome. The central role of c-MYC in cancer pathogenesis makes it a major therapeutic target in field of anticancer agent development. METHODS: We targeted the acetyl-lysine binding modules or bromodomains, which are associated with c-MYC transcriptional activation. RESULTS: Sequence specific inhibition of BET bromodomains with small hairpin RNAs (shRNAs) resulted in cessation of cellular proliferation in different cancer cell lines...
December 1, 2016: Clinical and Investigative Medicine. Médecine Clinique et Experimentale
https://www.readbyqxmd.com/read/27917783/understanding-thermal-sensitivity-at-the-molecular-level-and-developing-temperature-based-systems-using-rna-thermometers
#19
Fatih Gul, Ibrahim Y Orhan, Furkan S Ceylan, Nadir B Akdeniz, H Abdulkadir Karadag
PURPOSE: Temperature sensitivity is found in all multicelleular organisms, as well as in most primitive life forms. The ubiquity of this temperature sensitivity is an indicator of its effects at the multicellular, cellular and molecular levels [1]. Previous studies have shown that temperature-based regulation is present in the transcriptional process [2]. RNA Thermometers, temperature-sensitive sequences, have been shown to act on heat-shock genes to regulate temperature-dependant systems in many organisms [3,4]...
December 1, 2016: Clinical and Investigative Medicine. Médecine Clinique et Experimentale
https://www.readbyqxmd.com/read/27917677/infectious-bronchitis-vaccine-virus-detection-and-part-s1-genetic-variation-following-single-or-dual-inoculation-in-broiler-chicks
#20
Christopher Ball, Faez Awad, Sally Hutton, Anne Forrester, Matthew Baylis, Kannan Ganapathy
An investigation was undertaken of the extent of genetic variation occurring within infectious bronchitis virus (IBV) vaccine strains following vaccination of day-old broiler chicks. Chicks were divided into seven groups, with two groups receiving single Massachusetts (Mass) vaccinations and the other four were inoculated with combinations of different IBV serotypes; Mass, 793B, D274, and Arkansas (Ark). The remaining group was maintained as an unvaccinated control. Following vaccination, swabs and tissues collected at intervals were pooled and RNA was extracted for detection of IBV by reverse transcription polymerase chain reaction (RT PCR)...
December 5, 2016: Avian Pathology: Journal of the W.V.P.A
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