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https://www.readbyqxmd.com/read/29779262/-salivary-exrna-biomarkers-to-detect-gingivitis-and-monitor-disease-regression
#1
Karolina Elżbieta Kaczor-Urbanowicz, Harsh M Trivedi, Patricia O Lima, Paulo M Camargo, William V Giannobile, Tristan R Grogan, Frederico O Gleber-Netto, Yair Whiteman, Feng Li, Hyo Jung Lee, Karan Dharia, Katri Aro, Carmen Martin Carerras-Presas, Saarah Amuthan, Manjiri Vartak, David Akin, Hiba Al-Adbullah, Kanika Bembey, Perry R Klokkevold, David Elashoff, Virginia Monsul Barnes, Rose Richter, William DeVizio, James G Masters, David Wong
AIM: This study tests the hypothesis that salivary extracellular RNA (exRNA) biomarkers can be developed for gingivitis detection and monitoring disease regression. MATERIALS AND METHODS: Salivary exRNA biomarker candidates were developed from a total of 100 gingivitis and non-gingivitis individuals using Affymetrix's expression microarrays. The top ten differentially expressed exRNAs were tested in a clinical cohort to determine if the discovered salivary exRNA markers for gingivitis were associated with clinical gingivitis and disease regression...
May 19, 2018: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/29778942/transcriptomic-and-methylomic-analysis-reveal-the-toxicological-effect-of-2-3-7-8-tetrachlorodibenzodioxin-on-human-embryonic-stem-cell
#2
Keng Po Lai, Jing Woei Li, Ting Fung Chan, Andy Chen, Cherie Yin Lau Lee, William Shu Biu Yeung, Chris Kong Chu Wong
Cumulating epidemiological studies demonstrated that environmental exposure to endocrine disrupting chemicals (EDCs) during the early stages of fetal development is associated with the increase in disease susceptibility in later life. The fetal developmental plasticity is considered as a protective mechanism against an undesirable prenatal environment. Dioxin is one of the environmental contaminants and is considered a diabetogenic factor. Experimental animal and human epidemiological studies have revealed that dioxin exposure was associated with insulin resistance and altered beta cell function...
May 10, 2018: Chemosphere
https://www.readbyqxmd.com/read/29778844/identification-of-micrornas-with-heat-stress-responsive-and-immune-properties-in-marsupenaeus-japonicus-based-on-next-generation-sequencing-and-bioinformatics-analysis-essential-regulators-in-the-heat-stress-host-interactions
#3
Jinbin Zheng, Jiawen Cao, Yong Mao, Yongquan Su, Jun Wang
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29778628/environmentally-enriched-pigs-have-transcriptional-profiles-consistent-with-neuroprotective-effects-and-reduced-microglial-activity
#4
S M Brown, S J Bush, K M Summers, D A Hume, A B Lawrence
Environmental enrichment (EE) is widely used to study the effects of external factors on brain development, function and health in rodent models, but very little is known of the effects of EE on the brain in a large animal model such as the pig. Twenty-four young pigs (aged 5 weeks at start of study, 1:1 male: female ratio) were housed in environmentally enriched (EE) pens and provided with additional enrichment stimulation (a bag filled with straw) once daily. Litter, weight and sex matched controls n= (24) were housed in barren (B) conditions...
May 17, 2018: Behavioural Brain Research
https://www.readbyqxmd.com/read/29778390/next-generation-sequencing-reveals-differentially-expressed-small-noncoding-rnas-in-uterine-leiomyoma
#5
Tsai-Der Chuang, Yeming Xie, Wei Yan, Omid Khorram
OBJECTIVE: To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN: Laboratory-based investigation. SETTING: Academic center. PATIENT(S): Women undergoing hysterectomy for benign indications. INTERVENTION(S): Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR)...
May 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29778222/exploring-dinoflagellate-biology-with-high-throughput-proteomics
#6
REVIEW
David Morse, Sirius P K Tse, Samuel C L Lo
Dinoflagellates are notorious for their ability to form the harmful algal blooms known as "red tides," yet the mechanisms underlying bloom formation remain poorly understood. Despite recent advances in nucleic acid sequencing, which have generated transcriptomes from a wide range of species exposed to a variety of different conditions, measuring changes in RNA levels have not generally produced great insight into dinoflagellate cell biology or environmental physiology, nor do we have a thorough grasp on the molecular events underpinning bloom formation...
May 2018: Harmful Algae
https://www.readbyqxmd.com/read/29778014/expression-of-grape-acs1-in-tomato-decreases-ethylene-and-alters-the-balance-between-auxin-and-ethylene-during-shoot-and-root-formation
#7
Xia Ye, Mengmeng Fu, Yu Liu, Dongliang An, Xianbo Zheng, Bin Tan, Jidong Li, Jun Cheng, Wei Wang, Jiancan Feng
Ethylene plays an important role in the grape rachis, where its production can be 10 times higher than in the berry. VvACS1 is the only rachis-specific ACC synthase (ACS) gene, and its expression is coincident with ethylene production in the rachis of Vitis vinifera 'Thompson seedless'. VvACS1 was cloned and ectopically expressed in tomato (Solanum lycopersicum 'Moneymaker'). Lateral buds were increased in two- or four-week-old 35s∷VvACS1 transgenic tomato plants after transplanting. Compared with wild-type (WT) plants, the transgenic tomato plants showed higher expression of the VvACS1 gene in the flowers, leaves, rachis, and fruits...
May 4, 2018: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29777657/mcv-mir-m1-targets-the-host-cell-immune-response-resulting-in-the-attenuation-of-neutrophil-chemotaxis
#8
P Akhbari, D Tobin, K Poterlowicz, W Roberts, J R Boyne
Virus-encoded miRNAs are emerging as key regulators of persistent infection and host-cell immune evasion. Merkel cell polyomavirus (MCPyV), the predominant aetiological agent of Merkel cell carcinoma (MCC), encodes a single miRNA, MCV-miR-M1, which targets the oncogenic MCPyV large T antigen (LT). MCV-miR-M1 has previously been shown to play an important role in establishment of long-term infection, however, the underlying mechanism is not fully understood. A key unanswered question is whether, in addition to auto-regulating LT, MCV-miR-M1 also targets cellular transcripts to orchestrate an environment conducive for persistent infection...
May 16, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29777364/cell-division-and-turgor-mediate-enhanced-plant-growth-in-arabidopsis-plants-treated-with-the-bacterial-signalling-molecule-lumichrome
#9
Motlalepula Pholo, Beatrix Coetzee, Hans J Maree, Philip R Young, James R Lloyd, Jens Kossmann, Paul N Hills
Transcriptomic analysis indicates that the bacterial signalling molecule lumichrome enhances plant growth through a combination of enhanced cell division and cell enlargement, and possibly enhances photosynthesis. Lumichrome (7,8 dimethylalloxazine), a novel multitrophic signal molecule produced by Sinorhizobium meliloti bacteria, has previously been shown to elicit growth promotion in different plant species (Phillips et al. in Proc Natl Acad Sci USA 96:12275-12280, https://doi.org/10.1073/pnas.96.22.12275 , 1999)...
May 17, 2018: Planta
https://www.readbyqxmd.com/read/29777111/knockdown-of-rna-interference-pathway-genes-impacts-the-fitness-of-western-corn-rootworm
#10
Courtney Davis-Vogel, Angel Ortiz, Lisa Procyk, Jonathan Robeson, Adane Kassa, Yiwei Wang, Emily Huang, Carl Walker, Amit Sethi, Mark E Nelson, Dipali G Sashital
Western corn rootworm (Diabrotica virgifera virgifera) is a serious agricultural pest known for its high adaptability to various management strategies, giving rise to a continual need for new control options. Transgenic maize expressing insecticidal RNAs represents a novel mode of action for rootworm management that is dependent on the RNA interference (RNAi) pathways of the insect for efficacy. Preliminary evidence suggests that western corn rootworm could develop broad resistance to all insecticidal RNAs through changes in RNAi pathway genes; however, the likelihood of field-evolved resistance occurring through this mechanism remains unclear...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29776339/differential-gene-transcription-across-the-life-cycle-in-daphnia-magna-using-a-new-all-genome-custom-made-microarray
#11
Bruno Campos, Danielle Fletcher, Benjamín Piña, Romà Tauler, Carlos Barata
BACKGROUND: Unravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29776334/swi-snf-regulates-half-of-its-targets-without-the-need-of-atp-driven-nucleosome-remodeling-by-brahma
#12
Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann-Kristin Östlund Farrants, Neus Visa
BACKGROUND: Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. RESULTS: Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29776125/post-transcriptional-bursting-in-genes-regulated-by-small-rna-molecules
#13
Guillermo Rodrigo
Gene expression programs in living cells are highly dynamic due to spatiotemporal molecular signaling and inherent biochemical stochasticity. Here we study a mechanism based on molecule-to-molecule variability at the RNA level for the generation of bursts of protein production, which can lead to heterogeneity in a cell population. We develop a mathematical framework to show numerically and analytically that genes regulated post transcriptionally by small RNA molecules can exhibit such bursts due to different states of translation activity (on or off), mostly revealed in a regime of few molecules...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29775646/the-rna-binding-protein-ars2-supports-hematopoiesis-at-multiple-levels
#14
Seerat Elahi, Shawn M Egan, G Aaron Holling, Rachel L Kandefer, Michael J Nemeth, Scott H Olejniczak
Recent biochemical characterization of Arsenic resistance protein 2 (Ars2) has established it as central to determining the fate of nascent RNA polymerase II (RNAPII) transcripts. Through interactions with the nuclear 5'-7-methylguanosine (7mG) cap binding complex (CBC), Ars2 promotes co-transcriptional processing coupled with nuclear export or degradation of several classes of RNAPII transcripts, allowing for gene expression programs that facilitate rapid and sustained proliferation of immortalized cells in culture...
May 15, 2018: Experimental Hematology
https://www.readbyqxmd.com/read/29775608/regulation-of-the-gyr-operon-of-mycobacterium-tuberculosis-by-overlapping-promoters-dna-topology-and-reiterative-transcription
#15
Rajiv Kumar Jha, Priyanka Tare, Valakunja Nagaraja
DNA gyrase introduces negative supercoils into DNA to maintain topological homeostasis. The genes encoding gyrase, gyrB and gyrA, form a dicistronic operon in Mycobacterium tuberculosis (Mtb) and other actinobacteria. Earlier work indicated that DNA relaxation stimulates the expression of the gyr genes, a phenomenon termed relaxation-stimulated transcription (RST). The present study addresses the underlying mechanism of gyr operon regulation. The operon is regulated by overlapping and divergently oriented promoters located upstream of gyrB...
May 15, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29775585/an-optogenetic-platform-for-real-time-single-cell-interrogation-of-stochastic-transcriptional-regulation
#16
Marc Rullan, Dirk Benzinger, Gregor W Schmidt, Andreas Milias-Argeitis, Mustafa Khammash
Transcription is a highly regulated and inherently stochastic process. The complexity of signal transduction and gene regulation makes it challenging to analyze how the dynamic activity of transcriptional regulators affects stochastic transcription. By combining a fast-acting, photo-regulatable transcription factor with nascent RNA quantification in live cells and an experimental setup for precise spatiotemporal delivery of light inputs, we constructed a platform for the real-time, single-cell interrogation of transcription in Saccharomyces cerevisiae...
May 17, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29775583/correlating-transcription-initiation-and-conformational-changes-by-a-single-subunit-rna-polymerase-with-near-base-pair-resolution
#17
Hye Ran Koh, Rahul Roy, Maria Sorokina, Guo-Qing Tang, Divya Nandakumar, Smita S Patel, Taekjip Ha
We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies...
May 17, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29775485/plasmodium-parasite-exploits-host-aquaporin-3-during-liver-stage-malaria-infection
#18
Dora Posfai, Kayla Sylvester, Anupama Reddy, Jack G Ganley, Johannes Wirth, Quinlan E Cullen, Tushar Dave, Nobutaka Kato, Sandeep S Dave, Emily R Derbyshire
Within the liver a single Plasmodium parasite transforms into thousands of blood-infective forms to cause malaria. Here, we use RNA-sequencing to identify host genes that are upregulated upon Plasmodium berghei infection of hepatocytes with the hypothesis that host pathways are hijacked to benefit parasite development. We found that expression of aquaporin-3 (AQP3), a water and glycerol channel, is significantly induced in Plasmodium-infected hepatocytes compared to uninfected cells. This aquaglyceroporin localizes to the parasitophorous vacuole membrane, the compartmental interface between the host and pathogen, with a temporal pattern that correlates with the parasite's expansion in the liver...
May 18, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29774630/the-emerging-roles-of-long-non-coding-rna-in-cancer
#19
Anna Sanchez Calle, Yumi Kawamura, Yusuke Yamamoto, Fumitaka Takeshita, Takahiro Ochiya
Since comprehensive analysis of the mammalian genome has revealed that the vast majority of genomic products are transcribed in long non-coding RNAs (lncRNAs), increasing attention has been paid towards these transcripts. The applied next-generation sequencing technologies have provided accumulating evidence of dysregulated lncRNAs in cancer. The implication of this finding may be seen in many forms and at multiple levels. With impacts ranging from integrating chromatin remodeling complexes to regulating transcription and post-transcriptional processes, aberrant expression of lncRNAs may have repercussions in cell proliferation, tumor progression or metastasis...
May 17, 2018: Cancer Science
https://www.readbyqxmd.com/read/29774544/functional-molecules-in-mesothelial-to-mesenchymal-transition-revealed-by-transcriptome-analyses
#20
Sara Namvar, Adrian S Woolf, Leo A H Zeef, Thomas Wilm, Bettina Wilm, Sarah E Herrick
Peritoneal fibrosis is a common complication of abdominal and pelvic surgery, and can also be triggered by peritoneal dialysis, resulting in treatment failure. In these settings, fibrosis is driven by activated myofibroblasts that are considered to be partly derived by mesothelial-to-mesenchymal transition (MMT). We hypothesised that if the molecular signature of MMT could be better defined, these insights could be exploited to block this pathological cellular transition. Rat peritoneal mesothelial cells were purified, using an antibody to HBME1, a protein present on mesothelial cell microvilli, and streptavidin nanobead technology...
May 17, 2018: Journal of Pathology
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