STING Mediates Neuronal Innate Immune Response Following Japanese Encephalitis Virus Infection : Scientific Reports. Ethics statement All animal experiments were approved by the Institutional Animal and Ethics Committee of the National Brain Research Centre (approval no.
NBRC/IAEC/2007/36 and NBRC/IAEC/2011/66). Towards the understanding of microRNA and environmental factor interactions and their relationships to human diseases : Scientific Reports. MiRNA–EF interaction is correlated with miRNA characteristics It is interesting to investigate whether miRNA characteristics have roles in miRNA–EF interactions.
Hence, we analyzed the correlation between the number of miRNA-interacting EFs with the expression level, tissue specificity, conservation, and disease spectrum width (DSW) of the miRNAs. The miRNA–EF interactions showed significantly regular patterns. The number of EFs interacting with a miRNA has a significant positive correlation with the expression level of the miRNA (R = 0.50, P = 1.784×10−14, Spearman's correlation, Figure 1A). This result suggests that highly expressed miRNAs tend to interact with more EFs. An EF–EF interaction network linked by miRNAs Next, we evaluated the relationship between any two EFs through their miRNA signatures. RNA editing study under intense scrutiny. Three groups1–3 today throw fuel on the debate surrounding a researcher’s claim to have discovered a twist in the mechanism whereby genes are translated into proteins.
The paper, published in Science last May4, suggested a revision in the central dogma, which holds that the RNA transcripts used as templates for protein assembly are generally faithful matches to the original DNA. In technical commentaries published today in Science, the groups suggest that errors in multiple aspects of the study, led by Vivian Cheung of the University of Pennsylvania in Philadelphia, seriously undermine its claim to have found a new mechanism of genetic regulation.
The idea that RNA is often edited after being transcribed from DNA is a controversial one. Stilbene derivatives promote Ago2-dependent tumour-suppressive microRNA activity : Scientific Reports : Nature Publishing Group. Reagents.
Self-circularizing 5′-ETS RNAs accumulate along with unprocessed pre ribosomal RNAs in growth-stressed Entamoeba histolytica : Scientific Reports. Mapping the second promoter of rDNA in E. histolytica The rDNA promoter had earlier been mapped 2.672 kb upstream of the 5′-end of 18S rRNA21, 22.
We now show the presence of a second stronger promoter downstream to the previously mapped promoter. This was discovered when the expression of luciferase reporter gene (1.6 kb) cloned downstream of the full length 5′-ETS (construct A spanning – 277 to + 2.672 kb) was checked by northern blot analysis in a stably transfected cell line (Figure 1a, b). The size of transcript expected from the promoter (marked P1) was 4.27 kb but the observed size was 2.7 kb (Figure 1b, lane 4). Stable lines were made with the indicated deletion constructs B, C and D. Top panel shows the location of ETS probes used for northern analysis. Full size image (206 KB) Pre rRNA and etsRNA accumulate under growth stress. Cholinergic and non-cholinergic functions of two acetylcholinesterase genes revealed by gene-silencing in Tribolium castaneum : Scientific Reports. Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses : Scientific Reports.
Small Molecule-MiRNA Networks (SMirNs) in human cancers In order to identify the relationships between small molecules and miRNAs in human cancers, the transcriptional responses to 1,309 compounds and the differentially expressed genes in 23 human cancers were obtained from the Connectivity Map (cMap)15 and the unifying caner microarray resource (ONCOMINE)16, respectively.
The miRNA target genes were obtained from our integrated database, which included seven widely used miRNA target genes prediction tools. Here, using the hypergeometric test we evaluated the extent to which the miRNA target genes appeared in the differentially expressed genes in cancer. At the significance level of 0.05, we identified 406 cancer-related miRNAs (CRMs) for 23 human cancers. Fine-Scale Temporal Dynamics of a Fragmented Lotic Microbial Ecosystem : Scientific Reports. Sampling site and sample collection Sequential samples were collected from the “Seven mills” weir of the Yarqon stream (32°096′N; 34°81′W; 5 m altitude) during a 7-day period, every 7 hours, encompassing day and night as well as the low and high tides changes, from July 6th to July 12th 2009, resulting in a total of 23 samplings.
At each time point, two samples were taken, one from the upstream section of the weir, and the other from the downstream section below the weir, at the origin of the estuary. The delay in taking these paired samples, taken 50 meters apart, was less than 10 minutes. Samples were taken from 0.5 m deep surface water, using 0.25 L plastic collection bottles. Accurate RT-qPCR gene expression analysis on cell culture lysates : Scientific Reports. Accuracy First, the ability of the Cells-to-CT workflow to accurately quantify relative gene expression levels and resulting fold changes between samples was assessed.
To this end, cDNA from duplicate cultures of four neuroblastoma cell lines, two bearing amplification of the MYCN transcription factor gene (NGP and IMR-32) and two without the amplification (SH-EP, SK-N-AS), was prepared using either the classic or the Cells-to-CT workflow. Relative expression levels of 10 genes of interest (DKK3, INHBA, PLAT, RGS4, MYC, MTHFD2, MYCN, TGFBI, PMP22, NTRK2) known to be differentially expressed between cells with and without MYCN-amplification3 were then quantified, yielding a theoretical number of 80 expression level data points for both workflows. Discrimination of the oral microbiota associated with high hydrogen sulfide and methyl mercaptan production : Scientific Reports. We investigated the salivary bacterial populations of 43 subjects whose mouth air showed three different VSC profiles: high H2S but low CH3SH concentration (H2S group, n = 14), high CH3SH but low H2S concentration (CH3SH group, n = 16), and no VSC (no-odor group, n = 13) (Figure 1).
The general and clinical parameters of the study populations are given in Table 1. Age and tongue coating scores of the two malodor groups were significantly higher than those of the no-odor group, whereas no significant difference was observed between the two malodor groups. In addition, the mean periodontal pocket depth of the CH3SH group was significantly greater than that of the no-odor group.
Subjects with low VSC in mouth air (•, H2S ≤ 0.075 ppm and CH3SH = 0 ppm, n = 13), those with high H2S but low CH3SH concentrations (∇, H2S ≥ 1 ppm and CH3SH/H2S < 0.6, n = 14), and those with high CH3SH but low H2S concentrations (▴, CH3SH ≥ 0.5 ppm and CH3SH/H2S ≥ 1.0, n = 16) were enrolled in this study. Video animation: RNA interference. Cdc14b regulates mammalian RNA polymerase II and represses cell cycle transcription : Scientific Reports.
Cell cycle alterations in Cdc14b-deficient cells We have generated a new Cdc14b null allele in the mouse by excising exons 8-9 which encode most of the phosphatase catalytic domain.
As reported recently13, Cdc14b(−/−) mice are viable although develop some pathologies that will be described elsewhere. Cucumber mosaic virus and its 2b RNA silencing suppressor modify plant-aphid interactions in tobacco : Scientific Reports. Aphid survival is altered on tobacco infected with CMV and CMV Δ 2b. Bacterial biogeography of the human digestive tract : Scientific Reports. Patient samples and Illumina libraries For each healthy individual (two males, two females), the samples included dental plaque (left and right supra-gingival and sub-gingival, tongue), stomach (antrum and body), duodenum, colon (transverse and descending), rectum and stool. The stool was collected within 24 hours of GI sampling and prior to Klean Prep of the colon whereas all other GI and oral samples were collected on the same day for each individual at the time of gastroscopy and colonoscopy.
Libraries were constructed for all samples by amplification of the V3 region of the bacterial 16S rRNA gene. A unique index was used to label each sample and multiplex Illumina sequencing resulted in 46,960,900 paired-end reads. Removal of low-quality and short (<100 nucleotide) sequences followed by perfect-match assembly reduced the total to 32,770,833 assembled sequences with an average length of 149.3 ± 10.9 bases (sequenced primer regions removed). Essential role of microfibrillar-associated protein 4 in human cutaneous homeostasis and in its photoprotection : Scientific Reports. Human skin Full-thickness abdominal skin from a healthy 41-year-old Caucasian female with type II skin undergoing abdominoplasty and breast skin from a healthy 46-year-old Caucasian female with type II skin undergoing breast reduction (University Pointe, Cincinnati, OH, USA), were used for skin xenografts.
Three to four punch biopsies of skin at the ventral upper arm or the dorsal lower arm from healthy Caucasian females with type II skin in their twenties, thirties, fifties and sixties (Stephens and Associates, Carrollton, TX, USA) were also used for the investigation of mRNA transcript expression or protein localisation. Huntingtin mediates dendritic transport of β-actin mRNA in rat neurons : Scientific Reports. RNA editing may not be as widespread as claimed. A paper that appeared to find evidence for a new mechanism of genetic regulation has been challenged by an analysis released today. In May, a team led by Vivian Cheung of the University of Pennsylvania in Philadelphia reported that in an analysis of 27 people, it had found 10,210 sites where transcribed RNA differed from an individual’s corresponding DNA sequence.
The finding was startling because it implied that there might be an as-yet undiscovered mechanism of ‘RNA editing’ that could disrupt the central dogma, the process whereby DNA is faithfully transcribed into matching sequences of RNA, which are translated into proteins. But other researchers pointed out that Cheung’s team had not performed some crucial analyses to ensure that it was actually observing mismatches rather than genetic sequencing errors or accurately transcribed regions of DNA.
Today, Daniel R. Schrider, Jean-Francois Gout and Matthew W. Hahn says his team did contact Cheung’s group, but did not receive a reply. Argument over RNA editing study deepens. The geneticist whose claimed to find a new mechanism of genetic regulation is defending her work against critics. Vivian Cheung of the University of Pennsylvania in Philadelphia says that her team stands by a May paper in which it reported that it had found more than ten thousand sites where transcribed RNA differed from an individual’s corresponding DNA sequence.