E. coli OxyS non-coding RNA does not trigger RNAi in C. elegans.

The discovery of RNA interference (RNAi) in C. elegans has had a major impact on scientific research, led to the rapid development of RNAi tools and has inspired RNA-based therapeutics. Astonishingly, nematodes, planaria and many insects take up double-stranded RNA (dsRNA) from their environment to elicit RNAi; the biological function of this mechanism is unclear. Recently, the E. coli OxyS non-coding RNA was shown to regulate gene expression in C. elegans when E. coli is offered as food. This was surprising given that C. elegans is unlikely to encounter E. coli in nature. To directly test the hypothesis that the E. coli OxyS non-coding RNA triggers the C. elegans RNAi pathway, we sequenced small RNAs from C. elegans after feeding with bacteria. We clearly demonstrate that the OxyS non-coding RNA does not trigger an RNAi response in C. elegans. We conclude that the biology of environmental RNAi remains to be discovered.PS is funded by a research fellowship from the Gonville and Caius College, University of Cambridge. AA and EAM are supported by a Cancer Research UK programme grant to EAM.This is the final published version. It first appeared at http://www.nature.com/srep/2015/150411/srep09597/full/srep09597.html

Preoperative Lipid Profile of Patients Operated For Coronary Bypass Surgery

DergiPark: 379072tmsjAims: Dyslipidemia is a major risk factor for atherosclerosis and coronary heart disease. Evidence showed that an atherogenic lipid pattern is characterized by high levels of small, dense low-density lipoprotein, low levels of high-density lipoprotein cholesterol, elevated triglyceride and total cholesterol levels; similar with the lipid profiles of diabetics.Methods: In this study, 91 patients who underwent coronary artery bypass grafting in Trakya University Hospital Department of Cardiovascular Surgery from April 2017 to September 2017 were analyzed retrospectively. As for statistical analysis, Student’s t-test and Mann Whitney U tests were performed.Results: The lipid profiles of patients were not significantly related to their ages and genders. However, when diabetic patients’ lipid profiles were analyzed, their low-density lipoprotein, and total cholesterol values were found to be significantly lower.Conclusion: It is unexpected to see that patients with diabetes had significantly lower total cholesterol and low-density lipoprotein levels than non-diabetic patients. As for the reason, it is thought that patients with diabetes are more conscious of their health conditio

Parallel population-based algorithm portfolios::An empirical study

Although many algorithms have been proposed, no single algorithm is better than others on all types of problems. Therefore, the search characteristics of different algorithms that show complementary behavior can be combined through portfolio structures to improve the performance on a wider set of problems. In this work, a portfolio of the Artificial Bee Colony, Differential Evolution and Particle Swarm Optimization algorithms was constructed and the first parallel implementation of the population-based algorithm portfolio was carried out by means of a Message Passing Interface environment. The parallel implementation of an algorithm or a portfolio can be performed by different models such as master-slave, coarse-grained or a hybrid of both, as used in this study. Hence, the efficiency and running time of various parallel implementations with different parameter values and combinations were investigated on benchmark problems. The performance of the parallel portfolio was compared to those of the single constituent algorithms. The results showed that the proposed models reduced the running time and the portfolio delivered a robust performance compared to each constituent algorithm. It is observed that the speedup gained over the sequential counterpart changed significantly depending on the structure of the portfolio. The portfolio is also applied to a training of neural networks which has been used for time series prediction. Result demonstrate that, portfolio is able to produce good prediction accuracy. (C) 2017 Elsevier B.V. All rights reserved

Risk Factors and Management of Hepatitis B Virus Reactivation in Patients With Hematological Disorders

DergiPark: 420829tmsjAims: The aim of this study is to evaluate hepatitis B virus serological status and to categorize the risks of our treatmentmodalities in patients with both benign and malignant hematological disorders.Methods: This was a retrospective study of 552 patients who were admitted to the Trakya University Hospital Hematologyunit between 01.01.2017 and 31.12.2017. All data regarding the diagnosis, treatment and HBV serologicalstatus were collected from patient files. Data were analyzed with IBM SPSS V.20 using descriptive statistical analysis.Results: Hepatitis B surface antigen was positive in 45 (8.2%) patients, antibody to the hepatitis B surface antigenwas positive in 279 (50.5%) patients and antibody to the hepatitis B core antigen was positive in 247 (44.7%) patients.According to these results, 32 patients were found to be vaccinated for hepatitis B virus. Reactivation was observed in4 (0.7%) patients who have been hepatitis B surface antigen positive and have received adequate duration of antiviralprophylaxis with tenofovir. These 4 patients have received monoclonal antibody for immunosuppressive treatment.Conclusion: To conclude, although the rate of hepatitis B surface antigen reactivation is quite low, as many patientsas possible should be vaccinated to reduce the costs of antiviral treatments and monitorization. If there is notime to vaccinate, patients should be categorized according to guidelines by their hepatitis B surface antigen serologicalstatus and by the planned immunosuppressive treatments

U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of <i>C. elegans</i> mRNAs

pre-mRNA splicing is a critical feature of eukaryotic gene expression. Many eukaryotes use cis-splicing to remove intronic sequences from pre-mRNAs. In addition to cis-splicing, many organisms use trans-splicing to replace the 5′ ends of mRNAs with a non-coding spliced-leader RNA. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that m6A modification of U6 snRNA A43 by the RNA methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of U6 snRNA m6A modification primarily leads to alternative splicing at 5′ splice sites. Furthermore, weaker 5′ splice site recognition by the unmodified U6 snRNA A43 affects splicing at 3′ splice sites. U6 snRNA m6A43 and the splicing factor SNRNP27K function to recognise an overlapping set of 5′ splice sites with an adenosine at +4 position. Finally, we show that U6 snRNA m6A43 is required for efficient SL trans-splicing at weak 3′ trans-splice sites. We conclude that the U6 snRNA m6A modification is important for accurate and efficient cis- and trans-splicing in C. elegans

U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of <i>C. elegans</i> mRNAs

pre-mRNA splicing is a critical feature of eukaryotic gene expression. Many eukaryotes use cis-splicing to remove intronic sequences from pre-mRNAs. In addition to cis-splicing, many organisms use trans-splicing to replace the 5′ ends of mRNAs with a non-coding spliced-leader RNA. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that m6A modification of U6 snRNA A43 by the RNA methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of U6 snRNA m6A modification primarily leads to alternative splicing at 5′ splice sites. Furthermore, weaker 5′ splice site recognition by the unmodified U6 snRNA A43 affects splicing at 3′ splice sites. U6 snRNA m6A43 and the splicing factor SNRNP27K function to recognise an overlapping set of 5′ splice sites with an adenosine at +4 position. Finally, we show that U6 snRNA m6A43 is required for efficient SL trans-splicing at weak 3′ trans-splice sites. We conclude that the U6 snRNA m6A modification is important for accurate and efficient cis- and trans-splicing in C. elegans

Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans.

Methylation of carbon-5 of cytosines (m5 C) is a post-transcriptional nucleotide modification of RNA found in all kingdoms of life. While individual m5 C-methyltransferases have been studied, the impact of the global cytosine-5 methylome on development, homeostasis and stress remains unknown. Here, using Caenorhabditis elegans, we generated the first organism devoid of m5 C in RNA, demonstrating that this modification is non-essential. Using this genetic tool, we determine the localisation and enzymatic specificity of m5 C sites in the RNome in vivo. We find that NSUN-4 acts as a dual rRNA and tRNA methyltransferase in C. elegans mitochondria. In agreement with leucine and proline being the most frequently methylated tRNA isoacceptors, loss of m5 C impacts the decoding of some triplets of these two amino acids, leading to reduced translation efficiency. Upon heat stress, m5 C loss leads to ribosome stalling at UUG triplets, the only codon translated by an m5 C34-modified tRNA. This leads to reduced translation efficiency of UUG-rich transcripts and impaired fertility, suggesting a role of m5 C tRNA wobble methylation in the adaptation to higher temperatures

Identification of functional long non-coding RNAs in C. elegans.

BACKGROUND: Functional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing 20 years ago. The last decade of research has seen a tremendous increase in the number of non-coding RNAs identified in various organisms. While we have mechanistic understandings of small non-coding RNA pathways, long non-coding RNAs represent a diverse class of active transcripts whose function remains less well characterised. RESULTS: By analysing hundreds of published transcriptome datasets, we annotated 3392 potential lncRNAs including 143 multi-exonic loci that showed increased nucleotide conservation and GC content relative to other non-coding regions. Using CRISPR/Cas9 genome editing, we generated deletion mutants for ten long non-coding RNA loci. Using automated microscopy for in-depth phenotyping, we show that six of the long non-coding RNA loci are required for normal development and fertility. Using RNA interference-mediated gene knock-down, we provide evidence that for two of the long non-coding RNA loci, the observed phenotypes are dependent on the corresponding RNA transcripts. CONCLUSIONS: Our results highlight that a large section of the non-coding regions of the C. elegans genome remains unexplored. Based on our in vivo analysis of a selection of high-confidence lncRNA loci, we expect that a significant proportion of these high-confidence regions is likely to have a biological function at either the genomic or the transcript level

The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription.

PIWI-interacting RNAs (piRNAs) are genome-encoded small RNAs that regulate germ cell development and maintain germline integrity in many animals. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. piRNA biogenesis mechanisms are diverse and remain poorly understood. Here, we identify the RNA polymerase II (RNA Pol II) core subunit RPB-9 as required for piRNA-mediated silencing in the nematode Caenorhabditis elegans. We show that rpb-9 initiates heritable piRNA-mediated gene silencing at two DNA transposon families and at a subset of somatic genes in the germline. We provide genetic and biochemical evidence that RPB-9 is required for piRNA biogenesis by recruiting the Integrator complex at piRNA genes, hence promoting transcriptional termination. We conclude that, as a part of its rapid evolution, the piRNA pathway has co-opted an ancient machinery for high-fidelity transcription

DEPS-1 is required for piRNA-dependent silencing and PIWI condensate organisation in Caenorhabditis elegans

Abstract: Membraneless organelles are sites for RNA biology including small non-coding RNA (ncRNA) mediated gene silencing. How small ncRNAs utilise phase separated environments for their function is unclear. We investigated how the PIWI-interacting RNA (piRNA) pathway engages with the membraneless organelle P granule in Caenorhabditis elegans. Proteomic analysis of the PIWI protein PRG-1 reveals an interaction with the constitutive P granule protein DEPS-1. DEPS-1 is not required for piRNA biogenesis but piRNA-dependent silencing: deps-1 mutants fail to produce the secondary endo-siRNAs required for the silencing of piRNA targets. We identify a motif on DEPS-1 which mediates a direct interaction with PRG-1. DEPS-1 and PRG-1 form intertwining clusters to build elongated condensates in vivo which are dependent on the Piwi-interacting motif of DEPS-1. Additionally, we identify EDG-1 as an interactor of DEPS-1 and PRG-1. Our study reveals how specific protein-protein interactions drive the spatial organisation and piRNA-dependent silencing within membraneless organelles