Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation

Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research to date has focused on the regulatory effect of individual RBPs or miRNAs. Here, we mapped both RBP and miRNA binding sites on human 3′UTRs and utilized this collection to better understand PTR. We show that the transcripts that lack competition for HuR binding are destabilized more after HuR depletion. We also confirm this finding for PUM1(2) by measuring genome-wide expression changes following the knockdown of PUM1(2) in HEK293 cells. Next, to find potential cooperative interactions, we identified the pairs of factors whose sites co-localize more often than expected by random chance. Upon examining these results for PUM1(2), we found that transcripts where the sites of PUM1(2) and its interacting miRNA form a stem-loop are more stabilized upon PUM1(2) depletion. Finally, using dinucleotide frequency and counts of regulatory sites as features in a regression model, we achieved an AU-ROC of 0.86 in predicting mRNA half-life in BEAS-2B cells. Altogether, our results suggest that future studies of PTR must consider the combined effects of RBPs and miRNAs, as well as their interactions.No sponso

Influence of Reoperations on Long-Term Quality of Life After Restrictive Procedures: A Prospective Study

Quality of life improves after bariatric surgery. However, long-term results and the influence of reoperations are not well known. A prospective quality of life assessment before, 1 and 7 years after laparoscopic adjustable gastric banding (LAGB) and vertical banded gastroplasty (VBG) was performed in order to determine the influence of reoperations during follow-up. One hundred patients were included in the study. Fifty patients underwent VBG and 50 LAGB. Patients completed the quality of life questionnaires prior to surgery and two times during follow-up. Health-related quality of life (HRQoL) questionnaires included the Nottingham Health Profile I and II and the Sickness Impact Profile 68. Follow-up was 84% with a mean duration of 84 months (7 years). During follow-up, 65% of VBG patients underwent conversion to Roux-en-Y gastric bypass while 44% of LAGB patients underwent a reoperation or conversion. One year after the procedure, nearly all quality-of-life parameters significantly improved. After 7 years, the Nottingham Health Profile (NHP)-I domain “physical ability”, the NHP-II and the SIP-68 domains “mobility control”, “social behavior”, and “mobility range” were still significantly improved in both groups. The domains “emotional reaction”, “social isolation” (NHP-I), and “emotional stability” (SIP-68) remained significantly improved in the VBG group while this was true for the domain “energy level” (NHP-I) in the LAGB group. Both the type of procedure and reoperations during follow-up were not of significant influence on the HRQoL results. Weight loss and decrease in comorbidities were the only significant factors influencing quality of life. Restrictive bariatric surgery improves quality of life. Although results are most impressive 1 year after surgery, the improvement remains significant after long-term follow-up. Postoperative quality of life is mainly dependent on weight loss and decrease in comorbidities and not on the type of procedure or surgical complications

Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression

A hallmark of inflammatory diseases is the excessive recruitment and influx of monocytes to sites of tissue damage and their ensuing differentiation into macrophages. Numerous stimuli are known to induce transcriptional changes associated with macrophage phenotype, but posttranscriptional control of human macrophage differentiation is less well understood. Here we show that expression levels of the RNA-binding protein Quaking (QKI) are low in monocytes and early human atherosclerotic lesions, but are abundant in macrophages of advanced plaques. Depletion of QKI protein impairs monocyte adhesion, migration, differentiation into macrophages and foam cell formation in vitro and in vivo. RNA-seq and microarray analysis of human monocyte and macrophage transcriptomes, including those of a unique QKI haploinsufficient patient, reveal striking changes in QKI-dependent messenger RNA levels and splicing of RNA transcripts. The biological importance of these transcripts and requirement for QKI during differentiation illustrates a central role for QKI in posttranscriptionally guiding macrophage identity and function.No sponso

Targeting the RNA-Binding Protein QKI in Myeloid Cells Ameliorates Macrophage-Induced Renal Interstitial Fibrosis

In the pathophysiologic setting of acute and chronic kidney injury, the excessive activation and recruitment of blood-borne monocytes prompts their differentiation into inflammatory macrophages, a process that leads to progressive glomerulosclerosis and interstitial fibrosis. Importantly, this differentiation of monocytes into macrophages requires the meticulous coordination of gene expression at both the transcriptional and post-transcriptional level. The transcriptomes of these cells are ultimately determined by RNA-binding proteins such as QUAKING (QKI), that define their pre-mRNA splicing and mRNA transcript patterns. Using two mouse models, namely (1) quaking viable mice (qkv) and (2) the conditional deletion in the myeloid cell lineage using the lysozyme 2-Cre (QKIFL/FL;LysM-Cre mice), we demonstrate that the abrogation of QKI expression in the myeloid cell lineage reduces macrophage infiltration following kidney injury induced by unilateral urethral obstruction (UUO). The qkv and QKIFL/FL;LysM-Cre mice both showed significant diminished interstitial collagen deposition and fibrosis in the UUO-damaged kidney, as compared to wild-type littermates. We show that macrophages isolated from QKIFL/FL;LysM-Cre mice are associated with defects in pre-mRNA splicing. Our findings demonstrate that reduced expression of the alternative splice regulator QKI in the cells of myeloid lineage attenuates renal interstitial fibrosis, suggesting that inhibition of this splice regulator may be of therapeutic value for certain kidney diseases

OMAE2011-49910 35 YEARS OLD JACKETS REMOVED AS A SINGLE PIECE OMAE2011-49910

ABSTRACT Heerema Marine Contractors (HMC) have removed and will be removing various platforms from the North Sea. For these projects Heerema has developed an unconventional method to remove and transport jackets: Jackets are lifted as one single piece and transported to the recycling yard whilst being suspended from both cranes of the Heavy Lift Vessel (HLV) Thialf. Two purpose built structures at the stern restrain the jackets from horizontal motions during transport. In summer 2010 three eight-legged jackets were removed and transported using this method (see The transport distance with the jacket suspended from both Thialf cranes ranged from 200-300 nautical miles (1½-2½ days sailing). The final cuts and the jacket lifting required relatively low sea states. The wave climate for transport was determined with the assumption of a preceding weather sensitive operation, which is different to a transport that assumes a start at a random time. Model tests for these design sea states have been performed to accurately assess the Thialf dynamic behavior at its shallow transit draught. Additional analyses were performed to confirm the vessel-jacket dynamic interaction. During transport the so called 'restraints' gripped around the jacket corner legs, restraining the structure horizontally and preventing side loads on the cranes. During the three transports, motions have been measured and dynamic behavior corresponded well with the analyses. Removing and transporting these jackets as a single piece was a unique operation. The method worked well and resulted in a predictable, safe and time efficient jacket removal. This paper will address the removal method, including structural aspects, model tests and full scale verification

Effect of long-term aspirin use on the risk for neovascular age-related macular degeneration

Background: Results from several cohort studies have indicated that long-term low-dose aspirin (acetylsalicylic acid, ASA) use markedly increases the risk for neovascular age-related macular degeneration (nAMD). nAMD is a serious condition that causes rapid decline in central-field vision over the course of days to weeks. The studies currently available obtained data from questionnaires, therefore lacking high-quality information regarding exposure to low-dose ASA, and had few nAMD cases. Objectives: To quantify the risk for nAMD associated with long-term low-dose ASA use. Methods: A case-control study was conducted, including all cases of nAMD in the period 1 January 1987 - 31 December 2012 aged 50 years and older from the UK Clinical Practice Research Datalink (CPRD) database. Cases were matched to up to five controls on age, gender and general practice. Conditional logistic regression was used to estimate odds ratios for the risk of nAMD associated with increasing durations of low-dose ASA use, adjusting for smoking status, obesity, glaucoma, hypercholesterolaemia, and lipid lowering medication, and cardiovascular diseases. Results: 4,125 cases were matched to 20,173 controls. Cases had a median age of 80.1 years and were in majority female (64.7%). Overall, the risk for nAMD associated with low-dose ASA use was a small but significantly increased adjusted risk of 1.12 (95% confidence interval 1.03 - 1.21). We observed a trend for increasing risk with prolonged use: odds ratios were 1.06 (use for less than twoand- a-half years; 95% CI 0.96 - 1.17), 1.07 (twoand- a-half to five years; 95% CI 0.94 - 1.21), 1.17 (five to ten years; 95% CI 1.04 - 1.31), 1.23 (ten to fifteen years; 95% CI 1.05 - 1.45), and 1.33 (more than fifteen years; 95% CI 1.08 - 1.63), compared to no ASA use. Conclusions: Long-term use of low-dose ASA is associated with an increased risk for nAMD. This risk is lower than previously observed and small compared to other risk factors and the benefit-risk balance of low-dose ASA for the prevention of cardiovascular disease will not be impacted

Scatterplot displaying the total number of patients studied before approval plotted against the number of patients studied long term (for 6 and 12 mo) for chronic medication.

<p>Reference lines are added to indicate the minimum criteria from the ICH E1 guideline: 1,000 patients in total and 300 and 100 patients studied for 6 and 12 mo, respectively. Any products not meeting the ICH E1 guideline recommendations are shown in red.</p