Influence of ionic liquids on the crystalline structure of nanocolloids

This communication demonstrates that ionic liquids can alter the crystallinity and chemical ordering of nanocolloids synthesized in solution.

Hydrodynamic cavitation in micro channels with channel sizes of 100 and 750 micrometers

Decreasing the constriction size and residence time in hydrodynamic cavitation is predicted to give increased hot spot temperatures at bubble collapse and increased radical formation rate. Cavitation in a 100 x 100 mu m(2) rectangular micro channel and in a circular 750 mu m diameter milli channel has been investigated with computational fluid dynamics software and with imaging and radical production experiments. No radical production has been measured in the micro channel. This is probably because there is no spherically symmetrical collapse of the gas pockets in the channel which yield high hot spot temperatures. The potassium iodide oxidation yield in the presence of chlorohydrocarbons in the milli channel of up to 60 nM min(-1) is comparable to values reported on hydrodynamic cavitation in literature, but lower than values for ultrasonic cavitation. These small constrictions can create high apparent cavitation collapse frequencies.

Fetch Gating Control through Speculative Instruction Window Weighting

In a dynamic reordering superscalar processor, the front-end fetches instructions and places them in the issue queue. Instructions are then issued by the back-end execution core. Till recently, the front-end was designed to maximize performance without considering energy consumption. The front-end fetches instructions as fast as it can until it is stalled by a filled issue queue or some other blocking structure. This approach wastes energy: (i) speculative execution causes many wrong-path instructions to be fetched and executed, and (ii) back-end execution rate is usually less than its peak rate, but front-end structures are dimensioned to sustained peak performance. Dynamically reducing the front-end instruction rate and the active size of front-end structure (e.g. issue queue) is a required performance-energy trade-off. Techniques proposed in the literature attack only one of these effects.
In previous work, we have proposed Speculative Instruction Window Weighting (SIWW) [21], a fetch gating technique that allows to address both fetch gating and instruction issue queue dynamic sizing. SIWW computes a global weight on the set of inflight instructions. This weight depends on the number and types of inflight instructions (non-branches, high confidence or low confidence branches, ...). The front-end instruction rate can be continuously adapted based on this weight. This paper extends the analysis of SIWW performed in previous work. It shows that SIWW performs better than previously proposed fetch gating techniques and that SIWW allows to dynamically adapt the size of the active instruction queue.

Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration

Despite significant progress in the identification of genetic loci for age-related macular degeneration (AMD), not all of the heritability has been explained. To identify variants which contribute to the remaining genetic susceptibility, we performed the largest meta-analysis of genome-wide association studies to date for advanced AMD. We imputed 6 036 699 single-nucleotide polymorphisms with the 1000 Genomes Project reference genotypes on 2594 cases and 4134 controls with follow-up replication of top signals in 5640 cases and 52 174 controls. We identified two new common susceptibility alleles, rs1999930 on 6q21-q22.3 near FRK/COL10A1 [odds ratio (OR) 0.87; P = 1.1 × 10(-8)] and rs4711751 on 6p12 near VEGFA (OR 1.15; P = 8.7 × 10(-9)). In addition to the two novel loci, 10 previously reported loci in ARMS2/HTRA1 (rs10490924), CFH (rs1061170, and rs1410996), CFB (rs641153), C3 (rs2230199), C2 (rs9332739), CFI (rs10033900), LIPC (rs10468017), TIMP3 (rs9621532) and CETP (rs3764261) were confirmed with genome-wide significant signals in this large study. Loci in the recently reported genes ABCA1 and COL8A1 were also detected with suggestive evidence of association with advanced AMD. The novel variants identified in this study suggest that angiogenesis (VEGFA) and extracellular collagen matrix (FRK/COL10A1) pathways contribute to the development of advanced AMD.

Detecting sequence dependent transcriptional pauses from RNA and protein number time series

Background: Evidence suggests that in prokaryotes sequence-dependent transcriptional pauses a?ect the dynamics of transcription and translation, as well as of small genetic circuits. So far, a few pause-prone sequences have been identi?ed from in vitro measurements of transcription elongation kinetics.

Results: Using a stochastic model of gene expression at the nucleotide and codon levels with realistic parameter values, we investigate three di?erent but related questions and present statistical methods for their analysis. First, we show that information from in vivo RNA and protein temporal numbers is su?cient to discriminate between models with and without a pause site in their coding sequence. Second, we demonstrate that it is possible to separate a large variety of models from each other with pauses of various durations and locations in the template by means of a hierarchical clustering and a random forest classi?er. Third, we introduce an approximate likelihood function that allows to estimate the location of a pause site.

Conclusions: This method can aid in detecting unknown pause-prone sequences from temporal measurements of RNA and protein numbers at a genome-wide scale and thus elucidate possible roles that these sequences play in the dynamics of genetic networks and phenotype.

CO2 uptake by a soil microcosm

Sequestration of CO2 via biological sinks is a matter of great scientific importance due to the potential lowering of atmospheric CO2. In this study, a custom built incubation chamber was used to cultivate a soil microbial community to instigate chemoautotrophy of a temperate soil. Real-time atmospheric CO2 concentrations were monitored and estimations of total CO2 uptake were made. After careful background flux corrections, 4.52 +/- 0.05 g CO2 kg I dry soil was sequestered from the chamber atmosphere over 40 h. Using isotopically labelled (CO2)-C-13 and GCMS-IRMS, labelled fatty acids were identified after only a short incubation, hence confirming CO2 sequestration for soil. The results of this in vivo study provide the ground work for future studies intending to mimic the in situ environment by providing a reliable method for investigating CO2 uptake by soil microorganisms.(C) 2012 Elsevier Ltd. All rights reserved.

MicroRNA-34c inversely couples the biological functions of the runt-related transcription factor RUNX2 and the tumor suppressor p53 in osteosarcoma

Osteosarcoma (OS) is a primary bone tumor that is most prevalent during adolescence. RUNX2, which stimulates differentiation and suppresses proliferation of osteoblasts, is deregulated in OS. Here, we define pathological roles of RUNX2 in the etiology of OS and mechanisms by which RUNX2 expression is stimulated. RUNX2 is often highly expressed in human OS biopsies and cell lines. Small interference RNA (siRNA)-mediated depletion of RUNX2 inhibits growth of U2OS OS cells. RUNX2 levels are inversely linked to loss of p53 (which predisposes to OS) in distinct OS cell lines and osteoblasts. RUNX2 protein levels decrease upon stabilization of p53 with the MDM2 inhibitor Nutlin-3. Elevated RUNX2 protein expression is post-transcriptionally regulated and directly linked to diminished expression of several validated RUNX2 targeting microRNAs (miRNAs) in human OS cells compared to mesenchymal progenitor cells. The p53-dependent miR-34c is the most significantly down-regulated RUNX2 targeting miRNA in OS. Exogenous supplementation of miR-34c markedly decreases RUNX2 protein levels, while 3UTR reporter assays establish RUNX2 as a direct target of miR-34c in OS cells. Importantly, Nutlin-3 mediated stabilization of p53 increases expression of miR-34c and decreases RUNX2. Thus, a novel RUNX2-p53-miR34 network controls cell growth of osseous cells and is compromised in OS.

Tracking the Fate of Microbially Sequestered Carbon Dioxide in Soil Organic Matter

The microbial contribution to soil organic matter (SOM) has recently been shown to be much larger than previously thought and thus its role in carbon sequestration may also be underestimated. In this study we employ C-13 ((CO2)-C-13) to assess the potential CO2 sequestration capacity of soil chemoautotrophic bacteria and combine nuclear magnetic resonance (NMR) with stable isotope probing (SIP), techniques that independently make use of the isotopic enrichment of soil microbial biomass. In this way molecular information generated from NMR is linked with identification of microbes responsible for carbon capture. A mathematical model is developed to determine real-time CO2 flux so that net sequestration can be calculated. Twenty-eight groups of bacteria showing close homologies with existing species were identified. Surprisingly, Ralstonia eutropha was the dominant group. Through NMR we observed the formation of lipids, carbohydrates, and proteins produced directly from CO2 utilized by microbial biomass. The component of SOM directly associated with CO2 capture was calculated at 2.86 mg C (89.21 mg kg(-1)) after 48 h. This approach can,differentiate between SOM derived through microbial uptake of CO2 and other SOM constituents and represents a first step in tracking the fate and dynamics of microbial biomass in soil.

A Variant in LDLR is Associated with Abdominal Aortic Aneurysm

Background—Abdominal aortic aneurysm (AAA) is a common cardiovascular disease among older people and demonstrates significant heritability. In contrast to similar complex diseases, relatively few genetic associations with AAA have been confirmed. We reanalysed our genome-wide study and carried through to replication suggestive discovery associations at a lower level of significance.

Methods and Results—A genome-wide association study was conducted using 1,830 cases from the UK, New Zealand and Australia with infra-renal aorta diameter =30mm or ruptured AAA and 5,435 unscreened controls from the 1958 Birth Cohort and National Blood Service cohort from the Wellcome Trust Case Control Consortium. Eight suggestive associations with P<1x10-4 were carried through to in silico replication in 1,292 AAA cases and 30,503 controls. One SNP associated with P<0.05 after Bonferroni correction in the in silico study underwent further replication (706 AAA cases and 1,063 controls from the UK, 507 AAA cases and 199 controls from Denmark and 885 AAA cases and 1,000 controls from New Zealand). Low density lipoprotein receptor (LDLR) rs6511720 A, was significantly associated overall and in three of five individual replication studies. The full study showed an association that reached genome-wide significance (odds ratio 0.76; 95% confidence interval 0.70 to 0.83; P=2.08x10-10).

Conclusions—LDLR rs6511720 is associated with abdominal aortic aneurysm. This finding is consistent with established effects of this variant on coronary artery disease. Shared aetiological pathways with other cardiovascular diseases may present novel opportunities for preventative and therapeutic strategies for AAA.