Association Of G-Quadruplex Forming Sequences With Human MtDNA Deletion Breakpoints

Background: Mitochondrial DNA (mtDNA) deletions cause disease and accumulate during aging, yet our understanding of the molecular mechanisms underlying their formation remains rudimentary. Guanine-quadruplex (GQ) DNA structures are associated with nuclear DNA instability in cancer; recent evidence indicates they can also form in mitochondrial nucleic acids, suggesting that these non-B DNA structures could be associated with mtDNA deletions. Currently, the multiple types of GQ sequences and their association with human mtDNA stability are unknown. Results: Here, we show an association between human mtDNA deletion breakpoint locations (sites where DNA ends rejoin after deletion of a section) and sequences with G-quadruplex forming potential (QFP), and establish the ability of selected sequences to form GQ in vitro. QFP contain four runs of either two or three consecutive guanines (2G and 3G, respectively), and we identified four types of QFP for subsequent analysis: intrastrand 2G, intrastrand 3G, duplex derived interstrand (ddi) 2G, and ddi 3G QFP sequences. We analyzed the position of each motif set relative to either 5\u27 or 3\u27 unique mtDNA deletion breakpoints, and found that intrastrand QFP sequences, but not ddi QFP sequences, showed significant association with mtDNA deletion breakpoint locations. Moreover, a large proportion of these QFP sequences occur at smaller distances to breakpoints relative to distribution-matched controls. The positive association of 2G QFP sequences persisted when breakpoints were divided into clinical subgroups. We tested in vitro GQ formation of representative mtDNA sequences containing these 2G QFP sequences and detected robust GQ structures by UV–VIS and CD spectroscopy. Notably, the most frequent deletion breakpoints, including those of the common deletion , are bounded by 2G QFP sequence motifs. Conclusions: The potential for GQ to influence mitochondrial genome stability supports a high-priority investigation of these structures and their regulation in normal and pathological mitochondrial biology. These findings emphasize the potential importance of helicases that subsequently resolve GQ to maintain the stability of the mitochondrial genome

G-Quadruplex Dynamics Contribute To Regulation Of Mitochondrial Gene Expression

Single-stranded DNA or RNA sequences rich in guanine (G) can adopt non-canonical structures known as G-quadruplexes (G4). Mitochondrial DNA (mtDNA) sequences that are predicted to form G4 are enriched on the heavy-strand and have been associated with formation of deletion breakpoints. Increasing evidence supports the ability of mtDNA to form G4 in cancer cells; however, the functional roles of G4 structures in regulating mitochondrial nucleic acid homeostasis in non-cancerous cells remain unclear. Here, we demonstrate by live cell imaging that the G4-ligand RHPS4 localizes primarily to mitochondria at low doses. We find that low doses of RHPS4 do not induce a nuclear DNA damage response but do cause an acute inhibition of mitochondrial transcript elongation, leading to respiratory complex depletion. We also observe that RHPS4 interferes with mtDNA levels or synthesis both in cells and isolated mitochondria. Importantly, a mtDNA variant that increases G4 stability and anti-parallel G4-forming character shows a stronger respiratory defect in response to RHPS4, supporting the conclusion that mitochondrial sensitivity to RHPS4 is G4-mediated. Taken together, our results indicate a direct role for G4 perturbation in mitochondrial genome replication, transcription processivity, and respiratory function in normal cells

Contributions of transported Prudhoe Bay oil field emissions to the aerosol population in Utqiaġvik, Alaska

Loss of sea ice is opening the Arctic to increasing development involving oil and gas extraction and shipping. Given the significant impacts of absorbing aerosol and secondary aerosol precursors emitted within the rapidly warming Arctic region, it is necessary to characterize local anthropogenic aerosol sources and compare to natural conditions. From August to September 2015 in Utqiaġvik (Barrow), AK, the chemical composition of individual atmospheric particles was measured by computer-controlled scanning electron microscopy with energy-dispersive X-ray spectroscopy (0.13-4 μm projected area diameter) and real-time single-particle mass spectrometry (0.2-1.5 μm vacuum aerodynamic diameter). During periods influenced by the Arctic Ocean (70 % of the study), our results show that fresh sea spray aerosol contributed ∼ 20 %, by number, of particles between 0.13 and 0.4 μm, 40-70 % between 0.4 and 1 μm, and 80-100 % between 1 and 4 μm particles. In contrast, for periods influenced by emissions from Prudhoe Bay (10 % of the study), the third largest oil field in North America, there was a strong influence from submicron (0.13-1 μm) combustion-derived particles (20-50 % organic carbon, by number; 5-10 % soot by number). While sea spray aerosol still comprised a large fraction of particles (90 % by number from 1 to 4 μm) detected under Prudhoe Bay influence, these particles were internally mixed with sulfate and nitrate indicative of aging processes during transport. In addition, the overall mode of the particle size number distribution shifted from 76 nm during Arctic Ocean influence to 27 nm during Prudhoe Bay influence, with particle concentrations increasing from 130 to 920 cm-3 due to transported particle emissions from the oil fields. The increased contributions of carbonaceous combustion products and partially aged sea spray aerosol should be considered in future Arctic atmospheric composition and climate simulations

Macrophage-Engineered Vesicles for Therapeutic Delivery and Bidirectional Reprogramming of Immune Cell Polarization

Macrophages, one of the most important phagocytic cells of the immune system, are highly plastic and are known to exhibit diverse roles under different pathological conditions. The ability to repolarize macrophages from pro-inflammatory (M1) to anti-inflammatory (M2) or vice versa offers a promising therapeutic approach for treating various diseases such as traumatic injury and cancer. Herein, it is demonstrated that macrophage-engineered vesicles (MEVs) generated by disruption of macrophage cellular membranes can be used as nanocarriers capable of reprogramming macrophages and microglia toward either pro- or anti-inflammatory phenotypes. MEVs can be produced at high yields and easily loaded with diagnostic molecules or chemotherapeutics and delivered to both macrophages and cancer cells in vitro and in vivo. Overall, MEVs show promise as potential delivery vehicles for both therapeutics and their ability to controllably modulate macrophage/microglia inflammatory phenotypes

FFTF FUEL PIN AND SUBASSEMBLY CONCEPTUAL DESIGN METHODS AND DATA

The major technical bases for the FFTF first core fuel assembly conceptual design are presented in four general categories: (1) thermal, (2) hydraulic, (3) structural and (4) performance-manufacturing design characteristics. Recommended design values and conceptual engineering drawings of the fuel pin and subassembly are included

Top-k String Auto-Completion with Synonyms

Auto-completion is one of the most prominent features of modern information systems. The existing solutions of auto-completion provide the suggestions based on the beginning of the currently input character sequence (i.e. prefix). However, in many real applications, one entity often has synonyms or abbreviations. For example, "DBMS" is an abbreviation of "Database Management Systems". In this paper, we study a novel type of auto-completion by using synonyms and abbreviations. We propose three trie-based algorithms to solve the top-k auto-completion with synonyms; each one with different space and time complexity trade-offs. Experiments on large-scale datasets show that it is possible to support effective and efficient synonym-based retrieval of completions of a million strings with thousands of synonyms rules at about a microsecond per-completion, while taking small space overhead (i.e. 160-200 bytes per string).Peer reviewe

Metagenes Associated with Survival in Non-Small Cell Lung Cancer

NSCLC (non-small cell lung cancer) comprises about 80% of all lung cancer cases worldwide. Surgery is most effective treatment for patients with early-stage disease. However, 30%–55% of these patients develop recurrence within 5 years. Therefore, markers that can be used to accurately classify early-stage NSCLC patients into different prognostic groups may be helpful in selecting patients who should receive specific therapies

Pi-eta scattering and the resummation of vacuum fluctuation in three-flavour ChPT

We discuss various aspects of resummed chiral perturbation theory, which was developed recently in order to consistently include the possibility of large vacuum fluctuations of the ss-pairs and the scenario with smaller value of the chiral condensate for N_f=3. The subtleties of this approach are illustrated using a concrete example of observables connected with pi-eta scattering. This process seems to be a suitable theoretical laboratory for this purpose due to its sensitivity to the values of the O(p^4) LEC's, namely to the values of the fluctuation parameters L4 and L6. We discuss several issues in detail, namely the choice of `good' observables and properties of their bare expansions, the `safe' reparametrization in terms of physical observables, the implementation of exact perturbative unitarity and exact renormalization scale independence, the role of higher order remainders and their estimates. We make a detailed comparison with standard chiral perturbation theory and use generalized ChPT as well as resonance chiral theory to estimate the higher order remainders.Comment: Version submitted to EPJ

Rationale and design of the hip fracture accelerated surgical treatment and care track (hip attack) trial : A protocol for an international randomised controlled trial evaluating early surgery for hip fracture patients

Introduction Annually, millions of adults suffer hip fractures. The mortality rate post a hip fracture is 7%-10% at 30 days and 10%-20% at 90 days. Observational data suggest that early surgery can improve these outcomes in hip fracture patients. We designed a clinical trial - HIP fracture Accelerated surgical TreaTment And Care tracK (HIP ATTACK) to determine the effect of accelerated surgery compared with standard care on the 90-day risk of all-cause mortality and major perioperative complications. Methods and analysis HIP ATTACK is a multicentre, international, parallel group randomised controlled trial (RCT) that will include patients ≥45 years of age and diagnosed with a hip fracture from a low-energy mechanism requiring surgery. Patients are randomised to accelerated medical assessment and surgical repair (goal within 6 h) or standard care. The co-primary outcomes are (1) all-cause mortality and (2) a composite of major perioperative complications (ie, mortality and non-fatal myocardial infarction, pulmonary embolism, pneumonia, sepsis, stroke, and life-threatening and major bleeding) at 90 days after randomisation. All patients will be followed up for a period of 1 year. We will enrol 3000 patients. Ethics and dissemination All centres had ethics approval before randomising patients. Written informed consent is required for all patients before randomisation. HIP ATTACK is the first large international trial designed to examine whether accelerated surgery can improve outcomes in patients with a hip fracture. The dissemination plan includes publishing the results in a policy-influencing journal, conference presentations, engagement of influential medical organisations, and providing public awareness through multimedia resources. Trial registration number NCT02027896; Pre-results