APLF (C2orf13) is a novel human protein involved in the cellular response to chromosomal DNA strand breaks

Aprataxin and polynucleotide kinase (PNK) are DNA end processing factors that are recruited into the DNA single- and double-strand break repair machinery through phosphorylation-specific interactions with XRCC1 and XRCC4, respectively. These interactions are mediated through a divergent class of forkhead-associated (FHA) domain that binds to peptide sequences in XRCC1 and XRCC4 that are phosphorylated by casein kinase 2 (CK2). Here, we identify the product of the uncharacterized open reading frame C2orf13 as a novel member of this FHA domain family of proteins and we denote this protein APLF (aprataxin- and PNK-like factor). We show that APLF interacts with XRCC1 in vivo and in vitro in a manner that is stimulated by CK2. Yeast two-hybrid analyses suggest that APLF also interacts with the double-strand break repair proteins XRCC4 and XRCC5 (Ku86). We also show that endogenous and yellow fluorescent protein-tagged APLF accumulates at sites of H(2)O(2) or UVA laser-induced chromosomal DNA damage and that this is achieved through at least two mechanisms: one that requires the FHA domain-mediated interaction with XRCC1 and a second that is independent of XRCC1 but requires a novel type of zinc finger motif located at the C terminus of APLF. Finally, we demonstrate that APLF is phosphorylated in a DNA damage- and ATM-dependent manner and that the depletion of APLF from noncycling human SH-SY5Y neuroblastoma cells reduces rates of chromosomal DNA strand break repair following ionizing radiation. These data identify APLF as a novel component of the cellular response to DNA strand breaks in human cells

Emergence of the Shackleton Range from beneath the Antarctic Ice Sheet due to glacial erosion

This paper explores the long-term evolution of a subglacial fjord landscape in the Shackleton Range, Antarctica. We propose that prolonged ice-sheet erosion across a passive continental margin caused troughs to deepen and lower the surrounding ice-sheet surface, leaving adjacent mountains exposed. Geomorphological evidence suggests a change in the direction of regional ice flow accompanied emergence. Simple calculations suggest that isostatic compensation caused by the deepening of bounding ice-stream troughs lowered the ice-sheet surface relative to the mountains by ~800m. Use of multiple cosmogenic isotopes on bedrock and erratics (26Al, 10Be, 21Ne) provides evidence that overriding of the massif and the deepening of the adjacent troughs occurred earlier than the Quaternary. Perhaps this occurred in the mid-Miocene, as elsewhere in East Antarctica in the McMurdo Dry Valleys and the Lambert basin. The implication is that glacial erosion instigates feedback that can change ice-sheet thickness, extent, and direction of flow. Indeed, as the subglacial troughs evolve over millions of years, they increase topographic relief; and this changes the dynamics of the ice sheet. © 2013 Elsevier B.V

Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis

Despite extensive study, the mechanism by which retroviral reverse transciptases (RTs) specifically utilize polypurine tract (PPT) RNA for initiation of plus-strand DNA synthesis remains unclear. Three sequence motifs within or adjacent to the purine-rich elements are highly conserved, namely, a rU:dA tract region immediately 5′ to the PPT, an rA:dT-rich sequence constituting the upstream portion of the PPT and a downstream rG:dC tract. Using an in vitro HIV-1 model system, we determined that the former two elements define the 5′ terminus of the (+)-strand primer, whereas the rG:dC tract serves as the primary determinant of initiation specificity. Subsequent analysis demonstrated that G→A or A→G substitution at PPT positions −2, −4 and +1 (relative to the scissile phosphate) substantially reduces (+)-strand priming. We explored this observation further using PPT substrates substituted with a variety of nucleoside analogs [inosine (I), purine riboside (PR), 2-aminopurine (2-AP), 2,6-diaminopurine (2,6-DAP), isoguanine (iG)], or one of the naturally occurring bases at these positions. Our results demonstrate that for PPT positions −2 or +1, substituting position 2 of the purine was an important determinant of cleavage specificity. In addition, cleavage specificity was greatly affected by substituting −4G with an analog containing a 6-NH2 moiety

Self-consistent field predictions for quenched spherical biocompatible triblock copolymer micelles

We have used the Scheutjens-Fleer self-consistent field (SF-SCF) method to predict the self-assembly of triblock copolymers with a solvophilic middle block and sufficiently long solvophobic outer blocks. We model copolymers consisting of polyethylene oxide (PEO) as solvophilic block and poly(lactic-co-glycolic) acid (PLGA) or poly({\ko}-caprolactone) (PCL) as solvophobic block. These copolymers form structurally quenched spherical micelles provided the solvophilic block is long enough. Predictions are calibrated on experimental data for micelles composed of PCL-PEO-PCL and PLGA-PEO-PLGA triblock copolymers prepared via the nanoprecipitation method. We establish effective interaction parameters that enable us to predict various micelle properties such as the hydrodynamic size, the aggregation number and the loading capacity of the micelles for hydrophobic species that are consistent with experimental finding.Comment: accepted for publication in Soft Matte

Selection Of A Novel Aptamer Against Vitronectin Using Capillary Electrophoresis And Next Generation Sequencing

Breast cancer (BC) results in ≃40,000 deaths each year in the United States and even among survivors treatment of the disease may have devastating consequences, including increased risk for heart disease and cognitive impairment resulting from the toxic effects of chemotherapy. Aptamer-mediated drug delivery can contribute to improved treatment outcomes through the selective delivery of chemotherapy to BC cells, provided suitable cancer-specific antigens can be identified. We report here the use of capillary electrophoresis in conjunction with next generation sequencing to develop the first vitronectin (VN) binding aptamer (VBA-01; Kd 405 nmol/l, the first aptamer to vitronectin (VN; Kd = 405 nmol/l), a protein that plays an important role in wound healing and that is present at elevated levels in BC tissue and in the blood of BC patients relative to the corresponding nonmalignant tissues. We used VBA-01 to develop DVBA-01, a dimeric aptamer complex, and conjugated doxorubicin (Dox) to DVBA-01 (7:1 ratio) using pH-sensitive, covalent linkages. Dox conjugation enhanced the thermal stability of the complex (60.2 versus 46.5°C) and did not decrease affinity for the VN target. The resulting DVBA-01-Dox complex displayed increased cytotoxicity to MDA-MB-231 BC cells that were cultured on plasticware coated with VN (1.8 × 10⁻⁶mol/l) relative to uncoated plates (2.4 × 10⁻⁶ mol/l), or plates coated with the related protein fibronectin (2.1 × 10⁻⁶ mol/l). The VBA-01 aptamer was evaluated for binding to human BC tissue using immunohistochemistry and displayed tissue specific binding and apparent association with BC cells. In contrast, a monoclonal antibody that preferentially binds to multimeric VN primarily stained extracellular matrix and vessel walls of BC tissue. Our results indicate a strong potential for using VN-targeting aptamers to improve drug delivery to treat BC

Crop expansion and conservation priorities in tropical countries

Expansion of cropland in tropical countries is one of the principal causes of biodiversity loss, and threatens to undermine progress towards meeting the Aichi Biodiversity Targets. To understand this threat better, we analysed data on crop distribution and expansion in 128 tropical countries, assessed changes in area of the main crops and mapped overlaps between conservation priorities and cultivation potential. Rice was the single crop grown over the largest area, especially in tropical forest biomes. Cropland in tropical countries expanded by c. 48,000 km2 per year from 1999–2008. The countries which added the greatest area of new cropland were Nigeria, Indonesia, Ethiopia, Sudan and Brazil. Soybeans and maize are the crops which expanded most in absolute area. Other crops with large increases included rice, sorghum, oil palm, beans, sugar cane, cow peas, wheat and cassava. Areas of high cultivation potential—while bearing in mind that political and socio-economic conditions can be as influential as biophysical ones—may be vulnerable to conversion in the future. These include some priority areas for biodiversity conservation in tropical countries (e.g., Frontier Forests and High Biodiversity Wilderness Areas), which have previously been identified as having ‘low vulnerability’, in particular in central Africa and northern Australia. There are also many other smaller areas which are important for biodiversity and which have high cultivation potential (e.g., in the fringes of the Amazon basin, in the Paraguayan Chaco, and in the savanna woodlands of the Sahel and East Africa). We highlight the urgent need for more effective sustainability standards and policies addressing both production and consumption of tropical commodities, including robust land-use planning in agricultural frontiers, establishment of new protected areas or REDD+ projects in places agriculture has not yet reached, and reduction or elimination of incentives for land-demanding bioenergy feedstock

Gravitational Collapse with a Cosmological Constant

We consider the effect of a positive cosmological constant on spherical gravitational collapse to a black hole for a few simple, analytic cases. We construct the complete Oppenheimer-Snyder-deSitter (OSdS) spacetime, the generalization of the Oppenheimer-Snyder solution for collapse from rest of a homogeneous dust ball in an exterior vacuum. In OSdS collapse, the cosmological constant may affect the onset of collapse and decelerate the implosion initially, but it plays a diminishing role as the collapse proceeds. We also construct spacetimes in which a collapsing dust ball can bounce, or hover in unstable equilibrium, due to the repulsive force of the cosmological constant. We explore the causal structure of the different spacetimes and identify any cosmological and black hole event horizons which may be present.Comment: 7 pages, 10 figures; To appear in Phys. Rev.

The Mass Inflow Rate in the Barred Galaxy NGC 1530

Mass inflow in barred galaxies has been invoked to account for a wide variety of phenomena, but until now direct evidence for inflow has been lacking. We present Fabry-Perot H-alpha observations of the barred spiral galaxy NGC 1530 from which we determine velocities of the ionized gas for the entire region swept by the bar. We compare the velocity field to models of gas flow in barred spirals and show that it is well reproduced by ideal gas hydrodynamic models. Inspection of the models and observations reveals that gas entering the bar dust lanes streams directly down the dust lanes toward the 2 kpc radius nuclear ring. The models predict that approximately 20% of the gas flowing down the dust lane enters the nuclear ring; the remaining gas sprays around the ring to the other bar dust lane. The fraction of the gas entering the ring is relatively insensitive to the shape or size of the bar. Our observations of the velocity field and dust optical depth yield a mass inflow rate into the nuclear ring of 1 solar mass per year.Comment: 13 pages, 3 figures, aastex 4.0, accepted for publication in Ap J Letter

Statistical methods in cosmology

The advent of large data-set in cosmology has meant that in the past 10 or 20 years our knowledge and understanding of the Universe has changed not only quantitatively but also, and most importantly, qualitatively. Cosmologists rely on data where a host of useful information is enclosed, but is encoded in a non-trivial way. The challenges in extracting this information must be overcome to make the most of a large experimental effort. Even after having converged to a standard cosmological model (the LCDM model) we should keep in mind that this model is described by 10 or more physical parameters and if we want to study deviations from it, the number of parameters is even larger. Dealing with such a high dimensional parameter space and finding parameters constraints is a challenge on itself. Cosmologists want to be able to compare and combine different data sets both for testing for possible disagreements (which could indicate new physics) and for improving parameter determinations. Finally, cosmologists in many cases want to find out, before actually doing the experiment, how much one would be able to learn from it. For all these reasons, sophisiticated statistical techniques are being employed in cosmology, and it has become crucial to know some statistical background to understand recent literature in the field. I will introduce some statistical tools that any cosmologist should know about in order to be able to understand recently published results from the analysis of cosmological data sets. I will not present a complete and rigorous introduction to statistics as there are several good books which are reported in the references. The reader should refer to those.Comment: 31, pages, 6 figures, notes from 2nd Trans-Regio Winter school in Passo del Tonale. To appear in Lectures Notes in Physics, "Lectures on cosmology: Accelerated expansion of the universe" Feb 201

Knee Osteoarthritis and the Efficacy of Kinesthesia, Balance & Agility Exercise Training: A Pilot Study

Kinesthesia, balance and agility (KBA) neuromuscular exercises are commonly used for rehabilitation of lower extremity injuries. KBA combined with strength training (ST) reportedly improves function among persons with knee osteoarthritis (OA), but independent effects of KBA are unknown. The purpose of this study was to determine the efficacy of KBA exercises, independent of ST, to improve function among persons with knee OA. Twenty participants (69.3, SD 11.4 y) were randomized to 8 weeks, 3-days per week, instructor-lead KBA or ST groups. Self-reported physical function (difficulty with daily living activities such as walking, bending, stair climbing, etc.) was measured at baseline and every two weeks. Community physical activity level, negative and positive outcome expectancies for exercise, self-reported knee stability, and timed 10-stair climb, 10-stair descent, and ‘get up and go’ 15 m walk were measured at baseline and follow-up. Physical function improved 59% (p = 0.02) with KBA and 40% (p = 0.02) with ST at 8 weeks. Community physical activity level improved only in KBA (p = 0.04); knee stability improved in both KBA (p = 0.04) and ST (p = 0.01). There were no significant between-group differences (p \u3e 0.05). In conclusion, both interventions appear to improve function and knee stability among persons with symptomatic knee OA. As KBA has never been studied as an independent treatment program, our results indicate it is a promising stand-alone intervention worthy of further study