Kinetic Mechanism for Single stranded DNA binding and Translocation by S. cerevisiae Isw2

The chromatin remodeling complex Isw2 from S. cerevisiae (yIsw2) mobilizes nucleosomes through an ATP-dependent reaction that is coupled to the translocation of the helicase domain of the enzyme along intranucleosomal DNA. In this study we demonstrate that yIsw2 is capable of translocating along single-stranded DNA in a reaction that is coupled to ATP hydrolysis. We propose that single-stranded DNA translocation by yIsw2 occurs through a series of repeating uniform steps with an overall macroscopic processivity of P = (0.90 ± 0.02), corresponding to an average translocation distance of (20 ± 2) nucleotides before dissociation. This processivity corresponds well to the processivity of nucleosome sliding by yIsw2 thus arguing that single-stranded DNA translocation or tracking may be fundamental to the double-stranded DNA translocation required for effective nucleosome mobilization. Furthermore, we find evidence that a slow initiation process, following DNA binding, may be required to make yIsw2 competent for DNA translocation. We also provide evidence that this slow initiation process may correspond to the second step of a two-step DNA binding mechanism by yIsw2 and a quantitative description of the kinetics of this DNA binding mechanism

Measuring Organization of Large Surficial Clasts in Heterogeneous Gravel Beach Sediments

The natural stratification and interlocking “organization” of armored sediments in heterogeneous, coarse-grained, beaches provides protection and enhances habitat for borrowing sedentary megafauna and macrofauna such as hard-shelled clams. Here, we develop a novel metric for quantifying sediment organization of large surficial beach clasts through sedimentologic and photogrammetric analyses of 37 lower intertidal heterogeneous gravel beaches in western Prince William Sound, Alaska (USA). Grain size, photogrammetric, and Wolman Pebble Count clast-size data from 64, ~1-m2 study plots are combined into a clast-size-independent “Organization Metric” to quantify the degree of organization in the meshed arrangement of larger surficial sediments. This metric was validated through field manipulation experiments and comparisons of adjacent plots characterized by different clast sizes. Application of this metric to subsets of Prince William Sound beaches that underwent differential treatment following the Exxon Valdez oil spill reveals persistent physical effects of artificial beach disturbance even 21 years after the cleanup. This has important implications for beach management (e.g., cleaning or dredging) and for the diverse and productive sedentary megafaunal assemblages that live within these sediments. Overall, this study provides a new approach for quantifying organization of heterogenous coarse sediments in diverse natural settings; in particular, heterogenous gravel beaches

Use of an Observational Coding System with Families of Adolescents: Psychometric Properties among Pediatric and Healthy Populations

Objective: To examine reliability and validity data for the Family Interaction Macro-coding System (FIMS) with adolescents with spina bifida (SB), adolescents with type 1 diabetes mellitus (T1DM), and healthy adolescents and their families.Methods: Sixty-eight families of children with SB, 58 families of adolescents with T1DM, and 68 families in a healthy comparison group completed family interaction tasks and self-report questionnaires. Trained coders rated family interactions using the FIMS.Results: Acceptable interrater and scale reliabilities were obtained for FIMS items and subscales. Observed FIMS parental acceptance, parental behavioral control, parental psychological control, family cohesion, and family conflict scores demonstrated convergent validity with conceptually similar self-report measures.Conclusions: Preliminary evidence supports the use of the FIMS with families of youths with SB and T1DM and healthy youths. Future research on overall family functioning may be enhanced by use of the FIMS

Termite resistance of DMDHEU-treated wood.

Four field trials were conducted with wood modified with dimethyloldihydroxy-ethyleneurea (DMDHEU) in contact with subterranean termites. Trials 1 to 3 were conducted with Coptotermes acinaciformis (Froggatt); 1 and 2 in south-east Queensland, and 3 in northern Queensland, Australia. Trial 4 was conducted in northern Queensland with Mastotermes darwiniensis (Froggatt). Four timber species (Scots pine, beech, Slash pine and Spotted gum) and two levels (1.3 M and 2.3 M) of DMDHEU were used. The tests were validated. DMDHEU successfully prevented damage by C. acinaciformis in south-east Queensland, but not in northern Queensland. It also did not protect the wood against M. darwiniensis. Except for beech in trial 4, DMDHEU led to reduced mass losses caused by termite attack compared to the unmodified feeder stakes. Slash pine (in trials 1 and 3) and Spotted gum (in trial 1) presented low mass losses. Modification of Scots pine was more effective against termite damage than the modification of beech

Following the Sand Grains

When longshore transport systems encounter tidal inlets, complex mechanisms are involved in bypassing sand to downdrift barriers. Here, this process is examined at Plum Island Sound and Essex Inlets, Massachusetts, USA. One major finding from this study is that sand is transferred along the coast—especially at tidal inlets—by parcels, in discrete steps, and over decadal-scale periods. The southerly orientation of the main-ebb channel at Plum Island Sound, coupled with the landward migration of bars from the ebb delta to the central portion of the downdrift Castle Neck barrier island, have formed a beach protuberance. During the constructional phase, sand is sequestered at the protuberance and the spit-end of the barrier becomes sediment starved, leading to shoreline retreat and a broadening of the spit platform at the mouth to Essex Bay (downdrift side of Castle Neck). Storm-induced sand transport from erosion of the spit and across the spit platform is washed into Essex Bay, filling channels and enlarging flood deltas. This study illustrates the pathways and processes of sand transfer along the shoreline of a barrier-island/tidal-inlet system and provides an important example of the processes that future hydrodynamic and sediment-transport modeling should strive to replicate

A review of ventilation opening area terminology

This is the author accepted manuscript. The final version is available from Elsevier via https://doi.org/10.1016/j.enbuild.2016.02.053The design of a natural ventilation strategy requires the establishment of the location and size of a series of purpose provided ventilation openings (PPOs). The success of the design is dependent on knowledge of the aerodynamic performance of the PPOs often described by their geometry (normally an area) and resistance to airflow. The incorrect interpretation of this information can lead inappropriate ventilation strategies and buildings that overheat and have an excessive energy demand. Many definitions of PPO area are used by standards, guidelines, text books, and software tools. Each can be assigned multiple terms and a single term can be assigned to different definitions. There is evidence that this leads to errors in practice. An effective area of a PPO, defined as the product of its discharge coefficient and its free area, is proposed as a standard description because it is unambiguous and its measurement is governed by recognised standards. It is hoped that PPO manufacturers will provide an effective area as standard and that its use will be recognised as best practice. It is intended that these steps will reduce design errors and lead to successful natural ventilation strategies and better building

Ultrasound-triggered antibiotic release from PEEK clips to prevent spinal fusion infection: Initial evaluations.

Despite aggressive peri-operative antibiotic treatments, up to 10% of patients undergoing instrumented spinal surgery develop an infection. Like most implant-associated infections, spinal infections persist through colonization and biofilm formation on spinal instrumentation, which can include metal screws and rods for fixation and an intervertebral cage commonly comprised of polyether ether ketone (PEEK). We have designed a PEEK antibiotic reservoir that would clip to the metal fixation rod and that would achieve slow antibiotic release over several days, followed by a bolus release of antibiotics triggered by ultrasound (US) rupture of a reservoir membrane. We have found using human physiological fluid (synovial fluid), that higher levels (100–500 μg) of vancomycin are required to achieve a marked reduction in adherent bacteria vs. that seen in the common bacterial medium, trypticase soy broth. To achieve these levels of release, we applied a polylactic acid coating to a porous PEEK puck, which exhibited both slow and US-triggered release. This design was further refined to a one-hole or two-hole cylindrical PEEK reservoir that can clip onto a spinal rod for clinical use. Short-term release of high levels of antibiotic (340 ± 168 μg), followed by US-triggered release was measured (7420 ± 2992 μg at 48 h). These levels are sufficient to prevent adhesion of Staphylococcus aureus to implant materials. This study demonstrates the feasibility of an US-mediated antibiotic delivery device, which could be a potent weapon against spinal surgical site infection. Statement of Significance: Spinal surgical sites are prone to bacterial colonization, due to presence of instrumentation, long surgical times, and the surgical creation of a dead space (≥5 cm 3 ) that is filled with wound exudate. Accordingly, it is critical that new approaches are developed to prevent bacterial colonization of spinal implants, especially as neither bulk release systems nor controlled release systems are available for the spine. This new device uses non-invasive ultrasound (US) to trigger bulk release of supra-therapeutic doses of antibiotics from materials commonly used in existing surgical implants. Thus, our new delivery system satisfies this critical need to eradicate surviving bacteria, prevent resistance, and markedly lower spinal infection rates

Data-driven Planning for the Conservation of Grassland Birds in the Central Hardwoods Bird Conservation Region

The Central Hardwoods Joint Venture held two workshops in 2006 to delineate bobwhite focus areas across the Central Hardwoods Bird Conservation Region (BCR) for targeting on-the-ground conservation efforts. From 2008 – 2012, we conducted randomized sets of point counts within counties containing bobwhite focal areas to assess the efficacy of that method for monitoring grassland birds within focal areas, and to assess relationships of conservation practices with bird species occupancy and abundance. We collected data on nine species of Partners in Flight priority species, including northern bobwhite (Colinus virginianus). Land cover types within a 200-m buffer of each point were derived from year National Agricultural Statistics Service data, and information related to the location of conservation practices deemed beneficial to grassland birds was attained from the National Resources Conservation Service. We fit occupancy and abundance models for each species using Akaike’s Information Criterion adjusted for small sample sizes. We then used the model covariates to map predicted abundances of three species, northern bobwhite, eastern meadowlark (Sturnella magna), and Henslow’s sparrow (Ammodramus henslowii) across the BCR. The spatial patterns of predicted abundance varied among species, suggesting that focus areas should be somewhat species-specific. We will use data collected around the nests of each species at Ft. Campbell, a military base straddling the Kentucky-Tennessee border where grassland management has occurred at relatively large scales over more than two decades, to assess the with-in patch structure preferred by each species to develop grazing practices that will result in the desired structure for the species suite

Complex coastal change in response to autogenic basin infilling: An example from a sub-tropical Holocene strandplain

Thick bay-fill sequences that often culminate in strandplain development serve as important sedimentary archives of land-ocean interaction, although distinguishing between internal and external forcings is an ongoing challenge. This study employs sediment cores, ground-penetrating radar surveys, radiocarbon dates, palaeogeographic reconstructions and hydrodynamic modelling to explore the role of autogenic processes - notably a reduction in wave energy in response to coastal embayment infilling - in coastal evolution and shoreline morphodynamics. Following a regional 2 to 4m highstand at ca 58ka, the 75km(2) Tijucas Strandplain in southern Brazil built from fluvial sediments deposited into a semi-enclosed bay. Holocene regressive deposits are underlain by fluvial sands and a Pleistocene transgressive-regressive sequence, and backed by a highstand barrier-island. The strandplain is immediately underlain by 5 to 16m of seaward-thickening, fluvially derived, Holocene-age, basin-fill mud. Several trends are observed from the landward (oldest) to the seaward (youngest) sections of the strandplain: (i) the upper shoreface and foreshore become finer and thinner and shift from sand-dominated to mud-dominated; (ii) beachface slopes decrease from \u3e11 degrees to ca 7 degrees; and (iii) progradation rates increase from 04 to 18myr(-1). Hydrodynamic modelling demonstrates a correlation between progressive shoaling of Tijucas Bay driven by sea-level fall and sediment infilling and a decrease in onshore wave-energy transport from 18 to 4kWm(-1). The combination of allogenic (sediment supply, falling relative sea-level and geology) and autogenic (decrease in wave energy due to bay shoaling) processes drove the development of a regressive system with characteristics that are rare, if not unique, in the Holocene and rock records. These findings demonstrate the complexities in architecture styles of highstand and regressive systems tracts. Furthermore, this article highlights the diverse internal and external processes and feedbacks responsible for the development of these intricate marginal marine sedimentary systems

Treatment recommendations for psoriatic arthritis

Objective: To develop comprehensive recommendations for the treatment of the various clinical manifestations of psoriatic arthritis (PsA) based on evidence obtained from a systematic review of the literature and from consensus opinion. Methods: Formal literature reviews of treatment for the most significant discrete clinical manifestations of PsA (skin and nails, peripheral arthritis, axial disease, dactylitis and enthesitis) were performed and published by members of the Group for Research and Assessment of Psoriasis and Psoriatic Arthritis (GRAPPA). Treatment recommendations were drafted for each of the clinical manifestations by rheumatologists, dermatologists and PsA patients based on the literature reviews and consensus opinion. The level of agreement for the individual treatment recommendations among GRAPPA members was assessed with an online questionnaire. Results: Treatment recommendations were developed for peripheral arthritis, axial disease, psoriasis, nail disease, dactylitis and enthesitis in the setting of PsA. In rotal, 19 recommendations were drafted, and over 80% agreement was obtained on 16 of them. In addition, a grid that factors disease severity into each of the different disease manifestations was developed to help the clinician with treatment decisions for the individual patient from an evidenced-based perspective. Conclusions: Treatment recommendations for the cardinal physical manifestations of PsA were developed based on a literature review and consensus between rheumatologists and dermatologists. In addition, a grid was established to assist in therapeutic reasoning and decision making for individual patients. It is anticipated that periodic updates will take place using this framework as new data become available