Base Orientation of Second DNA in RecA·DNA Filaments. Analysis by combination of linear dichroism and small angle neutron scattering in flow-oriented solution

To gain insight into the mechanism of pairing two complementary DNA strands by the RecA protein, we have determined the nucleobase orientation of the first and the second bound DNA strands in the RecA·DNA filament by combined measurements of linear dichroism and small angle neutron scattering on flow-oriented samples. An etheno-modified DNA, poly(depsilon A) was adapted as the first DNA and an oligo(dT) as the second DNA, making it possible to distinguish between the linear dichroism signals of the two DNA strands. The results indicate that binding of the second DNA does not alter the nucleobase orientation of the first bound strand and that the bases of the second DNA are almost coplanar to the bases of the first strand although somewhat more tilted (60 degrees relative to the fiber axis compared with 70 degrees for the first DNA strand). Similar results were obtained for the RecA·DNA complex formed with unmodified poly(dA) and oligo(dT). An almost coplanar orientation of nucleobases of two DNA strands in a RecA-DNA filament would facilitate scanning for, and recognition of, complementary base sequences. The slight deviation from co-planarity could increase the free energy of the duplex to facilitate dissociation in case of mismatching base sequences

A Room-Temperature High-Conductivity Metal Printing Paradigm with Visible-Light Projection Lithography

Fabricating electronic devices require integrating metallic conductors and polymeric insulators in complex structures. Current metal-patterning methods such as evaporation and laser sintering require vacuum, multistep processes, and high temperature during sintering or postannealing to achieve desirable electrical conductivity, which damages low-temperature polymer substrates. Here reports a facile ecofriendly room-temperature metal printing paradigm using visible-light projection lithography. With a particle-free reactive silver ink, photoinduced redox reaction occurs to form metallic silver within designed illuminated regions through a digital mask on substrate with insignificant temperature change (<4 °C). The patterns exhibit remarkably high conductivity achievable at room temperature (2.4 × 107 S m−1, ≈40% of bulk silver conductivity) after simple room-temperature chemical annealing for 1–2 s. The finest silver trace produced reaches 15 µm. Neither extra thermal energy input nor physical mask is required for the entire fabrication process. Metal patterns were printed on various substrates, including polyethylene terephthalate, polydimethylsiloxane, polyimide, Scotch tape, print paper, Si wafer, glass coverslip, and polystyrene. By changing inks, this paradigm can be extended to print various metals and metal–polymer hybrid structures. This method greatly simplifies the metal-patterning process and expands printability and substrate materials, showing huge potential in fabricating microelectronics with one system

Sex Differences in a Cross Sectional Study of Age-related Hearing Loss in Korean

ObjectivesThe purpose of this study was to obtain sex- and age-specific reference level for hearing threshold of normal aging in Korean and to determine if the rate of change in pure-tone hearing thresholds differed by sex.MethodsSubjects were clients who visited the Health Promotion Center, Daegu Fatima Hospital, Daegu, Korea, from January 2004 to September 2005. Pure-tone audiometric measures were obtained from 3,470 subjects who also completed a hearing questionnaire. The slope of a linear regression was used to estimate the rate of change in pure-tone thresholds at 0.25 to 8 kHz for each ear in 214 men and 902 women without past history of otorrhea, usage of ototoxic drugs, head injury, job in noisy environment, and military service.ResultsHearing thresholds were elevated with age in all test frequencies. Significant sex differences were found in pure-tone thresholds at 4 and 8 kHz after adjusting for age using analysis of covariance. In those high frequencies, hearing was worse in men than in women. The average rate of change in threshold was 0.28 and 0.24 dB per year at 0.25 kHz, increasing gradually to 1.27 and 1.05 dB per year at 8 kHz for men and women, respectively. Men had significantly faster rates of threshold increase at 4 and 8 kHz than women.ConclusionThese cross-sectional measures of hearing levels and rate of threshold increases at 4 and 8 kHz showed significant sex differences in Korean men and women with little evidence of noise-induced hearing loss

A randomised controlled trial comparing graded exercise treatment and usual physiotherapy for patients with non-specific neck pain (the GET UP neck pain trial).

Evidence supports exercise-based interventions for the management of neck pain, however there is little evidence of its superiority over usual physiotherapy. This study investigated the effectiveness of a group neck and upper limb exercise programme (GET) compared with usual physiotherapy (UP) for patients with non-specific neck pain. A total of 151 adult patients were randomised to either GET or UP. The primary measure was the Northwick Park Neck pain Questionnaire (NPQ) score at six weeks, six months and 12 months. Mixed modelling identified no difference in neck pain and function between patients receiving GET and those receiving UP at any follow-up time point. Both interventions resulted in modest significant and clinically important improvements on the NPQ score with a change score of around 9% between baseline and 12 months. Both GET and UP are appropriate clinical interventions for patients with non-specific neck pain, however preferences for treatment and targeted strategies to address barriers to adherence may need to be considered in order to maximise the effectiveness of these approaches

Local and global modes of drug action in biochemical networks

It becomes increasingly accepted that a shift is needed from the traditional target-based approach of drug development to an integrated perspective of drug action in biochemical systems. We here present an integrative analysis of the interactions between drugs and metabolism based on the concept of drug scope. The drug scope represents the set of metabolic compounds and reactions that are potentially affected by a drug. We constructed and analyzed the scopes of all US approved drugs having metabolic targets. Our analysis shows that the distribution of drug scopes is highly uneven, and that drugs can be classified into several categories based on their scopes. Some of them have small scopes corresponding to localized action, while others have large scopes corresponding to potential large-scale systemic action. These groups are well conserved throughout different topologies of the underlying metabolic network. They can furthermore be associated to specific drug therapeutic properties

Replication and shedding kinetics of infectious hematopoietic necrosis virus in juvenile rainbow trout

Viral replication and shedding are key components of transmission and fitness, the kinetics of which are heavily dependent on virus, host, and environmental factors. To date, no studies have quantified the shedding kinetics of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss), or how they are associated with replication, making it difficult to ascertain the transmission dynamics of this pathogen of high agricultural and conservation importance. Here, the replication and shedding kinetics of two M genogroup IHNV genotypes were examined in their naturally co-evolved rainbow trout host. Within host virus replication began rapidly, approaching maximum values by day 3 post-infection, after which viral load was maintained or gradually dropped through day 7. Host innate immune response measured as stimulation of Mx-1 gene expression generally followed within host viral loads. Shedding also began very quickly and peaked within 2 days, defining a generally uniform early peak period of shedding from 1 to 4 days after exposure to virus. This was followed by a post-peak period where shedding declined, such that the majority of fish were no longer shedding by day 12 post-infection. Despite similar kinetics, the average shedding rate over the course of infection was significantly lower in mixed compared to single genotype infections, suggesting a competition effect, however, this did not significantly impact the total amount of virus shed. The data also indicated that the duration of shedding, rather than peak amount of virus shed, was correlated with fish mortality. Generally, the majority of virus produced during infection appeared to be shed into the environment rather than maintained in the host, although there was more retention of within host virus during the post-peak period. Viral virulence was correlated with shedding, such that the more virulent of the two genotypes shed more total virus. This fundamental understanding of IHNV shedding kinetics and variation at the individual fish level could assist with management decisions about how to respond to disease outbreaks when they occur. (C) 2016 Elsevier B.V. All rights reserved

Mining metabolites: extracting the yeast metabolome from the literature

Text mining methods have added considerably to our capacity to extract biological knowledge from the literature. Recently the field of systems biology has begun to model and simulate metabolic networks, requiring knowledge of the set of molecules involved. While genomics and proteomics technologies are able to supply the macromolecular parts list, the metabolites are less easily assembled. Most metabolites are known and reported through the scientific literature, rather than through large-scale experimental surveys. Thus it is important to recover them from the literature. Here we present a novel tool to automatically identify metabolite names in the literature, and associate structures where possible, to define the reported yeast metabolome. With ten-fold cross validation on a manually annotated corpus, our recognition tool generates an f-score of 78.49 (precision of 83.02) and demonstrates greater suitability in identifying metabolite names than other existing recognition tools for general chemical molecules. The metabolite recognition tool has been applied to the literature covering an important model organism, the yeast Saccharomyces cerevisiae, to define its reported metabolome. By coupling to ChemSpider, a major chemical database, we have identified structures for much of the reported metabolome and, where structure identification fails, been able to suggest extensions to ChemSpider. Our manually annotated gold-standard data on 296 abstracts are available as supplementary materials. Metabolite names and, where appropriate, structures are also available as supplementary materials

The Clinical Outcome of FLAG Chemotherapy without Idarubicin in Patients with Relapsed or Refractory Acute Myeloid Leukemia

A refractory and resistant disease to conventional induction chemotherapy and relapsed disease are considered as the most important adverse prognostic factors for acute myeloid leukemia (AML). Sixty-one patients (median age, 33.6 yr) with relapsed or refractory AML were treated with the FLAG regimen that consisted of fludarabine (30 mg/m2, days 1-5), cytarabine (2.0 g/m2, days 1-5) and granulocyte colony-stimulating factor. Of the treated patients 29 patients (47.5%) achieved complete remission (CR). Higher CR rates were observed for patients with a first or second relapse as compared to patients with a primary refractory response or relapse after stem cell transplantation (HSCT). There was a significant difference in the response rates according to the duration of leukemia-free survival (pre-LFS) before chemotherapy (P=0.05). The recovery time of both neutrophils (≥500/µL) and platelets (≥20,000/µL) required a median of 21 and 18 days, respectively. Treatment-related mortality (TRM) occurred in seven patients (11.4%), of which 71.4% of TRM was caused by an invasive aspergillosis infection. After achieving CR, 18 patients underwent consolidation chemotherapy and six patients underwent allogeneic HSCT. In conclusion, FLAG chemotherapy without idarubicin is a relatively effective and well-tolerated regimen for relapsed or refractory AML and the use of FLAG chemotherapy has allowed intensive post-remission therapy including HSCT

Listening In on the Past: What Can Otolith δ18O Values Really Tell Us about the Environmental History of Fishes?

Oxygen isotope ratios from fish otoliths are used to discriminate marine stocks and reconstruct past climate, assuming that variations in otolith δ18O values closely reflect differences in temperature history of fish when accounting for salinity induced variability in water δ18O. To investigate this, we exploited the environmental and migratory data gathered from a decade using archival tags to study the behaviour of adult plaice (Pleuronectes platessa L.) in the North Sea. Based on the tag-derived monthly distributions of the fish and corresponding temperature and salinity estimates modelled across three consecutive years, we first predicted annual otolith δ18O values for three geographically discrete offshore sub-stocks, using three alternative plausible scenarios for otolith growth. Comparison of predicted vs. measured annual δ18O values demonstrated >96% correct prediction of sub-stock membership, irrespective of the otolith growth scenario. Pronounced inter-stock differences in δ18O values, notably in summer, provide a robust marker for reconstructing broad-scale plaice distribution in the North Sea. However, although largely congruent, measured and predicted annual δ18O values of did not fully match. Small, but consistent, offsets were also observed between individual high-resolution otolith δ18O values measured during tag recording time and corresponding δ18O predictions using concomitant tag-recorded temperatures and location-specific salinity estimates. The nature of the shifts differed among sub-stocks, suggesting specific vital effects linked to variation in physiological response to temperature. Therefore, although otolith δ18O in free-ranging fish largely reflects environmental temperature and salinity, we counsel prudence when interpreting otolith δ18O data for stock discrimination or temperature reconstruction until the mechanisms underpinning otolith δ18O signature acquisition, and associated variation, are clarified