Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK.

Short-patch repair of DNA single-strand breaks and gaps (SSB) is coordinated by XRCC1, a scaffold protein that recruits the DNA polymerase and DNA ligase required for filling and sealing the damaged strand. XRCC1 can also recruit end-processing enzymes, such as PNK (polynucleotide kinase 3'-phosphatase), Aprataxin and APLF (aprataxin/PNK-like factor), which ensure the availability of a free 3'-hydroxyl on one side of the gap, and a 5'-phosphate group on the other, for the polymerase and ligase reactions respectively. PNK binds to a phosphorylated segment of XRCC1 (between its two C-terminal BRCT domains) via its Forkhead-associated (FHA) domain. We show here, contrary to previous studies, that the FHA domain of PNK binds specifically, and with high affinity to a multiply phosphorylated motif in XRCC1 containing a pSer-pThr dipeptide, and forms a 2:1 PNK:XRCC1 complex. The high-resolution crystal structure of a PNK-FHA-XRCC1 phosphopeptide complex reveals the basis for this unusual bis-phosphopeptide recognition, which is probably a common feature of the known XRCC1-associating end-processing enzymes

Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

Active flow control systems architectures for civil transport aircraft

Copyright @ 2010 American Institute of Aeronautics and AstronauticsThis paper considers the effect of choice of actuator technology and associated power systems architecture on the mass cost and power consumption of implementing active flow control systems on civil transport aircraft. The research method is based on the use of a mass model that includes a mass due to systems hardware and a mass due to the system energy usage. An Airbus A320 aircraft wing is used as a case-study application. The mass model parameters are based on first-principle physical analysis of electric and pneumatic power systems combined with empirical data on system hardware from existing equipment suppliers. Flow control methods include direct fluidic, electromechanical-fluidic, and electrofluidic actuator technologies. The mass cost of electrical power distribution is shown to be considerably less than that for pneumatic systems; however, this advantage is reduced by the requirement for relatively heavy electrical power management and conversion systems. A tradeoff exists between system power efficiency and the system hardware mass required to achieve this efficiency. For short-duration operation the flow control solution is driven toward lighter but less power-efficient systems, whereas for long-duration operation there is benefit in considering heavier but more efficient systems. It is estimated that a practical electromechanical-fluidic system for flow separation control may have a mass up to 40% of the slat mass for a leading-edge application and 5% of flap mass for a trailing-edge application.This work is funded by the Sixth European Union Framework Programme as part of the AVERT project (Contract No. AST5-CT-2006-030914

A Novel 14C-Postlabeling Assay Using Accelerator Mass Spectrometry For the Detection of O6-Methyldeoxyguanosine Adducts

Accelerator mass spectrometry (AMS) is currently one of the most sensitive methods available for the trace detection of DNA adducts and is particularly valuable for measuring adducts in humans or animal models. However, the standard approach requires administration of a radiolabeled compound. As an alternative, we have developed a preliminary {sup 14}C-postlabeling assay for detection of the highly mutagenic O{sup 6}-MedG, by AMS. Procedures were developed for derivatizing O{sup 6}-MedG using unlabeled acetic anhydride. Using conventional LC-MS analysis, the limit of detection for the major product, triacetylated O{sup 6}-MedG, was 10 fmoles. On reaction with {sup 14}C-acetic anhydride, using a specially designed enclosed system, the predominant product was {sup 14}C-di-acetyl O{sup 6}-MedG. This change in reaction profile was due to a modification of the reaction procedure, introduced as a necessary safety precaution. The limit of detection for {sup 14}C-diacetyl O{sup 6}-MedG by AMS was determined as 79 attomoles, {approx}18,000 fold lower than that achievable by LSC. Although the assay has so far only been carried out with labeled standards, the degree of sensitivity obtained illustrates the potential of this assay for measuring O{sup 6}-MedG levels in humans

Factors Associated with Access to Immunotherapy and Its Impact on Survival in Mucosal Melanoma

Mucosal melanoma is rare, comprising only 1.4% of all melanomas in the United States. Yet it is associated with a worse prognosis compared to cutaneous melanoma due to aggressive biology and advanced stage at diagnosis with a reported 5-year survival rate of less than 30%. Although there are no established guidelines for the treatment of mucosal melanoma, immunotherapy has been increasingly used for the management of advanced mucosal melanoma

The mTOR regulated RNA-binding protein LARP1 requires PABPC1 for guided mRNA interaction.

The mammalian target of rapamycin (mTOR) is a critical regulator of cell growth, integrating multiple signalling cues and pathways. Key among the downstream activities of mTOR is the control of the protein synthesis machinery. This is achieved, in part, via the co-ordinated regulation of mRNAs that contain a terminal oligopyrimidine tract (TOP) at their 5'ends, although the mechanisms by which this occurs downstream of mTOR signalling are still unclear. We used RNA-binding protein (RBP) capture to identify changes in the protein-RNA interaction landscape following mTOR inhibition. Upon mTOR inhibition, the binding of LARP1 to a number of mRNAs, including TOP-containing mRNAs, increased. Importantly, non-TOP-containing mRNAs bound by LARP1 are in a translationally-repressed state, even under control conditions. The mRNA interactome of the LARP1-associated protein PABPC1 was found to have a high degree of overlap with that of LARP1 and our data show that PABPC1 is required for the association of LARP1 with its specific mRNA targets. Finally, we demonstrate that mRNAs, including those encoding proteins critical for cell growth and survival, are translationally repressed when bound by both LARP1 and PABPC1

Identification of Five Developmental Processes during Chondrogenic Differentiation of Embryonic Stem Cells

Chondrogenesis is the complex process that leads to the establishment of cartilage and bone formation. Due to their ability to differentiate in vitro and mimic development, embryonic stem cells (ESCs) show great potential for investigating developmental processes. In this study, we used chondrogenic differentiation of ESCs as a model to analyze morphogenetic events during chondrogenesis.ESCs were differentiated into the chondrocyte lineage, forming small cartilaginous aggregates in suspension. Differentiated ESCs showed that chondrogenesis was typically characterized by five overlapping stages. During the first stage, cell condensation and aggregate formation was observed. The second stage was characterized by differentiation into chondrocytes and fibril scaffold formation within spherical aggregates. Deposition of cartilaginous extracellular matrix and cartilage formation were hallmarks of the third stage. Apoptosis of chondrocytes, hypertrophy and/or degradation of cartilage occurred during the fourth stage. Finally, during the fifth stage, bone replacement with membranous calcified tissues took place.We demonstrate that ESCs show the chondrogenic differentiation pathway from the pluripotent stem cell to terminal skeletogenesis through these five stages in vitro. During each stage, morphological changes acquired in preceding stages played an important role in further development as a scaffold or template in subsequent stages. The study of chondrogenesis via ESC differentiation may be informative to our further understanding of skeletal growth and regeneration

Identifying an essential package for school-age child health: economic analysis

This chapter presents the investment case for providing an integrated package of essential health services for children attending primary schools in low- and middle- income countries (LMICs). In doing so, it builds on chapter 20 in this volume (Bundy, Schultz, and others 2017), which presents a range of relevant health services for the school- age population and the economic rationale for adminis- tering them through educational systems. This chapter identifies a package of essential health services that low- and middle-income countries (LMICs) can aspire to implement through the primary and secondary school platforms. In addition, the chapter considers the design of such programs, including targeting strategies. Upper- middle-income countries and high-income countries (HICs) typically aim to implement such interventions on a larger scale and to include and promote additional health services relevant to their populations. Studies have docu- mented the contribution of school health interventions to a range of child health and educational outcomes, partic- ularly in the United States (Durlak and others 2011; Murray and others 2007; Shackleton and others 2016). Health services selected for the essential package are those that have demonstrated benefits and relevance for children in LMICs. The estimated costs of implementation are drawn from the academic literature. The concept of a package of essential school health interventions and its justification through a cost-benefit perspective was pioneered by Jamison and Leslie (1990). As chapter 20 notes, health services for school-age children can promote educational outcomes, including access, attendance, and academic achievement, by mitigat- ing earlier nutrition and health deprivations and by addressing current infections and nutritional deficiencies (Bundy, Schultz, and others 2017). This age group is partic- ularly at risk for parasitic helminth infections (Jukes, Drake, and Bundy 2008), and malaria has become prevalent in school-age populations as control for younger children delays the acquisition of immunity from early childhood to school age (Brooker and others 2017). Furthermore, school health services are commonly viewed as a means for build- ing and reinforcing healthy habits to lower the risk of non- communicable disease later in life (Bundy 2011). This chapter focuses on packages and programs to reach school-age children, while the previous chapter, chapter 24 (Horton and Black 2017), focuses on early childhood inter- ventions, and the next chapter, chapter 26 (Horton and others 2017), focuses on adolescent interventions. These packages are all part of the same continuum of care from age 5 years to early adulthood, as discussed in chapter 1 (Bundy, de Silva, and others 2017). A particular emphasis of the economic rationale for targeting school-age children is to promote their health and education while they are in the process of learning; many of the interventions that are part of the package have been shown to yield substantial benefits in educational outcomes (Bundy 2011; Jukes, Drake, and Bundy 2008). They might be viewed as health interventions that leverage the investment in education. Schools are an effective platform through which to deliver the essential package of health and nutrition ser- vices (Bundy, Schultz, and others 2017). Primary enroll- ment and attendance rates increased substantially during the Millennium Development Goals era, making schools a delivery platform with the potential to reach large num- bers of children equitably. Furthermore, unlike health centers, almost every community has a primary school, and teachers can be trained to deliver simple health inter- ventions, resulting in the potential for high returns for relatively low costs by using the existing infrastructure. This chapter identifies a core set of interventions for children ages 5–14 years that can be delivered effectively through schools. It then simulates the returns to health and education and benchmarks them against the costs of the intervention, drawing on published estimates. The invest- ment returns illustrate the scale of returns provided by school-based health interventions, highlighting the value of integrated health services and the parameters driving costs, benefits, and value for money (the ratio of benefits to costs). Countries seeking to introduce such a package need to undertake context-specific analyses of critical needs to ensure that the package responds to the specific local needs

Nutrition issues in Codex: health claims, nutrient reference values and WTO agreements: a conference report

BACKGROUND: Codex documents may be used as educational and consensus materials for member governments. Also, the WTO SPS Agreement recognizes Codex as the presumptive international authority on food issues. Nutrient bioavailability is a critical factor in determining the ability of nutrients to provide beneficial effects. Bioavailability also influences the quantitative dietary requirements that are the basis of nutrient intake recommendations and NRVs. HEALTH CLAIMS: Codex, EFSA and some national regulatory authorities have established guidelines or regulations that will permit several types of health claims. The scientific basis for claims has been established by the US FDA and EFSA, but not yet by Codex. Evidence-based nutrition differs from evidence-based medicine, but the differences are only recently gaining recognition. Health claims on foods may provide useful information to consumers, but many will interpret the information to mean that they can rely upon the food or nutrient to eliminate a disease risk. NUTRIENT REFERENCE VALUES: NRVs are designed to provide a quantitative basis for comparing the nutritive values of foods, helping to illustrate how specific foods fit into the overall diet. The INL-98 and the mean of adult male and female values provide NRVs that are sufficient when used as targets for individual intakes by most adults. WORLD TRADE ORGANIZATION AGREEMENTS: WTO recognizes Codex as the primary international authority on food issues. Current regulatory schemes based on recommended dietary allowances are trade restrictive. A substantial number of decisions by the EFSA could lead to violation of WTO agreements

Improving educational achievement and anaemia of school children: design of a cluster randomised trial of school-based malaria prevention and enhanced literacy instruction in Kenya

BACKGROUND: Improving the health of school-aged children can yield substantial benefits for cognitive development and educational achievement. However, there is limited experimental evidence on the benefits of school-based malaria prevention or how health interventions interact with other efforts to improve education quality. This study aims to evaluate the impact of school-based malaria prevention and enhanced literacy instruction on the health and educational achievement of school children in Kenya. DESIGN: A factorial, cluster randomised trial is being implemented in 101 government primary schools on the coast of Kenya. The interventions are (i) intermittent screening and treatment of malaria in schools by public health workers and (ii) training workshops and support for teachers to promote explicit and systematic literacy instruction. Schools are randomised to one of four groups: receiving either (i) the malaria intervention alone; (ii) the literacy intervention alone; (iii) both interventions combined; or (iv) control group where neither intervention is implemented. Children from classes 1 and 5 are randomly selected and followed up for 24 months. The primary outcomes are educational achievement and anaemia, the hypothesised mediating variables through which education is affected. Secondary outcomes include malaria parasitaemia, school attendance and school performance. A nested process evaluation, using semi-structured interviews, focus group discussion and a stakeholder analysis will investigate the community acceptability, feasibility and cost-effectiveness of the interventions. DISCUSSION: Across Africa, governments are committed to improve health and education of school-aged children, but seek clear policy and technical guidance as to the optimal approach to address malaria and improved literacy. This evaluation will be one of the first to simultaneously evaluate the impact of health and education interventions in the improvement of educational achievement. Reflection is made on the practical issues encountered in conducting research in schools in Africa. TRIAL REGISTRATION: National Institutes of Health NCT00878007