A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, genome-genome alignment, and annotation. For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered phylogenies from multiple datasets that were consistent with previous conflicting estimates of the relationships among mammals. SISRS is open source and freely available at https://github.com/rachelss/SISRS.Comment: 12 pages plus36 figures, 1 supplementary table, 3 supplementary figure

EVALUATION OF THE 2006/7 AGRICULTURAL INPUT SUBSIDY PROGRAMME, MALAWI. FINAL REPORT

This report evaluates the 2006/7 Malawi Government Agricultural Input Subsidy Programme (AISP). The main objective of the evaluation is to assess the impact and implementation of the AISP in order to provide lessons for future interventions in growth and social protection. The evaluation combined qualitative and quantitative methods of data collection and analysis. Quantitative data were collected through a national survey in 2007 of 2,491 households who were previously interviewed in the 2004/05 Integrated Household Survey, a survey of retail shops selling inputs in six districts and data on stocks and sales from manufacturers, large-scale importers and dealers of fertilizers and seeds. The quantitative data was triangulated by qualitative data from focus group discussions with smallholder farmers in 12 districts, and key informant interviews with government staff, input distributors and beneficiary and non-beneficiary households. The analysis is based on descriptive statistics, econometric modelling and livelihood and rural economy modelling. An Interim Report in March 2007 provides fuller details of the implementation of the programme.Agribusiness, Agricultural and Food Policy, Community/Rural/Urban Development, Food Consumption/Nutrition/Food Safety, Food Security and Poverty, Productivity Analysis,

Enzymatic Characterization of Leishmania major Phosphatidylethanolamine Methyltransferases LmjPEM1 and LmjPEM2

Phosphatidylcholine (PC) is the most abundant phospholipid in the membranes of the human parasite Leishmania. It is synthesized via two metabolic routes, the de novo pathway that starts with the uptake of choline, and the threefold methylation of phosphatidylethanolamine. Choline was shown to be dispensable for Leishmania; thus, the methylation pathway likely represents the primary route for PC production. Here, we have identified and characterized two phosphatidylethanolamine methyltransferases, LmjPEM1and LmjPEM2. Both enzymes are expressed in promastigotes as well as in the vertebrate form amastigotes, suggesting that these methyltransferases are important for the development of the parasite throughout its life cycle. Heterologous expression in yeast has demonstrated that LmjPEM1 and LmjPEM2 complement the choline auxotrophy phenotype of a yeast double null mutant lacking phosphatidylethanolamine methyltransferase activity. LmjPEM1 catalyzes the first, and to a lesser extent, the second methylation reaction. In contrast, LmjPEM2 has the capacity to add the second and third methyl group onto phosphatidylethanolamine to yield (lyso)PC; it can also add the first methyl group, albeit with very low efficiency

Georgia Library Association - Technical Services Interest Group

Published in Georgia Library Quarterl

Manipulating adenovirus hexon hypervariable loops dictates immune neutralisation and coagulation factor X-dependent cell interaction in vitro and in vivo

Adenoviruses are common pathogens, mostly targeting ocular, gastrointestinal and respiratory cells, but in some cases infection disseminates, presenting in severe clinical outcomes. Upon dissemination and contact with blood, coagulation factor X (FX) interacts directly with the adenovirus type 5 (Ad5) hexon. FX can act as a bridge to bind heparan sulphate proteoglycans, leading to substantial Ad5 hepatocyte uptake. FX “coating” also protects the virus from host IgM and complement-mediated neutralisation. However, the contribution of FX in determining Ad liver transduction whilst simultaneously shielding the virus from immune attack remains unclear. In this study, we demonstrate that the FX protection mechanism is not conserved amongst Ad types, and identify the hexon hypervariable regions (HVR) of Ad5 as the capsid proteins targeted by this host defense pathway. Using genetic and pharmacological approaches, we manipulate Ad5 HVR interactions to interrogate the interplay between viral cell transduction and immune neutralisation. We show that FX and inhibitory serum components can co-compete and virus neutralisation is influenced by both the location and extent of modifications to the Ad5 HVRs. We engineered Ad5-derived HVRs into the rare, native non FX-binding Ad26 to create Ad26.HVR5C. This enabled the virus to interact with FX at high affinity, as quantified by surface plasmon resonance, FX-mediated cell binding and transduction assays. Concomitantly, Ad26.HVR5C was also sensitised to immune attack in the absence of FX, a direct consequence of the engineered HVRs from Ad5. In both immune competent and deficient animals, Ad26.HVR5C hepatic gene transfer was mediated by FX following intravenous delivery. This study gives mechanistic insight into the pivotal role of the Ad5 HVRs in conferring sensitivity to virus neutralisation by IgM and classical complement-mediated attack. Furthermore, through this gain-of-function approach we demonstrate the dual functionality of FX in protecting Ad26.HVR5C against innate immune factors whilst determining liver targeting

Interviewer: 'Are women and girls ever responsible for the domestic violence they encounter?' Student: 'No, well, unless they did something really, really bad …'

Research shows the ‘gendered nature’ of domestic violence, with Women’s Aid (a UK-based charity) estimating that 1 in 4 women are affected (2014). This paper reports on a project - funded by Comic Relief, completed by Nottinghamshire Domestic Violence Forum (now known as Equation) and evaluated by Nottingham Trent University. The project adopts a Whole School Approach in seeking to prevent domestic violence. Students at three secondary schools attended between one and five blocks of work, and special events. There is evidence of positive developments - with young people showing understanding of domestic violence as well as the margins between healthy and unhealthy relationships. However, not all students could reply ‘never’ to the question of ‘are women and girls to blame for the domestic violence they experience?’, remarking that if the woman had done something ‘really, really bad’ then violence might be justified. We argue that young people’s uncertainties need to be situated within the gender-unequal socio-contexts of contemporary society, and further call for a WSA to domestic violence prevention to be a compulsory part of the UK national curriculum

Is there some degree of unmet need in primary care?: analysis of a patient cohort accessing a new out of hours units

Background The increasing demands on Emergency Departments has led to considerable rhetoric on the availability of general practitioner (GP) appointments of which one perceived solution is to offer more out of hours (OOH) care. In England, OOH healthcare provision is regarded as urgent care only and offered as a mixture of telephone triage, drop-in centres, emergency departments (ED), and triaged appointments. This evaluation describes the patients who used new OOH appointments offered through the UK Prime Minister’s Challenge Fund scheme which was intended to extend patient access to primary care. The aim of this paper is to report on the demographic profile of attendees and to offer some indication of the impact on ED. Methods The study used de-identifiable cohort data from 14 months of OOH appointments offered in 4 units in Sheffield and the responses to the standard NHS patient-opinion questionnaire modified for this programme. Descriptive analysis of the appointment data was conducted. Multivariate logistic regression analysis of the survey data examined the characteristics of the patients who would have gone to the Emergency Department (ED) had the OOH appointments not been available. Results There were 24,448 appointments for 19,701 different patients resulting in 29,629 service outcomes (i.e. clinical advice, prescription issued). Six percent of appointments were deemed urgent and two-thirds were non-urgent but needed follow-up. Less than 1% of appointments were judged inappropriate by the consulting GP. The non-attendance rate was 1.8%. Females accounted for 60% of all attendances and 70% in the under 35 age group. The patients from the poorest 5th of the population used nearly 40% of the appointments. The patient survey found OOH appointments were extremely popular - 93% selecting ‘extremely likely’ or ‘likely’ to recommend the service. Regression analysis of patient opinion survey data on whether ED would have been an alternative to the OOH service found that males, young children, people of Asian heritage and the most deprived were more likely to have gone to ED without this service. Conclusion Similar to the published literature, the users of the OOH service were substantially different from in-hours service users; consisting of young adults and children as opposed to the elderly. The findings of this analysis also support the idea that there may be unmet need in the poorest fifth of the population. Future analysis of access to primary care services needs to incorporate patient perceptions and not just statistical data

The concluding chapter: Recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification

© 2020. Close scrutiny of Goodenia (Goodeniaceae) and allied genera in the \u27Core Goodeniaceae\u27 over recent years has clarified our understanding of this captivating group. While expanded sampling, sequencing of multiple regions, and a genome skimming reinforced backbone clearly supported Goodenia s.l. as monophyletic and distinct from Scaevola and Coopernookia, there appears to be no synapomorphic characters that uniquely characterise this morphologically diverse clade. Within Goodenia s.l., there is strong support from nuclear, chloroplast and mitochondrial data for three major clades (Goodenia Clades A, B and C) and various subclades, which lead to earlier suggestions for the possible recognition of these as distinct genera. Through ongoing work, it has become evident that this is impractical, as conflict remains within the most recently diverged Clade C, likely due to recent radiation and incomplete lineage sorting. In light of this, it is proposed that a combination of morphological characters is used to circumscribe an expanded Goodenia that now includes Velleia, Verreauxia, Selliera and Pentaptilon, and an updated infrageneric classification is proposed to accommodate monophyletic subclades. A total of twenty-five new combinations, three reinstatements, and seven new names are published herein including Goodenia subg. Monochila sect. Monochila subsect. Infracta K.A. Sheph. subsect. nov. Also, a type is designated for Goodenia subg. Porphyranthus sect. Ebracteolatae (K. Krause) K.A. Sheph. comb. et stat. nov., and lectotypes or secondstep lectotypes are designated for a further three names

Putting health workers at the centre of health system investments in COVID-19 and beyond

The COVID-19 pandemic highlights the implications of chronic underinvestment in health workforce development, particularly in resource-constrained health systems. Inadequate health workforce diversity, insufficient training and remuneration, and limited support and protection reduce health system capacity to equitably maintain health service delivery while meeting urgent health emergency demands. Applying the Health Worker Life Cycle Approach provides a useful conceptual framework that adapts a health labour market approach to outline key areas and recommendations for health workforce investment-building, managing and optimising-to systematically meet the needs of health workers and the systems they support. It also emphasises the importance of protecting the workforce as a cross-cutting investment, which is especially important in a health crisis like COVID-19. While the global pandemic has spurred intermittent health workforce investments required to immediately respond to COVID-19, applying this 'lifecycle approach' to guide policy implementation and financing interventions is critical to centering health workers as stewards of health systems, thus strengthening resilience to public health threats, sustainably responding to community needs and providing more equitable, patient-centred care