Reviews

Judith Jeffcoate, Multimedia in Practice ‐Technology and Applications, BCS Practitioner Series, Prentice‐Hall International, 1995. ISBN: 0–13–123324–6. £24.95

Predicting the impact of promoter variability on regulatory outputs

The increased availability of whole genome sequences calls for quantitative models of global gene expression, yet predicting gene expression patterns directly from genome sequence remains a challenge. We examine the contributions of an individual regulator, the ferrous iron-responsive regulatory element, BqsR, on global patterns of gene expression in Pseudomonas aeruginosa. The position weight matrix (PWM) derived for BqsR uncovered hundreds of likely binding sites throughout the genome. Only a subset of these potential binding sites had a regulatory consequence, suggesting that BqsR/DNA interactions were not captured within the PWM or that the broader regulatory context at each promoter played a greater role in setting promoter outputs. The architecture of the BqsR operator was systematically varied to understand how binding site parameters influence expression. We found that BqsR operator affinity was predicted by the PWM well. At many promoters the surrounding regulatory context, including overlapping operators of BqsR or the presence of RhlR binding sites, were influential in setting promoter outputs. These results indicate more comprehensive models that include local regulatory contexts are needed to develop a predictive understanding of global regulatory outputs

A House with Two Rooms: Final Report of the Truth and Reconciliation Commission of Liberia Diaspora Project

From 1979 to 2003, more than 1.5 million Liberians were forced from their homes to escape from the violence and destruction of a protracted civil conflict. Hundreds of thousands became refugees and many eventually made their way to countries of resettlement including the United States and the United Kingdom. Most of their stories have never been told. This report on the experience of the Liberian diaspora, entitled A House with Two Rooms, is the culmination of three years of work in the United States, the United Kingdom and Buduburam Refugee Settlement in Ghana. The report has been submitted to the Liberian Truth and Reconciliation Commission (TRC), the body charged by the Liberian government with determining the facts of the human rights violations that occurred during the civil war. The Liberian TRC officially completed its mandate June 30, 2009.https://open.mitchellhamline.edu/dri_press/1006/thumbnail.jp

Effects of transmission reduction by insecticide-treated bed nets (ITNs) on parasite genetics population structure: I. The genetic diversity of Plasmodium falciparum parasites by microsatellite markers in western Kenya

<p>Abstract</p> <p>Background</p> <p>Insecticide-treated bed nets (ITNs) reduce malaria transmission and are an important prevention tool. However, there are still information gaps on how the reduction in malaria transmission by ITNs affects parasite genetics population structure. This study examined the relationship between transmission reduction from ITN use and the population genetic diversity of <it>Plasmodium falciparum </it>in an area of high ITN coverage in western Kenya.</p> <p>Methods</p> <p>Parasite genetic diversity was assessed by scoring eight single copy neutral multilocus microsatellite (MS) markers in samples collected from <it>P. falciparum-</it>infected children (< five years) before introduction of ITNs (1996, baseline, n = 69) and five years after intervention (2001, follow-up, n = 74).</p> <p>Results</p> <p>There were no significant changes in overall high mixed infections and unbiased expected heterozygosity between baseline (%M_A= 94% and H_e= 0.75) and follow up (%M_A= 95% and H_e= 0.79) years. However, locus specific analysis detected significant differences for some individual loci between the two time points. Pfg377 loci, a gametocyte-specific MS marker showed significant increase in mixed infections and H_ein the follow up survey (%M_A= 53% and H_e= 0.57) compared to the baseline (%M_A= 30% and H_e= 0.29). An opposite trend was observed in the erythrocyte binding protein (EBP) MS marker. There was moderate genetic differentiation at the Pfg377 and TAA60 loci (F_ST= 0.117 and 0.137 respectively) between the baseline and post-ITN parasite populations. Further analysis revealed linkage disequilibrium (LD) of the microsatellites in the baseline (14 significant pair-wise tests and <it>I^S_A</it>= 0.016) that was broken in the follow up parasite population (6 significant pairs and <it>I^S_A</it>= 0.0003). The locus specific change in H_e, the moderate population differentiation and break in LD between the baseline and follow up years suggest an underlying change in population sub-structure despite the stability in the overall genetic diversity and multiple infection levels.</p> <p>Conclusions</p> <p>The results from this study suggest that although <it>P. falciparum </it>population maintained an overall stability in genetic diversity after five years of high ITN coverage, there was significant locus specific change associated with gametocytes, marking these for further investigation.</p

Effects of transmission reduction by insecticide-treated bed nets (ITNs) on parasite genetics population structure: I. The genetic diversity of Plasmodium falciparum parasites by microsatellite markers in western Kenya

<p>Abstract</p> <p>Background</p> <p>Insecticide-treated bed nets (ITNs) reduce malaria transmission and are an important prevention tool. However, there are still information gaps on how the reduction in malaria transmission by ITNs affects parasite genetics population structure. This study examined the relationship between transmission reduction from ITN use and the population genetic diversity of <it>Plasmodium falciparum </it>in an area of high ITN coverage in western Kenya.</p> <p>Methods</p> <p>Parasite genetic diversity was assessed by scoring eight single copy neutral multilocus microsatellite (MS) markers in samples collected from <it>P. falciparum-</it>infected children (< five years) before introduction of ITNs (1996, baseline, n = 69) and five years after intervention (2001, follow-up, n = 74).</p> <p>Results</p> <p>There were no significant changes in overall high mixed infections and unbiased expected heterozygosity between baseline (%M_A= 94% and H_e= 0.75) and follow up (%M_A= 95% and H_e= 0.79) years. However, locus specific analysis detected significant differences for some individual loci between the two time points. Pfg377 loci, a gametocyte-specific MS marker showed significant increase in mixed infections and H_ein the follow up survey (%M_A= 53% and H_e= 0.57) compared to the baseline (%M_A= 30% and H_e= 0.29). An opposite trend was observed in the erythrocyte binding protein (EBP) MS marker. There was moderate genetic differentiation at the Pfg377 and TAA60 loci (F_ST= 0.117 and 0.137 respectively) between the baseline and post-ITN parasite populations. Further analysis revealed linkage disequilibrium (LD) of the microsatellites in the baseline (14 significant pair-wise tests and <it>I^S_A</it>= 0.016) that was broken in the follow up parasite population (6 significant pairs and <it>I^S_A</it>= 0.0003). The locus specific change in H_e, the moderate population differentiation and break in LD between the baseline and follow up years suggest an underlying change in population sub-structure despite the stability in the overall genetic diversity and multiple infection levels.</p> <p>Conclusions</p> <p>The results from this study suggest that although <it>P. falciparum </it>population maintained an overall stability in genetic diversity after five years of high ITN coverage, there was significant locus specific change associated with gametocytes, marking these for further investigation.</p

Systems for grading the quality of evidence and the strength of recommendations I: Critical appraisal of existing approaches The GRADE Working Group

BACKGROUND: A number of approaches have been used to grade levels of evidence and the strength of recommendations. The use of many different approaches detracts from one of the main reasons for having explicit approaches: to concisely characterise and communicate this information so that it can easily be understood and thereby help people make well-informed decisions. Our objective was to critically appraise six prominent systems for grading levels of evidence and the strength of recommendations as a basis for agreeing on characteristics of a common, sensible approach to grading levels of evidence and the strength of recommendations. METHODS: Six prominent systems for grading levels of evidence and strength of recommendations were selected and someone familiar with each system prepared a description of each of these. Twelve assessors independently evaluated each system based on twelve criteria to assess the sensibility of the different approaches. Systems used by 51 organisations were compared with these six approaches. RESULTS: There was poor agreement about the sensibility of the six systems. Only one of the systems was suitable for all four types of questions we considered (effectiveness, harm, diagnosis and prognosis). None of the systems was considered usable for all of the target groups we considered (professionals, patients and policy makers). The raters found low reproducibility of judgements made using all six systems. Systems used by 51 organisations that sponsor clinical practice guidelines included a number of minor variations of the six systems that we critically appraised. CONCLUSIONS: All of the currently used approaches to grading levels of evidence and the strength of recommendations have important shortcomings

Genetic diversity of Plasmodium falciparum parasite by microsatellite markers after scale-up of insecticide-treated bed nets in western Kenya

Background: An initial study of genetic diversity of Plasmodium falciparum in Asembo, western Kenya showed that the parasite maintained overall genetic stability 5 years after insecticide-treated bed net (ITN) introduction in 1997. This study investigates further the genetic diversity of P. falciparum 10 years after initial ITN introduction in the same study area and compares this with two other neighbouring areas, where ITNs were introduced in 1998 (Gem) and 2004 (Karemo). Methods: From a cross-sectional survey conducted in 2007, 235 smear-positive blood samples collected from children ≤15-year-old in the original study area and two comparison areas were genotyped employing eight neutral microsatellites. Differences in multiple infections, allele frequency, parasite genetic diversity and parasite population structure between the three areas were assessed. Further, molecular data reported previously (1996 and 2001) were compared to the 2007 results in the original study area Asembo. Results: Overall proportion of multiple infections (M A ) declined with time in the original study area Asembo (from 95.9 %-2001 to 87.7 %-2007). In the neighbouring areas, M A was lower in the site where ITNs were introduced in 1998 (Gem 83.7 %) compared to where they were introduced in 2004 (Karemo 96.7 %) in 2007. Overall mean allele count (M AC ~ 2.65) and overall unbiased heterozygosity (H e ~ 0.77) remained unchanged in 1996, 2001 and 2007 in Asembo and was the same level across the two neighbouring areas in 2007. Overall parasite population differentiation remained low over time and in the three areas at F ST < 0.04. Both pairwise and multilocus linkage disequilibrium showed limited to no significant association between alleles in Asembo (1996, 2001 and 2007) and between three areas. Conclusions: This study showed the P. falciparum high genetic diversity and parasite population resilience on samples collected 10 years apart and in different areas in western Kenya. The results highlight the need for long-term molecular monitoring after implementation and use of combined and intensive prevention and intervention measures in the region

Use of Field Based Loop Mediated Isothermal Amplification (LAMP) Technology for a Prevalence Survey and Proof of Freedom Survey for African Swine Fever in Timor-Leste in 2019

African Swine Fever (ASF) has been spreading in numerous southeast Asian countries since a major incursion in mainland China in 2018. Timor-Leste confirmed an outbreak of ASF in September 2019 which resulted in high mortalities in affected pigs. Pigs in Timor-Leste are the second most common type of livestock kept by villagers and represent a traditionally important source of income and prestige for householders. In order to understand the extent of ASF infected villages in Timor-Leste a prevalence survey was designed and conducted in November-December 2019. Timor-Leste has limited laboratory facilities and access to qPCR diagnostic tests. Therefore, a loop mediated isothermal amplification (LAMP) assay was used to detect ASF positive blood samples collected during the prevalence survey. The LAMP assay was proven to be a robust, highly specific and sensitive laboratory test for ASF suitable for use in the field and where there are limited laboratory facilities. The results of the prevalence survey allowed the extent of the ASF incursion to be delineated and the introduction of a disease response strategy to limit the spread of ASF and assist in the recovery of the pig population in Timor-Leste