Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients

Naturally acquired blood-stage infections of the malaria parasite Plasmodium falciparum typically harbour multiple haploid clones. The apparent number of clones observed in any single infection depends on the diversity of the polymorphic markers used for the analysis, and the relative abundance of rare clones, which frequently fail to be detected among PCR products derived from numerically dominant clones. However, minority clones are of clinical interest as they may harbour genes conferring drug resistance, leading to enhanced survival after treatment and the possibility of subsequent therapeutic failure. We deployed new generation sequencing to derive genome data for five non-propagated parasite isolates taken directly from 4 different patients treated for clinical malaria in a UK hospital. Analysis of depth of coverage and length of sequence intervals between paired reads identified both previously described and novel gene deletions and amplifications. Full-length sequence data was extracted for 6 loci considered to be under selection by antimalarial drugs, and both known and previously unknown amino acid substitutions were identified. Full mitochondrial genomes were extracted from the sequencing data for each isolate, and these are compared against a panel of polymorphic sites derived from published or unpublished but publicly available data. Finally, genome-wide analysis of clone multiplicity was performed, and the number of infecting parasite clones estimated for each isolate. Each patient harboured at least 3 clones of P. falciparum by this analysis, consistent with results obtained with conventional PCR analysis of polymorphic merozoite antigen loci. We conclude that genome sequencing of peripheral blood P. falciparum taken directly from malaria patients provides high quality data useful for drug resistance studies, genomic structural analyses and population genetics, and also robustly represents clonal multiplicity.     

Household energy and recycling of nutrients and carbon to the soil in integrated crop‐livestock farming systems: a case study in Kumbursa village,Central Highlands of Ethiopia

Soil amendment with organic wastes in the Highlands of Ethiopia has been greatly reduced by widespread use of dung cakes and crop residues as fuels. This study assessed the interaction between household energy and recycling of nutrients and carbon to the soil using household survey, focus group discussions, key informant interviews, direct observations and measurements between 2014 and 2015 in Kumbursa village (Central Highlands of Ethiopia). All surveyed households were entirely dependent on biomass fuel for cooking, with production and consumption rates directly related to wealth status, which significantly varied (P < 0.001) among three farm wealth groups (poor, medium and rich). Crop residues and dung cakes accounted for 80(±3)% by energy content and 85(±4)% by dry mass weight of total biomass fuel consumption. Mean losses were 59(±2) kg ha^?1 yr^?1 nitrogen (109(±8) kg yr^?1 per household), 13.9(±0.3) kg ha^?1 yr^?1 phosphorus (26(±2) kg yr^?1 per household), 79(±2) kg ha^?1 yr^?1 potassium (150(±11) kg yr^?1 per household) and 2100(±40) kg ha^?1 yr^?1 organic carbon (3000(±300) kg yr^?1 per household). Rich farmers lost significantly more carbon and nutrients in fuel than farmers in other wealth groups. However, these losses were spread over a larger area, so losses per land area were significantly higher for medium and poor than for rich farmers. This means that the land of poorer farmers is likely to become degraded more rapidly due to fuel limitations than that of rich farmers, so increasing the poverty gap. The estimated financial loss per household due to not using dung and crop residues as organic fertilizer was 162(±8) USSoil amendment with organic wastes in the Highlands of Ethiopia has been greatly reduced by widespread use of dung cakes and crop residues as fuels. This study assessed the interaction between household energy and recycling of nutrients and carbon to the soil using household survey, focus group discussions, key informant interviews, direct observations and measurements between 2014 and 2015 in Kumbursa village (Central Highlands of Ethiopia). All surveyed households were entirely dependent on biomass fuel for cooking, with production and consumption rates directly related to wealth status, which significantly varied (P < 0.001) among three farm wealth groups (poor, medium and rich). Crop residues and dung cakes accounted for 80(±3)% by energy content and 85(±4)% by dry mass weight of total biomass fuel consumption. Mean losses were 59(±2) kg ha^?1 yr^?1 nitrogen (109(±8) kg yr^?1 per household), 13.9(±0.3) kg ha^?1 yr^?1 phosphorus (26(±2) kg yr^?1 per household), 79(±2) kg ha^?1 yr^?1 potassium (150(±11) kg yr^?1 per household) and 2100(±40) kg ha^?1 yr^?1 organic carbon (3000(±300) kg yr^?1 per household). Rich farmers lost significantly more carbon and nutrients in fuel than farmers in other wealth groups. However, these losses were spread over a larger area, so losses per land area were significantly higher for medium and poor than for rich farmers. This means that the land of poorer farmers is likely to become degraded more rapidly due to fuel limitations than that of rich farmers, so increasing the poverty gap. The estimated financial loss per household due to not using dung and crop residues as organic fertilizer was 162(±8) US$ yr^?1. However, this is less than their value as fuels, which was 490(±20) US$ yr^?1. Therefore, farmers will only be persuaded to use these valuable assets as soil improvers if an alternative, cheaper fuel source can be found.     

Methodological framework to find links between life cycle sustainability assessment categories and the UN Sustainable Development Goals based on literature

Life cycle sustainability assessment (LCSA) can be used as a tool to understand how products and operating systems can meet the United Nations’ Sustainable Development Goals (SDGs). However, existing linkages between SDGs and LCSA are limited and an analysis of coverage in literature is needed. In this paper, we propose a generic methodological framework establishing connections between LCSA categories at micro-level and SDGs at macro-level based on derivation from the literature. The qualitative heuristic research method developed builds on keyword literature search, bibliometric analysis, mapping, and narrative literature review for connection rationales. By using qualitative assessment levels, an assessment of linkages between LCSA categories and SDGs reveal that “technology development,” “public commitment to sustainability issues,” “access to material resources,” and “education provided in the local community” have the highest number of reported relationships with SDGs. Twenty-two LCSA categories were found with no direct/indirect connection with any SDG; reasons include absence of life cycle thinking perspective in SDGs and lack of sustainability-based discussion for workers, consumers, and value chain actors' stakeholder groups. Despite these gaps, the results provide new insights for industries looking to measure the contribution of their product systems along their life cycle in the context of SDGs supporting them to some extent, to select LCSA categories with either highest number of identified relationships to SDGs or that contribute to prioritized list of SDGs. The approach provides a starting point to improve transparency and consistency of reporting of sustainability performance of product systems by connecting LCSA to the global agenda for sustainable development.     

Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity

Background

Genome wide sequence analyses of malaria parasites from widely separated areas of the world have identified contrasting population structures and signatures of selection. To compare relatively closely situated but ecologically contrasting regions within an endemic African country, population samples of Plasmodium falciparum clinical isolates were collected in Ghana from Kintampo in the central forest-savannah area, and Navrongo in a drier savannah area ~350 km to the north with more seasonally-restricted transmission. Parasite DNA was sequenced and paired-end reads mapped to the P. falciparum reference genome.

Results

High coverage genome wide sequence data for 85 different clinical isolates enabled analysis of 121,712 single nucleotide polymorphisms (SNPs). The local populations had similar proportions of mixed genotype infections, similar SNP allele frequency distributions, and eleven chromosomal regions had elevated integrated haplotype scores (|iHS|) in both. A between-population Rsb metric comparing extended haplotype homozygosity indicated a stronger signal within Kintampo for one of these regions (on chromosome 14) and in Navrongo for two of these regions (on chromosomes 10 and 13). At least one gene in each of these identified regions is a potential target of locally varying selection. The candidates include genes involved in parasite development in mosquitoes, members of variant-expressed multigene families, and a leading vaccine-candidate target of immunity.

Conclusions

Against a background of very similar population structure and selection signatures in the P. falciparum populations of Ghana, three narrow genomic regions showed evidence indicating local differences in historical timing or intensity of selection. Sampling of closely situated populations across heterogeneous environments has potential to refine the mapping of important loci under temporally or spatially varying selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1746-3) contains supplementary material, which is available to authorized users.     

Trends of Modern Contraceptive Use among Young Married Women Based on the 2000, 2005, and 2011 Ethiopian Demographic and Health Surveys: A Multivariate Decomposition Analysis

Introduction

Accessing family planning can reduce a significant proportion of maternal, infant, and childhood deaths. In Ethiopia, use of modern contraceptive methods is low but it is increasing. This study aimed to analyze the trends and determinants of changes in modern contraceptive use over time among young married women in Ethiopia.

Methods

The study used data from the three Demographic Health Surveys conducted in Ethiopia, in 2000, 2005, and 2011. Young married women age 15–24 years with sample sizes of 2,157 in 2000, 1,904 in 2005, and 2,146 in 2011 were included. Logit-based decomposition analysis technique was used for analysis of factors contributing to the recent changes. STATA 12 was employed for data management and analyses. All calculations presented in this paper were weighted for the sampling probabilities and non-response. Complex sampling procedures were also considered during testing of statistical significance.

Results

Among young married women, modern contraceptive prevalence increased from 6% in 2000 to 16% in 2005 and to 36% in 2011. The decomposition analysis indicated that 34% of the overall change in modern contraceptive use was due to difference in women’s characteristics. Changes in the composition of young women’s characteristics according to age, educational status, religion, couple concordance on family size, and fertility preference were the major sources of this increase. Two-thirds of the increase in modern contraceptive use was due to difference in coefficients. Most importantly, the increase was due to change in contraceptive use behavior among the rural population (33%) and among Orthodox Christians (16%) and Protestants (4%).

Conclusions

Modern contraceptive use among young married women has showed a remarkable increase over the last decade in Ethiopia. Programmatic interventions targeting poor, younger (adolescent), illiterate, and Muslim women would help to maintain the increasing trend in modern contraceptive use.     

Breastfeeding practice and associated factors among female nurses and midwives at North Gondar Zone,Northwest Ethiopia: a cross-sectional institution based study

Background

Health care workers have a duty to promote and support breastfeeding among their clients. Although their ability to do this may be influenced by their knowledge and personal experience; little is known about breastfeeding practices and the perceived barriers. The objective of this study was to assess the breastfeeding practices and the associated factors among female nurses and midwives in North Gondar Zone; Northwest Ethiopia.

Methods

An institution based cross-sectional study design was conducted in 2013 among 178 nurses and midwives. In this study exclusive breastfeeding refers to breastfeeding exclusively for the first six months of a child’s life. Bivariate and multivariate logistic regressions were performed to identify the presence and strength of association. Odds ratios with 95% confidence interval were computed to determine the level of significance.

Results

Exclusive breastfeeding rate among respondents was found to be 35.9%. Nearly half (49.4%) of the respondents exclusively breastfed for only 3 months or less. The mean duration exclusive breastfeeding was 4.1?±?1.7 months. Older women (AOR?=?2.8; 95% CI 2.16, 3.24), rural residence (AOR?=?3.01; 95% CI 2.65, 3.84), being midwife (AOR?=?2.01; 95% CI 1.83, 2.56), a women who gave birth through vaginal delivery (AOR?=?2.0; 95% CI 1.68, 2.87), multiparous women (AOR?=?2.20; 95% CI 1.74, 2.67) and resumption of work after 3 months (AOR?=?1.61; 95% CI 1.24, 2.35) were independently associated with exclusive breastfeeding.

Conclusion

Though respondents had adequate knowledge on breastfeeding, the practice of exclusive breastfeeding was low. Maternal age, place of residence, profession, mode of delivery, parity and the time before resuming work were factors associated with exclusive breastfeeding. Appropriate education concerning breastfeeding, directed at nurses and midwives is required to enhance exclusive breastfeeding and duration of breastfeeding.

     

Comparison of genomic signatures of selection on <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> between different regions of a country with high malaria endemicity

Background

Genome wide sequence analyses of malaria parasites from widely separated areas of the world have identified contrasting population structures and signatures of selection. To compare relatively closely situated but ecologically contrasting regions within an endemic African country, population samples of Plasmodium falciparum clinical isolates were collected in Ghana from Kintampo in the central forest-savannah area, and Navrongo in a drier savannah area ~350 km to the north with more seasonally-restricted transmission. Parasite DNA was sequenced and paired-end reads mapped to the P. falciparum reference genome.

Results

High coverage genome wide sequence data for 85 different clinical isolates enabled analysis of 121,712 single nucleotide polymorphisms (SNPs). The local populations had similar proportions of mixed genotype infections, similar SNP allele frequency distributions, and eleven chromosomal regions had elevated integrated haplotype scores (|iHS|) in both. A between-population Rsb metric comparing extended haplotype homozygosity indicated a stronger signal within Kintampo for one of these regions (on chromosome 14) and in Navrongo for two of these regions (on chromosomes 10 and 13). At least one gene in each of these identified regions is a potential target of locally varying selection. The candidates include genes involved in parasite development in mosquitoes, members of variant-expressed multigene families, and a leading vaccine-candidate target of immunity.

Conclusions

Against a background of very similar population structure and selection signatures in the P. falciparum populations of Ghana, three narrow genomic regions showed evidence indicating local differences in historical timing or intensity of selection. Sampling of closely situated populations across heterogeneous environments has potential to refine the mapping of important loci under temporally or spatially varying selection.

     

Agrobiodiversity and gender: the role of women in farm diversification among smallholder farmers in Sinana district,Southeastern Ethiopia

Biodiversity and Conservation - Women’s knowledge and conservation of agrobiodiversity are under-valued and less documented and recognized in the scientific spheres regardless of the...     

Kinome screening for regulators of the estrogen receptor identifies LMTK3 as a new therapeutic target in breast cancer

Therapies targeting estrogen receptor α (ERα, encoded by ESR1) have transformed the treatment of breast cancer. However, large numbers of women relapse, highlighting the need for the discovery of new regulatory targets modulating ERα pathways. An siRNA screen identified kinases whose silencing alters the estrogen response including those previously implicated in regulating ERα activity (such as mitogen-activated protein kinase and AKT). Among the most potent regulators was lemur tyrosine kinase-3 (LMTK3), for which a role has not previously been assigned. In contrast to other modulators of ERα activity, LMTK3 seems to have been subject to Darwinian positive selection, a noteworthy result given the unique susceptibility of humans to ERα+ breast cancer. LMTK3 acts by decreasing the activity of protein kinase C (PKC) and the phosphorylation of AKT (Ser473), thereby increasing binding of forkhead box O3 (FOXO3) to the ESR1 promoter. LMTK3 phosphorylated ERα, protecting it from proteasomal degradation in vitro. Silencing of LMTK3 reduced tumor volume in an orthotopic mouse model and abrogated proliferation of ERα+ but not ERα- cells, indicative of its role in ERα activity. In human cancers, LMTK3 abundance and intronic polymorphisms were significantly associated with disease-free and overall survival and predicted response to endocrine therapies. These findings yield insights into the natural history of breast cancer in humans and reveal LMTK3 as a new therapeutic target.