Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm

KEY MESSAGE: Loci conferring resistance to the highly virulent African stem rust race TTKSK were identified in advanced barley breeding germplasm and positioned to chromosomes 5H and 7H using an association mapping approach. ABSTRACT: African races of the stem rust pathogen (Puccinia graminis f. sp. tritici) are a serious threat to barley production worldwide because of their wide virulence. To discover and characterize resistance to African stem rust race TTKSK in US barley breeding germplasm, over 3,000 lines/cultivars were assessed for resistance at the seedling stage in the greenhouse and also the adult plant stage in the field in Kenya. Only 12 (0.3 %) and 64 (2.1 %) lines exhibited a resistance level comparable to the resistant control at the seedling and adult plant stage, respectively. To map quantitative trait loci (QTL) for resistance to race TTKSK, an association mapping approach was conducted, utilizing 3,072 single nucleotide polymorphism (SNP) markers. At the seedling stage, two neighboring SNP markers (0.8 cM apart) on chromosome 7H (11_21491 and 12_30528) were found significantly associated with resistance. The most significant one found was 12_30528; thus, the resistance QTL was named Rpg-qtl-7H-12_30528. At the adult plant stage, two SNP markers on chromosome 5H (11_11355 and 12_31427) were found significantly associated with resistance. This resistance QTL was named Rpg-qtl-5H-11_11355 for the most significant marker identified. Adult plant resistance is of paramount importance for stem rust. The marker associated with Rpg-qtl-5H-11_11355 for adult plant resistance explained only a small portion of the phenotypic variation (0.02); however, this QTL reduced disease severity up to 55.0 % under low disease pressure and up to 21.1 % under heavy disease pressure. SNP marker 11_11355 will be valuable for marker-assisted selection of adult plant stem rust resistance in barley breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-014-2297-8) contains supplementary material, which is available to authorized users

The Association Between Social Networks and Self-rated risk of HIV Infection among Secondary School Students in Moshi Municipality, Tanzania.

Abstract This study describes the social networks of secondary school students in Moshi Municipality, and their association with self-rated risk of human immunodeficiency virus (HIV) infection. A cross-sectional analytical study was conducted among 300 students aged 15-24 years in 5 secondary schools in Moshi, Tanzania. Bonding networks were defined as social groupings of students participating in activities within the school, while bridging networks were groups that included students participating in social groupings from outside of the school environs. A structured questionnaire was used to ask about participation in bonding and bridging social networks and self-rated HIV risk behavior. More participants participated in bonding networks (72%) than in bridging networks (29%). Participation in bridging networks was greater among females (25%) than males (12%, p < .005). Of 300 participants, 88 (29%) were sexually experienced, and of these 62 (70%) considered themselves to be at low risk of HIV infection. Factors associated with self-rated risk of HIV included: type of school (p < .003), family structure (p < .008), being sexually experienced (p < .004), having had sex in the past three months (p < .009), having an extra sexual partner (p < .054) and non-condom use in last sexual intercourse (p < .001), but not the presence or type of social capital. The study found no association between bonding and bridging social networks on self-rated risk of HIV among study participants. However, sexually experienced participants rated themselves at low risk of HIV infection despite practicing unsafe sex. Efforts to raise adolescents' self-awareness of risk of HIV infection through life skills education and HIV/acquired immunodeficiency syndrome risk reduction strategies may be beneficial to students in this at-risk group

Sociodemographic and Other Characteristics Associated With Behavioural Risk Factors of HIV Infection Among Male Mountain-Climbing Porters in Kilimanjaro Region, Tanzania.

BACKGROUND: Alcohol consumption, marijuana use, unprotected sex, and multiple concurrent sexual partnerships are prevalent among youth globally. These factors are regarded as important behavioural risk factors for HIV infection. The aim of this study was to assess the sociodemographic and other characteristics associated with behavioural risk factors of HIV infection among male mountain-climbing porters working on Mount Kilimanjaro in Tanzania. METHODS: This cross-sectional study enrolled a representative sample of 384 male mountain-climbing porters from 7 tour companies in the Kilimanjaro region using a multi-stage sampling technique. Local interviewers completed a structured questionnaire with porters in the local language, Kiswahili. The questionnaire covered demographics, alcohol and marijuana use, sexual history, sexual partners, and condom use. In-person interviews were completed between April and May 2013. Univariate and bivariate analysis were used to describe data and determine significant predictors of behavioural risk factors of HIV infection. RESULTS: Of 384 participants, 381 (99.2%) were sexually experienced, 353 (92.6%) were sexually active, and 168 (44.1%), reported condom use at last sex. The prevalence of ever-use of alcohol was 62%, and 68% of participants reported being current alcohol users. The prevalence of ever-use of marijuana was 15%, and 49% of participants reported being current marijuana users, with 12% reporting daily use. Age, marital status, working duration as a porter, transactional sex practices, and number of concurrent sexual partners were factors that were significantly associated with unprotected sex, alcohol consumption, and marijuana use (P<.05). CONCLUSIONS: Age, marital status, working duration, transactional sex practices, and number of concurrent sexual partners were significantly associated with unprotected sex, alcohol consumption, and marijuana use, among porters in this setting. The findings suggest the need for efforts to motivate sexually active male porters to engage in HIV prevention interventions, including condom use and reduction of multiple concurrent sexual partners, transactional sexual practices, alcohol consumption, and marijuana use

Routine delivery of artemisinin-based combination treatment at fixed health facilities reduces malaria prevalence in Tanzania: an observational study

BACKGROUND Artemisinin-based combination therapy (ACT) has been promoted as a means to reduce malaria transmission due to their ability to kill both asexual blood stages of malaria parasites, which sustain infections over long periods and the immature derived sexual stages responsible for infecting mosquitoes and onward transmission. Early studies reported a temporal association between ACT introduction and reduced malaria transmission in a number of ecological settings. However, these reports have come from areas with low to moderate malaria transmission, been confounded by the presence of other interventions or environmental changes that may have reduced malaria transmission, and have not included a comparison group without ACT. This report presents results from the first large-scale observational study to assess the impact of case management with ACT on population-level measures of malaria endemicity in an area with intense transmission where the benefits of effective infection clearance might be compromised by frequent and repeated re-infection. METHODS A pre-post observational study with a non-randomized comparison group was conducted at two sites in Tanzania. Both sites used sulphadoxine-pyrimethamine (SP) monotherapy as a first-line anti-malarial from mid-2001 through 2002. In 2003, the ACT, artesunate (AS) co-administered with SP (AS + SP), was introduced in all fixed health facilities in the intervention site, including both public and registered non-governmental facilities. Population-level prevalence of Plasmodium falciparum asexual parasitaemia and gametocytaemia were assessed using light microscopy from samples collected during representative household surveys in 2001, 2002, 2004, 2005 and 2006. FINDINGS Among 37,309 observations included in the analysis, annual asexual parasitaemia prevalence in persons of all ages ranged from 11% to 28% and gametocytaemia prevalence ranged from <1% to 2% between the two sites and across the five survey years. A multivariable logistic regression model was fitted to adjust for age, socioeconomic status, bed net use and rainfall. In the presence of consistently high coverage and efficacy of SP monotherapy and AS + SP in the comparison and intervention areas, the introduction of ACT in the intervention site was associated with a modest reduction in the adjusted asexual parasitaemia prevalence of 5 percentage-points or 23% (p < 0.0001) relative to the comparison site. Gametocytaemia prevalence did not differ significantly (p = 0.30). INTERPRETATION The introduction of ACT at fixed health facilities only modestly reduced asexual parasitaemia prevalence. ACT is effective for treatment of uncomplicated malaria and should have substantial public health impact on morbidity and mortality, but is unlikely to reduce malaria transmission substantially in much of sub-Saharan Africa where individuals are rapidly re-infected.Financial support for IMPACT-Tz came primarily from CDC, the U.S. Agency for International Development and the Wellcome Trust

Cost variations in prevention of mother-to-child HIV transmission services integrated within maternal and child health services in rural Tanzania.

We estimated the costs of Option B+ for HIV-infected pregnant women in 12 facilities in Morogoro Region, Tanzania, from a provider perspective. Costs of prevention of mother-to-child (PMTCT) HIV services were measured over 12 months to September 2017 to estimate the average costs per HIV testing episode, per HIV-positive case diagnosed, per patient-year on antiretroviral therapy (ART), and per neonatal HIV care. A one-way sensitivity analysis was undertaken to understand how staffing levels and other core resource inputs affected costs. The total number of HIV testing episodes was 25,593 with 279 HIV cases identified yielding a 1.1% positivity rate. The average cost per testing episode was US$5.49 (range US$2.13 to US$13.93), and the average cost per HIV case detected was US$503.29 (range US$230.61 to US$3330.38). The number of pregnant women initiated on ART was 278. The mean cost per patient-year on ART was US$159.89 (range US$100.91 to US$812.23). The average cost of neonatal HIV care was US$90.09 (range US$41.53 to US$180.26). PMTCT service costs varied widely across facilities due to variations in resource use, number of women testing, and HIV prevalence. The study provides further evidence against generalising cost estimates, and that budgeting and planning requires context specific cost information

The carnivorous feeding behavior of early Homo at HWK EE, Bed II, Olduvai Gorge, Tanzania

The regular consumption of large mammal carcasses, as evidenced by butchery marks on fossils recovered from Early Stone Age archaeological sites, roughly coincides with the appearance of Homo habilis. However, the significance of this niche expansion cannot be appreciated without an understanding of hominin feeding behavior and their ecological interactions with mammalian carnivores. The Olduvai Geochronology and Archaeology Project (OGAP) has recovered a large and well-preserved fossil assemblage from the HWK EE site, which was deposited just prior to the first appearance of Acheulean technology at Olduvai Gorge and likely represents one of the last H. habilis sites at Olduvai. This taphonomic analysis of the larger mammal fossil assemblage excavated from HWK EE shows evidence of multiple occupations over a long period of time, suggesting the site offered resources that were attractive to hominins. There was a water source indicated by the presence of fish, crocodiles, and hippos, and there was possible tree cover in an otherwise open habitat. The site preserves several stratigraphic intervals with large fossil and artifact assemblages within two of these intervals. Feeding traces on bone surfaces suggest hominins at the site obtained substantial amounts of flesh and marrow, particularly from smaller size group 1-2 carcasses, and exploited a wide range of taxa, including megafauna. A strong carnivore signal suggests hominins scavenged much of their animal foods during the two main stratigraphic intervals. In the later interval, lower carnivore tooth mark and hammerstone percussion mark frequencies, in addition to high epiphyseal to shaft fragment ratios, suggest hominins and carnivores did not fully exploit bone marrow and grease, which may have been acquired from nutritionally-stressed animals that died during a dry period at Olduvai. The diversity of fauna that preserve evidence of butchery suggests that the HWK EE hominins were opportunistic in their acquisition of carcass foods

Evidence of fatal skeletal injuries on Malapa Hominins 1 and 2

Malapa is one of the richest early hominin sites in Africa and the discovery site of the hominin species, Australopithecus sediba. The holotype and paratype (Malapa Hominin 1 and 2, or MH1 and MH2, respectively) skeletons are among the most complete in the early hominin record. Dating to approximately two million years BP, MH1 and MH2 are hypothesized to have fallen into a natural pit trap. All fractures evident on MH1 and MH2 skeletons were evaluated and separated based on wet and dry bone fracture morphology/characteristics. Most observed fractures are post-depositional, but those in the right upper limb of the adult hominin strongly indicate active resistance to an impact, while those in the juvenile hominin mandible are consistent with a blow to the face. The presence of skeletal trauma independently supports the falling hypothesis and supplies the first evidence for the manner of death of an australopith in the fossil record that is not attributed to predation or natural death

Potential opportunities and challenges of deploying next generation sequencing and CRISPR-cas systems to support diagnostics and surveillance towards malaria control and elimination in Africa

Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent

What factors influence HIV testing? Modeling preference heterogeneity using latent classes and class-independent random effects.

Efforts to eliminate the HIV epidemic will require increased HIV testing rates among high-risk populations. To inform the design of HIV testing interventions, a discrete choice experiment (DCE) with six policy-relevant attributes of HIV testing options elicited the testing preferences of 300 female barworkers and 440 male Kilimanjaro mountain porters in northern Tanzania. Surveys were administered between September 2017 and July 2018. Participants were asked to complete 12 choice tasks, each involving first- and second-best choices from 3 testing options. DCE responses were analyzed using a random effects latent class logit (RELCL) model, in which the latent classes summarize common participant preference profiles, and the random effects capture additional individual-level preference heterogeneity with respect to three attribute domains: (a) privacy and confidentiality (testing venue, pre-test counseling, partner notification); (b) invasiveness and perceived accuracy (method for obtaining the sample for the HIV test); and (c) accessibility and value (testing availability, additional services provided). The Bayesian Information Criterion indicated the best model fit for a model with 8 preference classes, with class sizes ranging from 6% to 19% of participants. Substantial preference heterogeneity was observed, both between and within latent classes, with 12 of 16 attribute levels having positive and negative coefficients across classes, and all three random effects contributing significantly to participants' choices. The findings may help identify combinations of testing options that match the distribution of HIV testing preferences among high-risk populations; the methods may be used to systematically design heterogeneity-focused interventions using stated preference methods

A randomized, open-label, comparative efficacy trial of artemether-lumefantrine suspension versus artemether-lumefantrine tablets for treatment of uncomplicated Plasmodium falciparum malaria in children in western Kenya

<p>Abstract</p> <p>Background</p> <p>Artemether/lumefantrine (AL) has been adopted as the treatment of choice for uncomplicated malaria in Kenya and other countries in the region. Six-dose artemether/lumefantrine tablets are highly effective and safe for the treatment of infants and children weighing between five and 25 kg with uncomplicated <it>Plasmodium falciparum </it>malaria. However, oral paediatric formulations are urgently needed, as the tablets are difficult to administer to young children, who cannot swallow whole tablets or tolerate the bitter taste of the crushed tablets.</p> <p>Methods</p> <p>A randomized, controlled, open-label trial was conducted comparing day 28 PCR corrected cure-rates in 245 children aged 6–59 months, treated over three days with either six-dose of artemether/lumefantrine tablets (Coartem^®) or three-dose of artemether/lumefantrine suspension (Co-artesiane^®) for uncomplicated falciparum malaria in western Kenya. The children were followed-up with clinical, parasitological and haematological evaluations over 28 days.</p> <p>Results</p> <p>Ninety three percent (124/133) and 90% (121/134) children in the AL tablets and AL suspension arms respectively completed followed up. A per protocol analysis revealed a PCR-corrected parasitological cure rate of 96.0% at Day 28 in the AL tablets group and 93.4% in the AL suspension group, p = 0.40. Both drugs effectively cleared gametocytes and were well tolerated, with no difference in the overall incidence of adverse events.</p> <p>Conclusion</p> <p>The once daily three-dose of artemether-lumefantrine suspension (Co-artesiane^®) was not superior to six-dose artemether-lumefantrine tablets (Coartem^®) for the treatment of uncomplicated malaria in children below five years of age in western Kenya.</p> <p>Trial registration</p> <p>ClinicalTrials.gov NCT00529867</p