Cereal grain mineral micronutrient and soil chemistry data from GeoNutrition surveys in Ethiopia and Malawi.

The dataset comprises primary data for the concentration of 29 mineral micronutrients in cereal grains and up to 84 soil chemistry properties from GeoNutrition project surveys in Ethiopia and Malawi. The work provided insights on geospatial variation in the micronutrient concentration in staple crops, and the potential influencing soil factors. In Ethiopia, sampling was conducted in Amhara, Oromia, and Tigray regions, during the late-2017 and late-2018 harvest seasons. In Malawi, national-scale sampling was conducted during the April-June 2018 harvest season. The concentrations of micronutrients in grain were measured using inductively coupled plasma mass spectrometry (ICP-MS). Soil chemistry properties reported include soil pH; total soil nitrogen; total soil carbon (C); soil organic C; effective cation exchange capacity and exchangeable cations; a three-step sequential extraction scheme for the fractionation of sulfur and selenium; available phosphate; diethylenetriaminepentaacetic acid (DTPA)-extractable trace elements; extractable trace elements using 0.01 M Ca(NO3)2 and 0.01 M CaCl2; and isotopically exchangeable Zn. These data are reported here according to FAIR data principles to enable users to further explore agriculture-nutrition linkages.

Soil and landscape factors influence geospatial variation in maize grain zinc concentration in Malawi.

Dietary zinc (Zn) deficiency is widespread globally, and in particular among people in sub-Saharan Africa (SSA). In Malawi, dietary sources of Zn are dominated by maize and spatially dependent variation in grain Zn concentration, which will affect dietary Zn intake, has been reported at distances of up to ~ 100 km. The aim of this study was to identify potential soil properties and environmental covariates which might explain this longer-range spatial variation in maize grain Zn concentration. Data for maize grain Zn concentrations, soil properties, and environmental covariates were obtained from a spatially representative survey in Malawi (n = 1600 locations). Labile and non-labile soil Zn forms were determined using isotopic dilution methods, alongside conventional agronomic soil analyses. Soil properties and environmental covariates as potential predictors of the concentration of Zn in maize grain were tested using a priori expert rankings and false discovery rate (FDR) controls within the linear mixed model (LMM) framework that informed the original survey design. Mean and median grain Zn concentrations were 21.8 and 21.5 mg kg-1, respectively (standard deviation 4.5; range 10.0-48.1). A LMM for grain Zn concentration was constructed for which the independent variables: soil pH(water), isotopically exchangeable Zn (ZnE), and diethylenetriaminepentaacetic acid (DTPA) extractable Zn (ZnDTPA) had predictive value (p < 0.01 in all cases, with FDR controlled at < 0.05). Downscaled mean annual temperature also explained a proportion of the spatial variation in grain Zn concentration. Evidence for spatially dependent variation in maize grain Zn concentrations in Malawi is robust within the LMM framework used in this study, at distances of up to ~ 100 km. Spatial predictions from this LMM provide a basis for further investigation of variations in the contribution of staple foods to Zn nutrition, and where interventions to increase dietary Zn intake (e.g. biofortification) might be most effective. Other soil and landscape factors influencing spatially dependent variation in maize grain Zn concentration, along with factors operating over shorter distances such as choice of crop variety and agronomic practices, require further exploration beyond the scope of the design of this survey.

The nutritional quality of cereals varies geospatially in Ethiopia and Malawi.

Micronutrient deficiencies (MNDs) remain widespread among people in sub-Saharan Africa1-5, where access to sufficient food from plant and animal sources that is rich in micronutrients (vitamins and minerals) is limited due to socioeconomic and geographical reasons4-6. Here we report the micronutrient composition (calcium, iron, selenium and zinc) of staple cereal grains for most of the cereal production areas in Ethiopia and Malawi. We show that there is geospatial variation in the composition of micronutrients that is nutritionally important at subnational scales. Soil and environmental covariates of grain micronutrient concentrations included soil pH, soil organic matter, temperature, rainfall and topography, which were specific to micronutrient and crop type. For rural households consuming locally sourced food-including many smallholder farming communities-the location of residence can be the largest influencing factor in determining the dietary intake of micronutrients from cereals. Positive relationships between the concentration of selenium in grain and biomarkers of selenium dietary status occur in both countries. Surveillance of MNDs on the basis of biomarkers of status and dietary intakes from national- and regional-scale food-composition data1-7 could be improved using subnational data on the composition of grain micronutrients. Beyond dietary diversification, interventions to alleviate MNDs, such as food fortification8,9 and biofortification to increase the micronutrient concentrations in crops10,11, should account for geographical effects that can be larger in magnitude than intervention outcomes.

Measurement and determinants of tuberculosis outcome in Karonga District, Malawi.

Evaluation of disease outcome is central to the assessment of tuberculosis (TB) control programmes. In the study reported in this article we examined the factors influencing the measurement of outcome, survival rates during and after treatment, smear conversion rates, and relapse rates for patients diagnosed with TB in a rural area of Malawi between 1986 and mid-1994. Patients with less certain diagnoses of TB were more likely to die than those with confirmed TB, both among those who were seropositive and those who were seronegative to human immunodeficiency virus (HIV). The mortality rate among smear-positive patients with a separate culture-positive specimen was half that of patients with no such diagnostic confirmation. Patients not registered by the Ministry of Health had much higher mortality and default rates than did registered patients. Among smear-positive patients, HIV serostatus was the most important influence on mortality both during and after treatment (crude hazard ratios (95% confidence intervals) = 5.6 (3.0-10) and 7.7 (3.4-17), resp.), but HIV serostatus did not influence smear conversion rates. The initial degree of smear positivity influenced smear conversion rates, but not mortality rates. No significant predictors of relapse were identified. Unless considerable care is taken to include all TB patients, and to exclude nontuberculous patients, recorded TB outcome statistics are difficult to interpret and may be misleading. In populations with high rates of HIV infection, TB target cure rates of 85% are unrealistic. When new interventions are assessed it cannot be assumed that factors which influence the smear conversion rate will also influence the mortality rate.

PIP: Measurement of treatment outcome is central to tuberculosis control programs. A study conducted in Malawi's rural Karonga District in 1986-94 examined factors influencing the measurement of outcome: survival rates during and after treatment, smear conversion rates, and relapse rates for patients diagnosed with tuberculosis. Information was available on 1655 certain, probable, or possible tuberculosis patients. Overall, 22.5% of patients died before the end of treatment, 57.9% completed treatment and were discharged, 4.3% moved out of the district, and 15.3% defaulted or were lost to follow-up. 35% of HIV-positive patients, compared with 11% of HIV-negative patients, died before the end of treatment. Patients with uncertain tuberculosis diagnoses were more likely to die than those with certain diagnoses, regardless of their HIV serostatus. The mortality rate among smear-positive patients with a separate culture-positive specimen was half that of patients with no such diagnostic confirmation. Patients not registered by the Ministry of Health had substantially higher mortality and default rates than registered patients. HIV serostatus was the most important determinant of mortality both during and after treatment in smear-positive patients (crude hazards ratios, 5.6 and 7.7, respectively; 95% confidence intervals, 3.0-10 and 3.4-17, respectively), but HIV status did not influence smear conversion rates. The initial degree of smear positivity influenced smear conversion rates but not mortality rates. No significant predictors of relapse were identified. These findings indicate that tuberculosis outcome statistics may be misleading unless care is taken to include all tuberculosis patients and exclude nontubercular patients.

Household and dwelling contact as risk factors for leprosy in northern Malawi.

Data on household and dwelling contact with known leprosy cases were available on more than 80,000 initially disease-free individuals followed up during the 1980s in a rural district of northern Malawi. A total of 331 new cases of leprosy were diagnosed among them. Individuals recorded as living in household or dwelling contact with multibacillary patients at the start of follow-up were at approximately five- to eightfold increased risk of leprosy, respectively, compared with individuals not living in such households or dwellings. Individuals living in household or dwelling contact with paucibacillary cases were both at approximately twofold increased risk. The higher risk associated with multibacillary contact and the fact that dwelling contact entailed a greater risk than household contact if the association was with multibacillary, but not with paucibacillary, disease suggest that paucibacillary cases may not themselves be sources of transmission, but rather just markers that a household has had contact with some (outside) source of infection. When household contact was considered alone, the risks of disease were appreciably higher for younger than for older contacts and for male compared with female contacts. Despite the elevated risk of leprosy associated with household or dwelling contact, only 15% of all incidence cases arose among recognized household contacts. Given the dynamic nature of household membership and consequent misclassification of contact status, the true contribution to overall incidence of contact within household or dwelling settings is likely to be much higher than this, perhaps 30% or higher. Considering the predilection of males for infectious multibacillary forms of the disease, the transmission of Mycobacterium leprae at an early age, in particular to males, may be of particular importance for the persistence of leprosy in endemic communities. Although residential contact with a multibacillary case is the strongest known determinant of leprosy risk, the vast majority of such contacts never manifest disease, which indicates a crucial role for genetic and/or environmental factors in the transmission of M. leprae infection and/or the pathogenesis of clinical leprosy.

Polymerase chain reaction of nasal swabs from tuberculosis patients and their contacts.

Previous studies have found Mycobacterium leprae in nasal swabs from leprosy patients, their contacts, and persons living in endemic areas. It might be expected that M. tuberculosis would be present on nasal mucosa of pulmonary tuberculosis patients, but whether they can be detected in patients or contacts is unknown. We used the polymerase chain reaction (PCR) technique on nasal swabs from tuberculosis patients, contacts of tuberculosis patients, leprosy patients, and London controls to look for both M. tuberculosis and M. leprae. Swabs dipped in sputum specimens from smear-positive patients were used as positive controls. The PCRs were conducted in two independent laboratories. M. tuberculosis was detected in nasal swabs from 6/16 smear-positive tuberculosis patients and from 1/10 household contacts by one of the laboratories. All of the sputum swabs were positive for M. tuberculosis, and all of the London controls were negative. M. leprae were found in nasal swabs from 2/5 leprosy patients, but one laboratory also reported M. leprae in swabs from 4/21 tuberculosis patients and from one sputum specimen. The results show that M. tuberculosis can be found in the noses of some tuberculosis patients, and suggest that the bacilli also may be detected in some household contacts. The comparisons with M. leprae and between the two laboratories give further insights into the sensitivity and specificity of the technique.

Use of colicin e3 for biological containment of microorganisms.

The genetic determinant of the lethal antibiotic colicin E3 was cloned under the control of a tightly regulated promoter in the absence of the gene for its cognate inhibitor. Combination of this killing cassette with a stringent regulatory element provided a substrate-dependent conditional suicide system that was exploited for the biological containment of a Pseudomonas putida strain. The lethality of a single gene copy and the distinct and universal cellular target of the antibiotic suggest colicin E3 as an ideal candidate for combination with other lethal functions to design highly efficient containment systems for microorganisms.

Does bacille Calmette-Guérin scar size have implications for protection against tuberculosis or leprosy?

SETTING: Total population study in Karonga District, northern Malawi, in which the overall vaccine efficacy of bacille Calmette-Guérin (BCG) has been found to be -7% against tuberculosis and 54% against leprosy. OBJECTIVE: To examine the relationship between BCG scar size and protection against tuberculosis and leprosy. DESIGN: Cohort study in which 85,134 individuals were screened for tuberculosis and 82,265 for leprosy between 1979 and 1984, and followed up between 1986 and 1989. RESULTS: Of the BCG scar positive individuals whose scars were measured, 31/3 2471 were later identified with tuberculosis and 81/31 879 with leprosy. In 19,114 individuals, of whom 17 developed tuberculosis, tuberculin induration was measured at first examination. Mean scar sizes increased with increasing tuberculin induration in all except the oldest individuals. Mean scar sizes were lowest in individuals aged < 10 years, highest in individuals aged 10-29 years and intermediate in older individuals. There was some evidence (P = 0.08) for an increase in tuberculosis risk with increasing scar size, which probably reflects the known correlation between scar size and tuberculin status at the time of vaccination. There was no clear association between BCG scar size and leprosy incidence. CONCLUSIONS: We find no evidence that increased BCG scar size is a correlate of vaccine-induced protective immunity against either tuberculosis or leprosy.

The two-step lysis system of pneumococcal bacteriophage EJ-1 is functional in gram-negative bacteria: triggering of the major pneumococcal autolysin in Escherichia coli.

The holin function Ejh of the pneumococcal bacteriophage EJ-1 has been characterized. It shows structural features similar to, and functionally complemented, the prototype member of the holin family. In Escherichia coli and Pseudomonas putida the Ejh product caused cellular death, and changes in cell morphology could be accounted for by lesions in the cytoplasmic membrane. Expression of ejh resulted in the inhibition of growth in a variety of phylogenetically distant bacterial genera, suggesting a broad spectrum of action. Concomitant expression of the ejh and ejl (encodes a lysin) genes led to lysis of E. coli and P. putida cells. Remarkably, the Ejl lysin was able to attack murein from bacteria lacking choline in their sacculi, which suggests that pneumococcal lysins have a broader substrate specificity than previously assumed. Furthermore, the Ejh holin was able to trigger activity of the major pneumococcal autolysin cloned and expressed in E. coli, and this raised new questions about the regulation of this model autolysin. A new function for holins in systems where the phage lysin is supposed to be associated with the membrane is proposed.

The detection of somaclonal variants of beet using RAPD.

Plantlets were regenerated by adventitious shoot budding in tissue culture from leaf explants of a single genotype of sugar beet. DNA was extracted from the parental plant and from 120 regenerants. RAPD analysis was carried out using five decanucleotide primers; 4,557 RAPD marker bands were examined and two polymorphisms were observed. Thirty secondary regenerants were then derived, using the same tissue culture technique, from thirty of the primary regenerants. Again RAPD analysis was employed and a single band polymorphism was observed out of 1,050 bands examined. The overall frequency of detection of somaclonal polymorphisms using RAPD (3 in 5,607 = 0.05%) is similar to frequencies previously reported using isozyme and RFLP technologies.

Universal barrier to lateral spread of specific genes among microorganisms.

A genetic circuit to suppress the lateral spread of cloned genes from recombinant to indigenous microorganisms in the environment has been developed. It is based on the endonucleolytic activity of the bacterial toxin colicin E3, which has a distinct target at the 3' end of the 16S ribosomal RNA; this sequence is conserved in virtually all prokaryotic and many eukaryotic genera. Cleavage at this sequence separates the mRNA binding sites from the remainder of the 16S rRNA, thereby inhibiting protein synthesis. While host bacteria carrying the genes for both colicin production and colicin immunity are perfectly viable, lateral transfer of the E3 gene to non-immune recipients results in killing of such recipients. This genetic circuit decreases operational transfer frequencies of cloned genes linked to the E3 gene among a variety of bacterial genera by four to five orders of magnitude. In combination with transposon cloning vectors, the circuit is predicted to reduce the rate of lateral spread of specific genes to ecologically insignificant levels. This system therefore represents a useful tool both to explore the evolutionary and ecological consequences of experimentally reducing lateral gene spread among microorganisms, and to increase the ecological predictability of novel recombinant microorganisms.