Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome

Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ~1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a "liquid biopsy," while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 μL plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimer's disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinson's disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 ± 0.06.

Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling

Tandem mass tags data-dependent acquisition (TMT-DDA) as well as data-independent acquisition-based label-free quantification (LFQ-DIA) have become the leading workflows to achieve deep proteome and phosphoproteome profiles. We present a modular pipeline for TMT-DDA and LFQ-DIA that integrates steps to perform scalable phosphoproteome profiling, including protein lysate extraction, clean-up, digestion, phosphopeptide enrichment, and TMT-labeling. We also detail peptide and/or phosphopeptide fractionation and pre-mass spectrometry desalting and provide researchers guidance on choosing the best workflow based on sample number and input. For complete details on the use and execution of this protocol, please refer to Koenig et al.1 and Martínez-Val et al.2.

Effectiveness of a large-scale, sustained and comprehensive community health worker program in improving population health: the experience of an urban health district in South Africa

INTRODUCTION

South Africa is an upper middle-income country with wide wealth inequality. It faces a quadruple burden of disease and poor health outcomes, with access to appropriate and adequate health care a challenge for millions of South Africans. The introduction of large-scale, comprehensive community health worker (CHW) programs in the country, within the context of implementing universal health coverage, was anticipated to improve population health outcomes. However, there is inadequate local (or global) evidence on whether such programs are effective, especially in urban settings.

METHODS

This study is part of a multi-method, quasi-experimental intervention study measuring effectiveness of a large-scale CHW program in a health district in an urban province of South Africa, where CHWs now support approximately one million people in 280,000 households. Using interviewer administered questionnaires, a 2019 cross-sectional survey of 417 vulnerable households with long-term CHW support (intervention households) are compared to 417 households with no CHW support (control households). Households were selected from similar vulnerable areas from all sub-levels of the Ekurhuleni health district.

RESULTS

The 417 intervention and control households each had good health knowledge. Compared to controls, intervention households with long-term comprehensive CHW support were more likely to access early care, get diagnosed for a chronic condition, be put on treatment and be well controlled on chronic treatment. They were also more likely to receive a social grant, and have a birth certificate or identity document. The differences were statistically significant for social support, health seeking behavior, and health outcomes for maternal, child health and chronic care.

CONCLUSION

A large-scale and sustained comprehensive CHW program in an urban setting improved access to social support, chronic and minor acute health services at household and population level through better health-seeking behavior and adherence to treatment. Direct evidence from households illustrated that such community health worker programs are therefore effective and should be part of health systems in low- and middle-income countries.

Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment

Phosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as immobilized metal-ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC). We compared zirconium(IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used titanium(IV) IMAC (Ti-IMAC) and TiO₂ magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior to phosphopeptide sequencing and characterization by mass spectrometry (liquid chromatography-tandem mass spectrometry, LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC-, Ti-IMAC-, and TiO₂-based workflows by 22, 24, and 35%, respectively. The optimized protocol resulted in improved performance of Zr-IMAC over Ti-IMAC and TiO₂ as well as high-performance liquid chromatography-based Fe(III)-IMAC with up to 23% more identified phosphopeptides. The different enrichment chemistries showed a high degree of overlap but also differences in phosphopeptide selectivity and complementarity. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this complementary and scalable affinity enrichment method is more widely used in biological and biomedical studies of cell signaling and the search for biomarkers. Data are available via ProteomeXchange with identifier PXD018273.

Are large scale, urban, comprehensive CHW programs effective? The South African experience

Background

South Africa is an upper middle-income country, but has one of the widest GINI co-efficients in the world. It faces a heavy burden of disease and poor health outcomes remain a challenge for millions of South Africans. Slow economic growth, rapid urbanization and high unemployment could de-rail the efforts to improve access to health care and health outcomes amongst the most vulnerable in the country. Within this context, the introduction of large scale, comprehensive community health worker (CHW) programs, in urban areas are seen to be game changers. However, there is inadequate global evidence on whether such programs work.

Methods

This is a multi-method, quasi-experimental intervention study measuring the effectiveness of a CHW program in the Ekurhuleni health district; set in an urban province of South Africa, where CHWs support approximately one million people. Health indicator performance was compared in clinics with good coverage of CHWs and those with low or no CHW support. Poor and vulnerable households with CHW support were compared to those with no CHW support.

Results

Over a nine-year period since implementation, clinics with CHW programs improved better than clinics without; on identified pregnancy, child health, infectious disease and non-communicable disease indicators. Odds ratios showed that households with good CHW coverage had better social support, health-seeking behavior, morbidity and mortality than households without. p-values were statistically significant (&lt;0.05) for social support, chronic disease diagnosis and chronic disease control outputs.

Conclusions

This CHW program has shown its worth as it has been effective in improving early screening, referrals, diagnosis and disease control across a number of health conditions in an urban setting.

Key messages

Large-scale comprehensive CHW programs are a good investment towards achieving universal health coverage for all by improving access and care to the poor and vulnerable. Community Health Worker services in households are effective and should be a legitimate level of health care delivery in developing countries.

Sustainable production of nucleoside analogues by a high-efficient purine 2'-deoxyribosyltransferase immobilized onto Ni2+ chelate magnetic microparticles

The present work aims to develop a magnetic biocatalyst for customized production of nucleoside analogues using mutant His-tagged purine 2'-deoxyribosyltransferase from Trypanosoma brucei (TbPDT_V11S) immobilized onto Ni²⁺ chelate magnetic iron oxide porous microparticles (MTbPDT_V11S). Biochemical characterization revealed MTbPDT_V11S5 as optimal candidate for further studies (10,552 IU g^-1; retained activity 54% at 50 °C and pH 6.5). Interestingly, MTbPDT_V11S5 displayed the highest activity value described up to date for an immobilized NDT. Moreover, MTbPDT_V11S5 was successfully employed in the one-pot, one-step production of different therapeutic nucleoside analogues, such as cladribine or 2'-deoxy-2-fluoroadenosine, among others. Finally, MTbPDT_V11S5 proved to be stable when stored at 50 °C for 8 h and pH 6.0 and reusable up to 10 times without negligible loss of activity in the enzymatic production of the antitumor prodrug 2'-deoxy-2-fluoroadenosine.

A comparative study of the psychological problems of HIV-infected and HIV-uninfected children in a South African sample

According to research children living with HIV experience elevated levels of depression, anxiety, ADHD and disruptive behavioural disorders. Although South Africa's paediatric population that is infected with the human immunodeficiency virus (HIV) is the largest worldwide, little research has been conducted on their mental health challenges. However, attributing high levels of mental health problems solely to their HIV status can be problematic as there may be other contributory factors. This research explored the mental health problems of HIV-infected children and compared these to the mental health problems of their HIV-unaffected peers from similar backgrounds. Data was gathered from two samples of child and caregiver pairs. HIV-infected children (aged 6-12 years) and their caregivers/mothers (n = 54) were recruited from the Kalafong paediatric clinic where they received medical treatment and routine ART. A comparison group of 113 HIV-uninfected children and their uninfected mothers were recruited from primary care clinics in the same community. Caregivers completed the Child Behaviour Checklist (CBCL) to assess children's mental health. Children completed the Self-Description Questionnaire (SDQ-I) and the Revised Children's Manifest Anxiety Scale (RCMAS). The scores of the psychometric sub-scales of the two groups were compared using parametric and non-parametric statistics. HIV-infected children experienced more somatic and affective problems, physiological anxiety, less ADHD and lower self-esteem than HIV-uninfected children in the comparison group, while controlling for age differences. The high levels of mental health problems of both groups of children may be attributed to similar difficult socio-economic circumstances. The fact that most infected children were not aware of their HIV-status could have influenced the results. Mental health services should not be limited to HIV-infected children but should form part of all health care services.

The medico-legal investigation of abandoned fetuses and newborns--a review of cases admitted to the Pretoria Medico-Legal Laboratory, South Africa

There is a dearth of literature on the extent of fetal or newborn abandonment or "dumping" and the medico-legal investigation procedures these cases require. This is despite the fact that these occurrences are a worldwide phenomenon and by definition involve criminal law concerns such as illegal abortion, concealment of birth, murder, or neonaticide, depending on the country concerned. This article contributes to current literature in both respects and provides a retrospective case audit for the period 2004-2008 pertaining to all abandoned newborns and fetuses admitted to the Pretoria Medico-Legal Laboratory (PMLL) in South Africa. Demographic details, scope, and nature of the medico-legal investigation as well as formulation of cause of death were recorded. A total of 289 cases were identified for inclusion in this study, 57% of which were considered to have been non-viable fetuses, while 45 of the viable fetuses were deemed to have been stillborn. These instances involve the crimes of concealment of birth and at times illegal abortion, yet prosecution of these cases are relatively unheard of. Signs of live birth were identified in 38 of the cases in the study. Of these infants, 9 were deemed to have died from injuries they have sustained, and in a further 9 cases, no anatomical cause of death could be identified. Homicidal cases should be brought in cases where death ensued as a result of abandonment; however, it is not known how many cases were prosecuted. A comparatively large number of cases were found to have been admitted to the Pretoria Medico-Legal Laboratory. This is alarming because South African abortion laws are liberal and services are free at point of access in the public health care sector. A substantial percentage of cases of abandoned infants were found to have shown signs of life after birth implying a homicidal manner of death or death by abandonment, but it seems these cases are merely shelved.

Sudden loss of vision in an Acute Medical Unit

We present a case report of young man with Type 1 diabetes who developed acute visual loss after initially presenting with diabetic ketoacidosis. The diagnosis of invasive paranasal sinusoidal aspergillosis was made following CT and biopsy. Although uncommon, visual loss is a recognised complication of disseminated aspergillosis and is more likely in immune-compromised patients and those with diabetes. Early investigation with appropriate sinus imaging and involvement of the Ear Nose and Throat team in recommended when patients with diabetes develop acute visual loss in the context of a non-specific infective illness.

Spectrophotometric activity microassay for pure and recombinant cytochrome P450-type nitric oxide reductase

Nitric oxide reductase (NOR) of the P450 oxidoreductase family accepts electrons directly from its cofactor, NADH, to reduce two nitric oxide (NO) molecules to one nitrous oxide molecule and water. The enzyme plays a key role in the removal of radical NO produced during respiratory metabolism, and applications in bioremediation and biocatalysis have been identified. However, a rapid, accurate, and sensitive enzyme assay has not yet been developed for this enzyme family. In this study, we optimized reaction conditions for the development of a spectrophotometric NOR activity microassay using NOC-5 for the provision of NO in solution. We also demonstrate that the assay is suitable for the quantification and characterization of P450-type NOR. The K(m) and k(cat) kinetic constants obtained by this assay were comparable to the values determined by gas chromatography, but with improved convenience and cost efficiency, effectively by miniaturization. To our knowledge, this is the first study to present the quantification of NOR activity in a kinetic microassay format.

Spherezymes: a novel structured self-immobilisation enzyme technology

BACKGROUND

Enzymes have found extensive and growing application in the field of chemical organic synthesis and resolution of chiral intermediates. In order to stabilise the enzymes and to facilitate their recovery and recycle, they are frequently immobilised. However, immobilisation onto solid supports greatly reduces the volumetric and specific activity of the biocatalysts. An alternative is to form self-immobilised enzyme particles.

RESULTS

Through addition of protein cross-linking agents to a water-in-oil emulsion of an aqueous enzyme solution, structured self-immobilised spherical enzyme particles of Pseudomonas fluorescens lipase were formed. The particles could be recovered from the emulsion, and activity in aqueous and organic solvents was successfully demonstrated. Preliminary data indicates that the lipase tended to collect at the interface.

CONCLUSION

The immobilised particles provide a number of advantages. The individual spherical particles had a diameter of between 0.5-10 mum, but tended to form aggregates with an average particle volume distribution of 100 mum. The size could be controlled through addition of surfactant and variations in protein concentration. The particles were robust enough to be recovered by centrifugation and filtration, and to be recycled for further reactions. They present lipase enzymes with the active sites selectively orientated towards the exterior of the particle. Co-immobilisation with other enzymes, or other proteins such as albumin, was also demonstrated. Moreover, higher activity for small ester molecules could be achieved by the immobilised enzyme particles than for free enzyme, presumably because the lipase conformation required for catalysis had been locked in place during immobilisation. The immobilised enzymes also demonstrated superior activity in organic solvent compared to the original free enzyme. This type of self-immobilised enzyme particle has been named spherezymes.

Staphylococcus lugdunensis endocarditis following cardiac catheterisation

We report the case of a 77 year old with Staphylococcus lugdunensis endocarditis following cardiac catheterisation via a femoral approach. We underline the association between this pathogen and inguinal skin breaks, and discuss the potential diagnostic pitfalls in clinical and laboratory diagnosis.

Isolation, purification and characterization of a novel glucose oxidase from Penicillium sp. CBS 120262 optimally active at neutral pH

A novel glucose oxidase (GOX), a flavoenzyme, from Penicillium sp. was isolated, purified and partially characterised. Maximum activities of 1.08U mg(-1)dry weight intracellular and 6.9U ml(-1) extracellular GOX were obtained. Isoelectric focussing revealed two isoenzymes present in both intra- and extracellular fractions, having pI's of 4.30 and 4.67. GOX from Penicillium sp. was shown to be dimeric with a molecular weight of 148kDa, consisting of two equal subunits with molecular weight of 70k Da. The enzyme displayed a temperature optimum between 25 and 30 degrees C, and an optimum pH range of 6-8 for the oxidation of beta-d-glucose. The enzyme was stable at 25 degrees C for a minimum of 10h, with a half-life of approximately 30 min at 37 degrees C without any prior stabilisation. The lyophilized enzyme was stable at -20 degrees C for a minimum of 6 months. GOX from Penicillium sp. Tt42 displayed the following kinetic characteristics: Vmax, 240.5U mg(-1); Km, 18.4mM; kcat, 741 s(-1) and kcat/Km, 40 s(-1)mM(-1). Stability at room temperature, good shelf-life without stabilisation and the neutral range for the pH optimum of this GOX contribute to its usefulness in current GOX-based biosensor applications.

Morality as a predictor of loneliness: a cross-cultural study

Loneliness is currently regarded as one of the most common and prevalent problems experienced by adolescents, and it is also observed as a painful, unpleasant and negative experience. South African adolescents also have to face and cope with this predicament daily. The main objective of this study was to establish the perception of adolescents of different cultures regarding loneliness and morality and to investigate the relationship between them. It was also determined which of the independent variables, namely morality, gender, age, mother tongue and ethnicity, contributed significantly to the prediction of loneliness. A total of 714 adolescents from three different secondary schools in the greater Bloemfontein area between the ages of 13 and 17 were selected. Adolescents were used because they are increasingly being confronted with moral issues and because loneliness occurs more commonly during adolescence. The focus was on three ethnic groups, namely Coloured, black and white. Three different questionnaires, namely the Le Roux Loneliness Scale, the Morally Debatable Behaviours Scale and a biographical questionnaire were completed to obtain the necessary data.