Upconverting luminescent nanoparticles for bioimaging applications

The synthesis and surface modification of upconverting nanoparticles (UCNPs) composed of a host lattice NaYF4 doped with sensitizers (Yb3+, Nd3+) and luminescent emitters (Er3+) were investigated for potential integration in biological applications.The fascination of NaYF4: Nd3+, Yb3+, Er3+ upconverting nanoparticles derives from their capacity to be excited in the biologically transparent window (650-950 nm) enabling deep tissue penetration. In particular, the ability to convert near infrared radiation into visible light (upconversion), which prevents autofluorescence and over-heating effect of biological tissues.In biological applications especially in vivo, morphology and size of the nanoparticles plays a crucial role in determination of cellular responses and fate in living organism. Heterogeneously sized nanoparticles, in contrast to uniform ones, might be distributed unevenly in the organism causing undesirable toxic side effects. Therefore, precise control of the nanoparticle size, distribution, and reproducibility were main tasks in the first part of this work. Colloidal upconverting nanoparticles were synthesized using coprecipitation method. Synthetic parameters such as reaction temperature (280-320 °C), and time (5-30 min) were used to tailor the nanoparticle morphology, crystal phase (cubic or hexagonal) and particle size (sub-10 - 20 nm). Integration of these nanoparticles in biological applications requires dispersibility in aqueous media. Hence hydrophobic UCNPs were surface-modified with low molecular weight ligands including O-phospho-L-threonine, alendronic acid, and PEG-phosphate ligands to generate water-dispersible UCNPs. Furthermore, in this work, photocrosslinking of diacetylenes is presented as an effective way to create robust UCNPs with a crosslinked shell. Finally, the protein corona formation on UCNPs coated with charged, zwitterionic and nearly neutral ligands was investigated. The composition of protein binding to UCNP is notably influenced by the surface charges of the UCNPs. Overall, the results obtained in the frame of this work show that the NaYF4: Nd3+, Yb3+, Er3+ UCNPS have the potential to replace conventional fluorophores in bioimaging applications due to their remarkable optical properties, as well as the derivatization flexibility of their surfac

Analysis and monitoring of equitable access and full participation in education in South Africa: the challenge of data quality

Indicators to measure educational access serve the useful purpose of facilitating theevaluation and analysis of progress made towards achieving stated educational accessobjectives. In South Africa, data from the Gross Enrolment Ratio (GER) and Net EnrolmentRatio (NER) are commonly used to report on progress made towards universal educationalaccess. The critique in the use of these data is threefold; first, that they are computed frominaccurate school data and second, that their conceptual basis stems from a structuralapproach to educational access that gives primacy to the onset or final phases of theschooling process (primary or secondary) rather than also to what not only happens duringschool but also in classrooms. Subsumed and arising from the first two, the third critiquerelates to the nature of indicators used to measure educational access. Put differently,conceptualisations premised on a structural approach have not only had consequences forthe source of data and indicators used to measure educational access but also for its analysisand interpretation.Established therefore, is that conceptions of educational access not onlyinfluence the choice of indicators that are regarded to be effective and suitable to describeeducational access (Fataar, 1997; Lewin, 2007; Hill, Baxen, Craig and Namakula, 2012) butthey also impact the nature of data generated for this purpose.Through a review of conceptualisations of educational access and through the use of datadrawn from a study of two Eastern Cape secondary schools, this paper argues that a shift indiscourses on education access is necessary for this country to fully understand and respondto the discontinuities that persist to characterise the education system. It calls for a shiftfrom a structural discourse to one that intersects equity and full participation concerns. Thepaper highlights how such a shift in conceptualisation not only has implications for thenature of data gathered but importantly for indicators produced and applied to describe andmeasure educational access

The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda

The General Population Cohort (GPC) in south-western Uganda has a low HIV-1 incidence rate (25 years (aOR = 1.52; 95% CI, 1.16-2.0) and being a resident in the GPC (aOR = 6.90; 95% CI, 5.22-9.21). Phylogeographic analysis showed significant viral dissemination (Bayes Factor test, BF > 3) from the GPC without significant viral introductions (BF < 3) into the GPC. The findings suggest localized HIV-1 transmission in the GPC. Intensifying geographically focused combination interventions in the GPC would contribute towards controlling HIV-1 infections

Rates of HIV-1 virological suppression and patterns of acquired drug resistance among fisherfolk on first-line antiretroviral therapy in Uganda.

OBJECTIVES: We examined virological outcomes, patterns of acquired HIV drug resistance (ADR), correlates of virological failure (VF) and acquired drug resistance among fisherfolk on first-line ART. METHODS: We enrolled 1169 adults on ART for a median duration of 6, 12, 24, 36 and ≥48 months and used a pooled VL testing approach to identify VF (VL ≥1000 copies/mL). We performed genotyping among VF cases and determined correlates of VF and ADR by logistic regression. RESULTS: The overall virological suppression rate was 91.7% and ADR was detected in 71/97 (73.2%) VF cases. The most prevalent mutations were M184V/I (53.6%) for NRTIs and K103N (39.2%) for NNRTIs. Thymidine analogue mutations were detected in 21.6% of VF cases while PI mutations were absent. A zidovudine-based ART regimen, duration on ART (≥24 months) and secondary/higher education level were significantly associated with VF. A nevirapine-based regimen [adjusted OR (aOR): 1.87; 95% CI: 0.03-0.54)] and VL ≥10000 copies/mL (aOR: 3.48; 95% CI: 1.37-8.85) were ADR correlates. The pooling strategies for VL testing with a negative predictive value (NPV) of ≥95.2% saved US $20320 (43.5%) in VL testing costs. CONCLUSIONS: We observed high virological suppression rates among these highly mobile fisherfolk; however, there was widespread ADR among those with VF at the first VL testing prior to intensive adherence counselling. Timely treatment switching and adherence support is recommended for better treatment outcomes. Adoption of pooled VL testing could be cost effective, particularly in resource-limited settings

Gender Differences in HIV Disease Progression and Treatment Outcomes among HIV Patients One Year after Starting Antiretroviral Treatment (ART) in Dar es Salaam, Tanzania.

We investigated gender differences in treatment outcome during first line antiretroviral treatment (ART) in a hospital setting in Tanzania, assessing clinical, social demographic, virological and immunological factors. We conducted a cohort study involving HIV infected patients scheduled to start ART and followed up to 1 year on ART. Structured questionnaires and patients file review were used to collect information and blood was collected for CD4 and viral load testing. Gender differences were assessed using Kruskal-Wallis test and chi-square test for continuous and categorical data respectively. Survival distributions for male and female patients were estimated using the Kaplan-Meier method and compared using Cox proportional hazards models. Of 234 patients recruited in this study, 70% were females. At baseline, women had significantly lower education level; lower monthly income, lower knowledge on ARV, less advanced HIV disease (33% women; 47% men started ART at WHO stage IV, p = 0.04), higher CD4 cell count (median 149 for women, 102 for men, p = 0.02) and higher BMI (p = 0.002). After 1 year of standard ART, a higher proportion of females survived although this was not significant, a significantly higher proportion of females had undetectable plasma viral load (69% women, 45% men, p = 0.003), however females ended at a comparable CD4 cell count (median CD4, 312 women; 321 men) signifying a worse CD4 cell increase (p = 0.05), even though they still had a higher BMI (p = 0.02). The unadjusted relative hazard for death for men compared to women was 1.94. After correcting for confounding factors, the Cox proportional hazards showed no significant difference in the survival rate (relative hazard 1.02). We observed women were starting treatment at a less advanced disease stage, but they had a lower socioeconomical status. After one year, both men and women had similar clinical and immunological conditions. It is not clear why women lose their immunological advantage over men despite a better virological treatment response. We recommend continuous follow up of this and more cohorts of patients to better understand the underlying causes for these differences and whether this will translate also in longer term differences

Viruses associated with measles-like illnesses in Uganda

Objectives: In this study, we investigated the causes of measles-like illnesses (MLI) in the Uganda national surveillance programme in order to inform diagnostic assay selection and vaccination strategies. Methods: We used metagenomic next-generation sequencing (M-NGS) on the Illumina platform to identify viruses associated with MLI (defined as fever and rash in the presence of either cough, coryza or conjunctivitis) in patient samples that had tested IgM negative for measles between 2010 and 2019. Results: Viral genomes were identified in 87/271 (32%) of samples, of which 44/271 (16%) contained 12 known viral pathogens. Expected viruses included rubella, human parvovirus B19, Epstein Barr virus, human herpesvirus 6B, human cytomegalovirus, varicella zoster virus and measles virus (detected within the seronegative window-period of infection) and the blood-borne hepatitis B virus. We also detected Saffold virus, human parvovirus type 4, the human adenovirus C2 and vaccine-associated poliovirus type 1. Conclusions: The study highlights the presence of undiagnosed viruses causing MLI in Uganda, including vaccine-preventable illnesses. NGS can be used to monitor common viral infections at a population level, especially in regions where such infections are prevalent, including low and middle income countries to guide vaccination policy and optimize diagnostic assays

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Upconverting luminescent nanoparticles for bioimaging applications

The synthesis and surface modification of upconverting nanoparticles (UCNPs) composed of a host lattice NaYF4 doped with sensitizers (Yb3+, Nd3+) and luminescent emitters (Er3+) were investigated for potential integration in biological applications.The fascination of NaYF4: Nd3+, Yb3+, Er3+ upconverting nanoparticles derives from their capacity to be excited in the biologically transparent window (650-950 nm) enabling deep tissue penetration. In particular, the ability to convert near infrared radiation into visible light (upconversion), which prevents autofluorescence and over-heating effect of biological tissues.In biological applications especially in vivo, morphology and size of the nanoparticles plays a crucial role in determination of cellular responses and fate in living organism. Heterogeneously sized nanoparticles, in contrast to uniform ones, might be distributed unevenly in the organism causing undesirable toxic side effects. Therefore, precise control of the nanoparticle size, distribution, and reproducibility were main tasks in the first part of this work. Colloidal upconverting nanoparticles were synthesized using coprecipitation method. Synthetic parameters such as reaction temperature (280-320 °C), and time (5-30 min) were used to tailor the nanoparticle morphology, crystal phase (cubic or hexagonal) and particle size (sub-10 - 20 nm). Integration of these nanoparticles in biological applications requires dispersibility in aqueous media. Hence hydrophobic UCNPs were surface-modified with low molecular weight ligands including O-phospho-L-threonine, alendronic acid, and PEG-phosphate ligands to generate water-dispersible UCNPs. Furthermore, in this work, photocrosslinking of diacetylenes is presented as an effective way to create robust UCNPs with a crosslinked shell. Finally, the protein corona formation on UCNPs coated with charged, zwitterionic and nearly neutral ligands was investigated. The composition of protein binding to UCNP is notably influenced by the surface charges of the UCNPs. Overall, the results obtained in the frame of this work show that the NaYF4: Nd3+, Yb3+, Er3+ UCNPS have the potential to replace conventional fluorophores in bioimaging applications due to their remarkable optical properties, as well as the derivatization flexibility of their surfac