Single tube allele specific PCR: a low cost technique for molecular screening of sickle cell anaemia in Nigeria

Background: Sickle cell anaemia (SCA) is a hereditary blood disorder caused by a single mutation in the haemoglobin gene. The disease burden of SCA is highest in Nigeria. The allele specific polymerase chain reaction (ASPCR) method is applicable for the direct detection of known single nucleotide polymorphisms (SNPs). Objective: To investigate the use of the single tube ASPCR as an accurate and affordable method for SCA screening in Nigeria. Methods: DNA was extracted from study subjects with normal haemoglobin, HbAA (20), sickle cell anaemia, HbSS (20) and carriers, HbAS (1). Haemoglobin was genotyped by ASPCR using two primer sets that amplifies the wildtype and mutant haemoglobins in each sample. Amplicon sizes were analyzed by gel electrophoresis. Results: Amplicons were visible after electrophoresis at regions 517 base pair (bp) for HbA and 267 bp for HbS. ASPCR correctly and unambiguously detected the presence or absence of haemoglobins A and S from all samples collected, demonstrating its accuracy and precision for the screening of SCA. Conclusion: This study validates ASPCR as an effective, low cost approach for the clinical screening of SCA in Nigeria. ASPCR is also applicable for other genetic diseases, paternity testing, and forensics where more expensive fluorescence-based approaches are not obtainable.Keywords: Sickle cell anaemia, polymerase chain reaction, molecular diagnostic techniques

Human immunodeficiency virus type 1 envelope-mediated neuropathogenesis: targeted gene delivery by a Sindbis virus expression vector

AbstractSindbis virus (SIN) expression vectors offer the opportunity for studying neuropathogenesis because of their distinct neural cell tropism. Here, we demonstrate that a recombinant SIN vector expressing EGFP (SINrep5-EGFP) infected multiple cell types including neural cells from several species relevant to lentivirus pathogenesis with high levels of transgene expression. Infection of human neurons by a recombinant SIN (SINrep5-JRFL) expressing the full-length envelope from a neurovirulent human immunodeficiency virus type 1 (HIV-1) strain (JRFL) caused increased cytotoxicity compared to infection with SINrep5-EGFP (P < 0.001), while no cytotoxicity was observed among infected human astrocytes or monocytoid cells. Both human monocyte-derived macrophages (MDM) (P < 0.01) and astrocytes (P < 0.001) infected with SINrep5-JRFL released soluble neurotoxins in contrast to SINrep5-EGFP or mock-infected cells, although this was most prominent for the astrocytes. Implantation of SINrep5-JRFL into the brains of SCID/NOD mice induced neuroinflammation, neuronal loss, and neurobehavioral changes characteristic of HIV-1 infection, which were not present in SINrep5-EGFP or mock-infected animals. Thus SIN expression vectors represent novel tools for studying in vitro and in vivo HIV-1 neuropathogenesis because of their high levels of transgene expression in specific cell types within the brain

Evolution of HIV-1 in the Gut

The high mutation rate of Human Immunodeficiency Virus (HIV) is a significant contributor to its ability to develop drug resistance. While much research has been directed towards developing new drugs and treatments in response to resistance, it is also critical to gain a better understanding of the nature of the virus’s replication. Previous studies (van Marle et al., 2007; van Marle et al., 2010) have demonstrated that viral replication and evolution are compartmentalized in different gut tissues. However, these studies focused on the reverse transcriptase (rt) region of the proviral DNA. This project examined whether the same patterns of viral evolution would be found in the nef (negative factor) encoding region. The Nef protein contributes to the infectivity and pathogenicity of the virus and is therefore under different selection pressures than reverse transcriptase. For this project, gut biopsy samples were taken from a patient cohort at the Southern Alberta HIV Clinic from 1993-1996 and again from 2007-2010. Proviral DNA was isolated and the nef region was subsequently sequenced and analyzed using Molecular Evolutionary Genetic Analysis (MEGA) software. The results indicated that evolution of the nef region over time is consistent with compartmentalization of the gut in each patient. Overall diversity of the Nef protein encoding region is similar among all tissue types. Finally, the majority of mutations suggest that HIV-1 is under neutral or purifying selection. These observations are consistent with the observations of the rt region, suggesting a similar evolutionary pattern for the nef region

Compartmentalization of the gut viral reservoir in HIV-1 infected patients

<p>Abstract</p> <p>Background</p> <p>Recently there has been an increasing interest and appreciation for the gut as both a viral reservoir as well as an important host-pathogen interface in human immunodefiency virus type 1 (HIV-1) infection. The gut associated lymphoid tissue (GALT) is the largest lymphoid organ infected by HIV-1. In this study we examined if different HIV-1 quasispecies are found in different parts of the gut of HIV-1 infected individuals.</p> <p>Results</p> <p>Gut biopsies (esophagus, stomach, duodenum and colorectum) were obtained from eight HIV-1 infected preHAART (highly active antiretroviral therapy) patients. HIV-1 Nef and Reverse transcriptase (RT) encoding sequences were obtained through nested PCR amplification from DNA isolated from the gut biopsy tissues. The PCR fragments were cloned and sequenced. The resulting sequences were subjected to various phylogenetic analyses. Expression of the <it>nef </it>gene and viral RNA in the different gut tissues was determined using real-time RT-PCR. Phylogenetic analysis of the Nef protein-encoding region revealed compartmentalization of viral replication in the gut within patients. Viral diversity in both the Nef and RT encoding region varied in different parts of the gut. Moreover, increased <it>nef </it>gene expression (p < 0.05) and higher levels of viral genome were observed in the colorectum (p < 0.05). These differences could reflect an adaptation of HIV-1 to the various tissues.</p> <p>Conclusion</p> <p>Our results indicated that different HIV-1 quasispecies populate different parts of the gut, and that viral replication in the gut is compartmentalized. These observations underscore the importance of the gut as a host-pathogen interface in HIV-1 infection.</p

New land-use-change emissions indicate a declining CO₂ airborne fraction

About half of the anthropogenic CO2 emissions remain in the atmosphere and half are taken up by the land and ocean1. If the carbon uptake by land and ocean sinks becomes less efficient, for example, owing to warming oceans2 or thawing permafrost3, a larger fraction of anthropogenic emissions will remain in the atmosphere, accelerating climate change. Changes in the efficiency of the carbon sinks can be estimated indirectly by analysing trends in the airborne fraction, that is, the ratio between the atmospheric growth rate and anthropogenic emissions of CO2 (refs. 4–10). However, current studies yield conflicting results about trends in the airborne fraction, with emissions related to land use and land cover change (LULCC) contributing the largest source of uncertainty7,11,12. Here we construct a LULCC emissions dataset using visibility data in key deforestation zones. These visibility observations are a proxy for fire emissions13,14, which are — in turn — related to LULCC15,16. Although indirect, this provides a long-term consistent dataset of LULCC emissions, showing that tropical deforestation emissions increased substantially (0.16 Pg C decade−1) since the start of CO2 concentration measurements in 1958. So far, these emissions were thought to be relatively stable, leading to an increasing airborne fraction4,5. Our results, however, indicate that the CO2 airborne fraction has decreased by 0.014 ± 0.010 decade−1 since 1959. This suggests that the combined land–ocean sink has been able to grow at least as fast as anthropogenic emissions

Single tube allele specific PCR: a low cost technique for molecular screening of sickle cell anaemia in Nigeria

Background: Sickle cell anaemia (SCA) is a hereditary blood disorder caused by a single mutation in the haemoglobin gene. The disease burden of SCA is highest in Nigeria. The allele specific polymerase chain reaction (ASPCR) method is applicable for the direct detection of known single nucleotide polymorphisms (SNPs). Objective: To investigate the use of the single tube ASPCR as an accurate and affordable method for SCA screening in Nigeria. Methods: DNA was extracted from study subjects with normal haemoglobin, HbAA (20), sickle cell anaemia, HbSS (20) and carriers, HbAS (1). Haemoglobin was genotyped by ASPCR using two primer sets that amplifies the wildtype and mutant haemoglobins in each sample. Amplicon sizes were analyzed by gel electrophoresis. Results: Amplicons were visible after electrophoresis at regions 517 base pair (bp) for HbA and 267 bp for HbS. ASPCR correctly and unambiguously detected the presence or absence of haemoglobins A and S from all samples collected, demonstrating its accuracy and precision for the screening of SCA. Conclusion: This study validates ASPCR as an effective, low cost approach for the clinical screening of SCA in Nigeria. ASPCR is also applicable for other genetic diseases, paternity testing, and forensics where more expensive fluorescence-based approaches are not obtainable

Global fire emissions estimates during 1997-2016

Climate, land use, and other anthropogenic and natural drivers have the potential to influence fire dynamics in many regions. To develop a mechanistic understanding of the changing role of these drivers and their impact on atmospheric composition, long-term fire records are needed that fuse information from different satellite and in situ data streams. Here we describe the fourth version of the Global Fire Emissions Database (GFED) and quantify global fire emissions patterns during 1997-2016. The modeling system, based on the Carnegie-Ames-Stanford Approach (CASA) biogeochemical model, has several modifications from the previous version and uses higher quality input datasets. Significant upgrades include (1) new burned area estimates with contributions from small fires, (2) a revised fuel consumption parameterization optimized using field observations, (3) modifications that improve the representation of fuel consumption in frequently burning landscapes, and (4) fire severity estimates that better represent continental differences in burning processes across boreal regions of North America and Eurasia. The new version has a higher spatial resolution (0.25) and uses a different set of emission factors that separately resolves trace gas and aerosol emissions from temperate and boreal forest ecosystems. Global mean carbon emissions using the burned area dataset with small fires (GFED4s) were 2.21015 grams of carbon per year (Pg Cyr-1) during 1997-2016, with a maximum in 1997 (3.0 Pg C yr-1) and minimum in 2013 (1.8 Pg C yr-1). These estimates were 11% higher than our previous estimates (GFED3) during 1997-2011, when the two datasets overlapped. This net increase was the result of a substantial increase in burned area (37 %), mostly due to the inclusion of small fires, and a modest decrease in mean fuel consumption (-19 %) to better match estimates from field studies, primarily in savannas and grasslands. For trace gas and aerosol emissions, differences between GFED4s and GFED3 were often larger due to the use of revised emission factors. If small fire burned area was excluded (GFED4 without the s for small fires), average emissions were 1.5 Pg C yr-1. The addition of small fires had the largest impact on emissions in temperate North America, Central America, Europe, and temperate Asia. This small fire layer carries substantial uncertainties; improving these estimates will require use of new burned area products derived from high-resolution satellite imagery. Our revised dataset provides an internally consistent set of burned area and emissions that may contribute to a better understanding of multi-decadal changes in fire dynamics and their impact on the Earth system. GFED data are available from http://www.globalfiredata.org

Using the social entrepreneurship approach to generate innovative and sustainable malaria diagnosis interventions in Tanzania: a case study

<p>Abstract</p> <p>Background</p> <p>There have been a number of interventions to date aimed at improving malaria diagnostic accuracy in sub-Saharan Africa. Yet, limited success is often reported for a number of reasons, especially in rural settings. This paper seeks to provide a framework for applied research aimed to improve malaria diagnosis using a combination of the established methods, participatory action research and social entrepreneurship.</p> <p>Methods</p> <p>This case study introduces the idea of using the social entrepreneurship approach (SEA) to create innovative and sustainable applied health research outcomes. The following key elements define the SEA: (1) identifying a locally relevant research topic and plan, (2) recognizing the importance of international multi-disciplinary teams and the incorporation of local knowledge, (3) engaging in a process of continuous innovation, adaptation and learning, (4) remaining motivated and determined to achieve sustainable long-term research outcomes and, (5) sharing and transferring ownership of the project with the international and local partner.</p> <p>Evaluation</p> <p>The SEA approach has a strong emphasis on innovation lead by local stakeholders. In this case, innovation resulted in a unique holistic research program aimed at understanding patient, laboratory and physician influences on accurate diagnosis of malaria. An evaluation of milestones for each SEA element revealed that the success of one element is intricately related to the success of other elements.</p> <p>Conclusions</p> <p>The SEA will provide an additional framework for researchers and local stakeholders that promotes innovation and adaptability. This approach will facilitate the development of new ideas, strategies and approaches to understand how health issues, such as malaria, affect vulnerable communities.</p

Global fire emissions buffered by the production of pyrogenic carbon

Landscape fires burn 3–5 million km2 of the Earth’s surface annually. They emit 2.2 Pg of carbon per year to the atmosphere, but also convert a significant fraction of the burned vegetation biomass into pyrogenic carbon. Pyrogenic carbon can be stored in terrestrial and marine pools for centuries to millennia and therefore its production can be considered a mechanism for long-term carbon sequestration. Pyrogenic carbon stocks and dynamics are not considered in global carbon cycle models, which leads to systematic errors in carbon accounting. Here we present a comprehensive dataset of pyrogenic carbon production factors from field and experimental fires and merge this with the Global Fire Emissions Database to quantify the global pyrogenic carbon production flux. We found that 256 (uncertainty range: 196–340) Tg of biomass carbon was converted annually into pyrogenic carbon between 1997 and 2016. Our central estimate equates to 12% of the annual carbon emitted globally by landscape fires, which indicates that their emissions are buffered by pyrogenic carbon production. We further estimate that cumulative pyrogenic carbon production is 60 Pg since 1750, or 33–40% of the global biomass carbon lost through land use change in this period. Our results demonstrate that pyrogenic carbon production by landscape fires could be a significant, but overlooked, sink for atmospheric CO2