Isolation and characterisation of novel DNA aptamers against Mycobacterium tuberculosis biomarkers: new tools for tuberculosis diagnostics

Tuberculosis is a curable disease with an average treatment success rate of 86 %. Despite this, there were an estimated 1.5 million deaths due to tuberculosis in 2013, most of which occurred in low and middle income countries. In order to overcome tuberculosis in developing countries innovation in diagnostics is key to administering treatment. While detection of whole mycobacteria has been favoured in the past to diagnose tuberculosis, culturing mycobacteria is costly and microscopy is often not sensitive enough due to low bacterial loads. Detection of Mycobacterium tuberculosis biomarkers in urine, a safe and easy specimen to test, could offer a cost effective and simple solution to identify patients with tuberculosis. Enzyme linked immunosorbent assays (ELISAs) were performed on concentrated tuberculosis patient urine to detect two M. tuberculosis biomarkers: lipoarabinomannan (LAM) and early secreted antigen-6 kDa (ESAT-6). Concentrating urine improved the detection of LAM in human immunodeficiency virus (HIV) negative patients and patients with a CD4 count > 200 cells/µl. ESAT-6 was not detected by ELISA due to a high background signal caused by the available antibodies cross reacting with a human protein present in urine which was identified by western blot and mass spectrometry. Targeted mass spectrometry did not detect ESAT-6 or its dimer partner, culture filtrate protein-10 kDa (CFP-10) in tuberculosis positive patient urine. Since concentrating urine samples is impractical in a clinical setting a more sensitive diagnostic is needed to detect LAM in urine and ESAT-6 or CFP-10 in other samples. Aptamers can be packed more densely on biosensor surfaces increasing the dynamic range of detection while matching the affinity that an antibody has for a biomarker. Chemically modified DNA aptamers were isolated for LAM and the ESAT-6.CFP-10 dimer. The aptamers were characterised by enzyme linked oligonucleotide assays (ELONAs) and biolayer interferometry. One aptamer bound with high affinity to ESAT-6 while one aptamer bound with low affinity to LAM. The use of aptamers as capture agents for detecting biomarkers in biological specimens thus appears to be a viable option for diagnosing tuberculosis, although availability and concentration of individual biomarkers seems likely to remain key to the choice of specimen in which to make diagnostic measurements

Plurilingual practices in Lx Turkish learning: A case study from an online summer intensive program

Drawing on a case study in a beginner-level intensive program held online by a US university, this article examines when and how learners sought out plurilingual and pluricultural connections relevant to Turkish learning. Compared to a monolingual orientation, a plurilingual approach to Lx learning encourages learners to draw upon diverse languages, cultural knowledge, and experiences in approaching the target language. Learners of less commonly taught languages often have unique motivations for learning (Dörnyei & Al-Hoorie, 2017), and prior experiences in language learning, making them particularly poised to mobilize diverse resources and benefit from a plurilingual approach (Wei & Ho, 2018). Data collection included a language history questionnaire, pre- and post - program plurilingual and pluricultural competence measures, semi-structured interviews, and classroom recordings. Findings reveal the activation of plurilingual practices is not limited to occurrences of lexical and cultural overlap and emphasize the centrality of the instructor in drawing upon plurilingual resources

The Technologies Required for Fusing HPC and Real-Time Data to Support Urgent Computing

The use of High Performance Computing (HPC) to compliment urgent decision making in the event of disasters is an important future potential use of supercomputers. However, the usage modes involved are rather different from how HPC has been used traditionally. As such, there are many obstacles that need to be overcome, not least the unbounded wait times in the batch system queues, to make the use of HPC in disaster response practical. In this paper, we present how the VESTEC project plans to overcome these issues and develop a working prototype of an urgent computing control system. We describe the requirements for such a system and analyse the different technologies available that can be leveraged to successfully build such a system. We finally explore the design of the VESTEC system and discuss ongoing challenges that need to be addressed to realise a production level system.Comment: Preprint of paper in 2019 IEEE/ACM HPC for Urgent Decision Making (UrgentHPC

Higher measured than modeled ozone production at increased NOx levels in the Colorado Front Range

Abstract. Chemical models must correctly calculate the ozone formation rate, P(O3), to accurately predict ozone levels and to test mitigation strategies. However, air quality models can have large uncertainties in P(O3) calculations, which can create uncertainties in ozone forecasts, especially during the summertime when P(O3) is high. One way to test mechanisms is to compare modeled P(O3) to direct measurements. During summer 2014, the Measurement of Ozone Production Sensor (MOPS) directly measured net P(O3) in Golden, CO, approximately 25 km west of Denver along the Colorado Front Range. Net P(O3) was compared to rates calculated by a photochemical box model that was constrained by measurements of other chemical species and that used a lumped chemical mechanism and a more explicit one. Median observed P(O3) was up to a factor of 2 higher than that modeled during early morning hours when nitric oxide (NO) levels were high and was similar to modeled P(O3) for the rest of the day. While all interferences and offsets in this new method are not fully understood, simulations of these possible uncertainties cannot explain the observed P(O3) behavior. Modeled and measured P(O3) and peroxy radical (HO2 and RO2) discrepancies observed here are similar to those presented in prior studies. While a missing atmospheric organic peroxy radical source from volatile organic compounds co-emitted with NO could be one plausible solution to the P(O3) discrepancy, such a source has not been identified and does not fully explain the peroxy radical model–data mismatch. If the MOPS accurately depicts atmospheric P(O3), then these results would imply that P(O3) in Golden, CO, would be NOx-sensitive for more of the day than what is calculated by models, extending the NOx-sensitive P(O3) regime from the afternoon further into the morning. These results could affect ozone reduction strategies for the region surrounding Golden and possibly other areas that do not comply with national ozone regulations. Thus, it is important to continue the development of this direct ozone measurement technique to understand P(O3), especially under high-NOx regimes

Regional Invasive Species & Climate Change Management Challenge: Embracing the Future. Promoting adaptation and resilience to invasive species and climate change

Climate change and invasive species can interact to increase disturbances and magnify changes in ecosystem form and function (Double Trouble). Increasing resilience is one of several management approaches for enabling healthy ecosystems to persist despite these changes. While resilience can be complicated and take many forms, it can generally be thought of as the “ability [of an ecosystem] to experience disturbances or environmental change without changing to a fundamentally different state” [Holling, 1973]. The accumulating effects of climate change, invasive species, or interacting effects of multiple disturbances can push an ecosystem past a tipping point and into a new ecological state. These alternative states are characterized by a different suite of species or functions, which are difficult or impossible to recover from (e.g. a shift from a closed-canopy to an open-canopy forested wetland). Actions to increase resilience help an ecosystem to maintain or return to its fundamental structure or function after a disturbance. Resilience falls in the middle of a spectrum of management goals ranging from preventing change (resistance) to promoting change (transformation) in the species composition, structure, or functions provided by an ecosystem. Clear management goals (See Table) and an understanding of the range of disturbances affecting focal ecosystems are necessary for deciding between managing for resistance, resilience, or transformation and what actions are required for successful management outcomes

The role of interactive super-computing in using HPC for urgent decision making

Technological advances are creating exciting new opportunities that have the potential to move HPC well beyond traditional computational workloads. In this paper we focus on the potential for HPC to be instrumental in responding to disasters such as wildfires, hurricanes, extreme flooding, earthquakes, tsunamis, winter weather conditions, and accidents. Driven by the VESTEC EU funded H2020 project, our research looks to prove HPC as a tool not only capable of simulating disasters once they have happened, but also one which is able to operate in a responsive mode, supporting disaster response teams making urgent decisions in real-time. Whilst this has the potential to revolutionise disaster response, it requires the ability to drive HPC interactively, both from the user's perspective and also based upon the arrival of data. As such interactivity is a critical component in enabling HPC to be exploited in the role of supporting disaster response teams so that urgent decision makers can make the correct decision first time, every time

Prenatal Vitamin D Levels in Maternal Sera and Offspring Specific Learning Disorders

Recent evidence has suggested potential harmful effects of vitamin D deficiency during pregnancy on offspring brain development, for example, elevated risks for neuropsychiatric disorders. Findings on general cognition and academic achievement are mixed, and no studies have examined the effect of prenatal 25-hydroxyvitamin D (25(OH)D) levels on diagnosed specific learning disorders, which was the aim of this study. We examined a nested case–control sample from the source cohort of all singleton-born children in Finland between 1996 and 1997 (n = 115,730). A total of 1607 cases with specific learning disorders (mean age at diagnosis: 9.9 years) and 1607 matched controls were identified from Finnish nationwide registers. Maternal 25(OH)D levels were analyzed from serum samples collected during the first trimester of pregnancy and stored in a national biobank. Conditional logistic regression was used to test the association between maternal 25(OH)D and offspring specific learning disorders. There were no significant associations between maternal 25(OH)D levels and specific learning disorders when vitamin D was examined as a log-transformed continuous variable (adjusted OR 0.98, 95% CI 0.82–1.18, p = 0.84) or as a categorical variable (25(OH)D 50 nmol/L), nor when it was divided into quintiles (adjusted OR for the lowest quintile 1.00, 95% CI 0.78–1.28, p = 0.99 compared to the highest quintile). This study found no association between low maternal 25(OH)D in early pregnancy and offspring specific learning disorders

Prenatal Vitamin D Levels in Maternal Sera and Offspring Specific Learning Disorders

Recent evidence has suggested potential harmful effects of vitamin D deficiency during pregnancy on offspring brain development, for example, elevated risks for neuropsychiatric disorders. Findings on general cognition and academic achievement are mixed, and no studies have examined the effect of prenatal 25-hydroxyvitamin D (25(OH)D) levels on diagnosed specific learning disorders, which was the aim of this study. We examined a nested case–control sample from the source cohort of all singleton-born children in Finland between 1996 and 1997 (n = 115,730). A total of 1607 cases with specific learning disorders (mean age at diagnosis: 9.9 years) and 1607 matched controls were identified from Finnish nationwide registers. Maternal 25(OH)D levels were analyzed from serum samples collected during the first trimester of pregnancy and stored in a national biobank. Conditional logistic regression was used to test the association between maternal 25(OH)D and offspring specific learning disorders. There were no significant associations between maternal 25(OH)D levels and specific learning disorders when vitamin D was examined as a log-transformed continuous variable (adjusted OR 0.98, 95% CI 0.82–1.18, p = 0.84) or as a categorical variable (25(OH)D 50 nmol/L), nor when it was divided into quintiles (adjusted OR for the lowest quintile 1.00, 95% CI 0.78–1.28, p = 0.99 compared to the highest quintile). This study found no association between low maternal 25(OH)D in early pregnancy and offspring specific learning disorders

Molecular phylogenetics reveals convergent evolution in lower Congo River spiny eels

Background The lower Congo River (LCR) is a region of exceptional species diversity and endemism in the Congo basin, including numerous species of spiny eels (genus Mastacembelus). Four of these exhibit distinctive phenotypes characterized by greatly reduced optic globes deeply embedded into the head (cryptophthalmia) and reduced (or absent) melanin pigmentation, among other characteristics. A strikingly similar cryptophthalmic phenotype is also found in members of a number of unrelated fish families, strongly suggesting the possibility of convergent evolution. However, little is known about the evolutionary processes that shaped diversification in LCR Mastacembelus, their biogeographic origins, or when colonization of the LCR occurred. Methods We sequenced mitochondrial and nuclear genes from Mastacembelus species collected in the lower Congo River, and compared them with other African species and Asian representatives as outgroups. We analyzed the sequence data using Maximum Likelihood and Bayesian phylogenetic inference. Results Bayesian and Maximum Likelihood phylogenetic analyses, and Bayesian coalescent methods for species tree reconstruction, reveal that endemic LCR spiny eels derive from two independent origins, clearly demonstrating convergent evolution of the cryptophthalmic phenotype. Mastacembelus crassus, M. aviceps, and M. simbi form a clade, allied to species found in southern, eastern and central Africa. Unexpectedly, M. brichardi and brachyrhinus fall within a clade otherwise endemic to Lake Tanganikya (LT) ca. 1500 km east of the LCR. Divergence dating suggests the ages of these two clades of LCR endemics differ markedly. The age of the crassus group is estimated at ~4 Myr while colonization of the LCR by the brichardi-brachyrhinus progenitor was considerably more recent, dated at ~0.5 Myr. Conclusions The phylogenetic framework of spiny eels presented here, the first to include LCR species, demonstrates that cryptophthalmia and associated traits evolved at least twice in Mastacembelus: once in M. brichardi and at least once in the M. crassus clade. Timing of diversification is broadly consistent with the onset of modern high-energy flow conditions in the LCR and with previous studies of endemic cichlids. The close genetic relationship between M. brichardi and M. brachyrhinus is particularly notable given the extreme difference in phenotype between these species, and additional work is needed to better understand the evolutionary history of diversification in this clade. The findings presented here demonstrate strong, multi-trait convergence in LCR spiny eels, suggesting that extreme selective pressures have shaped numerous phenotypic attributes of the endemic species of this region. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0507-x) contains supplementary material, which is available to authorized users

Biological Reduction of a U(V)-Organic Ligand Complex

Metal-reducing microorganisms such as Shewanella oneidensis MR-1 reduce highly soluble species of hexavalent uranyl (U(VI)) to less mobile tetravalent uranium (U(IV)) compounds. The biologically mediated immobilization of U(VI) is being considered for the remediation of U contamination. However, the mechanistic underpinnings of biological U(VI) reduction remain unresolved. It has become clear that a first electron transfer occurs to form pentavalent (U(V)) intermediates, but it has not been definitively established whether a second one-electron transfer can occur or if disproportionation of U(V) is required. Here, we utilize the unusual properties of dpaea2– ((dpaeaH2═bis(pyridyl-6-methyl-2-carboxylate)-ethylamine)), a ligand forming a stable soluble aqueous complex with U(V), and investigate the reduction of U(VI)–dpaea and U(V)–dpaea by S. oneidensis MR-1. We establish U speciation through time by separating U(VI) from U(IV) by ion exchange chromatography and characterize the reaction end-products using U M4-edge high resolution X-ray absorption near-edge structure (HR-XANES) spectroscopy. We document the reduction of solid phase U(VI)–dpaea to aqueous U(V)–dpaea but, most importantly, demonstrate that of U(V)–dpaea to U(IV). This work establishes the potential for biological reduction of U(V) bound to a stabilizing ligand. Thus, further work is warranted to investigate the possible persistence of U(V)–organic complexes followed by their bioreduction in environmental systems