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BACKGROUND: Control of latent tuberculosis infection (LTBI) is a priority in the World Health Organization strategy to eliminate tuberculosis (TB). Many high-income low TB incidence countries have prioritised LTBI screening and treatment in recent migrants. We tested whether a novel model of care, based entirely within primary care, was effective and safe as compared to secondary care. METHODS: This was a pragmatic cluster-randomised, parallel group, superiority trial conducted in 34 general practices in London, UK, comparing LTBI treatment in recent migrants in primary care to secondary care. The primary outcome was treatment completion, defined as taking at least 90% of antibiotic doses. Secondary outcomes included treatment acceptance, adherence, adverse effects, patient satisfaction, TB-incidence and a cost-effectiveness analysis. The trial is registered at ClinicalTrials.gov (NCT03069807). Analyses were performed on an intention-to-treat basis. RESULTS: Between September 2016 and May 2019, 362 recent migrants with LTBI were offered treatment and 276 accepted. Treatment completion was similar in primary and secondary care (82·6% versus 86·0%, aOR:0·64, 95%CI:0·31-1·29). There was no difference in drug induced liver injury (DILI) between primary and secondary care (0·7% versus 2·3%, aOR:0·29, 95%CI:0·03-2·84). Treatment acceptance was lower in primary care (65·2% (146/224) versus 94.2% (130/138), aOR:0·10, 95%CI:0·03-0·31). The estimated cost per patient completing treatment was lower in primary care, with an incremental saving of £315. 27(£313.47-£317.07). CONCLUSIONS: The treatment of LTBI in recent migrants within primary care does not result in higher rates of treatment completion but is safe and costs less when compared to secondary care.
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Sire is a Python/C++ library that is used both to prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. This empowers researchers to use sire to write a single script that can, for example, load a molecule from a PDBx/mmCIF file via Gemmi, perform SMARTS searches via RDKit, parameterize molecules using BioSimSpace, run GPU-accelerated molecular dynamics via OpenMM, and then display the resulting dynamics trajectory in a NGLView Jupyter notebook 3D molecular viewer. This functionality is built on by BioSimSpace, which uses sire's molecular information engine to interconvert with programs such as GROMACS, NAMD, Amber, and AmberTools for automated molecular parameterization and the running of molecular dynamics, metadynamics, and alchemical free energy workflows. Sire comes complete with a powerful molecular information search engine, plus trajectory loading and editing, analysis, and energy evaluation engines. This, when combined with an in-built computer algebra system, gives substantial flexibility to researchers to load, search for, edit, and combine molecular information from multiple sources and use that to drive novel algorithms by combining functionality from other programs. Sire is open source (GPL3) and is available via conda and at a free Jupyter notebook server at https://try.openbiosim.org. Sire is supported by the not-for-profit OpenBioSim community interest company.
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The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA, which is an open software that calculates elastic parameters of double-stranded nucleic acids from dinucleotide length up to the whole molecule using ensembles from numerical simulations. The program reveals that global bendability emerge from local periodic bending angles in phase with the DNA helicoidal shape. We apply SerraNA to the whole set of 136 tetra-bp combinations and we observe a high degree of sequence-dependence with differences over 200% for all elastic parameters. Tetramers with TA and CA base-pair steps are especially flexible, while the ones containing AA and AT tend to be the most rigid. Thus, AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly. Our results also indicate base mismatches would make DNA more flexible, while protein binding would make it more rigid. SerraNA is a tool to be applied in the next generation of interdisciplinary investigations to further understand what determines the elasticity of DNA.
Assuntos
DNA/química , Simulação de Dinâmica Molecular , Software , Elasticidade , Conformação de Ácido NucleicoRESUMO
Latent tuberculosis infection (LTBI) screening is an important intervention for tuberculosis (TB) elimination in low-incidence countries and is, therefore, a key component of England's TB control strategy. This study describes outcomes from a LTBI screening programme in a high-incidence area to inform national LTBI screening in England and other low-incidence countries.We conducted a retrospective cohort study of LTBI screening among eligible migrants (from high-incidence countries and entered the UK within the last 5â years), who were identified at primary-care clinics in Newham, London between August 2014 and August 2015. Multivariable logistic regression was used to identify factors associated with LTBI testing uptake, interferon-γ release assay (IGRA) positivity and treatment uptake.40% of individuals offered LTBI screening received an IGRA test. The majority of individuals tested were 16-35â years old, male and born in India, Bangladesh or Pakistan. Country of birth, smoking status and co-morbidities were associated with LTBI testing uptake. IGRA positivity was 32% among those tested and was significantly associated with country of birth, age, sex and co-morbidities.This study identifies factors associated with screening uptake, IGRA positivity and treatment uptake, and improves understanding of groups that should be supported to increase acceptability of LTBI testing and treatment in the community.
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Controle de Doenças Transmissíveis/métodos , Tuberculose Latente/diagnóstico , Migrantes , Adolescente , Adulto , Bangladesh , Inglaterra , Feminino , Humanos , Incidência , Índia , Infectologia/métodos , Testes de Liberação de Interferon-gama , Masculino , Pessoa de Meia-Idade , Paquistão , Valor Preditivo dos Testes , Estudos Retrospectivos , Teste Tuberculínico , Adulto JovemRESUMO
Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.
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DNA , Fenômenos Mecânicos , DNA/química , Biopolímeros , Microscopia de Fluorescência , Pinças Ópticas , Fenômenos MagnéticosAssuntos
Antituberculosos/efeitos adversos , Síndrome do QT Longo/induzido quimicamente , Síndrome do QT Longo/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Cardiotoxicidade , Estudos Transversais , Diarilquinolinas/efeitos adversos , Eletrocardiografia , Europa (Continente) , Humanos , Internacionalidade , Nitroimidazóis/efeitos adversos , Oxazóis/efeitos adversosAssuntos
Antituberculosos/provisão & distribuição , Epidemias/prevenção & controle , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Antituberculosos/uso terapêutico , Humanos , Tuberculose Resistente a Múltiplos Medicamentos/diagnóstico , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Ucrânia/epidemiologiaRESUMO
RNA-catalyzed RNA replication is widely considered a key step in the emergence of life's first genetic system. However, RNA replication can be impeded by the extraordinary stability of duplex RNA products, which must be dissociated for re-initiation of the next replication cycle. Here, we have explored rolling circle synthesis (RCS) as a potential solution to this strand separation problem. We observe sustained RCS by a triplet polymerase ribozyme beyond full-length circle synthesis with strand displacement yielding concatemeric RNA products. Furthermore, we show RCS of a circular Hammerhead ribozyme capable of self-cleavage and re-circularization. Thus, all steps of a viroid-like RNA replication pathway can be catalyzed by RNA alone. Finally, we explore potential RCS mechanisms by molecular dynamics simulations, which indicate a progressive build-up of conformational strain upon RCS with destabilization of nascent strand 5'- and 3'-ends. Our results have implications for the emergence of RNA replication and for understanding the potential of RNA to support complex genetic processes.
Many organisms today rely on a trio of molecules for their survival: DNA, to store their genetic information; proteins, to conduct the biological processes required for growth or replication; and RNA, to mainly act as an intermediary between DNA and proteins. Yet, how these inanimate molecules first came together to form a living system remains unclear. Circumstantial evidence suggests that the first lifeforms relied to a much greater exrtent on RNA to conduct all necessary biological processes. There is no trace of this 'RNA world' today, but molecular 'fossils' may exist in current biology. Viroids, for example, are agents which can infect and replicate inside plant cells. They are formed of nothing but a circular strand of RNA that serves not only as genetic storage but also as ribozymes (RNA-based enzymes). Viroids need proteins from the host plant to replicate, but scientists have been able to engineer ribozymes that can copy complex RNA strands. This suggests that viroid-like replication could be achieved using only RNA. Kristoffersen et al. put this idea to the test and showed that it is possible to use RNA enzymatic activity alone to carry out all the steps of a viroid-like copying mechanism. This process included copying a viroid-like RNA circle with RNA, followed by trimming the copy to the right size and reforming the circle. These two latter steps could be carried out by a ribozyme that could itself be encoded on the RNA circle. A computer simulation indicated that RNA synthesis on the circle caused increasing tension that could ease some of the barriers to replication. These results increase our understanding of how RNA copying by RNA could be possible. This may lead to developing molecular models of a primordial RNA-based replication, which could be used to investigate early genetic systems and may have potential applications in synthetic biology.
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RNA , Viroides , Catálise , RNA Viral/genética , RNA Viral/metabolismo , Recombinação Genética , Viroides/genética , Viroides/metabolismo , Replicação ViralRESUMO
OBJECTIVES: To describe demographic features, clinical outcomes and diagnostic delay amongst patients with extra-spinal articular tuberculosis (TB) in a low-incidence setting. METHODS: Cases of TB treated at our institution between 2004 and 2014 were identified via the London TB register (LTBR). Demographic features of extra-spinal articular TB cases were compared to controls with TB at all other sites. For articular cases (excluding individuals <16 years or with spinal TB without peripheral joint involvement) clinical data were retrospectively collected. RESULTS: 6,146â¯TB patients were identified over the study period; 146 (2.4%) cases had extra-spinal articular infection. There was no difference in median age between extra-spinal articular TB cases and controls with TB at other sites (31â¯vs 32 years, pâ¯=â¯0.57). Articular cases were more likely to be male (70.6% vs 59.5%, pâ¯=â¯0.007), Bangladeshi (28.7% vs 18.0%) or Pakistani (24.0% vs 16.1%) and were less likely to be Black-African (9.5% vs 19.8%) (p < 0.001). 93 cases were included in the case series; 85 (88.5%) were migrants and 83 (89.2%) were South Asian. Knee and elbow joints were affected in 22 (23.7%) and 18 (19.4%) cases respectively. The median durations of pre-healthcare and healthcare associated delay were 16 and 6 weeks respectively. Where mycobacterial culture was performed, 57/75 (76%) were positive for Mycobacterium tuberculosis. 86 (92.5%) cases received standard quadruple therapy for a median of 6 months (IQR 6-9). Recurrence of TB infection occurred in 4 (4.3%) cases and there were no TB related deaths. Seven (7.6%) cases required surgical intervention. CONCLUSIONS: Extra-spinal articular TB more commonly affected men and people of South Asian ethnicity. Significant diagnostic delays were identified, including avoidable healthcare-associated delays.