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1.
Plant Cell ; 35(10): 3809-3827, 2023 09 27.
Artigo em Inglês | MEDLINE | ID: mdl-37486356

RESUMO

Engineering the plant immune system offers genetic solutions to mitigate crop diseases caused by diverse agriculturally significant pathogens and pests. Modification of intracellular plant immune receptors of the nucleotide-binding leucine-rich repeat (NLR) receptor superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defense responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signaling networks that coevolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. The sensor and helper NLRs of the rice (Oryza sativa) NLR pair Pik have coevolved, and mismatching between noncoevolved alleles triggers constitutive activation and cell death. This limits the extent to which protein modifications can be used to engineer pathogen recognition and enhance disease resistance mediated by these NLRs. Here, we dissected incompatibility determinants in the Pik pair in Nicotiana benthamiana and found that heavy metal-associated (HMA) domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely coevolved with other NLR domains to maintain immune homeostasis. This explains why changes in integrated domains can lead to autoactivation. We then used this knowledge to facilitate engineering of new effector recognition specificities, overcoming initial autoimmune penalties. We show that by mismatching alleles of the rice sensor and helper NLRs Pik-1 and Pik-2, we can enable the integration of synthetic domains with novel and enhanced recognition specificities. Taken together, our results reveal a strategy for engineering NLRs, which has the potential to allow an expanded set of integrations and therefore new disease resistance specificities in plants.


Assuntos
Resistência à Doença , Proteínas de Plantas , Resistência à Doença/genética , Proteínas de Plantas/metabolismo , Alelos , Plantas/genética , Imunidade Vegetal/genética , Doenças das Plantas/genética
2.
J Microsc ; 2024 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-38349020

RESUMO

Colocalisation microscopy analysis provides an intuitive and straightforward way of determining if two biomolecules occupy the same diffraction-limited volume. A popular colocalisation coefficient, the Pearson's correlation coefficient (PCC), can be calculated using different pixel selection criteria: PCCALL includes all image pixels, PCCOR only pixels exceeding the intensity thresholds for either one of the detection channels, and PCCAND only pixels exceeding the intensity thresholds for both detection channels. Our results show that PCCALL depends on the foreground to background ratio, producing values influenced by factors unrelated to biomolecular association. PCCAND focuses on areas with the highest intensities in both channels, which allows it to detect low levels of colocalisation, but makes it inappropriate for evaluating spatial cooccurrence between the signals. PCCOR produces values influenced both by signal proportionality and spatial cooccurrence but can sometimes overemphasise the lack of the latter. Overall, PCCAND excels at detecting low levels of colocalisation, PCCOR provides a balanced quantification of signal proportionality and spatial coincidence, and PCCALL risks misinterpretation yet avoids segmentation challenges. Awareness of their distinct properties should inform their appropriate application with the aim of accurately representing the underlying biology.

3.
Environ Health ; 21(1): 122, 2022 12 05.
Artigo em Inglês | MEDLINE | ID: mdl-36464683

RESUMO

BACKGROUND: Air quality is a major public health threat linked to poor birth outcomes, respiratory and cardiovascular disease, and premature mortality. Deprived groups and children are disproportionately affected. Bradford will implement a Clean Air Zone (CAZ) as part of the Bradford Clean Air Plan (B-CAP) in 2022 to reduce pollution, providing a natural experiment. The aim of the current study is to evaluate the impact of the B-CAP on health outcomes and air quality, inequalities and explore value for money. An embedded process and implementation evaluation will also explore barriers and facilitators to implementation, impact on attitudes and behaviours, and any adverse consequences. METHODS: The study is split into 4 work packages (WP). WP1A: 20 interviews with decision makers, 20 interviews with key stakeholders; 10 public focus groups and documentary analysis of key reports will assess implementation barriers, acceptability and adverse or unanticipated consequences at 1 year post-implementation (defined as point at which charging CAZ goes 'live'). WP1B: A population survey (n = 2000) will assess travel behaviour and attitudes at baseline and change at 1 year post-implementation). WP2: Routine air quality measurements will be supplemented with data from mobile pollution sensors in 12 schools collected by N = 240 pupil citizen scientists (4 within, 4 bordering and 4 distal to CAZ boundary). Pupils will carry sensors over four monitoring periods over a 12 month period (two pre, and two post-implementation). We will explore whether reductions in pollution vary by CAZ proximity. WP3A: We will conduct a quasi-experimental interrupted time series analysis using a longitudinal routine health dataset of > 530,000 Bradford residents comparing trends (3 years prior vs 3 years post) in respiratory health (assessed via emergency/GP attendances. WP3B: We will use the richly-characterised Born in Bradford cohort (13,500 children) to explore health inequalities in respiratory health using detailed socio-economic data. WP4: will entail a multi-sectoral health economic evaluation to determine value for money of the B-CAP. DISCUSSION: This will be first comprehensive quasi-experimental evaluation of a city-wide policy intervention to improve air quality. The findings will be of value for other areas implementing this type of approach. TRIAL REGISTRATION: ISRCTN67530835 https://doi.org/10.1186/ISRCTN67530835.


Assuntos
Poluição do Ar , Conservação dos Recursos Naturais , Saúde Pública , Criança , Humanos , Poluição do Ar/análise , Poluição do Ar/prevenção & controle , Reino Unido , Saúde Pública/instrumentação , Saúde Pública/métodos , Entrevistas como Assunto , Conservação dos Recursos Naturais/métodos
4.
Biochemistry ; 58(11): 1492-1500, 2019 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-30817136

RESUMO

The field of synthetic biology is already beginning to realize its potential, with a wealth of examples showcasing the successful genetic engineering of microorganisms for the production of valuable compounds. The chassis Saccharomyces cerevisiae has been engineered to function as a microfactory for producing many of these economically and medically relevant compounds. However, strain construction and optimization to produce industrially relevant titers necessitate a wealth of underpinning biological knowledge alongside large investments of capital and time. Over the past decade, advances in DNA synthesis and editing tools have enabled multiplex genome engineering of yeast, permitting access to more complex modifications that could not have been easily generated in the past. These genome engineering efforts often result in large populations of strains with genetic diversity that can pose a significant challenge to screen individually via traditional methods such as mass spectrometry. The large number of samples generated would necessitate screening methods capable of analyzing all of the strains generated to maximize the explored genetic space. In this Perspective, we focus on recent innovations in multiplex genome engineering of S. cerevisiae, together with biosensors and high-throughput screening tools, such as droplet microfluidics, and their applications in accelerating chassis optimization.


Assuntos
Engenharia de Proteínas/métodos , Proteínas de Saccharomyces cerevisiae/biossíntese , Biologia Sintética/métodos , Sistemas CRISPR-Cas , Engenharia Genética/métodos , Engenharia Metabólica/métodos , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
5.
Mov Disord ; 30(5): 736-9, 2015 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-25546340

RESUMO

BACKGROUND: Limited trial evidence suggests that cognitive-behavioral therapy (CBT) may be effective in managing impulse control behavior (ICBs) in Parkinson's disease. AIMS: To examine predictors of outcome in trial, participants (N=42) receiving treatment immediately or after a waiting time. METHODS: Dependent variables were Clinical Global Impression of Change (CGI-C) and the Neuropsychiatric Inventory (NPI). Baseline demographic and clinical variables were independent variables. RESULTS: Better CGI-C was predicted by fewer ICBs, taking a dopamine agonist, lower levodopa (l-dopa) equivalent dose (LEDD), higher social functioning, and lower NPI severity before treatment. Improvement on the NPI was predicted by lower LEDD, lower anxiety, lower baseline global clinical severity, and higher social functioning. CONCLUSIONS: Patients with lower burden of ICBs and other psychiatric symptomatology, better social functioning, and lower dose of antiparkinsonian medication may benefit more from CBT. However, we cannot yet identify individual patients with sufficient confidence at this stage to target treatment.


Assuntos
Terapia Cognitivo-Comportamental/métodos , Transtornos Disruptivos, de Controle do Impulso e da Conduta/etiologia , Transtornos Disruptivos, de Controle do Impulso e da Conduta/reabilitação , Doença de Parkinson/complicações , Idoso , Feminino , Humanos , Modelos Lineares , Masculino , Pessoa de Meia-Idade , Escalas de Graduação Psiquiátrica , Resultado do Tratamento
6.
Crit Care ; 18(3): R98, 2014 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-24887537

RESUMO

INTRODUCTION: Blunt chest wall trauma accounts for over 15% of all trauma admissions to Emergency Departments worldwide. Reported mortality rates vary between 4 and 60%. Management of this patient group is challenging as a result of the delayed on-set of complications. The aim of this study was to develop and validate a prognostic model that can be used to assist in the management of blunt chest wall trauma. METHODS: There were two distinct phases to the overall study; the development and the validation phases. In the first study phase, the prognostic model was developed through the retrospective analysis of all blunt chest wall trauma patients (n = 274) presenting to the Emergency Department of a regional trauma centre in Wales (2009 to 2011). Multivariable logistic regression was used to develop the model and identify the significant predictors for the development of complications. The model's accuracy and predictive capabilities were assessed. In the second study phase, external validation of the model was completed in a multi-centre prospective study (n = 237) in 2012. The model's accuracy and predictive capabilities were re-assessed for the validation sample. A risk score was developed for use in the clinical setting. RESULTS: Significant predictors of the development of complications were age, number of rib fractures, chronic lung disease, use of pre-injury anticoagulants and oxygen saturation levels. The final model demonstrated an excellent c-index of 0.96 (95% confidence intervals: 0.93 to 0.98). CONCLUSIONS: In our two phase study, we have developed and validated a prognostic model that can be used to assist in the management of blunt chest wall trauma patients. The final risk score provides the clinician with the probability of the development of complications for each individual patient.


Assuntos
Modelos Teóricos , Traumatismos Torácicos/diagnóstico , Ferimentos não Penetrantes/diagnóstico , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Valor Preditivo dos Testes , Prognóstico , Estudos Prospectivos , Estudos Retrospectivos , Traumatismos Torácicos/terapia , Resultado do Tratamento , Ferimentos não Penetrantes/terapia
7.
Neurophysiol Clin ; 54(5): 102997, 2024 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-38991470

RESUMO

OBJECTIVES: Aberrant movement-related cortical activity has been linked to impaired motor function in Parkinson's disease (PD). Dopaminergic drug treatment can restore these, but dosages and long-term treatment are limited by adverse side-effects. Effective non-pharmacological treatments could help reduce reliance on drugs. This experiment reports the first study of home-based electroencephalographic (EEG) neurofeedback training as a non-pharmacological candidate treatment for PD. Our primary aim was to test the feasibility of our EEG neurofeedback intervention in a home setting. METHODS: Sixteen people with PD received six home visits comprising symptomology self-reports, a standardised motor assessment, and a precision handgrip force production task while EEG was recorded (visits 1, 2 and 6); and 3 × 1-hr EEG neurofeedback training sessions to supress the EEG mu rhythm before initiating handgrip movements (visits 3 to 5). RESULTS: Participants successfully learned to self-regulate mu activity, and this appeared to expedite the initiation of precision movements (i.e., time to reach target handgrip force off-medication pre-intervention = 628 ms, off-medication post-intervention = 564 ms). There was no evidence of wider symptomology reduction (e.g., Movement Disorder Society Unified Parkinson's Disease Rating Scale Part III Motor Examination, off-medication pre-intervention = 29.00, off-medication post intervention = 30.07). Interviews indicated that the intervention was well-received. CONCLUSION: Based on the significant effect of neurofeedback on movement-related cortical activity, positive qualitative reports from participants, and a suggestive benefit to movement initiation, we conclude that home-based neurofeedback for people with PD is a feasible and promising non-pharmacological treatment that warrants further research.

8.
J Neuropsychiatry Clin Neurosci ; 25(2): 141-9, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23686032

RESUMO

The aim of this study was to investigate the clinical, neuropsychological, and self-awareness correlates of impulse-control disorder (ICD) in a group of 17 Parkinson's disease (PD) subjects with an active ICD and a comparison group of 17 PD subjects without ICD. Self-awareness was assessed with the Beck Cognitive Insight Scale and patient-caregiver discrepancy scores from ratings on the Dysexecutive Questionnaire and the Everyday Memory Questionnaire-Revised. Self-awareness was comparable or increased in those with ICD, versus those without, and measures of neuropsychological functioning did not differ between the two groups. Those with ICD had more motor complications of PD therapy and were more likely to be on an antidepressant than those without ICD, whereas dopaminergic medication profiles were comparable between the two groups. In this group, PD patients with current ICDs were aware of their impulsivity. Although executive dysfunction may contribute to ICD behavior, it is not a necessary component. The awareness of the inability to resist these motivated behaviors may be a source of increased depression.


Assuntos
Conscientização , Transtornos Cognitivos/etiologia , Comportamento Impulsivo/complicações , Comportamento Impulsivo/psicologia , Doença de Parkinson/complicações , Doença de Parkinson/psicologia , Idoso , Cuidadores/psicologia , Transtornos Cognitivos/psicologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Testes Neuropsicológicos , Escalas de Graduação Psiquiátrica , Autorrelato , Inquéritos e Questionários
9.
Clin Med (Lond) ; 13(6): 561-4, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24298101

RESUMO

The decision to admit a frail older patient is rarely made by a geriatrician and often falls to staff in the emergency department (ED), who may not have the training to balance the risks, benefits and alternatives. We based a consultant geriatrician in the ED with the primary aim of facilitating admission prevention for older patients and this was achieved for 64% (543/848) of patients. A secondary aim was to facilitate direct admission to elderly care wards when admission was necessary, and this was achieved for 57% of admitted patients (174/305). The geriatrician was able to facilitate discharge from the ED for over half of potential 30-day readmissions seen. The overall 7-day ED re-attendance rate was 10.1%, but only 3.4% of patients were admitted with the same problem, indicating true admission prevention rather than admission delay. In conclusion, the placement of a consultant geriatrician in the ED is effective in facilitating admission prevention for older patients.


Assuntos
Serviço Hospitalar de Emergência/normas , Idoso Fragilizado , Avaliação Geriátrica/métodos , Admissão do Paciente/normas , Alta do Paciente/normas , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade
10.
Mov Disord Clin Pract ; 10(9): 1360-1367, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37772283

RESUMO

Background: Impulse control behaviors (ICBs) are problematic, reward-based behaviors, affecting 15% to 35% of patients with Parkinson's disease. Evidence exists of increased carer burden as a result of these behaviors; however, little is known about the variables mediating this effect and their management. Objective: To identify factors predictive of carer burden in a cohort of patients with Parkinson's disease with ICBs to enable the development of targeted therapeutic interventions for carers. Methods: Data were collected from 45 patients with clinically significant ICBs and their carers, including levodopa equivalent daily dosage, motor and neuropsychiatric symptoms, cognitive function, and ICB severity. Carer burden was quantified by Zarit Burden Interview (ZBI). Univariate analyses were performed using the Spearman rank correlation. Linear regression was used to create a multivariate model for predicting ZBI. Results: Univariate analysis identified significant correlations between ZBI and patient total Neuropsychiatric Inventory (NPI) (r s = 0.50), 4 NPI subscores (agitation/aggression, r s = 0.41; depression/dysphoria, r s = 0.47; apathy/indifference, r s = 0.49; and irritability/lability, r s = 0.38; all P < 0.02), and the carer 28-item General Health Questionnaire (GHQ-28) (r s = 0.52, P < 0.0005). Multivariate linear regression retained total NPI and GHQ-28 scores and were collectively predictive of 36.6% of the variance in the ZBI. Conclusions: Our study suggests that depressive symptoms and aspects of executive dysfunction (apathy and disinhibition) in the patient are potential drivers of carer burden in patients with ICBs. Such findings suggest the presence of executive difficulties and/or mood disturbance should point the clinician to inquire about burden in the caring role and encourage the carer to seek help for any of their own general health problems, which may compound carer burden.

11.
ACS Synth Biol ; 11(2): 579-586, 2022 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-35050610

RESUMO

Computational design tools are the cornerstone of synthetic biology and have underpinned its rapid development over the past two decades. As the field has matured, the scale of biological investigation has expanded dramatically, and researchers often must rely on computational tools to operate in the high-throughput investigational space. This is especially apparent in the modular design of DNA expression circuits, where complexity is accumulated rapidly. Alongside our automated pipeline for the high-throughput construction of Extensible Modular Mammalian Assembly (EMMA) expression vectors, we recognized the need for an integrated software solution for EMMA vector design. Here we present EMMA-CAD (https://emma.cailab.org), a powerful web-based computer-aided design tool for the rapid design of bespoke mammalian expression vectors. EMMA-CAD features a variety of functionalities, including a user-friendly design interface, automated connector selection underpinned by rigorous computer optimization algorithms, customization of part libraries, and personalized design spaces. Capable of translating vector assembly designs into human- and machine-readable protocols for vector construction, EMMA-CAD integrates seamlessly into our automated EMMA pipeline, hence completing an end-to-end design to production workflow.


Assuntos
Software , Biologia Sintética , Algoritmos , Animais , Automação , DNA/genética , Humanos , Mamíferos/genética , Biologia Sintética/métodos
12.
Commun Biol ; 5(1): 853, 2022 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-35996019

RESUMO

Targeting host processes that allow pathogens to thrive can be invaluable in resistance breeding. Here, we generated a deep-sequencing transcriptome time course for Puccinia striiformis f. sp. tritici (Pst) infection on wheat and compared datasets from three wheat varieties with different levels of susceptibility to two tested pathogen isolates. We sought genes specifically altered in a susceptible host as candidates that might support colonisation. Host responses differed between Pst-varietal pairs most prominently early during infection. Notably, however, nuclear genes encoding chloroplast-localised proteins (NGCPs) exhibited temporal coordination of expression profiles that differed at later time points in relation to Pst susceptibility. Disrupting one such NGCP, encoding the chloroplast-localised RNA binding protein TaCSP41a, led to lower Pst susceptibility. These analyses thus highlight NGCPs as prime targets for Pst manipulation during infection and point to TaCSP41a disruption as a potential source of Pst resistance for breeding programmes.


Assuntos
Basidiomycota , Triticum , Basidiomycota/genética , Proteínas de Cloroplastos/metabolismo , Melhoramento Vegetal , Doenças das Plantas/genética , Puccinia , Triticum/genética , Triticum/metabolismo
13.
ACS Synth Biol ; 11(2): 587-595, 2022 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-35061373

RESUMO

With applications from functional genomics to the production of therapeutic biologics, libraries of mammalian expression vectors have become a cornerstone of modern biological investigation and engineering. Multiple modular vector platforms facilitate the rapid design and assembly of vectors. However, such systems approach a technical bottleneck when a library of bespoke vectors is required. Utilizing the flexibility and robustness of the Extensible Mammalian Modular Assembly (EMMA) toolkit, we present an automated workflow for the library-scale design, assembly, and verification of mammalian expression vectors. Vector design is simplified using our EMMA computer-aided design tool (EMMA-CAD), while the precision and speed of acoustic droplet ejection technology are applied in vector assembly. Our pipeline facilitates significant reductions in both reagent usage and researcher hands-on time compared with manual assembly, as shown by system Q-metrics. To demonstrate automated EMMA performance, we compiled a library of 48 distinct plasmid vectors encoding either CRISPR interference or activation modalities. Characterization of the workflow parameters shows that high assembly efficiency is maintained across vectors of various sizes and design complexities. Our system also performs strongly compared with manual assembly efficiency benchmarks. Alongside our automated pipeline, we present a straightforward strategy for integrating gRNA and Cas modules into the EMMA platform, enabling the design and manufacture of valuable genome editing resources.


Assuntos
Edição de Genes , RNA Guia de Cinetoplastídeos , Animais , Automação , Sistemas CRISPR-Cas , Biblioteca Gênica , Vetores Genéticos/genética , Mamíferos/genética , RNA Guia de Cinetoplastídeos/genética
14.
J Patient Saf ; 18(3): e672-e679, 2022 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-34570002

RESUMO

OBJECTIVE: Adverse event (AE) reporting is crucial for determining safety of trials. Adverse events are captured manually by clinical research associates (CRAs) and research nurses (RNs), and prior studies show underreporting. It is necessary to understand AE reporting training, processes, and institution-level differences to improve AE capture. METHODS: A 26-item questionnaire regarding AE reporting training, identification, tracking, and challenges was distributed to all Children's Oncology Group (COG) CRAs and RNs from February 15 to March 11, 2019, regardless of if they report AEs based on limitations of COG rosters. Results were tabulated. Institutions were grouped by self-reported full-time equivalents and compared using χ2 tests. RESULTS: Of 1315 CRAs and 2703 RNs surveyed, 509 (12.7%) responded. Of those, 369 (64.9%) representing 71.8% of COG institutions report AEs. Only data from respondents who report AEs were collected and analyzed. There was a range in AE training; COG training modules were most common (79.7%). There was wide variability in AE ascertainment; only 51.2% use standardized approaches at their site. There was no standard AE tracking method; larger sites more commonly use spreadsheets (P = 0.002) and smaller sites more commonly use paper (P = 0.028). The greatest AE reporting challenges were differences between protocols (70%) and between AE definitions and documentation (53%). Half of the respondents endorsed 6 of 13 proposed tools for improving reporting including online AE reporting modules (75.3%), tip sheets for interpreting Common Terminology Criteria for Adverse Events definitions (67.5%), and standardized AE tracking forms (66.9%). Only half of the respondents reported that all colleagues at their site followed the same AE reporting practices, and there was no dominant AE tracking approach across the respondents. DISCUSSION: There is wide variability in AE reporting training and practices. Numerous challenges exist, including differences between trials, challenges in interpreting AE definitions, and engaging clinicians. CONCLUSIONS: Respondents are eager for additional central resources. These results provide a roadmap for areas of potential improvement.


Assuntos
Projetos de Pesquisa , Criança , Humanos , Autorrelato , Inquéritos e Questionários
15.
J Women Aging ; 23(3): 246-62, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21767088

RESUMO

Attention Deficit Hyperactivity Disorder (ADHD), usually diagnosed in children, is known to persist into adulthood. However, the research has not examined the disorder in older adults. This article describes a preliminary qualitative study of the experiences of women over age 62 who were diagnosed with ADHD after the age of 60. Participants reported experiencing peer rejection, feeling different, and a tendency to become advocates for others. Although they reported difficulties in work and relationships, they also described finding creative solutions to their attention problems. Diagnosis and treatment appears to have assisted with self-acceptance and appreciation of the strengths of having ADHD.


Assuntos
Transtorno do Deficit de Atenção com Hiperatividade/psicologia , Relações Interpessoais , Idoso , Idoso de 80 Anos ou mais , Transtorno do Deficit de Atenção com Hiperatividade/diagnóstico , Transtorno do Deficit de Atenção com Hiperatividade/tratamento farmacológico , Educação , Feminino , Humanos , Entrevistas como Assunto , Pessoa de Meia-Idade , Trabalho/psicologia
16.
Methods Mol Biol ; 2205: 305-327, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32809206

RESUMO

The synthetic chromosome rearrangement and modification by LoxP-mediated evolution (SCRaMbLE) system is a key component of the synthetic yeast genome (Sc2.0) project, an international effort to construct an entire synthetic genome in yeast. SCRaMbLE involves the introduction of thousands of symmetrical LoxP (LoxPsym) recombination sites downstream of every nonessential gene in all 16 chromosomes, enabling numerous genome rearrangements in the form of deletions, inversions, duplications, and translocations by the Cre-LoxPsym recombination system. We highlight a two-step protocol for SCRaMbLE-in (Liu, Nat Commun 9(1):1936, 2018), a recombinase-based combinatorial method to expedite genetic engineering and exogenous pathway optimization, using a synthetic ß-carotene pathway as an example. First, an in vitro phase uses a recombinase toolkit to diversify gene expression by integrating various regulatory elements into the target pathway. This combinatorial pathway library can be transformed directly into yeast for traditional screening. Once an optimized pathway which is flanked by LoxPsym sites is identified, it is transformed into Sc2.0 yeast for the in vivo SCRaMbLE phase, where LoxPsym sites in the synthetic yeast genome and Cre recombinase catalyze massive genome rearrangements. We describe all the conditions necessary to perform SCRaMbLE and post-SCRaMbLE experiments including screening, spot test analysis, and PCRTag analysis to elucidate genotype-phenotype relationships.


Assuntos
Engenharia Genética/métodos , Saccharomyces cerevisiae/genética , Biologia Sintética/métodos , Cromossomos Artificiais de Levedura/genética , Cromossomos Fúngicos/genética , Expressão Gênica/genética , Regulação Fúngica da Expressão Gênica/genética , Biblioteca Gênica , Genes Sintéticos/genética , Genoma Fúngico/genética , Genótipo , Integrases/genética , Fenótipo , Recombinação Genética/genética
17.
Methods Enzymol ; 617: 463-493, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30784414

RESUMO

Construction of expression vectors is imperative for many areas of biological research and the biotechnology industry. Modular cloning systems for expression vector construction offer a labor- and cost-effective alternative to overcome drawbacks associated with traditional cloning methods. We developed an Extensible Mammalian Modular Assembly toolkit (EMMA) as an efficient and versatile tool to facilitate the construction of functionally diverse mammalian expression vectors from a standardized library of DNA parts. This system supports both hierarchical and combinatorial assembly, and is adaptable for automation. In this chapter, we describe the protocols to construct libraries of DNA parts and assemble these parts into mammalian expression vectors using EMMA.


Assuntos
Clonagem Molecular/métodos , Biblioteca Gênica , Vetores Genéticos/genética , Animais , Sequência de Bases , DNA/genética , Escherichia coli/genética , Humanos , Reação em Cadeia da Polimerase/métodos
18.
BMJ Open ; 9(7): e029187, 2019 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-31350248

RESUMO

OBJECTIVE: A new prognostic model has been developed and externally validated, the aim of which is to assist in the management of the blunt chest wall trauma patient in the emergency department (ED). The aim of this trial is to assess the feasibility and acceptability of a definitive impact trial investigating the clinical and cost-effectiveness of a new prognostic model for the management of patients with blunt chest wall trauma in the ED. DESIGN: Stepped wedge feasibility trial. SETTING: Four EDs in England and Wales. PARTICIPANTS: Adult blunt chest wall trauma patients presenting to the ED with no concurrent, life-threatening injuries. INTERVENTION: A prognostic model (the STUMBL score) to guide clinical decision-making. OUTCOME MEASURES: Primary: participant recruitment rate and clinicians' use of the STUMBL score. Secondary: composite outcome measure (mortality, pulmonary complications, delayed upgrade in care, unplanned representations to the ED), physical and mental components of quality of life, clinician feedback and health economic data gathering methodology for healthcare resource utilisation. RESULTS: Quantitative data were analysed using the intention-to-treat principle. 176 patients were recruited; recruitment targets were achieved at all sites. Clinicians used the model in 96% of intervention cases. All feasibility criteria were fully or partially met. After adjusting for predefined covariates, there were no statistically significant differences between the control and intervention periods. Qualitative analysis highlighted that STUMBL was well-received and clinicians would support a definitive trial. Collecting data on intervention costs, health-related quality of life and healthcare resource use was feasible. DISCUSSION: We have demonstrated that a fully powered randomised clinical trial of the STUMBL score is feasible and desirable to clinicians. Minor methodological modifications will be made for the full trial. TRIAL REGISTRATION NUMBER: ISRCTN95571506; Post-results.


Assuntos
Modelos Estatísticos , Traumatismos Torácicos/terapia , Ferimentos não Penetrantes/terapia , Adulto , Idoso , Análise Custo-Benefício , Serviço Hospitalar de Emergência , Estudos de Viabilidade , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Prognóstico , Estudos Prospectivos , Resultado do Tratamento
19.
J Pediatr Oncol Nurs ; 35(5): 314-319, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29633658

RESUMO

A chemotherapy roadmap is a summary of the chemotherapy plan for a pediatric oncology patient. Chemotherapy roadmaps exist as paper documents for most, if not all, pediatric oncology programs. Paper chemotherapy roadmaps are associated with risks that can negatively affect the safety of the chemotherapy process. This institution explored the feasibility of converting paper chemotherapy roadmaps into an electronic form. The pediatric information systems team developed an innovative computer application that can generate electronic chemotherapy roadmaps, and the pediatric oncology program established a novel workflow that can operationalize them. Electronic chemotherapy roadmaps have been produced for 36 treatment protocols, and 369 electronic chemotherapy roadmaps have been used for 352 pediatric oncology patients. They have functioned as designed and have not had any unintended effects. In the 5 years after their implementation, the average proportion of patient safety events involving paper or electronic chemotherapy roadmaps decreased by 78.7%. This report is the first to demonstrate the feasibility of creating and implementing electronic chemotherapy roadmaps. Continued expansion of the current library will be necessary to formally test the hypothesis that electronic chemotherapy roadmaps can decrease the risks associated with their paper counterparts and increase the safety of the chemotherapy process.


Assuntos
Tomada de Decisão Clínica , Registros Eletrônicos de Saúde/normas , Oncologia/normas , Neoplasias/tratamento farmacológico , Criança , Prática Clínica Baseada em Evidências/normas , Humanos , Software
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