Biocontainment Principles for Pediatric Patients
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ABSTRACT:
SUBMITTER: Hewlett A
PROVIDER: S-EPMC7123203 | biostudies-literature | 2018 Jul
REPOSITORIES: biostudies-literature
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Project description:Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
| S-EPMC4422498 | biostudies-literature
Project description:Genetically modified microorganisms (GMMs) can enable a wide range of important applications including environmental sensing and responsive engineered living materials. However, containment of GMMs to prevent environmental escape and satisfy regulatory requirements is a bottleneck for real-world use. While current biochemical strategies restrict unwanted growth of GMMs in the environment, there is a need for deployable physical containment technologies to achieve redundant, multi-layered and robust containment. We developed a hydrogel-based encapsulation system that incorporates a biocompatible multilayer tough shell and an alginate-based core. This deployable physical containment strategy (DEPCOS) allows no detectable GMM escape, bacteria to be protected against environmental insults including antibiotics and low pH, controllable lifespan and easy retrieval of genomically recoded bacteria. To highlight the versatility of DEPCOS, we demonstrated that robustly encapsulated cells can execute useful functions, including performing cell-cell communication with other encapsulated bacteria and sensing heavy metals in water samples from the Charles River.
| S-EPMC9269716 | biostudies-literature
Project description:We sought to identify proteins that enable differentiation between CD and UC in children with new onset IBD. Mucosal biopsies were obtained from children undergoing baseline diagnostic endoscopy prior to therapeutic interventions. Using a super-stable isotope labeling with amino acids in cell culture (SILAC)-based approach, the proteomes of 99 paediatric control and biopsies of patients with CD and UC were compared. Multivariate analysis of a subset of these (n=50) was applied to identify novel biomarkers, which were validated in a second subset (n=49). In the discovery cohort, a panel of five proteins was sufficient to distinguish control from IBD-affected tissue biopsies with an AUC of 1.0 (95% CI 0.99 to 1.0); a second panel of 12 proteins segregated inflamed CD from UC within an AUC of 0.95 (95% CI 0.86 to 1.0). Application of the two panels to the validation cohort resulted in accurate classification of 95.9% (IBD from control) and 80% (CD from UC) of patients. 116 proteins were identified to have correlation with the severity of disease, four of which were components of the two panels, including visfatin and metallothionein-2. This study has identified two panels of candidate biomarkers for the diagnosis of IBD and the differentiation of IBD subtypes to guide appropriate therapeutic interventions in paediatric patients.
2018-11-06 | PXD005086 | Pride
Project description:Biocontainment systems are needed to neutralize genetically modified organisms (GMOs) that pose ecological threats outside of controlled environments. In contrast, benign selection markers complement GMOs with reduced fitness. Benign selection agents serve as alternatives to antibiotics, which are costly and risk spread of antibiotic resistance. Here, we present a yeast biocontainment strategy leveraging engineered fluoride sensitivity and DNA vectors enabling use of fluoride as a selection agent. The biocontainment system addresses the scarcity of platforms available for yeast despite their prevalent use in industry and academia. In the absence of fluoride, the biocontainment strain exhibits phenotypes nearly identical to those of the wildtype strain. Low fluoride concentrations severely inhibit biocontainment strain growth, which is restored upon introduction of fluoride-based vectors. The biocontainment strategy is stringent, easily implemented, and applicable to several eukaryotes. Further, the DNA vectors enable genetic engineering at reduced costs and eliminate risks of propagating antibiotic resistance.
| S-EPMC7596524 | biostudies-literature
Project description:Whole blood transcriptional profiles in children with or without tuberculous meningitis (TBM) were compared using RNA-Seq and a biomarker signature driven by inflammasome activation and signaling was identified
2019-08-06 | GSE111459 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore ChIPseq results for pediatric AML patients.
2022-07-20 | GSE188605 | GEO
Project description:There is a growing demand to develop biocontainment strategies that prevent unintended proliferation of genetically modified organisms in the open environment. We found that the hypophosphite (H3PO2, HPt) transporter HtxBCDE from Pseudomonas stutzeri WM88 was also capable of transporting phosphite (H3PO3, Pt) but not phosphate (H3PO4, Pi), suggesting the potential for engineering a Pt/HPt-dependent bacterial strain as a biocontainment strategy. We disrupted all Pi and organic Pi transporters in an Escherichia coli strain expressing HtxABCDE and a Pt dehydrogenase, leaving Pt/HPt uptake and oxidation as the only means to obtain Pi. Challenge on non-permissive growth medium revealed that no escape mutants appeared for at least 21 days with a detection limit of 1.94?×?10-13 per colony forming unit. This represents, to the best of our knowledge, the lowest escape frequency among reported strategies. Since Pt/HPt are ecologically rare and not available in amounts sufficient for the growth of the Pt/HPt-dependent bacteria, this strategy offers a reliable and practical method for biocontainment.
| S-EPMC5357788 | biostudies-literature
Project description:Introduction:The cost of health care in the US is rapidly rising. Understanding the financial cost of medical care is an important competency for physicians and physicians-in-training. Medical students in their clinical clerkships are being exposed to health care decision-making often for the first time and are forming habits they will carry throughout their training and careers. Teaching high-value care (HVC) principles is crucial for students as they will be the future leaders in health care. Methods:This 1-hour workshop was interactive and aimed to prepare medical students to apply HVC when making medical decisions. The topic of HVC was initially introduced by eliciting tests that students want to order and highlighting the concept of whether or not a test changes the management of the patient. This exercise was followed by a PowerPoint presentation which discussed HVC, Choosing Wisely guidelines in pediatrics, and how to communicate with parents and patients about this topic. Results:Of third-year medical students, 125 participated in the workshop, with a survey response rate of 90% (n = 112). Ninety-nine percent reported that this workshop was helpful, and 97% reported that they will change their practice to reflect more cost-conscious care. Most students reported that their knowledge of HVC improved after the session, with 88% reporting scores of 3 (moderately improved) or 4 (significantly improved). Discussion:This ready-to-implement workshop offered students an understanding of how the cost of medical care impacts patients and families and how to practice cost-conscious care in pediatrics.
| S-EPMC7678025 | biostudies-literature
Project description:Background and objectivesFixed-dose combination formulations where several drugs are included in one tablet are important for the implementation of many long-term multidrug therapies. The selection of optimal dose ratios and tablet content of a fixed-dose combination and the design of individualized dosing regimens is a complex task, requiring multiple simultaneous considerations.MethodsIn this work, a methodology for the rational design of a fixed-dose combination was developed and applied to the case of a three-drug pediatric anti-tuberculosis formulation individualized on body weight. The optimization methodology synthesizes information about the intended use population, the pharmacokinetic properties of the drugs, therapeutic targets, and practical constraints. A utility function is included to penalize deviations from the targets; a sequential estimation procedure was developed for stable estimation of break-points for individualized dosing. The suggested optimized pediatric anti-tuberculosis fixed-dose combination was compared with the recently launched World Health Organization-endorsed formulation.ResultsThe optimized fixed-dose combination included 15, 36, and 16% higher amounts of rifampicin, isoniazid, and pyrazinamide, respectively. The optimized fixed-dose combination is expected to result in overall less deviation from the therapeutic targets based on adult exposure and substantially fewer children with underexposure (below half the target).ConclusionThe development of this design tool can aid the implementation of evidence-based formulations, integrating available knowledge and practical considerations, to optimize drug exposures and thereby treatment outcomes.
| S-EPMC5904239 | biostudies-literature
Project description:BackgroundParents who have to make tracheostomy decisions for their critically ill child may face forecasting errors and wish to learn from peer parents. We sought to develop an intervention with peer parent narratives to help parents anticipate and prepare for future challenges before making a decision.MethodsTo ensure that the intervention reflects parents' needs (rather than experts' opinions), we adapted a user-centered design (UCD) process to identify decision-critical information and refine the presentation format by interviewing parents who had tracheostomy decision making experience. Phase 1 (n = 10) presented 15 possible forecasting errors and asked participants to prioritize and justify the problematic ones. It also asked participants to comment on the draft narratives and preferred delivery mode and time of the intervention. Phase 2 (n = 9 additional parents and 1 previous parent) iteratively collected feedback over four waves of user interviews to guide revisions to the informational booklet.ResultsPhase 1 revealed that parents wanted information to address all forecasting errors as soon as tracheostomy becomes an option. They also highlighted diverse family situations and the importance of offering management strategies. The resulting prototype booklet contained five sections: introduction, child's quality of life, home care, practical challenges, and resources. Feedback from Phase 2 focused on emphasizing individualized situations, personal choice, seriousness of the decision, and caregiver health as well as presenting concrete illustrations of future challenges with acknowledgement of positive outcomes and advice. We also learned that parents preferred to use the booklet with support from the care team rather than read it alone.ConclusionsA UCD process enabled inclusion of parental perspectives that were initially overlooked and tailoring of the intervention to meet parental expectations. Similar UCD-based approaches may be valuable in the design of other types of patient communications (e.g., decision aids).
| S-EPMC9316812 | biostudies-literature