The mismatch repair system protects against intergenerational GAA repeat instability in a Friedreich ataxia mouse model

Copyright @ 2012 Elsevier. The article can be accessed from the link below.This article has been made available through the Brunel Open Access Publishing Fund.Friedreich ataxia (FRDA) is an autosomal recessive neurodegenerative disorder caused by a dynamic GAA repeat expansion mutation within intron 1 of the FXN gene. Studies of mouse models for other trinucleotide repeat (TNR) disorders have revealed an important role of mismatch repair (MMR) proteins in TNR instability. To explore the potential role of MMR proteins on intergenerational GAA repeat instability in FRDA, we have analyzed the transmission of unstable GAA repeat expansions from FXN transgenic mice which have been crossed with mice that are deficient for Msh2, Msh3, Msh6 or Pms2. We find in all cases that absence of parental MMR protein not only maintains transmission of GAA expansions and contractions, but also increases GAA repeat mutability (expansions and/or contractions) in the offspring. This indicates that Msh2, Msh3, Msh6 and Pms2 proteins are not the cause of intergenerational GAA expansions or contractions, but act in their canonical MMR capacity to protect against GAA repeat instability. We further identified differential modes of action for the four MMR proteins. Thus, Msh2 and Msh3 protect against GAA repeat contractions, while Msh6 protects against both GAA repeat expansions and contractions, and Pms2 protects against GAA repeat expansions and also promotes contractions. Furthermore, we detected enhanced occupancy of Msh2 and Msh3 proteins downstream of the FXN expanded GAA repeat, suggesting a model in which Msh2/3 dimers are recruited to this region to repair mismatches that would otherwise produce intergenerational GAA contractions. These findings reveal substantial differences in the intergenerational dynamics of expanded GAA repeat sequences compared with expanded CAG/CTG repeats, where Msh2 and Msh3 are thought to actively promote repeat expansions.This study is funded under European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement number 242193/EFACTS. This article is made available through the Brunel Open Access Publishing Fund

Air quality self-management in asthmatic patients with COPD: An integrative review for developing nursing interventions to prevent exacerbations

Objectives: Asthma-chronic obstructive pulmonary disease (COPD) overlap (ACO) patients experience a lower quality of life, frequent exacerbations, and worse pulmonary function. Environmental management is essential in a complex chronic condition, as pollutant exposure can worsen symptoms and increase morbidity and mortality. We aimed to identify evidence that informs nursing interventions in promoting self-management of air quality in asthmatic people with COPD. Methods: We conducted an integrative review in March of 2023. We searched the databases CINAHL, MEDLINE, Academic Search Complete, Cochrane Database of Systematic Reviews (CDSR), Scopus, Web of Science, Joanna Briggs Institute (JBI) Evidence-Based Practice Database, and Google Scholar. We included articles whose participants were adults with asthma, COPD, or both; the intervention was air quality management and the outcome of any exacerbations. We excluded editorials, letters, commentaries, opinion papers, position papers, study protocols, conference abstracts, and reviews. Data extraction and synthesis were performed, categorizing interventions according to nursing actions. Methodological quality assessment was conducted using the JBI Critical Appraisal Checklist tools. The review protocol was registered at Open Science Framework (https://doi.org/10.17605/OSF.IO/5Y4KW). Results: We included five articles from different countries. The interventions promoting air quality self-management for individuals with asthma and COPD included vigilance interventions (health professional regular visits, assessment of symptoms), monitoring interventions (measurement of indoor and outdoor trigger factors), and educational interventions (air quality alerts, allergen avoidance). Policy interventions such as smoke-free policies and comprehensive strategies to improve air quality were also identified. These areas of focus represent critical components of nurses' interventions and can integrate the fundamental patterns of knowing in nursing. Although the studies reveal heterogeneous interventions and the methodological quality is variable, these interventions showed potential for preventing exacerbations, reducing emergency department visits, and minimizing hospitalizations. Conclusions: The study emphasizes the need for a comprehensive approach involving nurses in multidisciplinary teams to air quality self-management. They can use these results to inform their interventions and ways of knowing, benefiting individuals with asthma and COPD. Further research is needed to expand the evidence base and refine these interventions.info:eu-repo/semantics/publishedVersio

Cyclin D 1‐induced proliferation is independent of beta‐catenin in H ead and N eck C ancer

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106775/1/odi12124.pd

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

Objective Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H. pylori infection leads to reduced acid secretion, which may allow the growth of a different gastric bacterial community. This change in the microbiome may increase aggression to the gastric mucosa and contribute to malignancy. Our aim was to evaluate the composition of the gastric microbiota in chronic gastritis and in gastric carcinoma. Design The gastric microbiota was retrospectively investigated in 54 patients with gastric carcinoma and 81 patients with chronic gastritis by 16S rRNA gene profiling, using next-generation sequencing. Differences in microbial composition of the two patient groups were assessed using linear discriminant analysis effect size. Associations between the most relevant taxa and clinical diagnosis were validated by real-time quantitative PCR. Predictive functional profiling of microbial communities was obtained with PICRUSt. Results The gastric carcinoma microbiota was characterised by reduced microbial diversity, by decreased abundance of Helicobacter and by the enrichment of other bacterial genera, mostly represented by intestinal commensals. The combination of these taxa into a microbial dysbiosis index revealed that dysbiosis has excellent capacity to discriminate between gastritis and gastric carcinoma. Analysis of the functional features of the microbiota was compatible with the presence of a nitrosating microbial community in carcinoma. The major observations were confirmed in validation cohorts from different geographic origins. Conclusions Detailed analysis of the gastric microbiota revealed for the first time that patients with gastric carcinoma exhibit a dysbiotic microbial community with genotoxic potential, which is distinct from that of patients with chronic gastritis.This research was supported by a Worldwide Cancer Research grant to CF and JCM (Reference 16-1352). RMF, JPM and IPR have fellowships from Fundacao para a Ciencia e a Tecnologia (FCT; SFRH/BPD/84084/2012, PD/BD/114014/2015 and SFRH/BD/110803/2015, respectively) through Programa Operacional Capital Humano (POCH) and the European Union. JPM's fellowship is in the framework of FCT's PhD Programme BiotechHealth (Ref PD/0016/2012). i3S-Instituto de Investigacao e Inovacao em Saude is funded by Fundo Europeu de Desenvolvimento Regional (FEDER) funds through the COMPETE 2020-Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, and by Portuguese funds through Fundacao para a Ciencia e a Tecnologia (FCT)/Ministerio da Ciencia, Tecnologia e Inovacao (POCI-01-0145-FEDER-007274)

Delivering amoxicillin at the infection site-a rational design through lipid nanoparticles

Purpose: Amoxicillin is a commonly used antibiotic, although degraded by the acidic pH of the stomach. This is an important limitation for the treatment of Helicobacter pylori infections. The purpose of this work was to encapsulate amoxicillin in lipid nanoparticles, increasing the retention time at the site of infection (gastric mucosa), while protecting the drug from the harsh conditions of the stomach lumen. Materials and methods: The nanoparticles were produced by the double emulsion technique and optimized by a three-level Box-Behnken design. Tween 80 and linolenic acid were used as potential therapeutic adjuvants and dioleoylphosphatidylethanolamine as a targeting agent to Helicobacter pylori. Nanoparticles were characterized regarding their physico-chemical features, their storage stability, and their usability for oral administration (assessment of in vitro release, in vitro cell viability, permeability, and interaction with mucins). Results: The nanoparticles were stable for at least 6 months at 4°C. In vitro release studies revealed a high resistance to harsh conditions, including acidic pH and physiologic temperature. The nanoparticles have a low cytotoxicity effect in both fibroblasts and gastric cell lines, and they have the potential to be retained at the gastric mucosa. Conclusion: Overall, the designed formulations present suitable physico-chemical features for being henceforward used by oral administration to treat Helicobacter pylori infections.DLC, RMP, TS, and CN are thankful to Fundação para a Ciência e Tecnologia (FCT) for the PhD Grant (PD/ BD/105957/2014), Research Grant (PD/BI/128326/2017), post-doctorate grant (SFRH/BPD/103113/2014), and Investigator Grant (IF/00293/2015), respectively. This work was supported by FCT through the FCT PhD Programmes and by Programa Operacional Capital Humano (POCH), specifically by the BiotechHealth Programe (Doctoral Programme on Cellular and Molecular Biotechnology Applied to Health Sciences). The authors are also grateful to Dr Rui Fernandes (Histology and Electron Microscopy Service – Instituto de Investigação e Inovação em Saúde, Universidade do Porto) for the expertise and technical assistance with transmission electron microscopy and to Manuela Barros for administrative and technical support. The authors thank the financial support under Program PT2020 (UID/QUI/50006/2019). SACL and BS thanks Operação NORTE-01-0145-FEDER-000011 and NORTE-01-0145-FEDER-000012, respectively, for their Investigator contract

Impact of host DNA and sequencing depth on the taxonomic resolution of whole metagenome sequencing for microbiome analysis

The amount of host DNA poses a major challenge to metagenome analysis. However, there is no guidance on the levels of host DNA, nor on the depth of sequencing needed to acquire meaningful information from whole metagenome sequencing (WMS). Here, we evaluated the impact of a wide range of amounts of host DNA and sequencing depths on microbiome taxonomic profiling using WMS. Synthetic samples with increasing levels of host DNA were created by spiking DNA of a mock bacterial community, with DNA from a mouse-derived cell line. Taxonomic analysis revealed that increasing proportions of host DNA led to decreased sensitivity in detecting very low and low abundant species. Reduction of sequencing depth had major impact on the sensitivity of WMS for profiling samples with 90% host DNA, increasing the number of undetected species. Finally, analysis of simulated datasets with fixed depth of 10 million reads confirmed that microbiome profiling becomes more inaccurate as the level of host DNA increases in a sample. In conclusion, samples with high amounts of host DNA coupled with reduced sequencing depths, decrease WMS coverage for characterization of the microbiome. This study highlights the importance of carefully considering these aspects in the design of WMS experiments to maximize microbiome analyses.This work was supported by European Regional Development Funds (ERDF) funds through the COMPETE 2020 – Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by FCT – Fundação para a Ciência e a Tecnologia (POCI-01-0145-FEDER-032532). JP-M and IP-R have fellowships from FCT (PD/BD/114014/2015 and SFRH/BD/110803/2015, respectively) through Programa Operacional Capital Humano (POCH) and the European Social Fund. JP-M’s have fellowship from the framework of FCT’s Ph.D. Program Biotech Health (Ref. PD/0016/2012)

Modeling the quantum evolution of the universe through classical matter

It is well known that the canonical quantization of the Friedmann-Lema\^itre-Robertson-Walker (FLRW) filled with a perfect fluid leads to nonsingular universes which, for later times, behave as their classical counterpart. This means that the expectation value of the scale factor $(t)$ never vanishes and, as $t\to\infty$, we recover the classical expression for the scale factor. In this paper, we show that such universes can be reproduced by classical cosmology given that the universe is filled with an exotic matter. In the case of a perfect fluid, we find an implicit equation of state (EoS). We then show that this single fluid with an implict EoS is equivalent to two non-interacting fluids, one of them representing stiff matter with negative energy density. In the case of two non-interacting scalar fields, one of them of the phantom type, we find their potential energy. In both cases we find that quantum mechanics changes completely the configuration of matter for small values of time, by adding a fluid or a scalar field with negative energy density. As time passes, the density of negative energy decreases and we recover the ordinary content of the classical universe. The more the initial wave function of the universe is concentrated around the classical big bang singularity, the more it is necessary to add negative energy, since this type of energy will be responsible for the removal of the classical singularity.Comment: updated version as accepted by Gen. Relativ. Gravi

GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology

Friedreich ataxia (FRDA) is a neurodegenerative disorder caused by an unstable GAA repeat expansion mutation within intron 1 of the FXN gene. However, the origins of the GAA repeat expansion, its unstable dynamics within different cells and tissues, and its effects on frataxin expression are not yet completely understood. Therefore, we have chosen to generate representative FRDA mouse models by using the human FXN GAA repeat expansion itself as the genetically modified mutation. We have previously reported the establishment of two lines of human FXN YAC transgenic mice that contain unstable GAA repeat expansions within the appropriate genomic context. We now describe the generation of FRDA mouse models by crossbreeding of both lines of human FXN YAC transgenic mice with heterozygous Fxn knockout mice. The resultant FRDA mice that express only human-derived frataxin show comparatively reduced levels of frataxin mRNA and protein expression, decreased aconitase activity, and oxidative stress, leading to progressive neurodegenerative and cardiac pathological phenotypes. Coordination deficits are present, as measured by accelerating rotarod analysis, together with a progressive decrease in locomotor activity and increase in weight. Large vacuoles are detected within neurons of the dorsal root ganglia (DRG), predominantly within the lumbar regions in 6-month-old mice, but spreading to the cervical regions after 1 year of age. Secondary demyelination of large axons is also detected within the lumbar roots of older mice. Lipofuscin deposition is increased in both DRG neurons and cardiomyocytes, and iron deposition is detected in cardiomyocytes after 1 year of age. These mice represent the first GAA repeat expansion-based FRDA mouse models that exhibit progressive FRDA-like pathology and thus will be of use in testing potential therapeutic strategies, particularly GAA repeat-based strategies. (c) 2006 Elsevier Inc. All rights reserved