iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.

Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of A. baumannii would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of A. baumannii AYE, named iCN718, that improves and standardizes previous A. baumannii AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an A. baumannii reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other A. baumannii strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen

Norovirus whole genome sequencing by SureSelect target enrichment: a robust and sensitive method

Norovirus full genome sequencing is challenging due to sequence heterogeneity between genomes. Previous methods have relied on PCR amplification, which is problematic due to primer design, and RNASeq which non-specifically sequences all RNA in a stool specimen, including host and bacterial RNA.Target enrichment uses a panel of custom-designed 120-mer RNA baits which are complementary to all publicly available norovirus sequences, with multiple baits targeting each position of the genome, thus overcoming the challenge of primer design. Norovirus genomes are enriched from stool RNA extracts to minimise sequencing non-target RNA.SureSelect target enrichment and Illumina sequencing was used to sequence full genomes from 507 norovirus positive stool samples with RT-qPCR Ct values 10-43. Sequencing on an Illumina MiSeq in batches of 48 generated on average 81% on-target-reads per sample and 100% genome coverage with >12,000-fold read depth. Samples included genotypes GI.1, GI.2, GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14 and GII.17. Once outliers are accounted for, we generate over 80% genome coverage for all positive samples, regardless of Ct value.164 samples were tested in parallel with conventional PCR genotyping of the capsid shell domain. 164/164 samples were successfully sequenced, compared to 158/164 that were amplified by PCR. Four of the samples that failed capsid PCR had low titres, suggesting target enrichment is more sensitive than gel-based PCR. Two samples failed PCR due to primer mismatches; target enrichment uses multiple baits targeting each position, thus accommodating sequence heterogeneity between norovirus genomes

Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK

Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineages (1983-1995, Ia, I/IIa and I/IIb; 1996-2014, Ic; and 2015-2018, IIb). The acquisition of a stx2a-encoding bacteriophage by these five sub-lineages appears to have coincided with their respective emergences. The Oxford Nanopore Technologies (ONT) system was used to sequence, characterize and compare the stx-encoding prophages harboured by each sub-lineage to investigate the integration of this key virulence factor. The stx2a-encoding prophages from each of the lineages causing clinical disease in the UK were all different, including the two UK sub-lineages (Ia and I/IIa) circulating concurrently and causing severe disease in the early 1980s. Comparisons between the stx2a-encoding prophage in sub-lineages I/IIb and IIb revealed similarity to the prophage commonly found to encode stx2c, and the same site of bacteriophage integration (sbcB) as stx2c-encoding prophage. These data suggest independent acquisition of previously unobserved stx2a-encoding phage is more likely to have contributed to the emergence of STEC O157:H7 sub-lineages in the UK than intra-UK lineage to lineage phage transmission. In contrast, the stx2c-encoding prophage showed a high level of similarity across lineages and time, consistent with the model of stx2c being present in the common ancestor to extant STEC O157:H7 and maintained by vertical inheritance in the majority of the population. Studying the nature of the stx-encoding bacteriophage contributes to our understanding of the emergence of highly pathogenic strains of STEC O157:H7

Avaliação da eficácia do aluminosilicato de sódio hidratado na prevenção de câncer hepático induzido por aflatoxina em truta arco-íris

The use of aluminum silicates for decontaminating animal feed containing aflatoxins has yielded encouraging results in chicken and turkey poults. In contrast, very few studies have tested these substances in aquaculture. In this work, we investigated the efficacy of a trout diet containing 0.5% hydrated sodium aluminosilicate (HSAS) in protecting against contamination with aflatoxin B1. Trout were reared on these diets for one year and the experimental groups were examined monthly for hepatic presumptive preneoplastic and neoplastic lesions. Regardless of the presence of HSAS, all of the fish that received aflatoxin in their diet have shown hepatic lesions indicative of a carcinogenic process, presenting also the development of cancer in some fish. The concentration of HSAS used in this study was ineffective in preventing the onset of hepatic lesions induced by aflatoxin B1 in rainbow trout.Resultados encorajadores têm sido observados com o emprego de aluminosilicatos para descontaminação de ração contendo aflatoxina destinada à avicultura. No entanto, raros estudos têm sido destinados a testar essa substância em aqüicultura. Assim, no presente trabalho, foi investigada a eficácia do aluminosilicato de sódio hidratado (HSAS, 0,5%) em proteger a truta arco-íris dos danos hepáticos causados por ração contaminada com aflatoxina B1. Os grupos experimentais foram alimentados com suas respectivas dietas durante 12 meses, mensalmente cada grupo foi amostrado para análises anatomopatológica e histopatológica para verificação da presença de lesões hepáticas. Apesar da presença de HSAS, todos os grupos que receberam dieta contaminada com aflatoxina B1 apresentaram lesões hepáticas indicativas do processo carcinogênico, sendo que exemplares alimentados com essas dietas por mais longo prazo apresentaram hepatocarcinoma ou colangiocarcinoma. Estes resultados indicaram que a concentração de HSAS usada no presente estudo não foi efetiva em prevenir o desenvolvimento de lesões hepáticas induzidas por aflatoxina B1 em truta arco-íris.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundo de Apoio ao Ensino, Pesquisa e Extensão da Universidade Estadual de Campina

Problems with Sleep Do Not Predict Self-Reported Driving Factors and Perception in Older Drivers: Evidences from the Candrive II Prospective Cohort

Given that sleep problems and serious motor vehicle collisions are increasingly prevalent in older adults, even minor drowsiness could potentially contribute to driving patterns in older drivers. To date, it is unknown whether less serious problems with sleep influence driving frequency and ability in older adults. We investigated the influence of everyday sleep disturbances on driving practices and driver perceptions in a large cohort of healthy older drivers. Selfreported measures of sleep problems were used to investigate the influence of sleep disturbance on self-reported driving practices and perceived driving abilities. On two measures of self-reported driving outcomes, participants with problems with rated themselves more poorly. However, this relationship disappeared when health and demographic variables were entered prior in hierarchical regression analyses. Our results show that the relationship between sleep problems, driving frequency and perceived abilities is better explained by mediating demographic, health, and cognitive factors

Identifying Potential Risks and Benefits of Using Cloud in Distributed Software Development

Cloud-based infrastructure has been increasingly adopted by the industry in distributed software development (DSD) environments. Its proponents claim that its several benefits include reduced cost, increased speed and greater productivity in software development. Empirical evaluations, however, are in the nascent stage of examining both the benefits and the risks of cloud-based in-frastructure. The objective of this paper is to identify potential benefits and risks of using cloud in a DSD project conducted by teams based in Helsinki and Ma-drid. A cross-case qualitative analysis is performed based on focus groups con-ducted at the Helsinki and Madrid sites. Participants’ observations are used to supplement the analysis. The results of the analysis indicated that the main ben-efits of using cloud are rapid development, continuous integration, cost savings, code sharing, and faster ramp-up. The key risks determined by the project are dependencies, unavailability of access to the cloud, code commitment and inte-gration, technical debt, and additional support costs. The results revealed that if such environments are not planned and set up carefully, the benefits of using cloud in DSD projects might be overshadowed by the risks associated with it.Peer reviewe

Photodynamic Therapy of Inorganic Complexes for the Treatment of Cancer

Photodynamic therapy (PDT) is a medicinal tool that uses a photosensitiser and a light source to treat several conditions, including cancer. PDT uses reactive oxygen species (ROS) such as cytotoxic singlet oxygen 1O2 to induce cell death in cancer cells. Chemotherapy has historically utilized the cytotoxic effects of many metals, especially transition-metal complexes. However, chemotherapy is a systemic treatment so all cells in a patient\u27s body are exposed to the same cytotoxic effects. Transition metal complexes have also shown high cytotoxicity as PDT agents. PDT is a potential localized method for treating several cancer types by using inorganic complexes as photosensitizing agents. This review covers several in vitro and in vivo studies, as well as clinical trials that reported on the anti-cancer properties of inorganic pharmaceuticals used in PDT against different types of cancer