COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia

The COLOMBOS database (http://www.colombos.net) features comprehensive organism-specific cross-platform gene expression compendia of several bacterial model organisms and is supported by a fully interactive web portal and an extensive web API. COLOMBOS was originally published in PLoS One, and COLOMBOS v2.0 includes both an update of the expression data, by expanding the previously available compendia and by adding compendia for several new species, and an update of the surrounding functionality, with improved search and visualization options and novel tools for programmatic access to the database. The scope of the database has also been extended to incorporate RNA-seq data in our compendia by a dedicated analysis pipeline. We demonstrate the validity and robustness of this approach by comparing the same RNA samples measured in parallel using both microarrays and RNA-seq. As far as we know, COLOMBOS currently hosts the largest homogenized gene expression compendia available for seven bacterial model organisms

Development of an NGS-based workflow for improved monitoring of circulating plasmids in support of risk assessment of antimicrobial resistance gene dissemination

Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR. Next-generation sequencing (NGS) technologies are ideal for the detection of AMR genes; however, reliable reconstruction of plasmids is still a challenge due to large repetitive regions. This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads (Oxford Nanopore Technologies) and a combination of both (hybrid). Furthermore, the added value of conjugation of a plasmid to a known host was evaluated. As a case study, an isolate harboring a large, low-copymcr-1-carrying plasmid (>200 kb) was used. Hybrid assemblies of NGS data obtained from whole-genome DNA extractions of the original isolates resulted in the most complete reconstruction of plasmids. The optimal workflow was successfully applied to multidrug-resistantSalmonellaKentucky isolates, where the transfer of an ESBL-gene-containing fragment from a plasmid to the chromosome was detected. This study highlights a strategy including wet and dry lab parameters that allows accurate plasmid reconstruction, which will contribute to an improved monitoring of circulating plasmids and the assessment of their risk of transfer

Biochar characterization of raw versus spent common ivy: Inorganic nutrient behavior

Hedera sp., common Ivy, a lignocellulosic evergreen vine, is commonly seen in gardens and yards all over the globe. It is an excellent candidate to be applied in vertical green walls to improve ecosystems in future green cities (e.g. fine particulate matter adsorption). These green walls need to be trimmed regularly, thus leaving a major residue stream which could be promising as biomass feedstock for biochar fertilizer production. However, common Ivy contains valuable compounds (e.g. etheric oils and triterpene saponins) increasing the process’ added value. These should preferably be extracted prior to thermal conversion. The aim of this study is therefore to investigate the influence of extraction methods on the final properties of common ivy’s biochar using conventional pyrolysis. Investigated extraction methods include a Soxhlet ethanol extraction and a steam distillation, to obtain respectively a triterpene saponin and volatile oil extract. The influence of these extractions on the biochar properties was studied by comparing the thermal conversion and biochar properties of spent, extracted, biomass with raw biomass. Studied properties include biochar yield, elemental composition (CHNO), amount of inorganic nutrients, specific surface area, and presence of harmful heavy metals. The guidelines of the European Biochar Certificate are used to evaluate said properties. Furthermore, the pyrolysis process parameters, temperature and heating rate, were optimized to improve said biochar properties for application as fertilizer. Tested pyrolysis temperatures were 400, 550 and 700 °C. Results show that biochar yield from raw ivy was inversely proportional with pyrolysis temperature ranging from 29.6 ± 0.6% at 400 °C, 25.4% ± 0.03 at 550 °C and 23.0 ± 0.06 % at 700 °C. It was found that steam distillation lowers the amount of heavy metals in the material, whilst the inorganic nutrients are retained, thus enhancing the biochar’s potential as fertilizer. Furthermore, nitrogen content remained constant, around 2%, before and after pyrolysis both for raw and spent ivy, these results indicate that high-quality biochars were produced. To further understand biochar’s chemical behavior in soils, structural properties and morphology are being investigated further, specific surface area via BET, general pore structure using SEM, surface functional groups with FT-IR and, aromaticity with CP/MAS 13C NMR results will be presented accordingly

The attenuated end of the phenotypic spectrum in MPS III: from late-onset stable cognitive impairment to a non-neuronopathic phenotype

BACKGROUND: The phenotypic spectrum of many rare disorders is much wider than previously considered. Mucopolysaccharidosis type III (Sanfilippo syndrome, MPS III), is a lysosomal storage disorder traditionally considered to be characterized by childhood onset, progressive neurocognitive deterioration with a rapidly or slowly progressing phenotype. The presented MPS III case series demonstrates adult onset phenotypes with mild cognitive impairment or non-neuronopathic phenotypes. METHODS: In this case series all adult MPS III patients with a mild- or non-neuronopathic phenotype, who attend the outpatient clinic of 3 expert centers for lysosomal storage disorders were included. A mild- or non-neuronopathic phenotype was defined as having completed regular secondary education and attaining a level of independency during adulthood, involving either independent living or a paid job. RESULTS: Twelve patients from six families, with a median age at diagnosis of 43 years (range 3-68) were included (11 MPS IIIA, 1 MPS IIIB). In the four index patients symptoms which led to diagnostic studies (whole exome sequencing and metabolomics) resulting in the diagnosis of MPS III; two patients presented with retinal dystrophy, one with hypertrophic cardiomyopathy and one with neurocognitive decline. The other eight patients were diagnosed by family screening. At a median age of 47 years (range 19-74) 9 out of the 12 patients had normal cognitive functions. Nine patients had retinal dystrophy and 8 patients hypertrophic cardiomyopathy. CONCLUSION: We show the very mild end of the phenotypic spectrum of MPS III, ranging from late-onset stable neurocognitive impairment to a fully non-neuronopathic phenotype. Awareness of this phenotype could lead to timely diagnosis and genetic counseling

Elucidation of the Mode of Action of a New Antibacterial Compound Active against Staphylococcus aureus and Pseudomonas aeruginosa.

Nosocomial and community-acquired infections caused by multidrug resistant bacteria represent a major human health problem. Thus, there is an urgent need for the development of antibiotics with new modes of action. In this study, we investigated the antibacterial characteristics and mode of action of a new antimicrobial compound, SPI031 (N-alkylated 3, 6-dihalogenocarbazol 1-(sec-butylamino)-3-(3,6-dichloro-9H-carbazol-9-yl)propan-2-ol), which was previously identified in our group. This compound exhibits broad-spectrum antibacterial activity, including activity against the human pathogens Staphylococcus aureus and Pseudomonas aeruginosa. We found that SPI031 has rapid bactericidal activity (7-log reduction within 30 min at 4x MIC) and that the frequency of resistance development against SPI031 is low. To elucidate the mode of action of SPI031, we performed a macromolecular synthesis assay, which showed that SPI031 causes non-specific inhibition of macromolecular biosynthesis pathways. Liposome leakage and membrane permeability studies revealed that SPI031 rapidly exerts membrane damage, which is likely the primary cause of its antibacterial activity. These findings were supported by a mutational analysis of SPI031-resistant mutants, a transcriptome analysis and the identification of transposon mutants with altered sensitivity to the compound. In conclusion, our results show that SPI031 exerts its antimicrobial activity by causing membrane damage, making it an interesting starting point for the development of new antibacterial therapies

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Cognitive development in patients with Mucopolysaccharidosis type III (Sanfilippo syndrome)

Mucopolysaccharidosis type III (MPS III, Sanfilippo syndrome) is a lysosomal storage disorder caused by a deficiency of one of the enzymes involved in the degradation of heparan sulfate. MPS III is characterized by progressive mental deterioration resulting in severe dementia. A number of potentially disease-modifying therapies are studied. As preservation of cognitive function is the ultimate goal of treatment, assessment of cognitive development will be essential in order to evaluate treatment efficacy. However, no large scale studies on cognitive levels in MPS III patients, using formal psychometric tests, have been reported. We aimed to assess cognitive development in all 73 living patients with MPS III in the Netherlands. Cognitive development could be assessed in 69 patients. In 39 of them developmental level was estimated > 3 months and formal psychometric testing was attempted. A remarkable variation in the intellectual disability was detected. Despite special challenges encountered, testing failed in only three patients. The observed broad variation in intellectual disability, should be taken into account when designing therapeutic trial

Cognitive development in patients with Mucopolysaccharidosis type III (Sanfilippo syndrome)

Mucopolysaccharidosis type III (MPS III, Sanfilippo syndrome) is a lysosomal storage disorder caused by a deficiency of one of the enzymes involved in the degradation of heparan sulfate. MPS III is characterized by progressive mental deterioration resulting in severe dementia. A number of potentially disease-modifying therapies are studied. As preservation of cognitive function is the ultimate goal of treatment, assessment of cognitive development will be essential in order to evaluate treatment efficacy. However, no large scale studies on cognitive levels in MPS III patients, using formal psychometric tests, have been reported. We aimed to assess cognitive development in all 73 living patients with MPS III in the Netherlands. Cognitive development could be assessed in 69 patients. In 39 of them developmental level was estimated > 3 months and formal psychometric testing was attempted. A remarkable variation in the intellectual disability was detected. Despite special challenges encountered, testing failed in only three patients. The observed broad variation in intellectual disability, should be taken into account when designing therapeutic trial

Mothers and fathers of young Dutch adolescents with Down syndrome: Health related quality of life and family functioning

Like any child, children with Down syndrome (DS) affect the lives of their families. Most studies focus on the adaptation of parents and families of young children with DS, while relatively few studies include the perspective of fathers. To determine 1) whether mothers and fathers of 11 to 13-year-olds with DS differ from reference parents in health related quality of life (HRQoL) and family functioning, and 2) whether HRQoL in parents of children with DS changes over time, from when the child was 6-8 years old to when the child was 11-13 years old. 80 mothers and 44 fathers completed HRQoL and family functioning questionnaires. 58 parents (53 mothers) had completed the HRQoL-questionnaire in a previous study. Mothers differed from reference mothers in one HRQoL-domain (Sexuality), while fathers' HRQoL did not significantly differ from reference fathers. Both mothers and fathers scored in the (sub)clinical range more frequently than reference parents in Total family functioning, and in the domains Partner relation and Social network. Furthermore, fathers scored in the (sub)clinical range more frequently than reference parents in Responsiveness and Organization. HRQoL showed no significant change over time. Our findings indicate frequent family functioning problems but few HRQoL problems in parents and families of children with DS. In offering care, a family based approach with special attention for partner relation and social functioning is neede