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Doing different things – or doing things differently? : Outcome of the consultation process NLandscape, Five years landscapes – what have we learned?
No full textPectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence
Full text linkPectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain
Genetics of colostrum, milk, and serum antibodies in dairy cattle : Implications for health and production
No full textColostrum with sufficient IgG content is essential for the newborn calf, as it requires this passive immunity to survive during its rearing. Failure of passive transfer (FPT) occurs when a calf does not absorb enough antibodies (<10 g/L of IgG in serum) from the colostrum, which besides timely access to colostrum, can be due to low IgG production of the mother or poor IgG absorption of the calf. The aim of this thesis was to explore the genetics of antibody content in colostrum and newborn calf serum and how they correlate with production and health traits. The first three studies were conducted on Swedish Red and Swedish Holstein animals from three experimental farms in Sweden. Colostrum samples from 1313 cows calving from January 2015 to April 2017 were collected. For two of the farms, serum samples from 868 newborn calves were collected at 1 to 12 days after birth. Genetic parameters were estimated for antibody traits (total IgG and natural antibodies (NAb)) and indicators (Brix and Serum Total Protein) in colostrum and calf serum. Colostrum traits had heritabilities ranging from 0.16 to 0.31 with repeatabilities from 0.21 to 0.55. Brix had positive genetic correlations with all the other colostrum traits including total IgG (0.68). Genetic correlations with milk yield, protein and fat were non-significant. A negative genetic correlation was observed for Brix and IgG traits with Lactation Average Somatic Cell Score (LASCS), but it was also non-significant. Calf serum traits had heritabilities from 0.25 to 0.59, with a significant maternal effect accounting for 17 to 27% of the variance. Genetic correlations of calf serum traits and calf health for the first three months of life had a negative tendency, but were non-significant. LASCS for the first lactation of the animals studied as calves was negatively genetically correlated with 3 NAb traits. We also performed Genome-wide association studies (GWAS) using an imputed 50K SNP array on colostrum and calf serum. In colostrum, genomic regions were found for Brix, total IgG and NAbs, with candidate genes related to immunity. Similarly, calf serum GWAS revealed QTLs for S-IgG, IgM and IgG NAbs with genes linked to molecule transport, gastric acid and salivary secretion, among others. In the last study, 1,695 milk samples of Holstein Friesian cows from Dutch herds were analyzed for 16 different NAb traits. GWAS were performed using imputed 777K SNP genotypes. For IgM NAb, significant associations were found with candidate genes related to immunoglobulin structure and early B cell development. We have shown that antibodies in colostrum, milk and serum have an important genetic component and we can pinpoint genomic regions that influence these antibodies. Our results suggest that these traits can potentially provide a tool to reduce FPT using genetic selection
Distal colonic transit is linked to gut microbiota diversity and microbial fermentation in humans with slow colonic transit
No full textLonger colonic transit time and hard stools are associated with increased gut microbiota diversity. Here, we investigate to what extent quantitative measures of (segmental) colonic transit time were related to gut microbiota composition, microbial metabolites, and gut-related parameters in a human cross-sectional study. Using radiopaque markers, (segmental) colonic transit time (CTT) was measured in 48 lean/overweight participants with long colonic transit but without constipation. Fecal microbiota composition was determined using 16S rRNA gene amplicon sequencing. Associations between gastrointestinal transit (segmental CTT and stool frequency and consistency), microbiota diversity and composition, microbial metabolites [short-chain fatty acids (SCFA), branched-chain fatty acids, and breath hydrogen], habitual diet, and gut-related host parameters [lipopolysaccharide-binding protein (LBP) and fecal calprotectin] were investigated using univariate and multivariate approaches. Long descending (i.e., distal) colonic transit was associated with increased microbial α-diversity but not with stool consistency. Using unweighted and weighted UniFrac distance, microbiota variation was not related to (segmental) CTT but to demographics, diet, plasma LBP, and fecal calprotectin. Bray-Curtis dissimilarity related only to stool consistency. Rectosigmoid and descending colonic transit were negatively associated with fecal SCFA and plasma acetate, respectively. This study suggests that the distal colon transit may affect not only microbiota diversity but also microbial metabolism.NEW & NOTEWORTHY We extend previous findings showing that long distal colonic transit time influences microbial diversification and fermentation, whereas stool consistency is related to microbiota composition in humans with a long colonic transit. This study puts the importance of the (distal) colonic site in microbiota ecology forward, which should be considered in future therapeutic studies targeting, for instance, short-chain fatty acid production to improve metabolic health.</p
Differential Network Analysis Reveals Metabolic Determinants Associated with Mortality in Acute Myocardial Infarction Patients and Suggests Potential Mechanisms Underlying Different Clinical Scores Used To Predict Death
Full text linkWe present here the differential analysis of metabolite-metabolite association networks constructed from an array of 24 serum metabolites identified and quantified via nuclear magnetic resonance spectroscopy in a cohort of 825 patients of which 123 died within 2 years from acute myocardial infarction (AMI). We investigated differences in metabolite connectivity of patients who survived, at 2 years, the AMI event, and we characterized metabolite-metabolite association networks specific to high and low risks of death according to four different risk parameters, namely, acute coronary syndrome classification, Killip, Global Registry of Acute Coronary Events risk score, and metabolomics NOESY RF risk score. We show significant differences in the connectivity patterns of several low-molecular-weight molecules, implying variations in the regulation of several metabolic pathways regarding branched-chain amino acids, alanine, creatinine, mannose, ketone bodies, and energetic metabolism. Our results demonstrate that the characterization of metabolite-metabolite association networks is a promising and powerful tool to investigate AMI patients according to their outcomes at a molecular level.</p
Mediterranean style diet and kidney function loss in kidney transplant recipients
No full textBackground and objectives Despite improvement of short-term graft survival over recent years, long-term graft survival after kidney transplantation has not improved. Studies in the general population suggest the Mediterranean diet benefits kidney function preservation. We investigated whether adherence to the Mediterranean diet is associated with kidney outcomes in kidney transplant recipients. Design, setting, participants, & measurements We included 632 adult kidney transplant recipients with a functioning graft for ≥1 year. Dietary intake was inquired using a 177-item validated food frequency questionnaire. Adherence to the Mediterranean diet was assessed using a nine-point Mediterranean Diet Score. Primary end point of the study was graft failure and secondary end points included kidney function decline (doubling of serum creatinine or graft failure) and graft loss (graft failure or death with a functioning graft). Cox regression analyses were used to prospectively study the associations of the Mediterranean Diet Score with study end points. Results During median follow-up of 5.4 (interquartile range, 4.9–6.0) years, 76 participants developed graft failure, 119 developed kidney function decline, and 181 developed graft loss. The Mediterranean Diet Score was inversely associated with all study end points (graft failure: hazard ratio [HR], 0.68; 95% confidence interval [95% CI], 0.50 to 0.91; kidney function decline: HR, 0.68; 95% CI, 0.55 to 0.85; and graft loss: HR, 0.74; 95% CI, 0.63 to 0.88 per two-point increase in Mediterranean Diet Score) independent of potential confounders. We identified 24-hour urinary protein excretion and time since transplantation to be an effect modifier, with stronger inverse associations between the Mediterranean Diet Score and kidney outcomes observed in participants with higher urinary protein excretion and participants transplanted more recently. Conclusions Adherence to the Mediterranean diet is associated with better kidney function outcomes in kidney transplant recipients.</p
Ecosystem services or nature's contributions? Reasons behind different interpretations in Latin America
No full textPeople depend on nature in multiple ways and there is increasing concern about how the current unsustainable use of natural resources will compromise human well-being. In this context, there is a debate about the usefulness of the terms ecosystem services (ES) and nature's contributions to people (NCP) in addressing this problem, but so far no research has been dedicated to investigating the reasons behind this. We, therefore, performed a data-based study to explore the potential explanations for the use and perceptions of the differences between the ES and NCP terms. Based on a questionnaire among 150 participants in the ESP Latin America and the Caribbean conference in 2018, we demonstrate that the choice for using one or both terms is related to the perception of the differences between them and to specific professional traits. We detected that researchers that use quantitative methods are predominantly inclined to use ES while researchers using qualitative methods use the NCP-term. Despite the predominant preference for one of the two terms, a considerable percentage of researchers used both. Our results suggest that rather than emphasizing perceived conflicts between ES and NCP terms, they can be used in a complementary way and have the potential to reach multiple audiences.</p
Certain flexibilities in land-use plans Towards a method for assessing flexibility
No full textThe trade-off between flexibility and legal certainty is inherent in every planning system. This trade-off is especially apparent within a land-use plan. Flexibility and legal certainty are often seen as communicating vessels: the demise of one leads to an increase in the other. Within land-use plans, however, the connection between the two is more subtle. For a land-use plan, the choice between being specific or open, and rigid or adaptable, determine the amount of flexibility. With these choices a land-use plan can increase its flexibility without decreasing legal certainty. Within reason the legal certainty can even benefit from more flexibility. However, current academic literature lacks a structured way to analyse flexibility contained within a land-use plan. Such a method is necessary for analysing and comparing different land-use plans. This paper will provide such a method and analyse thirteen different land-use plans in the Netherlands on their flexibility. It will show that a structured method can prove to be useful for analysing and comparing different land-use plans. The research provides insight into the complex balance between flexibility and legal certainty and presents an assessment tool which can be used for further academic research.</p
An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida
Full text linkOwing to its wide metabolic versatility and physiological robustness, together with amenability to genetic manipulations and high resistance to stressful conditions, Pseudomonas putida is increasingly becoming the organism of choice for a range of applications in both industrial and environmental applications. However, a range of applied synthetic biology and metabolic engineering approaches are still limited by the lack of specific genetic tools to effectively and efficiently regulate the expression of target genes. Here, we present a single‐plasmid CRISPR‐interference (CRISPRi) system expressing a nuclease‐deficient cas9 gene under the control of the inducible XylS/Pm expression system, along with the option of adopting constitutively expressed guide RNAs (either sgRNA or crRNA and tracrRNA). We showed that the system enables tunable, tightly controlled gene repression (up to 90%) of chromosomally expressed genes encoding fluorescent proteins, either individually or simultaneously. In addition, we demonstrate that this method allows for suppressing the expression of the essential genes pyrF and ftsZ, resulting in significantly low growth rates or morphological changes respectively. This versatile system expands the capabilities of the current CRISPRi toolbox for efficient, targeted and controllable manipulation of gene expression in P. putida.<br/