Metabolic Induction of Trained Immunity through the Mevalonate Pathway

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Computing approximate standard errors for genetic parameters derived from random regression models fitted by average information REML

Approximate standard errors (ASE) of variance components for random regression coefficients are calculated from the average information matrix obtained in a residual maximum likelihood procedure. Linear combinations of those coefficients define variance components for the additive genetic variance at given points of the trajectory. Therefore, ASE of these components and heritabilities derived from them can be calculated. In our example, the ASE were larger near the ends of the trajectory.     

Depressive Symptoms in Crohn's Disease: Relationship with Immune Activation and Tryptophan Availability

Crohn''s disease (CD) is associated with immune activation and depressive symptoms. This study determines the impact of anti-tumor necrosis factor (TNF)-α treatment in CD patients on depressive symptoms and the degree to which tryptophan (TRP) availability and immune markers mediate this effect. Fifteen patients with CD, eligible for anti-TNF-α treatment were recruited. Disease activity (Harvey-Bradshaw Index (HBI), Crohn''s Disease Activity Index (CDAI)), fatigue (Multidimensional Fatigue Inventory (MFI)), quality of life (Inflammatory Bowel Disease Questionnaire (IBDQ)), symptoms of depression and anxiety (Symptom Checklist (SCL-90), Beck Depression Inventory (BDI), Hamilton Depression Rating Scale (HDRS)), immune activation (acute phase proteins (APP)), zinc and TRP availability were assessed before treatment and after 2, 4 and 8 weeks. Anti-TNF-α increased IBDQ scores and reduced all depression scores; however only SCL-90 depression scores remained decreased after correction for HBI. Positive APPs decreased, while negative APPs increased after treatment. After correction for HBI, both level and percentage of γ fraction were associated with SCL-90 depression scores over time. After correction for HBI, patients with current/past depressive disorder displayed higher levels of positive APPs and lower levels of negative APPs and zinc. TRP availability remained invariant over time and there was no association between SCL-90 depression scores and TRP availability. Inflammatory reactions in CD are more evident in patients with comorbid depression, regardless of disease activity. Anti-TNF-α treatment in CD reduces depressive symptoms, in part independently of disease activity; there was no evidence that this effect was mediated by immune-induced changes in TRP availability.     

ArrayIDer: automated structural re-annotation pipeline for DNA microarrays

Background  

Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedical model organisms, are often dated. In addition, most microarray analysis tools do not readily accept EST clone names, which are abundantly represented on arrays. Manual re-annotation of microarrays is impracticable and so we developed a computational re-annotation tool (ArrayIDer) to retrieve the most recent accession mapping files from public databases based on EST clone names or accessions and rapidly generate database accessions for entire microarrays.     

Characterization of Pseudomonas aeruginosa fatty acid profiles in biofilms and batch planktonic cultures

The fatty acid composition of Pseudomonas aeruginosa PAO1 was compared between biofilm and batch planktonic cultures. Strain PAO1 biofilms were able to maintain a consistent fatty acid profile for up to 6 days, whereas strain PAO1 batch planktonic cultures showed a gradual loss of cis-monounsaturated fatty acids over 4 days. Biofilms exhibited a greater proportion of hydroxy fatty acids but a lower proportion of both cyclopropane fatty acids and saturated fatty acids (SAFAs). SAFAs with >=16 carbons, in particular, decreased in biofilms when compared with that in batch planktonic cultures. A reduced proportion of SAFAs and a decline in overall fatty acid chain length indicate more fluidic biophysical properties for cell membranes of P. aeruginosa in biofilms. Separating the biofilms into 2 partitions and comparing their fatty acid compositions revealed additional trends that were not observed in the whole biofilm: the shear-nonremovable layer consistently showed greater proportions of hydroxy fatty acid than the bulk liquid + shear-removable portion of the biofilm. The shear-nonremovable portion demonstrated a relatively immediate decline in the proportion of monounsaturated fatty acids between days 2 and 4; which was offset by an increase in the proportion of cyclopropane fatty acids, specifically 19:0cyc(11,12). Simultaneously, the shear-removable portion of the biofilm showed an increase in the proportion of trans-monounsaturated fatty acids and cyclopropane fatty acids.     

Discursive Shifts in Dutch River Management: ‘Deep’ Institutional Change or Adaptation Strategy?

This paper argues that a discursive shift is taking place in Dutch water policy, from ‘a battle against water’ to ‘living with water’ or ‘accommodating water’. Yet we ask ourselves whether this shift is just an adaptation strategy of the existing elite group of water managers, who pay lip-service to new management approaches in order to maintain their vested interests, as some authors claim, or whether it implies ‘deep’ institutional change, e.g. in terms of the emergence of new water institutions, power relations and procedures. While investigating this question, we make use of the ‘policy arrangement approach’, which pays attention to institutional and discursive aspects of policy making alike. Our conclusion is that we are currently observing institutional changes beyond ‘policy talk’, particularly in terms of new legislation and procedures. However, it is too early to speak of ‘deep’ institutional change in Dutch water management, because the former water institutions are still maintaining their power positions, despite the availability of additional resources for policy and research as well as the emergence of several new modes of governance.     

Accelerating the reconstruction of genome-scale metabolic networks

Background  

The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method to accelerate the time-consuming process of network reconstruction for a query species. The method exploits the availability of well-curated metabolic networks and uses high-resolution predictions of gene equivalency between species, allowing the transfer of gene-reaction associations from curated networks.