In-depth characterization of genome-scale network reconstructions for the in vitro synthesis in cell-free systems

Cell-free systems containing multiple enzymes are becoming an increasingly interesting tool for one-pot syntheses of biochemical compounds. To extensively explore the enormous wealth of enzymes in the biological space, we present methods for assembling and curing data from databases to apply them for the prediction of pathway candidates for directed enzymatic synthesis. We use Kyoto Encyclopedia of Genes and Genomes to establish single organism models and a pan-organism model that is combining the available data from all organisms listed there. We introduce a filtering scheme to remove data that are not suitable, for example, generic metabolites and general reactions. In addition, a valid stoichiometry of reactions is required for acceptance. The networks created are analyzed by graph theoretical methods to identify a set of metabolites that are potentially reachable from a defined set of starting metabolites. Thus, metabolites not connected to such starting metabolites cannot be produced unless new starting metabolites or reactions are introduced. The network models also comprise stoichiometric and thermodynamic data that allow the definition of constraints to identify potential pathways. The resulting data can be directly applied using existing or future pathway finding tools.     

Wide spread invasion without sexual reproduction? A case study on European willows in Patagonia,Argentina

Willows of the Salix alba–Salix fragilis complex, native to western Eurasia, represent typical invaders of floodplain ecosystems worldwide. Introduced to South America by European settlers probably at the end of the nineteenth century, their distribution has increased significantly along the rivers in Northern Patagonia. This case study carried out mainly in the area around Lake Nahuel Huapi aims to analyze clonal structures and their spatial distribution using molecular markers as well as to relate the observed patterns to settlement history and life history traits of this species complex. Leaf material from 171 trees was collected along selected river floodplains in Northern Patagonia and genotypes were determined at six microsatellite loci. Including 62 reference samples of the S. alba–S. fragilis complex from German rivers, Probability of Identity (P _ID) was calculated and a Principal Coordinate Analysis (PCoA) conducted. From the altogether thirteen different genotypes detected, one dominant genotype (female) formed monoclonal stands along most of the studied river stretches. The maximum linear distance between the most remote ramets of this clone was 790 km. Evidence arose that the colonizing process so far is exclusively based on vegetative propagation in the focal study area and is obviously attributable to the pronounced brittleness of the hybrid parent S. fragilis. However, outside this area the occurrence of male trees and a diversity of genotypes indicate that evolutionary processes by recombination are involved within the willow complex. Therefore, an increase in genotypes can be assumed when male individuals and therefore sexual reproduction would appear in the area around Lake Nuhuel Huapi. This could be a crucial point for the long-term invasion success of the taxa when climatic and other environmental conditions will change in Southern Argentina.     

Early stress and chronic methylphenidate cross-sensitize dopaminergic responses in the adolescent medial prefrontal cortex and nucleus accumbens

Methylphenidate (MP) is widely used to treat attention deficit/hyperactivity disorder in children. However, basic research has been mainly focused on MP treatment in adult, behaviorally normal rodents. Here we analyzed MP-evoked changes of dopamine (DA) release in the limbic system of juvenile rodents with hyperactive and attention deficit-like symptoms. Using dual probe in vivo microdialysis, DA levels were quantified in the medial prefrontal cortex and nucleus accumbens of juvenile and adolescent degus ( Octodon degus ). Acute stress- and acute MP-evoked dopaminergic responses in normal juvenile and adolescent animals were compared with (i) animals showing symptoms of hyperactivity and attention deficits induced by early life stress, i.e. repeated parental separation during the first 3 weeks of life, and (ii) animals chronically treated with MP during pre-adolescence. Our main results revealed that (i) early life stress and (ii) chronic MP treatment during pre-adolescence cross-sensitize limbic dopaminergic functions in adolescent animals. Furthermore, we demonstrated a unique pattern of acute MP-evoked DA release in the juvenile compared with the adolescent medial prefrontal cortex and nucleus accumbens. Our findings that the functional maturation of dopaminergic limbic function is significantly altered by early life experience, i.e. repeated parental separation and chronic MP treatment, allow novel insights into the etiology of attention deficit/hyperactivity disorder and into the long-term consequences of MP treatment on brain development.     

Label-free live-cell imaging with confocal Raman microscopy

Confocal Raman spectroscopy is a noninvasive alternative to established cell imaging methods because it does not require chemical fixation, the use of fluorescent markers, or genetic engineering. In particular, single live-cell, high-resolution imaging by confocal Raman microscopy is desirable because it allows further experiments concerning the individually investigated cells. However, to derive meaningful images from the spectroscopic data, one must identify cell components within the dataset. Using immunofluorescence images as a reference, we derive Raman spectral signatures by means of information measures to identify cell components such as the nucleus, the endoplasmic reticulum, the Golgi apparatus, and mitochondria. The extracted signatures allow us to generate representations equivalent to conventional (immuno)fluorescence images with more than three cell components at a time, exploiting the Raman spectral information alone.     

Isolation of transgenic progeny of maize by embryo rescue under selective conditions

Summary Fertile transgenic maize plants (T₀) and progeny (T₁) were obtained using microprojectile bombardment and callus selection on hygromycin B. To quickly identify progeny expressing the transgene, embryos from T3 generation kernels were excised 20 days after pollination and exposed to different concentrations of hygromycin B. Surviving and non-surviving embryos were assayed for the presence of the hygromycin phosphotransferase (aphIV) gene using polymerase chain reaction. Embryos that germinated and survived on 25, 50, or 100 mg/liter hygromycin possessed theaphIV gene. Embryos that did not germinate lacked the gene. Progeny surviving selection were transferred to the greenhouse and tested for expression of the gene using a leaf disc assay. The results demonstrated that the gene construct was expressed in both embryo and leaf tissue and that selection during germination successfully eliminated progeny lacking the gene of interest. This method is also useful for rapid-cycling of maize generations.     

Azithromycin versus placebo for the treatment of HIV-associated chronic lung disease in children and adolescents (BREATHE trial): study protocol for a randomised controlled trial

Background

Human immunodeficiency virus (HIV)-related chronic lung disease (CLD) among children is associated with substantial morbidity, despite antiretroviral therapy. This may be a consequence of repeated respiratory tract infections and/or dysregulated immune activation that accompanies HIV infection. Macrolides have anti-inflammatory and antimicrobial properties, and we hypothesised that azithromycin would reduce decline in lung function and morbidity through preventing respiratory tract infections and controlling systemic inflammation.

Methods/design

We are conducting a multicentre (Malawi and Zimbabwe), double-blind, randomised controlled trial of a 12-month course of weekly azithromycin versus placebo. The primary outcome is the mean change in forced expiratory volume in 1 second (FEV₁) z-score at 12 months. Participants are followed up to 18 months to explore the durability of effect. Secondary outcomes are FEV₁ z-score at 18 months, time to death, time to first acute respiratory exacerbation, number of exacerbations, number of hospitalisations, weight for age z-score at 12 and 18 months, number of adverse events, number of malaria episodes, number of bloodstream Salmonella typhi infections and number of gastroenteritis episodes. Participants will be followed up 3-monthly, and lung function will be assessed every 6 months. Laboratory substudies will be done to investigate the impact of azithromycin on systemic inflammation and on development of antimicrobial resistance as well as impact on the nasopharyngeal, lung and gut microbiome.

Discussion

The results of this trial will be of clinical relevance because there are no established guidelines on the treatment and management of HIV-associated CLD in children in sub-Saharan Africa, where 80% of the world’s HIV-infected children live and where HIV-associated CLD is highly prevalent.

Trial registration

ClinicalTrials.gov, NCT02426112. Registered on 21 April 2015.

     

Cyclodextrins differentially mobilize free and esterified cholesterol from primary human foam cell macrophages

Human monocyte-derived foam cell macrophages (HMFCs) are resistant to cholesterol efflux mediated by physiological acceptors. The role of the plasma membrane in regulating depletion of free cholesterol (FC) and of cholesteryl ester (CE) was investigated using cyclodextrins (CDs). HMFCs were incubated in media containing CDs (1.0 mg/ml, approximately 0.7 mM) with low [hydroxypropyl-beta-CD (HP-CD)] or high [trimethyl-beta-CD (TM-CD)] affinity for cholesterol in the presence or absence of phospholipid vesicles (PLVs). Low-affinity HP-CD caused minimal cholesterol efflux on its own, but HP-CD+ PLV depleted cell FC and CE to 54.5 +/- 6.7% of control by 24 h. TM-CD depleted FC at least as well as HP-CD+PLV but without depleting CE, even when combined with PLV. This was not explained by acceptor saturation, instability of PLV vesicles, de novo cholesterol synthesis, kinetically distinct cholesterol pools, or inhibition of CE hydrolysis. TM-CD did, however, deplete CE when lower concentrations of TM-CD were combined with PLV and when acetyl-CoA cholesteryl acyltransferase was inhibited. TM-CD caused much greater depletion of plasma membrane cholesterol than HP-CD without depleting plasma membrane sphingomyelin. It is concluded that differential depletion of plasma membrane cholesterol pools regulates cholesterol efflux and CE clearance in human macrophages.     

Conditional and inducible transgene expression in mice through the combinatorial use of Cre-mediated recombination and tetracycline induction

Here we describe a triple transgenic mouse system, which combines the tissue specificity of any Cre-transgenic line with the inducibility of the reverse tetracycline transactivator (rtTA)/tetracycline-responsive element (tet-O)-driven transgenes. To ensure reliable rtTA expression in a broad range of cell types, we have targeted the rtTA transgene into the ROSA26 locus. The rtTA expression, however, is conditional to a Cre recombinase-mediated excision of a STOP region from the ROSA26 locus. We demonstrate the utility of this technology through the inducible expression of the vascular endothelial growth factor (VEGF-A) during embryonic development and postnatally in adult mice. Our results of adult induction recapitulate several different hepatic and immune cell pathological phenotypes associated with increased systemic VEGF-A protein levels. This system will be useful for studying genes in which temporal control of expression is necessary for the discovery of the full spectrum of functions. The presented approach abrogates the need to generate tissue-specific rtTA transgenes for tissues where well-characterized Cre lines already exist.     

UV effects on photosynthesis and DNA in propagules of three Antarctic seaweeds (<Emphasis Type="Italic">Adenocystis utricularis</Emphasis>, <Emphasis Type="Italic">Monostroma hariotii</Emphasis> and <Emphasis Type="Italic">Porphyra endiviifolium</Emphasis>)

Ozone depletion is highest during spring and summer in Antarctica, coinciding with the seasonal reproduction of most macroalgae. Propagules are the life-stage of an alga most susceptible to environmental perturbations therefore, reproductive cells of three intertidal macroalgal species Adenocystis utricularis (Bory) Skottsberg, Monostroma hariotii Gain, and Porphyra endiviifolium (A and E Gepp) Chamberlain were exposed to photosynthetically active radiation (PAR), PAR + UV-A and PAR + UV-A + UV-B radiation in the laboratory. During 1, 2, 4, and 8 h of exposure and after 48 h of recovery, photosynthetic efficiency, and DNA damage were determined. Saturation irradiance of freshly released propagules varied between 33 and 83 μmol photons m⁻² s⁻¹ with lowest values in P. endiviifolium and highest values in M. hariotii. Exposure to 22 μmol photons m⁻² s⁻¹ PAR significantly reduced photosynthetic efficiency in P. endiviifolium and M. hariotii, but not in A. utricularis. UV radiation (UVR) further decreased the photosynthetic efficiency in all species but all propagules recovered completely after 48 h. DNA damage was minimal or not existing. Repeated exposure of A. utricularis spores to 4 h of UVR daily did not show any acclimation of photosynthesis to UVR but fully recovered after 20 h. UVR effects on photosynthesis are shown to be species-specific. Among the tested species, A. utricularis propagules were the most light adapted. Propagules obviously possess good repair and protective mechanisms. Our study indicates that the applied UV dose has no long-lasting negative effects on the propagules, a precondition for the ecological success of macroalgal species in the intertidal.     

Blood volume-monitored regulation of ultrafiltration in fluid-overloaded hemodialysis patients: study protocol for a randomized controlled trial

Background

Governments and donors all over Africa are searching for sustainable, affordable and cost-effective ways to improve the quality of malaria case management. Widespread deficiencies have been reported in the prescribing and counselling practices of health care providers treating febrile patients in both public and private health facilities. Cameroon is no exception with low levels of adherence to national guidelines, the frequent selection of non-recommended antimalarials and the use of incorrect dosages. This study evaluates the effectiveness and cost-effectiveness of introducing two different provider training packages, alongside rapid diagnostic tests (RDTs), designed to equip providers with the knowledge and practical skills needed to effectively diagnose and treat febrile patients. The overall aim is to target antimalarial treatment better and to facilitate optimal use of malaria treatment guidelines.

Methods/Design

A 3-arm stratified, cluster randomized trial will be conducted to assess whether introducing RDTs with provider training (basic or enhanced) is more cost-effective than current practice without RDTs, and whether there is a difference in the cost effectiveness of the provider training interventions. The primary outcome is the proportion of patients attending facilities that report a fever or suspected malaria and receive treatment according to malaria guidelines. This will be measured by surveying patients (or caregivers) as they exit public and mission health facilities. Cost-effectiveness will be presented in terms of the primary outcome and a range of secondary outcomes, including changes in provider knowledge. Costs will be estimated from a societal and provider perspective using standard economic evaluation methodologies.

Trial Registration

ClinicalTrials.gov: NCT00981877