An Atypical Mitochondrial Carrier That Mediates Drug Action in Trypanosoma brucei

Elucidating the mechanism of action of trypanocidal compounds is an important step in the development of more efficient drugs against Trypanosoma brucei. In a screening approach using an RNAi library in T. brucei bloodstream forms, we identified a member of the mitochondrial carrier family, TbMCP14, as a prime candidate mediating the action of a group of anti-parasitic choline analogs. Depletion of TbMCP14 by inducible RNAi in both bloodstream and procyclic forms increased resistance of parasites towards the compounds by 7-fold and 3-fold, respectively, compared to uninduced cells. In addition, down-regulation of TbMCP14 protected bloodstream form mitochondria from a drug-induced decrease in mitochondrial membrane potential. Conversely, over-expression of the carrier in procyclic forms increased parasite susceptibility more than 13-fold. Metabolomic analyses of parasites over-expressing TbMCP14 showed increased levels of the proline metabolite, pyrroline-5-carboxylate, suggesting a possible involvement of TbMCP14 in energy production. The generation of TbMCP14 knock-out parasites showed that the carrier is not essential for survival of T. brucei bloodstream forms, but reduced parasite proliferation under standard culture conditions. In contrast, depletion of TbMCP14 in procyclic forms resulted in growth arrest, followed by parasite death. The time point at which parasite proliferation stopped was dependent on the major energy source, i.e. glucose versus proline, in the culture medium. Together with our findings that proline-dependent ATP production in crude mitochondria from TbMCP14-depleted trypanosomes was reduced compared to control mitochondria, the study demonstrates that TbMCP14 is involved in energy production in T. brucei. Since TbMCP14 belongs to a trypanosomatid-specific clade of mitochondrial carrier family proteins showing very poor similarity to mitochondrial carriers of mammals, it may represent an interesting target for drug action or targeting.     

Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet

Proteomics by mass spectrometry technology is widely used for identifying and quantifying peptides and proteins. The breadth and sensitivity of peptide detection have been advanced by the advent of data-independent acquisition mass spectrometry. Analysis of such data, however, is challenging due to the complexity of fragment ion spectra that have contributions from multiple co-eluting precursor ions. We present SWATHProphet software that identifies and quantifies peptide fragment ion traces in data-independent acquisition data, provides accurate probabilities to ensure results are correct, and automatically detects and removes contributions to quantitation originating from interfering precursor ions. Integration in the widely used open source Trans-Proteomic Pipeline facilitates subsequent analyses such as combining results of multiple data sets together for improved discrimination using iProphet and inferring sample proteins using ProteinProphet. This novel development should greatly help make data-independent acquisition mass spectrometry accessible to large numbers of users.Mass spectrometry is widely used to identify and quantify protein samples. Proteins are typically cleaved into peptides (either enzymatically or chemically), separated by at least one-dimensional fractionation (e.g. liquid chromatography), and collisionally fragmented, and fragment ions are detected by their unique m/z values in a mass spectrometer (1). Data-dependent acquisition (shotgun) selects individual precursor ions for fragmentation and is limited in its ability to consistently detect large numbers of peptides, particularly those of lower intensity, in samples (2). In contrast, selective reaction monitoring (SRM)¹ is a targeted approach in which known precursor and a set of fragment ions are monitored over time upon selection by mass filters in a triple quadrupole instrument. The selected fragment ions in conjunction with the parent ion constitute a highly sensitive molecular assay specific for a precursor ion of interest. Although this strategy has been successfully applied for a large number of biological studies, it is limited by low throughput.An alternative approach, data-independent acquisition (DIA), aims to overcome the low throughput limitation of SRM while maintaining full quantitative analyses. It selects all ions within a sliding m/z precursor window for fragmentation (3–7) and effectively creates a digital record of the complete peptide contents of the sample. Its increased sensitivity, however, is limited by the challenge of interpreting fragment ion spectra generated from multiple precursors. This can be done by spectral deconvolution followed by database search (1, 8) or by query of the data with preselected fragment ions in a spectral library in a manner similar to targeted approaches such as SRM (3).Software packages currently available for targeted analysis of DIA MS data with precursor ion assays contained within a spectral library include PeakView^TM from (Sciex, Framingham, MA), for data generated on a TripleTOF mass spectrometer. The proprietary Spectronaut (Biognosys AG, Zurich, Switzerland) and open source OpenSWATH software (9) are adaptations of the mProphet software suite (10) originally designed for SRM data, and the widely used SRM software Skyline (11) now also incorporates mProphet software to handle DIA MS data. None of these available programs, however, provide validation of results with computed probabilities or detection and removal of fragment ion interferences that give rise to inaccurate quantitation and decreased sensitivity.Here we present SWATHProphet software that performs these functions in conjunction with a high quality spectral library. SWATHProphet validates results with accurate probabilities of being correct. These probabilities serve as input to downstream analyses in the highly developed Trans-Proteomic Pipeline (TPP) (12), such as combining together results of multiple runs for improved discrimination with iProphet (13) and inferring sample proteins with ProteinProphet (14). In addition, SWATHProphet uses these probabilities to help cope with complex spectra by automatically detecting fragment ion interferences and removing them in silico to yield accurate quantitation and adjusted probabilities.     

Reading a Suspenseful Literary Text Activates Brain Areas Related to Social Cognition and Predictive Inference

Stories can elicit powerful emotions. A key emotional response to narrative plots (e.g., novels, movies, etc.) is suspense. Suspense appears to build on basic aspects of human cognition such as processes of expectation, anticipation, and prediction. However, the neural processes underlying emotional experiences of suspense have not been previously investigated. We acquired functional magnetic resonance imaging (fMRI) data while participants read a suspenseful literary text (E.T.A. Hoffmann''s “The Sandman”) subdivided into short text passages. Individual ratings of experienced suspense obtained after each text passage were found to be related to activation in the medial frontal cortex, bilateral frontal regions (along the inferior frontal sulcus), lateral premotor cortex, as well as posterior temporal and temporo-parietal areas. The results indicate that the emotional experience of suspense depends on brain areas associated with social cognition and predictive inference.     

Population size estimates based on the frequency of genetically assigned parent–offspring pairs within a subsample

Estimating population density as precise as possible is a key premise for managing wild animal species. This can be a challenging task if the species in question is elusive or, due to high quantities, hard to count. We present a new, mathematically derived estimator for population size, where the estimation is based solely on the frequency of genetically assigned parent–offspring pairs within a subsample of an ungulate population. By use of molecular markers like microsatellites, the number of these parent–offspring pairs can be determined. The study's aim was to clarify whether a classical capture–mark–recapture (CMR) method can be adapted or extended by this genetic element to a genetic‐based capture–mark–recapture (g‐CMR). We numerically validate the presented estimator (and corresponding variance estimates) and provide the R‐code for the computation of estimates of population size including confidence intervals. The presented method provides a new framework to precisely estimate population size based on the genetic analysis of a one‐time subsample. This is especially of value where traditional CMR methods or other DNA‐based (fecal or hair) capture–recapture methods fail or are too difficult to apply. The DNA source used is basically irrelevant, but in the present case the sampling of an annual hunting bag is to serve as data basis. In addition to the high quality of muscle tissue samples, hunting bags provide additional and essential information for wildlife management practices, such as age, weight, or sex. In cases where a g‐CMR method is ecologically and hunting‐wise appropriate, it enables a wide applicability, also through its species‐independent use.     

Uropathogenic Escherichia coli use d-serine deaminase to modulate infection of the murine urinary tract

Although once thought to be unique to bacteria, d-amino acids are also produced by mammals. For example, d-serine is excreted in human urine at concentrations ranging from 3.0 to 40 micro g ml-1. An epidemiological survey demonstrated that urine isolates of E. coli are more likely to catabolise d-serine via expression of d-serine deaminase, DsdA than enteric disease isolates. The urosepsis strain, CFT073, and an isogenic dsdA mutant have similar growth kinetics in minimal or complex media. However, relative to the wild type, the dsdA mutant has a pleiomorphic cell shape and a prolonged, 4-6 h lag phase when grown in human urine. This suggests that d-serine catabolism provides a growth advantage in the urinary tract. Unexpectedly, in a direct competition model of urinary tract infection, the dsdA mutant was recovered 300-times more frequently than the wild type in the bladders of mice 48 h after infection. A new model of E. coli uropathogenesis is proposed where growth and gene expression are modulated in response to environmental d-serine levels. In support of this, the CFT073 dsdA mutant is hyperflagellated and more motile than the wild type indicating that intracellular levels of d-serine may directly or indirectly influence the expression of regulons associated with E. coli uropathogenesis.     

Antibodies against beta-amyloid slow cognitive decline in Alzheimer's disease

To test whether antibodies against beta-amyloid are effective in slowing progression of Alzheimer's disease, we assessed cognitive functions in 30 patients who received a prime and a booster immunization of aggregated Abeta(42) over a 1 year period in a placebo-controlled, randomized trial. Twenty patients generated antibodies against beta-amyloid, as determined by tissue amyloid plaque immunoreactivity assay. Patients who generated such antibodies showed significantly slower rates of decline of cognitive functions and activities of daily living, as indicated by the Mini Mental State Examination, the Disability Assessment for Dementia, and the Visual Paired Associates Test of delayed recall from the Wechsler Memory Scale, as compared to patients without such antibodies. These beneficial clinical effects were also present in two of three patients who had experienced transient episodes of immunization-related aseptic meningoencephalitis. Our results establish that antibodies against beta-amyloid plaques can slow cognitive decline in patients with Alzheimer's disease.     

Multi-biomarker analysis in patients after transcatheter aortic valve implantation (TAVI)

Abstract

Background: In this study we sought to examine whether transcatheter aortic valve implantation (TAVI) is followed by a change in the plasma levels of novel cardiovascular biomarkers.

Methods: We collected blood samples of 79 patients with severe aortic valve stenosis undergoing TAVI before and at 7 days, 1 month, 3 months and 6 months post TAVI and analyzed the plasma concentrations of GDF-15, H-FABP, fetuin-A, galectin 3, sST2 and suPAR by means of ELISA.

Results: There was a significant increase in the concentration of fetuin-A (median: 52.44 mg/ml to 113.2 mg/ml, p?<?0.001) and a significant decrease of H–FABP after TAVI (median: 4.835 ng/ml to 2.534 ng/ml, p?<?0.001). The concentrations of suPAR and sST2 showed an initial increase (suPAR median: 2755 pg/ml 3489 pg/ml, p?<?0.001; sST2 median: 5832 pg/ml to 7137 pq/ml, p?<?0.001) and subsequently decreased significantly.

Conclusion: We hypothesize that the decrease of H-FABP and the increase of fetuin-A could be due to a hemodynamic improvement after valve replacement. The initial increase of suPAR could indicate an inflammatory stimulus and the significant increase in sST2 could be due to the mechanical strain caused by implantation of the valve.     

A microsatellite DNA toolkit for studying population structure in Apis mellifera

We present a set of 18 microsatellite DNA markers that can be run in two multiplex polymerase chain reactions as standard tool for assessing molecular ecological problems in honeybees (Apis mellifera). In addition to a set of six unlinked loci testing for classical population genetic parameters, we present three sets of four tightly linked loci, each located on three different chromosomes. These linked markers are useful for determining the number of colonies in a population as well as the parentage of drones and workers. Moreover, the tool kit can test for various modes of natural selection in honeybee populations.     

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