Proteogenomic Refinement of the Neomegalonema perideroedesT Genome Annotation.

Neomegalonema perideroedes (formerly Meganema perideroedes) str. G1 is the type strain and only described isolate of the genus Neomegalonema (formerly Meganema) which belongs to the Alphaproteobacteria. N. perideroedes is distinguished by the ability to accumulate high amounts of polyhydroxyalkanoates and has been associated with bulking problems in wastewater treatment plants due to its filamentous morphology. In 2013, its genome was sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which aims to improve the sequencing coverage of the poorly represented regions of the bacterial and archaeal branches of the tree of life. As N. perideroedes str. G1 is relatively distantly related to well described species-being the only sequenced member of its proposed family-the in silico prediction of genes by nucleotide homology to reference genes might be less reliable. Here, a proteomic dataset for the refinement of the N. perideroedes genome annotations is generated which clearly indicates the shortcomings of high-throughput in silico genome annotation.

Spectral and temporal multiplexing for multispectral fluorescence and reflectance imaging using two color sensors.

Fluorescence imaging can reveal functional, anatomical or pathological features of high interest in medical interventions. We present a novel method to record and display in video rate multispectral color and fluorescence images over the visible and near infrared range. The fast acquisition in multiple channels is achieved through a combination of spectral and temporal multiplexing in a system with two standard color sensors. Accurate color reproduction and high fluorescence unmixing performance are experimentally demonstrated with a prototype system in a challenging imaging scenario. Through spectral simulation and optimization we show that the system is sensitive to all dyes emitting in the visible and near infrared region without changing filters and that the SNR of multiple unmixed components can be kept high if parameters are chosen well. We propose a sensitive per-pixel metric of unmixing quality in a single image based on noise propagation and present a method to visualize the high-dimensional data in a 2D graph, where up to three fluorescent components can be distinguished and segmented.

Simultaneous real-time multicomponent fluorescence and reflectance imaging method for fluorescence-guided surgery.

Fluorescence-guided surgical procedures are employed in an increasing number of applications such as tumor delineation, blood perfusion, and sentinel lymph node detection. A new generation of fluorescent probes is expected to increase the number of applications and improve efficiency. Yet, there are no available imaging methods to take full advantage of the forthcoming targeting technologies. We present a novel concept for imaging multiple agents for fluorescence-guided surgery. The system operates without any moving parts and can resolve images of three different fluorochromes while simultaneously recording conventional reflectance images.

Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation.

The relative quantification of proteins is one of the major techniques used to elucidate physiological reactions. Because it allows one to avoid artifacts due to chemical labeling, the metabolic introduction of heavy isotopes into proteins and peptides is the preferred method for relative quantification. For eukaryotic cells, stable isotope labeling by amino acids in cell culture (SILAC) has become the gold standard and can be readily applied in a vast number of scenarios. In the microbial realm, with its highly versatile metabolic capabilities, SILAC is often not feasible, and the use of other (13)C or (15)N labeled substrates might not be practical. Here, the incorporation of heavy sulfur isotopes is shown to be a useful alternative. We introduce (34)S stable isotope labeling of amino acids for quantification and the corresponding tools required for spectra extraction and disintegration of the isotopic overlaps caused by the small mass shift. As proof of principle, we investigated the proteomic changes related to naphthalene degradation in P. fluorescens ATCC 17483 and uncovered a specific oxidative-stress-like response.

Optimizing of thienopyridine therapy by multiple electrode platelet aggregometry in clopidogrel low responders undergoing PCI.

AIMS: One possible cause of stent thrombosis is an insufficient effect of clopidogrel. In a prospective study, we aimed to optimize the platelet inhibition of clopidogrel low responders (CLR) by multiple electrode platelet aggregometry (MEA)-guided therapy modifications and to evaluate specific major adverse cardiac and cerebrovascular events (MACCE). METHODS AND RESULTS: ADP-induced platelet aggregation was measured by MEA in 1,005 consecutive patients after stent implantation and 600 mg clopidogrel loading dose. All patients received at least 100 mg aspirin/day. In 118 patients (11.7%), ADP values remained in the reference range generated in 150 controls and were defined as CLR. Significant independent predictors of CLR were acute coronary syndrome (ACS) (OR = 6.54), diabetes (OR = 2.07), use of diuretics (OR = 1.93) or proton pump inhibitors (OR = 1.64) and male gender (OR = 1.83). Ninety-nine CLR were switched to clopidogrel 150 mg/day, leading to an adequate response in 54/99. Subsequently, 44 patients were changed to ticlopidine 2 × 250 mg/day, resulting in an inhibition in 24/44. The remaining 20 patients received 2 × 100 mg cilostazol/day in addition to 75 mg clopidogrel/day. After its recent availability, 19/118 primary CLR were treated with 5-10 mg prasugrel/day. One patient was a prasugrel low responder. The total thienopyridine low response-rate was 2% in our population. The specific MACCE rate (death, non-fatal target vessel myocardial infarction, non-fatal stroke) of the CLR under optimized treatment (except prasugrel) was 2.0% at 30 days and 3.0% during a mean follow-up of 44 weeks. CONCLUSION: Clopidogrel low response is present in 1/10 patients and more frequent in ACS-PCI. MEA-guided optimizing of thienopyridine therapy is feasible and results in a very low specific MACCE rate. Low response to all thienopyridines is rare.