Analysis of the Aspergillus fumigatus Proteome Reveals Metabolic Changes and the Activation of the Pseurotin A Biosynthesis Gene Cluster in Response to Hypoxia

The mold Aspergillus fumigatus is the most important airborne fungal pathogen. Adaptation to hypoxia represents an important virulence attribute for A. fumigatus. Therefore, we aimed at obtaining a comprehensive overview about this process on the proteome level. To ensure highly reproducible growth conditions, an oxygen-controlled, glucose-limited chemostat cultivation was established. Two-dimensional gel electrophoresis analysis of mycelial and mitochondrial proteins as well as two-dimensional Blue Native/SDS-gel separation of mitochondrial membrane proteins led to the identification of 117 proteins with an altered abundance under hypoxic in comparison to normoxic conditions. Hypoxia induced an increased activity of glycolysis, the TCA-cycle, respiration, and amino acid metabolism. Consistently, the cellular contents in heme, iron, copper, and zinc increased. Furthermore, hypoxia induced biosynthesis of the secondary metabolite pseurotin A as demonstrated at proteomic, transcriptional, and metabolite levels. The observed and so far not reported stimulation of the biosynthesis of a secondary metabolite by oxygen depletion may also affect the survival of A. fumigatus in hypoxic niches of the human host. Among the proteins so far not implicated in hypoxia adaptation, an NO-detoxifying flavohemoprotein was one of the most highly up-regulated proteins which indicates a link between hypoxia and the generation of nitrosative stress in A. fumigatus

An Extreme Precision Radial Velocity Pipeline: First Radial Velocities from EXPRES

The EXtreme PREcision Spectrograph (EXPRES) is an environmentally stabilized, fiber-fed, $R=137,500$, optical spectrograph. It was recently commissioned at the 4.3-m Lowell Discovery Telescope (LDT) near Flagstaff, Arizona. The spectrograph was designed with a target radial-velocity (RV) precision of 30$\mathrm{~cm~s^{-1}}$. In addition to instrumental innovations, the EXPRES pipeline, presented here, is the first for an on-sky, optical, fiber-fed spectrograph to employ many novel techniques---including an "extended flat" fiber used for wavelength-dependent quantum efficiency characterization of the CCD, a flat-relative optimal extraction algorithm, chromatic barycentric corrections, chromatic calibration offsets, and an ultra-precise laser frequency comb for wavelength calibration. We describe the reduction, calibration, and radial-velocity analysis pipeline used for EXPRES and present an example of our current sub-meter-per-second RV measurement precision, which reaches a formal, single-measurement error of 0.3$\mathrm{~m~s^{-1}}$ for an observation with a per-pixel signal-to-noise ratio of 250. These velocities yield an orbital solution on the known exoplanet host 51 Peg that matches literature values with a residual RMS of 0.895$\mathrm{~m~s^{-1}}$

Deep Sequencing Whole Transcriptome Exploration of the σE Regulon in Neisseria meningitidis

Bacteria live in an ever-changing environment and must alter protein expression promptly to adapt to these changes and survive. Specific response genes that are regulated by a subset of alternative σ70-like transcription factors have evolved in order to respond to this changing environment. Recently, we have described the existence of a σE regulon including the anti-σ-factor MseR in the obligate human bacterial pathogen Neisseria meningitidis. To unravel the complete σE regulon in N. meningitidis, we sequenced total RNA transcriptional content of wild type meningococci and compared it with that of mseR mutant cells (ΔmseR) in which σE is highly expressed. Eleven coding genes and one non-coding gene were found to be differentially expressed between H44/76 wildtype and H44/76ΔmseR cells. Five of the 6 genes of the σE operon, msrA/msrB, and the gene encoding a pepSY-associated TM helix family protein showed enhanced transcription, whilst aniA encoding a nitrite reductase and nspA encoding the vaccine candidate Neisserial surface protein A showed decreased transcription. Analysis of differential expression in IGRs showed enhanced transcription of a non-coding RNA molecule, identifying a σE dependent small non-coding RNA. Together this constitutes the first complete exploration of an alternative σ-factor regulon in N. meningitidis. The results direct to a relatively small regulon indicative for a strictly defined response consistent with a relatively stable niche, the human throat, where N. meningitidis resides

State of the Field: Extreme Precision Radial Velocities

The Second Workshop on Extreme Precision Radial Velocities defined circa 2015 the state of the art Doppler precision and identified the critical path challenges for reaching 10 cm/s measurement precision. The presentations and discussion of key issues for instrumentation and data analysis and the workshop recommendations for achieving this precision are summarized here. Beginning with the HARPS spectrograph, technological advances for precision radial velocity measurements have focused on building extremely stable instruments. To reach still higher precision, future spectrometers will need to produce even higher fidelity spectra. This should be possible with improved environmental control, greater stability in the illumination of the spectrometer optics, better detectors, more precise wavelength calibration, and broader bandwidth spectra. Key data analysis challenges for the precision radial velocity community include distinguishing center of mass Keplerian motion from photospheric velocities, and the proper treatment of telluric contamination. Success here is coupled to the instrument design, but also requires the implementation of robust statistical and modeling techniques. Center of mass velocities produce Doppler shifts that affect every line identically, while photospheric velocities produce line profile asymmetries with wavelength and temporal dependencies that are different from Keplerian signals. Exoplanets are an important subfield of astronomy and there has been an impressive rate of discovery over the past two decades. Higher precision radial velocity measurements are required to serve as a discovery technique for potentially habitable worlds and to characterize detections from transit missions. The future of exoplanet science has very different trajectories depending on the precision that can ultimately be achieved with Doppler measurements.Comment: 45 pages, 23 Figures, workshop summary proceeding

Isozyme-Specific Ligands for O-acetylserine sulfhydrylase, a Novel Antibiotic Target

Conceived and designed the experiments: FS PC BC ES AM. Performed the experiments: FS RS ES PF SR. Analyzed the data: FS BC ES PF GEK PFC AM. Contributed reagents/materials/analysis tools: PC PB GC. Wrote the paper: FS GEK BC AM.The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, have been identified that share similar binding sites, although the respective specific functions are still debated. O-acetylserine sulfhydrylase plays a key role in the adaptation of bacteria to the host environment, in the defense mechanisms to oxidative stress and in antibiotic resistance. Because mammals synthesize cysteine from methionine and lack O-acetylserine sulfhydrylase, the enzyme is a potential target for antimicrobials. With this aim, we first identified potential inhibitors of the two isozymes via a ligand- and structure-based in silico screening of a subset of the ZINC library using FLAP. The binding affinities of the most promising candidates were measured in vitro on purified O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B from Salmonella typhimurium by a direct method that exploits the change in the cofactor fluorescence. Two molecules were identified with dissociation constants of 3.7 and 33 µM for O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, respectively. Because GRID analysis of the two isoenzymes indicates the presence of a few common pharmacophoric features, cross binding titrations were carried out. It was found that the best binder for O-acetylserine sulfhydrylase-B exhibits a dissociation constant of 29 µM for O-acetylserine sulfhydrylase-A, thus displaying a limited selectivity, whereas the best binder for O-acetylserine sulfhydrylase-A exhibits a dissociation constant of 50 µM for O-acetylserine sulfhydrylase-B and is thus 8-fold selective towards the former isozyme. Therefore, isoform-specific and isoform-independent ligands allow to either selectively target the isozyme that predominantly supports bacteria during infection and long-term survival or to completely block bacterial cysteine biosynthesis.Yeshttp://www.plosone.org/static/editorial#pee

Stroke genetics informs drug discovery and risk prediction across ancestries

Previous genome-wide association studies (GWASs) of stroke — the second leading cause of death worldwide — were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries

The similarity renormalization group for three-body interactions in one dimension

We report on recent progress of the implementation of the similarity renormalization group (SRG) for three-body interactions in a one-dimensional, bosonic model system using the plane-wave basis. We discuss our implementation of the flow equations and show results that confirm that results in the three-body sector remain unchanged by the transformation of the Hamiltonian. We also show how the SRG transformation decouples low- from high-momentum nodes in the three-body sector and therefore simplifies the numerical calculation of observables