Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.

Bottom-up proteomics relies on the proteolytic or chemical cleavage of proteins into peptides, the identification of those peptides via mass spectrometry, and the mapping of the identified peptides back to the reference proteome to infer which possible proteins are identified. Reliable mapping of peptides to proteins still poses substantial challenges when considering similar proteins, protein families, splice isoforms, sequence variation, and possible residue mass modifications, combined with an imperfect and incomplete understanding of the proteome. The ProteoMapper tool enables a comprehensive and rapid mapping of peptides to a reference proteome. The indexer component creates a segmented index for an input proteome from a FASTA or PEFF file. The ProMaST component provides ultrafast mapping of one or more input peptides against the index. ProteoMapper allows searches that take into account known sequence variation encoded in PEFF files. It also enables fuzzy searches to find highly similar peptides with residue order changes or other isobaric or near-isobaric substitutions within a specified mass tolerance. We demonstrate an example of a one-hit-wonder identification in PeptideAtlas that may be better explained by a combination of catalogued and uncatalogued sequence variation in another highly observed protein. ProteoMapper is a free and open source, available for local use after downloading, embedding in other applications, as an online web tool at http://www.peptideatlas.org/map , and as a web service

OPT3 is a component of the iron-signaling network between leaves and roots and misregulation of OPT3 leads to an over-accumulation of cadmium in seeds.

Plants and seeds are the main dietary sources of zinc, iron, manganese, and copper, but are also the main entry point for toxic elements such as cadmium into the food chain. We report here that an Arabidopsis oligopeptide transporter mutant, opt3-2, over-accumulates cadmium (Cd) in seeds and roots but, unexpectedly, under-accumulates Cd in leaves. The cadmium distribution in opt3-2 differs from iron, zinc, and manganese, suggesting a metal-specific mechanism for metal partitioning within the plant. The opt3-2 mutant constitutively up-regulates the Fe/Zn/Cd transporter IRT1 and FRO2 in roots, indicative of an iron-deficiency response. No genetic mutants that impair the shoot-to-root signaling of iron status in leaves have been identified. Interestingly, shoot-specific expression of OPT3 rescues the Cd sensitivity and complements the aberrant expression of IRT1 in opt3-2 roots, suggesting that OPT3 is required to relay the iron status from leaves to roots. OPT3 expression was found in the vasculature with preferential expression in the phloem at the plasma membrane. Using radioisotope experiments, we found that mobilization of Fe from leaves is severely affected in opt3-2, suggesting that Fe mobilization out of leaves is required for proper trace-metal homeostasis. When expressed in yeast, OPT3 does not localize to the plasma membrane, precluding the identification of the OPT3 substrate. Our in planta results show that OPT3 is important for leaf phloem-loading of iron and plays a key role regulating Fe, Zn, and Cd distribution within the plant. Furthermore, ferric chelate reductase activity analyses provide evidence that iron is not the sole signal transferred from leaves to roots in leaf iron status signaling

Thickness-Dependent Differential Reflectance Spectra of Monolayer and Few-Layer MoS2, MoSe2, WS2 and WSe2

The research field of two dimensional (2D) materials strongly relies on optical microscopy characterization tools to identify atomically thin materials and to determine their number of layers. Moreover, optical microscopy-based techniques opened the door to study the optical properties of these nanomaterials. We presented a comprehensive study of the differential reflectance spectra of 2D semiconducting transition metal dichalcogenides (TMDCs), MoS2, MoSe2, WS2, and WSe2, with thickness ranging from one layer up to six layers. We analyzed the thickness-dependent energy of the different excitonic features, indicating the change in the band structure of the different TMDC materials with the number of layers. Our work provided a route to employ differential reflectance spectroscopy for determining the number of layers of MoS2, MoSe2, WS2, and WSe2.Comment: Main text (3 Figures) and Supp. Info. (23 Figures

Three Dimensional Lattice-Boltzmann Model for Electrodynamics

In this paper we introduce a novel 3D Lattice-Boltzmann model that recovers in the continuous limit the Maxwell equations in materials. In order to build conservation equations with antisymmetric tensors, like the Faraday law, the model assigns four auxiliary vectors to each velocity vector. These auxiliary vectors, when combined with the distribution functions, give the electromagnetic fields. The evolution is driven by the usual BGK collision rule, but with a different form for the equilibrium distribution functions. This LBGK model allows us to consider for both dielectrics and conductors with realistic parameters, and therefore it is adequate to simulate the most diverse electromagnetic problems, like the propagation of electromagnetic waves (both in dielectric media and in waveguides), the skin effect, the radiation pattern of a small dipole antenna and the natural frequencies of a resonant cavity, all with 2% accuracy. Actually, it shows to be one order of magnitude faster than the original FDTD formulation by Yee to reach the same accuracy. It is, therefore, a valuable alternative to simulate electromagnetic fields and opens lattice Boltzmann for a broad spectrum of new applications in electrodynamics. In this paper we develop a 3D Lattice-Boltzmann model that recovers in the continuous limit the Maxwell equations for macroscopic mediums. The model can sucessfully reproduces the propagation of the electromagnetic waves in dielectric mediums and waveguide, the skin effect, the electrical dipole radiation and the electromagnetic response of a resonant cavity.Comment: Accepted for publication in Phys. Rev.

Centerscope

Centerscope, formerly Scope, was published by the Boston University Medical Center "to communicate the concern of the Medical Center for the development and maintenance of improved health care in contemporary society.

Lunar occultations events from the Earth-Moon equilateral Lagrangian point: Simulations and scientific potential

Recently, a novel idea has been proposed to use a spacecraft orbiting closely around the L4 or L5 Lagrangian points of the Earth–Moon system as a vantage location for astronomical observations under unique and advantageous conditions, e.g. to investigate the Solar corona or Kordylewski clouds. In this paper, we explore the scientific advantages of this configuration to observe lunar occultations. By using simulations based on actual orbital parameters and detector performance, we find that even a telescope as small as 10 cm in a L4 orbit would enable better light-curve sampling and higher angular resolution than from ground, and open up at the same time new spectral windows such as e.g. in the UV. We focus in particular on angular diameter measurements, which we find would be possible at the 100 as level even at magnitudes normally considered faint in the context of ground-based LOs. Considerable benefits would also be afforded in the area of small separation binary objects, not just in terms of angular resolution but also by the capability of L4-based observations to repeat an LO scan of a source at multiple different position angles. Additional science cases would be made possible by the high time resolution intrinsic to the LO technique and the access to UV wavelengths. On-board data pipeline codes already exist, greatly simplifying the automatic pre-processing and the data transfer requirements

Shape-sensing robotic-assisted bronchoscopy for pulmonary nodules: initial multicenter experience using the Ion™ Endoluminal System

BACKGROUND: Traditional bronchoscopy provides limited approach to peripheral nodules. Shape-sensing robotic-assisted bronchoscopy (SSRAB, Ion™ Endoluminal System) is a new tool for minimally invasive peripheral nodule biopsy. We sought to answer the research question: Does SSRAB facilitate sampling of pulmonary nodules during bronchoscopists\u27 initial experience? METHODS: The lead-in stage of a multicenter, single-arm, prospective evaluation of the Ion Endoluminal System (PRECIsE) is described. Enrolled subjects ≥ 18 years old had recent computed tomography evidence of one or more solid or semi-solid pulmonary nodules ≥ 1.0 to ≤ 3.5 cm in greatest dimension and in any part of the lung. Subjects were followed at 10- and 30-days post-procedure. This stage provided investigators and staff their first human experience with the SSRAB system; safety and procedure outcomes were analyzed descriptively. Neither diagnostic yield nor sensitivity for malignancy were assessed in this stage. Categorical variables are summarized by percentage; continuous variables are summarized by median/interquartile range (IQR). RESULTS: Sixty subjects were enrolled across 6 hospitals; 67 nodules were targeted for biopsy. Median axial, coronal and sagittal diameters were \u3c 18 mm with a largest cardinal diameter of 20.0 mm. Most nodules were extraluminal and distance from the outer edge of the nodule to the pleura or nearest fissure was 4.0 mm (IQR: 0.0, 15.0). Median bronchial generation count to the target location was 7.0 (IQR: 6.0, 8.0). Procedure duration (catheter-in to catheter-out) was 66.5 min (IQR: 50.0, 85.5). Distance from the catheter tip to the closest edge of the virtual nodule was 7.0 mm (IQR: 2.0, 12.0). Biopsy completion was 97.0%. No pneumothorax or airway bleeding of any grade was reported. CONCLUSIONS: Bronchoscopists leveraged the Ion SSRAB\u27s functionality to drive the catheter safely in close proximity of the virtual target and to obtain biopsies. This initial, multicenter experience is encouraging, suggesting that SSRAB may play a role in the management of pulmonary nodules. Clinical Trial Registration identifier and date NCT03893539; 28/03/2019

Impaired Mitochondrial Fat Oxidation Induces FGF21 in Muscle

SummaryFatty acids are the primary fuel source for skeletal muscle during most of our daily activities, and impaired fatty acid oxidation (FAO) is associated with insulin resistance. We have developed a mouse model of impaired FAO by deleting carnitine palmitoyltransferase-1b specifically in skeletal muscle (Cpt1bm−/−). Cpt1bm−/− mice have increased glucose utilization and are resistant to diet-induced obesity. Here, we show that inhibition of mitochondrial FAO induces FGF21 expression specifically in skeletal muscle. The induction of FGF21 in Cpt1b-deficient muscle is dependent on AMPK and Akt1 signaling but independent of the stress signaling pathways. FGF21 appears to act in a paracrine manner to increase glucose uptake under low insulin conditions, but it does not contribute to the resistance to diet-induced obesity