This letter analyzes two large-scale proteomics studies published in the same issue of Nature. At the time of the release, both studies were portrayed as draft maps of the human proteome and great ...advances in the field. As with the initial publication of the human genome, these papers have broad appeal and will no doubt lead to a great deal of further analysis by the scientific community. However, we were intrigued by the number of protein-coding genes detected by the two studies, numbers that far exceeded what has been reported for the multinational Human Proteome Project effort. We carried out a simple quality test on the data using the olfactory receptor family. A high-quality proteomics experiment that does not specifically analyze nasal tissues should not expect to detect many peptides for olfactory receptors. Neither of the studies carried out experiments on nasal tissues, yet we found peptide evidence for more than 100 olfactory receptors in the two studies. These results suggest that the two studies are substantially overestimating the number of protein coding genes they identify. We conclude that the experimental data from these two studies should be used with caution.
Using decoy databases to estimate the number of false positive assignations is one of the most widely used methods to calculate false discovery rates in large-scale peptide identification studies. ...However, in spite of their widespread use, the decoy approach has not been fully standardized. In conjunction with target databases, decoy databases may be used separately or in the form of concatenated databases, allowing a competition strategy; depending on the method used, two alternative formulations are possible to calculate error rates. Although both methods are conservative, the separate database approach overestimates the number of false positive assignations due to the presence of MS/MS spectra produced by true peptides, while the concatenated approach calculates the error rate in a population that has a higher size than that obtained after searching a target database. In this work, we demonstrate that by analyzing as a whole the joint distribution of matches obtained after performing a separate database search, and applying the competition strategy, it is possible to make a more accurate calculation of false discovery rates. We show that both separate and concatenated approaches clearly overestimate error rates with respect to those calculated by the new algorithm, using several kinds of scores. We conclude that the new indicator provides a more sensitive alternative, and establishes for the first time a unique and integrated framework to calculate error rates in large-scale peptide identification studies
This paper evaluates the accuracy of shoreline positions obtained from the infrared (IR) bands of Landsat 7, Landsat 8, and Sentinel-2 imagery on natural beaches. A workflow for sub-pixel shoreline ...extraction, already tested on seawalls, is used. The present work analyzes the behavior of that workflow and resultant shorelines on a micro-tidal (<20 cm) sandy beach and makes a comparison with other more accurate sets of shorelines. These other sets were obtained using differential GNSS surveys and terrestrial photogrammetry techniques through the C-Pro monitoring system. 21 sub-pixel shorelines and their respective high-precision lines served for the evaluation. The results prove that NIR bands can easily confuse the shoreline with whitewater, whereas SWIR bands are more reliable in this respect. Moreover, it verifies that shorelines obtained from bands 11 and 12 of Sentinel-2 are very similar to those obtained with bands 6 and 7 of Landsat 8 (−0.75 ± 2.5 m; negative sign indicates landward bias). The variability of the brightness in the terrestrial zone influences shoreline detection: brighter zones cause a small landward bias. A relation between the swell and shoreline accuracy is found, mainly identified in images obtained from Landsat 8 and Sentinel-2. On natural beaches, the mean shoreline error varies with the type of image used. After analyzing the whole set of shorelines detected from Landsat 7, we conclude that the mean horizontal error is 4.63 m (±6.55 m) and 5.50 m (±4.86 m), respectively, for high and low gain images. For the Landsat 8 and Sentinel-2 shorelines, the mean error reaches 3.06 m (±5.79 m).
Implementing proteins in optoelectronics represents a fresh idea toward a sustainable new class of materials with bio‐functions that can replace environmentally unfriendly and/or toxic components ...without losing device performance. However, their native activity (fluorescence, catalysis, and so on) is easily lost under device fabrication/operation as non‐native environments (organic solvents, organic/inorganic interfaces, and so on) and severe stress (temperature, irradiation, and so on) are involved. Herein, a gift bow genetically‐encoded macro‐oligomerization strategy is showcased to promote protein–protein solid interaction enabling i) high versatility with arbitrary proteins, ii) straightforward electrostatic driven control of the macro‐oligomer size by ionic strength, and iii) stabilities over months in pure organic solvents and stress scenarios, allowing to integrate them into classical water‐free polymer‐based materials/components for optoelectronics. Indeed, rainbow‐/white‐emitting protein‐based light‐emitting diodes are fabricated, attesting a first‐class performance compared to those with their respective native proteins: significantly enhanced device stabilities from a few minutes up to 100 h keeping device efficiency at high power driving conditions. Thus, the oligomerization concept is a solid bridge between biological systems and materials/components to meet expectations in bio‐optoelectronics, in general, and lighting schemes, in particular.
The integration of proteins into optoelectronics offers a novel approach toward the development of eco‐friendly materials, replacing non‐sustainable elements while maintaining device efficiency. In this work, a genetically‐encoded macro‐oligomerization strategy which enables versatile, electrostatic‐controlled protein–protein interactions, ensuring the protein stability in non‐native environments and stressful conditions, is developed.
Shotgun proteomics is the method of choice for high-throughput protein identification; however, robust statistical methods are essential to automatize this task while minimizing the number of false ...identifications. The standard method for estimating the false discovery rate (FDR) of individual identifications and keeping it below a threshold (typically 1%) is the target-decoy approach. However, numerous works have shown that FDR at the protein level may become much larger than FDR at the peptide level. The development of an appropriate scoring model to identify proteins from their peptides using high-throughput shotgun proteomics is highly needed. In this study, we present a novel protein-level scoring algorithm that uses the scores of the identified peptides and maintains all of the properties expected for a true protein probability. We also present a refinement of the picked method to calculate FDR at the protein level. These algorithms can be used together as a robust identification workflow suitable for large-scale proteomics, and we show that the identification performance of this workflow is superior to that of other widely used methods in several samples and using different search engines. Our protein probability model offers the scientific community an algorithm that is easy to integrate into protein identification workflows for the automated analysis of shotgun proteomics data.
The antimicrobial functions of neutrophils are facilitated by a defensive armamentarium of proteins stored in granules, and by the formation of neutrophil extracellular traps (NETs). However, the ...toxic nature of these structures poses a threat to highly vascularized tissues, such as the lungs. Here, we identified a cell-intrinsic program that modified the neutrophil proteome in the circulation and caused the progressive loss of granule content and reduction of the NET-forming capacity. This program was driven by the receptor CXCR2 and by regulators of circadian cycles. As a consequence, lungs were protected from inflammatory injury at times of day or in mouse mutants in which granule content was low. Changes in the proteome, granule content and NET formation also occurred in human neutrophils, and correlated with the incidence and severity of respiratory distress in pneumonia patients. Our findings unveil a 'disarming' strategy of neutrophils that depletes protein stores to reduce the magnitude of inflammation.
We present a semiclassical surface-hopping method which is able to treat arbitrary couplings in molecular systems including all degrees of freedom. A reformulation of the standard surface-hopping ...scheme in terms of a unitary transformation matrix allows for the description of interactions like spin−orbit coupling or transitions induced by laser fields. The accuracy of our method is demonstrated in two systems. The first one, consisting of two model electronic states, validates the semiclassical approach in the presence of an electric field. In the second one, the dynamics in the IBr molecule in the presence of spin−orbit coupling after laser excitation is investigated. Due to an avoided crossing that originates from spin−orbit coupling, IBr dissociates into two channels: I + Br(2P3/2) and I + Br*(2P1/2). In both systems, the obtained results are in very good agreement with those calculated from exact quantum dynamical simulations.
The conformational study of saccharides and glycomimetics in solution is critical for a comprehensive understanding of their interactions with biological receptors and enabling the design of ...optimized glycomimetics. Here, we report a nuclear magnetic resonance (NMR) study centered on the conformational properties of the hydroxymethyl group and glycosidic bond of four series of aryl S-glucosides. We found that in acetyl-protected and free aryl S-β-glucosides, the rotational equilibrium around the C5–C6 bond (hydroxymethyl group) exhibits a linear dependence on the electronic properties of the aglycone, namely, as the aryl’s substituent electron-withdrawing character increases, the dominance of the gg rotamer declines and the gt contribution rises. Likewise, the conformational equilibrium around the glycosidic C1–S bond also depends on the aglycone’s electronic properties, where glucosides carrying electron-poor aglycones exhibit stiffer glycosidic bonds in comparison to their electron-rich counterparts. In the case of the α anomers, the aglycone’s effect over the glycosidic bond conformation is like that observed on their β isomers; however, we observe no aglycone’s influence over the hydroxymethyl group conformation in the α-glucosides.
Ab initio molecular dynamics including nonadiabatic and spin–orbit couplings on equal footing is used to unravel the deactivation of cytosine after UV light absorption. Intersystem crossing (ISC) is ...found to compete directly with internal conversion in tens of femtoseconds, thus making cytosine the organic compound with the fastest triplet population calculated so far. It is found that close degeneracy between singlet and triplet states can more than compensate for very small spin–orbit couplings, leading to efficient ISC. The femtosecond nature of the ISC process highlights its importance in photochemistry and challenges the conventional view that large singlet–triplet couplings are required for an efficient population flow into triplet states. These findings are important to understand DNA photostability and the photochemistry and dynamics of organic molecules in general.
There is much interest in Na-ion batteries for grid storage because of the lower projected cost compared with Li-ion. Identifying Earth-abundant, low-cost, and safe materials that can function as ...intercalation cathodes in Na-ion batteries is an important challenge facing the field. Here we investigate such a material, β-NaMnO2, with a different structure from that of NaMnO2 polymorphs and other compounds studied extensively in the past. It exhibits a high capacity (of ca. 190 mA h g–1 at a rate of C/20), along with a good rate capability (142 mA h g–1 at a rate of 2C) and a good capacity retention (100 mA h g–1after 100 Na extraction/insertion cycles at a rate of 2C). Powder XRD, HRTEM, and 23Na NMR studies revealed that this compound exhibits a complex structure consisting of intergrown regions of α-NaMnO2 and β-NaMnO2 domains. The collapse of the long-range structure at low Na content is expected to compromise the reversibility of the Na extraction and insertion processes occurring upon charge and discharge of the cathode material, respectively. Yet stable, reproducible, and reversible Na intercalation is observed.
PDF
