Plastome (plastid genome) sequences provide valuable information for understanding the phylogenetic relationships and evolutionary history of plants. Although the rapid development of high-throughput ...sequencing technology has led to an explosion of plastome sequences, annotation remains a significant bottleneck for plastomes. User-friendly batch annotation of multiple plastomes is an urgent need.
We introduce Plastid Genome Annotator (PGA), a standalone command line tool that can perform rapid, accurate, and flexible batch annotation of newly generated target plastomes based on well-annotated reference plastomes. In contrast to current existing tools, PGA uses reference plastomes as the query and unannotated target plastomes as the subject to locate genes, which we refer to as the reverse query-subject BLAST search approach. PGA accurately identifies gene and intron boundaries as well as intron loss. The program outputs GenBank-formatted files as well as a log file to assist users in verifying annotations. Comparisons against other available plastome annotation tools demonstrated the high annotation accuracy of PGA, with little or no post-annotation verification necessary. Likewise, we demonstrated the flexibility of reference plastomes within PGA by annotating the plastome of
using that of
as a reference. The program, user manual and example data sets are freely available at https://github.com/quxiaojian/PGA.
PGA facilitates rapid, accurate, and flexible batch annotation of plastomes across plants. For projects in which multiple plastomes are generated, the time savings for high-quality plastome annotation are especially significant.
Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. Here, we introduce an experimental workflow ...that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in a proteomics experiment. These coordinates calibrate protein databases or spectrum libraries to a specific mass spectrometer and chromatography setup, facilitating DIA-only pipelines and the reuse of global resource libraries. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect 20-25% more peptides from DIA experiments than with data dependent acquisition-based spectrum libraries alone.
Abstract
Microbial communities comprised of phototrophs and heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of ...appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting
Synechococcus elongatus
with heterotrophic
Escherichia coli
K-12,
Escherichia coli
W,
Yarrowia lipolytica
, or
Bacillus subtilis
. Model simulations reveae metabolic exchanges that sustain the heterotrophs in minimal media devoid of any organic carbon source, pointing to
S. elongatus-E. coli
K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.
The development of new techniques and materials that can separate ethylene from ethane is highly relevant in modern applications. Although adsorption-based separation techniques using metal–organic ...frameworks (MOFs) have gained increasing attention, the relatively low stability (especially water resistance) and unscalable synthesis of MOFs severely limit their application in real industrial scenarios. Addressing these challenges, we rationally designed and synthesized two new C2H6-selective MOF adsorbents (NKMOF-8-Br and -Me) with ultrahigh chemical and thermal stability, including water resistance. Attributed to the nonpolar/hydrophobic pore environments and appropriate pore apertures, the MOFs can capture C2 hydrocarbon gases at ambient conditions even in high humidity. The single-crystal structures of gas@NKMOF-8 realized the direct visualization of adsorption sites of the gases. Both the single-crystal data and simulated data elucidate the mechanism of selective adsorption. Moreover, the NKMOF-8 possesses high C2H6 adsorption capacity and high selectivity, allowing for efficient C2H6/C2H4 separation, as verified by experimental breakthrough tests. Most importantly, NKMOF-8-Br and -Me can be scalably synthesized through stirring at room temperature in minutes, which confers them with great potential for industrial application. This work offers new adsorbents that can address major chemical industrial challenges and provides an in-depth understanding of the gas binding sites in a visual manner.
Guanine-rich DNA sequences occur throughout the human genome and can transiently form G-quadruplex (G4) structures that may obstruct DNA replication, leading to genomic instability. Here, we apply ...multi-color single-molecule localization microscopy (SMLM) coupled with robust data-mining algorithms to quantitatively visualize replication fork (RF)-coupled formation and spatial-association of endogenous G4s. Using this data, we investigate the effects of G4s on replisome dynamics and organization. We show that a small fraction of active replication forks spontaneously form G4s at newly unwound DNA immediately behind the MCM helicase and before nascent DNA synthesis. These G4s locally perturb replisome dynamics and organization by reducing DNA synthesis and limiting the binding of the single-strand DNA-binding protein RPA. We find that the resolution of RF-coupled G4s is mediated by an interplay between RPA and the FANCJ helicase. FANCJ deficiency leads to G4 accumulation, DNA damage at G4-associated replication forks, and silencing of the RPA-mediated replication stress response. Our study provides first-hand evidence of the intrinsic, RF-coupled formation of G4 structures, offering unique mechanistic insights into the interference and regulation of stable G4s at replication forks and their effect on RPA-associated fork signaling and genomic instability.
Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based technique for unbiased and reproducible measurement of protein mixtures. DIA tandem mass spectrometry spectra are often ...highly multiplexed, containing product ions from multiple cofragmenting precursors. Detecting peptides directly from DIA data is therefore challenging; most DIA data analyses require spectral libraries. Here we present PECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECAN reports evidence of detection based on product ion scoring, which enables detection of low-abundance analytes with poor precursor ion signal. We demonstrate the chromatographic peak picking accuracy and peptide detection capability of PECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECAN to build a plasma proteome library from DIA data and to query known sequence variants.
Several recent studies have reported different intrinsic correlations between the active galactic nucleus (AGN) mid-IR luminosity ( ) and the rest-frame 2-10 keV luminosity (LX) for luminous quasars. ...To understand the origin of the difference in the observed relations, we study a sample of 3247 spectroscopically confirmed type 1 AGNs collected from Boötes, XMM-COSMOS, XMM-XXL-North, and the Sloan Digital Sky Survey quasars in the Swift/XRT footprint spanning over four orders of magnitude in luminosity. We carefully examine how different observational constraints impact the observed relations, including the inclusion of X-ray-nondetected objects, possible X-ray absorption in type 1 AGNs, X-ray flux limits, and star formation contamination. We find that the primary factor driving the different relations reported in the literature is the X-ray flux limits for different studies. When taking these effects into account, we find that the X-ray luminosity and mid-IR luminosity (measured at rest-frame , or ) of our sample of type 1 AGNs follow a bilinear relation in the log-log plane: erg s−1 + (44.60 0.01) for erg s−1, and erg s−1 + (44.51 0.01) for erg s−1. This suggests that the luminous type 1 quasars have a shallower correlation than the approximately linear relations found in local Seyfert galaxies. This result is consistent with previous studies reporting a luminosity-dependent relation and implies that assuming a linear relation to infer the neutral gas column density for X-ray absorption might overestimate the column densities in luminous quasars.
In situ x-ray spectroscopies offer a powerful way to understand the electronic structure of the electrode-electrolyte interface under operating conditions. However, most x-ray techniques require ...vacuum, making it necessary to design spectro-electrochemical cells with a delicate interface to the wet electrochemical environment. The design of the cell often dictates what measurements can be done and which electrochemical processes can be studied. Hence, it is important to pick the right spectro-electrochemical cell for the process of interest. To facilitate this choice, and to highlight the challenges in cell design, we critically review four recent, successful cell designs. Using several case studies, we investigate the opportunities and limitations that arise in practical experiments.
Countermeasures to prevent and treat coronavirus disease 2019 (COVID-19) are a global health priority. We enrolled a cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-recovered ...participants, developed neutralization assays to investigate antibody responses, adapted our high-throughput antibody generation pipeline to rapidly screen more than 1800 antibodies, and established an animal model to test protection. We isolated potent neutralizing antibodies (nAbs) to two epitopes on the receptor binding domain (RBD) and to distinct non-RBD epitopes on the spike (S) protein. As indicated by maintained weight and low lung viral titers in treated animals, the passive transfer of a nAb provides protection against disease in high-dose SARS-CoV-2 challenge in Syrian hamsters. The study suggests a role for nAbs in prophylaxis, and potentially therapy, of COVID-19. The nAbs also define protective epitopes to guide vaccine design.
The efficacy of glucocorticoids in COVID‐19 is unclear. This study was designed to determine whether systemic glucocorticoid treatment in COVID‐19 patients is associated with reduced mortality or ...mechanical ventilation. This observational study included 1,806 hospitalized COVID‐19 patients; 140 were treated with glucocorticoids within 48 hours of admission. Early use of glucocorticoids was not associated with mortality or mechanical ventilation. However, glucocorticoid treatment of patients with initial C‐reactive protein (CRP) ≥20 mg/dL was associated with significantly reduced risk of mortality or mechanical ventilation (odds ratio, 0.23; 95% CI, 0.08‐0.70), while glucocorticoid treatment of patients with CRP <10 mg/dL was associated with significantly increased risk of mortality or mechanical ventilation (OR, 2.64; 95% CI, 1.39‐5.03). Whether glucocorticoid treatment is associated with changes in mortality or mechanical ventilation in patients with high or low CRP needs study in prospective, randomized clinical trials.
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