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We performed an RNA-Seq analysis of nine of E.coli single knockout strains from the Keio collection carrying deletions in tRNA modification genes (dusB, truA, truD, thiI, miaA, rlmN, mnmA, mnmC, mnmG) and wildtype. RNA was isolated from each of the different strains at grown in LB at 37˚C up to mid-exponential phase (OD(A600nm) ~0.6) in three biological replicates.
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Human coronaviruses (HCoVs) HCoV-NL63, HCoV-229E, HCoV-HKU1 and HCoV-OC43 have been circulated in the human population worldwide, and they are associated with a broad range of respiratory diseases with varying severity. However, there are neither effective therapeutic drugs nor licensed vaccines available for the treatment and prevention of infections by the four HCoVs. In this study, we collected nasopharyngeal aspirates of children hospitalized for respiratory tract infection in China during 2014–2018 and conducted next-generation sequencing. Sequences of four HCoVs were then selected for an in-depth analysis. Genome sequences of 2 HCoV-NL63, 8 HCoV-229E, 2 HCoV-HKU1, and 6 HCoV-OC43 were obtained. Based on the full-length S gene, a strong temporal signal was found in HCoV-229E and the molecular evolutionary rate was 6 × 10 −4 substitutions/site/year. Based on the maximum-likelihood (ML) phylogenetic tree of complete S gene, we designated H78 as a new sub-genotype C2 of HCoV-HKU1, and the obtained P43 sequence was grouped into the reported novel genotype K of HCoV-OC43 circulating in Guangzhou, China. Based on the complete genome, potential recombination events were found to occur as two phenomena, namely intraspecies and interspecies. Moreover, we observed two amino acid substitutions in the S1 subunit of obtained HCoV-NL63 (G534V) and HCoV-HKU1 (H512R), while residues 534 and 512 are important for the binding of angiotensin-converting enzyme 2 and neutralizing antibodies, respectively. Our findings might provide a clue for the molecular evolution of the four HCoVs and help in the early diagnosis, treatment and prevention of broad-spectrum HCoV infection.
The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction.
This review focuses on diffractive physics, which involves the long-range interactions of strong nuclear force at high energies described by SU(3) gauge symmetry. It is expected that diffractive processes account for nearly 40% of the total cross-section at LHC energies. These processes consist of soft-scale physics where perturbation theory cannot be applied. Although highly successful and often described as a perfect theory, quantum chromodynamics relies heavily on perturbation theory, a model best suited for hard-scale physics. The study of pomerons could help bridge the soft and hard processes and provide a complete description of the theory of the strong interaction across the full momentum spectrum. Here, we will discuss some of the features of diffractive physics, experimental results from SPS, HERA, and the LHC, and where the field could potentially lead. With the recent publication of the odderon discovery in 2021 by the D0 and TOTEM collaborations and the new horizon of physics that lies ahead with the upcoming Electron-Ion Collider at Brookhaven National Laboratory, interest is seemingly piquing in high energy diffractive physics.
The scaling relationship is a fundamental probe of the evolution of galaxies. Using the integral field spectroscopic data from the Mapping Nearby Galaxies at Apache Point Observatory survey, we select 1698 spaxels with a significant detection of the auroral emission line [O ιιι]λ4363 from 52 galaxies to investigate the scaling relationships at the low-metallicity end. We find that our sample’s star formation rate is higher and its metallicity is lower in the scaling relationship than the star-forming sequence after removing the contribution of the Fundamental Metallicity Relation. We also find that the stellar ages of our sample are younger (<1 Gyr) and the stellar metallicities are also lower. Morphological parameters from the Deep Learning catalog indicate that our galaxies are more likely to be mergers. These results suggest that their low-metallicity regions may be related to interaction; the inflow of metal-poor gas may dilute the interstellar medium and form new metal-poor stars in these galaxies during interactions.
The data included in this Dryad submission was collected in order to understand how the model organism* Escherichia coli* overcomes stabilized G-quadruplexes. This work involved a multi-omics approach to studying how the G-quadruplex stabilizers NMM and Braco-19 impact growth, gene importance, and mRNA/proteomic abundance in G-quadruplex stabilizing conditions.
We review recent theoretical progress in describing collective effects in photon+nucleus collisions. The approaches considered range from the color glass condensate, where correlations are encoded in the initial state, to hydrodynamic frameworks, where a strong final-state response to the initial geometry of the collision is the key ingredient to generate momentum-space correlations.
The Energy to Communities (E2C) peer-learning cohort program provides technical assistance to groups of 15 community entities around a common energy topic over the course of 6 months. Every month, participants join a virtual meeting where they hear from experts and exchange strategies and best practices with their peers. This cohort, "Successful Energy Project Implementation" will explore common challenges in implementing energy projects and learn strategies to turn project plans into reality. Each participant will focus on a local energy project or priority as a cornerstone for their learning throughout the series.This presentation overviews the basics of developing electric mobility projects with emphasis on leveraging the right tools to advance technical scoping and program design.
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.
The price data for four regions (CAISO, ERCOT, MISO-W, and PJM-W) are developed using the ReEDS to PLEXOS conversion as described in (Gagnon et al. 2020). The reference ReEDS case chosen is based on the 2020 Standard Scenario Mid-case, which uses the 2020 ReEDS model version (Cole et al. 2020; Ho et al. 2021). All ReEDS model inputs use 2020 Standard Scenarios Mid-case assumptions except for CO2 prices, which are implemented as linearly increasing CO2 price trajectories beginning at $0/tCO2 in 2020 and ending at either $100/tCO2 or $150/tCO2 in 2035 to dive capacity expansion towards a low-carbon system that could support CCS deployment. However, these scenarios also prohibit CCS deployment in this time frame so that resulting price data are not influenced by the deployment and operation of CCS itself. Implementing the ReEDS to PLEXOS conversion tool, PLEXOS is then simulated using the 2035 ReEDS infrastructure for both CO2 price scenarios, with the following model version and setup: PLEXOS Version: 8.2 Solver: Xpress-MP 35.01.01 Mixed integer optimization relative gap 1% System configuration: • Total number of nodes: 134 (consistent with ReEDS balancing areas) • Line losses enforced using piecewise linear approximation • Energy dump was enabled Price data is aggregated to the ISO/RTO level using load-weighted averages. References: Cole, Wesley, Sean Corcoran, Nathaniel Gates, Daniel Mai, Trieu, and Paritosh Das. 2020. “2020 Standard Scenarios Report: A U.S. Electricity Sector Outlook.” NREL/TP-6A20-77442. Golden, CO: National Renewable Energy Laboratory. https://www.nrel.gov/docs/fy21osti/77442.pdf. Gagnon, Pieter, Will Frazier, Elaine Hale, and Wesley Cole. 2020. “Cambium Documentation: Version 2020.” NREL/TP-6A20-78239. National Renewable Energy Lab. (NREL), Golden, CO (United States). https://doi.org/10.2172/1734551. Ho, Jonathan, Jonathon Becker, Maxwell Brown, Patrick Brown, Ilya (ORCID:0000000284917814) Chernyakhovskiy, Stuart Cohen, Wesley (ORCID:000000029194065X) Cole, et al. 2021. “Regional Energy Deployment System (ReEDS) Model Documentation: Version 2020.” NREL/TP-6A20-78195. Golden, CO: National Renewable Energy Laboratory. https://doi.org/10.2172/1788425.
To investigate the effects of stabilizing G-quadruplexes on Escherichia coli, cells were grown in the presence of the G-quadruplex stabilizing compound, NMM, and RNA-seq was performed. This was done for the control cell strain (MG1655 dtolC) as well as a strain with a decrease in a translation elongation factor (MG1655 dtolC tufA::kan). TPM values were used for differential gene expression analysis between each growth condition. All samples were grown and sequenced in triplicate.
Genomic DNA from each sample was prepared using the Wizard Genomic DNA Purification Kit (Promega) and after, DNA was quantified using the QuantiFluor ONE dsDNA System (Promega). Genomic DNA underwent shearing to ~200 bp fragments via sonication and the gDNA fragments were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Bead-based size selection was used to select ~200 bp fragments and the fragments then underwent a splinkerette PCR using a Tn5-enriching forward primer and custom reverse primers for multiplexing. A final bead-based size selection was used to select for the correct length DNA. DNA was sequenced at the University of Michigan Advanced Genomics Core using Illumina sequencing with a custom read primer reading the last 10 nt of the transposon. PhiX174 DNA spike was added to the run to ensure sufficient sequence diversity on the flow cell. Then, a custom index read primer and standard Illumina primer were used to sequence the index reads and PhiX174, respectively.
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