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Citrobacter freundii is a species of facultative anaerobic Gram-negative bacteria of the family Enterobacteriaceae. The complete genome is composed of a single chromosomal circle of 4,957,773 bp with a G+C content of 52%.
ABSTRACT Cellulomonas sp. strain ES6 is a chromate-reducing bacterium isolated from chromium contaminated subsurface sediment. Illumina MiSeq and Oxford Nanopore sequencing were used to assemble the genome sequence which consisted of a single circular chromosome of 4.13 Mb, contained 3,960 protein encoding genes and with an overall G + C content 75.38%.
Enterobacter hormaechei DVZ29 was isolated from a sediment trap incubated in an 129 I plume at the Hanford Site (Washington State, USA). Whole genome sequencing of the strain resulted in 32 contigs and revealed that the genome is 4.90 Mb, with a G+C content of 55.61%.
Pseudomonas strains DVZ6 and DVZ24 were isolated from a sediment trap incubated in an 129 I plume at the Hanford Site (Washington State, USA). Whole-genome sequencing of the strains revealed that both genomes are 5.77 Mb in size, with a G + C content of 64.75%.
Cupriavidus basilensis SRS was isolated from stream sediments from the Savannah River Site in South Carolina. Here, we report the draft genome sequence and annotation of Cupriavidus basilensis SRS. The genome contains 8,918,236 bp and 7,916 predicted protein-coding genes, with a total G+C content of 65.2%.
We grew a soil enrichment culture to identify organisms that anaerobically oxidize phenazine-1-carboxylic acid. A strain of Citrobacter portucalensis was isolated from this enrichment and sequenced by both Illumina and PacBio technologies. It has a genome with a length of 5.3 Mb, a G+C content of 51.8%, and at least one plasmid.
“ Candidatus Dehalogenimonas etheniformans” strain GP couples growth with the reductive dechlorination of vinyl chloride and several polychlorinated ethenes. The genome sequence comprises a circular 2.07-Mb chromosome with a G+C content of 51.9% and harbors 50 putative reductive dehalogenase gene
This study describes the whole genome sequence of Dolosicoccus paucivorans 2991-95 (DSM 15742) isolated from human blood in Cleveland, Ohio. The genome length is approximately 1.8 Mbp with 107 contigs and a G + C content of 37.91%. Annotation identified 1,752 coding genes and multiple virulence factors.
Electrochemical reduction of Sr 2+ and Ba 2+ into liquid Bi was investigated in dilute concentrations of SrCl 2 /BaCl 2 (0-5 mol%) in LiCl-KCl electrolytes at 500 °C to ascertain the limit of liquid Bi electrodes for alkaline-earth recovery. Analysis of the electrodes after constant current electrolysis to the specific charge of 270 C g -1 showed Sr 2+ ions consuming 29% of charge at 5 mol% before dropping to 8%-10% of the total charge at 0.45-0.72 mol% SrCl 2 . Ba 2+ ions consumed 54% at 5 mol% BaCl 2 before decreasing to 22%-24% at 0.42-0.89 mol% BaCl 2 ; substantial co-deposition of Li was observed in all chemistries, consuming up to 53% of charge. Considering only 1% of the total charge was consumed for depositing Ba 2+ and Sr 2+ ions in ~0.1 mol% SrCl 2 /BaCl 2 electrolyte, the lower recovery limit of Bi for alkaline-earth elements is suggested to be at ~0.4 mol% SrCl 2 /BaCl 2 to achieve appreciable deposition of alkaline-earths (>1.5 mol% Ba/Sr in liquid Bi). The overpotentials of liquid Bi at 5 mol% of SrCl 2 /BaCl 2 were evaluated by electrochemical impedance spectroscopy. The co-deposition of Sr and Li exhibited the largest increase in charge transfer resistances implying sluggish charge transfer kinetics whereas the co-deposition of Ba and Li exhibited a large increase in mass transport resistances due to the slow diffusion of Ba 2+ ions in the electrolyte.
Background: Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. Results: A high quality draft genome (7.8Mb) of S. yeochonensis CN732 was obtained with a G+C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. Conclusions: This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.
Background Processing of archaeal 16S and 23S rRNAs is believed to involve excision of individual rRNAs from polycistronic precursors, circularization of excised rRNAs, and re-linearization before the incorporation into ribosomes. However, all the knowledge is derived from several isolated species, leaving open the possibility that different processes may occur in other archaeal groups. Results Here, we investigate rRNAs from diverse and mostly uncultivated archaea. Sequencing of total cellular RNA from eight phylum-level lineages indicates that archaeal circular 23S rRNA transcript abundances vastly exceed those of linear counterparts, and linear versions are often undetectable. As the majority of rRNAs derive from mature ribosomes, the data suggest that ribosomes contain circular 23S rRNAs. Thus, we directly sequence RNA extracted from isolated ribosomes of a model archaeon, Methanosarcina acetivorans, and confirm that the 23S rRNAs in the ribosomes are circular. Structural modeling places the 5′ and 3′ ends of the linear precursors of archaeal 23S rRNAs in close proximity to form a GNRA tetraloop (in which N is A, C, G, or U and R is A or G), consistent with their existence as circular molecules. We also confirm the existence of circular 16S rRNA intermediates in transcriptomes of most archaea, yet a circular form is not evident in some distinct archaeal groups, suggesting that certain archaea do not circularize 16S rRNA during processing. Conclusions Our findings uncover unexpected variations in the processing required to generate mature rRNAs and the conformation of functional molecules in archaeal ribosomes.
Over the last four years, each successive wave of the COVID-19 pandemic has been caused by variants with mutations that improve the transmissibility of the virus. Despite this, we still lack tools for predicting clinically important features of the virus. In this study, we show that it is possible to predict the PCR cycle threshold (Ct) values from clinical detection assays using sequence data. Ct values often correspond with patient viral load and the epidemiological trajectory of the pandemic. Using a collection of 36,335 high quality genomes, we built models from SARS-CoV-2 intrahost single nucleotide variant (iSNV) data, computing XGBoost models from the frequencies of A, T, G, C, insertions, and deletions at each position relative to the Wuhan-Hu-1 reference genome. Our best model had an R 2 of 0.604 [0.593–0.616, 95% confidence interval] and a Root Mean Square Error (RMSE) of 5.247 [5.156–5.337], demonstrating modest predictive power. Overall, we show that the results are stable relative to an external holdout set of genomes selected from SRA and are robust to patient status and the detection instruments that were used. This study highlights the importance of developing modeling strategies that can be applied to publicly available genome sequence data for use in disease prevention and control.
Abstract The detection of GW170817/AT2017gfo inaugurated an era of multimessenger astrophysics, in which gravitational-wave and multiwavelength photon observations complement one another to provide unique insight into astrophysical systems. A broad theoretical consensus exists, in which the photon phenomenology of neutron star mergers largely rests upon the evolution of the small amount of matter left on bound orbits around the black hole or massive neutron star remaining after the merger. Because this accretion disk is far from inflow equilibrium, its subsequent evolution depends very strongly on its initial state, yet very little is known about how this state is determined. Using both snapshot and tracer particle data from a numerical relativity/MHD simulation of an equal-mass neutron star merger that collapses to a black hole, we show how gravitational forces arising in a nonaxisymmetric, dynamical spacetime supplement hydrodynamical effects in shaping the initial structure of the bound debris disk. The work done by hydrodynamical forces is ∼10 times greater than that due to time-dependent gravity. Although gravitational torques prior to remnant relaxation are an order of magnitude larger than hydrodynamical torques, their intrinsic sign symmetry leads to strong cancellation; as a result, hydrodynamical and gravitational torques have a comparable effect. We also show that the debris disk’s initial specific angular momentum distribution is sharply peaked at roughly the specific angular momentum of the merged neutron star’s outer layers, a fewr g c, and identify the regulating mechanism.
While supermassive binary black holes (SMBBHs) inspiral toward merger they may also accrete matter from a surrounding disk. To study the dynamics of this system requires simultaneously describing the evolving spacetime and the magnetized plasma. We present the first relativistic calculation simulating two equal-mass, nonspinning black holes as they inspiral from a 20 M (G = c = 1) initial separation almost to merger. Our results imply important observational consequences: for instance, the accretion rate $\dot{M}$ onto the black holes first decreases and then plateaus, dropping by only a factor of ~3 despite the rapid inspiral. An estimated bolometric light curve follows the same profile, suggesting some merging SMBBHs may be significantly luminous past the predicted circumbinary disk decoupling. The minidisks are nonstandard: Reynolds, not Maxwell, stresses dominate, and they oscillate between two states. In one part of the cycle, "sloshing" streams transfer mass between minidisks, carrying kinetic energy at a rate sometimes as high as the peak minidisk bolometric luminosity. We also discover that episodic accretion drives time-varying minidisk tilts. These complex dynamics all contribute to unique cyclical behavior in the light curves of late-time inspiraling SMBBHs. The poloidal magnetic flux on the black holes is roughly constant at a dimensionless level $\phi$ ~ 2–3, but doubles just before merger; for significant black hole spin, this flux predicts powerful jets with variability driven by binary dynamics, another potentially unique electromagnetic signature. This simulation is the first to employ our multipatch infrastructure PATCHWORK MHD, decreasing the computational expense to ~3% of conventional single-grid methods' cost.
Ultrasonic paramagnetic resonance investigations of Pr ions ground state energy levels in calcium fluoride
Results are presented from a wind-tunnel investigation of the flow field around a 0.45-scale model of a Mars lander. The tests were conducted in air at values of Reynolds number equivalent to those anticipated on Mars. The effects of Reynolds number equivalent to those anticipated on Mars. The effects of Reynolds number, model orientation with respect to the airstream, and the position of a dish-type antenna on the flow field were determined. An appendix is included which describes the calibration and operational characteristics of hot-film anemometers under simulated Mars surface conditions.
Two existing function space algorithms, Davidon and projected gradient, are modified so that they may handle directly control variable inequality constraints. A third quasi-Newton type algorithm developed by C. G. Broyden is extended to optimal control problems. The Broyden algorithm is further modified so that it also may handle directly control variable inequality constraints. These methods along with a pure gradient and two conjugate gradient algorithms are simulated on three relatively simple yet representative bounded control problems, two of which have singular subarcs. Overall the Broyden algorithm was found to be superior. The most notable result of the study was the clear superiority of the Broyden and Davidon algorithms in producing a sharp interior control subarc.
Extrapolating from extensive field measurements on foliar emissions in the U.S. approximate global inputs of isoprene and terpenes of 3.5 times 10 to the 14th power and 4.8 times 10 to the 14th power g(C)/yr, respectively, are obtained. The oxidation of these hydrocarbons could contribute in an important way to the atmospheric sources of CO (4.2-13.3 times 10 to the 14th power g/yr) and H2 (10-35 times 10 to the 12th power g/yr), and to organic species soluble in rainwater