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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%.
The role of archaeal ammonia oxidizers often exceeds that of bacterial ammonia oxidizers in marine and terrestrial environments but has been understudied in permafrost, where thawing has the potential to release ammonia. Here, three thaumarchaea genomes were assembled and annotated from metagenomic data sets from carbon-poor Canadian High Arctic active-layer cryosols.
ABSTRACT Lactobacillus brevis Oregon-R-modENCODE strain BDGP6 was isolated from the gut of Drosophila melanogaster for functional host-microbial interaction studies. The bacterial chromosome is a single circular DNA molecule of 2,785,111 bp with a G+C content of 46%.
Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/μL of sample for SWGA and >129 genomic copies/μL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now.
Microorganisms frequently colonize surfaces within food production facilities. Detection of Listeria monocytogenes in this setting relies on culture-dependent methods, but the complex dynamics of bacterial interactions within these environments and their impact on pathogen detection remain largely unexplored. To address this challenge, we applied both 16S rRNA and shotgun quasimetagenomic (enriched microbiome) sequencing of swab culture enrichments from five seafood and seven dairy production environments. Utilizing 16S rRNA amplicon sequencing, we observed variability between 355 samples taken from these 12 production facilities and a distinctive microbiome for each environment. With shotgun quasimetagenomic sequencing, we were able to assemble L. monocytogenes metagenome-assembled genomes (MAGs) from 28 of the 32 culture-positive samples. We compared these MAGs to their corresponding whole-genome sequencing assemblies, which resulted in two polyphyletic clades consisting of L. monocytogenes lineages I and II with 13,195 and 25,556 single-nucleotide polymorphism sites, respectively. The remaining four MAGs did not produce sufficient genome coverage. To understand and establish limits for pathogen detection and subtyping using shotgun quasimetagenomics, these same data sets were downsampled in slilico to produce a titration series of abundances of L. monocytogenes and analyzed. Pathogen detection was achieved for all downsampled data sets, even those with only 3× genome coverage. This study contributes to the understanding of microbial diversity within food production environments and presents insights into the level of genome coverage needed in a metagenome sequencing data set to detect, subtype, and source track a foodborne pathogen.
The Laurentide Ice Sheet (LIS) was the largest ice sheet during the last glacial period. An accurate representation of its behavior during the last deglaciation is critical to understanding its influence on and response to a changing climate. Here we use 10 Be dating and Bayesian modeling to track the recession of the southwest sector of the Labrador Dome of the LIS along an ~500-km-long transect west of Lake Superior during the last deglaciation. This transect reflects terrestrial ice-margin retreat and crosses multiple moraine sets, with the southwestern part of the transect deglaciated by ca. 19 ka and the northeastern part deglaciated by ca. 10 ka. The predominant behavior of the ice margin during this interval is near-constant retreat with retreat rates varying between ~59 m/a and 38 m/a. The moraine sets mark standstills and/or readvances that in total constitute only ~17% of the retreat interval. The spatial and temporal pattern of ice-margin retreat tracked here differs from existing reconstructions that are based on using isochrons to define ice-margin positions. Acknowledging the uncertainties associated with the modeled ages of ice-margin retreat, we suggest that the overall retreat pattern is consistent with forcing by a gradual increase in Northern Hemisphere, high-latitude summer insolation. The pattern of ice-margin retreat is inconsistent with Greenland ice-core temperature records, and thus these records may not be suitable to drive models of the LIS.
Understanding the surface topographic change that results from underground explosions is important for global security. Current techniques to relate the surface change to underground explosion characteristics usually involve assuming the earth has homogenous properties, leading to highly variable interpretations. Here we use an unoccupied aerial platform and a digital single lens reflex camera along with 200+ ground control points surveyed with a real-time kinematic global navigation satellite system to measure the surface topographic change resulting from two underground explosions at the Dry Alluvium Geology site in Yucca Flat, Nevada National Security Site, southern Nevada, United States. We find areas of 5–7 cm of subsidence that are not directly above the explosion source but rather 200–300 m away. For experiment DAG2, this zone is located south and west of the explosion, while for DAG4, there is a zone of subsidence located northeast of the explosion. In addition, late-time measurements show as much as 5 cm of horizontal change without measurable associated vertical change in the weeks following DAG4 but not DAG2. These indicate that the deformation resulting from underground chemical explosions can be very complex and bear little to no resemblance to predictions using half-space models. It is likely the tectonic environment plays a significant role in controlling the surface change, but the details are not fully understood.
Observations of changes in phenology have provided some of the strongest signals of the effects of climate change on terrestrial ecosystems. The International Tundra Experiment (ITEX), initiated in the early 1990s, established a common protocol to measure plant phenology in tundra study areas across the globe. Today, this valuable collection of phenology measurements depicts the responses of plants at the colder extremes of our planet to experimental and ambient changes in temperature over the past decades. The database contains 150 434 phenology observations of 278 plant species taken at 28 study areas for periods of 1–26 years. Here we describe the full data set to increase the visibility and use of these data in global analyses and to invite phenology data contributions from underrepresented tundra locations. Portions of this tundra phenology database have been used in three recent syntheses, some data sets are expanded, others are from entirely new study areas, and the entirety of these data are now available at the Polar Data Catalogue (https://doi.org/10.21963/13215).
The use of heavy actinide targets, including 243 Am, 240,242,244 Pu, 245,248 Cm, 249 Bk, and 249 Cf, irradiated by intense heavy ion beams of 48 Ca has resulted in a significant expansion of the periodic table since 2000, including the discovery of five new heaviest elements and more than 50 new isotopes. These actinide materials can only be produced by intense neutron irradiation in very high flux reactors followed by chemical processing and purification in specialized hot cell facilities available in only a few locations worldwide. This paper reviews the reactor production of heavy actinides, the recovery and chemical separation of actinide materials, and the preparation of actinide targets for superheavy element experiments. The focus is on 248 Cm, 249 Bk, mixed 249–251 Cf, and 254 Es, including current availabilities and new production processes. The impacts of new facilities, including the Superheavy Element Factory at Dubna, accelerator and separator upgrades at RIKEN, and proposed upgrades to the High Flux Isotope Reactor at Oak Ridge are also described. Examples of recent superheavy element research are discussed as well as future opportunities for superheavy research using actinide targets.
Abstract Radiative corrections are crucial for modern high-precision physics experiments, and are an area of active research in the experimental and theoretical community. Here we provide an overview of the state of the field of radiative corrections with a focus on several topics: lepton–proton scattering, QED corrections in deep-inelastic scattering, and in radiative light-hadron decays. Particular emphasis is placed on the two-photon exchange, believed to be responsible for the proton form-factor discrepancy, and associated Monte-Carlo codes. We encourage the community to continue developing theoretical techniques to treat radiative corrections, and perform experimental tests of these corrections.
This summary of the second Terrestrial Very-Long-Baseline Atom Interferometry (TVLBAI) Workshop provides a comprehensive overview of our meeting held in London in April 2024 (Second Terrestrial Very-Long-Baseline Atom Interferometry Workshop, Imperial College, April 2024), building on the initial discussions during the inaugural workshop held at CERN in March 2023 (First Terrestrial Very-Long-Baseline Atom Interferometry Workshop, CERN, March 2023). Like the summary of the first workshop (Abend et al. in AVS Quantum Sci. 6:024701, 2024), this document records a critical milestone for the international atom interferometry community. It documents our concerted efforts to evaluate progress, address emerging challenges, and refine strategic directions for future large-scale atom interferometry projects. Our commitment to collaboration is manifested by the integration of diverse expertise and the coordination of international resources, all aimed at advancing the frontiers of atom interferometry physics and technology, as set out in a Memorandum of Understanding signed by over 50 institutions (Memorandum of Understanding for the Terrestrial Very Long Baseline Atom Interferometer Study).
Emerging quantum processors provide an opportunity to explore new approaches for solving traditional problems in the post Moore’s law supercomputing era. However, the limited number of qubits makes it infeasible to tackle massive real-world datasets directly in the near future, leading to new challenges in utilizing these quantum processors for practical purposes. Furthermore, hybrid quantum-classical algorithms that leverage both quantum and classical types of devices are considered as one of the main strategies to apply quantum computing to large-scale problems. In this article, we advocate the use of multilevel frameworks for combinatorial optimization as a promising general paradigm for designing hybrid quantum-classical algorithms. To demonstrate this approach, we apply this method to two well-known combinatorial optimization problems, namely, the Graph Partitioning Problem, and the Community Detection Problem. We develop hybrid multilevel solvers with quantum local search on D-Wave’s quantum annealer and IBM’s gate-model based quantum processor. We carry out experiments on graphs that are orders of magnitude larger than the current quantum hardware size, and we observe results comparable to state-of-the-art solvers in terms of quality of the solution.
As quantum computers become available to the general public, the need has arisen to train a cohort of quantum programmers, many of whom have been developing classical computer programs for most of their careers. While currently available quantum computers have less than 100 qubits, quantum computing hardware is widely expected to grow in terms of qubit count, quality, and connectivity. This review aims at explaining the principles of quantum programming, which are quite different from classical programming, with straightforward algebra that makes understanding of the underlying fascinating quantum mechanical principles optional. We give an introduction to quantum computing algorithms and their implementation on real quantum hardware. We survey 20 different quantum algorithms, attempting to describe each in a succinct and self-contained fashion. We show how these algorithms can be implemented on IBM’s quantum computer, and in each case, we discuss the results of the implementation with respect to differences between the simulator and the actual hardware runs. This article introduces computer scientists, physicists, and engineers to quantum algorithms and provides a blueprint for their implementations.
Biomass-derived energy sources represent a promising domestic route for fuel and chemical production, taking advantage of largely underutilized biological and waste resources. Heterogeneous catalysis plays a key role in these biomass conversion processes, as reflected by all American Society for Testing and Materials–approved pathways for producing sustainable aviation fuel proceeding through a catalytic step. This concise review seeks to establish the state of the art in thermal catalytic process development for various biomass-derived feedstocks and the current enabling capabilities that aid this development. Research needs are identified and described throughout the article, as further advancements in heterogeneous catalysis are required to improve the affordability and realize the full potential of biomass-derived products.
Rapid Arctic environmental change affects the entire Earth system as thawing permafrost ecosystems release greenhouse gases to the atmosphere. Understanding how much permafrost carbon will be released, over what time frame, and what the relative emissions of carbon dioxide and methane will be is key for understanding the impact on global climate. In addition, the response of vegetation in a warming climate has the potential to offset at least some of the accelerating feedback to the climate from permafrost carbon. Temperature, organic carbon, and ground ice are key regulators for determining the impact of permafrost ecosystems on the global carbon cycle. Together, these encompass services of permafrost relevant to global society as well as to the people living in the region and help to determine the landscape-level response of this region to a changing climate.
Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if these protein channels provide environments similar to the aqueous solution hydration environment. In fact, bulk aqueous solution is an important reference condition for the ion permeation process. Assessment of this hydration mimicry concept depends on understanding the hydration structure and free energies of metal ions in water in order to provide a comparison for the membrane channel environment. To refine these considerations, we review local hydration structures of ions in bulk water and the molecular quasi-chemical theory that provides hydration free energies. In doing so, we note some current views of ion binding to membrane channels and suggest new physical chemical calculations and experiments that might further clarify the hydration mimicry concept.
Enabling fast charging in lithium ion batteries (LIBs) is a key factor to make electric vehicles drive just like gasoline-powered vehicles when the time comes to refuel. However, fast charging to current LIBs (LiNi x Mn y Co 1–z O 2 /graphite) is limited by lithium plating, which is barely reversible and causes LIBs to lose capacity over time. Thus, research to quantify the lithium plating in LIB cells is extremely important in improving our fundamental understanding of lithium plating behavior and enabling fast charging for LIBs. Here, we precisely quantified the amount of fast-charge-driven lithium plating in a coin-cell composed of LiNi 0.5 Mn 0.3 Co 0.2 O 2 (NMC532)/graphite. We found that the amount of lithium plating gradually increases with the cycle count and reaches 25.59 μmole (26.80 mAh g –1 cathode ) by the 100th cycle. The study also reveals that the NMC532 has lost 19% of its original lithium content after 100 fast-charging cycles; this, correspondingly, causes a lattice volumetric strain of 0.59%.
Enabling fast charging in lithium-ion batteries (LIBs) is a key factor for resolving consumers’ “range anxiety” concerns in choosing an electric vehicle over a gasoline-powered one. The best-known issue in the fast charging of current LIBs (based on LiNi x Mn y Co 1–x–y O 2 /graphite) is lithium plating, which is barely reversible and is accompanied by capacity loss over time. Therefore, understanding the reasons for the irreversibility of lithium plating driven by fast charging is critical to enhancing the fast-charging capability of LIBs. Here, a study of the irreversibility and heterogeneity of lithium plating is carried out by using electrochemical analyses, inductively coupled plasma mass spectroscopy, and X-ray photoelectron spectroscopy. Further, the study shows that the majority of the lithium plated during fast charging remains inactive even with very slow discharging rates, implying that most of the plated lithium is irreversibly lost. The study also reveals that chemical compounds such as LiF, Li 2 O and Li 2 (CO 3 ) are formed heterogeneously within the lithium plating and are responsible for some of the irreversibility of the plated lithium.