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We report here the genome sequence of a Staphylococcus xylosus clinical isolate, strain SMA0341-04 (UGA5), which contains one chromosome and at least one plasmid. Notably, strain SMA0341-04 (UGA5) contains the tetracycline efflux major facilitator superfamily (MFS) transporter ( tetK ) gene.
Here, we report the sequence of a Staphylococcus pettenkoferi clinical isolate, strain SMA0010-04 (UGA20), which contains the PC1 beta-lactamase ( blaZ ) gene.
Here, we report the genome sequences of a Staphylococcus aureus clinical isolate, strain SMA0034-04 (UGA22), which contains one chromosome and one plasmid. We also reveal that isolate SMA0034-04 (UGA22) contains loci in the genome that encode multiple exotoxins.
Rhodobacter sphaeroides is an alphaproteobacterium found in freshwater and marine ecosystems. To better understand the metabolic diversity within this species, we isolated and sequenced four R. sphaeroides isolates obtained from Trunk River in Woods Hole, Massachusetts.
Here, we report the draft genome sequence of Rhodovulum robiginosum DSM 12329 T , an anoxygenic phototroph isolated from a marine sediment in the North Sea (Jadebusen, Germany). This is the first genome for a marine photoferrotrophic bacterium, and it provides a genetic basis to understand the mechanistic underpinnings of photoferrotrophy in future studies.
A method to generate Schroedinger cat states in free propagating optical fields based on the use of displaced states (or displacement operators) is developed. Some optical schemes with photon-added coherent states are studied. The schemes are modifications of the general method based on a sequence of displacements and photon additions or subtractions adjusted to generate Schroedinger cat states of a larger size. The effects of detection inefficiency are taken into account.
A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energy between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.
A symmetry analysis of monoclinic, orthorhombic, and trigonal M{sub 3}X{sub 2}-type superstructures that can be formed in strongly stoichiometric MX{sub y} compounds with B1 structure is carried out. Channels of order-disorder transitions MX{sub y} → M{sub 3}X{sub 2} are determined. It is shown that, as temperature decreases, two physically admissible sequences of transformations associated with the formation of M{sub 3}X{sub 2} superstructures are possible in nonstoichiometric MX{sub y} compounds of group IV transition metals. By an example of vanadium carbide VC{sub y}, it is demonstrated that orthorhombic or monoclinic V{sub 3}C{sub 2} superstructures can be obtained with the formation of a nanostructure.
We have studied the dynamics of an electronic microwave generator with backward-wave and traveling-wave tubes connected in the feedback circuit and operating in the regimes of amplification and nonlinear Kompfner absorption, respectively. It is shown that radiation generated in such a system can have the form of a periodic sequence of ultrashort pulses. The studied mechanism of pulse generation is analogous to the method of passive mode locking, which is widely used in laser physics.
Due to the high contents of protein and fat in rainbow trout, it is highly susceptible to spoilage, which limits the storage and transportation processes. Exploring the spoilage microbial community during rainbow trout storage is essential to develop an effective preservation method. Here, the changes in the total bacterial colony and total volatile base nitrogen (TVB-N) during the storage of rainbow trout were investigated. Storage at 0 °C can effectively slow down the spoilage process with bacterial counts and TVB-N contents decreased from 8.7 log CFU/g and 18.7 mg/100 g obtained at 4 °C to 5.6 log CFU/g and 14.5 mg/100 g, respectively. 16S rDNA high-throughput sequencing results showed that the diversity of microbial genera decreased during storage. Acinetobacter, Pseudomonas, and Shewanells gradually became the dominant spoilage genera with contents of 59.9%, 18.6%, and 1.7%, respectively, in the late stage of storage. The spoilage abilities of bacteria belonging to the Pseudomonas and Shewanells genera were analyzed. Shewanella sp. S5-52 showed the highest level of TVB-N content (100.6 mg/100 g) in sterile fish juice, indicating that it had a strong spoilage ability. This study confirmed the dominant spoilage bacterial genera and evaluated the spoilage abilities of isolated strains during the storage of rainbow trout, which laid the foundation for further investigation of the spoilage mechanism of rainbow trout and other aquatic products.
GPU-BSW is a version of Smith-Waterman alignment algorithm which has been optimized to perform large number of sequence alignments on GPUs.
The JGI's gRNA Designer software is a a web application for doing whole genome guide RNA selection. It uses open source software, CCTop to identify potential guide RNA sequences, but adds value.
The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files.
SAND2024-09978O The Launch Accident Sequence Evaluation Program is used to calculate the source term for the consequence analysis involving a launch vehicle accident with a space nuclear system. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Analyze virus genetic sequences to identify lineages that are spreading especially rapidly.
As part of the VGI work under the National Charging Experience (ChargeX) Consortium, reliability analysis of communication interfaces for multiple SCM/VGI use-cases was performed using a Process Failure Modes and Analysis (PFMEA) style framework. This repository hosts all the relevant files for each of these use-cases which include: *A visual representation of their communication architecture: Image file (.png) *UML sequence diagram: Plant-UML source file (.puml). Visio file (.vsdx) and image file (.png) derived from the UML sourceX` *The PFMEA table: Excel file (.xlsx) These files are meant to serve as a starting point and can be adapted to company / organization specific SCM implementation.
Researchers at University of Missouri have conducted ultra-deep RNA sequencing of viral concentrates from wastewater (1 billion Illumina reads per sample). The resulting dataset spans 321 samples collected weekly from 11 cities between 2023-2025. As part of a tri-lab collaboration, scientists at LLNL and LANL cleaned, assembled, and annotated this metagenomic data, identifying nearly 200,000 viral genomes. Careful data curation resulted in a database containing 21,015 high-quality, near-complete viral genomes from wastewater. This database contains viruses predicted to infect a range of hosts including bacteria (most common viruses), plants (most abundant viruses), and vertebrates (rarest viruses). There are also numerous novel viruses that could not be well identified and whose host(s) are unknown. Just 7% of all genomes in the wastewater virus database had genus-level matches in the public NCBI database, and 17% matched to a recently created metagenomic virus database at that level (metaVR). The database will provide baseline information about viruses in wastewater that may be used to additional identify novel viruses during ongoing monitoring
Cupriavidus sp. strain UYPR2.512 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida grown in soils from a native forest of Uruguay. Here we describe the features of Cupriavidus sp. strain UYPR2.512, together with sequence and annotation. We find the 7,858,949 bp high-quality permanent draft genome is arranged in 365 scaffolds of 369 contigs, contains 7,411 protein-coding genes and 76 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.