Engineering topics

Newton, ed., Irene L. G.

Publications and source records attributed to Newton, ed., Irene L. G..

15 records

DOE OSTI2023

A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile

ABSTRACT Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Draft Genome Sequence of Pedococcus sp. Strain 5OH_020, Isolated from California Grassland Soil

The draft genome sequence of the soil bacterium Pedococcus sp. strain 5OH_020, isolated on a natural cobalamin analog, comprises 4.4 Mbp, with 4,108 protein-coding genes. Its genome encodes cobalamin-dependent enzymes, including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests that it is a novel species within the genus Pedococcus .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Friend or Foe: Draft Genome Sequence of Bradyrhizobium sp. Strain SRS-191

We report the genomic features of Bradyrhizobium sp. strain SRS-191, which was isolated from a former nuclear legacy site in Aiken, South Carolina, USA. With a genome size of 7,621,400 bp, the strain harbored genes not only for environmentally beneficial traits (e.g., heavy metal resistance, nitrogen fixation, and aromatic biodegradation) but also for antimicrobial resistance.

Chauhan, Ashvini↗

DOE OSTI2022

Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate

Anaerobic microbiomes can be used to recover the chemical energy in agroindustrial and municipal wastes as useful products. Here, we report a total of 109 draft metagenome-assembled genomes from a bioreactor-fed carbohydrate-rich dairy manure hydrolysate. Studying these genomes will aid us in deciphering the metabolic networks in anaerobic microbiomes.

Ingle, Abel T.↗

DOE OSTI2022

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate

Fermentative microbial communities can be utilized for the conversion of various agroindustrial residues into valuable chemicals. Here, we report 34 metagenomes from anaerobic bioreactors fed lactose-rich ultrafiltered milk permeate and 278 metagenome-assembled genomes (MAGs). These MAGs can inform future studies aimed at generating renewable chemicals from dairy and other agroindustrial residues.

Walters, Kevin A.↗

DOE OSTI2022

Metagenomes from 25 Low-Abundance Microbes in a Partial Nitritation Anammox Microbiome

Microbial communities using anammox bacteria to remove nitrogen are increasingly important in wastewater treatment. We report on 25 metagenome-assembled genomes of low-abundance microbes from a partial nitritation anammox bioreactor system that have not been described previously. These data add to the body of information about this important wastewater treatment system.

Beach, Natalie K.↗

DOE OSTI2022

Complete Genome Sequence of Acidithiobacillus ferriphilus GT2, Isolated from Gold Mill Tailings

We report the complete genome sequence of Acidithiobacillus ferriphilus GT2, an acidophile isolated from gold mill tailings. The circular genome of GT2 contains 2,489 predicted protein-coding units and a single plasmid. Functional analysis indicates the metabolic potential to oxidize iron and reduced sulfur compounds and to fix N 2 and CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Metagenomes, Metatranscriptomes, and Metagenome-Assembled Genomes from Chesapeake and Delaware Bay (USA) Water Samples

Here, we present 36 metagenomes, 59 metatranscriptomes, and 373 metagenome-assembled genomes (MAGs) from Chesapeake and Delaware Bay water samples. This data set will be useful for studying microbial biogeochemical cycling in estuaries.

Ahmed, Mir Alvee↗

DOE OSTI2021

Delila-PY, a Pipeline for Utilizing the Delila Suite of Software to Identify Potential DNA Binding Motifs

Predicting potential DNA binding motifs is a critical part of understanding gene expression across all domains of life. Here, we report the development of Delila-PY, an easy-to-use pipeline to utilize the Delila suite to identify DNA binding motifs.

Myers, Kevin S.↗

DOE OSTI2021

Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

ABSTRACT The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Chromosomal Sequence of Lactobacillus brevis Oregon-R-modENCODE Strain BDGP6, a Lactic Acid Bacterium Isolated from the Gut of Drosophila melanogaster

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%.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Genome Sequences of Frankineae sp. Strain MT45 and Jatrophihabitans sp. Strain GAS493, Two Actinobacteria Isolated from Forest Soil

Frankiaceae are bacterial endosymbionts that are also found free-living in soil. Here, we present the genome sequences of two novel bacterial members of the order Frankiales , class Actinobacteria , isolated from temperate terrestrial forest soils. The genomes for MT45 and GAS493 indicate a genetic capacity for carbohydrate degradation but not nitrogen fixation.

DeAngelis, Kristen M.↗

DOE OSTI2020

Draft Genome Sequence of Agrobacterium fabrum ARqua1

Agrobacterium fabrum ARqua1 is a hybrid of Agrobacterium fabrum C58C bearing the megaplasmid pRiA4b. ARqua1 is used by many plant researchers to generate transgenic roots. The draft genome of ARqua1 includes a 249,350-bp contig that likely covers all of pRiA4b, and it will be a valuable resource to plant biologists.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Draft Genome Sequence of Yokenella regensburgei Strain WCD67, Isolated from the Boxelder Bug

We report here the draft genome sequence of Yokenella regensburgei strain WCD67, isolated from the boxelder bug ( Boisea trivittata ). The genome is 5,277,883 bp in size, has a GC content of 54.12%, and has 5,416 genes. A total of 17 mobile elements were discovered, 6 of which were predicted to be phages.

Meyers, Desiree J.↗

DOE OSTI2020

One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil

We report eight genomes from representatives of the phylum Acidobacteria subdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.

59 BASIC BIOLOGICAL SCIENCES↗