Search NASA⌕ Search

SEARCH · Search NASA

Results for “KBase”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2

KBase Educators Overview

KBase worked with a community of instructors to create a connected workflow that integrates genomics, metagenomics, phylogenetics, and pangenomic concepts in a “choose your own adventure” framework. Each concept is stand alone, while complementing one another as they flow from one topic to another across concepts. The pace of each workflow can be adjusted with the flexibility of modules that are shareable and allow students to copy and interact with data and analyses.

Data science, Education, Training, Genomics, Metag↗

KBase Narrative - Viral Analysis End-to-End

This pipeline processes a single metagenomic dataset (downloaded from NCBI SRA) from the Global Ocean Viromes dataset, identifies the viral sequences using VirSorter, and subsequently classifies them with vConTACT2. Along the way there are several intermediary steps to convert files from one KBase object to another - and though some of these can be skipped for this particular dataset - we're explicitly doing them here as to be more easily generalized to other datasets.

Bolduc, Benjamin↗

KBase Narrative - kb_DRAM E. coli annotation

Here we are annotating a E. coli K-12 genome using both DRAM and RAST then using those annotations to build models. The genome is from NCBI RefSeq ID NC_000913.

Shaffer, Michael↗

KBase Narrative - Mse_Genome_Assembly

Upon investigating the gut microbiome of mice for microbes related to Polycystic Ovary Syndrome (PCOS), our team found 2 metagenomes that could not be classified using alignment based methods. To further investigate microbial species from these samples, we used common MAGs workflow to create draft genomes which were then later taxonomically classified using GTDB-tk app.

Rastegar, Kiarash↗

KBase Narrative - Metagenome-assembled genomes from Amazonian soil microbial consortia

We report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils, in the Brazilian Eastern Amazon. Recovered MAGs constitute novel genomes with the potential to act in important ecological processes, including the degradation of carbohydrate and sulfur and nitrogen cycling.

Mandro, Jessica Adriele↗

KBase Narrative - Comparing Proteomes of Cupriavidus basilensis 4G11 and Cupriavidus necator H16

Species of Cupriavidus are among the best bioplastic producing microorganisms known, though intracellular poly-hydroxybutyrate (PHB) is made exclusively during unbalanced growth (e.g. nitrogen limitation), a state characterized by poor growth and cellular stress. Much work has been done studying bioplastic production in the model/type strain C. necator H16. We use an RB-TnSeq library of the closely related C. basilensis 4G11 to assess for genes which decouple PHB production from growth state. In this narrative we compute genome-wide protein homology between these two organisms, and generate a synteny plot across the genomes as well.

Sander, Kyle↗

KBase Narrative - Draft Genome of Exiguobacterium indicum strain LL15

Exiguobacterium indicum has often reported from a wide variety of environmental samples, ranging from extreme to common habitats. Here we report the 3.1-Mb draft genome of E. indicum strain LL15, discovered during an investigation of freshwater lakes in residential-urban environments.

Cooper, Joshua [Northern Kentucky University, Depa↗

KBase Narrative - Draft Genome of Roseomonas Strain GC11

This narrative was used for the draft genome of a Roseomonas species Strain GC11. This genus includes 6 known species. The specimen was collected using a water grab method in Conservancy Park, a freshwater site in Belleview, KY. This species is often identified in aquatic environments and is a known pathogen to humans1. It has been reported in healthcare settings from bacteremia in the blood and has also been reported to be found in human catheters. Due to the the prevelance as a human pathogen and lack of isolation in a non-human environment this strain was of particular interest.

Cooper, Joshua [Northern Kentucky University, Depa↗

KBase Narrative - BIT 295 MRA Isolate 106- Final

Arthrobactor is a bacteria that commonly resides in soil, plants, and wastewater (Gobbetti 2014). It is commonly used in the agricultural industry for degrading pesticides which will detox the soil and allow wildlife not to be harmed by said pesticides. The sample that is being tested came from an acid drain from a mine. The test sample was able to live and thrive in a metal ridden environment which could lead it to having some genes that could aid in e-waste recycling. A species of arthrobacter known as Arthrobacter citreus can be used for polyamide waste (Baxi 2019). Polyamide is used in fishing nets and industrial applications and the waste generated by this impacts ocean environments and ecosystems (Rietzler et all... 2021). Based on the resilience of arthrobacter as a genus, the hopes for this sample to aid in e-waste recycling are high.

Chadha, Aditya↗

KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Decontamination through Metagenomic Fractionation and analysis of Metabolic Potential-

Deep-sea microbiomes sampled with traditional or pressure-retaining instrumentation A fundamental property of life in the sea is that with increasing depth must come increased adaptation to elevated hydrostatic pressures. This project aims to assess technology for the accurate characterization of microbial biodiversity and biochemistry at greater depths, and validate its use in some of the deepest and least-explored waters in the Ocean: Hadal Trench. Compared to the 0.1 megapascal (MPa) of surface waters, organisms inhabiting at the average depth of the Ocean (3800 m) have to deal with pressures of 38 MPa (5,500 psi). The effects of these high pressure have been most thoroughly investigated in microorganisms, where it has been found to affect membrane integrity and transport, cytoskeletal assembly and both DNA and protein synthesis. We will explore the diversity and activity of microorganisms from 2000 m to >8,000 m depths within the highly productive water column of hadal trenches, comparing seawater samples obtained with and without substantial pressure changes during recovery. A pressure retaining device was used to sample the microbial communities of the watercolumn with reduced decompression during retreival (Peoples et. al., 2019). References: Peoples LM, Norenberg M, Price D, McGoldrick M, Novotny M, Bochdansky A, Bartlett DH. A full-ocean-depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions. Deep Sea Research Part I: Oceanographic Research Papers. 2019 Jan 1;143:50-7.

Plominsky, Alvaro M.↗

KBase Narrative - Timberlake Metagenomes

This narrative contains the MAG Analysis from: Clifton P Bueno de Mesquita, Wyatt H Hartman, Marcelo Ardón, Susannah G Tringe, Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland, ISME Communications, 2024; ycae040, https://doi.org/10.1093/ismeco/ycae040 Metagenomes were uploaded to IMG/M for other analyses.

de Mesquita, Clifton Bueno↗

KBase Narrative - MRA Genome Announcement Bradyrhizobium NP1

We report the complete genome sequence of Bradyrhizobium strain NP1, which was isolated from forest soil that had been subject to chronic warming. The diverse genus Bradyrhizobium is predicted to contain approximately 800 species (1) and includes non-symbiotic species that dominate forest soil (2). Bradyrhizobium NP1 was isolated from a Long-Term Ecological Research site in the Harvard Forest (HRF), in Petersham, MA (42.54, -72.18).

Morrow, Maureen↗

KBase Narrative - Metabolic_reconstruction_ETDI_mangrove

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

Laux, Marcele↗

KBase Narrative - Supplemental Data for "Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes"

Here we provide the complete set of circular elements produced by SCAPP from metagenomic data that may represent mobile genetic elements (MGEs). For the publication, these sequences were de-replicated within the high [U] and low [U] sample sets. Additionally, 98 of the circular elements were removed for downstream analysis due to high suspicion of being (1) chloroplast or mitochondrial sequences or (2) erroneously circularized long repeat regions. The complete list of circular elements used for the analysis along with metadata can be found in Tables S5 and S6.

Goff, Jennifer↗