Journal: PLOS One

Article Title: The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, sheds light on an environmentally widespread genus with remarkable metabolic potential

doi: 10.1371/journal.pone.0334406

Figure Lengend Snippet: (A) Phylogenetic relationship of the 16S rRNA gene sequences from strain 10A and other Gallaecimonas spp. found in the SILVA rRNA gene database v.138.1. The maximum-likelihood tree was built using 100 replicates and rooted with sequences from two strains of Escherichia coli (NCBI accession numbers: CP033092.1 and MT215717.1 ) as an outgroup. The value in the heatmap associated with the phylogenetic tree represents the average nucleotide identity (ANI) of 16S rRNA gene sequences between two strains on each of the x and y axes. (B) Phylogenomic tree of bacteria in the genus Gallaecimonas based on data in NCBI Reference Sequence Database (RefSeq, v.216). The tree was built based on the overall genome sequences and rooted with two genome sequences from Escherichia coli (GTDBtk accession numbers: RS_GCF_011881725.1 and RS_GCF_003697165.2) as an outgroup. Gallaecimonas pentaromativorans strain CEE_131 is also known as G. pentaromativorans strain DSM 21945.

Article Snippet: Annotation using the National Centre for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) v.6.0, revealed that strain 10A contains genes coding for 18 rRNA (six of each 5S, 16S, and 23S rRNAs), 86 tRNAs, and four ncRNAs, as well as 3,928 protein-coding sequences (CDS).

Techniques: Bacteria, Sequencing

Journal: PLOS One

Article Title: The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, sheds light on an environmentally widespread genus with remarkable metabolic potential

doi: 10.1371/journal.pone.0334406

Figure Lengend Snippet: (A) The global distribution of 16S rRNA gene sequences assigned to Gallaecimonas spp. was assessed using 536 sequences sourced from the GBIF Database. Orange and green indicate sequences assigned to G. pentaromativorans and G. xiamenensis , respectively, while “Other Gallaecimonas ” comprises G. kandeliae , G. mangrovi and unclassified Gallaecimonas spp. The circle size represents the relative abundance of sequences assigned to Gallaecimonas spp. within the prokaryotic community. The base map was generated using R package maps v.2.3−2, with internal boundary data derived from Natural Earth ( https://www.naturalearthdata.com ) via the maps package. (B) The proportion of 16S rRNA gene sequences assigned to Gallaecimonas spp. across environments. Seawater, estuary, and freshwater correspond to water samples from the respective environments. Polar represents the cryosphere and sediment includes samples from marine (e.g., pelagic sediment cores, benthic continental shelf), rivers, wetlands, saltmarshes and tidal mudflats.

Article Snippet: Annotation using the National Centre for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) v.6.0, revealed that strain 10A contains genes coding for 18 rRNA (six of each 5S, 16S, and 23S rRNAs), 86 tRNAs, and four ncRNAs, as well as 3,928 protein-coding sequences (CDS).

Techniques: Generated, Derivative Assay

Journal: NPJ Microgravity

Article Title: Rad-Bio-App: a discovery environment for biologists to explore spaceflight-related radiation exposures

doi: 10.1038/s41526-021-00143-x

Figure Lengend Snippet: The data within dashboard #4 of the Rad-Bio-App contains radiation data from Martian, lunar and spaceflight missions and ground-based radiation experiments. These data were filtered using radiation levels recorded on the lunar surface by the Chang’e 4 lander, with limits set to span a 2-fold range around the average dose rate (0.55 mGy/d). Results of this filtering were then exported to build a listing of spaceflight experiment datasets within the GeneLab data repository where their radiation exposure lies within this range of dose rates. Green numbers in table, datasets pre-processed by either the GeneLab uniform microarray or RNAseq analysis pipelines.

Article Snippet: These RR6 datasets were from five different tissues: dorsal skin, thymus, spleen, colon, and lung, respectively (i.e., GLDS 243, 244, 246, 247, and 248) and they were processed using the GeneLab RNAseq pipeline .

Techniques: Microarray