Brian C. Thomas
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View article: Multiple techniques confirm endogenous collagen in Edmontosaurus fossil bone
Multiple techniques confirm endogenous collagen in Edmontosaurus fossil bone Open
Reports of proteins in fossilized bones have ignited an on-going debate because previously it was generally assumed that fossilization results in destruction of all organic components. We combine Attenuated Total Reflection (ATR) Fourier T…
View article: FTIR, XPol, and LC-MS confirm endogenous collagen in Edmontosaurus fossil bone
FTIR, XPol, and LC-MS confirm endogenous collagen in Edmontosaurus fossil bone Open
Reports of proteins in fossilized bones have ignited an on-going debate because previously it was generally assumed that fossilization results in destruction of all organic components. We combine Attenuated Total Reflection (ATR) Fourier T…
View article: CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes Open
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deploy…
View article: CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes
CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes Open
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deploy…
View article: Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability
Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability Open
Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 nucleases have been extensively used in biotechnology and therapeutics. However, many applications are not possible owing to the size, targetability, and poten…
View article: Novel CRISPR-Associated Gene-Editing Systems Discovered in Metagenomic Samples Enable Efficient and Specific Genome Engineering
Novel CRISPR-Associated Gene-Editing Systems Discovered in Metagenomic Samples Enable Efficient and Specific Genome Engineering Open
Development of medicines using gene editing has been hampered by enzymological and immunological impediments. We described previously the discovery and characterization of improved, novel gene-editing systems from metagenomic data. In this…
View article: Testing the Cavefish Model: An Organism-Focused Theory of Biological Design
Testing the Cavefish Model: An Organism-Focused Theory of Biological Design Open
Poster Abstract\nThe Institute for Creation Research (ICR) is experimentally testing an engineering-based model of rapid biological adaptation: Continuous Environmental Tracking (CET). This model infers that organisms actively track condit…
View article: Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes
Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes Open
Programmable, RNA-guided nucleases are diverse enzymes that have been repurposed for biotechnological applications. However, to further expand the therapeutic application of these tools there is a need for targetable systems that are small…
View article: Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities
Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities Open
Cas12a enzymes are quickly being adopted for use in a variety of genome-editing applications. These programmable nucleases are part of adaptive microbial immune systems, the natural diversity of which has been largely unexplored. Here, we …
View article: Subsurface carbon monoxide oxidation capacity revealed through genome‐resolved metagenomics of a carboxydotroph
Subsurface carbon monoxide oxidation capacity revealed through genome‐resolved metagenomics of a carboxydotroph Open
Summary Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth's deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 to…
View article: Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph
Subsurface carbon monoxide oxidation capacity revealed through genome-resolved metagenomics of a carboxydotroph Open
Summary Microbial communities play important roles in the biogeochemical cycling of carbon in the Earth’s deep subsurface. Previously, we demonstrated changes to the microbial community structure of a deep aquifer (1.4 km) receiving 150 to…
View article: Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs
Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs Open
Little is currently known about biogeochemical mercury cycling in geothermal systems. The manuscript presents a new conceptual model, supported by genome-resolved metagenomic analysis and detailed geochemical measurements. The model illust…
View article: Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs
Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs Open
Geothermal systems emit substantial amounts of aqueous, gaseous and methylated mercury, but little is known about microbial influences on mercury speciation. Here we report results from genome-resolved metagenomics and mercury speciation a…
View article: Microbial communities across a hillslope‐riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock
Microbial communities across a hillslope‐riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock Open
Watersheds are important suppliers of freshwater for human societies. Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharge through soils and underlying …
View article: Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms
Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms Open
Gene expression profiles provide insight into how microorganisms respond to changing environmental conditions. However, few studies have integrated expression profile analyses of both coding genes and non-coding RNAs (ncRNAs) to characteri…
View article: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria Open
The evolution of aerobic respiration was likely linked to the origins of oxygenic Cyanobacteria. Close phylogenetic neighbors to Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria and Sericytoch…
View article: MOESM2 of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
MOESM2 of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Open
Additional file 2: FASTA-formatted file containing EMIRGE-reconstructed sequences from the complex simulated microbial community. (FASTA 35 KB)
View article: of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Open
of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
View article: MOESM1 of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
MOESM1 of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Open
Additional file 1: FASTA formatted file containing EMIRGE-reconstructed sequences from the simple simulated microbial community. (FASTA 14 KB)
View article: MOESM3 of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
MOESM3 of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Open
Additional file 3: FASTA-formatted file containing EMIRGE-reconstructed sequences from the natural microbial community. (FASTA 16 KB)
View article: of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Open
of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
View article: of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data Open
of EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
View article: Processing of grassland soil C-N compounds into soluble and volatile molecules is depth stratified and mediated by genomically novel bacteria and archaea
Processing of grassland soil C-N compounds into soluble and volatile molecules is depth stratified and mediated by genomically novel bacteria and archaea Open
Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by organisms with unknown metabolic capacities. Even Acidobacteria, among the mos…
View article: Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock
Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock Open
Watersheds are important suppliers of freshwater for human societies. Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharges through soils and underlying…
View article: Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome Open
Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an a…