James Hemp
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View article: A geological timescale for bacterial evolution and oxygen adaptation
A geological timescale for bacterial evolution and oxygen adaptation Open
Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously th…
View article: Diversity and evolution of nitric oxide reduction in bacteria and archaea
Diversity and evolution of nitric oxide reduction in bacteria and archaea Open
Nitrous oxide is a potent greenhouse gas whose production is catalyzed by nitric oxide reductase (NOR) members of the heme-copper oxidoreductase (HCO) enzyme superfamily. We identified several previously uncharacterized HCO families, four …
View article: An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event
An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event Open
Most of life’s diversity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time. However, the co-evolution of life and the Earth system has left signatures of bacterial me…
View article: Quantitative gastrointestinal function and corresponding symptom profiles in autonomic neuropathy
Quantitative gastrointestinal function and corresponding symptom profiles in autonomic neuropathy Open
Purpose Peripheral neuropathies with autonomic nervous system involvement are a recognized cause of gastrointestinal dysmotility for a wide spectrum of diseases. Recent advances in wireless motility capsule testing allow improved sampling …
View article: Diversity and evolution of nitric oxide reduction
Diversity and evolution of nitric oxide reduction Open
Nitrogen is an essential element for life, with the availability of fixed nitrogen limiting productivity in many ecosystems. The return of oxidized nitrogen species to the atmospheric N 2 pool is predominately catalyzed by microbial denitr…
View article: Evolution of the cytochrome <i>bd</i> oxygen reductase superfamily and the function of CydAA’ in Archaea
Evolution of the cytochrome <i>bd</i> oxygen reductase superfamily and the function of CydAA’ in Archaea Open
Cytochrome bd-type oxygen reductases (cytbd) belong to one of three enzyme superfamilies that catalyze oxygen reduction to water. They are widely distributed in Bacteria and Archaea, but the full extent of their biochemical diversity is un…
View article: Evolution of the cytochrome-<i>bd</i>type oxygen reductase superfamily and the function of cydAA’ in Archaea
Evolution of the cytochrome-<i>bd</i>type oxygen reductase superfamily and the function of cydAA’ in Archaea Open
Cytochrome bd -type oxygen reductases (cytbd) belong to one of three enzyme superfamilies that catalyze oxygen reduction to water. They are widely distributed in Bacteria and Archaea, but the full extent of their biochemical diversity is u…
View article: Neuroimmunogastroenterology: At the Interface of Neuroimmunology and Gastroenterology
Neuroimmunogastroenterology: At the Interface of Neuroimmunology and Gastroenterology Open
The central nervous system (CNS) is an important regulator of the gastrointestinal tract, and CNS dysfunction can result in significant and disabling gastrointestinal symptom manifestation. For patients with neuroimmunologic and neuroinfla…
View article: FIND: Identifying Functionally and Structurally Important Features in Protein Sequences with Deep Neural Networks
FIND: Identifying Functionally and Structurally Important Features in Protein Sequences with Deep Neural Networks Open
The ability to correctly predict the functional role of proteins from their amino acid sequences would significantly advance biological studies at the molecular level by improving our ability to understand the biochemical capability of bio…
View article: Genomic Evidence for Phototrophic Oxidation of Small Alkanes in a Member of the Chloroflexi Phylum
Genomic Evidence for Phototrophic Oxidation of Small Alkanes in a Member of the Chloroflexi Phylum Open
Recent genomic and microcosm based studies revealed a wide diversity of previously unknown microbial processes involved in alkane and methane metabolism. Here we described a new bacterial genome from a member of the Chloroflexi phylum—term…
View article: Phototrophic Methane Oxidation in a Member of the Chloroflexi Phylum
Phototrophic Methane Oxidation in a Member of the Chloroflexi Phylum Open
Biological methane cycling plays an important role in Earth’s climate and the global carbon cycle, with biological methane oxidation (methanotrophy) modulating methane release from numerous environments including soils, sediments, and wate…
View article: Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium
Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium Open
Respiratory ammonification and denitrification are two evolutionarily unrelated dissimilatory nitrogen (N) processes central to the global N cycle, the activity of which is thought to be controlled by carbon (C) to nitrate (NO3 -) ratio. H…
View article: Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications
Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications Open
Respiratory complex I is part of a large family of homologous enzymes that carry out the transfer of electrons between soluble cytoplasmic electron carriers and membrane-bound electron carriers. These complexes are vital bioenergetic enzym…
View article: Resource limitation modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium
Resource limitation modulates the fate of dissimilated nitrogen in a dual-pathway Actinobacterium Open
Respiratory ammonification and denitrification are two evolutionarily unrelated dissimilatory nitrogen (N) processes central to the global N cycle, the activity of which is thought to be controlled by carbon (C) to nitrate (NO 3 - ) ratio.…
View article: Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer
Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer Open
The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineag…
View article: Draft Genome Sequence of Hydrogenibacillus schlegelii MA48, a Deep-Branching Member of the <i>Bacilli</i> Class of <i>Firmicutes</i>
Draft Genome Sequence of Hydrogenibacillus schlegelii MA48, a Deep-Branching Member of the <i>Bacilli</i> Class of <i>Firmicutes</i> Open
We report here the draft genome sequence of Hydrogenibacillus schlegelii MA48, a thermophilic facultative anaerobe that can oxidize hydrogen aerobically. H. schlegelii MA48 belongs to a deep-branching clade of the Bacilli class and provide…
View article: Crown group Oxyphotobacteria postdate the rise of oxygen
Crown group Oxyphotobacteria postdate the rise of oxygen Open
The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by the evolution of oxygenic photosynthesis in the ancestors of Cyanobacteria. However, long‐standing …
View article: Evolution of Oxygenic Photosynthesis
Evolution of Oxygenic Photosynthesis Open
The origin of oxygenic photosynthesis was the most important metabolic innovation in Earth history. It allowed life to generate energy and reducing power directly from sunlight and water, freeing it from the limited resources of geochemica…
View article: A Purple Cupredoxin from <i>Nitrosopumilus maritimus</i> Containing a Mononuclear Type 1 Copper Center with an Open Binding Site
A Purple Cupredoxin from <i>Nitrosopumilus maritimus</i> Containing a Mononuclear Type 1 Copper Center with an Open Binding Site Open
Mononuclear cupredoxin proteins usually contain a coordinately saturated type 1 copper (T1Cu) center and function exclusively as electron carriers. Here we report a cupredoxin isolated from the nitrifying archaeon Nitrosopumilus maritimus …
View article: Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification
Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification Open
Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the …