Publications

Publications

Reproductive Microbiomes: Using the Microbiome as a Novel Diagnostic Tool for Endometriosis

Journal: Reproductive Immunology

Background: Endometriosis is a chronic inflammatory disease which results in significant pain and long term reproductive consequences for up to 50% of infertile women. This study was focused to understand how endometriosis altered the uterine and cervical bacterial community. Methods and findings: Urogenital swabs and...

Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil

Journal: Nature Ecology & Evolution

Phosphorus is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting phosphorus deficiency at the gene and protein levels remains unknown. Here, we report a metagenomic and metaproteomic comparison of microbial communities in phosphorus-deficient and phosphorus-rich...

"To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation

Journal: CellPress

Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in...

Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis

Journal: ACS Catalysis

The emergence and dissemination of bacterial resistance to β-lactam antibiotics via β-lactamase enzymes is a serious problem in clinical settings, often leaving few treatment options for infections resulting from multidrug-resistant superbugs. Understanding the catalytic mechanism of β-lactamases is important for...

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

Journal: American Society for Microbiology

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis, the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-...

Molecular Insights into Arctic Soil Organic Matter Degradation under Warming

Journal: Environmental Science & Technology

Molecular composition of the Arctic soil organic carbon (SOC) and its susceptibility to microbial degradation are uncertain due to heterogeneity and unknown SOC compositions. Using ultrahigh-resolution mass spectrometry, we determined the susceptibility and compositional changes of extractable dissolved organic matter...

A 5-enolpyruvylshikimate 3-phosphate synthase functions as a transcriptional repressor in Populus

Journal: The Plant Cell

Long-lived perennial plants, with distinctive habits of inter-annual growth, defense, and physiology, are of great economic and ecological importance. However, some biological mechanisms resulting from genome duplication and functional divergence of genes in these systems remain poorly studied. Here, we discovered an...

Polarization- and wavelength-resolved near-field imaging of complex plasmonic modes in Archimedean nanospirals

Journal: OSA Publishing

Asymmetric nanophotonic structures enable a wide range of opportunities in optical nanotechnology because they support efficient optical nonlinearities mediated by multiple plasmon resonances over a broad spectral range. The Archimedean nanospiral is a canonical example of a chiral plasmonic structure because it...

Robust Mercury Methylation across Diverse Methanogenic Archaea

Journal: American Society for Microbiology

Methylmercury (MeHg) production was compared among nine cultured methanogenic archaea that contain hgcAB, a gene pair that codes for mercury (Hg) methylation. The methanogens tested produced MeHg at inherently different rates, even when normalized to growth rate and Hg availability. Eight of the nine tested were...

Chemical nature of ferroelastic twin domains in CH3NH3PbI3 perovskite

Journal: Nature Materials

The extraordinary optoelectronic performance of hybrid organic–inorganic perovskites has resulted in extensive efforts to unravel their properties. Recently, observations of ferroic twin domains in methylammonium lead triiodide drew significant attention as a possible explanation for the current–voltage hysteretic...

Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree

Journal: PNAS

Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases typically relies on breeding programs that can take decades to complete. To demonstrate how this process can be accelerated,...

Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides)

Journal: New Phytologist Trust

While recent reports demonstrate that the direct emission of methane from living tree trunks may be a significant terrestrial emission source, there has been debate whether tree emissions are due to transport from soils or produced in the wood environment itself. Reports of methanogens from wood of trees were...

Impact of hydration and temperature history on the structure and dynamics of lignin

Journal: Royal Society of Chemistry

The full utilization of plant biomass for the production of energy and novel materials often involves high temperature treatment. Examples include melt spinning of lignin for manufacturing low-cost carbon fiber and the relocalization of lignin to increase the accessibility of cellulose for production of biofuels....

Construction and optimization of a heterologous pathway for protocatechuate catabolism in Escherichia coli enables bioconversion of model aromatic compounds

Journal: American Society for Microbiology Applied and Environmental Microbiology

The production of biofuels from lignocellulose yields a substantial lignin byproduct stream that currently has few applications. Biological conversion of lignin-derived compounds into chemicals and fuels has the potential to improve the economics of lignocellulose-derived biofuels, but few microbes are able both to...

Root and Phizosphere Bacterial Phosphatase Activity Varies with Tree Species and Soil Phosphorus Availability in Puerto Rico Tropical Forest

Journal: Frontiers in Plant Science

Climatic conditions in tropical forests combined with the immobility of phosphorus due to sorption on mineral surfaces or result in soils typically lacking in the form of phosphorus (orthophosphate) most easily metabolized by plants and microbes. In these soils, mineralization of organic phosphorus can be the major...

The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project

Journal: New Phytologist

Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even ‘extend’ to influence community structure and ecosystem level processes.Progress in this area is limited to model systems with deep...

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Journal: Nature Communications

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3...

Purinyl-cobamide is a native prosthetic group of reductive dehalogenases

Journal: Nature Chemical Biology

Cobamides such as vitamin B12 are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In organohalide respiration, a vital biological process for the global cycling of natural and anthropogenic organohalogens, cobamides are the requisite...

Structural relaxation, viscosity, and network connectivity in a hydrogen bonding liquid

Journal: Physical Chemistry Chemical Physics

In liquids, the ability of neighboring molecules to rearrange and jostle past each other is directly related to viscosity, the property which describes the propensity to flow. The presence of hydrogen bonds (H-bonds) complicates the molecular scale picture of viscosity. H-Bonds are attractive, directional interactions...

Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme

Journal: nautre communications

Enzymes dependent on pyridoxal 5′-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing...

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