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...

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...

Transgenic switch grass (Panicum virgatum L.) targeted for reduced recalcitrance to bioconversion: a 2-year comparative analysis of field grown lines modified for target gene or genetic element expression

Journal: Plant Biotechnology Journal

Transgenic Panicum virgatum L. silencing (KD) or over-expressing (OE) specific genes or a small RNA (GAUT4-KD, miRNA156-OE, MYB4-OE, COMT-KD and FPGS-KD) were grown in the field and aerial tissue analyzed for biofuel production traits. Clones representing independent transgenic lines were established and senesced...

An In-Depth Understanding of Biomass Recalcitrance Using Natural Poplar Variants as the Feedstock

Journal: ChemSusChem

In an effort to better understand the biomass recalcitrance, six natural poplar variants were selected as feedstocks based on previous sugar release analysis. Compositional analysis and physicochemical characterizations of these poplars were performed and the correlations between these physicochemical properties and...

A new method for qualitative multi-scale analysis of bacterial biofilms on filamentous fungal colonies using confocal and electron microscopy

Journal: JOVE

A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy

Comparison of autohydrolysis and ionic liquid 1-butyl-3-methylimidazolium acetate pretreatment to enhance enzymatic hydrolysis of sugarcane bagasse

Journal: Bioresource Technology

The aim of this work was to evaluate the efficiency of an ionic liquid (IL) 1-butyl-3-methylimidazolium acetate ([C4mim][OAc]) pretreatment (110 °C for 30 min) in comparison to high severity autohydrolysis pretreatment in terms of delignification, cellulose crystallinity and enzymatic digestibility. The increase in...

Study of traits and recalcitrance reduction of field-grown COMT down-regulated switchgrass

Journal: Biotechnology for Biofuels

The native recalcitrance of plants hinders the biomass conversion process using current biorefinery techniques. Down-regulation of the caffeic acid O-methyltransferase (COMT) gene in the lignin biosynthesis pathway of switchgrass reduced the thermochemical and biochemical conversion recalcitrance of biomass. Due to...

The extent of fermentative transformation of phenolic compounds in the bioanode controls exoelectrogenic activity in a microbial electrolysis cell

Journal: Water Research

Phenolic compounds in hydrolysate/pyrolysate and wastewater streams produced during the pretreatment of lignocellulosic biomass for biofuel production present a significant challenge in downstream processes. Bioelectrochemical systems are increasingly recognized as an alternative technology to handle biomass-derived...

Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cycteinexigens

Journal: Environmental Microbiology

Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi...

Identification of Mercury and Dissolved Organic Matter Complexes Using Ultrahigh Resolution Mass Spectrometry

Journal: Environmental Science and Technology Letters

The chemical speciation and bioavailability of mercury (Hg) is markedly influenced by its complexation with naturally dissolved organic matter (DOM) in aquatic environments. To date, however, analytical methodologies capable of identifying such complexes are scarce. Here, we utilize ultrahigh resolution Fourier...

Effects of Lignin Structure on Hydrodeoxygenation Reactivity of Pine Wood Lignin to Valuable Chemicals

Journal: ACS Sustainable Chemistry and Engineering

Hydrodeoxygenation (HDO) of two dilute acid flowthrough pretreated softwood lignin samples, including residual lignin in pretreated solid residues (ReL) and recovered insoluble lignin in pretreated liquid (RISL), with apparent different physical and chemical structures, was comprehensively studied. A combination of...

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