Publications

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...

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...

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...

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...

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...

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-...

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...

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...

Fractionation of Organosolv Lignin Using Acetone:Water and Properties of the Obtained Fractions

Journal: ACS Sustainable Chemistry and Engineering

Lignin fractions with different molecular weight were prepared using a simple and almost green method from switchgrass and pine organosolv lignin. Different proportions of acetone in water, ranging from 30 to 60%, were used for lignin fractionation. A higher concentration of acetone dissolved higher molecular...

Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

Journal: Biotechnology for Biofuels

Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe’s growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand...

Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth

Journal: Frontiers in Microbiology

Similar to mycorrhizal mutualists, the rhizospheric and endophytic fungi are also considered to act as active regulators of host fitness (e.g., nutrition and stress tolerance). Despite considerable work in selected model systems, it is generally poorly understood how plant-associated fungi are structured in...

Plant-Derived Terpenes: A Feedstock for Specialty Biofuels

Journal: Trends in Biotechnology

Research toward renewable and sustainable energy has identified specific terpenes capable of supplementing or replacing current petroleum-derived fuels. Despite being naturally produced and stored by many plants, there are few examples of commercial recovery of terpenes from plants because of low yields. Plant...

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

Journal: Journal of Visualized Experiments

This protocol describes a new method to grow and qualitatively analyze bacterial biofilms on fungal hyphae by confocal and electron microscopy.

Surface characterization of Populus during Caldicellulosiruptor bescii growth by TOF-SIMS analysis

Journal: ACS Sustainable Chemistry and Engineering

Caldicellulosiruptor bescii is a thermophilic, anaerobic bacterium that is capable of utilizing unpretreated biomass in addition to breaking down cellulose and hemicellulose into simple sugars. Despite the fact that C. bescii must first bind to the surface of the biomass, there has been no...

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

Journal: Environmental Science and Technology

Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average...

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

Journal: Journal of Physics: Condensed Matter

Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water...

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