Center for Bio Molecular Science and Engineering

Washington, DC, United States

Center for Bio Molecular Science and Engineering

Washington, DC, United States
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Strycharz-Glaven S.M.,Center for Bio Molecular Science and Engineering | Tender L.M.,Center for Bio Molecular Science and Engineering
ChemSusChem | Year: 2012

The number of investigations involving bioelectrochemical systems (BES), processes in which microorganisms catalyze electrode reactions, is increasing while their mechanisms remain unresolved. Geobacter sulfurreducens strain DL1 is a model electrode catalyst that forms multimicrobe-thick biofilms on anodes that catalyze the oxidation of acetate to result in an electric current. Here, we report the characterization by cyclic voltammetry (CV) of DL1 biofilm-modified anodes (biofilm anodes) performed during biofilm development. This characterization, based on our recently reported model of biofilm anode catalytic activity, indicates the following. 1) As a biofilm grows, catalytic activity scales linearly with the amount of anode-accessible redox cofactor in the biofilm. This observation is consistent with a catalytic activity that is limited during biofilm growth by electron transport from within cells to the extracellular redox cofactor. 2) Distinct voltammetric features are exhibited that reflect the presence of a redox cofactor expressed by cells that initially colonize an anode that is not involved in catalytic current generation © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tender L.M.,Center for Bio Molecular Science and Engineering
MRS Bulletin | Year: 2011

Dissimilatory metal-reducing bacteria (DMRB) are a fascinating group of microorganisms that inhabit many natural environments. They possess a distinct capability wherein they can acquire energy by coupling oxidation of organic matter with reduction of insoluble oxidants such as mineral deposits. This capability requires that DMRB transfer respired electrons to their outer surface where electron transfer can occur to an insoluble oxidant. This is distinct from the dominant paradigm, wherein soluble oxidants are transported into microbes for reduction during metabolism. This unique extracellular electron transfer (EET) capability of DMRB extends to reduction of electrodes on which they can proliferate and form persistent films (biofilms). This capability makes DMRB useful as anode catalysts in microbial fuel cells for alternative energy generation and for degradation of organic wastes. In the case of Geobacter spp., anode biofilms can grow to be many microbes thick. In such biofilms, individual microbes contribute to a flux of electrons to the underlying electrode surface, which may be many cell lengths away, confounding long-held notions about the inability of microbes to engage in such long-range EET. This article describes the electrode-reducing ability of DMRB and the latest results describing the mechanism of long-range extracellular electron transfer, which appears to involve filamentous appendages termed nanowires. © 2011 Materials Research Society.

Hotzer B.,CNRS Fundamental Electronics Institute | Medintz I.L.,Center for Bio Molecular Science and Engineering | Hildebrandt N.,CNRS Fundamental Electronics Institute
Small | Year: 2012

Nanobiotechnology is one of the fastest growing and broadest-ranged interdisciplinary subfields of the nanosciences. Countless hybrid bio-inorganic composites are currently being pursued for various uses, including sensors for medical and diagnostic applications, light- and energy-harvesting devices, along with multifunctional architectures for electronics and advanced drug-delivery. Although many disparate biological and nanoscale materials will ultimately be utilized as the functional building blocks to create these devices, a common element found among a large proportion is that they exert or interact with light. Clearly continuing development will rely heavily on incorporating many different types of fluorophores into these composite materials. This review covers the growing utility of different classes of fluorophores in nanobiotechnology, from both a photophysical and a chemical perspective. For each major structural or functional class of fluorescent probe, several representative applications are provided, and the necessary technological background for acquiring the desired nano-bioanalytical information are presented. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Robertson K.L.,Center for Bio Molecular Science and Engineering
PloS one | Year: 2012

Observations of enhanced growth of melanized fungi under low-dose ionizing radiation in the laboratory and in the damaged Chernobyl nuclear reactor suggest they have adapted the ability to survive or even benefit from exposure to ionizing radiation. However, the cellular and molecular mechanism of fungal responses to such radiation remains poorly understood. Using the black yeast Wangiella dermatitidis as a model, we confirmed that ionizing radiation enhanced cell growth by increasing cell division and cell size. Using RNA-seq technology, we compared the transcriptomic profiles of the wild type and the melanin-deficient wdpks1 mutant under irradiation and non-irradiation conditions. It was found that more than 3000 genes were differentially expressed when these two strains were constantly exposed to a low dose of ionizing radiation and that half were regulated at least two fold in either direction. Functional analysis indicated that many genes for amino acid and carbohydrate metabolism and cell cycle progression were down-regulated and that a number of antioxidant genes and genes affecting membrane fluidity were up-regulated in both irradiated strains. However, the expression of ribosomal biogenesis genes was significantly up-regulated in the irradiated wild-type strain but not in the irradiated wdpks1 mutant, implying that melanin might help to contribute radiation energy for protein translation. Furthermore, we demonstrated that long-term exposure to low doses of radiation significantly increased survivability of both the wild-type and the wdpks1 mutant, which was correlated with reduced levels of reactive oxygen species (ROS), increased production of carotenoid and induced expression of genes encoding translesion DNA synthesis. Our results represent the first functional genomic study of how melanized fungal cells respond to low dose ionizing radiation and provide clues for the identification of biological processes, molecular pathways and individual genes regulated by radiation.

Algar W.R.,University of British Columbia | Kim H.,University of British Columbia | Medintz I.L.,Center for Bio Molecular Science and Engineering | Hildebrandt N.,CNRS Fundamental Electronics Institute
Coordination Chemistry Reviews | Year: 2014

Förster resonance energy transfer (FRET) configurations incorporating colloidal semiconductor quantum dots (QDs) have proven to be a valuable tool for bioanalysis and bioimaging. Mirroring well established techniques with only fluorescent dyes, "traditional" FRET configurations with QDs have involved single-step energy transfer to organic dye acceptors mediated by biomolecular interactions. Here, we review recent progress in characterizing non-traditional FRET configurations incorporating QDs and their application to challenges in biosensing, energy conversion, and fabrication of optoelectronic devices. Such non-traditional FRET configurations with QDs include substitution of organic dyes with lanthanide complexes, polypyridyl transition metal complexes, azamacrocyclic metal complexes, graphene (oxide), carbon nanotubes, gold nanoparticles, and dyes exhibiting photochromism. Other non-traditional configurations of interest include FRET relays (with or without organic dyes) that feature multiple sequential energy transfer steps, and thin films of QDs where discrete FRET pairs cannot be defined, including those where QDs are layered in a size-sequential or "rainbow" structure. The calculation of FRET efficiencies and donor-acceptor distances in the above configurations are reviewed, as are distance scaling relationships for non-zero dimensional acceptors, and the related dipolar energy transfer mechanism, nanosurface energy transfer (NSET). To illustrate the utility of non-traditional QD-FRET configurations, we highlight examples of optically switchable probes, photonic wires, time-gated and multiplexed probes for biosensing, enhanced light harvesting in QD and dye sensitized solar cells (DSSC), and colour conversion in light emitting diodes (LEDs). We close by providing a perspective on how the combined utility of these non-traditional QD-FRET configurations may be useful for engineering complex nanoscale devices in the future. © 2013 Elsevier B.V.

Melde B.J.,Center for Bio Molecular Science and Engineering | Johnson B.J.,Center for Bio Molecular Science and Engineering
Analytical and Bioanalytical Chemistry | Year: 2010

Mesoporous materials are finding increasing utility in sensing applications. These applications can benefit from a surface area that may exceed 1,000 m2 g-1 and fast diffusion of analytes through a porous structure. This article reviews recent developments in mesoporous materials-based sensing and provides examples of the impact of different surface functionality, pore structure, and macro-morphology in an attempt to illustrate the contribution of these factors to the selectivity and sensitivity of a sensor response. The materials discussed include ordered mesoporous silicates synthesized with surfactants, hard templated ordered mesoporous carbons, and metal oxides with porous textures which have been applied to advantage in various detection schemes. Chemical functionalization of mesoporous materials through silane grafting, co-condensation, and adsorption are also addressed. © 2010 US Government.

Johnson B.J.,Center for Bio Molecular Science and Engineering | Russ Algar W.,University of British Columbia | Malanoski A.P.,Center for Bio Molecular Science and Engineering | Ancona M.G.,Washington Technology | Medintz I.L.,Center for Bio Molecular Science and Engineering
Nano Today | Year: 2014

The ability of enzymes to catalyze reactions and engage in complex syntheses has long made them attractive for use in a multitude of industrial, biotechnological, and research applications. Although this utility grows with each passing year, the exploitation of enzymes in ex vivo formats is still hampered by relatively low rates of turnover, particularly when attached to planar surfaces. However, a growing number of reports suggest that assembling enzymes or their substrates onto nanoparticle (NP) surfaces can accelerate or otherwise improve catalysis when compared to freely diffusing enzyme in bulk solution. Here, we present an in-depth review and discussion of what is currently known about this phenomenon with an emphasis on inorganic NPs. The assembly of enzyme-NP and substrate-NP bioconjugates is first described, emphasizing their heterogeneity and the expected impact on enzymatic activity within the framework of collision theory, biomolecular interactions, and the classic Michaelis-Menten model. We next discuss representative examples from the literature where accelerated enzyme activity has been reported in conjunction with NP materials, the mechanisms that have been proposed to account for the accelerated activity, and the challenges that remain to fully understand and optimize this potentially valuable phenomenon. Finally, approaches to quantitative modeling of NP-associated enzyme activity are discussed, including a kinetic analysis that we suggest can provide insight into the underlying mechanisms that may drive the observed rate enhancements. We conclude with a perspective on the future evolution and broader impact of this growing area of nanoresearch.

Gemill K.B.,Center for Bio Molecular Science and Engineering
Nature Nanotechnology | Year: 2016

Understanding the relationships between the physicochemical properties of engineered nanomaterials and their toxicity is critical for environmental and health risk analysis. However, this task is confounded by material diversity, heterogeneity of published data and limited sampling within individual studies. Here, we present an approach for analysing and extracting pertinent knowledge from published studies focusing on the cellular toxicity of cadmium-containing semiconductor quantum dots. From 307 publications, we obtain 1,741 cell viability-related data samples, each with 24 qualitative and quantitative attributes describing the material properties and experimental conditions. Using random forest regression models to analyse the data, we show that toxicity is closely correlated with quantum dot surface properties (including shell, ligand and surface modifications), diameter, assay type and exposure time. Our approach of integrating quantitative and categorical data provides a roadmap for interrogating the wide-ranging toxicity data in the literature and suggests that meta-analysis can help develop methods for predicting the toxicity of engineered nanomaterials. © 2016 Nature Publishing Group

Strycharz-Glaven S.M.,Center for Bio Molecular Science and Engineering | Tender L.M.,Center for Bio Molecular Science and Engineering
Energy and Environmental Science | Year: 2012

Geobacter sulfurreducens can acquire energy by coupling oxidation of acetate with extracellular electron transfer to an anode, forming an electrically conductive biofilm extending many cell lengths away from the anode surface. Owing to their conductivity, such biofilms may play important roles in emerging technologies referred to as bioelectrochemical systems (BES). In these systems, microbes are used to catalyze anode processes for which abiotic catalysts do not exist, such as wastewater treatment and energy generation from biomass by fuel cells. Two models describing the conductive nature of G. sulfurreducens biofilms grown on anodes (biofilm anodes) have recently been put forth; superexchange proposed by our group, recently published in Energy and Environmental Science, which invokes electron-transfer among a network of cytochromes, and metallic-like conductivity proposed by Malvankar et al., recently published in Nature Nanotechnology, which invokes intrinsic conductivity of certain secreted microbial filaments referred to as nanowires. Here, we respond to criticisms raised by Malvankar et al. in the preceding commentary concerning superexchange. © 2012 The Royal Society of Chemistry.

Robertson K.L.,Center for Bio Molecular Science and Engineering
Journal of visualized experiments : JoVE | Year: 2012

Fluorescence in situ hybridization (FISH) is a powerful technique that is used to detect and localize specific nucleic acid sequences in the cellular environment. In order to increase throughput, FISH can be combined with flow cytometry (flow-FISH) to enable the detection of targeted nucleic acid sequences in thousands of individual cells. As a result, flow-FISH offers a distinct advantage over lysate/ensemble-based nucleic acid detection methods because each cell is treated as an independent observation, thereby permitting stronger statistical and variance analyses. These attributes have prompted the use of FISH and flow-FISH methods in a number of different applications and the utility of these methods has been successfully demonstrated in telomere length determination, cellular identification and gene expression, monitoring viral multiplication in infected cells, and bacterial community analysis and enumeration. Traditionally, the specificity of FISH and flow-FISH methods has been imparted by DNA oligonucleotide probes. Recently however, the replacement of DNA oligonucleotide probes with nucleic acid analogs as FISH and flow-FISH probes has increased both the sensitivity and specificity of each technique due to the higher melting temperatures (T(m)) of these analogs for natural nucleic acids. Locked nucleic acid (LNA) probes are a type of nucleic acid analog that contain LNA nucleotides spiked throughout a DNA or RNA sequence. When coupled with flow-FISH, LNA probes have previously been shown to outperform conventional DNA probes and have been successfully used to detect eukaryotic mRNA and viral RNA in mammalian cells. Here we expand this capability and describe a LNA flow-FISH method which permits the specific detection of RNA in bacterial cells (Figure 1). Specifically, we are interested in the detection of small non-coding regulatory RNA (sRNA) which have garnered considerable interest in the past few years as they have been found to serve as key regulatory elements in many critical cellular processes. However, there are limited tools to study sRNAs and the challenges of detecting sRNA in bacterial cells is due in part to the relatively small size (typically 50-300 nucleotides in length) and low abundance of sRNA molecules as well as the general difficulty in working with smaller biological cells with varying cellular membranes. In this method, we describe fixation and permeabilzation conditions that preserve the structure of bacterial cells and permit the penetration of LNA probes as well as signal amplification steps which enable the specific detection of low abundance sRNA (Figure 2). Copyright © 2012 Creative Commons Attribution License

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