Open Access. Powered by Scholars. Published by Universities.®

Biomedical Engineering and Bioengineering Commons

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 16 of 16

Full-Text Articles in Biomedical Engineering and Bioengineering

Genome Sequence Of The Psychrophilic Deep-Sea Bacterium Moritella Marina Mp-1 (Atcc 15381), Kumar Babu Kautharapu, Laura R. Jarboe Nov 2012

Genome Sequence Of The Psychrophilic Deep-Sea Bacterium Moritella Marina Mp-1 (Atcc 15381), Kumar Babu Kautharapu, Laura R. Jarboe

Chemical and Biological Engineering Publications

Moritella marina MP-1 is a bacterial species known for its production of docosahexaenoic acid. We present the draft genome sequence of the type strainMoritella marina MP-1 (ATCC 15381), having 4,636,778 bp with a G+C content of 40.5% and consisting of 83 contigs.


Metabolic Engineering Of Biocatalysts For Carboxylic Acids Production, Ping Liu, Laura R. Jarboe Oct 2012

Metabolic Engineering Of Biocatalysts For Carboxylic Acids Production, Ping Liu, Laura R. Jarboe

Chemical and Biological Engineering Publications

Fermentation of renewable feedstocks by microbes to produce sustainable fuels and chemicals has the potential to replace petrochemical-based production. For example, carboxylic acids produced by microbial fermentation can be used to generate primary building blocks of industrial chemicals by either enzymatic or chemical catalysis. In order to achieve the titer, yield and productivity values required for economically viable processes, the carboxylic acid-producing microbes need to be robust and wellperforming. Traditional strain development methods based on mutagenesis have proven useful in the selection of desirable microbial behavior, such as robustness and carboxylic acid production. On the other hand, rationally-based metabolic engineering ...


Structural Classification Of Biotin Carboxyl Carrier Proteins, Yingfei Chen, Armando Elizondo-Noriega, David C. Cantu, Peter J. Reilly Oct 2012

Structural Classification Of Biotin Carboxyl Carrier Proteins, Yingfei Chen, Armando Elizondo-Noriega, David C. Cantu, Peter J. Reilly

Chemical and Biological Engineering Publications

We gathered primary and tertiary structures of acyl-CoA carboxylases from public databases, and established that members of their biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains occur in one family each and that members of their carboxyl transferase (CT) domains occur in two families. Protein families have members similar in primary and tertiary structure that probably have descended from the same protein ancestor. The BCCP domains complexed with biotin in acyl and acyl-CoA carboxylases transfer bicarbonate ions from BC domains to CT domains, enabling the latter to carboxylate acyl and acyl-CoA moieties. We separated the BCCP domains into ...


Optimization Of Enzyme Parameters For Fermentative Production Of Biorenewable Fuels And Chemicals, Laura R. Jarboe, Ping Liu, Kumar Babu Kautharapu, Lonnie O. Ingram Oct 2012

Optimization Of Enzyme Parameters For Fermentative Production Of Biorenewable Fuels And Chemicals, Laura R. Jarboe, Ping Liu, Kumar Babu Kautharapu, Lonnie O. Ingram

Chemical and Biological Engineering Publications

Microbial biocatalysts such as Escherichia coli and Saccharomyces cerevisiae have been extensively subjected to Metabolic Engineering for the fermentative production of biorenewable fuels and chemicals. This often entails the introduction of new enzymes, deletion of unwanted enzymes and efforts to fine-tune enzyme abundance in order to attain the desired strain performance. Enzyme performance can be quantitatively described in terms of the Michaelis-Menten type parameters Km, turnover number kcat and Ki, which roughly describe the affinity of an enzyme for its substrate, the speed of a reaction and the enzyme sensitivity to inhibition by regulatory molecules. Here we describe examples of ...


Docking Studies On Glycoside Hydrolase Family 47 Endoplasmic Reticulum Α-(1→2)-Mannosidase I To Elucidate The Pathway To The Substrate Transition State, Chandrika Mulakala, Wim Nerinckx, Peter J. Reilly Sep 2012

Docking Studies On Glycoside Hydrolase Family 47 Endoplasmic Reticulum Α-(1→2)-Mannosidase I To Elucidate The Pathway To The Substrate Transition State, Chandrika Mulakala, Wim Nerinckx, Peter J. Reilly

Chemical and Biological Engineering Publications

α-(1→2)-Mannosidase I from the endoplasmic reticulum (ERManI), a Family 47 glycoside hydrolase, is a key enzyme in the N-glycan synthesis pathway. Catalytic-domain crystal structures of yeast and human ERMan1s have been determined, the former with a hydrolytic product and the latter without ligands, with the inhibitors 1-deoxymannojirimycin and kifunensine, and with a thiodisaccharide substrate analog. Both inhibitors were bound at the base of the funnel-shaped active site as the unusual 1C4 conformer, while the substrate analog glycon is a 3S1 conformer. In the current study, AutoDock was used to dock α-d-mannopyranosyl-(1 ...


Combinatorial Synthesis Of And High-Throughput Protein Release From Polymer Film And Nanoparticle Libraries, Latrisha K. Petersen, Ana Vianey Chavez-Santoscoy, Balaji Narasimhan Sep 2012

Combinatorial Synthesis Of And High-Throughput Protein Release From Polymer Film And Nanoparticle Libraries, Latrisha K. Petersen, Ana Vianey Chavez-Santoscoy, Balaji Narasimhan

Chemical and Biological Engineering Publications

Polyanhydrides are a class of biomaterials with excellent biocompatibility and drug delivery capabilities. While they have been studied extensively with conventional one-sample-at-a-time synthesis techniques, a more recent high-throughput approach has been developed enabling the synthesis and testing of large libraries of polyanhydrides(1). This will facilitate more efficient optimization and design process of these biomaterials for drug and vaccine delivery applications. The method in this work describes the combinatorial synthesis of biodegradable polyanhydride film and nanoparticle libraries and the high-throughput detection of protein release from these libraries. In this robotically operated method (Figure 1), linear actuators and syringe pumps are ...


High-Throughput Synthesis Of Carbohydrates And Functionalization Of Polyanhydride Nanoparticles, Brenda Rocio Carrillo-Conde, Rajarshi Roychoudhury, Ana Vianey Chavez-Santoscoy, Balaji Narasimhan, Nicola L.B. Pohl Jul 2012

High-Throughput Synthesis Of Carbohydrates And Functionalization Of Polyanhydride Nanoparticles, Brenda Rocio Carrillo-Conde, Rajarshi Roychoudhury, Ana Vianey Chavez-Santoscoy, Balaji Narasimhan, Nicola L.B. Pohl

Chemical and Biological Engineering Publications

Transdisciplinary approaches involving areas such as material design, nanotechnology, chemistry, and immunology have to be utilized to rationally design efficacious vaccines carriers. Nanoparticle-based platforms can prolong the persistence of vaccine antigens, which could improve vaccine immunogenicity 1. Several biodegradable polymers have been studied as vaccine delivery vehicles 1; in particular, polyanhydride particles have demonstrated the ability to provide sustained release of stable protein antigens and to activate antigen presenting cells and modulate immune responses 2-12. The molecular design of these vaccine carriers needs to integrate the rational selection of polymer properties as well as the incorporation of appropriate targeting agents ...


Harvesting Murine Alveolar Macrophages And Evaluating Cellular Activation Induced By Polyanhydride Nanoparticles., Ana Vianey Chavez-Santoscoy, Lucas Mark Huntimer, Amanda Ellen Ramer-Tait, Michael J. Wannemuehler, Balaji Narasimhan Jun 2012

Harvesting Murine Alveolar Macrophages And Evaluating Cellular Activation Induced By Polyanhydride Nanoparticles., Ana Vianey Chavez-Santoscoy, Lucas Mark Huntimer, Amanda Ellen Ramer-Tait, Michael J. Wannemuehler, Balaji Narasimhan

Chemical and Biological Engineering Publications

Biodegradable nanoparticles have emerged as a versatile platform for the design and implementation of new intranasal vaccines against respiratory infectious diseases. Specifically, polyanhydride nanoparticles composed of the aliphatic sebacic acid (SA), the aromatic 1,6-bis(p-carboxyphenoxy)hexane (CPH), or the amphiphilic 1,8-bis(p-carboxyphenoxy)-3,6-dioxaoctane (CPTEG) display unique bulk and surface erosion kinetics and can be exploited to slowly release functional biomolecules (e.g., protein antigens, immunoglobulins, etc.) in vivo. These nanoparticles also possess intrinsic adjuvant activity, making them an excellent choice for a vaccine delivery platform. In order to elucidate the mechanisms governing the activation of innate immunity ...


Mixed-Surface, Lipid-Tethered Quantum Dots For Targeting Cells And Tissues, Yanjie Zhang, Amanda Haage, Elizabeth M. Whitley, Ian C. Schneider, Aaron R. Clapp Jun 2012

Mixed-Surface, Lipid-Tethered Quantum Dots For Targeting Cells And Tissues, Yanjie Zhang, Amanda Haage, Elizabeth M. Whitley, Ian C. Schneider, Aaron R. Clapp

Chemical and Biological Engineering Publications

Quantum dots (QDs), with their variable luminescent properties, are rapidly transcending traditional labeling techniques in biological imaging and hold vast potential for biosensing applications. An obstacle in any biosensor development is targeted specificity. Here we report a facile procedure for creating QDs targeted to the cell membrane with the goal of cell-surface protease biosensing. This procedure generates water-soluble QDs with variable coverage of lipid functional groups. The resulting hydrophobicity is quantitatively controlled by the molar ratio of lipids per QD. Appropriate tuning of the hydrophobicity ensures solubility in common aqueous cell culture media and while providing affinity to the lipid ...


Analyzing Cellular Internalization Of Nanoparticles And Bacteria By Multi-Spectral Imaging Flow Cytometry., Yashdeep Phanse, Amanda Ellen Ramer-Tait, Sherree L. Friend, Brenda Rocio Carrillo-Conde, Paul A. Lueth, Carrie Jo Oster, Gregory J. Phillips, Balaji Narasimhan, Michael J. Wannemuehler, Bryan H. Bellaire Jun 2012

Analyzing Cellular Internalization Of Nanoparticles And Bacteria By Multi-Spectral Imaging Flow Cytometry., Yashdeep Phanse, Amanda Ellen Ramer-Tait, Sherree L. Friend, Brenda Rocio Carrillo-Conde, Paul A. Lueth, Carrie Jo Oster, Gregory J. Phillips, Balaji Narasimhan, Michael J. Wannemuehler, Bryan H. Bellaire

Chemical and Biological Engineering Publications

Nanoparticulate systems have emerged as valuable tools in vaccine delivery through their ability to efficiently deliver cargo, including proteins, to antigen presenting cells. Internalization of nanoparticles (NP) by antigen presenting cells is a critical step in generating an effective immune response to the encapsulated antigen. To determine how changes in nanoparticle formulation impact function, we sought to develop a high throughput, quantitative experimental protocol that was compatible with detecting internalized nanoparticles as well as bacteria. To date, two independent techniques, microscopy and flow cytometry, have been the methods used to study the phagocytosis of nanoparticles. The high throughput nature of ...


Organic Materials And Organic/Inorganic Heterostructures In Atom Probe Tomography, Derk Joester, Andrew C. Hillier, Yi Zhang, Ty J. Prosa May 2012

Organic Materials And Organic/Inorganic Heterostructures In Atom Probe Tomography, Derk Joester, Andrew C. Hillier, Yi Zhang, Ty J. Prosa

Chemical and Biological Engineering Publications

Nano-scale organic/inorganic interfaces are key to a wide range of materials. In many biominerals, for instance bone or teeth, outstanding fracture toughness and wear resistance can be attributed to buried organic/inorganic interfaces. Organic/inorganic interfaces at very small length scales are becoming increasingly important also in nano and electronic materials. For example, functionalized inorganic nanomaterials have great potential in biomedicine or sensing applications. Thin organic films are used to increase the conductivity of LiFePO4 electrodes in lithium ion batteries, and solid electrode interphases (SEI) form by uncontrolled electrolyte decomposition. Organics play a key role in dye-sensitized solar cells ...


Amphiphilic Polyanhydride Nanoparticles Stabilize Bacillus Anthracis Protective Antigen, L. K. Petersen, Yashdeep Phanse, Amanda Ellen Ramer-Tait, Michael J. Wannemuehler, Balaji Narasimhan Jan 2012

Amphiphilic Polyanhydride Nanoparticles Stabilize Bacillus Anthracis Protective Antigen, L. K. Petersen, Yashdeep Phanse, Amanda Ellen Ramer-Tait, Michael J. Wannemuehler, Balaji Narasimhan

Chemical and Biological Engineering Publications

Advancements toward an improved vaccine against Bacillus anthracis, the causative agent of anthrax, have focused on formulations composed of the protective antigen (PA) adsorbed to aluminum hydroxide. However, due to the labile nature of PA, antigen stability is a primary concern for vaccine development. Thus, there is a need for a delivery system capable of preserving the immunogenicity of PA through all the steps of vaccine fabrication, storage, and administration. In this work, we demonstrate that biodegradable amphiphilic polyanhydride nanoparticles, which have previously been shown to provide controlled antigen delivery, antigen stability, immune modulation, and protection in a single dose ...


Production Of 5-Hydroxymethylfurfural From Glucose Using A Combination Of Lewis And Brønsted Acid Catalysts In Water In A Biphasic Reactor With An Alkylphenol Solvent, Yomaira J. Pagan-Torres, Tianfu Wang, Jean Marcel R. Gallo, Brent H. Shanks, James A. Dumesic Jan 2012

Production Of 5-Hydroxymethylfurfural From Glucose Using A Combination Of Lewis And Brønsted Acid Catalysts In Water In A Biphasic Reactor With An Alkylphenol Solvent, Yomaira J. Pagan-Torres, Tianfu Wang, Jean Marcel R. Gallo, Brent H. Shanks, James A. Dumesic

Chemical and Biological Engineering Publications

We report the catalytic conversion of glucose in high yields (62%) to 5-hydroxymethylfurfural (HMF), a versatile platform chemical. The reaction system consists of a Lewis acid metal chloride (e.g., AlCl 3) and a Bronsted acid (HCl) in a biphasic reactor consisting of water and an alkylphenol compound (2-sec-butylphenol) as the organic phase. The conversion of glucose in the presence of Lewis and Bronsted acidity proceeds through a tandem pathway involving isomerization of glucose to fructose, followed by dehydration of fructose to HMF. The organic phase extracts 97% of the HMF produced, while both acid catalysts remain in the aqueous ...


Block Copolymer-Quantum Dot Micelles For Multienzyme Colocalization, Feng Jia, Yanjie Zhang, Balaji Narasimhan, Surya K. Mallapragada Jan 2012

Block Copolymer-Quantum Dot Micelles For Multienzyme Colocalization, Feng Jia, Yanjie Zhang, Balaji Narasimhan, Surya K. Mallapragada

Chemical and Biological Engineering Publications

To mimic the structure and functionality of multienzyme complexes, which are widely present in Nature, Pluronic-based micelles were designed to colocalize multiple enzymes. To stabilize the micelles as well as to enable characterization of single enzyme immobilization and multienzyme colocalization by Förster resonance energy transfer (FRET), quantum dots (QDs) were incorporated into the micelles to form Pluronic-QD micelles using a novel microreactor. Model enzymes glucose oxidase (GOX) and horseradish peroxidase (HRP) were respectively labeled with fluorescent dyes. The results indicated that FRET occurred between the QDs and dyes that labeled each type of enzyme in single enzyme immobilization studies ...


Resonance Quenching And Guided Modes Arising From The Coupling Of Surface Plasmons With A Molecular Resonance, Wei-Hsun Yeh, Joseph W. Petefish, Andrew C. Hillier Jan 2012

Resonance Quenching And Guided Modes Arising From The Coupling Of Surface Plasmons With A Molecular Resonance, Wei-Hsun Yeh, Joseph W. Petefish, Andrew C. Hillier

Chemical and Biological Engineering Publications

In this paper, we describe experimental and modeling results that illucidate the nature of coupling between surface plasmon polaritons in a thin silver film with the molecular resonance of a zinc phthalocyanine dye film. This coupling leads to several phenomena not generally observed when plasmons are coupled to transparent materials. The increased absorption coefficient near a molecular resonance leads to a discontinuity in the refractive index, which causes branching of the plasmon resonance condition and the appearance of two peaks in the p-polarized reflectance spectrum. A gap exists between these peaks in the region of the spectrum associated with the ...


Dendrimer-Fullerenol Soft-Condensed Nanoassembly, Priyanka Bhattacharya, Seung Ha Kim, Pengyu Chen, Ran Chen, Anne M. Spuches, Jared M. Brown, Monica H. Lamm, Pu Chun Ke Jan 2012

Dendrimer-Fullerenol Soft-Condensed Nanoassembly, Priyanka Bhattacharya, Seung Ha Kim, Pengyu Chen, Ran Chen, Anne M. Spuches, Jared M. Brown, Monica H. Lamm, Pu Chun Ke

Chemical and Biological Engineering Publications

Nanoscale assembly is an area of research that has vast implications for molecular design, sensing, nanofabrication, supramolecular chemistry, catalysis, and environmental remediation. Here we show that poly(amidoamine) (PAMAM) dendrimers of both generations 1 (G1) and 4 (G4) can host 1 fullerenol per 2 dendrimer primary amines as evidenced by isothermal titration calorimetry, dynamic light scattering, and spectrofluorometry. Thermodynamically, the interactions were similarly spontaneous between both generations of dendrimers and fullerenols, however, G4 formed stronger complexes with fullerenols resulting from their higher surface charge density and more internal voids, as demonstrated by spectrofluorometry. In addition to hydrogen bonding that existed ...