Articles

Designing and engineering evolutionary robust genetic circuits

One problem with engineered genetic circuits in synthetic microbes is their stability over evolutionary time in the absence of selective pressure. Since design of a selective environment for maintaining functi...

Authors: Sean C Sleight, Bryan A Bartley, Jane A Lieviant and Herbert M Sauro

Environment-sensitive behavior of fluorescent molecular rotors

Molecular rotors are a group of fluorescent molecules that form twisted intramolecular charge transfer (TICT) states upon photoexcitation. When intramolecular twisting occurs, the molecular rotor returns to th...

Authors: Mark A Haidekker and Emmanuel A Theodorakis

A synthetic three-color scaffold for monitoring genetic regulation and noise

Current methods for analyzing the dynamics of natural regulatory networks, and quantifying synthetic circuit function, are limited by the lack of well-characterized genetic measurement tools. Fluorescent repor...

Authors: Robert Sidney Cox III, Mary J Dunlop and Michael B Elowitz

Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system

A large amount of recombinant proteins can be synthesized in a few hours with Escherichia coli cell-free expression systems based on bacteriophage transcription. These cytoplasmic extracts are used in many applic...

Authors: Jonghyeon Shin and Vincent Noireaux

Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70

Escherichia coli cell-free expression systems use bacteriophage RNA polymerases, such as T7, to synthesize large amounts of recombinant proteins. These systems are used for many applications in biotechnology, suc...

Authors: Jonghyeon Shin and Vincent Noireaux

Four suggestions for addressing public concern regarding synthetic biology

The following essay was written by Mr. Alex Hatch, a junior undergraduate student majoring in Biological Engineering at Utah State University. Mr. Hatch submitted a 1000-1200 word essay to the 5^th Annual Bioethic...

Authors: Alex David Hatch

A positive feedback-based gene circuit to increase the production of a membrane protein

Membrane proteins are an important class of proteins, playing a key role in many biological processes, and are a promising target in pharmaceutical development. However, membrane proteins are often difficult t...

Authors: Karan Bansal, Ke Yang, Goutam J Nistala, Robert B Gennis and Kaustubh D Bhalerao

Polarized light based scheme to monitor column performance in a continuous foam fractionation column

A polarized light scattering technique was used to monitor the performance of a continuously operated foam fractionation process. The S₁₁ and S₁₂ parameters, elements of the light scattering matrix, combined toge...

Authors: Janakiraman N Swamy, Czarena L Crofcheck and MP Mengüç

A modular positive feedback-based gene amplifier

Positive feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical cir...

Authors: Goutam J Nistala, Kang Wu, Christopher V Rao and Kaustubh D Bhalerao

Insulation of a synthetic hydrogen metabolism circuit in bacteria

The engineering of metabolism holds tremendous promise for the production of desirable metabolites, particularly alternative fuels and other highly reduced molecules. Engineering approaches must redirect the t...

Authors: Christina M Agapakis, Daniel C Ducat, Patrick M Boyle, Edwin H Wintermute, Jeffrey C Way and Pamela A Silver

Chitosan nanoparticle-based neuronal membrane sealing and neuroprotection following acrolein-induced cell injury

The highly reactive aldehyde acrolein is a very potent endogenous toxin with a long half-life. Acrolein is produced within cells after insult, and is a central player in slow and progressive "secondary injury"...

Authors: Youngnam Cho, Riyi Shi and Richard Ben Borgens

BglBricks: A flexible standard for biological part assembly

Standard biological parts, such as BioBricks™ parts, provide the foundation for a new engineering discipline that enables the design and construction of synthetic biological systems with a variety of applicati...

Authors: JChristopher Anderson, John E Dueber, Mariana Leguia, Gabriel C Wu, Jonathan A Goler, Adam P Arkin and Jay D Keasling

Antimicrobial effect of silver-impregnated cellulose: potential for antimicrobial therapy

Silver has long been known to have antimicrobial activity. To incorporate this property into multiple applications, a silver-impregnated cellulose (SIC) with low cytotoxicity to human cells was developed. SIC ...

Authors: Juyoung Kim, Soonjo Kwon and Erik Ostler

TinkerCell: modular CAD tool for synthetic biology

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and bio...

Authors: Deepak Chandran, Frank T Bergmann and Herbert M Sauro

Fluorometric determination of ethidium bromide efflux kinetics in Escherichia coli

Efflux pump activity has been associated with multidrug resistance phenotypes in bacteria, compromising the effectiveness of antimicrobial therapy. The development of methods for the early detection and quanti...

Authors: Laura Paixão, Liliana Rodrigues, Isabel Couto, Marta Martins, Pedro Fernandes, Carla CCR de Carvalho, Gabriel A Monteiro, Filipe Sansonetty, Leonard Amaral and Miguel Viveiros

Puncture mechanics of cnidarian cnidocysts: a natural actuator

Cnidocysts isolated from cnidarian organisms are attractive as a drug-delivery platform due to their fast, efficient delivery of toxins. The cnidocyst could be utilized as the means to deliver therapeutics in ...

Authors: Shawn C Oppegard, Peter A Anderson and David T Eddington

Grand challenges for biological engineering

Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE) released a doc...

Authors: Jeong-Yeol Yoon and Mark R Riley

A switchable light-input, light-output system modelled and constructed in yeast

Advances in synthetic biology will require spatio-temporal regulation of biological processes in heterologous host cells. We develop a light-switchable, two-hybrid interaction in yeast, based upon the Arabidop...

Authors: Oxana Sorokina, Anita Kapus, Kata Terecskei, Laura E Dixon, Laszlo Kozma-Bognar, Ferenc Nagy and Andrew J Millar

Engineering and validation of a novel lipid thin film for biomembrane modeling in lipophilicity determination of drugs and xenobiotics

Determination of lipophilicity as a tool for predicting pharmacokinetic molecular behavior is limited by the predictive power of available experimental models of the biomembrane. There is current interest, the...

Authors: Sunday Olakunle Idowu, Morenikeji Ambali Adeyemo and Udochi Ihechiluru Ogbonna

Transcriptional effects of CRP* expression in Escherichia coli

Escherichia coli exhibits diauxic growth in sugar mixtures due to CRP-mediated catabolite repression and inducer exclusion related to phosphotransferase system enzyme activity. Replacement of the native crp gene ...

Authors: Reza Khankal, Jonathan W Chin, Debashis Ghosh and Patrick C Cirino

Solving a Hamiltonian Path Problem with a bacterial computer

The Hamiltonian Path Problem asks whether there is a route in a directed graph from a beginning node to an ending node, visiting each node exactly once. The Hamiltonian Path Problem is NP complete, achieving s...

Authors: Jordan Baumgardner, Karen Acker, Oyinade Adefuye, Samuel Thomas Crowley, Will DeLoache, James O Dickson, Lane Heard, Andrew T Martens, Nickolaus Morton, Michelle Ritter, Amber Shoecraft, Jessica Treece, Matthew Unzicker, Amanda Valencia, Mike Waters, AMalcolm Campbell…

Enhanced production of bacterial cellulose by using a biofilm reactor and its material property analysis

Bacterial cellulose has been used in the food industry for applications such as low-calorie desserts, salads, and fabricated foods. It has also been used in the paper manufacturing industry to enhance paper st...

Authors: Kuan-Chen Cheng, Jeff M Catchmark and Ali Demirci

Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter

Gradients of morphogens pattern cell fate – a phenomenon that is especially important during development. A simple model system for studying how morphogens pattern cell behavior would overcome difficulties inh...

Authors: Takayuki Sohka, Richard A Heins and Marc Ostermeier

Antimicrobial activities of commercial nanoparticles against an environmental soil microbe, Pseudomonas putida KT2440

The release of heavy metal-containing nanoparticles (NP) into the environment may be harmful to the efficacy of beneficial microbes that function in element cycling, pollutant degradation and plant growth. Nan...

Authors: Priyanka Gajjar, Brian Pettee, David W Britt, Wenjie Huang, William P Johnson and Anne J Anderson

Engineering fusogenic molecules to achieve targeted transduction of enveloped lentiviral vectors

Lentiviral vectors with broad tropism are one of the most promising gene delivery systems capable of efficiently delivering genes of interest into both dividing and non-dividing cells while maintaining long-te...

Authors: Yuning Lei, Kye-Il Joo and Pin Wang

Mapping the moral boundaries of biological engineering

The following essay was written by a sophomore undergraduate student majoring in Bioengineering at the University of Maryland, Mr. Zachary Russ. Mr. Russ was one of 174 students who submitted a 1000–1200 word ...

Authors: Zachary N Russ

Reusable, polyethylene glycol-structured microfluidic channel for particle immunoassays

A microfluidic channel made entirely out of polyethylene glycol (PEG), not PEG coating to silicon or polydimethylsiloxane (PDMS) surface, was fabricated and tested for its reusability in particle immunoassays ...

Authors: Jin-Hee Han and Jeong-Yeol Yoon

Soluble aggregates of the amyloid-β peptide are trapped by serum albumin to enhance amyloid-β activation of endothelial cells

Self-assembly of the amyloid-β peptide (Aβ) has been implicated in the pathogenesis of Alzheimer's disease (AD). As a result, synthetic molecules capable of inhibiting Aβ self-assembly could serve as therapeut...

Authors: Adriana A Reyes Barcelo, Francisco J Gonzalez-Velasquez and Melissa A Moss

Measuring the activity of BioBrick promoters using an in vivo reference standard

The engineering of many-component, synthetic biological systems is being made easier by the development of collections of reusable, standard biological parts. However, the complexity of biology makes it diffic...

Authors: Jason R Kelly, Adam J Rubin, Joseph H Davis, Caroline M Ajo-Franklin, John Cumbers, Michael J Czar, Kim de Mora, Aaron L Glieberman, Dileep D Monie and Drew Endy

Microbial inactivation and shelf life of apple juice treated with high pressure carbon dioxide

Apple juice prepared from 'Annurca' apple puree was treated with a HPCD batch system. The pH, °Brix, color parameters and microbial load of the treated apple juice were compared with those of thermally process...

Authors: Giovanna Ferrentino, Mariacarmela Bruno, Giovanna Ferrari, Massimo Poletto and Murat O Balaban

Synthesizing non-natural parts from natural genomic template

The current knowledge of genes and proteins comes from 'naturally designed' coding and non-coding regions. It would be interesting to move beyond natural boundaries and make user-defined parts. To explore this...

Authors: Pawan K Dhar, Chaw Su Thwin, Kyaw Tun, Yuko Tsumoto, Sebastian Maurer-Stroh, Frank Eisenhaber and Uttam Surana

Synthetic control of a fitness tradeoff in yeast nitrogen metabolism

Microbial communities are involved in many processes relevant to industrial and medical biotechnology, such as the formation of biofilms, lignocellulosic degradation, and hydrogen production. The manipulation ...

Authors: Travis S Bayer, Kevin G Hoff, Chase L Beisel, Jack J Lee and Christina D Smolke

Large naturally-produced electric currents and voltage traverse damaged mammalian spinal cord

Immediately after damage to the nervous system, a cascade of physical, physiological, and anatomical events lead to the collapse of neuronal function and often death. This progression of injury processes is ca...

Authors: Mahvash Zuberi, Peishan Liu-Snyder, Aeraj ul Haque, David M Porterfield and Richard B Borgens

Review of Career Development in Bioengineering and Biotechnology by Guruprasad Madhavan, Barbara Oakley, and Luis Kun (editors), Springer Science+Business Media, LLC, 2008

Authors: Mark R Riley

Backscattering particle immunoassays in wire-guide droplet manipulations

A simpler way for manipulating droplets on a flat surface was demonstrated, eliminating the complications in the existing methods of open-surface digital microfluidics. Programmed and motorized movements of 10...

Authors: Jeong-Yeol Yoon and David J You

The role of casein in supporting the operation of surface bound kinesin

Microtubules and associated motor proteins such as kinesin are envisioned for applications such as bioseparation and molecular sorting to powering hybrid synthetic mechanical devices. One of the challenges in ...

Authors: Vivek Verma, William O Hancock and Jeffrey M Catchmark

Fast quantitative determination of microbial rhamnolipids from cultivation broths by ATR-FTIR Spectroscopy

Vibrational spectroscopic techniques are becoming increasingly important and popular because they have the potential to provide rapid and convenient solutions to routine analytical problems. Using these techni...

Authors: Frank Leitermann, Christoph Syldatk and Rudolf Hausmann

In vivo analysis of fracture toughness of thyroid gland tumors

Human solid tumors that are hard or firm on physical palpation are likely to be cancerous, a clinical maxim that has been successfully applied to cancer screening programs, such as breast self-examination. How...

Authors: Nagesh Ragavendra, JW Ju, James W Sayre, Sharon Hirschowitz, Inder Chopra and Michael W Yeh

Pyrene fate affected by humic acid amendment in soil slurry systems

Humic acid (HA) has been found to affect the solubility, mineralization, and bound residue formation of polycyclic aromatic hydrocarbons (PAHs). However, most of the studies on the interaction between HA and P...

Authors: Yanna Liang, Darwin L Sorensen, Joan E McLean and Ronald C Sims

Characterization of seed nuclei in glucagon aggregation using light scattering methods and field-flow fractionation

Glucagon is a peptide hormone with many uses as a therapeutic agent, including the emergency treatment of hypoglycemia. Physical instability of glucagon in solution leads to problems with the manufacture, form...

Authors: Cindy C Hoppe, Lida T Nguyen, Lee E Kirsch and John M Wiencek

Behavioral recovery from traumatic brain injury after membrane reconstruction using polyethylene glycol

Polyethylene glycol (PEG; 2000 MW, 30% by volume) has been shown to mechanically repair damaged cellular membranes and reduce secondary axotomy after traumatic brain and spinal cord injury (TBI and SCI respect...

Authors: Andrew O Koob, Julia M Colby and Richard B Borgens

Engineering bacteria to solve the Burnt Pancake Problem

We investigated the possibility of executing DNA-based computation in living cells by engineering Escherichia coli to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP). The BPP is solve...

Authors: Karmella A Haynes, Marian L Broderick, Adam D Brown, Trevor L Butner, James O Dickson, W Lance Harden, Lane H Heard, Eric L Jessen, Kelly J Malloy, Brad J Ogden, Sabriya Rosemond, Samantha Simpson, Erin Zwack, A Malcolm Campbell, Todd T Eckdahl, Laurie J Heyer…

Synthetic biology: enormous possibility, exaggerated perils

The following essay was written by a freshman undergraduate student majoring in Bioengineering at the University of Maryland, Mr. Zachary Russ. Mr. Russ was one of 94 students who submitted a 1000 to 1200 word...

Authors: Zachary N Russ

Effects of Dielectrophoresis on Growth, Viability and Immuno-reactivity of Listeria monocytogenes

Dielectrophoresis (DEP) has been regarded as a useful tool for manipulating biological cells prior to the detection of cells. Since DEP uses high AC electrical fields, it is important to examine whether these ...

Authors: Liju Yang, Padmapriya P Banada, Arun K Bhunia and Rashid Bashir

Engineering BioBrick vectors from BioBrick parts

The underlying goal of synthetic biology is to make the process of engineering biological systems easier. Recent work has focused on defining and developing standard biological parts. The technical standard th...

Authors: Reshma P Shetty, Drew Endy and Thomas F Knight Jr

Response coefficient analysis of a fed-batch bioreactor to dissolved oxygen perturbation in complementary cultures during PHB production

Although the production of poly-β-hydroxybutyrate (PHB) has many biological, energetic and environmental advantages over chemically synthesized polymers, synthetic polymers continue to be produced industrially si...

Authors: Pratap R Patnaik

Cellular automata simulation of topological effects on the dynamics of feed-forward motifs

Feed-forward motifs are important functional modules in biological and other complex networks. The functionality of feed-forward motifs and other network motifs is largely dictated by the connectivity of the i...

Authors: Advait A Apte, John W Cain, Danail G Bonchev and Stephen S Fong

A co-fermentation strategy to consume sugar mixtures effectively

We report a new approach for the simultaneous conversion of xylose and glucose sugar mixtures into products by fermentation. The process simultaneously uses two substrate-selective strains of Escherichia coli, on...

Authors: Mark A Eiteman, Sarah A Lee and Elliot Altman

Measuring variability in trophic status in the Lake Waco/Bosque River Watershed

Nutrient management in rivers and streams is difficult due to the spatial and temporal variability of algal growth responses. The objectives of this project were to determine the spatial and seasonal in situ vari...

Authors: Angela D Rodriguez and Marty D Matlock

Fractionation of the rice bran layer and quantification of vitamin E, oryzanol, protein, and rice bran saccharide

Value-added processing with respect to rice milling has traditionally treated the rice bran layer as a homogenous material that contains significant concentrations of high-value components of interest for phar...

Authors: Rebecca Schramm, Alicia Abadie, Na Hua, Zhimin Xu and Marybeth Lima