Articles

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…

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

Authentic teaching and learning through synthetic biology

Synthetic biology is an emerging engineering discipline that, if successful, will allow well-characterized biological components to be predictably and reliably built into robust organisms that achieve specific...

Authors: Natalie Kuldell

Rapid single step subcloning procedure by combined action of type II and type IIs endonucleases with ligase

The subcloning of a DNA fragment from an entry vector into a destination vector is a routinely performed task in molecular biology labs.

Authors: Tobias Fromme and Martin Klingenspor

Role of reaction kinetics and mass transport in glucose sensing with nanopillar array electrodes

The use of nanopillar array electrodes (NAEs) for biosensor applications was explored using a combined experimental and simulation approach to characterize the role of reaction kinetics and mass transport in g...

Authors: Venkataramani Anandan, Xiaoling Yang, Euihyeon Kim, Yeswanth L Rao and Guigen Zhang

Development of a Cryptosporidium oocyst assay using an automated fiber optic-based biosensor

An intestinal protozoan parasite, Cryptosporidium parvum, is a major cause of waterborne gastrointestinal disease worldwide. Detection of Cryptosporidium oocysts in potable water is a high priority for the water ...

Authors: Marianne F Kramer, Graham Vesey, Natasha L Look, Ben R Herbert, Joyce M Simpson-Stroot and Daniel V Lim

Amyloglucosidase enzymatic reactivity inside lipid vesicles

Efficient functioning of enzymes inside liposomes would open new avenues for applications in biocatalysis and bioanalytical tools. In this study, the entrapment of amyloglucosidase (AMG) (EC 3.2.1.3) from Aspergi...

Authors: Mian Li, Michael J Hanford, Jin-Woo Kim and Tonya L Peeples

Electrospun nitrocellulose and nylon: Design and fabrication of novel high performance platforms for protein blotting applications

Electrospinning is a non-mechanical processing strategy that can be used to process a variety of native and synthetic polymers into highly porous materials composed of nano-scale to micron-scale diameter fiber...

Authors: Ashley E Manis, James R Bowman, Gary L Bowlin and David G Simpson

Engineering education in the wake of hurricane Katrina

Living through hurricane Katrina and its aftermath and reflecting on these experiences from technical and non-technical standpoints has led me to reconsider my thoughts and philosophy on engineering education....

Authors: Marybeth Lima

Introducing Journal of Biological Engineering

Authors: Mark R Riley