This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ http://www.jbioleng.org The latest articles from Journal of Biological Engineering (ISSN 1754-1611) published by BioMed Central Book details Guruprasad Madhavan, Barbara Oakley, and Luis Kun (editors) Career Development in Bioengineering and Biotechnology, published by Springer, Series in Biomedical Engineering an official publication of the International Federation for Medical and Biological Engineering, 2008. ISBN 978-0-387-76494-8; DOI 10.1007/978-0-387-76495-5. Web: http://www.springer.com/engineering/biomedical+eng/book/978-0-387-76494-8 http://www.jbioleng.org/content/2/1/16 Mark R Riley Journal of Biological Engineering 2008, 2:16 2008-11-25 doi:10.1186/1754-1611-2-16 Journal of Biological Engineering 1754-1611 2 16 2008-11-25 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 uL droplets were demonstrated using stepper motors and microcontrollers, including merging, complicated movement along the programmed path, and rapid mixing. Latex immunoagglutination assays for mouse immunoglobulin G, bovine viral diarrhea virus and Escherichia coli were demonstrated by merging two droplets on a superhydrophobic surface (contact angle = 155 degrees) and using subsequent back light scattering detection, with detection limits of 50 pg/mL, 2.5 TCID50/mL and 85 CFU/mL, respectively, all significantly lower than the other immunoassay demonstrations in conventional microfluidics (~1 ng/mL for proteins, ~100 TCID50/mL for viruses and ~100 CFU/mL for bacteria). Advantages of this system over conventional microfluidics or microwell plate assays include: (1) minimized biofouling and repeated use (>100 times) of a platform; (2) possibility of nanoliter droplet manipulation; (3) reprogrammability with a computer or a game pad interface. http://www.jbioleng.org/content/2/1/15 Jeong-Yeol Yoon and David J. You Journal of Biological Engineering 2008, 2:15 2008-11-17 doi:10.1186/1754-1611-2-15 Journal of Biological Engineering 1754-1611 2 15 2008-11-17 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 realizing such systems is retaining motor functionality on device surfaces. Kinesin motors adsorbed onto glass surfaces lose their functionality or ability to interact with microtubules if not adsorbed with other supporting proteins. Casein, a milk protein, is commonly used in microtubule motility assays to preserve kinesin functionality. However, the mechanism responsible for this preservation of motor function is unknown. To study casein and kinesin interaction, a series of microtubule motility assays were performed where whole milk casein, or its αs1 and αs2, β or κ subunits, were introduced or omitted at various steps of the motility assay. In addition, a series of epifluorescence and total internal reflection microscopy (TIRF) experiments were conducted where fluorescently labeled casein was introduced at various steps of the motility assay to assess casein-casein and casein-glass binding dynamics. From these experiments it is concluded that casein forms a bi-layer which supports the operation of kinesin. The first tightly bound layer of casein mainly performs the function of anchoring the kinesin while the second more loosely bound layer of casein positions the head domain of the kinesin to more optimally interact with microtubules. Studies on individual casein subunits indicate that β casein was most effective in supporting kinesin functionality while κ casein was found to be least effective. http://www.jbioleng.org/content/2/1/14 Vivek Verma, William O Hancock and Jeffrey M Catchmark Journal of Biological Engineering 2008, 2:14 2008-10-20 doi:10.1186/1754-1611-2-14 Journal of Biological Engineering 1754-1611 2 14 2008-10-20 Background: 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 techniques, a variety of substances can be characterized, identified and also quantified rapidly. Results: The rapid ATR-FTIR (Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy) in time technique has been applied, which is suitable to quantify the concentrations of microbial rhamnolipids in a typical cultivation process. While the usually applied HPLC analysis requires an extensive and time consuming multi step extraction protocol for sample preparation, the ATR-FTIR-method allows the quantification of the rhamnolipids within 20 minutes. Accuracies between 0.5 g/l – 2.1 g/l for the different analytes were determined by cross validation of the calibration set. Even better accuracies between 0.28 g/l – 0.59 g/l were found for independent test samples of an arbitrarily selected cultivation. Conclusion: ATR-FTIR was found to be suitable for the rapid analysis of rhamnolipids in a biotechnological process with good reproducibility in sample determination and sufficient accuracy. An improvement in accuracy through continuous expansion and validation of the reference spectra set seems very likely. http://www.jbioleng.org/content/2/1/13 Frank Leitermann, Christoph Syldatk and Rudolf Hausmann Journal of Biological Engineering 2008, 2:13 2008-10-07 doi:10.1186/1754-1611-2-13 Journal of Biological Engineering 1754-1611 2 13 2008-10-07 Background: 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. However, the biological relevance or prognostic significance of tumor hardness remains poorly understood. Here we present a fracture mechanics based in vivo approach for characterizing the fracture toughness of biological tissue of human thyroid gland tumors. Methods: In a prospective study, 609 solid thyroid gland tumors were percutaneously probed using standard 25 gauge fine needles, their tissue toughness ranked on the basis of the nature and strength of the haptic force feedback cues, and subjected to standard fine needle biopsy. The tumors' toughness rankings and final cytological diagnoses were combined and analyzed. The interpreting cytopathologist was blinded to the tumors' toughness rankings. Results: Our data showed that cancerous and noncancerous tumors displayed remarkable haptically distinguishable differences in their material toughness. Conclusion: The qualitative method described here, though subject to some operator bias, identifies a previously unreported in vivo approach to classify fracture toughness of a solid tumor that can be correlated with malignancy, and paves the way for the development of a mechanical device that can accurately quantify the tissue toughness of a human tumor. http://www.jbioleng.org/content/2/1/12 Nagesh Ragavendra, JW Ju, James W Sayre, Sharon Hirschowitz, Inder Chopra and Michael W Yeh Journal of Biological Engineering 2008, 2:12 2008-10-06 doi:10.1186/1754-1611-2-12 Journal of Biological Engineering 1754-1611 2 12 2008-10-06 Background: 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 PAH concentrated on one or two of the three phases. Few studies have provided a simple protocol to demonstrate the overall effects of HA on PAH distribution in soil systems for all three phases. Methods: In this study, three doses of standard Elliott soil HA (ESHA), 15, 187.5, and 1,875 μg ESHA/g soil slurry, were amended to soil slurry systems. 14C-pyrene was added to the systems along with non-radiolabeled pyrene; 14C and 14CO2 were monitored for each system for a period of 120 days. Results: The highest amendment dose significantly increased the 14C fraction in the aqueous phase within 24 h, but not after that time. Pyrene mineralization was significantly inhibited by the highest dose over the 120-day study. While organic solvent extractable 14C decreased with time in all systems, non-extractable or bound 14C was significantly enhanced with the highest dose of ESHA addition. Conclusion: Amendment of the highest dose of ESHA to pyrene contaminated soil was observed to have two major functions. The first was to mitigate CO2 production significantly by reducing 14CO2 from 14C pyrene mineralization. The second was to significantly increase stable bound 14C formation, which may serve as a remediation end point. Overall, this study demonstrated a practical approach for decontamination of PAH contaminated soil. This approach may be applicable to other organic contaminated environments where active bioremediation is taking place. http://www.jbioleng.org/content/2/1/11 Yanna Liang, Darwin L Sorensen, Joan E McLean and Ronald C Sims Journal of Biological Engineering 2008, 2:11 2008-09-10 doi:10.1186/1754-1611-2-11 Journal of Biological Engineering 1754-1611 2 11 2008-09-10 Background: 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, formulation, and delivery of this pharmaceutical product. Glucagon has been shown to aggregate and form fibrils and gels in vitro. Small oligomeric precursors serve to initiate and nucleate the aggregation process. In this study, these initial aggregates, or seed nuclei, are characterized in bulk solution using light scattering methods and field-flow fractionation. Results: High molecular weight aggregates of glucagon were detected in otherwise monomeric solutions using light scattering techniques. These aggregates were detected upon initial mixing of glucagon powder in dilute HCl and NaOH. In the pharmaceutically relevant case of acidic glucagon, the removal of aggregates by filtration significantly slowed the aggregation process. Field-flow fractionation was used to separate aggregates from monomeric glucagon and determine relative mass. The molar mass of the large aggregates was shown to grow appreciably over time as the glucagon solutions gelled. Conclusion: The results of this study indicate that initial glucagon solutions are predominantly monomeric, but contain small quantities of large aggregates. These results suggest that the initial aggregates are seed nuclei, or intermediates which catalyze the aggregation process, even at low concentrations. http://www.jbioleng.org/content/2/1/10 Cindy C Hoppe, Lida T Nguyen, Lee E Kirsch and John M Wiencek Journal of Biological Engineering 2008, 2:10 2008-07-09 doi:10.1186/1754-1611-2-10 Journal of Biological Engineering 1754-1611 2 10 2008-07-09 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 respectively). This repair is achieved following spontaneous reassembly of cell membranes made possible by the action of targeted hydrophilic polymers which first seal the compromised portion of the plasmalemma, and secondarily, allow the lipidic core of the compromised membranes to resolve into each other. Here we compared PEG-treated to untreated rats using a computer-managed open-field behavioral test subsequent to a standardized brain injury. Animals were evaluated after a 2-, 4-, and 6-hour delay in treatment after TBI. Treated animals receive a single subcutaneous injection of PEG. When treated within 2 hours of the injury, injured PEG-treated rats showed statistically significant improvement in their exploratory behavior recorded in the activity box when compared to untreated but brain-injured controls. A delay of 4 hours reduced this level of achievement, but a statistically significant improvement due to PEG injection was still clearly evident in most outcome measures compared at the various evaluation times. A further delay of 2 more hours, however, eradicated the beneficial effects of PEG injection as revealed using this behavioral assessment. Thus, there appears to be a critical window of time in which PEG administration after TBI can provide neuroprotection resulting in an enhanced functional recovery. As is often seen in clinically applied acute treatments for trauma, the earlier the intervention can be applied, the better the outcome. http://www.jbioleng.org/content/2/1/9 Andrew O Koob, Julia M Colby and Richard B Borgens Journal of Biological Engineering 2008, 2:9 2008-06-27 doi:10.1186/1754-1611-2-9 Journal of Biological Engineering 1754-1611 2 9 2008-06-27 Background: 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 solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack. We have designed a system that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA. Results: Inversions (or "flips") of the DNA fragment pancakes are driven by the Salmonella typhimurium Hin/hix DNA recombinase system that we reconstituted as a collection of modular genetic elements for use in E. coli. Our system sorts DNA segments by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; E. coli cells become antibiotic resistant when the segments are properly sorted. Hin recombinase can mediate all possible inversion operations on adjacent flippable DNA fragments. Mathematical modeling predicts that the system reaches equilibrium after very few flips, where equal numbers of permutations are randomly sorted and unsorted. Semiquantitative PCR analysis of in vivo flipping suggests that inversion products accumulate on a time scale of hours or days rather than minutes. Conclusion: The Hin/hix system is a proof-of-concept demonstration of in vivo computation with the potential to be scaled up to accommodate larger and more challenging problems. Hin/hix may provide a flexible new tool for manipulating transgenic DNA in vivo. http://www.jbioleng.org/content/2/1/8 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 and Jeffrey L Poet Journal of Biological Engineering 2008, 2:8 2008-05-20 doi:10.1186/1754-1611-2-8 Journal of Biological Engineering 1754-1611 2 8 2008-05-20 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 essay to the 3rd Annual Bioethics Essay Contest sponsored by the Institute of Biological Engineering (IBE). A group of professionals in Biological Engineering assessed and ranked the essays in a blinded process. Five semi-finalists were invited to present their essays at a session at the annual meeting of IBE in Chapel Hill, NC on March 8, 2008. Five judges scored the presentations at the annual meeting and selected Mr. Russ's contribution as the overall winner (1st Place). Below is his essay. http://www.jbioleng.org/content/2/1/7 Zachary N Russ Journal of Biological Engineering 2008, 2:7 2008-04-25 doi:10.1186/1754-1611-2-7 Journal of Biological Engineering 1754-1611 2 7 2008-04-25