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 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 received 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 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 electrical fields in any way damage cells or affect their characteristics in subsequent analytical procedures. In this study, we investigated the effects of DEP manipulation on the characteristics of Listeria monocytogenes cells, including the immuno-reactivity to several Listeria-specific antibodies, the cell growth profile in liquid medium, and the cell viability on selective agar plates. It was found that a 1-h DEP treatment increased the cell immuno-reactivity to the commercial Listeria species-specific polyclonal antibodies (from KPL) by ~31.8% and to the C11E9 monoclonal antibodies by ~82.9%, whereas no significant changes were observed with either anti-InlB or anti-ActA antibodies. A 1-h DEP treatment did not cause any change in the growth profile of Listeria in the low conductive growth medium (LCGM); however, prolonged treatments (4 h or greater) caused significant delays in cell growth. The results of plating methods showed that a 4-h DEP treatment (5 MHz, 20 Vpp) reduced the viable cell numbers by 56.8–89.7 %. These results indicated that DEP manipulation may or may not affect the final detection signal in immuno-based detection depending on the type of antigen-antibody reaction involved. However, prolonged DEP treatment for manipulating bacterial cells could produce negative effects on the cell detection by growth-based methods. Careful selection of DEP operation conditions could avoid or minimize negative effects on subsequent cell detection performance. http://www.jbioleng.org/content/2/1/6 Liju Yang, Padmapriya P Banada, Arun K Bhunia and Rashid Bashir Journal of Biological Engineering 2008, 2:6 2008-04-16 doi:10.1186/1754-1611-2-6 Journal of Biological Engineering 1754-1611 2 6 2008-04-16 Background: 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 that has gained the most traction in the synthetic biology community is the BioBrick standard for physical composition of genetic parts. Parts that conform to the BioBrick assembly standard are BioBrick standard biological parts. To date, over 2,000 BioBrick parts have been contributed to, and are available from, the Registry of Standard Biological Parts. Results: Here we extended the same advantages of BioBrick standard biological parts to the plasmid-based vectors that are used to provide and propagate BioBrick parts. We developed a process for engineering BioBrick vectors from BioBrick parts. We designed a new set of BioBrick parts that encode many useful vector functions. We combined the new parts to make a BioBrick base vector that facilitates BioBrick vector construction. We demonstrated the utility of the process by constructing seven new BioBrick vectors. We also successfully used the resulting vectors to assemble and propagate other BioBrick standard biological parts. Conclusion: We extended the principles of part reuse and standardization to BioBrick vectors. As a result, myriad new BioBrick vectors can be readily produced from all existing and newly designed BioBrick parts. We invite the synthetic biology community to (1) use the process to make and share new BioBrick vectors; (2) expand the current collection of BioBrick vector parts; and (3) characterize and improve the available collection of BioBrick vector parts. http://www.jbioleng.org/content/2/1/5 Reshma P Shetty, Drew Endy and Thomas F Knight Journal of Biological Engineering 2008, 2:5 2008-04-14 doi:10.1186/1754-1611-2-5 Journal of Biological Engineering 1754-1611 2 5 2008-04-14 Background: 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 since the productivities of fermentation processes fr PHB are not yet economically competitive. Improvement of a PHB fermentation requires good understanding and optimization under the realistic conditions of large bioreactors.Laboratory-scale studies have shown that co-cultures of Ralstonia eutropha and Lactobacillus delbrueckii generate better fermentation efficiencies than R. eutropha alone. In large bioreactors, incomplete dispersioin and perturbations in the dissolved oxygen (DO) concentration, both of which affect the fermentation, have to be considered. This study analyzes the effect of DO fluctuations on bioreactor performance for both ideal and optimally dispersed broths. Results: Response coefficient analysis was employed to obtain quantitative information on the effect of DO perturbations on different variables. Three values of the Peclet number (Pe) cheracterized three levels of dispersion: Pe = 0.01 for nearly complete dispersion, Pe = 20 for optimum dispersion and Pe = 60 for insufficient dispersion. The response coefficients (RCs) of the pairs of bacterial concentrations and the main substrates, glucose and ammonium chloride, showed contrasting variations with time. Lactate, a critical intermediate, and PHB had similar RC profiles but those of lactate were one to two orders of magnitude larger than other RCs. Significantly, the optimum Pe also resulted in the largest RCs, suggesting a balance between productivity and reactor stability. Conclusion: Since R. eutropha requires oxygen for its growth whereas L. delbrueckii does not, fluctuations in the DO concentartion have a strong influence on the fermentation. Apart from this, the mechanism of PHB biosynthesis indicates that control of lactate is a critical determinant of fermentation efficiency. The RC profiles indicate that, under non-ideal conditions, a compromise may be required between PHB formation and reactor stability, especially in the latter half of the process. http://www.jbioleng.org/content/2/1/4 Pratap R Patnaik Journal of Biological Engineering 2008, 2:4 2008-03-27 doi:10.1186/1754-1611-2-4 Journal of Biological Engineering 1754-1611 2 4 2008-03-27 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, one which is unable to consume glucose and one which is unable to consume xylose. The xylose-selective (glucose deficient) strain E. coli ZSC113 has mutations in the glk, ptsG and manZ genes while the glucose-selective (xylose deficient) strain E. coli ALS1008 has a mutation in the xylA gene. By combining these two strains in a single process, xylose and glucose are consumed more quickly than by a single-organism approach. Moreover, we demonstrate that the process is able to adapt to changing concentrations of these two sugars, and therefore holds promise for the conversion of variable sugar feed streams, such as lignocellulosic hydrolysates. http://www.jbioleng.org/content/2/1/3 Mark A Eiteman, Sarah A Lee and Elliot Altman Journal of Biological Engineering 2008, 2:3 2008-02-27 doi:10.1186/1754-1611-2-3 Journal of Biological Engineering 1754-1611 2 3 2008-02-27 Background: 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 individual network components. While studies on the dynamics of motifs and networks are usually devoted to the temporal or spatial description of processes, this study focuses on the relationship between the specific architecture and the overall rate of the processes of the feed-forward family of motifs, including double and triple feed-forward loops. The search for the most efficient network architecture could be of particular interest for regulatory or signaling pathways in biology, as well as in computational and communication systems. Results: Feed-forward motif dynamics were studied using cellular automata and compared with differential equation modeling. The number of cellular automata iterations needed for a 100% conversion of a substrate into a target product was used as an inverse measure of the transformation rate. Several basic topological patterns were identified that order the specific feed-forward constructions according to the rate of dynamics they enable. At the same number of network nodes and constant other parameters, the bi-parallel and tri-parallel motifs provide higher network efficacy than single feed-forward motifs. Additionally, a topological property of isodynamicity was identified for feed-forward motifs where different network architectures resulted in the same overall rate of the target production. Conclusion: It was shown for classes of structural motifs with feed-forward architecture that network topology affects the overall rate of a process in a quantitatively predictable manner. These fundamental results can be used as a basis for simulating larger networks as combinations of smaller network modules with implications on studying synthetic gene circuits, small regulatory systems, and eventually dynamic whole-cell models. http://www.jbioleng.org/content/2/1/2 Advait A Apte, John W Cain, Danail G Bonchev and Stephen S Fong Journal of Biological Engineering 2008, 2:2 2008-02-27 doi:10.1186/1754-1611-2-2 Journal of Biological Engineering 1754-1611 2 2 2008-02-27 Background: 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 variability of trophic status in the Lake Waco/Bosque River watershed, determine the variability in the lotic ecosystem trophic status index (LETSI) at each site as indicators of the system's nutrient sensitivity, and determine if passive diffusion periphytometers could provide threshold algal responses to nutrient enrichment. Methods: We used the passive diffusion periphytometer to measure in-situ nutrient limitation and trophic status at eight sites in five streams in the Lake Waco/Bosque River Watershed in north-central Texas from July 1997 through October 1998. The chlorophyll a production in the periphytometers was used as an indicator of baseline chlorophyll a productivity and of maximum primary productivity (MPP) in response to nutrient enrichment (nitrogen and phosphorus). We evaluated the lotic ecosystem trophic status index (LETSI) using the ratio of baseline primary productivity to MPP, and evaluated the trophic class of each site. Results: The rivers and streams in the Lake Waco/Bosque River Watershed exhibited varying degrees of nutrient enrichment over the 18-month sampling period. The North Bosque River at the headwaters (NB-02) located below the Stephenville, Texas wastewater treatment outfall consistently exhibited the highest degree of water quality impact due to nutrient enrichment. Sites at the outlet of the watershed (NB-04 and NB-05) were the next most enriched sites. Trophic class varied for enriched sites over seasons. Conclusion: Seasonality played a significant role in the trophic class and sensitivity of each site to nutrients. Managing rivers and streams for nutrients will require methods for measuring in situ responses and sensitivities to nutrient enrichment. Nutrient enrichment periphytometers show significant potential for use in nutrient gradient studies. http://www.jbioleng.org/content/2/1/1 Angela D Rodriguez and Marty D Matlock Journal of Biological Engineering 2008, 2:1 2008-01-11 doi:10.1186/1754-1611-2-1 Journal of Biological Engineering 1754-1611 2 1 2008-01-11 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 pharmaceutical and nutraceutical applications. Investigators have shown that high-value components in the rice bran layer vary from differences in kernel-thickness, bran fraction, rice variety, and environmental conditions during the growing season. The objectives of this study were to quantify the amount of rice bran removed at pre-selected milling times and to correlate the amount of rice bran removed at each milling time with the concentration of vitamin E, gamma-oryzanol, rice bran saccharide, and protein obtained. The ultimate goal of this research is to show that rice bran fractionation is a useful method to obtain targeted, nutrient-rich bran samples for value-added processing. Two long grain rice cultivars, Cheniere and Cypress, were milled at discrete times between 3 and 40 seconds using a McGill mill to obtain bran samples for analysis. Results showed that the highest oryzanol and protein concentrations were found in the outer portion of the rice bran layer, while the highest rice bran saccharide concentration was found in the inner portion of the bran layer. Vitamin E concentration showed no significant difference across the bran layer within a variety, though the highest magnitude of concentration occurs within the first 10 seconds of milling for both varieties. To extract the higher concentration of oryzanol and protein only the outer portion of the bran layer requires processing, while to extract the higher concentration of rice bran saccharide, only the inner portion of the bran layer requires processing. Rice bran fractionation allows for the selective use of portions of the bran layer and is advantageous for two reasons: (1) bran fractions contain higher concentrations of components of interest with respect to the overall bran layer average, and (2) less bran needs to be processed to obtain components of interest. http://www.jbioleng.org/content/1/1/9 Rebecca Schramm, Alicia Abadie, Na Hua, Zhimin Xu and Marybeth Lima Journal of Biological Engineering 2007, 1:9 2007-12-28 doi:10.1186/1754-1611-1-9 Journal of Biological Engineering 1754-1611 1 9 2007-12-28