Articles

Blue and UV LED-induced fluorescence in cotton foreign matter

Cotton is an important domesticated fiber used to manufacture a variety of products and industrial goods. During harvesting with cotton strippers and cotton pickers, it is contaminated with foreign matter from...

Authors: Adnan Mustafic, Changying Li and Mark Haidekker

The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts

The Registry of Standard Biological Parts only accepts genetic parts compatible with the RFC 10 BioBrick format. This combined assembly and submission standard requires that four unique restriction enzyme site...

Authors: Razan N Alnahhas, Ben Slater, Yunle Huang, Catherine Mortensen, Jordan W Monk, Yousef Okasheh, Marco D Howard, Neil R Gottel, Michael J Hammerling and Jeffrey E Barrick

Erratum to: A fibrin/hyaluronic acid hydrogel for the delivery of mesenchymal stem cells and potential for articular cartilage repair

Authors: Timothy N Snyder, Krishna Madhavan, Miranda Intrator, Ryan C Dregalla and Daewon Park

A library of mammalian effector modules for synthetic morphology

In mammalian development, the formation of most tissues is achieved by a relatively small repertoire of basic morphogenetic events (e.g. cell adhesion, locomotion, apoptosis, etc.), permutated in various seque...

Authors: Elise Cachat, Weijia Liu, Peter Hohenstein and Jamie A Davies

A DNA-based pattern classifier with in vitro learning and associative recall for genomic characterization and biosensing without explicit sequence knowledge

Genetic material extracted from in situ microbial communities has high promise as an indicator of biological system status. However, the challenge is to access genomic information from all organisms at the popula...

Authors: Ju Seok Lee, Junghuei Chen, Russell Deaton and Jin-Woo Kim

Large area micropatterning of cells on polydimethylsiloxane surfaces

Precise spatial control and patterning of cells is an important area of research with numerous applications in tissue engineering, as well as advancing an understanding of fundamental cellular processes. Poly ...

Authors: Mahmoud E Moustafa, Venkat S Gadepalli, Ahmed A Elmak, Woomin Lee, Raj R Rao and Vamsi K Yadavalli

Parameter-less approaches for interpreting dynamic cellular response

Cellular response such as cell signaling is an integral part of information processing in biology. Upon receptor stimulation, numerous intracellular molecules are invoked to trigger the transcription of genes ...

Authors: Kumar Selvarajoo

Minireactor-based high-throughput temperature profiling for the optimization of microbial and enzymatic processes

Bioprocesses depend on a number of different operating parameters and temperature is one of the most important ones. Unfortunately, systems for rapid determination of temperature dependent reaction kinetics ar...

Authors: Martin Kunze, Clemens Lattermann, Sylvia Diederichs, Wolfgang Kroutil and Jochen Büchs

Challenges in predicting the evolutionary maintenance of a phage transgene

In prior work, a phage engineered with a biofilm-degrading enzyme (dispersin B) cleared artificial, short-term biofilms more fully than the phage lacking the enzyme. An unresolved question is whether the trans...

Authors: Matthew Schmerer, Ian J Molineux, Dilara Ally, Jabus Tyerman, Nicole Cecchini and James J Bull

Endometrial stem cells in regenerative medicine

First described in 2004, endometrial stem cells (EnSCs) are adult stem cells isolated from the endometrial tissue. EnSCs comprise of a population of epithelial stem cells, mesenchymal stem cells, and side popu...

Authors: Javad Verdi, Aaron Tan, Alireza Shoae-Hassani and Alexander M Seifalian

“NiCo Buster”: engineering E. coli for fast and efficient capture of cobalt and nickel

Metal contamination is widespread and results from natural geogenic and constantly increasing anthropogenic sources (mainly mining and extraction activities, electroplating, battery and steel manufacturing or ...

Authors: Alexandre Duprey, Viviane Chansavang, Franck Frémion, Clémence Gonthier, Yoann Louis, Philippe Lejeune, Fanny Springer, Valérie Desjardin, Agnès Rodrigue and Corinne Dorel

Cross-section perimeter is a suitable parameter to describe the effects of different baffle geometries in shaken microtiter plates

Biotechnological screening processes are performed since more than 8 decades in small scale shaken bioreactors like shake flasks or microtiter plates. One of the major issues of such reactors is the sufficient...

Authors: Clemens Lattermann, Matthias Funke, Sven Hansen, Sylvia Diederichs and Jochen Büchs

Characterization of hydromechanical stress in aerated stirred tanks up to 40 m³ scale by measurement of maximum stable drop size

Turbulence intensity, or hydromechanical stress, is a parameter that influences a broad range of processes in the fields of chemical engineering and biotechnology. Fermentation processes are often characterize...

Authors: Andreas Daub, Marina Böhm, Stefanie Delueg, Markus Mühlmann, Gerhard Schneider and Jochen Büchs

An instrument design for non-contact detection of biomolecules and minerals on Mars using fluorescence

We discuss fluorescence as a method to detect polycyclic aromatic hydrocarbons and other organic molecules, as well as minerals on the surface of Mars. We present an instrument design that is adapted from the ...

Authors: Heather D Smith, Christopher P McKay, Andrew G Duncan, Ronald C Sims, Anne J Anderson and Paul R Grossl

Engineered protein A ligands, derived from a histidine-scanning library, facilitate the affinity purification of IgG under mild acidic conditions

In antibody purification processes, the acidic buffer commonly used to elute the bound antibodies during conventional affinity chromatograph, can damage the antibody. Herein we describe the development of seve...

Authors: Masayuki Tsukamoto, Hideki Watanabe, Ayako Ooishi and Shinya Honda

Comparative in vitro study regarding the biocompatibility of titanium-base composites infiltrated with hydroxyapatite or silicatitanate

The development of novel biomaterials able to control cell activities and direct their fate is warranted for engineering functional bone tissues. Adding bioactive materials can improve new bone formation and b...

Authors: Ioana-Carmen Brie, Olga Soritau, Noemi Dirzu, Cristian Berce, Adriana Vulpoi, Catalin Popa, Milica Todea, Simion Simon, Maria Perde-Schrepler, Piroska Virag, Otilia Barbos, Gabriela Chereches, Petru Berce and Valentin Cernea

Influence of surface topography on the human epithelial cell response to micropatterned substrates with convex and concave architectures

Understanding the fundamental mechanisms underlying the cellular response to topographical surface features will extend our knowledge regarding the regulation of cell functions. Analyzing the cellular response...

Authors: Mee-Hae Kim, Yoshiko Sawada, Masahito Taya and Masahiro Kino-oka

Effect of tumor shape, size, and tissue transport properties on drug delivery to solid tumors

The computational methods provide condition for investigation related to the process of drug delivery, such as convection and diffusion of drug in extracellular matrices, drug extravasation from microvessels o...

Authors: Mostafa Sefidgar, M Soltani, Kaamran Raahemifar, Hossein Bazmara, Seyed Mojtaba Mousavi Nayinian and Majid Bazargan

Investigation of antimicrobial activity of photothermal therapeutic gold/copper sulfide core/shell nanoparticles to bacterial spores and cells

Au/CuS core/shell nanoparticles (NPs) were designed as a new type of transducer agent for photothermal therapy (PTT), with attractive features of easy preparation, low cost and small size for targeting. This p...

Authors: Ebenezer Addae, Xiuli Dong, Eric McCoy, Chang Yang, Wei Chen and Liju Yang

A fibrin/hyaluronic acid hydrogel for the delivery of mesenchymal stem cells and potential for articular cartilage repair

Osteoarthritis (OA) is a degenerative joint disease affecting approximately 27 million Americans, and even more worldwide. OA is characterized by degeneration of subchondral bone and articular cartilage. In th...

Authors: Timothy N Snyder, Krishna Madhavan, Miranda Intrator, Ryan C Dregalla and Daewon Park

Optimization of 3-D organotypic primary colonic cultures for organ-on-chip applications

New advances enable long-term organotypic culture of colonic epithelial stem cells that develop into structures known as colonoids. Colonoids represent a primary tissue source acting as a potential starting ma...

Authors: Asad A Ahmad, Yuli Wang, Adam D Gracz, Christopher E Sims, Scott T Magness and Nancy L Allbritton

Optimized conditions for successful transfection of human endothelial cells with in vitro synthesized and modified mRNA for induction of protein expression

The induction of protein synthesis by exogenous delivery of coding synthetic mRNA in desired cells is an auspicious strategy in the fields of basic cell biology, regenerative medicine, treatment of diseases, a...

Authors: Meltem Avci-Adali, Andreas Behring, Timea Keller, Stefanie Krajewski, Christian Schlensak and Hans Peter Wendel

Modular assembly of designer PUF proteins for specific post-transcriptional regulation of endogenous RNA

Due to their modular repeat structure, Pumilio/fem-3 mRNA binding factor (PUF) proteins are promising candidates for designer RNA-binding protein (RBP) engineering. To further facilitate the application of the...

Authors: Zhanar Abil, Carl A Denard and Huimin Zhao

In silico design and in vivoimplementation of yeast gene Boolean gates

In our previous computational work, we showed that gene digital circuits can be automatically designed in an electronic fashion. This demands, first, a conversion of the truth table into Boolean formulas with ...

Authors: Mario A Marchisio

Half-life measurements of chemical inducers for recombinant gene expression

Inducible promoters are widely spread genetic tools for triggering, tuning and optimizing the expression of recombinant genes in engineered biological systems. Most of them are controlled by the addition of a ...

Authors: Nicolo’ Politi, Lorenzo Pasotti, Susanna Zucca, Michela Casanova, Giuseppina Micoli, Maria Gabriella Cusella De Angelis and Paolo Magni

Design and analysis of LacI-repressed promoters and DNA-looping in a cyanobacterium

Cyanobacteria are solar-powered prokaryotes useful for sustainable production of valuable molecules, but orthogonal and regulated promoters are lacking. The Lac repressor (LacI) from Escherichia coli is a well-st...

Authors: Daniel Camsund, Thorsten Heidorn and Peter Lindblad

Towards an integrated systems-based modelling framework for drug transport and its effect on tumour cells

A systematic understanding of chemotherapeutic influence on solid tumours is highly challenging and complex as it encompasses the interplay of phenomena occurring at multiple scales. It is desirable to have a ...

Authors: Cong Liu, Cong Krishnan and Xiao Yun Xu

An improved Escherichia colistrain to host gene regulatory networks involving both the AraC and LacI inducible transcription factors

Many of the gene regulatory networks used within the field of synthetic biology have extensively employed the AraC and LacI inducible transcription factors. However, there is no Escherichia coli strain that provi...

Authors: Manjunatha Kogenaru and Sander J Tans

Comparison of lignin derivatives as substrates for laccase-catalyzed scavenging of oxygen in coatings and films

Lignin derivatives are phenylpropanoid biopolymers derived from pulping and biorefinery processes. The possibility to utilize lignin derivatives from different types of processes in advanced enzyme-catalyzed o...

Authors: Kristin Johansson, Thomas Gillgren, Sandra Winestrand, Lars Järnström and Leif J Jönsson

Polylactic acid composites incorporating casein functionalized cellulose nanowhiskers

Polylactic acid (PLA) is considered to be a sustainable alternative to petroleum-based polymers for many applications. Using cellulose fiber to reinforce PLA is of great interest recently due to its complete b...

Authors: Jin Gu and Jeffrey M Catchmark

Assembly of eukaryotic algal chromosomes in yeast

Synthetic genomic approaches offer unique opportunities to use powerful yeast and Escherichia coli genetic systems to assemble and modify chromosome-sized molecules before returning the modified DNA to the target...

Authors: Bogumil J Karas, Bhuvan Molparia, Jelena Jablanovic, Wolfgang J Hermann, Ying-Chi Lin, Christopher L Dupont, Christian Tagwerker, Isaac T Yonemoto, Vladimir N Noskov, Ray-Yuan Chuang, Andrew E Allen, John I Glass, Clyde A Hutchison III, Hamilton O Smith, J Craig Venter and Philip D Weyman

The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis

Standardized and well-characterized genetic building blocks are a prerequisite for the convenient and reproducible assembly of novel genetic modules and devices. While numerous standardized parts exist for Escher...

Authors: Jara Radeck, Korinna Kraft, Julia Bartels, Tamara Cikovic, Franziska Dürr, Jennifer Emenegger, Simon Kelterborn, Christopher Sauer, Georg Fritz, Susanne Gebhard and Thorsten Mascher

Correlation between mass transfer coefficient k_La and relevant operating parameters in cylindrical disposable shaken bioreactors on a bench-to-pilot scale

Among disposable bioreactor systems, cylindrical orbitally shaken bioreactors show important advantages. They provide a well-defined hydrodynamic flow combined with excellent mixing and oxygen transfer for mam...

Authors: Wolf Klöckner, Riad Gacem, Tibor Anderlei, Nicole Raven, Stefan Schillberg, Clemens Lattermann and Jochen Büchs

Development of growth selection systems to isolate a-type or α-type of yeast cells spontaneously emerging from MAT a/α diploids

Manufacture of MAT a and MAT α yeast cells is required for crossbreeding, a procedure that permits hybridization and the generation of new heterozygous strains. Crossbreeding also can be performed with a- and α-t...

Authors: Nobuo Fukuda and Shinya Honda

Design and analysis of a tunable synchronized oscillator

The use of in silico simulations as a basis for designing artificial biological systems (and experiments to characterize them) is one of the tangible differences between Synthetic Biology and “classical” Genetic ...

Authors: Brendan M Ryback, Dorett I Odoni, Ruben GA van Heck, Youri van Nuland, Matthijn C Hesselman, Vítor AP Martins dos Santos, Mark WJ van Passel and Floor Hugenholtz

Engineering biodegradable and multifunctional peptide-based polymers for gene delivery

The complex nature of in vivo gene transfer establishes the need for multifunctional delivery vectors capable of meeting these challenges. An additional consideration for clinical translation of synthetic deliver...

Authors: Julie Shi, Joan G Schellinger and Suzie H Pun

Secretion of polyhydroxybutyrate in Escherichia coli using a synthetic biological engineering approach

Polyhydroxyalkanoates (PHAs) are a group of biodegradable plastics that are produced by a wide variety of microorganisms, mainly as a storage intermediate for energy and carbon. Polyhydroxybutyrate (PHB) is a ...

Authors: Asif Rahman, Elisabeth Linton, Alex D Hatch, Ronald C Sims and Charles D Miller

Influence of substrate curvature on osteoblast orientation and extracellular matrix deposition

The effects of microchannel diameter in hydroxyapatite (HAp) substrates on osteoblast behavior were investigated in this study. Microchannels of 100, 250 and 500 μm diameter were created on hydroxyapatite disk...

Authors: Marcello Pilia, Teja Guda, Stefanie M Shiels and Mark R Appleford

Dilution and the theoretical description of growth-rate dependent gene expression

Expression of a gene is not only tuned by direct regulation, but also affected by the global physiological state of the (host) cell. This global dependence complicates the quantitative understanding of gene re...

Authors: Marius Hintsche and Stefan Klumpp

Targeting a heterologous protein to multiple plant organelles via rationally designed 5′ mRNA tags

Plant bioengineers require simple genetic devices for predictable localization of heterologous proteins to multiple subcellular compartments.

Authors: Mathias J Voges, Pamela A Silver, Jeffrey C Way and Matthew D Mattozzi

Contribution of cytoskeletal elements to the axonal mechanical properties

Microtubules, microfilaments, and neurofilaments are cytoskeletal elements that affect cell morphology, cellular processes, and mechanical structures in neural cells. The objective of the current study was to ...

Authors: Hui Ouyang, Eric Nauman and Riyi Shi

Dual effects of single-walled carbon nanotubes coupled with near-infrared radiation on Bacillus anthracis spores: inactivates spores and stimulates the germination of surviving spores

Bacillus anthracis is a pathogen that causes life-threatening disease--anthrax. B. anthracis spores are highly resistant to extreme temperatures and harsh chemicals. Inactivation of B. anthracis spores is importa...

Authors: Xiuli Dong, Yongan Tang, Marvin Wu, Branislav Vlahovic and Liju Yang

Endothelial cells derived from embryonic stem cells respond to cues from topographical surface patterns

The generation of micro- and nano-topography similar to those found in the extra cellular matrix of three-dimensional tissues is one technique used to recapitulate the cell-tissue physiology found in the nativ...

Authors: Rachel Hatano, Kevin Mercurio, Jesus Isaac Luna, Drew E Glaser, Valerie J Leppert and Kara E McCloskey

Dual organism design cycle reveals small subunit substitutions that improve [NiFe] hydrogenase hydrogen evolution

Photosynthetic microorganisms that directly channel solar energy to the production of molecular hydrogen are a potential future biofuel system. Building such a system requires installation of a hydrogenase in ...

Authors: Isaac T Yonemoto, Christopher W Matteri, Thao Amy Nguyen, Hamilton O Smith and Philip D Weyman

Hidden hysteresis – population dynamics can obscure gene network dynamics

Positive feedback is a common motif in gene regulatory networks. It can be used in synthetic networks as an amplifier to increase the level of gene expression, as well as a nonlinear module to create bistable ...

Authors: Phillip Poisson and Kaustubh D Bhalerao

Pushing the science forward: chitosan nanoparticles and functional repair of CNS tissue after spinal cord injury

We continue our exploration of the large polysaccharide polymer Chitosan as an acute therapy for severe damage to the nervous system. We tested the action of subcutaneously injected nanoparticles (~ 100 – 200 ...

Authors: Bojun Chen, Debra Bohnert, Richard Ben Borgens and Youngnam Cho

Model-driven elucidation of the inherent capacity of Geobacter sulfurreducens for electricity generation

G. sulfurreducens is one of the commonest microbes used in microbial fuel cells (MFCs) for organic-to-electricity biotransformation. In MFCs based on this microorganism, electrons can be conveyed to the anode via...

Authors: Longfei Mao and Wynand S Verwoerd

A survey of enabling technologies in synthetic biology

Realizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. B...

Authors: Linda J Kahl and Drew Endy

A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli

The chromosomal integration of biological parts in the host genome enables the engineering of plasmid-free stable strains with single-copy insertions of the desired gene networks. Although different integrativ...

Authors: Susanna Zucca, Lorenzo Pasotti, Nicolò Politi, Maria Gabriella Cusella De Angelis and Paolo Magni

Wide-dynamic-range promoters engineered for cyanobacteria

Cyanobacteria, prokaryotic cells with oxygenic photosynthesis, are excellent bioengineering targets to convert solar energy into solar fuels. Tremendous genetic engineering approaches and tools have been and s...

Authors: Hsin-Ho Huang and Peter Lindblad