Articles

A novel approach for metabolic pathway optimization: Oligo-linker mediated assembly (OLMA) method

Imbalances in gene expression of a metabolic pathway can result in less-yield of the desired products. Several targets were intensively investigated to balance the gene expression, such as promoter, ribosome b...

Authors: Shasha Zhang, Xuejin Zhao, Yong Tao and Chunbo Lou

Stimulating effect of graphene oxide on myogenesis of C2C12 myoblasts on RGD peptide-decorated PLGA nanofiber matrices

In the field of biomedical engineering, many studies have focused on the possible applications of graphene and related nanomaterials due to their potential for use as scaffolds, coating materials and delivery ...

Authors: Yong Cheol Shin, Jong Ho Lee, Min Jeong Kim, Suck Won Hong, Bongju Kim, Jung Keun Hyun, Yu Suk Choi, Jong-Chul Park and Dong-Wook Han

Engineering dynamic cell cycle control with synthetic small molecule-responsive RNA devices

The cell cycle plays a key role in human health and disease, including development and cancer. The ability to easily and reversibly control the mammalian cell cycle could mean improved cellular reprogramming, ...

Authors: Kathy Y. Wei and Christina D. Smolke

Dual functional nisin-multi-walled carbon nanotubes coated filters for bacterial capture and inactivation

Removal of pathogens from water is one way to prevent waterborne illness. In this paper, we developed dual functional carbon nanotube (CNT) modified filters for bacterial capture and inactivation, utilizing mu...

Authors: Xiuli Dong and Liju Yang

Collective cell migration of smooth muscle and endothelial cells: impact of injury versus non-injury stimuli

Cell migration is a vital process for growth and repair. In vitro migration assays, utilized to study cell migration, often rely on physical scraping of a cell monolayer to induce cell migration. The physical act...

Authors: Kaitlyn R. Ammann, Katrina J. DeCook, Phat L. Tran, Valerie M. Merkle, Pak K. Wong and Marvin J. Slepian

Patterned polymer matrix promotes stemness and cell-cell interaction of adult stem cells

The interaction of stem cells with their culture substrates is critical in controlling their fate and function. Declining stemness of adult-derived human mesenchymal stem cells (hMSCs) during in vitro expansion o...

Authors: Lucas H. Hofmeister, Lino Costa, Daniel A. Balikov, Spencer W. Crowder, Alexander Terekhov, Hak-Joon Sung and William H. Hofmeister

Gold nanoparticle-labeled biosensor for rapid and sensitive detection of bacterial pathogens

Escherichia coli O157:H7 is one of the major foodborne bacterial pathogens and also a biodefense agent. To ensure food safety and public health, it is very important to develop rapid m...

Authors: Yun Wang and Evangelyn C. Alocilja

Standards not that standard

There is a general assent on the key role of standards in Synthetic Biology. In two consecutive letters to this journal, suggestions on the assembly methods for the Registry of standard biological parts have b...

Authors: Cristina Vilanova, Kristie Tanner, Pedro Dorado-Morales, Paula Villaescusa, Divya Chugani, Alba Frías, Ernesto Segredo, Xavier Molero, Marco Fritschi, Lucas Morales, Daniel Ramón, Carlos Peña, Juli Peretó and Manuel Porcar

QuickStep-Cloning: a sequence-independent, ligation-free method for rapid construction of recombinant plasmids

Molecular cloning is an essential step in biological engineering. Methods involving megaprimer-based PCR of a whole plasmid are promising alternatives to the traditional restriction-ligation-based molecular cl...

Authors: Pawel Jajesniak and Tuck Seng Wong

Development of a miniaturized stimulation device for electrical stimulation of cells

Directing cell behaviour using controllable, on-demand non-biochemical methods, such as electrical stimulation is an attractive area of research. While there exists much potential in exploring different modes ...

Authors: Gordon Minru Xiong, Anh Tuan Do, Jun Kit Wang, Chee Leong Yeoh, Kiat Seng Yeo and Cleo Choong

Artificial cell-cell communication as an emerging tool in synthetic biology applications

Cell-cell communication is a widespread phenomenon in nature, ranging from bacterial quorum sensing and fungal pheromone communication to cellular crosstalk in multicellular eukaryotes. These communication mod...

Authors: Stefan Hennig, Gerhard Rödel and Kai Ostermann

Lipase-catalyzed biodiesel production and quality with Jatropha curcas oil: exploring its potential for Central America

Extensive native Jatropha curcas L. (Jatropha) crop areas have been planted in Central America marginal lands since 2008 as a non-edible prospective feedstock alternative to high-value, edible palm oil. Jatropha ...

Authors: Francisco Bueso, Luis Moreno, Mathew Cedeño and Karla Manzanarez

Essential validation methods for E. coli strains created by chromosome engineering

Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used ...

Authors: Sriram Tiruvadi Krishnan, M. Charl Moolman, Theo van Laar, Anne S. Meyer and Nynke H. Dekker

No training required: experimental tests support homology-based DNA assembly as a best practice in synthetic biology

The Registry of Standard Biological Parts imposes sequence constraints to enable DNA assembly using restriction enzymes. Alnahhas et al. (Journal of Biological Engineering 2014, 8:28) recently argued that thes...

Authors: Afnan Azizi, Wilson Lam, Hilary Phenix, Lioudmila Tepliakova, Ian J Roney, Daniel Jedrysiak, Alex Power, Vaibhav Gupta, Nada Elnour, Martin Hanzel, Alexandra C Tzahristos, Shihab Sarwar and Mads Kærn

Chemical lysis of cyanobacteria

We have developed a mixture of enzymes and chemicals that completely lyse cyanobacteria. Since the treatment involves only readily-available chemicals and simple proteins that degrade the components of the cya...

Authors: Kunal K. Mehta, Niklaus H. Evitt and James R. Swartz

Parallel use of shake flask and microtiter plate online measuring devices (RAMOS and BioLector) reduces the number of experiments in laboratory-scale stirred tank bioreactors

Conventional experiments in small scale are often performed in a ‘Black Box’ fashion, analyzing only the product concentration in the final sample. Online monitoring of relevant process characteristics and par...

Authors: S. J. Wewetzer, M. Kunze, T. Ladner, B. Luchterhand, S. Roth, N. Rahmen, R. Kloß, A. Costa e Silva, L. Regestein and J. Büchs

Employing aromatic tuning to modulate output from two-component signaling circuits

Two-component signaling circuits (TCSs) govern the majority of environmental, pathogenic and industrial processes undertaken by bacteria. Therefore, controlling signal output from these circuits in a stimulus-...

Authors: Rahmi Yusuf and Roger R Draheim

Engineering pH responsive fibronectin domains for biomedical applications

Engineered antibodies with pH responsive cell surface target antigen-binding affinities that decrease at the acidic pH (5.5-5.8) within the endosomes have been found to have reduced susceptibility to degradati...

Authors: Pete Heinzelman, John Krais, Eliza Ruben and Robert Pantazes

Synthetic feedback control using an RNAi-based gene-regulatory device

Homeostasis within mammalian cells is achieved through complex molecular networks that can respond to changes within the cell or the environment and regulate the expression of the appropriate genes in response...

Authors: Ryan J Bloom, Sally M Winkler and Christina D Smolke

Recent advances in 3D printing of biomaterials

3D Printing promises to produce complex biomedical devices according to computer design using patient-specific anatomical data. Since its initial use as pre-surgical visualization models and tooling molds, 3D ...

Authors: Helena N Chia and Benjamin M Wu

Autonomous buckling of micrometer-sized lipid-protein membrane patches constructed by Dictyostelium discoideum

The cytosol of amoeba cells controls the membrane deformation during their motion in vivo. To investigate such ability of the cytosol of amoeba cell, Dictyostelium discoideum (Dictyostelium), in vitro, we used li...

Authors: Kei Takahashi and Taro Toyota

Molecular cloning using polymerase chain reaction, an educational guide for cellular engineering

Over the last decades, molecular cloning has transformed biological sciences. Having profoundly impacted various areas such as basic science, clinical, pharmaceutical, and environmental fields, the use of reco...

Authors: Sayed Shahabuddin Hoseini and Martin G Sauer

TGF-β1 conjugated chitosan collagen hydrogels induce chondrogenic differentiation of human synovium-derived stem cells

Unlike bone tissue, articular cartilage regeneration has not been very successful and has many challenges ahead. We have previously developed injectable hydrogels using photopolymerizable chitosan (MeGC) that ...

Authors: Jinku Kim, Brian Lin, Soyon Kim, Bogyu Choi, Denis Evseenko and Min Lee

Electrospun nanofibers as versatile interfaces for efficient gene delivery

The integration of gene delivery technologies with electrospun nanofibers is a versatile strategy to increase the potential of gene therapy as a key platform technology that can be readily utilized for numerou...

Authors: Slgirim Lee, Gyuhyung Jin and Jae-Hyung Jang

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

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

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

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

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

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

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