Articles

Streamlining recombination-mediated genetic engineering by validating three neutral integration sites in Synechococcus sp. PCC 7002

Synechococcus sp. PCC 7002 (henceforth Synechococcus) is developing into a powerful synthetic biology chassis. In order to streamline the integration of genes into the Synechococcus ch...

Authors: Anne Ilse Maria Vogel, Rahmi Lale and Martin Frank Hohmann-Marriott

Significantly enhanced biomass production of a novel bio-therapeutic strain Lactobacillus plantarum (AS-14) by developing low cost media cultivation strategy

Probiotic bacteria are becoming an important tool for improving human health, controlling diseases and enhancing immune responses. The availability of a cost effective cultivation conditions has profound effec...

Authors: Asma Manzoor, Javed Iqbal Qazi, Ikram ul Haq, Hamid Mukhtar and Akhtar Rasool

Application of denitrifying wood chip bioreactors for management of residential non-point sources of nitrogen

Two important and large non-point sources of nitrogen in residential areas that adversely affect water quality are stormwater runoff and effluent from on-site treatment systems. These sources are challenging t...

Authors: E. V. Lopez-Ponnada, T. J. Lynn, M. Peterson, S. J. Ergas and J. R. Mihelcic

Synthesis of umbelliferone derivatives in Escherichia coli and their biological activities

Umbelliferone, also known as 7-hydroxycoumarin, is a phenolic metabolite found in many familiar plants. Its derivatives have been shown to have various pharmacological and chemo-preventive effects on human hea...

Authors: Luan Luong Chu, Ramesh Prasad Pandey, Haet Nim Lim, Hye Jin Jung, Nguyen Huy Thuan, Tae-Su Kim and Jae Kyung Sohng

Directing three-dimensional multicellular morphogenesis by self-organization of vascular mesenchymal cells in hyaluronic acid hydrogels

Physical scaffolds are useful for supporting cells to form three-dimensional (3D) tissue. However, it is non-trivial to develop a scheme that can robustly guide cells to self-organize into a tissue with the de...

Authors: Xiaolu Zhu, Shiva Gojgini, Ting-Hsuan Chen, Peng Fei, Siyan Dong, Chih-Ming Ho and Tatiana Segura

Portable nuclear magnetic resonance biosensor and assay for a highly sensitive and rapid detection of foodborne bacteria in complex matrices

Nuclear magnetic resonance (NMR) technique is a powerful analytical tool in determining the presence of bacterial contaminants in complex biological samples. In this paper, a portable NMR-based (pNMR) biosenso...

Authors: Yilun Luo and Evangelyn C. Alocilja

Strategies for using nanoprobes to perceive and treat cancer activity: a review

Nanomedicine has seen a significant increase in research on stimuli-responsive activatable nanoprobes for tumor-specific delivery and diagnosis. The tumor microenvironment has particular characteristics that c...

Authors: Byunghoon Kang, Aastha Kukreja, Daesub Song, Yong-Min Huh and Seungjoo Haam

Aptamer-based sandwich-type biosensors

Sandwich-type biosensor platforms have drawn lots of attentions due to its superior features, compared to other platforms, in terms of its stable and reproducible responses and easy enhancement in the detectio...

Authors: Ho Bin Seo and Man Bock Gu

Technical advances in global DNA methylation analysis in human cancers

Prototypical abnormalities of genome-wide DNA methylation constitute the most widely investigated epigenetic mechanism in human cancers. Errors in the cellular machinery to faithfully replicate the global 5-me...

Authors: Basudev Chowdhury, Il-Hoon Cho and Joseph Irudayaraj

Reliable measurement of E. coli single cell fluorescence distribution using a standard microscope set-up

Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system...

Authors: Marilisa Cortesi, Lucia Bandiera, Alice Pasini, Alessandro Bevilacqua, Alessandro Gherardi, Simone Furini and Emanuele Giordano

Detection of extremely low concentration waterborne pathogen using a multiplexing self-referencing SERS microfluidic biosensor

It is challenging to achieve ultrasensitive and selective detection of waterborne pathogens at extremely low levels (i.e., single cell/mL) using conventional methods. Even with molecular methods such as ELISA ...

Authors: Chao Wang, Foram Madiyar, Chenxu Yu and Jun Li

Influence of gold nanoparticle surface chemistry and diameter upon Alzheimer’s disease amyloid-β protein aggregation

Deposits of aggregated amyloid-β protein (Aβ) are a pathological hallmark of Alzheimer’s disease (AD). Thus, one therapeutic strategy is to eliminate these deposits by halting Aβ aggregation. While a variety o...

Authors: Kelly A. Moore, Kayla M. Pate, Deborah D. Soto-Ortega, Samuel Lohse, Nicholas van der Munnik, Mihyun Lim, Kaliah S. Jackson, Venetia D. Lyles, Lemeisha Jones, Nisha Glassgow, Vanessa M. Napumecheno, Shanee Mobley, Mark J. Uline, Rahina Mahtab, Catherine J. Murphy and Melissa A. Moss

Future developments in biosensors for field-ready Zika virus diagnostics

Since early reports of the recent Zika virus outbreak in May 2015, much has been learned and discussed regarding Zika virus infection and transmission. However, many opportunities still remain for translating ...

Authors: Ariana M. Nicolini, Katherine E. McCracken and Jeong-Yeol Yoon

Pretreatment of vinasse from the sugar refinery industry under non-sterile conditions by Trametes versicolor in a fluidized bed bioreactor and its effect when coupled to an UASB reactor

During hydrous ethanol production from the sugar refinery industry in Mexico, vinasse is generated. Phenolic compounds and melanoidins contribute to its color and make degradation of the vinasse a difficult ta...

Authors: Elda España-Gamboa, Teresa Vicent, Xavier Font, Jorge Dominguez-Maldonado, Blondy Canto-Canché and Liliana Alzate-Gaviria

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction

Microbial consortia composed of autotrophic and heterotrophic species abound in nature, yet examples of synthetic communities with mixed metabolism are limited in the laboratory. We previously engineered a mod...

Authors: Stephanie G. Hays, Leo L. W. Yan, Pamela A. Silver and Daniel C. Ducat

Towards the 10-year milestone of Journal of Biological Engineering

October 10^th, 2016 marked the 9^th anniversary for the Journal of Biological Engineering (JBE), the official journal of Institute of Biological Engineering (IBE), published by BioMed Central. We are entering into ...

Authors: Jeong-Yeol Yoon

Single cell isolation process with laser induced forward transfer

A viable single cell is crucial for studies of single cell biology. In this paper, laser-induced forward transfer (LIFT) was used to isolate individual cell with a closed chamber designed to avoid contaminatio...

Authors: Yu Deng, Philippe Renaud, Zhongning Guo, Zhigang Huang and Ying Chen

Cellulolytic RoboLector – towards an automated high-throughput screening platform for recombinant cellulase expression

Cellulases are key player in the hydrolyzation of cellulose. Unfortunately, this reaction is slow and a bottleneck in the process chain from biomass to intermediates and biofuels due to low activities of the e...

Authors: Martina Mühlmann, Martin Kunze, Joaquim Ribeiro, Bertram Geinitz, Christian Lehmann, Ulrich Schwaneberg, Ulrich Commandeur and Jochen Büchs

Can terminators be used as insulators into yeast synthetic gene circuits?

In bacteria, transcription units can be insulated by placing a terminator in front of a promoter. In this way promoter leakage due to the read-through from an upstream gene or RNA polymerase unspecific binding...

Authors: Wenjiang Song, Jing Li, Qiang Liang and Mario Andrea Marchisio

Algae-based biofilm productivity utilizing dairy wastewater: effects of temperature and organic carbon concentration

Biofilm-based microalgal growth was determined as functions of organic chemical loading and water temperature utilizing dairy wastewater from a full-scale dairy farm. The dairy industry is a significant source...

Authors: Zachary T. Fica and Ronald C. Sims

Bioelectronic nose and its application to smell visualization

There have been many trials to visualize smell using various techniques in order to objectively express the smell because information obtained from the sense of smell in human is very subjective. So far, well-...

Authors: Hwi Jin Ko and Tai Hyun Park

The extracellular microscape governs mesenchymal stem cell fate

Each cell forever interacts with its extracellular matrix (ECM); a stem cell relies on this interaction to guide differentiation. The stiffness, nanotopography, protein composition, stress and strain inherent ...

Authors: William J. Hadden and Yu Suk Choi

Exploiting the dynamic properties of covalent modification cycle for the design of synthetic analog biomolecular circuitry

Cycles of covalent modification are ubiquitous motifs in cellular signalling. Although such signalling cycles are implemented via a highly concise set of chemical reactions, they have been shown to be capable ...

Authors: Mathias Foo, Rucha Sawlekar and Declan G. Bates

Respiration activity monitoring system for any individual well of a 48-well microtiter plate

Small-scale micro-bioreactors have become the cultivation vessel of choice during the first steps of bioprocess development. They combine high cultivation throughput with enhanced cost efficiency per cultivati...

Authors: David Flitsch, Sebastian Krabbe, Tobias Ladner, Mario Beckers, Jana Schilling, Stefan Mahr, Uwe Conrath, Werner K. Schomburg and Jochen Büchs

Significantly enhancing recombinant alkaline amylase production in Bacillus subtilis by integration of a novel mutagenesis-screening strategy with systems-level fermentation optimization

Alkaline amylase has significant potential for applications in the textile, paper and detergent industries, however, low yield of which cannot meet the requirement of industrial application. In this work, a no...

Authors: Yingfang Ma, Wei Shen, Xianzhong Chen, Long Liu, Zhemin Zhou, Fei Xu and Haiquan Yang

Design and engineering of a transmissible antiviral defense

We propose, model, and implement a novel system of population-level intervention against a virus. One context is a treatment against a chronic infection such as HIV. The underlying principle is a form of virus...

Authors: Matthew L. Paff, Scott L. Nuismer, Andrew D. Ellington, Ian J. Molineux, Ryan H. May and James J. Bull

Probing unnatural amino acid integration into enhanced green fluorescent protein by genetic code expansion with a high-throughput screening platform

Genetic code expansion has developed into an elegant tool to incorporate unnatural amino acids (uAA) at predefined sites in the protein backbone in response to an amber codon. However, recombinant production a...

Authors: Georg Wandrey, Joel Wurzel, Kyra Hoffmann, Tobias Ladner, Jochen Büchs, Lorenz Meinel and Tessa Lühmann

Design and integration of a problem-based biofabrication course into an undergraduate biomedical engineering curriculum

The rapidly evolving discipline of biological and biomedical engineering requires adaptive instructional approaches that teach students to target and solve multi-pronged and ill-structured problems at the cutt...

Authors: Ritu Raman, Marlon Mitchell, Pablo Perez-Pinera, Rashid Bashir and Lizanne DeStefano

Treatment of saline municipal wastewater using hybrid growth system

In this study, a hybrid treatment system (Fluidized Bed positioned in a biological reactor of an Activated Sludge process) was used to treat saline domestic wastewater. The performance of the mentioned hybrid ...

Authors: N. Salmanikhas, M. Tizghadam and A. Rashidi Mehrabadi

Optimization of the fermentation process of Cordyceps sobolifera Se-CEPS and its anti-tumor activity in vivo

Cordyceps sobolifera (C. sobolifera) isolated from cicadae was used as the starting fungus to produce selenium-enriched C. sobolifera extracellular polysaccharide (Se-CEPS). An orthogo...

Authors: Shengli Yang and Hui Zhang

CE-UV/VIS and CE-MS for monitoring organic impurities during the downstream processing of fermentative-produced lactic acid from second-generation renewable feedstocks

During the downstream process of bio-based bulk chemicals, organic impurities, mostly residues from the fermentation process, must be separated to obtain a pure and ready-to-market chemical. In this study, cap...

Authors: Hendrik Laube, Frank-Michael Matysik, Andreas Schmidberger, Kerstin Mehlmann, Andreas Toursel and Jana Boden

Seamless site-directed mutagenesis of the Saccharomyces cerevisiae genome using CRISPR-Cas9

CRISPR assisted homology directed repair enables the introduction of virtually any modification to the Saccharomyces cerevisiae genome. Of obvious interest is the marker-free and seamless introduction of point mu...

Authors: Damien Biot-Pelletier and Vincent J. J. Martin

Modulating the import of medium-chain alkanes in E. coli through tuned expression of FadL

In recent years, there have been intensive efforts to develop synthetic microbial platforms for the production, biosensing and bio-remediation of fossil fuel constituents such as alkanes. Building predictable ...

Authors: Toby P. Call, M. Kalim Akhtar, Frank Baganz and Chris Grant

Respirator masks protect health but impact performance: a review

Respiratory protective masks are used whenever it is too costly or impractical to remove airborne contamination from the atmosphere. Respirators are used in a wide range of occupations, form the military to me...

Authors: Arthur T. Johnson

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functi...

Authors: Gregory Linshiz, Erik Jensen, Nina Stawski, Changhao Bi, Nick Elsbree, Hong Jiao, Jungkyu Kim, Richard Mathies, Jay D. Keasling and Nathan J. Hillson

Rational design of Raman-labeled nanoparticles for a dual-modality, light scattering immunoassay on a polystyrene substrate

Surface-enhanced Raman scattering (SERS) is a powerful light scattering technique that can be used for sensitive immunoassay development and cell labeling. A major obstacle to using SERS is the complexity of f...

Authors: Nathan D. Israelsen, Donald Wooley, Cynthia Hanson and Elizabeth Vargis

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

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

Heterologous expression of the isopimaric acid pathway in Nicotiana benthamiana and the effect of N-terminal modifications of the involved cytochrome P450 enzyme

Plant terpenoids are known for their diversity, stereochemical complexity, and their commercial interest as pharmaceuticals, food additives, and cosmetics. Developing biotechnology approaches for the productio...

Authors: Thiyagarajan Gnanasekaran, Konstantinos Vavitsas, Johan Andersen-Ranberg, Agnieszka Zygadlo Nielsen, Carl Erik Olsen, Björn Hamberger and Poul Erik Jensen

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