Articles

Modeling the architecture of the regulatory system controlling methylenomycin production in Streptomyces coelicolor

The antibiotic methylenomycin A is produced naturally by Streptomyces coelicolor A3(2), a model organism for streptomycetes. This compound is of particular interest to synthetic biologists because all of the a...

Authors: Jack E. Bowyer, Emmanuel LC. de los Santos, Kathryn M. Styles, Alex Fullwood, Christophe Corre and Declan G. Bates

In-vitro evaluation of Polylactic acid (PLA) manufactured by fused deposition modeling

With additive manufacturing (AM) individual and biocompatible implants can be generated by using suitable materials. The aim of this study was to investigate the biological effects of polylactic acid (PLA) man...

Authors: Matthias C. Wurm, Tobias Möst, Bastian Bergauer, Dominik Rietzel, Friedrich Wilhelm Neukam, Sandra C. Cifuentes and Cornelius von Wilmowsky

Construction of an easy-to-use CRISPR-Cas9 system by patching a newly designed EXIT circuit

Plasmid-borne genetic editing tools, including the widely used CRISPR-Cas9 system, have greatly facilitated bacterial programming to obtain novel functionalities. However, the lack of effective post-editing pl...

Authors: Qiang Tang, Chunbo Lou and Shuang-Jiang Liu

Facing the challenge of sustainable bioenergy production: Could halophytes be part of the solution?

Due to steadily growing population and economic transitions in the more populous countries, renewable sources of energy are needed more than ever. Plant biomass as a raw source of bioenergy and biofuel product...

Authors: Ahmed Debez, Ikram Belghith, Jan Friesen, Carsten Montzka and Skander Elleuche

Nucleotides upstream of the Kozak sequence strongly influence gene expression in the yeast S. cerevisiae

In the yeast Saccharomyces cerevisiae, as in every eukaryotic organism, the mRNA 5^′-untranslated region (UTR) is important for translation initiation. However, the patterns and mechanisms that determine the effic...

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

Three-dimensional (3D) evaluation of liquid distribution in shake flask using an optical fluorescence technique

Biotechnological development in shake flask necessitates vital engineering parameters e.g. volumetric power input, mixing time, gas liquid mass transfer coefficient, hydromechanical stress and effective shear ...

Authors: Amizon Azizan and Jochen Büchs

Flow-dependent fluorescence of CCVJ

The molecular rotor 9-(2-Carboxy-2-cyanovinyl)julolidine (CCVJ) is presumed to have a sensitivity towards velocity or shear which is supposed to result in a change in fluorescence quantum yield. Furthermore, a...

Authors: Markus J. Schmidt, David Sauter and Thomas Rösgen

A computational study of VEGF production by patterned retinal epithelial cell colonies as a model for neovascular macular degeneration

The configuration of necrotic areas within the retinal pigmented epithelium is an important element in the progression of age-related macular degeneration (AMD). In the exudative (wet) and non-exudative (dry) ...

Authors: Qanita Bani Baker, Gregory J. Podgorski, Elizabeth Vargis and Nicholas S. Flann

Investigation of poly(γ-glutamic acid) production via online determination of viscosity and oxygen transfer rate in shake flasks

Poly(γ-glutamic acid) (γ-PGA) is a biopolymer with many useful properties making it applicable for instance in food and skin care industries, in wastewater treatment, in biodegradable plastics or in the pharma...

Authors: Lena Regestein née Meissner, Julia Arndt, Thomas G. Palmen, Tim Jestel, Hitoshi Mitsunaga, Eiichiro Fukusaki and Jochen Büchs

Human pluripotent stem cell differentiation to functional pancreatic cells for diabetes therapies: Innovations, challenges and future directions

Recent advances in the expansion and directed pancreatogenic differentiation of human pluripotent stem cells (hPSCs) have intensified efforts to generate functional pancreatic islet cells, especially insulin-s...

Authors: Elena F. Jacobson and Emmanuel S. Tzanakakis

Prediction of Escherichia coli expression performance in microtiter plates by analyzing only the temporal development of scattered light during culture

Escherichia coli is often used for recombinant protein production. The expression of recombinant proteins negatively affects the microbial growth, thus, a balance between protein expre...

Authors: Tobias Ladner, Martina Mühlmann, Andreas Schulte, Georg Wandrey and Jochen Büchs

Delivery of stromal cell-derived factor 1α for in situ tissue regeneration

In situ tissue regeneration approach aims to exploit the body’s own biological resources and reparative capability and recruit host cells by utilizing cell-instructive biomaterials. In or...

Authors: Wen Zhao, Kaixiang Jin, Jiaojiao Li, Xuefeng Qiu and Song Li

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

AAV-based dual-reporter circuit for monitoring cell signaling in living human cells

High-throughput methods based on molecular reporters have greatly advanced our knowledge of cell signaling in mammalian cells. However, their ability to monitor various types of cells is markedly limited by th...

Authors: Zhiwen Zhang, Zachary Stickney, Natalie Duong, Kevin Curley and Biao Lu

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