Using synthetic biological parts and microbioreactors to explore the protein expression characteristics of Escherichia coli

Synthetic biology has developed numerous parts for the precise control of protein expression. However, relatively little is known about the burden these place on a host, or their reliability under varying environmental conditions. To address this, we made use of synthetic transcriptional and translational elements to create a combinatorial library of constructs that modulated expression strength of a green fluorescent protein. Combining this library with a microbioreactor platform, we were able to perform a detailed large-scale assessment of transient expression and growth characteristics of two <i>Escherichia coli</i> strains across several temperatures. This revealed significant differences in the robustness of both strains to differing types of protein expression, and a complex response of transcriptional and translational elements to differing temperatures. This study supports the development of reliable synthetic biological systems capable of working across different hosts and environmental contexts. Plasmids developed during this work have been made publicly available to act as a reference set for future research

Peptide dendrimer-conjugates of ketoprofen: synthesis and ex vivo and in vivo evaluations of passive diffusion, sonophoresis and iontophoresis for skin delivery

The aim of this study was to evaluate skin delivery of ketoprofen when covalently tethered to mildly cationic (2or 4) peptide dendrimers prepared wholly by solid phase peptide synthesis. The amino acids glycine, arginine and lysine formed the dendrimer with ketoprofen tethered either to the lysine side-arm (N) or periphery of dendrimeric branches. Passive diffusion, sonophoresis- and iontophoresis-assisted permeation of each peptide dendrimer-drug conjugate (D1–D4) was studied across mouse skin, both in vitro and in vivo. In addition, skin toxicity of dendrimeric conjugates when trialed with iontophoresis or sonophoresis was also evaluated. All dendrimeric conjugates improved aqueous solubility at least 5-fold, compared to ketoprofen alone, while also exhibiting appreciable lipophilicity. In vitro passive diffusion studies revealed that ketoprofen in its native form was delivered to a greater extent, compared with a dendrimer-conjugated form at the end of 24\ua0h (Q(μg/cm): ketoprofen (68.06\ua0±\ua03.62)\ua0>\ua0D2 (49.62\ua0±\ua02.92)\ua0>\ua0D4 (19.20\ua0±\ua00.89)\ua0>\ua0D1 (6.45\ua0±\ua00.40)\ua0>\ua0D3 (2.21\ua0±\ua00.19). However, sonophoresis substantially increased the skin permeation of ketoprofen-dendrimer conjugates in 30\ua0min (Q(μg/cm): D4 (122.19\ua0±\ua07.14)\ua0>\ua0D2 (66.74\ua0±\ua03.86)\ua0>\ua0D1 (52.10\ua0±\ua03.22)\ua0>\ua0D3 (41.66\ua0±\ua03.22)) although ketoprofen alone again proved superior (Q: 167.99\ua0±\ua09.11\ua0μg/cm). Next, application of iontophoresis was trialed and shown to considerably increase permeation of dendrimeric ketoprofen in 6\ua0h (Q(μg/cm): D2 (711.49\ua0±\ua039.14)\ua0>\ua0D4 (341.23\ua0±\ua016.43)\ua0>\ua0D3 (89.50\ua0±\ua04.99)\ua0>\ua0D1 (50.91\ua0±\ua02.98), with a Qvalue of 96.60\ua0±\ua05.12\ua0μg/cmfor ketoprofen alone). In vivo studies indicated that therapeutically relevant concentrations of ketoprofen could be delivered transdermally when iontophoresis was paired with D2 (985.49\ua0±\ua043.25\ua0ng/mL). Further, histopathological analysis showed that the dendrimeric approach was a safe mode as ketoprofen alone. The present study successfully demonstrates that peptide dendrimer conjugates of ketoprofen, when combined with non-invasive modalities, such as iontophoresis can enhance skin permeation with clinically relevant concentrations achieved transdermally

Razvoj matriksnih sustava za transdermalnu isporuku pentazocina: In vitro/in vivo ispitivanje

The present study aimed to develop hydroxypropyl methylcellulose based transdermal delivery of pentazocine. In formulations containing lower proportions of polymer, the drug released followed the Higuchi kinetics while, with an increase in polymer content, it followed the zero-order release kinetics. Release exponent (n) values imply that the release of pentazocine from matrices was non-Fickian. FT-IR, DSC and XRD studies indicated no interaction between drug and polymer. The in vitro dissolution rate constant, dissolution half-life and pharmacokinetic parameters (Cmax, tmax, AUC(s), t1/2, Kel, and MRT) were evaluated statistically by two-way ANOVA. A significant difference was observed between but not within the tested products. Statistically, a good correlation was found between per cent of drug absorbed from patches vs. Cmax, and AUC(s). A good correlation was also observed when per cent drug released was correlated with the blood drug concentration obtained at the same time point. The results of this study indicate that the polymeric matrix films of pentazocine hold potential for transdermal drug delivery.U radu je opisan razvoj transdermalnih sustava na bazi hidroksipropil metilceluloze za isporuku pentazocina. U pripravcima koji sadrže manje udjele polimera, otpuštanje lijeka slijedilo je Higuchijevu kinetiku. Međutim, ako je udio polimera veći oslobađanje je najbolje odgovaralo kinetici nultog reda. Vrijednost eksponenta n implicira da oslobađanje pentazocina iz matriksa nije po Fickovom zakonu. FT-IR, DSC i X RD studije ukazuju da nema interakcije između ljekovite tvari i polimera. In vitro konstanta oslobađanja, poluvrijeme oslobađanja i farmakokinetički parametri (Cmax, tmax, AUC(s), t1/2, Kel, i MRT) procijenjeni su statistički koristeći ANOVA program. Značajna razlika primijećena je između, ali ne i unutar testiranih pripravaka. Pronađena je dobra korelacija između lijeka apsorbiranog iz flastera i Cmax i AUC(s) te oslobođenog lijeka i koncentracije lijeka u krvi. Rezultati ukazuju da su polimerni matriksni filmovi pentazocina potencijalno dobri sustavi za transdermalnu primjenu lijeka

Principles of genetic circuit design

Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.National Institute of General Medical Sciences (U.S.) (Grant P50 GM098792)National Institute of General Medical Sciences (U.S.) (Grant R01 GM095765)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (EEC0540879)Life Technologies, Inc. (A114510)National Science Foundation (U.S.). Graduate Research FellowshipUnited States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant 4500000552

Doing synthetic biology with photosynthetic microorganisms

The use of photosynthetic microbes as synthetic biology hosts for the sustainable production of commodity chemicals and even fuels has received increasing attention over the last decade. The number of studies published, tools implemented, and resources made available for microalgae have increased beyond expectations during the last few years. However, the tools available for genetic engineering in these organisms still lag those available for the more commonly used heterotrophic host organisms. In this mini-review, we provide an overview of the photosynthetic microbes most commonly used in synthetic biology studies, namely cyanobacteria, chlorophytes, eustigmatophytes and diatoms. We provide basic information on the techniques and tools available for each model group of organisms, we outline the state-of-the-art, and we list the synthetic biology tools that have been successfully used. We specifically focus on the latest CRISPR developments, as we believe that precision editing and advanced genetic engineering tools will be pivotal to the advancement of the field. Finally, we discuss the relative strengths and weaknesses of each group of organisms and examine the challenges that need to be overcome to achieve their synthetic biology potential.Peer reviewe

Negated bio-events: Analysis and identification

Background: Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event annotations.Results: We have conducted a detailed analysis of three open access bio-event corpora containing negation information (i.e., GENIA Event, BioInfer and BioNLP'09 ST), and have identified the main types of negated bio-events. We have analysed the key aspects of a machine learning solution to the problem of detecting negated events, including selection of negation cues, feature engineering and the choice of learning algorithm. Combining the best solutions for each aspect of the problem, we propose a novel framework for the identification of negated bio-events. We have evaluated our system on each of the three open access corpora mentioned above. The performance of the system significantly surpasses the best results previously reported on the BioNLP'09 ST corpus, and achieves even better results on the GENIA Event and BioInfer corpora, both of which contain more varied and complex events.Conclusions: Recently, in the field of biomedical text mining, the development and enhancement of event-based systems has received significant interest. The ability to identify negated events is a key performance element for these systems. We have conducted the first detailed study on the analysis and identification of negated bio-events. Our proposed framework can be integrated with state-of-the-art event extraction systems. The resulting systems will be able to extract bio-events with attached polarities from textual documents, which can serve as the foundation for more elaborate systems that are able to detect mutually contradicting bio-events. © 2013 Nawaz et al.; licensee BioMed Central Ltd