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Synthetic biology

Mitchell S Weisenberger, Tara L Deans
Synthetic biologists use engineering principles to design and construct genetic circuits for programming cells with novel functions. A bottom-up approach is commonly used to design and construct genetic circuits by piecing together functional modules that are capable of reprogramming cells with novel behavior. While genetic circuits control cell operations through the tight regulation of gene expression, a diverse array of environmental factors within the extracellular space also has a significant impact on cell behavior...
March 19, 2018: Journal of Industrial Microbiology & Biotechnology
Matthew M Crane, Matt Kaeberlein
Aging is a fundamental aspect of life, yet also one of the most confounding. In individual cells, aging results in a progressive decline which affects all organelles and reduces a cell's ability to maintain homeostasis. Because of the interconnected nature of cellular systems, the failure of even a single organelle can have cascading effects. We are just beginning to understand the dramatic physiological changes that occur during aging. Because most aging research has focused on population dynamics, or differences between wild-type and mutant populations, single-cell behavior has been largely overlooked...
April 2018: Current Opinion in Systems Biology
Erqing Jin, Lynn Wong, Yun Jiao, Jake Engel, Benjamin Holdridge, Peng Xu
Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements...
December 2017: Synthetic and Systems Biotechnology
Jian Zha, Mattheos A G Koffas
Microbial production of plant-derived natural products by engineered microorganisms has achieved great success thanks to large extend to metabolic engineering and synthetic biology. Anthocyanins, the water-soluble colored pigments found in terrestrial plants that are responsible for the red, blue and purple coloration of many flowers and fruits, are extensively used in food and cosmetics industry; however, their current supply heavily relies on complex extraction from plant-based materials. A promising alternative is their sustainable production in metabolically engineered microbes...
December 2017: Synthetic and Systems Biotechnology
Lisa A Sawicki, Leila H Choe, Katherine L Wiley, Kelvin H Lee, April M Kloxin
Cells interact with and remodel their microenvironment, degrading large extracellular matrix (ECM) proteins (e.g., fibronectin, collagens) and secreting new ECM proteins and small soluble factors (e.g., growth factors, cytokines). Synthetic mimics of the ECM have been developed as controlled cell culture platforms for use in both fundamental and applied studies. However, how cells broadly remodel these initially well-defined matrices remains poorly understood and difficult to probe. In this work, we have established methods for widely examining both large and small proteins that are secreted by cells within synthetic matrices...
March 12, 2018: ACS Biomaterials Science & Engineering
Joselle M McCracken, Sheng Xu, Adina Badea, Kyung-In Jang, Zheng Yan, David J Wetzel, Kewang Nan, Qing Lin, Mengdi Han, Mikayla A Anderson, Jung Woo Lee, Zijun Wei, Matt Pharr, Renhan Wang, Jessica Su, Stanislav S Rubakhin, Jonathan V Sweedler, John A Rogers, Ralph G Nuzzo
Complex 3D organizations of materials represent ubiquitous structural motifs found in the most sophisticated forms of matter, the most notable of which are in life-sustaining hierarchical structures found in biology, but where simpler examples also exist as dense multilayered constructs in high-performance electronics. Each class of system evinces specific enabling forms of assembly to establish their functional organization at length scales not dissimilar to tissue-level constructs. This study describes materials and means of assembly that extend and join these disparate systems-schemes for the functional integration of soft and biological materials with synthetic 3D microscale, open frameworks that can leverage the most advanced forms of multilayer electronic technologies, including device-grade semiconductors such as monocrystalline silicon...
September 2017: Advanced Biosystems
Jeffrey R Watkins, Michael S Truitt, Houssam Osman, Rohan D Jeyarajah
Background and Objectives: Laparoscopic paraesophageal hernia repair (LPEHR) is the new standard, but the use of mesh is still debated. Biologic mesh has shown great promise, but only the U-shaped onlay has been extensively studied. Postoperative dysphagia has historically been a concern with the use of synthetic keyhole mesh and subsequently slowed its adoption. The purpose of our study was to identify the incidence of postoperative dysphagia in a series of patients who underwent laparoscopic paraesophageal hernia repair with novel placement of keyhole biologic mesh...
January 2018: JSLS: Journal of the Society of Laparoendoscopic Surgeons
J Carlos Rodríguez-Cabello, I González de Torre, A Ibañez-Fonzeca, M Alonso
Wound healing is a complex process that, in healthy tissues, starts immediately after the injury. Even though it is a natural well-orchestrated process, large trauma wounds, or injuries caused by acids or other chemicals, usually produce a non-elastic deformed tissue that not only have biological reduced properties but a clear aesthetic effect. One of the main drawbacks of the scaffolds used for wound dressing is the lack of elasticity, driving to non-elastic and contracted tissues. In the last decades, elastin based materials have gained in importance as biomaterials for tissue engineering applications due to their good cyto- and bio-compatibility, their ease handling and design, production and modification...
March 15, 2018: Advanced Drug Delivery Reviews
Masaki Matsumoto, Keiichi I Nakayama
Proteomics is a powerful tool for obtaining information on a large number of proteins with regard to their expression levels, interactions with other molecules, and posttranslational modifications. Whereas nontargeted, discovery proteomics uncovers differences in the proteomic landscape under different conditions, targeted proteomics has been developed to overcome the limitations of this approach with regard to quantitation. In addition to technical advances in instruments and informatics tools, the advent of the synthetic proteome composed of synthetic peptides or recombinant proteins has advanced the adoption of targeted proteomics across a wide range of research fields...
March 15, 2018: Current Opinion in Biotechnology
Zachary Js Mays, Nikhil U Nair
The trillions of microbes hosted by humans can dictate health or illness depending on a multitude of genetic, environmental, and lifestyle factors that help define the human ecosystem. As the human microbiota is characterized, so can the interconnectivity of microbe-host-disease be realized and manipulated. Designing microbes as therapeutic agents can not only enable targeted drug delivery but also restore homeostasis within a perturbed microbial community. Used for centuries in fermentation and preservation of food, lactic acid bacteria (LAB) have a long history of safe, and occasionally health promoting, interactions with the human gut, making them ideal candidates for engineered functionality...
March 15, 2018: Current Opinion in Biotechnology
Maria J Rodriguez, Thomas A Dixon, Eliad Cohen, Wenwen Huang, Fiorenzo G Omenetto, David L Kaplan
Freeform fabrication has emerged as a key direction in printing biologically-relevant materials and structures. With this emerging technology, complex structures with microscale resolution can be created in arbitrary geometries and without the limitations found in traditional bottom-up or top-down additive manufacturing methods. Recent advances in freeform printing have used the physical properties of microparticle-based granular gels as a medium for the submerged extrusion of bioinks. However, most of these techniques require post-processing or crosslinking for the removal of the printed structures [1,2]...
March 14, 2018: Acta Biomaterialia
Janardhan Reddy Koduru, Suresh Kumar Kailasa, Jigna R Bhamore, Ki-Hyun Kim, Tanushree Dutta, Kowsalya Vellingiri
Silver nanoparticles (Ag NPs) have recently emerged as promising materials in the biomedical sciences because of their antimicrobial activities towards a wide variety of microorganisms. Nanomaterial-based drug delivery systems with antimicrobial activity are critical as they may lead to novel treatments for cutaneous pathogens. In this review, we explore the recent progress on phytochemical-mediated synthesis of Ag NPs for antimicrobial treatment and associated infectious diseases. We discuss the biological activity of Ag NPs including mechanisms, antimicrobial activity, and antifungal/antiviral effects towards various microorganisms...
March 9, 2018: Advances in Colloid and Interface Science
Ya-Wen Cheng, Chia-Jung Chou, Pei-Ming Yang
DNA 5-methylcytosine (5-mC) methylation, a key epigenetic mark, is critical for biological and pathological processes. Aberrant DNA methylation occurs in all tumor types and correlates with tumor suppressor gene silencing. DNA methylation is thought to be very stable, and active DNA demethylation remains a long-standing enigma. Recently, the ten-eleven translocation (TET) family of oxygenases are found to oxidize 5-mC to 5-hydroxymethylcytosine (5-hmC), which is prerequisite for active DNA demethylation. Both TET1 expression and global 5-hmC content are significantly reduced in colorectal cancer (CRC), the top leading cause of cancer-related death in the world...
March 2018: Surgical Oncology
Cho Rong Lee, Changman Kim, Young Eun Song, Hyeonsung Im, You-Kwan Oh, Sunghoon Park, Jung Rae Kim
The biological conversion of carbon monoxide (CO) has been highlighted for the development of a C1 gas biorefinery process. Despite this, the toxicity and low reducing equivalent of CO uptake make biological conversion difficult. The use of synthetic co-cultures is an alternative way of enhancing the performance of CO bioconversion. This study evaluated a synthetic co-culture consisting of Citrobacter amalonaticus Y19 and Sporomusa ovata for acetate production from CO. In this consortium, the CO2 and H2 produced by the water-gas shift reaction of C...
March 2, 2018: Bioresource Technology
Marie Mardal, Petur Weihe Dalsgaard, Bing Qi, Christian Brinch Mollerup, Pieter Annaert, Kristian Linnet
The main analytical targets of synthetic cannabinoids are often metabolites. With the high number of new psychoactive substances entering the market, suitable workflows are needed for analytical target identification in biological samples. The aims of this study were to identify the main metabolites of the synthetic cannabinoids, AMB-CHMICA and 5C-AKB48, using an in silico-assisted workflow with analytical data acquired using ultra-high-performance liquid chromatography-(ion mobility spectroscopy)-high resolution-mass spectrometry in data-independent acquisition mode (UHPLC-(IMS)-HR-MSE )...
March 10, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Robert Sidney Cox, Curtis Madsen, James McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Thomas Gorochowski, Raik Grünberg, Augustin Luna, Nicolas Le Novere, Matthew Pocock, Herbert Sauro, John T Sexton, Guy-Bart Stan, Jeffrey J Tabor, Christopher A Voigt, Zach Zundel, Chris Myers, Jacob Beal, Anil Wipat
People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs...
March 19, 2018: Journal of Integrative Bioinformatics
Katerina Kaziani, Alice G Vassiliou, Anastasia Kotanidou, Chariclea Athanasiou, Ioanna Korovesi, Konstantinos Glynos, Stylianos E Orfanos
INTRODUCTION: Pulmonary capillary endothelium-bound (PCEB) angiotensin-converting enzyme (ACE) activity is a direct and quantifiable index of pulmonary endothelial function that decreases early in acute respiratory distress syndrome (ARDS) and correlates with its severity. Endothelial dysfunction is a major pathophysiology that underlies sepsis-related ARDS. Recombinant human activated protein C (rhAPC), now withdrawn from the market, has been used in the recent past as an endothelial-protective treatment in patients with septic organ dysfunction...
March 2018: Infectious Diseases and Therapy
Mairi M Littleson, Christopher M Baker, Anne J Dalençon, Elizabeth C Frye, Craig Jamieson, Alan R Kennedy, Kenneth B Ling, Matthew M McLachlan, Mark G Montgomery, Claire J Russell, Allan J B Watson
Natural phytotoxins are valuable starting points for agrochemical design. Acting as a jasmonate agonist, coronatine represents an attractive herbicidal lead with novel mode of action, and has been an important synthetic target for agrochemical development. However, both restricted access to quantities of coronatine and a lack of a suitably scalable and flexible synthetic approach to its constituent natural product components, coronafacic and coronamic acids, has frustrated development of this target. Here, we report gram-scale production of coronafacic acid that allows a comprehensive structure-activity relationship study of this target...
March 16, 2018: Nature Communications
Christian Greunke, Elke Regina Duell, Paul Michael D'Agostino, Anna Glöckle, Katharina Lamm, Tobias Alexander Marius Gulder
Specialized metabolites from bacteria are an important source of inspiration for drug development. The genes required for the biosynthesis of such metabolites in bacteria are usually organized in so-called biosynthetic gene clusters (BGCs). Using modern bioinformatic tools, the wealth of genomic data can be scanned for such BGCs and the expected products can often structurally be predicted in silico. This facilitates the directed discovery of putatively novel bacterial metabolites. However, the production of these molecules often requires genetic manipulation of the BGC for activation or the expression of the pathway in a heterologous host...
March 13, 2018: Metabolic Engineering
Asmaa E Kassab, Ehab M Gedawy
As we are interested in synthetizing biologically active leads with dual anticancer and antibacterial activity, we adopted biology oriented drug synthesis (BIODS) strategy to synthesize a series of novel ciprofloxacin (CP) hybrids. The National Cancer Institute (USA) selected seventeen newly synthesized compounds for anticancer evaluation against 59 different human tumor cell lines. Five compounds 3e, 3f, 3h, 3o and 3p were further studied through determination of IC50 values against the most sensitive cancer cell lines...
March 9, 2018: European Journal of Medicinal Chemistry
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