scholarly journals Blueprints for Biosensors: Design, Limitations, and Applications

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 375 ◽  
Author(s):  
Alexander Carpenter ◽  
Ian Paulsen ◽  
Thomas Williams
Keyword(s):  
Transcription Factors ◽  
Synthetic Biology ◽  
Nucleic Acids ◽  
Dynamic Range ◽  
Optimal Performance ◽  
Ease Of Use ◽  
Ligand Specificity ◽  
Biotechnological Application ◽  
Wide Range ◽  
Output Time

Biosensors are enabling major advances in the field of analytics that are both facilitating and being facilitated by advances in synthetic biology. The ability of biosensors to rapidly and specifically detect a wide range of molecules makes them highly relevant to a range of industrial, medical, ecological, and scientific applications. Approaches to biosensor design are as diverse as their applications, with major biosensor classes including nucleic acids, proteins, and transcription factors. Each of these biosensor types has advantages and limitations based on the intended application, and the parameters that are required for optimal performance. Specifically, the choice of biosensor design must consider factors such as the ligand specificity, sensitivity, dynamic range, functional range, mode of output, time of activation, ease of use, and ease of engineering. This review discusses the rationale for designing the major classes of biosensor in the context of their limitations and assesses their suitability to different areas of biotechnological application.

scholarly journals Robust gene expression control in human cells with a novel universal TetR aptamer splicing module

2019 ◽  
Vol 47 (20) ◽  
pp. e132-e132 ◽  
Author(s):  
Adam A Mol ◽  
Florian Groher ◽  
Britta Schreiber ◽  
Ciaran Rühmkorff ◽  
Beatrix Suess
Keyword(s):  
Gene Expression ◽  
Synthetic Biology ◽  
Dynamic Range ◽  
Intron Retention ◽  
Human Cells ◽  
Fine Tuning ◽  
Genomic Context ◽  
Mammalian Cell Lines ◽  
Gene Expression Control ◽  
Wide Range

Abstract Fine-tuning of gene expression is desirable for a wide range of applications in synthetic biology. In this context, RNA regulatory devices provide a powerful and highly functional tool. We developed a versatile, robust and reversible device to control gene expression by splicing regulation in human cells using an aptamer that is recognized by the Tet repressor TetR. Upon insertion in proximity to the 5′ splice site, intron retention can be controlled via the binding of TetR to the aptamer. Although we were able to demonstrate regulation for different introns, the genomic context had a major impact on regulation. In consequence, we advanced the aptamer to develop a splice device. Our novel device contains the aptamer integrated into a context of exonic and intronic sequences that create and maintain an environment allowing a reliable and robust splicing event. The exon-born, additional amino acids will then be cleaved off by a self-cleaving peptide. This design allows portability of the splicing device, which we confirmed by demonstrating its functionality in different gene contexts. Intriguingly, our splicing device shows a high dynamic range and low basal activity, i.e. desirable features that often prove a major challenge when implementing synthetic biology in mammalian cell lines.

scholarly journals Poxviral Targeting of Interferon Regulatory Factor Activation

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1191 ◽  
Author(s):  
Clara Lawler ◽  
Gareth Brady
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Nucleic Acids ◽  
Viral Gene Expression ◽  
Host Cells ◽  
Viral Gene ◽  
Type I ◽  
Adaptive Responses ◽  
Regulatory Factor ◽  
Wide Range

As viruses have a capacity to rapidly evolve and continually alter the coding of their protein repertoires, host cells have evolved pathways to sense viruses through the one invariable feature common to all these pathogens—their nucleic acids. These genomic and transcriptional pathogen-associated molecular patterns (PAMPs) trigger the activation of germline-encoded anti-viral pattern recognition receptors (PRRs) that can distinguish viral nucleic acids from host forms by their localization and subtle differences in their chemistry. A wide range of transmembrane and cytosolic PRRs continually probe the intracellular environment for these viral PAMPs, activating pathways leading to the activation of anti-viral gene expression. The activation of Nuclear Factor Kappa B (NFκB) and Interferon (IFN) Regulatory Factor (IRF) family transcription factors are of central importance in driving pro-inflammatory and type-I interferon (TI-IFN) gene expression required to effectively restrict spread and trigger adaptive responses leading to clearance. Poxviruses evolve complex arrays of inhibitors which target these pathways at a variety of levels. This review will focus on how poxviruses target and inhibit PRR pathways leading to the activation of IRF family transcription factors.

From the history of the development of electronic dictionaries: foreign and domestic experience

2020 ◽  
Vol 11 (1) ◽  
pp. 6-12
Author(s):  
O. Y. Balalaieva ◽  
Keyword(s):  
Human Activity ◽  
Current Level ◽  
Ease Of Use ◽  
Advanced Search ◽  
Wide Range ◽  
Promising Area ◽  
History Of ◽  
Machine Readable ◽  
Everyday Communication ◽  
Educational Professional

The purpose of the article is to study the dynamics of electronic dictionaries development abroad and in Ukraine using methods of analysis of scientific sources, comparison, generalization and systematization. Electronic dictionaries have been found to be a relatively new phenomenon in the lexicographic market, evolving from machine-readable dictionaries, exact copies of paper editions to complex digital lexicographic systems with a powerful arsenal of functions over the decades. The stages of development of autonomous and online dictionaries are described. Electronic dictionaries due to the advanced search capabilities, speed, simplicity, ease of use, accessibility and compactness have gained popularity among a wide range of users. Today they are used in many spheres of human activity – scientific, educational, professional, everyday communication. However, the analysis of the current level of development of Ukrainian electronic resources indicates a shortage of electronic dictionaries both common and terminological vocabulary. The lack of electronic dictionaries is due to a number of objective problems, both practical and theoretical, that is why research in the field of domestic computer lexicography is a promising area of further research.

scholarly journals Detectivity optimization to detect of ultraweak light fluxes with an EM-CCD as binary photon counter array

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ibtissame Khaoua ◽  
Guillaume Graciani ◽  
Andrey Kim ◽  
François Amblard
Keyword(s):  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Photon Counting ◽  
Detection Methods ◽  
Strong Nonlinearity ◽  
Wide Range ◽  
Depth Analysis ◽  
Spatially Extended ◽  
Extended Sources ◽  
Photon Counting Mode

AbstractFor a wide range of purposes, one faces the challenge to detect light from extremely faint and spatially extended sources. In such cases, detector noises dominate over the photon noise of the source, and quantum detectors in photon counting mode are generally the best option. Here, we combine a statistical model with an in-depth analysis of detector noises and calibration experiments, and we show that visible light can be detected with an electron-multiplying charge-coupled devices (EM-CCD) with a signal-to-noise ratio (SNR) of 3 for fluxes less than $$30\,{\text{photon}}\,{\text{s}}^{ - 1} \,{\text{cm}}^{ - 2}$$ 30 photon s - 1 cm - 2 . For green photons, this corresponds to 12 aW $${\text{cm}}^{ - 2}$$ cm - 2 ≈ $$9{ } \times 10^{ - 11}$$ 9 × 10 - 11 lux, i.e. 15 orders of magnitude less than typical daylight. The strong nonlinearity of the SNR with the sampling time leads to a dynamic range of detection of 4 orders of magnitude. To detect possibly varying light fluxes, we operate in conditions of maximal detectivity $${\mathcal{D}}$$ D rather than maximal SNR. Given the quantum efficiency $$QE\left( \lambda \right)$$ Q E λ of the detector, we find $${ \mathcal{D}} = 0.015\,{\text{photon}}^{ - 1} \,{\text{s}}^{1/2} \,{\text{cm}}$$ D = 0.015 photon - 1 s 1 / 2 cm , and a non-negligible sensitivity to blackbody radiation for T > 50 °C. This work should help design highly sensitive luminescence detection methods and develop experiments to explore dynamic phenomena involving ultra-weak luminescence in biology, chemistry, and material sciences.

scholarly journals Biosynthesis of Nature-Inspired Unnatural Cannabinoids

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2914
Author(s):  
Kevin J. H. Lim ◽  
Yan Ping Lim ◽  
Yossa D. Hartono ◽  
Maybelle K. Go ◽  
Hao Fan ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Cannabis Sativa ◽  
Genetic Manipulation ◽  
Therapeutic Agents ◽  
Orphan Receptors ◽  
Complex Chemical ◽  
Biological Targets ◽  
Chemical Structures ◽  
Commercial Use ◽  
Wide Range

Natural products make up a large proportion of medicine available today. Cannabinoids from the plant Cannabis sativa is one unique class of meroterpenoids that have shown a wide range of bioactivities and recently seen significant developments in their status as therapeutic agents for various indications. Their complex chemical structures make it difficult to chemically synthesize them in efficient yields. Synthetic biology has presented a solution to this through metabolic engineering in heterologous hosts. Through genetic manipulation, rare phytocannabinoids that are produced in low yields in the plant can now be synthesized in larger quantities for therapeutic and commercial use. Additionally, an exciting avenue of exploring new chemical spaces is made available as novel derivatized compounds can be produced and investigated for their bioactivities. In this review, we summarized the biosynthetic pathways of phytocannabinoids and synthetic biology efforts in producing them in heterologous hosts. Detailed mechanistic insights are discussed in each part of the pathway in order to explore strategies for creating novel cannabinoids. Lastly, we discussed studies conducted on biological targets such as CB1, CB2 and orphan receptors along with their affinities to these cannabinoid ligands with a view to inform upstream diversification efforts.

scholarly journals Bulk Relativistic Motion in a Complete Sample of Radio Selected AGN

1987 ◽  
Vol 121 ◽  
pp. 287-293
Author(s):  
C.J. Schalinski ◽  
P. Biermann ◽  
A. Eckart ◽  
K.J. Johnston ◽  
T.Ph. Krichbaum ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Radio Sources ◽  
Relativistic Motion ◽  
Complete Sample ◽  
Superluminal Motion ◽  
Spectrum Radio ◽  
Wide Range ◽  
Show Evidence

A complete sample of 13 flat spectrum radio sources is investigated over a wide range of frequencies and spatial resolutions. SSC-calculations lead to the prediction of bulk relativistic motion in all sources. So far 6 out of 7 sources observed with sufficient dynamic range by means of VLBI show evidence for apparent superluminal motion.

scholarly journals Optical whispering-gallery mode barcodes for high-precision and wide-range temperature measurements

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Jie Liao ◽  
Lan Yang
Keyword(s):  
High Precision ◽  
Dynamic Range ◽  
Single Mode ◽  
Whispering Gallery Mode ◽  
Temperature Measurements ◽  
Laser Source ◽  
Multiple Modes ◽  
Whispering Gallery ◽  
Wide Range ◽  
Thermal Sensing

AbstractTemperature is one of the most fundamental physical properties to characterize various physical, chemical, and biological processes. Even a slight change in temperature could have an impact on the status or dynamics of a system. Thus, there is a great need for high-precision and large-dynamic-range temperature measurements. Conventional temperature sensors encounter difficulties in high-precision thermal sensing on the submicron scale. Recently, optical whispering-gallery mode (WGM) sensors have shown promise for many sensing applications, such as thermal sensing, magnetic detection, and biosensing. However, despite their superior sensitivity, the conventional sensing method for WGM resonators relies on tracking the changes in a single mode, which limits the dynamic range constrained by the laser source that has to be fine-tuned in a timely manner to follow the selected mode during the measurement. Moreover, we cannot derive the actual temperature from the spectrum directly but rather derive a relative temperature change. Here, we demonstrate an optical WGM barcode technique involving simultaneous monitoring of the patterns of multiple modes that can provide a direct temperature readout from the spectrum. The measurement relies on the patterns of multiple modes in the WGM spectrum instead of the changes of a particular mode. It can provide us with more information than the single-mode spectrum, such as the precise measurement of actual temperatures. Leveraging the high sensitivity of WGMs and eliminating the need to monitor particular modes, this work lays the foundation for developing a high-performance temperature sensor with not only superior sensitivity but also a broad dynamic range.

Designing Soft Reactive Adhesives by Controlling Polymer Chemistry

MRS Bulletin ◽  
2003 ◽  
Vol 28 (6) ◽  
pp. 424-427 ◽  
Author(s):  
Agnès Aymonier ◽  
Eric Papon
Keyword(s):  
Automotive Industry ◽  
Ease Of Use ◽  
Large Strains ◽  
Structural Adhesives ◽  
Wide Range ◽  
Step Growth ◽  
Visible Irradiation ◽  
Step Growth Polymerization ◽  
Uv Visible ◽  
Activation Heat

AbstractSoft reactive adhesives (SRAs) are polymer-based materials (e.g., polyurethanes, polysiloxanes, polydienes) designed to be further vulcanized or slightly cross-linked through external activation (heat, moisture, oxygen, UV–visible irradiation, etc.), either at the time of their application or within a subsequent predefined period. They are used mainly as mastics, or sealing compounds, in a wide range of industrial and commercial fields such as construction, footwear, and the automotive industry. Generally deposited as thick films, SRAs behave as structural adhesives; their low elastic moduli accommodate large strains between the bonded parts without incurring permanent damage. Other outstanding attributes of SRAs are their resistance to solvents, their ability to withstand aggressive environments, and their ease of use. This article discusses examples of SRAs and, more specifically, shows how the cross-linking chemistry, mainly through step-growth polymerization, provides their primary advantages.

Detector commissioning and development for PETRA-III

2010 ◽  
Vol 1 (SRMS-7) ◽  
Author(s):  
David Pennicard ◽  
Heinz Graafsma ◽  
Michael Lohmann
Keyword(s):  
High Speed ◽  
Materials Science ◽  
Dynamic Range ◽  
Photon Counting ◽  
High Energy ◽  
X Rays ◽  
Silicon Detectors ◽  
Time Resolved ◽  
Wide Range ◽  
Synchrotron Light

The new synchrotron light source PETRA-III produced its first beam last year. The extremely high brilliance of PETRA-III and the large energy range of many of its beamlines make it useful for a wide range of experiments, particularly in materials science. The detectors at PETRA-III will need to meet several requirements, such as operation across a wide dynamic range, high-speed readout and good quantum efficiency even at high photon energies. PETRA-III beamlines with lower photon energies will typically be equipped with photon-counting silicon detectors for two-dimensional detection and silicon drift detectors for spectroscopy and higher-energy beamlines will use scintillators coupled to cameras or photomultiplier tubes. Longer-term developments include ‘high-Z’ semiconductors for detecting high-energy X-rays, photon-counting readout chips with smaller pixels and higher frame rates and pixellated avalanche photodiodes for time-resolved experiments.

scholarly journals A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Karen A. Hudson ◽  
Matthew E. Hudson
Keyword(s):  
Transcription Factors ◽  
Genome Sequence ◽  
Search Algorithm ◽  
Soybean Genome ◽  
Binding Potential ◽  
Future Research ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Genes ◽  
Wide Range

The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH) family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281) of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

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