scholarly journals A memory switch for plant synthetic biology based on the phage ϕC31 integration system

2020 ◽  
Vol 48 (6) ◽  
pp. 3379-3394 ◽  
Author(s):  
Joan Miquel Bernabé-Orts ◽  
Alfredo Quijano-Rubio ◽  
Marta Vazquez-Vilar ◽  
Javier Mancheño-Bonillo ◽  
Victor Moles-Casas ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Regulatory Element ◽  
Alternative States ◽  
Gene Circuits ◽  
Site Specific ◽  
Precise Control ◽  
Bacteriophage Φc31 ◽  
Whole Plants ◽  
Transcriptional State

Abstract Synthetic biology has advanced from the setup of basic genetic devices to the design of increasingly complex gene circuits to provide organisms with new functions. While many bacterial, fungal and mammalian unicellular chassis have been extensively engineered, this progress has been delayed in plants due to the lack of reliable DNA parts and devices that enable precise control over these new synthetic functions. In particular, memory switches based on DNA site-specific recombination have been the tool of choice to build long-term and stable synthetic memory in other organisms, because they enable a shift between two alternative states registering the information at the DNA level. Here we report a memory switch for whole plants based on the bacteriophage ϕC31 site-specific integrase. The switch was built as a modular device made of standard DNA parts, designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally operated by action of the ϕC31 integrase (Int), and its recombination directionality factor (RDF). The kinetics, memory, and reversibility of the switch were extensively characterized in Nicotiana benthamiana plants.

scholarly journals A reversible memory switch for plant synthetic biology based on the phage PhiC31 integration system

2019 ◽  
Author(s):  
Bernabé-Orts Joan Miquel ◽  
Quijano-Rubio Alfredo ◽  
Mancheño-Bonillo Javier ◽  
Moles-Casas Victor ◽  
Selma Sara ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Cell Fate ◽  
Regulatory Element ◽  
Living Organism ◽  
Inducible Promoter ◽  
Chemical Stimulus ◽  
Toggle Switch ◽  
Genetic Switch ◽  
Whole Plants ◽  
Plant Synthetic Biology

ABSTRACTPlant synthetic biology aims to contribute to global food security by engineering plants with new or improved functionalities. In recent years, synthetic biology has rapidly advanced from the setup of basic genetic devices to the design of increasingly complex gene circuits able to provide organisms with novel functions. While many bacterial, fungal and mammalian unicellular chassis have been extensively engineered, this progress has been delayed in plants due to their complex multicellular nature and the lack of reliable DNA devices that allow an accurate design of more sophisticated biological circuits. Among these basic devices, gene switches are crucial to deploying new layers of regulation into the engineered organisms. Of special interest are bistable genetic toggle switches, which allow a living organism to exist in two alternative states and switch between them with a minimal metabolic burden. Naturally occurring toggle switches control important decision-making processes such as cell fate and developmental events. We sought to engineer whole plants with an orthogonal genetic toggle switch to be able to regulate artificial functions with minimal interference with their natural pathways. Here we report a bistable toggle memory switch for whole plants based on the phage PhiC31 serine integrase and its cognate recombination directionality factor (RDF). This genetic device was designed to control the transcription of two genes of interest by inversion of a central DNA regulatory element. Each state of the device is defined by one transcriptionally active gene of interest, while the other one remains inactive. The state of the switch can be reversibly modified by the action of the recombination actuators, which were administered externally (e.g. via agroinfiltration), or produced internally in response to an inducible chemical stimulus. We extensively characterized the kinetics, memory, and reversibility of this genetic switch in Nicotiana benthamiana through transient and stable transformation experiments using transgenic plants and hairy roots. Finally, we coupled the integrase expression to an estradiol-inducible promoter as a proof of principle of inducible activation of the switch.

scholarly journals Gene-circuit therapy on the horizon: synthetic biology tools for engineered therapeutics

2021 ◽  
Author(s):  
Rafał Krzysztoń ◽  
Yiming Wan ◽  
Julia Petreczky ◽  
Gábor Balázsi
Keyword(s):  
Synthetic Biology ◽  
Transgene Expression ◽  
Quantitative Methods ◽  
Clinical Applications ◽  
Gene Circuits ◽  
Gene Circuit ◽  
Precise Control ◽  
Genome Modification ◽  
Therapeutic Function ◽  
Therapeutic Context

Therapeutic genome modification requires precise control over the introduced therapeutic functions. Current approaches of gene and cell therapy fail to deliver such command and rely on semi-quantitative methods with limited influence on timing, contextuality and levels of transgene expression, and hence on therapeutic function. Synthetic biology offers new opportunities for quantitative functionality in designing therapeutic systems and their components. Here, we discuss synthetic biology tools in their therapeutic context, with examples of proof-of-principle and clinical applications of engineered synthetic biomolecules and higher-order functional systems, i.e. gene circuits. We also present the prospects of future development towards advanced gene-circuit therapy.

scholarly journals Efficient Protocol for Improving the Development of Cryopreserved Embryonic Axes of Chestnut (Castanea sativa Mill.) by Encapsulation–Vitrification

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 231
Author(s):  
Mariam Gaidamashvili ◽  
Eka Khurtsidze ◽  
Tamari Kutchava ◽  
Maurizio Lambardi ◽  
Carla Benelli
Keyword(s):  
Activated Charcoal ◽  
Castanea Sativa ◽  
Alginate Beads ◽  
Embryonic Axes ◽  
Root Regrowth ◽  
Castanea Sativa Mill ◽  
Whole Plants ◽  
Long Term Preservation ◽  
Direct Immersion

An optimized cryopreservation protocol for embryonic axes (EAs) of chestnut (Castanea sativa Mill.) has been developed based on the encapsulation–vitrification procedure. EAs of mature seeds were aseptically dissected and encapsulated in alginate beads with or without 0.3% (w/v) activated charcoal (AC). Embedded EAs were dehydrated with Plant Vitrification Solution 2 for different treatment times up to 120 min, followed by direct immersion in liquid nitrogen. Cryopreserved embryonic axes encapsulated with AC showed higher survival (70%) compared to those encapsulated without AC (50%). Sixty-four percent of embryonic axes, from synthetic seeds with AC, subsequently developed as whole plants. Plantlet regrowth was faster in AC-encapsulated EAs and showed enhanced postcryopreservation shoot and root regrowth over 2 cm after five weeks from rewarming. Results indicate that encapsulation–vitrification with activated charcoal added to the beads is an effective method for the long-term preservation of Castaneasativa embryonic axes.

scholarly journals Applications, challenges, and needs for employing synthetic biology beyond the lab

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sierra M. Brooks ◽  
Hal S. Alper
Keyword(s):  
Synthetic Biology ◽  
Great Promise ◽  
Long Term Storage ◽  
Autonomous Function ◽  
Recent Advances ◽  
Resource Limited ◽  
Major Application ◽  
Further Development ◽  
Probiotic Delivery

AbstractSynthetic biology holds great promise for addressing global needs. However, most current developments are not immediately translatable to ‘outside-the-lab’ scenarios that differ from controlled laboratory settings. Challenges include enabling long-term storage stability as well as operating in resource-limited and off-the-grid scenarios using autonomous function. Here we analyze recent advances in developing synthetic biological platforms for outside-the-lab scenarios with a focus on three major application spaces: bioproduction, biosensing, and closed-loop therapeutic and probiotic delivery. Across the Perspective, we highlight recent advances, areas for further development, possibilities for future applications, and the needs for innovation at the interface of other disciplines.

scholarly journals Long-term effectiveness of faecal immunochemical test screening for proximal and distal colorectal cancers

Gut ◽  
2021 ◽  
pp. gutjnl-2020-322545
Author(s):  
Han-Mo Chiu ◽  
Grace Hsiao-Hsuan Jen ◽  
Ying-Wei Wang ◽  
Jean Ching-Yuan Fann ◽  
Chen-Yang Hsu ◽  
...  
Keyword(s):  
Large Scale ◽  
Distal Colon ◽  
Population Based ◽  
Proximal Colon ◽  
Advanced Stage ◽  
Site Specific ◽  
Faecal Immunochemical Test ◽  
Immunochemical Test ◽  
Selection Factors

ObjectiveTo measure the effects of faecal immunochemical test (FIT) for colorectal cancer (CRC) screening on overall and site-specific long-term effectiveness of population-based organised service screening.DesignA prospective cohort study of Taiwanese nationwide biennial FIT screening was performed. A total of 5 417 699 eligible subjects were invited to attend screening from 2004 through 2009 and were followed up until 2014. We estimated the adjusted relative rates (aRRs) on the effectiveness of reducing advanced-stage CRC (stage II+) and CRC death by Bayesian Poisson regression models with the full adjustment for a cascade of self-selection factors (including the screening rate and the colonoscopy rate) and the completeness of colonoscopy together with demographic features.ResultsFIT screening (exposed vs unexposed) reduced the incidence of advanced-stage CRC (48.4 vs 75.7 per 100 000) and mortality (20.3 vs 41.3 per 100 000). Statistically significant reductions of both incidence of advanced-stage CRCs (aRR=0.66, 95% CI 0.63 to 0.70) and deaths from CRC (aRR=0.60, 95% CI 0.57 to 0.64) were noted. FIT screening was more effective in reducing distal advanced-stage CRCs (aRR=0.61, 95% CI 0.58 to 0.64) and CRC mortality (aRR=0.56, 95% CI 0.53 to 0.69) than proximal advanced CRCs (aRR=0.84, 95% CI 0.77 to 0.92) and CRC mortality (aRR=0.72, 95% CI 0.66 to 0.80).ConclusionA large-scale population-based biennial FIT screening demonstrates 34% significant reduction of advanced-stage CRCs and 40% reduction of death from CRC with larger long-term effectiveness in the distal colon than the proximal colon. Our findings provide a strong and consistent evidence-based policy for supporting a sustainable population-based FIT organised service screening worldwide. The disparity of site-specific long-term effectiveness also provides an insight into the remedy for lower effectiveness of FIT screening in the proximal colon.

scholarly journals Virus Eradication and Synthetic Biology: Changes with SARS-CoV-2?

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 569
Author(s):  
Jean-Nicolas Tournier ◽  
Joseph Kononchik
Keyword(s):  
Clinical Trials ◽  
Synthetic Biology ◽  
Viral Disease ◽  
Virus Eradication ◽  
Disease Eradication ◽  
The Public ◽  
The Past ◽  
The World ◽  
Significant Effort

The eradication of infectious diseases has been achieved only once in history, in 1980, with smallpox. Since 1988, significant effort has been made to eliminate poliomyelitis viruses, but eradication is still just out of reach. As the goal of viral disease eradication approaches, the ability to recreate historically eradicated viruses using synthetic biology has the potential to jeopardize the long-term sustainability of eradication. However, the emergence of the severe acute respiratory syndrome-coronavirus (SARS-CoV)-2 pandemic has highlighted our ability to swiftly and resolutely respond to a potential outbreak. This virus has been synthetized faster than any other in the past and is resulting in vaccines before most attenuated candidates reach clinical trials. Here, synthetic biology has the opportunity to demonstrate its truest potential to the public and solidify a footing in the world of vaccines.

Testing Long-Term Predictions from Hydro-Geochemical Models

1993 ◽  
Vol 333 ◽  
Author(s):  
William E. Glassley ◽  
Carol J. Bruton ◽  
William L. Bourcier
Keyword(s):  
Yucca Mountain ◽  
Taupo Volcanic Zone ◽  
Ambient Conditions ◽  
Volcanic Zone ◽  
Site Specific ◽  
Thermally Induced ◽  
Induced Flow ◽  
Geochemical Models ◽  
Kinetics And Thermodynamic

ABSTRACTThermally induced flow of liquid water and water vapor at the potential repository site at Yucca Mountain, Nevada, will extend hundreds of meters away from the repository edge. The resultant transfer of heat and mass will sufficiently perturb the ambient conditions such that a variety of mineralogical and chemical reactions will occur that may modify hydrological properties. The consequences of this “coupling” of geochemical and hydrological processes will vary through time, and will occur to different degrees in four regimes (T < Tboiling; T = Tboiling; T > T boiling; cooling) that will develop within the repository block. The dominant processes in the regimes differ, and reflect the local balance between: 1) kinetics and equilibrium; 2) dissolution and precipitation; 3) evaporation and boiling; and 4) fluid flow in matrix and fractures. Simulations were conducted of the evolution of these regimes, using laboratory derived kinetics and thermodynamic data, and site specific mineralogical and hydrological properties. These simulations identify regions where chemical and mineralogical equilibrium is likely to be achieved, and where net changes in hydrological properties will be concentrated. Tests of the results of these simulations have been initiated using field data from the Taupo Volcanic Zone, New Zealand. A preliminary series of calculations suggest that relative changes in porosity of as much as ± 20% to 30% may be possible for rocks with an initial porosity of 10%.

The effect of long term under- and over-feeding on the expression of genes related to lipid metabolism in mammary tissue of sheep

2014 ◽  
Vol 82 (1) ◽  
pp. 107-112 ◽  
Author(s):  
Eleni Tsiplakou ◽  
Emmanouil Flemetakis ◽  
Evangelia-Diamanto Kouri ◽  
Kyriaki Sotirakoglou ◽  
George Zervas
Keyword(s):  
Fatty Acid ◽  
Regulatory Element ◽  
Fatty Acid Synthetase ◽  
Hormone Sensitive Lipase ◽  
Mammary Tissue ◽  
Positive Energy ◽  
Peroxisome Proliferator ◽  
Nutritional Regulation ◽  
Expression Of Genes

Milk fatty acid (FA) synthesis by the mammary gland involves expression of a large number of genes whose nutritional regulation remains poorly defined. In this study, we examined the effect of long-term under- and over-feeding on the expression of genes (acetyl Co A carboxylase, ACC; fatty acid synthetase, FAS; lipoprotein lipase, LPL; stearoyl Co A desaturase, SCD; peroxisome proliferator activated receptor γ2, PPARγ2; sterol regulatory element binding protein-1, SREBP-1c; and hormone sensitive lipase, HSL) related to FA metabolism in sheep mammary tissue (MT). Twenty-four lactating sheep were divided into three homogenous sub-groups and fed the same ration in quantities covering 70% (underfeeding), 100% (control) and 130% (overfeeding) of their energy and crude protein requirements. The results showed a significant reduction of mRNA of ACC, FAS, LPL and SCD in the MT of underfed sheep, and a significant increase on the mRNA of LPL and SREBP-1c in the MT of overfed compared with the control respectively. In conclusion, the negative, compared to positive, energy balance in sheep down-regulates ACC, FAS, LPL, SCD, SREBP-1c and PPARγ2 expression in their MT which indicates that the decrease in nutrient availability may lead to lower rates of lipid synthesis.

scholarly journals A method for reconstructing past lake water phosphorus concentrations using sediment geochemical records

2021 ◽  
Author(s):  
Madeleine Moyle ◽  
John F. Boyle
Keyword(s):  
Lake Water ◽  
Water Quality Monitoring ◽  
Specific Reference ◽  
Site Specific ◽  
Burial Rate ◽  
Steady State Model ◽  
Sediment Records ◽  
Current Water ◽  
Study Sites

AbstractAn existing steady state model of lake phosphorus (P) budgets has been adapted to allow reconstruction of long-term average historic lake water total phosphorus (TP) concentrations using lake sediment records of P burial. This model can be applied without site-specific parameterisation, thus potentially having universal application. In principle, it is applicable at any site where there is both a sediment P burial record and knowledge of the current water budget, although we advise caution applying it to problematic sediment records. Tested at six published case study sites, modelled lake water TP concentrations agree well with water-quality monitoring data, and limited testing finds good agreement with wholly independent diatom inferred lake water TP. Our findings, together with a review of the literature, suggest that well preserved lake sediments can usefully record a long-term average P burial rate from which the long-term mean lake water TP can be reliably estimated. These lake water TP reconstructions can provide meaningful site-specific reference values to support decision making in lake eutrophication management, including establishing targets for lake restoration.

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