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77 results for “Synthetic Biology”
Data from: A synthetic biology and green bioprocess approach to recreate agarwood sesquiterpenoid mixtures
<p>Certain endangered Thymelaeaceous trees are major sources of the fragrant and highly valued resinous agarwood, comprised of hundreds of oxygenated sesquiterpenoids (STPs). Despite growing pressure on natural agarwood sources, the chemical complexity of STPs severely limits synthetic production. Here, we catalogued the chemical diversity in 58 agarwood samples by two-dimensional gas chromatography–mass spectrometry and partially recreated complex STP mixtures through synthetic biology. We improved STP yields in the unicellular alga <em>Chlamydomonas reinhardtii </em>by combinatorial engineering to biosynthesise nine macrocyclic STP backbones found in agarwood. A bioprocess following green-chemistry principles was developed that exploits 'milking' of STPs without cell lysis, solvent–solvent STP extraction, solvent–STP nanofiltration, and bulk STP oxy-functionalisation to obtain terpene mixtures like those of agarwood. This process occurs with total solvent recycling and enables continuous production. Our synthetic-biology approach offers a sustainable alternative to harvesting agarwood trees to obtain mixtures of complex, fragrant, oxygenated STPs.</p>
Dataset for manuscript entitled "The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm"
<p>The following datasets were used for the 16s rRNA analysis in the manuscript entitled " The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm". BZ2 files were obtained from next generation sequencing with the Illumina Mi-Seq. Mothur was used to analyze the BZ2 files, creating the listed excel documents.</p>
A quantitative autonomous bioluminescence reporter system with a wide dynamic range for Plant Synthetic Biology
<p>This data set includes: Luminescence (NeoLuc Luminescence), Fluorescence (eGFP) , NeoLuc/eGFP ratios, Area Under The Curve of NeoLuc/eGFP ratios, Normalized Area Under The Curve of Neoluc/eGFP (FBP-RTAs), Firefly Luciferase luminescence (FLuc), Renilla Luciferase luminescence (RLuc), FLuc/RLuc ratios and Normalized FLuc/RLuc values of all experiments in this work. </p>
Raw data for Broaden the application of Yarrowia Lipolytica synthetic biology tools to explore the potential of Yarrowia clade biodiversity
<p>Raw data for growth curves and fluorescence/OD ratio for article "Broaden the application of Yarrowia Lipolytica synthetic biology tools to explore the potential of Yarrowia clade biodiversity"</p>
Complex Ventral Hernia Repair Using Biologic or Synthetic Mesh
ClinicalTrials.gov study NCT02041494. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Biological Mesh Versus Synthetic Mesh in Interdisciplinary RRP With SCP
ClinicalTrials.gov study NCT06245577. IPD Sharing: YES. Countries: 1. Publications: 7.
Biologic Mesh Versus Synthetic Mesh in Repair of Ventral Hernias
ClinicalTrials.gov study NCT02451176. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: A synthetic biology and green bioprocess approach to recreate agarwood sesquiterpenoid mixtures
Open the record for dataset details and reuse information.
Data from: Biomimicry of iridescent, patterned insect cuticles: comparison of biological and synthetic, cholesteric microcells using hyperspectral imaging
<p>Biological systems inspire the design of multifunctional materials and devices. However, current syynthetic replicas rarelyy capture the range of structural complexityy observed in natural materials. Prior to the definition of a biomimetic design, a dual investigation with a common set of criteria for comparing the biological material and the replica is required. Here, we deal with this issue by addressing the non-trivial case of insect cuticles tessellated with polygonal microcells with iridescent colors due to the twisted cholesteric organization of chitin fibers. By using hyperspectral imaging within a common methodology, we compare, at several length scales, the textural, structural and spectral properties of the microcells found in the two-band cuticle of the scarab beetle <i>Chrysina gloriosa</i> with those of the polygonal texture formed in flat films of cholesteric liquid crystal oligomers. The hyperspectral imaging technique offers a unique opportunity to reveal the common features and differences in the spectral-spatial signatures of biological and synthetic samples at a 6-nm spectral resolution over 400 nm-1000 nm and a spatial resolution of 150 nm. The biomimetic design of chiral tessellations is relevant to the field of non-specular properties such as deflection and lensing in geometric phase planar optics.</p>
A versatile plasmid architecture for mammalian synthetic biology (VAMSyB)
<p>Data underlying the figures in the publication “A versatile plasmid architecture for mammalian synthetic biology (VAMSyB)”, published in <em>Metabolic Engineering</em>, <strong>2021</strong>, 66, 41–50. <a href="https://doi.org/10.1016/j.ymben.2021.04.003">https://doi.org/10.1016/j.ymben.2021.04.003</a></p> <p>Table of contents:</p> <p><strong>1. Dataset 1</strong>; Excel file with the curated data underlying the figures.</p> <p><strong>Figure 1.</strong> (F) Comparison of promoters cloned in the tier-1 scaffold, including minimal promoters (PTKmin, Pmin, PCMVmin-2, PMLP, and PCMVmin-1) and constitutive promoters (PTK, PSV40, PmPGK1, PhCMV, PhEF1a, and PRPBSA) was assessed in terms of SEAP production. (G-H) Modulation of the rtTA-based tet-ON system with different (G) minimal promoters and (H) suppressor (TS) 5’UTR sequences or destabilizing ribozymes (sTRSV and env140) in the 3’UTR was assessed in terms of SEAP production.</p> <p><strong>Figure 2.</strong> (C-D) Expression characterization of each cassette of the tier-2 construct is tested by inserting expression cassettes controlled by the moderately strong phospho-glycerate kinase (PmPGK1) or strong human cytomegalovirus-derived (PhCMV) promoter. (C) Expression comparison of each cassette of the tier-2 construct tested individually was assessed in terms of Nluc production. (D) Characterization of interference between promoters of different strengths (PhCMV and PmPGK1) encoded in individual constructs or cloned into a single tier-2 construct. PhCMV expression was assessed in terms of SEAP production and PmPGK1 expression was assessed in terms of Nluc production. The reporters were transfected individually, cotransfected (+), or expressed from the same plasmid (|). (E) Characterization of interference between a constitutive promoter (PmPGK1) and an inducible promoter (PCRE). PmPGK1 driving firefly luciferase (Fluc) and a synthetic inducible cAMP-responsive (PCRE) promoter driving Nluc were cloned into different expression cassettes of a single tier-2 construct. Levels of Nluc activity are normalized to Fluc activity. (G-J) Generation of a single tier-2 construct encoding four different well-established synthetic gene switches: (G) the doxycycline-regulated rtTA system, (H) the doxycycline-regulated tTA system, (I) the vanillic acid-regulated VanA system, and (J) the phloretin-regulated TtgA system were all assessed in terms of SEAP production</p> <p> </p> <p><strong>Figure 3. </strong>(C) Characterization of polyclonal stable cell lines generated with the tier-3 PB and SB constructs encoding Tet-responsive inducible SEAP-p2A-iRFP670 in the first cassette (A1), constitutively expressed rtTA in the second cassette (A2), and constitutively expressed YPet-p2A-PuroR in the third cassette (A3) demonstrated dose-dependent induction of SEAP expression in response to doxycycline. (F) Characterization of polyclonal stable cell lines generated with the tier-3 lentiviral constructs encoding Tet-responsive inducible SEAP-p2A-iRFP670 in the first cassette (A1), constitutively expressed rtTA in the second cassette (A2), and constitutively expressed YPet-p2A-PuroR in the third cassette (A3) show dose-dependent induction of SEAP expression in response to doxycycline. (J) Characterization monoclonal lines generated with the CRISPR tier-3 constructs encoding Tet-responsive inducible SEAP-p2A-iRFP670 in the first cassette (A1), constitutively expressed rtTA in the second cassette (A2) show dose-dependent induction of SEAP expression in response to doxycycline.</p> <p> </p> <p><strong>Figure S1.</strong> Characterization of functional genetic elements that can reduce interference between promoters of different strengths (PhCMV and PmPGK1) encoded in a single tier-2 construct. PhCMV-driven expression was assessed in terms of SEAP production and PmPGK1-driven expression was assessed in terms of Nluc production. The reporters were transfected individually, cotransfected (+), or expressed from the same plasmid (|). Functional genetic elements, including a plasmid backbone spacer sequence [spacer], a synthetic poly(A) signal/transcriptional pause site derived from a commercial vector [pGL3], a co-transcriptional cleavage element [CoTC], a transcriptional termination sequence derived from the human β-globin gene [Tactb], or an insulator sequence consisting of two repeats of chicken hypersensitive site 4 [2xcHS4] were introduced directly 5’ of the PmPGK1-NLuc expression cassette encoded in either the (A) A2 or (B) A3 insertion site.</p> <p> </p> <p><strong>Figure S2. </strong>Selection of high-performing sub-populations derived from polyclonal stable cell lines generated with the tier-3 PiggyBac (PB; pcTS50), Sleeping Beauty (SB; pcTS51), or lentiviral (Lenti; pcVH38) construct as presented in Figure 3. The polyclonal stable cell lines were induced with doxycycline for 48 h and then sorted based on iRFP670 expression to isolated high-expressing clones. (A-B) The sorted PB generated sub-populations were assayed for (A) dose-dependent induction of SEAP, as well as (B) iRFP670 reporter mean fluorescence intensity (MFI) output in response to doxycycline. (D-E) The sorted SB generated sub-populations were assayed for (D) dose-dependent induction of SEAP expression, as well as (E) iRFP670 reporter MFI output in response to doxycycline. (G-H) The sorted lentiviral generated sub-population was assayed for (G) dose-dependent induction of SEAP expression, as well as (H) iRFP670 reporter MFI output in response to doxycycline.</p>
Data from: Varying the spatial arrangement of synthetic herbivore-induced plant volatiles and companion plants to improve conservation biological control
1.Conservation biological control aims to control pests by promoting wild populations of natural enemies. One challenge is to attract and retain efficient natural enemies in crop fields, which often are a suboptimal environment. Towards this goal, the attract-and-reward strategy relies on combining attractive synthetically produced herbivore-induced plant volatiles (HIPVs) with companion plants (non-crop plants which provide alternative resources to the targeted natural enemies). Although severely overlooked, the spatial arrangement of HIPV dispensers and rewards inside crop fields may strongly influence the foraging behaviour and persistence of natural enemies and thus the success of this pest management strategy. 2.We tested the impact of two contrasting spatial arrangements of HIPV dispensers and rewards, alternatively inside and around a block of target apple trees, on the efficacy of the biological control of Aphis citricola populations by the common predatory ladybird Propylea japonica in apple orchards in northern China. We used synthetic methyl salicylate (MeSA) as an attractant and the companion plant Calendula officinalis as a reward. To better understand how the spatial arrangement of MeSA dispensers and companion plants affected the attraction and foraging behaviour of adult ladybirds, we conducted indoor experiments in a flight mill, an olfactometer and a wind-tunnel. 3.Blocks of target trees treated with MeSA dispensers inside and companion plants around provided the most efficient pest control in orchards, compared with the opposite spatial arrangement. 4.The synthetic MeSA dispenser and the companion plant synergistically attracted ladybirds in the olfactometer and enhanced their flight activity in the flight mill. In the wind-tunnel, MeSA served as a spatial cue for ladybirds to find nearby prey, while companion plants were sought in the absence of prey. 5.Synthesis and applications. The present study will help further improvements of aphid control in apple orchards through a careful spatial arrangement of herbivore-induced plant volatiles dispensers (HIPVs) and rewards (companion plants) in optimized attract-and-reward strategies. Without such assessment, these strategies may be hazardous even with well-identified targeted natural enemies. Associated lab experiments highlight that HIPVs and companion plants interactively influence ladybird foraging pattern, and that their spatial arrangement can modulate the ability of such key predators to find their prey.
The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems. Source data
<p>Supplementary information for manuscript titled "The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems"</p>
(raw dataset) "Spatial biology of Ising-like synthetic genetic networks"
<p>This is the raw data for the manuscript Simpson et al "Spatial biology of Ising-like synthetic genetic<br> networks"</p>
Fig. 19 in A comprehensive review: Biological activity, modification and synthetic methodologies of prenylated flavonoids
Fig. 19. Synthesis of prenylated flavonoids 472–494 Reagents and conditions: (a): 3,3-dimethylallyl bromide, 10% KOH; (b): MOMCl, K CO, acetone, 0 ◦ C - RT; (c): 2 3 corresponding benzaldehyde, 10% KOH ethanol/H O, RT; (d): 5% HCl, MeOH/THF, reflux; (e) NaOAc, EtOH, reflux; (f) I, pyridine, 90 ◦ C.
Fig. 18 in A comprehensive review: Biological activity, modification and synthetic methodologies of prenylated flavonoids
Fig. 18. Synthesis of prenylated flavonoids (468–471). Reagents and conditions: (a) 1.3 N NaOH, acetone; 3,3-dimethylallyl bromide, benzene, reflux; (b) 3,3-dimethylallyl bromide, 10% KOH; (c) MOMCl, K CO, acetone, 0 ◦ C to RT; (d) p-methoxymethoxyl benzaldehyde, 10% KOH (H O/EtOH); (e) NaOAc, EtOH, reflux; (f) 3N 2 3 2 HCl, MeOH, reflux; (g) I, pyridine, 90 ◦ C.
Fig. 25 in A comprehensive review: Biological activity, modification and synthetic methodologies of prenylated flavonoids
Fig. 25. Synthetic route of C-6/C-8 prenylated flavonoids from natural precusor. Reagents and conditions: (a) CH3OCH2Cl, K2CO3, acetone, RT; (b) prenyl bromide, K CO, acetone, 45 ◦ C; (c) Florisil, toluene, reflux; (d) Montmorillonite K10, toluene, reflux; (e) dilute HCl (aq.), CH OH, RT.
Fig. 17 in A comprehensive review: Biological activity, modification and synthetic methodologies of prenylated flavonoids
Fig. 17. Chemical structures of prenylated flavonoids with anti-diabetes activity (445–465) and estrogenic activity (466–467).
Fig. 15 in A comprehensive review: Biological activity, modification and synthetic methodologies of prenylated flavonoids
Fig. 15. Synthesis of icaritin derivatives (403–412). Reagents and conditions: (f) α,ω-dibromoalkanes (15 equiv), K2CO3 (5 equiv), acetone, reflux, 12 h; (g) diethylamine or dimethylamine, DMSO, RT, 4 h; (h) 1-iodopentane, Cs2CO3, acetone, reflux, 12 h, then diethylamine, DMSO, RT, 4 h.
Fig. 14 in A comprehensive review: Biological activity, modification and synthetic methodologies of prenylated flavonoids
Fig. 14. Synthesis of icaritin derivatives (393–402). Reagents and conditions: (a) ethyl iodoacetate, K2CO3, acetone, reflux, 12 h; (b) LiOH, THF, H2O, RT, 1.5 h; (c) corresponding basic amino acid, DIC, HOBt, anhydrous DMF, RT, overnight, His = histidine, Arg = arginine, Lys = lysine; (d) corresponding basic amino acid, HATU, DIPEA, anhydrous DMF, RT, overnight; (e) piperidine, DMF, RT, 20 min.
Fig. 23 in A comprehensive review: Biological activity, modification and synthetic methodologies of prenylated flavonoids
Fig. 23. Synthetic route of C-8 prenylated flavonoids. Reagents and conditions: (a) CH3OCH2Cl, K2CO3, acetone, room temp., 83–90%; (b) 4-MOMO-benzaldehyde, KOH, EtOH, reflux, 85%; (c) I2, DMSO, reflux, 8 h, 70%; (d) oxone, acetone, CH2Cl2/NaHCO3/ Na2CO3, RT; then p-toluenesulfonic acid, RT, 76%; (e) dilute HCl (aq.), EtOH, RT, 89%; (f) prenyl bromide, K2CO3, acetone, reflux, 95%; (g) microwave, PhNEt2, reflux, 82%. (h) H2SO4 (20% aq.), CH3OH, reflux, 86%; (j) DDQ, 1,4-dioxane, reflux, 76%.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.