Find research datasets worth reusing

opencc-by-4.0Dec 2019View details →

Three-Enzyme Phosphorylase Cascade Immobilized on Solid Support for Biocatalytic Synthesis of Cello-oligosaccharides

We provide here the underlying data of the scientific publication "Three-Enzyme Phosphorylase Cascade Immobilized on Solid Support for Biocatalytic Synthesis of Cello-oligosaccharides". Please find the abstract below: Enzyme cascades are promising for multistep biocatalytic synthesis, but their effective use beyond the proof-of-concept stage is challenging. Strategies to recycle the individual enzymes are critical for the applicability of such cascades. Immobilization on solid support is well developed for single enzymes but remains difficult for enzyme ensembles. Here, we show a controlled co-immobilization of three glycoside phosphorylases to establish a highly active and recyclable biocatalyst for the conversion of sucrose and glucose into soluble (short-chain) cello-oligosaccharides. We use protein fusion with the binding module Zbasic2 to enable non-covalent surface tethering of all enzymes according to a uniform principle and in a programmable fashion. We thus achieve loading of the phosphorylases in an activity ratio optimal for the overall conversion rate and for controlling the cello-oligosaccharide chain length (≤ 6), hence the solubility, in the reaction. We demonstrate efficient production of ~12 g/L cello-oligosaccharides in 5 reaction cycles with integrated enzyme re-use. This study presents a major advance toward the practical use of systems bio-catalysis on solid support.

opencc-by-4.0Jul 2020View details →

TERMINUS WP4: Enzyme immobilization, protection, and triggering. TASK 4.2: Experimental data

A. E. Delorme, J.-M. Andanson and V. Verney: Improving Laccase Thermostability with aqueous Natural Deep Eutectic Solvents, Int. J. Biol. Macromol., (2020), <a href="https://doi.org/10.1016/j.ijbiomac.2020.07.022">doi.org/10.1016/j.ijbiomac.2020.07.022</a> Abstract The wide-spread use of laccases in industry is often limited due to the enzyme inactivation over time at conditions which exceeds the operating conditions of the enzymes, which are neutral pH and ambient temperatures (30-40 °C). Today, the most common strategies used to improve enzyme stability are chemical modifications and immobilization of enzymes on solid supports. Although, these techniques have shown promise in improving enzyme stability, they are often synthetically demanding and unsustainable in terms of costs and synthesis route.  Deep Eutectic Solvents (DESs) have attracted considerable attention as reaction media in biocatalysis due to their promising compatibility with enzymes and sustainable derivation. In this contribution we demonstrate the possibility of applying DESs as incubation media to inhibit thermal inactivation of laccase T. Versicolor. For example we show that by incubating laccase in 25 wt% of a betaine-xylitol based DES at 70 °C for 15 minutes, the measured residual activity of laccase is a near 10 fold greater than the measured residual activity of laccase when incubated without the DES.  The drastic enhancement of the enzyme thermostability by pre-incubation of laccase in DES media showcases a facile, cheap and green method of boosting the stability laccase.   Dataset This dataset contains all the UV-kinetic raw data used to calculate the laccase activity in the article “Improving Laccase Thermostability with aqueous Natural Deep Eutectic Solvents”. Data are available in a compressed .zip file with 1 folder (Laccase-thermostability-DES_v1.0_TER_WP4_D4-2) containing 3 files:   <ul> <li>one tabular file saved in .xlsx format containing all UV-kinetic raw data used to calculate the relative and residual laccase activities for figure 1-6 in the article (<a href="https://doi.org/10.1016/j.ijbiomac.2020.07.022">doi.org/10.1016/j.ijbiomac.2020.07.022</a>). The Laccase-thermostability-DES_v1.0_TER_WP4_D4-2.xlsx file contains the UV kinetic absorption spectra (at wavelength 417 nm) and each row in represent one spectrum. The spectra are grouped under laccase incubation temperature and length of time of incubation. For each incubation time, three solutions were prepared which signifies the three trials under each incubation times. Each sheet in the .xlsx file represent the data set collected for each laccase incubation medium</li> <li>The Materials_and_experimental_method-D4-2-Laccase-Thermostability-DES.pdf file details the experimental method and conditions for the data acquisition presented in the Laccase-thermostability-DES_v1.0_TER_WP4_D4-2.xlsx. Guidance is also provided on how to use the data to calculate the laccase activity and thermostability.</li> <li>The_metadata_information-D4-2-Laccase-Thermostability-DES.pdf includes more detailed metadata information for the dataset represented in the excel file Laccase-thermostability-DES_v1.0_TER_WP4_D4-2.xlsx.</li> </ul>

opencc-by-4.0Jun 2021View details →

TERMINUS WP4 Enzyme immobilization, protection, and triggering. TASK 4.1 TASK 4.2 Experimental data – Hydrolytic enzyme immobilization and triggering

The use of polymer-degrading enzymes is an attractive and effective method for the management of plastic waste. Synthetic polyesters such as poly(ethylene terephthalate) (PET) or polyurethane (PUR) have been shown to be susceptible to enzymatic degradation by microbial polyester hydrolases, as well as biopolyesters such as poly(lactic acid) (PLA), poly(butylene succinate) (PBS), and polycaprolactone (PCL). However, raw enzymes are not used in polymer formulations because the high processing temperatures would deteriorate the proteins (whose enzymes are made of), by destroying their macromolecular structure and catalytic center. The possibility of a direct use of enzyme in a polymer formulation thorough an opportune protective system, able to preserve the activity of the enzyme and increase its thermal stability, could open to new materials degradable “on-demand” at the end-of life. Therefore, significant progresses could be possible for example in the field of plastic packaging, which currently represents 40% of the total production of plastic in EU and requires the consumption of more than 19 million tons of oil and gas. This dataset includes some of the experimental raw data presented by UNIBO in deliverable D4.1 and D4.3, namely FT-IR analysis, X-ray diffraction analysis, TGA analysis, UV-Vis spectrophotometer. Data are available in a compressed .zip file with 1 folder (Hydrolytic enzyme immobilization and triggering_v1.0_TER_WP4_D4.1_D4.3) containing 6 files, 4 .xlsx files containing the FT-IR, XRD, TGA, Enzyme release kinetics and Thermostability raw data, 1 .pdf file describing the experimental methods and materials and a second .pdf file outlining the metadata and information. 1_Hydrolytic enzyme immobilization and triggering _FTIR.xlsx contains all the FTIR raw data and curves of the Immobilized enzyme systems prepared. 2_Hydrolytic enzyme immobilization and triggering _XRD.xlsx contains all the XRD raw data and profiles of the Immobilized enzyme systems prepared. 3_Hydrolytic enzyme immobilization and triggering _TGA.xlsx contains all the TGA raw data and curves of the Immobilized enzyme systems prepared. 4_Hydrolytic enzyme immobilization and triggering release activity and thermal resistance.xlsx contains all the raw data and graphs related to the protein content, activity of the Immobilized enzyme systems prepared after release and the thermal stress experiment data. Materials and experimental method_D4.1_D4.3_Hydrolytic enzyme immobilization and triggering.pdf contains the details of the experimental method and conditions for the data acquisition presented in the data set. Metadata information for WP4 dataset_D4.1_D4.3_Hydrolytic enzyme immobilization and triggering.pdf includes more detailed metadata information for the dataset presented.

opencc-by-4.0Dec 2023View details →

Selective Oxidation of 5-Hydroxymethylfurfural to 2,5-Diformylfuran in Biphasic Media using Immobilized Galactose Oxidase: Proof of Concept and Limitations

The oxidation of 5-hydroxymethylfurfural (HMF) to 2,5-diformylfuran (DFF) is a key reaction in valorizing biomass. DFF is hardly soluble in water, while HMF is often obtained from biorefineries in crude wet organic fractions. Thus, the reaction is challenging for both biocatalysis performed in aqueous media, and for chemocatalysis where the presence of water often results in catalyst poisoning. Galactose oxidase (GalOx) can selectively oxidize HMF to DFF and displays promising activity in aqueous-organic media. In this study, GalOx was immobilized on ten carriers, assessing the immobilization yield, activity, and stability. Covalently immobilized GalOx catalyzed the oxidation of HMF to DFF in neat and water-saturated EtOAc, and in biphasic systems of various water contents. At 50 % v/v H2O, the reaction was conducted at a semi-preparative scale (50 mL) with no adverse effect on DFF yield. Some limitations arise, such as enzyme deactivation, and adsorption of DFF to the support, particularly in the aqueous fraction. Future options to upgrade the route may include designed stable enzymes under the presence of HMF/DFF, and the setup of microaqueous systems where DFF adsorption is minimized. The use of wet EtOAc media would be a promising approach in future biorefineries employing inexpensive crude wet organic fractions.

opencc-by-4.0Mar 2024View details →

Data and supplementary files of the publication: "What Goes Around Should Not Move Around: Immobilizing Microplastics as a New Approach for Analytical Ring Trials"

Accompanying materials for the publication: <a href="https://doi.org/10.1021/acs.est.4c09427">https://doi.org/10.1021/acs.est.4c09427</a>

opencc-by-4.0Nov 2020View details →

Bathymetry of Large, Straight and Immobile bed-forms found in the Great South Channel (2015 - 2017)

Digital Bathymetry produced from the raw data set collected with a Reson Seabat 7125 Multibeam echo-sounder.  The grid cell size is 1 m×1m. The area is a representative sample of the Great South Channel seafloor describing Large, Straight, and Immobile bedforms (LSI). The survey data were collected during the 2015 and 2017 - NOAA annual federal Sea Scallop Survey on board R/V Hugh Sharp, operated by the University of Delaware, and funded by the Improve a Stock Assessment Program of the NOAA Northeast National Marine Fisheries Service (NEMFS) The data processing was supported by NOAA GRANT NA15NOS400002000.

opencc-by-4.0Dec 2020View details →

Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite"

Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite", by Paulina Szymoniak, Brian R. Pauw, Xintong Qu, and Andreas Schönhals. Datasets are in three-column ascii (processed and azimuthally averaged data) from a Xenocs NanoInXider SW instrument. Monte-Carlo analyses were performed using McSAS 1.3.1, other analyses are in the Python 3.7 worksheet. Graphics and result tables are output by the worksheet.

opencc-by-4.0Nov 2023View details →

Interactions of netrin-1 through its glycosylation sites immobilize DCC receptors by favoring its constitutive clustering

Open the record for dataset details and reuse information.

opencc-by-4.0Dec 2021View details →

Dataf from: Global patterns and controls of nutrient immobilization on decomposing cellulose in riverine ecosystems

Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature. Collectively, we demonstrated that exogenous nutrient supply and immobilization are critical control points for decomposition of organic matter.

opencc-by-nc-3.0Jun 2023View details →

FTIR Microscopy for Direct Observation of Conformational Changes on Immobilized ω-Transaminase: Effect of Water Activity and Organic Solvent on Biocatalyst Performance

Enzyme immobilization is a key strategy to expand the scope of enzyme applications and to enable the recycling of biocatalysts, resulting in greener and more cost-efficient processes. The full exploitation of the technology advantages is strictly connected to the optimal selection of the carriers and the rational development of the immobilization protocol. The present study achieved such objectives by investigating the activity of a ω-transaminase in organic solvent (toluene) upon immobilization on commercially controlled porosity glass carriers (EziG™) with diverse porosity and surface functionalization. In addition to more conventional wet-chemistry approaches and confocal microscopy, infrared microspectroscopy and imaging were exploited to highlight the enzyme distribution in a label-free manner and provide details on the immobilized enzyme's conformation with respect to the native form. Contrary to what could be expected, the highest activity of the enzyme in organic solvent was achieved for the immobilization protocol on the most hydrophilic support that more severely affects the enzyme secondary structure, promoting a beta-sheet rich folding. Experimental data show that values of water activity above 0.90 in the reaction system had a positive effect on the efficiency of the transaminase reaction. The present study represents the first example of rational development of immobilization protocols relying on direct observation of the enzyme conformation upon immobilization, shedding light on the mutual interaction between the diverse process parameters and the carrier properties.

opencc-by-4.0May 2023View details →

Biosynthesis of Furfurylamines in Batch and Continuous Flow by Immobilized Amine Transaminases

Building blocks with amine functionality are crucial in the chemical industry. Biocatalytic syntheses and chemicals derived from renewable resources are increasingly desired to achieve sustainable production of these amines. As a result, renewable materials such as furfurals, especially furfurylamines like 5-(hydroxymethyl)furfurylamine (HMFA) and 2,5-di(aminomethyl)furan (DAF), are gaining increasing attention. In this study, we identified four different amine transaminases (ATAs) that catalyze the reductive amination of 5-(hydroxymethyl)furfural (HMF) and 2,5-diformylfuran (DFF). We successfully immobilized these ATAs on glutaraldehyde-functionalized amine beads using multiple binding and on amine beads by site-selective binding of the unique Cα-formylglycine within an aldehyde tag. All immobilized ATAs were efficiently reused in five repetitive cycles of reductive amination of HMF with alanine as co-substrate, while the ATA from Silicibacter pomeroyi (ATA-Spo) also exhibited high stability for reuse when isopropylamine was used as an amine donor. Additionally, immobilized ATA-Spo yielded high conversion in the batch syntheses of HMFA and DAF using alanine (87% and 87%, respectively) or isopropylamine (99% and 98%, respectively) as amine donors. We further demonstrated that ATA-Spo was effective for the reductive amination of HMF with alanine or isopropylamine in continuous-flow catalysis with high conversion up to 12 days (48% and 41%, respectively).

opencc-by-4.0Jun 2023View details →

Immobilized fluorescently stained zebrafish through the eXtended Field of view Light Field Microscope 2D-3D dataset

Immobilized fluorescently stained zebrafish through the eXtended Field of view Light Field Microscope 2D-3D dataset This dataset comprises three immobilized fluorescently stained zebrafish imaged through the eXtended Field of view Light Field Microscope (XLFM, also known as Fourier Light Field Microscope). The images were preprocessed with the <a href="https://github.com/pvjosue/SLNet_XLFMNet">SLNet</a>, which extracts the sparse signals from the images (a.k.a. the neural activity). If you intend to use this with Pytorch, you can find a data loader and working source code to load and train networks <a href="https://github.com/pvjosue/CWFA">here</a>. This dataset is part of the publication: Fast light-field 3D microscopy with out-of-distribution detection and adaptation through Conditional Normalizing Flows.   The fish present are: <ul> <li>1x NLS GCaMP6s</li> <li>1x Pan-neuronal nuclear localized GCaMP6s Tg(HuC:H2B:GCaMP6s)</li> <li>1x Soma localized GCaMP7f Tg(HuC:somaGCaMP7f)</li> </ul>   The dataset is structured as follows:: XLFM_dataset <ul> <li>Dataset/ <ul> <li>GCaMP6s_NLS_1/ <ul> <li>SLNet_preprocessed/ <ul> <li>XLFM_image/ <ul> <li>XLFM_image_stack.tif: tif stack of 600 preprocessed XLFM images.</li> </ul> </li> <li>XLFM_stack/ <ul> <li>XLFM_stack_nnn.tif: 3D stack corresponding to frame nnn.</li> </ul> </li> <li>Neural_activity_coordinates.csv: 3D coordinates of neurons found through the <a href="https://www.biorxiv.org/content/10.1101/061507v2">suite2p framework</a>.</li> </ul> </li> <li>Raw/ <ul> <li>XLFM_image/ <ul> <li>XLFM_image_stack.tif: tif stack of 600 raw XLFM images.</li> </ul> </li> </ul> </li> </ul> </li> <li>(other samples)</li> </ul> </li> <li>lenslet_centers_python.txt: 2D coordinates of the lenset in the XLFM images.</li> <li>PSF_241depths_16bit.tif: 3D PSF of the microscope can be used for 3D deconvolution. Spanning  734 × 734 × 550𝜇𝑚3 used to deconvolve this volumes. </li> </ul>   In this dataset, we provide a subset of the images and volumes. Due to space constraints, we provide the 3D volumes only for: <ul> <li>SLNet_preprocessed/XLFM_stack/ <ul> <li>10 interleaved frames between frames 0-499 (can be used for training a network).</li> <li>20 consecutive frames, 500-520 (can be used for testing).</li> </ul> </li> <li>raw/ <ul> <li>No volumes are provided for raw data, but they can be reconstructed through 3D deconvolution.</li> </ul> </li> </ul>   Enjoy, and feel free to contact us for any information request, like the full PSF, 3 more samples or longer image sequences.

opencc-by-3.0Dec 2022View details →

2,5-Furandicarboxaldehyde as a Bio-based Crosslinking Agent Replacing Glutaraldehyde for Covalent Enzyme Immobilization

In the quest for a bio-based and safer substitute for glutaraldehyde, we have investigated 2,5 diformylfuran (DFF) as bifunctional crosslinking agent for the covalent immobilization of glucoamylase on amino-functionalized methacrylic resins. Immobilization experiments and systematic comparison with glutaraldehyde at four different concentrations for the activation step showed that DFF leads to comparable enzymatic activities at all tested concentrations. Continuous flow experiment confirms a similar long term stability of the immobilized formulations obtained with the two crosslinkers. The NMR study of DFF in aqueous solution evidenced a much simpler behaviour as compared to glutaraldehyde, since no enolic forms can form and only a mono-hydrated form was observed. Unlike in the case of glutaraldehyde, DFF reacts covalently with the primary amino groups via imine bond formation only. Nevertheless, the stability of the covalent immobilization was confirmed also at acidic pH (4.5), most probably because of the higher stability of the imine bonds formed with the aromatic aldehydes. In terms of toxicity DFF has the advantage of being poorly soluble in water and, more importantly, poorly volatile as compared to glutaraldehyde, which displays severe respiratory toxicity. We have performed preliminary ecotoxicity assays using Aliivibrio fischeri, a marine bacterium, evidencing comparable behaviour (below the toxicity threshold) for both dialdehydes at the tested concentrations.

opencc-by-4.0Nov 2023View details →

Analysis of immobilized triflogallate (III) IL catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents TGA and SEM-EDX analysis of immobilized triflogallate (III) IL catalyst on silica.

opencc-by-4.0Nov 2023View details →

Dataset for Aberration-Corrected STEM to Determine the Surface Coverage and Distribution of Immobilized Molecular Complexes

Raw image data used for the paper "Aberration-Corrected STEM to Determine the Surface Coverage and Distribution of Immobilized Molecular Complexes".

opencc-by-4.0Dec 2021View details →

Dataset to "Fine-sediment erosion and ridge morphodynamics in coarse-grained immobile beds"

The dataset is connected to the paper "Fine-sediment erosion and ridge morphodynamics in coarse-grained immobile beds". The dataset is subdivided in "topographic" and "PIV" data. Each dataset refers to an experiment presented in the paper. The filenames of the topographic data specify the location where the data were collected ("upstream" or "downstream"). The topographic data contain the bed elevations measured around each sphere over a measurement area as wide as the channel and covering nine patterns of spheres (see paper for a definition of the pattern of spheres). Each topographic dataset contains four structures: - A time vector "T" identifying the sampling times at which the bed topography was measured (unit: h) - A space vector "x" identifying the streamwise position of the spheres with the origin of the coordinate system positioned at the beginning of the measurement areas (upstream or downstream) - unit cm - A space vector "y" identifying the transverse position of the spheres with the coordinate system centred in the middle of the channel and positively oriented towards the left side of the flume looking in streamwise direction - unit cm - A matrix "Z" identifying the protrusion levels of the spheres  (as defined in the paper) as a function of space and time (x times y times T) - unit cm   The PIV data were acquired during experiments 1b and 5b at the upstream location. The data are a collection of the velocity fields measured above the top of the spheres and over two pattern of spheres in the middle "m" and in the quarter plane "q" of the channel for three different time instants (t1, t2, t3) during the experiments. Each dataset contains 6 variables: - the "sampling time" of the bursts - unit s - the "acquisition time" of the PIV run during the experiments - unit h - a vector "x" identifying the streamwise position of the velocity vectors for a coordinae system centred in the centre of the sphere and pointing in the longitudinal direction. - a vector "z" identifying the vertical direction of the coordinate system with the origin at the top of the sphere and pointing upwards - unit cm - a matrix "vx" containing 1000 fields of the streamwise velocity component - unit cm/s - a matrix "vz" containing 1000 fields of the vertical velocity component - unit cm/s

opencc-by-4.0Apr 2022View details →

Supplementary Material for Mapping Active Site Geometry to Activity in Immobilized Frustrated Lewis Pair Catalysts

Supplementary Material for "Mapping Active Site Geometry to Activity in Immobilized Frustrated Lewis Pair Catalysts".

opencc-by-4.0Dec 2022View details →

Figure 1 in Recent progress in magnetic nanoparticles and mesoporous materials for enzyme immobilization: an update

Figure 1. Mesoporous material-functioned MNPs.

opencc-by-4.0Feb 2019View details →

Immobilized Different Shape Gold Nanostructures on Printing Paper for Lable-Free Surface-enhanced Raman Spectroscopy

Surface Enhanced Raman Spectroscopy (SERS) is spectroscopic technique of a label-free with high selectivity, and sensitivity. Methods and Materials: Paper-based SERS active substrates with different grade gram per square meter (GSM) were prepared by adsorbing 40 nm spherical GNP and 40nm star-shaped gold nanostructures GNS. Besides the SERS evaluation and optimization, morphological parameters were found to strongly affect the substrates. The developed substrate was tested by the Raman reporter dye Methylene Blue (MB). Results: These paper-based SERS active substrates are simple to prepare, easy to handle and cheap solid SERS substrates. Conclusion: GNS with 135 GSM printing paper can easily use as highly active SERS active substrates, with enhancement factor EF= 105.