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108 results for “protein production”
Raw data to accompany the manuscript 'Data for Engineering Lipid Metabolism of Chinese Hamster Ovary (CHO) Cells for Enhanced Recombinant Protein Production' published in the Journal Data in Brief
<p>This repository consists of the raw western blot, microscopy and mass spectrometry data to accompany the manuscript 'Data for Engineering Lipid Metabolism of Chinese Hamster Ovary (CHO) Cells for Enhanced Recombinant Protein Production' published in the Journal Data in Brief and associated with the article '<a href="https://www.ncbi.nlm.nih.gov/pubmed/31805379">Engineering of Chinese hamster ovary cell lipid metabolism results in an expanded ER and enhanced recombinant biotherapeutic protein production</a>' published in the journal Metabolic Engineering (see DOI: 10.1016/j.ymben.2019.11.007). </p> <p>The western blot raw file is associated with Figure 1a and 1b of the Data in Brief manuscript.</p> <p>The confocal microscopy raw image files (x3) are associated with Figure 1c of the Data in Brief manuscript.</p> <p>The mass spectrometry files are the raw data that refers to the samples presented in Figure 5 of the Data in Brief manuscript. Files are labelled as in the Data in Brief and Metabolic Engineering manuscripts. The file name structures is as follows;</p> <p>CHO-Controlpoolai</p> <p>Where 'a' represents replicate 'a' of three biological replicates and 'i' refers to mass spectrometry technical analysis 1 of 3 technical analyses of each replicate (thus for each cell pool or line there are three biological replicates that are each analysed in triplicate such that there are 9 raw mass spectrometry files for each cell pool or line).</p> <p>All the mass spectrometry files are found in the compressed (zip) file named mass_spectrometry_raw_files_archive.zip</p>
Exploring Data Evaluation Strategies for Enhanced Identification of Host Cell Proteins in Drug Products of Therapeutic Antibodies and Fc-Fusion Proteins
<p>This data repository contains all previously unpublished raw data files for the manuscript “Exploring Data Evaluation Strategies for Enhanced Identification of Host Cell Proteins in Drug Products of Therapeutic Antibodies and Fc-Fusion Proteins” by Wolfgang Esser-Skala, Marius Segl, Therese Wohlschlager, Veronika Reisinger, Johann Holzmann, and Christian G. Huber. See <em>readme.md</em> for further information.</p>
Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches
<p>Raw experimental data associated with the manuscript "Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches", by Sosa-Carrillo and colleagues, bioRxiv, 10.1101/2022.11.02.514931.<br> The code to analyze this raw data and generate the figures for the manuscript is available on GitLab at https://gitlab.inria.fr/InBio/Public/yeastcybersecretion.</p>
Dataset for Diamond-coated quartz crystal microbalance sensors: Challenges in high yield production and enhanced detection of ethanol and sars-cov-2 proteins
<p>The data set to paper: </p> <p>Name: Diamond-coated quartz crystal microbalance challenges in mass production and enhanced detection of ethanol and sars-cov-2 proteins</p> <p>Authors: Tibor Izsák1*, Marian Varga1, Michal Kočí2,3, Ondrej Szabó2, Katarína Aubrechtová Dragounová2, Gabriel Vanko2, Miroslav Gál4, Jana Korčeková5, Michaela Hornychová 4, Alexandra Poturnayová5, Alexander Kromka2*</p> <p>Affiliations: 1 Department of Microelectronics and Sensors, Institute of Electrical Engineering, Slovak Academy of Sciences, Dúbravská Cesta 9, Bratislava, 841 04, Slovak Republic<br> 2 Department of Semiconductors, Institute of Physics of the Czech Academy of Sciences, Cukrovarnicka 10/112, Prague 6 162 00, Czech Republic<br> 3 Department of Microelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, Prague 6, 166 27, Czech Republic<br> 4 Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovak Republic<br> 5 Center of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Bratislava, Slovak Republic<br> *corresponding author: tibor.izsak@savba.sk</p> <p>Data manager: Kristýna Dostálová: dostalovak@fzu.cz</p> <p>Date of collection: 1. 5. 2023 - 31. 7. 2024</p> <p>Description: Figure 1: Photos of QCM substrates oriented horizontally or vertically on the substrate holder in the deposition chamber (left) and during the diamond CVD process with ignited plasma (right).<br> Figure 2: a) 3D model of the measurement setup and b) photograph of the open gas chamber with embedded QCM sample.<br> Figure 3: Photo of the a) measurement setup and b) disassembled flow cell with V-Dia-QCM. c) Side view photo of the assembled flow cell in the measurement setup.<br> Figure 4: a) SEM images revealing surface morphology and b) corresponding Raman spectra of Dia-QCM and Dia-Si substrates horizontally or vertically oriented on the substrate holder and corresponding optical photos. There is also the Raman spectrum of the bare QCM (Au-QCM) sample before the diamond deposition.<br> Figure 5: a) Raman spectra and b) SEM images depicting surface morphology of porous diamond film grown on Si (H-PorDia-Si) and QCM (H-PorDia-QCM) substrate. The inset in Fig. 5a represents the optical photo of diamond-coated QCM. Note: ‘H-’ in sample names means horizontally loaded samples.<br> Figure 6: The response delta fR of diamond-coated QCM sensors horizontally and vertically oriented, i.e., single-sided and double-sided diamond-coated QCMs, when applying periodic switching (at 3-minute intervals) of ethanol vapour (E) with various concentrations (from 10 ppm to 100 ppm) and synthetic air (Air).<br> Figure 7: a) First resonant frequency shift (delta fR) of individual QCM sensors and b) mean values of delta fR with corresponding error bars for each QCM sensor group dependent on ethanol concentration.<br> Figure 8: a) The changes of the resonant frequency, delta fR, after the addition of neutravidin (NA) dissolved in water, biotinylated 1C aptamers (1C APT) dissolved in PBS with MgCl2, and 50 pg/mL S-RBD protein in PBS. The addition of neutravidin, aptamers, proteins, and surface washings by water (H2O) or buffer (PBS) are highlighted by arrows. b) Zoom in on the highlighted area in Fig. 8a.<br> Figure 9: Decrease of the resonant frequency, fR, at various S-RBD protein concentrations. The comparison of the sensitivity of diamond and gold QCM surfaces on which S-RBD was determined is indicated in the graph legend.</p>
Data for thesis titled: The impact of processing conditions on enzymatic protein hydrolysis performance from sardine (Sardina pilchardus) by-products using Alcalase 2.4L, and the influence on final spray dried hydrolysate powder properties
<p>The data answer the objectives that focused on:</p> <ol> <li>determining the substrate-specific optimum hydrolysis temperature and pH for the particular enzyme-substrate (Alcalase-sardine by-product) combination,</li> <li>investigating the effect of mixing speed, solids concentration and enzyme dosage on dry solids yield and protein recovery during enzymatic hydrolysis of sardine processing by-products,</li> <li>evaluating the influence of solids concentration on emulsion formation during enzymatic hydrolysis,</li> <li>determining the effect of solids concentration and emulsion formation on molecular weight distribution of protein hydrolysates,</li> <li>investigating the effect of mixing speed and solids concentration on the viscosity and mixing regime of material during enzymatic hydrolysis,</li> <li>establishing the role played by processing conditions (degree of hydrolysis (DH), maltodextrin addition and inlet air temperature) on powder recovery during spray drying, and</li> <li>investigating the role of DH, maltodextrin concentration and spray drying temperature on handling and storage properties of spray dried protein hydrolysates.</li> </ol> <p>This data also appears in journal papers with the following titles:</p> <p>Chiodza, K. & Goosen, N.J. 2023a. Evaluation of handling and storage stability of spray dried protein hydrolysates from sardine (Sardina pilchardus) processing by-products: Effect of enzymatic hydrolysis time, spray drying temperature and maltodextrin concentration. <em>Food and Bioproducts Processing</em>. (June, 30). DOI: <a href="https://www.sciencedirect.com/science/article/pii/S0960308523000743?via%3Dihub">https://doi.org/10.1016/j.fbp.2023.06.009</a>.</p> <p>Chiodza, K. & Goosen, N.J. 2023b. Influence of mixing speed, solids concentration and enzyme dosage on dry solids yield and protein recovery during enzymatic hydrolysis of sardine (Sardina pilchardus) processing by-products using Alcalase 2.4L: a multivariable optimisation approach. <em>Biomass Conversion and Biorefinery</em>. 1:1–23. DOI: <a href="https://link.springer.com/article/10.1007/s13399-023-03829-2">https://doi.org/10.1007/s13399-023-03829-2</a>. </p> <p>Chiodza, K. & Goosen, N.J. 2023c. Emulsion formation during enzymatic protein hydrolysis and its effect on protein recovery and molecular weight distribution of protein hydrolysates from sardine (Sardina pilchardus) by-products. <em>Biomass Conversion and Biorefinery</em>. 1:1–12. DOI: <a href="https://link.springer.com/article/10.1007/s13399-023-04438-9">https://doi.org/10.1007/s13399-023-04438-9</a>.</p>
Production and purification of receptor-binding domain (RBD) of the Spike protein from a transiently transfected mammalian cell
<p> </p> <p>Production and purification of recombinant receptor-binding domain (RBD) of the Spike protein from a transiently transfected EXPI293 mammalian cell .</p>
Production and purification protocols for Ectodomain of SARS-CoV-2 Spike (S) protein
<p>Production and purification protocols for Ectodomain of SARS-CoV-2 Spike (S) protein </p>
Data from: Pharmacological HIF-1 activation upregulates extracellular vesicle production synergistically with adiponectin through transcriptional induction and protein stabilization of T-cadherin
<p>Pharmacological activation of hypoxia-inducible factor 1alpha (HIF-1α), a hypoxia-responsive transcription factor, has attracted increasing attention due to its efficacy not only in renal anemia but also in various disease models. Our study demonstrated that a HIF-1 activator enhanced exosome production from cultured endothelial cells synergistically with adiponectin, an adipocyte-derived factor, through both transcriptional induction and posttranscriptional stabilization of an adiponectin binding partner, T-cadherin. Increased exosome levels were observed in wild-type mice but not in T-cadherin null mice after consecutive administration of roxadustat. Adiponectin- and T-cadherin-dependent increased exosome production may be involved in the pleiotropic effects of HIF-1 activators.</p>
Mining Proteomic Databases of a Model Plant Medicago truncatula for Mosaic Proteins and Other Unconventional Translation Products
<p><strong>How many different proteins can be produced from a single spliced transcript? Genome annotation projects do not consider the coding potential of reading frames other than that of the reference open reading frames (refORFs). Recently, alternative open reading frames (altORFs) and their translational products, alternative proteins (altProts), have been shown to carry out important functions in various organisms. Overlapping altORFs may be involved in one fundamental mechanism so far overlooked. A few years ago, it was proposed that altORFs may act as building blocks for chimeric (mosaic) polypeptides, which are produced via multiple ribosomal frameshifting events from a single mature transcript. We adopt terminology from that earlier discussion and call this mechanism mosaic translation. This way of extracting and combining genetic information may significantly increase proteome diversity. Thus, we hypothesize that this mechanism may have contributed to the flexibility and adaptability of organisms to a variety of environmental conditions. The idea of mosaic translation is a testable hypothesis, although its direct demonstration is technically very challenging. If confirmed, this concept will revolutionize modern genetics. In this project, we would like to follow a unique strategy for the detection of mosaic proteins in proteomic databases publicly available for a very important model plant <em>Medicago truncatula</em>. The proposed analysis will be based on our own preliminary data already generated in the course of an ongoing TÜBİTAK1002 project. Regardless of whether the evidence for mosaic translation is found in this study, this effort will help identify such proteins later when more proteomic data become available. Finally, our approach can reveal unconventional frameshifting products that derive from the omission of several nucleotides by ribosomes (for example, +2 to +16 frameshifts). Regardless of whether such frameshifted products are parts of mosaic proteins, the potential for their detection makes this project very novel, because frameshifts longer than one nucleotide in the forward direction have not been described so far.</strong></p>
New protein production in primary pulmonary artery endothelial cells treated with insulin-like growth factor 1 treatment
<p>Maximum projections of flat-fielded and deconvolved epi-fluorescence imaging data for primary sheep pulmonary artery endothelial cells (PAEC) treated with vehicle or insulin-like growth factor 1 (IGF1) media.</p> <p>Two cell types: normal PAEC and persistent pulmonary hypertension of the newborn (PPHN) PAEC</p> <p>Three time points: 0 minutes, 1 hour, and 24 hours post-treatment</p> <p>Two fluorescence channels:<br> C0 - DAPI for nuclei (R37606, Life Technologies)<br> C1 - Click-IT new protein translation kit (C10428, C10429, Life Technologies)</p>
Increasing Recombinant Protein Production in E. coli via FACS-Based Selection of N-terminal Coding DNA Libraries
<p>Data for a manuscript to be deposited to the FEBS Journal. </p> <p>Abstract as deposited:</p> <p><span><span>We present a novel approach to modify N-terminal sequences of recombinant proteins to increase their production yield in <em><span>Escherichia coli</span></em>. Prior research has demonstrated a profound impact of a few nucleotides following the initiator codon (further to as N-terminal sequences) on their expression. Most of these investigations have been limited to selecting from a few rationally designed sequences. In contrast we used directed evolution-based methodology screening large numbers of diversified sequences derived from DNA libraries coding for the N-termini of investigated proteins. To facilitate the identification of cells with increasing expression of the target construct, we cloned a GFP gene at the C-terminus of the expressed genes and used fluorescent activated cell sorting (FACS) to separate cells based on their fluorescence. By following this systematic workflow, we successfully elevated the yield of soluble recombinant proteins of multiple constructs up to over 30-fold. </span></span></p>
Data from: Pharmacological HIF-1 activation upregulates extracellular vesicle production synergistically with adiponectin through transcriptional induction and protein stabilization of T-cadherin
Open the record for dataset details and reuse information.
Results for Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast
<p>This dataset contains the original results for the paper "Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast". To reproduce all figures in this paper, this dataset is required. The scripts can be found in Github (https://github.com/SysBioChalmers/pcSecYeast)</p>
Nutritional Intervention With Moderately High-protein, Low-glycemic Load Products in Type-2 Diabetes Patients
ClinicalTrials.gov study NCT01264523. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Physiological Response to Protein and Energy-enhanced Food Products During Winter Military Training
ClinicalTrials.gov study NCT05210205. IPD Sharing: NO. Countries: 1. Publications: 0.
Impact of FTO Gene Variation on Body Composition, Lipid Profile, Insulin Resistance, Advanced Glycation End-Products and Ghrelin Levels in Response to Hypocaloric, Protein Rich-Diet
ClinicalTrials.gov study NCT06426017. IPD Sharing: NO. Countries: 1. Publications: 4.
High Protein Dairy Products and Resistance Exercise in the Elderly
ClinicalTrials.gov study NCT06412302. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Determination of process parameters and precipitation methods for potential large-scale production of sugar beet leaf protein concentrate
<p>Abstract</p> <p><br>BACKGROUND</p> <p>Sugar beet is one of the most produced industrial plants in the world, and during manufacturing, it produces a large quantity of leaf waste. Because this waste is rich in protein, this study aimed to identify an efficient method for producing large-scale protein concentrate from sugar beet leaves.</p> <p><br>RESULTS</p> <p>Results showed that protein extraction from fresh leaves was more effective than dried leaves. Maximum protein extraction was achieved at pH 9, compared with pH 7 or 8. Blanching as a pretreatment reduced protein yield during isoelectric precipitation, with a yield of 2.31% compared to 20.20% without blanching. Consequently, blanching was excluded from the extraction process. After extraction, isoelectric precipitation, heat coagulation, and isoelectric–ammonium sulfate precipitation were compared. Although the latter resulted in the highest protein yield, Fourier transform infrared analysis revealed that excessive salt was not removed during dialysis, making it unsuitable for scale-up due to its additional cost and complexity. Therefore, isoelectric precipitation was selected as the appropriate method for protein precipitation from sugar beet leaves. To increase yield, extractions were assisted by ultrasound or enzyme addition. Ultrasound-assisted extraction resulted in an increased protein yield from 20.20% to 28.60%, while Pectinex Ultra SP-L-assisted extraction was the most effective, increasing protein yield from 20.20% to 38.09%.</p> <p><br>CONCLUSION</p> <p>Proteins were extracted from fresh sugar beet leaves using optimum conditions (50 °C, 30 min, pH 9) and precipitated at the isoelectric point, with enzymatic-assisted extraction yielding the maximum protein recovery.<br><br></p>
Rheological and sensorial behavior of tomato product enriched with pea protein and olive powder
<p>In this study, a new functional product using Mediterranean ingredients (tomato, tomato peel powder and olive powder) was formulated where two different concentrations of protein (1 and 2%) and peel (2 and 4%) were tested. Olive powder was kept at a constant concentration of 2%. Physico-chemical, Rheological, and Sensorial analysis were carried out on the formulated samples. Soluble protein content was found as the highest in the sample containing 4% peel and 2% protein and it was affected by the pH and tomato peel concentration. Rheological results reveal shear-thinning behavior, as defined by the HerschelBulkley model, with protein and peel concentrations having a major influence on yield stress and viscosity. A positive trend was noticed between apparent viscosity and peel concentration, meantime protein concentration affected apparent viscosity adversely. Contrary relation between consistency index (k) values and apparent viscosity illustrate the complex interaction between protein and peel, particularly at higher concentrations. Furthermore, Principal Component Analysis (PCA) was used to investigate the complicated sensory landscape of tomato products with different quantities of pea protein and tomato peel. While higher tomato peel and protein levels have no direct impact on rheological qualities, they do add to astringency and sourness, which influences overall acceptability. Remarkably, the sample with the greatest quantities of peel and protein exhibits a delicate balance, with a loss in perceived tomato taste intensity and overall acceptability offsetting an increase in astringency. In terms of overall acceptability, the most preferred beverage was selected as the sample formulated with 2% peel and 1% protein.</p>
African swine fever virus E120R protein inhibits interferon-β production by interacting with IRF3 to block its activation
<p><span><span>African swine fever is a devastating disease of swine caused by African swine fever virus (ASFV). The pathogenesis of the disease remains largely unknown, leaving the uncontrolled spreading of the disease in many countries and regions. Here, we identified the E120R, a structural protein of ASFV, as a key virulent factor and late phase expression protein of the virus. E120R revealed an activity to suppress host antiviral response through blocking IFN-β production, and the 72-73 amino acid sites in the C-terminal domain were essential for this function. E120R interacted with the interferon regulatory factor 3 (IRF3) and interfered with the recruitment of IRF3 to TBK1, which in turn suppressed IRF3 phosphorylation, decreasing interferon production. The recombinant mutant ASFV was further constructed to confirm the claimed mechanism. The ASFV lacking the complete E120R region could not be rescued, whereas the virus could tolerate the deletion of the 72nd and 73rd residuals in the E120R (ASFV E120R-Δ72-73aa). ASFV E120R with the two amino acids deletion failed to interact with IRF3 during ASFV E120R-Δ72-73aa infection, and the viral infection highly activated IRF3 phosphorylation and induced more robust type I interferon production in comparison with its parental ASFV. An unbiased transcriptome-wide analysis of gene expression also confirmed that a considerably higher level of ISGs was detected in ASFV E120R-Δ72-73aa-infected porcine alveolar macrophages (PAMs) than that in the wildtype ASFV-infected PAMs. Together, our findings found a novel mechanism evolved by ASFV to inhibit host antiviral response and provide a new target for guiding the development of ASFV live-attenuated vaccine.</span></span></p>
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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.