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> Disorders > Neoplastic Process > Choroid Plexus Papilloma

Choroid Plexus Papilloma

Choroid Plexus Papilloma: A rare, benign neoplasm originating from the choroid plexus epithelium.
It typically occurs in the ventricles of the brain, most commonly the lateral and fourth ventricles.
Choroid plexus papillomas can cause obstructive hydrocephalus due to their location and growth.
Accurate identification of the best research protocols and products is crucial for studying this condition.
PubCompare.ai's AI-driven platform can help optimize your research on choroid plexus papilloma by facilitating the discovery of relevant protocols from literature, preprints, and patents, and providing AI-powered comparisons to identify the most suitable approaches for your study.
Streamline your research with PubCompare.ai's powerful tools and experince enhanced results.

Most cited protocols related to «Choroid Plexus Papilloma»

1
Comprehensive CPP Structural Annotation
Data were compiled in two different tables as primary and secondary data. The manually curated information such as PubMed ID, CPP sequences, name, their category, chirality, nature, ends modifications, length and other relevant experimental information like uptake efficiency, uptake mechanism, sub-cellular localizations, model systems used for CPP testing, cargo types, etc. were organized as the primary information.
We have derived other important information from the primary data like physiochemical properties and amino acid composition of CPPs. This information was stored as secondary information in the database. Since structure plays a major role in defining the function of a peptide, we also performed the structural annotation of the peptides present in CPPsite 2.0. We followed a systematic approach for performing structural annotation. First, if the peptide was already available in Protein Data Bank (PDB) (25 (link)), we assigned the same structure to that peptide as present in PDB. We mapped the sequences of all the peptides of CPPsite 2.0 to that of PDB sequences to identify such peptides. If the peptide was not available in PDB, we predicted the structure of those peptides using structure prediction techniques. Peptides with length ranging between 5 and 30 residues were predicted using the web-service PEPstrMOD (in parallel communication). PEPstrMOD is an updated version of PEPstr method (26 (link)), which predicts the tertiary structure of peptides. PEPstrMOD is capable of handling peptides with natural as well as non-natural or modified amino acids. Many peptides in CPPsite2 contains modified residues like Ornithine, β-alanine, etc. which were predicted using PEPstrMOD which integrates force field libraries (FFNCAA (27 (link)), FFPTM (28 (link)) and SwissSideChain (29 (link)–30 (link)) to tackle non-natural residues. The peptides having natural amino acids but linked with fluorophores (used for labeling) at terminal residues or having other complex modifications were treated as natural and their structure was also predicted using PEPstrMOD.
Peptides having the length between 1 and 4 residues were predicted using an alternative approach. We used an extended conformation of the peptide (with phi and psi torsion angles of 180° for each residue) as initial structure, which is then subjected to energy minimization and molecular dynamics simulation to get the output predicted structure. The peptides with more than 30 natural amino acids were predicted using I-TASSER suite (31 (link)). I-TASSER (named as ‘Zhang-Server’) was among the best methods in the server category in recent CASP (2011 and 2010) experiments for the assessment of protein structure prediction (32 (link)).
The predicted tertiary structures of peptides were given as input to DSSP software (version 2.0.4) (33 (link)) which assigns eight types of secondary structure states. DSSP describes these states as helix (alpha helix (H), 3/10 helix (G) and pi helix (I)); strand (extended strand (E) and beta-bridge (B)); turn (T); bend (S) and loop (C).
Agrawal P., Bhalla S., Usmani S.S., Singh S., Chaudhary K., Raghava G.P, & Gautam A. (2015). CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides. Nucleic Acids Research, 44(Database issue), D1098-D1103.
Publication 2015
Amino Acids beta-Alanine Biological Models Cells Choroid Plexus Papilloma Decompression Sickness Helix (Snails) Ornithine Peptides Proteins
2
Comparative Analysis of CPP Datasets
In order to compare our method with existing methods, we have extracted datasets from literature that have been used in previous studies. Sanders et al. (2011) have developed a method for CPP prediction. In this study, they have used 111 experimentally validated CPPs and equal number of non-CPPs (generated randomly from the chicken proteome). We have named this dataset Sanders-2011a. Second dataset from Sanders et al. (2011) named Sanders-2011b, which contains 111 CPPs and 34 experimentally validated non-CPPs. We have also generated a third dataset Sanders-2011c consisting of 111 CPPs, and 111 non-CPPs randomly sampled from 34 known non-CPPs. Dobchev et al. (2010) have used 74 CPPs and 24 non-CPPs for developing method for CPP prediction. These peptides were collected from the literature. We have used this dataset in this study and named Dobchev-2010. Similarly, we have created datasets Hansen-2008 (containing 66 CPPs & 19 non-CPPs) [20 (link)] and Hallbrink-2005 (containing 53 CPPs & 16 non-CPPs) from previous studies [19 (link)].
Gautam A., Chaudhary K., Kumar R., Sharma A., Kapoor P., Tyagi A, & Raghava G.P. (2013). In silico approaches for designing highly effective cell penetrating peptides. Journal of Translational Medicine, 11, 74.
Publication 2013
Chickens Choroid Plexus Papilloma Peptides Proteome
3
Urological Measures for UCPPS
Urological measures were selected purposefully to provide continuity between MAPP and pre-existing literatures on IC/BPS and IC/CPPS. The urological measures thus sought to assess symptoms that have been historically considered relevant to UCPPS with instruments designed specifically for this population (Table 3).
Landis J.R., Williams D.A., Lucia M.S., Clauw D.J., Naliboff B.D., Robinson N.A., van Bokhoven A., Sutcliffe S., Schaeffer A.J., Rodriguez L.V., Mayer E.A., Lai H.H., Krieger J.N., Kreder K.J., Afari N., Andriole G.L., Bradley C.S., Griffith J.W., Klumpp D.J., Hong B.A., Lutgendorf S.K., Buchwald D., Yang C.C., Mackey S., Pontari M.A., Hanno P., Kusek J.W., Mullins C, & Clemens J.Q. (2014). The MAPP research network: design, patient characterization and operations. BMC Urology, 14, 58.
Publication 2014
Choroid Plexus Papilloma
4
Comprehensive Community Obesity Intervention Protocol

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2015
Action Potentials Behavior Therapy Child Choroid Plexus Papilloma Ethics Committees, Research Obesity Pediatric Obesity Youth
5
Experimentally Validated Cell-Penetrating Peptide Database
We have extracted 843 experimentally validated CPPs from the CPPsite database, which has been developed by our group [24 ]. The peptides containing non-natural amino acids (e.g. selenocysteine) or having D-amino acids (D-conformation) were removed. Finally, we have got 708 unique CPPs having natural amino acids. Three different datasets (CPPsite-1, CPPsite-2 and CPPsite-3) have been created from these peptides. Since very few peptides have been experimentally validated as non-CPPs (negative examples), equal number of peptides (15–30 amino acids) were generated randomly from SwissProt proteins, and considered them as non-CPPs. This strategy for creating negative dataset has already been used in previous studies [22 (link),25 (link)].
First dataset (CPPsite-1) contains 708 CPPs (positive examples) and 708 non-CPPs (negative examples). In CPPsite-1, CPPs having wide range of uptake efficiency (low and high) have been included, thus we have derived another dataset CPPsite-2 from CPPsite-1. CPPsite-2 contains 187 CPPs having high uptake efficiency and equal number of non-CPPs. We have created third dataset (CPPsite-3), which contains 187 CPPs having high uptake efficacy as positive examples and equal number of CPPs with low uptake efficiency were taken as negative examples. The model based on CPPsite-3 dataset can discriminate between high and low efficient CPPs.
All datasets (CPPsite-1, CPPsite-2 and CPPsite-3) consist of several CPPs with all possible Ala-scan mutants, or different truncations. Ideally redundancy in the datasets should be removed because it affects the performance of prediction method. In past, our group has removed the redundancy in various prediction methods [25 (link),26 (link)]. But in this study, we have not removed the redundancy in CPP datasets because a single residue can affect the uptake efficiency of CPPs, and this may also lead to the loss of information about CPPs. In order to check the performance of our model on redundant dataset, we have used some benchmark datasets, which are redundant.
Gautam A., Chaudhary K., Kumar R., Sharma A., Kapoor P., Tyagi A, & Raghava G.P. (2013). In silico approaches for designing highly effective cell penetrating peptides. Journal of Translational Medicine, 11, 74.
Publication 2013
Amino Acids Choroid Plexus Papilloma Peptides Proteins Radionuclide Imaging Selenocysteine

Most recents protocols related to «Choroid Plexus Papilloma»

1
Optimized Imiquimod Nanosuspension Cream
Preparation of the aqueous nanosuspension: to create an IMQ nanosuspension, the top-down method of a wet media ball-milling process was selected. CMAs and CPPs were identified by using an Ishikawa diagram and estimated for their criticality in a risk-estimation matrix. The CMAs have been previously studied by Gogoll [7 (link),22 ] and Denny [23 ]. In this study, the identified CPPs of the wet media ball-milling process’s milling time and rotational speed were evaluated by using DoE in a face-centered CCD and were set up by using Minitab Statistical Software (version 21.1). The CPPs were studied at two levels: low (−1) at 250 rpm for 60 min and high (+1) at 650 rpm for 240 min in 2 replicates with an alpha of 1. Milling time was segmented into 20 min cycles, each cycle with a 10 min pause interval in between each cycle, using a Fritsch Pulverisette 6 planetary mill. For the experimental runs with 150 min of milling time, a 10 min cycle was added after the seventh milling cycle. All experimental runs were randomized. The model contained 8 corner points, 10 center points and 8 star points, totaling 26 conducted experimental runs. For each experimental run, the z-average and PdI were measured in triplicates. The ratio of milling balls to drug substance mass, the media volume and the milling ball size were kept constant by following [7 (link),22 ]. For the study and manufacturing of IMPs, a total mass of 25 g of 1 mm diameter zirconium oxide milling balls, a volume of 17 mL of a 9% (w/w) polysorbate 80 solution and an IMQ mass of 3 g were added into a 45 mL zirconium oxide grinding vessel [23 ]. Based on the identified optimal process conditions, milling for IMP manufacturing was performed at 650 rpm for 7 20 min repetitive cycles, each with a 10 min pause interval in between each milling cycle.
Homogenization of the o/w emulsion: for the dispersion of jojoba wax in the aqueous IMQ suspension, a high-pressure homogenization (HPH) process was selected. The number of cycles and pressure necessary to disperse the jojoba wax were identified as a critical process parameter and empirically determined until the emulsion appeared homogeneously. For the manufacturing of IMPs, the emulsion was homogenized for 5 cycles at 500 bar and 10 cycles at 1000 bar after the addition of stochiometric amounts of jojoba wax, Aqua conservata DAC and polysorbate 80 using an Avestin Emulsiflex C3.
Adjustment of the cream consistency: to create a cream formulation, a neutralized 3% (w/w) Carbomer 974P gel was prepared (pH 6.5–7.0). After gelling, a stochiometric amount of the neutralized carbomer gel was added to the homogenized o/w emulsion after the HPH step. The emulsion was incorporated into the gel matrix in a bowl with a pestle and mixed until the gel had transitioned from a sol to the gel state, and the formulation appeared as a cream. The resulting formulation was packaged in a 7 mL Aponorm aluminum tube with 3 g ± 15% of the formulation and labeled according to regulatory requirements on the labeling of IMPs.
Pielenhofer J., Meiser S.L., Gogoll K., Ciciliani A.M., Denny M., Klak M., Lang B.M., Staubach P., Grabbe S., Schild H., Radsak M.P., Spahn-Langguth H, & Langguth P. (2023). Quality by Design (QbD) Approach for a Nanoparticulate Imiquimod Formulation as an Investigational Medicinal Product. Pharmaceutics, 15(2), 514.
Publication 2023
Aluminum Blood Vessel carbomer Chaperone-Mediated Autophagy Choroid Plexus Papilloma Emulsions Face jojoba wax Pharmaceutical Preparations Polysorbate 80 Pressure zirconium oxide
2
Lipid-based Delivery of Modified Oligonucleotides
SCO-705 (5′-CCUCUUACCUCAGUUACA-3′), SCO-654 (5′-GCUAUUACCUAAACCCAG-3′), and Cy5-SCO-654, all with a phosphorothioate backbone and 2′OMe modification, were purchased from Metabion (Planegg, Germany). The siRNA targeting luciferase (5′-GGACGAGGACGAGCACUUCTT-3′) and the negative control siRNA (5′-AGGUAGUGUAAUCGCCUUGTT-3′) were obtained from Microsynth (Balgach, Switzerland). The following CPPs were used: PF14, hPep3, and CADY (see Table S1). PF14 was obtained from PepMic (Suzhou, China), CADY was kindly provided by G. Divita and S. Deshayes, Montpellier CNRS, and hPep3 by T. Lehto, ITUT. For all peptides, 1 mM stock solutions were prepared and stored at −20 °C. Lipofectamine RNAiMAX Reagent was obtained from Invitrogen (Waltham, MA, USA). The used organic solvents were of p.a. grade with low water content (>99.5%): EtOH (Chem-Lab, Zedelgem, Belgium), 2-propanol and 2-butanol (Riedel-de Häen, Honeywell, Wabash, IN, USA), DMSO (AppliChem, Darmstadt, Germany), and THF (Lachner, Eurasburg, Germany). Trimethylene carbonate, i.e., 1,3-dioxan-2-one, was sourced from Apollo (Stockport, UK), and ethylene carbonate and glycerol carbonate were sourced from Acros Organics (Geel, Belgium). Other reagents, such as CaCl2, MgCl2, MeOH, DMF, etc., were obtained from Merck-Sigma-Aldrich (Darmstadt, Germany) if not stated otherwise. The cell culture lysis solution contained 1% (v:v) Triton X-100, 50 mM of Tris (pH 7.5), 150 mM of NaCl, and 1 mM of EDTA. Ready-to-use Cell Proliferation Colorimetric Reagent, WST-8, was purchased from BioVision (Milpitas, CA, USA). The luciferase activity measurement protocol was based on Rocha et al., 2016 [49 (link)] and Helmfors et al., 2015 [50 (link)]. The silicon wafers used for scanning electron microscopy and atomic force microscopy were obtained from Micro to Nano (Haarlem, The Netherlands).
Biswas A., Maloverjan M., Padari K., Abroi A., Rätsep M., Wärmländer S.K., Jarvet J., Gräslund A., Kisand V., Lõhmus R, & Pooga M. (2023). Choosing an Optimal Solvent Is Crucial for Obtaining Cell-Penetrating Peptide Nanoparticles with Desired Properties and High Activity in Nucleic Acid Delivery. Pharmaceutics, 15(2), 396.
Publication 2023
2-butanol Carbonates Cell Culture Techniques Cell Proliferation Choroid Plexus Papilloma Colorimetry dioxane Edetic Acid Ethanol ethylene carbonate Glycerin Isopropyl Alcohol Lipofectamine Luciferases Magnesium Chloride Microscopy, Atomic Force Peptides RNA, Small Interfering Scanning Electron Microscopy Silicon Sodium Chloride Solvents Sulfoxide, Dimethyl trimethylene carbonate Triton X-100 Tromethamine Vertebral Column WST-8
3
Visualizing Superoxide Production in HUVECs
To image superoxide (O2−) production, HUVECs exposed to secondary CPPs (24 hours) were incubated with 2.5 μmol/L MitoSOX Red Reagent (#M36008, Thermo Fisher Scientific), for 30 minutes at 37 °C. After incubation, cells were washed with serum-free ECM and fixed with 2% paraformaldehyde (PFA) for 30 minutes. Prior to the imaging, samples were incubated with DAPI (180 nmol/L) solution for 10 minutes in the dark. Fluorescent images were taken with the EVOS cell imaging system (Thermo Fisher Scientific).
Feenstra L., Kutikhin A.G., Shishkova D.K., Buikema H., Zeper L.W., Bourgonje A.R., Krenning G, & Hillebrands J.L. (2023). Calciprotein Particles Induce Endothelial Dysfunction by Impairing Endothelial Nitric Oxide Metabolism. Arteriosclerosis, Thrombosis, and Vascular Biology, 43(3), 443-455.
Publication 2023
Cells Choroid Plexus Papilloma DAPI paraform Serum Superoxides
4
Peroxynitrite-Induced Protein Nitration in ECs
To analyze peroxynitrite protein damage in ECs, indicated by the formation and presence of protein nitrotyrosine residues (3NT), an immunohistochemical nitrotyrosine staining was performed on HUVECs and paraffin-embedded RCA rings. With regard to the in vitro staining, HUVECs were cultured in Nunc Lab-Tek chamber slides (BD Biosciences) and exposed to secondary CPPs for 24 hours. After the stimulation, cells were fixed in 2% PFA and permeabilized with 0.5% Triton-X-100. Next, cells were blocked in 5% BSA-PBS and 0.1% H2O2 for 30 minutes at RT, followed by incubation with the primary anti-3NT antibody (#39B6, 1:50, Santa Cruz Biotechnologies) in 1% BSA-PBS at 4 °C overnight. Cells were blocked with both avidin and biotin for 15 minutes at RT (#SP-2001, Avidin-biotin kit, Vector Laboratories). For detection of the primary antibody, an isotype-specific IgG2a secondary antibody (#1081-08, 1:100, Southern Biotech, goat anti-mouse Biotin) and streptavidin-HRP conjugate diluted in 1% serum-PBS were used (#P039701-2, DAKO). Thereafter, tissue sections were incubated with 3’-diaminobenzidine (DAB) and counterstained with hematoxylin. Finally, stained HUVECs were mounted with Kaiser’s glycerol gelatin. Stained sections were scanned with the Hamamatsu slide scanner (Hamamatsu, Japan) and analyzed with the ImageJ Software.42 (link) Graphs showed the mean pixel intensity expressed as delta (Δ) to the experimental control.
For staining the RCA rings, a similar protocol was followed with a few modifications. Briefly, the tissue sections were deparaffinized, followed by overnight antigen retrieval in 10 mmol/L Tris-HCl (pH=9) at 80 °C. Tissue sections were blocked in 5% BSA-PBS and 0.1% H2O2 for 30 minutes at RT and incubated with the primary anti-3NT antibody (#39B6, 1:50, Santa Cruz Biotechnologies) in 1% BSA and 5% serum-PBS for 3 hours at RT. For the detection of the primary antibody, a donkey anti-mouse Alexa Fluor 647-conjugated secondary antibody (#A-31571, Invitrogen) was used. Additionally, tissue sections were incubated with Lycopersicon esculentum Lectin (LEA; #FL-1171, 1:100, Vector Laboratories) to visualize the endothelial glycocalyx. Nuclei were visualized with DAPI and sections were mounted with CitiFluor mounting medium. Stained sections were scanned the Olympus slide viewer VS200 (Olympus Nederland B.V., the Netherlands) and analyzed with the ImageJ Software afterward.42 (link) For analysis, 5 random LEA positive areas were selected, in which the mean fluorescent intensity of the 3NT positive pixels were quantified per sample.
Feenstra L., Kutikhin A.G., Shishkova D.K., Buikema H., Zeper L.W., Bourgonje A.R., Krenning G, & Hillebrands J.L. (2023). Calciprotein Particles Induce Endothelial Dysfunction by Impairing Endothelial Nitric Oxide Metabolism. Arteriosclerosis, Thrombosis, and Vascular Biology, 43(3), 443-455.
Publication 2023
3-nitrotyrosine Alexa Fluor 647 Antibodies, Anti-Idiotypic Antigens Avidin Biotin Cell Nucleus Cells Choroid Plexus Papilloma Cloning Vectors DAPI Endothelium Equus asinus Gelatins Glycerin Glycocalyx Goat Hematoxylin IgG2A Immunoglobulin Isotypes Immunoglobulins Mus Paraffin Peroxide, Hydrogen Peroxynitrite Proteins Serum Streptavidin Tissues tomato lectin Triton X-100 Tromethamine
5
Porcine Endothelial Function Assessment by Ex Vivo Assay
To assess the ex vivo endothelial cell function, RCA rings were incubated in Krebs-buffered CPP solutions (0=control condition, TBS in Krebs bicarbonate solution), 100, 200, and 400 μg/mL (CPPs) for 2 hours (37 °C) or overnight (≈20 hours, 4 °C). Rings were isolated from 3 individual porcine hearts and evenly distributed within groups (3–4 rings per heart per group; total 2 hours N=7–9 rings per group, overnight N=8–11 rings per group). After incubation, rings were placed into the organ baths for measurement of isotonic displacements as described previously.33 (link)–35 In brief, organ baths were filled with Krebs buffer (15 mL) and continuously aerated with 95% O2 and 5% CO2 at 37 °C. Rings were allowed to equilibrate for 60 minutes before the start of the experiments. After the equilibrium was reached, rings were stimulated twice with 60 mmol/L KCl, for reasons of priming and viability assessment. Rings not responding to KCl treatment were excluded from the experiment. Then, rings were pre-contracted with the thromboxane agonist U46619 (10−7 mol/L) in the presence of the COX inhibitor indomethacin (10−5 mol/L). Because COX-derived prostaglandins can cause interspecies variation and thereby influence vasoactive responses, a single dose of indomethacin was administered to inhibit the prostaglandin activity and rule out COX-derived variation between pigs.36 (link) Subsequently, increasing concentrations of bradykinin (10−10–10−6 mol/L) were added in a cumulative manner to measure endothelial-dependent relaxation of the rings. In this study, we used bradykinin as vasodilating compound, and not acetylcholine or H2O2 which are known to have vasoconstricting properties in various conditions.37 (link)–39 (link) To circumvent these vasoconstrictive effects, we chose to use bradykinin. Finally, a single dose of sodium nitroprusside (SNP; EC-independent NO donor; 10−4 mol/L) was added to assess maximal endothelium-independent VSMC relaxation. Both endothelial-dependent and endothelial-independent relaxation were calculated as percentage of the precontraction to U46619. Responses (in micrometer) were measured with LabView (National instruments, 2010). IC50 was calculated with GraphPad Prism 9.
Feenstra L., Kutikhin A.G., Shishkova D.K., Buikema H., Zeper L.W., Bourgonje A.R., Krenning G, & Hillebrands J.L. (2023). Calciprotein Particles Induce Endothelial Dysfunction by Impairing Endothelial Nitric Oxide Metabolism. Arteriosclerosis, Thrombosis, and Vascular Biology, 43(3), 443-455.
Publication 2023
Acetylcholine Bath Bicarbonates Bradykinin Buffers Cardiac Arrest Choroid Plexus Papilloma Displacement, Psychology Donors Endothelial Cells Endothelium Heart Indomethacin Krebs-Ringer solution Nitroprusside, Sodium Peroxide, Hydrogen Physiology, Cell Pigs prisma Prostaglandins Thromboxanes U-44619

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More about "Choroid Plexus Papilloma"

Choroid Plexus Papilloma (CPP) is a rare, benign neoplasm that originates from the choroid plexus epithelium, typically occurring in the ventricles of the brain, most commonly the lateral and fourth ventricles.
This condition can cause obstructive hydrocephalus due to its location and growth.
Accurate identification of the best research protocols and products is crucial for studying CPP.
PubCompare.ai's AI-driven platform can help optimize your research on CPP by facilitating the discovery of relevant protocols from literature, preprints, and patents, and providing AI-powered comparisons to identify the most suitable approaches for your study.
Streamline your research with PubCompare.ai's powerful tools and experince enhanced results.
When studying CPP, researchers may utilize various techniques and equipment, such as Tripsin/EDTA for cell dissociation, FITC for fluorescent labeling, and A1 confocal microscope with NIS-Elements software Ver4.4 for imaging.
The Zetasizer Nano ZS may be used for particle size analysis, while the BioTek Synergy H1 can be employed for assays.
DMSO may be used as a solvent, and the ChemiDoc XRS gel imaging system can be utilized for gel documentation.
Culturing cells in DMEM/F12 medium and imaging with the LSM 700 confocal microscope are also common in CPP research.