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Cytokinesis

Cytokinesis is the final phase of cell division, where the cytoplasm of a single cell divides into two or more daughter cells.
This critical process ensures the equitable distribution of genetic material and organelles between the newly formed cells.
PubCompare.ai, an AI-driven platform, can enhance the accuracy of your cytokinesis research by helping you locate the best research protocols from literature, pre-prints, and patents.
Its AI-powered comparisons can identify the optimal protocols and products for your needs, streamlining your research process and providing more reliable results.
Disocver the power of PubCompare.ai for your cytokinesis studies.

Most cited protocols related to «Cytokinesis»

1
Mass Spectrometry Data Processing Pipeline
Following
data acquisition, Thermo RAW files were processed using
a series of software tools that were developed in-house. First the
RAW files were converted to mzXML using a custom version of ReAdW.exe
(http://sashimi.svn.sourceforge.net/viewvc/sashimi/) that
had been modified to export ion accumulation times and FT peak noise.
During this initial processing we also corrected any erroneous assignments
of monoisotopic m/z. Using Sequest,24 (link) MS2 spectra were searched against the human
UniProt database (downloaded on 08/02/2011), supplemented with the
sequences of common contaminating proteins such as trypsin. This forward
database was followed by a decoy component, which included all target
protein sequences in reversed order.
Searches were performed
using a 50 ppm precursor ion tolerance.25 (link) When searching Orbitrap MS2 data, we used 0.02 Th fragment ion tolerance.
The fragment ion tolerance was set to 1.0 Th when searching ITMS2
data. Only peptide sequences with both termini consistent with the
protease specificity of LysC were considered in the database search,
and up to two missed cleavages were accepted. TMT tags on lysine residues
and peptide N-termini (+ 229.162932 Da) and carbamidomethylation of
cysteine residues (+ 57.02146 Da) were set as static modifications,
while oxidation of methionine residues (+ 15.99492 Da) was treated
as a variable modification. An MS2 spectral assignment false discovery
rate of less than 1% was achieved by applying the target-decoy strategy.26 (link) Filtering was performed using linear discriminant
analysis as described previously27 (link) to create
one composite score from the following peptide ion and MS2 spectra
properties: Sequest parameters XCorr and unique ΔCn, peptide
length and charge state, and precursor ion mass accuracy. The resulting
discriminant scores were used to sort peptides prior to filtering
to a 1% FDR, and the probability that each peptide-spectral-match
was correct was calculated using the posterior error histogram.
Following spectral assignment, peptides were assembled into proteins
and proteins were further filtered based on the combined probabilities
of their constituent peptides to a final FDR of 1%. In cases of redundancy,
shared peptides were assigned to the protein sequence with the most
matching peptides, thus adhering to principles of parsimony.28
McAlister G.C., Nusinow D.P., Jedrychowski M.P., Wühr M., Huttlin E.L., Erickson B.K., Rad R., Haas W, & Gygi S.P. (2014). MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes. Analytical Chemistry, 86(14), 7150-7158.
Publication 2014
Amino Acid Sequence Cytokinesis Immune Tolerance Lysine Methionine Peptides Proteins Trypsin tyrosyl-alanyl-glycine
2
SARS-CoV-2 Spike Protein Expression Protocols
The mammalian cell codon-optimized nucleotide sequence coding for the spike protein of the SARS-CoV-2 isolate (GenBank:MN908947.3) was synthesized commercially (Genewiz). The RBD (amino acids 319–541; RVQP…CVNF), along with the signal peptide (amino acids 1–14; MFVF…VSSQ) plus a hexahistidine tag, was cloned into mammalian expression vector pCAGGS as well as in a modified pFastBac Dual vector for baculovirus system expression. The soluble version of the spike protein (amino acids 1–1,213; MFVF…IKWP), including a C-terminal thrombin cleavage site, T4 foldon trimerization domain and hexahistidine tag, was also cloned into pCAGGS. The protein sequence was modified to remove the polybasic cleavage site (RRAR to A), and two stabilizing mutations were introduced as well (K986P and V987P; wild-type numbering). Recombinant proteins were produced using the well-established baculovirus expression system and this system has been published in detail in refs.20 (link)–22 , including a video guide. Recombinant proteins were also produced in Expi293F cells (Thermo Fisher Scientific) by transfections of these cells with purified DNA using an ExpiFectamine 293 Transfection Kit (Thermo Fisher Scientific). Supernatants from transfected cells were harvested on day 3 post-transfection by centrifugation of the culture at 4,000g for 20 min. Supernatant was then incubated with 6 ml Ni-NTA Agarose (Qiagen) for 1–2 h at room temperature. Next, gravity flow columns were used to collect the Ni-NTA agarose and the protein was eluted. Each protein was concentrated in Amicon centrifugal units (EMD Millipore) and re-suspended in phosphate-buffered saline (PBS). Proteins were analyzed by reducing SDS-PAGE. The DNA sequence for all constructs is available from the Krammer Laboratory and has also been deposited in GenBank (additional information in the ‘Data availability’ statement). Several of the expression plasmids and proteins have also been submitted to the BEI Resources repository and can be requested from their web page for free (https://www.beiresources.org/. S1 proteins of NL63 and 229E were obtained from Sino Biological (produced in hexahistidine-tagged 293HEK cells). A detailed protocol for protein expression of RBD and spike in mammalian cells is also available7 (link).
Amanat F., Stadlbauer D., Strohmeier S., Nguyen T.H., Chromikova V., McMahon M., Jiang K., Arunkumar G.A., Jurczyszak D., Polanco J., Bermudez-Gonzalez M., Kleiner G., Aydillo T., Miorin L., Fierer D.S., Lugo L.A., Kojic E.M., Stoever J., Liu S.T., Cunningham-Rundles C., Felgner P.L., Moran T., García-Sastre A., Caplivski D., Cheng A.C., Kedzierska K., Vapalahti O., Hepojoki J.M., Simon V, & Krammer F. (2020). A serological assay to detect SARS-CoV-2 seroconversion in humans. Nature medicine, 26(7), 1033-1036.
Publication 2020
Amino Acids Amino Acid Sequence Baculoviridae Biopharmaceuticals Cells Centrifugation Cloning Vectors Codon Cytokinesis DNA Sequence Gravity His-His-His-His-His-His isononanoyl oxybenzene sulfonate Mammals M protein, multiple myeloma Mutation Open Reading Frames Phosphates Plasmids Proteins Recombinant Proteins Saline Solution SARS-CoV-2 SDS-PAGE Sepharose Signal Peptides Staphylococcal Protein A Thrombin Transfection
3
Genomic DNA Extraction and CRISPR Indel Analysis

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2013
Buffers Cells Clustered Regularly Interspaced Short Palindromic Repeats Cytokinesis Genes Genome Gold INDEL Mutation Oligonucleotide Primers polyacrylamide gels Stains Taq Polymerase Transfection
4
CRISPR Efficiency Measurement by SURVEYOR Assay
293FT and HUES9 cells were transfected with DNA as described above. Cells were incubated at 37 °C for 72 h post-transfection before genomic DNA extraction. Genomic DNA was extracted using the QuickExtract DNA Extraction Solution (Epicentre) following the manufacturer's protocol. Briefly, pelleted cells were resuspended in QuickExtract solution and incubated at 65 °C for 15 min, 68 °C for 15 min, and 98 °C for 10 min.
The genomic region flanking the CRISPR target site for each gene was PCR amplified (target sites and primers listed in Supplementary Tables 1 and 2), and products were purified using QiaQuick Spin Column (Qiagen) following the manufacturer's protocol. 400 ng total of the purified PCR products were mixed with 2 μl 10× Taq DNA Polymerase PCR buffer (Enzymatics) and ultrapure water to a final volume of 20 μl, and subjected to a re-annealing process to enable heteroduplex formation: 95 °C for 10 min, 95 °C to 85 °C ramping at −2 °C/s, 85 °C to 25 °C at −0.25 °C/s, and 25 °C hold for 1 min. After re-annealing, products were treated with SURVEYOR nuclease and SURVEYOR enhancer S (Transgenomics) following the manufacturer's recommended protocol, and analyzed on 4–20% Novex TBE polyacrylamide gels (Life Technologies). Gels were stained with SYBR Gold DNA stain (Life Technologies) for 30 min and imaged with a Gel Doc gel imaging system (Bio-rad). Quantification was based on relative band intensities. Indel percentage was determined by the formula, 100 × (1 − (1 − (b + c)/(a + b + c))1/2), where a is the integrated intensity of the undigested PCR product, and b and c are the integrated intensities of each cleavage product.
Hsu P.D., Scott D.A., Weinstein J.A., Ran F.A., Konermann S., Agarwala V., Li Y., Fine E.J., Wu X., Shalem O., Cradick T.J., Marraffini L.A., Bao G, & Zhang F. (2013). DNA targeting specificity of RNA-guided Cas9 nucleases. Nature biotechnology, 31(9), 827-832.
Publication 2013
Buffers Cells Clustered Regularly Interspaced Short Palindromic Repeats Cytokinesis Genes Genome Gold H-DNA INDEL Mutation Oligonucleotide Primers polyacrylamide gels Stains Taq Polymerase Transfection
5
Genome-wide CRISPR Target Identification
Euchromatic regions of the dm3/BDGP release 5 Drosophila melanogaster genome were indexed as in Iseli et al. (2007) (link). PHP code was developed to (1) parse user-inputted DNA sequence to detect CRISPR targets on both strands, (2) execute fetchGWI (Iseli et al. 2007 (link)) to identify similar sequences elsewhere in the genome, (3) employ algorithms based on empirical rules and user-selected parameters to identify potential off-target cleavage sites, and (4) return CRISPR target sites ranked by specificity along with location information and a Gbrowse link for each potential off-target site. The following invertebrate genomes were processed identically: D. simulans (annotation DroSim1), D. yakuba (DroYak2), D. sechellia (DroSec1), D. virilis (DroVir3), two strains of Anopheles gambiae (AgamM1 and AgamS1), Aedes aegypti (AaegL1), Apis mellifera (apiMel3), Tribolium castaneum (TriCas2), and Caenorhabditis elegans (ce10). A detailed user manual is available at http://tools.flycrispr.molbio.wisc.edu/targetFinder/CRISPRTargetFinderManual.pdf.
Gratz S.J., Ukken F.P., Rubinstein C.D., Thiede G., Donohue L.K., Cummings A.M, & O’Connor-Giles K.M. (2014). Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila. Genetics, 196(4), 961-971.
Publication 2014
Aedes Anopheles gambiae Apis Caenorhabditis elegans Clustered Regularly Interspaced Short Palindromic Repeats Cytokinesis Drosophila melanogaster Drosophila simulans Genome Invertebrates Strains Tribolium, monocots

Most recents protocols related to «Cytokinesis»

1
CRISPR-Cas9 RNA Editing in iPSCs
Not available on PMC !

Example 2

iPS cells were prepared according to protocols known in the art and seeded in a Geltrex®-Matrix coated 12-well culture dish. Transfection was performed in iPSCs with 3 ul of Lipofectamine® 2000 or 3 ul of Lipofectamine® 3000 as indicated and according to manufacturer's instructions, to deliver a GeneArt® CRISPR Nuclease vector targeting the HPRT locus. Transfection was also performed with GeneArt® CRISPR Nuclease RNA editing system targeting the HPRT locus and 3 ul of Formulation 21 lipid aggregate complex. RNA editing system utilizes a Cas9 mRNA, which was prepared via in vitro transcription with the Ambion® mMESSAGE mMACHINE® Kit, and a gRNA which was transcribed using the Ambion® MEGAshortscript™ Kit. Cells were harvested 72-hours post-transfection and cleavage efficiency was determined using the GeneArt® Genomic Cleavage Detection Kit.

Results are shown in FIG. 2A and FIG. 2B, which clearly demonstrate that using an mRNA based form of Cas9 with a guide-RNA for gene editing with the lipid aggregates described herein for transfection results in at least 4-fold more targeted cleavage of the host cell genome when compared to standard DNA based editing approaches.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, the descriptions and examples should not be construed as limiting the scope of the invention. The disclosures of all patent and scientific literature cited herein are expressly incorporated in their entirety by reference.

US11872285B2. Compositions and methods for efficient delivery of molecules to cells (2024-01-16). LIFE TECHNOLOGIES CORPORATION [US]. Inventors: Xavier de Mollerat du Jeu [US], Nektaria Andronikou [US].
Full text: Click here
Patent 2024
Cells Cloning Vectors Clustered Regularly Interspaced Short Palindromic Repeats Cytokinesis Genes Genome Hyperostosis, Diffuse Idiopathic Skeletal Induced Pluripotent Stem Cells Lipids Lipofectamine lipofectamine 2000 RNA, Messenger Transcription, Genetic Transfection
2
Benchmarking MCA-Miner against FP-Growth in BRL
Not available on PMC !

Example 1

The MCA-miner method disclosed herein in FIGS. 2A-2C, when used together with BRL, offers the power of rule list interpretability while maintaining the predictive capabilities of already established machine learning methods.

The performance and computational efficiency of the new MCA-miner is benchmarked against the “Titanic” dataset, as well as the following five (5) datasets available in the UCI Machine Learning Repository: “Adult,” “Autism Screening Adult,” “Breast Cancer Wisconsin (Diagnostic),” “Heart Disease,” and “HIV-1 protease cleavage,” which are designated as Adult, ASD, Cancer, Heart, and HIV, respectively. These datasets represent a wide variety of real-world experiments and observations, thus enabling the improvements described herein to be compared against the original BRL implementation using the FP-Growth miner.

All six benchmark datasets correspond to binary classification tasks. The experiments were conducted using the same set up in each of the benchmarks. First, the dataset is transformed into a format that is compatible with the disclosed BRL implementation. Second, all continuous attributes are quantized into either two (2) or three (3) categories, while keeping the original categories of all other variables. It is worth noting that depending on the dataset and how its data was originally collected, the existing taxonomy and expert domain knowledge are prioritized in some instances to generate the continuous variable quantization. A balanced quantization is generated when no other information was available. Third, a model is trained and tested using 5-fold cross-validations, reporting the average accuracy and Area Under the ROC Curve (AUC) as model performance measurements.

Table 1 presents the empirical result of comparing both implementations. The notation in the table follows the definitions above. To strive for a fair comparison between both implementations, the parameters rmax=2 and smin=0:3 are fixed for both methods, and in particular for MCA-miner μmin=0:5 and M=70 are also set. The multi-core implementations for both the new MCA-miner and BRL were executed on six parallel processes, and stopped when the Gelman & Rubin parameter satisfied {circumflex over (R)}≤1.05. All the experiments were run using a single AWS EC2 c5.18×large instance with 72 cores.

TABLE 1
Performance evaluation of FP-Growth against MCA-miner
when used with BRL on benchmark datasets. ttrain is the full training wall time.
FP-GROWTH + BRLMCA-MINER + BRL
DATASETnpΣt-1p|α1|ACCURACYAUCttrain[s]ACCURACYAUCttrain[s]
Adult45.222141110.810.855120.810.85115
ASD24821890.870.901980.870.9016
Cancer569321500.920.971680.920.9422
Heart30313490.820.861170.820.8615
HIV5.84081600.870.884490.870.8836
Titanic2.201380.790.761180.790.7510

It is clear from the experiments in Table 1 that the new MCA-miner matches the performance of FP-Growth in each case, while significantly reducing the computation time required to mine rules and train a BRL model.

US11857322B2. Systems and methods for screening, diagnosing, and stratifying patients (2024-01-02). BlackThorn Therapeutics, Inc. [US]. Inventors: Qingzhu Gao [US], Humberto Andres Gonzalez Cabezas [US], Parvez Ahammad [US], Yuelu Liu [US].
Full text: Click here
Patent 2024
Adult Autistic Disorder Cytokinesis Diagnosis Figs Heart Heart Diseases HIV-2 Malignant Neoplasm of Breast Malignant Neoplasms p16 protease, Human immunodeficiency virus 1
3
Lantern Cleavage and Analysis
Not available on PMC !

Example 5

Lanterns are placed individually in 96-well plates and treated with 0.5 mL solution of 20% (V/V) HFIP in DCM for 1 h. Lanterns are removed and the cleaved products are concentrated using a stream of N2. Samples were dissolved for UPLC analysis and preparative HPLC.

The following compounds were prepared according to the general procedures of Part A.

US11857565B2. Hydrophobic Auristatin F compounds and conjugates thereof (2024-01-02). SEAGEN INC. [US]. Inventors: Svetlana O. Doronina [US], Philip Moquist [US].
Full text: Click here
Patent 2024
Cytokinesis High-Performance Liquid Chromatographies
4
CasX-Mediated Genome Editing in HEK293 Cells
Not available on PMC !

Example 3

FIG. 8. Experimental design for editing human cells using CasX. HEK293 cells expressing a destabilized GFP is treated with CasX using either lipofection of plasmid expressing CasX and its guide RNA or nucleofection of CasX preassembled with its guide RNA. Successful genome cleavage will result in indels in the GFP locus causing a loss of fluorescence signal, which can be detected by flow cytometry and/or surveyor assay (e.g., T7E1 assay).

US11873504B2. RNA-guided nucleic acid modifying enzymes and methods of use thereof (2024-01-16). The Regents of the University of California [US]. Inventors: Jennifer A Doudna [US], Jillian F. Banfield [US], David Burstein [US], Lucas Benjamin Harrington [US], Steven C. Strutt [US].
Full text: Click here
Patent 2024
Biological Assay Cells Cytokinesis Enzymes Flow Cytometry Fluorescence Genome HEK293 Cells Homo sapiens INDEL Mutation Nucleic Acids Plasmids
5
Recombinant Fascin 1 Protein Expression
Not available on PMC !

Example 2

Recombinant human fascin 1 was expressed as a GST fusion protein in BL21 Escherichia coli. One liter of 2YT medium with ampicillin was inoculated overnight with 3 mL of BL21/DE3 culture transformed with pGEX4T-fascin 1 plasmid and grown at 37° C. until attenuance at 600 nm (D600) reached about 0.8. The culture was then transferred to 18° C. and induced by the addition of 0.1 mM isopropyl β-d-thiogalactoside (IPTG) for 12 h. Bacteria were harvested by centrifugation at 5,000 r.p.m. for 10 min. The pellets were suspended in 30 mL of PBS supplemented with 0.2 mM PMSF, 1 mM DTT, 1% (v/v) Triton X-100 and 1 mM EDTA. After sonication, the suspension was centrifuged at 15,000 r.p.m. for 30 min to remove the cell debris. The supernatant was then incubated for 2 h with 4 mL of glutathione beads (Sigma) at 4° C. After extensive washing with PBS, the beads were resuspended in 10 mL of thrombin cleavage buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM CaCl2, 1 mM DTT). Fascin was released from the beads by incubation overnight with 40-100 U of thrombin at 4° C. After centrifugation, 0.2 mM PMSF was added to the supernatant to inactivate the remnant thrombin activity. The fascin protein was further concentrated with a Centricon® (Boca Raton, FL) filter to about 50 mg/mL.

US11866440B2. Methods for inhibiting fascin (2024-01-09). NOVITA PHARMACEUTICALS, INC. [US], CORNELL UNIVERSITY [US]. Inventors: Xin-Yun Huang [US], Christy Young Shue [US].
Full text: Click here
Patent 2024
Ampicillin Bacteria Brown Oculocutaneous Albinism Buffers Cells Centrifugation Cytokinesis D-600 Edetic Acid Escherichia coli fascin Glutathione Homo sapiens Isopropyl Thiogalactoside Pellets, Drug Plasmids Proteins Sodium Chloride Staphylococcal Protein A Thrombin Triton X-100 Tromethamine

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More about "Cytokinesis"

Cytokinesis is the final phase of cell division, where the cytoplasm of a single cell splits into two or more daughter cells.
This critical process ensures the equitable distribution of genetic material and organelles between the newly formed cells.
Cytokinesis is a key aspect of cellular reproduction and proliferation, and understanding its mechanisms is crucial for various fields of biological research.
One powerful tool for enhancing cytokinesis research is PubCompare.ai, an AI-driven platform that can help locate the best research protocols from literature, pre-prints, and patents.
Using advanced AI-powered comparisons, PubCompare.ai can identify the optimal protocols and products for your specific needs, streamlining your research process and providing more reliable results.
In addition to PubCompare.ai, other software and tools can also be useful for cytokinesis studies.
Proteome Discoverer, a popular proteomics analysis platform, can be used to identify and quantify proteins involved in cytokinesis.
Mascot, a powerful search engine, can be employed to match peptide sequences to protein databases, aiding in the identification of key cytokinesis-related proteins.
Furthermore, reagents such as Lipofectamine 2000, a transfection reagent, can be utilized to introduce genetic material into cells, enabling the study of cytokinesis-related genes and proteins.
Trypsin, a widely used enzyme, can also play a role in cytokinesis research by facilitating the dissociation of cells and the preparation of samples for analysis.
By leveraging these tools and resources, researchers can delve deeper into the complex mechanisms of cytokinesis, unraveling its intricacies and advancing our understanding of this critical cellular process.
Whether you're investigating the role of specific proteins, exploring the regulation of cytokinesis, or seeking to optimize your experimental protocols, the combination of PubCompare.ai and other bioinformatics tools can be a powerful asset in your cytokinesis research endeavors.