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Neutrophil

Neutrophils are a type of white blood cell that play a critical role in the body's immune response.
These granulocytes are the most abundant leukocytes in humans and are the first line of defense against invading pathogens.
Neutrophils are essential for the clearance of bacterial and fungal infections, as well as the regulation of inflammatory processes.
They are characterized by their segmented nuclei and the presence of cytoplasmic granules containing antimicrobial enzymes and proteins.
Neutrophils are rapidly mobilized to sites of infection or inflammation, where they phagocytose and destroy microorganisms through a variety of mechanisms, including the release of reactive oxygen species and the formation of neutrophil extracellular traps.
Optimizing neutrophil research is crucial for understanding immune system function and developing new therapeutic strategies for infectious and inflammatory diseases.
The AI-driven platform PubCompare.ai can enhance the reproducibility and accuracy of neutrophil studies by helping researchers easily locate the best protocols from literature, preprints, and patents, and identify the most effective products and methods to advance their neutrophil research with confidence.

Most cited protocols related to «Neutrophil»

Human gene annotations were acquired from GENCODE v17 (31 (link)). Protein-coding transcripts were defined as those with ‘protein_coding’ gene biotype and ‘protein_coding’ transcript biotype. The lncRNAs transcripts were defined as those with ‘processed_transcript’, ‘lincRNA’, ‘3prime_overlapping_ncrna’, ‘antisense’, ‘non_coding’, ‘sense_intronic’ or ‘sense_overlapping’ gene biotype. Small non-coding RNA (sncRNA) transcripts were defined as those with ‘snRNA’, ‘snoRNA’, ‘rRNA’, ‘Mt_tRNA’, ‘Mt_rRNA’, ‘misc_RNA’ or ‘miRNA’ gene biotype. Pseudogene transcripts were defined as those with ‘polymorphic_pseudogene’, ‘pseudogene’, ‘IG_C_pseudogene’, ‘IG_J_pseudogene’, ‘IG_V_pseudogene’, ‘TR_V_pseudogene’ or ‘TR_J_pseudogene’ gene biotype.
Mouse and Caenorhabditis elegans gene annotations were extracted from Ensembl Gene Release 72 and LiftOver to mm9/mm10 and ce6/ce10, respectively. Protein-coding, lncRNAs, sncRNAs and pseudogenes were classified using a similar method. Human, mouse and C. elegans circRNA annotations were downloaded from circBase v0.1 (6 (link)).
These transcripts were scanned to find conserved miRNAs target sites using miRanda v3.3a with the ‘-strict’ parameter. The target sites that overlap with any entry of the aforementioned AGO CLIP clusters were considered as the CLIP-supported target sites.
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Publication 2013
Caenorhabditis elegans Clip Gene Annotation Gene Products, Protein Genes Genes, Overlapping Homo sapiens Introns Long Intergenic Non-Protein Coding RNA MicroRNAs Mus Neutrophil Proteins Pseudogenes Ribosomal RNA RNA, Circular RNA, Long Untranslated RNA, Small Untranslated RNA, Untranslated Small Nuclear RNA Small Nucleolar RNA Transfer RNA
We check the scree plot to choose ten dimension as the intrinsic dimensions to reconstruct the developmental trajectory for the Paul dataset (cells used in Figure 1 of the original study9 (link)). Five branch points and six terminal lineages (monocytes, neutrophils or eosinophil, basophils, dendritic cells, megakaryocytes, and erythrocytes) are revealed. We ordered the cells using genes Paul et al. used to cluster their data rather than the genes from dpFeature, for the sake of consistency with their clusetering analysis. Similarly, we reconstruct Olsson datasets in four dimensions. The major bifurcation between the granulocyte and monocyte branch (GMP) as well as the intricate branch between GMP and megakaryocyte/erythrocyte (Ery/Meg) are revealed. Top 1, 000 genes from dpFeature based on WT cells are used in both of the WT and full datasets. The distribution (related to confusion matrix) of percentages of cells in each cluster from the original papers over each segment (state in Monocle 2) of the principal graph are calculated and visualized in the heatmap.
We applied BEAM analysis to identify genes significantly bifurcating between Ery/Meg and GMP branch on the Olsson wildtype dataset. We then calculate the instant log ratios (ILRs) of gene expression between Ery/Meg and GMP branch and find genes have mean ILR larger than 0.5. The ILRs are defined as:
ILRt=log(Y1tY2t)
So
ILRt is calculated as the log ratio of fitted value at interpolated pseudotime point
t for the Ery/Meg lineage and that for the GMP lineage. Those genes are used to calculate the lineage score (simply calculated as average expression of those genes in each cell, same as stemness score below) for both of the Olsson and the Paul dataset which is used to color the cells in a tree plot transformed from the high dimensional principal graph (see Supplementary Notes). The same genes are used to create the multi-way heatmap for both of the Paul and Olsson dataset (see plot multiple_branches_heatmap function). Critical functional genes from this procedure are identified. Car1, Car2 (important erythroid functional genes for reversible hydration of carbon dioxide) as well as Elane, Prtn3 (important proteases hydrolyze proteins within specialized neutrophil lysosomes as well as proteins of the extracellular matrix) are randomly chosen as example for creating multi-lineage kinetic curves in both of the Olsson and Paul dataset (see plot_multiple_branches_pseudotime function).
In addition, pseudotime dependent genes for the Ery/Meg and GMP branch are identified in the Olsson wildtype dataset. All genes that always have lower expression from both lineages than the average in the progenitor cells are selected. Those genes are used to calculate the stemness score for both of the Olsson and the Paul dataset which is used to color the cells in the tree plot.
Publication 2017
Basophils Carbon dioxide Dendritic Cells Endopeptidases Eosinophil Erythrocytes Extracellular Matrix Proteins Gene Expression Genes Genetic Engineering Granulocyte Kinetics lysosomal proteins Megakaryocytes Monocytes Neutrophil Stem Cells Trees
We check the scree plot to choose ten dimension as the intrinsic dimensions to reconstruct the developmental trajectory for the Paul dataset (cells used in Figure 1 of the original study9 (link)). Five branch points and six terminal lineages (monocytes, neutrophils or eosinophil, basophils, dendritic cells, megakaryocytes, and erythrocytes) are revealed. We ordered the cells using genes Paul et al. used to cluster their data rather than the genes from dpFeature, for the sake of consistency with their clusetering analysis. Similarly, we reconstruct Olsson datasets in four dimensions. The major bifurcation between the granulocyte and monocyte branch (GMP) as well as the intricate branch between GMP and megakaryocyte/erythrocyte (Ery/Meg) are revealed. Top 1, 000 genes from dpFeature based on WT cells are used in both of the WT and full datasets. The distribution (related to confusion matrix) of percentages of cells in each cluster from the original papers over each segment (state in Monocle 2) of the principal graph are calculated and visualized in the heatmap.
We applied BEAM analysis to identify genes significantly bifurcating between Ery/Meg and GMP branch on the Olsson wildtype dataset. We then calculate the instant log ratios (ILRs) of gene expression between Ery/Meg and GMP branch and find genes have mean ILR larger than 0.5. The ILRs are defined as:
ILRt=log(Y1tY2t)
So
ILRt is calculated as the log ratio of fitted value at interpolated pseudotime point
t for the Ery/Meg lineage and that for the GMP lineage. Those genes are used to calculate the lineage score (simply calculated as average expression of those genes in each cell, same as stemness score below) for both of the Olsson and the Paul dataset which is used to color the cells in a tree plot transformed from the high dimensional principal graph (see Supplementary Notes). The same genes are used to create the multi-way heatmap for both of the Paul and Olsson dataset (see plot multiple_branches_heatmap function). Critical functional genes from this procedure are identified. Car1, Car2 (important erythroid functional genes for reversible hydration of carbon dioxide) as well as Elane, Prtn3 (important proteases hydrolyze proteins within specialized neutrophil lysosomes as well as proteins of the extracellular matrix) are randomly chosen as example for creating multi-lineage kinetic curves in both of the Olsson and Paul dataset (see plot_multiple_branches_pseudotime function).
In addition, pseudotime dependent genes for the Ery/Meg and GMP branch are identified in the Olsson wildtype dataset. All genes that always have lower expression from both lineages than the average in the progenitor cells are selected. Those genes are used to calculate the stemness score for both of the Olsson and the Paul dataset which is used to color the cells in the tree plot.
Publication 2017
Basophils Carbon dioxide Dendritic Cells Endopeptidases Eosinophil Erythrocytes Extracellular Matrix Proteins Gene Expression Genes Genetic Engineering Granulocyte Kinetics lysosomal proteins Megakaryocytes Monocytes Neutrophil Stem Cells Trees
In the following two sections, we describe how to create a custom leukocyte signature matrix and apply it to study cellular heterogeneity and TIL survival associations in melanoma tumors profiled by The Cancer Genome Atlas (TCGA). Readers can follow along by creating ‘LM6’, a leukocyte RNA-Seq signature matrix comprised of six peripheral blood immune subsets (B cells, CD8 T cells, CD4 T cells, NK cells, monocytes/macrophages, neutrophils; GSE60424 [20 ]). Key input files are provided on the CIBERSORT website (‘Menu>Download’).
A custom signature file can be created by uploading the Reference sample file and the Phenotype classes file (section 3.3.2) to the online CIBERSORT application (SeeFigure 2) or can be created using the downloadable Java package. To build a custom gene signature matrix with the latter, the user should download the Java package from the CIBERSORT website and place all relevant files under the package folder. To link Java with R, run the following in R:
Within R:

> library(Rserve)

> Rserve(args=“–no-save”)

Command line:

> java -Xmx3g -Xms3g -jar CIBERSORT.jar -M Mixture_file -P Reference_sample_file -c phenotype_class_file -f

The last argument (-f) will eliminate non-hematopoietic genes from the signature matrix and is generally recommended for signature matrices tailored to leukocyte deconvolution. The user can also run this step on the website by choosing the corresponding reference sample file and phenotype class file (seeFigure 2). The CIBERSORT website will generate a gene signature matrix located under ‘Uploaded Files’ for future download.
Following signature matrix creation, quality control measures should be taken to ensure robust performance (see ‘Calibration of in silico TIL profiling methods’ in Newman et al.) [17 (link)]. Factors that can adversely affect signature matrix performance include poor input data quality, significant deviations in gene expression between cell types that reside in different tissue compartments (e.g., blood versus tissue), and cell populations with statistically indistinguishable expression patterns. Manual filtering of poorly performing genes in the signature matrix (e.g., genes expressed highly in the tumor of interest) may improve performance.
To benchmark our custom leukocyte matrix (LM6), we compared it to LM22 using a set of TCGA lung squamous cell carcinoma tumors profiled by RNA-Seq and microarray (n = 130 pairs). Deconvolution results were significantly correlated for all cell subsets shared between the two signature matrices (P < 0.0001). Notably, since LM6 was derived from leukocytes isolated from peripheral blood [20 ,21 (link)], we restricted the CD4 T cell comparison to naïve and resting memory CD4 T cells in LM22. Once validation is complete, a CIBERSORT signature matrix can be broadly applied to mixture samples as described in section 3.3 (e.g., SeeFigure 4).
Publication 2018
B-Lymphocytes BLOOD CD4 Positive T Lymphocytes CD8-Positive T-Lymphocytes cDNA Library Cells Genes, vif Genetic Diversity Genetic Heterogeneity Hematopoietic System Leukocytes Lung Neoplasms Macrophage Malignant Neoplasms Melanoma Memory Microarray Analysis Monocytes Natural Killer Cells Neoplasms Neutrophil Phenotype Population Group RNA-Seq RNA Motifs Squamous Cell Carcinoma Strains Tissues
In the eigenanalysis of the Shriver data, we examine no more than two markers as independent regression variables for each marker we analyze, insisting that any marker that enters the regression be within 100,000 bases of the marker being analyzed. This slightly sharpens the results. Varying these parameters made little difference.
For all STRUCTURE runs, we ran with a burn-in of 10,000 iterations with 20,000 follow-on iterations, and no admixture model was used. Computations were carried out on a cluster of Intel Xeon compute nodes, each node having a 3.06-GHz clock.
For our coalescent simulations, we assumed a phylogenetic tree on the populations, and at each simulated marker, ran the coalescent back in time to the root of the tree. At this point we have a set of ancestors A of the sampled chromosomes. We now assume that the marker is biallelic and that the population frequency f of the variant allele in the ancestral population is distributed uniformly on the unit interval. Sample the frequency f and then choose an allele for each ancestor of A, picking the allele for each ancestor with probability f. Now retain the marker if it is polymorphic in our samples. This process is mathematically equivalent to having a very large outgroup population diverging from the sampled populations at the phylogenetic root, with the population panmictic before any population divergence, and ascertaining by finding heterozygotes in the outgroup. If our simulated samples have n individuals, our procedure yields a sample frequency that is approximately uniform on (1,2,…,2n − 1).
For the admixture analysis that created the plot of Figure 8 we had a population C that was admixed with founder populations A and B. For each individual of C, we generated a mixing value x that is Beta-distributed B(3.5,1.5). Now for each marker independently, the individual was assigned to population A with probability x or B with probability 1 − x.
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Publication 2006
Alleles Chromosomes Heterozygote Neutrophil Plant Roots Trees

Most recents protocols related to «Neutrophil»

Example 14

In contrast to the previous experimental infection using specific pathogen-free Beagles (Crawford et al., 2005), the virus-inoculated mongrel dogs had pneumonia as evidenced by gross and histological analyses of the lungs from days 1 to 6 p.i. In addition to pneumonia, the dogs had rhinitis, tracheitis, bronchitis, and bronchiolitis similar to that described in naturally infected dogs (Crawford et al., 2005). There was epithelial necrosis and erosion of the lining of the airways and bronchial glands with neutrophil and macrophage infiltration of the submucosal tissues (FIG. 5, upper panels). Immunohistochemistry detected viral H3 antigen in the epithelial cells of bronchi, bronchioles, and bronchial glands (FIG. 5, lower panels). No bacterial superinfection was present. The respiratory tissues from the 2 sham-inoculated dogs were normal.

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Patent 2024
Antigens, Viral Autopsy Bacteria Bronchi Bronchioles Bronchiolitis Bronchitis Canis familiaris Epithelial Cells Immunohistochemistry Infection Lung Macrophage Necrosis Neutrophil Pneumonia Respiratory Rate Rhinitis Specific Pathogen Free Superinfection Tissues Tracheitis Virus

Example 5

As described above, vidofludimus, in both its free acid form and its calcium salt formulation (vidofludimus calcium), has undergone clinical trials for a variety of immune-related indications. Both formulations depend on the same active substance (vidofludimus) in vivo, and thus the two formulations share the same mechanism of action, pharmacology and toxicology. IMU-838 is the “Polymorph A” of the dihydrate of 1-cyclopentene-1-carboxylic acid, 2-(((3-fluoro-3′-methoxy(1,1′-biphenyl)-4-yl)amino)carbonyl)-, calcium salt (2:1), characterized by an X-ray powder diffraction pattern having characteristic peaks at 2 theta)(±0.2° of 5.91°, 9.64°, 16.78°, 17.81°, 19.81° and 25.41°. The preparation of this “Polymorph A” is described in WO 2019/175396, which is incorporated herein by this reference.

In the following Table 4 the amount (in mg) of active moiety of the compound is converted into μmol.

TABLE 4
mg
mgμmolvidofludimus
IMU-838IMU-838(free acid)
45115   41  
3076.5 27  
1025.5 9.1

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Patent 2024
Acids Calcium Carboxylic Acids Cyclopentenes diphenyl Drug Kinetics Neutrophil Powder Sodium Chloride vidofludimus X-Ray Diffraction

Example 6

Suspensions of Compound 1 were prepared at 50° C. and stirred for 2 hr. Clear solutions were obtained by filtering the suspensions with a 0.2 μm PTFE filter and followed by cooling from 50 to 5° C. at a cooling rate 0.1° C./min. The results from slow cooling are shown in Table 8. Form 1, Pattern 2, Form 8 minus some peaks, Pattern 12 and low crystallinity were observed.

TABLE 8
Summary of slow cooling
Polymorphic naturePolymorphic nature
Solvent system (v/v)(XRPD wet)(XRPD dry)
THF:water (1:2)Pattern 2N/A
IPA:water (1:2)Pattern 2N/A
Acetone:water (1:2)Pattern 2N/A
MeCN:water (1:2)Form 8Form 1
Dioxane:water (1:2)Low crystallinityForm 1
DMSO:water (1:1)Low crystallinityForm 1
DMSO:MIBK (1:1)Pattern 12Form 1
DMSO:MeCN (1:1)Low crystallinityForm 1
DMSO:DCM (1:1)Low crystallinityForm 1
DMSO:MeOH (1:1)Pattern 12Form 1
DMSO:THF (1:1)Low crystallinityForm 1
DMF:Toluene (1:1)N/AN/A
DMF:MEK (1:1)N/AN/A
DMF:MeCN (1:1)N/AN/A
DMF:Dioxane (1:1)N/AN/A
DMF:IPAc (1:1)N/AN/A
NMP:Acetone (1:1)N/AN/A
NMP:EtOAc (1:1)N/AN/A
NMP:IPA (1:1)N/AN/A
NMP:DCM (1:1)N/AN/A

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Patent 2024
Acetone COOL-1 protein, human dioxane MAP2K1 protein, human Neutrophil Polytetrafluoroethylene Solvents Sulfoxide, Dimethyl Toluene
Not available on PMC !

Example 16

Demonstrating CKA of CD34+ Stem Cell Derived Neutrophils (SCDNs)

Results were obtained via the xCELLigence assay with further populations of CD34+ Stem Cell Derived Neutrophils (FIG. 6), and were consistent with results obtained via the MTT assay as described above. SCDNs (generated ex vivo) were again shown to have differential CKA, with culture 5 representing low CKA neutrophils and culture 1 representing high CKA neutrophils.

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Patent 2024
Biological Assay Cells Malignant Neoplasms Neutrophil Population Group Stem Cells
Not available on PMC !

Example 3

Systemic Inflammatory Response Syndrome (SIRS) can occur in association with cardiopulmonary bypass (CPB) surgery, resulting in multiple organ dysfunction (MOD). Activated neutrophils have been implicated as major inciting factors in this process. This example describes in vitro and in vivo experiments that evaluate the effect of SCD cartridges for use during CPB surgery. The results demonstrate that the usage of SCD cartridges may disrupt the systemic leukocyte response during CPB surgery, leading to improved outcomes for CPB-mediated MOD.

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Patent 2024
Cardiopulmonary Bypass Leukocytes Medical Devices Neutrophil Systemic Inflammatory Response Syndrome

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Polymorphprep is a density gradient medium used for the isolation of polymorphonuclear cells, such as neutrophils, from whole blood. It is designed to separate these cells from other blood components, including erythrocytes and lymphocytes, through differential centrifugation.
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Histopaque-1077 is a density gradient medium used for the isolation of mononuclear cells from whole blood. It is a sterile, endotoxin-tested solution composed of polysucrose and sodium diatrizoate, adjusted to a density of 1.077 g/mL.
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The EasySep Direct Human Neutrophil Isolation Kit is a magnetic cell separation system designed to isolate human neutrophils from whole blood or bone marrow samples. The kit utilizes an immunomagnetic labeling approach to selectively target and separate neutrophils from the sample.

More about "Neutrophil"

Neutrophils, also known as polymorphonuclear leukocytes (PMNs) or granulocytes, are a critical component of the body's innate immune system.
These white blood cells play a vital role in the defense against pathogens, inflammation, and tissue repair.
Neutrophils are the most abundant leukocytes in humans, rapidly mobilizing to sites of infection or injury to eliminate threats.
Neutrophil research is essential for understanding immune system function and developing new therapies for infectious and inflammatory diseases.
Optimizing neutrophil studies involves utilizing the right tools and methods.
For example, flow cytometry techniques using instruments like the FACSCalibur and FACSCanto II can be used to analyze neutrophil phenotype and function.
Phorbol 12-myristate 13-acetate (PMA) is a common stimulant used to activate neutrophils in vitro, while fetal bovine serum (FBS) provides essential nutrients.
The DNA-binding dye SYTOX Green can be employed to assess neutrophil extracellular trap (NET) formation.
Neutrophil isolation is a critical step in many experiments.
Techniques like Polymorphprep and Histopaque-1077 density gradient centrifugation, as well as the EasySep Direct Human Neutrophil Isolation Kit, can be used to purify these cells from whole blood.
Researchers should also consider the cell culture media, such as RPMI 1640, to maintain neutrophil viability and function.
By leveraging the insights and tools available, scientists can enhance the reproducibility and accuracy of their neutrophil research, leading to a deeper understanding of these versatile immune cells and the development of innovative therapeutic strategies.