First, for each major cell-type, a gene-wise correlation coefficient (Spearman’s rank correlation coefficient) was computed using gene expression and AD-related neuropathological trait values across all the annotated cells as variables. The AD-related neuropathological traits included in this analysis were cogn_global_lv (global cognitive function - last valid score), age_death (age at death), educ (years of education), msex (self-reported sex), parksc_lv (global parkinsonian summary score - last valid score), gpath (global AD pathology burden), gpath_3neocort (global measure of neocortical pathology), pmi (post-mortem interval), amyloid (Overall amyloid level), plaq_d (diffuse plaque burden), plaq_n (neuritic plaque burden), nft (neurofibrillary tangle burden), and tangles (tangle density). Only significant correlations after Bonferroni correction at P<0.01 were considered. The resulting correlation matrices for each major cell-type were concatenated and analyzed using a computational algorithm (self-organizing map, SOM)37 . All SOMs were created using the Kohonen R package56 . To identify the territories of the SOM most strongly correlated with AD-related neuropathological traits, we used an image segmentation method and further manual curation to identify territories (gene-trait correlation modules) based on all the individual cell-type-specific SOM plots for each neuropathological trait. Enrichment analysis for Gene Ontology (GO) terms among the genes of a gene-trait correlation module was performed using Metascape53 . The robustness of gene-trait associations to single-cell heterogeneity and noise was confirmed examining individual-level correlations for the genes in gene-trait module. Individual-level correlations were computed by first averaging for each individual normalized gene expression profiles across cells of the same cell. This resulted in cell-type-specific averaged gene expression profiles across the 48 individuals. Average profiles were subsequently mean-centered and scaled to finally compute gene-wise correlation coefficients versus corresponding pathological values. Individual-level gen-trait correlations were computed independently for all 48 individuals, for only 24 male individuals, and for only 24 female individuals. The robustness of gene-trait associations to potential confounding variables was corroborated by confirming the cell-type specific recovery of identified gene-trait modules using partial correlation. Briefly, the partial Pearson’s correlation coefficient between average gene expression and each pathological trait, after correcting for the effect of PMI, age, gender, and education level of each individual; was computed by first orthogonalizing the normalized expression with respect to the normalized covariates and then computing the correlation in the residual subspace.
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Amyloid
Amyloid
Amyloid is a general term referring to an insoluble fibrous protein material that is deposited in various tissues, often in association with disease.
These fibrils typically have a beta-pleated sheet structure and are resistant to degradation.
Amyloid deposits can lead to disruption of normal tissue structure and function, contributing to a variety of conditions such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes.
Reseach into amyloid and amyloidosis is critical for understanding the mechanisims of these diseeases and developing effective treatments.
These fibrils typically have a beta-pleated sheet structure and are resistant to degradation.
Amyloid deposits can lead to disruption of normal tissue structure and function, contributing to a variety of conditions such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes.
Reseach into amyloid and amyloidosis is critical for understanding the mechanisims of these diseeases and developing effective treatments.
Most cited protocols related to «Amyloid»
Amyloid
Autopsy
Cell Microarray Analysis
Cells
Cognition
Cytosol
Females
Gene Expression
Gene Modules
Genes
Genetic Heterogeneity
Males
Neurofibrillary Tangle
Senile Plaques
Amyloid
Astrocytes
Biological Assay
Biopsy
Cloning Vectors
Diagnosis
DNA, Complementary
Endocytic Vesicles
Ethics Committees, Research
Fibroblasts
Homo sapiens
Induced Pluripotent Stem Cells
KLF4 protein, human
Microscopy, Confocal
Neurons
Oncogenes, myc
POU5F1 protein, human
SOX2 protein, human
Primary fibroblast cultures were established from dermal punch biopsies taken from individuals following informed consent and Institutional Review Board approval. To generate iPSCs, fibroblasts were transduced with MMLV vectors containing the complementary DNAs for OCT4, SOX2, KLF4, c-MYC and ± EGFP. IPSC-derived NPCs were differentiated for 3 weeks, neurons were purified by FACS, and amyloid-β, p-tau/total tau and aGSK-3β were measured on purified control and mutant neurons from multiple lines cultured in parallel for an additional 5 days by multi-spot electrochemiluminescence assays (Meso Scale Diagnostics). Early endosomes were analysed by confocal microscopy on purified neurons co-cultured with human astrocytes (Lonza) for 12 days. To ensure reproducible and consistent data, we found that it is important to differentiate and evaluate neurons from full sets of mutant and control iPSC lines together.
Amyloid
Astrocytes
Biological Assay
Biopsy
Cloning Vectors
Diagnosis
DNA, Complementary
Endocytic Vesicles
Ethics Committees, Research
Fibroblasts
Homo sapiens
Induced Pluripotent Stem Cells
KLF4 protein, human
Microscopy, Confocal
Neurons
Oncogenes, myc
POU5F1 protein, human
SOX2 protein, human
Amyloid
BLOOD
Brain
Cells
Cephalothin
Comb
Cortex, Cerebral
cytidylyl-3'-5'-guanosine
Dasen
DNA Methylation
Genetic Polymorphism
Methylation
Neurons
Python
Single Nucleotide Polymorphism
Tissues
Unithiol
Watermelon
A-factor (Streptomyces)
Amyloid
Brain
Cloning Vectors
factor A
Radionuclide Imaging
Technique, Dilution
Temporal Lobe
Tissues
Most recents protocols related to «Amyloid»
A consecutive series of 142 newly diagnosed AL amyloidosis patients, who presented to our hospital from November 2012 to December 2021, were analyzed retrospectively. A total of 80 of the 142 newly diagnosed AL amyloidosis patients had primary AL amyloidosis, and the other 62 patients were AL amyloidosis patients with concurrent MM. The diagnosis of AL amyloidosis was confirmed by a Congo-red-positive biopsy and immunohistochemistry of the amyloid [1 (link)]. Meanwhile, the presence of the kappa or lambda chain was confirmed through immunohistochemistry and/or immunofluorescence. Moreover, monoclonal plasma cell proliferation was investigated by multi-color flow cytometry on aspirated bone marrow cells. Patients were evaluated for the presence of symptomatic MM based on the International Myeloma Working Group (IMWG) criteria [11 (link)]: bone marrow clonal plasma cells > 10% and evidence of myeloma-defining events, including the slim-CRAB criteria. Patients with AL amyloidosis with >10% bone marrow plasma cells and any myeloma-defining events were described with coexistent MM. iFISH was performed for all the patients as part of their routine clinical testing. Patients gave written informed consent for the iFISH and data analysis in accordance with the Declaration of Helsinki. Approval was obtained by the Ethics Committee of Shanghai Changzheng Hospital.
Among the 80 primary AL amyloidosis patients, 71 patients were treated with bortezomib-based regimens (cyclophosphamide/bortezomib/dexmethasome (CBd) or bortezomib/dexamethasone (Vd)), five patients treated with lenalidomide-based regimens (lenalidomide/cyclophosphamide/dexmethasome (RCd) or lenalidomide/dexmethasome (Rd)), three patients were treated with thalidomide-based regimens (thalidomide/ cyclophosphamide/dexmethasome (TCd)), and one patient was treated with ixazomib-based regimens (ixazomib/dexmethasome (Id)) for induction therapy, and three of the 80 patients received autologous transplants as a consolidation therapy. Among the 62 AL amyloidosis patients with concurrent MM, 47 patients were treated with bortezomib-based regimens (CBd or Vd), seven patients were treated with lenalidomide-based regimens (RCd or Rd), five patients were treated with bortezomib combined with lenalidomide (bortezomib/lenalidomide/dexmethasome (VRd)), and three patients were treated with daratumumab-based regimens (daratumumab/bortezomib/dexmethasome (DVd)). A total of six of the 62 patients received autologous transplants as a consolidation therapy. None of the 142 patients received venetoclax.
Among the 80 primary AL amyloidosis patients, 71 patients were treated with bortezomib-based regimens (cyclophosphamide/bortezomib/dexmethasome (CBd) or bortezomib/dexamethasone (Vd)), five patients treated with lenalidomide-based regimens (lenalidomide/cyclophosphamide/dexmethasome (RCd) or lenalidomide/dexmethasome (Rd)), three patients were treated with thalidomide-based regimens (thalidomide/ cyclophosphamide/dexmethasome (TCd)), and one patient was treated with ixazomib-based regimens (ixazomib/dexmethasome (Id)) for induction therapy, and three of the 80 patients received autologous transplants as a consolidation therapy. Among the 62 AL amyloidosis patients with concurrent MM, 47 patients were treated with bortezomib-based regimens (CBd or Vd), seven patients were treated with lenalidomide-based regimens (RCd or Rd), five patients were treated with bortezomib combined with lenalidomide (bortezomib/lenalidomide/dexmethasome (VRd)), and three patients were treated with daratumumab-based regimens (daratumumab/bortezomib/dexmethasome (DVd)). A total of six of the 62 patients received autologous transplants as a consolidation therapy. None of the 142 patients received venetoclax.
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Amyloid
Autografts
Biopsy
Bone Marrow Cells
Bortezomib
Brachyura
Cell Proliferation
Clone Cells
Cyclophosphamide
daratumumab
Dexamethasone
Diagnosis
Ethics Committees, Clinical
Flow Cytometry
Immunofluorescence
Immunohistochemistry
ixazomib
Lenalidomide
Multiple Myeloma
Neoadjuvant Therapy
Patients
Plasma
Primary Amyloidosis
Thalidomide
Therapeutics
Treatment Protocols
venetoclax
Primary antibodies against β-secretase (BACE, Cat# 5606), phospho-Tau (p-Tau, Cat# 15013), Tau (Cat# 46687), Catalase (Cat# 12980), NOD-like receptor (NLR) family pyrin domain containing 3 (NLRP3, Cat# 13158), apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC, Cat# 67824), Caspase-1 (Cat# 3866), Bcl-2-associated X protein (Bax, Cat# 2772), B-cell lymphoma 2 (Bcl-2, Cat# 3498), cleaved caspase-9 (Cat# 20750), cleaved caspase-3 (Cat# 9664), cleaved poly (ADP-ribose) polymerase (PARP, Cat# 5625), FUN14 Domain-Containing 1 (FUNDC1, Cat# 49240), PTEN-induced putative kinase 1 (PINK1, Cat# 6946), Parkin (Cat# 4211), Beclin1 (Cat# 3495), microtubule-associated protein 1A/1B-light chain 3B (LC3B, Cat# 3868), p-cAMP response element-binding (p-CREB, Cat# 9198), CREB (Cat# 9197), choline acetyltransferase (ChAT, Cat# 27269), p-extracellular signal-regulated kinase (p-ERK, Cat# 4377), ERK (Cat# 4695), and β-actin (Cat# 8457) were obtained from Cell Signaling Technology (Danvers, MA, USA). Superoxide dismutase-1 (SOD-1, Cat# sc-515404), SOD-2 (Cat# sc-137254), β-amyloid (Aβ1–42, Cat# sc-28365), glutathione peroxidase-1 (GPx-1, Cat# sc-133160), glutathione reductase (GR, Cat# sc-133245), and acetylcholinesterase (AChE, Cat# sc-373901) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Nitric oxide synthase (iNOS, Cat# PA1-036) was obtained from Invitrogen Life Technologies (Carlsbad, CA, USA). Tumor necrosis factor α (TNFα, Cat# ab66579), IL-6 (Cat# ab9324), interleukin-1β (IL-1β, Cat# ab9722), and anti-brain-derived neurotrophic factor (BDNF, Cat# ab108319) were purchased from Abcam Inc. (Cambridge, CA, USA). Horseradish peroxidase (HRP)-linked anti-rabbit IgG and HRP-linked anti-mouse IgG antibodies were purchased from GenDEPOT (Barker, TX, USA).
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Acetylcholinesterase
Actins
Amyloid
anti-IgG
Antibodies
Apoptosis
B-Cell Lymphomas
Bax Protein
BCL2 protein, human
BECN1 protein, human
Caspase 1
Caspase 3
Caspase 9
Caspase Activation and Recruitment Domain
Catalase
Choline O-Acetyltransferase
Extracellular Signal Regulated Kinases
Glutathione Peroxidase GPX1
Glutathione Reductase
Horseradish Peroxidase
IL1B protein, human
Interleukin-1 beta
microtubule-associated protein 1B
Mus
Neurotrophic Factor, Brain-Derived
Nitric Oxide Synthase
NLR Proteins
NOS2A protein, human
Pain
PARK2 protein, human
PARP1 protein, human
Phosphorus
Phosphotransferases
Proteins
PTEN protein, human
Pyrin Domain
Rabbits
Secretase
Superoxide Dismutase-1
TNF protein, human
TNFSF14 protein, human
Data were analyzed using the R statistical software (version 4.0.2) [27 ]. For each group, quantitative variables were expressed as the median with the interquartile range (IQR, Q1 and Q3). Groups were compared using non-parametric Kruskal–Wallis or Mann–Whitney tests according to the group number. Pairwise comparisons were adjusted with Bonferroni correction. Correlations were assessed using Spearman’s rank correlation coefficient (ρ). The distribution of categorical variables was expressed with percentages and compared using Fisher’s exact test.
For comparisons of biomarker concentrations between diagnosis groups, to avoid the influence of extreme values, outliers were identified using Rosner’s test and discarded (n = 6). For each group, normal distribution was assessed using the Shapiro–Wilk test and homoscedasticity through Levene’s test. The assumption of normality was not obtained in only two groups, IPMS-Shim and Simoa Aβ42/40 for the AD diagnosis. ANCOVA’s assumptions of linearity, homogeneity of variance, non-collinearity of the factors (variance inflation factor <5), non-influential observations, and normality of residuals were evaluated. The impact of diagnosis on plasma amyloid biomarker concentrations was evaluated using ANCOVA controlling for age and APOE ε4 status. Multiple comparisons of the means were achieved using Tukey contrasts with diagnosis as a factor.
Plasma cutoffs were computed using expectation–maximization (EM) algorithms for mixtures of univariate normal distributions [28 ]. Cutoffs were visually determined at the intersection of two normal distributions.
A receiver operating characteristic (ROC) analysis was used to determine biomarker performances. A predictive formula adjusted for age and APOE ε4 status was built using a logistic regression analysis. The best values for sensitivity (se) and specificity (sp) were computed at an optimal cutoff point. Youden’s index was used to determine this optimal cutoff corresponding to the threshold maximizing the distance to the identity (diagonal) line and giving and equal weight to sensitivity and specificity. The area under the curve (AUC) was compared using the DeLong test. All tests were two-tailed, and significance was set at α = .05.
For comparisons of biomarker concentrations between diagnosis groups, to avoid the influence of extreme values, outliers were identified using Rosner’s test and discarded (n = 6). For each group, normal distribution was assessed using the Shapiro–Wilk test and homoscedasticity through Levene’s test. The assumption of normality was not obtained in only two groups, IPMS-Shim and Simoa Aβ42/40 for the AD diagnosis. ANCOVA’s assumptions of linearity, homogeneity of variance, non-collinearity of the factors (variance inflation factor <5), non-influential observations, and normality of residuals were evaluated. The impact of diagnosis on plasma amyloid biomarker concentrations was evaluated using ANCOVA controlling for age and APOE ε4 status. Multiple comparisons of the means were achieved using Tukey contrasts with diagnosis as a factor.
Plasma cutoffs were computed using expectation–maximization (EM) algorithms for mixtures of univariate normal distributions [28 ]. Cutoffs were visually determined at the intersection of two normal distributions.
A receiver operating characteristic (ROC) analysis was used to determine biomarker performances. A predictive formula adjusted for age and APOE ε4 status was built using a logistic regression analysis. The best values for sensitivity (se) and specificity (sp) were computed at an optimal cutoff point. Youden’s index was used to determine this optimal cutoff corresponding to the threshold maximizing the distance to the identity (diagonal) line and giving and equal weight to sensitivity and specificity. The area under the curve (AUC) was compared using the DeLong test. All tests were two-tailed, and significance was set at α = .05.
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Amyloid
ApoE protein, human
Biological Markers
Contrast Media
Diagnosis
Factor V
Plasma
SHIMS
CSF samples were collected from participants. They were centrifuged immediately and the supernatant was stored at − 80 °C until testing. The concentration of cytokines in blood was determined by a magnetic bead-based multiplex panel (Luminex™; Bio-Rad Laboratories, Hercules, CA, USA). In 14 patients, levels of the following cytokines in CSF were evaluated: TNF-α, IFN-γ, IL-1α, IL-1β, IL-2, IL-3, IL-4, IL-6, IL-8, IL-10, IL-12p40, IL-12p70, IL-13, IL-17A, interferon-gamma induced protein 10, monocyte chemotactic protein-1, macrophage inflammatory protein (MIP)-1α, MIP-1β, G-CSF, granulocyte–macrophage colony-stimulating factor, soluble CD40 ligand, complement C3, complement factor H (CFH), fibroblast growth factor-2, platelet-derived growth factor-AA, growth-related oncogene, alpha 2-macroglobulin (α2M), apolipoprotein AI (Apo AI), apolipoprotein E (Apo E), amyloid beta 1–42, total tau, and phosphorylated tau. Cytokine concentrations were expressed in pg/mL and determined before and after lenalidomide therapy (refer to Additional file 1 : Table S2 for explanation of abbreviations).
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alpha 2-Glucoproteins
Amyloid
Apolipoprotein A-I
Apolipoproteins E
BLOOD
CCL3 protein, human
CCL4 protein, human
CD40 Ligand
Complement 3
Complement factor H
Cytokine
Fibroblast Growth Factor 2
Granulocyte-Macrophage Colony-Stimulating Factor
Granulocyte Colony-Stimulating Factor
IL10 protein, human
Interferon Type II
Interleukin-1 beta
Interleukin-12
Interleukin-12 Subunit p40
Interleukin-13
Interleukin-17A
Lenalidomide
Monocyte Chemoattractant Protein-1
Oncogenes
Patients
PDGF AA
Proteins
Therapeutics
Tumor Necrosis Factor-alpha
The Korea University bone marrow transplantation registry is a longitudinal cohort containing data of patients who underwent SCT at the Korea University Medical Center (Korea University Anam, Guro, and Ansan Hospitals) from January 2007 to December 2018. According to this registry, 201 patients underwent auto-SCT: 107 with multiple myeloma; 50 with B-cell lymphoma; 35 with T-cell lymphoma; 8 with Hodgkin lymphoma, and 1 with amyloid light-chain (AL) amyloidosis. Patients with AL amyloidosis were excluded because critical medical data were missing. Of the 200 patients, 50 were not tested for CMV reactivation. Thus, we retrospectively analyzed data from 150 patients with multiple myeloma (n = 80), B-cell lymphoma (n = 39), T-cell lymphoma (n = 26), and Hodgkin lymphoma (n = 5). All methods were performed in accordance with relevant guidelines and regulations. This study was approved by the Institutional Review Board of the Korea University Medical Center, with a waiver of informed consent for the collection and analysis of retrospective data.
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Amyloid
Amyloidosis
B-Cell Lymphomas
Bone Marrow Transplantation
Ethics Committees, Research
Hodgkin Disease
Light
Multiple Myeloma
Patients
T-Cell Lymphoma
Top products related to «Amyloid»
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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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The FV3000 is a confocal laser scanning microscope system designed for advanced imaging applications. It features high-resolution scanning, a flexible optical configuration, and integrated software for image capture and analysis.
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Methylcellulose is a water-soluble, synthetic polymer derived from cellulose. It is a white, odorless, and tasteless powder that is commonly used as a thickening, stabilizing, and emulsifying agent in various industries, including pharmaceutical, food, and personal care products.
Sourced in United States
The UltraScan 1000 is a 2k×2k CCD camera designed for laboratory applications. It features a high-resolution sensor capable of capturing detailed images. The camera's core function is to provide high-quality image data for scientific analysis and documentation purposes.
Thioflavin T (ThT) is a fluorescent dye commonly used in research applications. It exhibits enhanced fluorescence upon binding to amyloid fibrils, making it a useful tool for detecting and studying protein aggregation.
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L-glutamine is an amino acid that is commonly used as a dietary supplement and in cell culture media. It serves as a source of nitrogen and supports cellular growth and metabolism.
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Quantitative real-time PCR is a laboratory instrument used for the amplification and quantification of DNA or RNA sequences. It measures the accumulation of amplified DNA or RNA in real-time during the PCR process, providing precise quantification of the target molecules.
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Ultrapure grade Thioflavin T (ThT) is a fluorescent dye used in the detection and quantification of amyloid fibrils. It exhibits an enhanced fluorescence signal upon binding to amyloid structures. The Ultrapure grade ensures high purity and consistency for reliable results in amyloid research applications.
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ZLN005 is a laboratory instrument designed for the quantitative analysis of various samples. It utilizes advanced detection technologies to provide accurate and reliable measurements. The core function of ZLN005 is to perform analytical tasks with precision and efficiency, supporting research and testing activities in multiple industries.
More about "Amyloid"
Amyloid is a general term referring to an insoluble, fibrous protein material that is deposited in various tissues, often in association with disease.
These amyloid fibrils typically have a beta-pleated sheet structure and are resistant to degradation.
Amyloid deposits can lead to disruption of normal tissue structure and function, contributing to a variety of conditions such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes.
Researching amyloid and amyloidosis is critical for understanding the mechanisms of these diseases and developing effective treatments.
PubCompare.ai can enhance amyloid research by helping users find the most effective protocols and products.
Its AI-driven comparisons analyze data from literature, preprints, and patents, ensuring reproducibility and accuracy.
This allows researchers to experience smarter, more efficient amyloid research.
When studying amyloid, researchers may utilize a variety of tools and techniques.
Fluorescence-based Spectroscopy (FBS) and Fluorescence Visiometry (FV3000) can be used to analyze the structural and morphological properties of amyloid fibrils.
Methylcellulose and the UltraScan 1000 (2k×2k) CCD camera can also be employed in amyloid research.
The Thioflavin T (ThT) dye is a common fluorescent probe used to detect and quantify amyloid aggregates, while L-glutamine may be used as a nutrient source for cell cultures.
Microplate readers are often utilized to measure fluorescence or absorbance in amyloid assays, and Quantitative real-time PCR can be used to study gene expression related to amyloid formation.
Ultrapure grade ThT and the compound ZLN005 may also be relevant to amyloid research and therapeutics.
These amyloid fibrils typically have a beta-pleated sheet structure and are resistant to degradation.
Amyloid deposits can lead to disruption of normal tissue structure and function, contributing to a variety of conditions such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes.
Researching amyloid and amyloidosis is critical for understanding the mechanisms of these diseases and developing effective treatments.
PubCompare.ai can enhance amyloid research by helping users find the most effective protocols and products.
Its AI-driven comparisons analyze data from literature, preprints, and patents, ensuring reproducibility and accuracy.
This allows researchers to experience smarter, more efficient amyloid research.
When studying amyloid, researchers may utilize a variety of tools and techniques.
Fluorescence-based Spectroscopy (FBS) and Fluorescence Visiometry (FV3000) can be used to analyze the structural and morphological properties of amyloid fibrils.
Methylcellulose and the UltraScan 1000 (2k×2k) CCD camera can also be employed in amyloid research.
The Thioflavin T (ThT) dye is a common fluorescent probe used to detect and quantify amyloid aggregates, while L-glutamine may be used as a nutrient source for cell cultures.
Microplate readers are often utilized to measure fluorescence or absorbance in amyloid assays, and Quantitative real-time PCR can be used to study gene expression related to amyloid formation.
Ultrapure grade ThT and the compound ZLN005 may also be relevant to amyloid research and therapeutics.