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Lipid A

Lipid A, a crucial component of lipopolysaccharides in Gram-negative bacteria, is a key target for research in immunology and infectious disease.
Lipid A plays a central role in the body's inflammatory response and can be a potent activator of the immune system.
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Most cited protocols related to «Lipid A»

The numbered positions of annotated residues in the Swiss-Prot sequence often do not align to the same numbered positions of the sequence from the PDB structure. Therefore, a mapping of positions between the Swiss-Prot sequence and the PDB sequence must be obtained. We use a variation of the Needleman and Wunsch algorithm to identify if a sequence of a PDB structure can be found to match the sequence containing annotated residues from the Swiss-Prot database.
Specifically, every Swiss-Prot sequence containing one or more annotated residues and a link to a PDB structure was aligned to the corresponding sequence of the PDB structure. Standard annotations of Swiss-Prot used include post-translational modifications (MOD_RES), covalent binding of a lipid moiety (LIPID), glycosylation sites (CARBOHYD), post-translational formed amino acid bonds (CROSSLNK), metal binding sites (METAL), chemical group binding sites (BINDING), calcium binding regions (CA_BIND), DNA binding regions (DNA_BIND), nucleotide phosphate binding regions (NP_BIND), zinc finger regions (ZN_FING), enzyme activity amino acids (ACT_SITE) and any interesting single amino acid site (SITE). To ensure that the mapping is accurate, only alignments of two sequences with a sequence identity greater than ninety five percent were used. The annotated positions from Swiss-Prot are then transferred onto the PDB sequence, as long as the position is not aligned to a gap.
Publication 2006
Amino Acids Binding Sites Calcium enzyme activity Lipid A Lipids Metals Nucleotides Phosphates Protein Biosynthesis Protein Glycosylation Sequence Alignment Zinc Fingers
The β2AR-Gs complex was crystallized from β2AR and Gs protein expressed in insect cells. Crystallogenesis was aided by fusing T4 lysozyme to the amino terminus of the β2AR and the addition of a nanobody (Nb35) that binds at the interface between the Gα and Gβ subunits. Crystals were grown in a lipidic cubic phase using MAG7.7, a lipid that accommodates membrane proteins with larger hydrophilic surfaces15 (link). Diffraction data were measured at beamline 23ID-B of the Advanced Photon Source and the structure was solved by molecular replacement. For more experimental details see Online Methods.
Publication 2011
Cells Cuboid Bone Insecta Lipid A Lipids Membrane Proteins Muramidase Proteins Protein Subunits
Eight acquisitions containing complete sets of MS and MS/MS spectra were independently submitted as *.raw files. The output was aligned by reported lipid species. Individual lipid species were considered as positively identified if they were recognized in four or more replicated analyses. In all tests the programs were prompted to identify species of PE, PI, PS, PG and PA classes. Mass tolerance was set at 0.3 Da in MS and MS/MS modes; fatty acid moieties were assumed to comprise 12 to 22 carbon atoms and 0 to 6 double bonds.
Settings specific for each tested program were as follows.
LipidXplorer: 'MS threshold' was set to 100 and 'MS/MS threshold' to 5 counts per peak area; 'Resolution gradient' was set to 1; other common spectra import settings were as in Additional file 13 (setting: 'FAS_LTQ').
LipidQA (spectra were imported as *.raw files): 'MS error' and the 'MS/MS error' were both set to 0.3 Da; 'Finnigan Filter', on; 'Quantification', off; 'Mode selection', Neg. Mode; 'If MS2 spectra were centroided', checked. Only species with a score above 0.5 were accepted. The current version of LipidQA is available at [51 ].
Lipid Search version 2.0 beta: 'SearchType' was set to 'MS2,MS3'; 'ExpType' to 'Infusion'; 'Precursor tol' to '0.3 Da'; 'Product peak tol' to 0.3 Da; 'Intensity threshold' to 0.01; 'Threshold type' to Relative; 'M-score Threshold' to 10.0. The current version of LipidSearch is available at [52 ].
LipidProfiler v.1.0.97: the software was used for creating a reference list of lipids in the E. coli extract and utilized a separate dataset acquired on a QSTAR Pulsar i mass spectrometer by the MPIS method. Intensity threshold was set to 0.2%; all lipid species reported as 'confirmed results' in at least four independent acquisitions.
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Publication 2011
Carbon-22 Escherichia coli Fatty Acids Immune Tolerance Lipid A Lipids Pulsar SLPI protein, human Tandem Mass Spectrometry
All pure lipid bilayer systems were built
using the CHARMM-GUI Membrane Builder.19 (link),40 (link)−42 (link) A total of 80 lipid molecules were placed in each
lipid bilayer (i.e., 40 lipids in each leaflet) with its center at z = 0. A water layer of 20-Å thickness was added above
and below the lipid bilayer for the DPPC, DOPC, POPC, and POPE systems
and that of 40-Å thickness for the POPS and PSM systems. The
corresponding hydration numbers of each membrane are 34 (DPPC), 34
(DOPC), 32 (POPC), 29 (POPE), 67 (POPS), and 58 (PSM) waters per lipid.
KCl ions corresponding to 0.15 M were added in the POPS (including
neutralizing ions) and PSM systems, and no ion was added in the DPPC,
DOPC, POPC, and POPE systems. While CHARMM and NAMD use the origin
for the periodic boundary conditions (PBC), GROMACS, AMBER, and OpenMM
use the PBC center at (LX/2, LY/2, LZ/2) where LX, LY, and LZ are the system
lengths along the xyz directions. Therefore, the
whole system is translated by LX/2, LY/2, and LZ/2 for the GROMACS, AMBER,
and OpenMM input generation in CHARMM-GUI.
Publication 2015
1,2-oleoylphosphatidylcholine 1-palmitoyl-2-oleoylphosphatidylethanolamine Amber Familial Mediterranean Fever Lipid A Lipid Bilayers lipid I Lipids Tissue, Membrane
We performed a set of experiments to characterize the precision and accuracy of MI for measuring the homogeneous absorption and reduced scattering optical properties. Sixteen turbid phantoms were constructed using a single batch of Liposyn lipid emulsion and water-soluble nigrosin dye stock solutions for the scattering and absorbing properties, respectively. In the first eight phantoms, we varied the absorption coefficient, μa, over two orders of magnitude (logarithmically spaced between 0.002 mm−1≤μa≤0.12 mm−1), with a constant scattering coefficient constant at μs=0.97mm1 . In the second set, we linearly varied μs(0.32mm1μs1.8mm1) , while holding the absorption coefficient constant at μa=0.0046 mm−1. These values were calculated based on infinite-geometry, multifrequency (50 to 500 MHz), multidistance (10 to 25 mm) frequency-domain photon migration measurements15 of one of the Liposyn/nigrosin phantoms.
MI measurements were performed on each sample. Thirty spatial frequencies of illumination were chosen between 0 mm−1 and 0.13 mm−1, corresponding to a total of 90 images per phantom (three spatial phases per frequency). The interfrequency spacing was chosen to accurately capture the MTF curvature of all phantoms, with finer spacing at low frequencies and coarser spacing at high frequencies, accordingly. All measurements were taken at 660 nm with an approximate 75×75 mm illumination area, a 50×50 mm camera field of view, and an integration time of 100 ms. The individual phantoms were measured in a randomized order, and measurements were repeated three times to allow for statistical averaging.
Modulation images of the AC reflectance were obtained at each frequency using Eq. (20). At full CCD resolution, the pixel-by-pixel demodulation approach results in approximately 250,000 separate measurements of reflectance per spatial frequency, highlighting the statistical power of the technique. As the lipid solutions were expected to be highly homogeneous, 20×20 pixel binning was performed on each image to speed computation, resulting in low-resolution, 15×15 pixel modulation images. The resulting 30 images provide a quantitative AC amplitude measurement at each of 100 spatial locations within the field of view. For calibration, a single phantom from the entire set of 16 was chosen as the reference (second-lowest absorption phantom). Using the reference’s known optical properties (determined from infinite-geometry FDPM measurements), we calculate a model-based prediction for the reflectance, Rd,ref,pred(fx). Then, for each spatial frequency and each spatial location, we use Eq. (23) to calculate Rd(fx) of the sample. Having retained some low-resolution spatial data, we can calculate a standard deviation of recovered values within an image as an indicator of measurement precision.
The diffusion model of Eq. (10) was used to solve for μa and μs using both least-squares minimization by a simplex search algorithm (in “fminsearch” MATLAB) and via the two-frequency lookup table approach using the lowest (0 mm−1) and highest (0.13 mm−1) spatial frequencies. For each phantom, each spatial sampling point was separately analyzed, generating images of recovered absorption and scattering values. As these were homogeneous samples, a mean and a standard deviation were calculated to represent each optical property image result, characterizing the accuracy and precision of MI, respectively.
Publication 2009
Diffusion Emulsions Light Lipid A Lipids Liposyn nigrosin Vision

Most recents protocols related to «Lipid A»

The measurements of anthropometric attributes and biochemical profiles have been described previously [23 (link)]. In brief, we used a digital system (BW-2200; NAGATA Scale Co. Ltd., Tainan, Taiwan) to measure the subject’s body weight and height. Waist circumference (WC) was measured at the level of mid-distance between the bottom of the rib cage and the top of the iliac crest. Hip circumference was the distance around the largest part of the subject’s hips. Blood pressure was measured three times, with an interval of 3 min, after 10 min of rest. The averages of repeated measurements of systolic blood pressure (SBP) and diastolic blood pressure (DBP) were used for analyses. The fasting blood levels of total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglycerides (FTG), and glucose (FPG) were determined by an autoanalyzer (Toshiba TBA c16000; Toshiba Medical System, Holliston, MA, USA) with commercial kits (Denka Seiken, Tokyo, Japan).
We also used a structured questionnaire to collect personal histories of common diseases in adults and health behaviors. In the study, hypertension was defined as subjects who had physician-diagnosed hypertension or a history of taking antihypertensive medications. Hyperlipidemia was defined as subjects having been diagnosed with high blood lipids by a physician or having a history of taking lipid-lowering medications. DM was defined as FPG ≥ 126 mg/dL or the use of insulin or other hypoglycemic agents. Cigarette smoking and alcohol drinking were defined as having smoked cigarettes or drank alcohol-containing beverages at least 4 days per week during the past month before enrollment.
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Publication 2023
Adult Alcoholic Beverages Antihypertensive Agents BLOOD Blood Pressure Body Weight Cholesterol Cholesterol, beta-Lipoprotein Coxa Fingers Glucose High Blood Pressures High Density Lipoprotein Cholesterol Hyperlipidemia Hypoglycemic Agents Iliac Crest Insulin Lipid A Lipids Pharmaceutical Preparations Physicians Pressure, Diastolic Rib Cage Systolic Pressure Triglycerides Waist Circumference
Stock solutions (1–10 mg/mL)
of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
(POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS, Avanti Polar Lipids, Alabaster, AL, USA), and
ATTO 390-1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine
(Atto 390-DPPE, ATTO-TEC, Siegen, Germany) were prepared in chloroform. l-α-Phosphatidylinositol-4,5-bisphosphate (PtdIns[4,5]P2, brain porcine, Avanti Polar Lipids, Alabaster, AL, USA)
was freshly dissolved in chloroform/methanol/H2O (10:20:8)
to a final concentration of 1 mg/mL. Lipid mixtures (0.4 mg) were
prepared in chloroform/methanol (10:1), and organic solvents were
evaporated with a nitrogen stream followed by 3 h in vacuum. The dried
lipid films were stored at 4 °C until needed.
Small unilamellar
vesicles (SUVs) were prepared by rehydrating a lipid film in spreading
buffer (50 mM KCl, 20 mM Na-citrate, 0.1 mM NaN3, 0.1 mM
ethylenediaminetetraacetic acid (EDTA), pH 4.8),38 (link) incubating for 30 min, subsequent vortexing (3 × 30
s at 5 min intervals), and a final sonification step for 30 min at
room temperature (cycle 4, 60%, Sonopuls HD2070, resonator cup; Bandelin,
Berlin, Germany). PtdIns[4,5]P2 containing SUVs were used
immediately for the preparation of SLBs to avoid PtdIns[4,5]P2 degradation.65 (link)
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Publication 2023
1-palmitoyl-2-oleoylphosphatidylcholine Acids Alabaster bis(diphenylphosphine)ethane Brain Chloroform Citrates Edetic Acid Lipid A Lipids Methanol Nitrogen Phosphatidylethanolamines Phosphatidylinositols Pigs Serine Sodium Azide Solvents Vacuum
Our mice strain came from the Nanjing Model Animal Resource Information Platform. Apoe−/− male C57BL/6 mice (16 weeks old) were used to establish control and experimental group. APOE is often produced in monocytes and macrophages (Curtiss et al., 2000 (link)) and plays a critical role in blood lipid metabolism (Chen et al., 2017 (link)) as ligands for receptors that clear chylomicron and VLDL residue (Meir and Leitersdorf, 2004 (link)). So when APOE is knocked out, total cholesterol in plasma increases (Maganto-Garcia, Tarrio, and Lichtman, 2012 (link)), and the effect is multiplied especially under a high-fat and high-cholesterol diet. Female mice secrete estrogen, which lowers the content of LDL in plasma and enhances endovascular blood coagulation (Aryan et al., 2020 (link)). For the experimental group, to accelerate the progression of atherosclerosis, the mice were fed with high-fat and high-cholesterol food for about 12 weeks after they had been weaned (4 weeks old); this group is referred to as the Western diet (HFD) group for short. (Formula of high fat, high cholesterol diet: 20% sucrose, 15% lard, 1.2% cholesterol, 0.2% sodium cholate, 10% casein, 0.6% calcium hydrogen phosphate, 0.4% stone powder, 0.4% premix and 52.2% basal feed.) Meanwhile, another group of mice, the control group, was administered with a chow diet. Mice were euthanized after 12 weeks of being administered different diets. Animal studies were performed in compliance with ethical guidelines and use of animals, and the experimental protocol was approved by the Shenzhen University Animal Care and Use Committee.
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Publication 2023
Animal Model Animals ApoE protein, human Atherosclerosis BLOOD Calculi Caseins Cholesterol Chylomicrons Coagulation, Blood dicalcium phosphate Diet Diet, High-Fat Disease Progression Estrogens Females Food Hypercholesterolemia lard Ligands Lipid A Macrophage Males Metabolism Mice, House Mice, Inbred C57BL Monocytes Plasma Powder Sodium Cholate Strains Sucrose Therapy, Diet
Chemically defined food (CDF) was made as described by Lee and Micchelli (2013) (link) by mixing 3 powder master mixes: essential amino acid mix 2.87 g/L for 100 kCal food and 11.49 g/L for 400 kCal food (TD.10473, Envigo Teklad, IN); nonessential amino acid mix (TD.110036) 2.03 g/L for 100 kCal food and 8.12 g/L for 400 kCal food; and basal mix 3.2 g/L for both 100 and 400 kCal food (TD. 10475). Then a 5X carbohydrate mix was added. A 100X slurry of lipids was added for 100 kCal food NS 400X was added for 400 kCal food before the CDF was adjusted to the final volume. We added the tracking dye Sulforhodamine B (SRB) at a final concentration of 0.5 mg/mL (Sigma-Aldrich, St. Louis, MO) to the CDF or PBS depending on the assay.
Conventional flies were reared on Cornmeal, Sucrose, and Yeast Media (agar 10 g/L, cornmeal 27 g/L, sugar 43 g/L, yeast 15 g/L, 2.8 g/L p-Hydroxybenzoic acid methyl ester in 10.8 mL/L of ethanol, from LabExpress). Germ-free flies were reared on 10:5 fly media (10% glucose, 5% yeast extract, Bacto Agar 1.2%, propionic acid 0.42%) Liquid 10:5 fly media (10% glucose, 5% yeast extract) was fed in the WAFFL. Liguid 10:5 fly media with Ex-Q dye was used for tracking the amount of food eaten per fly (10% glucose, 5% yeast extract, 1% w/v erioglaucine dye). Tissue homogenization buffer (THB) was PBS pH 7.4 plus 0.5% v/v Triton X.
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Publication 2023
Agar Amino Acids Amino Acids, Essential Biological Assay brilliant blue FCF Buffers Carbohydrates Eating Ethanol Food Glucose Lipid A lissamine rhodamine B methyl salicylate Powder propionic acid Sucrose Tissues Yeast, Dried
Glucose (enzymatic-colorimetric method, sensitivity: 0.06 mmol/L) and urea (kinetic method, sensitivity: 0.056 mmol/L) concentrations were determined in plasma with an automatic analyzer (Gernon, RAL S.A, Barcelona, Spain). The mean intra- and interassay CV were 1.5% and 1.9% for glucose and 3.2% and 4.8% for urea, respectively. Plasma BHB (kinetic enzymatic method, sensitivity: 0.100 mmol/L) and NEFA (colorimetric method, sensitivity: 0.072 mmol/L) were determined using Randox kits (Randox Laboratories Ltd., Country Antrim, UK). The mean intra- and interassay CV were respectively 3.3% and 3.7% for NEFA and 6.2% in both cases for BHB. Oxidative status was determined using MDA as a biomarker of lipid peroxidation. This indicator was determined by liquid chromatography using an Acquity UPLC H-Class liquid chromatograph (Waters, Milford, MA, USA) equipped with a silica-based bonded phase column (Acquity UPLC HSS PFP, 100 mm × 2.1 mm × 1.8 μm, Waters), an absorbance detector (Acquity UPLC Photodiode Array PDA eλ detector, Waters) and a fluorescence detector (2475 Multi λ Fluorescence Detector, Waters). The quantification of MDA was done by fluorescence detection at ʎexcitation = 530 nm and ʎemission = 550 nm following the chromatographic conditions described in Bertolín et al. (2019) (link). The mean intra- and interassay CV were 4.6% and 7.3%, respectively.
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Publication 2023
Biological Markers Chromatography Colorimetry Enzymes Fluorescence Glucose Hypersensitivity Kinetics Lipid A Lipid Peroxidation Liquid Chromatography Nonesterified Fatty Acids Plasma Randox Silicon Dioxide Urea

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Lipid A is a key component of the outer membrane of gram-negative bacteria. It serves as the hydrophobic anchor of lipopolysaccharides, which are crucial structural elements of the bacterial cell wall. Lipid A plays a central role in the innate immune response and is an important target for research in microbiology, immunology, and drug development.

More about "Lipid A"

Lipid A, a critical component of lipopolysaccharides (LPS) in Gram-negative bacteria, is a key focus of research in the fields of immunology and infectious disease.
As a central player in the body's inflammatory response, Lipid A can act as a potent activator of the immune system.
Researchers studying Lipid A often utilize advanced techniques and equipment such as mini-extruders, Zetasizer Nano ZS instruments, Bio-Beads SM-2, and polycarbonate filters to investigate its properties and interactions.
PubCompare.ai, an innovative AI-powered tool, can greatly enhance Lipid A research by helping scientists quickly identify the best protocols from the literature, preprints, and patents.
This time-saving platform can improve the reproducibility and accuracy of Lipid A studies, enabling researchers to focus on advancing their important work.
By leveraging the power of AI, PubCompare.ai can help researchers find the optimal methods for studying Lipid A, including its role in the inflammatory response and its interactions with cholesterol and other lipids.
Through the use of advanced techniques and cutting-edge tools like PubCompare.ai, scientists can make significant strides in understanding the critical role of Lipid A in immunology and infectious disease research.
This knowledge can lead to the development of more effective treatments and therapies, ultimately improving human health and wellbeing.