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Buffers

Buffers are aqueous solutions that maintain a relatively stable pH value, resisting changes in hydrogen ion concentration upon the addition of small amounts of an acid or base.
They are essential in biological research, ensuring optimal conditions for enzymes, proteins, and other biomolecules to function properly.
Buffers can be composed of various chemical compounds, such as phosphates, acetates, and tris, and their selection is crucial in experimental design.
Understanding the properties and appropriate use of buffers is key to achieving consistent and reproducabble results in a wide range of scientific applications, from cell culture to biochemical assays.

Most cited protocols related to «Buffers»

Initial helical conformations were defined as all amino acids having (φ, ψ)=(−60°, −40°). Initial extended conformations were defined as all (φ, ψ)=(180°, 180°). Native conformations, as appropriate, were defined for each system as below. Explicit solvation was achieved with truncated octahedra of TIP3P water16 with a minimum 8.0 Å buffer between solute atoms and box boundary. All structures were built via the LEaP module of Ambertools. Except where otherwise indicated, equilibration was performed with a weak-coupling (Berendsen) thermostat33 and barostat targeted to 1 bar with isotropic position scaling as follows. With 100 kcal mol−1 Å−2 positional restraints on protein heavy atoms, structures were minimized for up to 10000 cycles and then heated at constant volume from 100 K to 300 K over 100 ps, followed by another 100 ps at 300 K. The pressure was equilibrated for 100 ps and then 250 ps with time constants of 100 fs and then 500 fs on coupling of pressure and temperature to 1 bar and 300 K, and 100 kcal mol−1 Å−2 and then 10 kcal mol−1 Å−2 Cartesian positional restraints on protein heavy atoms. The system was again minimized, with 10 kcal mol−1 Å−2 force constant Cartesian restraints on only the protein main chain N, Cα, and C for up to 10000 cycles. Three 100 ps simulations with temperature and pressure time constants of 500 fs were performed, with backbone restraints of 10 kcal mol−1 Å−2, 1 kcal mol−1 Å−2, and then 0.1 kcal mol−1 Å−2. Finally, the system was simulated unrestrained with pressure and temperature time constants of 1 ps for 500 ps with a 2 fs time step, removing center-of-mass translation and rotation every picosecond.
SHAKE34 was performed on all bonds including hydrogen with the AMBER default tolerance of 10−5 Å for NVT and 10−6 Å for NVE. Non-bonded interactions were calculated directly up to 8 Å. Beyond 8 Å, electrostatic interactions were treated with cubic spline switching and the particle-mesh Ewald approximation35 in explicit solvent, with direct sum tolerances of 10−5 for NVT or 10−6 for NVE. A continuum model correction for energy and pressure was applied to long-range van der Waals interactions. The production timesteps were 2 fs for NVT and 1 fs for NVE.
Publication 2015
Amber Amino Acids Buffers Cuboid Bone Debility Electrostatics Helix (Snails) Hydrogen-5 Immune Tolerance nucleoprotein, Measles virus Pressure Proteins Solvents Vertebral Column
DNase treatment, cDNA synthesis, primer design and SYBR Green I RT-PCR were carried out as described [23 (link)]. In brief, 2 μg of each total RNA sample was treated with the RQ1 RNase-free DNase according to the manufacturer's instructions (Promega). Treated RNA samples were desalted (to prevent carry over of magnesium) before cDNA synthesis using Microcon-100 spin columns (Millipore). First-strand cDNA was synthesized using random hexamers and SuperscriptII reverse transcriptase according to the manufacturer's instructions (Invitrogen), and subsequently diluted with nuclease-free water (Sigma) to 12.5 ng/μl cDNA. RT-PCR amplification mixtures (25 μl) contained 25 ng template cDNA, 2x SYBR Green I Master Mix buffer (12.5 μl) (Applied Biosystems) and 300 nM forward and reverse primer. Reactions were run on an ABI PRISM 5700 Sequence Detector (Applied Biosystems). The cycling conditions comprised 10 min polymerase activation at 95°C and 40 cycles at 95°C for 15 sec and 60°C for 60 sec. Each assay included (in duplicate): a standard curve of four serial dilution points of SK-N-SH or IMR-32 cDNA (ranging from 50 ng to 50 pg), a no-template control, and 25 ng of each test cDNA. All PCR efficiencies were above 95%. Sequence Detection Software (version 1.3) (Applied Biosystems) results were exported as tab-delimited text files and imported into Microsoft Excel for further analysis. The median coefficient of variation (based on calculated quantities) of duplicated samples was 6%.
Publication 2002
Anabolism Biological Assay Buffers Deoxyribonucleases DNA, Complementary Endoribonucleases Magnesium Oligonucleotide Primers prisma Promega Reverse Transcriptase Polymerase Chain Reaction RNA-Directed DNA Polymerase SYBR Green I Technique, Dilution
The streptavidin alkaline phosphatase method was adapted to detect the viral antigen using a polyclonal anti-ZIKV antibody produced at the Evandro Chagas Institute2 (link). The biotin-streptavidin peroxidase method was used for immunostaining of tissues with antibodies specific for each marker studied. First, the tissue samples were deparaffinized in xylene and hydrated in a decreasing ethanol series (90%, 80%, and 70%). Endogenous peroxidase was blocked by incubating the sections in 3% hydrogen peroxide for 45 min. Antigen retrieval was performed by incubation in citrate buffer, pH 6.0, or EDTA, pH 9.0, for 20 min at 90 °C. Nonspecific proteins were blocked by incubating the sections in 10% skim milk for 30 min. The histological sections were then incubated overnight with the primary antibodies diluted in 1% bovine serum albumin (Supplementary Table S1). After this period, the slides were immersed in 1 × PBS and incubated with the secondary biotinylated antibody (LSAB, DakoCytomation) in an oven for 30 min at 37 °C. The slides were again immersed in 1X PBS and incubated with streptavidin peroxidase (LSAB, DakoCytomation) for 30 min at 37 °C. The reactions were developed with 0.03% diaminobenzidine and 3% hydrogen peroxide as the chromogen solution. After this step, the slides were washed in distilled water and counterstained with Harris hematoxylin for 1 min. Finally, the sections were dehydrated in an increasing ethanol series and cleared in xylene.
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Publication 2018
Alkaline Phosphatase Antibodies Antibodies, Anti-Idiotypic Antigens Antigens, Viral azo rubin S Biotin Buffers Citrates Edetic Acid Ethanol Hematoxylin Immunoglobulins Milk, Cow's Peroxidase Peroxide, Hydrogen Peroxides Proteins Serum Albumin, Bovine Streptavidin Tissues Tritium Xylene Zika Virus
Freshly isolated and cultivated skin samples were harvested at indicated time-points, embedded in optimum cutting tissue compound (Tissue-plus; Scigen Scientific, Gardena, CA, USA), snap frozen in liquid nitrogen and stored at −80 °C until further processing. Frozen tissues were sectioned (5 µm) (Cryotome–Leica Biosystems CM1850, Germany), fixed in ice-cold acetone (10 minutes) and washed with PBS. Fixed sections were stained with unconjugated and conjugated antibodies (Abs) (overnight, 4 °C) and Ab binding was detected using corresponding secondary Abs. Paraffin embedded tissues were deparaffinised by dipping them into Xylol (2x, 5 minutes), 100% ethanol (5 minutes), 70% ethanol (5 minutes) and washed in tap water (2x, 5 minutes). Then they were incubated in antigen retrieval buffer (Dako S1699, Denmark), washed in PBS and stained. Abs used are listed in Table S1.
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Publication 2020
Acetone Antibodies Antigens Buffers Cold Temperature Ethanol Freezing Nitrogen Paraffin Skin Tissues Xylene
One approach for simulating a small part of a large system (e.g.,
the enzyme active site region of a large protein) uses a solvent boundary
potential (SBP). In SBP simulations, the macromolecular system is separated
into an inner and an outer region. In the outer region, part of the
macromolecule may be included explicitly in a fixed configuration, while the
solvent is represented implicitly as a continuous medium. In the inner
region, the solvent molecules and all or part of the macromolecule are
included explicitly and are allowed to move using molecular or stochastic
dynamics. The SBP aims to “mimic” the average
influence of the surroundings, which are not included explicitly in the
simulation.27 ,28 There are several implementations of the SBP
method in CHARMM. The earliest implementation, called the stochastic
boundary potential (SBOU), uses a soft nonpolar restraining potential to
help maintain a constant solvent density in the inner or
“simulation” region while the molecules in a shell
or buffer region are propagated using Langevin dynamics.27 By virtue of its simplicity, this treatment
remains attractive and it is sufficient for many applications.320 (link),321 (link) To improve the treatment of systems with irregular
boundaries in which part of the protein is in the outer region, a refinement
of the method has been developed that first scales the exposed charges to
account for solvent shielding and then corrects for the scaling by
post-processing.307
The Spherical Solvent Boundary Potential (SSBP), which is part of
the Miscellaneous Mean Field Potential (MMFP) module (see Section III F), is
designed to simulate a molecular solute completely surrounded by an
isotropic bulk aqueous phase with a spherical boundary.28 In SSBP the radius of the spherical region is
allowed to fluctuate dynamically and the influence of long-range
electrostatic interactions is incorporated by including the dielectric
reaction field response of the solvent.28 ,29 This approach has
been used to study several systems.322 –325
Because SSBP incorporates the long-range electrostatic reaction field
contribution, the method is particularly useful in free energy calculations
that involve introducing charges.322 –325
Like the SBOU charge-scaling method,307 the Generalized Solvent Boundary Potential (GSBP) is
designed for irregular boundaries when part of the protein is outside the
simulation region.29 However, unlike
SBOU, GSBP includes long-range electrostatic effects and reaction fields. In
the GSBP approach, the influence of the outer region is represented in terms
of a solvent-shielded static field and a reaction field expressed in terms
of a basis set expansion of the charge density in the inner region, with the
basis set coefficients corresponding to generalized electrostatic
multipoles.29 ,326 The solvent-shielded static field from the
outer macromolecular atoms and the reaction field matrix representing the
coupling between the generalized multipoles are both invariant with respect
to the configuration of the explicit atoms in the inner region. They are
calculated only once (with the assumption that the size and shape of inner
region does not change during the simulation) using the finite-difference
Poisson-Boltzmann (PB) equation of the PBEQ module. This formulation is an
accurate and computationally efficient hybrid MD/continuum method for
simulating a small region of a large macromolecular system,326 and is also used in QM/MM approaches.281 (link),327 (link)
Publication 2009
Buffers Dietary Fiber Electrostatics Enzymes Hybrids Proteins Radius Solvents Staphylococcal Protein A

Most recents protocols related to «Buffers»

Example 6

Compound 3 was generated from the purification process of IL-2 mutein Ala-M1 polymer prodrug 5. During separation of compound 5 on a Capto MMC ImpRes resin the later eluting peak which contains 3 was collected. The collected fraction was diluted with 10 mM succinic acid, pH 5.0 to lower the conductivity to approx. 14 mS/cm and further purified on a Äkta system equipped with a HiScreen Capto Blue column using buffer A (20 mM sodium phosphate, pH 7.5), buffer B (20 mM sodium phosphate, 1 M NaCl, pH 7.5) and a gradient from 0 to 50% buffer B in 6 column volumes. The main peak was collected and concentrated using Amicon Ultra centrifugal device (3 kDa MWCO). The concentrated solution was buffer exchanged to 10 mM Hepes, 150 mM NaCl, 3 mM EDTA, 0.05% polysorbate 20, pH 7.4 by using an Äkta system and a HiPrep 26/10 column and the concentration was adjusted to 0.25 mg/mL to give compound 3.

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Patent 2024
Buffers Edetic Acid Electric Conductivity HEPES interleukin-2, polyethylene glycol-modified Medical Devices mutein 2 mutein 5 Polymers Polysorbate 20 Prodrugs Resins, Plant Sodium Chloride sodium phosphate Succinic Acid
Not available on PMC !

Example 1

The particles are synthesized by adding between about 5 mg and about 20 mg of rituximab (or non-specific IgG) to 20 mg of ABRAXANE. Saline is then added to a final volume of 2 ml for a final concentration of 10 mg/ml ABRAXANE, and the mixture is allowed to incubate at room temperature for 30 minutes to allow particle formation. Particles average about 160 nm and are termed “AR160” nanoparticles.

Optionally, the composition is divided into aliquots and frozen at −80° C. Once frozen the aliquots are optionally lyophilized overnight with the Virtis 3L benchtop lyophilizer (SP Scientific, Warmister, PA) with the refrigeration on. A lyophilized preparation is generated.

The dried aliquots are stored at room temperature. These samples are reconstituted in saline at room temperature for 30 minutes, followed by centrifugation for 7 minutes at 2000×g. The resulting sample is then resuspended in the appropriate buffer, as needed.

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Patent 2024
Abraxane Albumins Buffers Centrifugation Freezing Rituximab Saline Solution

Example 9

NEBT7EL-pA06238 was grown on LB with 50 μg/ml kanamycin. A 600 ml culture of TBkan50 was inoculated with NEBT7EL-pA06238 and incubated overnight at 37° C. at 200 rpm. The next morning, a 10 L fermentor was prepared with 9.5 L of TB and then inoculated with 500 ml of the overnight culture. The culture was grown at 37° C. The pH was maintained at 6.2 with NaOH and the dO2 was maintained ≥20%. After 2 hours of growth, the temperature was dropped to 25° C. The culture was grown for an additional 1 hour with the OD600 around 7. IPTG was added to a final concentration of 1 mM and CoCl2 was added to 25 μM. Additional CoCl2 was added 1 and 2 hours after induction to bring the final concentration to 300 μM. The cells were grown for 20 hours at which point the fermentor was chilled to 10° C. and the cells were harvested by centrifugation. The cell pellet was stored at −80° C. until use.

The cell pellet from the fermentation was lysed by stirring in buffer with lysozyme and DNAse. Cell debris was removed by centrifugation and the supernatant was filtered through a 0.45 micron filter. Filtered supernatant was incubated with Ni-NTA agarose resin and then enzyme was eluted with imidazole. Purified FC4E pA06238 was immobilized onto 5.25 grams of ECR8204F resin using the standard published protocol from Purolite.

The immobilized enzyme was loaded into a 11×300 mm glass fixed bed reactor and run for approximately 200 h at constant temperature (60° C.) with a constant feed composition of 30 wt % fructose+70 wt % aqueous buffer solution (20 mM KPO4, 50 mM NaCl, 300 uM CoCl2). Feed rate was held constant at 140 uL/min throughout the run. The fixed bed reaction reached a maximal conversion of approximately 30% tagatose and had a half-life of −50 hours (FIG. 15).

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Patent 2024
ARID1A protein, human Buffers Cells Centrifugation Deoxyribonucleases Enzymes Enzymes, Immobilized Fermentation Fermentors Fructose imidazole Isopropyl Thiogalactoside Kanamycin Muramidase Resins, Plant Sepharose Sodium Chloride tagatose

Example 3

Recombinant Protein Purification

FIG. 5 shows the steps of one of the purifications carried out on the chimera. In the case of GRNLY, this process was shown in an earlier paper [Ibáñez, R., University of Zaragoza. 2015]. It can be seen in FIG. 5A that the P. Pastoris supernatant obtained after induction (lane 1) contains rather diluted proteins. After concentrating same with Pellicom, protein bands are not seen in the permeate (lane 3), but proteins that are much more concentrated than in the supernatant are seen in the concentrate (lane 2). After dialysis (lane 4), the band profile remains similar to the concentrate. Furthermore, protein bands are not seen in the buffer in which the dialysis bag (lane 5) was introduced. Upon addition of the nickel resin, the chimera binds to said resin as it has a histidine tag. After adding the resin (lane 6), the intensity of a band corresponding to a protein of about 40 kDa decreases with respect to the concentrate and dialysate. This band may correspond to the chimera. The fact that this band does not altogether disappear may indicate that the nickel resin was saturated. In the washes performed on the resin, particularly in the first wash (lane 7), it can be seen how the residues of other proteins are removed. Finally, after the elution of the nickel column, a major protein with a molecular weight of about 40 kDa corresponding to the molecular weight of the chimera (lane 11) is clearly observed. As shown in FIG. 5B, it was confirmed by means of immunoblot that this band of about 40 kDa corresponds to the chimera (lane 11). It is also confirmed that the resin was saturated because a band appears in the post-resin dialysis phase (lane 6).

FIG. 6 shows different elution fractions and the pooling of all of them with the exception of elution fraction 1. FIG. 6A shows several bands in the different elution fractions and in the total eluate. The band with the highest intensity has a molecular weight corresponding to the chimera. Furthermore, other bands having intermediate molecular weights are observed, which means that the chimera undergoes partial proteolysis. The band with the second highest intensity has a molecular weight of about 10 kDa, which corresponds to 9-kDa GRNLY, as its molecular weight increases since it is bound to a histidine tag. In FIG. 6B, it was confirmed by means of immunoblot that these bands of about 40 and 10 kDa correspond to the chimeric recombinant protein and to recombinant GRNLY, respectively.

Once the chimera is generated, its functionality must be assured, that is, on one hand the scFv still recognizes the CEA antigen, and on the other hand GRNLY is still cytotoxic.

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Patent 2024
Antigens Buffers Chimera Chimeric Proteins, Recombinant Dialysis Dialysis Solutions GNLY protein, human Histidine Immunoblotting Nickel One-Step dentin bonding system Proteins Proteolysis Recombinant Proteins Resins, Plant Staphylococcal Protein A Vision

Example 49

The functional activity of compounds was determined in a cell line where p70S6K is constitutively activated. Test article was dissolved in DMSO to make a 10 μM stock. PathScan® Phospho-S6 Ribosomal Protein (Ser235/236) Sandwich ELISA Kit was purchased from Cell Signaling Technology. A549 lung cancer cell line, was purchased from American Type Culture Collection. A549 cells were grown in F-12K Medium supplemented with 10% FBS. 100 μg/mL penicillin and 100 μg/mL streptomycin were added to the culture media. Cultures were maintained at 37° C. in a humidified atmosphere of 5% CO2 and 95% air. 2.0×105 cells were seeded in each well of 12-well tissue culture plates for overnight. Cells were treated with DMSO or test article (starting at 100 μM, 10-dose with 3 fold dilution) for 3 hours. The cells were washed once with ice cold PBS and lysed with 1× cell lysis buffer. Cell lysates were collected and samples were added to the appropriate wells of the ELISA plate. Plate was incubated for overnight at 4° C. 100 μL of reconstituted Phospho-S6 Ribosomal Protein (Ser235/236) Detection Antibody was added to each well and the plate was incubated at 37° C. for 1 hour. Wells were washed and 100 μl of reconstituted HRP-Linked secondary antibody was added to each well. The plate was incubated for 30 minutes at 37° C. Wash procedure was repeated and 100 μL of TMB Substrate was added to each well. The plate was incubated for 10 minutes at 37° C. 100 μL of STOP Solution was added to each well and the absorbance was read at 460 nm using Envision 2104 Multilabel Reader (PerkinElmer, Santa Clara, CA). IC50 curves were plotted and IC50 values were calculated using the GraphPad Prism 4 program based on a sigmoidal dose-response equation.

TABLE 2
In vitro biological data for representative compounds of Formula
I-IX Unless otherwise noted, compounds that were tested had an IC50
of less than 50 μM in the S6K binding assay.
Example NumberS6K Binding Activity
1A
2B
3B
4A
5A
6A
7A
8A
9B
10B
11B
12C
13C
14C
15A
16A
17B
18A
19A
20A
21A
22C
23B
24A
25A
26C
27A
28C
29C
30C
31A
32A
33C
34C
35C
36C
37C
38A
39A
40A
41A

Unless otherwise noted, compounds that were tested had an IC50 of less than 50 μM in the S6K Binding assay. A=less than 0.05 μM; B=greater than 0.05 μM and less than 0.5 μM; C=greater than 0.5 μM and less than 10 μM;

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Patent 2024
A549 Cells Atmosphere Biological Assay Biopharmaceuticals Buffers Cell Lines Cells Cold Temperature Culture Media Enzyme-Linked Immunosorbent Assay Immunoglobulins Lung Cancer Penicillins prisma Psychological Inhibition Ribosomal Proteins Ribosomal Protein S6 Ribosomal Protein S6 Kinases, 70-kDa Streptomycin Sulfoxide, Dimethyl Technique, Dilution Tissues

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More about "Buffers"

Buffers are crucial in a wide range of scientific applications, from cell culture to biochemical assays.
These aqueous solutions help maintain a relatively stable pH value, resisting changes in hydrogen ion concentration upon the addition of small amounts of an acid or base.
Buffers are essential for ensuring optimal conditions for enzymes, proteins, and other biomolecules to function properly.
Buffers can be composed of various chemical compounds, such as phosphates, acetates, and tris.
The selection of the appropriate buffer is crucial in experimental design, as it can impact the performance and reproducibility of your results.
RIPA lysis buffer, for example, is a commonly used buffer for extracting proteins from cells and tissues, while the BCA protein assay kit and the Pierce BCA Protein Assay Kit are widely used for quantifying protein concentrations.
In addition to buffers, other important tools and techniques in biological research include PVDF membranes for protein transfer and detection, protease inhibitor cocktails for preserving protein integrity, and flow cytometry instruments like the FACSCalibur for analyzing cells.
Understanding the properties and appropriate use of buffers, as well as these related tools and techniques, is key to achieving consistent and reproducible results in your scientific work.
By optimizing your research protocols and enhancing reproducibility, you can unlock the true power of your research and drive scientific progress forward.