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PubMed2005

Crystallization Optimum Solubility Screening: using crystallization results to identify the optimal buffer for protein crystal formation.

An optimal solubility screen is described that uses the results of crystallization trials to identify buffers that improve protein solubility and, in turn, crystallization success. This screen is useful not only for standard crystallization experiments, but also can easily be implemented into any high-throughput structure-determination pipeline. As a proof of principle, the predicted novel-fold protein AF2059 from Archaeoglobus fulgidus, which was known to precipitate in most buffers and particularly during concentration experiments, was selected. Using the crystallization results of 192 independent crystallization trials, it was possible to identify a buffer containing 100 mM CHES pH 9.25 that significantly improves its solubility. After transferring AF2059 into this ;optimum-solubility' buffer, the protein was rescreened for crystal formation against these same 192 conditions. Instead of extensive precipitation, as observed initially, it was found that 24 separate conditions produced crystals and the exchange of AF2059 into CHES buffer significantly improved crystallization success. Fine-screen optimization of these conditions led to the production of a crystal suitable for high-resolution (2.2 A) structure determination.

Archaeoglobus fulgidus↗

PubMed1998

Analysis of synthetic peptides by capillary zone electrophoresis in organic/aqueous buffers.

Whereas synthetic peptides have been routinely analyzed for purity by reverse phase high performance liquid chromatography (RPHPLC) for a number of years, it is only in the last decade that the use of capillary zone electrophoresis (CZE) in aqueous buffers has been taken advantage of as an orthogonal method for the detection of impurities. However, we have found that hydrophobic amino acids and peptides often migrate as very broad, tailing absorbances or even precipitate in the aqueous buffers during CZE analysis. As a result, alternative buffer systems containing organic modifiers were sought. Varying concentrations of acetonitrile, methanol and isopropanol in sodium phosphate and triethylammonium phosphate buffers were used to study their effects on the electrophoretic migration of several synthetic peptides [gonadotropin releasing hormone (GnRH), corticotropin releasing factor (CRF) and analogs] and an enantiomeric synthetic amino acid. The organic/aqueous buffers used to obtain the best conditions for separation of porcine gonadotropin-releasing hormone (GnRH) and chicken II GnRH were then used to optimize a separation of nine native forms of GnRH decapeptides. Interestingly, several of these GnRHs have identical formal charges and yet could be separated. This suggests a mixed mechanism of separation that discriminates not only on the basis of peptide charge and structure but also of adsorptive properties (Van der Waals forces, dipole-dipole interactions and hydrogen bonding) of the capillaries.

Buffers↗

PubMed1979

Norepinephrine-stimulated fatty-acid release and oxygen consumption in isolated hamster brown-fat cells. Influence of buffers, albumin, insulin and mitochondrial inhibitors.

Brown fat cells isolated from adult golden hamsters have earlier been found to respond to addition of the physiological agonist norepinephrine with an increased rate of oxygen consumption and with fatty acid release. Working with these cells, we found the following. 1. The presence of albumin in the incubation medium (phosphate buffer) increases norepinephrine-induced fatty acid release and tends to stabilize the rate of oxygen consumption; bubbling of phosphate buffer with 5% CO2 in air has only a slight effect on fatty acid release. 2. In the presence of albumin, the norepinephrine-induced rate of oxygen consumption is also stable in bicarbonate buffer; it is higher than in the phosphate + CO2 buffer and the brown fat cells have a higher sensitivity to norepinephrine. 3. 20 mM phosphate (as e.g. present in a phosphate buffer) inhibits both fatty acid release and oxygen consumption. 4. Insulin inhibits the rate of oxygen consumption, but only at suboptimal concentrations of norepinephrine. 5. Atractylate inhibits submaximal norepinephrine-induced respiration, indicating that some oxidative phosphorylation takes place in norepinephrine-stimulated brown fat cells. 6. Fatty acid export from brown fat should be regarded as physiologically important.

Adipose Tissue, Brown↗

PubMed1999

Differential control of three after-hyperpolarizations in rat hippocampal neurones by intracellular calcium buffering.

1. The whole-cell recording technique, combined with internal perfusion, was used to study the effects of intracellular Ca2+ buffering on fast, medium and slow after-hyperpolarizations (fAHP, mAHP and sAHP) in hippocampal CA1 pyramidal neurones in rat brain slices at room temperature. 2. The action potentials and the fAHP were unaffected by 100 microM to 3 mM concentrations of the internally applied fast Ca2+ chelator BAPTA. At higher (10-15 mM) concentrations, BAPTA inhibited the fAHP and prolonged the decay of the action potential, suggesting that the corresponding large-conductance Ca2+-activated K+ channels are located close to the sites of Ca2+ entry during an action potential. Addition of Ca2+ to the BAPTA-containing solution (at a ratio of 4.5 [Ca2+] : 10 [BAPTA]) to maintain the control level of [Ca2+]i did not prevent the effects of high concentrations of BAPTA. 3. The mAHP, activated by a train of action potentials, was inhibited by internally applied BAPTA within the range of concentrations used (100 microM to 15 mM), and this effect could not be reversed or prevented by addition of Ca2+ to the BAPTA-containing solution. The inhibition of the mAHP by BAPTA could also be observed after blockade of the hyperpolarization-activated IQ type mixed Na+-K+ current (also known as Ih) component of the mAHP by bath-applied 3-5 mM Cs+, suggesting that the inhibition of the mAHP by BAPTA is due to inhibition of the depolarization-activated IM (muscarinic) type K+ current. 4. The sAHP, activated by a train of action potentials, was potentiated by 100-300 microM internally applied BAPTA, both with and without added Ca2+. At 1-2 mM or higher concentrations, the potentiation of the sAHP by BAPTA without added Ca2+ was transient and was followed by a fast decrease. With added Ca2+, however, BAPTA caused a persistent potentiation of the sAHP with more than a 10-fold increase in duration for periods exceeding 1 h even at concentrations of the buffer as high as 10-15 mM. Earlier reports showing a blockade of the sAHP by BAPTA, based on experiments without added Ca2+, were apparently due to a sharp reduction in intracellular free [Ca2+] and to a high intracellular concentration of the free buffer. 5. Internally applied BAPTA caused a prolongation of the spike discharge during an 800 ms-long depolarizing current step. At 100-300 microM BAPTA, but not at 1-2 mM or higher concentrations, this effect could be reversed by addition of Ca2+. The effects of BAPTA on the spike discharge occurred in parallel with the changes in the sAHP time course, which was more prolonged at higher concentrations of the buffer. 6. The concentration-dependent differential control of the three types of AHP in hippocampal neurones by BAPTA is related to modulation of intracellular Ca2+ diffusion by a fast acting mobile Ca2+ buffer.

Action Potentials↗

PubMed2006

Effect of phosphate buffer concentration on the batch xylitol production by Candida guilliermondii.

AIMS: To evaluate the effect of phosphate buffer concentration on growth and xylitol production by Candida guilliermondii FTI 20037. METHODS AND RESULTS: Fermentations runs were carried out in batch mode employing semisynthetic medium supplemented with phosphate buffer at different concentrations (from 200 to 600 mmol l(-1)). The xylitol yield (Y(P/S)) and volumetric productivity (Q(P)) were improved when the fermentation medium was supplemented with phosphate buffer at concentration of 600 mmol l(-1). Under this condition (Y(P/S)) and (Q(P)) values were 0.75 g g(-1) and 0.66 g l(-1) h(-1), respectively, whereas in the absence of the phosphate buffer these values decreased to 0.52 g g(-1) and 0.44 g l(-1)h(-1) respectively. CONCLUSIONS: The use of phosphate buffer at 600 mmol l(-1) promoted an easier pH control during shake flasks fermentation of C. guilliermondii. In addition the xylitol yield and productivity were significantly improved in response to the supplementation of potassium phosphate in the medium. The increase in these parameters could be related to both osmotic effect and pH control. SIGNIFICANCE AND IMPACT OF THE STUDY: This approach provided a method for improving the xylitol production from semisynthetic medium by C. guilliermondii, being possible their use as a simple strategy to achieve efficient fermentation processes employing complex medium such as lignocellulosic hydrolysates.

Biomass↗

PubMed1991

Alkaline buffers release EDRF from bovine cultured aortic endothelial cells.

1. Release of endothelium-derived relaxing factor (EDRF) and prostacyclin (PGI2) from bovine cultured aortic endothelial cells (EC) was measured by bioassay and radioimmunoassay, respectively. 2. Bradykinin (BK, 3-30 pmol), adenosine diphosphate (ADP, 2-6 nmol) or the sodium ionophore monensin (40-100 nmol) injected through a column of EC released EDRF. L-Arginine free base (FB; 10-20 mumol) or D-arginine FB (10-20 mumol) injected through the column of EC released similar amounts of EDRF and also caused an increase in pH of the Krebs solution perfusing the EC from 7.5-8.0 to 8.6-9.5. Sodium carbonate (Na2CO3) an alkaline buffer which caused the same changes in the pH of the Krebs solution also induced the same release of EDRF. The hydrochloride salts of L- or D-arginine did not cause either release of EDRF when injected through the column of EC or increases in the pH of the Krebs solution. 3. Inhibitors of either diacylglycerol lipase (RHC 80267) or kinase (R59022) inhibited the release of EDRF induced by BK or ADP but potentiated the release induced by L-arginine FB, monensin (40-100 nmol) or alkaline buffer (Na2CO3). R59022 and RHC 80267 infused through the EC increased the basal release of EDRF. 4. When calcium chloride was omitted from the Krebs solution the release of EDRF induced by alkaline buffer (Na2CO3; pH 8.6-9.5) or L-arginine FB (10-20 mumol) was selectively inhibited when compared to that induced by BK (3-30 pmol) or ADP (2-6 nmol). This inhibition was reversed when calcium (2.5 mM) was restored. 5. NG-monomethyl-L-arginine (NMMA; 30 microM) inhibited release of EDRF induced by BK (10-30 pmol) or alkaline buffers (Na2CO3 or D-arginine FB; pH 8.6-9.5). This inhibition was partially reversed by L- but not D-arginine FB or HCl (30-100 microM). 6. Prostacyclin was released when BK (10 pmol), ADP (2 nmol) or arachidonic acid (30 nmol) were injected through the column of EC. However, monensin (40 nmol) or alkaline buffers (pH 8.6-9.5) did not release detectable amounts of PGI2 as measured by radioimmunoassay for 6-oxo-prostaglandin F1 alpha. 7. Thus alkalinisation of the external bathing solution can release EDRF from cultured EC by a mechanism which does not involve receptor activation and which depends on the presence of extracellular calcium.

Animals↗

PubMed2006

Buffering and dilution in red blood cell storage.

BACKGROUND: Red blood cell (RBC) storage solutions work in a narrow pH range between 7.2 and 6.4. While keeping RBC within that pH range, ATP production can be increased by buffering or dilution. STUDY DESIGN AND METHODS: In the first study, 12 units of packed CP2D RBCs were pooled in groups of four, re-aliquoted, and added to one of four additive solutions (ASs): AS-3, 110 mL; EAS-61, 170 mL; EAS-78, 170 mL; or EAS-81, 110 mL. EAS-78 and -81 contain bicarbonate. Units were sampled approximately weekly for 10 weeks for biochemical measures. In the second study, 12 volunteers donated RBCs for measures of (51)Cr in vivo recovery after 6 or 8 weeks of storage in EAS-81. RESULTS: RBCs stored in the higher-volume or buffered ASs had higher RBC ATP concentrations. The combination had an additive effect. Hemolysis was reduced in dilute ASs and less so with buffering. RBCs stored for 8 weeks (n=6) in EAS-81 exhibited 87+/- 2 percent 24-hour (51)Cr in vivo recovery and 0.4+/- 0.2 percent hemolysis. CONCLUSIONS: It is possible to store RBCs for 8 weeks in buffered conventional volume ASs. Combining buffering and increased AS volume improves stored RBC characteristics further.

Blood Preservation↗

PubMed1991

Effect of repeated sampling and prestimulation on saliva buffer capacity and flow rate values in children.

Great variations reported in the frequency distribution of buffer capacity values may partly be due to methodological differences in saliva sampling. In this study we wanted to see to what extent these variations are due to repetition and prestimulation. 9-yr-old schoolchildren (n: 41, 23 girls and 18 boys), who had never had saliva samples taken before, participated in the present study. The repetition tests were carried out between 9 and 11 a.m. on three subsequent days. The effect of prestimulation was tested 4 days later with the same subjects. The buffer capacity of the samples was determined electrometrically immediately after sampling using the commercial Dentobuff-test. The intraindividual analysis revealed a significant increase in flow rate but not in buffer capacity along with repetition of the sampling. The analysis further showed that the buffer capacity of children accustomed to saliva sampling increased significantly through prestimulation of 1 min. The use of prestimulation resulted in substantial changes also in the frequency distribution of the buffer capacity values. Our results emphasize the importance of proper sampling conditions in saliva collection when screening children for high caries risk.

Buffers↗

PubMed1983

Comparison of portal vein responsiveness in Tris, HEPES or bicarbonate-phosphate buffered media.

The effects of using Tris or HEPES buffered solutions instead of bicarbonate-phosphate buffered solution on the spontaneous activity of the rat portal vein were studied. The effect of the solution buffered with Tris on the spontaneous contractile activity was a minor change in amplitude and frequency, increasing the integrated isometric force by about 20%. A small increase in the mechanical response to variations in [Ca2+]0 (1.0-2.5 mM) was also observed. The response to field stimulation of intramural nerves was significantly lowered in Tris but the response to exogenous noradrenaline was not affected. HEPES buffer does not significantly affect the spontaneous activity, the concentration-effect curve for Ca2+, the response to field stimulation or to exogenous noradrenaline. Transient changes in the spontaneous activity and the resting membrane potential were observed when the solution was changed from Krebs to Tris (or HEPES) solution or vice versa. These changes disappear if the Tris or HEPES solutions were aerated with 4% CO2 in O2 (at pH 7.4) instead of pure O2. A small change in extracellular pH (+/- 0.2 pH units) significantly affects the spontaneous activity. A change in pH may be the reason for the observed effects in the different buffer media.

Animals↗

PubMed1981

The stability of trifluorothymidine: hydrolysis in buffered aqueous solutions.

The decomposition of trifluorothymidine in aqueous solution, and borate and phosphate buffers has been studied using an h.p.l.c. method. In aqueous solution accelerated studies demonstrate that a storage life, to 10% loss, of more than 30 years at 4 degrees C is predicted, but steam sterilization causes extensive breakdown. Considerable differences occur in the kinetics and routes of decomposition in borate and phosphate buffers in the pH range 4-8. Hydroxide ion attack producing 5-carboxy-2'-deoxyuridine is suppressed in borate buffers. Complex kinetics of decomposition in phosphate buffer are found and possible explanations suggested. Steam sterilization in buffered solution also leads to unacceptable breakdown.

Borates↗

PubMed1988

Buffer and pH effects on propranolol binding by human albumin and alpha 1-acid glycoprotein.

Propranolol binding to isolated human alpha-1-acid glycoprotein (AGP) and human albumin (HSA) was studied by equilibrium dialysis at 37 degrees C. With AGP (0.067%) and HSA (4%), total propranolol concentration was varied from 0.7 to 93,000 ng mL-1. Over this concentration range the percentage drug bound to HSA declined from 49 to 39% while that to AGP declined from 68 to 4%. Two classes of sites were identified on AGP with n1k1 = 8.50 X 10(4) M-1 and n2k2 = 3.12 X 10(4) M-1. With a pH 7.4 phosphate buffer, propranolol binding to AGP was greatest when the protein was initially dissolved in pH 7.4 water compared with pH 7.2 water or the phosphate buffer. Thus, the method of AGP solution preparation affected propranolol binding by this protein. For both AGP and HSA, greater drug binding was noted with phosphate buffers in comparison with a physiological buffer. With phosphate buffers, decreasing pH from 7.4 to 7.0 decreased propranolol binding by AGP, while decreasing pH from 7.7 to 7.4 had little effect. With HSA, the percent propranolol bound consistently decreased on lowering pH from 7.7 to 7.0.

Buffers↗

PubMed1996

On the role of bicarbonate as a hydrogen ion buffer in rat CNS neurones.

The role of bicarbonate as a hydrogen ion buffer has been investigated using the fluorescent dye BCECF in individual rat cerebellar, hippocampal and neocortical neurones maintained in culture. The steady-state intracellular pH (pHi) was estimated to be 7.07 +/- 0.05 (n = 22) in CO2-HCO3(-)-buffered media. Buffering power (beta) estimated from the addition and removal of weak bases was ca 10 mM (pH unit)-1 and was found to be similar in both CO2-HCO3(-)- and Hepes-buffered media. The membrane-permeant carbonic anhydrase inhibitor, acetazolamide (10-20 microM), did not affect estimates of beta. The results indicate that CO2-HCO3- does not act as an open buffer system in these neurones.

Acetazolamide↗

PubMed1976

The effect of carbon dioxide on the intracellular pH and buffering power of snail neurones.

1. Intracellular pH (pHi) was measured using pH-sensitive glass micro-electrodes. The effects on pHi of CO2 applied externally and HCO3-, H+ and NH4+ injected iontophoretically, were investigated. 2. The transport numbers for iontophoretic injection into aqueous micro-droples were found by potentiometric titration to be 0-3 for HCO3- and 0-94 for H+. 3. Exposure to Ringer, pH 7-5, equilibrated with 2-2% CO2 caused a rapid, but only transient, fall in pHi. Within 1 or 2 min pHi began to return exponentially to normal, with a time constant of about 5 min. 4. When external CO2 was removed, pHi rapidly increased, and then slowly returned to normal. The pHi changes with CO2 application or removal gave a calculated intracellular buffer value of about 30 m-equiv H+/pH unit per litre. 5. Injection of HCO3- caused a rise in pHi very similar to that seen on removal of external CO2. 6. The pHi responses to CO2 application, CO2 removal and HCO3- injection were slowed by the carbonic anhydrase inhibitor acetazolamide. 7. H+ injection caused a transient fall in pHi. In CO2 Ringer pHi fell less and recovered faster than in CO2-free Ringer. Calculation of the internal buffer value from the pHi responses to H+ and HCO3- injection gave very similar values. 8. The internal buffer value (measured by H+ injection) was greatly increased by exposure to CO2 Ringer. Acetazolamide reduced this effect of CO2, suggesting that the function of intracellular carbonic anhydrase may be to maximize the internal buffering power in CO2. 9. It was concluded that the internal HCO3- was determined primarily by the CO2 level and pHi, that internal HCO3- made a large contribution to the buffering power, and that after internal acidfication pHi was restored to normal by active transport of H+, OH- or HCO3- across the cell membrane. The active transport was much faster in CO2 than in CO2-free Ringer.

Acetazolamide↗

PubMed1973

Fish viruses: buffers and methods for plaquing eight agents under normal atmosphere.

A universal procedure was sought for plaque assay of eight fish viruses (bluegill myxovirus, channel catfish virus, eel virus, Egtved virus, infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus, lymphocystis virus, and the agent of spring viremia of carp (Rhabdovirus carpio), in dish cultures of various fish cells. Eagle minimal essential medium with sodium bicarbonate-CO(2) buffer (Earle's salt solution) was compared with minimal essential medium buffered principally with tris (hydroxymethyl)aminomethane or N-2-hydroxyethylpiperazine-N'-2'-ethanesulfonic acid at a pH or in the range of 7.6 to 8.0 depending upon temperature. Five fish cell lines collectively capable of replicating all fish viruses thus far isolated were tested and quantitatively found to grow comparably well in the three media. Two-phase (gel-liquid) media incorporating the various buffer systems allowed plaquing at 15 to 33 C either in partial pressures of CO(2) or in normal atmosphere, but greater efficiency and sensitivity were obtained with the organic buffers, and, overall, the best results were obtained with tris(hydroxymethyl)aminomethane. Epizootiological data, specific fish cell line response, and plaque morphology permit presumptive identification of most of the agents. At proper pH, use of organic buffers obviates the need for CO(2) incubators.

Air↗

PubMed1977

Cell envelope of Neisseria gonorrhoeae: relationship between autolysis in buffer and the hydrolysis of peptidoglycan.

Neisseria gonorrhoeae readily underwent autolysis when suspended in N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) buffer at alkaline pH values. Autolysis was inhibited by the addition of Mg2+ or other divalent cations. Autolysis was also suppressed at acid pH (pH 6.0). Suspension of cells in buffer was accompanied by the hydrolysis of peptidoglycan. The rate of peptidoglycan hydrolysis in HEPES buffer was maximal at pH 8.5 and was similar in the presence or absence of Mg2+. Therefore, divalent cation stabilization against autolysis is not mediated by inhibition of peptidoglycan hydrolysis. Peptidoglycan hydrolysis occurred in HEPES buffer (pH 6.0), but at a rate that was 50% of the maximum. Incubation of cells with chloramphenicol or rifampin before suspension in HEPES buffer (pH 8.5) partially prevented autolysis; under these conditions, peptidoglycan hydrolysis still occurred, but at a reduced rate. Old and new peptidoglycans were hydrolyzed at similar rates. Peptidoglycan hydrolysis results in solubilization of both the peptide and glycan moieties.

Buffers↗

PubMed1981

Changes in potential difference across the human buccal mucosa with buffered or unbuffered aspirin and salicylate.

The potential difference (PD) across the gastric mucosa is an index of mucosal integrity, and is lowered by topical application of irritants such as aspirin. There are basic similarities in the PD across the buccal and gastric mucosae, and we have therefore investigated the actions of various salicylates in buffered or un-buffered solution on buccal PD in human subjects. Aspirin (at pH 2) and soluble aspirin (pH 4.4) applied topically reduced buccal PD, but this fall was abolished by buffering to pH 7. Sodium salicylate likewise reduced buccal PD at pH 4 and pH 6, but not when buffered to pH 7. Two other soluble aspirin mixtures also reduced buccal PD, indicating insufficient buffering capacity to prevent topical irritancy. Ingestion of aspirin (600 mg), avoiding topical contact with the buccal mucosa, did not alter buccal PD. Paracetamol applied topically likewise failed to reduce buccal PD. Measurement of buccal PD may be useful in the preliminary assessment of the gastrointestinal irritation provoked by anti-inflammatory and other compounds.

Acetaminophen↗

PubMed2004

Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR.

BACKGROUND: The isolation of good quality DNA from routinely fixed and processed biopsy samples is crucial for the success of subsequent molecular analysis. AIMS: To compare the amount of beta actin DNA extracted from upper gastrointestinal tract biopsies fixed in buffered and unbuffered formalin. METHODS: Amounts of beta actin DNA extracted from forceps biopsies of the upper gastrointestinal tract fixed in unbuffered (n = 22) and buffered formalin (n = 16) were estimated by quantitative real-time polymerase chain reaction. RESULTS: The yield of beta actin DNA was significantly higher in biopsies fixed in buffered formalin than in those fixed in unbuffered formalin (median 2.8 x 10(4) and 5.3 x 10(2) DNA molecules, respectively; p < 0.005). Furthermore, fixation in buffered formalin led to a more reproducible DNA extraction, as indicated by the coefficient of variation (1.0 and 2.2, respectively). CONCLUSIONS: This study indicates that tissue samples should be fixed in buffered formalin to facilitate the use of molecular pathology analysis in routine biopsy material.

Actins↗

PubMed1991

Cardiac hypothermia: 31P and 1H NMR spectroscopic studies of the effect of buffer on preservation of human heart atrial appendages.

31P and 1H nuclear magnetic resonance spectroscopy has been used to follow noninvasively the time course of energetic metabolite levels in human heart atrial appendages preserved under various temperatures and buffer conditions. From sample harvest up to the normal 5-h time limit for heart preservation, ATP levels in human atrial appendages are much better maintained in 0.9% saline and PIPES-buffered preservation solutions at 12 degrees C than at 4 degrees C. Furthermore, preservation at 12 degrees C can be improved considerably by using high extracellular buffer concentrations. The increased buffer concentration allows better maintenance of the intracellular pH and leads to a faster glycolytic rate as measured by lactate production. At 4 degrees C, ATP levels decline rapidly during the first 5 h but reached a stable plateau, which is well maintained over 15-20 h. At this temperature, the rate of lactate production is similar at all buffer concentrations (20, 60, and 100 mM PIPES). As a consequence of these observations, we postulate that the mechanisms of ATP production and utilization at 4 degrees C and at 12 degrees C are different. At 4 degrees C, the rate of glycolysis is temperature limited whereas at 12 degrees C, low intracellular pH inhibits glycolysis.

Adenosine Triphosphate↗