Assay Buffer Research Articles

Identification of Genes Preferentially Expressed in Stomatal Guard Cells of Arabidopsis thaliana and Involvement of the Aluminum-Activated Malate Transporter 6 Vacuolar Malate Channel in Stomatal Opening.

Stomatal guard cells (GCs) are highly specialized cells that respond to various stimuli, such as blue light (BL) and abscisic acid, for the regulation of stomatal aperture. Many signaling components that are involved in the stomatal movement are preferentially expressed in GCs. In this study, we identified four new such genes in addition to an aluminum-activated malate transporter, ALMT6, and GDSL lipase, Occlusion of Stomatal Pore 1 (OSP1), based on the expression analysis using public resources, reverse transcription PCR, and promoter-driven β-glucuronidase assays. Some null mutants of GC-specific genes evidenced altered stomatal movement. We further investigated the role played by ALMT6, a vacuolar malate channel, in stomatal opening. Epidermal strips from an ALMT6-null mutant exhibited defective stomatal opening induced by BL and fusicoccin, a strong plasma membrane H+-ATPase activator. The deficiency was enhanced when the assay buffer [Cl–] was low, suggesting that malate and/or Cl– facilitate efficient opening. The results indicate that the GC-specific genes are frequently involved in stomatal movement. Further detailed analyses of the hitherto uncharacterized GC-specific genes will provide new insights into stomatal regulation.

Isolation, Purify and Characterization of Lectin from the Seeds of Artocarpus Species

Aim: To isolate, partially purify and characterize lectin from the seeds of Artocarpus species - using ammonium sulphate, gel-filtration and ion exchange chromatography. 
 Methodology: ABO blood groups were screened for the assay of hemagglutinating property with seed lectins of both. heterophyllus and A. hirsutus. The seed lectins were extracted using suitable buffer system pH 7.0 and partially purified by gel filtration and ion exchange chromatographic techniques.
 Results and Discussion: Lectins were extracted from the defatted seed powders of A. heterophyllus and A. hirsutus. The extracts were used for optimization of assay buffer for hemagglutination activity and 50 mM Tris-HCl buffer, pH 8.8 containing 1 mM CaCl2 and 1 mM MnCl2 showed greater hemagglutinating property. Screening for optimum concentration of RBCs from different blood group (A, B, AB and O groups) indicated O group at 10 % concentration as ideal for the assay of hemagglutinating property with seed lectins of both A. heterophyllus and A. hirsutus.
 Conclusion: In this study, lectin from the seeds of Artocarpus heterophyllus and Artocarpus hirsutus were isolated and partially purified. The isolated lectins were characterized for their heamagglutination activity. Among the human blood types (A+, B+, AB+ and O+) used, all the blood groups showed agglutination while greater agglutination was observed with O+ blood group.

Analyzing the causes of method-to-method variability among Rubisco kinetic traits: from the first to the current measurements.

Due to the importance of Rubisco in the biosphere, its kinetic parameters have been measured by different methodologies in a large number of studies over the last 60 years. These parameters are essential to characterize the natural diversity in the catalytic properties of the enzyme and they are also required for photosynthesis and cross-scale crop modeling. The present compilation of Rubisco kinetic parameters in model species revealed a wide intraspecific laboratory-to-laboratory variability, which was partially solved by making corrections to account for differences in the assay buffer composition and in the acidity constant of dissolved CO2, as well as for differences in the CO2 and O2 solubilities. Part of the intraspecific variability was also related to the different analytical methodologies used. For instance, significant differences were found between the two main methods for the determination of the specificity factor (Sc/o), and also between Rubisco quantification methods, Rubisco purification versus crude extracts, and single-point versus CO2 curve measurements for the carboxylation turnover rate (kcatc) determination. Causes of the intraspecific laboratory-to-laboratory variability for Rubisco catalytic traits are discussed. This study provides a normalized kinetic dataset for model species to be used by the scientific community. Corrections and recommendations are also provided to reduce measurement variability, allowing the comparison of kinetic data obtained in different laboratories using different assay conditions.

Development of ELISA formats for polymyxin B monitoring in serum of critically ill patients

Treating infections in critically ill patients often requires the use of last-line antibacterial drugs such as polymyxins with a narrow therapeutic window and high toxicity. In critically ill patients, the drug pharmacokinetics changes significantly, and as a result, the antibiotic concentrations in blood and infection foci become suboptimal, which leads to therapeutic failures or toxic manifestations. For timely dosage adjustments, a competitive ELISA-based method using antibodies to polymyxin В (PMB) was developed. Among the several considered assays, a direct antibody-coated format was selected for its short duration (1.5 h) and the best agreement with the LC–MS/MS data (R2 = 98 %). The assay dynamic measurement range (IC20-IC80) could be substantially shifted by changing the ratio of immunoreagents. To conveniently measure the therapeutic range of PMB concentrations, it was adjusted to 5.0–192 ng/mL, allowing the samples to be analyzed after a simple 100-fold dilution with the assay buffer. The ELISA sensitivity expressed in half-inhibition concentration (IC50) and the limit of detection were 30.6 and 1.8 ng/mL, respectively. The assay cross-reactivity towards the related analogue colistin (COL) was 95 %, and this compound could also be adequately quantified by the same assay. The PMB and COL recovery from the spiked serum samples was similar and constituted 98–109 %. The trial drug monitoring was carried out in 3 patients with Gram-negative sepsis, and the established pharmacokinetic profiles of PMB revealed the necessity for individual dosage adjustment.

Vanillin Activates Human Bitter Taste Receptors TAS2R14, TAS2R20, and TAS2R39.

Vanilla is widely used in food preparation worldwide for its sensory properties, mainly related to its fragrance, being vanillin the major compound present in the processed vanilla. Vanillin is also known to elicit bitterness as a secondary sensory sensation, but the molecular mechanism of its bitterness has never been reported. Assay buffers of vanillin were tested in vitro on all known 25 human bitter taste receptors TAS2Rs. Three receptors, TAS2R14, TAS2R20, and TAS2R39, were activated, showing that these receptors are mediating the bitterness of vanillin. The result could be useful to improve the overall sensory profile of this broadly used food ingredient, but even more could represent the starting point for further studies to investigate the potential of vanillin in sensory nutrition and other pharmaceutical applications.

Lamellar Enzyme-Metal–Organic Framework Composites Enable Catalysis on Large Substrates

Lamellar Enzyme-Metal–Organic Framework Composites Enable Catalysis on Large Substrates

Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii.

Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and sequence‐related to other ATP‐dependent enzymes involved in lactam hydrolysis, like 5‐oxoprolinases and hydantoinases. Low sequence similarity also exists with ATP‐dependent acetone‐ and acetophenone carboxylases. The caprolactamase was produced in Escherichia coli, isolated by His‐tag affinity chromatography, and subjected to functional and structural studies. Activity toward caprolactam required ATP and was dependent on the presence of bicarbonate in the assay buffer. The hydrolysis product was identified as 6‐aminocaproic acid. Quantum mechanical modeling indicated that the hydrolysis of caprolactam was highly disfavored (ΔG0'= 23 kJ/mol), which explained the ATP dependence. A crystal structure showed that the enzyme exists as an (αβ)2 tetramer and revealed an ATP‐binding site in CapA and a Zn‐coordinating site in CapB. Mutations in the ATP‐binding site of CapA (D11A and D295A) significantly reduced product formation. Mutants with substitutions in the metal binding site of CapB (D41A, H99A, D101A, and H124A) were inactive and less thermostable than the wild‐type enzyme. These residues proved to be essential for activity and on basis of the experimental findings we propose possible mechanisms for ATP‐dependent lactam hydrolysis.

Effect of Serum on Electrochemical Detection of Bioassays Having Ag Nanoparticle Labels.

The effect of serum on electrochemical detection of bioassays having silver nanoparticle (AgNP) detection labels was investigated. Both a model assay and an antigen-specific sandwich bioassay for the heart failure marker NT-proBNP were examined. In both cases, the AgNP labels were conjugated to a detection antibody. Electrochemical detection was carried out using a galvanic exchange/anodic stripping voltammetry method in which Au3+ exchanges with AgNP labels. The assays were carried out using a paper-based electrode platform. The bioassays were exposed to different serum conditions prior to and during detection. There are three important outcomes reported in this article. First, both the model- and antigen-specific assays could be formed in undiluted serum with no detectable interferences from the serum components. Second, to achieve the maximum possible electrochemical signal, the highest percentage of serum that can remain in an assay buffer during electrochemical detection is 0.25% when no washing is performed. The assay results are rendered inaccurate when 0.50% or more of serum is present. Third, the factors inhibiting galvanic exchange in serum probably relate to surface adsorption of biomolecules onto the AgNP labels, chelation of Au3+ by serum components, or both. The results reported here provide general guidance for using metal NP labels for electrochemical assays in biofluids.

LncRNA MIR503HG inhibits cell proliferation and promotes apoptosis in TNBC cells via the miR-224-5p/HOXA9 axis

Triple-negative breast cancer (TNBC) is a highly invasive subtype of breast cancer. This study investigated the molecular mechanism and influences of MIR503HG, miR-224-5p, and homeobox A9 (HOXA9) on TNBC cell growth and migration. Dual-luciferase reporter gene and RNA immunoprecipitation were performed to examine the regulation of MIR503HG, miR-224-5p, and HOXA9. Cell proliferation, apoptosis, migration, and invasion were evaluated by colony formation, flow cytometry, and Transwell assays. Finally, nude mice were employed to investigate the influence of MIR503HG on TNBC tumor growth. HOXA9 protein levels were detected by immunohistochemical staining. MIR503HG and HOXA9 expression were reduced in TNBC, while miR-224-5p was increased. Overexpression of MIR503HG or HOXA9 reduced the cell migration ability and proliferation and promoted apoptosis, and knockdown of MIR503HG or overexpression of miR-224-5p exhibited the opposite effects. Furthermore, MIR503HG promoted HOXA9 expression by inhibiting miR-224-5p. Overexpression of miR-224-5p reversed the effects of MIR503HG overexpression on TNBC cells, while overexpression of HOXA9 reversed the effect of MIR503HG knockdown. Additionally, an in vivo study proved that MIR503HG inhibited TNBC tumor growth via the miR-224-5p/HOXA9 axis. MIR503HG inhibited cell proliferation and promoted the apoptosis of TNBC cells via the miR-224-5p/HOXA9 axis, which may function as a novel target for the treatment of TNBC.

Challenges for impedimetric affinity sensors targeting protein detection

The review provides articles discussing big challenges behind successful design of impedimetric biosensors and the way such challenges were/could be addressed for highly sensitive affinity detection of proteins. In particular, the effect of gold etching by chloride ions or by CN − ions (released from the redox probe [Fe(CN) 6 ] 3-/4- ), the effect of ionic strength of the assay buffer; the effect of initial interfacial properties (capacitance) and the effect of the high analyte:bioreceptor ratio on electrochemical impedance spectroscopy–based biosensing are discussed. The review provides also short discussion related to other factors, which can significantly affect operational performance of electrochemical impedance spectroscopy–based biosensing including novel conductive interfaces, small bioreceptors, strategies for improved selectivity (nonbiofouling interfaces) and sensitivity (use of nanoparticles). • The review paper provides a short introduction to electrochemical impedance spectroscopy (EIS). • Three EIS modes of operation are discussed in the review paper. • Novel trends in EIS sensing are provided, as well.

Preliminary Study of Buffer Ratio in Protein Extraction from Placental Cotyledons of Kedah-Kelantan Cattle

Protein extraction is a preliminary step of protein purification which mainly focus on maximization of total protein yield. The heterogeneous properties cause diversification of protein; therefore, there is no absolute protocol in protein extraction. The ratio of buffer gives different protein concentrations in different types of mammalian tissues, and this condition leads to the study of optimization of buffer ratio to obtain a better total protein yield. The objectives of this study were to compare the total protein yield based on three different ratios of buffer used. The phosphate buffer saline (PBS), radioimmunoprecipitation assay (RIPA) buffer, and RIPA buffer with the addition of protease inhibitor (Pi) were used with the ratios of 1:1, 1:3, and 1:5. Fetal cotyledons removed from the placenta have undergone mechanical disruption, incubation, sonication, and centrifugation. The supernatant was retained and quantified with Bradford assay to determine the total protein yield based on the standard curve of bovine serum albumin (BSA). There was a statistically significant different between buffer ratio (p<0.5) in RIPA and RIPA with addition of protease inhibitor buffers. RIPA buffer with the ration of 1:1 gave the best total protein yield (194.880±15.089 mg/g). As a conclusion, there was a significant interaction between buffer types and have greatly enhanced the total protein yield obtained from placental cotyledons of Kedah-Kelantan cattle.

Tryptophan Depletion Modulates Tryptophanyl-tRNA Synthetase-Mediated High-Affinity Tryptophan Uptake into Human Cells.

The novel high-affinity tryptophan (Trp)-selective transport system is present at elevated levels in human interferon-γ (IFN-γ)-treated and indoleamine 2,3-dioxygenase 1 (IDO1)-expressing cells. High-affinity Trp uptake into cells results in extracellular Trp depletion and immune suppression. We have previously shown that both IDO1 and tryptophanyl-tRNA synthetase (TrpRS), whose expression levels are increased by IFN-γ, have a crucial function in high-affinity Trp uptake into human cells. Here, we aimed to elucidate the relationship between TrpRS and IDO1 in high-affinity Trp uptake. We demonstrated that overexpression of IDO1 in HeLa cells drastically enhances high-affinity Trp uptake upon addition of purified TrpRS protein to uptake assay buffer. We also clarified that high-affinity Trp uptake by Trp-starved cells is significantly enhanced by the addition of TrpRS protein to the assay buffer. Moreover, we showed that high-affinity Trp uptake is also markedly elevated by the addition of TrpRS protein to the assay buffer of cells overexpressing another Trp-metabolizing enzyme, tryptophan 2,3-dioxygenase (TDO2). Taken together, we conclude that Trp deficiency is crucial for high-affinity Trp uptake mediated by extracellular TrpRS.

Pharmacokinetics of exogenous GIP(1-42) in C57Bl/6 mice; Extremely rapid degradation but marked variation between available assays

Like other peptide hormones, glucose-dependent insulinotropic polypeptide (GIP) is rapidly cleared from the circulation. Dipeptidyl peptidase-4 (DPP-4) is known to be involved. Information on the overall pharmacokinetics of GIP in rodents is, however, lacking. We investigated the pharmacokinetics of exogenous GIP after intravenous, subcutaneous and intraperitoneal injection with and without DPP-4 inhibition in conscious female C57Bl/6 mice. Secondly, we compared total and intact GIP levels measured by an in-house RIA and commercially available ELISA kits to determine the suitability of these methods for in vivo and in vitro measurements. GIP half-life following intravenous injection amounted to 93 ± 2 s, which was extended to 5 ± 0.6 min by inhibition of DPP-4. Intact GIP levels following subcutaneous and intraperitoneal GIP administration were approximately 15 % of total GIP. The area under the curve of intact GIP (GIP exposure) following GIP injection was significantly increased by DPP-4 inhibition, whereas total GIP levels remained unchanged. We found significant variation between measurements of total, but not intact GIP performed with our in-house RIA and ELISAs in samples obtained after in vivo administration of GIP. Different preanalytical sample preparation (EDTA plasma, heparin plasma, assay buffer and PBS) significantly influenced results for all ELISA kits used. Thus, in experiments involving exogenous GIP(1–42) administration in mice, it is important to consider that this will result in a very low ratio of intact:total peptide but co-administration of a DPP-4 inhibitor greatly elevates this ratio. Furthermore, for comparison of GIP levels, it is essential to maintain uniformity concerning assay methodology and sample preparation.

Potassium Glutamate and Glycine Betaine Induce Self-Assembly of the PCNA and β-Sliding Clamps

Sliding clamps are oligomeric ring-shaped proteins that increase the efficiency of DNA replication. The stability of the Escherichia coli β-clamp, a homodimer, is particularly remarkable. The dissociation equilibrium constant of the β-clamp is of the order of 10 pM in buffers of moderate ionic strength. Coulombic electrostatic interactions have been shown to contribute to this remarkable stability. Increasing NaCl concentration in the assay buffer results in decreased dimer stability and faster subunit dissociation kinetics in a way consistent with simple charge-screening models. Here, we examine non-Coulombic ionic effects on the oligomerization properties of sliding clamps. We determined relative diffusion coefficients of two sliding clamps using fluorescence correlation spectroscopy. Replacing NaCl by KGlu, the primary cytoplasmic salt in E. coli, results in a decrease of the diffusion coefficient of these proteins consistent with the formation of protein assemblies. The UV-vis spectrum of the β-clamp labeled with tetramethylrhodamine shows the characteristic absorption band of dimers of rhodamine when KGlu is present in the buffer. This suggests that KGlu induces the formation of assemblies that involve two or more rings stacked face-to-face. Results can be quantitatively explained on the basis of unfavorable interactions between KGlu and the functional groups on the protein surface, which drive biomolecular processes that bury exposed surface. Similar results were obtained with the Saccharomyces cerevisiae PCNA sliding clamp, suggesting that KGlu effects are not specific to the β-clamp. Clamp association is also promoted by glycine betaine, a zwitterionic compound that accumulates intracellularly when E. coli is exposed to high concentrations of extracellular solute. Possible biological implications are discussed.

Protein discrimination based on DNA induced perylene probe self-assembly

The development of a simple and effective method for the highly sensitive and selective discrimination of proteins is a subject of enormous interest. Herein, we report the construction of a novel fluorescence detection method based on a perylene probe for the highly efficient discrimination of multiple proteins. Single-stranded DNA (ssDNA) could induce aggregation of the perylene probe which caused quenching of probe fluorescence. After the addition of a protein, the protein could interact with the ssDNA-probe assembly complex with “turn-on” or further “turn-off” fluorescence response. A sensor array was designed based on the above phenomena which could realize the successful discrimination of proteins with 100% accuracy of cross validation. Nine representative proteins were successfully recognized. Moreover, it was observed that a protein could induce characteristic effect on the DNA-probe assembly with varying pH of assay buffer. Thus, different proteins showed unique fluorescence response towards assay buffers having different pH values. The assay buffer pH was then utilized as a sensing channel. Based on Linear Discriminant Analysis (LDA) nine proteins were successfully discriminated at the nanomolar concentration with 100% accuracy of cross validation. Furthermore, the sensor array also demonstrated differentiation of the nine proteins regardless of their concentration. The developed sensor array could also detect the proteins with great precision in human urine sample at a quite low concentration, which suggests its practical applicability for analysis of biological fluids.

Trophoblast Stem-Cell-Derived Exosomes Improve Doxorubicin-Induced Dilated Cardiomyopathy by Modulating the let-7i/YAP Pathway

Trophoblast stem cells (TSCs) have been confirmed to play a cardioprotective role in heart failure. However, whether TSC-derived exosomes (TSC-exos) can protect against cardiac injury remains unclear. In the present study, TSC-exos were isolated from the supernatant of TSCs using the ultracentrifugation method and characterized by transmission electron microscopy and western blotting. Utilizing the public Gene Expression Omnibus (GEO) database, we found that let-7i and Yes-associated protein 1 (YAP) could participate in the development of heart failure. In vitro, AC16 cardiomyocytes subjected to doxorubicin (DOX) were treated with TSC-exos or let-7i mimic. Flow cytometry showed that TSC-exos and let-7i both decreased cardiomyocyte apoptosis. In vivo, mice that were intraperitoneally injected into DOX received either PBS, TSC-exos, or AAV9-let7iup for let-7i overexpression. Mice receiving TSC-exos and AAV9-let7iup showed improved cardiac function and decreased inflammatory responses, accompanied by downregulated YAP signaling. Mechanistically, TSC-exos could transfer let-7i to cardiomyocytes and silence the YAP signaling pathway. In conclusion, TSC-exos could alleviate DOX-induced cardiac injury via the let-7i/YAP pathway, which sheds new light on the application of TSC-exos as a potential therapeutic tool for heart failure.

Angiotensin-converting Enzyme 2–containing Small Extracellular Vesicles and Exomeres Bind the Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein

Angiotensin-converting Enzyme 2–containing Small Extracellular Vesicles and Exomeres Bind the Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein

Ex vivo delivery of Mirococept: A dose-finding study in pig kidney after showing a low dose is insufficient to reduce delayed graft function in human kidney.

The complement system plays a pivotal role in the pathogenesis of ischemia-reperfusion injury in solid organ transplantation. Mirococept is a potent membrane-localizing complement inhibitor that can be administered ex vivo to the donor kidney prior to transplantation. To evaluate the efficacy of Mirococept in reducing delayed graft function (DGF) in deceased donor renal transplantation, we undertook the efficacy of mirococept (APT070) for preventing ischaemia-reperfusion injury in the kidney allograft (EMPIRIKAL) trial (ISRCTN49958194). A dose range of 5-25mg would be tested, starting with 10mg in cohort 1. No significant difference between Mirococept at 10mg and control was detected; hence the study was stopped to enable a further dose saturation study in a porcine kidney model. The optimal dose of Mirococept in pig kidney was 80mg. This dose did not induce any additional histological damage compared to controls or after a subsequent 3hours of normothermic machine perfusion. The amount of unbound Mirococept postperfusion was found to be within the systemic dose range considered safe in the Phase I trial. The ex vivo administration of Mirococept is a safe and feasible approach to treat DGF in deceased donor kidney transplantation. The porcine kidney study identified an optimal dose of 80mg (equivalent to 120mg in human kidney) that provides a basis for further clinical development.

High-Throughput Amenable MALDI-MS Detection of RNA and DNA with On-Surface Analyte Enrichment Using Fluorous Partitioning.

High-throughput matrix-assisted laser desorption/ionization mass spectrometry (HT-MALDI-MS) has garnered considerable attention within the drug discovery industry as an information-rich alternative to assays using light-based detection methods. To date, these efforts have been primarily focused on assays using protein or peptide substrates. Methods for RNA or DNA analysis by HT-MALDI-MS have not been extensively reported due to the challenges associated with MALDI-MS of oligonucleotides, including the propensity to form multiple salt adducts, low ionization potential, and ease of fragmentation. The objective of this work was to develop a platform suitable for HT-MS analysis of RNA and DNA substrates that overcomes these hurdles by combining on-surface sample preparation with soft ionization. This has been accomplished through the selective immobilization of fluorous-tagged oligonucleotides on a fluorous-modified MS target plate, followed by on-surface enrichment, matrix addition, and direct laser desorption/ionization, a process dubbed fluorous HT-MS (F-HT-MS). The work has resulted in methods by which RNA and DNA substrates can be detected at nanomolar concentrations from a typical assay buffer system using procedures that are amenable to full automation. The protocols were applied to an miRNA biogenesis assay, demonstrating its potential for RNA processes and thereby filling a prominent gap in RNA drug discovery: the paucity of in vitro functional assays.

Resolving the Interactome of the Human Macrophage Immunometabolism Regulator (MACIR) with Enhanced Membrane Protein Preparation and Affinity Proteomics.

Expression of the macrophage immunometabolism regulator gene (MACIR) is associated with severity of autoimmune disease pathology and with the regulation of macrophage biology through unknown mechanisms. The encoded 206 amino acid protein lacks homology to any characterized protein sequence and is a disordered protein according to structure prediction algorithms. To identify interactions of MACIR with proteins from all subcellular compartments, a membrane solubilization buffer is employed, that together with a high affinity EF hand based pull down method, increases the resolution of quantitative mass spectrometry analysis with significant enrichment of interactions from membrane bound nuclear and mitochondrial compartments compared to samples prepared with radioimmunoprecipitation assay buffer. A total of 63 significant interacting proteins are identified and interaction with the nuclear transport receptor TNPO1 and the trafficking proteins UNC119 homolog A and B are validated by immunoprecipitation. Mutational analysis in two candidate nuclear localization signal motifs in the MACIR amino acid sequence shows the interaction with TNPO1 is likely via a non-classical proline/tyrosine-nuclear localization signal motif (aa98-117). It is shown that employing a highly specific and high affinity pull down method that performs efficiently in this glycerol and detergent rich buffer is a powerful approach for the analysis of uncharacterized protein interactomes.