Apparent Dissociation Constant Research Articles

Pharmacological fingerprint of antipsychotic drugs at the serotonin 5-HT2A receptor.

The intricate involvement of the serotonin 5-HT2A receptor (5-HT2AR) both in schizophrenia and in the activity of antipsychotic drugs is widely acknowledged. The currently marketed antipsychotic drugs, although effective in managing the symptoms of schizophrenia to a certain extent, are not without their repertoire of serious side effects. There is a need for better therapeutics to treat schizophrenia for which understanding the mechanism of action of the current antipsychotic drugs is imperative. With bioluminescence resonance energy transfer (BRET) assays, we trace the signaling signature of six antipsychotic drugs belonging to three generations at the 5-HT2AR for the entire spectrum of signaling pathways activated by serotonin (5-HT). The antipsychotic drugs display previously unidentified pathway preference at the level of the individual Gα subunits and β-arrestins. In particular, risperidone, clozapine, olanzapine and haloperidol showed G protein-selective inverse agonist activity. In addition, G protein-selective partial agonism was found for aripiprazole and cariprazine. Pathway-specific apparent dissociation constants determined from functional analyses revealed distinct coupling-modulating capacities of the tested antipsychotics at the different 5-HT-activated pathways. Computational analyses of the pharmacological and structural fingerprints support a mechanistically based clustering that recapitulate the clinical classification (typical/first generation, atypical/second generation, third generation) of the antipsychotic drugs. The study provides a new framework to functionally classify antipsychotics that should represent a useful tool for the identification of better and safer neuropsychiatric drugs and allows formulating hypotheses on the links between specific signaling cascades and in the clinical outcomes of the existing drugs.

Abstract 7141: The novel microtubule-destabilizing compound AUS_001 maintains unique binding to the colchicine site of tubulin and elicits reversible cellular effects relative to other anti-tubulin agents

Abstract Our previous work showed that the prenylated hydroxy-stilbene AUS_001 exerts a strong safety profile and potent anti-proliferative responses, as assessed in 30 types of cancer cell lines, stemming from its microtubule destabilization activity. The aim of the current study was to delineate the molecular mechanism of microtubule destabilization by AUS_001 and to provide insight into its high potency and low toxicity. Surface plasmon resonance (SPR) experiments revealed the direct interaction of AUS_001 with tubulin with an apparent equilibrium dissociation constant, Kd, of 2.13 × 10−5M. Size exclusion competition assays and an X-ray crystal structure of the tubulin-AUS_001 complex at 2.1 Å resolution establish ligand binding within the colchicine site on tubulin. Since colchicine-site ligands are well known to inhibit the curved-to-straight conformational transition of tubulin, which is an essential process for microtubule formation, these results readily explain the microtubule-destabilizing activity of the compound. Notably, while both combretastatin A4 (CA-4) and AUS_001 are both colchicine-site stilbene ligands, CA-4 binds in the cis configuration, while AUS_001 maintains a trans configuration leading to a substantially different pocket engagement. Comparison of the tubulin-AUS_001 complex structure with the ones of tubulin-colchicine and tubulin-plinabulin revealed that AUS_001 elicits different rearrangements in the T7 loop of β-tubulin versus colchicine and occupies a different zone of the pocket relative to plinabulin, further elaborating its unique binding properties. Interestingly, AUS_001 exhibits a higher relative affinity than colchicine itself, as assessed by i) an ultrafiltration-based tubulin-ligand release assay and ii) a radioligand colchicine competition assay. However, fitting steady state SPR data for AUS_001 binding to tubulin revealed fast association and dissociation rates and was indicative of reversible binding. The latter finding is corroborated by AUS_001-triggered reverse biological effects including morphological alterations, cell cycle G2/M arrest, and by a decrease of cell viability upon discontinuation of the drug treatment in glioma and pancreatic cancer cells. Conversely, colchicine, CA-4 or paclitaxel administered at the same doses as those applied for AUS_001 failed to reverse the drug-induced phenotypes upon removal resulting in sustained cytotoxicity. In conclusion, we fully characterized the unique binding mode of AUS_001 to the colchicine site of tubulin and elucidated the reversible nature of the target engagement. AUS_001 features a distinctive and reversible molecular interaction with tubulin which provides a plausible explanation for its favorable safety profile compared to other microtubule targeting agents. Citation Format: Herman Lelie, Yao-Chieh Chou, Alastair J. King, Zlata Boiarska, Andrea E. Prota, Michel O. Steinmetz, Marina Koutsioumpa. The novel microtubule-destabilizing compound AUS_001 maintains unique binding to the colchicine site of tubulin and elicits reversible cellular effects relative to other anti-tubulin agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7141.

Aptamer-Based Multiparameter Analysis for Molecular Profiling of Hematological Malignancies.

The subtypes of hematological malignancies (HM) with minimal molecular profile differences display an extremely heterogeneous clinical course and a discrepant response to certain treatment regimens. Profiling the surface protein markers offers a potent solution for precision diagnosis of HM by differentiating among the subtypes of cancer cells. Herein, we report the use of Cell-SELEX technology to generate a panel of high-affinity aptamer probes that are able to discriminate subtle differences among surface protein profiles between different HM cells. Experimental results show that these aptamers with apparent dissociation constants (Kd) below 10 nM display a unique recognition pattern on different HM subtypes. By combining a machine learning model on the basis of partial least-squares discriminant analysis, 100% accuracy was achieved for the classification of different HM cells. Furthermore, we preliminarily validated the effectiveness of the aptamer-based multiparameter analysis strategy from a clinical perspective by accurately classifying complex clinical samples, thus providing a promising molecular tool for precise HM phenotyping.

The effect of membrane composition on the interaction between human CYP51 and its flavonoid inhibitor - luteolin 7,3′-disulfate

Cytochromes P450 (CYP) are a family of membrane proteins involved in the production of endogenous molecules and the metabolism of xenobiotics. It is well-known that the composition of the membrane can influence the activity and orientation of CYP proteins. However, little is known about how membrane composition affects the ligand binding properties of CYP. In this study, we utilized surface plasmon resonance and fluorescence lifetime analysis to examine the impact of membrane micro-environment composition on the interaction between human microsomal CYP51 (CYP51A1) and its inhibitor, luteolin 7,3′-disulphate (LDS). We observed that membranes containing cholesterol or sphingomyelin exhibited the lowest apparent equilibrium dissociation constant for the CYP51A1-LDS complex. Additionally, the tendency for relation between kinetic parameters of the CYP51A1-LDS complex and membrane viscosity and overall charge was observed. These findings suggest that the specific composition of the membrane, particularly the presence of cholesterol and sphingomyelin, plays a vital role in regulating the interaction between CYP enzymes and their ligands.

In Vitro Methods for the Investigation of sRNA-mRNA Interactions in Bacillus subtilis.

So far, in Bacillus subtilis, only four trans-encoded and 11 cis-encoded sRNAs and their targets have been investigated in detail, the majority of them in our group (rev. in 1, 2). Here, we describe in vitro methods for the analysis of sRNA/mRNA interactions. All these methods have been either elaborated or significantly improved in our group and successfully applied to characterize a number of sRNA/target mRNA systems in Bacillus subtilis for which we provide examples from our own work. The in vitro methods comprise the synthesis and purification of labeled and unlabeled RNA, the analysis of sRNA/mRNA interactions in electrophoretic mobility shift assays (EMSAs) including the calculation of their apparent binding rate constants (kapp) and equilibrium dissociation constants (Kd), the localization of minimal regulatory regions of an sRNA, the determination of the secondary structures of both interacting RNAs and their complex as well as the analysis of RNA chaperones that may promote the sRNA/mRNA interaction.

Interaction studies between human papillomavirus virus-like particles and laminin 332 by affinity capillary electrophoresis assisted by bio-layer interferometry

Human papillomavirus (HPV) interacts, in vitro, with laminin 332 (LN332), a key component of the extracellular matrix. In this study, we performed bio-layer interferometry (BLI) and affinity capillary electrophoresis (ACE) to investigate the binding properties of this interaction. Virus-like particles (VLPs), composed of the HPV16 L1 major capsid protein, were used as HPV model and LN332 as the VLPs binding partner. Using BLI, we quantitatively determined the kinetics of the interaction, via the measurement of VLP binding and release from LN332 immobilized onto the surface of aminopropylsilane biosensors. We found an averaged kon of 1.74 x 104 M−1s−1 and an averaged koff of 1.50 x 10−4 s−1. Furthermore, an ACE method was developed to study the interaction under physiological conditions, where the interactants are moving freely in solution, without any fluorescence labeling. Specifically, a constant amount of HPV16-VLPs was preincubated with increasing LN332 concentrations and then the samples were injected in the capillary electrophoresis instrument. A shift in the migration time of the HPV16-VLP/LN332 complexes, carrying an increasing number of LN332 molecules bound per VLP, was observed. The mobility of the complexes was found to decrease with increasing LN332 concentrations in the sample. It was used to quantify stability constant. From BLI and ACE approaches, we reported an apparent equilibrium dissociation constant in the nanomolar range (8.89 nM and 17.7 nM, respectively) for the complex between HPV16-VLPs and LN332.

C-terminal domain dimerization in yeast Hsp90 is moderately modulated by the other domains

Heat shock protein 90 (Hsp90) serves as a crucial regulator of cellular proteostasis by stabilizing and regulating the activity of numerous substrates, many of which are oncogenic proteins. Therefore, Hsp90 is a drug target for cancer therapy. Hsp90 comprises three structural domains, a highly conserved amino-terminal domain (NTD), a middle domain (MD), and a carboxyl-terminal domain (CTD). The CTD is responsible for protein dimerization, is crucial for Hsp90’s activity, and has therefore been targeted for inhibiting Hsp90. Here we addressed the question of whether the CTD dimerization in Hsp90, in the absence of bound nucleotides, is modulated by allosteric effects from the other domains. We studied full length (FL) and isolated CTD (isoC) yeast Hsp90 spin-labeled with a Gd(III) tag by double electron-electron resonance measurements to track structural differences and to determine the apparent dissociation constant (Kd). We found the distance distributions for both the FL and isoC to be similar, indicating that the removal of the NTD and MD does not significantly affect the structure of the CTD dimer. The low-temperature double electron-electron resonance-derived Kd values, as well as those obtained at room temperature using microscale thermophoresis and native mass spectrometry, collectively suggested the presence of some allosteric effects from the NTDs and MDs on the CTD dimerization stability in the apo state. This was evidenced by a moderate increase in the Kd for the isoC compared with the FL mutants. Our results reveal a fine regulation of the CTD dimerization by allosteric modulation, which may have implications for drug targeting strategies in cancer therapy.

Physiologically based pharmacokinetic model analysis of the inhibitory effect of vonoprazan on the metabolic activation of proguanil

We previously reported that repeated oral administration of vonoprazan (VPZ) followed by oral administration of proguanil (PG) in healthy adults increased blood concentration of PG and decreased blood concentration of its metabolite cycloguanil (CG) compared with administration of PG alone. In this study, we investigated whether this interaction can be quantitatively explained by VPZ inhibition of PG metabolism. In an in vitro study using human liver microsomes, VPZ inhibited CG formation from PG in a concentration-dependent manner, and the inhibition was enhanced depending on preincubation time. Then, a physiologically based pharmacokinetic (PBPK) model analysis was performed incorporating the obtained inhibition parameters. By fitting the blood concentration profiles of VPZ and PG/CG after VPZ and PG were orally administered alone to our PBPK model, parameters were obtained which can reproduce their concentration profiles. In contrast, when the VPZ inhibition parameters for CG formation from the in vitro study were incorporated, the predicted blood PG and CG concentrations were unchanged; the apparent dissociation constant had to be set to about 1/23 of the obtained in vitro value to reproduce the observed interaction. Further comprehensive evaluation is required, including the possibility that mechanisms other than metabolic inhibition may be involved.

Harnessing a 4-Formyl-Aniline Handle to Tune the Stability of a DNA Aptamer-Protein Complex via Fluorescent Surrogates.

Interactions between DNA aptamers and protein targets hold promise for the development of pharmaceuticals and diagnostics. As such, the utilization of fluorescent nucleobase surrogates in studying aptamer-protein interactions is a powerful tool due to their ability to provide site-specific information through turn-on fluorescence. Unfortunately, previously described turn-on probes serving as nucleobase replacements have only been strongly disruptive to the affinity of aptamer-protein interactions. Herein, we present a modified TBA15 aptamer for thrombin containing a fluorescent surrogate that provides site-specific turn-on emission with low nanomolar affinity. The modification, referred to as AnBtz, was substituted at position T3 and provided strong turn-on emission (Irel ≈ 4) and brightness (ε·Φ > 20 000 cm-1 M-1) with an apparent dissociation constant (Kd) of 15 nM to afford a limit of detection (LOD) of 10 nM for thrombin in 20% human serum. The probe was selected through a modular "on-strand" synthesis process that utilized a 4-formyl-aniline (4FA) handle. Using this platform, we were able to enhance the affinity of the final aptamer conjugate by ∼30-fold in comparison with the initial conjugate design. Molecular dynamics simulations provide insight into the structural basis for this phenomenon and highlight the importance of targeting hydrophobic protein binding sites with fluorescent nucleobase surrogates to create new contacts with protein targets.

Preparation of Protein A Membrane Adsorbers Using Strain-Promoted, Copper-Free Dibenzocyclooctyne (DBCO)-Azide Click Chemistry.

Protein A chromatography is the preferred unit operation for purifying Fc-based proteins. Convective chromatography technologies, like membrane adsorbers, can perform the purification rapidly and improve throughput dramatically. While the literature reports the preparation of Protein A membrane adsorbers utilizing traditional coupling chemistries that target lysine or thiol groups on the Protein A ligand, this study demonstrates a new approach utilizing copper-free dibenzocyclooctyne (DBCO)-azide click chemistry. The synthetic pathway consists of three main steps: bioconjugation of Protein A with a DBCO-polyethylene glycol (PEG) linker, preparation of an azide-functionalized membrane surface, and click reaction of DBCO-Protein A onto the membrane surface. Using polyclonal human immunoglobulins (hIgG) as the target molecule, Protein A membranes prepared by this synthetic pathway showed a flowrate-independent dynamic binding capacity of ~10 mg/mL membrane at 10% breakthrough. Fitting of static binding capacity measurements to the Langmuir adsorption isotherm showed a maximum binding (qmax) of 27.48 ± 1.31 mg/mL and an apparent equilibrium dissociation constant (Kd) of value of 1.72 × 10-1 ± 4.03 × 10-2 mg/mL. This work represents a new application for copper-less click chemistry in the membrane chromatography space and outlines a synthetic pathway that can be followed for immobilization of other ligands.

Myrcene: A Natural Compound Showing Anticancer Activity in HeLa Cells.

γ-terpinene, α-terpinene, p-cymene, and myrcene are monoterpenes found in many essential oils extracted from a variety of plants and spices. Myrcene also occurs naturally in plants such as hops, cannabis, lemongrass, and verbena and is used as a flavoring agent in food and beverage manufacturing. In this research, the biological efficacy of γ-terpinene, α-terpinene, p-cymene, and myrcene was studied in human cell lines (HeLa, SH-SY5Y, and HDFa). Cytotoxicity, cell proliferation, cell migration, and morphology assays were performed to obtain detailed information on the anticancer properties. Our results show that myrcene has potential biological activity, especially in HeLa cells. In this cell line, it leads to an arrest of proliferation, a decrease in motility and morphological changes with loss of sphericity and thickness, and DNA damage. In addition, the interaction of γ-terpinene, α-terpinene, p-terpinene, and myrcene with calf thymus DNA (ct-DNA) was studied by UV-visible spectrophotometry. DNA binding experiments show that only myrcene can interact with DNA with an apparent dissociation constant (Kd) of 29 × 10-6 M.

Carbon Nanotube Sensors Enable Visualization of Dopamine Neuromodulation at the Resolution of a Single Chemical Synapse

Among the organs in our body, the brain easily remains the most intriguing in terms of its complexity and function. Nerve cells, which are the functional building blocks of the brain, operate in complex networks that underpin most of the brain’s capabilities, including ability to learn, remember, initiate and orchestrate complex movement. In systems neuroscience, behavioral assays and large-scale neuronal activity recording have broadened our understanding of the role that specific brain regions and neuronal circuits play in a behaving animal. An equally exciting aspect of neuroscience concerns itself with the cellular and molecular underpinnings of nerve cell function. Unique among all the organs, the brain’s constituent cells, neurons, need to communicate with another in intricate networks that are responsible for circuit function, and most of this communication is enabled by chemical cues that are released between neurons. Better understanding of neuronal communication via chemical release from synapses requires technologies that can help us visualize and measure the spatial and temporal dynamics of these chemical signals. Our lab seeks to address this challenge by developing optical biosensors with ultra-low detection capabilities, high spatial resolution and signal-to-noise ratio.To study chemical synapses at high spatial resolution, we use primary dopamine neuron cultures derived from rats and mice as a model system. Dopamine neuron signaling is critical for learning and motor control, and its aberration is implicated in a wide range of neurological and psychiatric disorders. Furthermore, dopamine is a neuromodulator, and it is a neurochemical that is predicted to be highly diffusive in its spatial signaling. Our lab and several others have developed ssDNA functionalized SWCNT optical sensors to study catecholaminergic neurotransmitters, including dopamine. In a recent publication we reported an assay to study dopamine effluxes from primary dopaminergic neurons using a chemi-sensitive 2D substrate (DopaFilm). DopaFilm is fabricated from solution phase SWCNT-sensors in two simple steps: (1) surface functionalization of glass coverslips using silane chemistry to anchor nanosensors (2) drop casting of nanotube sensor solution to create the 2D nanofilm followed by passivation with a thin layer of poly(D-lysine). Primary dopamine neurons plated on DopaFilm are allowed to grow and mature (2 – 6 weeks depending on the experiment). Dopamine release activity can be imaged by recording the NIR emission (900-1400 nm) and at excitation with a 785nm laser. With this technology we were able to faithfully measure dopamine concentrations as low as 1nM with DopaFilm, which has an apparent dissociation constant of 268nM. In 2D cultures, we routinely observed spontaneous and evoked dendritic and axonal DA release events with bouton level spatial resolutions and sub-second temporal resolutions. With signal-to-noise ratios above 50 and comparable on and off-kinetics to latest genetically encoded dopamine sensors (dLight1 and GRABDA), DopaFilm is by far the most sensitive technology to study dopamine chemical signaling with the resolution of a single synapse. The technology allows the study of an entire neuron at the resolution of a single synapse. We combine functional imaging data with pharmacological and genetic perturbations to dissect the role that circuit effects and specific genes (proteins) play in dopamine synthesis, packaging, and release. Additionally, by taking advantage of the NIR emission of SWCNTs, we are able to multiplex dopamine release imaging with Ca2+ activity in orthogonal channels, a feat that is yet to be demonstrated with any competing technology.

Solvatochromic and Acid–Base Molecular Probes in Surfactant Micelles: Comparison of Molecular Dynamics Simulation with the Experiment

This article summarizes a series of seventeen publications by the authors devoted to molecular dynamics modeling of various indicator dyes (molecular probes) enclosed in surfactant micelles. These dyes serve as generally recognized tools for studying various types of organized solutions, among which surfactant micelles in water are the simplest and most explored. The modeling procedure involves altogether 50 to 95 surfactant molecules, 16 to 28 thousand water molecules, and a single dye molecule. The presentation of the simulation results was preceded by a brief review of the state of experimental studies. This article consists of three parts. First, despite numerous literature data devoted to modeling the micelles itself, we decided to revisit this issue. The structure and hydration of the surface of micelles of surfactants, first of all of sodium n-dodecylsulfate, SDS, and cetyltrimethylammonium bromide, CTAB, were studied. The values of the electrical potential, Ψ, were estimated as functions of the ionic strength and distance from the surface. The decrease in the Ψ value with distance is gradual. Attempts to consider both DS− and CTA+ micelles in water without counterions result in a decay into two smaller aggregates. Obviously, the hydrophobic interaction (association) of the hydrocarbon tails balances the repulsion of the charged headgroups of these small “bare” micelles. The second part is devoted to the study of seven pyridinium N-phenolates, known as Reichardt’s dyes, in ionic micelles. These most powerful solvatochromic indicators are now used for examining various colloidal systems. The localization and orientation of both zwitterionic and (colorless) cationic forms are generally consistent with intuitive ideas about the hydrophobicity of substituents. Hydration has been quantitatively described for both the dye molecule as a whole and the oxygen atom. A number of markers, including the visible absorption spectra of Reichardt’s dyes, enable assuming a better hydration of the micellar surface of SDS than that of CTAB. However, our data show that it is more correct to speak about the more pronounced hydrogen-bonding ability of water molecules in anionic micelles than about better hydration of the SDS micelles as compared to CTAB ones. Finally, a set of acid–base indicators firmly fixed in the micellar pseudophase were studied by molecular dynamics. They are instruments for estimating electrostatic potentials of micelles and related aggregates as Ψ= 2.303RTF−1 (pKai − pKaapp), where pKai and pKaapp are indices of so-called intrinsic and apparent dissociation constants. In this case, in addition to the location, orientation, and hydration, the differences between values of pKaapp and indices of the dissociation constants in water were estimated. Only a semi-quantitative agreement with the experimental data was obtained. However, the differences between pKaapp of a given indicator in two micellar solutions do much better agree with the experimental data. Accordingly, the experimental Ψ values of ionic micelles, as determined using the pKaapp in nonionic micelles as pKai, are reproduced with reasonable accuracy for the corresponding indicator. However, following the experimental data, a scatter of the Ψ values obtained with different indicators for given micelles is observed. This problem may be the subject of further research.

Time-Resolved Fluorescence Spectroscopy of Molecularly Imprinted Nanoprobes as an Ultralow Detection Nanosensing Tool for Protein Contaminants.

Currently, optical sensors based on molecularly imprinted polymers (MIPs) have been attracting significant interest. MIP sensing relies on the combination of the MIP's selective capability, which is conveyed to the polymeric material by a template-assisted synthesis, with optical techniques that offer exquisite sensitivity. In this work, we devised an MIP nanoparticle optical sensor for the ultralow detection of serum albumin through time-resolved fluorescence spectroscopy. The Fluo-nanoMIPs (∅~120 nm) were synthetized using fluorescein-O-methacrylate (0.1×, 1×, 10× mol:mol versus template) as an organic fluorescent reporter. The ability of 0.1× and 1×Fluo-nanoMIPs to bind albumin (15 fM-150 nM) was confirmed by fluorescence intensity analyses and isothermal titration calorimetry. The apparent dissociation constant (Kapp) was 30 pM. Conversely, the 10× fluorophore content did not enable monitoring binding. Then, the time-resolved fluorescence spectroscopy of the nanosensors was studied. The 1×Fluo-nanoMIPs showed a decrease in fluorescence lifetime upon binding to albumin (100 fM-150 nM), Kapp = 28 pM, linear dynamic range 3.0-83.5 pM, limit of detection (LOD) 1.26 pM. Selectivity was confirmed testing 1×Fluo-nanoMIPs against competitor proteins. Finally, as a proof of concept, the nanosensors demonstrated detection of the albumin (1.5 nM) spiked in wine samples, suggesting a possible scaling up of the method in monitoring allergens in wines.

Promising Gene Delivery Properties of Polycations Based on 2-(N,N-dimethylamino)ethyl Methacrylate and Polyethylene Glycol Monomethyl Ether Methacrylate Copolymers.

Cationic copolymers based on 2-(N,N-dimethylamino)ethyl methacrylate and polyethylene glycol monomethyl ether (pDMAEMA-co-PEO) with different molecular weights have been synthesized. Their physicochemical properties were studied by NMR spectroscopy, sedimentation, and potentiometric titration. According to the data of potentiometric titration for the synthesized pegylated cationic copolymers, the apparent dissociation constants were determined in the pH range from 4.5 to 8.5. The physicochemical properties of interpolyelectrolyte complexes of these polycations with circular DNA (IPEC DNA) were also studied by dynamic light scattering, electrophoretic mobility, and TEM methods. It has been established that the diameter and electrokinetic potential (ζ-potential) of interpolyelectrolyte complexes can be varied over a wide range (from 200 nm to 1.5 μm and from -25 mV to +30 mV) by changing the ratio of oppositely charged ionizable groups in pegylated cationic copolymers and DNA, as well as by regulating medium pH. The resistance of the IPEC DNA/polycation complex to the action of nucleases was studied by electrophoresis in agarose gel; the cytotoxic effect of the polymers in vitro, and the efficiency of penetration (transfection) of IPEC DNA with PDMAEMA-co-PEO-polycations into eukaryotic cells of a cell line derived from human embryonic kidneys HEK 293 in vitro.

DNA aptamers selection and characterization for development of impedimetric aptasensor for Bacillus cereus at different growing stages

The physiology (membrane integrity, intracellular esterase and redox activity) of individual pathogenic bacteria is various in different growing phase, which has a profound significance for food safety testing and control. In this work, the aptamers against B. cereus in different growing phase was firstly selected based on whole bacterium-SELEX screening approach. Out of 32 candidate aptamers screened, aptamer B15 and B16 showed relatively high binding affinity with an apparent dissociation constant (Kd value) of 16.13 ± 4.98 nM and 20.67 ± 5.23 nM, respectively. A label-free impedance based aptasensor was further fabricated based on the screened aptamer, immobilized onto the GCE/Au surface. With the addition of B. cereus, the electron transfer process was prevented and exhibited a significant decrease in the electron-transfer resistance. Under optimal conditions, the fabricated aptasensor can achieve high sensitive detection of B. cereus as low as 10 cfu/mL. A satisfactory recovery of 90.5%–105.3% was achieved for the B. cereus detection in spiked milk samples, exhibiting its prospect in the sensitive detection of B. cereus in daily life.

TitrationAnalysis: a tool for high throughput binding kinetics data analysis for multiple label-free platforms.

Label-free techniques including Surface Plasmon Resonance (SPR) and Biolayer Interferometry (BLI) are biophysical tools widely used to collect binding kinetics data of bimolecular interactions. To efficiently analyze SPR and BLI binding kinetics data, we have built a new high throughput analysis tool named the TitrationAnalysis. It can be used as a package in the Mathematica scripting environment and ultilize the non-linear curve-fitting module of Mathematica for its core function. This tool can fit the binding time course data and estimate association and dissociation rate constants ( k a and k d respectively) for determining apparent dissociation constant ( K D) values. The high throughput fitting process is automatic, requires minimal knowledge on Mathematica scripting and can be applied to data from multiple label-free platforms. We demonstrate that the TitrationAnalysis is optimal to analyze antibody-antigen binding data acquired on Biacore T200 (SPR), Carterra LSA (SPR imaging) and ForteBio Octet Red384 (BLI) platforms. The k a, k d and K D values derived using TitrationAnalysis very closely matched the results from the commercial analysis software provided specifically for these instruments. Additionally, the TitrationAnalysis tool generates user-directed customizable results output that can be readily used in downstream Data Quality Control associated with Good Clinical Laboratory Practice operations. With the versatility in source of data input source and options of analysis result output, the TitrationAnalysis high throughput analysis tool offers investigators a powerful alternative in biomolecular interaction characterization.

Organic alkalinity dynamics in Irish coastal waters: Case study Rogerstown Estuary

Total alkalinity (TA) is a popularly measured carbonate system parameter and is widely used in calculations of key carbonate system descriptors such as the calcium carbonate saturation state, an important indicator of ocean acidification. Organic alkalinity (OrgAlk) is recognised as a contributor to TA in coastal waters, with this having implications on the use of TA to calculate key carbonate chemistry descriptors. As titratable charge groups of OrgAlk can act as unknown acid-base species, the inclusion of the total concentration and apparent dissociation constants of OrgAlk in carbonate calculations involving TA is required to minimise uncertainty in computed speciation. Here we present an investigation of the prevalence and properties of OrgAlk as well as the impact of OrgAlk on carbonate chemistry calculations in a transitional waterbody. Water samples were collected during low and high tide over a 5-week period in Rogerstown Estuary, Dublin Ireland. TA and OrgAlk were measured using modified Global Ocean Acidification Observing Network (GOA-ON) titration apparatus in conjunction with OrgAlkCalc, an open-source Python based computational programme. pH was measured on the total scale using meta-cresol purple (mCP) as the indicator dye. Dissolved inorganic carbon (DIC), the partial pressure of CO2 (pCO2), in situ pH on the total scale (pHT) and the saturation state of aragonite (∆ΩA) were calculated using pH and both OrgAlk adjusted TA and measured TA as the input parameters. Optical analysis of DOM was conducted to compliment OrgAlk characterisations and to further elucidate OrgAlk sources and dynamics. OrgAlk charge groups concentrations ranged from 35,198 μmol·kg−1, with the highest concentrations observed in more marine waters. Two apparent charge groups were associated with OrgAlk, with pK values of 4.38 ± 0.27 and 6.95 ± 0.43. Differences between calculated carbonate system parameters when using OrgAlk adjusted TA and non-OrgAlk adjusted TA ranged from 88 to 254 μmol·kg−1 DIC, −98–67 μatm pCO2, −0.02–0.12 pHT and 0.02–0.64 ∆ΩA. Variability in the differences in calculated carbonate systems was largely a factor of OrgAlk charge group concentration and pK. This work highlights the importance of considering OrgAlk if using TA as an input parameter in carbonate system investigations of coastal waters.

Establishment of a Novel Anti-CD44 Variant 10 Monoclonal Antibody C44Mab-18 for Immunohistochemical Analysis against Oral Squamous Cell Carcinomas.

Head and neck squamous cell carcinoma (HNSCC) is the most common type of head and neck cancer, and has been revealed as the second-highest expression of CD44 in cancers. CD44 has been investigated as a cancer stem cell marker of HNSCC and plays a critical role in tumor malignant progression. Especially, splicing variant isoforms of CD44 (CD44v) are overexpressed in cancers and considered a promising target for cancer diagnosis and therapy. We developed monoclonal antibodies (mAbs) against CD44 by immunizing mice with CD44v3-10-overexpressed PANC-1 cells. Among the established clones, C44Mab-18 (IgM, kappa) reacted with CHO/CD44v3-10, but not with CHO/CD44s and parental CHO-K1 using flow cytometry. The epitope mapping using peptides that cover variant exon-encoded regions revealed that C44Mab-18 recognized the border sequence between variant 10 and the constant exon 16-encoded sequence. These results suggest that C44Mab-18 recognizes variant 10-containing CD44v, but not CD44s. Furthermore, C44Mab-18 could recognize the human oral squamous cell carcinoma (OSCC) cell line, HSC-3, in flow cytometry. The apparent dissociation constant (KD) of C44Mab-18 for CHO/CD44v3-10 and HSC-3 was 1.6 × 10-7 M and 1.7 × 10-7 M, respectively. Furthermore, C44Mab-18 detected CD44v3-10 but not CHO/CD44s in Western blotting, and endogenous CD44v10 in immunohistochemistry using OSCC tissues. These results indicate that C44Mab-18 is useful for detecting CD44v10 in flow cytometry and immunohistochemistry.

Posttranslational Modification of Human Cytochrome CYP4F11 by 4-Hydroxynonenal Impairs ω-Hydroxylation in Malaria Pigment Hemozoin-Fed Monocytes: The Role in Malaria Immunosuppression.

Malaria is a frequent parasitic infection becomes life threatening due to the disequilibrated immune responses of the host. Avid phagocytosis of malarial pigment hemozoin (HZ) and HZ-containing Plasmodium parasites incapacitates monocyte functions by bioactive lipoperoxidation products 4-hydroxynonenal (4-HNE) and hydroxyeicosatetraenoic acids (HETEs). CYP4F conjugation with 4-HNE is hypothesised to inhibit ω-hydroxylation of 15-HETE, leading to sustained monocyte dysfunction caused by 15-HETE accumulation. A combined immunochemical and mass-spectrometric approach identified 4-HNE-conjugated CYP4F11 in primary human HZ-laden and 4-HNE-treated monocytes. Six distinct 4-HNE-modified amino acid residues were revealed, of which C260 and H261 are localized in the substrate recognition site of CYP4F11. Functional consequences of enzyme modification were investigated on purified human CYP4F11. Palmitic acid, arachidonic acid, 12-HETE, and 15-HETE bound to unconjugated CYP4F11 with apparent dissociation constants of 52, 98, 38, and 73 µM, respectively, while in vitro conjugation with 4-HNE completely blocked substrate binding and enzymatic activity of CYP4F11. Gas chromatographic product profiles confirmed that unmodified CYP4F11 catalysed the ω-hydroxylation while 4-HNE-conjugated CYP4F11 did not. The 15-HETE dose dependently recapitulated the inhibition of the oxidative burst and dendritic cell differentiation by HZ. The inhibition of CYP4F11 by 4-HNE with consequent accumulation of 15-HETE is supposed to be a crucial step in immune suppression in monocytes and immune imbalance in malaria.