Nonlinear least-squares data fitting in Excel spreadsheets

Time-resolved fluorescence of tryptophan characterizes membrane perturbation by cyclic lipopeptides

Viscosin is a membrane-permeabilizing, cyclic lipopeptide (CLiP) produced by Pseudomonas species. Here, we have studied four synthetic analogs (L1W, V4W, L5W, and L7W), each with one leucine (Leu; L) or valine residue exchanged for tryptophan (Trp; W) by means of time-resolved fluorescence spectroscopy of Trp. To this end, we recorded the average fluorescence lifetime, rotational correlation time and limiting anisotropy, dipolar relaxation time and limiting extent of relaxation, rate constant of acrylamide quenching, effect of H2O-D2O exchange, and time-resolved half-width of the spectrum in the absence and presence of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) liposomes. Structure, localization, and hydration of the peptides were described by molecular dynamics simulations. The combination of the parameters provides a good description of the molecular environments of the Trp positions and the behavior of viscosin as a whole. Of particular value for characterizing the impact of viscosin on the membrane is the dipolar relaxation of Trp4 in V4W, which is deeply embedded in the hydrophobic core. The limiting relaxation level represents the membrane perturbation-unlike typical membrane probes-at the site of the perturbant. Fractions of Trp4 relax at different rates; the one not in contact with water upon excitation relaxes via recruitment of a water molecule on the 10-ns timescale. This rate is sensitive to the concerted membrane perturbation by more than one lipopeptide, which appears at high lipopeptide concentration and is assumed a prerequisite for the final formation of a membrane-permeabilizing defect. Trp7 relaxes primarily with respect to neighboring Ser residues. Trp5 flips between a membrane-inserted and surface-exposed orientation.

The Structural Stability of Membrane Proteins Revisited: Combined Thermodynamic and Spectral Phasor Analysis of SDS-induced Denaturation of a Thermophilic Cu(I)-transport ATPase

Assessing membrane protein stability is among the major challenges in protein science due to their inherent complexity, which complicates the application of conventional biophysical tools. In this work, sodium dodecyl sulfate-induced denaturation of AfCopA, a Cu(I)-transport ATPase from Archaeoglobus fulgidus, was explored using a combined model-free spectral phasor analysis and a model-dependent thermodynamic analysis. Decrease in tryptophan and 1-anilino-naphthalene-8-sulfonate fluorescence intensity, displacements in the spectral phasor space, and the loss of ATPase activity were reversibly induced by this detergent. Refolding from the SDS-induced denatured state yields an active enzyme that is functionally and spectroscopically indistinguishable from the native state of the protein. Phasor analysis of Trp spectra allowed us to identify two intermediate states in the SDS-induced denaturation of AfCopA, a result further supported by principal component analysis. In contrast, traditional thermodynamic analysis detected only one intermediate state, and including the second one led to overparameterization. Additionally, ANS fluorescence spectral analysis detected one more intermediate and a gradual change at the level of the hydrophobic transmembrane surface of the protein. Based on this evidence, a model for acquiring the native structure of AfCopA in a membrane-like environment is proposed.

Growth of complete ammonia oxidizers on guanidine

Guanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well known as a protein denaturant in biochemistry1-3. Guanidine occurs widely in nature and is used by several microorganisms as a nitrogen source, but microorganisms growing on guanidine as the only substrate have not yet been identified. Here we show that the complete ammonia oxidizer (comammox) Nitrospira inopinata and probably most other comammox microorganisms can grow on guanidine as the sole source of energy, reductant and nitrogen. Proteomics, enzyme kinetics and the crystal structure of a N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Incubation experiments with comammox-containing agricultural soil and wastewater treatment plant microbiomes suggested that guanidine serves as substrate for nitrification in the environment. The identification of guanidine as a growth substrate for comammox shows an unexpected niche of these globally important nitrifiers and offers opportunities for their isolation.

Assessment of oxygen kinetic parameters for closely related ammonia-oxidizing bacteria

The reaction kinetics of lithotrophic ammonia-oxidizing bacteria (AOB) are strongly dependent on dissolved oxygen (DO) as their metabolism is an aerobic process. In this study, we estimate the kinetic parameters, including the oxygen affinity constant (Km[O2]) and the maximum oxygen consumption rate (Vmax[O2]), of different AOB species, by fitting the data to the Michaelis-Menten equation using nonlinear regression analysis. An example for three different species of Nitrosomonas bacteria (N. europaea, N. eutropha, and N. mobilis) in monoculture is given, finding a Km[O2] of 0.25 ± 0.05 mg l-1, 0.47 ± 0.09 mg l-1, and 0.28 ± 0.08 mg l-1, and a Vmax[O2] of 0.07 ± 0.04 pg h-1cell-1, 0.25 ± 0.06 pg h-1cell-1, and 0.02 ± 0.001 pg h-1cell-1 for N. europaea, N. eutropha, and N. mobilis, respectively. This study shows that of the analyzed AOB, N. europaea has the highest affinity towards oxygen and N. eutropha the lowest affinity towards oxygen, indicating that the former can convert ammonia even under low DO conditions. These results improve the understanding of the ecophysiology of AOB in the environment. The accuracy of mathematically modelled ammonia oxidation can be improved, allowing the implementation of better management practices to restore the nitrogen cycle in natural and engineered water systems.

Ion Mobility-Mass Spectrometry Strategies to Elucidate the Anhydrous Structure of Noncovalent Guest/Host Complexes

Structural mass spectrometry (MS) techniques are fast and sensitive analytical methods to identify noncovalent guest/host complexation phenomena for desirable solution-phase properties. Current MS-based studies on guest/host complexes of drug and drug-like molecules are sparse, and there is limited guidance on how to interpret MS information in the context of host nanoencapsulation and inclusion. Here, we use structural MS strategies, combining energy-resolved MS (ERMS), ion mobility-MS (IM-MS), and computational modeling, to characterize 14 chemically distinct drug and drug-like compounds for their propensity to form guest/host complexes with the widely used excipient, beta-cyclodextrin (βCD). The majority (11/14) yielded a 1:1 guest/host complex, and ion mobility collision cross section (CCS) analysis provided subtle evidence of gas-phase compaction of complexes in both polarities. The three distinct dissociation channels observed in ERMS (i.e., charged βCD, charged guest, and partial guest loss) were used to direct charge-site assignments for computational modeling, and structural candidates were prioritized using helium-derived CCS measurements combined with root-mean-square distance analysis. The combined analytical information from ERMS, IM-MS, and computational modeling suggested that the majority of anhydrous complexes are inclusion complexes with βCD. Taken together, this work demonstrates a roadmap for how multiple MS-based analytical measurements can be combined to interpret the structures that guest/host complexes adopt in the absence of water.

Protocol to identify the ligand binding site of Mincle using NMR spectroscopy

Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor that can be targeted for inducing potent adjuvant effects. Mincle can recognize trehalose dimycolate and related glycolipids. Here, we present a protocol to identify the ligand binding mode of Mincle. We describe steps for preparing labeled Mincle ectodomain, data acquisition, and analysis of nuclear magnetic resonance experiments using non-detergent sulfobetaine-195. This protocol can be applied to other protein-ligand interactions that have aggregation problems for complex formation. For complete details on the use and execution of this protocol, please refer to Furukawa et al.1.

Inhibition profile of three biological nitrification inhibitors and their response to soil pH modification in two contrasting soils

Up to 70% of the nitrogen (N) fertilizer applied to agricultural soils is lost through microbially mediated processes, such as nitrification. This can be counteracted by synthetic and biological compounds that inhibit nitrification. However, for many biological nitrification inhibitors (BNIs), the interaction with soil properties, nitrifier specificity, and effective concentrations are unclear. Here, we investigated three synthetic nitrification inhibitors (SNIs) (DCD, DMPP, and nitrapyrin) and three BNIs [methyl 3(4-hydroxyphenyl) propionate (MHPP), methyl 3(4-hydroxyphenyl) acrylate (MHPA), and limonene] in two agricultural soils differing in pH and nitrifier communities. The efficacies of SNIs and BNIs were resilient to short-term pH changes in the neutral pH soil, whereas the efficacy of some BNIs increased by neutralizing the alkaline soil. Among the BNIs, MHPA showed the highest inhibition and was, together with MHPP, identified as a putative AOB/comammox-selective inhibitor. Additionally, MHPA and limonene effectively inhibited nitrification at concentrations comparable to those used for DCD. Moreover, we identified the effective concentrations at which 50% and 80% of inhibition is observed (EC50 and EC80) for the BNIs, and similar EC80 values were observed in both soils. Overall, our results show that these BNIs could potentially serve as effective alternatives to SNIs currently used.

Transfer of ANS-Like Drugs from Micellar Drug Delivery Systems to Albumin Is Highly Favorable and Protected from Competition with Surfactant by "Reserved" Binding Sites

Micellar drug delivery systems (MDDS) for the intravenous administration of poorly soluble drugs have great advantages over alternative formulations in terms of the safety of their excipients, storage stability, and straightforward production. A classic example is mixed micelles of glycocholate (GC) and lecithin, both endogenous substances in human blood. What limits the use of MDDS is the complexity of the transitions after injection. In particular, as the MDDS disintegrate partially or completely after injection, the drug has to be transferred safely to endogenous carriers in the blood, such as human serum albumin (HSA). If this transfer is compromised, the drug might precipitate─a process that needs to be excluded under all circumstances. The key question of this paper is whether the high local concentration of GC at the moment and site of MDDS dissolution might transiently saturate HSA binding sites and, hence, endanger quick drug transfer. To address this question, we have used a new approach, which is time-resolved fluorescence spectroscopy of the single tryptophan in HSA, Trp-214, to characterize the competitive binding of GC and the drug substitute anilinonaphthalenesulfonate (ANS) to HSA. Time-resolved fluorescence of Trp-214 showed important advantages over established methods for tackling this problem. ANS has been the standard "model drug" to study albumin binding for decades, given its structural similarity to the class of naphthalene-containing acidic drugs and the fact that it is displaced from HSA by numerous drugs (which presumably bind to the same sites). Our complex global fit uses the critical approximation that the average lifetimes behave similarly to a single lifetime, but the resulting errors are found to be moderate and the results provide a convincing explanation of the, at first glance, counterintuitive behavior. Accordingly, and largely in line with the literature, we observed two types of sites binding ANS at HSA: 3 type A, rather peripheral, and 2 type B, likely more central sites. The latter quench Trp-214 by Förster Resonance Energy Transfer (FRET) with a rate constant of ≈0.4 ns-1 per ANS. Adding millimolar concentrations of GC displaces ANS from the A sites but not from B sites. At incomplete ANS saturation, this causes a GC-induced translocation of ANS from A to the more FRET-active B sites. This leads to the apparent paradox that the partial displacement of ANS from HSA increases its quenching effect on Trp-214. The most important conclusion is that (ANS-like) drugs cannot be displaced from the type-B sites, and consequently, drug transfer to these sites is not impaired by competitive binding of GC in the vicinity of a dissolving micelle. The second conclusion is that for unbound GC above the CMC (9 mM), ANS equilibrates between HSA and GC micelles but with a strong preference for free sites on HSA. That means that even persisting micelles would lose their cargo readily once exposed to HSA. For all MDDS sharing this property, targeted drug delivery approaches involving them as the nanocarrier would be pointless.

A millimeter water-in-oil droplet as an alternative back exchange prevention strategy for hydrogen/deuterium exchange mass spectrometry of peptides/proteins

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a versatile bioanalytical technique for protein analysis. Since the reliability of HDX-MS analysis considerably depends on the retention of deuterium labels in the post-labeling workflow, deuterium/hydrogen (D/H) back exchange prevention strategies, including decreasing the pH, temperature, and exposure time to protic sources of the deuterated samples, are widely adopted in the conventional HDX-MS protocol. Herein, an alternative and effective back exchange prevention strategy based on the encapsulation of a millimeter droplet of a labeled peptide solution in a water-immiscible organic solvent (cyclohexane) is proposed. Cyclohexane was used to prevent the undesirable uptake of water by the droplet from the atmospheric vapor through the air-water interface. Using the pepsin digest of deuterated myoglobin, our results show that back exchange kinetics of deuterated peptides is retarded in a millimeter droplet as compared to that in the bulk solution. Performing pepsin digestion directly in a water-in-oil droplet at room temperature (18-21 °C) was found to preserve more deuterium labels than that in the bulk digestion with an ice-water bath. Based on the present findings, it is proposed that keeping deuterated peptides in the form of water-in-oil droplets during the post-labelling workflow will facilitate the preservation of deuterium labels on the peptide backbone and thereby enhance the reliability of the H/D exchange data.

Human mitochondrial glutathione transferases: Kinetic parameters and accommodation of a mitochondria-targeting group in substrates

Glutathione-S-transferases are key to the cellular detoxification of xenobiotics and products of oxidative damage. GSTs catalyse the reaction of glutathione (GSH) with electrophiles to form stable thioether adducts. GSTK1-1 is the main GST isoform in the mitochondrial matrix, but the GSTA1-1 and GSTA4-4 isoforms are also thought to be in the mitochondria with their distribution altering in transformed cells, thus potentially providing a cancer specific target. A mitochondria-targeted version of the GST substrate 1-chloro-2,4-dinitrobenzene (CDNB), MitoCDNB, has been used to manipulate the mitochondrial GSH pool. To finesse this approach to target particular GST isoforms in the context of cancer, here we have determined the kcat/Km for the human isoforms of GSTK1-1, GSTA1-1 and GSTA4-4 with respect to GSH and CDNB. We show how the rate of the GST-catalysed reaction between GSH and CDNB analogues can be modified by both the electron withdrawing substituents, and by the position of the mitochondria-targeting triphenylphosphonium on the chlorobenzene ring to tune the activity of mitochondria-targeted substrates. These findings can now be exploited to selectively disrupt the mitochondrial GSH pools of cancer cells expressing particular GST isoforms.

Effect of Pore Confinement of Ionic Liquids on Solute Diffusion within Mesoporous Silica Microparticles

The transport properties of the ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) confined within silica microparticles with well-ordered, accessible mesopores (5.4 or 9 nm diameter) were investigated. [BMIM][PF6] confinement was confirmed by using differential scanning calorimetry (DSC) and Fourier transform infrared (FTIR) spectroscopy. The transport properties of the confined IL were studied using the neutral and cationic fluorescent probes 4-(dicyanomethylene)-2-methyl-6-(4-dimethylaminostyryl)-4H-pyran (DCM) and rhodamine 6G, respectively, through fluorescence recovery after photobleaching (FRAP) in confocal microscopy. The diffusivity of DCM in 9 nm pores is 0.026 ± 0.0091 μm2/s, which is 2 orders of magnitude less than in the bulk ionic liquid. The pore size did not affect the diffusivity of DCM in unmodified silica nanopores. The diffusivity of the cationic probe is reduced by 63% relative to that of the neutral probe. Diffusivity is increased with water content, where equilibrium hydration of the system leads to a 37% increase in DCM diffusivity. The most dramatic impact on diffusivity was caused by tethering an IL-like methylimidazolium chloride group to the pores, which increased the pore hydrophobicity and resulted in 3-fold higher diffusivity of DCM compared to bare silica pores. Subsequent exchange of the chloride anion from the tethering group with PF6- decreased the diffusivity to half that of bare silica. The diffusion of probe molecules is affected most strongly by the pore wall effects on probe interactions rather than by the pore size itself, which suggests that understanding pore wall diffusion is critical to the design of nanoconfined ILs for separations, catalysis, and energy storage.

Warping Torsion in Sandwich Panels: Analyzing the Structural Behavior through Experimental and Numerical Studies

Recently, there has been a growing interest in the use of sandwich panels that, beyond handling well-known bending stress, can withstand torsional stresses. This is particularly relevant for wall applications when the panels are equipped with photovoltaic or supplemental curtain wall modules. This research article presents a detailed exploration of the structural behavior of eccentrically loaded sandwich panels, with a specific focus on warping torsion. Experimental and numerical studies were conducted on polyisocyanurate (PU) core sandwich panels, commonly employed in building envelopes. These studies involved various dimensions and material properties, while omitting longitudinal joints. The experimental study provided essential insights and validated the numerical model in ANSYS. Enabling parametric variation, the numerical analysis extends the analysis beyond the experimental scope. Results revealed a high degree of correlation between experimental, numerical, and analytical solutions, regarding the rotation, as well as the normal and shear stress of the panel. Confirming the general applicability of warping torsion in sandwich panels with certain limitations, the study contributes valuable data for applications and design of eccentrically loaded sandwich panels, laying the foundation for potential engineering calculation methods.

Quantitative Biochemical Analysis of Deadenylase Enzymes Using Fluorescence and Chemiluminescence-Based Assays

Deadenylase enzymes play a key role in mRNA degradation and RNA processing. In this chapter, we describe two activity assays for the quantitative biochemical analysis of deadenylase enzymes, which can easily be adapted for other nuclease enzymes. The assays use distinct principles of detection, which are based on differential annealing of a probe complementary to the substrate RNA or detection of adenosine monophosphate (AMP). The assays are sensitive, flexible, and can be used in low-throughput tube-based formats and 96-well or 384-well plate formats. The assays rely on plate reader detection and can be carried out using manual pipetting or robotic liquid handling equipment. In addition to two activity assays, we describe differential scanning fluorimetry (thermal shift assay) as a complementary assay that allows the direct characterization of ligand binding to deadenylase enzymes. The assays can be useful for the characterization of deadenylase variants and are particularly suitable for the discovery and development of small-molecule inhibitors of deadenylase enzymes.

Identification and Characterization of Novel Intracellular α-Xylosidase in Aspergillus oryzae

α-Xylosidase releases xylopyranosyl side chains from xyloglucan oligosaccharides and is vital for xyloglucan degradation. Previously, we identified and characterized two α-xylosidases, intracellular AxyA and extracellular AxyB, in Aspergillus oryzae. In this study, we identified a third α-xylosidase, termed AxyC, in A. oryzae. These three A. oryzae α-xylosidases belong to the glycoside hydrolase family 31, but there are clear differences in substrate specificity. Both AxyA and AxyB showed much higher hydrolytic activity toward isoprimeverose (α-D-xylopyranosyl-1,6-glucose) than p-nitrophenyl α-D-xylopyranoside. In contrast, the specific activity of AxyC toward the p-nitrophenyl substrate was approximately 950-fold higher than that toward isoprimeverose. Our study revealed that there are multiple α-xylosidases with different substrate specificities in A. oryzae.

Regression fitting megavoltage depth dose curves to determine material relative electron density in radiotherapy

The relative electron density (RED) parameter is ubiquitous throughout radiotherapy for clinical dosimetry and treatment planning purposes as it provides a more accurate description of the relevant radiological properties over mass density alone. RED is in practice determined indirectly from calibrated CT Hounsfield Units (HU). While CT images provide useful 3D information, the spectral differences between CT and clinical LINAC beams may impact the validity of the CT-ED calibration, especially in the context of novel tissue-mimicking materials where deviations from biologically typical atomic number to atomic weight ratios 〈Z/A〉 occur and/or high-Z materials are present. A theoretical basis for determining material properties directly in a clinical beam spectrum via an electron-density equivalent pathlength (eEPL) method has been previously established. An experimental implementation of this approach is introduced whereby material-specific measured percentage depth dose curves (PDDs) are regressed to a PDD measured in a reference material (water), providing an inference of 〈Z/A〉, which when combined with the physical density provides a determination of RED. This method is validated over a range of tissue-mimicking materials and compared against the standard CT output, as well as compositional information obtained from the manufacturer's specifications. The measured PDD regression method shows consistent results against both manufacturer-provided and CT-derived values between 0.9 and 1.15 RED. Outside of this soft-tissue range a trend was observed whereby the 〈Z/A〉 determined becomes unrealistic indicating the method is no longer reporting RED alone and the assumptions around the eEPL model are constrained. Within the soft-tissue RED range of validity, the regression method provides a practical and robust characterisation for unknown materials in the clinical setting and may be used to improve on the CT derived RED where high Z material components are suspected.

Susceptibility of Cu(I) transport ATPases to sodium dodecyl sulfate. Relevance of the composition of the micellar phase

Sodium dodecyl sulfate (SDS) is a well-known protein denaturing agent. A less known property of this detergent is that it can activate or inactivate some enzymes at sub-denaturing concentrations. In this work we explore the effect of SDS on the ATPase activity of a hyper-thermophilic and a mesophilic Cu(I) ATPases reconstituted in mixed micelles of phospholipids and a non-denaturing detergent. An iterative procedure was used to evaluate the partition of SDS between the aqueous and the micellar phases, allowing to determine the composition of micelles prepared from phospholipid/detergent mixtures. The incubation of enzymes with SDS in the presence of different amounts of phospholipids reveals that higher SDS concentrations are required to obtain the same degree of inactivation when the initial concentration of phospholipids is increased. Remarkably, we found that, if represented as a function of the mole fraction of SDS in the micelle, the degree of inactivation obtained at different amounts of amphiphiles converges to a single inactivation curve. To interpret this result, we propose a simple model involving active and inactive enzyme molecules in equilibrium. This model allowed us to estimate the Gibbs free energy change for the inactivation process and its derivative with respect to the mole fraction of SDS in the micellar phase, the latter being a measure of the susceptibility of the enzyme to SDS. Our results showed that the inactivation free energy changes are similar for both proteins. Conversely, susceptibility to SDS is significantly lower for the hyperthermophilic ATPase, suggesting an inverse relation between thermophilicity and susceptibility to SDS.

Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor

Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.

γ-2 and GSG1L bind with comparable affinities to the tetrameric GluA1 core

BACKGROUND

The AMPA-type ionotropic glutamate receptor mediates fast excitatory neurotransmission in the brain. A variety of auxiliary subunits regulate its gating properties, assembly, and trafficking, but it is unknown if the binding of these auxiliary subunits to the receptor core is dynamically regulated. Here we investigate the interplay of the two auxiliary subunits γ-2 and GSG1L when binding to the AMPA receptor composed of four GluA1 subunits.

METHODS

We use a three-color single-molecule imaging approach in living cells, which allows the direct observation of the receptors and both auxiliary subunits. Colocalization of different colors can be interpreted as interaction of the respective receptor subunits.

RESULTS

Depending on the relative expression levels of γ-2 and GSG1L, the occupancy of binding sites shifts from one auxiliary subunit to the other, supporting the idea that they compete for binding to the receptor. Based on a model where each of the four binding sites at the receptor core can be either occupied by γ-2 or GSG1L, our experiments yield apparent dissociation constants for γ-2 and GSG1L in the range of 2.0-2.5/µm2.

CONCLUSIONS

The result that both binding affinities are in the same range is a prerequisite for dynamic changes of receptor composition under native conditions.

A comprehensive and high-throughput screening method for multiple prohibited substances by UPLC-QE Plus-HRMS and HPLC-QQQ-MS in human urine for doping control

Since the World Anti-Doping Agency's (WADA) Prohibited List is updated on an annual basis, screening methods must be continually adapted to align with these changes. In accordance with Technical Document-MRPL 2022, a newly combined, comprehensive, rapid and high-throughput doping control screening method has been developed for the analysis of 350 substances with different polarities in human urine using ultra-high performance liquid chromatography coupled with Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer (UPLC-QE Plus-HRMS) and ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometer (UPLC-QQQ-MS). The limits of detection were in the range of 0.12-50 ng mL-1 for beta-2 agonists, hormone and metabolic modulators, narcotics, cannabinoids and glucocorticoids, 0.1-14 ng mL-1 for the manipulation of blood and blood components, beta blockers, anabolic agents and hypoxia-inducible factor (HIF) activating agents, and 2.5-100 000 ng mL-1 for substances of Appendix A, diuretics & masking agents and stimulants. The sample preparation consisted of two parts: one is the dilute & shoot part analyzed in UPLC-QQQ-MS, another is a mixture of the dilute & shoot part and a liquid-liquid extraction part of hydrolyzed human urine analyzed in UPLC-QE Plus-HRMS in full scan mode with polarity switching and parallel reaction monitoring (PRM) mode. The method has been fully validated for doping control purposes. All the substances were compliant with WADA's required 1/2 minimum requirement performance level (MRPL) or minimum reporting level (MRL), and this method was successfully used in the 2022 Beijing Winter Olympic Games and Winter Paralympic Games for anti-doping purpose.

Nitrite reductase activity in F420-dependent sulphite reductase (Fsr) from Methanocaldococcus jannaschii

Methanocaldococcus jannaschii (Mj), a hyperthermophilic and evolutionarily deeply rooted methanogenic archaeon from a deep-sea hydrothermal vent, produces F₄₂₀-dependent sulphite reductase (Fsr) in response to exposure to sulphite. This enzyme allows Mj to detoxify sulphite, a potent inhibitor of methyl coenzyme-M reductase (Mcr), by reducing it to sulphide with reduced coenzyme F₄₂₀ (F₄₂₀H₂) as an electron donor; Mcr is essential for energy production for a methanogen. Fsr allows Mj to utilize sulphite as a sulphur source. Nitrite is another potent inhibitor of Mcr and is toxic to methanogens. It is reduced by most sulphite reductases. In this study, we report that MjFsr reduced nitrite to ammonia with F₄₂₀H₂ with physiologically relevant K _m values (nitrite, 8.9 µM; F₄₂₀H₂, 9.7 µM). The enzyme also reduced hydroxylamine with a K _m value of 112.4 µM, indicating that it was an intermediate in the reduction of nitrite to ammonia. These results open the possibility that Mj could use nitrite as a nitrogen source if it is provided at a low concentration of the type that occurs in its habitat.

Optimization of the stability constants of the ternary system of diclofenac/famotidine/β-cyclodextrin by nonlinear least-squares method using theoretical equations

This study aimed to establish a new method for determining the stability constants of drug/β-cyclodextrin (β-CD) complexes when multiple drugs interacting with each other coexist in the solution of complexation. The basic drug famotidine (FAM) and the acidic drug diclofenac (DIC) were used as model drugs, their solubility decreasing owing to their mutual interaction. The dissolution of both FAM and DIC was characterized by A_L-type phase solubility diagrams in the presence of the other's 1:1 complex with β-CD. When the stability constant was calculated from the slope of the phase solubility diagram using the conventional phase solubility diagram method, it was modified in the presence of the other drug. However, by performing optimization calculations that considered the interactions between the drug/β-CD complex and the drug, drug/β-CD complexes, and drugs, we were able to accurately calculate the stability constant of DIC/β-CD and FAM/β-CD complexes even in the presence of FAM and DIC, respectively. The results of the solubility profile indicated that various molecular species, which are attributed to drug-drug and drug/β-CD interactions, interfere with the values of the dissolution rate constants and saturated concentration in the solubility profiles.

Online Fully Automated System for Hydrogen/Deuterium-Exchange Mass Spectrometry with Millisecond Time Resolution

Amide hydrogen/deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for analyzing the conformational dynamics of proteins in a solution. Current conventional methods have a measurement limit starting from several seconds and are solely reliant on the speed of manual pipetting or a liquid handling robot. Weakly protected regions of polypeptides, such as in short peptides, exposed loops and intrinsically disordered the protein exchange on the millisecond timescale. Typical HDX methods often cannot resolve the structural dynamics and stability in these cases. Numerous academic laboratories have demonstrated the considerable utility of acquiring HDX-MS data in the sub-second regimes. Here, we describe the development of a fully automated HDX-MS apparatus to resolve amide exchange on the millisecond timescale. Like conventional systems, this instrument boasts automated sample injection with software selection of labeling times, online flow mixing and quenching, while being fully integrated with a liquid chromatography-MS system for existing standard "bottom-up" workflows. HDX-MS's rapid exchange kinetics of several peptides demonstrate the repeatability, reproducibility, back-exchange, and mixing kinetics achieved with the system. Comparably, peptide coverage of 96.4% with 273 peptides was achieved, supporting the equivalence of the system to standard robotics. Additionally, time windows of 50 ms-300 s allowed full kinetic transitions to be observed for many amide groups; especially important are short time points (50-150 ms) for regions that are likely highly dynamic and solvent- exposed. We demonstrate that information on structural dynamics and stability can be measured for stretches of weakly stable polypeptides in small peptides and in local regions of a large enzyme, glycogen phosphorylase.

Lipid exchange among electroneutral Sulfo-DIBMA nanodiscs is independent of ion concentration

Polymer-encapsulated nanodiscs enable membrane proteins to be investigated within a native-like lipid-bilayer environment. Unlike other bilayer-based membrane mimetics, these nanodiscs are equilibrium structures that permit lipid exchange on experimentally relevant timescales. Therefore, examining the kinetics and mechanisms of lipid exchange is of great interest. Since the high charge densities of existing anionic polymers can interfere with protein-protein and protein-lipid interactions as well as charge-sensitive analysis techniques, electroneutral nanodisc-forming polymers have been recently introduced. However, it has remained unclear how the electroneutrality of these polymers affects the lipid-exchange behavior of the nanodiscs. Here, we use time-resolved Förster resonance energy transfer to study the kinetics and the mechanisms of lipid exchange among nanodiscs formed by the electroneutral polymer Sulfo-DIBMA. We also examine the role of coulombic repulsion and specific counterion association in lipid exchange. Our results show that Sulfo-DIBMA nanodiscs exchange lipids on a similar timescale as DIBMA nanodiscs. In contrast with nanodiscs made from polyanionic DIBMA, however, the presence of mono- and divalent cations does not influence lipid exchange among Sulfo-DIBMA nanodiscs, as expected from their electroneutrality. The robustness of Sulfo-DIBMA nanodiscs against varying ion concentrations opens new possibilities for investigating charge-sensitive processes involving membrane proteins.

Develop a hybrid machine learning model for promoting microbe biomass production

Since the cultivation condition of microbe biomass production (mycelia yield) involves a variety of factors, it's a laborious process to obtain the optimal cultivation condition of Antrodia cinnamomea (A. cinnamomea). This study proposed a hybrid machine learning approach (i.e., ANFIS-NM) to identify the potent factors and optimize the cultivation conditions of A. cinnamomea based on a 32 fractional factorial design with seven factors. The results indicate that the ANFIS-NM approach successfully identified three key factors (i.e., glucose, potato dextrose broth, and agar) and significantly boosted mycelia yield. The interpretability of ANFIS rules made the cultivation conditions visually interpretable. Subsequently, a three-factor five-level central composite design was used to probe the optimal yield. This study demonstrates the proposed hybrid machine learning approach could significantly reduce the time consumption in laboratory cultivation and increase mycelia yield that meets SDGs 7 and 12, hitting a new milestone for biomass production.

Interaction of a Homologous Series of Amphiphiles with P-glycoprotein in a Membrane Environment-Contributions of Polar and Non-Polar Interactions

The transport of drugs by efflux transporters in biomembranes limits their bioavailability and is a major determinant of drug resistance development by cancer cells and pathogens. A large number of chemically dissimilar drugs are transported, and despite extensive studies, the molecular determinants of substrate specificity are still not well understood. In this work, we explore the role of polar and non-polar interactions on the interaction of a homologous series of fluorescent amphiphiles with the efflux transporter P-glycoprotein. The interaction of the amphiphiles with P-glycoprotein is evaluated through effects on ATPase activity, efficiency in inhibition of [¹²⁵I]-IAAP binding, and partition to the whole native membranes containing the transporter. The results were complemented with partition to model membranes with a representative lipid composition, and details on the interactions established were obtained from MD simulations. We show that when the total concentration of amphiphile is considered, the binding parameters obtained are apparent and do not reflect the affinity for P-gp. A new formalism is proposed that includes sequestration of the amphiphiles in the lipid bilayer and the possible binding of several molecules in P-gp's substrate-binding pocket. The intrinsic binding affinity thus obtained is essentially independent of amphiphile hydrophobicity, highlighting the importance of polar interactions. An increase in the lipophilicity and amphiphilicity led to a more efficient association with the lipid bilayer, which maintains the non-polar groups of the amphiphiles in the bilayer, while the polar groups interact with P-gp's binding pocket. The presence of several amphiphiles in this orientation is proposed as a mechanism for inhibition of P-pg function.

Extending the Pseudo-Phase Model of Detergent-Lipid Dispersions by a Detergent-Binding Protein

Mixed micellar drug delivery systems for poorly soluble active pharmaceutical ingredients (APIs) are easy to produce and long-term stable, because they represent equilibrium structures. However, their fate after intravenous injection is still largely unknown. Once injected into the bloodstream, they can potentially convert to vesicles or disappear altogether, with both API and excipients being picked up by blood components. Our study aimed at reducing the gap between the good, quantitative understanding of aqueous glycocholate (GC)-lecithin dispersions alone and the highly complex situation in the blood. To this end, we extended the pseudophase model previously established for lipid-detergent dispersions to include the detergent-binding protein albumin as another component. The model predicted a quaternary phase diagram with planar phase boundaries defined by key parameters of the ternary subsystems, which were then determined by isothermal titration calorimetry. They include the aqueous GC concentration upon bilayer-micelle coexistence, 5.2 mM, the GC-to-lipid mole ratios in coexisting bilayers (R_e^sat = 0.2) and micelles (R_e^sol = 0.7), as well as the capacity of the albumin to bind 0.1 GC molecules with a dissociation constant of K_D = 0.1 mM and 6 GC molecules with K_D = 0.7 mM. Subsequent measurements in the quaternary system showed phase boundaries in good agreement with the model predictions. In addition, the critical micelle concentration of GC shows a minimal value (midpoint of transition) of 9.1 mM at the temperature of 24 °C where the demicellization enthalpy is zero. The demicellization process is accompanied by a heat capacity change of 29 cal/mol K. The model improves the understanding of the mixed micellar drug delivery systems. The success of the approach encourages including even more blood components, like lipoproteins, to a quantitative treatment.

Implementing re-configurable biological computation with distributed multicellular consortia

The use of synthetic biological circuits to deal with numerous biological challenges has been proposed in several studies, but its implementation is still remote. A major problem encountered is the complexity of the cellular engineering needed to achieve complex biological circuits and the lack of general-purpose biological systems. The generation of re-programmable circuits can increase circuit flexibility and the scalability of complex cell-based computing devices. Here we present a new architecture to produce reprogrammable biological circuits that allow the development of a variety of different functions with minimal cell engineering. We demonstrate the feasibility of creating several circuits using only a small set of engineered cells, which can be externally reprogrammed to implement simple logics in response to specific inputs. In this regard, depending on the computation needs, a device composed of a number of defined cells can generate a variety of circuits without the need of further cell engineering or rearrangements. In addition, the inclusion of a memory module in the circuits strongly improved the digital response of the devices. The reprogrammability of biological circuits is an intrinsic capacity that is not provided in electronics and it may be used as a tool to solve complex biological problems.

Thermal niche partitioning and phenology of Nearctic and Palearctic flea (Siphonaptera) communities on rodents (Mammalia: Rodentia) from five ecoregions

Seasonality of fleas (Siphonaptera) may be due to species competition, prompting the idea that flea species partition temperature, along with correlated variables such as moisture (thermal-niche partitioning hypothesis). I compared the fleas of five rodent-flea communities described from the literature for thermal-niche optima by fitting non-linear LRF (Lobry-Rosso-Flandrois) curves to examine whether flea species in a community show distinct, partitioned thermal niches. LRF curves estimate physiological parameters of temperature minimum, optimum, maximum, and maximum abundance, and facilitate comparison between species by summarizing seasonal data. Flea-communities were on Nearctic Southern flying squirrel (Glaucomys volans volans), Richardson's ground-squirrel (Urocitellus richardsonii), North American deer-mouse (Peromyscus maniculatus), and Palearctic Midday jird (Meriones meridianus), and Wagner's gerbil (Dipodillus dasyurus). Flea communities appeared to show seasonality consistent with thermal-niche partitioning. Several flea families and genera had characteristic thermal niches: Ceratophyllidae had broad tolerance to extreme temperature, Leptopsyllidae (one species in this study) to cold, and Pulicidae to hot. In contrast, at the local, species level, climatic speciation could be significant in flea diversification. Non-competition hypotheses (environmental filtering, neutrality) require testing, too. Thermal-niche partitioning may increase flea species richness on hosts and could occur in other insect and plant communities. Implications for biodiversity conservation and disease ecology under global warming are wide-ranging.

Electroneutral Polymer Nanodiscs Enable Interference-Free Probing of Membrane Proteins in a Lipid-Bilayer Environment

Membrane proteins can be examined in near-native lipid-bilayer environments with the advent of polymer-encapsulated nanodiscs. These nanodiscs self-assemble directly from cellular membranes, allowing in vitro probing of membrane proteins with techniques that have previously been restricted to soluble or detergent-solubilized proteins. Often, however, the high charge densities of existing polymers obstruct bioanalytical and preparative techniques. Thus, the authors aim to fabricate electroneutral-yet water-soluble-polymer nanodiscs. By attaching a sulfobetaine group to the commercial polymers DIBMA and SMA(2:1), these polyanionic polymers are converted to the electroneutral maleimide derivatives, Sulfo-DIBMA and Sulfo-SMA(2:1). Sulfo-DIBMA and Sulfo-SMA(2:1) readily extract proteins and phospholipids from artificial and cellular membranes to form nanodiscs. Crucially, the electroneutral nanodiscs avert unspecific interactions, thereby enabling new insights into protein-lipid interactions through lab-on-a-chip detection and in vitro translation of membrane proteins. Finally, the authors create a library comprising thousands of human membrane proteins and use proteome profiling by mass spectrometry to show that protein complexes are preserved in electroneutral nanodiscs.

A rapid and simple spectroscopic method for the determination of yeast cell viability using methylene blue

Determination of cell viability is important in various microbiological studies. The microscopic method, counting dead cells stained by methylene blue (MB), has often been used for the determination of viability, although it is not efficient for the measurement of a large number of samples. Alternatively, some spectroscopic methods have been proposed to avoid tedious cell counting. One of these proposed methods detects the decrease in MB absorbance in the supernatant of cell suspension, because dead cells incorporate MB more efficiently than viable cells. However, at present, this spectroscopic method is rarely used due to its low throughput. Therefore, we devised a small-scale, rapid and simple method by improving several points as follows. (1) The peak wavelength of MB absorbance, 665 nm, was used to detect MB efficiently at the microtube scale. (2) The composition of the MB solution was improved by adding trisodium citrate. (3) The reaction time was shortened. And (4) the concentration ranges of both MB and cells, with which absorbance is linearly related to cell viability, were determined. The improved method enabled us to evaluate the dose-dependent toxicities of alcohols, antifungal/antimalarial quinacrine, and UV-C irradiation. The results were compatible with those of conventional microscopic counting and colony formation. The method would be applicable to automated determination and to various organisms such as bacteria and filamentous fungi which are difficult to be counted microscopically.

In Vitro and In Silico Analysis of New n-Butyl and Isobutyl Quinoxaline-7-carboxylate 1,4-di-N-oxide Derivatives against Trypanosoma cruzi as Trypanothione Reductase Inhibitors

American trypanosomiasis is a worldwide health problem that requires attention due to ineffective treatment options. We evaluated n-butyl and isobutyl quinoxaline-7-carboxylate 1,4-di-N-oxide derivatives against trypomastigotes of the Trypanosoma cruzi strains NINOA and INC-5. An in silico analysis of the interactions of 1,4-di-N-oxide on the active site of trypanothione reductase (TR) and an enzyme inhibition study was carried out. The n-butyl series compound identified as T-150 had the best trypanocidal activity against T. cruzi trypomastigotes, with a 13% TR inhibition at 44 μM. The derivative T-147 behaved as a mixed inhibitor with Ki and Ki' inhibition constants of 11.4 and 60.8 µM, respectively. This finding is comparable to the TR inhibitor mepacrine (Ki = 19 µM).

Multienzyme activity profiling for evaluation of cell‐to‐cell variability of metabolic state

In solid organs, cells of the same “type” can vary in their molecular phenotype. The basis of this state variation is being revealed by characterizing cell features including the expression pattern of mRNAs and the internal distribution of proteins. Here, the variability of metabolic state between cells is probed by enzyme activity profiling. We study individual cells of types that can be identified during the post‐mitotic phase of oogenesis in Xenopus laevis. Whole‐cell homogenates of isolated oocytes are used for kinetic analysis of enzymes, with a focus on the initial reaction rate. For each oocyte type studied, the activity signatures of glyceraldehyde 3‐phosphate dehydrogenase (GAPDH) and malate dehydrogenase 1 (MDH1) vary more between the homogenates of single oocytes than between repeat samplings of control homogenates. Unexpectedly, the activity signatures of GAPDH and MDH1 strongly co‐vary between oocytes of each type and change in strength of correlation during oogenesis. Therefore, variability of the kinetic behavior of these housekeeping enzymes between “identical” cells is physiologically programmed. Based on these findings, we propose that single‐cell profiling of enzyme kinetics will improve understanding of how metabolic state heterogeneity is related to heterogeneity revealed by omics methods including proteomics, epigenomics, and metabolomics.

Escaping from the Cutoff Paradox by Accumulating Long-Chain Alcohols in the Cell Membrane

The mechanism for the cutoff, an activity cliff at which long-chain alcohols lose their biological effects, has not been elucidated. Highly hydrophobic oleyl alcohol (C_18:1) exists as a mixture of monomers and aggregated droplets in water. C_18:1 did not inhibit the yeast growth but inhibited the growth of the slime mold without a cell wall. C_18:1 exhibited toxicity to the yeast protoplast, which was enhanced by polyethylene glycol, a fusogen. Therefore, direct interactions of C_18:1 with the membrane are crucial for the toxicity. The cutoff alcohols, C₁₄ and C₁₆, also exhibited strong toxicity obeying the Meyer-Overton correlation, in intact yeast cells whose membrane growth was suppressed in water. Taken together, the cutoff is avoidable by securing sufficient accumulation of the wall-permeable monomers in the membrane, which supports the lipid theory. It would be important to distinguish the effective drug structure localizing in the membrane and deal with the amount in the membrane.

Fucoxanthin’s Optimization from Undaria pinnatifida Using Conventional Heat Extraction, Bioactivity Assays and In Silico Studies

Brown macroalgae are a potential source of natural pigments. Among them, Undaria pinnatifida is recognized for its high concentration of fucoxanthin (Fx), which is a pigment with a wide range of bioactivities. In this study, three independent parameters were optimized for conventional heat extraction (CHE) to maximize the recovery of Fx from Undaria pinnatifida. Optimal conditions (temperature = 45 °C, solvent = 70%, and time = 61 min) extracted 5.1 mg Fx/g dw. Later, the bioactivities of the Fx-rich extracts (antioxidant, antimicrobial, and neuroprotective) were assessed using in vitro and in silico approaches. In vitro assays indicated that Fx has a strong antioxidant capacity and even stronger antimicrobial activity against gram-positive bacteria. This data was supported in silico where Fx established a high binding affinity to DR, a Staphylococcus aureus protein, through aa ALA-8, LEU-21, and other alkane interactions. Finally, the in vitro enzymatic inhibition of AChE using Fx, was further supported using docking models that displayed Fx as having a high affinity for aa TYR72 and THR 75; therefore, the Fx extraction behavior explored in this work may reduce the costs associated with energy and solvent consumption. Moreover, this paper demonstrates the efficiency of CHE when recovering high amounts of Fx from Undaria pinnatifida. Furthermore, these findings can be applied in different industries.

A Reduced F420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon

Anaerobic methanotrophic archaea (ANME), which oxidize methane in marine sediments through syntrophic associations with sulfate-reducing bacteria, carry homologs of coenzyme F₄₂₀-dependent sulfite reductase (Fsr) of Methanocaldococcus jannaschii, a hyperthermophilic methanogen from deep-sea hydrothermal vents. M. jannaschii Fsr (MjFsr) and ANME-Fsr belong to two phylogenetically distinct groups, FsrI and FsrII, respectively. MjFsrI reduces sulfite to sulfide with reduced F₄₂₀ (F₄₂₀H₂), protecting methyl coenzyme M reductase (Mcr), an essential enzyme for methanogens, from sulfite inhibition. However, the function of FsrIIs in ANME, which also rely on Mcr and live in sulfidic environments, is unknown. We have determined the catalytic properties of FsrII from a member of ANME-2c. Since ANME remain to be isolated, we expressed ANME2c-FsrII in a closely related methanogen, Methanosarcina acetivorans. Purified recombinant FsrII contained siroheme, indicating that the methanogen, which lacks a native sulfite reductase, produced this coenzyme. Unexpectedly, FsrII could not reduce sulfite or thiosulfate with F₄₂₀H₂. Instead, it acted as an F₄₂₀H₂-dependent nitrite reductase (FNiR) with physiologically relevant K_m values (nitrite, 5 μM; F₄₂₀H_2, 14 μM). From kinetic, thermodynamic, and structural analyses, we hypothesize that in FNiR, F₄₂₀H₂-derived electrons are delivered at the oxyanion reduction site at a redox potential that is suitable for reducing nitrite (E⁰' [standard potential], +440 mV) but not sulfite (E⁰', -116 mV). These findings and the known nitrite sensitivity of Mcr suggest that FNiR may protect nondenitrifying ANME from nitrite toxicity. Remarkably, by reorganizing the reductant processing system, Fsr transforms two analogous oxyanions in two distinct archaeal lineages with different physiologies and ecologies. IMPORTANCE Coenzyme F₄₂₀-dependent sulfite reductase (Fsr) protects methanogenic archaea inhabiting deep-sea hydrothermal vents from the inactivation of methyl coenzyme M reductase (Mcr), one of their essential energy production enzymes. Anaerobic methanotrophic archaea (ANME) that oxidize methane and rely on Mcr, carry Fsr homologs that form a distinct clade. We show that a member of this clade from ANME-2c functions as F₄₂₀-dependent nitrite reductase (FNiR) and lacks Fsr activity. This specialization arose from a distinct feature of the reductant processing system and not the substrate recognition element. We hypothesize FNiR may protect ANME Mcr from inactivation by nitrite. This is an example of functional specialization within a protein family that is induced by changes in electron transfer modules to fit an ecological need.

Captivating color: evidence for optimal stimulus design in a polymorphic prey lure

Many species – humans included – employ color as an instrument of deception. One intriguing example of this resides in the conspicuous abstract color patterns displayed on the bodies of female orb weaving spiders. These displays increase prey interception rates and thereby function at least as visual lures. Their chromatic properties however vary extensively, both across and within species, with discrete forms often co-existing in the manner of a stable polymorphism. Variation is principally expressed in terms of signal hue (color per se), but it is unclear how attractiveness scales with this property and if extant morphs are maximally attractive relative to a graded range of potential alternatives. We examined these questions by assessing catch rates among color-manipulated females of the dimorphic jeweled spider Gasteracantha fornicata in their natural webs. The manipulation altered dorsal appearance in a manner akin to adding six new variants of their existing white/yellow phenotypes. This magnified the natural variation in stimulus hue independently of chroma (saturation) across a range spanning most of the color spectrum. Catch rate varied across treatments in simple accordance with how greatly stimulus hue deviated from either of the two extant spider phenotypes. Predictions based on fly-perceived chromatic and achromatic background contrast were clearly unsupported despite dipterans constituting ~60 % of identifiable prey. This study supports the importance of signal coloration per se in G. fornicata and suggests that extant lure phenotypes reside in a broadly optimal spectral range for stimulating their aggregate prey community.

Hot Ductility Prediction Model of Cast Steel with Low-Temperature Transformed Structure during Continuous Casting

When various alloying elements are added or the cooling rate is increased, steel grades with U- or V-typed ductility behavior show N-shaped ductility behavior in which the ductility decreases in the low-temperature region. This study proposes a method that uses N-shaped data fitting and random forest to predict ductility behavior of steel grades that have bainite microstructure. To include the phenomenon in which that ductility decreases below the intermediate temperature, the data range was extended to temperature T < 700 °C. To identify the T range in which the ductility decreases at T < 700 °C, an N-shaped data fitting method using six parameters was proposed. Comparison with the experimental values confirmed the effectiveness of the proposed model. Also, the model has better ability than models to predict bainite start temperature TBS. In a case study, the change of ductility behavior according to the cooling rate was observed for Nb-added steel. As the cooling rate increased from 1 °C/s to 10 °C/s, the formation of hard phase was relatively promoted, and different transformation behaviors appeared. This ability to predict the ductility behavior of alloy steels with a bainite microstructure, and to predict TBS below the intermediate temperature enables effective control of the secondary cooling conditions during continuous casting process, minimizing the formation of cracks on the slab surface.

Development of synaptic fidelity and action potential robustness at an inhibitory sound localization circuit: effects of otoferlin-related deafness

KEY POINTS

Inhibitory glycinergic inputs from the medial nucleus of the trapezoid body (MNTB) to the lateral superior olive (LSO) are involved in sound localization. This brainstem circuit performs reliably throughout life. How such reliability develops is unknown. Here we investigated the role of acoustic experience on the functional maturation of MNTB-LSO inputs at juvenile (postnatal day P11) and young-adult ages (P38) employing deaf mice lacking otoferlin (KO). We analyzed neurotransmission at single MNTB-LSO fibers in acute brainstem slices employing prolonged high-frequency stimulation (1-200 Hz|60 s). At P11, KO inputs still performed normally, as manifested by normal synaptic attenuation, fidelity, replenishment rate, temporal precision, and action potential robustness. Between P11-P38, several synaptic parameters increased substantially in WTs, collectively resulting in high-fidelity and temporally precise neurotransmission. In contrast, maturation of synaptic fidelity was largely absent in KOs after P11. Collectively, reliable neurotransmission at inhibitory MNTB-LSO inputs develops under the guidance of acoustic experience.

ABSTRACT

Sound localization involves information analysis in the lateral superior olive (LSO), a conspicuous nucleus in the mammalian auditory brainstem. LSO neurons weigh interaural level differences (ILDs) through precise integration of glutamatergic excitation from the cochlear nucleus (CN) and glycinergic inhibition from the medial nucleus of the trapezoid body (MNTB). Sound sources can be localized even during sustained perception, an accomplishment that requires robust neurotransmission. Virtually nothing is known about the sustained performance and the temporal precision of MNTB-LSO inputs after postnatal day (P)12 (time of hearing onset) and whether acoustic experience guides development. Here we performed whole-cell patch-clamp recordings to investigate neurotransmission of single MNTB-LSO fibers upon sustained electrical stimulation (1-200 Hz|60 s) at P11 and P38 in wild-type (WT) and deaf otoferlin (Otof) knock-out (KO) mice. At P11, WT and KO inputs performed remarkably similarly. In WTs, the performance increased drastically between P11-P38, e.g. manifested by an 8 to 11-fold higher replenishment rate (RR) of synaptic vesicles (SVs) and action potential robustness. Together, these changes resulted in reliable and highly precise neurotransmission at frequencies ≤ 100 Hz. In contrast, KO inputs performed similarly at both ages, implying impaired synaptic maturation. Computational modeling confirmed the empirical observations and established a reduced RR per release site for P38 KOs. In conclusion, acoustic experience appears to contribute massively to the development of reliable neurotransmission, thereby forming the basis for effective ILD detection. Collectively, our results provide novel insights into experience-dependent maturation of inhibitory neurotransmission and auditory circuits at the synaptic level. Abstract figure legend MNTB-LSO inputs are a major component of the mammalian auditory brainstem. Reliable neurotransmission at these inputs requires both failure-free conduction of action potentials and robust synaptic transmission. The development of reliable neurotransmission depends crucially on functional hearing, as demonstrated in a time series and by the fact that deafness - upon loss of the protein otoferlin - results in severely impaired synaptic release and replenishment machineries. These findings from animal research may have some implications towards optimizing cochlear implant strategies on newborn humans. This article is protected by copyright. All rights reserved.

Reliability Analysis of Military Vehicles Based on Censored Failures Data

The paper proposes a methodology of reliability testing as applied to vehicles used in military transport systems. After estimating the value of the reliability function using the Kaplan–Meier estimator, reliability models were developed and analysed. The neural model, which achieved the value of the correlation coefficient R exceeding 0.99, was determined to fit the empirical data the best. On the basis of the approximated reliability function of several models, the reliability characteristics of the tested sample of vehicles were determined. Plots of the failure probability density function for all three models had similar courses over a significant part of the function domain. A failure intensity function was also determined, which varied between models. For the exponential and Weibull model, the expected mileage between failures was calculated, which proved impossible for the neural model. The proposed methodology is capable of modelling reliability characteristics based on the observation of an assumed period of the exploitation process of the selected group of military vehicles.

Use of Worksheet events in Excel to save solver objective cell value from each iteration

Solver is a Microsoft Excel add-in program which is used to find an optimal value for a formula in the objective cell. Solver accomplishes this either by maximizing, minimizing or setting the objective cell value to a specific value. The article presents the utility of in built worksheet events in Excel VBA to save the value of objective cell from each iteration when solver is used for optimization.

Exchange of a single amino acid residue in the cryptophyte phycobiliprotein lyase GtCPES expands its substrate specificity

Cryptophytes are among the few eukaryotes employing phycobiliproteins (PBP) for light harvesting during oxygenic photosynthesis. In contrast to cyanobacterial PBP that are organized in membrane-associated phycobilisomes, those from cryptophytes are soluble within the chloroplast thylakoid lumen. Their light-harvesting capacity is due to covalent linkage of several open-chain tetrapyrrole chromophores (phycobilins). Guillardia theta utilizes the PBP phycoerythrin 545 with 15,16-dihydrobiliverdin (DHBV) in addition to phycoerythrobilin (PEB) as chromophores. The assembly of PBPs in cryptophytes involves the action of PBP-lyases as shown for cyanobacterial PBP. PBP-lyases facilitate the attachment of the chromophore in the right configuration and stereochemistry. Here we present the functional characterization of the eukaryotic S-type PBP lyase GtCPES. We show GtCPES-mediated transfer and covalent attachment of PEB to the conserved Cys82 of the acceptor PBP β-subunit (PmCpeB) of Prochlorococcus marinus MED4. On the basis of the previously solved crystal structure, the GtCPES binding pocket was investigated using site-directed mutagenesis. Thereby, amino acid residues involved in phycobilin binding and transfer were identified. Interestingly, exchange of a single amino acid residue Met67 to Ala extended the substrate specificity to phycocyanobilin (PCB), most likely by enlarging the substrate-binding pocket. Variant GtCPES_M67A binds both PEB and PCB forming a stable, colored complex in vitro and produced in Escherichia coli. GtCPES_M67A is able to mediate PCB transfer to Cys82 of PmCpeB. Based on these findings, we postulate that this single amino acid residue has a crucial role for bilin binding specificity of S-type phycoerythrin lyases but additional factors regulate handover to the target protein.

Self-Assembly of Protein-Containing Lipid-Bilayer Nanodiscs from Small-Molecule Amphiphiles

When membrane proteins are removed from their natural environment, the quality of the membrane-solubilizing agent used is critical for preserving their native structures and functions. Nanodiscs that retain a lipid-bilayer core around membrane proteins have attracted great attention because they offer a much more native-like environment than detergent micelles. Here, two small-molecule amphiphiles with diglucose headgroups and either a hydrocarbon or a fluorocarbon hydrophobic chain are shown to directly assemble lipids and membrane proteins to form native nanodiscs rather than mixed micelles. Self-assembly of nanodiscs of increasing complexity from both defined, artificial vesicles as well as complex, cellular membranes is demonstrated. A detailed investigation of bilayer integrity and membrane-protein activity in these nanodiscs reveals gentle effects on the encapsulated bilayer core. The fluorinated amphiphile appears particularly promising because its lipophobicity results in gentle, non-perturbing interactions with the nanoscale lipid bilayer. A sequential model of nanodisc self-assembly is proposed that proceeds through perforation of the original membrane followed by saturation and complete solubilization of the bilayer. On this basis, pseudophase diagrams are established for mixtures of lipids and nanodisc-forming diglucoside amphiphiles, and the latter are used for the extraction of a broad range of membrane proteins from cellular membranes.

Integrity and Stability of PTC Bearing CFTR mRNA and Relevance to Future Modulator Therapies in Cystic Fibrosis

Major advances have recently been made in the development and application of CFTR (cystic fibrosis transmembrane conductance regulator) mutation class-specific modulator therapies, but to date, there are no approved modulators for Class I mutations, i.e., those introducing a premature termination codon (PTC) into the CFTR mRNA. Such mutations induce nonsense-mediated decay (NMD), a cellular quality control mechanism that reduces the quantity of PTC bearing mRNAs, presumably to avoid translation of potentially deleterious truncated CFTR proteins. The NMD-mediated reduction of PTC-CFTR mRNA molecules reduces the efficacy of one of the most promising approaches to treatment of such mutations, namely, PTC readthrough therapy, using molecules that induce the incorporation of near-cognate amino acids at the PTC codon, thereby enabling translation of a full-length protein. In this study, we measure the effect of three different PTC mutations on the abundance, integrity, and stability of respective CFTR mRNAs, using CFTR specific RT-qPCR-based assays. Altogether, our data suggest that optimized rescue of PTC mutations has to take into account (1) the different steady-state levels of the CFTR mRNA associated with each specific PTC mutation; (2) differences in abundance between the 3' and 5' regions of CFTR mRNA, even following PTC readthrough or NMD inhibition; and (3) variable effects on CFTR mRNA stability for each specific PTC mutation.

Glucocorticoid-Responsive Transcription Factor Krüppel-Like Factor 9 Regulates fkbp5 and Metabolism

Krüppel-like factor 9 (Klf9) is a feedforward regulator of glucocorticoid receptor (GR) signaling. Here we show that in zebrafish klf9 is expressed with GR-dependent oscillatory dynamics in synchrony with fkbp5, a GR target that encodes a negative feedback regulator of GR signaling. We found that fkbp5 transcript levels are elevated in klf9 -/- mutants and that Klf9 associates with chromatin at the fkbp5 promoter, which becomes hyperacetylated in klf9 -/ - mutants, suggesting that the GR regulates fkbp5 via an incoherent feedforward loop with klf9. As both the GR and Fkbp5 are known to regulate metabolism, we asked how loss of Klf9 affects metabolic rate and gene expression. We found that klf9 -/- mutants have a decreased oxygen consumption rate (OCR) and upregulate glycolytic genes, the promoter regions of which are enriched for potential Klf9 binding motifs. Our results suggest that Klf9 functions downstream of the GR to regulate cellular glucocorticoid responsivity and metabolic homeostasis.

Membrane-water partitioning - Tackling the challenges of poorly soluble drugs using chaotropic co-solvents

Many newly developed drugs suffer from poor water solubility and low bioavailability and hence, need special formulation vehicles like vesicular or micellar drug delivery systems. The knowledge of their membrane-water partition coefficient K becomes critical as is governs drug loading and release from the vehicle, as well as absorption into the body. The dilemma is that measuring K is particularly challenging for these very compounds. Here we establish a strategy to resolve this problem. We added DMSO to shift K and solubility into a convenient range and extrapolated these results back to zero-DMSO. Isothermal titration calorimetry revealed that logK of the kinase inhibitor Lapatinib decreased proportionally to DMSO content (2.5 - 20v%) with a slope of -1/20v% (m value = 28 kJ/mol). This implies a K of 84 mM-1 in DMSO-free buffer. This strategy should be transferable to other poorly soluble drugs and further detection methods.

Re-Use of Caco-2 Monolayers in Permeability Assays-Validation Regarding Cell Monolayer Integrity

Caco-2 monolayers are a common in vitro model used to evaluate human intestinal absorption. The reference protocol requires 21 days post-seeding to establish a stable and confluent cell monolayer, which is used in a single permeability assay during the period of monolayer stability (up to day 30). In this work, we characterize variations in the tightness of the cell monolayer over the stable time interval and evaluate the conditions required for their re-use in permeability assays. The monolayer integrity was assessed through TEER measurements and permeability of the paracellular marker Lucifer Yellow (LY), complemented with nuclei and ZO-1 staining for morphological studies and the presence of tight junctions. Over 150 permeability assays were performed, which showed that manipulation of the cell monolayer in the permeability assay may contribute significantly to the flux of LY, leading to P_app values that are dependent on the sampling duration. The assay also leads to a small decrease in the cell monolayer TEER, which is fully recovered when cell monolayers are incubated with culture media for two full days. When this procedure is followed, the cell monolayers may be used for permeability assays on days 22, 25, and 28, triplicating the throughput of this important assay.