DataSheet1_Relative specificity as an important consideration in the big data era.xls

Technological breakthroughs such as high-throughput methods, genomics, single-cell studies, and machine learning have fundamentally transformed research and ushered in the big data era of biology. Nevertheless, current data collections, analyses, and modeling frequently overlook relative specificity, a crucial property of molecular interactions in biochemical systems. Relative specificity describes how, for example, an enzyme reacts with its many substrates at different rates, and how this discriminatory action alone is sufficient to modulate the substrates and downstream events. As a corollary, it is not only important to comprehensively identify an enzyme’s substrates, but also critical to quantitatively determine how the enzyme interacts with the substrates and to evaluate how it shapes subsequent biological outcomes. Genomics and high-throughput techniques have greatly facilitated the studies of relative specificity in the 21st century, and its functional significance has been demonstrated in complex biochemical systems including transcription, translation, protein kinases, RNA-binding proteins, and animal microRNAs (miRNAs), although it remains ignored in most work. Here we analyze recent findings in big data and relative specificity studies and explain how the incorporation of relative specificity concept might enhance our mechanistic understanding of gene functions, biological phenomena, and human diseases.</p

Solubility Measurement and Modeling for the NaCl–NH₄Cl–Monoethylene Glycol–H₂O System from (278 to 353) K

The solubilities of NH₄Cl and NaCl in the mixtures of monoethylene glycol (MEG) and water were determined, respectively, in the temperature range of (278 to 353) K by a dynamic method. The NaCl–NH₄Cl–MEG–H₂O system with MEG mole fraction of 0.30 on a salt-free basis was also investigated from (278 to 353) K to determine its phase equilibrium as a function of temperature and the concentration of electrolytes. The solubilities of both NH₄Cl and NaCl in the MEG–H₂O mixtures were found to decrease with the addition of MEG and the increasing concentration of the secondary electrolyte. The results show that the increment of temperature causes a marked increase in the solubility of NH₄Cl but only has a slight impact on the solubility of NaCl. The mixed-solvent electrolyte (MSE) model was applied to model solid–liquid equilibrium for the system containing NaCl, NH₄Cl, MEG, and H₂O. Binary interaction parameters for MEG–NH₄⁺, MEG–Na⁺, and Na⁺–NH₄⁺ were newly determined by regressing the experimental data. The MSE model with new parameters presented very high accuracy to calculate solubilities for the NaCl–NH₄Cl–MEG–H₂O system. The average absolute relative deviations (AARD) between the prediction and the experimental solubility are 0.75 and 0.88% for NH₄Cl and NaCl, respectively

Measurements and Modeling of the Phase Equilibria in AlCl₃ + NaCl + CaCl₂ + H₂O and AlCl₃ + CaCl₂ + NH₄Cl + H₂O Systems

Solid–liquid phase equilibrium for chloride salt systems plays a vital role in the utilization of liquid wastes generated from soda ash production by the Solvay process. The equilibrium data for ternary systems AlCl3–NaCl–H2O, AlCl3–NH4Cl–H2O, and CaCl2–NH4Cl–H2O from 283 to 353 K were determined by a dynamic method. A chemical model for these systems was developed with the mixed-solvent electrolyte model parameterization with the average absolute relative deviation less than 5%. The new model is capable of calculating solubilities of NaCl and NH4Cl in the AlCl3–CaCl2–H2O system, and the average absolute relative deviation of predicted points is less than 6%. The experimental and calculated phase equilibria have been used in developing a recovery method for NaCl and CaCl2 in the liquid wastes from the Solvay process and the subsequent utilization of CaCl2

Phase Equilibria for the Glycine–Methanol–NH₄Cl–H₂O System

An investigation of the phase equilibria of the glycine–methanol–NH₄Cl–H₂O system was carried out with the objective of optimizing the monochloroacetic acid (MCA) process for the production of glycine. Phase equilibrium of the glycine–NH₄Cl–H₂O system at temperatures over the range of 283.2–353.2 K was determined for concentrations ranging up to the multiple saturation points. The solubilities of both glycine and NH₄Cl were found to increase with increasing temperature, as well as with increasing concentration of other solutes. The Bromley–Zemaitis model for ions and the Pitzer formulation for glycine neutral species implemented in the OLI platform were used in the regression of the experimental solubilities. The average absolute deviations between the regressed solubility values and the experimental data were found to be 1.4% for glycine and 0.93% for NH₄Cl. Three binary interaction parameters of the Pitzer formulation were newly obtained and coupled with the Bromley–Zemaitis parameters documented in OLI’s databank to predict the multiple saturation points of the system. Additionally, the solubility of glycine in methanol–H₂O mixtures was also measured from 283.2 to 323.2 K, and a sharp decline was observed as a function of the content of methanol. Such thermodynamic information is definitely useful for improving the existing industrial process, as well as providing fundamentals for the development of new glycine production processes

Selective ATP Detection via Activation of MoS₂‑Based Artificial Nanozymes Inhibited by ZIF-90 Nanoparticles

In this paper, we presented an ATP detection platform based on the selective activation of an artificial nanozyme inhibited by ZIF-90 nanoparticles. For the first time, we found and reported the inhibitory effect of ZIF-90 nanoparticles on the MoS2 nanozyme, and this property was integrated with its ATP-responsive ability to develop an ATP detection biosensor. The presence of ATP triggers the decomposition of ZIF-90, thus eliminating the inhibition ability and recovering the catalytic ability of the MoS2 nanozyme. By measuring the catalytic activity in the H2O2–TMB reaction system with optical and electrochemical methods, the ATP detection performance was evaluated systematically. The proposed detection method exhibited excellent sensitivity and selectivity, and the optical and electrochemical modes satisfied the requirements of different application circumstances. In addition, taking advantage of the mild and rapid bacterial disintegration properties of antibiotic peptide-modified magnetic nanoparticles (M-AMPs), using the proposed platform based on selective activation of ZIF-90 nanoparticles inhibited the MoS2 nanozyme, discriminative ATP detection was performed. This work confirms that the inhibitory effect of ZIF-90 nanoparticles on the MoS2 artificial nanozyme provides an idea for developing biosensing systems based on enzyme inhibition and, more importantly, holds great potential for expanding the application of ZIF-90 nanoparticles in analytical fields

Impact of Polarization Effect on Exciton Binding Energies and Charge Transport for the Crystals of Chlorinated ITIC Derivatives

Exciton binding energy (Eb) and carrier mobility are the key parameters to determine organic photovoltaic performance. Here, the impact of polarization effect on the Eb and carrier mobility in the crystals of different end-group-chlorinated ITIC isomers have been investigated by the self-consistent quantum mechanics/embedded charge method. In contrast to large values and small fluctuation for the gas phase Eb, the Eb in the solid crystals is substantially decreased and ranges from 0.08 to 0.36 eV due to important charge polarization and distinct molecular packing. Because of the counteraction between the electrostatic effect of the hole and electron, a good linear relationship is found between the Eb and the charge induction term. Accordingly, the nonequivalent molecules in each crystal have similar Eb. However, their ionization potential and electron affinity can be much changed due to different electrostatic effects, leading to appreciable site energy differences. Thus, the carrier mobility is decreased to varying degrees, up to 3 orders of magnitude. Remarkably, benefiting from a three-dimensional dense packing, α-ITIC-2Cl possesses the smallest Eb and the highest electron mobility. These results underline that chlorination is an effective way to tune molecular packing to simultaneously reduce Eb and improve carrier mobility toward high-efficiency organic photovoltaics

Measurement and Chemical Modeling of the Solubility of Na₂SiO₃·9H₂O and Na₂SiO₃ in Concentrated NaOH Solution from 288 to 353 K

In order to comprehensively use magnesium and silicon resources existing in serpentine ore, an efficient process for decomposing serpentine by the use of concentrated NaOH solution is proposed at elevated temperature. In this new process, magnesium is obtained as residues with the form of Mg­(OH)₂ after filtration, while silicon is dissolved in an alkaline solution and then separated by a crystallization operation with the common ion effect of NaOH at relatively low temperature. Solubilities of sodium metasilicate nonahydrate (Na₂SiO₃·9H₂O) and anhydrous sodium metasilicate (Na₂SiO₃) in NaOH solutions were measured. The experiments were carried out at the temperature range from 288.2 to 313.2 K and 343.2 to 353.2 K for these two solids, respectively. Over the investigated concentration range from 0.0 to 11.2 mol·kg^–1, the addition of NaOH caused the solubility of both Na₂SiO₃·9H₂O and Na₂SiO₃ to decrease due to common ion effect. It was also found that increasing the temperature favored the solubility of sodium metasilicate nonahydrate but depressed the solubility of anhydrous sodium metasilicate in NaOH solutions. A chemical model has been established with newly obtained interaction parameters of the Bromley–Zemaitis model by regressing the experimental solubility of Na₂SiO₃·9H₂O in NaOH solutions from 288.2 to 313.2 K along with the experimental solubility data of Na₂SiO₃ in NaOH solutions at 353.2 K

A New Tetrathiafulvalene−Quinone−Tetrathiafulvalene Triad: Modulation of the Intramolecular Charge Transfer by the Electron-Transfer Process Promoted by Metal Ions

Electron transfer can occur from the TTF units to the substituted quinone unit in a new TTF−quinone−TTF triad 1 containing the N,N-dialkylaniline-substituted quinone unit flanked by two TTF units, in the presence of metal ions (Pb2+, Zn2+, and Sc3+). Simultaneously, the corresponding charge transfer within the substituted quinone unit becomes weak in the presence of metal ions. Moreover, the metal ion-promoted electron transfer and the intramolecular charge transfer can be tuned by alternating UV and visible light irradiation in the presence of spiropyran

Precise Localization and Simultaneous Bacterial Eradication of Biofilms Based on Nanocontainers with Successive Responsive Property toward pH and ATP

The bacterial colonization of surfaces and subsequent biofilm formation are a great threat in medical therapy and clinical diagnosis. The complex internal structure and composition sets an enormous obstacle for the localization and removal of biofilms. In this study, we proposed a novel biofilm-targeted nanocontainer with successive responsive property toward pH and ATP for precise localization and simultaneous bacterial eradication, with an acidic and adenosine triphosphate (ATP)-rich microenvironment within biofilms, formed due to the accumulation of fatty acids and ATP in the three-dimensional enclosed structure, integrated as two successive indicators to improve the precision of biofilm identification and removal. The biofilm-targeted nanocontainer was composed of a ATP-responsive zeolitic imidazolate framework-90 (ZIF-90) core loaded with Rho 6G and doxorubicin hydrochloride (DOX) encapsulated in the pH-responsive amorphous calcium carbonate/poly(acrylic acid) (ACC/PAA) shell. In the presence of biofilms, the ACC/PAA shell and ZIF-90 core were successively degraded by the accumulated H+ and ATP within biofilms, resulting in the release of fluorescence indicators and antimicrobial agents. On the other hand, to meet the application requirements of different biofilm scenarios, the pH response ability of the nanocontainers could be adjusted by changing the metallic ions (Ni2+, Zn2+, and Cu2+) doped into the structure of the ACC/PAA shell. Owing to excellent water dispersion of the pH/ATP double-responsive ZIF-90@Zn-ACC/PAA nanocontainer, precise localization and simultaneous bacterial eradication was successfully realized via a simple spray process. The successive pH/ATP two-step unlocking processes endowed the nanocontainers high precision for localization and simultaneous eradication of biofilms, which made the proposed nanocontainers high promising in food safety and medical treatment

Data_Sheet_1_Energy Availability Determines Strategy of Microbial Amino Acid Synthesis in Volatile Fatty Acid–Fed Anaerobic Methanogenic Chemostats.docx

In natural communities, microbes exchange a variety of metabolites (public goods) with each other, which drives the evolution of auxotroph and shapes interdependent patterns at community-level. However, factors that determine the strategy of public goods synthesis for a given community member still remains to be elucidated. In anaerobic methanogenic communities, energy availability of different community members is largely varied. We hypothesized that this uneven energy availability contributed to the heterogeneity of public goods synthesis ability among the members in these communities. We tested this hypothesis by analyzing the synthetic strategy of amino acids of the bacterial and archaeal members involved in four previously enriched anaerobic methanogenic communities residing in thermophilic chemostats. Our analyses indicate that most of the members in the communities did not possess ability to synthesize all the essential amino acids, suggesting they exchanged these essential public goods to establish interdependent patterns for survival. Importantly, we found that the amino acid synthesis ability of a functional group was largely determined by how much energy it could obtain from its metabolism in the given environmental condition. Moreover, members within a functional group also possessed different amino acid synthesis abilities, which are related to their features of energy metabolism. Our study reveals that energy availability is a key driver of microbial evolution in presence of metabolic specialization at community level and suggests the feasibility of managing anaerobic methanogenic communities for better performance through controlling the metabolic interactions involved.</p