Intelligent Image-Activated Cell Sorting.

A fundamental challenge of biology is to understand the vast heterogeneity of cells, particularly how cellular composition, structure, and morphology are linked to cellular physiology. Unfortunately, conventional technologies are limited in uncovering these relations. We present a machine-intelligence technology based on a radically different architecture that realizes real-time image-based intelligent cell sorting at an unprecedented rate. This technology, which we refer to as intelligent image-activated cell sorting, integrates high-throughput cell microscopy, focusing, and sorting on a hybrid software-hardware data-management infrastructure, enabling real-time automated operation for data acquisition, data processing, decision-making, and actuation. We use it to demonstrate real-time sorting of microalgal and blood cells based on intracellular protein localization and cell-cell interaction from large heterogeneous populations for studying photosynthesis and atherothrombosis, respectively. The technology is highly versatile and expected to enable machine-based scientific discovery in biological, pharmaceutical, and medical sciences.

Label-free chemical imaging flow cytometry by high-speed multicolor stimulated Raman scattering.

Combining the strength of flow cytometry with fluorescence imaging and digital image analysis, imaging flow cytometry is a powerful tool in diverse fields including cancer biology, immunology, drug discovery, microbiology, and metabolic engineering. It enables measurements and statistical analyses of chemical, structural, and morphological phenotypes of numerous living cells to provide systematic insights into biological processes. However, its utility is constrained by its requirement of fluorescent labeling for phenotyping. Here we present label-free chemical imaging flow cytometry to overcome the issue. It builds on a pulse pair-resolved wavelength-switchable Stokes laser for the fastest-to-date multicolor stimulated Raman scattering (SRS) microscopy of fast-flowing cells on a 3D acoustic focusing microfluidic chip, enabling an unprecedented throughput of up to ∼140 cells/s. To show its broad utility, we use the SRS imaging flow cytometry with the aid of deep learning to study the metabolic heterogeneity of microalgal cells and perform marker-free cancer detection in blood.

Spontaneous Combustion of 2-Bromo-3-Methoxythiophene: A Study on Reaction Pathways and Energetics by Quantum Chemical Calculations.

Reaction pathways and energetics for the dimerization and trimerization reactions of 2-bromo-3-methoxythiophene (2Br-3Met) molecules are investigated using hybrid density functional theory (DFT) calculations to obtain insight into the oligomerization reaction observed in the spontaneous combustion of pure liquid 2Br-3Met. The calculations show that the carbon-bromine bond in a 2Br-3Met molecule elongates easily, and the trans addition of this C-Br bond to a double bond in the neighboring 2Br-3Met molecule occurs easily at room temperature, reflecting the evaluated activation energy of ΔHa = 12.46 kcal/mol (enthalpy) or ΔGa = 35.68 kcal/mol (Gibbs free energy, 298.150 K and 1 atm). The formation process of trimers is calculated in a similar way. A model for the explanation of spontaneous combustion is proposed; large oligomers of the 2Br-3Met molecule are produced spontaneously following the initial formation of dimers or trimers. UV-vis spectra and vibration spectra are obtained for related molecular species, which show reasonable agreement with the experimental results.

Hydrogen storage mechanism and diffusion in metal-organic frameworks.

Diffusion and storage of hydrogen molecules in metal-organic frameworks are crucial for the development of next-generation energy storage devices. By resorting to the first principles modeling, we compute the diffusion coefficient of molecular hydrogen in these systems in a range of temperatures where MOF-based devices are expected to operate. The explicit inclusion of the electronic structure shows that diffusivities are one order of magnitude smaller than those reported by classical simulations, evidencing the insufficiency of the empirical force fields used so far. We show that hydrogen is mainly rolled up around the metal oxide nodes both in MOF-5 and IRMOF-6, and partly around the carbon atoms in the case of IRMOF-6, where charged linkers are present. Metal ions embedded in the junction sites exert an electrostatic attraction toward hydrogen and the resulting distribution shows some ordering around these same sites at low temperature, whereas this tendency vanishes at room temperature. The induced polarization of hydrogen molecules generates an electrostatic interaction with charged atoms inside these nano-scaffolds and this is a key factor for the enhancement in hydrogen storage both in MOF-5 and IRMOF-6. The mechanism discussed hereby provides a novel understanding of metal-organic frameworks and acts as a guide to tune their efficiency for hydrogen storage. Moreover it paves the way to a computer-aided design of effective MOFs indicating that a fine control of the distribution of electrostatic charges inside the hydrogen hosting structure is crucial.

Aggregation-induced emission effect on turn-off fluorescent switching of a photochromic diarylethene.

Background: Diarylethenes are well-known photochromic compounds, which undergo cyclization and cycloreversion reactions between open- and closed-ring isomers. Recently, diarylethene derivatives with photoswitchable fluorescent properties were prepared. They are applicable for fluorescence imaging including bio-imaging. On the other hand, a new system called "excited state intramolecular proton transfer (ESIPT)" is reported. In the system, absorption and emission bands are largely separated due to the proton transfer, hence it showed strong fluorescence even in the crystalline state. We aimed to construct the photochromic system incorporating the ESIPT mechanism. Results: A diarylethene incorporating a fluorescent moiety that exhibit ESIPT behavior was prepared. The ESIPT is one of the examples which express the mechanisms of aggregation-induced emission (AIE). This compound emits orange fluorescence with a large Stokes shift derived from ESIPT in aprotic solvents such as THF or hexane, while it exhibits only a photochromic reaction in protic solvents such as methanol. In addition, it shows turn-off type fluorescence switching in an aprotic solvent and in crystals. The fluorescence is quenched as the content of closed-ring isomers increases upon UV light irradiation. Conclusions: A diarylethene containing an ESIPT functional group was prepared. It showed fluorescent turn-off behavior during photochromism in aprotic solvents as well as in crystalline state upon UV light irradiation. Furthermore, it showed AIE in THF/water mixtures with blue-shift of the emission.

A detailed insight into the catalytic reduction of NO operated by Cr-Cu nanostructures embedded in a CeO2 surface.

Replacing rare and expensive elements, such as Pt, Pd, and Rh, commonly used in catalytic devices with more abundant and less expensive ones is mandatory to realize efficient, sustainable and economically appealing three-way catalysts. In this context, the surface of a Cr-Cu/CeO2 system represents a versatile catalyst for the conversion of toxic NO into harmless N2. Yet, a clear picture of the underlying mechanism is still missing. We provide here a detailed insight into such a reaction mechanism by means of a combined experimental and theoretical study. Fourier-transform infrared spectroscopy is used to detect all the products resulting from catalytic reactions of NO and CO on the surface of a Cr-Cu/CeO2 nanocatalyst. CO pulsing experiments unveil that reactions of CO with O atoms at the Cr-Cu/CeO2 surface are the major factors responsible for the formation of surface vacancies. On these grounds, a comprehensive picture of the NO reduction and the role of both Cu and Cr dopants and vacancies is rationalized by first-principles modeling. Our findings provide a general route for the realization of ceria-based cost-effective catalysts.

Simple but Efficient Method for Inhibiting Sintering and Aggregation of Catalytic Pt Nanoclusters on Metal-Oxide Supports.

A simple and efficient method to inhibit aggregation of Pt clusters supported on metal oxide was developed, preserving the accessible clusters surface where catalytically active sites are located even at relatively high temperatures up to 700 K. The key idea was the inclusion of transition metal atoms such as Ni into the Pt clusters, thus anchoring the clusters through formation of strong chemical bonds with oxygen atoms of the metal-oxide support. To elucidate the efficiency of the method, first-principles molecular dynamics enhanced with free-energy sampling methods were used. These virtual experiments showed how doped Ni atoms, having a stronger affinity to O than Pt, anchor the Pt clusters tightly to the metal-oxide supports and inhibit their tendency to aggregate on the support.

An atomic-level insight into the basic mechanism responsible for the enhancement of the catalytic oxidation of carbon monoxide on a Cu/CeO2 surface.

The reaction mechanisms of CO molecules interacting with a Cu/CeO2 surface and related morphological modifications occurring upon removal of O atoms to generate CO2 are investigated by first-principles dynamical simulations complemented by a free-energy sampling technique. We show that the reactivity of oxygen atoms located in the first layer in the vicinity of the Cu site is remarkably high because of a reduction of the O coordination number. Moreover, we evidence that the doped Cu atoms are responsible for an enhancement of the exposure of other surrounding O atoms, even below the first surface layer, which can then easily react with CO and are gradually removed from the system in the oxidation process. The underlying mechanism responsible for such a high catalytic reactivity of the Cu/CeO2 surface toward CO oxidation is rationalized in terms of the characteristics of the doped Cu. In fact, this copper site is responsible for providing an increasing number of O atoms participating in the catalysis by exposing subsequently all O atoms in the vicinity which are likely to react with an approaching CO. This peculiarity of the Cu atoms extends to O atoms which initially can be deeply buried up to the fourth layer underneath the surface. The mechanism unveiled here provides useful insights into the fundamental mechanism and suggests strategies for the engineering and design of more effective ceria-based catalysts via metal doping.

How seaweeds release the excess energy from sunlight to surrounding sea water.

We report an atomistic insight into the mechanism regulating the energy released by a porphyra-334 molecule, the ubiquitous photosensitive component of marine algae, in a liquid water environment upon an electron excitation. To quantify this rapidly occurring process, we resort to the Fourier analysis of the mass-weighted auto-correlation function, providing evidence for a remarkable dynamic change in the number of hydrogen bonds among water molecules and between the porphyra-334 and its surrounding hydrating water. Hydrogen bonds between the porphyra-334 and close by water molecules can act directly and rather easily to promote an efficient transfer of the excess kinetic energies of the porphyra-334 to the surrounding solvating water molecules via an activation of the collective modes identified as hydrogen-bond stretching modes in liquid water which eventually results in a disruption of the hydrogen bond network. Since porphyra-334 is present in seaweeds, aquatic cyanobacteria (blue-green algae) and red algae, our findings allow addressing the question how algae in oceans or lakes, upon sunlight absorption, can release large amounts of energy into surrounding water without destabilizing neither their own nor the H2O molecular structure.

Reducing the Cost and Preserving the Reactivity in Noble-Metal-Based Catalysts: Oxidation of CO by Pt and Al-Pt Alloy Clusters Supported on Graphene.

The oxidation mechanisms of CO to CO2 on graphene-supported Pt and Pt-Al alloy clusters are elucidated by reactive dynamical simulations. The general mechanism evidenced is a Langmuir-Hinshelwood (LH) pathway in which O2 is adsorbed on the cluster prior to the CO oxidation. The adsorbed O2 dissociates into two atomic oxygen atoms thus promoting the CO oxidation. Auxiliary simulations on alloy clusters in which other metals (Al, Co, Cr, Cu, Fe, Ni) replace a Pt atom have pointed to the aluminum doped cluster as a special case. In the nanoalloy, the reaction mechanism for CO oxidation is still a LH pathway with an activation barrier sufficiently low to be overcome at room temperature, thus preserving the catalyst efficiency. This provides a generalizable strategy for the design of efficient, yet sustainable, Pt-based catalysts at reduced cost.

The absence of a gap state and enhancement of the Mars-van Krevelen reaction on oxygen defective Cu/CeO2 surfaces.

We report a detailed first-principles analysis of the electronic structures of oxygen defective CeO2 and Cu/CeO2 surfaces aimed at elucidating the disappearance of the gap state of defective CeO2 when a Cu atom is added at the surface. The top of the valence band of Cu/CeO2 originates from the O 2p states around this Cu atom. We show that this redistribution of electronic states at the defective Cu/CeO2 surface enhances the reactivity of the surface O atoms. Indeed, dynamical simulations show an acceleration of catalytic NO oxidation occurring via the Mars-van Krevelen mechanism mediated by these highly reactive oxygens.

Molecular Design Learned from the Natural Product Porphyra-334: Molecular Generation via Chemical Variational Autoencoder versus Database Mining via Similarity Search, A Comparative Study.

A comparative study is presented. The method via chemical variational autoencoder (VAE) and the method via similarity search are compared, focusing on their generation ability for new functional molecular design. Focusing on the natural porphyra-334 as a model molecule, we generated three groups: molecules of mycosporine-like amino acids (MAAs) as seeds (G SEEDS ), molecules generated via chemical VAE (G VAE ) and molecules gathered via similarity search (G SIM ). The number of molecules that satisfy the condition for the light absorption ability of porphyra-334 in G SEEDS , G VAE , and G SIM are 52, 138, and 6, respectively. The method via chemical VAE shows a promising potential for future molecular design. By using quantum chemistry wave function properties for chemical VAE, we find new molecules that are comparable to porphyra-334, including some with unexpected geometries. At the end, we show a group of molecules found with this method.

Hybrid-DFT study on electronic structures of the active site of sweet potato purple acid phosphatase: the origin of stronger antiferromagnetic couplings than other purple acid phosphatases.

The electronic structure and magnetic interactions of the active site of sweet potato purple acid phosphatase (PAP) were investigated by using UHF, pure DFT (UBLYP), and hybrid DFT methods (UB3LYP and UB2LYP). PAP catalyzes the hydrolysis of a phosphate ester under acidic conditions and contains a binuclear metal center. Sweet potato PAP provides stronger antiferromagnetic coupling than other PAPs. UB3LYP showed reasonably good agreement with the experimental magnetic coupling, indicating that this stronger antiferromagnetic coupling is caused by a mu-oxo bridge in the Fe(III)-Mn(II) binuclear metal center, which is the origin of the asymmetric spin delocalization. The type of bridging ligand is essential for the reaction mechanism, because the bridging ligand is suggested to function as a nucleophile in the reaction. Analyses of the natural orbital and spin density distributions implied the asymmetric spin delocalization on the bridging oxygen. The mechanism and the pathway of the antiferromagnetic coupling between Fe(III) and Mn(II) were discussed, using chemical indices introduced with the occupation numbers of singly occupied natural orbitals.

Pharmacological evidence for the relationship between the NMDA receptor and nitric oxide pathway and the antidepressant-like effects of glucagon-like peptide-2 in the mouse forced-swim test.

We previously demonstrated that glucagon-like peptide-2 (GLP-2) exerted antidepressant-like effects in mice. The aim of the present study was to investigate the relationship between N-methyl-D-aspartate (NMDA) receptor-nitric oxide-cyclic guanosine monophosphate (NO-cGMP) pathway and the antidepressant-like effects of GLP-2 in the forced-swim test (FST) in mice. Intracerebroventricularly administered GLP-2 (3 µg/mouse) decreased the immobility time in the FST. The pretreatment of mice with l-arginine (750 mg/kg, i.p.), a substrate for nitric oxide synthase, sildenafil (5 mg/kg, i.p.), a phosphodiesterase 5 inhibitor, or d-serine (300 mg/kg, i.p.), a NMDA receptor co-agonist, inhibited the antidepressant-like effects of GLP-2 (3 µg/mouse) in the FST. Meanwhile, l-nitroarginine methyl ester (10 mg/kg, i.p.), a non-specific nitric oxide synthase (NOS) inhibitor, 7-nitroindazole (30 mg/kg, i.p.), a neuronal NOS inhibitor, methylene blue (10 mg/kg, i.p.), an inhibitor of both NOS and soluble guanylate cyclase (sGC), ODQ (30 pmol/site, i.c.v.), a sGC inhibitor, or MK-801 (0.05 mg/kg, i.p.), an NMDA receptor antagonist, in combination with a sub-effective dose of GLP-2 (1.5 µg/mouse) also decreased the immobility time in the FST. The present study provided evidence for the synergistic antidepressant-like effects of GLP-2 and inhibition of the NMDA receptor-l-arginine-NO-cGMP pathway in the FST, thereby contributing to our understanding of the mechanisms underlying the antidepressant-like effects of GLP-2.

Unique Structural Relaxations and Molecular Conformations of Porphyra-334 at the Excited State.

Quantum chemistry based simulations were used to examine the excited state of porphyra-334, one of the fundamental mycosporine-like amino acids present in a wide variety of aqueous organisms. Our calculations reveal three characteristic aspects of porphyra-334 related to either its ground or excited state. Specifically, (i) the ground state (S0) structure consists of a planar geometry in which three units can be identified, the central cyclohexene ring, the glycine branch, and the threonine branch, reflecting the π conjugation of the system; (ii) the first singlet excited state (S1) shows a large oscillator strength and a typical ππ* excitation character; and (iii) upon relaxation at S1, the originally ground state planar structure undergoes a relaxation to a nonplanar one, S1, especially at the carbon-nitrogen (CN) groups linking the cyclohexene ring to the glycine or threonine arm. The induced nonplanarity can be ascribed to the fact that the carbon atoms of the CN groups prefer an sp3 hybridization in the S1 state. At the singlet state, these processes are unlikely to be trapped by singlet-triplet intersystem crossing especially when these occur in the hydrophilic zwitter-ion forms of porphyra-334. These results provide the missing information for thorough interpretation of the stability of porphyra-334 upon UV irradiation.

A novel enzyme, 2'-hydroxybiphenyl-2-sulfinate desulfinase (DszB), from a dibenzothiophene-desulfurizing bacterium Rhodococcus erythropolis KA2-5-1: gene overexpression and enzyme characterization.

Dibenzothiophene (DBT), a model of organic sulfur compound in petroleum, is microbially desulfurized to 2-hydroxybiphenyl (2-HBP), and the gene operon dszABC was required for DBT desulfurization. The final step in the microbial DBT desulfurization is the conversion of 2'-hydroxybiphenyl-2-sulfinate (HBPSi) to 2-HBP catalyzed by DszB. In this study, DszB of a DBT-desulfurizing bacterium Rhodococcus erythropolis KA2-5-1 was overproduced in Escherichia coli by coexpression with chaperonin genes, groEL/groES, at 25 degrees C. The recombinant DszB was purified to homogeneity and characterized. The optimal temperature and pH for DszB activity were 35 degrees C and about 7.5, respectively. The K(m) and k(cat) values for HBPSi were 8.2 microM and 0.123.s(-1), respectively. DszB has only one cysteine residue, and the mutant enzyme completely lost the activity when the cysteine residue was changed to a serine residue. This result together with experiments using inhibitors showed that the cysteine residue contributes to the enzyme activity. DszB was also inhibited by a reaction product, 2-HBP (K(i)=0.25 mM), and its derivatives, but not by the other reaction product, sulfite. The enzyme showed a narrow substrate specificity: only 2-phenylbenzene sulfinate except HBPSi served as a substrate among the aromatic and aliphatic sulfinates or sulfonates tested. DszB was thought to be a novel enzyme (HBPSi desulfinase) in that it could specifically cleave the carbon-sulfur bond of HBPSi to give 2-HBP and sulfite ion without the aid of any other proteinic components and coenzymes.

Enhancement and stabilization of desulfurization activity of Rhodococcus erythropolis KA2-5-1 by feeding ethanol and sulfur components.

We developed a fed-batch culture system fed with ethanol and restricted amounts of sulfur compounds to enhance and stabilize the desulfurizing activity in bacterial cells. In this system using dibenzothiophene (DBT) as the sole sulfur source, a desulfurizing bacterium Rhodococcus erythropolis KA2-5-1 cultivated with small amounts of sulfur showed stable desulfurizing activity and a low rate of growth. However, the cells cultured with excess amounts of sulfur showed unstable activity and a high growth rate. DBT had disadvantages as a sulfur source for cultivation because it is immiscible with water and toxic to cells. We then investigated water-soluble sulfur compounds for use as the sole sulfur source for the cultivation of R. erythropolis KA2-5-1 with desulfurizing activity, and found 2-aminoethanesulfonic acid to be the most effective. When 2-aminoethanesulfonic acid was used instead of DBT as the sole sulfur source in the fed-batch fermentation system, R. erythropolis KA2-5-1 showed the highest desulfurizing activity, 111 mmol of 2-HBP/kg-cells/h, a high growth rate (mu = 0.37/h) and a final cell concentration of 20.0 g-dry cells/l during 89 h of cultivation. The production levels of the desulfurizing enzymes in the bacterial cells cultivated with DBT or 2-aminoethanesulfonic acid were evaluated by immunoblot analysis with specific antisera, indicating that the same quantity of desulfurizing enzymes was expressed in both cases.

Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene.

We report first-principles molecular dynamics calculations combined with rare events sampling techniques that clarify atom-scale mechanisms of oxygen plasma etching of graphene. The obtained reaction pathways and associated free-energy landscapes show that the etching proceeds near vacancies via a two-step mechanism, formation of precursor lactone structures and the subsequent exclusive CO2 desorption. We find that atomic oxygen among the plasma components is most efficient for etching, providing a guidline in tuning the plasma conditions.

Oxygen affinity of hemoglobin regulates O2 consumption, metabolism, and physical activity.

The oxygen affinity of hemoglobin is critical for gas exchange in the lung and O(2) delivery in peripheral tissues. In the present study, we generated model mice that carry low affinity hemoglobin with the Titusville mutation in the alpha-globin gene or Presbyterian mutation in the beta-globin gene. The mutant mice showed increased O(2) consumption and CO(2) production in tissue metabolism, suggesting enhanced O(2) delivery by mutant Hbs. The histology of muscle showed a phenotypical conversion from a fast glycolytic to fast oxidative type. Surprisingly, mutant mice spontaneously ran twice as far as controls despite mild anemia. The oxygen affinity of hemoglobin may control the basal level of erythropoiesis, tissue O(2) consumption, physical activity, and behavior in mice.

Impaired cell cycle control of neuronal precursor cells in the neocortical primordium of presenilin-1-deficient mice.

Recent studies have implicated presenilin-1 (PS-1) in the processing of the amyloid precursor protein and Notch-1. We show that PS-1 has biological effects on differentiation and cell cycle control of neuronal precursor cells in vivo using PS-1-deficient mice. The expression of Class III beta-tubulin was upregulated throughout the neocortical primordia of PS-1-deficient E14 embryos, especially on the ventricular surface. The increased speed of migration of the immature neurons from the ventricular zone outward in the PS-1-deficient neocortical primordia was indicated by an in vivo bromodeoxyuridine (BrdU)-labeling assay and a DiI-labeling assay in slice culture. Furthermore, we investigated the cell cycle of neuronal precursor cells in the neocortical ventricular zone using an in vivo cumulative BrdU-labeling assay. The length of the cell cycle in the neocortical precursor cells of wild-type mice was 11.4 hr whereas that of the PS-1-deficient mice was 15.4 hr. Among all phases of the cell cycle, S-phase exhibited the most prominent change in length, increasing from 2.4 hr in the wild-type mice to 7.4 hr in the mutant mice. The distribution of beta-catenin was specifically affected in the ventricular zone of the PS-1-deficient mice. These findings suggest that PS-1 is involved in the differentiation and the cell cycle control of neuronal precursor cells in the ventricular proliferating zone of the neocortical primordium.