Tracking B Cell Memory to SARS-CoV-2 Using Rare Cell Analysis System.

Rapid mutations within SARS-CoV-2 are driving immune escape, highlighting the need for in-depth and routine analysis of memory B cells (MBCs) to complement the important but limited information from neutralizing antibody (nAb) studies. In this study, we collected plasma samples and peripheral blood mononuclear cells (PBMCs) from 35 subjects and studied the nAb titers and the number of antigen-specific memory B cells at designated time points before and after vaccination. We developed an assay to use the MiSelect R II System with a single-use microfluidic chip to directly detect the number of spike-receptor-binding domain (RBD)-specific MBCs in PBMCs. Our results show that the number of spike-RBD-specific MBCs detected by the MiSelect R II System is highly correlated with the level of nAbs secreted by stimulated PBMCs, even 6 months after vaccination when nAbs were generally not present in plasma. We also found antigen-specific cells recognizing Omicron spike-RBD were present in PBMCs from booster vaccination of subjects, but with a high variability in the number of B cells. The MiSelect R II System provided a direct, automated, and quantitative method to isolate and analyze subsets of rare cells for tracking cellular immunity in the context of a rapidly mutating virus.

MiSelect R System: the validation of a new detection system of CTCs and their correlation with prognosis in non-metastatic CRC patients.

Circulating tumor cells (CTCs) in blood are accepted as a prognostic marker for patients with metastatic colorectal cancer (CRC). However, there is limited data on the use of CTCs as a prognostic marker for non-metastatic patients. In the current study, we used a rare cell automated analysis platform, the MiSelect R System, to enumerate CTCs from blood in non-metastatic CRC patients, and corelated the number of CTCs with the clinical staging and survival. The presence of CTCs in mesenteric vein blood (MVB) samples from 101 CRC patients was significantly associated with T stage. Patients with 1 or more CTCs per 8 mL of MVB exhibited significantly worse disease-free survival (DFS) and cancer-specific survival (CSS) compared to patient without CTCs. The presence of CTCs before surgery is an independent marker for both DFS and CSS. CTC presence after surgical resection is also a prognostic marker. CTCs are a potentially useful prognostic and predictive biomarker in non-metastatic CRC patients that may further stratify patient's risk status within different stages of disease.

Accurate prediction of terahertz spectra of molecular crystals of fentanyl and its analogs.

Fentanyl is a potent synthetic opioid pain reliever with a high bioavailability that can be used as prescription anesthetic. Rapid identification via non-contact methods of both known and emerging opioid substances in the fentanyl family help identify the substances and enable rapid medical attention. We apply PBEh-3c method to identify vibrational normal modes from 0.01 to 3 THz in solid fentanyl and its selected analogs. The molecular structure of each fentanyl analog and unique arrangement of H-bonds and dispersion interactions significantly change crystal packing and is subsequently reflected in the THz spectrum. Further, the study of THz spectra of a series of stereoisomers shows that small changes in molecular structure results in distinct crystal packing and significantly alters THz spectra as well. We discuss spectral features of synthetic opioids with higher potency than conventional fentanyl such as ohmefentanyl and sufentanil and discover the pattern of THz spectra of fentanyl analogs.

Impact of COVID-19 on Pregnancy.

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is an emerging disease. There has been a rapid increase in cases and deaths since it was identified in Wuhan, China, in early December 2019, with over 4,000,000 cases of COVID-19 including at least 250,000 deaths worldwide as of May 2020. However, limited data about the clinical characteristics of pregnant women with COVID-19 have been reported. Given the maternal physiologic and immune function changes during pregnancy, pregnant women may be at a higher risk of being infected with SARS-CoV-2 and developing more complicated clinical events. Information on severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) may provide insights into the effects of COVID-19's during pregnancy. Even though SARS and MERS have been associated with miscarriage, intrauterine death, fetal growth restriction and high case fatality rates, the clinical course of COVID-19 pneumonia in pregnant women has been reported to be similar to that in non-pregnant women. In addition, pregnant women do not appear to be at a higher risk of catching COVID-19 or suffering from more severe disease than other adults of similar age. Moreover, there is currently no evidence that the virus can be transmitted to the fetus during pregnancy or during childbirth. Babies and young children are also known to only experience mild forms of COVID-19. The aims of this systematic review were to summarize the possible symptoms, treatments, and pregnancy outcomes of women infected with COVID-19 during pregnancy.

High accuracy machine learning identification of fentanyl-relevant molecular compound classification via constituent functional group analysis.

Fentanyl is an anesthetic with a high bioavailability and is the leading cause of drug overdose death in the U.S. Fentanyl and its derivatives have a low lethal dose and street drugs which contain such compounds may lead to death of the user and simultaneously pose hazards for first responders. Rapid identification methods of both known and emerging opioid fentanyl substances is crucial. In this effort, machine learning (ML) is applied in a systematic manner to identify fentanyl-related functional groups in such compounds based on their observed spectral properties. In our study, accurate infrared (IR) spectra of common organic molecules which contain functional groups that are constituents of fentanyl is determined by investigating the structure-property relationship. The average accuracy rate of correctly identifying the functional groups of interest is 92.5% on our testing data. All the IR spectra of 632 organic molecules are from National Institute of Standards and Technology (NIST) database as the training set and are assessed. Results from this work will provide Artificial Intelligence (AI) based tools and algorithms increased confidence, which serves as a basis to detect fentanyl and its derivatives.

Molecular Dynamics of Combustion Reactions in Supercritical Carbon Dioxide. 6. Computational Kinetics of Reactions between Hydrogen Atom and Oxygen Molecule H + O2 ⇌ HO + O and H + O2 ⇌ HO2.

Reactions of the hydrogen atom and the oxygen molecule are among the most important ones in the hydrogen and hydrocarbon oxidation mechanisms, including combustion in a supercritical CO2 (sCO2) environment, known as oxy-combustion or the Allam cycle. Development of these energy technologies requires understanding of chemical kinetics of H + O2 ⇌ HO + O and H + O2 ⇌ HO2 in high pressures and concentrations of CO2. Here, we combine quantum treatment of the reaction system by the transition state theory with classical molecular dynamics simulation and the multistate empirical valence bonding method to treat environmental effects. Potential of mean force in the sCO2 solvent at various temperatures 1000-2000 K and pressures 100-400 atm was obtained. The reaction rate for H + O2 ⇌ HO + O was found to be pressure-independent and described by the extended Arrhenius equation 4.23 × 10-7 T-0.73 exp(-21 855.2 cal/mol/RT) cm3/molecule/s, while the reaction rate H + O2 ⇌ HO2 is pressure-dependent and can be expressed as 5.22 × 10-2 T-2.86 exp(-7247.4 cal/mol/RT) cm3/molecule/s at 300 atm.

Molecular Dynamics of Combustion Reactions in Supercritical Carbon Dioxide. Part 5: Computational Study of Ethane Dissociation and Recombination Reactions C2H6 ⇌ CH3 + CH3.

Fossil fuel oxy-combustion is an emerging technology where the habitual nitrogen diluent is replaced by high-pressure supercritical CO2 (sCO2), which increases the efficiency of energy conversion. In this study, the chemical kinetics of the combustion reaction C2H6 ⇌ CH3 + CH3 in the sCO2 environment is predicted at 30-1000 atm and 1000-2000 K. We adopt a multiscale approach, where the reactive complex is treated quantum mechanically in rigid rotor/harmonic oscillator approximation, while environment effects at different densities are taken into account by the potential of mean force, produced with classical molecular dynamics (MD). Here, we used boxed MD, where enhanced sampling of infrequent events of barrier crossing is accomplished without application of the bias potential. The multistate empirical valence bond model is applied to describe free radical formation accurately at the cost of the classical force field. Predicted rates at low densities agree well with the literature data. Rate constants at 300 atm are 2.41 × 1014 T-0.20 exp(-77.03 kcal/mol/ RT) 1/s for ethane dissociation and 8.44 × 10-19 T1.42 exp(19.89 kcal/mol/ RT) cm3/molecule/s for methyl-methyl recombination.

Atoh1 Controls Primary Cilia Formation to Allow for SHH-Triggered Granule Neuron Progenitor Proliferation.

During cerebellar development, granule neuron progenitors (GNPs) proliferate by transducing Sonic Hedgehog (SHH) signaling via the primary cilium. Precise regulation of ciliogenesis, thus, ensures proper GNP pool expansion. Here, we report that Atoh1, a transcription factor required for GNPs formation, controls the presence of primary cilia, maintaining GNPs responsiveness to SHH. Loss of primary cilia abolishes the ability of Atoh1 to keep GNPs in a proliferative state. Mechanistically, Atoh1 promotes ciliogenesis by transcriptionally regulating Cep131, which facilitates centriolar satellite (CS) clustering to the basal body. Importantly, ectopic expression of Cep131 counteracts the effects of Atoh1 loss in GNPs by restoring proper localization of CS and ciliogenesis. This Atoh1-CS-primary cilium-SHH pro-proliferative pathway is also conserved in SHH-type medulloblastoma, a pediatric brain tumor arising from the GNPs. Together, our data reveal how Atoh1 modulates the primary cilium to regulate GNPs development.

A rare human CEP290 variant disrupts the molecular integrity of the primary cilium and impairs Sonic Hedgehog machinery.

The primary cilium is a microtubule-enriched cell-communication organelle that participates in mechanisms controlling tissue development and maintenance, including cerebellar architecture. Centrosomal protein of 290 kDa (CEP290) is a protein important for centrosomal function and ciliogenesis. Mutations in CEP290 have been linked to a group of multi-organ disorders - termed ciliopathies. The neurophysiological deficits observed in ciliopathies are sometimes associated with the progression of autistic traits. Here, the cellular function of two rare variants of CEP290 identified from recent exome sequencing of autistic individuals are investigated. Cells expressing Cep290 carrying the missense mutation R1747Q in mouse exhibited a defective Sonic hedgehog (Shh) signalling response, mislocalisation of the Shh receptor Smoothened (Smo), and dysregulation of ciliary protein mobility, which ultimately disrupted the proliferation of cerebellar granule progenitors (CGPs). This data was furthermore corroborated in an autism patient-derived iPSC line harbouring the R1746Q rare CEP290 variant. Evidence from this study suggests that the R1746Q mutation interferes with the function of CEP290 to maintain the ciliary diffusion barrier and disrupts the integrity of the molecular composition in the primary cilium, which may contribute to alterations in neuroarchitecture.

Gli2 modulates cell cycle re-entry through autophagy-mediated regulation of the length of primary cilia.

The primary cilium is a tiny cell protrusion known to transduce key extracellular signals, including those of the sonic hedgehog pathway, which activates Gli transcription factors for various cellular functions. To understand the significance of the Gli2 transcription factor in fibroblasts, we establish a Gli2-knockout NIH3T3 cell line by CRISPR/Cas9 technology. Surprisingly, NIH3T3 fibroblasts lacking Gli2 expression through gene knockout or RNA interference possess longer primary cilia after stimulation of ciliogenesis by serum starvation. This lengthening of primary cilia is associated with enhanced autophagy-mediated Ofd1 degradation, and can be reversed by pharmacological and genetic inhibition of autophagy. Meanwhile, flow cytometry reveals that Gli2-/- NIH3T3 fibroblasts exhibit a delay in cell cycle re-entry after serum re-stimulation. Ablation of their primary cilia through Kif3a knockdown rescues the delay in cell cycle re-entry. These results suggest that Gli2 plays an unexpected role in cell cycle re-entry through an autophagy-mediated regulation on ciliary length in fibroblasts.

Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes.

In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput.2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of "water-in-water" model system.

Identification of genes associated with cortical malformation using a transposon-mediated somatic mutagenesis screen in mice.

Mutations in genes involved in the production, migration, or differentiation of cortical neurons often lead to malformations of cortical development (MCDs). However, many genetic mutations involved in MCD pathogenesis remain unidentified. Here we developed a genetic screening paradigm based on transposon-mediated somatic mutagenesis by in utero electroporation and the inability of mutant neuronal precursors to migrate to the cortex and identified 33 candidate MCD genes. Consistent with the screen, several genes have already been implicated in neural development and disorders. Functional disruption of the candidate genes by RNAi or CRISPR/Cas9 causes altered neuronal distributions that resemble human cortical dysplasia. To verify potential clinical relevance of these candidate genes, we analyzed somatic mutations in brain tissue from patients with focal cortical dysplasia and found that mutations are enriched in these candidate genes. These results demonstrate that this approach is able to identify potential mouse genes involved in cortical development and MCD pathogenesis.

Chloride Ion Transport by the E. coli CLC Cl-/H+ Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study.

We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl- ion migration through the transmembrane domain of a prototypical E. coli CLC Cl-/H+ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl-. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl- traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl- exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl- along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl- changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl- and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl- ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl- transport.

Peripheral 5-HT3 mediates mirror-image pain by a cross-talk with acid-sensing ion channel 3.

Mirror-image pain (MIP), which occurs along with complex regional pain syndrome, rheumatoid arthritis and chronic migraine, is characterized by increased pain sensitivity of healthy body regions other than the actual injured or inflamed sites. A high level of peripheral inflammation may activate central or peripheral glia, triggering mirror-image pain. However, which receptors mediate inflammatory signals to contribute glial activation remains unclear. Intraplantarly injecting mice with 5-hydroxytryptamine (5-HT) or acidic buffer (proton) caused only unilateral hyperalgesia, but co-injection of 5-HT/acid induced bilateral hyperalgesia (MIP). Blocking 5-HT3 or acid-sensing ion channel 3 (ASIC3) abolished satellite glial activation, inhibiting MIP. Interestingly, intraplantar administration of a 5-HT3 agonist induced MIP, and 5-HT3-mediated MIP can be reversed by a 5-HT3 antagonist or an ASIC3 blocker. Similar results were found using a ASIC3 agonist. Furthermore, 5-HT3 was observed to co-localize with ASIC3 in DRG neurons; 5-HT3 activation-induced an increase in intracellular calcium that was inhibited by an ASIC3 blocker and vice versa. A cross-talk between 5-HT3 and ASIC3 mediates satellite glial activation, thereby triggering mirror-image pain.

Factors that regulate the conformation of m-benziporphodimethene complexes: agostic metal-arene interaction, hydrogen bonding, and η2,π coordination.

Group 12 and silver(I) tetramethyl-m-benziporphodimethene (TMBPDM) complexes with phenyl, methylbenzoate, or nitrophenyl groups as meso substituents were synthesized and fully characterized. The dimeric silver(I) complex displays an unusual η(2),π coordination from the ß-pyrrolic C=C bond to the silver ion. All of the complexes displayed a close contact between the metal ion and the inner C(22)-H(22) on the m-phenylene ring. The downfield chemical shifts of H(22) and large coupling constants between Cd(II) and H(22) strongly support the presence of an agostic interaction between the metal ion and inner C(22)-H(22). Crystal structures revealed that the syn form is the predominant conformation for TMBPDM complexes. This is distinctively different from the exclusive anti conformation observed in m-benziporphyrin and tetraphenyl-m-benziporphodimethene (TPBPDM) complexes. Evidently, intramolecular hydrogen-bonding interactions between axial chloride and methyl groups stabilize syn conformations. Unlike the merely syn conformation observed in the solid-state structures of TMBPDM complexes that contain an axial chloride, in solution these complexes display highly solvent- and temperature-dependent syn/anti ratio changes. The observation of dynamic (1)H NMR spectroscopic scrambling between syn and anti conformations from the titration of chloride ion into the solution of the TMBPDM complex suggests that axial ligand exchange is a likely pathway for the conversion between syn and anti forms. Theoretical calculations revealed that intermolecular hydrogen-bonding interactions between the axial chloride and CHCl(3) stabilizes the anti conformation, which explains the increased ratio for the anti form when dichloromethane or chloroform was used as the solvent.

N-1- and N-2-anthryl succinimide derivatives: C-N bond rotational behaviors and fluorescence energy transfer.

New rigid bicyclic N-anthrylsuccinimide 1a, 1b, 2a, and 2b were prepared. The C(aryl)-N(imide) bond rotational barriers, intra/intermolecular arene-arene interactions, and photophysical properties were investigated. The rotational behaviors are more significantly controlled by the position of C(aryl)-N(imide) connection than the sidewall framework. The fluorescence energy transfer (Φ(ET)) in 1a and 1b was estimated to be 61% and 53%, respectively. The difference is attributed to the position of C(aryl)-N(imide) connection, which directly influences the relative orientation of donor (naphthalene) and acceptor (anthracene).

Polarization filters with an autocloned symmetric structure.

The process of fabricating photonic crystals comprised of alternately stacked high- and low-index dielectric materials on periodic substrates to form zigzag films is called the autocloning technique. In this study, we have fabricated TiO2/SiO2 two-dimensional polarization filters by using electron beam gun evaporation with ion-beam-assisted deposition. The shape of the zigzag structure is preserved, and the total thickness is 8 µm. The symmetric structural design can be utilized as an antireflection coating applied to reduce ripples and achieve a 200 nm working wavelength range.

Interaction of serotonin and fluoxetine: toward understanding the importance of the chirality of fluoxetine (S form and R form).

The present investigation reports the importance of the S and R forms of fluoxetine, as an antidepressant with regards to the chirality taking different types of interactions associated with the neurotransmitter, serotonin. The goal of the present study is to provide predictions and to help experimental and theoretical studies toward understanding the chirality of fluoxetine in drug-ligand interaction, associated with serotonin-reuptake inhibitor drug design studies. Several different conformations for serotonin and fluoxetine complexes have been considered for quantum mechanical calculations. Both the S and R forms of fluoxetine associated with serotonin and fluoxetine complexes are found to be similar in total energy and binding energy values. The present study also supports the conformational effect of the 3-phenyl group of fluoxetine as stereo independent and is consistent with in vitro and in vivo data which indicates that the the eudismic ratio of fluoxetine enantiomers is near unity. The calculated highest stabilization energy values, binding energy values, both in the gas and aqueous phases at MP2/6-31+G*//B3LYP/6-31+G* identify the most possible stable conformer for the serotonin-fluoxetine complex.

Environmental-sensitive micelles based on poly(2-ethyl-2-oxazoline)-b-poly(L-lactide) diblock copolymer for application in drug delivery.

Anticancer drug doxorubicin (DOX) was physically loaded into the micelles prepared from poly(2-ethyl-2-oxazoline)-b-poly(L-lactide) diblock copolymers (PEOz-PLLA). PEOz-PLLA consists of hydrophilic segment PEOz and hydrophobic segment PLLA showed pH-sensitivity in the aqueous solution. The DOX-loaded micelle exhibited a narrow size distribution with a mean diameter around 170 nm. The micellar structure can preserve hydrophobic drug DOX under the physiological condition (pH 7.4) and selectively release DOX by sensing the intracellular pH change in late endosomes and secondary lysosomes (pH 4-5). At 37 degrees C, the cumulated released rate of DOX from micelles was about 65% at pH 5.0 in the initial 24 h. Additionally, polymeric micelles had low cytotoxicity in human normal fibroblast HFW cells for 72 h by using MTT assay. Moreover, DOX-loaded micelles could slowly and efficiency decrease cell viability of non-small-cell lung carcinoma CL3 cells. Taken together, PEOz-b-PLLA diblock polymeric micelles may act as useful drug carriers for cancer therapy.

Polymeric micelles with a pH-responsive structure as intracellular drug carriers.

Polymeric micelles based on poly(L-lactide)-b-poly(2-ethyl-2-oxazoline)-b-poly(L-lactide) (PLLA-PEOz-PLLA) ABA triblock copolymers were designed as intracellular drug carriers. The PLLA-PEOz-PLLA micelles adopt a "flower-like" arrangement with A-blocks at the core and a B-block on the shell under neutral condition. The deformation of the core-shell structure is then promoted by the aggregation of PEOzs due to the formation of inter- and intra-hydrogen bonding between protonated nitrogen and carbonyl groups. The experiments on in vitro release have confirmed that the release of doxorubicin (DOX) from micelles was successfully inhibited at pH 7.4. In contrast, an accelerated release of DOX from micelles was observed at acidic conditions. The results of growth inhibition assay indicated that the cell-killing rate of DOX-loaded micelles gradually approached that of free DOX as increasing the concentration and the incubation time. The overlay of fluorescent images on CLSM observation clearly demonstrated the colocalization of DOX with acidic compartments, suggesting that the drug release was successfully triggered in the acidic organelles by means of micelle deformation.