Nicotinic Acid Adenine Dinucleotide Phosphate (NAADP)-Mediated Calcium Signaling Is Active in Memory CD4+ T Cells.

Nicotinic acid adenine dinucleotide phosphate (NAADP), identified as one of the most potent calcium-mobilizing second messengers, has been studied in different eukaryotic cell types, including lymphocytes. Although aspects of NAADP-mediated calcium release in lymphocytes are still under debate, the organelles pertaining to NAADP-mediated calcium release are often characterized as acidic and related to lysosomes. Although NAADP-mediated calcium release in different subsets of T cells, including naïve, effector and natural regulatory T cells, has been studied, it has not been widely studied in memory CD4+ T cells, which show a different calcium flux profile. Using a pharmacological approach, the effect of Ned-19, an NAADP pathway antagonist, on the involvement of NAADP in TCR activation in murine memory CD4+ T cells and their downstream effector functions, such as proliferation and cytokine production, was studied. According to this study, Ned-19 inhibited TCR-mediated calcium flux and its downstream effector functions in primary memory CD4+ T cells. The study also revealed that both extracellular and intracellular calcium stores, including endoplasmic reticulum and lysosome-like acidic calcium stores, contribute to the TCR-mediated calcium flux in memory CD4+ T cells. NAADP-AM, a cell permeable analogue of NAADP, was shown to release calcium in memory CD4+ T cells and calcium flux was inhibited by Ned-19.

The Sequential Recruitments of Rab-GTPase Ypt1p and the NNS Complex onto pre-HAC1 mRNA Promote Its Nuclear Degradation in Baker's Yeast.

Induction of unfolded protein response involves activation of transcription factor Hac1p that is encoded by HAC1 pre-mRNA harboring an intron and a bipartite element (BE), which is subjected to nuclear mRNA decay by the nuclear exosome/Cbc1p-Tif4631p-dependent Exosome Targeting (CTEXT) complex. Using a combination of genetic and biochemical approaches, we demonstrate that a Rab-GTPase Ypt1p controls unfolded protein response signaling dynamics. This regulation relies on the nuclear localization of a small fraction of the cellular Ypt1p pool in the absence of endoplasmic reticulum (ER)-stress causing a strong association of the nuclear Ypt1p with pre-HAC1 mRNA that eventually promotes sequential recruitments of NNS, CTEXT, and the nuclear exosome onto this pre-mRNA. Recruitment of these decay factors onto pre-HAC1 mRNA is accompanied by its rapid nuclear decay that produces a precursor RNA pool lacking functional BE thereby causing its inefficient targeting to Ire1p foci leading to their diminished splicing and translation. ER stress triggers rapid relocalization of the nuclear pool of Ypt1p to the cytoplasm leading to its dissociation from pre-HAC1 mRNA thereby causing decreased recruitment of these decay factors to precursor HAC1 RNA leading to its diminished degradation. Reduced decay results in an increased abundance of pre-HAC1 mRNA with intact functional BE leading to its enhanced recruitment to Ire1p foci.

Fixing the catastrophic breakdown of single reference coupled cluster theory for strongly correlated systems: Two paradigms toward the implicit inclusion of high-rank correlation with low-spin channels.

The dual exponential coupled cluster theory proposed by Tribedi et al.[J. Chem. Theory Comput. 16, 10, 6317-6328 (2020)] performs significantly better for a wide range of weakly correlated systems than the coupled cluster theory with singles and doubles excitations due to the implicit inclusion of high-rank excitations. The high-rank excitations are included through the action of a set of vacuum annihilating scattering operators that act non-trivially on certain correlated wavefunctions and are determined via a set of local denominators involving the energy difference between certain excited states. This often leads the theory to be prone to instabilities. In this paper, we show that restricting the correlated wavefunction, on which the scattering operators act, to be spanned by only the singlet-paired determinants can avoid catastrophic breakdown. For the first time, we present two nonequivalent approaches to arrive at the working equations, viz., the projective approach with sufficiency conditions and the amplitude form with many-body expansion. Although the effect of the triple excitation is quite small around molecular equilibrium geometry, this scheme leads to a better qualitative description of the energetics in the regions of strong correlation. With many pilot numerical applications, we have demonstrated the performance of the dual-exponential scheme with both the proposed solution strategies while restricting the excitation subspaces coupled to the corresponding lowest spin channels.

Novel characterization of CXCR4 expressing cells in uninfected and herpes simplex virus-1 infected corneas.

PURPOSE: To characterize CXCR4-expressing cells in uninfected and herpes simplex virus-1 (HSV-1) infected corneas. METHODS: The corneas of C57BL/6J mice were infected with HSV-1 McKrae. The RT-qPCR assay detected CXCR4 and CXCL12 transcripts in uninfected and HSV-1-infected corneas. Immunofluorescence staining for CXCR4 and CXCL12 protein was performed in the frozen sections of herpes stromal keratitis (HSK) corneas. Flow cytometry assay characterized the CXCR4-expressing cells in uninfected and HSV-1-infected corneas. RESULTS: Flow cytometry data showed CXCR4 expressing cells in the separated epithelium and stroma of uninfected corneas. In the uninfected stroma, CD11b + F4/80+ macrophages are the predominant CXCR4-expressing cells. In contrast, most CXCR4 expressing cells in the uninfected epithelium were CD207 (langerin)+, CD11c+, and expressed MHC class II molecule, documenting the Langerhans cells (LCs) phenotype. After corneal HSV-1 infection, CXCR4 and CXCL12 mRNA levels increased significantly in HSK corneas than in uninfected corneas. Immunofluorescence staining showed CXCR4 and CXCL12 protein localization in the newly formed blood vessels in the HSK cornea. Furthermore, the infection resulted in LCs proliferation, causing an increase in their numbers in the epithelium at 4 days post-infection (p.i.). However, by 9-day p.i., the LCs numbers declined to the counts observed in naïve corneal epithelium. Our results also showed neutrophils and vascular endothelial cells as the prominent CXCR4-expressing cell types in the stroma of HSK corneas. CONCLUSIONS: Together, our data demonstrate the expression of CXCR4 on resident antigen presenting cells in the uninfected cornea and on infiltrating neutrophils and newly formed blood vessels in the HSK cornea.

A Synergistic Approach towards Optimization of Coupled Cluster Amplitudes by Exploiting Dynamical Hierarchy.

The coupled cluster iteration scheme for determining the cluster amplitudes involves a set of nonlinearly coupled difference equations. In the space spanned by the amplitudes, the set of equations are analyzed as a multivariate time-discrete map where the concept of time appears in an implicit manner. With the observation that the cluster amplitudes have difference in their relaxation timescales with respect to the distributions of their magnitudes, the coupled cluster iteration dynamics are considered as a synergistic motion of coexisting slow and fast relaxing modes, manifesting a dynamical hierarchical structure. With the identification of the highly damped auxiliary amplitudes, their time variation can be neglected compared to the principal amplitudes which take much longer time to reach the fixed points. We analytically establish the adiabatic approximation where each of these auxiliary amplitudes are expressed as unique parametric functions of the collective principal amplitudes, allowing us to study the optimization with the latter taken as the independent degrees of freedom. Such decoupling of the amplitudes significantly reduces the computational scaling without sacrificing the accuracy in the ground state energy as demonstrated by a number of challenging molecular applications. A road-map to treat higher order post-adiabatic effects is also discussed.

Diphenyleneiodonium Treatment Inhibits the Development of Severe Herpes Stromal Keratitis Lesions.

Reactive oxygen species (ROS) play an important role in tissue inflammation. In this study, we measured the intracellular level of ROS in herpes stromal keratitis (HSK) corneas and determined the outcome of manipulating ROS level on HSK severity. Our results showed the predominance of ROS generation in neutrophils but not CD4 T cells in HSK corneas. NADPH oxidase 2 (NOX2) enzyme is known to generate ROS in myeloid cells. Our results showed baseline expression of different NOX2 subunits in uninfected corneas. After corneal herpes simplex virus-1 (HSV-1) infection, an enhanced expression of NOX2 subunits was detected in infected corneas. Furthermore, flow cytometry results showed a higher level of gp91 (Nox2 subunit) protein in neutrophils from HSK corneas, suggesting the involvement of NOX2 in generating ROS. However, no significant decrease in ROS level was noticed in neutrophils from HSV-1-infected gp91-/- mice than in C57BL/6J (B6) mice, suggesting NOX2 is not the major contributor in generating ROS in neutrophils. Next, we used diphenyleneiodonium (DPI), a flavoenzyme inhibitor, to pharmacologically manipulate the ROS levels in HSV-1-infected mice. Surprisingly, the neutrophils from peripheral blood and corneas of the DPI-treated group exhibited an increased level of ROS than the vehicle-treated group of infected B6 mice. Excessive ROS is known to cause cell death. Accordingly, DPI treatment resulted in a significant decrease in neutrophil frequency in peripheral blood and corneas of infected mice and was associated with reduced corneal pathology. Together, our results suggest that regulating ROS levels in neutrophils can ameliorate HSK severity. IMPORTANCE Neutrophils are one of the primary immune cell types involved in causing tissue damage after corneal HSV-1 infection. This study demonstrates that intracellular ROS production in the neutrophils in HSK lesions is not NOX2 dependent. Furthermore, manipulating ROS levels in neutrophils ameliorates the severity of HSK lesions. Our findings suggest that excessive intracellular ROS in neutrophils disrupt redox homeostasis and affect their survival, resulting in a decrease in HSK lesion severity.

A double exponential coupled cluster theory in the fragment molecular orbital framework.

Fragmentation-based methods enable electronic structure calculations for large chemical systems through partitioning them into smaller fragments. Here, we have developed and benchmarked a dual exponential operator-based coupled cluster theory to account for high-rank electronic correlation of large chemical systems within the fragment molecular orbital (FMO) framework. Upon partitioning the molecular system into several fragments, the zeroth order reference determinants for each fragment and fragment pair are constructed in a self-consistent manner with two-body FMO expansion. The dynamical correlation is induced through a dual exponential ansatz with a set of fragment-specific rank-one and rank-two operators that act on the individual reference determinants. While the single and double excitations for each fragment are included through the conventional rank-one and rank-two cluster operators, the triple excitation space is spanned via the contraction between the cluster operators and a set of rank-two scattering operators over a few optimized fragment-specific occupied and virtual orbitals. Thus, the high-rank dynamical correlation effects within the FMO framework are computed with rank-one and rank-two parametrization of the wave operator, leading to significant reduction in the number of variables and associated computational scaling over the conventional methods. Through a series of pilot numerical applications on various covalent and non-covalently bonded systems, we have shown the quantitative accuracy of the proposed methodology compared to canonical, as well as FMO-based coupled-cluster single double triple. The accuracy of the proposed method is shown to be systematically improvable upon increasing the number of contractible occupied and virtual molecular orbitals employed to simulate triple excitations.

Accelerating coupled cluster calculations with nonlinear dynamics and supervised machine learning.

In this paper, the iteration scheme associated with single reference coupled cluster theory has been analyzed using nonlinear dynamics. The phase space analysis indicates the presence of a few significant cluster amplitudes, mostly involving valence excitations, that dictate the dynamics, while all other amplitudes are enslaved. Starting with a few initial iterations to establish the inter-relationship among the cluster amplitudes, a supervised machine learning scheme with a polynomial kernel ridge regression model has been employed to express each of the enslaved amplitudes uniquely in terms of the former set of amplitudes. The subsequent coupled cluster iterations are restricted solely to determine those significant excitations, and the enslaved amplitudes are determined through the already established functional mapping. We will show that our hybrid scheme leads to a significant reduction in the computational time without sacrificing the accuracy.

Stability analysis of a double similarity transformed coupled cluster theory.

In this paper, we have analyzed the time series associated with the iterative scheme of a double similarity transformed coupled cluster theory. The coupled iterative scheme to solve the ground state Schrödinger equation is cast as a multivariate time-discrete map, and the solutions show the universal Feigenbaum dynamics. Using recurrence analysis, it is shown that the dynamics of the iterative process is dictated by a small subgroup of cluster operators, mostly those involving chemically active orbitals, whereas all other cluster operators with smaller amplitudes are enslaved. Using synergetics, we will indicate how the master-slave dynamics can suitably be exploited to develop a novel coupled-cluster algorithm in a much reduced dimension.

Formulation of a Dressed Coupled-Cluster Method with Implicit Triple Excitations and Benchmark Application to Hydrogen-Bonded Systems.

In this paper, we present a coupled-cluster theory based on a double-exponential wave operator ansatz, which is capable of mimicking the effects of connected triple excitations in an iterative manner. The triply excited manifold is spanned via the action of a set of scattering operators on doubly excited determinants, whereas their action annihilates the Hartree-Fock reference determinant. The effect of triple excitations is included at a computational scaling slightly higher than that of conventional coupled-cluster singles and doubles. Furthermore, we demonstrate two approximate schemes, which arise naturally, and argue that both these schemes come equipped with certain renormalization terms capable of handling nonbonding interactions due to robust inclusion of the screened Coulomb interaction. We justify our claims from both a theoretical perspective and a number of numerical applications to prototypical water clusters, in a number of basis functions. Our methods show overall comparable performance to the canonical coupled-cluster theory with singles, doubles, and perturbative triples (CCSD(T)) and allied methods, however, at a lower computational scaling.

Effect of hockey-stick-shaped molecules on the critical behavior at the nematic to isotropic and smectic-A to nematic phase transitions in octylcyanobiphenyl.

In the field of soft matter research, the characteristic behavior of both nematic-isotropic (N-I) and smectic-A nematic(Sm-A N) phase transitions has gained considerable attention due to their several attractive features. In this work, a high-resolution measurement of optical birefringence (Δn) has been performed to probe the critical behavior at the N-I and Sm-A N phase transitions in a binary system comprising the rodlike octylcyanobiphenyl and a laterally methyl substituted hockey-stick-shaped mesogen, 4-(3-n-decyloxy-2-methyl-phenyliminomethyl)phenyl 4-n-dodecyloxycinnamate. For the investigated mixtures, the critical exponent ß related to the limiting behavior of the nematic order parameter close to the N-I phase transition has come out to be in good conformity with the tricritical hypothesis. Moreover, the yielded effective critical exponents (α', ß', γ') characterizing the critical fluctuation near the Sm-A N phase transition have appeared to be nonuniversal in nature. With increasing hockey-stick-shaped dopant concentration, the Sm-A N phase transition demonstrates a strong tendency to be driven towards a first-order nature. Such a behavior has been accounted for by considering a modification of the effective intermolecular interactions and hence the related coupling between the nematic and smectic order parameters, caused by the introduction of the angular mesogenic molecules.