Theory of polarization-averaged core-level molecular-frame photoelectron angular distributions: III. new formula for p- and s-wave interference analogous to Young's double-slit experiment for core-level photoemission from hetero-diatomic molecules

We present a new variation of Young's double-slit formula for polarization-averaged molecular-frame photoelectron angular distributions (PA-MFPADs) of hetero-diatomic molecules, which may be used to extract the bond length. So far, empirical analysis of the PA-MFPADs has often been carried out employing Young's formula in which each of the two atomic centers emits a s-photoelectron wave. The PA-MFPADs, on the other hand, can consist of an interference between the p-wave from the X-ray absorbing atom emitted along the molecular axis and the s-wave scattered by neighboring atom, within the framework of Multiple Scattering theory. The difference of this p-s wave interference from the commonly used s-s wave interference causes a dramatic change in the interference pattern, especially near the angles perpendicular to the molecular axis. This change involves an additional fringe, urging us to caution when using the conventional Young's formula for retrieving the bond length. We have derived a new formula analogous to Young's formula but for the p-s wave interference. The bond lengths retrieved from the PA-MFPADs via the new formula reproduce the original C-O bond lengths used in the reference ab-initio PA-MFPADs within the relative error of 5 %. In the high energy regime, this new formula for p-s wave interference converges to the ordinary Young’s formula for the s-s wave interference. We expect it to be used to retrieve the bond length for time-resolved PA-MFPADs instead of the conventional Young's formula.

Reply to the comment by Amano on “Linear and bent triatomic molecules are not qualitatively different!”

In Amano’s comment on Jensen’s paper, we notice two important misconceptions: (i) Amano overlooks the fact that all features special for a linear molecule originate in the double degeneracy in the bending motion (i.e., in the fact that for a linear triatomic molecule, the description of the bending motion must necessarily also involve the rotation about the axis of least moment of inertia, the a axis, which becomes the molecular axis at equilibrium), and (ii) the expectation value generated from the wavefunction gives an “average” value of the relevant observable (coordinate); the expectation value can, in principle, be obtained experimentally as the average of very many repeated measurements of the observable. In our previous papers on this subject, in particular the paper by Jensen discussed here, we have attempted to explain our results as coherently and “pedagogically” as we can, starting with the fundamental principles of quantum mechanics, and we encourage interested readers to refer to our previous works on the subject. Thus, we maintain our assertion that the vibrationally averaged structure of a linear molecule is observed as being bent, as we have demonstrated previously from both theoretical and experimental viewpoints.

Serotonin transporter-mediated molecular axis regulates regional retinal ganglion cell vulnerability and axon regeneration after nerve injury

Molecular insights into the selective vulnerability of retinal ganglion cells (RGCs) in optic neuropathies and after ocular trauma can lead to the development of novel therapeutic strategies aimed at preserving RGCs. However, little is known about what molecular contexts determine RGC susceptibility. In this study, we show the molecular mechanisms underlying the regional differential vulnerability of RGCs after optic nerve injury. We identified RGCs in the mouse peripheral ventrotemporal (VT) retina as the earliest population of RGCs susceptible to optic nerve injury. Mechanistically, the serotonin transporter (SERT) is upregulated on VT axons after injury. Utilizing SERT-deficient mice, loss of SERT attenuated VT RGC death and led to robust retinal axon regeneration. Integrin β3, a factor mediating SERT-induced functions in other systems, is also upregulated in RGCs and axons after injury, and loss of integrin β3 led to VT RGC protection and axon regeneration. Finally, RNA sequencing analyses revealed that loss of SERT significantly altered molecular signatures in the VT retina after optic nerve injury, including expression of the transmembrane protein, Gpnmb. GPNMB is rapidly downregulated in wild-type, but not SERT- or integrin β3-deficient VT RGCs after injury, and maintaining expression of GPNMB in RGCs via AAV2 viruses even after injury promoted VT RGC survival and axon regeneration. Taken together, our findings demonstrate that the SERT-integrin β3-GPNMB molecular axis mediates selective RGC vulnerability and axon regeneration after optic nerve injury.

Anomalous dependence of ionization probability and electron angular distributions on orientation of molecular axis in photoionization of H+ 2: effect of two-center interference

A theoretical and computational study of photoionization of the one-electron molecular ion H+ 2 initially in the 1σu state is performed. The laser pulse is linearly polarized with the carrier wavelength in the extreme ultraviolet region. The electron wave function is obtained by solving the time-dependent Schrödinger equation with the help of the generalized pseudospectral method. The dependence of the total ionization probability and photoelectron spectra on the orientation of the molecular axis is analyzed. At the wavelength of 12.5 nm, anomalous behavior of the ionization probability is found, where the ionization probability increases with an increase of the angle between the polarization vector of the external field and the molecular axis and reaches a maximum at the perpendicular orientation of the molecule. The phenomenon is explained as resulting from the two-center interference in the wave function of the emitted electron. When the wavelength or internuclear distance change, the effect disappears, and the ionization probability exhibits its usual behavior with the maximum at the parallel orientation of the molecular axis.

Long Noncoding RNA KCNQ1OT1 Induces Resistance of HCC Cells To Cisplatin Through Regulating The miR-26a/CCND2 Molecular Axis

Objective: To explore the molecular mechanism by which LncRNA KCNQ1OT1 regulated the miR-26a/CCND2 molecular axis to participate in the resistance of Hepatocellular carcinoma(HCC) cells to cisplatin.Methods: Cancer tissue and corresponding para-carcinoma tissue specimens were collected from 25 HCC patients with complete data admitted from January 2018 to December 2018 at The Transplantation Center of the Third Xiangya Hospital. Then, the expression levels of KCNQ1OT1, miR-26a and CCND2 in HCCtissues and cell lines were detected through qRT-PCR. Meanwhile, the sensitivity of HCC cells to cisplatin was examined through Transwell and Annexin V-FITC/PI double staining flow cytometry. Further, the targeted relationships among KCNQ1OT1, miR-26a and CCND were verified through dual-luciferase reporter gene assay, and the regulatory relationships were detected through Western blotting and qRT-PCR.Results: KCNQ1OT1 was highly expressed in HCC tissues and cisplatin-resistant cell lines; meanwhile, over-expression of KCNQ1OT1 promoted the resistance of Huh7/CDDP cells to cisplatin. Dual-luciferase reporter gene assay verified that, KCNQ1OT1 targeted miR-26a and down-regulated its expression level. miR-26a suppressed Huh7/CDDP cell proliferation and invasion, while promoting their apoptosis, thus down-regulating the promoting effect of KCNQ1OT1 on the cisplatin resistance of HCC cells. miR-26a negatively regulated CCND2 expression, while KCNQ1OT1 down-regulated the suppression of miR-26a on CCND2 to promote Huh7/CDDP cell proliferation and invasion and to suppress apoptosis, thereby up-regulating the resistance of HCCcells to cisplatin. Conclusions: LncRNA KCNQ1OT1 regulates the miR-26a/CCND2 molecular axis to induce the resistance of HCC cells to cisplatin.

A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency

SUMMARYTET1 maintains hypomethylation at bivalent promoters through its catalytic activity in embryonic stem cells (ESCs). However, whether and how TET1 exerts catalytic activity-independent functions in regulating bivalent genes is not well understood. Using a proteomics approach, we mapped the TET1 interactome in mouse ESCs and identified PSPC1 as a novel TET1 partner. Genome-wide location analysis reveals that PSPC1 functionally associates with TET1 and Polycomb repressive complex-2 (PRC2) complex. We establish that PSPC1 and TET1 repress, and Neat1, the PSPC1 cognate lncRNA, activates the bivalent gene expression. In ESCs, Neat1 tethers the TET1-PSPC1 pair with PRC2 at bivalent promoters. During the ESC-to-formative epiblast-like stem cell (EpiLC) transition, PSPC1 and TET1 promote PRC2 chromatin occupancy at bivalent gene promoters while restricting Neat1 functions in facilitating PRC2 binding to bivalent gene transcripts. Our study uncovers a novel TET1-PSPC1-Neat1 molecular axis that modulates PRC2 binding affinity to chromatin and bivalent gene transcripts in controlling stem cell bivalency.In BriefTET1 is a transcriptional repressor for bivalent genes in pluripotent stem cells, but its mechanistic action on stem cell bivalency is unclear. Huang et al. use proteomics and genetic approaches to reveal that catalytic activity-independent functions of TET1, coordinated with the paraspeckle components PSPC1 and its cognate lncRNA Neat1, dynamically regulates stem cell bivalency by modulating PRC2 binding affinity to chromatin and bivalent gene transcripts in pluripotent state transition.HighlightsThe TET1 interactome identifies PSPC1 as a novel partner in ESCsTET1 and PSPC1 repress bivalent genes by promoting PRC2 chromatin occupancyNeat1 facilitates bivalent gene activation by promoting PRC2 binding to their mRNAsNeat1 bridges the TET1-PSPC1 and PRC2 complexes in regulating bivalent gene transcription

O-100 The follicular fluid derived exosomes facilitate the differentiation of oocytes from human induced pluripotent stem cells through miR218 / PI3K / Akt molecular axis

Abstract withdrawn by the authors

Molecular Mechanism of circRAPGEF5 in Regulating the Molecular Axis of microRNA-4712-5p/Tyrosine 3-Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Epsilon Affecting Cellular Proliferation and Apoptosis in Mammary Cancer

To understand the molecular mechanism of circRAPGEF5, its effect on the proliferation and apoptosis of mammary cancer cells, and its regulatory effect on the molecular axis of miRNA-4712-5p/YWHAE. qRT-PCR and Western blot were used to test circRAPGEF5, miRNA-4712-5p, and YWHAE expression in mammary cancer and paracancerous tissues. The human mammary cancer cell, MDA-MB-231, was cultured in vitro, and pcDNA-NC, pcDNA-circRAPGEF5, anti-miRNA-NC, anti-miRNA-4712-5p, pcDNA-circRAPGEF5, and miRNA-NC, pcDNA-circRAPGEF5 were transfected into MDA-MB-231 cells with miRNA-4712-5p mimics. qRT-PCR and Western blot were employed to detect circRAPGEF5, miRNA-4712-5p, and YWHAE expression in cells. The CCK-8 methodand plate clone formation experiment were conducted to test cellular proliferation ability. Flow cytometry was performed to detect apoptosis rate. Dual luciferase reporter assays were used to test the targeting association between circRAPGEF5 and miRNA-4712-5p, and the targeting association between miRNA-4712-5p and YWHAE. Western blot was utilized to detect Bcl-2, Bax, and Cleared Caspase-3 protein expression. In comparison with paracancerous tissues, circRAPGEF5 and YWHAE expression levels in mammary cancer tissues were significantly reduced (P < 0.05), and miRNA-4712-5p expression levels were significantly increased (P < 0.05). Transfection of pcDNA-circRAPGEF5 or trans-anti-miRNA-4712-5p could reduce the optical density (OD) value, Bcl-2 protein level and clonal formation number to a significant extent (P < 0.05), and it increases Bax and Cleaved Caspase-3 apoptosis rate and protein levels (P < 0.05). Dual luciferase reporter assays confirmed that there was target binding between circRAPGEF5 and miRNA-4712-5p and between miRNA-4712-5p and YWHAE. Co-transfection of pcDNA-circRAP GEF5 and miRNA-4712-5p could greatly reduce transfection of pcDNA-circRAP GEF5 and its effect on the proliferation and apoptosis of MDA-MB-231 cells. Overexpression of circRAPGEF5 can inhibit the proliferation of mammary cancer cells and induce apoptosis by regulating the molecular axis of miRNA-4712-5p/YWHAE.

Artificial Symmetries for Calculating Vibrational Energies of Linear Molecules

Linear molecules usually represent a special case in rotational-vibrational calculations due to a singularity of the kinetic energy operator that arises from the rotation about the a (the principal axis of least moment of inertia, becoming the molecular axis at the linear equilibrium geometry) being undefined. Assuming the standard ro-vibrational basis functions, in the 3N−6 approach, of the form ∣ν1,ν2,ν3ℓ3;J,k,m⟩, tackling the unique difficulties of linear molecules involves constraining the vibrational and rotational functions with k=ℓ3, which are the projections, in units of ℏ, of the corresponding angular momenta onto the molecular axis. These basis functions are assigned to irreducible representations (irreps) of the C2v(M) molecular symmetry group. This, in turn, necessitates purpose-built codes that specifically deal with linear molecules. In the present work, we describe an alternative scheme and introduce an (artificial) group that ensures that the condition ℓ3=k is automatically applied solely through symmetry group algebra. The advantage of such an approach is that the application of symmetry group algebra in ro-vibrational calculations is ubiquitous, and so this method can be used to enable ro-vibrational calculations of linear molecules in polyatomic codes with fairly minimal modifications. To this end, we construct a—formally infinite—artificial molecular symmetry group D∞h(AEM), which consists of one-dimensional (non-degenerate) irreducible representations and use it to classify vibrational and rotational basis functions according to ℓ and k. This extension to non-rigorous, artificial symmetry groups is based on cyclic groups of prime-order. Opposite to the usual scenario, where the form of symmetry adapted basis sets is dictated by the symmetry group the molecule belongs to, here the symmetry group D∞h(AEM) is built to satisfy properties for the convenience of the basis set construction and matrix elements calculations. We believe that the idea of purpose-built artificial symmetry groups can be useful in other applications.

Angular dependence of the Wigner time delay upon tunnel ionization of H2

When a very strong light field is applied to a molecule an electron can be ejected by tunneling. In order to quantify the time-resolved dynamics of this ionization process, the concept of the Wigner time delay can be used. The properties of this process can depend on the tunneling direction relative to the molecular axis. Here, we show experimental and theoretical data on the Wigner time delay for tunnel ionization of H2 molecules and demonstrate its dependence on the emission direction of the electron with respect to the molecular axis. We find, that the observed changes in the Wigner time delay can be quantitatively explained by elongated/shortened travel paths of the emitted electrons, which occur due to spatial shifts of the electrons’ birth positions after tunneling. Our work provides therefore an intuitive perspective towards the Wigner time delay in strong-field ionization.