Ocular A-to-I RNA editing signatures associated with SARS-CoV-2 infection.

Ophthalmic manifestations have recently been observed in acute and post-acute complications of COVID-19 caused by SARS-CoV-2 infection. Our precious study has shown that host RNA editing is linked to RNA viral infection, yet ocular adenosine to inosine (A-to-I) RNA editing during SARS-CoV-2 infection remains uninvestigated in COVID-19. Herein we used an epitranscriptomic pipeline to analyze 37 samples and investigate A-to-I editing associated with SARS-CoV-2 infection, in five ocular tissue types including the conjunctiva, limbus, cornea, sclera, and retinal organoids. Our results revealed dramatically altered A-to-I RNA editing across the five ocular tissues. Notably, the transcriptome-wide average level of RNA editing was increased in the cornea but generally decreased in the other four ocular tissues. Functional enrichment analysis showed that differential RNA editing (DRE) was mainly in genes related to ubiquitin-dependent protein catabolic process, transcriptional regulation, and RNA splicing. In addition to tissue-specific RNA editing found in each tissue, common RNA editing was observed across different tissues, especially in the innate antiviral immune gene MAVS and the E3 ubiquitin-protein ligase MDM2. Analysis in retinal organoids further revealed highly dynamic RNA editing alterations over time during SARS-CoV-2 infection. Our study thus suggested the potential role played by RNA editing in ophthalmic manifestations of COVID-19, and highlighted its potential transcriptome impact, especially on innate immunity.

Dysregulated RNA editing of EIF2AK2 in polycystic ovary syndrome: clinical relevance and functional implications.

BACKGROUND: Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder affecting women of reproductive ages. Our previous study has implicated a possible link between RNA editing and PCOS, yet the actual role of RNA editing, its association with clinical features, and the underlying mechanisms remain unclear. METHODS: Ten RNA-Seq datasets containing 269 samples of multiple tissue types, including granulosa cells, T helper cells, placenta, oocyte, endometrial stromal cells, endometrium, and adipose tissues, were retrieved from public databases. Peripheral blood samples were collected from twelve PCOS and ten controls and subjected to RNA-Seq. Transcriptome-wide RNA-Seq data analysis was conducted to identify differential RNA editing (DRE) between PCOS and controls. The functional significance of DRE was evaluated by luciferase reporter assays and overexpression in human HEK293T cells. Dehydroepiandrosterone and lipopolysaccharide were used to stimulate human KGN granulosa cells to evaluate gene expression. RESULTS: RNA editing dysregulations across multiple tissues were found to be associated with PCOS in public datasets. Peripheral blood transcriptome analysis revealed 798 DRE events associated with PCOS. Through weighted gene co-expression network analysis, our results revealed a set of hub DRE events in PCOS blood. A DRE event in the eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2:chr2:37,100,559) was associated with PCOS clinical features such as luteinizing hormone (LH) and the ratio of LH over follicle-stimulating hormone. Luciferase assays, overexpression, and knockout of RNA editing enzyme adenosine deaminase RNA specific (ADAR) showed that the ADAR-mediated editing cis-regulated EIF2AK2 expression. EIAF2AK2 showed a higher expression after dehydroepiandrosterone and lipopolysaccharide stimulation, triggering changes in the downstrean MAPK pathway. CONCLUSIONS: Our study presented the first evidence of cross-tissue RNA editing dysregulation in PCOS and its clinical associations. The dysregulation of RNA editing mediated by ADAR and the disrupted target EIF2AK2 may contribute to PCOS development via the MPAK pathway, underlining such epigenetic mechanisms in the disease.

Hydrogen Bonding-Assisted and Nonheme Manganese-Catalyzed Remote Hydroxylation of C-H Bonds in Nitrogen-Containing Molecules.

The development of catalytic systems capable of oxygenating unactivated C-H bonds with excellent site-selectivity and functional group tolerance under mild conditions remains a challenge. Inspired by the secondary coordination sphere (SCS) hydrogen bonding in metallooxygenases, reported herein is an SCS solvent hydrogen bonding strategy that employs 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) as a strong hydrogen bond donor solvent to enable remote C-H hydroxylation in the presence of basic aza-heteroaromatic rings with a low loading of a readily available and inexpensive manganese complex as a catalyst and hydrogen peroxide as a terminal oxidant. We demonstrate that this strategy represents a promising compliment to the current state-of-the-art protection approaches that rely on precomplexation with strong Lewis and/or Brønsted acids. Mechanistic studies with experimental and theoretical approaches reveal the existence of a strong hydrogen bonding between the nitrogen-containing substrate and HFIP, which prevents the catalyst deactivation by nitrogen binding and deactivates the basic nitrogen atom toward oxygen atom transfer and the α-C-H bonds adjacent to the nitrogen center toward H-atom abstraction. Moreover, the hydrogen bonding exerted by HFIP has also been demonstrated not only to facilitate the O-O bond heterolytic cleavage of a putative MnIII-OOH precursor to generate MnV(O)(OC(O)CH2Br) as an active oxidant but also to affect the stability and the activity of MnV(O)(OC(O)CH2Br).

Background-free single-beam coherent Raman spectroscopy assisted by air lasing.

We develop a background-free single-beam coherent Raman scattering technique enabling the high-sensitivity detection of greenhouse gases. In this scheme, Raman coherence prepared by a femtosecond laser is interrogated by self-generated narrowband air lasing, thus allowing single-beam measurements without complex pulse shaping. The unique temporal and spectral characteristics of air lasing are beneficial for improving the signal-to-noise ratio and spectral resolution of Raman signals. With this method, SF6 gas present at a concentration of 0.38% was detected in an SF6-air mixture. This technique provides a simple and promising route for remote detection due to the low divergence of Raman signals and the availability of high-energy pump lasers, which may broaden the potential applications of air lasing.

Retrieval of molecular alignment and identification of multiple-orbital contribution by using polarized high harmonics from aligned N2 molecules.

With the parallel and perpendicular components of high harmonics generated by using aligned N2 molecules, we propose a method to retrieve the alignment distribution induced by the aligning laser based on the quantitative rescattering theory. And the intensity of pump laser and gas temperature can be precisely determined as well. We find that the intensity ratio between two harmonic components is very sensitive to the inclusion of multiple-orbital contribution in the theory. We thus suggest that it could be used to identify the interference from inner orbitals by tuning input laser power or extending the spectral region of high harmonics.

Vibrational Raman scattering from coherently excited molecular ions in a strong laser field.

We report on a pump-probe investigation of vibrational Raman scattering from coherently excited N2+ ions. It is found that the Raman signals produced by the inelastic scattering of the probe pulse from molecular ions can be dramatically enhanced when the probe laser is resonant with electronic transitions in N2+ ions. The Raman signal can be amplified at 428 nm wavelength due to the presence of population inversion in N2+ ions.

Free-space Ν2+ lasers generated in strong laser fields: the role of molecular vibration.

We investigate free-space lasing actions from molecular nitrogen ions (N2+) at the wavelengths of ~391 nm and ~428 nm. Our results show that pronounced gain can be measured at either 391 nm or 428 nm laser wavelength with a pump laser centered at 800 nm wavelength, whereas the gain at 391 nm laser wavelength completely disappears when the wavelength of the pump laser is tuned to 1500 nm. Our theoretical analysis reveals that the different gain behaviors can be attributed to the vibrational distribution of populations in X2Σg+(v=0) and X2Σg+(v=1) states as the N2+ ions are generated by photoionization in the laser fields, giving rise to more robust (i.e., less sensitive to the pump laser wavelength) population inversion for generating the 428 nm laser.

Near-Resonant Raman Amplification in the Rotational Quantum Wave Packets of Nitrogen Molecular Ions Generated by Strong Field Ionization.

The generation of laserlike narrow bandwidth emissions from nitrogen molecular ions (N_{2}^{+}) generated in intense near- and mid infrared femtosecond laser fields has aroused much interest because of the mysterious physics underlying such a phenomenon. Here, we perform a pump-probe measurement on the nonlinear interaction of rotational quantum wave packets of N_{2}^{+} generated in midinfrared (e.g., at a wavelength centered at 1580 nm) femtosecond laser fields with an ultrashort probe pulse whose broad spectrum overlaps both P- and R-branch rotational transition lines between the electronic states N_{2}^{+}(B^{2}Σ_{u}^{+},v^{'}=0) and N_{2}^{+}(X^{2}Σ_{g}^{+},v=0). The results indicate the occurrence of highly efficient near-resonant stimulated Raman scattering in the quantum wave packets of N_{2}^{+} ions generated in strong laser fields in the midinfrared region, of which the underlying mechanism is different from that of the air lasers generated in atmospheric environment when pumping with 800 nm intense pulses.

Population Redistribution Among Multiple Electronic States of Molecular Nitrogen Ions in Strong Laser Fields.

We carry out a combined theoretical and experimental investigation on the population distributions in the ground and excited states of tunnel-ionized nitrogen molecules at various driver wavelengths in the near- and midinfrared range. Our results reveal that efficient couplings (i.e., population exchanges) between the ground N_{2}^{+}(X^{2}Σ_{g}^{+}) state and the excited N_{2}^{+}(A^{2}Π_{u}) and N_{2}^{+}(B^{2}Σ_{u}^{+}) states occur in strong laser fields. The couplings result in a population inversion between the N_{2}^{+}(X^{2}Σ_{g}^{+}) and N_{2}^{+}(B^{2}Σ_{u}^{+}) states at wavelengths near 800 nm, which is verified by our experimental observation of the amplification of a seed at ∼391 nm. The result provides insight into the mechanism of free-space nitrogen ion lasers generated in remote air with strong femtosecond laser pulses.

Fabrication of a microresonator-fiber assembly maintaining a high-quality factor by CO2 laser welding.

We demonstrate fabrication of a microtoroid resonator of a high-quality (high-Q) factor using femtosecond laser three-dimensional (3D) micromachining. A fiber taper is reliably assembled to the microtoroid using CO2 laser welding. Specifically, we achieve a high-Q-factor of 2.12 × 10(6) in the microresonator-fiber assembly by optimizing the contact position between the fiber taper and the microtoroid.

Quantum path selection in high-order harmonic generation from aligned molecules.

We theoretically investigate high-order harmonic generation (HHG) from aligned N(2) molecules with a driving field composed of two-color circularly polarized laser pulses. It is shown that the combination of N(2) molecules and the waveform-controlled laser field allows us to select either long or short quantum path, depending on molecular alignment angles, while in atom Ar, two paths show comparable contribution to HHG. The selection of single quantum path in aligned N(2) molecules leads to an ultrabroad and smooth XUV supercontinuum, giving rise to isolated attosecond pulses generation. Moreover, we can control the intensity ratio of two attosecond pulses by adjusting the molecular alignment angles, providing an opportunity for attosecond pump-probe technique.

Gain dynamics of a free-space nitrogen laser pumped by circularly polarized femtosecond laser pulses.

We experimentally demonstrate ultrafast dynamic of generation of the 337-nm nitrogen laser by injecting an external seed pulse into a femtosecond laser filament pumped by a circularly polarized laser pulse. In the pump-probe scheme, it is revealed that the population inversion between the C(3)Π(u) and B(3)Π(g) states of N(2) for the free-space 337-nm laser is firstly built up on the timescale of several picoseconds, followed by a relatively slow decay on the timescale of tens of picoseconds, depending on the nitrogen gas pressure. By measuring the intensities of 337-nm signal from nitrogen gas mixed with different concentrations of oxygen gas, it is also found that oxygen molecules have a significant quenching effect on the nitrogen laser signal. Our experimental observations agree with the picture of electron-impact excitation.

Generation of an air laser at extended distances by femtosecond laser filamentation with telescope optics.

We present the generation of self-induced-white-light-seeded lasing action of nitrogen molecules in air by a Ti:sapphire femtosecond laser (800 nm, 5.5 mJ) and demonstrate that such lasing action is strongly influenced by external focusing conditions. It is found that the self-seeded lasing signal of N(2)(+) at ~391 nm decreases dramatically by orders of magnitude and ultimately disappears when the focal length of an external lens increases from 0.5 m to 1 m. By using a telescope, it is shown that such limitation can be overcome and the 391 nm lasing can be controlled to occur at remotely designated distance, providing a possibility for practical applications in standoff spectroscopy.

Second harmonic generation in centrosymmetric gas with spatiotemporally focused intense femtosecond laser pulses.

We demonstrate unexpectedly strong second harmonic generation (SHG) in argon gas by use of spatio-temporally focused (SF) femtosecond laser pulses. The resulting SHG by the SF scheme at a 75 cm distance shows a significantly enhanced efficiency than that achieved with conventional focusing schemes, which offers a new promising possibility for standoff applications. Our theoretical calculations reasonably reproduce the experimental observations, which indicate that the observed SHG mainly originates from the gradient of non-uniform plasma dynamically controlled by the SF laser field.

Impulsive rotational Raman scattering of N2 by a remote "air laser" in femtosecond laser filament.

We report on experimental realization of impulsive rotational Raman scattering from neutral nitrogen molecules in a femtosecond laser filament using an intense self-induced white-light seeding "air laser" generated during the filamentation of an 800 nm Ti:sapphire laser in nitrogen gas. The impulsive rotational Raman fingerprint signals are observed with a maximum conversion efficiency of ∼0.8%. Our observation provides a promising way of remote identification and location of chemical species in the atmosphere by a rotational Raman scattering of molecules.

Spatiotemporal vortex strings.

Light carrying orbital angular momentum (OAM) holds unique properties and boosts myriad applications in diverse fields. However, the generation of an ultrafast wave packet carrying numerous vortices with various transverse OAM modes, i.e., vortex string, remains challenging, and the corresponding detection method is lacking. Here, we demonstrate that a vortex string with 28 spatiotemporal optical vortices (STOVs) with customizable topological charge (TC) arrangements can be generated in one wave packet. The diffraction rules of STOV strings are revealed theoretically and experimentally. Following these rules, the TC values and positions of all STOVs in a vortex string can be simultaneously recognized from the diffraction pattern. Such STOV strings facilitate STOV-based optical communication. As a proof-of-principle demonstration, the transmission of an image is realized with 16-STOV strings. This work provides guidance for revealing the underlying properties of the transverse OAM light and opens up opportunities for applications of the structured light in optical communication, quantum information processing, etc.

PAFAH1B3 is a KLF9 target gene that promotes proliferation and metastasis in pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal human malignancies. Uncontrolled cell proliferation, invasion and migration of pancreatic cancer cells are the fundamental causes of death in PDAC patients. Our previous studies showed that KLF9 inhibits the proliferation, invasion and migration of pancreatic cancer cells. However, the underlying mechanisms are not fully understood. In this study, we found that platelet-activating factor acetylhydrolase IB3 (PAFAH1B3) is highly expressed in pancreatic cancer tissues and cells. In vitro and in vivo studies showed that overexpression of PAFAH1B3 promoted the proliferation and invasion of pancreatic cancer cells, while downregulation of PAFAH1B3 inhibited these processes. We found that KLF9 expression is negatively correlated with PAFAH1B3 expression in pancreatic cancer tissues and cells. Western blotting revealed that KLF9 negatively regulates the expression of PAFAH1B3 in pancreatic cancer tissues and cells. Rescue experiments showed that overexpression of PAFAH1B3 could partially attenuate the suppression of pancreatic cancer cell proliferation, invasion and migration induced by KLF9 overexpression. Finally, chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays were carried out, and the results showed that KLF9 directly binds to the promoter of PAFAH1B3 and inhibits its transcriptional activity. In conclusion, our study indicated that KLF9 can inhibit the proliferation, invasion, migration and metastasis of pancreatic cancer cells by inhibiting PAFAH1B3.

Measurement of Carbon Dioxide Isotopes with Air-Lasing-Based Coherent Raman Spectroscopy.

Isotope detection is crucial for geological research, medical diagnostics, industrial production, and environmental monitoring. Various spectroscopic techniques are continually emerging for isotopic identification and accurate measurement. Herein, coherent Raman scattering (CRS) spectroscopy is developed for the quantitative detection of carbon dioxide isotopes, in which the N2+ air lasing coherently created in the interaction region is used as the probe. Benefiting from the narrow spectral width of air lasing, the Raman peaks of 12CO2 and 13CO2 can be well discerned, although their spectra partially overlap. The overlapped signals were proven to be the result of the coherent superposition of individual Raman signals. Based on that fact, a deconvolution algorithm was designed to retrieve the concentration ratio of the two isotopes. The relative error of the measurement is less than 6%. The CRS technique based on air lasing offers a potential approach for the quantitative characterization of molecular isotopes, especially in application scenarios of remote sensing or in situ detection.

Enhanced narrow-bandwidth emission during high-order harmonic generation from aligned molecules.

We theoretically investigate the selective enhancement of high-harmonic generation (HHG) in a small spectral range when an orthogonal-polarized two-color laser field interacts with aligned O(2) molecules. It is shown clearly that the enhanced narrow-bandwidth emission near the cutoff of the HHG spectrum can be effectively controlled by the molecular alignment angle, laser intensity and the relative phase of two-color laser fields. Furthermore, the strong dependence of narrow-bandwidth HHG on molecular alignment angle indicates that it encodes information about O(2) molecular orbitals, so it may be an alternative method for reconstruction of O(2) molecular orbitals.

Identification of the physical mechanism of generation of coherent N2(+) emissions in air by femtosecond laser excitation.

Recently, amplification of harmonic-seeded radiation generated through femtosecond laser filamentation in air has been observed, giving rise to coherent emissions at wavelengths corresponding to transitions between different vibrational levels of the electronic B(2)Σ(u)(+) and X(2)Σ(g)(+) states of molecular nitrogen ions [Phys. Rev. A. 84, 051802(R) (2011)]. Here, we carry out systematic investigations on its physical mechanism. Our experimental results do not support the speculation that such excellent coherent emissions could originate from nonlinear optical processes such as four-wave mixing or stimulated Raman scattering, leaving stimulated amplification of harmonic seed due to the population inversion generated in molecular nitrogen ions the most likely mechanism.