SIRT1 mediates central circadian control in the SCN by a mechanism that decays with aging.

SIRT1 is a NAD(+)-dependent protein deacetylase that governs many physiological pathways, including circadian rhythm in peripheral tissues. Here, we show that SIRT1 in the brain governs central circadian control by activating the transcription of the two major circadian regulators, BMAL1 and CLOCK. This activation comprises an amplifying circadian loop involving SIRT1, PGC-1α, and Nampt. In aged wild-type mice, SIRT1 levels in the suprachiasmatic nucleus are decreased, as are those of BMAL1 and PER2, giving rise to a longer intrinsic period, a more disrupted activity pattern, and an inability to adapt to changes in the light entrainment schedule. Young mice lacking brain SIRT1 phenocopy these aging-dependent circadian changes, whereas mice that overexpress SIRT1 in the brain are protected from the effects of aging. Our findings indicate that SIRT1 activates the central pacemaker to maintain robust circadian control in young animals, and a decay in this activity may play an important role in aging.

Base-edited cynomolgus monkeys mimic core symptoms of STXBP1 encephalopathy.

Presynaptic syntaxin binding protein 1 (STXBP1) is essential for neurotransmitter release. Heterozygous mutations in this protein cause STXBP1 encephalopathy (STXBP1-E), which is characterized by intellectual disabilities and epilepsies. Since nonhuman primates closely resemble humans, monkey models may advance studies on the pathogenesis and therapeutic treatments of STXBP1-E. We generated cynomolgus monkeys carrying STXBP1 (R292H) mutation through base editing of in vitro fertilized embryos to mimic a clinical condition. The newborn STXBP1-edited monkeys exhibited focal epilepsy, and the animal that survived beyond the first week postpartum presented typical EEG phenotypes. Biochemical analysis of brain biopsy samples showed reduced levels of STXBP1 (MUNC18-1) and SNARE complex proteins. Single-cell sequencing identified one specific cell cluster that may contribute to encephalopathy. Thus, our case report shows that base-edited STXBP1 mutant monkeys are a good animal model for STXBP1-E, and that a base-editing approach is useful for generating primate models of human genetic disorders.

Influenza a virus NS1 resembles a TRAF3-interacting motif to target the RNA sensing-TRAF3-type I IFN axis and impair antiviral innate immunity.

BACKGROUND: Influenza A virus (IAV) evolves strategies to counteract the host antiviral defense for establishing infection. The influenza A virus (IAV) non-structural protein 1 (NS1) is a key viral factor shown to counteract type I IFN antiviral response mainly through targeting RIG-I signaling. Growing evidence suggests that viral RNA sensors RIG-I, TLR3, and TLR7 function to detect IAV RNA in different cell types to induce type I IFN antiviral response to IAV infection. Yet, it remains unclear if IAV NS1 can exploit a common mechanism to counteract these RNA sensing pathways to type I IFN production at once, then promoting viral propagation in the host. METHODS: Luciferase reporter assays were conducted to determine the effect of NS1 and its mutants on the RIG-I and TLR3 pathways to the activation of the IFN-ß and NF-κB promoters. Coimmunoprecipitation and confocal microscopic analyses were used to the interaction and colocalization between NS1 and TRAF3. Ubiquitination assays were performed to study the effect of NS1 and its mutants on TRAF3 ubiquitination. A recombinant mutant virus carrying NS1 E152A/E153A mutations was generated by reverse genetics for biochemical, ex vivo, and in vivo analyses to explore the importance of NS1 E152/E153 residues in targeting the RNA sensing-TRAF3-type I IFN axis and IAV pathogenicity. RESULTS: Here we report that NS1 subverts the RIG-I, TLR3, and TLR7 pathways to type I IFN production through targeting TRAF3 E3 ubiquitin ligase. NS1 harbors a conserved FTEE motif (a.a. 150-153), in which the E152/E153 residues are critical for binding TRAF3 to block TRAF3 ubiquitination and type I IFN production by these RNA sensing pathways. A recombinant mutant virus carrying NS1 E152A/E153A mutations induces higher type I IFN production ex vivo and in vivo, and exhibits the attenuated phenotype in infected mice, indicating the importance of E152/E153 residues in IAV pathogenicity. CONCLUSIONS: Together our work uncovers a novel mechanism of IAV NS1-mediated immune evasion to promote viral infection through targeting the RNA sensing-TRAF3-type I IFN axis.

CDK9 modulates circadian clock by attenuating REV-ERBα activity.

Circadian clock and cell cycle are vital cellular programs acting in a timely-regulated, cyclic manner. The two cellular oscillators are coupled in various ways to facilitate biological processes. Here we report CDK9, a kinase belongs to the CDK family in regulating cell cycle and RNA Pol II activity, can serve as a modulator for circadian clock. We identified CDK inhibitor LY2857785 potently blocked PER2:LUC expression in MEFs from a screen of 17 commonly-used CDK inhibitors. We further analyzed the possible targets of LY2857785 by siRNA approach, and confirmed CDK9 as the main effector. LY2857785 treatment, as well as Cdk9 knock-down, led to lowered expression of Bmal1 in accordance with elevated expression of Rev-Erbα. CDK9 associated with REV-ERBα thus attenuated REV-ERBα binding to the RORE for Bmal1 suppression. To conform the circadian-modulating activity of CDK9 in vivo, we knocked down CDK9 in mice at the anterior hypothalamus covering the central oscillator SCN, and found the respiratory exchange ratio, daily activity and circadian period were altered in the Cdk9-knockdown mice. Together, our finding designated CDK9 as a novel modulator in circadian clock. CDK9 may serve as a vital basis to understand circadian- and cell cycle-misregulated ailments such as cancer.

Leaky property of the Dyakonov-like wave at the surface of a semi-infinite metal-dielectric multilayered structure.

We investigate the Dyakonov-like surface wave (DLSW) at the interface of a dielectric and a metal-dielectric multilayered (MDM) structure when this MDM structure serves as an elliptic medium according to the effective medium approximation (EMA). Different from the conventional Dyakonov surface waves, we find that this kind of DLSW possesses an unexpected leaky property due to an additional hyperbolic-like wave in the MDM structure, resulting in a significant increase of propagation loss compared to the results estimated by a simple effective model based on the EMA. Moreover, such leaky property is found to be sensitive to the period of the MDM structure. Thus, to diminish this non-negligible leaky loss, one can suppress the amplitude of the leaky component by designing the MDM structure with a smaller period. On the other hand, as the MDM structure sometimes can also support an additional elliptic-like dispersion when it is regarded as a hyperbolic medium, we discuss this condition for completeness. Based on this elliptic-like dispersion, an apparent leaky property is observed in the resultant DLSW. This DLSW propagates with a wider range of propagation direction but suffers from a poor field confinement to the interface it is propagating along.

Determination of dissipative Dyakonov surface waves using a finite element method based eigenvalue algorithm.

A full-vectorial finite element method is developed to analyze the surface waves propagating at the interface between two media which could be dissipative particularly. The dissipative wave possessing a complex-valued propagation constant can be determined precisely for any given propagation direction and thus the property of losses could be thoroughly analyzed. Besides, by applying a special characteristic of the implicit circular block matrix, we reduce the computational consumptions in the analysis. By utilizing this method, the Dyakonov surface wave (DSW) at the interface between a dielectric and a metal-dielectric multilayered (MDM) structure which serves as a hyperbolic medium is discussed. Its propagation loss is smaller for larger period of the MDM structure but its field becomes less confined to the interface.

Periodic anti-ring back reflectors for hydrogenated amorphous silicon thin-film solar cells.

Large and periodic anti-ring arrays are fabricated by using a monolayer of polymer/nanosphere hybrid technique and applied as back reflectors in substrate-type hydrogenated amorphous silicon (a-Si:H) thin-film solar cells. The structure of each anti-ring comprises a nanodome centered inside a nanohole. The excitation of Bloch wave surface plasmon polaritons is observed in the Ag-coated anti-ring arrays. The nanodomes of the anti-ring arrays turn out to enhance large-angle light scattering and increase the effective optical path in the solar cell. The resulting efficiency of an ultrathin a-Si:H (thickness: 150 nm) solar cell is enhanced by 39% compared to that with a flat back reflector and by 13% compared to that with a nanohole back reflector.

Enhancing bright-field image of microorganisms by local plasmon of Ag nanoparticle array.

Inspecting biological cells with bright-field light microscopy often engenders a challenge, owing to their optical transparency. We show that imaging contrast can be greatly enhanced as yeast cells are placed on a silver nanoparticle array. Its near- and far-field traits, revealed by electrodynamic simulations, illustrate that the enhancement is attributed to the sensitivity of its plasmonic characteristics to the attached cells. This study demonstrates that the silver nanoparticle array can serve as the agent for concurrently enhancing Raman scattering and imaging contrast of microorganisms for identification and examination.

High-frequency neural activity dysregulation is associated with sleep and psychiatric disorders in BMAL1-deficient animal models.

Sleep disturbance led by BMAL1-deficiency has been recognized both in rodent and non-human primate models. Yet it remained unclear how their diurnal brain oscillations were affected upon BMAL1 ablation and what caused the discrepancy in the quantity of sleep between the two species. Here, we investigated diurnal electroencephalographs of BMAL1-deficient mice and cynomolgus monkeys at young adult age and uncovered a shared defect of dysregulated high-frequency oscillations by Kullback-Leibler divergence analysis. We found beta and gamma oscillations were significantly disturbed in a day versus night manner in BMAL1-deficient monkeys, while in mice the beta band difference was less evident. Notably, the dysregulation of beta oscillations was particularly associated with psychiatric behaviors in BMAL1-deficient monkeys, including the occurrence of self-injuring and delusion-like actions. As such psychiatric phenotypes were challenging to uncover in rodent models, our results offered a unique method to study the correlation between circadian clock dysregulation and psychiatric disorders.

Essential role of the chaperonin folding compartment in vivo.

The GroEL/GroES chaperonin system of Escherichia coli forms a nano-cage allowing single protein molecules to fold in isolation. However, as the chaperonin can also mediate folding independently of substrate encapsulation, it remained unclear whether the folding cage is essential in vivo. To address this question, we replaced wild-type GroEL with mutants of GroEL having either a reduced cage volume or altered charge properties of the cage wall. A stepwise reduction in cage size resulted in a gradual loss of cell viability, although the mutants bound non-native protein efficiently. Strikingly, a mild reduction in cage size increased the yield and the apparent rate of green fluorescent protein folding, consistent with the view that an effect of steric confinement can accelerate folding. As shown in vitro, the observed acceleration of folding was dependent on protein encapsulation by GroES but independent of GroES cycling regulated by the GroEL ATPase. Altering the net-negative charge of the GroEL cage wall also strongly affected chaperonin function. Based on these findings, the GroEL/GroES compartment is essential for protein folding in vivo.

Real-time observation of trigger factor function on translating ribosomes.

The contribution of co-translational chaperone functions to protein folding is poorly understood. Ribosome-associated trigger factor (TF) is the first molecular chaperone encountered by nascent polypeptides in bacteria. Here we show, using fluorescence spectroscopy to monitor TF function and structural rearrangements in real time, that TF interacts with ribosomes and translating polypeptides in a dynamic reaction cycle. Ribosome binding stabilizes TF in an open, activated conformation. Activated TF departs from the ribosome after a mean residence time of approximately 10 s, but may remain associated with the elongating nascent chain for up to 35 s, allowing entry of a new TF molecule at the ribosome docking site. The duration of nascent-chain interaction correlates with the occurrence of hydrophobic motifs in translating polypeptides, reflecting a high aggregation propensity. These findings can explain how TF prevents misfolding events during translation and may provide a paradigm for the regulation of nucleotide-independent chaperones.

ISX-9 potentiates CaMKIIδ-mediated BMAL1 activation to enhance circadian amplitude.

Circadian dysregulation associates with numerous diseases including metabolic dysfunction, sleep disorder, depression and aging. Given that declined circadian amplitude is a trait commonly found with compromised health, interventions that design in precluding circadian amplitude from dampening will aid to mitigate complex, circadian-related diseases. Here we identify a neurogenic small molecule ISX-9 that is able to support persistent and higher amplitude of circadian oscillations. ISX-9 improves diurnal metabolic rhythms in middle-aged mice. Moreover, the ISX-9-treated mice show better sleep homeostasis with increased delta power during the day time and higher locomotive activity in the dark period. ISX-9 augments CaMKIIδ expression and increases BMAL1 activity via eliciting CaMKIIδ-mediated phosphorylation on BMAL1 residues S513/S515/S516, accordingly composes a positive feedback effect on enhancing circadian amplitude. CaMKIIδ-targeting, and the use of ISX-9 may serve as decent choices for treating circadian-related disorders.

Effect of perfectly matched layer reflection coefficient on modal analysis of leaky waveguide modes.

The reflection coefficient is one important parameter of the perfectly matched layer (PML). Here we investigate its effect on the modal analysis of leaky waveguide modes by examining three different leaky waveguide structures, i.e., the holey fiber, the air-core terahertz pipe waveguide, and the gain-guided and index-antiguided slab waveguide. Numerical results reveal that the typical values 10(-8) ~10(-12) are inadequate for obtaining the imaginary part of the complex propagation constant, and the suggested reflection coefficient would be much smaller, for example, 10(-50) or 10(-100). With such a small coefficient, both the computational window size and the PML thickness can be significantly reduced without loss of stability. Moreover, in some cases, the modal field profiles can only be accurately obtained with such a small coefficient.

A high-accuracy pseudospectral full-vectorial leaky optical waveguide mode solver with carefully implemented UPML absorbing boundary conditions.

The previously developed full-vectorial optical waveguide eigenmode solvers using pseudospectral frequency-domain (PSFD) formulations for optical waveguides with arbitrary step-index profile is further implemented with the uniaxial perfectly matched layer (UPML) absorption boundary conditions for treating leaky waveguides and calculating their complex modal effective indices. The role of the UPML reflection coefficient in achieving high-accuracy mode solution results is particularly investigated. A six-air-hole microstructured fiber is analyzed as an example to compare with published high-accuracy multipole method results for both the real and imaginary parts of the effective indices. It is shown that by setting the UPML reflection coefficient values as small as on the order of 10(-40) ∼ 10(-70), relative errors in the calculated complex effective indices can be as small as on the order of 10(-12).

Application of metal-clad antiresonant reflecting hollow waveguides to tunable terahertz notch filter.

A novel tunable terahertz notch filter is demonstrated using antiresonant reflecting hollow waveguides with movable metal layers outside dielectric claddings. Based on the Fabry-Pérot resonance of the dielectric cladding, multiple deep notches are observed in a broad THz transmission spectrum. Continuous shift of notch frequencies is for the first time experimentally observed by lateral translation of metal layers from dielectric claddings. The measured maximum frequency-tuning-range approached 60GHz, equaling to 50% of the bandwidth of every passband, and a 20dB rejection notch-depth with a linewidth as narrow as 6GHz at frequency of around 0.2THz was also achieved. Numerical simulations match the measurements and verify the spectral-tuning mechanism.

Terahertz polarization-sensitive rectangular pipe waveguides.

We propose square and rectangular pipe waveguides for low-loss THz waveguiding and polarization control. Different from common circular-symmetric THz fibers and waveguides, the proposed rectangular pipe waveguides successfully remove the transmission degeneracy of two orthogonal polarizations and possess polarization sensitivity to the guided THz waves. By measuring the attenuation spectra, we find that the polarization sensitivity depends on the structure of the pipe waveguides. With butt coupling method, it is easy to combine circular pipe waveguides and the rectangular ones.

Terahertz pipe-waveguide-based directional couplers.

We experimentally demonstrate a terahertz (THz) leaky mode directional coupler for future THz applications. The proposed directional coupler comprises two square pipe waveguides. The coupling efficiency is investigated for different frequencies, polarizations, and core sizes. Rectangular pipe-waveguide-based directional couplers and the issue of insertion loss are also discussed. It is found that the THz directional coupler works most efficiently in the minimal-attenuation wavelength regime.

Terahertz antiresonant-reflecting-hollow-waveguide-based directional coupler operating at antiresonant frequencies.

We report a particular coupling phenomenon occurring in the directional coupler composed of two touching terahertz antiresonant reflecting hollow waveguides. Unlike conventional directional couplers where one even system mode and one odd system mode are excited, numerical results indicate that three (one even and two odd) system modes participate in the power transfer process at the antiresonant frequencies. As a result, the coupling length can be significantly reduced, and it is shown here to be less than 300 wavelengths.

Modal characteristics of antiresonant reflecting pipe waveguides for terahertz waveguiding.

Modal characteristics of the THz pipe waveguide, which is a thin pipe consisting of a large air core and a thin dielectric layer with uniform but low index, are investigated. Modal indices and attenuation constants are calculated for various core diameters, cladding thicknesses, and cladding refractive indices. Numerical results reveal that the guiding mechanism of the leaky core modes, which transmit most of the power in the air-core region, is that of the antiresonant reflecting guiding. Moreover, modal patterns including modal intensity distributions and electric field vector distributions are shown for the fundamental and higher order modes. Experiments using time-domain spectroscopy with PMMA pipes also confirm the antiresonant reflecting guiding mechanism.