Timeless noncoding DNA contains cell-type preferential enhancers important for proper Drosophila circadian regulation.

To address the contribution of transcriptional regulation to Drosophila clock gene expression and to behavior, we generated a series of CRISPR-mediated deletions within two regions of the circadian gene timeless (tim), an intronic E-box region and an upstream E-box region that are both recognized by the key transcription factor Clock (Clk) and its heterodimeric partner Cycle. The upstream deletions but not an intronic deletion dramatically impact tim expression in fly heads; the biggest upstream deletion reduces peak RNA levels and tim RNA cycling amplitude to about 15% of normal, and there are similar effects on tim protein (TIM). The cycling amplitude of other clock genes is also strongly reduced, in these cases due to increases in trough levels. These data underscore the important contribution of the upstream E-box enhancer region to tim expression and of TIM to clock gene transcriptional repression in fly heads. Surprisingly, tim expression in clock neurons is only modestly affected by the biggest upstream deletion and is similarly affected by a deletion of the intronic E-box region. This distinction between clock neurons and glia is paralleled by a dramatically enhanced accessibility of the intronic enhancer region within clock neurons. This distinctive feature of tim chromatin was revealed by ATAC-seq (assay for transposase-accessible chromatin with sequencing) assays of purified neurons and glia as well as of fly heads. The enhanced cell type-specific accessibility of the intronic enhancer region explains the resilience of clock neuron tim expression and circadian behavior to deletion of the otherwise more prominent upstream tim E-box region.

Light and dopamine impact two circadian neurons to promote morning wakefulness.

In both mammals and flies, circadian brain neurons orchestrate physiological oscillations and behaviors like wake and sleep; these neurons can be subdivided by morphology and by gene expression patterns. Recent single-cell sequencing studies identified 17 Drosophila circadian neuron groups. One of these include only two lateral neurons (LNs), which are marked by the expression of the neuropeptide ion transport peptide (ITP). Although these two ITP+ LNs have long been grouped with five other circadian evening activity cells, inhibiting the two neurons alone strongly reduces morning activity; this indicates that they are prominent morning neurons. As dopamine signaling promotes activity in Drosophila like in mammals, we considered that dopamine might influence this morning activity function. Moreover, the ITP+ LNs express higher mRNA levels than other LNs of the type 1-like dopamine receptor Dop1R1. Consistent with the importance of Dop1R1, CRISPR/Cas9 mutagenesis of this receptor only in the two ITP+ LNs renders flies significantly less active in the morning, and ex vivo live imaging shows that dopamine increases cAMP levels in these two neurons; cell-specific mutagenesis of Dop1R1 eliminates this cAMP response to dopamine. Notably, the response is more robust in the morning, reflecting higher morning Dop1R1 mRNA levels in the two neurons. As morning levels are not elevated in constant darkness, this suggests light-dependent upregulation of morning Dop1R1 transcript levels. Taken together with enhanced morning cAMP response to dopamine, the data indicate how light stimulates morning wakefulness in flies, which mimics the important effect of light on morning wakefulness in humans.

Neural connectivity molecules best identify the heterogeneous clock and dopaminergic cell types in the Drosophila adult brain.

Our recent single-cell sequencing of most adult Drosophila circadian neurons indicated notable and unexpected heterogeneity. To address whether other populations are similar, we sequenced a large subset of adult brain dopaminergic neurons. Their gene expression heterogeneity is similar to that of clock neurons, i.e., both populations have two to three cells per neuron group. There was also unexpected cell-specific expression of neuron communication molecule messenger RNAs: G protein-coupled receptor or cell surface molecule (CSM) transcripts alone can define adult brain dopaminergic and circadian neuron cell type. Moreover, the adult expression of the CSM DIP-beta in a small group of clock neurons is important for sleep. We suggest that the common features of circadian and dopaminergic neurons are general, essential for neuronal identity and connectivity of the adult brain, and that these features underlie the complex behavioral repertoire of Drosophila.

Fast all-fiber ultraviolet photodetector based on an Ag-decorated ZnO micro-pillar.

There are urgent demands of ultraviolet (UV) photodetectors with high sensitivity and fast response due to the wide application of ultraviolet light in the fields of medical treatment, space exploration, optical communication and semiconductor industry. The response speed of traditional ZnO-based UV photodetectors is always limited by the carrier mobility and electrical resistance caused by the external circuits. Utilizing the all-optical detection method may replace the complex circuit structure and effectively improve the response speed of photodetectors. Here, a fast-response fiber-optic UV photodetector is proposed, where a ZnO micro-pillar is fixed on the end face of a fiber-tip and acts as a Fabry-Pérot interferometer (FPI). Under the irradiation of UV light, the photo-generated carriers change the refractive index of the ZnO micro-pillar, leading to a redshift of the interference wavelengths of the ZnO FPI. To enhance this effect, a discontinuous Ag film with an island-like structure is coated on the surface of ZnO micro-pillars through magnetron sputtering, and therefore the sensitivity of the proposed device achieves to 1.13 nm/(W·cm-2), which is 3.9 times higher than that of without Ag-decoration, due to the intensification of photo-carrier change with the help of the Schottky junction formed between Ag film and ZnO micro-pillar. Meanwhile, since the response speed of the proposed device is mainly determined by the temporal RI change of ZnO micro-pillar, the fiber-optic UV photodetector also shows very fast response with a rise time of 35 ns and a decay time of 40 µs. The demonstrated structure takes full advantage of optical fiber devices, exhibiting compactness, flexibility, fast response and immune to electromagnetic interference, which paves a new way for the next generation of photodetection devices.

Focused vortex beam generator suitable for optical fiber spanners in a complex liquid environment.

We experimentally demonstrated an all-fiber focused vortex beam (FVB) generator which was prepared by milling a spiral zone plate (SZP) on the Au-coated end face of a hybrid fiber by focused ion beam (FIB). In this generator, the fundamental modes propagating in the hybrid fiber are focused while being modulated into high-order orbital angular momentum (OAM) mode by the SZP at the end face. The focus length and topological charge were designed and then were both theoretically and experimentally verified. The results show that, the obtained characteristics of the FVB agree with the designed ones. The measured diameters of the focal spots are 2.2 µm, 4.4 µm, and 5.2 µm for the FVB with the topological charge of 0, 1, and 2, respectively. The simulated results show that the proposed FVB generators can maintain good focusing characteristics in different liquids, so it is a good candidate for optical fiber spanner use in a complex liquid environment. Moreover, the processing efficiency of the proposed FVB generators is nearly ten times higher than that of the previously reported ones due to the Au-coated film.

Polarimetric fiber laser for relative humidity sensing based on graphene oxide-coated D-shaped fiber and beat frequency demodulation.

We first propose and demonstrate a polarimetric fiber laser system for relative humidity (RH) sensing based on the beat frequency demodulation. A graphene oxide-coated D-shaped fiber (GDF) with a low insertion loss of 0.8 dB was embedded into a laser cavity to form an RH sensing probe. The output of the fiber laser could generate mode splitting between two orthogonal polarization modes due to birefringence of the GDF device. Hence, two types of beat signals, i.e., longitudinal mode beat frequency (LMBF) and polarization mode beat frequency (PMBF) could be generated synchronously. The experimental results indicated that the LMBFs of the fiber laser had almost no response to the ambient humidity, and the PMBFs of the fiber laser were very sensitive to the various RH levels. There was a good linear relationship between the PMBF and RH changes in the range of 30% to 98%. This fiber-optic RH sensor exhibited a sensitivity of 34.7 kHz/RH% with a high quality of fit (R2>0.997) during the ambient RH increase and decrease. Moreover, the average response and recovery times of the fiber-optic RH sensor were measured to be about 64.2 ms and 97.8 ms, respectively. Due to its long stability, reversibility, quick response time and low temperature cross-sensitivity (i.e., 0.12 RH%/°C), the proposed fiber-optic RH sensor could offer attractive applications in many fields, such as biology, chemical processing and food processing, etc.

Dopamine and GPCR-mediated modulation of DN1 clock neurons gates the circadian timing of sleep.

The metronome-like circadian regulation of sleep timing must still adapt to an uncertain environment. Recent studies in Drosophila indicate that neuromodulation not only plays a key role in clock neuron synchronization but also affects interactions between the clock network and brain sleep centers. We show here that the targets of neuromodulators, G Protein Coupled Receptors (GPCRs), are highly enriched in the fly brain circadian clock network. Single-cell sequencing indicates that they are not only enriched but also differentially expressed and contribute to clock neuron identity. We generated a comprehensive guide library to mutagenize individual GPCRs in specific neurons and verified the strategy by introducing a targeted sequencing approach. Combined with a behavioral screen, the mutagenesis strategy revealed a role of dopamine in sleep regulation by identifying two dopamine receptors and a clock neuron subpopulation that gate the timing of sleep.

The Drosophila microRNA bantam regulates excitability in adult mushroom body output neurons to promote early night sleep.

Sleep circuitry evolved to have both dedicated and context-dependent modulatory elements. Identifying modulatory subcircuits and understanding their molecular machinery is a major challenge for the sleep field. Previously, we identified 25 sleep-regulating microRNAs in Drosophila melanogaster, including the developmentally important microRNA bantam. Here we show that bantam acts in the adult to promote early nighttime sleep through a population of glutamatergic neurons that is intimately involved in applying contextual information to behaviors, the γ5ß'2a/ß'2mp/ß'2mp_bilateral Mushroom Body Output Neurons (MBONs). Calcium imaging revealed that bantam inhibits the activity of these cells during the early night, but not the day. Blocking synaptic transmission in these MBONs rescued the effect of bantam knockdown. This suggests bantam promotes early night sleep via inhibition of the γ5ß'2a/ß'2mp/ß'2mp_bilateral MBONs. RNAseq identifies Kelch and CCHamide-2 receptor as possible mediators, establishing a new role for bantam as an active regulator of sleep and neural activity in the adult fly.

A transcriptomic taxonomy of Drosophila circadian neurons around the clock.

Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of Drosophila circadian neurons, we optimized a single-cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.

Development of a Saliva-Optimized RT-LAMP Assay for SARS-CoV-2.

Conventional reverse transcription quantitative polymerase chain reaction (RT-qPCR) technology has struggled to fulfill the unprecedented need for diagnostic testing created by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Complexity and cost hinder access to testing, and long turnaround time decreases its utility. To ameliorate these issues, we focus on saliva and introduce several advances to colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) technology; RT-LAMP offers a minimal equipment alternative to RT-qPCR. First, we validated the use of the novel dye LAMPShade Violet (LSV), which improves the visual clarity and contrast of the colorimetric readout. Second, we compared different inactivation conditions on infectivity and RNA yield from saliva. Third, we developed a 10-minute RNA purification protocol from saliva. We call this magnetic bead protocol SalivaBeads. Finally, we developed a magnetic stick, StickLAMP, which provides reliable bead-based RNA purification as well as simple and low-cost access to scalable testing from saliva.

COR27 and COR28 Are Novel Regulators of the COP1-HY5 Regulatory Hub and Photomorphogenesis in Arabidopsis.

Plants have evolved sensitive signaling systems to fine-tune photomorphogenesis in response to changing light environments. Light and low temperatures are known to regulate the expression of the COLD REGULATED (COR) genes COR27 and COR28, which influence the circadian clock, freezing tolerance, and flowering time. Blue light stabilizes the COR27 and COR28 proteins, but the underlying mechanism is unknown. We therefore performed a yeast two-hybrid screen using COR27- and COR28 as bait and identified the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) as an interactor. COR27 and COR28 physically interact with COP1, which is in turn responsible for their degradation in the dark. Furthermore, COR27 and COR28 promote hypocotyl elongation and act as negative regulators of photomorphogenesis in Arabidopsis (Arabidopsis thaliana). Genome-wide gene expression analysis showed that HY5, COR27, and COR28 co-regulate many common genes. COR27 interacts directly with HY5 and associates with the promoters of the HY5 target genes HY5 and PIF4, then regulates their transcription together with HY5. Our results demonstrate that COR27 and COR28 act as key regulators in the COP1-HY5 regulatory hub, by regulating the transcription of HY5 target genes together with HY5 to ensure proper skotomorphogenic growth in the dark and photomorphogenic development in the light.

Controllable two-dimensional movement and redistribution of lithium ions in metal oxides.

Rechargeable lithium batteries are the most practical and widely used power sources for portable and mobile devices in modern society. Manipulation of the electronic and ionic charge transport and accumulation in solid materials has always been crucial for rechargeable lithium batteries. The transport and accumulation of lithium ions in electrode materials, which is a diffusion process, is determined by the concentration distribution of lithium ions and the intrinsic structure of the electrode material and thus far has not been manipulated by an external force. Here, we report the realization of controllable two-dimensional movement and redistribution of lithium ions in metal oxides. This achievement is one kind of centimeter-scale control and is achieved by a magnetic field based on the 'current-driving model'. This work provides additional insight for building safe and high-capacity rechargeable lithium batteries.

BES1-regulated BEE1 controls photoperiodic flowering downstream of blue light signaling pathway in Arabidopsis.

BRI1-EMS-SUPPRESSOR 1 (BES1) functions as a key regulator in the brassinosteroid (BR) pathway that promotes plant growth. However, whether BES1 is involved in photoperiodic flowering is unknown. Here we report that BES1 acts as a positive regulator of photoperiodic flowering, but it cannot directly bind FLOWERING LOCUS T (FT) promoter. BR ENHANCED EXPRESSION 1 (BEE1) is the direct target of BES1 and acts downstream of BES1. BEE1 is also a positive regulator of photoperiodic flowering. BEE1 binds directly to the FT chromatin to activate the transcription of FT and promote flowering initiation. More importantly, BEE1 promotes flowering in a blue light photoreceptor CRYPTOCHROME 2 (CRY2)  partially dependent manner, as it physically interacts with CRY2 under the blue light. Furthermore, BEE1 is regulated by both BRs and blue light. The transcription of BEE1 is induced by BRs, and the BEE1 protein is stabilized under the blue light. Our findings indicate that BEE1 is the integrator of BES1 and CRY2 mediating flowering, and BES1-BEE1-FT is a new signaling pathway in regulating photoperiodic flowering.

CIB1 and CO interact to mediate CRY2-dependent regulation of flowering.

Cryptochromes are photolyase-like photoreceptors. Arabidopsis CRY2 (cryptochrome 2) primarily mediates the photoperiodic regulation of floral initiation. CRY2 has been shown to promote FT (FLOWERING LOCUS T) mRNA expression in response to blue light by suppressing the degradation of the CO (CONSTANS) protein and activating CIB1 (CRY2-interacting bHLH1). Although CIB1 and CO are both transcriptional activators of FT, their relationship is unknown. Here, we show that CIB1 physically interacts with CO and promotes FT transcription in a CO-dependent manner. CRY2, CIB1, and CO form a protein complex in response to blue light to activate FT transcription, and the complex is regulated by the photoperiod and peaks at dusk along with higher FT expression. We also determined that CRY2 was recruited to the FT chromatin by CIB1 and CO and that all three proteins are bound to the same region within the FT promoter. Therefore, there is crosstalk between the CRY2-CO and CRY2-CIBs pathways, and CIB1 and CO act together to regulate FT transcription and flowering.

Blue Light- and Low Temperature-Regulated COR27 and COR28 Play Roles in the Arabidopsis Circadian Clock.

Light and temperature are two key environmental signals that profoundly affect plant growth and development, but underlying molecular mechanisms of how light and temperature signals affect the circadian clock are largely unknown. Here, we report that COR27 and COR28 are regulated not only by low temperatures but also by light signals. COR27 and COR28 are negative regulators of freezing tolerance but positive regulators of flowering, possibly representing a trade-off between freezing tolerance and flowering. Furthermore, loss-of-function mutations in COR27 and COR28 result in period lengthening of various circadian output rhythms and affect central clock gene expression. Also, the cor27 cor28 double mutation affects the pace of the circadian clock. Additionally, COR27 and COR28 are direct targets of CCA1, which represses their transcription via chromatin binding. Finally, we report that COR27 and COR28 bind to the chromatin of TOC1 and PRR5 to repress their transcription, suggesting that their effects on rhythms are in part due to their regulation of TOC1 and PRR5 These data demonstrate that blue light and low temperature-regulated COR27 and COR28 regulate the circadian clock as well as freezing tolerance and flowering time.

Cryptochrome 1 interacts with PIF4 to regulate high temperature-mediated hypocotyl elongation in response to blue light.

Cryptochrome 1 (CRY1) is a blue light receptor that mediates primarily blue-light inhibition of hypocotyl elongation. Very little is known of the mechanisms by which CRY1 affects growth. Blue light and temperature are two key environmental signals that profoundly affect plant growth and development, but how these two abiotic factors integrate remains largely unknown. Here, we show that blue light represses high temperature-mediated hypocotyl elongation via CRY1. Furthermore, CRY1 interacts directly with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) in a blue light-dependent manner to repress the transcription activity of PIF4. CRY1 represses auxin biosynthesis in response to elevated temperature through PIF4. Our results indicate that CRY1 signal by modulating PIF4 activity, and that multiple plant photoreceptors [CRY1 and PHYTOCHROME B (PHYB)] and ambient temperature can mediate morphological responses through the same signaling component-PIF4.