A gradient phage-assisted continuous evolution method for screening suppressor tRNAs in Escherichia coli.

Suppressor tRNAs, notable for their capability of reading through the stop codon while maintaining normal peptide synthesis, are promising in treating diseases caused by premature termination codons (PTC). However, the lack of effective engineering methods for suppressor tRNAs has curtailed their application potential. Here, we introduce a directed evolution technology that employs phage-assisted continuous evolution (PACE), combined with gradient biosensors featuring various PTCs in the M13 gene III. Utilizing this novel methodology, we have successfully evolved tRNATrp (UGG) reading through the UGA stop codon in Escherichia coli. Massively parallel sequencing revealed that these mutations predominantly occurred in the anticodon loop. Finally, two suppressor tRNATrp (UGA) mutants exhibited over fivefold increases in readthrough efficiency.

Dynamic variation in the aroma characteristics of Rhus chinensis honey at different stages after capping.

The ripening characteristics after capping of honey are favourable for improving its quality. However, research on the variation and formation of aroma characteristics of honey in this process is lacking. Therefore, the present study was carried out with different stages of Rhus chinensis honeys (RCHs) after capping and identified 192 volatiles with varying levels of concentration. "Fruity" was the main aroma characteristic of RCHs at different stages after capping, mainly contributed by (E)-ß-damascenone. Methyl salicylate might be a potential indicator for differentiating RCHs at different stages after capping. The metabolic pathway analyses revealed that the aroma compounds in RCHs undergo transformation at different stages after capping, which subsequently affects its aroma characteristics formation. This work is the first to study the dynamic changes in honey aroma characteristics after capping from multiple perspectives, and the results are of great significance for understanding the aroma characteristics after capping and quality control of honey.

Large herbivore grazing accelerates litter decomposition in terrestrial ecosystems.

Plant litter decomposition is critical for carbon and nutrient cycling globally. However, the effect of large herbivore grazing on litter decomposition and its mechanisms remain less explored. Here, 1203 paired observations and 381 independent experiments were analyzed to determine how litter decomposition and nutrient cycling respond to changes in grazing intensity. Grazing significantly increased litter decomposition rate by 14.08 % and litter carbon release by 5.03 %, and this effect was observed in grasslands and croplands but not in forests. The positive grazing effect was also found under sheep and cattle/yak grazing. Moderate grazing advanced the home-field advantage effect but inhibited under heavy grazing for grazed litters. The grazing effect was larger for high quality litter than for low quality litter. Litter decomposition slowed under >10 years heavy grazing but accelerated under moderate grazing. The effects of large herbivore grazing on litter decomposition were jointly influenced by grazing intensity, livestock type, climate condition, decomposition duration, litter quality, and soil properties. Our results demonstrated that large herbivore grazing accelerates litter decomposition globally and emphasized the significance and importance of grazing intensity on litter decomposition, which should be integrated into terrestrial ecosystem models.

Directed Evolution of Escherichia coli Nissle 1917 to Utilize Allulose as Sole Carbon Source.

Sugar substitutes are popular due to their akin taste and low calories. However, excessive use of aspartame and erythritol can have varying effects. While D-allulose is presently deemed a secure alternative to sugar, its excessive consumption is not devoid of cellular stress implications. In this study, the evolution of Escherichia coli Nissle 1917 (EcN) is directed to utilize allulose as sole carbon source through a combination of adaptive laboratory evolution (ALE) and fluorescence-activated droplet sorting (FADS) techniques. Employing whole genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats interference (CRISPRi) in conjunction with compensatory expression displayed those genetic mutations in sugar and amino acid metabolic pathways, including glnP, glpF, gmpA, nagE, pgmB, ybaN, etc., increased allulose assimilation. Enzyme-substrate dynamics simulations and deep learning predict enhanced substrate specificity and catalytic efficiency in nagE A247E and pgmB G12R mutants. The findings evince that these mutations hold considerable promise in enhancing allulose uptake and facilitating its conversion into glycolysis, thus signifying the emergence of a novel metabolic pathway for allulose utilization. These revelations bear immense potential for the sustainable utilization of D-allulose in promoting health and well-being.

Electrooxidative Rhodium(III)/Chiral Carboxylic Acid-Catalyzed Enantioselective C-H Annulation of Sulfoximines with Alkynes.

The combination of achiral Cp*Rh(III) with chiral carboxylic acids (CCAs) represents an efficient catalytic system in transition metal-catalyzed enantioselective C-H activation. However, this hybrid catalysis is limited to redox-neutral C-H activation reactions and the adopt to oxidative enantioselective C-H activation remains elusive and pose a significant challenge. Herein, we describe the development of an electrochemical Cp*Rh(III)-catalyzed enantioselective C-H annulation of sulfoximines with alkynes enabled by chiral carboxylic acid (CCA) in an operationally friendly undivided cell at room temperature. A broad range of enantioenriched 1,2-benzothiazines are obtained in high yields with excellent enantioselectivities (up to 99 % yield and 98 : 2 er). The practicality of this method is demonstrated by scale-up reaction in a batch reactor with external circulation. A crucial chiral Cp*Rh(III) intermediate is isolated, characterized, and transformed, providing rational support for a Rh(III)/Rh(I) electrocatalytic cycle.

Aromatic profiles and enantiomeric distributions of volatile compounds during the ripening of Dendropanax dentiger honey.

Dendropanax dentiger honey (DDH) is a specialty herbal honey from China. Previous research on DDH has mostly focused on its composition and potential chemical markers, no studies have been conducted on the changes in aroma characteristics and chiral odorants during its maturation. Therefore, the present study aims to address the missing parts. The proportions and total concentrations of 185 volatile compounds identified in different classes varied with DDHs ripening. Fourteen common odor-active compounds were identified by odor activity values (OAVs) and GC-olfactometry (GC-O) analysis. The aroma profiles of DDHs were observed to vary at different ripening stages, although the dominant aroma characteristic was "fruity" aroma, which became more pronounced with increasing maturity. The enantiomeric contents and distributions of 7 volatile enantiomers were related to specific physicochemical indicators and the maturity of DDHs, among which the enantiomers of linalool oxide A may be a potential indicator to identify its maturity. Furthermore, precise quantification and OAVs calculation showed that the enantiomer (2S, 5S)-linalool oxide A presented the highest concentration (8.83-27.39 ng/mL) and only the enantiomer R-linalool (OAVs: 5.56-6.14) was an important contributor to the aroma profiles of DDHs at different stages of maturity. These results provided a new research idea for quality control and identification of DDHs at different maturity stages.

Microglia trigger the structural plasticity of GABAergic neurons in the hippocampal CA1 region of a lipopolysaccharide-induced neuroinflammation model.

It is well-established that microglia-mediated neuroinflammatory response involves numerous neuropsychiatric and neurodegenerative diseases. While the role of microglia in excitatory synaptic transmission has been widely investigated, the impact of innate immunity on the structural plasticity of GABAergic inhibitory synapses is not well understood. To investigate this, we established an inflammation model using lipopolysaccharide (LPS) and observed a prolonged microglial response in the hippocampal CA1 region of mice, which was associated with cognitive deficits in the open field test, Y-maze test, and novel object recognition test. Furthermore, we found an increased abundance of GABAergic interneurons and GABAergic synapse formation in the hippocampal CA1 region. The cognitive impairment caused by LPS injection could be reversed by blocking GABA receptor activity with (-)-Bicuculline methiodide. These findings suggest that the upregulation of GABAergic synapses induced by LPS-mediated microglial activation leads to cognitive dysfunction. Additionally, the depletion of microglia by PLX3397 resulted in a decrease in GABAergic interneurons and GABAergic inhibitory synapses, which blocked the cognitive decline induced by LPS. In conclusion, our findings indicate that excessive reinforcement of GABAergic inhibitory synapse formation via microglial activation contributes to LPS-induced cognitive impairment.

SMDB: a Spatial Multimodal Data Browser.

Understanding the relationship between fine-scale spatial organization and biological function necessitates a tool that effectively combines spatial positions, morphological information, and spatial transcriptomics (ST) data. We introduce the Spatial Multimodal Data Browser (SMDB, https://www.biosino.org/smdb), a robust visualization web service for interactively exploring ST data. By integrating multimodal data, such as hematoxylin and eosin (H&E) images, gene expression-based molecular clusters, and more, SMDB facilitates the analysis of tissue composition through the dissociation of two-dimensional (2D) sections and the identification of gene expression-profiled boundaries. In a digital three-dimensional (3D) space, SMDB allows researchers to reconstruct morphology visualizations based on manually filtered spots or expand anatomical structures using high-resolution molecular subtypes. To enhance user experience, it offers customizable workspaces for interactive exploration of ST spots in tissues, providing features like smooth zooming, panning, 360-degree rotation in 3D and adjustable spot scaling. SMDB is particularly valuable in neuroscience and spatial histology studies, as it incorporates Allen's mouse brain anatomy atlas for reference in morphological research. This powerful tool provides a comprehensive and efficient solution for examining the intricate relationships between spatial morphology, and biological function in various tissues.

The effect of colour environments on visual tracking and visual strain during short-term simulation of three gravity states.

This study investigated the effects of nine colour environments on visual tracking accuracy and visual strain during normal sitting (SP), -12° head-down bed (HD) and 9.6° head-up tilt bed (HU). In a standard posture change laboratory study, fifty-four participants performed visual tracking tasks in nine colour environments while in the three postures. Visual strain was measured by means of a questionnaire. The results showed that in all colour environments, the -12° head-down bed rest posture significantly affected visual tracking accuracy and visual strain. During the three postures, the participants' visual tracking accuracy in the cyan environment was significantly higher than that in other colour environments, and their visual strain was the lowest. Overall, the study adds to our understanding of how environmental and postural factors impact on visual tracking and visual strain.

NSUN2-mediated M5c methylation of IRF3 mRNA negatively regulates type I interferon responses during various viral infections.

5-Methylcytosine (m5C) is a widespread post-transcriptional RNA modification and is reported to be involved in manifold cellular responses and biological processes through regulating RNA metabolism. However, its regulatory role in antiviral innate immunity has not yet been elucidated. Here, we report that NSUN2, a typical m5C methyltransferase, negatively regulates type I interferon responses during various viral infections, including SARS-CoV-2. NSUN2 specifically mediates m5C methylation of IRF3 mRNA and accelerates its degradation, resulting in low levels of IRF3 and downstream IFN-ß production. Knockout or knockdown of NSUN2 enhanced type I interferon and downstream ISGs during various viral infection in vitro. And in vivo, the antiviral innate response is more dramatically enhanced in Nsun2+/- mice than in Nsun2+/+ mice. The highly m5C methylated cytosines in IRF3 mRNA were identified, and their mutation enhanced cellular IRF3 mRNA levels. Moreover, infection with Sendai virus (SeV), vesicular stomatitis virus (VSV), herpes simplex virus 1 (HSV-1), or Zika virus (ZIKV) resulted in a reduction of endogenous NSUN2 levels. Especially, SARS-CoV-2 infection (WT strain and BA.1 omicron variant) also decreased endogenous levels of NSUN2 in COVID-19 patients and K18-hACE2 KI mice, further increasing type I interferon and downstream ISGs. Together, our findings reveal that NSUN2 serves as a negative regulator of interferon response by accelerating the fast turnover of IRF3 mRNA, while endogenous NSUN2 levels decrease during SARS-CoV-2 and various viral infections to boost antiviral responses for effective elimination of viruses.

The Effect of Correlated Colour Temperature on Physiological, Emotional and Subjective Satisfaction in the Hygiene Area of a Space Station.

The hygiene area is one of the most important facilities in a space station. If its environmental lighting is appropriately designed, it can significantly reduce the psychological pressure on astronauts. This study investigates the effect of correlated colour temperature (CCT) on heart rate, galvanic skin response, emotion and satisfaction in the hygiene area of a space station. Forty subjects participated in experiments in a hygiene area simulator with a controlled lighting environment. The lighting conditions included 2700 K, 3300 K, 3600 K, 5000 K and 6300 K; physiological responses (heart rate, galvanic skin response), as well as emotion and satisfaction, were recorded. The results showed that CCT significantly influenced the participants' physiological and subjective responses in the space station hygiene area. 6300 K led to the best emotion and satisfaction levels, the highest galvanic skin response and the lowest heart rate. The opposite was true for 2700 K.

Molecular Dynamics Simulation Study on the Interactions of Mixed Cationic/Anionic Collectors on Muscovite (001) Surface in Aqueous Solution.

In this study, the adsorption mechanisms of dodecylamine hydrochloride(DDAHC), sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate(SDBS), and their mixed anionic/cationic collectors at ten different molar ratios on a muscovite (Mcv) surface in neutral aqueous solution were assessed by molecular dynamics simulations (MDS). According to the snapshot, interaction energy, radial distribution function (RDF), and density profile between the Mcv surface and collector molecules, the individual DDAHC collector was an effective collector for the flotation of Mcv. The molar ratio of anionic/cationic collectors was determined to be an essential factor in the flotation recovery of Mcv. The DDAHC collector was involved in the adsorption of the mixed anionic/cationic collectors on the Mcv (001) surface, whereas SDS and SDBS collectors were co-adsorbed with DDAHC. The mixed cationic/anionic collector showed the best adsorption on the Mcv surface in a molar ratio of 2. Additionally, SDBS, which has one more benzene ring than SDS, was more likely to form spherical micelles with DDAHC, thus resulting in better adsorption on the Mcv surface. The results of micro-flotation experiments indicated that the DDAHC collector could improve the flotation recovery of Mcv in neutral aqueous solution, which was in agreement with MDS-derived findings. In conclusion, DDAHC alone is the optimum collector for Mcv flotation under the neutral aqueous conditions, while the mixture of DDAHC and SDBS collectors (molar ratio = 2:1) exhibits the similar flotation performance.

Histone methyltransferase Dot1L recruits O-GlcNAc transferase to target chromatin sites to regulate histone O-GlcNAcylation.

O-GlcNAc transferase (OGT) is the distinctive enzyme responsible for catalyzing O-GlcNAc addition to the serine or threonine residues of thousands of cytoplasmic and nuclear proteins involved in such basic cellular processes as DNA damage repair, RNA splicing, and transcription preinitiation and initiation complex assembly. However, the molecular mechanism by which OGT regulates gene transcription remains elusive. Using proximity labeling-based mass spectrometry, here, we searched for functional partners of OGT and identified interacting protein Dot1L, a conserved and unique histone methyltransferase known to mediate histone H3 Lys79 methylation, which is required for gene transcription, DNA damage repair, cell proliferation, and embryo development. Although this specific interaction with OGT does not regulate the enzymatic activity of Dot1L, we show that it does facilitate OGT-dependent histone O-GlcNAcylation. Moreover, we demonstrate that OGT associates with Dot1L at transcription start sites and that depleting Dot1L decreases OGT associated with chromatin globally. Notably, we also show that downregulation of Dot1L reduces the levels of histone H2B S112 O-GlcNAcylation and histone H2B K120 ubiquitination in vivo, which are associated with gene transcription regulation. Taken together, these results reveal that O-GlcNAcylation of chromatin is dependent on Dot1L.

Advances in Self-Powered Ultraviolet Photodetectors Based on P-N Heterojunction Low-Dimensional Nanostructures.

Self-powered ultraviolet (UV) photodetectors have attracted considerable attention in recent years because of their vast applications in the military and civil fields. Among them, self-powered UV photodetectors based on p-n heterojunction low-dimensional nanostructures are a very attractive research field due to combining the advantages of low-dimensional semiconductor nanostructures (such as large specific surface area, excellent carrier transmission channel, and larger photoconductive gain) with the feature of working independently without an external power source. In this review, a selection of recent developments focused on improving the performance of self-powered UV photodetectors based on p-n heterojunction low-dimensional nanostructures from different aspects are summarized. It is expected that more novel, dexterous, and intelligent photodetectors will be developed as soon as possible on the basis of these works.

Molecular dynamics simulations of adsorption behavior of DDAH, NaOL and mixed DDAH/NaOL surfactants on muscovite (001) surface in aqueous solution.

The adsorption mechanism of collectors on minerals is of fundamental importance in the research and development of flotation science and processing technology. To examine the effect of cationic dodecylamine hydrochloride (DDAH), anionic sodium oleate (NaOL) and mixed DDAH/NaOL surfactants with different molar ratios on the adsorption behavior on the muscovite (001) surface, the adsorption mechanism of DDAH, NaOL and their mixture on the muscovite (001) surface in neutral aqueous solution was investigated by molecular dynamics (MD) simulations. The results showed that the cationic DDAH molecules absorb on the muscovite (001) surface by electrostatic interactions and hydrogen bonding, whereas the anionic NaOL molecules cannot independently adsorb on the muscovite surface. Based on the analysis of the density distribution profile, radial distribution function (RDF) and interaction energy between surfactant molecules and muscovite surface, and the root mean square displacement (RMSD) of surfactants on water-muscovite interface, individual DDAH surfactant is a superior collector for the muscovite flotation. The molar ratio of DDAH/NaOL surfactants is found to be a key factor in the flotation response of muscovite. No significant adsorption of 1:2, 1:3 and 1:4 mixed DDAH/NaOL surfactants on the muscovite surface can be detected, while an effective adsorption was observed for the DDAH/NaOL mixture in molar ratios of 1:1, 2:1, 3:1 and 4:1. The cationic DDAH surfactant was determined to play a primary role in the adsorption of the mixed surfactants on the muscovite surface, while the anionic NaOL molecules co-adsorb with the DDAH molecules. The additional micro-flotation experiments under neutral aqueous conditions also showed that the flotation recovery of muscovite was the highest in the presence of DDAH surfactant, which was consistent with the findings derived from MD simulations.

ILF3 represses repeat-derived microRNAs targeting RIG-I mediated type I interferon response.

MicroRNAs (miRNAs) play important roles in regulated gene expression and miRNA biogenesis is also subject to regulation, together constituting critical regulatory circuitries in numerous physiological and pathological processes. As a dsRNA binding protein, interleukin enhancer binding factor 3 (ILF3) has been implicated as a negative regulator in miRNA biogenesis, but the mechanism and specificity have remained undefined. Here, combining small-RNA-seq and CLIP-seq, we showed that ILF3 directly represses many miRNAs or perhaps other types of small RNAs annotated in both miRBase and MirGeneDB. We demonstrated that ILF3 preferentially binds to A/U-enriched motifs, which tend to lengthen and/or stabilize the stem-loop in pri-miRNAs, thereby effectively competing with the Microprocessor to block miRNA biogenesis. Focusing on the biological function of ILF3-suppressed miR-582-3p, we discovered that this LINE-derived miRNA targets a critical interferon-inducible gene RIG-I for repression, thus establishing a novel ILF3/miR-582/RIG-I axis in the antiviral response.

Colour schemes to reduce stress response in the hygiene area of a space station: A Delphi study.

This paper aims to explore colour schemes to reduce stress response in the hygiene area of a space station. We conducted a two-stage exploratory Delphi-study with 30 international experts. It was found that the overall environment, stool-urine collection device, garbage collection interface and negative pressure package interface of the hygiene area most affected astronauts' experience. Remarkably, experts have highest visual requirements for the cleanliness of the overall environment and for stool and urine collection devices in the hygiene area. These tend to have low saturation and low blackness colours, while the garbage collection interface and negative pressure package interface have conspicuity and discernibility visual requirements. It was found that experts tend to choose high saturation and high brightness colours.

Optical properties of natural small molecules and their applications in imaging and nanomedicine.

Natural small molecules derived from plants have fascinated scientists for centuries due to their practical applications in various fields, especially in nanomedicine. Some of the natural molecules were found to show intrinsic optical features such as fluorescence emission and photosensitization, which could be beneficial to provide spatial temporal information and help tracking the drugs in biological systems. Much efforts have been devoted to the investigation of optical properties and practical applications of natural molecules. In this review, optical properties of natural small molecules and their applications in fluorescence imaging, and theranostics will be summarized. First, we will introduce natural small molecules with different fluorescence emission, ranging from blue to near infrared emission. Second, imaging applications in biological samples will be covered. Third, we will discuss the applications of theranostic nanomedicines or drug delivering systems containing fluorescent natural molecules acting as imaging agents or photosensitizers. Finally, future perspectives in this field will be discussed.

The SARS-CoV-2 subgenome landscape and its novel regulatory features.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently a global pandemic. CoVs are known to generate negative subgenomes (subgenomic RNAs [sgRNAs]) through transcription-regulating sequence (TRS)-dependent template switching, but the global dynamic landscapes of coronaviral subgenomes and regulatory rules remain unclear. Here, using next-generation sequencing (NGS) short-read and Nanopore long-read poly(A) RNA sequencing in two cell types at multiple time points after infection with SARS-CoV-2, we identified hundreds of template switches and constructed the dynamic landscapes of SARS-CoV-2 subgenomes. Interestingly, template switching could occur in a bidirectional manner, with diverse SARS-CoV-2 subgenomes generated from successive template-switching events. The majority of template switches result from RNA-RNA interactions, including seed and compensatory modes, with terminal pairing status as a key determinant. Two TRS-independent template switch modes are also responsible for subgenome biogenesis. Our findings reveal the subgenome landscape of SARS-CoV-2 and its regulatory features, providing a molecular basis for understanding subgenome biogenesis and developing novel anti-viral strategies.

ß-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus.

Mouse embryonic stem cells cultured with MEK (mitogen-activated protein kinase kinase) and GSK3 (glycogen synthase kinase 3) inhibitors (2i) more closely resemble the inner cell mass of preimplantation blastocysts than those cultured with SL [serum/leukemia inhibitory factor (LIF)]. The transcriptional mechanisms governing this pluripotent ground state are unresolved. Release of promoter-proximal paused RNA polymerase II (Pol2) is a multistep process necessary for pluripotency and cell cycle gene transcription in SL. We show that ß-catenin, stabilized by GSK3 inhibition in medium with 2i, supplies transcriptional coregulators at pluripotency loci. This selectively strengthens pluripotency loci and renders them addicted to transcription initiation for productive gene body elongation in detriment to Pol2 pause release. By contrast, cell cycle genes are not bound by ß-catenin, and proliferation/self-renewal remains tightly controlled by Pol2 pause release under 2i conditions. Our findings explain how pluripotency is reinforced in the ground state and also provide a general model for transcriptional resilience/adaptation upon network perturbation in other contexts.