DDX21 mediates co-transcriptional RNA m6A modification to promote transcription termination and genome stability.

N6-methyladenosine (m6A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m6A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21's helicase activity is needed for METTL3-mediated m6A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m6A, coordinating transcription termination and genome stability.

Sterically Controlled Synthesis of Amine-Free CsPbBr3 Nanoplatelets for Stable, Pure-Blue Light Emission.

Metal halide perovskite nanoplatelets (NPLs) have demonstrated excellent optical properties for light-emitting applications and achieved tunable blue luminescence through thickness control. However, their translation into electronic devices has lagged behind due to poor colloidal and film stability. The main reason for this is the deprotonation of their surface-capped ammonium passivating ligands, resulting in NPL aggregation. Here we report the first facile synthesis of amine-free pure-blue CsPbBr3 NPLs with outstanding thermal and light stability. This is achieved by utilizing an amine-free phosphine oxide route with a surface capping molecule exhibiting large steric hindrance to prevent NPL aggregation. Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy suggests slower ligand exchange in amine-free NPLs compared to the conventional NPLs, which can be attributed to the strong binding strength of the designated ligand. Consequently, the amine-free NPLs exhibited superior stability against radiation, heat and moisture. We further demonstrate the importance of acid-base equilibrium in this amine-free synthesis route. Through solvent neutralization and passivation with various alkali carbonates, the resulting NPLs attained near-unity photoluminescence quantum yield (PLQY) and pure blue emission.

Enhanced CO2 Reactive Capture and Conversion Using Aminothiolate Ligand-Metal Interface.

Metallic catalyst modification by organic ligands is an emerging catalyst design in enhancing the activity and selectivity of electrocatalytic carbon dioxide (CO2) reactive capture and reduction to value-added fuels. However, a lack of fundamental science on how these ligand-metal interfaces interact with CO2 and key intermediates under working conditions has resulted in a trial-and-error approach for experimental designs. With the aid of density functional theory calculations, we provided a comprehensive mechanism study of CO2 reduction to multicarbon products over aminothiolate-coated copper (Cu) catalysts. Our results indicate that the CO2 reduction performance was closely related to the alkyl chain length, ligand coverage, ligand configuration, and Cu facet. The aminothiolate ligand-Cu interface significantly promoted initial CO2 activation and lowered the activation barrier of carbon-carbon coupling through the organic (nitrogen (N)) and inorganic (Cu) interfacial active sites. Experimentally, the selectivity and partial current density of the multicarbon products over aminothiolate-coated Cu increased by 1.5-fold and 2-fold, respectively, as compared to the pristine Cu at -1.16 VRHE, consistent with our theoretical findings. This work highlights the promising strategy of designing the ligand-metal interface for CO2 reactive capture and conversion to multicarbon products.

Bcl-3 regulates T cell function through energy metabolism.

BACKGROUND: Bcl-3 is a member of the IκB protein family and an essential modulator of NF-κB activity. It is well established that Bcl-3 is critical for the normal development, survival and differentiation of adaptive immune cells, especially T cells. However, the regulation of immune cell function by Bcl-3 through metabolic pathways has rarely been studied. RESULTS: In this study, we explored the role of Bcl-3 in the metabolism and function of T cells via the mTOR pathway. We verified that the proliferation of Bcl-3-deficient Jurkat T cells was inhibited, but their activation was promoted, and Bcl-3 depletion regulated cellular energy metabolism by reducing intracellular ATP and ROS production levels and mitochondrial membrane potential. Bcl-3 also regulates cellular energy metabolism in naive CD4+ T cells. In addition, the knockout of Bcl-3 altered the expression of mTOR, Akt, and Raptor, which are metabolism-related genes, in Jurkat cells. CONCLUSIONS: This finding indicates that Bcl-3 may mediate the energy metabolism of T cells through the mTOR pathway, thereby affecting their function. Overall, we provide novel insights into the regulatory role of Bcl-3 in T-cell energy metabolism for the prevention and treatment of immune diseases.

S1P/S1PR signaling pathway advancements in autoimmune diseases.

Sphingosine-1-phosphate (S1P) is a versatile sphingolipid that is generated through the phosphorylation of sphingosine by sphingosine kinase (SPHK). S1P exerts its functional effects by binding to the G protein-coupled S1P receptor (S1PR). This lipid mediator plays a pivotal role in various cellular activities. The S1P/S1PR signaling pathway is implicated in the pathogenesis of immune-mediated diseases, significantly contributing to the functioning of the immune system. It plays a crucial role in diverse physiological and pathophysiological processes, including cell survival, proliferation, migration, immune cell recruitment, synthesis of inflammatory mediators, and the formation of lymphatic and blood vessels. However, the full extent of the involvement of this signaling pathway in the development of autoimmune diseases remains to be fully elucidated. Therefore, this study aims to comprehensively review recent research on the S1P/S1PR axis in diseases related to autoimmunity.

Selective pyrophosphate detection via metal complexes.

Pyrophosphate (PPi) anions are crucial in numerous biological and ecological processes involved in energy conversion, enzymatic reactions, and metabolic regulation along with adenosine. They are also significant biological markers for various processes related to diseases. Fluorescent PPi sensors would enable visual and/or biological detection in convenient settings. However, the current availability of commercial sensors has been limited to costly enzymes that are not compatible for imaging. Sensor development has also encountered challenges such as poor selectivity and stability, and limited practical applications. In this review, we analyze the situation of PPi sensing via commercial kits and focus on sensors that use metal complexes. We address their designs, sensing mechanisms, selectivities and detection limits. Finally, we discuss limitations and perspectives for PPi detection and imaging.

Expression of PmACRE1 in Arabidopsis thaliana enables host defence against Bursaphelenchus xylophilus infection.

BACKGROUND: Pine wilt disease (PWD) is a destructive disease that endangers pine trees, resulting in the wilting, with yellowing and browning of the needles, and eventually the death of the trees. Previous studies showed that the Avr9/Cf-9 rapidly elicited (PmACRE1) gene was downregulated by Bursaphelenchus xylophilus infection, suggesting a correlation between PmACRE1 expression and pine tolerance. Here, we used the expression of PmACRE1 in Arabidopsis thaliana to evaluate the role of PmACRE1 in the regulation of host defence against B. xylophilus infection. RESULTS: Our results showed that the transformation of PmACRE1 into A. thaliana enhanced plant resistance to the pine wood nematode (PWN); that is, the leaves of the transgenic line remained healthy for a longer period than those of the blank vector group. Ascorbate peroxidase (APX) activity and total phenolic acid and total flavonoid contents were higher in the transgenic line than in the control line. Widely targeted metabolomics analysis of the global secondary metabolites in the transgenic line and the vector control line showed that the contents of 30 compounds were significantly different between these two lines; specifically, the levels of crotaline, neohesperidin, nobiletin, vestitol, and 11 other compounds were significantly increased in the transgenic line. The studies also showed that the ACRE1 protein interacted with serine hydroxymethyltransferase, catalase domain-containing protein, myrosinase, dihydrolipoyl dehydrogenase, ketol-acid reductoisomerase, geranylgeranyl diphosphate reductase, S-adenosylmethionine synthase, glutamine synthetase, and others to comprehensively regulate plant resistance. CONCLUSIONS: Taken together, these results indicate that PmACRE1 has a potential role in the regulation of plant defence against PWNs.

The impact of genetic modified Ma bamboo on soil microbiome.

Evaluating the potential alteration of microbial communities is a vital step for biosafety of genetic modified plants. Recently, we have produced genetic modified Ma bamboo with increased cold and drought tolerance by anthocyanin accumulation. In this work, we aim to study the potential effects on microbial communities in rhizosphere soils during the cultivation of genetic modified bamboo. Rhizosphere and surrounding soil were collected at 3-month post-transplant. The amplicon (16S rDNA and ITS1) were sequenced for analysis of bacterial and fungal communities. Multiple software and database (Picrust2, FAPROTAX and FUNGulid) were applied to predict and compare the microbial functions involving basic metabolisms, nitrogen usage and presence of plant pathogens. There were no substantial change of the structure and abundance of rhizosphere soil microbial communities between genetic modified and wild type bamboo. For the surrounding soil, the bacterial biota α-diversity increased (chao1: 1,001 ± 80-1,276 ± 84, observed species: 787 ± 52-1,194 ± 137, PD whole tree: 75 ± 4-117 ± 18) and fungal biota α-diversity decreased (chao1: 187 ± 18-145 ± 10) in samples of genetic modified bamboo compared to those of wild type bamboo. The microbiota predicted functions did not change or had no negative alteration between genetic modified and wild type bamboo, in both rhizosphere and surrounding soils. As a conclusion, the growth of genetic modified bamboo had no substantial change on rhizosphere soil microbial communities, while minor alteration on bamboo surrounding soil microbial communities with no harmful effects. Moreover, the genetic modified bamboo had no negative effect on the predicted functions of microbiota in soil.

Analysis of Transcriptome and Terpene Constituents of Scots Pine Genotypes Inherently Resistant or Susceptible to Heterobasidion annosum.

Root and stem rot caused by Heterobasidion annosum is a severe problem in boreal Scots pine. Dissecting the features of disease resistance is generally an essential step in resistance breeding in plants and forest trees. In this study, we explored inherent resistance factors of Scots pine against H. annosum. A total of 236 families consisting of 85 full-sib (FS), 35 half-sib population mix (HSpm), and 116 half-sib (HS) families of Scots pine seedlings were inoculated with a H. annosum isolate. We sampled needle tissues before inoculation for terpene measurements and RNA sequencing. Based on the lesion area, the extremes of 12 resistant and 12 susceptible families were selected for further analyses. Necrotic lesions resulting from fungal infection were in a weak to moderate relationship with the plant height. Monoterpenes were the principal terpene compounds observed in Scots pine seedlings. Concentrations of 3-carene were significantly higher in pine genotypes inherently resistant compared with susceptible seedlings. By contrast, susceptible genotypes had significantly higher proportions of α-pinene. Gene ontology analysis of differential expressed transcripts (DETs) revealed that response to biotic factors was enriched in resistant seedlings. Functional characterization of individual DETs revealed that higher expression of transcripts involved in response to abiotic stress was common in susceptible genotypes. This observation was supported by the annotation of hub genes in a key module that was significantly correlated with the lesion trait through weighted gene co-expression network analysis (WGCNA) of 16 HS and HSpm samples. These findings contribute to our understanding of constitutive resistance factors of Scots pine against Heterobasidion root and stem rot diseases.

Fast Near-Infrared Photodetection Using III-V Colloidal Quantum Dots.

Colloidal quantum dots (CQDs) are promising materials for infrared (IR) light detection due to their tunable bandgap and their solution processing; however, to date, the time response of CQD IR photodiodes is inferior to that provided by Si and InGaAs. It is reasoned that the high permittivity of II-VI CQDs leads to slow charge extraction due to screening and capacitance, whereas III-Vs-if their surface chemistry can be mastered-offer a low permittivity and thus increase potential for high-speed operation. In initial studies, it is found that the covalent character in indium arsenide (InAs) leads to imbalanced charge transport, the result of unpassivated surfaces, and uncontrolled heavy doping. Surface management using amphoteric ligand coordination is reported, and it is found that the approach addresses simultaneously the In and As surface dangling bonds. The new InAs CQD solids combine high mobility (0.04 cm2 V-1 s-1 ) with a 4× reduction in permittivity compared to PbS CQDs. The resulting photodiodes achieve a response time faster than 2 ns-the fastest photodiode among previously reported CQD photodiodes-combined with an external quantum efficiency (EQE) of 30% at 940 nm.

Characteristics of N6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii.

The unicellular green alga Chlamydomonas reinhardtii (hereafter Chlamydomonas) possesses both plant and animal attributes, and it is an ideal model organism for studying fundamental processes such as photosynthesis, sexual reproduction, and life cycle. N6-methyladenosine (m6A) is the most prevalent mRNA modification, and it plays important roles during sexual reproduction in animals and plants. However, the pattern and function of m6A modification during the sexual reproduction of Chlamydomonas remain unknown. Here, we performed transcriptome and methylated RNA immunoprecipitation sequencing (MeRIP-seq) analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle. The results show that m6A modification frequently occurs at the main motif of DRAC (D = G/A/U, R = A/G) in Chlamydomonas mRNAs. Moreover, m6A peaks in Chlamydomonas mRNAs are mainly enriched in the 3' untranslated regions (3' UTRs) and negatively correlated with the abundance of transcripts at each stage. In particular, there is a significant negative correlation between the expression levels and the m6A levels of genes involved in the microtubule-associated pathway, indicating that m6A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement. In summary, our findings are the first to demonstrate the distribution and the functions of m6A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m6A modification in the process of sexual reproduction in other plant organisms.

Alternating Current Field Effects in Atomically Ferroelectric Ultrathin Films.

In this work, atomically K1-xNaxNbO3 thin films are taken as examples to investigate the reversible and irreversible effects in a horizon plane, i.e., the changes of domain structures, phase states, free energies, etc., under a z-axis alternating current field via a phase-field method. The simulation results show the driving forces during the charging and discharging process, where there is a variation for the angles of the domain walls from 180° to 90° (and then an increase to 135°), which are the external electric field and domain wall evolution, respectively. As for the phase states, there is a transformation between the orthorhombic and rhombohedral phases which can't be explained by the traditional polarization switching theory. This work provides a reasonable understanding of the alternating current field effect, which is essential in information and energy storage.

Ultrafast exciton transport at early times in quantum dot solids.

Quantum dot (QD) solids are an emerging platform for developing a range of optoelectronic devices. Thus, understanding exciton dynamics is essential towards developing and optimizing QD devices. Here, using transient absorption microscopy, we reveal the initial exciton dynamics in QDs with femtosecond timescales. We observe high exciton diffusivity (~102 cm2 s-1) in lead chalcogenide QDs within the first few hundred femtoseconds after photoexcitation followed by a transition to a slower regime (~10-1-1 cm2 s-1). QD solids with larger interdot distances exhibit higher initial diffusivity and a delayed transition to the slower regime, while higher QD packing density and heterogeneity accelerate this transition. The fast transport regime occurs only in materials with exciton Bohr radii much larger than the QD sizes, suggesting the transport of delocalized excitons in this regime and a transition to slower transport governed by exciton localization. These findings suggest routes to control the optoelectronic properties of QD solids.

RNA N6-methyladenosine modulates endothelial atherogenic responses to disturbed flow in mice.

Atherosclerosis preferentially occurs in atheroprone vasculature where human umbilical vein endothelial cells are exposed to disturbed flow. Disturbed flow is associated with vascular inflammation and focal distribution. Recent studies have revealed the involvement of epigenetic regulation in atherosclerosis progression. N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic mRNA, but its function in endothelial atherogenic progression remains unclear. Here, we show that m6A mediates the epidermal growth factor receptor (EGFR) signaling pathway during EC activation to regulate the atherosclerotic process. Oscillatory stress (OS) reduced the expression of methyltransferase like 3 (METTL3), the primary m6A methyltransferase. Through m6A sequencing and functional studies, we determined that m6A mediates the mRNA decay of the vascular pathophysiology gene EGFR which leads to EC dysfunction. m6A modification of the EGFR 3' untranslated regions (3'UTR) accelerated its mRNA degradation. Double mutation of the EGFR 3'UTR abolished METTL3-induced luciferase activity. Adenovirus-mediated METTL3 overexpression significantly reduced EGFR activation and endothelial dysfunction in the presence of OS. Furthermore, thrombospondin-1 (TSP-1), an EGFR ligand, was specifically expressed in atheroprone regions without being affected by METTL3. Inhibition of the TSP-1/EGFR axis by using shRNA and AG1478 significantly ameliorated atherogenesis. Overall, our study revealed that METTL3 alleviates endothelial atherogenic progression through m6A-dependent stabilization of EGFR mRNA, highlighting the important role of RNA transcriptomics in atherosclerosis regulation.

Molecular and Chemical Screening for Inherent Disease Resistance Factors of Norway Spruce (Picea abies) Clones Against Conifer Stem Rot Pathogen Heterobasidion parviporum.

Root and stem rot of conifer trees caused by Heterobasidion annosum species complex leads to huge economic losses in Europe, yet not much is known about the molecular and chemical basis for host resistance. To identify inherent chemical or molecular markers in clones found to be either resistant or susceptible, we sampled needle tissues of all the clones before pathogen inoculation. We conducted a short-term resistance screening by using the pathogen H. parviporum to inoculate 70 Norway spruce clones. Based on lesion size, subsets of highly susceptible and resistant clones were further analyzed. Terpene detection and RNA sequencing were performed to explore inherent variations in genotypes differing in resistance to pathogenic challenge at chemical and transcriptional levels. A negative correlation emerged between resistance and growth. Terpene profiles of resistant clones showed higher content of monoterpenes and sesquiterpenes, with concomitant increased transcript abundance of genes involved in the terpenoid pathway. A set of upregulated genes relevant to flavonoid biosynthesis was observed in resistant genotypes, whereas higher transcripts of lignin biosynthetic genes were prevalent in susceptible clones. Genes involved in flavonoid and lignin biosynthesis as well as terpene content may have a role in facilitating resistance of Norway spruce against H. parviporum. Our results provide strong support on the feasibility of sampling needle tissues before pathogen inoculation, and the approach could be of value for large-scale screening of novel biomarkers for durable resistance. The additional insights could form a basis for further research on resistance screening in this pathosystem.

Nonequilibrium Carrier Transport in Quantum Dot Heterostructures.

Understanding carrier dynamics and transport in quantum dot based heterostructures is crucial for unlocking their full potential for optoelectronic applications. Here we report the direct visualization of carrier propagation in PbS CQD solids and quantum-dot-in-perovskite heterostructures using femtosecond transient absorption microscopy. We reveal three distinct transport regimes: an initial superdiffusive transport persisting over hundreds of femtoseconds, an Auger-assisted subdiffusive transport before thermal equilibrium is achieved, and a final hopping regime. We demonstrate that the superdiffusive transport lengths correlate strongly with the degree of energetic disorder and carrier delocalization. By tailoring the perovskite content in heterostructures, we obtained a superdiffusive transport length exceeding 90 nm at room temperature and an equivalent diffusivity of up to 106 cm2 s-1, which is 4 orders of magnitude higher than the steady-state values. These findings introduce promising strategies to harness nonequilibrium transport phenomena for more efficient optoelectronic devices.

Switchable Synthesis of Sulfoxides and α-Alkoxy-ß-ketothioethers Regulated by Temperature in a Selectfluor-Methanol System.

A switchable and benign protocol for chemoselective synthesis of sulfoxides and α-alkoxy-ß-ketothioethers has been developed. It was determined that various thiophenols and alkenes/alkynes are compatible to realize the target compounds from a medium to a high yield by regulating the reaction temperature. In particular, methanol not only served as a solvent but also participated in the reaction process as a hydrogen donor. In this study, Selectfluor has been proved to be an efficient multifunctional reagent in the reaction system.

Single-step-fabricated disordered metasurfaces for enhanced light extraction from LEDs.

While total internal reflection (TIR) lays the foundation for many important applications, foremost fibre optics that revolutionised information technologies, it is undesirable in some other applications such as light-emitting diodes (LEDs), which are a backbone for energy-efficient light sources. In the case of LEDs, TIR prevents photons from escaping the constituent high-index materials. Advances in material science have led to good efficiencies in generating photons from electron-hole pairs, making light extraction the bottleneck of the overall efficiency of LEDs. In recent years, the extraction efficiency has been improved, using nanostructures at the semiconductor/air interface that outcouple trapped photons to the outside continuum. However, the design of geometrical features for light extraction with sizes comparable to or smaller than the optical wavelength always requires sophisticated and time-consuming fabrication, which causes a gap between lab demonstration and industrial-level applications. Inspired by lightning bugs, we propose and realise a disordered metasurface for light extraction throughout the visible spectrum, achieved with single-step fabrication. By applying such a cost-effective light extraction layer, we improve the external quantum efficiency by a factor of 1.65 for commercialised GaN LEDs, demonstrating a substantial potential for global energy-saving and sustainability.

A simple phenol-free isolation method for high-quality RNA from bilberry.

High-quality RNA is required for accurate gene expression and transcriptome analysis. The current methods of RNA extraction from berry fruits are either time-consuming or expensive. To simplify the conventional phenol-chloroform based RNA extraction method, we modified the protocol with less steps as well as the removal of the use of phenol. In this protocol, the extraction buffer is composed of hexadecyltrimethyl ammonium bromide (CTAB), polyvinylpyrrolidone (PVP), and Dithiothreitol (DTT). The method facilitates efficient removal of polysaccharides and phenolic compounds from both fruit pulp and fruit peel. Additionally, the protocol is phenol-free and less toxic than traditional phenol-containing method. High-quality RNA, with RNA Integrity Number value > 8, isolated by this method is applicable for RNA sequencing and qPCR. Only 3-4 working hours are required for one batch of RNA isolation.•Our method replaces the use of phenol-chloroform with chloroform, making the extraction less toxic.•The bilberry friut RNA is of high-quality and purity with less time input.

Nanocrystal Quantum Dot Devices: How the Lead Sulfide (PbS) System Teaches Us the Importance of Surfaces.

Semiconducting thin films made from nanocrystals hold potential as composite hybrid materials with new functionalities. With nanocrystal syntheses, composition can be controlled at the sub-nanometer level, and, by tuning size, shape, and surface termination of the nanocrystals as well as their packing, it is possible to select the electronic, phononic, and photonic properties of the resulting thin films. While the ability to tune the properties of a semiconductor from the atomistic- to macro-scale using solution-based techniques presents unique opportunities, it also introduces challenges for process control and reproducibility. In this review, we use the example of well-studied lead sulfide (PbS) nanocrystals and describe the key advances in nanocrystal synthesis and thin-film fabrication that have enabled improvement in performance of photovoltaic devices. While research moves forward with novel nanocrystal materials, it is important to consider what decades of work on PbS nanocrystals has taught us and how we can apply these learnings to realize the full potential of nanocrystal solids as highly flexible materials systems for functional semiconductor thin-film devices. One key lesson is the importance of controlling and manipulating surfaces.