TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors.

The high mobility group (HMG) transcription factor TCF-1 is essential for early T cell development. Although in vitro biochemical assays suggest that HMG proteins can serve as architectural elements in the assembly of higher-order nuclear organization, the contribution of TCF-1 on the control of three-dimensional (3D) genome structures during T cell development remains unknown. Here, we investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and the architectural protein CTCF altered the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes at late stages of T cell development. The TCF-1-dependent gain in long-range interactions was linked to deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in controlling global genome organization during T cell development.

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression.

Genetics is a major determinant of susceptibility to autoimmune disorders. Here, we examined whether genome organization provides resilience or susceptibility to sequence variations, and how this would contribute to the molecular etiology of an autoimmune disease. We generated high-resolution maps of linear and 3D genome organization in thymocytes of NOD mice, a model of type 1 diabetes (T1D), and the diabetes-resistant C57BL/6 mice. Multi-enhancer interactions formed at genomic regions harboring genes with prominent roles in T cell development in both strains. However, diabetes risk-conferring loci coalesced enhancers and promoters in NOD, but not C57BL/6 thymocytes. 3D genome mapping of NODxC57BL/6 F1 thymocytes revealed that genomic misfolding in NOD mice is mediated in cis. Moreover, immune cells infiltrating the pancreas of humans with T1D exhibited increased expression of genes located on misfolded loci in mice. Thus, genetic variation leads to altered 3D chromatin architecture and associated changes in gene expression that may underlie autoimmune pathology.

Conserved and divergent gene regulatory programs of the mammalian neocortex.

Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.

Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling.

Addressing the ongoing antibiotic crisis requires the discovery of compounds with novel mechanisms of action that are capable of treating drug-resistant infections1. Many antibiotics are sourced from specialized metabolites produced by bacteria, particularly those of the Actinomycetes family2. Although actinomycete extracts have traditionally been screened using activity-based platforms, this approach has become unfavourable owing to the frequent rediscovery of known compounds. Genome sequencing of actinomycetes reveals an untapped reservoir of biosynthetic gene clusters, but prioritization is required to predict which gene clusters may yield promising new chemical matter2. Here we make use of the phylogeny of biosynthetic genes along with the lack of known resistance determinants to predict divergent members of the glycopeptide family of antibiotics that are likely to possess new biological activities. Using these predictions, we uncovered two members of a new functional class of glycopeptide antibiotics-the known glycopeptide antibiotic complestatin and a newly discovered compound we call corbomycin-that have a novel mode of action. We show that by binding to peptidoglycan, complestatin and corbomycin block the action of autolysins-essential peptidoglycan hydrolases that are required for remodelling of the cell wall during growth. Corbomycin and complestatin have low levels of resistance development and are effective in reducing bacterial burden in a mouse model of skin MRSA infection.

Anodic Reconstructed p+-GaAs/a-InAsN for Stable and Efficient Photoelectrochemical Hydrogen Evolution.

The extremely poor solution stability and massive carrier recombination have seriously prevented III-V semiconductor nanomaterials from efficient and stable hydrogen production. In this work, an anodic reconstruction strategy based on group III-V active semiconductors is proposed for the first time, resulting in 19-times photo-gain. What matters most is that the device after anodic reconstruction shows very superior stability under the protracted photoelectrochemical (PEC) test over 8100 s, while the final photocurrent density does not decrease but rather increases by 63.15%. Using the experiment and DFT theoretical calculation, the anodic reconstruction mechanism is elucidated: through the oxidation of indium clusters and the migration of arsenic atoms, the reconstruction formed p+-GaAs/a-InAsN. The hole concentration of the former is increased by 10 times (5.64 × 1018 cm-1 increases up to 5.95 × 1019 cm-1) and the band gap of the latter one is reduced to a semi-metallic state, greatly strengthening the driving force of PEC water splitting. This work turns waste into treasure, transferring the solution instability into better efficiency.

CRISPR-Cas9 mediated genome editing of Kluyveromyces marxianus for iterative, multiplexed gene disruption and pathway integration.

Kluyveromyces marxianus, a thermotolerant, fast-growing, Crabtree-negative yeast, is a promising chassis for the manufacture of various bioproducts. Although several genome editing tools are available for this yeast, these tools still require refinement to enable more convenient and efficient genetic modification. In this study, we engineered the K. marxianus NBRC 104275 strain by impairing the nonhomologous end joining and enhancing the homologous recombination machinery, which resulted in improved homology-directed repair effective on homology arms of up to 40 bp in length. Additionally, we simplified the CRISPR-Cas9 editing system by constructing a strain for integrative expression of Cas9 nuclease and plasmids bearing different selection markers for gRNA expression, thereby facilitating iterative genome editing without the need for plasmid curing. We demonstrated that tRNA was more effective than the hammerhead ribozyme for processing gRNA primary transcripts, and readily assembled tRNA-gRNA arrays were used for multiplexed editing of at least four targets. This editing tool was further employed for simultaneous scarless in vivo assembly of a 12-kb cassette from three fragments and marker-free integration for expressing a fusion variant of fatty acid synthase, as well as the integration of genes for starch hydrolysis. Together, the genome editing tool developed in this study makes K. marxianus more amenable to genetic modification and will facilitate more extensive engineering of this nonconventional yeast for chemical production.

Reversible, Covalent DNA Condensation Approach Using Chemical Linkers for Enhanced Gene Delivery.

Nonviral gene delivery has emerged as a promising technology for gene therapy. Nonetheless, these approaches often face challenges, primarily associated with lower efficiency, which can be attributed to the inefficient transportation of DNA into the nucleus. Here, we report a two-stage condensation approach to achieve efficient nuclear transport of DNA. First, we utilize chemical linkers to cross-link DNA plasmids via a reversible covalent bond to form smaller-sized bundled DNA (b-DNA). Then, we package the b-DNA into cationic vectors to further condense b-DNA and enable efficient gene delivery to the nucleus. We demonstrate clear improvements in the gene transfection efficiency in vitro, including with 11.6 kbp plasmids and in primary cultured neurons. Moreover, we also observed a remarkable improvement in lung-selective gene transfection efficiency in vivo by this two-stage condensation approach following intravenous administration. This reversible covalent assembly strategy demonstrates substantial value of nonviral gene delivery for clinical therapeutic applications.

Ultrasound-Triggered In Situ Photon Emission for Noninvasive Optogenetics.

Optogenetics has revolutionized neuroscience understanding by allowing spatiotemporal control over cell-type specific neurons in neural circuits. However, the sluggish development of noninvasive photon delivery in the brain has limited the clinical application of optogenetics. Focused ultrasound (FUS)-derived mechanoluminescence has emerged as a promising tool for in situ photon emission, but there is not yet a biocompatible liquid-phase mechanoluminescence system for spatiotemporal optogenetics. To achieve noninvasive optogenetics with a high temporal resolution and desirable biocompatibility, we have developed liposome (Lipo@IR780/L012) nanoparticles for FUS-triggered mechanoluminescence in brain photon delivery. Synchronized and stable blue light emission was generated in solution under FUS irradiation due to the cascade reactions in liposomes. In vitro tests revealed that Lipo@IR780/L012 could be triggered by FUS for light emission at different stimulation frequencies, resulting in activation of opsin-expressing spiking HEK cells under the FUS irradiation. In vivo optogenetic stimulation further demonstrated that motor cortex neurons could be noninvasively and reversibly activated under the repetitive FUS irradiation after intravenous injection of lipid nanoparticles to achieve limb movements.

Lessons from assembling a microbial natural product and pre-fractionated extract library in an academic laboratory.

Microbial natural products are specialized metabolites that are sources of many bioactive compounds including antibiotics, antifungals, antiparasitics, anticancer agents, and probes of biology. The assembly of libraries of producers of natural products has traditionally been the province of the pharmaceutical industry. This sector has gathered significant historical collections of bacteria and fungi to identify new drug leads with outstanding outcomes-upwards of 60% of drug scaffolds originate from such libraries. Despite this success, the repeated rediscovery of known compounds and the resultant diminishing chemical novelty contributed to a pivot from this source of bioactive compounds toward more tractable synthetic compounds in the drug industry. The advent of advanced mass spectrometry tools, along with rapid whole genome sequencing and in silico identification of biosynthetic gene clusters that encode the machinery necessary for the synthesis of specialized metabolites, offers the opportunity to revisit microbial natural product libraries with renewed vigor. Assembling a suitable library of microbes and extracts for screening requires the investment of resources and the development of methods that have customarily been the proprietary purview of large pharmaceutical companies. Here, we report a perspective on our efforts to assemble a library of natural product-producing microbes and the establishment of methods to extract and fractionate bioactive compounds using resources available to most academic labs. We validate the library and approach through a series of screens for antimicrobial and cytotoxic agents. This work serves as a blueprint for establishing libraries of microbial natural product producers and bioactive extract fractions suitable for screens of bioactive compounds. ONE-SENTENCE SUMMARY: Natural products are key to discovery of novel antimicrobial agents: Here, we describe our experience and lessons learned in constructing a microbial natural product and pre-fractionated extract library.

Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels.

Chimeric antigen receptor (CAR)-T immunotherapy has yielded impressive results in several B cell malignancies, establishing itself as a powerful means to redirect the natural properties of T lymphocytes. In this strategy, the T cell genome is modified by the integration of lentiviral vectors encoding CAR that direct tumor cell killing. However, this therapeutic approach is often limited by the extent of CAR-T cell expansion in vivo. A major outstanding question is whether or not CAR-T integration itself enhances the proliferative competence of individual T cells by rewiring their regulatory landscape. To address this question, it is critical to define the identity of an individual CAR-T cell and simultaneously chart where the CAR-T vector integrates into the genome. Here, we report the development of a method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, leading to the discovery of cellular factors associated with durable treatment.

Salt-Assisted Selective Growth of H-phase Monolayer VSe2 with Apparent Hole Transport Behavior.

Vanadium diselenide (VSe2) exhibits versatile electronic and magnetic properties in the trigonal prismatic (H-) and octahedral (T-) phases. Compared to the metallic T-phase, the H-phase with a tunable semiconductor property is predicted to be a ferrovalley material with spontaneous valley polarization. Herein we report an epitaxial growth of the monolayer 2D VSe2 on a mica substrate via the chemical vapor deposition (CVD) method by introducing salt in the precursor. Our first-principles calculations suggest that the monolayer H-phase VSe2 with a large lateral size is thermodynamically favorable. The honeycomb-like structure and the broken symmetry are directly observed by spherical aberration-corrected scanning transmission electron microscopy (STEM) and confirmed by giant second harmonic generation (SHG) intensity. The p-type transport behavior is further evidenced by the temperature-dependent resistance and field-effect device study. The present work introduces a new phase-stable 2D transition metal dichalcogenide, opening the prospect of novel electronic and spintronics device design.

Unlocking Migratory Insertion in Gold Redox Catalysis.

Exploration of elementary reactions in organometallic catalysis is an important method with which to discover new reactions. In this article, we report a gold(I)-catalyzed iodo-alkynylation of benzyne involving the merging of challenging migratory insertion and an oxidative addition process in gold catalytic cycle. A wide range of structurally diverse alkynyl iodides are good coupling partners in this iodo-alkynylation transformation. Both aliphatic and aromatic alkynyl iodides can react with benzynes smoothly to afford highly functionalized 1,2-disubstituted aromatics in moderate to good yields. Its good functional group compatibility and late-stage application of complex molecules demonstrate its synthetic robustness. Studies of the mechanism reveals the feasibility of oxidative addition and the DFT calculations demonstrate the possible migratory insertion of benzyne into AuIII -carbon bonds in the AuI /AuIII redox catalytic cycle, representing an important step towards an elementary reaction in gold chemistry research.

RNAi and chemogenetic reporter co-regulation in primate striatal interneurons.

Using genetic tools to study the functional roles of molecularly specified neuronal populations in the primate brain is challenging, primarily because of specificity and verification of virus-mediated targeting. Here, we report a lentivirus-based system that helps improve specificity and verification by (a) targeting a selected molecular mechanism, (b) in vivo reporting of expression, and (c) allowing the option to independently silence all regional neural activity. Specifically, we modulate cholinergic signaling of striatal interneurons by shRNAmir and pair it with hM4Di_CFP, a chemogenetic receptor that can function as an in vivo and in situ reporter. Quantitative analyses by visual and deep-learning assisted methods show an inverse linear relation between hM4Di_CFP and ChAT protein expression for several shRNAmir constructs. This approach successfully applies shRNAmir to modulating gene expression in the primate brain and shows that hM4Di_CFP can act as a readout for this modulation.

High-speed graphene/InGaN heterojunction photodetectors for potential application in visible light communication.

Due to the wavelength-selective absorption characteristic of indium gallium nitride (InGaN) ternary alloy, the InGaN-based photodetectors (PDs) show great potential as high signal-to-noise ratio (SNR) receivers in the visible light communication (VLC) system. However, the application of InGaN-based PDs with simple structure in the VLC system is limited by slow speed. Integration of graphene (Gr) with InGaN is an effective strategy for overcoming the limitation. Herein, we report on a high responsivity and fast response PDs based on Gr/InGaN heterojunctions. It finds that the three-layer Gr (T-Gr) can effectively improve the InGaN-based PDs photoelectric properties. The T-Gr/InGaN PDs show a high responsivity of 1.39 A/W@-3 V and a short rise/fall time of 60/200 µs, which are attributed to the combination of the high-quality InGaN epitaxial films and finite density of states of three-layer graphene. The fast response with high responsivity endows the T-Gr/InGaN PDs with great potential for selective detection of the VLC system.

Parallel micro-LED arrays with a high modulation bandwidth for a visible light communication.

Over the past few decades, GaN-based LEDs have been widely used in solid-state lighting (SSL) due to their energy-saving and long-lifetime characteristics. However, the limited modulation bandwidth of conventional commercial LED chips limits their application in a high-speed visible light communication (VLC) system. Herein, this work designs vertical parallel micro-LED arrays with different array numbers to develop LED sources for communication and lighting. The as-prepared micro-LEDs in a 2 × 2 array reveal a high modulation bandwidth of ∼785 MHz at 6.67 kA/cm2. Meanwhile, the light output power is over 7 mW, which is more suitable for VLC in free space.

Kinetic and Mechanistic Investigations of OH-Initiated Atmospheric Degradation of Methyl Butyl Ketone.

Methyl butyl ketone (MBK, 2-hexanone) is a common atmospheric oxygenated volatile organic compound (OVOC) owing to broad industrial applications, but its atmospheric oxidation mechanism remains poorly understood. Herein, the detailed mechanisms and kinetic properties of MBK oxidation initiated by OH radicals and subsequent transformation of the resulting intermediates are performed by employing quantum chemical and kinetic modeling methods. The calculations show that H-abstraction at the C4 position of MBK is more favorable than those at the other positions, with the total rate coefficient of k(T) = 4.13 × 10-14 exp(1576/T) cm3 molecule-1 s-1 at 273-400 K. The dominant pathway of unimolecular degradation of the C-centered alkyl radical is 1,2-acyl group migration. For the isomerization of the peroxy radical RO2, 1,5- and 1,6-H shifts are more favorable than 1,3- and 1,4-H shifts. The multiconformer rate coefficient kMC-TST of the first H-shift of the RO2 radical is estimated to be 1.40 × 10-3 s-1 at room temperature. Compared to the H-shifts of analogous aliphatic RO2 radicals, it can be concluded that the carbonyl group enhances the H-shift rates by as much as 2-4 orders of magnitude. The rate coefficients of the RO2 radical reaction with the HO2 radical exhibit a weakly negative temperature dependence, and the pseudo-first-order rate constant k'HO2 = kHO2[HO2] is calculated to be 3.32-22.10 × 10-3 s-1 at ambient temperature. The bimolecular reaction of the RO2 radical with NO leads to the formation of 3-oxo-butanal as the main product with the formation concentration of 2.2-7.4 µg/m3 in urban areas. The predicted pseudo-first-order rate constant k'NO = kNO[NO] is 2.20-9.98 s-1 at room temperature. By comparing the kMC-TST, k'HO2, and k'NO, it can be concluded that reaction with NO is the dominant removal pathway for the RO2 radical formed from the OH-initiated oxidation of MBK. These findings are expected to deepen our understanding of the photochemical oxidation of ketones under realistic atmospheric conditions.

Dinuclear gold catalysis.

Gold chemistry has developed extensively in the past decade, and a dozen good reviews have been presented discussing this progress. Few however have paid close attention to the progress in organic synthesis of dinuclear gold-catalysis. A dinuclear gold catalyst is defined here as a gold complex with two gold centers linked by a bidentate ligand. With theoretical analysis and some representative studies in recent years, this comprehensive review highlights the particular properties of dinuclear gold-complexes, especially aurophilic interactions, and systematically summarizes the recent achievements of dinuclear gold-catalyzed coupling reactions, asymmetric catalysis, and photocatalysis, where dinuclear gold catalysts tend to show a greater advantage than the mononuclear gold catalysts.

Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations.

KEY MESSAGE: We provided a study on homeologous gene evolution of homeologous genes by comparing Brassica genomes. Polyploidy has played fundamental roles during the evolution of plants. Following polyploidization, many duplicated genes are diversified or lost in a process termed diploidization. Understanding the retention and diversification of homeologs after polyploidization will help elucidate the process of diploidization. Here, we investigated the evolution of homeologous genes in Brassica genomes and observed similarly asymmetrical gene retention among different functional groups and consistent retention after recurrent polyploidizations. In the comparative analysis of Brassica diploid genomes, we found that preferentially retained genes show different patterns on sequence and expression divergence: genes with the function of 'biosynthetic process' and 'transport' were under much stronger purifying selection, while transcriptional regulatory genes diverged much faster than other genes. Duplicate pairs of the former two functional groups show conserved high expression patterns, while most of transcriptional regulatory genes are simultaneously lowly expressed. Furthermore, homeologs in diploids and allotetraploids showed similar loss and retention patterns: duplicates in progenitor genomes were more likely to be retained and accumulated fewer substitutions. However, transcriptional regulation is also enriched in the genes that do not have any non-synonymous mutations in the Brassica allotetraploids, indicating that some of these genes were under strong purifying selection. Overall, our study provided insight into the evolution of homeologs genes during diploidization process.

Two-dimensional group-III nitrides and devices: a critical review.

As third-generation semiconductors, group-III nitrides are promising for high power electronic and optoelectronic devices because of their wide bandgap, high electron saturation mobility, and other unique properties. Inspired by the thickness-dependent properties of two-dimensional (2D) materials represented by graphene, it is predicted that the 2D counterparts of group-III nitrides would have similar properties. However, the preparation of 2D group-III nitride-based materials and devices is limited by the large lattice mismatch in heteroepitaxy and the low rate of lateral migration, as well as the unsaturated dangling bonds on the surfaces of group-III nitrides. The present review focuses on theoretical and experimental studies on 2D group-III nitride materials and devices. Various properties of 2D group-III nitrides determined using simulations and theoretical calculations are outlined. Moreover, the breakthroughs in their synthesis methods and their underlying physical mechanisms are detailed. Furthermore, devices based on 2D group-III nitrides are discussed accordingly. Based on recent progress, the prospect for the further development of the 2D group-III nitride materials and devices is speculated. This review provides a comprehensive understanding of 2D group-III nitride materials, aiming to promote the further development of the related fields of nano-electronic and nano-optoelectronics.