Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.

The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe the consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or "CRISPR D-BUGS," to map phenotypic variants caused by specific designer modifications, known as "bugs." We first fine-mapped a bug in synthetic chromosome II (synII) and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism, and tRNASerCGA abundance. Finally, to expedite consolidation, we employed chromosome substitution to incorporate the largest chromosome (synIV), thereby consolidating >50% of the Sc2.0 genome in one strain.

Design, construction, and functional characterization of a tRNA neochromosome in yeast.

Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.

A close quasar pair in a disk-disk galaxy merger at z = 2.17.

Galaxy mergers produce pairs of supermassive black holes (SMBHs), which may be witnessed as dual quasars if both SMBHs are rapidly accreting. The kiloparsec (kpc)-scale separation represents a physical regime sufficiently close for merger-induced effects to be important1 yet wide enough to be directly resolvable with the facilities currently available. Whereas many kpc-scale, dual active galactic nuclei-the low-luminosity counterparts of quasars-have been observed in low-redshift mergers2, no unambiguous dual quasar is known at cosmic noon (z ≈ 2), the peak of global star formation and quasar activity3,4. Here we report multiwavelength observations of Sloan Digital Sky Survey (SDSS) J0749 + 2255 as a kpc-scale, dual-quasar system hosted by a galaxy merger at cosmic noon (z = 2.17). We discover extended host galaxies associated with the much brighter compact quasar nuclei (separated by 0.46″ or 3.8 kpc) and low-surface-brightness tidal features as evidence for galactic interactions. Unlike its low-redshift and low-luminosity counterparts, SDSS J0749 + 2255 is hosted by massive compact disk-dominated galaxies. The apparent lack of stellar bulges and the fact that SDSS J0749 + 2255 already follows the local SMBH mass-host stellar mass relation, suggest that at least some SMBHs may have formed before their host stellar bulges. While still at kpc-scale separations where the host-galaxy gravitational potential dominates, the two SMBHs may evolve into a gravitationally bound binary system in around 0.22 Gyr.

DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage.

DNA storage is one of the most promising ways for future information storage due to its high data storage density, durable storage time and low maintenance cost. However, errors are inevitable during synthesizing, storing and sequencing. Currently, many error correction algorithms have been developed to ensure accurate information retrieval, but they will decrease storage density or increase computing complexity. Here, we apply the Bloom Filter, a space-efficient probabilistic data structure, to DNA storage to achieve the anti-error, or anti-contamination function. This method only needs the original correct DNA sequences (referred to as target sequences) to produce a corresponding data structure, which will filter out almost all the incorrect sequences (referred to as non-target sequences) during sequencing data analysis. Experimental results demonstrate the universal and efficient filtering capabilities of our method. Furthermore, we employ the Counting Bloom Filter to achieve the file version control function, which significantly reduces synthesis costs when modifying DNA-form files. To achieve cost-efficient file version control function, a modified system based on yin-yang codec is developed.

Rapid generation of high-quality structure figures for publication with PyMOL-PUB.

MOTIVATION: The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity. RESULTS: We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions, and predict performances of biomacromolecules. AVAILABILITY AND IMPLEMENTATION: Our tool is publicly available at https://github.com/BGI-SynBio/PyMOL-PUB.

In situ p-block protective layer plating in carbonate-based electrolytes enables stable cell cycling in anode-free lithium batteries.

'Anode-free' Li metal batteries offer the highest possible energy density but face low Li coulombic efficiency when operated in carbonate electrolytes. Here we report a performance improvement of anode-free Li metal batteries using p-block tin octoate additive in the carbonate electrolyte. We show that the preferential adsorption of the octoate moiety on the Cu substrate induces the construction of a carbonate-less protective layer, which inhibits the side reactions and contributes to the uniform Li plating. In the mean time, the reduction of Sn2+ at the initial charging process builds a stable lithophilic layer of Cu6Sn5 alloy and Sn, improving the affinity between the Li and the Cu substrate. Notably, anode-free Li metal pouch cells with tin octoate additive demonstrate good cycling stability with a high coulombic efficiency of ~99.1%. Furthermore, this in situ p-block layer plating strategy is also demonstrated with other types of p-block metal octoate, as well as a Na metal battery system, demonstrating the high level of universality.

HLA Class I Supertype Classification Based on Structural Similarity.

HLA class I proteins, a critical component in adaptive immunity, bind and present intracellular Ags to CD8+ T cells. The extreme polymorphism of HLA genes and associated peptide binding specificities leads to challenges in various endeavors, including neoantigen vaccine development, disease association studies, and HLA typing. Supertype classification, defined by clustering functionally similar HLA alleles, has proven helpful in reducing the complexity of distinguishing alleles. However, determining supertypes via experiments is impractical, and current in silico classification methods exhibit limitations in stability and functional relevance. In this study, by incorporating three-dimensional structures we present a method for classifying HLA class I molecules with improved breadth, accuracy, stability, and flexibility. Critical for these advances is our finding that structural similarity highly correlates with peptide binding specificity. The new classification should be broadly useful in peptide-based vaccine development and HLA-disease association studies.

Photosynthetic biohybrid coculture for tandem and tunable CO2 and N2 fixation.

Solar-driven bioelectrosynthesis represents a promising approach for converting abundant resources into value-added chemicals with renewable energy. Microorganisms powered by electrochemical reducing equivalents assimilate CO2, H2O, and N2 building blocks. However, products from autotrophic whole-cell biocatalysts are limited. Furthermore, biocatalysts tasked with N2 reduction are constrained by simultaneous energy-intensive autotrophy. To overcome these challenges, we designed a biohybrid coculture for tandem and tunable CO2 and N2 fixation to value-added products, allowing the different species to distribute bioconversion steps and reduce the individual metabolic burden. This consortium involves acetogen Sporomusa ovata, which reduces CO2 to acetate, and diazotrophic Rhodopseudomonas palustris, which uses the acetate both to fuel N2 fixation and for the generation of a biopolyester. We demonstrate that the coculture platform provides a robust ecosystem for continuous CO2 and N2 fixation, and its outputs are directed by substrate gas composition. Moreover, we show the ability to support the coculture on a high-surface area silicon nanowire cathodic platform. The biohybrid coculture achieved peak faradaic efficiencies of 100, 19.1, and 6.3% for acetate, nitrogen in biomass, and ammonia, respectively, while maintaining product tunability. Finally, we established full solar to chemical conversion driven by a photovoltaic device, resulting in solar to chemical efficiencies of 1.78, 0.51, and 0.08% for acetate, nitrogenous biomass, and ammonia, correspondingly. Ultimately, our work demonstrates the ability to employ and electrochemically manipulate bacterial communities on demand to expand the suite of CO2 and N2 bioelectrosynthesis products.

Novel compound heterozygous variants in ARL13B lead to Joubert syndrome.

Joubert syndrome (JBTS) is a systematic developmental disorder mainly characterized by a pathognomonic mid-hindbrain malformation. All known JBTS-associated genes encode proteins involved in the function of antenna-like cellular organelle, primary cilium, which plays essential roles in cellular signal transduction and development. Here, we identified four unreported variants in ARL13B in two patients with the classical features of JBTS. ARL13B is a member of the Ras GTPase family and functions in ciliogenesis and cilia-related signaling. The two missense variants in ARL13B harbored the substitutions of amino acids at evolutionarily conserved positions. Using model cell lines, we found that the accumulations of the missense variants in cilia were impaired and the variants showed attenuated functions in ciliogenesis or the trafficking of INPP5E. Overall, these findings expanded the ARL13B pathogenetic variant spectrum of JBTS.

DNA Self-Assembly Optimization by Betaine and Its Analogs.

The self-assembly yield of DNA nanostructures can be exponentially lower with increasing structural complexity. Few optimizing strategies are available in the DNA nanotechnology field for the assembly yield improvement. Here, betaine and its analogs are applied as supplementary ingredients in DNA self-assembly. Such a simple implementation results in effective yield improvement. Through a comprehensive investigation, a reliable yield improvement of two- to threefold is achieved for a number of DNA nanostructures with considerable complexity.

Dimensionality Engineering of Organic-Inorganic Halide Perovskites for Next-Generation X-Ray Detector.

The next-generation X-ray detectors require novel semiconductors with low material/fabrication cost, excellent X-ray response characteristics, and robust operational stability. The family of organic-inorganic hybrid perovskites (OIHPs) materials comprises a range of crystal configuration (i.e., films, wafers, and single crystals) with tunable chemical composition, structures, and electronic properties, which can perfectly meet the multiple-stringent requirements of high-energy radiation detection, making them emerging as the cutting-edge candidate for next-generation X-ray detectors. From the perspective of molecular dimensionality, the physicochemical and optoelectronic characteristics of OIHPs exhibit dimensionality-dependent behavior, and thus the structural dimensionality is recognized as the key factor that determines the device performance of OIHPs-based X-ray detectors. Nevertheless, the correlation between dimensionality of OIHPs and performance of their X-ray detectors is still short of theoretical guidance, which become a bottleneck that impedes the development of efficient X-ray detectors. In the review, the advanced studies on the dimensionality engineering of OIHPs are critically assessed in X-ray detection application, discussing the current understanding on the "dimensionality-property" relationship of OIHPs and the state-of-the-art progresses on the dimensionality-engineered OIHPs-based X-ray detector, and highlight the open challenges and future outlook of this field.

Mechanisms of biodiversity loss under nitrogen enrichment: unveiling a shift from light competition to cation toxicity.

The primary mechanisms contributing to nitrogen (N) addition induced grassland biodiversity loss, namely light competition and soil cation toxicity, are often examined separately in various studies. However, their relative significance in governing biodiversity loss along N addition gradient remains unclear. We conducted a 4-yr field experiment with five N addition rates (0, 2, 10, 20, and 50 g N m-2 yr-1) and performed a meta-analysis using global data from 239 observations in N-fertilized grassland ecosystems. Results from our field experiment and meta-analysis indicate that both light competition and soil cation (e.g. Mn2+ and Al3+) toxicity contribute to plant diversity loss under N enrichment. The relative importance of these mechanisms varied with N enrichment intensity. Light competition played a more significant role in influencing species richness under low N addition (≤ 10 g m-2 yr-1), while cation toxicity became increasingly dominant in reducing biodiversity under high N addition (>10 g m-2 yr-1). Therefore, a transition from light competition to cation toxicity occurs with increasing N availability. These findings imply that the biodiversity loss along the N gradient is regulated by distinct mechanisms, necessitating the adoption of differential management strategies to mitigate diversity loss under varying intensities of N enrichment.

The 1400 metabolite-mediated relationship between 91 inflammatory cytokines and migraine: An exploratory two-step Mendelian randomization study.

BACKGROUND: Inflammatory cytokines and migraines have been associated in previous research, but the underlying mechanisms of action are still elusive. The biological functions of metabolites are crucial in the onset of migraine. Our goals were to clarify the cause-and-effect connection between inflammatory cytokines and migraines and explore the potential mediating function of metabolites. METHODS: Utilizing summary-level data from genome-wide association studies (GWAS), we conducted two-sample Mendelian randomization (MR) analyses to evaluate the possible causal connection between inflammatory cytokines and migraines. A two-step MR analysis was employed to further investigate the potential mediating pathways of metabolites. RESULTS: MR analysis identified a total of 9 inflammatory cytokines that were genetically associated with migraines, and we subsequently identified 21 mediated relationships, with 20 metabolites (13 metabolites, 7 ratios) acting as potential mediators between 8 inflammatory cytokines and migraine. The 9 inflammatory cytokines were beta-nerve growth factor levels (ß-NGF), T-cell surface glycoprotein CD5 levels (CD5), T-cell surface glycoprotein CD6 isoform levels (CD6), C-X-C motif chemokine 11 levels (CXCL11), interleukin-4 levels (IL-4), oncostatin-M levels (OSM), signalling lymphocytic activation molecule levels (SLAM), C-C motif chemokine 25 levels (CCL25) and monocyte chemoattractant protein-1 levels (MCP-1). CONCLUSION: Our research findings provide evidence for both a causal connection between inflammatory cytokines and migraines, as well as a metabolite-mediated pathway. These biomarkers facilitate the detection, diagnosis and treatment of migraines while offering fresh perspectives on their underlying mechanisms.

LP-118 is a novel B-cell lymphoma 2 / extra-large inhibitor that demonstrates efficacy in models of venetoclax-resistant chronic lymphocytic leukemia.

Patients with chronic lymphocytic leukemia (CLL) respond well to initial treatment with the Bcell lymphoma 2 (BCL2) inhibitor venetoclax. Upon relapse, they often retain sensitivity to BCL2 targeting, but durability of response remains a concern. We hypothesize that targeting both BCL2 and B-cell lymphoma-extra large (BCLXL) will be a successful strategy to treat CLL, including for patients who relapse on venetoclax. To test this hypothesis, we conducted a pre-clinical investigation of LP-118, a highly potent inhibitor of BCL2 with moderate BCLXL inhibition to minimize platelet toxicity. This study demonstrated that LP-118 induces efficient BAK activation, cytochrome C release, and apoptosis in both venetoclax naïve and resistant CLL cells. Significantly, LP-118 is effective in cell lines expressing the BCL2 G101V mutation and in cells expressing BCLXL but lacking BCL2 dependence. Using an immunocompetent mouse model, Eµ-TCL1, LP-118 demonstrates low platelet toxicity, which hampered earlier BCLXL inhibitors. Finally, LP-118 in the RS4;11 and OSU-CLL xenograft models results in decreases in tumor burden and survival advantage, respectively. These results provide a mechanistic rationale for the evaluation of LP-118 for the treatment of venetoclax responsive and relapsed CLL.

Long-term outcomes of endoscopic resection for well-differentiated nonampullary duodenal neuroendocrine tumors.

BACKGROUND AND AIMS: Nonampullary duodenal neuroendocrine tumors (NAD-NETs) are rare, with limited evidence regarding endoscopic treatment. This study investigated the efficacy and safety of endoscopic resection of well-differentiated NAD-NETs and evaluated long-term outcomes, including local recurrence and metastasis. METHODS: Seventy-eight patients with NAD-NETs who underwent endoscopic resection between January 2011 and August 2022 were included. Clinicopathologic characteristics and treatment outcomes were collected and analyzed. RESULTS: En-bloc resection was achieved for 74 tumors (94.9%) and R0 resection for 68 tumors (87.2%). Univariate analysis identified tumors in the second part of the duodenum, tumor size ≥10 mm, and muscularis propria invasion as risk factors for noncurative resection. Two patients with R1 resection (vertical margin involvement) and 2 patients with lymphovascular invasion underwent additional surgery. Four patients experienced adverse events (5.1%), including 2 cases of delayed bleeding and 2 cases of perforation, all successfully managed conservatively. During a median follow-up period of 62.6 months, recurrence and lymph node metastasis were only detected in 1 patient with R1 resection 3 months after the original procedure. CONCLUSIONS: Endoscopic resection is safe and effective and provides a favorable long-term outcome for patients with well-differentiated NAD-NETs without regional lymph node or distant metastasis.

Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches.

Accurate prediction of nucleic binding residues is essential for the understanding of transcription and translation processes. Integration of feature- and template-based strategies could improve the prediction of these key residues in proteins. Nevertheless, traditional hybrid algorithms have been surpassed by recently developed deep learning-based methods, and the possibility of integrating deep learning- and template-based approaches to improve performance remains to be explored. To address these issues, we developed a novel structure-based integrative algorithm called NABind that can accurately predict DNA- and RNA-binding residues. A deep learning module was built based on the diversified sequence and structural descriptors and edge aggregated graph attention networks, while a template module was constructed by transforming the alignments between the query and its multiple templates into features for supervised learning. Furthermore, the stacking strategy was adopted to integrate the above two modules for improving prediction performance. Finally, a post-processing module dependent on the random walk algorithm was proposed to further correct the integrative predictions. Extensive evaluations indicated that our approach could not only achieve excellent performance on both native and predicted structures but also outperformed existing hybrid algorithms and recent deep learning methods. The NABind server is available at http://liulab.hzau.edu.cn/NABind/.

B2(OH)4-Mediated Reductive Ring-Opening of N-Tosyl Aziridines by Nitroarenes: A Green and Regioselective Access to Vicinal Diamines.

The nucleophilic ring-opening of aziridine derivatives provides an important synthetic tool for the preparation of various ß-functionalized amines. Amines as nucleophiles are employed to prepare synthetically useful 1,2-diamines in the presence of various catalysts or activators. Herein, the B2(OH)4-mediated reductive ring-opening transformation of N-tosyl aziridines by nitroarenes was developed. This aqueous protocol employed nitroarenes as cheap and readily available amino sources and proceeds under external catalyst-free conditions. Control experiments and DFT calculations pointed to the in situ reduction of nitroarenes to aryl amines via N-aryl boramidic acid (E) and an SN1-type ring-opening of N-tosylaziridines by the resultant aryl amines with high regioselectivity.

A Synthesis of α-Alkyl Cycloenones by Pd-Catalyzed Suzuki-Miyaura Coupling with Cyclic Morita-Baylis-Hillman Adducts.

We herein disclose a Pd-catalyzed Suzuki-Miyaura coupling of cyclic Morita-Baylis-Hillman adducts with organoboronic acids under mild conditions, which allows for a rapid access to diverse α-alkyl substituted cycloenones. The advantage of this method resides in the employment of functionalized allyl alcohols as the unprecedented electrophilic partners in the absence of external activators.

Palladium-Catalyzed Suzuki-Miyaura Reactions with Triazenyl-Tethered Aryl Bromides: Exploiting the Orthogonal Coupling Sites under Different Conditions.

Transition-metal-catalyzed cross-coupling of arenes bearing two or more potential coupling sites is often challenging because of the chemoselectivity issue. If orthogonal cross-couplings were applicable, one can develop a synthetically useful approach for consecutive functionalization of the starting arenes compounds. We herein reported a Suzuki-Miyaura coupling of triazenyl-substituted aryl bromides catalyzed by PdCl2(PCy3)2/PPh3 under basic conditions. The resultant polyfunctionalized aryl triazenes could undergo Suzuki-Miyaura couplings under acidic conditions or be converted to many other functionalized arenes. This orthogonal coupling strategy allows for a sequential functionalization of arenes with same type of nucleophilic reagents toward the synthesis of diverse biaryls and teraryls.

Dual-loaded nano pesticide system based on industrial grade scaleable carrier materials with combinatory efficacy and improved safety.

Repeated and widespread use of single chemical pesticides raises concerns about efficiency and safety, developing multi-component synergistic pesticides provides a new route for efficient control of diseases. Most commercial compound formulations are open systems with non-adjustable released rates, resulting in a high frequency of applications. Meanwhile, although nano pesticide delivery systems constructed with different carrier materials have been extensively studied, realizing their actual scale-up production still has important practical significance due to the large-scale field application. In this study, a boscalid and pyraclostrobin dual-loaded nano pesticide system (BPDN) was constructed with industrial-grade carrier materials to facilitate the realization of large-scale production. The optimal industrial-scale preparation mechanism of BPDN was studied with surfactants as key factors. When agricultural emulsifier No.600 and polycarboxylate are used as the ratio of 1:2 in the preparation process, the BPDN has a spherical structure with an average size of 270 nm and exhibits superior physical stability. Compared with commercial formulation, BPDN maintains rate-stabilized release up to 5 times longer, exhibits better dispersion and spreading performance on foliar, has more than 20% higher deposition amounts, and reduces loss. A single application of BPDN could efficiently control tomato gray mold during the growing period of tomatoes due to extended duration and combinatory effectiveness, reducing two application times and labor costs. Toxicology tests on various objects systematically demonstrated that BPDN has improved safety for HepG2 cells, and nontarget organism earthworms. This research provides insight into creating safe, efficient, and environmentally friendly pesticide production to reduce manual operation times and labor costs. Accompanied by production strategies that can be easily scaled up industrially, this contributes to the efficient use of resources for sustainable agriculture.