bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequential co-reduction of nitrate and carbon dioxide enables selective urea electrosynthesis
Authors: Li Yang , Zheng Shisheng , Liu Hao , Xiong Qi , Yi Haocong , Yang Haibin , Mei Zongwei , Zhao Qinghe , Yin Zu-Wei , Huang Ming , Lin Yuan , Lai Weihong , Dou Shi-Xue , Pan Feng , Li Shunning
Published: January 2024

Despite the recent achievements in urea electrosynthesis from co-reduction of nitrogen wastes (such as NO3−) and CO2, the product selectivity remains fairly mediocre due to the competing nature of the two parallel reduction reactions. Here we report a catalyst design that affords high selectivity to urea by sequentially reducing NO3− and CO2 at a dynamic catalytic centre, which not only alleviates the competition issue but also facilitates C−N coupling. We exemplify this strategy on a nitrogen-doped carbon catalyst, where a spontaneous switch between NO3− and CO2 reduction paths is enabled by reversible hydrogenation on the nitrogen functional groups. A high urea yield rate of 596.1 µg mg−1 h−1 with a promising Faradaic efficiency of 62% is obtained. These findings, rationalized by in situ spectroscopic techniques and theoretical calculations, are rooted in the proton-involved dynamic catalyst evolution that mitigates overwhelming reduction of reactants and thereby minimizes the formation of side products.
Integrative genotyping of cancer and immune phenotypes by long-read sequencing
Authors: Penter Livius , Borji Mehdi , Nagler Adi , Lyu Haoxiang , Lu Wesley S. , Cieri Nicoletta , Maurer Katie , Oliveira Giacomo , Al’Khafaji Aziz M. , Garimella Kiran V. , Li Shuqiang , Neuberg Donna S. , Ritz Jerome , Soiffer Robert J. , Garcia Jacqueline S. , Livak Kenneth J. , Wu Catherine J.
Published: January 2024

Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural ‘barcodes’, we define the optimal targets for nanoranger, namely those loci close to the 5’ end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.
Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication
Authors: Maffei Enea , Woischnig Anne-Kathrin , Burkolter Marco R. , Heyer Yannik , Humolli Dorentina , Thürkauf Nicole , Bock Thomas , Schmidt Alexander , Manfredi Pablo , Egli Adrian , Khanna Nina , Jenal Urs , Harms Alexander
Published: January 2024

Bacteriophages are ubiquitous viral predators that have primarily been studied using fast-growing laboratory cultures of their bacterial hosts. However, microbial life in nature is mostly in a slow- or non-growing, dormant state. Here, we show that diverse phages can infect deep-dormant bacteria and suspend their replication until the host resuscitates (“hibernation”). However, a newly isolated Pseudomonas aeruginosa phage, named Paride, can directly replicate and induce the lysis of deep-dormant hosts. While non-growing bacteria are notoriously tolerant to antibiotic drugs, the combination with Paride enables the carbapenem meropenem to eradicate deep-dormant cultures in vitro and to reduce a resilient bacterial infection of a tissue cage implant in mice. Our work might inspire new treatments for persistent bacterial infections and, more broadly, highlights two viral strategies to infect dormant bacteria (hibernation and direct replication) that will guide future studies on phage-host interactions.
Field-induced compensation of magnetic exchange as the possible origin of reentrant superconductivity in UTe2
Authors: Helm Toni , Kimata Motoi , Sudo Kenta , Miyata Atsuhiko , Stirnat Julia , Förster Tobias , Hornung Jacob , König Markus , Sheikin Ilya , Pourret Alexandre , Lapertot Gerard , Aoki Dai , Knebel Georg , Wosnitza Joachim , Brison Jean-Pascal
Published: January 2024

The potential spin-triplet heavy-fermion superconductor UTe2exhibits signatures of multiple distinct superconducting phases. For field aligned along thebaxis, a metamagnetic transition occurs atμ0Hm ≈ 35 T. It is associated with magnetic fluctuations that may be beneficial for the field-reinforced superconductivity surviving up toHm. Once the field is tilted away from thebtowards thecaxis, a reentrant superconducting phase emerges just aboveHm. In order to better understand this remarkably field-resistant superconducting phase, we conducted magnetic-torque and magnetotransport measurements in pulsed magnetic fields. We determine the record-breaking upper critical field ofμ0Hc2 ≈ 73 T and its evolution with angle. Furthermore, the normal-state Hall effect experiences a drastic suppression indicative of a reduced band polarization aboveHmin the angular range around 30° caused by a partial compensation between the applied field and an exchange field. This promotes the Jaccarino-Peter effect as a likely mechanism for the reentrant superconductivity aboveHm.
Towards a transferable fermionic neural wavefunction for molecules
Authors: Scherbela Michael , Gerard Leon , Grohs Philipp
Published: January 2024

Deep neural networks have become a highly accurate and powerful wavefunction ansatz in combination with variational Monte Carlo methods for solving the electronic Schrödinger equation. However, despite their success and favorable scaling, these methods are still computationally too costly for wide adoption. A significant obstacle is the requirement to optimize the wavefunction from scratch for each new system, thus requiring long optimization. In this work, we propose a neural network ansatz, which effectively maps uncorrelated, computationally cheap Hartree-Fock orbitals, to correlated, high-accuracy neural network orbitals. This ansatz is inherently capable of learning a single wavefunction across multiple compounds and geometries, as we demonstrate by successfully transferring a wavefunction model pre-trained on smaller fragments to larger compounds. Furthermore, we provide ample experimental evidence to support the idea that extensive pre-training of such a generalized wavefunction model across different compounds and geometries could lead to a foundation wavefunction model. Such a model could yield high-accuracy ab-initio energies using only minimal computational effort for fine-tuning and evaluation of observables.
Mutant p53 gains oncogenic functions through a chromosomal instability-induced cytosolic DNA response
Authors: Zhao Mei , Wang Tianxiao , Gleber-Netto Frederico O. , Chen Zhen , McGrail Daniel J. , Gomez Javier A. , Ju Wutong , Gadhikar Mayur A. , Ma Wencai , Shen Li , Wang Qi , Tang Ximing , Pathak Sen , Raso Maria Gabriela , Burks Jared K. , Lin Shiaw-Yih , Wang Jing , Multani Asha S. , Pickering Curtis R. , Chen Junjie , Myers Jeffrey N. , Zhou Ge
Published: January 2024

Inactivating TP53 mutations leads to a loss of function of p53, but can also often result in oncogenic gain-of-function (GOF) of mutant p53 (mutp53) proteins which promotes tumor development and progression. The GOF activities of TP53 mutations are well documented, but the mechanisms involved remain poorly understood. Here, we study the mutp53 interactome and find that by targeting minichromosome maintenance complex components (MCMs), GOF mutp53 predisposes cells to replication stress and chromosomal instability (CIN), leading to a tumor cell-autonomous and cyclic GMP–AMP synthase (cGAS)-stimulator of interferon genes (STING)-dependent cytosolic DNA response that activates downstream non-canonical nuclear factor kappa light chain enhancer of activated B cell (NC-NF-κB) signaling. Consequently, GOF mutp53-MCMs-CIN-cytosolic DNA-cGAS-STING-NC-NF-κB signaling promotes tumor cell metastasis and an immunosuppressive tumor microenvironment through antagonizing interferon signaling and regulating genes associated with pro-tumorigenic inflammation. Our findings have important implications for understanding not only the GOF activities of TP53 mutations but also the genome-guardian role of p53 and its inactivation during tumor development and progression.
Structure-guided design of a selective inhibitor of the methyltransferase KMT9 with cellular activity
Authors: Wang Sheng , Klein Sebastian O. , Urban Sylvia , Staudt Maximilian , Barthes Nicolas P. F. , Willmann Dominica , Bacher Johannes , Sum Manuela , Bauer Helena , Peng Ling , Rennar Georg A. , Gratzke Christian , Schüle Katrin M. , Zhang Lin , Einsle Oliver , Greschik Holger , MacLeod Calum , Thomson Christopher G. , Jung Manfred , Metzger Eric , Schüle Roland
Published: January 2024

Inhibition of epigenetic regulators by small molecules is an attractive strategy for cancer treatment. Recently, we characterised the role of lysine methyltransferase 9 (KMT9) in prostate, lung, and colon cancer. Our observation that the enzymatic activity was required for tumour cell proliferation identified KMT9 as a potential therapeutic target. Here, we report the development of a potent and selective KMT9 inhibitor (compound 4, KMI169) with cellular activity through structure-based drug design. KMI169 functions as a bi-substrate inhibitor targeting the SAM and substrate binding pockets of KMT9 and exhibits high potency, selectivity, and cellular target engagement. KMT9 inhibition selectively downregulates target genes involved in cell cycle regulation and impairs proliferation of tumours cells including castration- and enzalutamide-resistant prostate cancer cells. KMI169 represents a valuable tool to probe cellular KMT9 functions and paves the way for the development of clinical candidate inhibitors as therapeutic options to treat malignancies such as therapy-resistant prostate cancer.
BCG vaccination-induced acquired control of mycobacterial growth differs from growth control preexisting to BCG vaccination
Authors: van Meijgaarden Krista E. , Li Wenchao , Moorlag Simone J. C. F. M. , Koeken Valerie A. C. M. , Koenen Hans J. P. M. , Joosten Leo A. B. , Vyakarnam Annapurna , Ahmed Asma , Rakshit Srabanti , Adiga Vasista , Ottenhoff Tom H. M. , Li Yang , Netea Mihai G. , Joosten Simone A.
Published: January 2024

Bacillus Calmette-Guèrin - vaccination induces not only protection in infants and young children against severe forms of tuberculosis, but also against non-tuberculosis related all-cause mortality. To delineate different factors influencing mycobacterial growth control, here we first investigate the effects of BCG-vaccination in healthy Dutch adults. About a quarter of individuals already control BCG-growth prior to vaccination, whereas a quarter of the vaccinees acquires the capacity to control BCG upon vaccination. This leaves half of the population incapable to control BCG-growth. Single cell RNA sequencing identifies multiple processes associated with mycobacterial growth control. These data suggest (i) that already controllers employ different mechanisms to control BCG-growth than acquired controllers, and (ii) that half of the individuals fail to develop measurable growth control irrespective of BCG-vaccination. These results shed important new light on the variable immune responses to mycobacteria in humans and may impact on improved vaccination against tuberculosis and other diseases.
DomiRank Centrality reveals structural fragility of complex networks via node dominance
Authors: Engsig Marcus , Tejedor Alejandro , Moreno Yamir , Foufoula-Georgiou Efi , Kasmi Chaouki
Published: January 2024

Determining the key elements of interconnected infrastructure and complex systems is paramount to ensure system functionality and integrity. This work quantifies the dominance of the networks’ nodes in their respective neighborhoods, introducing a centrality metric, DomiRank, that integrates local and global topological information via a tunable parameter. We present an analytical formula and an efficient parallelizable algorithm for DomiRank centrality, making it applicable to massive networks. From the networks’ structure and function perspective, nodes with high values of DomiRank highlight fragile neighborhoods whose integrity and functionality are highly dependent on those dominant nodes. Underscoring this relation between dominance and fragility, we show that DomiRank systematically outperforms other centrality metrics in generating targeted attacks that effectively compromise network structure and disrupt its functionality for synthetic and real-world topologies. Moreover, we show that DomiRank-based attacks inflict more enduring damage in the network, hindering its ability to rebound and, thus, impairing system resilience. DomiRank centrality capitalizes on the competition mechanism embedded in its definition to expose the fragility of networks, paving the way to design strategies to mitigate vulnerability and enhance the resilience of critical infrastructures.
Dynamic stability of Sgt2 enables selective and privileged client handover in a chaperone triad
Authors: Cho Hyunju , Liu Yumeng , Chung SangYoon , Chandrasekar Sowmya , Weiss Shimon , Shan Shu-ou
Published: January 2024

Membrane protein biogenesis poses acute challenges to protein homeostasis, and how they are selectively escorted to the target membrane is not well understood. Here we address this question in the guided-entry-of-tail-anchored protein (GET) pathway, in which tail-anchored membrane proteins (TAs) are relayed through an Hsp70-Sgt2-Get3 chaperone triad for targeting to the endoplasmic reticulum. We show that the Hsp70 ATPase cycle and TA substrate drive dimeric Sgt2 from a wide-open conformation to a closed state, in which TAs are protected by both substrate binding domains of Sgt2. Get3 is privileged to receive TA from closed Sgt2, whereas off-pathway chaperones remove TAs from open Sgt2. Sgt2 closing is less favorable with suboptimal GET substrates, which are rejected during or after the Hsp70-to-Sgt2 handover. Our results demonstrate how fine-tuned conformational dynamics in Sgt2 enable hydrophobic TAs to be effectively funneled onto their dedicated targeting factor while also providing a mechanism for substrate selection.
Exact inversion of partially coherent dynamical electron scattering for picometric structure retrieval
Authors: Diederichs Benedikt , Herdegen Ziria , Strauch Achim , Filbir Frank , Müller-Caspary Knut
Published: January 2024

The greatly nonlinear diffraction of high-energy electron probes focused to subatomic diameters frustrates the direct inversion of ptychographic data sets to decipher the atomic structure. Several iterative algorithms have been proposed to yield atomically-resolved phase distributions within slices of a 3D specimen, corresponding to the scattering centers of the electron wave. By pixelwise phase retrieval, current approaches do not only involve orders of magnitude more free parameters than necessary, but also neglect essential details of scattering physics such as the atomistic nature of the specimen and thermal effects. Here, we introduce a parametrized, fully differentiable scheme employing neural network concepts which allows the inversion of ptychographic data by means of entirely physical quantities. Omnipresent thermal diffuse scattering in thick specimens is treated accurately using frozen phonons, and atom types, positions and partial coherence are accounted for in the inverse model as relativistic scattering theory demands. Our approach exploits 4D experimental data collected in an aberration-corrected momentum-resolved scanning transmission electron microscopy setup. Atom positions in a 20 nm thick PbZr0.2Ti0.8O3 ferroelectric are measured with picometer precision, including the discrimination of different atom types and positions in mixed columns.
Dipeptide coacervates as artificial membraneless organelles for bioorthogonal catalysis
Authors: Cao Shoupeng , Ivanov Tsvetomir , Heuer Julian , Ferguson Calum T. J. , Landfester Katharina , Caire da Silva Lucas
Published: January 2024

Artificial organelles can manipulate cellular functions and introduce non-biological processes into cells. Coacervate droplets have emerged as a close analog of membraneless cellular organelles. Their biomimetic properties, such as molecular crowding and selective partitioning, make them promising components for designing cell-like materials. However, their use as artificial organelles has been limited by their complex molecular structure, limited control over internal microenvironment properties, and inherent colloidal instability. Here we report the design of dipeptide coacervates that exhibit enhanced stability, biocompatibility, and a hydrophobic microenvironment. The hydrophobic character facilitates the encapsulation of hydrophobic species, including transition metal-based catalysts, enhancing their efficiency in aqueous environments. Dipeptide coacervates carrying a metal-based catalyst are incorporated as active artificial organelles in cells and trigger an internal non-biological chemical reaction. The development of coacervates with a hydrophobic microenvironment opens an alternative avenue in the field of biomimetic materials with applications in catalysis and synthetic biology.
AI-driven projection tomography with multicore fibre-optic cell rotation
Authors: Sun Jiawei , Yang Bin , Koukourakis Nektarios , Guck Jochen , Czarske Juergen W.
Published: January 2024

Optical tomography has emerged as a non-invasive imaging method, providing three-dimensional insights into subcellular structures and thereby enabling a deeper understanding of cellular functions, interactions, and processes. Conventional optical tomography methods are constrained by a limited illumination scanning range, leading to anisotropic resolution and incomplete imaging of cellular structures. To overcome this problem, we employ a compact multi-core fibre-optic cell rotator system that facilitates precise optical manipulation of cells within a microfluidic chip, achieving full-angle projection tomography with isotropic resolution. Moreover, we demonstrate an AI-driven tomographic reconstruction workflow, which can be a paradigm shift from conventional computational methods, often demanding manual processing, to a fully autonomous process. The performance of the proposed cell rotation tomography approach is validated through the three-dimensional reconstruction of cell phantoms and HL60 human cancer cells. The versatility of this learning-based tomographic reconstruction workflow paves the way for its broad application across diverse tomographic imaging modalities, including but not limited to flow cytometry tomography and acoustic rotation tomography. Therefore, this AI-driven approach can propel advancements in cell biology, aiding in the inception of pioneering therapeutics, and augmenting early-stage cancer diagnostics.
Synovial microenvironment-influenced mast cells promote the progression of rheumatoid arthritis
Authors: Lei Yunxuan , Guo Xin , Luo Yanping , Niu Xiaoyin , Xi Yebin , Xiao Lianbo , He Dongyi , Bian Yanqin , Zhang Yong , Wang Li , Peng Xiaochun , Wang Zhaojun , Chen Guangjie
Published: January 2024

Mast cells are phenotypically and functionally heterogeneous, and their state is possibly controlled by local microenvironment. Therefore, specific analyses are needed to understand whether mast cells function as powerful participants or dispensable bystanders in specific diseases. Here, we show that degranulation of mast cells in inflammatory synovial tissues of patients with rheumatoid arthritis (RA) is induced via MAS-related G protein-coupled receptor X2 (MRGPRX2), and the expression of MHC class II and costimulatory molecules on mast cells are upregulated. Collagen-induced arthritis mice treated with a combination of anti-IL-17A and cromolyn sodium, a mast cell membrane stabilizer, show significantly reduced clinical severity and decreased bone erosion. The findings of the present study suggest that synovial microenvironment-influenced mast cells contribute to disease progression and may provide a further mast cell-targeting therapy for RA.
Neoadjuvant camrelizumab and apatinib combined with chemotherapy versus chemotherapy alone for locally advanced gastric cancer: a multicenter randomized phase 2 trial
Authors: Lin Jian-Xian , Tang Yi-Hui , Zheng Hua-Long , Ye Kai , Cai Jian-Chun , Cai Li-Sheng , Lin Wei , Xie Jian-Wei , Wang Jia-Bin , Lu Jun , Chen Qi-Yue , Cao Long-Long , Zheng Chao-Hui , Li Ping , Huang Chang-Ming
Published: January 2024

Prospective evidence regarding the combination of programmed cell death (PD)−1 and angiogenesis inhibitors in treating locally advanced gastric cancer (LAGC) is limited. In this multicenter, randomized, phase 2 trial (NCT04195828), patients with gastric adenocarcinoma (clinical T2-4N + M0) were randomly assigned (1:1) to receive neoadjuvant camrelizumab and apatinib combined with nab-paclitaxel plus S-1 (CA-SAP) or chemotherapy SAP alone (SAP) for 3 cycles. The primary endpoint was the major pathological response (MPR), defined as <10% residual tumor cells in resection specimens. Secondary endpoints included R0 resection rate, radiologic response, safety, overall survival, and progression-free survival. The modified intention-to-treat population was analyzed (CA-SAP [n = 51] versus SAP [n = 53]). The trial has met pre-specified endpoints. CA-SAP was associated with a significantly higher MPR rate (33.3%) than SAP (17.0%, P = 0.044). The CA-SAP group had a significantly higher objective response rate (66.0% versus 43.4%, P = 0.017) and R0 resection rate (94.1% versus 81.1%, P = 0.042) than the SAP group. Nonsurgical grade 3-4 adverse events were observed in 17 patients (33.3%) in the CA-SAP group and 14 (26.4%) in the SAP group. Survival results were not reported due to immature data. Camrelizumab and apatinib combined with chemotherapy as a neoadjuvant regimen was tolerable and associated with favorable responses for LAGC.
IL-12 reprograms CAR-expressing natural killer T cells to long-lived Th1-polarized cells with potent antitumor activity
Authors: Landoni Elisa , Woodcock Mark G. , Barragan Gabriel , Casirati Gabriele , Cinella Vincenzo , Stucchi Simone , Flick Leah M. , Withers Tracy A. , Hudson Hanna , Casorati Giulia , Dellabona Paolo , Genovese Pietro , Savoldo Barbara , Metelitsa Leonid S. , Dotti Gianpietro
Published: January 2024

Human natural killer T cells (NKTs) are innate-like T lymphocytes increasingly used for cancer immunotherapy. Here we show that human NKTs expressing the pro-inflammatory cytokine interleukin-12 (IL-12) undergo extensive and sustained molecular and functional reprogramming. Specifically, IL-12 instructs and maintains a Th1-polarization program in NKTs in vivo without causing their functional exhaustion. Furthermore, using CD62L as a marker of memory cells in human NKTs, we observe that IL-12 maintains long-term CD62L-expressing memory NKTs in vivo. Notably, IL-12 initiates a de novo programming of memory NKTs in CD62L-negative NKTs indicating that human NKTs circulating in the peripheral blood possess an intrinsic differentiation hierarchy, and that IL-12 plays a role in promoting their differentiation to long-lived Th1-polarized memory cells. Human NKTs engineered to co-express a Chimeric Antigen Receptor (CAR) coupled with the expression of IL-12 show enhanced antitumor activity in leukemia and neuroblastoma tumor models, persist long-term in vivo and conserve the molecular signature driven by the IL-12 expression. Thus IL-12 reveals an intrinsic plasticity of peripheral human NKTs that may play a crucial role in the development of cell therapeutics.
Initial-site characterization of hydrogen migration following strong-field double-ionization of ethanol
Authors: Severt Travis , Weckwerth Eleanor , Kaderiya Balram , Feizollah Peyman , Jochim Bethany , Borne Kurtis , Ziaee Farzaneh , P Kanaka Raju , Carnes Kevin D. , Dantus Marcos , Rolles Daniel , Rudenko Artem , Wells Eric , Ben-Itzhak Itzik
Published: January 2024

An essential problem in photochemistry is understanding the coupling of electronic and nuclear dynamics in molecules, which manifests in processes such as hydrogen migration. Measurements of hydrogen migration in molecules that have more than two equivalent hydrogen sites, however, produce data that is difficult to compare with calculations because the initial hydrogen site is unknown. We demonstrate that coincidence ion-imaging measurements of a few deuterium-tagged isotopologues of ethanol can determine the contribution of each initial-site composition to hydrogen-rich fragments following strong-field double ionization. These site-specific probabilities produce benchmarks for calculations and answer outstanding questions about photofragmentation of ethanol dications; e.g., establishing that the central two hydrogen atoms are 15 times more likely to abstract the hydroxyl proton than a methyl-group proton to form H$${}_{3}^{+}$$3+and that hydrogen scrambling, involving the exchange of hydrogen between different sites, is important in H2O+formation. The technique extends to dynamic variables and could, in principle, be applied to larger non-cyclic hydrocarbons.
TMEM55B links autophagy flux, lysosomal repair, and TFE3 activation in response to oxidative stress
Authors: Jeong Eutteum , Willett Rose , Rissone Alberto , La Spina Martina , Puertollano Rosa
Published: January 2024

Lysosomes have emerged as critical regulators of cellular homeostasis. Here we show that the lysosomal protein TMEM55B contributes to restore cellular homeostasis in response to oxidative stress by three different mechanisms: (1) TMEM55B mediates NEDD4-dependent PLEKHM1 ubiquitination, causing PLEKHM1 proteasomal degradation and halting autophagosome/lysosome fusion; (2) TMEM55B promotes recruitment of components of the ESCRT machinery to lysosomal membranes to stimulate lysosomal repair; and (3) TMEM55B sequesters the FLCN/FNIP complex to facilitate translocation of the transcription factor TFE3 to the nucleus, allowing expression of transcriptional programs that enable cellular adaptation to stress. Knockout oftmem55genes in zebrafish embryos increases their susceptibility to oxidative stress, causing early death oftmem55-KO animals in response to arsenite toxicity. Altogether, our work identifies a role for TMEM55B as a molecular sensor that coordinates autophagosome degradation, lysosomal repair, and activation of stress responses.
Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing
Authors: Klaproth-Andrade Daniela , Hingerl Johannes , Bruns Yanik , Smith Nicholas H. , Träuble Jakob , Wilhelm Mathias , Gagneur Julien
Published: January 2024

Unlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins are lacking, hindering the utility of proteomics in applications where the sequences are unknown including variant calling, neoepitope identification, and metaproteomics. We introduce Spectralis, a de novo peptide sequencing method for tandem mass spectrometry. Spectralis leverages several innovations including a convolutional neural network layer connecting peaks in spectra spaced by amino acid masses, proposing fragment ion series classification as a pivotal task for de novo peptide sequencing, and a peptide-spectrum confidence score. On spectra for which database search provided a ground truth, Spectralis surpassed 40% sensitivity at 90% precision, nearly doubling state-of-the-art sensitivity. Application to unidentified spectra confirmed its superiority and showcased its applicability to variant calling. Altogether, these algorithmic innovations and the substantial sensitivity increase in the high-precision range constitute an important step toward broadly applicable peptide sequencing.
Modular access to chiral bridged piperidine-γ-butyrolactones via catalytic asymmetric allylation/aza-Prins cyclization/lactonization sequences
Authors: Fu Cong , He Ling , Xu Hui , Zhang Zongpeng , Chang Xin , Dang Yanfeng , Dong Xiu-Qin , Wang Chun-Jiang
Published: January 2024

Chiral functionalized piperidine and lactone heterocycles are widely spread in natural products and drug candidates with promising pharmacological properties. However, there remains no general asymmetric methodologies that enable rapid assemble both critical biologically important units into one three-dimensional chiral molecule. Herein, we describe a straightforward relay strategy for the construction of enantioenriched bridged piperidine-γ-butyrolactone skeletons incorporating three skipped stereocenters via asymmetric allylic alkylation and aza-Prins cyclization/lactonization sequences. The excellent enantioselectivity control in asymmetric allylation with the simplest allylic precursor is enabled by the synergistic Cu/Ir-catalyzed protocol; the success of aza-Prins cyclization/lactonization can be attributed to the pivotal role of the ester substituent, which acts as a preferential intramolecular nucleophile to terminate the aza-Prins intermediacy of piperid-4-yl cation species. The resulting chiral piperidine-γ-butyrolactone bridged-heterocyclic products show impressive preliminary biological activities against a panel of cancer cell lines.
Multiplexed multicolor antiviral assay amenable for high-throughput research
Authors: Li Li-Hsin , Chiu Winston , Huang Yun-An , Rasulova Madina , Vercruysse Thomas , Thibaut Hendrik Jan , ter Horst Sebastiaan , Rocha-Pereira Joana , Vanhoof Greet , Borrenberghs Doortje , Goethals Olivia , Kaptein Suzanne J. F. , Leyssen Pieter , Neyts Johan , Dallmeier Kai
Published: January 2024

To curb viral epidemics and pandemics, antiviral drugs are needed with activity against entire genera or families of viruses. Here, we develop a cell-based multiplex antiviral assay for high-throughput screening against multiple viruses at once, as demonstrated by using three distantly related orthoflaviviruses: dengue, Japanese encephalitis and yellow fever virus. Each virus is tagged with a distinct fluorescent protein, enabling individual monitoring in cell culture through high-content imaging. Specific antisera and small-molecule inhibitors are employed to validate that multiplexing approach yields comparable inhibition profiles to single-virus infection assays. To facilitate downstream analysis, a kernel is developed to deconvolute and reduce the multidimensional quantitative data to three cartesian coordinates. The methodology is applicable to viruses from different families as exemplified by co-infections with chikungunya, parainfluenza and Bunyamwera viruses. The multiplex approach is expected to facilitate the discovery of broader-spectrum antivirals, as shown in a pilot screen of approximately 1200 drug-like small-molecules.
Discrete symmetries tested at 10−4 precision using linear polarization of photons from positronium annihilations
Authors: Moskal Paweł , Czerwiński Eryk , Raj Juhi , Bass Steven D. , Beyene Ermias Y. , Chug Neha , Coussat Aurélien , Curceanu Catalina , Dadgar Meysam , Das Manish , Dulski Kamil , Gajos Aleksander , Gorgol Marek , Hiesmayr Beatrix C. , Jasińska Bożena , Kacprzak Krzysztof , Kaplanoglu Tevfik , Kapłon Łukasz , Klimaszewski Konrad , Konieczka Paweł , Korcyl Grzegorz , Kozik Tomasz , Krzemień Wojciech , Kumar Deepak , Moyo Simbarashe , Mryka Wiktor , Niedźwiecki Szymon , Parzych Szymon , del Río Elena Pérez , Raczyński Lech , Sharma Sushil , Choudhary Shivani , Shopa Roman Y. , Silarski Michał , Skurzok Magdalena , Stępień Ewa Ł. , Tanty Pooja , Ardebili Faranak Tayefi , Ardebili Keyvan Tayefi , Eliyan Kavya Valsan , Wiślicki Wojciech
Published: January 2024

Discrete symmetries play an important role in particle physics with violation of CP connected to the matter-antimatter imbalance in the Universe. We report the most precise test of P, T and CP invariance in decays of ortho-positronium, performed with methodology involving polarization of photons from these decays. Positronium, the simplest bound state of an electron and positron, is of recent interest with discrepancies reported between measured hyperfine energy structure and theory at the level of 10−4 signaling a need for better understanding of the positronium system at this level. We test discrete symmetries using photon polarizations determined via Compton scattering in the dedicated J-PET tomograph on an event-by-event basis and without the need to control the spin of the positronium with an external magnetic field, in contrast to previous experiments. Our result is consistent with QED expectations at the level of 0.0007 and one standard deviation.
KRAS allelic imbalance drives tumour initiation yet suppresses metastasis in colorectal cancer in vivo
Authors: Najumudeen Arafath K. , Fey Sigrid K. , Millett Laura M. , Ford Catriona A. , Gilroy Kathryn , Gunduz Nuray , Ridgway Rachel A. , Anderson Eve , Strathdee Douglas , Clark William , Nixon Colin , Morton Jennifer P. , Campbell Andrew D. , Sansom Owen J.
Published: January 2024

OncogenicKRASmutations are well-described functionally and are known to drive tumorigenesis. Recent reports describe a significant prevalence ofKRASallelic imbalances or gene dosage changes in human cancers, including loss of the wild-type allele inKRASmutant cancers. However, the role of wild-type KRAS in tumorigenesis and therapeutic response remains elusive. We report an in vivo murine model of colorectal cancer featuring deletion of wild-typeKrasin the context of oncogenicKras. Deletion of wild-typeKrasexacerbates oncogenic KRAS signalling through MAPK and thus drives tumour initiation. Absence of wild-typeKraspotentiates the oncogenic effect of KRASG12D, while incidentally inducing sensitivity to inhibition of MEK1/2. Importantly, loss of the wild-type allele in aggressive models of KRASG12D-driven CRC significantly alters tumour progression, and suppresses metastasis through modulation of the immune microenvironment. This study highlights the critical role for wild-typeKrasupon tumour initiation, progression and therapeutic response inKrasmutant CRC.
Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL
Authors: Sun Linhua , Zhou Jingru , Xu Xiao , Liu Yi , Ma Ni , Liu Yutong , Nie Wenchao , Zou Ling , Deng Xing Wang , He Hang
Published: January 2024

Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.
Gene regulation and speciation in a migratory divide between songbirds
Authors: Louder Matthew I. M. , Justen Hannah , Kimmitt Abigail A. , Lawley Koedi S. , Turner Leslie M. , Dickman J. David , Delmore Kira E.
Published: January 2024

Behavioral variation abounds in nature. This variation is important for adaptation and speciation, but its molecular basis remains elusive. Here, we use a hybrid zone between two subspecies of songbirds that differ in migration – an ecologically important and taxonomically widespread behavior---to gain insight into this topic. We measure gene expression in five brain regions. Differential expression between migratory states was dominated by circadian genes in all brain regions. The remaining patterns were largely brain-region specific. For example, expression differences between the subspecies that interact with migratory state likely help maintain reproductive isolation in this system and were documented in only three brain regions. Contrary to existing work on regulatory mechanisms underlying species-specific traits, two lines of evidence suggest that trans- (vs. cis) regulatory changes underlie these patterns – no evidence for allele-specific expression in hybrids and minimal associations between genomic differentiation and expression differences. Additional work with hybrids shows expression levels were often distinct (transgressive) from parental forms. Behavioral contrasts and functional enrichment analyses allowed us to connect these patterns to mitonuclear incompatibilities and compensatory responses to stress that could exacerbate selection on hybrids and contribute to speciation.
A plant cell death-inducing protein from litchi interacts with Peronophythora litchii pectate lyase and enhances plant resistance
Authors: Li Wen , Li Peng , Deng Yizhen , Situ Junjian , He Zhuoyuan , Zhou Wenzhe , Li Minhui , Xi Pinggen , Liang Xiangxiu , Kong Guanghui , Jiang Zide
Published: January 2024

Cell wall degrading enzymes, including pectate lyases (PeLs), released by plant pathogens, break down protective barriers and/or activate host immunity. The direct interactions between PeLs and plant immune-related proteins remain unclear. We identify two PeLs, PlPeL1 and PlPeL1-like, critical for full virulence of Peronophythora litchii on litchi (Litchi chinensis). These proteins enhance plant susceptibility to oomycete pathogens in a PeL enzymatic activity-dependent manner. However, LcPIP1, a plant immune regulator secreted by litchi, binds to PlPeL1/PlPeL1-like, and attenuates PlPeL1/PlPeL1-like induced plant susceptibility to Phytophthora capsici. LcPIP1 also induces cell death and various immune responses in Nicotiana benthamiana. Conserved in plants, LcPIP1 homologs bear a conserved “VDMASG” motif and exhibit immunity-inducing activity. Furthermore, SERK3 interacts with LcPIP1 and is required for LcPIP1-induced cell death. NbPIP1 participates in immune responses triggered by the PAMP protein INF1. In summary, our study reveals the dual roles of PlPeL1/PlPeL1-like in plant-pathogen interactions: enhancing pathogen virulence through PeL enzymatic activity while also being targeted by LcPIP1, thus enhancing plant immunity.
Fatty acid synthesis suppresses dietary polyunsaturated fatty acid use
Authors: Worthmann Anna , Ridder Julius , Piel Sharlaine Y. L. , Evangelakos Ioannis , Musfeldt Melina , Voß Hannah , O’Farrell Marie , Fischer Alexander W. , Adak Sangeeta , Sundd Monica , Siffeti Hasibullah , Haumann Friederike , Kloth Katja , Bierhals Tatjana , Heine Markus , Pertzborn Paul , Pauly Mira , Scholz Julia-Josefine , Kundu Suman , Fuh Marceline M. , Neu Axel , Tödter Klaus , Hempel Maja , Knippschild Uwe , Semenkovich Clay F. , Schlüter Hartmut , Heeren Joerg , Scheja Ludger , Kubisch Christian , Schlein Christian
Published: January 2024

Dietary polyunsaturated fatty acids (PUFA) are increasingly recognized for their health benefits, whereas a high production of endogenous fatty acids – a process called de novo lipogenesis (DNL) - is closely linked to metabolic diseases. Determinants of PUFA incorporation into complex lipids are insufficiently understood and may influence the onset and progression of metabolic diseases. Here we show that fatty acid synthase (FASN), the key enzyme of DNL, critically determines the use of dietary PUFA in mice and humans. Moreover, the combination of FASN inhibition and PUFA-supplementation decreases liver triacylglycerols (TAG) in mice fed with high-fat diet. Mechanistically, FASN inhibition causes higher PUFA uptake via the lysophosphatidylcholine transporter MFSD2A, and a diacylglycerol O-acyltransferase 2 (DGAT2)-dependent incorporation of PUFA into TAG. Overall, the outcome of PUFA supplementation may depend on the degree of endogenous DNL and combining PUFA supplementation and FASN inhibition might be a promising approach to target metabolic disease.
Mosaic: in-memory computing and routing for small-world spike-based neuromorphic systems
Authors: Dalgaty Thomas , Moro Filippo , Demirağ Yiğit , De Pra Alessio , Indiveri Giacomo , Vianello Elisa , Payvand Melika
Published: January 2024

The brain’s connectivity is locally dense and globally sparse, forming a small-world graph—a principle prevalent in the evolution of various species, suggesting a universal solution for efficient information routing. However, current artificial neural network circuit architectures do not fully embrace small-world neural network models. Here, we present the neuromorphic Mosaic: a non-von Neumann systolic architecture employing distributed memristors for in-memory computing and in-memory routing, efficiently implementing small-world graph topologies for Spiking Neural Networks (SNNs). We’ve designed, fabricated, and experimentally demonstrated the Mosaic’s building blocks, using integrated memristors with 130 nm CMOS technology. We show that thanks to enforcing locality in the connectivity, routing efficiency of Mosaic is at least one order of magnitude higher than other SNN hardware platforms. This is while Mosaic achieves a competitive accuracy in a variety of edge benchmarks. Mosaic offers a scalable approach for edge systems based on distributed spike-based computing and in-memory routing.
IKKε and TBK1 prevent RIPK1 dependent and independent inflammation
Authors: Eren Remzi Onur , Kaya Göksu Gökberk , Schwarzer Robin , Pasparakis Manolis
Published: January 2024

TBK1 and IKKε regulate multiple cellular processes including anti-viral type-I interferon responses, metabolism and TNF receptor signaling. However, the relative contributions and potentially redundant functions of IKKε and TBK1 in cell death, inflammation and tissue homeostasis remain poorly understood. Here we show that IKKε compensates for the loss of TBK1 kinase activity to prevent RIPK1-dependent and -independent inflammation in mice. Combined inhibition of IKKε and TBK1 kinase activities caused embryonic lethality that was rescued by heterozygous expression of kinase-inactive RIPK1. Adult mice expressing kinase-inactive versions of IKKε and TBK1 developed systemic inflammation that was induced by both RIPK1-dependent and -independent mechanisms. Combined inhibition of IKKε and TBK1 kinase activities in myeloid cells induced RIPK1-dependent cell death and systemic inflammation mediated by IL-1 family cytokines. Tissue-specific studies showed that IKKε and TBK1 were required to prevent cell death and inflammation in the intestine but were dispensable for liver and skin homeostasis. Together, these findings revealed that IKKε and TBK1 exhibit tissue-specific functions that are important to prevent cell death and inflammation and maintain tissue homeostasis.
The impact of extreme heat on lake warming in China
Authors: Wang Weijia , Shi Kun , Wang Xiwen , Zhang Yunlin , Qin Boqiang , Zhang Yibo , Woolway R. Iestyn
Published: January 2024

Global lake ecosystems are subjected to an increased occurrence of heat extremes, yet their impact on lake warming remains poorly understood. In this study, we employed a hybrid physically-based/statistical model to assess the contribution of heat extremes to variations in surface water temperature of 2260 lakes in China from 1985 to 2022. Our study indicates that heat extremes are increasing at a rate of about 2.08 days/decade and an intensity of about 0.03 °C/ day·decade in China. The warming rate of lake surface water temperature decreases from 0.16 °C/decade to 0.13 °C/decade after removing heat extremes. Heat extremes exert a considerable influence on long-term lake surface temperature changes, contributing 36.5% of the warming trends within the studied lakes. Given the important influence of heat extremes on the mean warming of lake surface waters, it is imperative that they are adequately accounted for in climate impact studies.
Dual-wavelength metalens enables Epi-fluorescence detection from single molecules
Authors: Barulin Aleksandr , Kim Yeseul , Oh Dong Kyo , Jang Jaehyuck , Park Hyemi , Rho Junsuk , Kim Inki
Published: January 2024

Single molecule fluorescence spectroscopy is at the heart of molecular biophysics research and the most sensitive biosensing assays. The growing demand for precision medicine and environmental monitoring requires the creation of miniaturized and portable sensing platforms. However, the need for highly sophisticated objective lenses has precluded the development of single molecule detection systems for truly portable devices. Here, we propose a dielectric metalens device of submicrometer thickness to excite and collect light from fluorescent molecules instead of an objective lens. The high numerical aperture, high focusing efficiency, and dual-wavelength operation of the metalens enable the implementation of fluorescence correlation spectroscopy with a single Alexa 647 molecule in the focal volume. Moreover, the metalens enables real-time monitoring of individual fluorescent nanoparticle transitions and identification of hydrodynamic diameters ranging from a few to hundreds of nanometers. This advancement in sensitivity extends the application of the metalens technology to ultracompact single-molecule sensors.
The evolution of centriole degradation in mouse sperm
Authors: Khanal Sushil , Jaiswal Ankit , Chowdanayaka Rajanikanth , Puente Nahshon , Turner Katerina , Assefa Kebron Yeshitela , Nawras Mohamad , Back Ezekiel David , Royfman Abigail , Burkett James P. , Cheong Soon Hon , Fisher Heidi S. , Sindhwani Puneet , Gray John , Ramachandra Nallur Basappa , Avidor-Reiss Tomer
Published: January 2024

Centrioles are subcellular organelles found at the cilia base with an evolutionarily conserved structure and a shock absorber-like function. In sperm, centrioles are found at the flagellum base and are essential for embryo development in basal animals. Yet, sperm centrioles have evolved diverse forms, sometimes acting like a transmission system, as in cattle, and sometimes becoming dispensable, as in house mice. How the essential sperm centriole evolved to become dispensable in some organisms is unclear. Here, we test the hypothesis that this transition occurred through a cascade of evolutionary changes to the proteins, structure, and function of sperm centrioles and was possibly driven by sperm competition. We found that the final steps in this cascade are associated with a change in the primary structure of the centriolar inner scaffold protein FAM161A in rodents. This information provides the first insight into the molecular mechanisms and adaptive evolution underlying a major evolutionary transition within the internal structure of the mammalian sperm neck.