bluuebunny/crossref_metadata_2025 huggingface dataset:
Change of deep subduction seismicity after a large megathrust earthquake
Authors: Gardonio Blandine , Marsan David , Bodin Thomas , Socquet Anne , Durand Stéphanie , Radiguet Mathilde , Ricard Yanick , Schubnel Alexandre
Published: January 2024

Subduction zones are home to the world’s largest and deepest earthquakes. Recently, large-scale interactions between shallow (0-60 km) and intermediate (80-150 km) seismicity have been evidenced during the interseismic period but also before and after megathrust earthquakes along with large-scale changes in surface motion. Large-scale deformation transients following major earthquakes have also been observed possibly due to a post-seismic change in slab pull or to a bending/unbending of the plates, which suggests the existence of interactions between the deep and shallow parts of the slab. In this study, we analyze the spatio-temporal variations of the declustered seismicity in Japan from 2000 to 2011/3/11 and from 2011/3/11 to 2013/3/11. We observe that the background rate of the intermediate to deep (150-450 km) seismicity underwent a deceleration of 55% south of the rupture zone and an acceleration of 30% north of it after the Tohoku-oki earthquake, consistent with the GPS surface displacements. This shows how a megathrust earthquake can affect the stress state of the slab over a 2500 km lateral range and a large depth range, demonstrating that earthquakes interact at a much greater scale than the surrounding rupture zone usually considered.
Waveguide holography for 3D augmented reality glasses
Authors: Jang Changwon , Bang Kiseung , Chae Minseok , Lee Byoungho , Lanman Douglas
Published: January 2024

Near-eye displays are fundamental technology in the next generation computing platforms for augmented reality and virtual reality. However, there are remaining challenges to deliver immersive and comfortable visual experiences to users, such as compact form factor, solving vergence-accommodation conflict, and achieving a high resolution with a large eyebox. Here we show a compact holographic near-eye display concept that combines the advantages of waveguide displays and holographic displays to overcome the challenges towards true 3D holographic augmented reality glasses. By modeling the coherent light interactions and propagation via the waveguide combiner, we demonstrate controlling the output wavefront using a spatial light modulator located at the input coupler side. The proposed method enables 3D holographic displays via exit-pupil expanding waveguide combiners, providing a large software-steerable eyebox. It also offers additional advantages such as resolution enhancement capability by suppressing phase discontinuities caused by pupil replication process. We build prototypes to verify the concept with experimental results and conclude the paper with discussion.
Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection
Authors: Hou Jiakai , Wei Yanjun , Zou Jing , Jaffery Roshni , Sun Long , Liang Shaoheng , Zheng Ningbo , Guerrero Ashley M. , Egan Nicholas A. , Bohat Ritu , Chen Si , Zheng Caishang , Mao Xiaobo , Yi S. Stephen , Chen Ken , McGrail Daniel J. , Sahni Nidhi , Shi Pei-Yong , Chen Yiwen , Xie Xuping , Peng Weiyi
Published: January 2024

Host anti-viral factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill in this knowledge gap, we perform a genome-wide CRISPR dropout screen and integrate analyses of the multi-omics data of the CRISPR screen, genome-wide association studies, single-cell RNA-Seq, and host-virus proteins or protein/RNA interactome. This study uncovers many host factors that are currently underappreciated, including the components of V-ATPases, ESCRT, and N-glycosylation pathways that modulate viral entry and/or replication. The cohesin complex is also identified as an anti-viral pathway, suggesting an important role of three-dimensional chromatin organization in mediating host-viral interaction. Furthermore, we discover another anti-viral regulator KLF5, a transcriptional factor involved in sphingolipid metabolism, which is up-regulated, and harbors genetic variations linked to COVID-19 patients with severe symptoms. Anti-viral effects of three identified candidates (DAZAP2/VTA1/KLF5) are confirmed individually. Molecular characterization of DAZAP2/VTA1/KLF5-knockout cells highlights the involvement of genes related to the coagulation system in determining the severity of COVID-19. Together, our results provide further resources for understanding the host anti-viral network during SARS-CoV-2 infection and may help develop new countermeasure strategies.
Reprogramming biocatalytic futile cycles through computational engineering of stereochemical promiscuity to create an amine racemase
Authors: Han Sang-Woo , Jang Youngho , Kook Jihyun , Jang Jeesu , Shin Jong-Shik
Published: January 2024

Repurposing the intrinsic properties of natural enzymes can offer a viable solution to current synthetic challenges through the development of novel biocatalytic processes. Although amino acid racemases are ubiquitous in living organisms, an amine racemase (AR) has not yet been discovered despite its synthetic potential for producing chiral amines. Here, we report the creation of an AR based on the serendipitous discovery that amine transaminases (ATAs) can perform stereoinversion of 2-aminobutane. Kinetic modeling revealed that the unexpected off-pathway activity results from stereochemically promiscuous futile cycles due to incomplete stereoselectivity for 2-aminobutane. This finding motivated us to engineer an S-selective ATA through in silico alanine scanning and empirical combinatorial mutations, creating an AR with broad substrate specificity. The resulting AR, carrying double point mutations, enables the racemization of both enantiomers of diverse chiral amines in the presence of a cognate ketone. This strategy may be generally applicable to a wide range of transaminases, paving the way for the development of new-to-nature racemases.
Robust changes in global subtropical circulation under greenhouse warming
Authors: Zhou Shijie , Huang Ping , Wang Lin , Hu Kaiming , Huang Gang , Hu Peng
Published: January 2024

The lower tropospheric subtropical circulation (SC) is characterized by monsoons and subtropical highs, playing an important role in global teleconnections and climate variability. The SC changes in a warmer climate are influenced by complex and region-specific mechanisms, resulting in uneven projections worldwide. Here, we present a method to quantify the overall intensity change in global SC, revealing a robust weakening across CMIP6 models. The weakening is primarily caused by global-mean surface warming, and partly counteracted by the direct CO2 effect. The direct CO2 effect is apparent in the transient response but is eventually dominated by the surface warming effect in a slow response. The distinct response timescales to global-mean warming and direct CO2 radiative forcing can well explain the time-varying SC changes in other CO2 emission scenarios. The declined SC implies a contracted monsoon range and drying at its boundary with arid regions under CO2-induced global warming.
Ultrafast entropy production in pump-probe experiments
Authors: Caprini Lorenzo , Löwen Hartmut , Geilhufe R. Matthias
Published: January 2024

The ultrafast control of materials has opened the possibility to investigate non-equilibrium states of matter with striking properties, such as transient superconductivity and ferroelectricity, ultrafast magnetization and demagnetization, as well as Floquet engineering. The characterization of the ultrafast thermodynamic properties within the material is key for their control and design. Here, we develop the ultrafast stochastic thermodynamics for laser-excited phonons. We calculate the entropy production and heat absorbed from experimental data for single phonon modes of driven materials from time-resolved X-ray scattering experiments where the crystal is excited by a laser pulse. The spectral entropy production is calculated for SrTiO3 and KTaO3 for different temperatures and reveals a striking relation with the power spectrum of the displacement-displacement correlation function by inducing a broad peak beside the eigenmode-resonance.
The psychological, computational, and neural foundations of indebtedness
Authors: Gao Xiaoxue , Jolly Eshin , Yu Hongbo , Liu Huiying , Zhou Xiaolin , Chang Luke J.
Published: January 2024

Receiving a favor from another person may induce a negative feeling of indebtedness for the beneficiary. In this study, we explore these hidden costs by developing and validating a conceptual model of indebtedness across three studies that combine a large-scale online questionnaire, an interpersonal game, computational modeling, and neuroimaging. Our model captures how individuals perceive the altruistic and strategic intentions of the benefactor. These inferences produce distinct feelings of guilt and obligation that together comprise indebtedness and motivate reciprocity. Perceived altruistic intentions convey care and communal concern and are associated with activity in insula, ventromedial prefrontal cortex and dorsolateral prefrontal cortex, while inferred strategic intentions convey expectations of future reciprocity and are associated with activation in temporal parietal junction and dorsomedial prefrontal cortex. We further develop a neural utility model of indebtedness using multivariate patterns of brain activity that captures the tradeoff between these feelings and reliably predicts reciprocity behavior.
Serglycin secreted by late-stage nucleus pulposus cells is a biomarker of intervertebral disc degeneration
Authors: Chen Fan , Lei Linchuan , Chen Shunlun , Zhao Zhuoyang , Huang Yuming , Jiang Guowei , Guo Xingyu , Li Zemin , Zheng Zhaomin , Wang Jianru
Published: January 2024

Intervertebral disc degeneration is a natural process during aging and a leading cause of lower back pain. Here, we generate a comprehensive atlas of nucleus pulposus cells using single-cell RNA-seq analysis of human nucleus pulposus tissues (three males and four females, age 41.14 ± 18.01 years). We identify fibrotic late-stage nucleus pulposus cells characterized by upregulation of serglycin expression which facilitate the local inflammatory response by promoting the infiltration of inflammatory cytokines and macrophages. Finally, we discover that daphnetin, a potential serglycin ligand, substantially mitigates the local inflammatory response by downregulating serglycin expression in an in vivo mouse model, thus alleviating intervertebral disc degeneration. Taken together, we identify late-stage nucleus pulposus cells and confirm the potential mechanism by which serglycin regulates intervertebral disc degeneration. Our findings indicate that serglycin is a latent biomarker of intervertebral disc degeneration and may contribute to development of diagnostic and therapeutic strategies.
Aspergillus fumigatus mitogen-activated protein kinase MpkA is involved in gliotoxin production and self-protection
Authors: Alves de Castro Patrícia , Figueiredo Pinzan Camila , dos Reis Thaila Fernanda , Valero Clara , Van Rhijn Norman , Menegatti Carla , de Freitas Migliorini Ivan Lucas , Bromley Michael , Fleming Alastair B. , Traynor Aimee M. , Sarikaya-Bayram Özlem , Bayram Özgür , Malavazi Iran , Ebel Frank , Barbosa Júlio César Jerônimo , Fill Taícia , Pupo Monica Tallarico , Goldman Gustavo H.
Published: January 2024

Aspergillus fumigatus is a saprophytic fungus that can cause a variety of human diseases known as aspergillosis. Mycotoxin gliotoxin (GT) production is important for its virulence and must be tightly regulated to avoid excess production and toxicity to the fungus. GT self-protection by GliT oxidoreductase and GtmA methyltransferase activities is related to the subcellular localization of these enzymes and how GT can be sequestered from the cytoplasm to avoid increased cell damage. Here, we show that GliT:GFP and GtmA:GFP are localized in the cytoplasm and in vacuoles during GT production. The Mitogen-Activated Protein kinase MpkA is essential for GT production and self-protection, interacts physically with GliT and GtmA and it is necessary for their regulation and subsequent presence in the vacuoles. The sensor histidine kinase SlnASln1 is important for modulation of MpkA phosphorylation. Our work emphasizes the importance of MpkA and compartmentalization of cellular events for GT production and self-defense.
Mcam inhibits macrophage-mediated development of mammary gland through non-canonical Wnt signaling
Authors: Yang Xing , Xu Haibo , Yang Xu , Wang Hui , Zou Li , Yang Qin , Qi Xiaopeng , Li Li , Duan Hongxia , Yan Xiyun , Fu Nai Yang , Tan Jing , Hou Zongliu , Jiao Baowei
Published: January 2024

While canonical Wnt signaling is well recognized for its crucial regulatory functions in cell fate decisions, the role of non-canonical Wnt signaling in adult stem cells remains elusive and contradictory. Here, we identified Mcam, a potential member of the non-canonical Wnt signaling, as an important negative regulator of mammary gland epithelial cells (MECs) by genome-scale CRISPR-Cas9 knockout (GeCKO) library screening. Loss of Mcam increases the clonogenicity and regenerative capacity of MECs, and promotes the proliferation, differentiation, and ductal morphogenesis of mammary epithelial in knockout mice. Mechanically, Mcam knockout recruits and polarizes macrophages through the Il4-Stat6 axis, thereby promoting secretion of the non-canonical Wnt ligand Wnt5a and its binding to the non-canonical Wnt signaling receptor Ryk to induce the above phenotypes. These findings reveal Mcam roles in mammary gland development by orchestrating communications between MECs and macrophages via a Wnt5a/Ryk axis, providing evidences for non-canonical Wnt signaling in mammary development.
Organohydrogel-based transparent terahertz absorber via ionic conduction loss
Authors: Xie Wenke , Tang Qian , Xie Jinlong , Fei Yang , Wan Hujie , Zhao Tao , Ding Tianpeng , Xiao Xu , Wen Qiye
Published: January 2024

The fast-growing terahertz technologies require high-performance terahertz absorber for suppressing electromagnetic interference. Since the dissipation mechanism in terahertz band usually focuses on electronic conduction loss, almost all terahertz absorbers are constructed with electronically conducting materials being opaque, which limits their applications in scenarios requiring high visible transmittance. Here, we demonstrate a transparent terahertz absorber based on permittivity-gradient elastomer-encapsulated-organohydrogel. Our organohydrogel-based terahertz absorber exhibits a high absorbing property (average reflection loss of 49.03 dB) in 0.5–4.5 THz band with a thin thickness of 700 μm and a high average visible transmittance of 85.51%. The terahertz absorbing mechanism mainly derives from the ionic conduction loss of the polar liquid in organohydrogel. Besides, the hydrophobic and adhesive elastomer coating endows this terahertz absorber high absorbing stability and interfacial adhesivity. This work paves a viable way to designing transparent terahertz absorbers.
Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64
Authors: Wang Ruobing , Zhang Anru , Sun Shijun , Yin Guankun , Wu Xingyu , Ding Qi , Wang Qi , Chen Fengning , Wang Shuyi , van Dorp Lucy , Zhang Yawei , Jin Longyang , Wang Xiaojuan , Balloux Francois , Wang Hui
Published: January 2024

The acquisition of exogenous mobile genetic material imposes an adaptive burden on bacteria, whereas the adaptational evolution of virulence plasmids upon entry into carbapenem-resistant Klebsiella pneumoniae (CRKP) and its impact remains unclear. To better understand the virulence in CRKP, we characterize virulence plasmids utilizing a large genomic data containing 1219 K. pneumoniae from our long-term surveillance and publicly accessible databases. Phylogenetic evaluation unveils associations between distinct virulence plasmids and serotypes. The sub-lineage ST11-KL64 CRKP acquires a pK2044-like virulence plasmid from ST23-KL1 hypervirulent K. pneumoniae, with a 2698 bp region deletion in all ST11-KL64. The deletion is observed to regulate methionine metabolism, enhance antioxidant capacity, and further improve survival of hypervirulent CRKP in macrophages. The pK2044-like virulence plasmid discards certain sequences to enhance survival of ST11-KL64, thereby conferring an evolutionary advantage. This work contributes to multifaceted understanding of virulence and provides insight into potential causes behind low fitness costs observed in bacteria.
The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients
Authors: Chu Victoria T. , Tsitsiklis Alexandra , Mick Eran , Ambroggio Lilliam , Kalantar Katrina L. , Glascock Abigail , Osborne Christina M. , Wagner Brandie D. , Matthay Michael A. , DeRisi Joseph L. , Calfee Carolyn S. , Mourani Peter M. , Langelier Charles R.
Published: January 2024

Antimicrobial resistant lower respiratory tract infections are an increasing public health threat and an important cause of global mortality. The lung microbiome can influence susceptibility of respiratory tract infections and represents an important reservoir for exchange of antimicrobial resistance genes. Studies of the gut microbiome have found an association between age and increasing antimicrobial resistance gene burden, however, corollary studies in the lung microbiome remain absent. We performed an observational study of children and adults with acute respiratory failure admitted to the intensive care unit. From tracheal aspirate RNA sequencing data, we evaluated age-related differences in detectable antimicrobial resistance gene expression in the lung microbiome. Using a multivariable logistic regression model, we find that detection of antimicrobial resistance gene expression was significantly higher in adults compared with children after adjusting for demographic and clinical characteristics. This association remained significant after additionally adjusting for lung bacterial microbiome characteristics, and when modeling age as a continuous variable. The proportion of adults expressing beta-lactam, aminoglycoside, and tetracycline antimicrobial resistance genes was higher compared to children. Together, these findings shape our understanding of the lung resistome in critically ill patients across the lifespan, which may have implications for clinical management and global public health.
Cultured meat with enriched organoleptic properties by regulating cell differentiation
Authors: Lee Milae , Park Sohyeon , Choi Bumgyu , Choi Woojin , Lee Hyun , Lee Jeong Min , Lee Seung Tae , Yoo Ki Hyun , Han Dongoh , Bang Geul , Hwang Heeyoun , Koh Won-Gun , Lee Sangmin , Hong Jinkee
Published: January 2024

Research on cultured meat has primarily focused on the mass proliferation or differentiation of muscle cells; thus, the food characteristics of cultured meat remain relatively underexplored. As the quality of meat is determined by its organoleptic properties, cultured meat with similar sensory characteristics to animal-derived meat is highly desirable. In this study, we control the organoleptic and nutritional properties of cultured meat by tailoring the 2D differentiation of primary bovine myoblasts and primary bovine adipose-derived mesenchymal stem cells on gelatin/alginate scaffolds with varying stiffness. We assess the effect of muscle and adipose differentiation quality on the sensory properties of cultured meat. Thereafter, we fabricate cultured meat with similar sensory profiles to that of conventional beef by assembling the muscle and adipose constructs composed of highly differentiated cells. We introduce a strategy to produce cultured meat with enriched food characteristics by regulating cell differentiation with scaffold engineering.
Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions
Authors: Schöpf Julia , Uhrig Sebastian , Heilig Christoph E. , Lee Kwang-Seok , Walther Tatjana , Carazzato Alexander , Dobberkau Anna Maria , Weichenhan Dieter , Plass Christoph , Hartmann Mark , Diwan Gaurav D. , Carrero Zunamys I. , Ball Claudia R. , Hohl Tobias , Kindler Thomas , Rudolph-Hähnel Patricia , Helm Dominic , Schneider Martin , Nilsson Anna , Øra Ingrid , Imle Roland , Banito Ana , Russell Robert B. , Jones Barbara C. , Lipka Daniel B. , Glimm Hanno , Hübschmann Daniel , Hartmann Wolfgang , Fröhling Stefan , Scholl Claudia
Published: January 2024

Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.
Gut microbiota facilitate chronic spontaneous urticaria
Authors: Zhu Lei , Jian Xingxing , Zhou Bingjing , Liu Runqiu , Muñoz Melba , Sun Wan , Xie Lu , Chen Xiang , Peng Cong , Maurer Marcus , Li Jie
Published: January 2024

Chronic spontaneous urticaria (CSU) comes with gut dysbiosis, but its relevance remains elusive. Here we use metagenomics sequencing and short-chain fatty acids metabolomics and assess the effects of human CSU fecal microbial transplantation, Klebsiella pneumoniae, Roseburia hominis, and metabolites in vivo. CSU gut microbiota displays low diversity and short-chain fatty acids production, but high gut Klebsiella pneumoniae levels, negatively correlates with blood short-chain fatty acids levels and links to high disease activity. Blood lipopolysaccharide levels are elevated, link to rapid disease relapse, and high gut levels of conditional pathogenic bacteria. CSU microbiome transfer and Klebsiella pneumoniae transplantation facilitate IgE-mediated mast cell(MC)-driven skin inflammatory responses and increase intestinal permeability and blood lipopolysaccharide accumulation in recipient mice. Transplantation of Roseburia hominis and caproate administration protect recipient mice from MC-driven skin inflammation. Here, we show gut microbiome alterations, in CSU, may reduce short-chain fatty acids and increase lipopolysaccharide levels, respectively, and facilitate MC-driven skin inflammation.
Colloidal pathways of amorphous calcium carbonate formation lead to distinct water environments and conductivity
Authors: Gindele Maxim B. , Vinod-Kumar Sanjay , Rochau Johannes , Boemke Daniel , Groß Eduard , Redrouthu Venkata SubbaRao , Gebauer Denis , Mathies Guinevere
Published: January 2024

CaCO3 is the most abundant biomineral and a major constituent of incrustations arising from water hardness. Polycarboxylates play key roles in controlling mineralization. Herein, we present an analytical and spectroscopic study of polycarboxylate-stabilized amorphous CaCO3 (ACC) and its formation via a dense liquid precursor phase (DLP). Polycarboxylates facilitate pronounced, kinetic bicarbonate entrapment in the DLP. Since bicarbonate is destabilized in the solid state, DLP dehydration towards solid ACC necessitates the formation of locally calcium deficient sites, thereby inhibiting nucleation. Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy of poly-aspartate-stabilized ACC reveals the presence of two distinct environments. The first contains immobile calcium and carbonate ions and structural water molecules, undergoing restricted, anisotropic motion. In the second environment, water molecules undergo slow, but isotropic motion. Indeed, conductive atomic force microscopy (C-AFM) reveals that ACC conducts electrical current, strongly suggesting that the mobile environment pervades the bulk of ACC, with dissolved hydroxide ions constituting the charge carriers. We propose that the distinct environments arise from colloidally stabilized interfaces of DLP nanodroplets, consistent with the pre-nucleation cluster (PNC) pathway.
p53 suppresses MHC class II presentation by intestinal epithelium to protect against radiation-induced gastrointestinal syndrome
Authors: Wang Jianming , Chang Chun-Yuan , Yang Xue , Zhou Fan , Liu Juan , Bargonetti Jill , Zhang Lanjing , Xie Ping , Feng Zhaohui , Hu Wenwei
Published: January 2024

Radiation-induced gastrointestinal syndrome is a major complication and limiting factor for radiotherapy. Tumor suppressor p53 has a protective role in radiation-induced gastrointestinal toxicity. However, its underlying mechanism remains unclear. Here we report that regulating the IL12-p40/MHC class II signaling pathway is a critical mechanism by which p53 protects against radiation-induced gastrointestinal syndrome. p53 inhibits the expression of inflammatory cytokine IL12-p40, which in turn suppresses the expression of MHC class II on intestinal epithelial cells to suppress T cell activation and inflammation post-irradiation that causes intestinal stem cell damage. Anti-IL12-p40 neutralizing antibody inhibits inflammation and rescues the defects in intestinal epithelial regeneration post-irradiation in p53-deficient mice and prolongs mouse survival. These results uncover that the IL12-p40/MHC class II signaling mediates the essential role of p53 in ensuring intestinal stem cell function and proper immune reaction in response to radiation to protect mucosal epithelium, and suggest a potential therapeutic strategy to protect against radiation-induced gastrointestinal syndrome.
Mammalian cell growth characterisation by a non-invasive plate reader assay
Authors: Grob Alice , Enrico Bena Chiara , Di Blasi Roberto , Pessina Daniele , Sood Matthew , Yunyue Zhou , Bosia Carla , Isalan Mark , Ceroni Francesca
Published: January 2024

Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here, we report the development of a high throughput non-invasive method for tracking mammalian cell growth and performance based on plate reader measurements. We show the method to be suitable for both suspension and adhesion cell lines, and we demonstrate it can be adopted when cells are grown under different environmental conditions. We establish that the method is suitable to inform on effective drug treatments to be used depending on the cell line considered, and that it can support characterisation of engineered mammalian cells over time. This work provides the scientific community with an innovative approach to mammalian cell screening, also contributing to the current efforts towards high throughput and automated mammalian cell engineering.
Leucine aminopeptidase1 controls egg deposition and hatchability in male Aedes aegypti mosquitoes
Authors: Sun Xiaomei , Wang Xueli , Shi Kai , Lyu Xiangyang , Sun Jian , Raikhel Alexander S. , Zou Zhen
Published: January 2024

Aedes aegypti are vectors for several arboviruses infecting hundreds of millions of people annually. Controlling mosquito populations by regulating their reproduction is a potential strategy to minimize viral transmission in the absence of effective antiviral therapies or vaccines. Here, we demonstrate that leucine aminopeptidase1 (LAP1), detected by a SWATH-MS-based proteomic screen of female spermathecae, is a crucial determinant in mosquito population expansion. Mitochondrial defects and aberrant autophagy of sperm in LAP1 mutant males (LAP1−/−), prepared using CRISPR/Cas9 system, result in a reduction of reproduction in wild-type females that mated with them. The fitness of LAP1−/− males is strong enough to efficiently transmit genetic changes to mosquito populations through a low number of hatchable offspring. Thus, LAP1−/− males represent an opportunity to suppress mosquito populations and further studies should be undertaken to characterize LAP1’s suitability for gene drive usage.
rworkflows: automating reproducible practices for the R community
Authors: Schilder Brian M. , Murphy Alan E. , Skene Nathan G.
Published: January 2024

Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have any default built-in checks for minimal coding standards or software usability. This makes it difficult to assess the current quality R packages, or to consistently use them over time and across platforms. While GitHub-native solutions are technically possible, they require considerable time and expertise for each developer to write, implement, and maintain. To address this, we developrworkflows; a suite of tools to make robust continuous integration and deployment (https://github.com/neurogenomics/rworkflows).rworkflowscan be implemented by developers of all skill levels using a one-time R function call which has both sensible defaults and extensive options for customisation. Once implemented, any updates to the GitHub repository automatically trigger parallel workflows that install all software dependencies, run code checks, generate a dedicated documentation website, and deploy a publicly accessible containerised environment. By making therworkflowssuite free, automated, and simple to use, we aim to promote widespread adoption of reproducible practices across a continually growing R community.
Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean
Authors: Deutschmann Ina M. , Delage Erwan , Giner Caterina R. , Sebastián Marta , Poulain Julie , Arístegui Javier , Duarte Carlos M. , Acinas Silvia G. , Massana Ramon , Gasol Josep M. , Eveillard Damien , Chaffron Samuel , Logares Ramiro
Published: January 2024

Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.
A conserved graft formation process in Norway spruce and Arabidopsis identifies the PAT gene family as central regulators of wound healing
Authors: Feng Ming , Zhang Ai , Nguyen Van , Bisht Anchal , Almqvist Curt , De Veylder Lieven , Carlsbecker Annelie , Melnyk Charles W.
Published: January 2024

The widespread use of plant grafting enables eudicots and gymnosperms to join with closely related species and grow as one. Gymnosperms have dominated forests for over 200 million years, and despite their economic and ecological relevance, we know little about how they graft. Here we developed a micrografting method in conifers using young tissues that allowed efficient grafting with closely related species and between distantly related genera. Conifer graft junctions rapidly connected vasculature and differentially expressed thousands of genes including auxin and cell-wall-related genes. By comparing these genes to those induced during Arabidopsis thaliana graft formation, we found a common activation of cambium, cell division, phloem and xylem-related genes. A gene regulatory network analysis in Norway spruce (Picea abies) predicted that PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) acted as a core regulator of graft healing. This gene was strongly up-regulated during both spruce and Arabidopsis grafting, and Arabidopsis mutants lacking PAT genes failed to attach tissues or successfully graft. Complementing Arabidopsis PAT mutants with the spruce PAT1 homolog rescued tissue attachment and enhanced callus formation. Together, our data show an ability for young tissues to graft with distantly related species and identifies the PAT gene family as conserved regulators of graft healing and tissue regeneration.
Absolute quantification of nicotinamide mononucleotide in biological samples by double isotope-mediated liquid chromatography-tandem mass spectrometry (dimeLC-MS/MS)
Authors: Unno Junya , Mills Kathryn F. , Ogura Tairo , Nishimura Masayuki , Imai Shin-ichiro
Published: January 2024

Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite for fundamental biological phenomena, including aging. Nicotinamide mononucleotide (NMN) is a key NAD+ intermediate that has been extensively tested as an effective NAD+-boosting compound in mice and humans. However, the accurate measurement of NMN in biological samples has long been a challenge in the field. Here, we have established an accurate, quantitative methodology for measuring NMN by using liquid chromatography-triple quadrupole mass spectrometry (LC-MS/MS) with double isotopic NMN standards. In this new methodology, the matrix effects of biological samples were properly adjusted, and the fate of NMN could be traced during sample processing. We have demonstrated that this methodology can accurately quantitate NMN levels in mouse plasma and confirmed quick, direct NMN uptake into blood circulation and cells. This double isotope-mediated LC-MS/MS (dimeLC-MS/MS) can easily be expanded to other NAD+-related metabolites as a reliable standard methodology for NAD+ biology.
Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer
Authors: Guerriero Jennifer L. , Lin Jia-Ren , Pastorello Ricardo G. , Du Ziming , Chen Yu-An , Townsend Madeline G. , Shimada Kenichi , Hughes Melissa E. , Ren Siyang , Tayob Nabihah , Zheng Kelly , Mei Shaolin , Patterson Alyssa , Taneja Krishan L. , Metzger Otto , Tolaney Sara M. , Lin Nancy U. , Dillon Deborah A. , Schnitt Stuart J. , Sorger Peter K. , Mittendorf Elizabeth A. , Santagata Sandro
Published: January 2024

Emerging data suggests that HER2 intratumoral heterogeneity (ITH) is associated with therapy resistance, highlighting the need for new strategies to assess HER2 ITH. A promising approach is leveraging multiplexed tissue analysis techniques such as cyclic immunofluorescence (CyCIF), which enable visualization and quantification of 10–60 antigens at single-cell resolution from individual tissue sections. In this study, we qualified a breast cancer-specific antibody panel, including HER2, ER, and PR, for multiplexed tissue imaging. We then compared the performance of these antibodies against established clinical standards using pixel-, cell- and tissue-level analyses, utilizing 866 tissue cores (representing 294 patients). To ensure reliability, the CyCIF antibodies were qualified against HER2 immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) data from the same samples. Our findings demonstrate the successful qualification of a breast cancer antibody panel for CyCIF, showing high concordance with established clinical antibodies. Subsequently, we employed the qualified antibodies, along with antibodies for CD45, CD68, PD-L1, p53, Ki67, pRB, and AR, to characterize 567 HER2+ invasive breast cancer samples from 189 patients. Through single-cell analysis, we identified four distinct cell clusters within HER2+ breast cancer exhibiting heterogeneous HER2 expression. Furthermore, these clusters displayed variations in ER, PR, p53, AR, and PD-L1 expression. To quantify the extent of heterogeneity, we calculated heterogeneity scores based on the diversity among these clusters. Our analysis revealed expression patterns that are relevant to breast cancer biology, with correlations to HER2 ITH and potential relevance to clinical outcomes.
cGAS-STING pathway expression correlates with genomic instability and immune cell infiltration in breast cancer
Authors: Chen Mengting , Yu Shibo , van der Sluis Tineke , Zwager Mieke C. , Schröder Carolien P. , van der Vegt Bert , van Vugt Marcel A. T. M.
Published: January 2024

Genomic instability, as caused by oncogene-induced replication stress, can lead to the activation of inflammatory signaling, involving the cGAS-STING and JAK-STAT pathways. Inflammatory signaling has been associated with pro-tumorigenic features, but also with favorable response to treatment, including to immune checkpoint inhibition. In this study, we aim to explore relations between inflammatory signaling, markers of replication stress, and immune cell infiltration in breast cancer. Expression levels of cGAS-STING signaling components (STING, phospho-TBK1, and phospho-STAT1), replication stress markers (γH2AX and pRPA), replication stress-related proto-oncogenes (Cyclin E1 and c-Myc) and immune cell markers (CD20, CD4, and CD57) are determined immunohistochemically on primary breast cancer samples (n = 380). RNA-sequencing data from TCGA (n = 1082) and METABRIC (n = 1904) are used to calculate cGAS-STING scores. pTBK1, pSTAT1 expression and cGAS-STING pathway scores are all increased in triple-negative breast cancers compared to other subtypes. Expression of γH2AX, pRPA, Cyclin E1, c-Myc, and immune cell infiltration positively correlate with p-STAT1 expression (P < 0.001). Additionally, we observe significant positive associations between expression of pTBK1 and γH2AX, pRPA, c-Myc, and number of CD4+ cells and CD20+ cells. Also, cGAS-STING scores are correlated with genomic instability metrics, such as homologous recombination deficiency (P < 0.001) and tumor mutational burden (P < 0.01). Moreover, data from the I-SPY2 clinical trial (n = 71) confirms that higher cGAS-STING scores are observed in breast cancer patients who responded to immunotherapy combined with chemotherapy. In conclusion, the cGAS-STING pathway is highly expressed in TNBCs and is correlated with genomic instability and immune cell infiltration.
Linking acetylated α-Tubulin redistribution to α-Synuclein pathology in brain of Parkinson’s disease patients
Authors: Mazzetti Samanta , Giampietro Federica , Calogero Alessandra Maria , Isilgan Huseyin Berkcan , Gagliardi Gloria , Rolando Chiara , Cantele Francesca , Ascagni Miriam , Bramerio Manuela , Giaccone Giorgio , Isaias Ioannis Ugo , Pezzoli Gianni , Cappelletti Graziella
Published: January 2024

Highly specialized microtubules in neurons are crucial to both health and disease of the nervous system, and their properties are strictly regulated by different post-translational modifications, including α-Tubulin acetylation. An imbalance in the levels of acetylated α-Tubulin has been reported in experimental models of Parkinson’s disease (PD) whereas pharmacological or genetic modulation that leads to increased acetylated α-Tubulin successfully rescues axonal transport defects and inhibits α-Synuclein aggregation. However, the role of acetylation of α-Tubulin in the human nervous system is largely unknown as most studies are based on in vitro evidence. To capture the complexity of the pathological processes in vivo, we analysedpost-mortemhuman brain of PD patients and control subjects. In the brain of PD patients at Braak stage 6, we found a redistribution of acetylated α-Tubulin, which accumulates in the neuronal cell bodies in subcortical structures but not in the cerebral cortex, and decreases in the axonal compartment, both in putamen bundles of fibres and in sudomotor fibres. High-resolution and 3D reconstruction analysis linked acetylated α-Tubulin redistribution to α-Synuclein oligomerization and to phosphorylated Ser 129 α-Synuclein, leading us to propose a model for Lewy body (LB) formation. Finally, inpost-mortemhuman brain, we observed threadlike structures, resembling tunnelling nanotubes that contain α-Synuclein oligomers and are associated with acetylated α-Tubulin enriched neurons. In conclusion, we support the role of acetylated α-Tubulin in PD pathogenesis and LB formation.
Quantum key distribution using deterministic single-photon sources over a field-installed fibre link
Authors: Zahidy Mujtaba , Mikkelsen Mikkel T. , Müller Ronny , Da Lio Beatrice , Krehbiel Martin , Wang Ying , Bart Nikolai , Wieck Andreas D. , Ludwig Arne , Galili Michael , Forchhammer Søren , Lodahl Peter , Oxenløwe Leif K. , Bacco Davide , Midolo Leonardo
Published: January 2024

Quantum-dot-based single-photon sources are key assets for quantum information technology, supplying on-demand scalable quantum resources for computing and communication. However, long-lasting issues such as limited long-term stability and source brightness have traditionally impeded their adoption in real-world applications. Here, we realize a quantum key distribution field trial using true single photons across an 18-km-long dark fibre, located in the Copenhagen metropolitan area, using an optimized, state-of-the-art, quantum-dot single-photon source frequency-converted to the telecom wavelength. A secret key generation rate of > 2 kbits/s realized over a 9.6 dB channel loss is achieved with a polarization-encoded BB84 scheme, showing remarkable stability for more than 24 hours of continuous operation. Our results highlight the maturity of deterministic single-photon source technology while paving the way for advanced single-photon-based communication protocols, including fully device-independent quantum key distribution, towards the goal of a quantum internet.
Myeloid cell-associated aromatic amino acid metabolism facilitates CNS myelin regeneration
Authors: Hu Jingwen , Melchor George S. , Ladakis Dimitrios , Reger Joan , Kim Hee Won , Chamberlain Kelly A. , Shults Nataliia V. , Oft Helena C. , Smith Victoria N. , Rosko Lauren M. , Li Erqiu , Baydyuk Maryna , Fu Meng-Meng , Bhargava Pavan , Huang Jeffrey K.
Published: January 2024

Regulation of myeloid cell activity is critical for successful myelin regeneration (remyelination) in demyelinating diseases, such as multiple sclerosis (MS). Here, we show aromatic alpha-keto acids (AKAs) generated from the amino acid oxidase, interleukin-4 induced 1 (IL4I1), promote efficient remyelination in mouse models of MS. During remyelination, myeloid cells upregulated the expression of IL4I1. Conditionally knocking out IL4I1 in myeloid cells impaired remyelination efficiency. Mice lacking IL4I1 expression exhibited a reduction in the AKAs, phenylpyruvate, indole-3-pyruvate, and 4-hydroxyphenylpyruvate, in remyelinating lesions. Decreased AKA levels were also observed in people with MS, particularly in the progressive phase when remyelination is impaired. Oral administration of AKAs modulated myeloid cell-associated inflammation, promoted oligodendrocyte maturation, and enhanced remyelination in mice with focal demyelinated lesions. Transcriptomic analysis revealed AKA treatment induced a shift in metabolic pathways in myeloid cells and upregulated aryl hydrocarbon receptor activity in lesions. Our results suggest myeloid cell-associated aromatic amino acid metabolism via IL4I1 produces AKAs in demyelinated lesions to enable efficient remyelination. Increasing AKA levels or targeting related pathways may serve as a strategy to facilitate the regeneration of myelin in inflammatory demyelinating conditions.
Immunogenicity and reactogenicity of intradermal mRNA-1273 SARS-CoV-2 vaccination: a non-inferiority, randomized-controlled trial
Authors: Prins Manon L. M. , Roozen Geert V. T. , Pothast Cilia. R. , Huisman Wesley , van Binnendijk Rob , den Hartog Gerco , Kuiper Vincent P. , Prins Corine , Janse Jacqueline J. , Lamers Olivia. A. C. , Koopman Jan Pieter R. , Kruithof Annelieke C. , Kamerling Ingrid M. C. , Dijkland Romy C. , de Kroon Alicia. C. , Azimi Shohreh , Feltkamp Mariet C. W. , Kuijer Marjan , Jochems Simon P. , Heemskerk Mirjam H. M. , Rosendaal Frits R. , Roestenberg Meta , Visser Leo G. , Roukens Anna H. E.
Published: January 2024

Fractional dosing can be a cost-effective vaccination strategy to accelerate individual and herd immunity in a pandemic. We assessed the immunogenicity and safety of primary intradermal (ID) vaccination, with a 1/5th dose compared with the standard intramuscular (IM) dose of mRNA-1273 in SARS-CoV-2 naïve persons. We conducted an open-label, non-inferiority, randomized controlled trial in the Netherlands between June and December 2021. One hundred and fifty healthy and SARS-CoV-2 naïve participants, aged 18–30 years, were randomized (1:1:1) to receive either two doses of 20 µg mRNA-1273 ID with a standard needle (SN) or the Bella-mu® needle (BM), or two doses of 100 µg IM, 28 days apart. The primary outcome was non-inferiority in seroconversion rates at day 43 (D43), defined as a neutralizing antibody concentration threshold of 465 IU/mL, the lowest response in the IM group. The non-inferiority margin was set at −15%. Neutralizing antibody concentrations at D43 were 1789 (95% CI: 1488–2150) in the IM and 1263 (951–1676) and 1295 (1020–1645) in the ID-SN and ID-BM groups, respectively. The absolute difference in seroconversion proportion between fractional and standard-dose groups was −13.95% (−24.31 to −3.60) for the ID-SN and −13.04% (−22.78 to −3.31) for the ID-BM group and exceeded the predefined non-inferiority margin. Although ID vaccination with 1/5th dose of mRNA-1273 did not meet the predefined non-inferior criteria, the neutralizing antibody concentrations in these groups are far above the proposed proxy for protection against severe disease (100 IU/mL), justifying this strategy in times of vaccine scarcity to accelerate mass protection against severe disease.