bluuebunny/crossref_metadata_2025_split huggingface dataset:
Membrane-localized expression, production and assembly of Vibrio parahaemolyticus T3SS2 provides evidence for transertion
Authors: Kaval Karan Gautam , Chimalapati Suneeta , Siegel Sara D. , Garcia Nalleli , Jaishankar Jananee , Dalia Ankur B. , Orth Kim 
Published: March 2023

AbstractIt has been proposed that bacterial membrane proteins may be synthesized and inserted into the membrane by a process known as transertion, which involves membrane association of their encoding genes, followed by coupled transcription, translation and membrane insertion. Here, we provide evidence supporting that the pathogen Vibrio parahaemolyticus uses transertion to assemble its type III secretion system (T3SS2), to inject virulence factors into host cells. We propose a two-step transertion process where the membrane-bound co-component receptor (VtrA/VtrC) is first activated by bile acids, leading to membrane association and expression of its target gene, vtrB, located in the T3SS2 pathogenicity island. VtrB, the transmembrane transcriptional activator of T3SS2, then induces the localized expression and membrane assembly of the T3SS2 structural components and its effectors. We hypothesize that the proposed transertion process may be used by other enteric bacteria for efficient assembly of membrane-bound molecular complexes in response to extracellular signals.
Viscoelastic coarsening of quasi-2D foam
Authors: Guidolin Chiara , Mac Intyre Jonatan , Rio Emmanuelle , Puisto Antti , Salonen Anniina 
Published: March 2023

AbstractFoams are unstable jammed materials. They evolve over timescales comparable to their “time of use", which makes the study of their destabilisation mechanisms crucial for applications. In practice, many foams are made from viscoelastic fluids, which are observed to prolong their lifetimes. Despite their importance, we lack understanding of the coarsening mechanism in such systems. We probe the effect of continuous phase viscoelasticity on foam coarsening with foamed emulsions. We show that bubble size evolution is strongly slowed down and foam structure hugely impacted. The main mechanisms responsible are the absence of continuous phase redistribution and a non-trivial link between foam structure and mechanical properties. These combine to give spatially heterogeneous coarsening. Beyond their importance in the design of foamy materials, the results give a macroscopic vision of phase separation in a viscoelastic medium.
Turning dead leaves into an active multifunctional material as evaporator, photocatalyst, and bioplastic
Authors: Fang Siyuan , Lyu Xingyi , Tong Tian , Lim Aniqa Ibnat , Li Tao , Bao Jiming , Hu Yun Hang 
Published: March 2023

AbstractLarge numbers of leaves fall on the earth each autumn. The current treatments of dead leaves mainly involve completely destroying the biocomponents, which causes considerable energy consumption and environmental issues. It remains a challenge to convert waste leaves into useful materials without breaking down their biocomponents. Here, we turn red maple dead leaves into an active three-component multifunctional material by exploiting the role of whewellite biomineral for binding lignin and cellulose. Owing to its intense optical absorption spanning the full solar spectrum and the heterogeneous architecture for effective charge separation, films of this material show high performance in solar water evaporation, photocatalytic hydrogen production, and photocatalytic degradation of antibiotics. Furthermore, it also acts as a bioplastic with high mechanical strength, high-temperature tolerance, and biodegradable features. These findings pave the way for the efficient utilization of waste biomass and innovations of advanced materials.
Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor
Authors: Glasgow Anum , Hobbs Helen T. , Perry Zion R. , Wells Malcolm L. , Marqusee Susan , Kortemme Tanja 
Published: March 2023

AbstractBiological regulation ubiquitously depends on protein allostery, but the regulatory mechanisms are incompletely understood, especially in proteins that undergo ligand-induced allostery with few structural changes. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to map allosteric effects in a paradigm ligand-responsive transcription factor, the lac repressor (LacI), in different functional states (apo, or bound to inducer, anti-inducer, and/or DNA). Although X-ray crystal structures of the LacI core domain in these states are nearly indistinguishable, HDX/MS experiments reveal widespread differences in flexibility. We integrate these results with modeling of protein-ligand-solvent interactions to propose a revised model for allostery in LacI, where ligand binding allosterically shifts the conformational ensemble as a result of distinct changes in the rigidity of secondary structures in the different states. Our model provides a mechanistic basis for the altered function of distal mutations. More generally, our approach provides a platform for characterizing and engineering protein allostery.
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat
Authors: Zhao Wei , Johnston Kevin G. , Ren Honglei , Xu Xiangmin , Nie Qing 
Published: March 2023

AbstractNeural communication networks form the fundamental basis for brain function. These communication networks are enabled by emitted ligands such as neurotransmitters, which activate receptor complexes to facilitate communication. Thus, neural communication is fundamentally dependent on the transcriptome. Here we develop NeuronChat, a method and package for the inference, visualization and analysis of neural-specific communication networks among pre-defined cell groups using single-cell expression data. We incorporate a manually curated molecular interaction database of neural signaling for both human and mouse, and benchmark NeuronChat on several published datasets to validate its ability in predicting neural connectivity. Then, we apply NeuronChat to three different neural tissue datasets to illustrate its functionalities in identifying interneural communication networks, revealing conserved or context-specific interactions across different biological contexts, and predicting communication pattern changes in diseased brains with autism spectrum disorder. Finally, we demonstrate NeuronChat can utilize spatial transcriptomics data to infer and visualize neural-specific cell-cell communication.
N6-methyladenosine of Spi2a attenuates inflammation and sepsis-associated myocardial dysfunction in mice
Authors: Wang Xiangyu , Ding Yan , Li Ran , Zhang Rujun , Ge Xuejun , Gao Ruifang , Wang Miao , Huang Yubing , Zhang Fang , Zhao Bin , Liao Wang , Du Jie 
Published: March 2023

AbstractBacteria-triggered sepsis is characterized by systemic, uncontrolled inflammation in affected individuals. Controlling the excessive production of pro-inflammatory cytokines and subsequent organ dysfunction in sepsis remains challenging. Here, we demonstrate that Spi2a upregulation in lipopolysaccharide (LPS)-stimulated bone marrow-derived macrophages reduces the production of pro-inflammatory cytokines and myocardial impairment. In addition, exposure to LPS upregulates the lysine acetyltransferase, KAT2B, to promote METTL14 protein stability through acetylation at K398, leading to the increased m6A methylation of Spi2a in macrophages. m6A-methylated Spi2a directly binds to IKKβ to impair IKK complex formation and inactivate the NF-κB pathway. The loss of m6A methylation in macrophages aggravates cytokine production and myocardial damage in mice under septic conditions, whereas forced expression of Spi2a reverses this phenotype. In septic patients, the mRNA expression levels of the human orthologue SERPINA3 negatively correlates with those of the cytokines, TNF, IL-6, IL-1β and IFNγ. Altogether, these findings suggest that m6A methylation of Spi2a negatively regulates macrophage activation in the context of sepsis.
rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly
Authors: Sekulski Kamil , Cruz Victor Emmanuel , Weirich Christine S. , Erzberger Jan P. 
Published: March 2023

AbstractBiogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation. Spb1 methylates the A-loop nucleotide G2922 and a catalytically deficient mutant strain (spb1D52A) has a severe 60S biogenesis defect. However, the assembly function of this modification is currently unknown. Here, we present cryo-EM reconstructions that reveal that unmethylated G2922 leads to the premature activation of Nog2 GTPase activity and capture a Nog2-GDP-AlF4− transition state structure that implicates the direct involvement of unmodified G2922 in Nog2 GTPase activation. Genetic suppressors and in vivo imaging indicate that premature GTP hydrolysis prevents the efficient binding of Nog2 to early nucleoplasmic 60S intermediates. We propose that G2922 methylation levels regulate Nog2 recruitment to the pre-60S near the nucleolar/nucleoplasmic phase boundary, forming a kinetic checkpoint to regulate 60S production. Our approach and findings provide a template to study the GTPase cycles and regulatory factor interactions of the other K-loop GTPases involved in ribosome assembly.
Wearable perovskite solar cells by aligned liquid crystal elastomers
Authors: Huang Zengqi , Li Lin , Wu Tingqing , Xue Tangyue , Sun Wei , Pan Qi , Wang Huadong , Xie Hongfei , Chi Jimei , Han Teng , Hu Xiaotian , Su Meng , Chen Yiwang , Song Yanlin 
Published: March 2023

AbstractIn a flexible perovskite solar cell, the bottom interface between perovskite and the electron-transporting layer is critical in determining its efficiency and reliability. High defect concentrations and crystalline film fracturing at the bottom interface substantially reduce the efficiency and operational stability. In this work, a liquid crystal elastomer interlayer is intercalated into a flexible device with the charge transfer channel toughened by the aligned mesogenic assembly. The molecular ordering is instantly locked upon photopolymerization of liquid crystalline diacrylate monomers and dithiol-terminated oligomers. The optimized charge collection and the minimized charge recombination at the interface boost the efficiency up to 23.26% and 22.10% for rigid and flexible devices, respectively. The liquid crystal elastomer-induced suppression of phase segregation endows the unencapsulated device maintaining >80% of the initial efficiency for 1570 h. Moreover, the aligned elastomer interlayer preserves the configuration integrity with remarkable repeatability and mechanical robustness, which enables the flexible device to retain 86% of its original efficiency after 5000 bending cycles. The flexible solar cell chips are further integrated into a wearable haptic device with microneedle-based arrays of sensors to demonstrate a pain sensation system in virtual reality.
TGFβ-mediated MMP13 secretion drives myoepithelial cell dependent breast cancer progression
Authors: Gibson Shayin V. , Tomas Bort Elena , Rodríguez-Fernández Lucía , Allen Michael D. , Gomm Jennifer J. , Goulding Iain , auf dem Keller Ulrich , Agnoletto Andrea , Brisken Cathrin , Peck Barrie , Cameron Angus J. , Marshall John F. , Jones J. Louise , Carter Edward P. , Grose Richard P. 
Published: March 2023

AbstractDuctal carcinoma in situ (DCIS) is a non-obligate precursor of invasive breast cancer. Virtually all women with DCIS are treated, despite evidence suggesting up to half would remain with stable, non-threatening, disease. Overtreatment thus presents a pressing issue in DCIS management. To understand the role of the normally tumour suppressive myoepithelial cell in disease progression we present a 3D in vitro model incorporating both luminal and myoepithelial cells in physiomimetic conditions. We demonstrate that DCIS-associated myoepithelial cells promote striking myoepithelial-led invasion of luminal cells, mediated by the collagenase MMP13 through a non-canonical TGFβ – EP300 pathway. In vivo, MMP13 expression is associated with stromal invasion in a murine model of DCIS progression and is elevated in myoepithelial cells of clinical high-grade DCIS cases. Our data identify a key role for myoepithelial-derived MMP13 in facilitating DCIS progression and point the way towards a robust marker for risk stratification in DCIS patients.
LRRK2 and GBA1 variant carriers have higher urinary bis(monacylglycerol) phosphate concentrations in PPMI cohorts
Authors: Merchant Kalpana M. , Simuni Tanya , Fedler Janel , Caspell-Garcia Chelsea , Brumm Michael , Nudelman Kelly N. H. , Tengstrandt Elizabeth , Hsieh Frank , Alcalay Roy N. , Coffey Christopher , Chahine Lana , Foroud Tatiana , Singleton Andrew , Weintraub Daniel , Hutten Samantha , Sherer Todd , Mollenhauer Brit , Siderowf Andrew , Tanner Caroline , Marek Ken ,   the Parkinson’s Progression Markers Initiative
Published: March 2023

AbstractWe quantified concentrations of three isoforms of the endolysosomal lipid, bis(monoacylglycerol) phosphate (BMP) in the urine of deeply phenotyped cohorts in the Parkinson’s Progression Markers Initiative: LRRK2 G2019S PD (N = 134) and non-manifesting carriers (NMC) (G2019S+ NMC; N = 182), LRRK2 R1441G PD (N = 15) and R1441G+ NMC (N = 15), GBA1 N409S PD (N = 76) and N409S+ NMC (N = 178), sporadic PD (sPD, N = 379) and healthy controls (HC) (N = 190). The effects of each mutation and disease status were analyzed using nonparametric methods. Longitudinal changes in BMP levels were analyzed using linear mixed models. At baseline, all LRRK2 carriers had 3–7× higher BMP levels compared to HC, irrespective of the disease status. GBA1 N409S carriers also showed significant, albeit smaller, elevation (~30–40%) in BMP levels compared to HC. In LRRK2 G2019S PD, urinary BMP levels remained stable over two years. Furthermore, baseline BMP levels did not predict disease progression as measured by striatal DaT imaging, MDS-UPDRS III Off, or MoCA in any of the cohorts. These data support the utility of BMP as a target modulation biomarker in therapeutic trials of genetic and sPD but not as a prognostic or disease progression biomarker.
Glycolysis-enhancing α1-adrenergic antagonists modify cognitive symptoms related to Parkinson’s disease
Authors: Weber Matthew A. , Sivakumar Kartik , Tabakovic Ervina E. , Oya Mayu , Aldridge Georgina M. , Zhang Qiang , Simmering Jacob E. , Narayanan Nandakumar S. 
Published: March 2023

AbstractTerazosin is an α1-adrenergic receptor antagonist that enhances glycolysis and increases cellular ATP by binding to the enzyme phosphoglycerate kinase 1 (PGK1). Recent work has shown that terazosin is protective against motor dysfunction in rodent models of Parkinson’s disease (PD) and is associated with slowed motor symptom progression in PD patients. However, PD is also characterized by profound cognitive symptoms. We tested the hypothesis that terazosin protects against cognitive symptoms associated with PD. We report two main results. First, in rodents with ventral tegmental area (VTA) dopamine depletion modeling aspects of PD-related cognitive dysfunction, we found that terazosin preserved cognitive function. Second, we found that after matching for demographics, comorbidities, and disease duration, PD patients newly started on terazosin, alfuzosin, or doxazosin had a lower hazard of being diagnosed with dementia compared to tamsulosin, an α1-adrenergic receptor antagonist that does not enhance glycolysis. Together, these findings suggest that in addition to slowing motor symptom progression, glycolysis-enhancing drugs protect against cognitive symptoms of PD.
Romanian young adult perceptions on using heated tobacco products following exposure to direct marketing methods
Authors: Chirila Sergiu , Antohe Adriana , Isar Cristina , Panaitescu Catalina , Malpass Alice 
Published: March 2023

AbstractHeated tobacco products have a rapid uptake, especially among young people, mostly where advertising is unregulated, as is the case in Romania. This qualitative study explores the influence of direct marketing methods of heated tobacco products on young people, their perception and behaviour towards smoking. We have carried out 19 interviews with smokers of heated tobacco products (HTPs) or/and combustible cigarettes (CCs) or non-smokers (NS), aged 18–26. Using the thematic analysis, we have identified three overarching themes: (1) people, places, and subjects of marketing, (2) engagement with risk narratives and (3) social body, family bonds, and autonomous self. Even if most of the participants have been exposed to a mix of marketing methods, they did not acknowledge the influence that marketing has on their decision to experience smoking. Young adults’ decision to use heated tobacco products seems to be influenced by a cluster of reasons: overcoming the legislation gap which prohibits indoor use of combustible cigarettes but not heated tobacco products; the attractivity of the product (novelty, inviting appearance, technological appeal and price) and presumed less damaging effects on health.
Experimental metrology beyond the standard quantum limit for a wide resources range
Authors: Cimini Valeria , Polino Emanuele , Belliardo Federico , Hoch Francesco , Piccirillo Bruno , Spagnolo Nicolò , Giovannetti Vittorio , Sciarrino Fabio 
Published: March 2023

AbstractAdopting quantum resources for parameter estimation discloses the possibility to realize quantum sensors operating at a sensitivity beyond the standard quantum limit. Such an approach promises to reach the fundamental Heisenberg scaling as a function of the employed resources N in the estimation process. Although previous experiments demonstrated precision scaling approaching Heisenberg-limited performances, reaching such a regime for a wide range of N remains hard to accomplish. Here, we show a method that suitably allocates the available resources permitting them to reach the same power law of Heisenberg scaling without any prior information on the parameter. We demonstrate experimentally such an advantage in measuring a rotation angle. We quantitatively verify sub-standard quantum limit performances for a considerable range of N (O(30,000)) by using single-photon states with high-order orbital angular momentum, achieving an error reduction, in terms of the obtained variance, >10 dB below the standard quantum limit. Such results can be applied to different scenarios, opening the way to the optimization of resources in quantum sensing.
Enhanced star formation through the high-temperature formation of H2 on carbonaceous dust grains
Authors: Grieco Francesco , Theulé Patrice , De Looze Ilse , Dulieu François 
Published: March 2023

AbstractThe microphysics of molecular hydrogen formation has an influence on galactic-scale star-formation rates over cosmic time. H2 is the cooling agent needed to initiate the cloud collapse regulating the star-formation efficiency. H2 formation is inefficient in the gas phase under typical interstellar conditions, requiring dust grain surfaces to act as catalysts. Small carbonaceous grains with sizes from roughly 4 to 100–200 Å, including polycyclic aromatic hydrocarbons (PAHs), have been shown to increase the H2 formation rates due to their large surface-to-volume ratios. H2 formation rates on PAHs were previously thought to reduce above temperatures of 50 K and H atom recombination was believed to be highly efficient only below 20 K. Until now, both laboratory experiments and theoretical modelling have suggested that H2 cannot form on grains with temperatures above 100 K. Here we report evidence, through direct laboratory measurements, of the highly efficient formation of H2 at temperatures up to 250 K on carbonaceous surfaces mimicking interstellar dust. By pushing their formation towards warmer temperatures, the H2 molecules could start contributing substantially to the cooling of warmer gas (temperatures of roughly 50–250 K). This will have a marked impact on our understanding of H2 formation in nearby galaxies and its efficiency in high-redshift galaxies where the Cosmic Microwave Background already pushes dust temperatures to more than 20 K.
The impact of satellite trails on Hubble Space Telescope observations
Authors: Kruk Sandor , García-Martín Pablo , Popescu Marcel , Aussel Ben , Dillmann Steven , Perks Megan E. , Lund Tamina , Merín Bruno , Thomson Ross , Karadag Samet , McCaughrean Mark J. 
Published: March 2023

AbstractThe recent launch of low Earth orbit satellite constellations is creating a growing threat for astronomical observations with ground-based telescopes1–10 that has alarmed the astronomical community 11–16. Observations affected by artificial satellites can become unusable for scientific research, wasting a growing fraction of the research budget on costly infrastructures and mitigation efforts. Here we report the first measurements, to our knowledge, of artificial satellite contamination on observations from a low Earth orbit made with the Hubble Space Telescope. With the help of volunteers on a citizen science project (www.asteroidhunter.org) and a deep learning algorithm, we scanned the archive of Hubble Space Telescope images taken between 2002 and 2021. We find that a fraction of 2.7% of the individual exposures with a typical exposure time of 11 minutes are crossed by satellites and that the fraction of satellite trails in the images increases with time. This fraction depends on the size of the field of view, exposure time, filter used and pointing. With the growing number of artificial satellites currently planned, the fraction of Hubble Space Telescope images crossed by satellites will increase in the next decade and will need further close study and monitoring.
Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet
Authors: Yan Haidong , Sun Min , Zhang Zhongren , Jin Yarong , Zhang Ailing , Lin Chuang , Wu Bingchao , He Min , Xu Bin , Wang Jing , Qin Peng , Mendieta John Pablo , Nie Gang , Wang Jianping , Jones Chris S. , Feng Guangyan , Srivastava Rakesh K. , Zhang Xinquan , Bombarely Aureliano , Luo Dan , Jin Long , Peng Yuanying , Wang Xiaoshan , Ji Yang , Tian Shilin , Huang Linkai 
Published: March 2023

AbstractPearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.