bluuebunny/crossref_metadata_2025_split huggingface dataset:
A computational framework for resolving the microbiome diversity conundrum
Authors: Daybog Itay , Kolodny Oren 
Published: December 2023

AbstractRecent empirical studies offer conflicting findings regarding the relation between host fitness and the composition of its microbiome, a conflict which we term ‘the microbial β- diversity conundrum’. The microbiome is crucial for host wellbeing and survival. Surprisingly, different healthy individuals’ microbiome compositions, even in the same population, often differ dramatically, contrary to the notion that a vital trait should be highly conserved. Moreover, gnotobiotic individuals exhibit highly deleterious phenotypes, supporting the view that the microbiome is paramount to host fitness. However, the introduction of almost arbitrarily selected microbiota into the system often achieves a significant rescue effect of the deleterious phenotypes. This is true even for microbiota from soil or phylogenetically distant host species, highlighting an apparent paradox. We suggest several solutions to the paradox using a computational framework, simulating the population dynamics of hosts and their microbiomes over multiple generations. The answers invoke factors such as host population size, the specific mode of microbial contribution to host fitness, and typical microbiome richness, offering solutions to the conundrum by highlighting scenarios where even when a host’s fitness is determined in full by its microbiome composition, this composition has little effect on the natural selection dynamics of the population.
Enhanced TARP-γ8-PSD-95 coupling in excitatory neurons contributes to the rapid antidepressant-like action of ketamine in male mice
Authors: Xue Shi-Ge , He Jin-Gang , Lu Ling-Li , Song Shi-Jie , Chen Mei-Mei , Wang Fang , Chen Jian-Guo 
Published: December 2023

AbstractKetamine produces rapid antidepressant effects at sub-anesthetic dosage through early and sustained activation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), however, the exact molecular mechanism still remains unclear. Transmembrane AMPAR regulatory protein-γ8 (TARP-γ8) is identified as one of AMPAR auxiliary subunits, which controls assemblies, surface trafficking and gating of AMPARs. Here, we show that ketamine rescues both depressive-like behaviors and the decreased AMPARs-mediated neurotransmission by recruitment of TARP-γ8 at the postsynaptic sites in the ventral hippocampus of stressed male mice. Furthermore, the rapid antidepressant effects of ketamine are abolished by selective blockade of TARP-γ8-containing AMPAR or uncoupling of TARP-γ8 from PSD-95. Overexpression of TARP-γ8 reverses chronic stress-induced depressive-like behaviors and attenuation of AMPARs-mediated neurotransmission. Conversely, knockdown of TARP-γ8 in excitatory neurons prevents the rapid antidepressant effects of ketamine.
Sharp zero-phonon lines of single organic molecules on a hexagonal boron-nitride surface
Authors: Smit Robert , Tebyani Arash , Hameury Jil , van der Molen Sense Jan , Orrit Michel 
Published: December 2023

AbstractSingle fluorescent molecules embedded in the bulk of host crystals have proven to be sensitive probes of the dynamics in their nano environment, thanks to their narrow (about 30–50 MHz or 0.1–0.2 μeV) optical linewidth of the 0-0 zero-phonon line (0-0 ZPL) at cryogenic temperatures. However, the optical linewidths of the 0-0 ZPL have been found to increase dramatically as the single molecules are located closer to a surface or interface, while no 0-0 ZPL has been detected for single molecules on any surface. Here we study single terrylene molecules adsorbed on the surface of hexagonal boron-nitride (hBN) substrates. Our low-temperature results show that it is possible to observe the 0-0 ZPL of fluorescent molecules on a surface. We compare our results for molecules deposited on the surfaces of annealed and non-annealed hBN flakes and we see a marked improvement in the spectral stability of the emitters after annealing.
Accurate de novo peptide sequencing using fully convolutional neural networks
Authors: Liu Kaiyuan , Ye Yuzhen , Li Sujun , Tang Haixu 
Published: December 2023

AbstractDe novo peptide sequencing, which does not rely on a comprehensive target sequence database, provides us with a way to identify novel peptides from tandem mass spectra. However, current de novo sequencing algorithms suffer from low accuracy and coverage, which hinders their application in proteomics. In this paper, we present PepNet, a fully convolutional neural network for high accuracy de novo peptide sequencing. PepNet takes an MS/MS spectrum (represented as a high-dimensional vector) as input, and outputs the optimal peptide sequence along with its confidence score. The PepNet model is trained using a total of 3 million high-energy collisional dissociation MS/MS spectra from multiple human peptide spectral libraries. Evaluation results show that PepNet significantly outperforms current best-performing de novo sequencing algorithms (e.g. PointNovo and DeepNovo) in both peptide-level accuracy and positional-level accuracy. PepNet can sequence a large fraction of spectra that were not identified by database search engines, and thus could be used as a complementary tool to database search engines for peptide identification in proteomics. In addition, PepNet runs around 3x and 7x faster than PointNovo and DeepNovo on GPUs, respectively, thus being more suitable for the analysis of large-scale proteomics data.
Targeted mutagenesis of the herpesvirus fusogen central helix captures transition states
Authors: Zhou Momei , Vollmer Benjamin , Machala Emily , Chen Muyuan , Grünewald Kay , Arvin Ann M. , Chiu Wah , Oliver Stefan L. 
Published: December 2023

AbstractHerpesviruses remain a burden for animal and human health, including the medically important varicella-zoster virus (VZV). Membrane fusion mediated by conserved core glycoproteins, the fusogen gB and the heterodimer gH-gL, enables herpesvirus cell entry. The ectodomain of gB orthologs has five domains and is proposed to transition from a prefusion to postfusion conformation but the functional relevance of the domains for this transition remains poorly defined. Here we describe structure-function studies of the VZV gB DIII central helix targeting residues 526EHV528. Critically, a H527P mutation captures gB in a prefusion conformation as determined by cryo-EM, a loss of membrane fusion in a virus free assay, and failure of recombinant VZV to spread in cell monolayers. Importantly, two predominant cryo-EM structures of gB[H527P] are identified by 3D classification and focused refinement, suggesting they represented gB conformations in transition. These studies reveal gB DIII as a critical element for herpesvirus gB fusion function.
Multi-step nucleation pathway of C-S-H during cement hydration from atomistic simulations
Authors: Aretxabaleta Xabier M. , López-Zorrilla Jon , Etxebarria Iñigo , Manzano Hegoi 
Published: December 2023

AbstractThe Calcium Silicate Hydrate (C-S-H) nucleation is a crucial step during cement hydration and determines to a great extent the rheology, microstructure, and properties of the cement paste. Recent evidence indicates that the C-S-H nucleation involves at least two steps, yet the underlying atomic scale mechanism, the nature of the primary particles and their stability, or how they merge/aggregate to form larger structures is unknown. In this work, we use atomistic simulation methods, specifically DFT, evolutionary algorithms (EA), and Molecular Dynamics (MD), to investigate the structure and formation of C-S-H primary particles (PPs) from the ions in solution, and then discuss a possible formation pathway for the C-S-H nucleation. Our simulations indicate that even for small sizes the most stable clusters encode C-S-H structural motifs, and we identified a C4S4H2 cluster candidate to be the C-S-H basic building block. We suggest a formation path in which small clusters formed by silicate dimers merge into large elongated aggregates. Upon dehydration, the C-S-H basic building blocks can be formed within the aggregates, and eventually crystallize.
A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers
Authors: Wranik Maximilian , Kepa Michal W. , Beale Emma V. , James Daniel , Bertrand Quentin , Weinert Tobias , Furrer Antonia , Glover Hannah , Gashi Dardan , Carrillo Melissa , Kondo Yasushi , Stipp Robin T. , Khusainov Georgii , Nass Karol , Ozerov Dmitry , Cirelli Claudio , Johnson Philip J. M. , Dworkowski Florian , Beale John H. , Stubbs Scott , Zamofing Thierry , Schneider Marco , Krauskopf Kristina , Gao Li , Thorn-Seshold Oliver , Bostedt Christoph , Bacellar Camila , Steinmetz Michel O. , Milne Christopher , Standfuss Jörg 
Published: December 2023

AbstractSerial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.
Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone
Authors: Nam Donggeon , Bacik John-Paul , Khade Rahul L. , Aguilera Maria Camila , Wei Yang , Villada Juan D. , Neidig Michael L. , Zhang Yong , Ando Nozomi , Fasan Rudi 
Published: December 2023

AbstractHemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.
Diversification of division mechanisms in endospore-forming bacteria revealed by analyses of peptidoglycan synthesis in Clostridioides difficile
Authors: Shrestha Shailab , Taib Najwa , Gribaldo Simonetta , Shen Aimee 
Published: December 2023

AbstractThe bacterial enzymes FtsW and FtsI, encoded in the highly conserved dcw gene cluster, are considered to be universally essential for the synthesis of septal peptidoglycan (PG) during cell division. Here, we show that the pathogen Clostridioides difficile lacks a canonical FtsW/FtsI pair, and its dcw-encoded PG synthases have undergone a specialization to fulfill sporulation-specific roles, including synthesizing septal PG during the sporulation-specific mode of cell division. Although these enzymes are directly regulated by canonical divisome components during this process, dcw-encoded PG synthases and their divisome regulators are dispensable for cell division during normal growth. Instead, C. difficile uses a bifunctional class A penicillin-binding protein as the core divisome PG synthase, revealing a previously unreported role for this class of enzymes. Our findings support that the emergence of endosporulation in the Firmicutes phylum facilitated the functional repurposing of cell division factors. Moreover, they indicate that C. difficile, and likely other clostridia, assemble a distinct divisome that therefore may represent a unique target for therapeutic interventions.
Operando analysis of a solid oxide fuel cell by environmental transmission electron microscopy
Authors: Jeangros Q. , Bugnet M. , Epicier T. , Frantz C. , Diethelm S. , Montinaro D. , Tyukalova E. , Pivak Y. , Van herle J. , Hessler-Wyser A. , Duchamp M. 
Published: December 2023

AbstractCorrelating the microstructure of an energy conversion device to its performance is often a complex exercise, notably in solid oxide fuel cell research. Solid oxide fuel cells combine multiple materials and interfaces that evolve in time due to high operating temperatures and reactive atmospheres. We demonstrate here that operando environmental transmission electron microscopy can identify structure-property links in such devices. By contacting a cathode-electrolyte-anode cell to a heating and biasing microelectromechanical system in a single-chamber configuration, a direct correlation is found between the environmental conditions (oxygen and hydrogen partial pressures, temperature), the cell open circuit voltage, and the microstructural evolution of the fuel cell, down to the atomic scale. The results shed important insights into the impact of the anode oxidation state and its morphology on the cell electrical properties.
Assembly mechanism of the inflammasome sensor AIM2 revealed by single molecule analysis
Authors: Sharma Meenakshi , de Alba Eva 
Published: December 2023

AbstractPathogenic dsDNA prompts AIM2 assembly leading to the formation of the inflammasome, a multimeric complex that triggers the inflammatory response. The recognition of foreign dsDNA involves AIM2 self-assembly concomitant with dsDNA binding. However, we lack mechanistic and kinetic information on the formation and propagation of the assembly, which can shed light on innate immunity’s time response and specificity. Combining optical traps and confocal fluorescence microscopy, we determine here the association and dissociation rates of the AIM2-DNA complex at the single molecule level. We identify distinct mechanisms for oligomer growth via the binding of incoming AIM2 molecules to adjacent dsDNA or direct interaction with bound AIM2 assemblies, resembling primary and secondary nucleation. Through these mechanisms, the size of AIM2 oligomers can increase fourfold in seconds. Finally, our data indicate that single AIM2 molecules do not diffuse/scan along the DNA, suggesting that oligomerization depends on stochastic encounters with DNA and/or DNA-bound AIM2.
Programmable de novo designed coiled coil-mediated phase separation in mammalian cells
Authors: Ramšak Maruša , Ramirez Dominique A. , Hough Loren E. , Shirts Michael R. , Vidmar Sara , Eleršič Filipič Kristina , Anderluh Gregor , Jerala Roman 
Published: December 2023

AbstractMembraneless liquid compartments based on phase-separating biopolymers have been observed in diverse cell types and attributed to weak multivalent interactions predominantly based on intrinsically disordered domains. The design of liquid-liquid phase separated (LLPS) condensates based on de novo designed tunable modules that interact in a well-understood, controllable manner could improve our understanding of this phenomenon and enable the introduction of new features. Here we report the construction of CC-LLPS in mammalian cells, based on designed coiled-coil (CC) dimer-forming modules, where the stability of CC pairs, their number, linkers, and sequential arrangement govern the transition between diffuse, liquid and immobile condensates and are corroborated by coarse-grained molecular simulations. Through modular design, we achieve multiple coexisting condensates, chemical regulation of LLPS, condensate fusion, formation from either one or two polypeptide components or LLPS regulation by a third polypeptide chain. These findings provide further insights into the principles underlying LLPS formation and a design platform for controlling biological processes.
Colliding heavy nuclei take multiple identities on the path to fusion
Authors: Cook Kaitlin J. , Rafferty Dominic C. , Hinde David J. , Simpson Edward C. , Dasgupta Mahananda , Corradi Lorenzo , Evers Maurits , Fioretto Enrico , Jeung Dongyun , Lobanov Nikolai , Luong Duc Huy , Mijatović Tea , Montagnoli Giovanna , Stefanini Alberto M. , Szilner Suzana 
Published: December 2023

AbstractThe properties of superheavy elements probe extremes of physics and chemistry. They are synthesised at accelerator laboratories using nuclear fusion, where two atomic nuclei collide, stick together (capture), then with low probability evolve to a compact superheavy nucleus. The fundamental microscopic mechanisms controlling fusion are not fully understood, limiting predictive capability. Even capture, considered to be the simplest stage of fusion, is not matched by models. Here we show that collisions of 40Ca with 208Pb, experience an ‘explosion’ of mass and charge transfers between the nuclei before capture, with unexpectedly high probability and complexity. Ninety different partitions of the protons and neutrons between the projectile-like and target-like nuclei are observed. Since each is expected to have a different probability of fusion, the early stages of collisions may be crucial in superheavy element synthesis. Our interpretation challenges the current view of fusion, explains both the successes and failures of current capture models, and provides a framework for improved models.
Single-crystal ZrCo nanoparticle for advanced hydrogen and H-isotope storage
Authors: Li Zhenyang , Liu Shiyuan , Pu Yanhui , Huang Gang , Yuan Yingbo , Zhu Ruiqi , Li Xufeng , Chen Chunyan , Deng Gao , Zou Haihan , Yi Peng , Fang Ming , Sun Xin , He Junzhe , Cai He , Shang Jiaxiang , Liu Xiaofang , Yu Ronghai , Shui Jianglan 
Published: December 2023

AbstractHydrogen-isotope storage materials are essential for the controlled nuclear fusion. However, the currently used smelting-ZrCo alloy suffers from rapid degradation of performance due to severe disproportionation. Here, we reveal a defect-derived disproportionation mechanism and report a nano-single-crystal strategy to solve ZrCo’s problems. Single-crystal nano-ZrCo is synthesized by a wet-chemistry method and exhibits excellent comprehensive hydrogen-isotope storage performances, including ultrafast uptake/release kinetics, high anti-disproportionation ability, and stable cycling, far superior to conventional smelting-ZrCo. Especially, a further incorporation of Ti into nano-ZrCo can almost suppress the disproportionation reaction. Moreover, a mathematical relationship between dehydrogenation temperature and ZrCo particle size is established. Additionally, a microwave method capable of nondestructively detecting the hydrogen storage state of ZrCo is developed. The proposed disproportionation mechanism and anti-disproportionation strategy will be instructive for other materials with similar problems.
Precise synthesis and photovoltaic properties of giant molecule acceptors
Authors: Zhuo Hongmei , Li Xiaojun , Zhang Jinyuan , Zhu Can , He Haozhe , Ding Kan , Li Jing , Meng Lei , Ade Harald , Li Yongfang 
Published: December 2023

AbstractSeries of giant molecule acceptors DY, TY and QY with two, three and four small molecule acceptor subunits are synthesized by a stepwise synthetic method and used for systematically investigating the influence of subunit numbers on the structure-property relationship from small molecule acceptor YDT to giant molecule acceptors and to polymerized small molecule acceptor PY-IT. Among these acceptors-based devices, the TY-based film shows proper donor/acceptor phase separation, higher charge transfer state yield and longer charge transfer state lifetime. Combining with the highest electron mobility, more efficient exciton dissociation and lower charge carrier recombination properties, the TY-based device exhibits the highest power conversion efficiency of 16.32%. These results indicate that the subunit number in these acceptors has significant influence on their photovoltaic properties. This stepwise synthetic method of giant molecule acceptors will be beneficial to diversify their structures and promote their applications in high-efficiency and stable organic solar cells.
Synthesizing evidence for the external cycling of NOx in high- to low-NOx atmospheres
Authors: Ye Chunxiang , Zhou Xianliang , Zhang Yingjie , Wang Youfeng , Wang Jianshu , Zhang Chong , Woodward-Massey Robert , Cantrell Christopher , Mauldin Roy L. , Campos Teresa , Hornbrook Rebecca S. , Ortega John , Apel Eric C. , Haggerty Julie , Hall Samuel , Ullmann Kirk , Weinheimer Andrew , Stutz Jochen , Karl Thomas , Smith James N. , Guenther Alex , Song Shaojie 
Published: December 2023

AbstractExternal cycling regenerating nitrogen oxides (NOx ≡ NO + NO2) from their oxidative reservoir, NOz, is proposed to reshape the temporal–spatial distribution of NOx and consequently hydroxyl radical (OH), the most important oxidant in the atmosphere. Here we verify the in situ external cycling of NOx in various environments with nitrous acid (HONO) as an intermediate based on synthesized field evidence collected onboard aircraft platform at daytime. External cycling helps to reconcile stubborn underestimation on observed ratios of HONO/NO2 and NO2/NOz by current chemical model schemes and rationalize atypical diurnal concentration profiles of HONO and NO2 lacking noontime valleys specially observed in low-NOx atmospheres. Perturbation on the budget of HONO and NOx by external cycling is also found to increase as NOx concentration decreases. Consequently, model underestimation of OH observations by up to 41% in low NOx atmospheres is attributed to the omission of external cycling in models.
Potential window alignment regulating ion transfer in faradaic junctions for efficient photoelectrocatalysis
Authors: Dong Hongzheng , Pan Xiangyu , Gong Yuancai , Xue Mengfan , Wang Pin , Ho-Kimura SocMan , Yao Yingfang , Xin Hao , Luo Wenjun , Zou Zhigang 
Published: December 2023

AbstractIn the past decades, a band alignment theory has become a basis for designing different high-performance semiconductor devices, such as photocatalysis, photoelectrocatalysis, photoelectrostorage and third-generation photovoltaics. Recently, a faradaic junction model (coupled electron and ion transfer) has been proposed to explain charge transfer phenomena in these semiconductor heterojunctions. However, the classic band alignment theory cannot explain coupled electron and ion transfer processes because it only regulates electron transfer. Therefore, it is very significant to explore a suitable design concept for regulating coupled electron and ion transfer in order to improve the performance of semiconductor heterojunctions. Herein, we propose a potential window alignment theory for regulating ion transfer and remarkably improving the photoelectrocatalytic performance of a MoS2/Cd-Cu2ZnSnS4 heterojunction photocathode. Moreover, we find that a faradaic potential window, rather than the band position of the intermediate layer, is a criterion for identifying interface charge transfer direction. This finding can offer different perspectives for designing high-performance semiconductor heterojunctions with suitable potential windows for solar energy conversion and storage.