bluuebunny/crossref_metadata_2025_split huggingface dataset:
CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper
Authors: Orlov Igor , Roche Stéphane , Brasilès Sandrine , Lukoyanova Natalya , Vaney Marie-Christine , Tavares Paulo , Orlova Elena V. 
Published: November 2022

AbstractNumerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 (gp612gp1512gp166) in the post-DNA packaging state at 2.7 Å resolution obtained by single particle cryo-electron microscopy. Comparison of the native SPP1 complex with assembly-naïve structures of individual components uncovered the complex program of conformational changes leading to its assembly. After DNA packaging, gp15 binds via its C-terminus to the gp6 oligomer positioning gp15 subunits for oligomerization. Gp15 refolds its inner loops creating an intersubunit β-barrel that establishes different types of contacts with six gp16 subunits. Gp16 binding and oligomerization is accompanied by folding of helices that close the portal channel to keep the viral genome inside the capsid. This mechanism of assembly has broad functional and evolutionary implications for viruses of the prokaryotic tailed viruses-herpesviruses lineage.
Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1
Authors: Hirano Rina , Ehara Haruhiko , Kujirai Tomoya , Uejima Tamami , Takizawa Yoshimasa , Sekine Shun-ichi , Kurumizaka Hitoshi 
Published: November 2022

AbstractIn chromatin, linker histone H1 binds to nucleosomes, forming chromatosomes, and changes the transcription status. However, the mechanism by which RNA polymerase II (RNAPII) transcribes the DNA in the chromatosome has remained enigmatic. Here we report the cryo-electron microscopy (cryo-EM) structures of transcribing RNAPII-chromatosome complexes (forms I and II), in which RNAPII is paused at the entry linker DNA region of the chromatosome due to H1 binding. In the form I complex, the H1 bound to the nucleosome restricts the linker DNA orientation, and the exit linker DNA is captured by the RNAPII DNA binding cleft. In the form II complex, the RNAPII progresses a few bases ahead by releasing the exit linker DNA from the RNAPII cleft, and directly clashes with the H1 bound to the nucleosome. The transcription elongation factor Spt4/5 masks the RNAPII DNA binding region, and drastically reduces the H1-mediated RNAPII pausing.
Creb5 coordinates synovial joint formation with the genesis of articular cartilage
Authors: Zhang Cheng-Hai , Gao Yao , Hung Han-Hwa , Zhuo Zhu , Grodzinsky Alan J. , Lassar Andrew B. 
Published: November 2022

AbstractWhile prior work has established that articular cartilage arises from Prg4-expressing perichondrial cells, it is not clear how this process is specifically restricted to the perichondrium of synovial joints. We document that the transcription factor Creb5 is necessary to initiate the expression of signaling molecules that both direct the formation of synovial joints and guide perichondrial tissue to form articular cartilage instead of bone. Creb5 promotes the generation of articular chondrocytes from perichondrial precursors in part by inducing expression of signaling molecules that block a Wnt5a autoregulatory loop in the perichondrium. Postnatal deletion of Creb5 in the articular cartilage leads to loss of both flat superficial zone articular chondrocytes coupled with a loss of both Prg4 and Wif1 expression in the articular cartilage; and a non-cell autonomous up-regulation of Ctgf. Our findings indicate that Creb5 promotes joint formation and the subsequent development of articular chondrocytes by driving the expression of signaling molecules that both specify the joint interzone and simultaneously inhibit a Wnt5a positive-feedback loop in the perichondrium.
Persistent high latitude amplification of the Pacific Ocean over the past 10 million years
Authors: Liu Xiaoqing , Huber Matthew , Foster Gavin L. , Dessler Andrew , Zhang Yi Ge 
Published: November 2022

AbstractWhile high latitude amplification is seen in modern observations, paleoclimate records, and climate modeling, better constraints on the magnitude and pattern of amplification would provide insights into the mechanisms that drive it, which remain actively debated. Here we present multi-proxy multi-site paleotemperature records over the last 10 million years from the Western Pacific Warm Pool (WPWP) – the warmest endmember of the global ocean that is uniquely important in the global radiative feedback change. These sea surface temperature records, based on lipid biomarkers and seawater Mg/Ca-adjusted foraminiferal Mg/Ca, unequivocally show warmer WPWP in the past, and a secular cooling over the last 10 million years. Compiling these data with existing records reveals a persistent, nearly stationary, extratropical response pattern in the Pacific in which high latitude (~50°N) temperatures increase by ~2.4° for each degree of WPWP warming. This relative warming pattern is also evident in model outputs of millennium-long climate simulations with quadrupling atmospheric CO2, therefore providing a strong constraint on the future equilibrium response of the Earth System.
A diverse Ediacara assemblage survived under low-oxygen conditions
Authors: Cherry Lucas B. , Gilleaudeau Geoffrey J. , Grazhdankin Dmitriy V. , Romaniello Stephen J. , Martin Aaron J. , Kaufman Alan J. 
Published: November 2022

AbstractThe Ediacaran biota were soft-bodied organisms, many with enigmatic phylogenetic placement and ecology, living in marine environments between 574 and 539 million years ago. Some studies hypothesize a metazoan affinity and aerobic metabolism for these taxa, whereas others propose a fundamentally separate taxonomic grouping and a reliance on chemoautotrophy. To distinguish between these hypotheses and test the redox-sensitivity of Ediacaran organisms, here we present a high-resolution local and global redox dataset from carbonates that contain in situ Ediacaran fossils from Siberia. Cerium anomalies are consistently >1, indicating that local environments, where a diverse Ediacaran assemblage is preserved in situ as nodules and carbonaceous compressions, were pervasively anoxic. Additionally, δ238U values match other terminal Ediacaran sections, indicating widespread marine euxinia. These data suggest that some Ediacaran biotas were tolerant of at least intermittent anoxia, and thus had the capacity for a facultatively anaerobic lifestyle. Alternatively, these soft-bodied Ediacara organisms may have colonized the seafloor during brief oxygenation events not recorded by redox proxy data. Broad temporal correlations between carbon, sulfur, and uranium isotopes further highlight the dynamic redox landscape of Ediacaran-Cambrian evolutionary events.
Fast light-switchable polymeric carbon nitride membranes for tunable gas separation
Authors: Ashirov Timur , Siena Julya Stein , Zhang Mengru , Ozgur Yazaydin A. , Antonietti Markus , Coskun Ali 
Published: November 2022

AbstractSwitchable gas separation membranes are intriguing systems for regulating the transport properties of gases. However, existing stimuli-responsive gas separation membranes suffer from either very slow response times or require high energy input for switching to occur. Accordingly, herein, we introduced light-switchable polymeric carbon nitride (pCN) gas separation membranes with fast response times prepared from melamine precursor through in-situ formation and deposition of pCN onto a porous support using chemical vapor deposition. Our systematic analysis revealed that the gas transport behavior upon light irradiation is fully governed by the polarizability of the permeating gas and its interaction with the charged pCN surface, and can be easily tuned either by controlling the power of the light and/or the duration of irradiation. We also demonstrated that gases with higher polarizabilities such as CO2 can be separated from gases with lower polarizability like H2 and He effectively with more than 22% increase in the gas/CO2 selectivity upon light irradiation. The membranes also exhibited fast response times (<1 s) and can be turned “on” and “off” using a single light source at 550 nm.
Arginine-modified black phosphorus quantum dots with dual excited states for enhanced electrochemiluminescence in bioanalysis
Authors: Yu Siqi , Du Yu , Niu Xianghong , Li Guangming , Zhu Da , Yu Qian , Zou Guizheng , Ju Huangxian 
Published: November 2022

AbstractThe electrochemiluminescence (ECL) is generally emitted via radiative transition of singlet or triplet excited state (S1 or T1). Herein, an ECL mechanism with the transitions of both S1 and T1 of black phosphorus quantum dots (BPQDs) is found, and an arginine (Arg) modification strategy is proposed to passivate the surface oxidation defects of BPQDs, which could modulate the excited states for enhancing the ECL efficiency of BPQDs. The Arg modification leads to greater spatial overlap of highest and lowest occupied molecular orbitals, and spectral shift of radiative transitions, and improves the stability of anion radical of BPQDs. To verify the application of the proposed mechanism, it is used to construct a sensitive method for conveniently evaluating the inhibiting efficiency of cyclo-arginine-glycine-aspartic acid-d-tyrosine-lysine to cell surface integrin by using Arg containing peptide modified BPQDs as signal tag. The dual excited states mediated ECL emitters provide a paradigm for adjustable ECL generation and extend the application of ECL analysis.
Chiral nanocrystals grown from MoS2 nanosheets enable photothermally modulated enantioselective release of antimicrobial drugs
Authors: Li Bang Lin , Luo Jun Jiang , Zou Hao Lin , Zhang Qing-Meng , Zhao Liu-Bin , Qian Hang , Luo Hong Qun , Leong David Tai , Li Nian Bing 
Published: November 2022

AbstractThe transfer of the concept of chirality from molecules to synthesized nanomaterials has attracted attention amongst multidisciplinary teams. Here we demonstrate heterogeneous nucleation and anisotropic accumulation of Au nanoparticles on multilayer MoS2 planes to form chiroptically functional nanomaterials. Thiol amino acids with chiral conformations modulate asymmetric growth of gold nanoarchitectures on seeds of highly faceted Au/MoS2 heterostructures. Consequently, dendritic plasmonic nanocrystals with partial chiral morphologies are synthesized. The chirality of dendritic nanocrystals inherited from cysteine molecules refers to the structural characteristics and includes specific recognition of enantiomeric molecules. With integration of the intrinsic photothermal properties and inherited enantioselective characteristics, dendritic Au/MoS2 heterostructures exhibit chirality-dependent release of antimicrobial drugs from hydrogel substrates when activated by exogenous infrared irradiation. A three-in-one strategy involving synthesis of chiral dendritic heterostructures, enantioselective recognition, and controlled drug release system is presented, which improves nanomaterial synthetic technology and enhances our understanding of crucial chirality information.
Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase
Authors: King Edward , Maxel Sarah , Zhang Yulai , Kenney Karissa C. , Cui Youtian , Luu Emma , Siegel Justin B. , Weiss Gregory A. , Luo Ray , Li Han 
Published: November 2022

AbstractNoncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN+) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN+-based reducing power. This is based on an orthogonal, NMN+-dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN+. With a throughput of >106 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme’s global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme’s access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.
Dynamic complex opto-magnetic holography
Authors: Makowski M. , Bomba J. , Frej A. , Kolodziejczyk M. , Sypek M. , Shimobaba T. , Ito T. , Kirilyuk A. , Stupakiewicz A. 
Published: November 2022

AbstractDespite recent significant progress in real-time, large-area computer-generated holography, its memory requirements and computational loads will be hard to tackle for several decades to come with the current paradigm based on a priori calculations and bit-plane writing to a spatial light modulator. Here we experimentally demonstrate a holistic approach to serial computation and repeatable writing of computer-generated dynamic holograms without Fourier transform, using minimal amounts of computer memory. We use the ultrafast opto-magnetic recording of holographic patterns in a ferrimagnetic film with femtosecond laser pulses, driven by the on-the-fly hardware computation of a single holographic point. The intensity-threshold nature of the magnetic medium allows sub-diffraction-limited, point-by-point toggling of arbitrarily localized magnetic spots on the sample, according to the proposed circular detour-phase encoding, providing complex modulation and symmetrical suppression of upper diffractive orders and conjugated terms in holographically reconstructed 3-D images.
Energy cascades in donor-acceptor exciton-polaritons observed by ultrafast two-dimensional white-light spectroscopy
Authors: Son Minjung , Armstrong Zachary T. , Allen Ryan T. , Dhavamani Abitha , Arnold Michael S. , Zanni Martin T. 
Published: November 2022

AbstractExciton-polaritons are hybrid states formed when molecular excitons are strongly coupled to photons trapped in an optical cavity. These systems exhibit many interesting, but not fully understood, phenomena. Here, we utilize ultrafast two-dimensional white-light spectroscopy to study donor-acceptor microcavities made from two different layers of semiconducting carbon nanotubes. We observe the delayed growth of a cross peak between the upper- and lower-polariton bands that is oftentimes obscured by Rabi contraction. We simulate the spectra and use Redfield theory to learn that energy cascades down a manifold of new electronic states created by intermolecular coupling and the two distinct bandgaps of the donor and acceptor. Energy most effectively enters the manifold when light-matter coupling is commensurate with the energy distribution of the manifold, contributing to long-range energy transfer. Our results broaden the understanding of energy transfer dynamics in exciton-polariton systems and provide evidence that long-range energy transfer benefits from moderately-coupled cavities.
Rad52’s DNA annealing activity drives template switching associated with restarted DNA replication
Authors: Kishkevich Anastasiya , Tamang Sanjeeta , Nguyen Michael O. , Oehler Judith , Bulmaga Elena , Andreadis Christos , Morrow Carl A. , Jalan Manisha , Osman Fekret , Whitby Matthew C. 
Published: November 2022

AbstractIt is thought that many of the simple and complex genomic rearrangements associated with congenital diseases and cancers stem from mistakes made during the restart of collapsed replication forks by recombination enzymes. It is hypothesised that this recombination-mediated restart process transitions from a relatively accurate initiation phase to a less accurate elongation phase characterised by extensive template switching between homologous, homeologous and microhomologous DNA sequences. Using an experimental system in fission yeast, where fork collapse is triggered by a site-specific replication barrier, we show that ectopic recombination, associated with the initiation of recombination-dependent replication (RDR), is driven mainly by the Rad51 recombinase, whereas template switching, during the elongation phase of RDR, relies more on DNA annealing by Rad52. This finding provides both evidence and a mechanistic basis for the transition hypothesis.
Chiral aldehyde-nickel dual catalysis enables asymmetric α−propargylation of amino acids and stereodivergent synthesis of NP25302
Authors: Zhu Fang , Li Chao-Xing , Wu Zhu-Lian , Cai Tian , Wen Wei , Guo Qi-Xiang 
Published: November 2022

AbstractThe combined catalytic systems derived from organocatalysts and transition metals exhibit powerful activation and stereoselective-control abilities in asymmetric catalysis. This work describes a highly efficient chiral aldehyde-nickel dual catalytic system and its application for the direct asymmetric α−propargylation reaction of amino acid esters with propargylic alcohol derivatives. Various structural diversity α,α−disubstituted non-proteinogenic α−amino acid esters are produced in good-to-excellent yields and enantioselectivities. Furthermore, a stereodivergent synthesis of natural product NP25302 is achieved, and a reasonable reaction mechanism is proposed to illustrate the observed stereoselectivity based on the results of control experiments, nonlinear effect investigation, and HRMS detection.
Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase
Authors: Ramírez Ana S. , de Capitani Mario , Pesciullesi Giorgio , Kowal Julia , Bloch Joël S. , Irobalieva Rossitza N. , Reymond Jean-Louis , Aebi Markus , Locher Kaspar P. 
Published: November 2022

AbstractOligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAc2Man9Glc3, from a dolichyl-pyrophosphate donor to acceptor sites in secretory proteins in the lumen of the endoplasmic reticulum. Precise recognition of the fully assembled glycan by OST is essential for the subsequent quality control steps of glycoprotein biosynthesis. However, the molecular basis of the OST-donor glycan interaction is unknown. Here we present cryo-EM structures of S. cerevisiae OST in distinct functional states. Our findings reveal that the terminal glucoses (Glc3) of a chemo-enzymatically generated donor glycan analog bind to a pocket formed by the non-catalytic subunits WBP1 and OST2. We further find that binding either donor or acceptor substrate leads to distinct primed states of OST, where subsequent binding of the other substrate triggers conformational changes required for catalysis. This alternate priming allows OST to efficiently process closely spaced N-glycosylation sites.
Increased fire activity under high atmospheric oxygen concentrations is compatible with the presence of forests
Authors: Vitali Rayanne , Belcher Claire M. , Kaplan Jed O. , Watson Andrew J. 
Published: November 2022

AbstractThroughout Earth’s history, the abundance of oxygen in our atmosphere has varied, but by how much remains debated. Previously, an upper limit for atmospheric oxygen has been bounded by assumptions made regarding the fire window: atmospheric oxygen concentrations higher than 30–40% would threaten the regeneration of forests in the present world. Here we have tested these assumptions by adapting a Dynamic Global Vegetation Model to run over high atmospheric oxygen concentrations. Our results show that whilst global tree cover is significantly reduced under high O2 concentrations, forests persist in the wettest parts of the low and high latitudes and fire is more dependent on fuel moisture than O2 levels. This implies that the effect of fire on suppressing global vegetation under high O2 may be lower than previously assumed and questions our understanding of the mechanisms involved in regulating the abundance of oxygen in our atmosphere, with moisture as a potentially important factor.
Aerobic oxidation of methane significantly reduces global diffusive methane emissions from shallow marine waters
Authors: Mao Shi-Hai , Zhang Hong-Hai , Zhuang Guang-Chao , Li Xiao-Jun , Liu Qiao , Zhou Zhen , Wang Wei-Lei , Li Chun-Yang , Lu Ke-Yu , Liu Xi-Ting , Montgomery Andrew , Joye Samantha B. , Zhang Yu-Zhong , Yang Gui-Peng 
Published: November 2022

AbstractMethane is supersaturated in surface seawater and shallow coastal waters dominate global ocean methane emissions to the atmosphere. Aerobic methane oxidation (MOx) can reduce atmospheric evasion, but the magnitude and control of MOx remain poorly understood. Here we investigate methane sources and fates in the East China Sea and map global MOx rates in shallow waters by training machine-learning models. We show methane is produced during methylphosphonate decomposition under phosphate-limiting conditions and sedimentary release is also source of methane. High MOx rates observed in these productive coastal waters are correlated with methanotrophic activity and biomass. By merging the measured MOx rates with methane concentrations and other variables from a global database, we predict MOx rates and estimate that half of methane, amounting to 1.8 ± 2.7 Tg, is consumed annually in near-shore waters (<50 m), suggesting that aerobic methanotrophy is an important sink that significantly constrains global methane emissions.
Plant genetic diversity affects multiple trophic levels and trophic interactions
Authors: Wan Nian-Feng , Fu Liwan , Dainese Matteo , Hu Yue-Qing , Pødenphant Kiær Lars , Isbell Forest , Scherber Christoph 
Published: November 2022

AbstractIntraspecific genetic diversity is an important component of biodiversity. A substantial body of evidence has demonstrated positive effects of plant genetic diversity on plant performance. However, it has remained unclear whether plant genetic diversity generally increases plant performance by reducing the pressure of plant antagonists across trophic levels for different plant life forms, ecosystems and climatic zones. Here, we analyse 4702 effect sizes reported in 413 studies that consider effects of plant genetic diversity on trophic groups and their interactions. We found that that increasing plant genetic diversity decreased the performance of plant antagonists including invertebrate herbivores, weeds, plant-feeding nematodes and plant diseases, while increasing the performance of plants and natural enemies of herbivores. Structural equation modelling indicated that plant genetic diversity increased plant performance partly by reducing plant antagonist pressure. These results reveal that plant genetic diversity often influences multiple trophic levels in ways that enhance natural pest control in managed ecosystems and consumer control of plants in natural ecosystems for sustainable plant production.
Transfer efficiency of organic carbon in marine sediments
Authors: Bradley James A. , Hülse Dominik , LaRowe Douglas E. , Arndt Sandra 
Published: November 2022

AbstractQuantifying the organic carbon (OC) sink in marine sediments is crucial for assessing how the marine carbon cycle regulates Earth’s climate. However, burial efficiency (BE) – the commonly-used metric reporting the percentage of OC deposited on the seafloor that becomes buried (beyond an arbitrary and often unspecified reference depth) – is loosely defined, misleading, and inconsistent. Here, we use a global diagenetic model to highlight orders-of-magnitude differences in sediment ages at fixed sub-seafloor depths (and vice-versa), and vastly different BE’s depending on sediment depth or age horizons used to calculate BE. We propose using transfer efficiencies (Teff’s) for quantifying sediment OC burial: Teff is numerically equivalent to BE but requires precise specification of spatial or temporal references, and emphasizes that OC degradation continues beyond these horizons. Ultimately, quantifying OC burial with precise sediment-depth and sediment-age-resolved metrics will enable a more consistent and transferable assessment of OC fluxes through the Earth system.