bluuebunny/crossref_metadata_2025 huggingface dataset:
Galactose oxidase oxidation and glycosidase digestion for glycoRNA analysis
Authors: Deng Jianbo , Miao Xinyu , Wang Xiaotong , Wen Sheng-Ye , Zhou Zeyang , Li Shuwei , Jiang Junhong , Yang Xiaodong , Yang Shuang
Published: December 2024

Solid-phase glycoRNA enrichment provides a universal approach for capturing glycosylated RNAs, enabling the identification of glycoRNAs and facilitating functional studies.
Single-wall carbon nanotube separations via aqueous two-phase extraction: new prospects enabled by high-throughput methods
Authors: Sims Christopher M. , Zheng Ming , Fagan Jeffrey A.
Published: December 2024

This feature article describes how high-throughput metrology developments have led to large advances in single-wall carbon nanotube (SWCNT) separations science and theorizes how these advances could be leveraged towards commercial technologies.
The substituent effect on the heat-induced pyrolysis mechanism of energetic materials: a case of reactive molecular dynamics simulations on nitrobenzene compounds
Authors: Zhu Shuangfei , Yang Chaowen , Zheng Shufen , Zhang Shuhai , Chen Yahong , Liu Yang
Published: December 2024

The initial decomposition reactions of TNB, TNT, PA, TNA and Tetryl were studied using ReaxFF-lg molecular dynamics simulations, and the substituent effect on the thermal decomposition behaviours of nitrobenzene compounds was evaluated.
Dynamics of hydrogen shift reactions between peroxy radicals
Authors: Mandal Imon , Daub Christopher David , Valiev Rashid , Kurtén Theo , Benny Gerber R.
Published: December 2024

The hydrogen shift reaction occurs on the singlet potential energy surface.
Sensing of n-butanol vapours using an oxygen vacancy-enriched Zn2SnO4–SnO2 hybrid-composite
Authors: Parayil Reshmi Thekke , Paine Snehangshu , Mukherjee K. , Tyagi D. , Mohapatra Manoj , Gupta Santosh K.
Published: December 2024

The precise identification of various toxic gases is important to prevent health and environmental hazards using cost-effective, efficient, metal oxide-based chemiresistive sensing methods.
Insight into photocatalytic CO2 reduction on TiO2-supported Cu nanorods: a DFT study on the reaction mechanism and selectivity
Authors: Liu Ying , Zhang Jinyang , Jin Jiamin , Liu Huihui , Ren Guanhua , Hu Peijun , Wang Haifeng
Published: December 2024

This study explores photocatalytic CO2 reduction on nanorod-Cu/TiO2, identifying H2COOH as a key species for C–O bond cleavage. Both CO and CH3OH share the H2CO intermediate, with CH3OH formation being favored over CO via a forth-back mechanism.
Carotenoid profile in maternal and cord plasma and its trends in breast milk during lactation: a comparative study among three cities in northern China
Authors: Tian Luojia , Wang Liang , Li Fei , Sun Anran , Ni Mengmei , Sun Hanxiao , Wang He , Li Xiang , Zhao Yanrong , Zhang Lishi , Li Xiaomeng , Kuchan Matthew , Mao Yingyi , Chen Jinyao
Published: December 2024

Our study aimed to assess the levels of carotenoids in maternal and cord plasma and breast milk during the lactation stages and explore the differences in carotenoids in breast milk among three cities in northern China.
Bovine lactopontin promotes bone development in growing rats by altering the composition of intestinal flora and bile acid metabolism
Authors: Lyu Yipin , Hu Jianqiang , Wang Xinyan , Zhang Jie , Li Xue , Cui Mengjun , Liu Dasong , Tang Xue , Zhou Peng
Published: December 2024

Bovine lactopontin alters intestinal flora and bile acid composition, improves bone microstructure, and promotes bone growth and development.
Shell structure, magnetic and magnetodynamic properties of oxidized iron nanoparticles with partial gold coating
Authors: Lyaschenko Sergey , Tarasov Ivan , Andryushchenko Tatyana , Yakovlev Ivan , Velikanov Dmitry , Volochaev Mikhail , Nemtsev Ivan , Kriukov Ruslan , Maximova Olga , Shevtsov Dmitry , Varnakov Sergey , Ovchinnikov Sergei
Published: December 2024

Oxidized Fe nanoparticles with partial Au coating were fabricated by spontaneous nucleation on NaCl. The chemical structure of the hydrated surface and ellipsometric control of magnetodynamics indicated their potential for magnetomechanical therapy.
Nanosized core–shell bio-hybrid microgels and their internal structure
Authors: Lenßen Pia , Hengsbach Rebecca , Frommelius Anne , Cammeraat Samira , Linssen Koen , Simon Ulrich , Wöll Dominik
Published: December 2024

Super-resolution fluorescence microscopy (SRFM) allowed for an investigation of the morphology and accessibility for guest molecules in core–shell bio-hybrid DNA-poly(N-isopropylmethacrylamide) microgels.
Optimizing gelation time for cell shape control through active learning
Authors: Luo Yuxin , Chen Juan , Gu Mengyang , Luo Yimin
Published: December 2024

We present an efficient method for investigating kinetics of gelling system, demonstrating that combining active learning and microrheology can streamline response surface construction and predict how gelation times influence the cell morphology.
Buried interface passivation with bis(3-aminopyrid-2-yl) sulfide for carbon-based perovskite solar cells
Authors: Wang Jiating , Gao Xinrui , Zhuansun Yingjia , Zhu Decai , Liu Jie , Tang Long , Wei Qingbo
Published: December 2024

Electron layer defects are one of the key factors affecting the performance of perovskite solar cells.
A bubble-templating strategy to construct CeO2 aerogels and their potential application for fast detection of acetone
Authors: Liu Sen , Zhao Liang , Yu Chengchao , Xing Yunpeng , Zhang Hongda , Zhi Sihao , Fei Teng , Zhang Haiyan , Zhang Tong
Published: December 2024

A facile bubble-templating strategy is proposed to prepare CeO2 and metal-doped CeO2 aerogels. The synergy of the sugar-blowing property of glucose and gases generated from precursors contributes to form the CeO2 aerogel.
Equilibrating bonding energy between solvent and solute for optimized crystallization enables efficient perovskite solar cells
Authors: Zhang Hanzhi , Bi Weihui , Wang Jin , Mao Peng , Lv Jun , Xing Shen , Yang Po-Chuan , Hai Guangtong , Han Gaorong , Zhong Yufei
Published: December 2024

Solvent engineering by introducing δ-valerolactone into DMF/DMSO mix-solvents for balancing solvent–solute interactions and diminishing the transformation barrier of α-FAPbI3.
Well pad-level geospatial differences in the carbon footprint and direct land use change impacts of natural gas extraction
Authors: Sharafi Amir , Fortier Marie-Odile P.
Published: December 2024

Well pad level life cycle assessment demonstrates the influence of geospatial parameters, including direct land use change impacts, on the carbon footprint of natural gas extraction.
Candidate bus identification for voltage stability enhancement of wind‐penetrated power system based on spectral learning technique
Authors: Zhou Niancheng , Guo Jinsheng , Chi Yuan , Zheng Xinying , Wang Qianggang , Luo Yongjie , Ye Jia
Published: December 2024

Dynamic reactive power sources can efficiently address the voltage stability problem of a wind‐penetrated power system and the possibility of cascading failures, which are caused by the decreasing inertia and the increasing complexity of the system dynamics. However, their applications are limited by the high investment cost. Identifying appropriate buses for the deployment can improve the economy and efficiency of reactive power source configuration and reduce the complexity of deployment models. Here, a new metric is proposed to guide the selection of candidate buses, based on the improved spectral learning technique and the quantitative assessment of the short‐term voltage stability. Specifically, a new short‐term voltage stability metric is developed to assess the dynamic voltage responses of different stages after a contingency. Then, an improved spectral learning algorithm with objective priorities assigned to different buses is used for the bus selection, aiming to identify the most influential buses, in terms of short‐term voltage stability and propagation potentials. A two‐dimensional decision‐making methodology is proposed, considering both the capacity sensitivity and the bus's structural characteristics. The effectiveness of the proposed methodology is validated on a New England 39‐bus system using an electromechanical transient model.
Suppression of photospheric velocity fluctuations in strongly magnetic O stars in radiation-magnetohydrodynamic simulations
Authors: ud-Doula A. , Sundqvist J. O. , Narechania N. , Debnath D. , Moens N. , Keppens R.
Published: December 2024

Context. O stars generally show clear signs of strong line broadening (in addition to rotational broadening) in their photospheric absorption lines (typically referred to as macroturbulence), believed to originate in a turbulent sub-surface zone associated with enhanced opacities due to the recombination of iron-group elements (at T ~ 150–200 kK). O stars with detected global magnetic fields also display such macroturbulence; the sole exception to this is NGC 1624-2, which also has the strongest (by far) detected field of the known magnetic O stars. It has been suggested that this lack of additional line broadening is due to NGC 1624-2’s exceptionally strong magnetic field, which might be able to suppress the turbulent velocity field generated in the iron opacity peak zone.

Aims. We tested this hypothesis based on two-dimensional (2D), time-dependent, radiation magnetohydrodynamical (RMHD) box- in-a-star simulations for O stars that encapsulate the deeper sub-surface atmosphere (down to T ~ 400 kK), the stellar photosphere, and the onset of the supersonic line-driven wind in one unified approach. To study the potential suppression of atmospheric velocity fluctuations, we extended our previous non-magnetic O star radiation-hydrodynamic (RHD) simulations to include magnetic fields of varying strengths and orientations.

Methods. We used MPI-AMRVAC, which is a Fortran 90 based publically available parallel finite volume code that is highly modular. We used the recently added RMHD module to perform all our simulations here.

Results. For moderately strong magnetic cases (~1 kG), the simulated atmospheres are highly structured and characterised by large root-mean-square velocities, and our results are qualitatively similar to those found in previous non-magnetic studies. By contrast, we find that a strong horizontal magnetic field in excess of 10 kG can indeed suppress the large velocity fluctuations, and can thus stabilise (and thereby also inflate) the atmosphere of a typical early O star in the Galaxy. On the other hand, an equally strong radial field is only able to suppress horizontal motions, and as a consequence these models exhibit significant radial fluctuations.

Conclusions. Our simulations provide an overall physical rationale as to why NGC 1624-2 with its strong ~20 kG dipolar field lacks the large macroturbulent line broadening that all other known slowly rotating early O stars exhibit. However, our simulations also highlight the importance of field geometry for controlling the atmospheric dynamics in massive and luminous stars that are strongly magnetic, tentatively suggesting latitudinal dependence of macroturbulence and basic photospheric parameters.
Analysis of the Potential Mechanism of Sanhua Decoction in Treating Ischemic Stroke Based on Network Pharmacology and Molecular Docking Technology
Authors: Zhao Wei , Li Dan , Yue Min , Yan Cheng , Li Feng , Qi Yonghua
Published: December 2024

Objective The aim of this study was to explore the action mechanism of Sanhua decoction in treating ischemic stroke through network pharmacology and molecular docking technology.

Methods Active components and related targets of Sanhua decoction were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. A “drug-active component-target” network was constructed, and core components were selected through topological analysis. Disease targets related to ischemic stroke were screened based on the Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), GeneCards, DrugBank, and PharmGKB databases. The intersection of active component–related targets and ischemic stroke disease targets was identified to obtain potential targets of Sanhua decoction for treating ischemic stroke, represented using a Venn diagram. The STRING database was used to construct a protein–protein interaction (PPI) network of potential targets and filter for core targets. Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of core targets were performed using the DAVID database and Metascape platform. Molecular docking verification of core targets and core components was conducted using AutoDock.

Results A total of 52 active components and 142 related targets were screened from Sanhua decoction, with core active components including luteolin, nobiletin, β-sitosterol, eucalyptol, and aloe-emodin. There were 2,991 ischemic stroke–related targets, with 98 potential targets identified in the intersection with active component–related targets. An analysis of the PPI network analysis revealed 23 core targets, including serine/threonine-protein kinase 1 (AKT1), tumor protein p53 (TP53), and mitogen-activated protein kinase 3 (MAPK3). Enrichment analysis obtained 35 GO results and 41 signaling pathways. Molecular docking results indicated good binding between core components and core targets.

Conclusion Multiple components in the classic formula Sanhua decoction, such as luteolin and nobiletin, may play a role in treating ischemic stroke by regulating core targets like AKT1, TP53, and MAPK3, and participating in multiple signaling pathways.
Analysis of the effect of the Fermi surface matching at Co–Fe and Cu interface on giant magnetoresistance effect using a combinatorial technique
Authors: Kushwaha Varun Kumar , Toyama Ryo , Miura Yoshio , Iwasaki Yuma , Sakuraba Yuya
Published: December 2024

Interfacial electronic band-matching (EBM) plays a crucial role in determining the spin-dependent transport properties and performance of spintronic devices. The final goal of this study is to establish a method to search for new material combinations that exhibit favorable EBM at the interfaces to achieve a superior performance in various spintronic devices using the machine learning technique combined with the first-principles calculations. As a first step, we investigate the effect of interfacial EBM on magnetoresistance (MR) by fabricating the current-in-plane giant magnetoresistive devices with compositionally graded Co1−βFeβ layers and Cu spacer. The MR ratio varies significantly across β = 0.11–1.0, with the highest MR of 17.5% observed at β ≈ 0.46, followed by a sharp decrease beyond β = 0.6. To analyze the β dependence of MR in terms of EBM with low computational cost, we calculate the simple Fermi surfaces of bcc Co1−βFeβ and Cu and evaluate the wave number (k) distance between their Fermi surfaces. The closest (furthest) Fermi surface match occurs at β ≈ 0.4 (1.0), which tends to be in good agreement with the observed MR trend. This suggests that a simple Fermi surface similarity analysis, when integrated with a machine learning technique, can be an effective method for efficiently identifying new material combinations with high EBM.
Enhanced structural, magnetic, and dielectric properties in Cr3+-substituted Mg0.5R0.5Fe1.5Cr0.5O4 (R = Cu, Zn) ferrites
Authors: Parajuli D. , Raju M. K. , Reddy T. Amaranatha , Shanmukhi P. S. V. , Ratnaraju M. , Chohan Jasgurpreet Singh , Murali N. , Samatha K. , Ramesh Avala , Manepalli R. K. N. R.
Published: December 2024

This study examines the structural, microstructural, magnetic, and dielectric properties of Cr3+-substituted ferrites, specifically Mg0.5Cu0.5Fe1.5Cr0.5O4 and Mg0.5Zn0.5Fe1.5Cr0.5O4, synthesized using the solid-state reaction method. Structural and phase purity assessments were conducted via x-ray diffraction (XRD), Scanning Electron Microscopy (SEM), Fourier Transform Infrared (FTIR) spectroscopy, and Vibrating Sample Magnetometry. XRD patterns confirmed the formation of a single-phase cubic spinel structure in both ferrites, with derived lattice parameters (8.402 and 8.497 Å) and crystallite sizes (44.70 and 30.05 nm) supporting consistent structural integrity. SEM analysis in association with ImageJ software showed grain sizes between 732 and 324 nm, while FTIR spectra revealed characteristic tetrahedral and octahedral vibration bands. Notably, the saturation magnetization increased significantly with Cu2+ concentration, from 38.67 to 60.45 emu/g, indicating an enhancement in magnetic properties. The dielectric behavior, analyzed over a 100–105 Hz range, exhibited Maxwell–Wagner interfacial polarization and electron hopping effects between Fe2+ and Fe3+ ions, contributing to typical dispersion patterns. This improvement in magnetic and dielectric properties, particularly in the Cu-doped samples, underscores the effectiveness of Cr3+ substitution in tuning material characteristics. The findings suggest that these modified ferrites hold promise for high-frequency electronic applications, such as inductors, transformers, and electromagnetic interference shielding materials, where both magnetic stability and efficient dielectric performance are critical. This research contributes valuable insights into the development of advanced ferrites for multifunctional electronic devices.
Efficacy of GABA aminotransferase inactivator OV329 in models of neuropathic and inflammatory pain without tolerance or addiction
Authors: Wirt Jonah L. , Assis Ferreira Luana , Jesus Carlos Henrique Alves , Woodward Taylor J. , Oliva Idaira , Xu Zhili , Crystal Jonathon D. , Pepin Robert H. , Silverman Richard B. , Hohmann Andrea G.
Published: December 2024

Dysregulation of GABAergic inhibition is associated with pathological pain. Consequently, enhancement of GABAergic transmission represents a potential analgesic strategy. However, therapeutic potential of current GABA agonists and modulators is limited by unwanted side effects. We postulated that inhibition of GABA’s degradation enzyme, GABA aminotransferase (GABA-AT), would increase endogenous GABA levels and produce analgesia. We evaluated antinociceptive efficacy of the potent GABA-AT inhibitor OV329 in rodent models of neuropathic and inflammatory pain and assessed possible side effects (i.e., reward and motor impairment). OV329 attenuated the development and maintenance of mechanical and cold hypersensitivities induced by the chemotherapeutic agent paclitaxel. Prophylactic OV329, administered systemically, normalized paclitaxel-induced increases in glutamate levels and suppressed neuropathic nociception. Intrathecal OV329 suppressed paclitaxel-induced mechanical hypersensitivity, elevating GABA, and reducing glutamate levels in the lumbar spinal cord, consistent with a spinal site of action. Furthermore, OV329 largely synergized with paclitaxel to enhance 4T1 tumor cell line cytotoxicity without altering viability of nontumor cells. OV329 also attenuated inflammation-induced mechanical hypersensitivity induced by intraplanar injection of complete Freund’s adjuvant (CFA) with efficacy comparable to morphine. Unlike morphine, OV329 did not produce reward in a conditioned place preference assay in mice and was not self-administered intravenously by rats. Antinociceptive efficacy of OV329 was observed at doses that did not impair motor function or produce tolerance following chronic dosing. Thus, inhibition of GABA-AT with OV329 represents a unique therapeutic strategy to alleviate neuropathic and inflammatory pain with no apparent abuse liability, potentially producing a beneficial spectrum of pharmacological effects through enzymatic regulation.
Boreal forests are heading for an open state
Authors: Rotbarth Ronny , van Nes Egbert H. , Scheffer Marten , Holmgren Milena
Published: December 2024

The boreal forest biome is warming four times faster than the global average. Changes so far are moderate, but time lags in responses may transiently maintain forest states which are no longer supported by current environmental conditions. Here, we explore whether tree cover dynamics hint at the state to which the biome may be shifting. Our results suggest that global boreal tree cover is heading for a unimodal state of open forest (30 to 50%), contrasting starkly to the bimodal distribution of dense forests (>60%) and sparse woodlands (5 to 15%) found today. A future open forest in a warmer world would likely increase the risk of forest fires, leading to potentially substantial releases of stored carbon.
ANAC044 orchestrates mitochondrial stress signaling to trigger iron-induced stem cell death in root meristems
Authors: Yan Juanmei , Feng Zhihang , Xiao Yihui , Zhou Ming , Zhao Xiaobo , Lin Xianyong , Shi Weiming , Busch Wolfgang , Li Baohai
Published: December 2024

While iron (Fe) is essential for life and plays important roles for almost all growth related processes, it can trigger cell death in both animals and plants. However, the underlying mechanisms for Fe-induced cell death in plants remain largely unknown. S-nitrosoglutathione reductase (GSNOR) has previously been reported to regulate nitric oxide homeostasis to prevent Fe-induced cell death within root meristems. Here, we found that in the absence of
GSNOR
, exposure to high Fe treatment results in DNA damage–dependent cell death specifically in vascular stem cells in root meristems within 48 h. Through a series of time-course transcriptomic analyses, we unveil that in the absence of
GSNOR
, mitochondrial dysfunction emerges as the most prominent response to high Fe treatment. Consistently, the application of mitochondrial respiratory inhibitors leads to stem cell death in root meristems, and pharmacological blockage of the voltage-dependent anion channel that is responsible for the release of mitochondrial-derived molecules into the cytosol or genetic changes that abolish the ANAC017- and ANAC013-mediated mitochondrial retrograde signaling effectively eliminate Fe-induced stem cell death in
gsnor
root meristems. We further identify the nuclear transcription factor ANAC044 as a mediator of this mitochondrial retrograde signaling. Disruption of
ANAC044
completely abolishes the GSNOR-dependent, Fe-induced stem cell death in root meristems, while ectopic expression of
ANAC044
causes severe root stem cell death. Collectively, our findings reveal a mechanism responsible for initiating Fe-induced stem cell death in the root meristem, which is the ANAC044-mediated GSNOR-regulated mitochondrial stress signaling pathway.
Binding mode–guided development of high-performance antibodies targeting site-specific posttranslational modifications
Authors: Riso Mariapia , Shah Rohan N. , Koide Akiko , Ruthenburg Alexander J. , Koide Shohei , Hattori Takamitsu
Published: December 2024

Posttranslational modifications (PTMs) of proteins play critical roles in regulating many cellular events. Antibodies targeting site-specific PTMs are essential tools for detecting and enriching PTMs at sites of interest. However, fundamental difficulties in molecular recognition of both PTM and surrounding peptide sequence have hindered the efficient generation of highly sequence-specific anti-PTM antibodies. Furthermore, the widespread use of potentially inconsistent, nonrenewable, and molecularly undefined antibodies presents experimental challenges thought to contribute to the reproducibility problem in biomedical research. In this study, we describe the binding mode-guided development of a platform that efficiently generates potent and selective recombinant antibodies to PTMs that are molecularly defined and renewable. Our platform is built on our previous discovery of an unconventional binding mode of anti-PTM antibodies, antigen clasping, where two antigen binding sites cooperatively sandwich a single antigen, creating extensive interactions with the antigen and leading to high selectivity and potency. We designed the platform that generates clasping antibodies with two distinct binding units, resulting in efficient generation of antibodies to a set of trimethylated histone H3 with high levels of specificity and affinity. Performance comparison in chromatin immunoprecipitation, a common application in epigenomics, revealed that a clasping antibody to trimethylated histone H3 at lysine 27 exhibited superior specificity to a widely used conventional antibody and captured symmetric and asymmetric nucleosomes in a less biased manner. We further generated clasping antibodies to phosphotyrosine antigens by using the same principle. These results suggest the broad applicability of our platform to generating high-performance clasping antibodies to diverse PTMs.
Chromatin enables precise and scalable gene regulation with factors of limited specificity
Authors: Perkins Mindy Liu , Crocker Justin , Tkačik Gašper
Published: December 2024

Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error.
Dynamic treeline and cryosphere response to pronounced mid-Holocene climatic variability in the US Rocky Mountains
Authors: Pederson Gregory T. , Stahle Daniel , McWethy David B. , Toohey Matthew , Jungclaus Johann , Lee Craig , Martin Justin , Alt Mio , Kichas Nickolas , Chellman Nathan , McConnell Joseph R. , Whitlock Cathy
Published: December 2024

Climate-driven changes in high-elevation forest distribution and reductions in snow and ice cover have major implications for ecosystems and global water security. In the Greater Yellowstone Ecosystem of the Rocky Mountains (United States), recent melting of a high-elevation (3,091 m asl) ice patch exposed a mature stand of whitebark pine (
Pinus albicaulis
) trees, located ~180 m in elevation above modern treeline, that date to the mid-Holocene (c. 5,950 to 5,440 cal y BP). Here, we used this subfossil wood record to develop tree-ring-based temperature estimates for the upper-elevation climate conditions that resulted in ancient forest establishment and growth and the subsequent regional ice-patch growth and downslope shift of treeline. Results suggest that mid-Holocene forest establishment and growth occurred under warm-season (May-Oct) mean temperatures of 6.2 °C (±0.2 °C), until a multicentury cooling anomaly suppressed temperatures below 5.8 °C, resulting in stand mortality by c. 5,440 y BP. Transient climate model simulations indicate that regional cooling was driven by changes in summer insolation and Northern Hemisphere volcanism. The initial cooling event was followed centuries later (c. 5,100 y BP) by sustained Icelandic volcanic eruptions that forced a centennial-scale 1.0 °C summer cooling anomaly and led to rapid ice-patch growth and preservation of the trees. With recent warming (c. 2000–2020 CE), warm-season temperatures now equal and will soon exceed those of the mid-Holocene period of high treeline. It is likely that perennial ice cover will again disappear from the region, and treeline may expand upslope so long as plant-available moisture and disturbance are not limiting.
Tetrameric PilZ protein stabilizes stator ring in complex flagellar motor and is required for motility in
Campylobacter jejuni
Authors: Chen Yuanyuan , Tachiyama Shoichi , Li Yuqian , Feng Xueyin , Zhao Hang , Wu Yanmin , Guo Yu , Lara-Tejero María , Hua Canfeng , Liu Jun , Gao Beile
Published: December 2024

Rotation of the bacterial flagellum, the first identified biological rotary machine, is driven by its stator units. Knowledge gained about the function of stator units has increasingly led to studies of rotary complexes in different cellular pathways. Here, we report that a tetrameric PilZ family protein, FlgX, is a structural component underneath the stator units in the flagellar motor of
Campylobacter jejuni
. FlgX forms a stable tetramer that does not bind cyclic di-GMP (c-di-GMP), unlike other canonical PilZ domain–containing proteins. Cryoelectron tomography and subtomogram averaging of flagellar motors in situ provide evidence that FlgX interacts with each stator unit and plays a critical role in stator ring assembly and stability. Furthermore, FlgX is conserved and was most likely present in the common ancestor of the phylum
Campylobacterota
. Overall, FlgX represents a divergence in function for PilZ superfamily proteins as well as a player in the key stator–rotor interaction of complex flagellar motors.
PsDMAP1/PsTIP60-regulated H4K16ac is required for ROS-dependent virulence adaptation of
Phytophthora sojae
on host plants
Authors: Zhang Fan , Chen Shanshan , Zhang Can , Wang Zhiwen , Miao Jianqiang , Dai Tan , Hao Jianjun , Liu Xili
Published: December 2024

Host plants and various fungicides inhibit plant pathogens by inducing the release of excessive reactive oxygen species (ROS) and causing DNA damage, either directly or indirectly leading to cell death. The mechanisms by which the oomycete
Phytophthora sojae
manages ROS stress resulting from plant immune responses and fungicides remains unclear. This study elucidates the role of histone acetylation in ROS-induced DNA damage responses (DDR) to adapt to stress. Mechanistically, the
P. sojae
DNA methyltransferase 1-associated protein (PsDMAP1) binds Tat-interactive protein 60 (PsTIP60) to comediate histone H4 acetylation on lysine 16 (H4K16ac). This regulation affects RNA polymerase II (pol II) recruitment, transcriptional induction of DDR-related genes, and the enrichment of histone H2Ax phosphorylated on serine 137 (γH2Ax) in response to both plant immunity and fungicide stress. The resulting H4K16ac serves as a crucial transgenerational epigenetic signal for virulence adaptation of
P. sojae
on plants, as a result of adaptation to ROS stress.
Gonadal sex and temperature independently influence germ cell differentiation and meiotic progression in
Trachemys scripta
Authors: Hatkevich Talia , Tezak Boris M. , Acemel Rafael D. , Yee Chung Vicky Wai , Lupiáñez Dario G. , Capel Blanche
Published: December 2024

In species with genetic sex determination (GSD), the sex identity of the soma determines germ cell fate. For example, in mice, XY germ cells that enter an ovary differentiate as oogonia, whereas XX germ cells that enter a testis initiate differentiation as spermatogonia. However, numerous species lack a GSD system and instead display temperature-dependent sex determination (TSD). In the red-eared slider turtle,
Trachemys scripta
, a TSD model species with a warm female promoting temperature (FPT) and cool male promoting temperature (MPT) system, temperature directly affects germ cell number. In this study, we examined whether temperature directly affects other aspects of germ cell differentiation/sex identity. We uncoupled temperature and the sexual fate of the gonad by incubating eggs at MPT and treating with 17β-estradiol, a scheme that invariably produces ovaries. Through analysis of meiotic spreads, we showed that germ cells in FPT ovaries follow the typical pattern of initiating meiosis and progress through prophase I. However, in E2-induced ovaries that incubated at MPT, germ cells entered prophase I yet fail to exhibit synapsis. These results, combined with our single-cell transcriptome analysis, reveal a direct effect of temperature on germ cell sexual differentiation independent of its effect on the gonadal soma. These results imply that not all events of meiosis are under somatic control, at least not in this TSD species.
Mechanism-guided engineering of a minimal biological particle for genome editing
Authors: Ngo Wayne , Peukes Julia , Baldwin Alisha , Xue Zhiwei Wayne , Hwang Sidney , Stickels Robert R. , Lin Zhi , Satpathy Ansuman T. , Wells James A. , Schekman Randy , Nogales Eva , Doudna Jennifer A.
Published: December 2024

The widespread application of genome editing to treat and cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped delivery vehicles (EDVs) are engineered virally derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication proteins in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. Here, we show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV-mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs and demonstrated increased editing in cell lines and therapeutically relevant primary human T cells. These results show that virally derived particles can be streamlined to create efficacious genome editing delivery vehicles with simpler production and manufacturing.
The return of stagnant slab recorded by intraplate volcanism
Authors: Zhou Zhong-Biao , Chen Li-Hui , Huang Zhou-Chuan , Hofmann Albrecht W. , Wang Xiao-Jun , Zeng Gang , Bi Ya-Jing , Zhao Jian
Published: December 2024

Subducted plates often stagnate in the mantle transition zone (MTZ), and the fate of the stagnant slabs is still debatable. They may sink into the lower mantle, or remain partially trapped in the MTZ, but it is uncertain whether they can return to the upper mantle. We report geochemical evidence of late-Miocene (~6 Ma) basalts from, and upper mantle seismic evidence beneath Shuangyashan, an area above the slab tear of the stagnant Pacific plate in eastern Asia, to show how the slab returns to the upper mantle from the MTZ. Remarkably high δ
57
Fe, Gd/Yb and low δ
26
Mg, Ti/Eu, CaO/Al
2
O
3
values of Shuangyashan basalts suggest that the subducted Pacific oceanic crust had been entrained to their upper mantle source. Therefore, the return of oceanic crust from the MTZ to the upper mantle appears to have been driven by upwelling triggered by tearing of the stagnant slab right beneath this area. Meanwhile, local shear splitting measurements reveal a circular pattern of anisotropy in the upper mantle with delay times diminishing toward the slab tear, suggesting that the slab-fragment-bearing upwelling subsequently turned into lateral flows in the upper mantle, and contributed to a wider intraplate magmatism above the stagnant slab. This finding, together with other widespread intraplate volcanism from eastern Asia, extending for approximately 6,000 km, demonstrates that a subduction-induced tear can lead to the destruction and partial return of stagnant slab material, and thus lead to the cycling of subducted crustal materials and the generation of subduction-induced intraplate magmatism.
Retinal ganglion cells encode the direction of motion outside their classical receptive field
Authors: Riccitelli Serena , Yaakov Hadar , Heukamp Alina S. , Ankri Lea , Rivlin-Etzion Michal
Published: December 2024

Retinal ganglion cells (RGCs) typically respond to light stimulation over their spatially restricted receptive field. Using large-scale recordings in the mouse retina, we show that a subset of non- direction-selective (DS) RGCs exhibit asymmetric activity, selective to motion direction, in response to a stimulus crossing an area far beyond the classic receptive field. The extraclassical response arises via inputs from an asymmetric distal zone and is enhanced by desensitization mechanisms and an inherent DS component, creating a network of neurons responding to motion toward the optic disc. Pharmacological manipulations revealed the necessity of glycinergic amacrine cells for this response. Using in vivo recordings, we identified similar extraclassical responses in lateral geniculate nucleus neurons, suggesting such non conventional DS information is transferred to downstream structures. Our results suggest a complex integration of motion direction processing across the visual field, which arises beyond the classical receptive field boundaries.
Structural insight into sodium ion pathway in the bacterial flagellar stator from marine
Vibrio
Authors: Nishikino Tatsuro , Takekawa Norihiro , Kishikawa Jun-ichi , Hirose Mika , Kojima Seiji , Homma Michio , Kato Takayuki , Imada Katsumi
Published: December 2024

Many bacteria swim in liquid or swarm on surface using the flagellum rotated by a motor driven by specific ion flow. The motor consists of the rotor and stator, and the stator converts the energy of ion flow to mechanical rotation. However, the ion pathway and the mechanism of stator rotation coupled with specific ion flow are still obscure. Here, we determined the structures of the sodium-driven stator of
Vibrio
, namely PomAB, in the presence and absence of sodium ions and the structure with its specific inhibitor, phenamil, by cryo-electron microscopy. The structures and following functional analysis revealed the sodium ion pathway, the mechanism of ion selectivity, and the inhibition mechanism by phenamil. We propose a model of sodium ion flow coupled with the stator rotation based on the structures. This work provides insights into the molecular mechanisms of ion specificity and conversion of the electrochemical potential into mechanical functions.
Metabolic enhancement contributed by horizontal gene transfer is essential for dietary specialization in leaf beetles
Authors: Zhang Yuxin , Tu Chengjie , Bai Jianyang , Li Xiayu , Sun Ziyue , Xu Letian
Published: December 2024

Horizontal gene transfer (HGT) from bacteria to insects is widely reported and often associated with the adaptation and diversification of insects. However, compelling evidence demonstrating how HGT-conferred metabolic adjustments enable species to adapt to surrounding environment remains scarce. Dietary specialization is an important ecological strategy adopted by animals to reduce inter- and intraspecific competition for limited resources. Adults of the leaf beetle
Plagiodera versicolora
(Coleoptera) preferentially consume new leaves; nevertheless, we found that they selectively oviposit on mature leaves, thereby establishing a distinct dietary niche separation between adults and larvae. Based on the de novo assembled chromosome-level genome, we identified two horizontally transferred genes with cellulose degradation potential, belonging to the glycosyl hydrolase 48 family (
GH48-1
and
GH48-2
). Prokaryotic expression of the HGTs confirmed the cellulose degradation capability of the two genes. Knockdown of GH48 significantly hampered the growth and survival rate of larvae feeding on mature leaves compared to wild-type larvae, with no similar effect observed in adults. Replenishing the GH48-expressing bacteria compensated for the knockdown of these two genes and recurred larval adaptability to mature leaves. Taken together, our results highlight the advantage and metabolic enhancement conferred by the two cellulose-degrading HGTs in
P. versicolora
larvae, enabling their development on cellulose-enriched mature leaves and underscoring the indispensable role of HGTs in facilitating the adaptation of leaf beetles to plants.
Metastable state preceding shear zone instability: Implications for earthquake-accelerated landslides and dynamic triggering
Authors: Li Yan , Hu Wei , Xu Qiang , Luo Hui , Chang Chingshung , Jia Xiaoping
Published: December 2024

Understanding the dynamic response of granular shear zones under cyclic loading is fundamental to elucidating the mechanisms triggering earthquake-induced landslides, with implications for broader fields such as seismology and granular physics. Existing prediction methods struggle to accurately predict many experimental and in situ landslide observations due to inadequate consideration of the underlying physical mechanisms. The mechanisms that influence landslide dynamic triggering, a transition from static (or extremely slow creeping) to rapid runout, remain elusive. Herein, we focus on the inherent physics of granular shear zones under dynamic loading using ring shear experiments. Except for coseismic slip caused by the dynamic load, varying magnitudes of postseismic creep with increasing cycles of dynamic loading are observed, highlighting the effects of coseismic weakening (shear zone fatigue) and subsequent postseismic healing. A metastable state, characterized by a significant increase in postseismic creep, typically precedes shear zone instability. The metastable state may arise as weakened shear resistance approaches the applied shear stress, demonstrating a phase transition from a solid-like state to a fluid state (plastic granular flow). The metastable state may potentially indicate the shear zone’s stress state and serve as a precursor to impending instability. Furthermore, the proposed mechanisms offer a compelling explanation for the widespread postseismic landslide movement following earthquakes. Incorporating these mechanisms into the Newmark method has the potential to improve the prediction of earthquake-induced landslide displacement and enhance our understanding of dynamic triggering.
A lever hypothesis for Synaptotagmin-1 action in neurotransmitter release
Authors: Jaczynska Klaudia , Esser Victoria , Xu Junjie , Sari Levent , Lin Milo M. , Rosenmund Christian , Rizo Josep
Published: December 2024

Neurotransmitter release is triggered in microseconds by Ca
2+
-binding to the Synaptotagmin-1 C
2
-domains and by SNARE complexes that form four-helix bundles between synaptic vesicles and plasma membranes, but the coupling mechanism between Ca
2+
-sensing and membrane fusion is unknown. Release requires extension of SNARE helices into juxtamembrane linkers that precede transmembrane regions (linker zippering) and binding of the Synaptotagmin-1 C
2
B domain to SNARE complexes through a “primary interface” comprising two regions (I and II). The Synaptotagmin-1 Ca
2+
-binding loops were believed to accelerate membrane fusion by inducing membrane curvature, perturbing lipid bilayers, or helping bridge the membranes, but SNARE complex binding through the primary interface orients the Ca
2+
-binding loops away from the fusion site, hindering these putative activities. To clarify this paradox, we have used NMR and fluorescence spectroscopy. NMR experiments reveal that binding of C
2
B domain arginines to SNARE acidic residues at region II remains after disruption of region I, and that a mutation that impairs spontaneous and Ca
2+
-triggered neurotransmitter release enhances binding through region I. Moreover, fluorescence assays show that Ca
2+
does not induce dissociation of Synaptotagmin-1 from membrane-anchored SNARE complex but causes reorientation of the C
2
B domain. Based on these results and electrophysiological data described by Toulme et al. (
https://doi.org/10.1073/pnas.2409636121
), we propose that upon Ca
2+
binding the Synaptotagmin-1 C
2
B domain reorients on the membrane and dissociates from the SNAREs at region I but not region II, acting remotely as a lever that pulls the SNARE complex and facilitates linker zippering or other SNARE structural changes required for fast membrane fusion.
Moisture-driven carbonation kinetics for ultrafast CO
2
mineralization
Authors: Gao Yining , Tao Yong , Li Gen , Shen Peiliang , Pellenq Roland J.-M. , Poon Chi Sun
Published: December 2024

CO
2
mineralization, a process where CO
2
reacts with minerals to form stable carbonates, presents a sustainable approach for CO
2
sequestration and mitigation of global warming. While the crucial role of water in regulating CO
2
mineralization efficiency is widely acknowledged, a comprehensive understanding of the underlying mechanisms remains elusive. This study employs a combined experimental and atomistic simulation approach to elucidate the intricate mechanisms governing moisture-driven carbonation kinetics of calcium-bearing minerals. A self-designed carbonation reactor equipped with an ultrasonic atomizer is used to meticulously control the water content during carbonation experiments. Grand Canonical Monte Carlo simulations reveal that maximum CO
2
uptake occurs at a critical water content where the initiation of capillary condensation significantly enhanced liquid–gas interactions. This phenomenon leads to CO
2
adsorption–driven ultrafast carbonation at an optimal moisture content (0.1 to 0.2 g/g, water mass ratio to total wet mass of the mineral). A higher moisture content decimates the carbonation rate by crippling CO
2
intake within mineral pores. However, at exceptionally high moisture levels, the carbonation reaction sites shift from internal mesopores to the grain surface. This results in surface dissolution–driven ultrafast carbonation, attributed to the monotonically decreasing free energy of dissolution with increasing surface water thickness, as revealed by metadynamics simulations. This study provides a fundamental and unified understanding of the multifaceted role of water in mineral carbonation, paving the way for optimizing ultrafast CO
2
mineralization strategies for global decarbonization efforts.
Synapse-specific catecholaminergic modulation of neuronal glutamate release
Authors: Bakshinska Dariya , Liu William YuChen , Schultz Ryan , Stowers R. Steven , Hoagland Adam , Cypranowska Caroline , Stanley Cherise , Younger Susan H. , Newman Zachary L. , Isacoff Ehud Y.
Published: December 2024

Norepinephrine in vertebrates and its invertebrate analog, octopamine, regulate the activity of neural circuits. We find that, when hungry,
Drosophila
larvae switch activity in type II octopaminergic motor neurons (MNs) to high-frequency bursts, which coincide with locomotion-driving bursts in type I glutamatergic MNs that converge on the same muscles. Optical quantal analysis across hundreds of synapses simultaneously reveals that octopamine potentiates glutamate release by tonic type Ib MNs, but not phasic type Is MNs, and occurs via the G
q
-coupled octopamine receptor (OAMB). OAMB is more abundant in type Ib terminals and acts through diacylglycerol and its target Unc13A, a key component of the glutamate release machinery. Potentiation varies significantly—by up to 1,000%—across synapses of a single Ib axon, with synaptic Unc13A levels determining both release probability and potentiation. We propose that a dual molecular mechanism—an upstream neuromodulator receptor and a downstream transmitter release controller—fine-tunes catecholaminergic modulation so that strong tonic synapses exhibit large potentiation, while weaker tonic and all phasic synapses maintain consistency, yielding a sophisticated regulation of locomotor behavior.