bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-resolved proteomic profiling reveals compositional and functional transitions across the stress granule life cycle
Authors: Hu Shuyao , Zhang Yufeng , Yi Qianqian , Yang Cuiwei , Liu Yanfen , Bai Yun 
Published: November 2023

AbstractStress granules (SGs) are dynamic, membrane-less organelles. With their formation and disassembly processes characterized, it remains elusive how compositional transitions are coordinated during prolonged stress to meet changing functional needs. Here, using time-resolved proteomic profiling of the acute to prolonged heat-shock SG life cycle, we identify dynamic SG proteins, further segregated into early and late proteins. Comparison of different groups of SG proteins suggests that their biochemical properties help coordinate SG compositional and functional transitions. In particular, early proteins, with high phase-separation-propensity, drive the rapid formation of the initial SG platform, while late proteins are subsequently recruited as discrete modules to further functionalize SGs. This model, supported by immunoblotting and immunofluorescence imaging, provides a conceptual framework for the compositional transitions throughout the acute to prolonged SG life cycle. Additionally, an early SG constituent, non-muscle myosin II, is shown to promote SG formation by increasing SG fusion, underscoring the strength of this dataset in revealing the complexity of SG regulation.
RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms
Authors: Mugunthan Sudarsan , Wong Lan Li , Winnerdy Fernaldo Richtia , Summers Stephen , Bin Ismail Muhammad Hafiz , Foo Yong Hwee , Jaggi Tavleen Kaur , Meldrum Oliver W. , Tiew Pei Yee , Chotirmall Sanjay H. , Rice Scott A. , Phan Anh Tuân , Kjelleberg Staffan , Seviour Thomas 
Published: November 2023

AbstractThe extracellular matrix of bacterial biofilms consists of diverse components including polysaccharides, proteins and DNA. Extracellular RNA (eRNA) can also be present, contributing to the structural integrity of biofilms. However, technical difficulties related to the low stability of RNA make it difficult to understand the precise roles of eRNA in biofilms. Here, we show that eRNA associates with extracellular DNA (eDNA) to form matrix fibres in Pseudomonas aeruginosa biofilms, and the eRNA is enriched in certain bacterial RNA transcripts. Degradation of eRNA associated with eDNA led to a loss of eDNA fibres and biofilm viscoelasticity. Compared with planktonic and biofilm cells, the biofilm matrix was enriched in specific mRNA transcripts, including lasB (encoding elastase). The mRNA transcripts colocalised with eDNA fibres in the biofilm matrix, as shown by single molecule inexpensive FISH microscopy (smiFISH). The lasB mRNA was also observed in eDNA fibres in a clinical sputum sample positive for P. aeruginosa. Thus, our results indicate that the interaction of specific mRNAs with eDNA facilitates the formation of viscoelastic networks in the matrix of Pseudomonas aeruginosa biofilms.
Ancient diversity in host-parasite interaction genes in a model parasitic nematode
Authors: Stevens Lewis , Martínez-Ugalde Isaac , King Erna , Wagah Martin , Absolon Dominic , Bancroft Rowan , Gonzalez de la Rosa Pablo , Hall Jessica L. , Kieninger Manuela , Kloch Agnieszka , Pelan Sarah , Robertson Elaine , Pedersen Amy B. , Abreu-Goodger Cei , Buck Amy H. , Blaxter Mark 
Published: November 2023

AbstractHost-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These interactions can lead to negative frequency-dependent selection, a form of balancing selection that is hypothesised to explain the high levels of polymorphism seen in many host immune and parasite antigen loci. Here, we sequence the genomes of several individuals of Heligmosomoides bakeri, a model parasite of house mice, and Heligmosomoides polygyrus, a closely related parasite of wood mice. Although H. bakeri is commonly referred to as H. polygyrus in the literature, their genomes show levels of divergence that are consistent with at least a million years of independent evolution. The genomes of both species contain hyper-divergent haplotypes that are enriched for proteins that interact with the host immune response. Many of these haplotypes originated prior to the divergence between H. bakeri and H. polygyrus, suggesting that they have been maintained by long-term balancing selection. Together, our results suggest that the selection pressures exerted by the host immune response have played a key role in shaping patterns of genetic diversity in the genomes of parasitic nematodes.
Molecular basis for the catalytic mechanism of human neutral sphingomyelinases 1 (hSMPD2)
Authors: Yi Jingbo , Qi Boya , Yin Jian , Li Ruochong , Chen Xudong , Hu Junhan , Li Guohui , Zhang Sensen , Zhang Yuebin , Yang Maojun 
Published: November 2023

AbstractEnzymatic breakdown of sphingomyelin by sphingomyelinase (SMase) is the main source of the membrane lipids, ceramides, which are involved in many cellular physiological processes. However, the full-length structure of human neutral SMase has not been resolved; therefore, its catalytic mechanism remains unknown. Here, we resolve the structure of human full-length neutral SMase, sphingomyelinase 1 (SMPD2), which reveals that C-terminal transmembrane helices contribute to dimeric architecture of hSMPD2 and that D111 − K116 loop domain is essential for substrate hydrolysis. Coupled with molecular docking, we clarify the binding pose of sphingomyelin, and site-directed mutagenesis further confirms key residues responsible for sphingomyelin binding. Hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamic (MD) simulations are utilized to elaborate the catalysis of hSMPD2 with the reported in vitro substrates, sphingomyelin and lyso-platelet activating fator (lyso-PAF). Our study provides mechanistic details that enhance our knowledge of lipid metabolism and may lead to an improved understanding of ceramide in disease and in cancer treatment.
Non-equilibrium dynamics of spin-lattice coupling
Authors: Ueda Hiroki , Mankowsky Roman , Paris Eugenio , Sander Mathias , Deng Yunpei , Liu Biaolong , Leroy Ludmila , Nag Abhishek , Skoropata Elizabeth , Wang Chennan , Ukleev Victor , Perren Gérard Sylvester , Dössegger Janine , Gurung Sabina , Svetina Cristian , Abreu Elsa , Savoini Matteo , Kimura Tsuyoshi , Patthey Luc , Razzoli Elia , Lemke Henrik Till , Johnson Steven Lee , Staub Urs 
Published: November 2023

AbstractQuantifying the dynamics of normal modes and how they interact with other excitations is of central importance in condensed matter. Spin-lattice coupling is relevant to several sub-fields of condensed matter physics; examples include spintronics, high-Tc superconductivity, and topological materials. However, experimental approaches that can directly measure it are rare and incomplete. Here we use time-resolved X-ray diffraction to directly access the ultrafast motion of atoms and spins following the coherent excitation of an electromagnon in a multiferroic hexaferrite. One striking outcome is the different phase shifts relative to the driving field of the two different components. This phase shift provides insight into the excitation process of such a coupled mode. This direct observation of combined lattice and magnetization dynamics paves the way to access the mode-selective spin-lattice coupling strength, which remains a missing fundamental parameter for ultrafast control of magnetism and is relevant to a wide variety of materials.
Resting-state global brain activity affects early β-amyloid accumulation in default mode network
Authors: Han Feng , Liu Xufu , Mailman Richard B. , Huang Xuemei , Liu Xiao 
Published: November 2023

AbstractIt remains unclear why β-amyloid (Aβ) plaque, a hallmark pathology of Alzheimer’s disease (AD), first accumulates cortically in the default mode network (DMN), years before AD diagnosis. Resting-state low-frequency ( < 0.1 Hz) global brain activity recently was linked to AD, presumably due to its role in glymphatic clearance. Here we show that the preferential Aβ accumulation in the DMN at the early stage of Aβ pathology was associated with the preferential reduction of global brain activity in the same regions. This can be partly explained by its failure to reach these regions as propagating waves. Together, these findings highlight the important role of resting-state global brain activity in early preferential Aβ deposition in the DMN.
CAR+ and CAR− T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies
Authors: Louie Raymond Hall Yip , Cai Curtis , Samir Jerome , Singh Mandeep , Deveson Ira W. , Ferguson James M. , Amos Timothy G. , McGuire Helen Marie , Gowrishankar Kavitha , Adikari Thiruni , Balderas Robert , Bonomi Martina , Ruella Marco , Bishop David , Gottlieb David , Blyth Emily , Micklethwaite Kenneth , Luciani Fabio 
Published: November 2023

AbstractChimeric antigen receptor (CAR) T cell therapy is effective in treating B cell malignancies, but factors influencing the persistence of functional CAR+ T cells, such as product composition, patients’ lymphodepletion, and immune reconstitution, are not well understood. To shed light on this issue, here we conduct a single-cell multi-omics analysis of transcriptional, clonal, and phenotypic profiles from pre- to 1-month post-infusion of CAR+ and CAR− T cells from patients from a CARTELL study (ACTRN12617001579381) who received a donor-derived 4-1BB CAR product targeting CD19. Following infusion, CAR+ T cells and CAR− T cells shows similar differentiation profiles with clonally expanded populations across heterogeneous phenotypes, demonstrating clonal lineages and phenotypic plasticity. We validate these findings in 31 patients with large B cell lymphoma treated with CD19 CAR T therapy. For these patients, we identify using longitudinal mass-cytometry data an association between NK-like subsets and clinical outcomes at 6 months with both CAR+ and CAR− T cells. These results suggest that non-CAR-derived signals can provide information about patients’ immune recovery and be used as correlate of clinically relevant parameters.
DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis
Authors: Li Qin , Zhou Jincong , Li Shuai , Zhang Weifeng , Du Yingxue , Li Kuan , Wang Yingxiang , Sun Qianwen 
Published: November 2023

AbstractGenome topology is tied to R-loop formation and genome stability. However, the regulatory mechanism remains to be elucidated. By establishing a system to sense the connections between R-loops and genome topology states, we show that inhibiting DNA topoisomerase 1 (TOP1i) triggers the global increase of R-loops (called topoR-loops) and DNA damages, which are exacerbated in the DNA damage repair-compromised mutant atm. A suppressor screen identifies a mutation in POL2A, the catalytic subunit of DNA polymerase ε, rescuing the TOP1i-induced topoR-loop accumulation and genome instability in atm. Importantly we find that a highly conserved junction domain between the exonuclease and polymerase domains in POL2A is required for modulating topoR-loops near DNA replication origins and facilitating faithful DNA replication. Our results suggest that DNA replication acts in concert with genome topological states to fine-tune R-loops and thereby maintain genome integrity, revealing a likely conserved regulatory mechanism of TOP1i resistance in chemotherapy for ATM-deficient cancers.
Lithium carbonate-promoted mixed rare earth oxides as a generalized strategy for oxidative coupling of methane with exceptional yields
Authors: Zhao Kun , Gao Yunfei , Wang Xijun , Lis Bar Mosevitzky , Liu Junchen , Jin Baitang , Smith Jacob , Huang Chuande , Gao Wenpei , Wang Xiaodong , Wang Xin , Zheng Anqing , Huang Zhen , Hu Jianli , Schömacker Reinhard , Wachs Israel E. , Li Fanxing 
Published: November 2023

AbstractThe oxidative coupling of methane to higher hydrocarbons offers a promising autothermal approach for direct methane conversion, but its progress has been hindered by yield limitations, high temperature requirements, and performance penalties at practical methane partial pressures (~1 atm). In this study, we report a class of Li2CO3-coated mixed rare earth oxides as highly effective redox catalysts for oxidative coupling of methane under a chemical looping scheme. This catalyst achieves a single-pass C2+ yield up to 30.6%, demonstrating stable performance at 700 °C and methane partial pressures up to 1.4 atm. In-situ characterizations and quantum chemistry calculations provide insights into the distinct roles of the mixed oxide core and Li2CO3 shell, as well as the interplay between the Pr oxidation state and active peroxide formation upon Li2CO3 coating. Furthermore, we establish a generalized correlation between Pr4+ content in the mixed lanthanide oxide and hydrocarbons yield, offering a valuable optimization strategy for this class of oxidative coupling of methane redox catalysts.
Ocean fronts as decadal thermostats modulating continental warming hiatus
Authors: Sung Mi-Kyung , An Soon-Il , Shin Jongsoo , Park Jae-Heung , Yang Young-Min , Kim Hyo-Jeong , Chang Minhee 
Published: November 2023

AbstractOver the past decade, an unexpected cooling trend has been observed in East Asia and North America during winter. Climate model simulations suggest that this pattern of stalled warming, besides accelerated warming, will repeat throughout the course of global warming, influenced by the natural decade-long variations in the climate system. However, understanding the exact factors affecting the pace of warming remains a challenge. Here we show that a pause in warming over continental areas—namely, local warming hiatus—can be accompanied by excessive heat accumulation north of the ocean fronts. This oceanic condition, often manifesting in the form of marine heatwaves, constrains the subseasonal growth of atmospheric planetary waves, significantly increasing the likelihood of cold extremes in downstream continents. Our results underscore the importance of closely monitoring changing ocean fronts in response to human-induced warming, which can potentially reshape the inherent decade-long fluctuations within regional climates over the long term.
COPI vesicle formation and N-myristoylation are targetable vulnerabilities of senescent cells
Authors: McHugh Domhnall , Sun Bin , Gutierrez-Muñoz Carmen , Hernández-González Fernanda , Mellone Massimiliano , Guiho Romain , Duran Imanol , Pombo Joaquim , Pietrocola Federico , Birch Jodie , Kallemeijn Wouter W. , Khadayate Sanjay , Dharmalingam Gopuraja , Vernia Santiago , Tate Edward W. , Martínez-Barbera Juan Pedro , Withers Dominic J. , Thomas Gareth J. , Serrano Manuel , Gil Jesús 
Published: November 2023

AbstractDrugs that selectively kill senescent cells (senolytics) improve the outcomes of cancer, fibrosis and age-related diseases. Despite their potential, our knowledge of the molecular pathways that affect the survival of senescent cells is limited. To discover senolytic targets, we performed RNAi screens and identified coatomer complex I (COPI) vesicle formation as a liability of senescent cells. Genetic or pharmacological inhibition of COPI results in Golgi dispersal, dysfunctional autophagy, and unfolded protein response-dependent apoptosis of senescent cells, and knockdown of COPI subunits improves the outcomes of cancer and fibrosis in mouse models. Drugs targeting COPI have poor pharmacological properties, but we find that N-myristoyltransferase inhibitors (NMTi) phenocopy COPI inhibition and are potent senolytics. NMTi selectively eliminated senescent cells and improved outcomes in models of cancer and non-alcoholic steatohepatitis. Our results suggest that senescent cells rely on a hyperactive secretory apparatus and that inhibiting trafficking kills senescent cells with the potential to treat various senescence-associated diseases.
Loss-of-function gs3 allele decreases methane emissions and increases grain yield in rice
Authors: Kwon Youngho , Lee Ji-Yoon , Choi Jisu , Lee So-Myeong , Kim Dajeong , Cha Jin-Kyung , Park Hyeonjin , Kang Ju-Won , Kim Tae Hee , Chae Ho Gyeong , Kabange Nkulu Rolly , Oh Ki-Won , Kim Pil Joo , Kwak Youn-Sig , Lee Jong-Hee , Ryu Choong-Min 
Published: November 2023

AbstractRice paddies are a major source of methane emissions. To meet the food demand of the growing population and to cope with global warming, reducing greenhouse gases and enhancing yields are critical. Here we demonstrate that a loss-of-function rice allele, gs3, mitigates methane emissions from methanogens by allocating more photosynthates to the grain and less to the root and increases yield by enlarging grain size and weight.
Comparison of a gelatin thrombin versus a modified absorbable polymer as a unique treatment for severe hepatic hemorrhage in swine
Authors: Sánchez del Valle Francisco José , De Nicolás Luis , Fernández Guillermo , Fernández Pedro , Gómez Esther , Aranaz Corral Inmaculada 
Published: November 2023

AbstractThere are many surgical techniques (packing, Pringle maneuver, etc.) and hemostatic agents to manage hepatic bleeding in trauma surgery. This study compares the effectiveness of two different types of hemostatic agents, one is an active flowable hemostat and the other is a passive hemostat made of modified absorbable polymers [MAP]. Both surgical technique and hemostatic agents can be used together as a means of controlling bleeding. We have hypothesized that a single hemostatic agent might be as effective as a unique hemostatic surgical technique. Twenty swine were prospectively randomized to receive either active Flowable (Floseal) or passive MAP powder (PerClot) hemostatic agents. We used a novel severe liver injury model that caused exsanguinating hemorrhage. The main outcome measure was total blood loss volume. The total volume of blood loss, from hepatic injury to minute 120, was significantly lower in the Flowable group (407.5 cm3; IqR: 195.0–805.0 cm3) compared to MAP group (1107.5 cm3; IqR: 822.5 to 1544.5 cm3) (Hodges–Lehmann median difference: − 645.0 cm3; 95% CI: − 1144.0 to − 280.0 cm3; p = 0.0087). The rate of blood loss was significantly lower in the flowable group compared with the MAP group as measured from time of injury to minutes 3, 9, 12, and 120 (except for 6 min). The mean arterial pressure gradually recovered in the flowable group by 24 h, whereas in the MAP group, the mean arterial pressure was consistently stayed below baseline values. Kaplan–Meier survival analysis indicated similar rates of death between study groups (Logrank test p = 0.3395). Both the flowable and the MAP hemostatic agents were able to effectively control surgical bleeding in a novel severe liver injury model, however, the flowable gelatin–thrombin agent provided quicker and better bleed control.
Attention-based solubility prediction of polysulfide and electrolyte analysis for lithium–sulfur batteries
Authors: Lee Jaewan , Yang Hongjun , Park Changyoung , Park Seong-Hyo , Jang Eunji , Kwack Hobeom , Lee Chang Hoon , Song Chang-ik , Choi Young Cheol , Han Sehui , Lee Honglak 
Published: November 2023

AbstractDuring the continuous charge and discharge process in lithium-sulfur batteries, one of the next-generation batteries, polysulfides are generated in the battery’s electrolyte, and impact its performance in terms of power and capacity by involving the process. The amount of polysulfides in the electrolyte could be estimated by the change of the Gibbs free energy of the electrolyte, $$\Delta _{mix}\textrm{G}$$

Δ

mix

G

in the presence of polysulfide. However, obtaining $$\Delta _{mix}\textrm{G}$$

Δ

mix

G

of the diverse mixtures of components in the electrolyte is a complex and expensive task that shows itself as a bottleneck in optimization of electrolytes. In this work, we present a machine-learning approach for predicting $$\Delta _{mix}\textrm{G}$$

Δ

mix

G

of electrolytes. The proposed architecture utilizes (1) an attention-based model (Attentive FP), a contrastive learning model (MolCLR) or morgan fingerprints to represent chemical components, and (2) transformers to account for the interactions between chemicals in the electrolyte. This architecture was not only capable of predicting electrolyte properties, including those of chemicals not used during training, but also providing insights into chemical interactions within electrolytes. It revealed that interactions with other chemicals relate to the logP and molecular weight of the chemicals.
Social opportunities and mate preference improve breeding success in Caribbean iguanas
Authors: Lemm Jeffrey M. , Martin Meghan S. 
Published: November 2023

AbstractConservation breeding of West Indian rock iguanas (Cyclura) has met with limited success historically. Many facilities witness high levels of aggression and mate incompatibility resulting in failed breeding introductions which often require animals to be separated. This may be due, in part, to lack of knowledge of how mate familiarity and preference affect reproductive outcomes in these species. We investigated whether social exposure during the pre-breeding season influenced copulation success, egg production, and breeding behaviors. Additionally, we examined whether mate preference, as determined by pre-mating dichotomous choice tests, increased these reproductive outcomes. Female rock iguanas that were socialized with males prior to breeding opportunities copulated with familiar males for longer periods of time than females that were not socialized. Socialization opportunities did not alter male reproductive success measurements or breeding behavior. Female rock iguanas introduced for mating to their preferred partners had a higher probability of successful copulations, higher average number of copulations, and less resting behavior during introductions than females mated to non-preferred males. Male mate preference had no effect on reproductive success measurements during mating introductions. These results indicate that socializing animals and providing mate choice opportunities increase breeding success of rock iguanas under managed care.
Assessment of green technology innovation on energy-environmental efficiency in China under the influence of environmental regulation considering spatial effects
Authors: Li Wei , Xu Xiaomin , Huang Shengzhong , Cheng Tong , Liu Mengkai , Zhang Can 
Published: November 2023

AbstractEnhancing energy-environmental efficiency (EEE) is crucial for achieving energy conservation and emission reduction goals. Investigating the mechanism through which green technology innovation (GTI) affects EEE and understanding the role of environmental regulation (ER) in this process provides a theoretical basis for efficient utilization of GTI and ER. This study employs a Dynamic Spatial Durbin Model and utilizes panel data from 2003 to 2017 for 30 Chinese provinces to examine the impact of GTI on EEE in the presence of ER. The empirical results reveal: (1) GTI has a U-shaped impact on EEE, primarily driven by SubGI. (2) GTI’s influence on EEE is predominantly reflected in PTE, also stemming from SubGI. (3) The interaction term between ER and GTI is 0.0022, while the GTI coefficient is − 0.0741, and the GTI quadratic term coefficient is 0.0007, all statistically significant. This implies that ER mitigates the negative impact of GTI on EEE while strengthening its positive effect. These findings provide empirical evidence and policy insights for more effectively utilizing GTI and ER to enhance EEE and achieve energy conservation and emissions reduction goals.