bluuebunny/crossref_metadata_2025_split huggingface dataset:
HSPB1 facilitates chemoresistance through inhibiting ferroptotic cancer cell death and regulating NF-κB signaling pathway in breast cancer
Authors: Liang Yiran , Wang Yajie , Zhang Yan , Ye Fangzhou , Luo Dan , Li Yaming , Jin Yuhan , Han Dianwen , Wang Zekun , Chen Bing , Zhao Wenjing , Wang Lijuan , Chen Xi , Ma Tingting , Kong Xiaoli , Yang Qifeng 
Published: July 2023

AbstractChemoresistance is one of the major causes of therapeutic failure and poor prognosis for breast cancer patients, especially for triple-negative breast cancer patients. However, the underlying mechanism remains elusive. Here, we identified novel functional roles of heat shock protein beta-1 (HSPB1), regulating chemoresistance and ferroptotic cell death in breast cancer. Based on TCGA and GEO databases, HSPB1 expression was upregulated in breast cancer tissues and associated with poor prognosis of breast cancer patients, which was considered an independent prognostic factor for breast cancer. Functional assays revealed that HSPB1 could promote cancer growth and metastasis in vitro and in vivo. Furthermore, HSPB1 facilitated doxorubicin (DOX) resistance through protecting breast cancer cells from drug-induced ferroptosis. Mechanistically, HSPB1 could bind with Ikβ-α and promote its ubiquitination-mediated degradation, leading to increased nuclear translocation and activation of NF-κB signaling. In addition, HSPB1 overexpression led to enhanced secretion of IL6, which further facilitated breast cancer progression. These findings revealed that HSPB1 upregulation might be a key driver to progression and chemoresistance through regulating ferroptosis in breast cancer while targeting HSPB1 could be an effective strategy against breast cancer.
miR-221/222 induce instability of p53 By downregulating deubiquitinase YOD1 in acute myeloid leukemia
Authors: Pei Han Zhong , Peng Zhiyong , Zhuang Xiaomei , Wang Xiaobo , Lu Bo , Guo Yao , Zhao Yuming , Zhang Dengyang , Xiao Yunjun , Gao Tianshun , Yu Liuting , He Chunxiao , Wu Shunjie , Baek Suk-Hwan , Zhao Zhizhuang Joe , Xu Xiaojun , Chen Yun 
Published: July 2023

AbstractAcute myeloid leukemia (AML) is a hematological malignancy characterized by the impaired differentiation and uncontrolled proliferation of myeloid blasts. Tumor suppressor p53 is often downregulated in AML cells via ubiquitination-mediated degradation. While the role of E3 ligase MDM2 in p53 ubiquitination is well-accepted, little is known about the involvement of deubiquitinases (DUBs). Herein, we found that the expression of YOD1, among several DUBs, is substantially reduced in blood cells from AML patients. We identified that YOD1 deubiqutinated and stabilized p53 through interaction via N-terminus of p53 and OTU domain of YOD1. In addition, expression levels of YOD1 were suppressed by elevated miR-221/222 in AML cells through binding to the 3′ untranslated region of YOD1, as verified by reporter gene assays. Treatment of cells with miR-221/222 mimics and inhibitors yielded the expected effects on YOD1 expressions, in agreement with the negative correlation observed between the expression levels of miR-221/222 and YOD1 in AML cells. Finally, overexpression of YOD1 stabilized p53, upregulated pro-apoptotic p53 downstream genes, and increased the sensitivity of AML cells to FLT3 inhibitors remarkably. Collectively, our study identified a pathway connecting miR-221/222, YOD1, and p53 in AML. Targeting miR-221/222 and stimulating YOD1 activity may improve the therapeutic effects of FLT3 inhibitors in patients with AML.
Loss of PML nuclear bodies in familial amyotrophic lateral sclerosis-frontotemporal dementia
Authors: Antoniani Francesco , Cimino Marco , Mediani Laura , Vinet Jonathan , Verde Enza M. , Secco Valentina , Yamoah Alfred , Tripathi Priyanka , Aronica Eleonora , Cicardi Maria E. , Trotti Davide , Sterneckert Jared , Goswami Anand , Carra Serena 
Published: July 2023

AbstractAmyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurodegenerative disorders that share genetic causes and pathogenic mechanisms. The critical genetic players of ALS and FTD are the TARDBP, FUS and C9orf72 genes, whose protein products, TDP-43, FUS and the C9orf72-dipeptide repeat proteins, accumulate in form of cytoplasmic inclusions. The majority of the studies focus on the understanding of how cells control TDP-43 and FUS aggregation in the cytoplasm, overlooking how dysfunctions occurring at the nuclear level may influence the maintenance of protein solubility outside of the nucleus. However, protein quality control (PQC) systems that maintain protein homeostasis comprise a cytoplasmic and a nuclear arm that are interconnected and share key players. It is thus conceivable that impairment of the nuclear arm of the PQC may have a negative impact on the cytoplasmic arm of the PQC, contributing to the formation of the cytoplasmic pathological inclusions. Here we focused on two stress-inducible condensates that act as transient deposition sites for misfolding-prone proteins: Promyelocytic leukemia protein (PML) nuclear bodies (PML-NBs) and cytoplasmic stress granules (SGs). Upon stress, PML-NBs compartmentalize misfolded proteins, including defective ribosomal products (DRiPs), and recruit chaperones and proteasomes to promote their nuclear clearance. SGs transiently sequester aggregation-prone RNA-binding proteins linked to ALS-FTD and mRNAs to attenuate their translation. We report that PML assembly is impaired in the human brain and spinal cord of familial C9orf72 and FUS ALS-FTD cases. We also show that defective PML-NB assembly impairs the compartmentalization of DRiPs in the nucleus, leading to their accumulation inside cytoplasmic SGs, negatively influencing SG dynamics. Although it is currently unclear what causes the decrease of PML-NBs in ALS-FTD, our data highlight the existence of a cross-talk between the cytoplasmic and nuclear PQC systems, whose alteration can contribute to SG accumulation and cytoplasmic protein aggregation in ALS-FTD.
Soft corrugated channel with synergistic exclusive discrimination gating for CO2 recognition in gas mixture
Authors: Gu Yifan , Zheng Jia-Jia , Otake Ken-ichi , Sakaki Shigeyoshi , Ashitani Hirotaka , Kubota Yoshiki , Kawaguchi Shogo , Yao Ming-Shui , Wang Ping , Wang Ying , Li Fengting , Kitagawa Susumu 
Published: July 2023

AbstractDeveloping artificial porous systems with high molecular recognition performance is critical but very challenging to achieve selective uptake of a particular component from a mixture of many similar species, regardless of the size and affinity of these competing species. A porous platform that integrates multiple recognition mechanisms working cooperatively for highly efficient guest identification is desired. Here, we designed a flexible porous coordination polymer (PCP) and realised a corrugated channel system that cooperatively responds to only target gas molecules by taking advantage of its stereochemical shape, location of binding sites, and structural softness. The binding sites and structural deformation act synergistically, exhibiting exclusive discrimination gating (EDG) effect for selective gate-opening adsorption of CO2 over nine similar gas molecules, including N2, CH4, CO, O2, H2, Ar, C2H6, and even higher-affinity gases such as C2H2 and C2H4. Combining in-situ crystallographic experiments with theoretical studies, it is clear that this unparalleled ability to decipher the CO2 molecule is achieved through the coordination of framework dynamics, guest diffusion, and interaction energetics. Furthermore, the gas co-adsorption and breakthrough separation performance render the obtained PCP an efficient adsorbent for CO2 capture from various gas mixtures.
Inheritance of associative memories and acquired cellular changes in C. elegans
Authors: Deshe Noa , Eliezer Yifat , Hoch Lihi , Itskovits Eyal , Bokman Eduard , Ben-Ezra Shachaf , Zaslaver Alon 
Published: July 2023

AbstractExperiences have been shown to modulate behavior and physiology of future generations in some contexts, but there is limited evidence for inheritance of associative memory in different species. Here, we trained C. elegans nematodes to associate an attractive odorant with stressful starvation conditions and revealed that this associative memory was transmitted to the F1 progeny who showed odor-evoked avoidance behavior. Moreover, the F1 and the F2 descendants of trained animals exhibited odor-evoked cellular stress responses, manifested by the translocation of DAF-16/FOXO to cells’ nuclei. Sperm, but not oocytes, transmitted these odor-evoked cellular stress responses which involved H3K9 and H3K36 methylations, the small RNA pathway machinery, and intact neuropeptide secretion. Activation of a single chemosensory neuron sufficed to induce a serotonin-mediated systemic stress response in both the parental trained generation and in its progeny. Moreover, inheritance of the cellular stress responses increased survival chances of the progeny as exposure to the training odorant allowed the animals to prepare in advance for an impending adversity. These findings suggest that in C. elegans associative memories and cellular changes may be transferred across generations.
Complementarity in Allen’s and Bergmann’s rules among birds
Authors: Baldwin Justin W. , Garcia-Porta Joan , Botero Carlos A. 
Published: July 2023

AbstractBiologists have long noted that endotherms tend to have larger bodies (Bergmann’s rule) and shorter appendages (Allen’s rule) in colder environments. Nevertheless, many taxonomic groups appear not to conform to these ‘rules’, and general explanations for these frequent exceptions are currently lacking. Here we note that by combining complementary changes in body and extremity size, lineages could theoretically respond to thermal gradients with smaller changes in either trait than those predicted by either Bergmann’s or Allen’s rule alone. To test this idea, we leverage geographic, ecological, phylogenetic, and morphological data on 6,974 non-migratory terrestrial bird species, and show that stronger family-wide changes in bill size over thermal gradients are correlated with more muted changes in body size. Additionally, we show that most bird families exhibit weak but appropriately directed changes in both traits, supporting the notion of complementarity in Bergmann’s and Allen’s rules. Finally, we show that the few families that exhibit significant gradients in either bill or body size, tend to be more speciose, widely distributed, or ecologically constrained. Our findings validate Bergmann’s and Allen’s logic and remind us that body and bill size are simply convenient proxies for their true quantity of interest: the surface-to-volume ratio.
The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel
Authors: Irie Katsumasa , Oda Yoshinori , Sumikama Takashi , Oshima Atsunori , Fujiyoshi Yoshinori 
Published: July 2023

AbstractDivalent cation block is observed in various tetrameric ion channels. For blocking, a divalent cation is thought to bind in the ion pathway of the channel, but such block has not yet been directly observed. So, the behaviour of these blocking divalent cations remains still uncertain. Here, we elucidated the mechanism of the divalent cation block by reproducing the blocking effect into NavAb, a well-studied tetrameric sodium channel. Our crystal structures of NavAb mutants show that the mutations increasing the hydrophilicity of the inner vestibule of the pore domain enable a divalent cation to stack on the ion pathway. Furthermore, non-equilibrium molecular dynamics simulation showed that the stacking calcium ion repel sodium ion at the bottom of the selectivity filter. These results suggest the primary process of the divalent cation block mechanism in tetrameric cation channels.
Carbene-catalyzed chemoselective reaction of unsymmetric enedials for access to Furo[2,3-b]pyrroles
Authors: Fan Guodong , Wang Qingyun , Xu Jun , Zheng Pengcheng , Chi Yonggui Robin 
Published: July 2023

AbstractA carbene-catalyzed chemoselective reaction of unsymmetric enedials is disclosed. The reaction provides a concise access to bicyclic furo[2,3-b]pyrroles derivatives in excellent selectivity. A main challenge in this reaction is chemoselective reaction of the two aldehyde moieties in the enedial substrates. Mechanistic studies via experiments suggest that our chemoselectivity controls are mostly achieved on the reducing properties of different sited Breslow intermediates. Several side reactions processes and the corresponding side adducts are also studied by high resolution mass spectroscopy analysis. Our method allows for efficient assembly of the furo[2,3-b]pyrrole structural moieties and their analogues widely found in natural products and pharmaceuticals.
Cooperative microbial interactions drive spatial segregation in porous environments
Authors: Wu Yichao , Fu Chengxia , Peacock Caroline L. , Sørensen Søren J. , Redmile-Gordon Marc A. , Xiao Ke-Qing , Gao Chunhui , Liu Jun , Huang Qiaoyun , Li Zixue , Song Peiyi , Zhu Yongguan , Zhou Jizhong , Cai Peng 
Published: July 2023

AbstractThe role of microbial interactions and the underlying mechanisms that shape complex biofilm communities are poorly understood. Here we employ a microfluidic chip to represent porous subsurface environments and show that cooperative microbial interactions between free-living and biofilm-forming bacteria trigger active spatial segregation to promote their respective dominance in segregated microhabitats. During initial colonization, free-living and biofilm-forming microbes are segregated from the mixed planktonic inoculum to occupy the ambient fluid and grain surface. Contrary to spatial exclusion through competition, the active spatial segregation is induced by cooperative interactions which improves the fitness of both biofilm and planktonic populations. We further show that free-living Arthrobacter induces the surface colonization by scavenging the biofilm inhibitor, D-amino acids and receives benefits from the public goods secreted by the biofilm-forming strains. Collectively, our results reveal how cooperative microbial interactions may contribute to microbial coexistence in segregated microhabitats and drive subsurface biofilm community succession.
Photothermal recycling of waste polyolefin plastics into liquid fuels with high selectivity under solvent-free conditions
Authors: Miao Yingxuan , Zhao Yunxuan , Waterhouse Geoffrey I. N. , Shi Run , Wu Li-Zhu , Zhang Tierui 
Published: July 2023

AbstractThe widespread use of polyolefin plastics in modern societies generates huge amounts of plastic waste. With a view toward sustainability, researchers are now seeking novel and low-cost strategies for recycling and valorizing polyolefin plastics. Herein, we report the successful development of a photothermal catalytic recycling system for transforming polyolefin plastics into liquid/waxy fuels under concentrated sunlight or xenon lamp irradiation. Photothermal heating of a Ru/TiO2 catalyst to 200–300 °C in the presence of polyolefin plastics results in intimate catalyst-plastic contact and controllable hydrogenolysis of C-C and C-H bonds in the polymer chains (mediated by Ru sites). By optimizing the reaction temperature and pressure, the complete conversion of waste polyolefins into valuable liquid fuels (86% gasoline- and diesel-range hydrocarbons, C5-C21) is possible in short periods (3 h). This work demonstrates a simple and efficient strategy for recycling waste polyolefin plastics using abundant solar energy.
In vitro and in vivo characterization of SARS-CoV-2 resistance to ensitrelvir
Authors: Kiso Maki , Yamayoshi Seiya , Iida Shun , Furusawa Yuri , Hirata Yuichiro , Uraki Ryuta , Imai Masaki , Suzuki Tadaki , Kawaoka Yoshihiro 
Published: July 2023

AbstractEnsitrelvir, an oral antiviral agent that targets a SARS-CoV-2 main protease (3CLpro or Nsp5), is clinically useful against SARS-CoV-2 including its omicron variants. Since most omicron subvariants have reduced sensitivity to most monoclonal antibody therapies, SARS-CoV-2 resistance to other antivirals including main protease inhibitors such as ensitrelvir is a major public health concern. Here, repeating passages of SARS-CoV-2 in the presence of ensitrelvir revealed that the M49L and E166A substitutions in Nsp5 are responsible for reduced sensitivity to ensitrelvir. Both substitutions reduced in vitro virus growth in the absence of ensitrelvir. The combination of the M49L and E166A substitutions allowed the virus to largely evade the suppressive effect of ensitrelvir in vitro. The virus possessing Nsp5-M49L showed similar pathogenicity to wild-type virus, whereas the virus possessing Nsp5-E166A or Nsp5-M49L/E166A slightly attenuated. Ensitrelvir treatment of hamsters infected with the virus possessing Nsp5-M49L/E166A was ineffective; however, nirmatrelvir or molnupiravir treatment was effective. Therefore, it is important to closely monitor the emergence of ensitrelvir-resistant SARS-CoV-2 variants to guide antiviral treatment selection.
Mass spectrometry imaging for biosolids characterization to assess ecological or health risks before reuse
Authors: Villette Claire , Maurer Loïc , Zumsteg Julie , Mutterer Jérôme , Wanko Adrien , Heintz Dimitri 
Published: July 2023

AbstractBiosolids are byproducts of wastewater treatment. With the increasing global population, the amounts of wastewater to be treated are expanding, along with the amounts of biosolids generated. The reuse of biosolids is now accepted for diversified applications in fields such as agriculture, engineering, agro-forestry. However, biosolids are known to be potential carriers of compounds that can be toxic to living beings or alter the environment. Therefore, biosolid reuse is subject to regulations, mandatory analyses are performed on heavy metals, persistent organic pollutants or pathogens. Conventional methods for the analysis of heavy metals and persistent organic pollutants are demanding, lengthy, and sometimes unsafe. Here, we propose mass spectrometry imaging as a faster and safer method using small amounts of material to monitor heavy metals and persistent organic pollutants in different types of biosolids, allowing for ecological and health risk assessment before reuse. Our methodology can be extended to other soil-like matrices.
A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint
Authors: Singh Vidisha , Naldi Aurelien , Soliman Sylvain , Niarakis Anna 
Published: July 2023

AbstractRheumatoid arthritis (RA) is a complex autoimmune disease with an unknown aetiology. However, rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) play a significant role in initiating and perpetuating destructive joint inflammation by expressing immuno-modulating cytokines, adhesion molecules, and matrix remodelling enzymes. In addition, RA-FLS are primary drivers of inflammation, displaying high proliferative rates and an apoptosis-resistant phenotype. Thus, RA-FLS-directed therapies could become a complementary approach to immune-directed therapies by predicting the optimal conditions that would favour RA-FLS apoptosis, limit inflammation, slow the proliferation rate and minimise bone erosion and cartilage destruction. In this paper, we present a large-scale Boolean model for RA-FLS that consists of five submodels focusing on apoptosis, cell proliferation, matrix degradation, bone erosion and inflammation. The five-phenotype-specific submodels can be simulated independently or as a global model. In silico simulations and perturbations reproduced the expected biological behaviour of the system under defined initial conditions and input values. The model was then used to mimic the effect of mono or combined therapeutic treatments and predict novel targets and drug candidates through drug repurposing analysis.
Altered neutrophil-to-lymphocyte ratio in patients with non-affective first episode psychosis and its relationship with symptom severity and cognitive impairment
Authors: Leung Kwan Keung , Wong Yip Chau , Shea Ka Sin , Chan Sheung Chun , Chang Wing Chung , Mo Yi Man Flora , Chan Sau Man Sandra 
Published: July 2023

AbstractSignatures of immune dysregulation as clinical biomarker for psychosis have remained unclear. We aimed to compare the Neutrophil-to-lymphocyte ratio (NLR) of patients with acute non-affective first-episode psychosis (FEP) with healthy controls after accounting for emotional states. We also explored the associations of NLR with symptom severity, onset profile and cognitive functions. The NLR was enumerated from complete blood count taken within a week of assessment. All FEP patients were rated on the Positive and Negative Syndrome Scale (PANSS) and the Clinician Global Impression-Severity (CGI-S) with verbal memory and executive functions assessed with the Cambridge Neuropsychological Test Automated Battery. Prevailing emotional state was measured with Beck Depression Inventory-II and Beck Anxiety Inventory. Out of seventy-nine consecutive FEP patients presenting to the study site, twenty-seven subjects were eligible and recruited. Twenty-seven age-/sex-matched controls were recruited. FEP patients had an NLR of 1.886 over the controls after accounting for scores on emotional states. The NLR of FEP patients was positively associated with CGI-S scores, PANSS positive symptom, disorganization and excitation scores. There was no significant correlation between NLR with the duration of untreated psychosis and cognitive performances. These findings support using NLR as a clinical biomarker in FEP, purporting further prospective study to measure NLR changes in the course of treatment.
Advantages and potential limitations of applying AFM kymograph analysis to pharmaceutically relevant membrane proteins in lipid bilayers
Authors: Schaefer Katherine G. , Roberts Arthur G. , King Gavin M. 
Published: July 2023

AbstractMembrane proteins play critical roles in disease and in the disposition of many pharmaceuticals. A prime example is P-glycoprotein (Pgp) which moves a diverse range of drugs across membranes and out of the cell before a therapeutic payload can be delivered. Conventional structural biology methods have provided a valuable framework for comprehending the complex conformational changes underlying Pgp function, which also includes ATPase activity, but the lack of real-time information hinders understanding. Atomic force microscopy (AFM) is a single-molecule technique that is well-suited for studying active membrane proteins in bilayers and is poised to advance the field beyond static snapshots. After verifying Pgp activity in surface-support bilayers, we used kymograph analysis in conjunction with AFM imaging and simulations to study structural transitions at the 100 ms timescale. Though kymographs are frequently employed to boost temporal resolution, the limitations of the method have not been well characterized, especially for sparse non-crystalline distributions of pharmaceutically relevant membrane proteins like Pgp. Common experimental challenges are analyzed, including protein orientation, instrument noise, and drift. Surprisingly, a lateral drift of 75% of the protein dimension leads to only a 12% probability of erroneous state transition detection; average dwell time error achieves a maximum value of 6%. Rotational drift of proteins like Pgp, with azimuthally-dependent maximum heights, can lead to artifactual transitions. Torsional constraints can alleviate this potential pitfall. Confidence in detected transitions can be increased by adding conformation-altering ligands such as non-hydrolysable analogs. Overall, the data indicate that AFM kymographs are a viable method to access conformational dynamics for Pgp, but generalizations of the method should be made with caution.