bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protection Against Pneumonia Induced By Vaccination With Fimbriae Subunits
FromKlebsiella pneumoniae
Authors: Assoni Lucas , Ciaparin Isabelle , Trentini Monalisa , Baboghlian Juliana , Rodrigo Gabriel , Ferreira Brenda Vieira , Pereira José Aires , Martinez Carlos Augusto Real , Caldas Ferraz Lucio Fabio , Girardello Raquel , de Carvalho Lucas Miguel , Hakansson Anders P. , Converso Thiago Rojas , Darrieux Michelle 
Published: January 2025

ABSTRACT
Klebsiella pneumoniaeinfections pose a great
burden worldwide, causing high morbidity and mortality, which are worsened by
the increase in multidrug resistant strains. New therapeutic/prophylactic
strategies are urgently needed to overcome antibiotic resistance and reduce the
health and economic impacts of diseases caused by this pathogen. Fimbriae are
important virulence factors involved in biofilm formation and adhesion to host
cells. Their exposed location, conservation among clinical isolates and adjuvant
properties make them interesting candidates for inclusion in protein-based
vaccines. Therefore, the present work investigated the immunological potential
of type 1 and 3 fimbriae subunits in a murine model ofK.
pneumoniaelung infection. Subcutaneous immunization with
recombinant FimA and MrkA induced high IgG1 production; the antibodies
efficiently recognized the native proteins at the bacterial surface, promoted C3
deposition and reduced biofilm formation byK. pneumoniae in
vitro. Mice vaccinated with the co-administered proteins
reduced the bacterial loads in the lungs after intranasal challenge, less
inflammation and tissue damage. The results suggest that both type 1 and type 3
fimbriae contribute to protection againstK.
pneumoniaelung infection, inducing antibodies that bind to the
bacteria and favor complement deposition and clearance by the host, while
inhibiting biofilm formation.
An ultra-long heavy chain bovine antibody neutralizes SARS-CoV-2 and reacts
broadly with sarbecoviruses
Authors: Tsoleridis Theocharis , Fan Chengcheng , Park Emily J. , Duncan Joshua D. , Sharma Parul , Wartnaby Sophie , Chappell Joseph G. , Kipar Anja , Bentley Eleanor G. , Kirby Adam , Han Ximeng , Coleman Christopher M. , Flyak Andrew I. , McClure C Patrick , Rho Semi , Johansson Daniel X. , Persson Mats A.A. , Tarr Alexander W. , Haig David , Stewart James P. , Bjorkman Pamela J. , Urbanowicz Richard A. , Ball Jonathan K. 
Published: January 2025

Abstract
The threat of emergence of further SARS-CoV-2 variants, and the future
spillover potential of other sarbecoviruses has prompted continued efforts to
isolate broadly reactive monoclonal antibodies for therapeutic use. In this
study, we generated monoclonal antibodies from immunised cattle, primarily
because of their ability to produce antibodies with ultra-long heavy chain
complementarity determining region 3 (CDRH3) domains. Such antibodies have been
shown to have potent and cross-reactive neutralisation phenotypes in other virus
infections. Following extended immunisation with different forms of spike
protein and using single B-cell sorting and phage display techniques, we
isolated 33 mAbs, including 10 with ultra-long CDRH3s (>50 amino acids). Of
these, mAbs P7 and 99 exhibited remarkable neutralisation breadth and potency.
Notably, mAb P7, which possessed an ultra-long CDRH3, neutralised all tested
variants, including SARS-CoV-1, with IC50values ranging
from 0.01 µg/mL to 1.06 µg/mL. This antibody was also cross-reactive against a
panel of RBDs from diverse sarbecovirus species. Structural studies revealed
that mAb 99 targets a region of the receptor-binding domain (RBD) of the spike
protein that overlaps with the ACE2 binding site. Although the structure of the
P7 Fab-RBD complex was not resolvable, data suggest P7 induces trimer
dissociation by binding to an occluded RBD epitope, likely mediated by the
extended CDRH3 structure. Syrian hamster challenge experiments, using several
VOCs, showed that mAbs P7 and 99 significantly reduced lung viral load. These
findings highlight the potential of bovine-derived, especially those possessing
ultra-long CDRH3s, as effective therapeutics against current and future
sarbecovirus threats.

One Sentence Summary
Monoclonal antibodies derived from SARS-CoV-2 immunised cows exhibit
pan-sarbecovirus reactivity, highlighting their potential use as
therapeutics
Dissection of ergosterol metabolism reveals a pathway optimized for membrane
phase separation
Authors: Juarez-Contreras Israel , Lopes Laura J.S. , Holt Jamie , Yu-Liao Lorena , O’Shea Katherine , Ruiz-Ruiz Jose , Sodt Alexander , Budin Itay 
Published: January 2025

Abstract
Sterols are among the most abundant lipids in eukaryotic cells, yet are
synthesized through notoriously long metabolic pathways. It has been proposed
that the molecular evolution of such pathways must have required each step to
increase the capacity of its product to condense and order phospholipids. Here
we carry out a systematic analysis of the ergosterol pathway that leverages the
yeast vacuole’s capacity to phase-separate as a predictive biophysical readout
for each intermediate. In the post-synthetic steps specific to ergosterol
biosynthesis, we find that successive modifications act to oscillate ordering
capacity, settling on a level that supports phase separation while retaining
fluidity of the resulting domains. Simulations carried out with each
intermediate showed how conformers in the sterol’s alkyl tail are capable of
modulating long-range ordering of phospholipids, which could underlie changes in
phase behavior. Our results indicate that the complexity of sterol metabolism
could have resulted from the need to balance lipid interactions required for
membrane organization.
Development of Severity Index for Oral Epithelial Dysplasia Using Fuzzy Group Decision Making Algorithm
Authors: Nawn Debaleena , Lahiri Pooja , Dey Budhaditya , Pal Mousumi , Paul Ranjan Rashmi , Adhya Debashree Guha , Chakraborty Debjani , Chatterjee Jyotirmoy 
Published: January 2025

AbstractBackgroundOral epithelial dysplasia (OED) grading suffers from several levels of uncertainties and imprecision. An index is preferred in this context to improve reliability and reduce subjectivity in diagnostic decision making. In this study, a fuzzy logic-based disease severity index (SI) is formulated considering standard histopathological features used in OED grading.MethodsOral onco-pathologists were asked to independently provide weights of different features, according to their clinical significance in the context of dysplasia. Aggregated weight of each feature was calculated from individual assessment of different onco-pathologists by a fuzzy logic-based group decision making algorithm. Confidence levels of experts were also included to improve robustness of the method. SI was generated by integrating abnormality score of each feature with its weight. Abnormality degree of each feature was expressed in linguistic terms by onco-pathologists which were subsequently represented by a triangular fuzzy number. Fuzzy membership function was used as it can capture the ambiguity of experts’ opinion regarding abnormality of individual feature. Finally, defuzzification was used to get a crisp index from weighted sum of all features.ResultSI was found to be statistically different (p<0.01) for different grades of dysplasia i.e mild, moderate and severe with added advantage of stratifying each grade in low and high subcategory.ConclusionKey contribution of our work is that we have developed a fuzzy logic-based group consensus process regarding weights of histopathological features for OED grading. Present methodology of developing SI can be applied to other medical decision-making problems as well.HighlightsA severity index is proposed to improve reproducibility of oral epithelial dysplasia grading.Clinical significance of each histopathological and cytopathological feature in the context of dysplasia is reflected by its weight.A fuzzy logic-based group decision making algorithm is used to reduce subjectivity of features’ weights.Confidence level of oral onco-pathologists are given due importance in derivation of aggregated weight of each feature.Abnormality score of each feature is evaluated in fuzzy scale to capture clinicians’ ambiguity.Present methodology may be useful for developing indices of other diseases.Abstract FigureGraphical abstract
Hyperacute Response Proteins (HARPs) synthesized on γ-tubulin-FTO-MARK4 translation microdomains upon exposure to stress, regulate stress response in cancer
Authors: Saleme Bruno , Tejay Saymon , Dembele Paul , Farraj Rabih Abou , Zhang Yongneng , Liu Yongsheng , Boukouris Aristeidis E. , Zervopoulos Sotirios D. , Haromy Alois , Zhao Yuan-Yuan , Braun Shelly , Saleme William , Sun Xuejun , Fahlman Richard , Glover Mark , Kinnaird Adam , Sutendra Gopinath , Michelakis Evangelos D. 
Published: January 2025

SummaryCompared to normal, cancer cells are particularly resistant to stress, and their immediate response to stress is critical for their subsequent multilayered adaptation programs which pose a major clinical challenge. With unbiased proteomics and transcriptomics analysis, we identified a list of HARPs synthesized from pre-existing mRNAs within 20 min of diverse stresses in A549 cancer cells, despite the known suppressed global translation in stress. HARP mRNAs were translated on microtubule-associated translation microdomains (MATMs) located on γ-tubulin, that host FTO and specialized cytoskeletal ribosomes, structurally and functionally distinct from ER and cytosolic ribosomes. FTO exited the nucleus immediately after stress and was activated by the microtubule-associated stress kinase MARK4 via T6 phosphorylation. Activated FTO demethylated a translation-inhibiting mRNA methylation (m6A) signature, facilitating compartmentalized HARP translation on MATMs, while non-HARP mRNA remained inhibited. FTO or MARK4 inhibition suppressed HARP synthesis and increased apoptosis post various stresses, including chemotherapy. These data were confirmed in 4 additional cancer cell lines and normal fibroblasts. Using the Protein Atlas database, we found that high levels of our identified HARPs had on average a 35% decrease on patient 5-year survival in prevalent and resistant cancers (breast, lung, liver, pancreas). γ-tubulin, FTO and MARK4 are therapeutic targets for many cancers, through their ability to comprehensively promote HARPs translation, a potential Achille’s heel for cancer’s resistance to physiologic or therapeutic stress, offering a new window in stress biology.
Functional interplay between condensin I and topoisomerase IIα in single-molecule DNA compaction
Authors: Tsubota Yuko , Shintomi Keishi , Kinoshita Kazuhisa , Masahara-Negishi Yuki , Aizawa Yuuki , Shima Masami , Hirano Tatsuya , Nishiyama Tomoko 
Published: January 2025

AbstractCondensin I and topoisomerase IIα (topo IIα) are chromosomal ATPases essential for mitotic chromosome assembly. Mechanistically how the two ATPases cooperate to assemble mitotic chromosomes remains unknown. Here we use total internal reflection fluorescence microscopy to analyze the interplay between condensin I and topo IIα at single-molecule resolution. As observed in previous studies, condensin I alone predominantly forms DNA loops in an ATP-dependent manner. However, when topo IIα is included in the reaction, condensin I forms stable compact structures (termed “lumps”) in a manner dependent on the C-terminal domain of topo IIα. Each of the stable lumps contains a single condensin I complex and a single topo IIα dimer. Remarkably, we find that topo IIα, when catalytically active, renders the lumps resistant to protease treatment. Several lines of evidence show that the protease-resistant lumps contain knotted DNA. A mutant condensin I complex defective in ATP hydrolysis, together with topo IIα, forms smaller lumps in which the probability of DNA knotting is greatly reduced. Our results demonstrate how topo IIα-mediated strand passage is coupled with condensin I-mediated loop extrusion to generate a compact DNA structure. Together with recent studies, we discuss the functional implications of these observations in mitotic chromosome assembly and stabilization.
Protein Kinase C positively regulates peroxisome biogenesis by promoting peroxisome-endoplasmic reticulum interaction
Authors: Borisyuk Anya , Howman Charlotte , Pattabiraman Sundararaghavan , Kaganovich Daniel , Amen Triana 
Published: January 2025

AbstractPeroxisomes carry out a diverse set of metabolic functions, including oxidation of very long-chained fatty acids, degradation of D-amino acids and hydrogen peroxide, and bile acid production. Many of these functions are upregulated on demand, therefore cells control peroxisome abundance, and by extension peroxisome function, in response to environmental and developmental cues. The mechanisms upregulating peroxisomes in mammalian cells have remained unclear. Here we identify a signaling regulatory network and a mechanism that coordinate cellular demand for peroxisomes and peroxisome abundance by regulating peroxisome proliferation. We show that protein kinase C (PKC) promotes peroxisome PEX11b-dependent formation. PKC activation leads to an increase in peroxisome formation, promoting peroxisome-ER contact site formation through inactivation of GSK3β. We show that removal of VAPA and VAPB impairs peroxisome biogenesis and PKC regulation. Inhibition of PKC reduces peroxisome-ER interactions, leading to a decrease in peroxisome abundance. During neuronal differentiation, active PKC leads to a significant increase in peroxisome formation. We propose that peroxisomal regulation by transient active PKC signaling enables rapid and fine-tuned responses to the need for peroxisomal activity.
The effect of surface properties on the interactions of particles and marine mucous filters
Authors: Jacobi Yuval , Epstein José A. , Paz Ariella , Shavit Uri , Yahel Gitai , Ramon Guy Z. 
Published: January 2025

AbstractFree-living suspended cells form the foundation of marine food webs, making suspension feeding a key mode in aquatic ecosystems. Suspension feeders across phyla use diverse filtration mechanisms, often relying on mucus and low-pressure pumps with high filtration efficiencies and self-cleaning capabilities. Traditionally, particle capture was thought to depend on size alone, but recent evidence highlights the importance of physicochemical surface interactions between prey cells and filtration apparatuses. In this study, we investigated the capture of 0.3-3 µm particles by ascidians and found that coating particles with amphiphilic polymers altered their mobility within the mucous filter, affecting capture efficiency. Surface interactions, such as steric repulsion, significantly influence particle mobility and inversely correlate with capture success. Furthermore, we discovered that the mucous filter in ascidians is much thicker (∼5 µm) than previously believed, functioning as a continuous sheet. These findings suggest a need to reevaluate suspension feeding models, with implications for marine ecosystems and filtration technology development.
Macromolecular Diamidobenzimidazole Conjugates Activate STING
Authors: Arora Karan , Sheehy Taylor L. , Schulman Jacob A. , Kimmel Blaise R. , McAtee Caitlin , Bharti Vijaya , Weaver Alissa M. , Wilson John T. 
Published: January 2025

AbstractPharmacologic activation of the stimulator of interferon genes (STING) pathway has broad potential applications, including the treatment of cancer and viral infections, which has motivated the synthesis and testing of a diversity of STING agonists as next generation immunotherapeutics. A promising class of STING agonists are the non-nucleotide, small molecule, dimeric-amidobenzimidazoles (diABZI), which have been recently used in the synthesis of polymer- and antibody-drug conjugates to improve pharmacokinetics, modulate biodistribution, and to confer other favorable properties for specific disease applications. These approaches have leveraged diABZI variants functionalized with reactive handles and enzyme-cleavable linkers at the 7-position of the benzimidazole for conjugation to and tunable drug release from carriers. However, since this position does not interact with STING and is exposed from the binding pocket when bound in an “open lid” configuration, we sought to evaluate the activity of macromolecular diABZI conjugates that lack enzymatic release and are instead conjugated to polymers via a stable linker. By covalently ligating diABZI to 5 or 20 kDa mPEG chains via an amide bond, we surprisingly found that these conjugates could activate STINGin vitro.To further evaluate this phenomenon, we designed a diABZI-functionalized RAFT chain transfer agent that provided an enabling tool for synthesis of large, hydrophilic, dimethylacrylamide (DMA) polymers directly from a single agonist and we found that these conjugates also elicited STING activationin vitrowith similar kinetics to highly potent small molecule analogs. We further demonstrated thein vivoactivity of these macromolecular diABZI platforms, which inhibited tumor growth to a similar extent as small molecule variants. Using flow cytometry and fluorescence microscopy to evaluate intracellular uptake and distribution of Cy5-labeled analogs, our data indicate that although diABZI-DMA conjugates enter cells via endocytosis, they can still colocalize with the ER, suggesting that intracellular trafficking processes can promote delivery of endocytosed macromolecular diABZI compounds to STING. In conclusion, we have described new chemical strategies for the synthesis of stable macromolecular diABZI conjugates with unexpectedly high immunostimulatory potency, findings with potential implications for the design of polymer-drug conjugates for STING agonist delivery that also further motivate investigation of endosomal and intracellular trafficking as an alternative route for achieving STING activation.
A hydrophobic core in the coiled-coil domain essential for NRC resistosome function
Authors: Wang Hung-Yu , Lee Kim-Teng , Goh Foong-Jing , Bozkurt Tolga O. , Wu Chih-Hang 
Published: January 2025

AbstractThe NRC (Nucleotide-binding leucine-rich repeat protein (NLR)-required for cell death) family represents a group of helper NLRs that are required by sensor NLRs to execute cell death during pathogen infection. NRC proteins are classified as CNL, which contain a coiled-coil (CC) domain in their N-terminal region. Previous studies highlighted the importance of the MADA motif in the first alpha helix of the CC domain for NRC-mediated defense responses. However, how other alpha helices in the CC domain contribute to NRC function remains unclear. In this study, we identified a novel hydrophobic feature localized in the CC domain barrel that contributes to NRC-mediated immunity. We screened the conserved hydrophobic residues among NRCs and identified seven required for NRC4-mediated cell death. Structural analysis revealed that four of these residues form a hydrophobic center in the CC domain. We further demonstrated that this hydrophobic core is important for NRC4 subcellular localization, oligomerization, and phospholipid association, but not for NRC4 focal accumulation on the extra-haustorial membrane duringPhytophthora infestansinfection. By comparing sequences of multiple NLRs in the NRC superclade, we found that the residues of the hydrophobic core in sensor NLRs exhibit greater diversity than those in helper NLRs. Cell death assays indicated that the function of the hydrophobic core has degenerated in certain sensor NLRs but remains essential in NRCs and ZAR1. Overall, our study highlights a novel hydrophobic feature in the CC domain of the NRC and its contribution to NLR-mediated immunity.SignificancePlant intracellular immune receptors known as NRCs (NLR-required for cell death) form resistosome complexes to activate pathogen defense, yet the contributions of coiled-coil (CC) domain features beyond the MADA motif remain unclear. Here, we uncover a novel hydrophobic core in the CC domain of NRC4 that is critical for subcellular localization, oligomerization, and phospholipid association, and thus for effective immune signaling. Intriguingly, while this hydrophobic feature is highly conserved among helper NRCs and singleton NLR ZAR1, the corresponding amino acid residues show greater sequence diversity or has been functionally degenerated in most other sensor NLRs, suggesting a divergence in sequences and in function. Our findings highlight the importance of this previously uncharacterized structural element for NRC-mediated cell death.
Spatial profiling identifies regionally distinct microenvironments and targetable immunosuppressive mechanisms in pediatric osteosarcoma pulmonary metastases
Authors: Eigenbrood Jason , Wong Nathan , Mallory Paul , Pereira Janice , Morris Douglass W , Beck Jessica A , Cronk James C , Sayers Carly M , Mendez Monica , Kaiser Linus , Galindo Julie , Singh Jatinder , Cardamone Ashley , Pore Milind , Kelly Michael , LeBlanc Amy K , Cotter Jennifer , Kaplan Rosandra N , McEachron Troy A 
Published: January 2025

ABSTRACTOsteosarcoma is the most common malignant bone tumor in young patients and remains a significant clinical challenge, particularly in the context of metastatic disease. Despite extensive documentation of genomic alterations in osteosarcoma, studies detailing the immunosuppressive mechanisms within the metastatic osteosarcoma microenvironment are lacking. Our objective was to characterize the spatial transcriptional landscape of metastatic osteosarcoma to reveal these immunosuppressive mechanisms and identify promising therapeutic targets. Here, we performed spatial transcriptional profiling on a cohort of osteosarcoma pulmonary metastases from pediatric patients. We reveal a conserved spatial gene expression pattern resembling a foreign body granuloma, characterized by peripheral inflammatory signaling, fibrocollagenous encapsulation, lymphocyte exclusion, and peritumoral macrophage accumulation. We also show that the intratumoral microenvironment of these lesions lack inflammatory signaling. Additionally, we identified CXCR4 as an actionable immunomodulatory target that bridges both the intratumoral and extratumoral microenvironments and highlights the spatial heterogeneity and complexity of this pathway. Collectively, this study reveals that metastatic osteosarcoma specimens are comprised of multiple regionally distinct immunosuppressive microenvironments.