bluuebunny/crossref_metadata_2025_split huggingface dataset:
Male and female gametophytes meet after winter: Testing the overwintering hypothesis for delayed fertilization in Japanese stone oak
Authors: Shagawa Takenori , Ogawa Kota , Kanaoka Masahiro M , Satake Akiko 
Published: October 2024

ABSTRACTPremiseFertilization delays of nearly a year have been observed in many acorn-producing Fagaceae trees. Despite this long-standing recognition, the underlying mechanisms and adaptive significance of delayed fertilization remain largely unexplored. It has been hypothesized that these prolonged delays may serve as an adaptive strategy, allowing ovules to be fertilized and seeds to develop during more favorable seasons, thereby avoiding the adverse conditions of winter. However, empirical evidence to support this hypothesis is still lacking.MethodsTo test the overwintering hypothesis, we observed the seasonal progression of pollen tube growth and ovule development inLithocarpus edulis, a species exhibiting two flowering seasons, spring and autumn. We conducted monthly observations of pollen tube growth and ovule development in both spring and autumn flower samples. We employed microtome techniques and scanning confocal microscopy to closely examine the seasonal progression of pollen tube growth and ovule development.ResultsWe found that pollen tubes were arrested at the style-joining site, and ovules remained immature in both spring and autumn samples prior to winter. Following winter, pollen tube regrowth and ovule maturation were synchronized in the subsequent spring in both spring and autumn samples.ConclusionsOur results support the overwintering hypothesis, suggesting that delayed fertilization may serve as an adaptive strategy to ensure fertilization in spring, overcoming the reproductive challenges posed by cold winter conditions. Our study introduces a new avenue for studying the temporal organization of plant reproductive phenology, specifically the alignment of flowering, pollination, fertilization, and fruiting in seasonal environments.
Mapping DHPS Evolvability: Identification of Novel Evolutionarily Critical Sub-Structure through Evolutionary and Structural Analyses of DHPS
Authors: Sanyal Dwipanjan , Shivram A. , Banerjee Suharto , Uversky Vladimir N. , Chivukula Aneesh , Chattopadhyay Krishnananda , Chowdhury Sourav 
Published: October 2024

AbstractProtein evolution shapes pathogen adaptation-landscape, particularly in developing drug resistance. The rapid evolution of target proteins under antibiotic pressure leads to escape mutations leading to the problem of antibiotic resistance. A deep understanding of the evolutionary dynamics of antibiotic target proteins presents a plausible intervention strategy for disrupting the evolutionary trajectory of resistance. Mutations in Dihydropteroate synthase (DHPS), an essential folate pathway protein and a key target for sulfonamide antibiotics, result in reduced antibiotic binding, leading to resistance. Deploying an array of statistical analyses on the DHPS sequence-space and integrating those with deep mutational analysis and structure-based network-topology models we identified critical DHPS-subsequences. Our analysis of the frustration landscape of DHPS predicts how conformational and mutational changes shift the energy distributions within the DHPS substructures. Combining dimensionality reduction and optimality analysis we identified a substructure critical to DHPS evolvability, and computed its druggablity. Our integrated evolution and structure-informed framework identified a DHPS-substructure with significant evolutionary and structural impact. Targeting this region could constrain DHPS evolvability and disrupt the resistome, presenting a new avenue for antibiotic development and contributing to the broader effort to address the problem of antibiotic resistance.
Long-read Spatial Transcriptomic Profiling of Patient-derived ccRCC Tumoroids Reveals Heterogeneity in Isoform and Gene Expression
Authors: Elshani Mustafa , Abdullah Hazem , Zhang Ying , Laird Alexander , Mullen Peter , Harrison David J. 
Published: October 2024

AbstractClear cell renal cell carcinoma (ccRCC) is the most prevalent type of kidney cancer characterized by its diverse tumor composition featuring various subclonal populations that hinder effective treatment responses. Tumoroids present an avenue for modelling this diversity and replicating the intricate tumor heterogeneity. Spatial transcriptomics preserves the spatial context of gene expression enabling us to study distinct tumor areas and the influence on overall diversity.Our spatial transcriptomics analysis uncovered tumor clusters with distinct genetic profiles that showcase various functional areas in depth and offer valuable understandings into the diversity of ccRCC types. Some of these tumor clusters exhibited activity in genes responsible for protein catabolism and reduced abundance of genes related to mitochondrial respiration processes. We also show isoform expression within tumoroids, in particular glutaminase (GLS) especially with the prevalence of the highly metabolically active GAC isoform that is expressed in regions where mitochondrial gene abundance is lower; whereas the KGA isoform displayed a more focal expression pattern. Combining long-read spatial transcriptomics with organoid models presents a novel strategy for unravelling gene and transcript level complexity.
CXCL10/CXCR3 Signaling Induces Neural Senescence and Cognitive Impairments
Authors: Patel Monika , Kumar Sakesh , Singh Aditya , Yadav Prem N 
Published: October 2024

AbstractChemokine receptors belong to the G-protein-coupled receptors family and multiple lines of emerging evidence suggest that several chemokines are elevated in aging associated with central nervous system disorders. Increased level of CXCL10 in central nervous system is reported in several neurodegenerative diseases, including Multiple sclerosis, Alzheimer’s disease, and Virus-associated dementia. We also observed significantly increased expression of CXCL10 and CXCR3 in the prefrontal cortex and hippocampus of aged C57BL/6J mice (12- and 18-month-old mice). This leads us to hypothesize that CXCL10, being a component of SASPs, may aggravate/perpetuate the brain aging process and, finally, neurodegenerative diseases. To test this hypothesis, we administered CXCL10 (intracerebroventricular: ICV, 0.5 pg/ hrs, 28 days) in 8-month-old C57BL/6J mice. We observed increased expression of senescent marker proteins p16INK4a, p21Cip1, p53 and decreased expression of pRB in the prefrontal cortex, which was blocked by CXCR3-specific antagonist AMG487. Furthermore, chronic infusion of CXCL10 induced learning and memory deficits in Y-maze, social recognition, contextual freeze tests and c-FOS expression in the prefrontal cortex. To further determine the specificity of CXCL10/CXCR3 signaling, we treated the primary cortical neuron (Daysin vitro: DIV 7-8) with CXCL10 and found increased senescence in CXCR3 dependent fashion. Using RFP-EGFP-LC3-tagged transgenic mice, we also showed CXCL10/CXCR3 signaling attenuates autophagic flux in primary cortical neurons. Lastly, using a c-FOS-iRFP reporter, we observed that increased CXCL10/CXCR3 signaling impairs glutamatergic signaling in primary cortical neurons. These results support the hypothesis that increased CXCL10/CXCR3 facilitates brain aging and could be targeted for the management of aging-associated CNS disorders.
The cGAS-STING pathway is anin vivomodifier of genomic instability syndromes
Authors: Bergman Marva , Goshtchevsky Uri , Atlan Tehila , Astre Gwendoline , Halabi Ryan , El Hosniyah , Moses Eitan , Lemus Aaron J.J. , Benayoun Bérénice A. , Tzfati Yehuda , Ben-Ami Ido , Harel Itamar 
Published: October 2024

AbstractMutations in genes involved in DNA damage repair (DDR) often lead to premature aging syndromes. While recent evidence suggests that inflammation, alongside mutation accumulation and cell death, may drive disease phenotypes, its precise contribution toin vivopathophysiology remains unclear. Here, by modeling Ataxia Telangiectasia (A-T) and Bloom Syndrome in the African turquoise killifish (N. furzeri), we replicate key phenotypes of DDR syndromes, including infertility, cytoplasmic DNA fragments, and reduced lifespan. The link between DDR defects and inflammation is attributed to the activation of the cGAS-STING pathway and interferon signaling by cytoplasmic DNA. Accordingly, mutating cGAS partially rescues germline defects and senescence in A-T fish. Double mutants also display reversal of telomere abnormalities and suppression of transposable elements, underscoring cGAS’s non-canonical role as a DDR inhibitor. Our findings emphasize the role of interferon signaling in A-T pathology and identify the cGAS-STING pathway as a potential therapeutic target for genomic instability syndromes.
The Src family kinase inhibitor drug Dasatinib and glucocorticoids display synergistic activity against tongue squamous cell carcinoma and reduce MET kinase activity
Authors: Hmedat Ali N.A. , Doondeea Jessica , Ebner Daniel , Feller Stephan M. , Lewitzky Marc 
Published: October 2024

AbstractBackgroundTongue squamous cell carcinoma (TSCC) is an aggressive cancer associated with a poor prognosis and limited treatment options, necessitating new drug targets to improve therapeutic outcomes. Our current work focuses on protein tyrosine kinases as well-known targets for successful cancer therapies.MethodsWestern blot analysis of tyrosine phosphorylation patterns in 34 TSCC lines identified Src family kinases (SFKs) as the main contributors. Inhibition of SFKs with PP2 and Dasatinib led to profound biological effects. A high-throughput screen with 1600 FDA-approved drugs was performed with three TSCC lines to discover drugs that act synergistically with Dasatinib against TSCC cell viability. Glucocorticoids emerged as potential candidates and were further investigated in 2D culture and by 3D soft agar colony formation. Dexamethasone was chosen as the major tool for our analyses. Since Dasatinib and glucocorticoids are known for their pleiotropic actions on cells, we analyzed effects on cell cycle, senescence, autophagy and cell signaling.ResultsA panel of 34 TSCC lines showed a surprisingly homogenous pTyr-protein pattern and a prominent 130 kDa pTyr-protein. Inhibition of SFK activity greatly reduced overall pTyr-protein levels and p130Cas tyrosine phosphorylation. It also impaired TSCC viability in 2D cell culture and 3D soft agar colony formation. A high-throughput drug combination screen with Dasatinib identified glucocorticoids as promising candidates for synergistic activity. Dasatinib and Dexamethasone combination treatment showed strong synergistic effects on Src and p130Cas phosphorylation and led to reduced p130Cas expression. Dexamethasone also suppressed phosphorylation of the MET kinase and its key substrate Gab1. On the cellular level, Dasatinib combination with glucocorticoids led to G1 cell cycle arrest, increased senescence and enhanced autophagy. This was also reflected by effects on cell cycle regulatory proteins, including CDKs and cyclins.ConclusionThis work is the first to show a strong synergistic activity of Dasatinib in combination with clinically used glucocorticoids in solid tumors. Furthermore, the tyrosine kinase MET and its effector protein Gab1 are newly identified glucocorticoid targets. Given the extensive research on MET as a drug target in various cancers, our findings have the potential to advance future cancer treatments.
Lung epithelial progenitor-mediated release of TGF-β regulates induction and persistence of lung CD8+TRMcells following mucosal BCG vaccination
Authors: Blake Judith A. , Seifert Julia , Ruscher Roland , Giacomin Paul R. , Doolan Denise L. , Kupz Andreas 
Published: October 2024

AbstractA principal reason for the high global morbidity and mortality of tuberculosis (TB) is the lack of efficacy of the only licensed TB vaccine, Bacillus Calmette-Guérin (BCG), as parenteral BCG does not induce local pulmonary immune memory. Animal studies have shown that mucosal BCG vaccination provides superior protection against TB due to generation of lung resident memory T cells (TRM). Here, we demonstrated that following mucosal vaccination with the genetically modified virulent BCG strain, BCG::RD1, distal airway epithelial progenitors were mobilized to assist with restoration of alveolar epithelium. By way of their migration-mediated activation of latent TGF-β, lung CD8+TRMdifferentiation was induced. Mucosal vaccinations using nonvirulent strains of BCG in which airway epithelial progenitors were not mobilized, as well as genetic inhibition of migration-mediated activation of TGF-β, resulted in significantly lower numbers of lung CD8+TRM. In addition, we discovered CD8+cells with ex-lung and stem-like TRMphenotypes that persisted in the lung-draining mediastinal lymph nodes for up to four months following mucosal BCG vaccination. These results link airway epithelial progenitor-mediated repair of injured lung tissue with induction of resident T cell memory and delineate why persistence of TRMin the lung is short-lived. These findings may explain why mucosal vaccination with virulent BCG strains is more protective against TB and thus have notable implications for future TB vaccine development.One Sentence SummaryFollowing lung damage due to inhalation of virulent BCG, distal airway epithelial progenitor cells interact with lung CD8+T cells to induce their differentiation into resident memory T cells via migration-mediated activation of TGF-β.
A First-in-Class Dual Degrader of Bcl-2/Bcl-xL Reverses HIV Latency and Eliminates Ex Vivo Reservoirs
Authors: Chang Lin-Chun , Yin Michael T , Laird Gregory M. , Ritter Kristen D. , Shah Jayesh , Debnath Asim K. 
Published: October 2024

ABSTRACTThe persistence of latent HIV-1 proviruses in CD4+ T cells is a major obstacle to curing HIV. The “shock and kill” strategy involves reversing latency with latency-reversing agents (LRAs) and selectively inducing cell death in infected cells. However, current LRAs have shown limited efficacy in eliminating the ex vivo HIV reservoir. We repurposed PZ703b, a pro-apoptotic protein degrader initially developed for anti-leukemia therapy, to target HIV eradication. PZ703b induced degradation of Bcl-2 and Bcl-xL, activating the non-canonical NF-kB pathway and caspases cascade, resulting in latency reversal and selective apoptosis of infected cells. Treatment of ex vivo CD4+ T cells from ART-suppressed HIV-1 patients achieved a ∼50% reduction in the replication-competent reservoir. Our study provides proof-of-concept for using protein degraders to reverse HIV latency and induce cell death, highlighting PZ703b’s potential in HIV cure strategies. This approach may pave the way for novel therapeutic interventions aimed at eliminating the HIV-inducible reservoir.
Blood cultures contain populations of genetically diverseCandida albicansstrains that may differ in echinocandin tolerance and virulence
Authors: Fleres Giuseppe , Cheng Shaoji , Badrane Hassan , Dupont Christopher L. , Espinoza Josh L. , Abbey Darren , Driscoll Eileen , Newbrough Anthony , Hao Binghua , Mansour Akila , Nguyen M. Hong , Clancy Cornelius J. 
Published: October 2024

AbstractIt is unknown whether within-patientCandida albicansdiversity is common during bloodstream infections (BSIs). We determined whole genome sequences of 10C. albicansstrains from blood cultures (BCs) in each of 4 patients. BCs in 3 patients contained mixed populations of strains that differed by large-scale genetic variants, including chromosome (Chr) 5 or 7 aneuploidy (n=2) and Chr1 loss of heterozygosity (n=1). Chr7 trisomy (Tri7) strains from patient MN were attenuated for hyphal and biofilm formation in vitro compared to euploid strains, due at least in part toNRG1over-expression. Nevertheless, representative Tri7 strain M1 underwent filamentation during disseminated candidiasis (DC) in mice. M1 was more fit than euploid strain M2 during DC and mouse gastrointestinal colonization, and in blood ex vivo. M1 and M2 exhibited identical echinocandin minimum inhibitory concentrations, but M2 was more tolerant to micafungin in vitro. Furthermore, M2 was more competitive with M1 in mouse kidneys following micafungin treatment than it was in absence of micafungin. Tri7 strains represented 74% of patient MN’s baseline BC population, but after 1d and 3d of echinocandin treatment, euploid strains were 93% and 98% of the BC population, respectively. Findings suggest that echinocandin tolerant, euploid strains were a subpopulation to more virulent Tri7 strains at baseline and then were selected upon echinocandin exposure. In conclusion, BCs in at least some patients are comprised of diverseC. albicanspopulations not recognized by the clinical lab, rather than single strains. Clinical relevance ofC. albicansdiversity and antifungal tolerance merits further investigation.
Geometric analysis of airway trees shows that lung anatomy evolved to enable explosive ventilation and prevent barotrauma in cetaceans
Authors: Cieri Robert L. , Tawhai Merryn H. , Piscitelli-Doshkov Marina , Vogl A. Wayne , Shadwick Robert E. 
Published: October 2024

ABSTRACTTwo new biomechanical challenges faced cetacean lungs compared to their terrestrial ancestors. First, hydrostatic pressures encountered during deep dives are sufficient to cause nearly full lung collapse, risking substantial barotrauma during surfacing if air is trapped in the fragile smaller airways. Second, rapid ventilation in large cetaceans requires correspondingly high ventilatory flow rates. In order to investigate how airway geometry evolved in response to these challenges, we characterized airway geometry from 12 species of cetaceans that vary in common dive depth and ventilatory behavior and a domestic pig using computed tomography. After segmenting the major airways, we generated centerline networks models for the larger airways and computed geometric parameters for each tree including mean branching angle, percent volume fraction, and Strahler branching, diameter, and length ratios. When airway geometry was regressed against ventilatory and diving parameters with phylogenetic least squares, neither average branching angle, percent volume fraction, Strahler length ratio or Strahler branching ratio significantly varied with common ventilatory mode or common diving depth. Higher Strahler diameter ratios were associated with slower ventilation and deeper diving depth, suggesting that cetacean lungs have responded to biomechanical pressures primarily with changes in airway diameter. High Strahler diameter ratios lungs in deeper diving species may help to facilitate more complete collapse of the delicate terminal airways by providing for a greater incompressible volume for air storage at depth. On the other hand, lungs with low Strahler diameter ratios would be better for fast ventilation because the gradual decrease in diameter moving distally should keep peripheral flow resistance low, maximizing ventilatory flow rates.
A brain-shuttled antibody targeting alpha synuclein aggregates for the treatment of synucleinopathies
Authors: An Sungwon , McInnis John J. , Kim Dongin , Li Yihang , Yilmaz Ozge , Ahn Jinhyung , Mackness Brian C , Park Jinyoung , Bonner Julia Maeve , Yun Hyesu , Dujardin Simon , Kim Donghwan , Kwon Seung-Hwan , Tang Yi , Pradier Laurent , Hyeon Sumin , Song Daehae , Sung Byungje , Krishnan Rajaraman , Spencer Brian , Rissman Robert , Sandhu Jagdeep K. , Haqqani Arsalan S. , Lee Hyeran , Jung Jinwon , You Weon-Kyoo , Star Alexandra T. , Delaney Christie E. , Stanimirovic Danica B. , Sardi Sergio Pablo , Lee Sang Hoon , Kayatekin Can 
Published: October 2024

AbstractParkinson’s disease and multiple system atrophy are members of a class of devastating neurodegenerative diseases called synucleinopathies, which are characterized by the presence of alpha-synuclein (α-Syn) rich aggregates in the brains of patients. Passive immunotherapy targeting these aggregates is an attractive disease-modifying strategy. Such an approach must not only demonstrate target selectivity towards α-Syn aggregates, but also achieve appropriate brain exposure to have the desired therapeutic effect. Here we present preclinical data for a next-generation antibody for the treatment of synucleinopathies. SAR446159 (ABL301) is a bispecific antibody composed of an α-Syn-binding immunoglobulin (IgG) and an engineered insulin-like growth factor receptor 1 (IGF1R) binding single-chain variable fragment (scFv), acting as a shuttle to transport an antibody across the blood-brain barrier (BBB). SAR446159 binds tightly and preferentially to α-Syn aggregates and prevents their seeding capacityin vitroandin vivo. Incubation with SAR446159 reduced α-Syn preformed fibrils (PFFs) uptake in neurons and facilitated uptake and clearance by microglia. In wild type mice injected in the striatum with α-Syn PFFs, treatment with SAR446159 reduced the spread of aSyn pathology as measured by phosphorylated α-Syn staining and lessened the severity of motor phenotypes. Additionally, in 9-month-old transgenic mice overexpressing α-Syn (mThy1-α-Syn, Line 61), repeated treatment with SAR446159 reduced markers of α-Syn aggregation in the brain. SAR446159 had significantly higher brain and CSF penetration over a sustained period than its monospecific counterpart (1E4) in rats and monkeys. The binding properties of SAR446159 combined with its brain-shuttle technology make it a potent, next-generation immunotherapeutic for treating synucleinopathies.
AI-QuIC: Machine Learning for Automated Detection of Misfolded Proteins in Seed Amplification Assays
Authors: Howey Kyle D. , Li Manci , Christenson Peter R. , Larsen Peter A. , Oh Sang-Hyun 
Published: October 2024

AbstractAdvancements in AI, particularly deep learning, have revolutionized protein folding modeling, offering insights into biological processes and accelerating drug discovery for protein misfolding diseases. However, detecting misfolded proteins associated with neurodegenerative disorders, such as Alzheimer’s, Parkinson’s, ALS, and prion diseases, relies on Seed Amplification Assays (SAAs) analyzed through manual, time-consuming, and potentially inconsistent methods. We introduce AI-QuIC, an AI-driven platform that automates the analysis of Real-Time Quaking- Induced Conversion (RT-QuIC) assay data, a type of SAA crucial for detecting misfolded proteins. Utilizing a well-labeled RT-QuIC dataset of over 8,000 wells—the largest curated dataset for chronic wasting disease prion detection—we applied various AI models to classify true positive, false positive, and negative reactions. Notably, our deep-learning-based model achieved over 98% sensitivity and 97% specificity. By learning directly from raw fluorescence data, deep learning simplifies the SAA-analysis workflow. Automating and standardizing SAA data interpretation with AI-QuIC provides robust, scalable, and consistent diagnostic solutions.