bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Drosophila model of mucopolysaccharidosis IIIB
Authors: Simkhada Bibhu , Nazario-Yepiz Nestor O , Freymuth Patrick S , Lyman Rachel A , Shankar Vijay , Wiggins Kali , Flanagan-Steet Heather , Basu Amrita , Weiss Ryan J , Anholt Robert R H , Mackay Trudy F C 
Published: December 2024

Abstract
Mucopolysaccharidosis type IIIB is a rare lysosomal storage disorder caused by defects in alpha-N-acetylglucosaminidase (NAGLU) and characterized by severe effects in the central nervous system. Mutations in NAGLU cause accumulation of partially degraded heparan sulfate in lysosomes. The consequences of these mutations on whole-genome gene expression and their causal relationships to neural degeneration remain unknown. Here, we used the functional Drosophila melanogaster ortholog of NAGLU, Naglu, to develop a fly model for MPS IIIB induced by gene deletion (NagluKO), missense (NagluY160C), and nonsense (NagluW422X) mutations. We used the Drosophila activity monitoring system to analyze activity and sleep and found sex- and age-dependent hyperactivity and sleep defects in mutant flies. Fluorescence microscopy on mutant fly brains using Lysotracker dye revealed a significant increase in acidic compartments. Differentially expressed genes determined from RNA sequencing of fly brains are involved in biological processes that affect nervous system development. A genetic interaction network constructed using known interacting partners of these genes consists of 2 major subnetworks, one of which is enriched in genes associated with synaptic function and the other with neurodevelopmental processes. Our data indicate that lysosomal dysfunction arising from disruption of heparan sulfate breakdown has widespread effects on the steady state of intracellular vesicle transport, including vesicles associated with synaptic transmission. Evolutionary conservation of fundamental biological processes predicts that the Drosophila model of mucopolysaccharidosis type IIIB can serve as an in vivo system for the future development of therapies for mucopolysaccharidosis type IIIB and related disorders.
The ATP-dependent DEAD-box RNA helicase Dbp2 regulates the glucose/nitrogen stress response in baker’s yeast by modulating reversible nuclear retention and decay of SKS1 mRNA
Authors: Paul Soumita , Das Subhadeep , Banerjea Mayukh , Chaudhuri Shouvik , Das Biswadip 
Published: December 2024

Abstract
In Saccharomyces cerevisiae, SKS1 mRNA encoding a glucose-sensing serine/threonine kinase belongs to “nucleus-retained” (NR) mRNAs representing a subset of otherwise normal transcripts, which exhibits slow nuclear export and excessively long nuclear dwell time. Nuclear retention of the SKS1 mRNA triggered by a 202 nt “export-retarding” nuclear zip code element promotes its rapid degradation in the nucleus by the nuclear exosome/CTEXT. In this investigation, we demonstrate that Dbp2p, an ATP-dependent DEAD-box RNA helicase binds to SKS1 and other NR-mRNAs and thereby inhibits their export by antagonizing with the binding of the export factors Mex67p/Yra1p. Consistent with this observation, a significant portion of these NR-mRNAs was found to localize into the cytoplasm in a yeast strain carrying a deletion in the DBP2 gene with the concomitant enhancement of its steady-state level and stability. This observation supports the view that Dbp2p promotes the nuclear retention of NR-mRNAs to trigger their subsequent nuclear degradation. Further analysis revealed that Dbp2p-dependent nuclear retention of SKS1 mRNA is reversible, which plays a crucial role in the adaptability and viability of the yeast cells in low concentrations of glucose/nitrogen in the growth medium. At high nutrient levels when the function of Sks1p is not necessary, SKS1 mRNA is retained in the nucleus and degraded. In contrast, during low glucose/nitrogen levels when Sks1p is vital to respond to such situations, the nuclear retention of SKS1 mRNA is relieved to permit its increased nuclear export and translation leading to a huge burst of cytoplasmic Sks1p.
A single-cell transcriptomic atlas reveals the cell differentiation trajectory and the response to virus invasion in swelling clove of garlic
Authors: Gao Song , Li Fu , Zeng Zheng , He Qiaoyun , Mostafa Hassan H A , Zhang Suling , Wang Taotao , Wang Yanzhou , Liu Touming 
Published: December 2024

Abstract
The garlic bulb comprises several cloves, the swelling growth of which is significantly hindered by the accumulation of viruses. Herein, we describe a single-cell transcriptomic atlas of swelling cloves with virus accumulation, which comprised 19 681 high-quality cells representing 11 distinct cell clusters. Cells of two clusters, clusters 7 (C7) and 11 (C11), were inferred to be from the meristem. Cell trajectory analysis suggested the differentiation of clove cells to start from the meristem cells, along two pseudo-time paths. Investigation into the cell-specific activity of invasive viruses demonstrated that garlic virus genes showed relatively low expression activity in cells of the clove meristem. There were 2060 garlic genes co-expressed with virus genes, many of which showed an association with the defense response. Five glutathione synthase/reductase genes co-expressed with virus genes displayed up-regulated expression, and the glutathione and related metabolites level showed an alteration in virus-invasive garlic clove, implying the role of glutathione in viral immunity of garlic. Our study offers valuable insights into the clove organogenesis and interaction between garlic and virus at single-cell resolution.
The antibacterial and antibiofilm role of cannabidiol against periodontopathogenic bacteria
Authors: Santos Anna Livia Oliveira , Santiago Mariana Brentini , Silva Nagela Bernadelli Sousa , Souza Sara Lemes , Almeida Joaquim Maurício Duarte , Martins Carlos Henrique Gomes 
Published: December 2024

Abstract

Aims
Bacterial resistance and systemic risks associated with periodontitis underscore the need for novel antimicrobial agents. Cannabis sativa is a promising source of antimicrobial molecules, and cannabidiol (CBD) attracts significant interest. This study evaluated the antibacterial and antibiofilm activity of CBD against periodontopathogens, and assessed its toxicity in vivo model.

Methods and results
Antibacterial activity was determined by the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). Biofilm inhibition was determined the minimum inhibitory concentration of biofilm (MICB50). Toxicity was assessed using Caeonorhabditis elegans. The periodontopathogens tested were Actinomyces naeslundii (ATCC 19039), Peptostreptococcus anaerobius (ATCC 27337), Veillonella parvula (ATCC 17745), Fusobacterium nucleatum (ATCC 10953), and Aggregatibacter actinomycetemcomitans (ATCC 43717). CBD exhibited antibacterial effects with MICs of 0.39 to 3.12 µg ml−1 and MICB50 of 0.39 µg ml−1 to 1.56 µg ml−1 against biofilms, without toxicity below 375 µg ml−1.

Conclusion
The results suggest that CBD is a non-toxic product with antibacterial and antibiofilm potential, exhibiting promise as a therapeutic alternative for oral diseases.
Hybrid exons evolved by coupling transcription initiation and splicing at the nucleotide level
Authors: Mick Steven T , Carroll Christine L , Uriostegui-Arcos Maritere , Fiszbein Ana 
Published: December 2024

Abstract
Exons within transcripts are traditionally classified as first, internal or last exons, each governed by different regulatory mechanisms. We recently described the widespread usage of ‘hybrid’ exons that serve as terminal or internal exons in different transcripts. Here, we employ an interpretable deep learning pipeline to dissect the sequence features governing the co-regulation of transcription initiation and splicing in hybrid exons. Using ENCODE data from human tissues, we identified 80 000 hybrid first-internal exons. These exons often possess a relaxed chromatin state, allowing transcription initiation within the gene body. Interestingly, transcription start sites of hybrid exons are typically centered at the 3′ splice site, suggesting tight coupling between splicing and transcription initiation. We identified two subcategories of hybrid exons: the majority resemble internal exons, maintaining strong 3′ splice sites, while a minority show enrichment in promoter elements, resembling first exons. Diving into the evolution of their sequences, we found that human hybrid exons with orthologous first exons in other species usually gained 3′ splice sites or whole exons upstream, while those with orthologous internal exons often gained promoter elements. Overall, our findings unveil the intricate regulatory landscape of hybrid exons and reveal stronger connections between transcription initiation and RNA splicing than previously acknowledged.
Broad repression of DNA repair genes in senescent cells identified by integration of transcriptomic data
Authors: Frey Yann , Haj Majd , Ziv Yael , Elkon Ran , Shiloh Yosef 
Published: December 2024

Abstract
Cellular senescence plays a significant role in tissue aging. Senescent cells, which resist apoptosis while remaining metabolically active, generate endogenous DNA-damaging agents, primarily reactive oxygen species. Efficient DNA repair is therefore crucial in these cells, especially when they undergo senescence escape, resuming DNA replication and cellular proliferation. To investigate whether senescent cell transcriptomes reflect adequate DNA repair capacity, we conducted a comprehensive meta-analysis of 60 transcriptomic datasets comparing senescent to proliferating cells. Our analysis revealed a striking downregulation of genes encoding essential components across DNA repair pathways in senescent cells. This includes pathways active in different cell cycle phases such as nucleotide excision repair, base excision repair, nonhomologous end joining and homologous recombination repair of double-strand breaks, mismatch repair and interstrand crosslink repair. The downregulation observed suggests a significant accumulation of DNA lesions. Experimental monitoring of DNA repair readouts in cells that underwent radiation-induced senescence supported this conclusion. This phenomenon was consistent across various senescence triggers and was also observed in primary cell lines from aging individuals. These findings highlight the potential of senescent cells as ‘ticking bombs’ in aging-related diseases and tumors recurring following therapy-induced senescence.
Neutrophil extracellular traps have active DNAzymes that promote bactericidal activity
Authors: Ku Ti-Hsuan , Ram-Mohan Nikhil , Zudock Elizabeth J , Abe Ryuichiro , Yang Samuel 
Published: December 2024

Abstract
The mechanisms of bacterial killing by neutrophil extracellular traps (NETs) are unclear. DNA, the largest component of NETs was believed to merely be a scaffold with antimicrobial activity only through the charge of the backbone. Here, we demonstrate for the first time that NETs DNA is beyond a mere scaffold to trap bacteria and it produces hydroxyl free radicals through the spatially concentrated G-quadruplex/hemin DNAzyme complexes, driving bactericidal effects. Immunofluorescence staining showed potential colocalization of G-quadruplex and hemin in extruded NETs DNA, and Amplex UltraRed assay portrayed its peroxidase activity. Proximity labeling of bacteria revealed localized concentration of radicals resulting from NETs bacterial trapping. Ex vivo bactericidal assays revealed that G-quadruplex/hemin DNAzyme is the primary driver of bactericidal activity in NETs. NETs are DNAzymes that may have important biological consequences.
Generative design-enabled exploration of wireframe DNA origami nanostructures
Authors: Vetturini Anthony J , Cagan Jonathan , Taylor Rebecca E 
Published: December 2024

Abstract
Recent advances in computer-aided design tools have helped rapidly advance the development of wireframe DNA origami nanostructures. Specifically, automated tools now exist that can convert an input polyhedral mesh into a DNA origami nanostructure, greatly reducing the design difficulty for wireframe DNA origami nanostructures. However, one limitation of these automated tools is that they require a designer to fully conceptualize their intended nanostructure, which may be limited by their own preconceptions. Here, a generative design framework is introduced capable of generating many wireframe DNA origami nanostructures without the need for a predefined mesh. User-defined objectives that guide the generative process are input as either single- or multi-objective optimization problems. A graph grammar is used to both contextualize physical properties of the DNA nanostructure and control the types of generated design features. This framework allows a designer to explore upon and ideate among many generated nanostructures that comply with their own unique constraints. A web-based graphical user interface is provided, allowing users to compare various generated solutions side by side in an interactive environment. Overall, this work illustrates how a constrained generative design framework can be implemented as an assistive tool in exploring design-feature trade-offs of wireframe DNA nanostructures, resulting in novel wireframe nanostructures.
A scaleable inducible knockout system for studying essential gene function in the malaria parasite
Authors: Ramaprasad Abhinay , Blackman Michael J 
Published: December 2024

Abstract
The malaria parasite needs nearly half of its genes to propagate normally within red blood cells. Inducible ways to interfere with gene expression like the DiCre-lox system are necessary to study the function of these essential genes. However, existing DiCre-lox strategies are not well-suited to be deployed at scale to study several genes simultaneously. To overcome this, we have developed SHIFTiKO (frameshift-based trackable inducible knockout), a novel scaleable strategy that uses short, easy-to-construct, barcoded repair templates to insert loxP sites around short regions in target genes. Induced DiCre-mediated excision of the flanked region causes a frameshift mutation resulting in genetic ablation of gene function. Dual DNA barcodes inserted into each mutant enables verification of successful modification and induced excision at each locus and collective phenotyping of the mutants, not only across multiple replication cycles to assess growth fitness but also within a single cycle to identify specific phenotypic impairments. As a proof of concept, we have applied SHIFTiKO to screen the functions of malarial rhomboid proteases, successfully identifying their blood stage-specific essentiality. SHIFTiKO thus offers a powerful platform to conduct inducible phenotypic screens to study essential gene function at scale in the malaria parasite.
Synthetic anti-RNA antibody derivatives for RNA visualization in mammalian cells
Authors: Banna Hasan Al , Berg Kimberley , Sadat Tasnia , Das Naba Krishna , Paudel Roshan , D'Souza Victoria , Koirala Deepak 
Published: December 2024

Abstract
Although antibody derivatives, such as Fabs and scFvs, have revolutionized the cellular imaging, quantification and tracking of proteins, analogous tools and strategies are unavailable for cellular RNA visualization. Here, we developed four synthetic anti-RNA scFv (sarabody) probes and their green fluorescent protein (GFP) fusions and demonstrated their potential to visualize RNA in live mammalian cells. We expressed these sarabodies and sarabody–GFP modules, purified them as soluble proteins, characterized their binding interactions with their corresponding epitopes and finally employed two of the four modules, sara1-GFP and sara1c-GFP, to visualize a target messenger RNA in live U2OS cells. Our current RNA imaging strategy is analogous to the existing MCP-MS2 system for RNA visualization, but additionally, our approach provides robust flexibility for developing target RNA-specific imaging modules, as epitope-specific probes can be selected from a library generated by diversifying the sarabody complementarity determining regions. While we continue to optimize these probes, develop new probes for various target RNAs and incorporate other fluorescence proteins like mCherry and HaloTag, our groundwork results demonstrated that these first-of-a-kind immunofluorescent probes will have tremendous potential for tracking mature RNAs and may aid in visualizing and quantifying many cellular processes as well as examining the spatiotemporal dynamics of various RNAs.
The target of rapamycin kinase is a positive regulator of plant fatty acid and lipid synthesis
Authors: Liu Hui , Blanford Jantana , Shi Hai , Schwender Jorg , Shanklin John , Zhai Zhiyang 
Published: December 2024

Abstract
In eukaryotes, target of rapamycin (TOR), a conserved protein sensor kinase, integrates diverse environmental cues, including growth factor signals, energy availability, and nutritional status, to direct cell growth. In plants, TOR is activated by light and sugars and regulates a wide range of cellular processes, including protein synthesis and metabolism. Fatty acid (FA) synthesis is a key to membrane biogenesis that is required for cell growth. To elucidate the primary regulatory role(s) of TOR in lipid metabolism, we followed FA and lipid changes in plants with altered TOR protein levels or activity for short durations, using Nicotiana benthamiana leaves, Arabidopsis seedlings, and Brassica napus cell suspension cultures. Transient expression of TOR significantly elevated the levels of total FA (TFA) in N. benthamiana leaves. Conversely, treatment of Arabidopsis seedlings with the TOR-specific inhibitor Torin 2 for 1 d caused significant reductions in FA and membrane lipids. Similarly, incubating oil–producing B. napus suspension culture cells with Torin 2 for 8 h led to significant decreases in the levels of TFA and triacylglycerol. The results from 3 independent systems presented here establish that TOR positively regulates lipid synthesis in plants, consistent with its role in animals. Furthermore, RNA-seq analysis of Torin 2-treated Arabidopsis seedlings showed that TOR promotes the upregulation of several genes involved in de novo FA synthesis while downregulating several genes involved in lipid turnover, which we propose as a mechanistic explanation for its promotion of lipid synthesis and accumulation.
Rare Cutaneous Primary Presentation of Extracavitary Primary Effusion Lymphoma
Authors: Mehta Apoorva , Luyten Sophia , Vencato da Silva Tiago , Bacchi Carlos , Gru Alejandro 
Published: December 2024

Abstract:
Primary effusion lymphoma (PEL) is a rare and aggressive B-cell lymphoma typically associated with human herpesvirus 8 (HHV-8) and Epstein–Barr virus infections. It classically presents as a malignant effusion in body cavities, but rarely presents with an extracavitary variant characterized by solid tumors in lymph nodes or extranodal sites such as the gastrointestinal tract, skin, lungs, and nervous system. This case report describes an unusual presentation of primary cutaneous extracavitary PEL in an HIV-positive patient that has only been reported in 8 cases previously. The patient presented with a skin nodule in the right supraclavicular area. Histopathologic examination showed a malignant infiltrate in the dermis composed of sheets of plasmablasts. The immunophenotype of the cells shows the characteristic coinfection with HHV-8 and Epstein–Barr virus. The case presented herein contributes to expand the reported literature on primary cutaneous extracavitary PEL and performs a comprehensive review of this entity, which most dermatopathologists are unfamiliar with.
“Pathway Leap”: A New Molecular Phenomenon to Consider in the Pathogenesis of Melanocytic Tumors
Authors: Fernandez-Flores Angel 
Published: December 2024

Introduction:
The current WHO classification of melanocytic tumors distinguishes 9 pathogenic routes. This classification is based on the conceptual interpretation that melanocytic tumors evolve from benign counterparts, accumulating mutations, eventually developing into melanomas with metastatic and potentially lethal capacity. In this article, we present a molecular study of 2 melanocytic tumors that suggest a “leap” from pathogenic routes IV to I.

Materials and Methods:
Two recent melanocytic tumors were selected, each exhibiting 2 contiguous melanocytic populations of distinct morphology, without separation between them. One population corresponded to a common melanocytic nevus (with morphology consistent with route I), while the other population displayed epithelioid morphology, consistent with route IV. Immunohistochemical studies were performed in both cases, as well as molecular studies using PCR to search for mutations in the NRAS and BRAF genes. For the molecular study, both populations were manually separated by microdissection.

Results:
In both cases, the melanocytic population consistent with route I showed a BRAF mutation. In both cases, the epithelioid population did not present a BRAF mutation. No NRAS mutations were observed in any of the populations.

Conclusions:
These findings suggest the existence of a molecular phenomenon of “leap” between pathways, which we have termed “pathway leap.” This could explain the enigmatic group of tumors that the WHO classifies under the heading of “combined nevi.” This group could be more frequent than suspected, because microdissection is not a technique commonly used in the daily diagnosis of melanocytic tumors.
Vegetative Pyoderma Gangrenosum Mimicking Squamous Cell Carcinoma: A Poorly Recognized Diagnostic Challenge
Authors: Hoang Megan , Maymone Mayra B. C. , Telang Gladys H. , Seo Su-Jean , Robinson-Bostom Leslie 
Published: December 2024

Abstract:
Pyoderma gangrenosum (PG) is a rare inflammatory neutrophilic dermatosis that is difficult to diagnose due to non-specific clinical, laboratory, and histopathologic features. Distinguishing pseudoepitheliomatous hyperplasia (PEH) from squamous cell carcinoma (SCC) is also histopathologically challenging. The connection between PEH and PG is not well recognized, and instances of PG mimicking SCC are rare. We report a case of vegetative PG accompanied by PEH, originally mistaken for SCC. A 78-year-old woman presented with a 3-month history of an ulcerated, exophytic, and painful mass on her right lower leg. An incisional biopsy revealed PEH and neutrophilic microabscesses, initially raising concerns for SCC keratoacanthoma type with PEH or well-differentiated, infiltrative SCC. However, following additional review of clinical and histopathologic findings at the cutaneous oncology tumor board, the diagnosis of vegetative PG with associated PEH was favored. This case highlights the significance of recognizing PEH as a histopathology feature that can be seen in PG and lead to difficulty distinguishing PG with PEH from SCC. We stress the importance of promptly diagnosing PG through clinical and histopathologic correlation to prevent diagnostic delays and unnecessary surgeries or treatments.
Drug Delivery in PROSE Device as Alternative to Frequent Drop Administration in Severe Ocular Surface Disease
Authors: Bian Yandong , Jacobs Deborah S. 
Published: December 2024

Abstract:
The design of the prosthetic replacement of the ocular surface ecosystem (PROSE) device allows it to serve as a novel drug delivery system. In this article, we describe the off-label administration of amphotericin B and cenegermin by instillation in the PROSE device reservoir for the treatment of Candida keratitis in the setting of a persistent epithelial defect.