bluuebunny/crossref_metadata_2025_split huggingface dataset:
PbrSYP71regulates pollen tube growth by maintaining uneven distribution of the ERin Pyrus
Authors: Zhang Mingliang , Tang Chao , Lan Chi , Zhang Ningyi , Yue Dong , Xie Zhihua , Qian Ming , Sun Mengjun , Liu Zongqi , Xie Zhu , Zhang Hao , Liu Zhuqin , Zhang Shaoling , Wang Peng , Wu Juyou 
Published: January 2024

AbstractThe uneven distribution of endoplasmic reticulum (ER) underlies the rapid polar growth of pollen tubes. However, the mechanism governing ER distribution remains elusive. In this study, we have identified a pollen tube-specific syntaxin protein, PbrSYP71. Our findings reveal that both overexpression and knocking down ofPbrSYP71inhibited pollen tube growth. Subcellular localization analysis demonstrates that PbrSYP71 anchors to the ER via its transmembrane structure. Overexpression ofPbrSYP71leads to clustered ER distribution in the pollen tube, while knocking down ofPbrSYP71abolishes the uneven ER distribution. Remarkably, transient overexpression ofPbrSYP71ΔABD, lacking the actin binding domain (ABD) of PbrSYP71, has no impact on ER distribution or pollen tube growth. Further investigation indicates that ABD is positioned on F-actin in the pollen tube and has a direct interaction with F-actin. PbrSYP71 assists the ER in moving towards the apex of pollen tube, with ABD displaying autonomous mobility. Our study elucidates that PbrSYP71 maintains uneven distribution of the ER by tethering ER to F-actin, facilitating ER movement towards the pollen tube apex for pear pollen tube elongation. These insights shed light on the mechanisms governing ER distribution in polarized cell growth.
Geometric changes in the nucleoids of Deinococcus radiodurans reveal involvement of new proteins in recovery from ionizing radiation
Authors: Cordova Antonio , Niese Brandon , Sweet Philip , Kamat Pratik , Phillip Jude M , Gordon Vernita , Contreras Lydia M. 
Published: January 2024

AbstractThe extremophileDeinococcus radioduransmaintains a highly-organized and condensed nucleoid as its default state, possibly contributing to high tolerance of ionizing radiation (IR). Previous studies of theD. radioduransnucleoid were limited by reliance on manual image annotation and qualitative metrics. Here, we introduce a high-throughput approach to quantify the geometric properties of cells and nucleoids, using confocal microscopy, digital reconstructions of cells, and computational modeling. We utilize this novel approach to investigate the dynamic process of nucleoid condensation in response to IR stress. Our quantitative analysis reveals that at the population level, exposure to IR induced nucleoid compaction and decreased size ofD. radioduranscells. Morphological analysis and clustering identified six distinct sub-populations across all tested experimental conditions. Results indicate that exposure to IR induces fractional redistributions of cells across sub-populations to exhibit morphologies that associate with greater nucleoid condensation, and decreased abundance of sub-populations associated with cell division. Nucleoid associated proteins (NAPs) may link nucleoid compaction and stress tolerance, but their roles in regulating compaction inD. radioduransis unknown. Imaging of genomic mutants of known and suspected NAPs that contribute to nucleoid condensation found that deletion of nucleic acid binding proteins, not previously described as NAPs, can remodel the nucleoid by driving condensation or decondensation in the absence of stress and that IR increases the abundance of these morphological states. Thus, our integrated analysis introduces a new methodology for studying environmental influences on bacterial nucleoids and provides an opportunity to further investigate potential regulators of nucleoid condensation.ImportanceD. radiodurans, an extremophile known for its stress tolerance, constitutively maintains a highly-condensed nucleoid. Qualitative studies have described nucleoid behavior under a variety of conditions. However, a lack of quantitative data regarding nucleoid organization and dynamics have limited our understanding of regulatory mechanisms controlling nucleoid organization inD. radiodurans. Here, we introduce a quantitative approach that enables high-throughput quantitative measurements of subcellular spatial characteristics in bacterial cells. Applying this to wild-type or single-protein-deficient populations ofD. radioduranssubjected to ionizing radiation, we identified significant stress-responsive changes in cell shape, nucleoid organization, and morphology. These findings highlight this methodology’s adaptability and capacity for quantitatively analyzing the cellular response to stressors for screening cellular proteins involved in bacterial nucleoid organization.
Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the GastrotrichLepidodermella squamata(Dujardin, 1841)
Authors: Roberts Nickellaus G. , Gilmore Michael J. , Struck Torsten H. , Kocot Kevin M. 
Published: January 2024

AbstractBackgroundObtaining adequate DNA for long-read genome sequencing remains a roadblock to producing contiguous genomes from small-bodied organisms. Multiple displacement amplification (MDA) leverages Phi29 DNA polymerase to produce micrograms of DNA from picograms of input. Few genomes have been generated using this approach, due to concerns over biases in amplification related to GC and repeat content and chimera production. Here, we explored the utility of MDA for generating template DNA for PacBio HiFi sequencing usingCaenorhabditis elegans(Nematoda) andLepidodermella squamata(Gastrotricha).ResultsHiFi sequencing of libraries prepared from MDA DNA produced highly contiguous and complete genomes for bothC. elegans(102 Mbp assembly; 336 contigs; N50 = 868 Kbp; L50 = 39; BUSCO_nematoda: S:92.2%, D:2.7%) andL. squamata(122 Mbp assembly; 157 contigs; N50 = 3.9 Mb; L50 = 13; BUSCO_metazoa: S: 78.0%, D: 2.8%). AmplifiedC. elegansreads mapped to the reference genome with a rate of 99.92% and coverage of 99.75% with just one read (of 708,811) inferred to be chimeric. Coverage uniformity was nearly identical for reads from MDA DNA and reads from pooled worm DNA when mapped to the reference genome. The genome ofLepidodermella squamata, the first of its phylum, was leveraged to infer the phylogenetic position of Gastrotricha, which has long been debated, as the sister taxon of Platyhelminthes.ConclusionsThis methodology will help generate contiguous genomes of microscopic taxa whose body size precludes standard long-read sequencing.L. squamatais an emerging model in evolutionary developmental biology and this genome will facilitate further work on this species.
Constitutive Plasma Membrane Turnover in T-REx293 cells via Ordered Membrane Domain Endocytosis under Mitochondrial Control
Authors: Deisl Christine , Moe Orson W. , Hilgemann Donald W. 
Published: January 2024

AbstractClathrin/dynamin-independent endocytosis of ordered plasma membrane domains (orderedmembranedomainendocytosis, OMDE) can become massive in response to cytoplasmic Ca elevations, G protein activation by non-hydrolyzable GTP analogs, and enhanced oxidative metabolism. In patch-clamped murine bone marrow macrophages (BMMs), cytoplasmic succinate and pyruvate, but not β-hydroxybutyrate, induce OMDE of 75% of the plasma membrane within 2 min. The responses require palmitoylation of membrane proteins, being decreased by 70% in BMMs lacking the acyltransferase, DHHC5, by treatment with carnitine to shift long-chain acyl groups from cytoplasmic to mitochondrial acyl-CoAs, by bromopalmitate/albumin complexes to block DHHCs, and by the mitochondria-specific cyclosporin, NIM811, to block permeability transition pores that may release mitochondrial coenzyme A into the cytoplasm. Using T-REx293 cells, OMDE amounts to 40% with succinate, pyruvate, or GTPγS, and it is inhibited by actin cytoskeleton disruption. Pyruvate-induced OMDE is blocked by the hydrophobic antioxidant, edaravone, which prevents permeability transition pore openings. Using fluorescent 3kD dextrans to monitor endocytosis, OMDE appears to be constitutively active in T-REx293 cells but not in BMMs. After 1 h without substrates or bicarbonate, pyruvate and hydroxybutyrate inhibit constitutive OMDE, as expected for a shift of CoA from long-chain acyl-CoAs to other CoA metabolites. In the presence of bicarbonate, pyruvate strongly enhances OMDE, which is then blocked by β-hydroxybutyrate, bromopalmitate/albumin complexes, cyclosporines, or edaravone. After pyruvate responses, T-REx293 cells grow normally with no evidence for apoptosis. Fatty acid-free albumin (15 μM) inhibits basal OMDE in T-REx293 cells, as do cyclosporines, carnitine, and RhoA blockade. Surprisingly, OMDE in the absence of substrates and bicarbonate is not inhibited by siRNA knockdown of the acyltransferases, DHHC5 or DHHC2, which are required for activated OMDE in patch clamp experiments. We verify biochemically that small CoA metabolites decrease long-chain acyl-CoAs. We verify also that palmitoylations of many PM-associated proteins decrease and increase when OMDE is inhibited and stimulated, respectively, by different metabolites. STED microscopy reveals that vesicles formed during constitutive OMDE in T-REX293 cells have 90 to 130 nm diameters. In summary, OMDE is likely a major G-protein-dependent endocytic mechanism that can be constitutively active in some cell types, albeit not BMMs. OMDE depends on different DHHC acyltransferases in different circumstances and can be limited by local supplies of fatty acids, CoA, and long-chain acyl-CoAs.
Retinal neuroanatomy of two emerging model organisms, the spiny mouse (Acomys dimidiatus) and the Mongolian gerbil (Meriones unguiculatus)
Authors: Bills Jessica D. , Seifert Ashley W. , Morris Ann C. 
Published: January 2024

AbstractPurposeDegenerative eye diseases such as macular degeneration and retinitis pigmentosa slowly deteriorate vision, ultimately leading to blindness. Current research with laboratory animal models largely utilizes small mammals that are nocturnal and lack the ability to restore lost vision. In contrast, the Mongolian gerbil is a diurnal rodent with good photopic vision, and the eastern spiny mouse is a small desert-dwelling rodent with remarkable regenerative capabilities. The goal of this study was to identify several antibodies that detect retinal cell classes inMerionesandAcomys, and to describe the retinal anatomy of these two species in comparison to outbred laboratory mice (Mus musculus).MethodsRetinal sections were obtained from adult eyes and subjected to histological or immuno-staining with antibodies for various retinal cell types. Sections were imaged by light, fluorescence, and confocal microscopy, assessing cell number and morphology. Cell density, morphology, and placement were compared between species qualitatively and quantitatively.ResultsImmunohistochemical visualization and analysis of all general classes of retinal neurons and Müller glia revealed a classic assembly of retinal cells with a few deviations compared toMus.Merionesdisplayed the highest density of cone photoreceptors andAcomysthe lowest. A higher density of bipolar cell bodies in the proximal portion of the inner nuclear layer was observed in bothAcomysandMerionescompared toMus, and both species exhibited an increase in amacrine cell density compared toMus.ConclusionWe have characterized similarities and differences in the retinal anatomy and cellular density betweenMeriones,Acomys, andMus. We identified several commercially available antibodies that reliably detect retinal cell types in theAcomysandMerionesretina. Our results provide a foundation for future research into the visual system adaptations of both of these interesting rodent species.
Infant vocal category exploration as a foundation for speech development
Authors: Yoo Hyunjoo , Su Pumpki Lei , Ramsay Gordon , Long Helen L. , Bene Edina R. , Kimbrough Oller D. 
Published: January 2024

AbstractNon-random exploration of infant speech-like vocalizations (e.g., squeals, growls, and vowel- like sounds or “vocants”) is pivotal in speech development. This type of vocal exploration, often noticed when infants produce particular vocal types in clusters, serves two crucial purposes: it establishes a foundation for speech because speech requires formation of new vocal categories, and it serves as a basis for vocal signaling of wellness and interaction with caregivers. Despite the significance of clustering, existing research has largely relied on subjective descriptions and anecdotal observations regarding early vocal category formation. In this study, we aim to address this gap by presenting the first large-scale empirical evidence of vocal category exploration and clustering throughout the first year of life. We observed infant vocalizations longitudinally using all-day home recordings from 130 typically developing infants across the entire first year of life. To identify clustering patterns, we conducted Fisher’s exact tests to compare the occurrence of squeals versus vocants, as well as growls versus vocants. We found that across the first year, infants demonstrated clear clustering patterns of squeals and growls, indicating that these categories were not randomly produced, but rather, it seemed, infants actively engaged in practice of these specific categories. The findings lend support to the concept of infants as manifesting active vocal exploration and category formation, a key foundation for vocal language.
Bitter taste receptor T2R14 and autophagy flux in gingival epithelial cells
Authors: Singh Nisha , Ulmer Ben , Medapati Manoj , Schroth Robert , Ghavami Saeid , Chelikani Prashen 
Published: January 2024

AbstractMacroautophagy (hereafterautophagy) is a lysosomal degradation pathway that functions in nutrient recycling and as a mechanism of innate immunity. Previously we reported, a novel host-bacteria interaction between cariogenicS. mutansand bitter taste receptor (T2R14) in gingival epithelial cells (GEC) leading to an innate immune response. Further,S. mutansmight be using the host immune system to inhibit other Gram-positive bacteria, such asS. aureus. To determine whether these bacteria exploit the autophagic machinery of GEC, it is first necessary to evaluate the role of T2R14 in modulating autophagic flux. So far, the the role of T2R14 in the regulation of autophagy is not well charcterized. Therefore, in this study, for the first time, we report that T2R14 downregulates autophagy flux in GECs and T2R14 knockout increases acidic vacuoles. Transmission electron microscopy morphometric results also suggested increased number of autophagic vesicles in T2R14 knockout GEC. Further, our results suggest thatS. mutanscompetence stimulating peptide CSP-1 showed robust intracellular calcium release and this effect is both T2R14 and autophagy protein 7 dependent. In this study we provide the first evidence that T2R14 modulates autophagy flux in GEC. The results of current study culd have benefitial impact on the identifying the impact of T2R in regulation of immuno microenviroment of GEC and its impact in oral health.
Identification of a novel mosaicMTORvariant in purified neuronal DNA from depth electrodes in a patient with focal cortical dysplasia
Authors: Klein Karl Martin , Mascarenhas Rumika , Merrikh Daria , Khanbabaei Maryam , Maroilley Tatiana , Kaur Navprabhjot , Liu Yiping , Soule Tyler , Manalo Minette , Tamura Goichiro , Jacobs Julia , Hader Walter , Pfeffer Gerald , Tarailo-Graovac Maja 
Published: January 2024

AbstractBackgroundRecent studies have identified brain somatic variants as a cause of focal epilepsy. These studies relied on resected tissue from epilepsy surgery which is not available in most patients. The use of trace tissue adherent to depth electrodes used for stereo electroencephalography (stereo EEG) has been proposed as an alternative but is hampered by the low cell quality and contamination by non-brain cells. Here, we use our improved depth electrode harvesting technique that purifies neuronal nuclei to achieve molecular diagnosis in a patient with focal cortical dysplasia (FCD).MethodsDepth electrode tips were collected, pooled by brain region and seizure onset zone, nuclei isolated and sorted using fluorescence-activated nuclei sorting (FANS). Somatic DNA was amplified from neuronal and astrocyte nuclei using primary template amplification followed by exome sequencing of neuronal DNA from the affected pool, unaffected pool, and saliva. The identified variant was validated using droplet digital PCR.ResultsAn adolescent male with drug-resistant genetic-structural epilepsy due to left anterior insula FCD had daily focal aware seizures. Stereo EEG confirmed seizure onset in the left anterior insula. The two anterior insula electrodes were combined as the affected pool and three frontal electrodes as the unaffected pool. FANS isolated 140 neuronal nuclei from the affected and 245 neuronal nuclei from the unaffected pool. A novel somatic missenseMTORvariant (p.Leu489Met, CADD score 23.7) was identified in the affected neuronal sample. Droplet digital PCR confirmed a mosaic gradient (VAF 0.78% in affected neuronal sample, variant was absent in all other samples).ConclusionsOur finding confirms that harvesting neuronal DNA from depth electrodes followed by molecular analysis to identify brain somatic variants is feasible. Our novel method represents a significant improvement compared to the previous method by focusing the analysis on high quality cells of the cell type of interest.
Evaluation of four interventions using behavioural economics insights to increase demand for voluntary medical male circumcision in South Africa through the MoyaApp: A quasi-experimental study
Authors: Mistri Preethi , Tomescu Silviu , Bokolo Simamkele , De Nooy Alexandra , Pisa Pedro T. , Grove Skye , Schmucker Laura , Chetty-Makkan Candice , Long Lawrence , Buttenheim Alison , Maughan-Brown Brendan 
Published: January 2024

AbstractBackgroundWhile voluntary medical male circumcision (VMMC) reduces the risk of HIV transmission by 60%, circumcision coverage falls short of the UNAIDS 90% target. We investigated whether behaviourally informed message framing increased demand for VMMC.SettingAdult users of the MoyaApp, a data free application in South Africa, who viewed a form designed to generate interest in VMMC during August-November 2022.MethodsA quasi-experimental study was conducted to evaluate four MoyaApp VMMC intervention forms against the Standard of Care (SOC) form. All forms enabled users to provide contact details for follow-up engagement by a call centre. The primary outcome was the proportion of forms submitted. Secondary outcomes included successful contact with the user, VMMC bookings/referrals and confirmed circumcision. Multivariable ordinary least-squares regression was used for the analysis.ResultsMoyaApp VMMC form viewers totalled 118,337 of which 6% submitted a form. Foot-in-the-Door form viewers were more likely (+1.3 percentage points, p<0.01) to submit a form compared to the SOC group (6.3%). Active Choice (-1.1 percentage points, p<0.01) and Reserved for You (-0.05 percentage points, p<0.05) form viewers were less likely to submit a form compared to SOC. Users submitting on Foot-in-the-Door were less likely to be booked/referred compared to SOC (-5 percentage points, p<0.05). There were no differences between the intervention and SOC forms for successful contact and circumcisions.ConclusionsMessage framing using behavioural insights was able to nudge men to engage with VMMC services. However, more work is needed to understand how to convert initial interest into bookings and circumcisions.Trial registrationSouth African Clinical Trials Registry DOH-27-062022-7811Pan-African Clinical Trials Registry PACTR202112699416418
Early detection of malignant and pre-malignant peripheral nerve tumors using cell-free DNA fragmentomics
Authors: Sundby R. Taylor , Szymanski Jeffrey J. , Pan Alexander , Jones Paul A. , Mahmood Sana Z. , Reid Olivia H. , Srihari Divya , Armstrong Amy E , Chamberlain Stacey , Burgic Sanita , Weekley Kara , Murray Béga , Patel Sneh , Qaium Faridi , Lucas Andrea N. , Fagan Margaret , Dufek Anne , Meyer Christian F. , Collins Natalie B. , Pratilas Christine A. , Dombi Eva , Gross Andrea M. , Kim AeRang , Chrisinger John S.A. , Dehner Carina A. , Widemann Brigitte C. , Hirbe Angela C. , Chaudhuri Aadel A. , Shern Jack F. 
Published: January 2024

AbstractEarly detection of neurofibromatosis type 1 (NF1) associated peripheral nerve sheath tumors (PNST) informs clinical decision-making, potentially averting deadly outcomes. Here, we describe a cell-free DNA (cfDNA) fragmentomic approach which distinguishes non-malignant, pre-malignant and malignant forms of NF1 PNST. Using plasma samples from a novel cohort of 101 NF1 patients and 21 healthy controls, we validated that our previous cfDNA copy number alteration (CNA)-based approach identifies malignant peripheral nerve sheath tumor (MPNST) but cannot distinguish among benign and premalignant states. We therefore investigated the ability of fragment-based cfDNA features to differentiate NF1-associated tumors including binned genome-wide fragment length ratios, end motif analysis, and non-negative matrix factorization deconvolution of fragment lengths. Fragmentomic methods were able to differentiate pre-malignant states including atypical neurofibromas (AN). Fragmentomics also adjudicated AN cases suspicious for MPNST, correctly diagnosing samples noninvasively, which could have informed clinical management. Overall, this study pioneers the early detection of malignant and premalignant peripheral nerve sheath tumors in NF1 patients using plasma cfDNA fragmentomics. In addition to screening applications, this novel approach distinguishes atypical neurofibromas from benign plexiform neurofibromas and malignant peripheral nerve sheath tumors, enabling more precise clinical diagnosis and management.