bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex sphingolipids are essential for cell division and plasmodesmal development in the mossPhyscomitrium patens
Authors: Wegner Linus , Herrfurth Cornelia , Feussner Ivo , Ehlers Katrin , Haslam Tegan M. 
Published: November 2024

AbstractDevelopmental patterning and organ structure are elegantly simple in the mossPhyscomitrium patens. In molecular genetic studies, this facilitates both the cultivation of severe mutant alleles and their phenotypic characterization. Essential membrane lipids, such as complex phosphosphingolipids (in plants, glycosyl inositol phosphorylceramides, GIPCs), have been difficult to functionally characterize due to non-viable and pleiotropic phenotypes of mutants affected in their synthesis inArabidopsis thaliana. Following the isolation and biochemical characterization of mutants affected in GIPC synthesis inP. patens, includingsphinganine-C4-hydroxylase(s4h/sbh) andinositol phosphorylceramide synthase(ipcs), we now report some of their morphological, histological, and cytological phenotypes. We observed alteration in cell division, expansion, and differentiation. Specifically, thes4hknock-out mutant had abnormal cell division planes, as well as irregular depositions attached to cell walls. Severeipcsmutant alleles showed frequent incomplete cell divisions, causing compromised cell autonomy as demonstrated by intercellular motility assays. These phenotypes suggest that sphingolipids impact both the orientation and proper formation of the cell plate during cytokinesis. Transmission electron microscopy revealed dramatic plasmodesmal structural defects in all three mutants, however, qualitative aspects of plasmodesmal transport do not seem to be severely impacted. Our methods can be used as a toolkit for quantifying growth, and specifically cell division and plasmodesmal phenotypes in mosses; our present results elucidate the specific contributions of GIPCs to fundamental cell functions. Finally, the severity of the observed defects in cell functions and ultrastructure highlight the resilience and utility ofP. patensfor studying basic cellular functions and severe mutant phenotypes.
Solution-phase indexing by kinetic confinement enables rapid, simple, and instrument-free single cell transcriptional profiling
Authors: Marafini P. , Smith DG. , Lamstaes AR. , Contreras RE. , Williams I. , West I. , Ambridge O. , Sanders-Brown V. , Intaite E. , Hii CY. , Hume BCC. , Munagala U. , Plumbly W. , Brown FL. , Shlyakhtina Y. , Woods L. , Bibby JA. , Williams L. , Yang JHM. , Steffy B. , Zawada L. , Harger JW. , McKenzie D. , Laing AG. , Stubbington MJT. , Edelman LB. 
Published: November 2024

AbstractExisting tools for single cell genomics require complex physical frameworks for the indexing of cellular nucleic acids, including proprietary instrumentation, droplet emulsions, and laborious combinatorial indexing schemes. The complexity and cost of these tools significantly constrains the use of single cell technologies across basic and translational research.Here, we describe an instrument-free method that uses novel, bifunctional indexing reagents to deliver index sequences directly to single cells followed by a biophysical process known as ‘Kinetic Confinement’ to perform high-fidelity indexing of target molecules across thousands of single cells simultaneously in single-tube, solution-phase reactions.Kinetic Confinement enables simple, fast, and flexible single cell experiments, and allows straightforward scaling to very large sample numbers. We anticipate that assays based on Kinetic Confinement will significantly expand the scope, use, and impact of single cell analysis across fundamental and applied research, as well as within therapeutic development and ultimately applied clinical diagnostics.
Differential Regulation of Large-scale Chromosome Conformations in Osteoblasts and Osteosarcoma
Authors: Bisht Madhoolika , Chung Yu-Chieh , He Siou-Luan , Willey Sydney , Sunkel Benjamin D. , Wang Meng , Stanton Benjamin Z. , Tu Li-Chun 
Published: November 2024

ABSTRACTCorrect chromosome organization in the cell nucleus is essential for genome function. However, dynamics and regulations of large-scale chromosomal conformations beyond single compartments at larger than ten megabasesin vivoin single cells remain largely unknown. Here we use CRISPR-Sirius, a high-resolution and high-sensitivity real-time imaging technique, to directly visualize distinctions in large-scale chromosomal conformations between live osteosarcoma (OS) cells and osteoblasts, suggesting extensive chromatin reorganization during cell transformation. A surprising discovery is that chromosome 19 long arm is primarily extended in osteoblasts and maintained by H3K27me3. Extended chromosome conformation has been reported in fly and mouse but not in human cells yet. However, in OS cells, chromosome 19 primarily folded into collapsed conformations, which reshape in minutes and are regulated by the chromosome architectural proteins CTCF and cohesin in the presence of H3K27ac. Changes in chromosome conformations by knocking down the cohesin subunit RAD21 resulted in altered gene expression, including proto-oncogenes. Transcription inhibition by a small molecule inhibitor did not have detectable effects on large-scale chromosome conformation, suggesting that local transcription events have limited effects on large-scale chromosomal architecture. Our results provide unique insights into the complex regulatory mechanisms of endogenous large-scale chromosome organization in normal and transformed osteogenic tissues.One-sentence summaryRegulations of chromosome territory organization in normal and cancer bone cells visualized by CRISPR-based live-cell imaging.
From the fly connectome to exact ring attractor dynamics
Authors: Biswas Tirthabir , Stanoev Angel , Romani Sandro , Fitzgerald James E. 
Published: November 2024

AbstractA cognitive compass enabling spatial navigation requires neural representation of heading direction (HD), yet the neural circuit architecture enabling this representation remains unclear. While various network models have been proposed to explain HD systems, these models rely on simplified circuit architectures that are incompatible with empirical observations from connectomes. Here we construct a novel network model for the fruit fly HD system that satisfies both connectome-derived architectural constraints and the functional requirement of continuous heading representation. We characterize an ensemble of continuous attractor networks where compass neurons providing local mutual excitation are coupled to inhibitory neurons. We discover a new mechanism where continuous heading representation emerges from combining symmetric and anti-symmetric activity patterns. Our analysis reveals three distinct realizations of these networks that all match observed compass neuron activity but differ in their predictions for inhibitory neuron activation patterns. Further, we found that deviations from these realizations can be compensated by cell-type-specific rescaling of synaptic weights, which could be potentially achieved through neuromodulation. This framework can be extended to incorporate the complete fly central complex connectome and could reveal principles of neural circuits representing other continuous quantities, such as spatial location, across insects and vertebrates.
Species-specific phyllosphere responses to external pH change
Authors: Lopez-Gonzalez Cristal , Floc’h Jean-Baptiste , Renner Tanya , Gilbert Kadeem J. 
Published: November 2024

AbstractThe leaf surface, known as the phylloplane, represents the initial point of contact for plants in their interaction with the aboveground environment. Although prior research has assessed how leaves respond to external pH variations, particularly in the context of acid rain, there remains a limited understanding of the molecular mechanisms through which plants detect, respond to, and mitigate cellular damage. To look at plant responses to external pH changes, we measured the phylloplane pH for five species with variable phylloplane pH that ranged in the dry control. Moreover, we investigated the phylloplane pH in response to three pH treatments (pH 6.5, 4, and 2) and found that plants can modify their phylloplane pH, and this buffering ability is species-specific. Among the species analyzed, onlyGossypiumdisplayed a strong buffering ability. For treatments where leaves were exposed to either pH 6.5 or pH 4,Gossypiumalkalinized the phylloplane pH slightly higher than the dry control pH. Remarkably, when leaves were exposed to pH 2,Gossypiumwas able to buffer the pH to 6 within five minutes. Furthermore, our transcriptional analysis indicated that the responses to external pH changes varied among species, highlighting differentially expressed genes associated with calcium (Ca2+) signaling pathways, as well as Ca2+and H+-ATPases pumps. These findings also suggest that pH stress negatively impacts photosynthesis, and that both wetness and moderate pH shifts may trigger additional abiotic and biotic stress signaling pathways.
Multi-modal characterization of rodent tooth development
Authors: Jiang Yuchen , Katsura Kaitlin A. , Badt Nir Z. , Didziokas Marius , Dougherty Sonia , Goldsby David L. , Bhoj Elizabeth J. , Vining Kyle 
Published: November 2024

AbstractCraniofacial tissues undergo hard tissue development through mineralization and changes in physicochemical properties. This study investigates the mechanical and chemical properties of developing enamel, dentin, and bone in the mouse mandible. We employ a multi-modal, multi-scale analysis of the developing incisor and first molar at postnatal day 12 by integrating micro-computed tomography (microCT), nanoindentation (NI), energy dispersive spectroscopy (EDS), and Raman spectroscopy. Our findings demonstrate distinct patterns of mechanical, elemental, and chemical changes across mineralized tissues. These results suggest that mineral composition drives mechanical properties across different craniofacial hard tissues. Integrating multi-modal characterization of mineralized tissues opens new opportunities for investigating structure-function relationships in craniofacial biology and genetics.
Using BONCAT To Dissect The Proteome OfS. aureusPersisters
Authors: George Matlalcuatzi Eva D. C. , Bakkum Thomas , Thomas Pooja S. , Hacker Stephan M. , Florea Bogdan I. , Vriesendorp Bastienne , Rozen Daniel E. , van Kasteren Sander I. 
Published: November 2024

AbstractBacterial persisters are a subpopulation of cells that exhibit a transient non-susceptible phenotype in the presence of bactericidal antibiotic concentrations. This phenotype can lead to the survival and regrowth of bacteria after treatment, resulting in relapse of infections. As such, it is also a contributing factor to antibacterial resistance. Multiple processes are believed to cause persister formation, yet identifying the proteins expressed during the induction of the persister state has been difficult, because the persister-state is rare, transient and does not lead to genetic changes. In this study, we used Bio-Orthogonal Non-Canonical Amino Acid Tagging (BONCAT) to label, and retrieve, the proteome expressed during the persister state for different strains of methicillin-resistantStaphylococcus aureus. After incubating antibiotic-exposed bacteria with the methionine ortholog L-azidohomoalanine to label the proteins of persister cells, we retrieved labeled proteins using click chemistry-pulldown methodology. Analysis of the retrieved proteome fraction of Methicillin resistantStaphylococcus aureus(MRSA) and Vancomycin resistantStaphylococcus aureus(VRSA) under challenge with β-lactam and fluoroquinolone antibiotics with Label Free Quantification - Liquid chromatography mass spectrometry (LFQ-LCMS) based proteomics reveals the upregulation of proteins involved in stringent response, cell wall biosynthesis, purine metabolism, ppGpp biosynthesis, two component systems (TCS), lipid metabolism, ABC transporters, D-alanine biosynthesis and L-proline degradation. Conversely, we observed a decline of proteins associated with amino acid biosynthesis and degradation, protein biosynthesis, protein modification, and carbohydrate metabolism, among others. These findings indicate that modification of translational activity in persister cells enables bacterial cells to induce an active defense to survive antibiotic pressure.
Reinforced identity confers cells with cancer hallmarks
Authors: Yang Haixia , Wang Pengqi , Tan Pengcheng , Xue Qiaomei , Wu Hua , He Kezhang , Wang Bowen , Wang Dan , Ma Tianhua , Ding Sheng 
Published: November 2024

AbstractGenetic alterations trigger tumorigenesis in a cell type-specific manner, but the biological basis for this, remains unclear. Here we define reinforced original cell identity established by interaction between genetic alterations and original cell type is a pivotal determinant of tumor development. Using AML-M5MLL-AF9as a model system, we demonstrated that MLL-AF9 enhanced key transcriptional factors (TFs) expression of promonocyte and cooperated with them to amplify their downstream programs for AML hallmarks. Interactions between MLL-AF9 and promonocyte endowed cancer cells with a reinforced promonocyte identity. Reinforced intrinsic cell identity also sustained cancer hallmarks across cancer types. Furthermore, we identified narciclasine, as an effective disruptor of reinforced promonocyte identity, effectively treating AML-M5MLL-AF9. This study not only identified reinforced cell identity as a fundamental tumor driver beyond genetic mutations but also offers a proof-of-concept for reinforced identity- targeted cancer therapy.
An Assessment of the Effects of Coronavirus Disease 2019 (COVID-19) on Community Pharmacy Service Delivery in Lagos State
Authors: Ajibola Olufunke G. , Joda Arinola 
Published: November 2024

ABSTRACTBackgroundCommunity pharmacists play an important role as frontline health care workers during the COVID-19 pandemic. Therefore, the delivery of pharmaceutical care and the availability of drugs is compromised. The objective of this study was to evaluate the effect of coronavirus disease 2019 (COVID-19) on community pharmacy service delivery in Lagos state.MethodsA cross-sectional study with an online questionnaire created using Google Forms software was sent to community pharmacists in Lagos State, Nigeria via the Association of Community Pharmacists in Nigeria WhatsApp platforms. The sample size was 120 respondents conveniently chosen. Ethical approval was obtained from Health Research Ethics Committee, Lagos University Teaching Hospital (LUTH), Idi-Araba, Lagos State. Collected data was analyzed using Microsoft Excel.ResultsA total of 125 respondents participated in the study. The result showed 56% were female respondents and the mean age of respondents was 32.4 ± 4.7 years. Measures such as the use of face masks (90.4%) and restricted number of patients for access at a time (89.6%) were implemented to reduce the spread of COVID-19. Majority of the respondents (61.6%) believe the measures have reduced the interaction between patients and pharmacists. Most of the respondents (81.6%) believe the pandemic has affected the availability and almost average (48%) of the respondents think that there was inflation in the prices of products like antimalarials, antibiotics, protective and preventive equipment and multivitamins.ConclusionThe COVID-19 pandemic has affected the delivery of pharmaceutical care to clients as well as the availability of medicines to patients. To improve the delivery of pharmaceutical care, tele-pharmacy and online pharmaceutical services may be employed.
A genome wide code to define cell-type specific CTCF binding and chromatin organization
Authors: Do Catherine , Jiang Guimei , Zappile Paul , Heguy Adriana , Skok Jane A 
Published: November 2024

AbstractCTCF-mediated chromatin folding plays a key role in gene regulation, however the mechanisms underlying cell type-specific control are not fully elucidated. Comprehensive analyses reveal that CTCF binding stability and cohesin overlap in mice and humans is regulated by species specific differences in accessibility, the presence of CTCF extended Up and Downstream binding site sequences and motifs corresponding to expressed TFs enriched at most bound sites. CTCF repositions nucleosomes asymmetrically, with linker spacing altered by accessibility, while cohesin-mediated nucleosome phasing is affected by surrounding motifs that similarly impact chromatin insulation. Importantly, cell type-specific transcriptional programs determine motif enrichment at CTCF bound sites, reflecting the stabilizing/destabilizing effect of individual TFs. These studies identify mechanisms underlying cell type-specific CTCF profiles, linked to local and long-range chromatin organization.
Atrans-translation inhibitor is potentiated by zinc and killsMycobacterium tuberculosisand non-tuberculous mycobacteria
Authors: Varshney Akanksha , Jia Ziyi , Howe Michael D. , Keiler Kenneth C. , Baughn Anthony D. 
Published: November 2024

SUMMARYMycobacterium tuberculosisposes a serious challenge for human health, and new antibiotics with novel targets are needed. Here we demonstrate that an acylaminooxadiazole, MBX-4132, specifically inhibits thetrans-translation ribosome rescue pathway to killM. tuberculosis. Our data demonstrate that MBX-4132 is bactericidal against multiple pathogenic mycobacterial species and killsM. tuberculosisin macrophages. We also show that acylaminooxadiazole activity is antagonized by iron but is potentiated by zinc. Our transcriptomic data reveals dysregulation of multiple metal homeostasis pathways after exposure to MBX-4132. Furthermore, we see differential expression of genes related to zinc sensing and efflux whentrans-translation is inhibited. Taken together, these data suggest that there is a link between disturbing intracellular metal levels and acylaminooxadiazole-mediated inhibition oftrans-translation. These findings provide an important proof-of-concept thattrans-translation is a promising antitubercular drug target.
CILP Inhibits Hyaline Cartilage Fibrosis and Chondrocyte Ferroptosis via Keap1-Nrf2 Axis in Early Osteoarthritis Exercise Therapy
Authors: Jia Shuangshuo , Hu Zhehan , Li Zihan , Zhang Weiming , Chen Liang , Niu Changping , Zhao Ziqi , Sun Yuhan , Yao Gang , Wang Yang , Yang Yue 
Published: November 2024

AbstractBy analyzing the single-cell RNA-Seq libraries, the roles of cartilage intermediate layer protein (CILP) and the cartilage intermediate zone in early osteoarthritis (OA) exercise therapy were explored. An early OA rat model was established via a 4-week anterior cruciate ligament transection. The effect of moderate exercise was confirmed using histology, the open-field test, and gait analysis. The response of the cartilage intermediate zone to mechanical stimulation was explored using multiplex fluorescent immunohistochemical staining. Radiomics was used to evaluate the relatively damaged and undamaged areas in the cartilage of patients with OA. CILP was OE and KD in early OA chondrocytes, and quantitative proteomics, yeast one-hybrid, co-immunoprecipitation, Nrf2 and ubiquitination assays were used to investigate its mechanism. We found that moderate exercise upregulates CILP in the cartilage intermediate zone. CILP recovers the type II/I collagen, Sox9, and α-SMA expression ratios, and reduces Keap1-Nrf2 dimer stability, inhibiting Nrf2 ubiquitination and promoting Nrf2 nuclear translocation. Nrf2 nuclear translocation activates SLC7A11, HO-1, GPX4, and SOD-1 expression, decreases MDA content, and increases GSH content, inhibiting chondrocyte ferroptosis and promoting fibrocartilage hyalinization. In conclusion, the exercise-induced cartilage intermediate zone and CILP-Keap1-Nrf2 axis inhibit hyaline cartilage fibrosis and chondrocyte ferroptosis to alleviate early OA.
Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells
Authors: Fegraeus Kim , Riihimäki Miia , Nordlund Jessica , Akula Srinivas , Wernersson Sara , Raine Amanda 
Published: November 2024

AbstractSingle-cell RNA sequencing (scRNA-seq) is a valuable tool for investigating cellular heterogeneity in diseases such as equine asthma (EA). This study evaluates the HIVE™ scRNA-seq method, a pico-well-based technology, for processing bronchoalveolar lavage (BAL) cells from horses with EA. The HIVE method offers practical advantages, including compatibility with both field and clinical settings, as well as a gentle workflow suited for handling sensitive cells.Our results show that the major cell types in equine BAL were successfully identified; however, the proportions of T cells and macrophages deviated from cytological expectations, with macrophages being overrepresented and T cells underrepresented. Despite these limitations, the HIVE method confirmed previously identified T cell and macrophage subpopulations and defined other BAL cell subsets. However, compared to previous studies T helper subsets were less clearly defined.Additionally, consistent with previous scRNA-seq studies, the HIVE method detected fewer granulocytes and mast cells than anticipated in the total BAL samples. Nevertheless, applying the method to purified mast cells recovered an expected number of cells. A small set of eosinophils were also detected which have not been characterized in earlier studies. In summary these findings suggest that while the HIVE method shows promise for certain applications, further optimization is needed to improve the accuracy of cell type representation, particularly for granulocytes and mast cells, in BAL samples.
Quantification of thermal side effects during pulsed field ablation
Authors: Mercado-Montoya Marcela , Gomez-Bustamante Tatiana , Mickelsen Steven R , Kulstad Erik , González-Suárez Ana , Overzet Lawrence J. 
Published: November 2024

AbstractBackground and AimsPulsed field ablation (PFA) has been described as non-thermal, but abundant data exist in oncology applications, and growing data are emerging in cardiology, highlighting that thermal effects are in fact present with PFA. Our objective was to develop a reliable model of the thermal effects arising from PFA of myocardial and esophageal tissue over a range of typical peak voltage operating conditions.MethodsWe developed a three-dimensional computer model of the left atrium that can quantify the thermal effects from PFA applications. Energy was applied using a bipolar configuration, and far-field and symmetry boundaries were set as electrically insulating. The model utilizes a monophasic waveform with a pulse width of 100 μs and gap between pulses of 1 s was applied for a total of 50 pulses in a single train, with variations to this easily implemented to accommodate various conditions.ResultsOver a range of peak voltage operating conditions (1 kV, 1.5 kV, and 2 kV), minimal temperature rise in the esophagus was seen with 1 kV pulses (corresponding to 215 J input), but with 1.5 kV and 2 kV peak voltages (corresponding to 570 J and 1.23 kJ), temperature elevations reaching 46.3°C and > 62 °C were seen, respectively. These elevations occurred after only a single pulse train of 50 pulses, implying that further elevations in temperature would be seen with subsequent applications. These findings concur with data published in other fields of medicine where pulsed field treatments are utilized.ConclusionsThermal effects from PFA occur and can be quantified with in-silico modeling. The model described here offers an efficient means of determining temperature effects from PFA over various operating conditions. Energy levels used clinically appear to have the potential to induce collateral thermal injury with repeated applications of pulsed field energy.