bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel structure and composition of the unusually large germline determinant of the wasp Nasonia vitripennis
Authors: Kemph Allie , Kharel Kabita , Tindell Samuel J. , Arkov Alexey L. , Lynch Jeremy A.
Published: November 2024

Specialized, maternally derived ribonucleoprotein (RNP) granules play an important role in specifying the primordial germ cells in many animal species. Typically, these germ granules are small (∼100 nm to a few microns in diameter) and numerous; in contrast, a single, extremely large granule called the oosome plays the role of germline determinant in the waspNasonia vitripennis.The organizational basis underlying the form and function of this unusually large membraneless RNP granule remains an open question. Here we use a combination of super-resolution and transmission electron microscopy to investigate the composition and morphology of the oosome. We show that the oosome has properties of a viscous liquid or elastic solid. The most prominent feature of the oosome is a branching mesh-like network of high abundance mRNAs that pervades the entire structure. Homologs of the core polar granule proteins Vasa and Oskar do not appear to nucleate this network, but rather are distributed adjacently as separate puncta. Low abundance RNAs appear to cluster in puncta that similarly do not overlap with the protein puncta. Several membrane-bound organelles, including lipid droplets and rough ER-like vesicles, are incorporated within the oosome, whereas mitochondria are nearly entirely excluded. Our findings show that the remarkably large size of the oosome is reflected in a complex sub-granular organization and suggest that the oosome is a powerful model for probing interactions between membraneless and membrane-bound organelles, structural features that contribute to granule size, and the evolution of germ plasm in insects.
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

Developmental 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

Existing 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

Correct 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 summary

Regulations 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

A 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

The 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

Craniofacial 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

Bacterial 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

Genetic 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

Background

Community 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.

Methods

A 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.

Results

A 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.

Conclusion

The 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.
On the neural substrates of mind wandering and dynamic thought: A drug and brain stimulation study
Authors: Rasmussen Tara , Dux Paul E , Filmer Hannah
Published: November 2024

The impact of mind wandering on our daily lives ranges from diminishing productivity, to facilitating creativity and problem solving. There is evidence that distinct internal thought types can be modulated by transcranial direct current stimulation (tDCS), although little is known about optimal stimulation parameters or the mechanisms behind such effects. In addition, recent findings suggest changes in dopamine availability may alter the effect tDCS has on neural and behavioural outcomes. Dopaminergic functioning has also been implicated in executive processes anticorrelated with mind wandering such as attention and working memory, however the neurochemical mechanisms involved in internal thoughts are largely unknown. Here, we investigated the role of dopamine, and tDCS, on internal thought processes. Specifically, using an attentional control task, we tested whether dopamine availability (levodopa or placebo) mediated the effects of online high definition tDCS (HD-tDCS; 2mA, or sham). There was no evidence for our hypothesised effect of left prefrontal cortex HD-tDCS reducing task unrelated thought, nor freely moving thought. This failure to replicate previous HD-tDCS findings emphasises the importance of employing robust methodological practices within this field to improve confidence in the findings. However, we did find that levodopa reduced freely moving thought, relative to placebo. We also found preliminary evidence that dopamine availability may moderate the relationship between stimulation and behavioural variability performance during periods of task unrelated thought. Overall, these findings suggest that stimulation does not affect dynamic internal thought, however there is initial evidence for the potential effectiveness of targeting the dopaminergic system to reduce spontaneous internal thoughts and improve behavioural performance.
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

CTCF-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

Mycobacterium 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

By 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

Single-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

Background and Aims

Pulsed 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.

Methods

We 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.

Results

Over 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.

Conclusions

Thermal 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.
Low Dose Radiation by Radiopharmaceutical Therapy Enhances GD2TRAC-CAR T Cells Efficacy in Localized Neuroblastoma
Authors: Sodji Quaovi H. , Shea Amanda , Cappabianca Dan , Forsberg Matthew H. , Eickhoff Jens C. , Idrissou Malick Bio , Ollendorff Andy S. , Kwon Ohyun , Ong Irene M. , Hernandez Reinier , Weichert Jamey , Bednarz Bryan P. , Saha Krishanu , Sondel Paul M. , Capitini Christian M. , Morris Zachary S.
Published: November 2024

Background

While chimeric antigen receptor (CAR) T cells have achieved significant success against hematological malignancies, efficacy against neuroblastoma has been limited. Virus-free CRISPR-edited GD2TRAC-CAR T cells have been developed as a potential means of improving CAR T efficacy but are not curative. Radiopharmaceutical therapy (RPT) is a promising approach to enhance the effectiveness of immunotherapies, including immune checkpoint inhibitors. However, it remains unclear whether RPT can synergize with GD2TRAC-CAR T cells to improve outcomes in neuroblastoma.

Methods

Dosimetry studies were conducted to measure the absorbed radiation dose delivered by lutetium-177 (177Lu) in bothin vitroandin vivomodels. Tumor-bearing mice were treated sequentially with low dose radiation by177Lu-NM600, an alkylphosphocholine mimetic radiopharmaceutical agent, followed 9 days later by GD2TRAC-CAR T cells generated in a virus-free manner by CRISPR/Cas9. Tumor burden was monitored through bioluminescence imaging and tumor size measurements. Mechanistic studies were performed using flow cytometry, multiplex assay and single-cell proteomic analysis.

Results

Low dose radiation delivered by177Lu-NM600 synergized with GD2TRAC-CAR T cells in a localized neuroblastoma model, resulting in complete tumor regression in all mice. The optimal combination was dependent on both the radiation dose and timing to minimize the negative impact of radiation on CAR T cell viability. Irradiation of neuroblastoma cells by low-dose RPT before GD2TRAC-CAR T cells enhanced the release by CAR T cells of perforin, granzyme B and cytokines like TNF-α and IL-7 while abrogating TGF-β1 secretion. Additionally, low-dose RPT upregulated Fas on neuroblastoma cells, potentially enabling a CAR-independent killing.

Conclusions

This study demonstrates that low-dose RPT can enhance CAR T cell efficacy to treat a solid tumor. Findings suggest that optimization of radiation dose and timing may be needed for each patient and RPT to account for effects of varied tumor radiosensitivity and dosimetry.

Graphical Abstract
Impact of prenatal delta-9-tetrahydrocannabinol exposure on mouse brain development: a fetal-to-adulthood magnetic resonance imaging study
Authors: Cupo Lani , Vecchiarelli Haley A. , Gallino Daniel , VanderZwaag Jared , Bradshaw Katerina , Phan Annie , Khakpour Mohammadparsa , Ben-Azu Benneth , Guma Elisa , Fouquet Jérémie , Spring Shoshana , Nieman Brian J. , Devenyi Gabriel A. , Tremblay Marie-Eve , Chakravarty M. Mallar
Published: November 2024

While cannabis use during pregnancy is often perceived as harmless, little is known about its consequences on offspring neurodevelopment. There is an urgent need to map the effects of prenatal cannabis exposure on the brain through the course of the lifespan. We used magnetic resonance imaging spanning nine timepoints, behavioral assays, and electron microscopy to build a trajectory from gestation to adulthood in mice exposed prenatally to delta-9-tetrahydrocannabinol (THC). Our results demonstrate a spatio-temporal patterning, with ventriculomegaly in THC-exposed embryos followed by a deceleration of brain growth in neonates that is sustained until adulthood, especially in females. We observed consistently impacted regions in both the cortex and subcortex, aligned with sex-dependent changes to social behavior in neonates and increased anxiety-like behavior in adolescents. Our results suggest prenatal THC exposure has a sustained sex-dependent impact on neurodevelopment that may persist into early adulthood.
Pyramidal cell types and 5-HT2Areceptors are essential for psilocybin’s lasting drug action
Authors: Shao Ling-Xiao , Liao Clara , Davoudian Pasha A. , Savalia Neil K. , Jiang Quan , Wojtasiewicz Cassandra , Tan Diran , Nothnagel Jack D. , Liu Rong-Jian , Woodburn Samuel C. , Bilash Olesia M. , Kim Hail , Che Alicia , Kwan Alex C.
Published: November 2024

Psilocybin is a serotonergic psychedelic with therapeutic potential for treating mental illnesses1–4. At the cellular level, psychedelics induce structural neural plasticity5,6, exemplified by the drug-evoked growth and remodeling of dendritic spines in cortical pyramidal cells7–9. A key question is how these cellular modifications map onto cell type-specific circuits to produce psychedelics’ behavioral actions10. Here, we usein vivooptical imaging, chemogenetic perturbation, and cell type-specific electrophysiology to investigate the impact of psilocybin on the two main types of pyramidal cells in the mouse medial frontal cortex. We find that a single dose of psilocybin increased the density of dendritic spines in both the subcortical-projecting, pyramidal tract (PT) and intratelencephalic (IT) cell types. Behaviorally, silencing the PT neurons eliminates psilocybin’s ability to ameliorate stress-related phenotypes, whereas silencing IT neurons has no detectable effect. In PT neurons only, psilocybin boosts synaptic calcium transients and elevates firing rates acutely after administration. Targeted knockout of 5-HT2Areceptors abolishes psilocybin’s effects on stress-related behavior and structural plasticity. Collectively these results identify a pyramidal cell type and the 5-HT2Areceptor in the medial frontal cortex as playing essential roles for psilocybin’s long-term drug action.
DSA-DeepFM: A Dual-Stage Attention-Enhanced DeepFM Model for Predicting Anticancer Synergistic Drug Combinations
Authors: Gu Yuexi , Sun Yongheng , Zhang Louxin , Zu Jian
Published: November 2024

Motivation

Drug combinations are crucial in combating drug resistance, reducing toxicity, and improving therapeutic outcomes in the treatment of complex diseases. As the number of available drugs grows, the potential combinations increase exponentially, making it impractical to rely solely on biological experiments to identify synergistic drug pairs. Consequently, machine learning methods are increasingly used to systematically screen for synergistic drug combinations. However, most current approaches prioritize predictive performance by integrating auxiliary information or increasing model complexity. By overlooking the biological mechanisms behind feature interactions, their effectiveness in predicting drug synergy can be limited.

Results

We present DSA-DeepFM, a deep learning model that integrates a dual-stage attention (DSA) mechanism with Factorization Machines (FMs) to improve drug synergy prediction by addressing complex biological feature interactions. The model incorporates categorical and auxiliary numerical inputs, embedding them into high-dimensional spaces and then fusing them through the DSA mechanism to capture both field-aware and embedding-aware patterns. These patterns are then processed by a DeepFM module, which captures low-order and high-order feature interactions before making final predictions. Validation testing demonstrates that DSA-DeepFM significantly outperforms traditional machine learning and state-of-the-art deep learning models. Additionally, t-SNE visualizations confirm the model’s discriminative power at various stages. As a case study, we use our model to identify eight novel synergistic drug combinations, three of which are well-supported by existing wet-lab experiments, underscoring its practical utility and potential for future applications.
Synaptic and Somatic Targeting of ArcLight, a Genetically Encoded Voltage Indicator
Authors: Zhong Sheng , Cohen Lawrence B.
Published: November 2024

Voltage signals in neurons are highly compartmentalized, which can influence their specific functions within neuronal circuits. Targeting of a genetically encoded voltage indicator (GEVI) to specific subcellular compartments can enhance the signal-to-noise ratio and provide more precise information about the location and timing of synaptic firing across different neuronal regions, reducing spatiotemporal signal convolution. To achieve subcellular targeting of the GEVI, ArcLight, we utilized five different postsynaptic targeting sequences (ShakerK+channel C-terminus, stargazin C-terminus, rat Neuroligin-1 C-terminus, and anti-homer1 nanobodies HC20 & HC87) to direct ArcLight expression to the excitatory postsynaptic density. Additionally, we assessed a presynaptic-targeting tag (rat Neurexin-1β C-terminus) and a somatodendritic targeting tag (Kv2.1-Lk-Tlcn C-terminus). Patch clamp experiments in HEK293 cells showed that the targeting tags used in this study did not significantly alter ArcLight’s voltage sensitivity compared to controls. AAV infection in the mouse olfactory bulb demonstrated that the subcellular targeting sequences effectively localized GEVI expression to specific compartments of mitral/tufted cells, including postsynaptic densities, presynaptic terminals, and somatodendritic regions. Furthermore, in vivovoltage imaging in mice expressing targeting-enhanced ArcLight variants revealed odorant-evoked responses similar to those observed with the original ArcLight. This indicates that subcellular targeting did not significantly impact the voltage sensing capability of ArcLight in mitral/tufted cells.
Structural variations contribute to genetic diversity and heterosis in rice
Authors: Dan Zhiwu , Chen Yunping , Huang Wenchao
Published: November 2024

The contributions of structural variants (SVs) to rice heterosis, which has significantly boosted crop yield, remain largely unexplored. In this study, we assembled 12 high-quality rice genomes and revealed that SVs are pivotal in the evolution and variation ofindicaandjaponica. Our findings indicate that SVs trigger gene expression changes which explain the variance in heterosis of 17 traits, highlighting the importance of SVs in harnessing rice heterosis.
Conversion of somatic sex identity in the testis induces female-specific cellular behaviors in the soma and early oocyte specification in the germline
Authors: Roach Tiffany V. , Harsh Sneh , Sainath Rajiv , Bach Erika A. , Lenhart Kari F.
Published: November 2024

Establishment and maintenance of cellular sex identity is essential for reproduction. Critically, the sex identity of somatic and germline cells must correspond for sperm or oocytes to be produced, with mismatched identity causing infertility in all organisms from flies to humans. In theDrosophilatestis, Chronologically inappropriate morphogenesis (Chinmo) is required for maintenance of adult male somatic identity. Loss ofchinmoleads to progressive feminization of the male soma, including adoption of female-specific cell morphologies, tissue organization and gene expression. However, the degree to which this feminized soma in the male engages female-specific cellular behaviors or influences the associated XY germline is unknown. Using extended live imaging, we have visualized the process of male-to-female somatic sex conversion uponchinmoloss of function. We find that feminized soma in the testis engage cell behaviors characteristic of ovarian follicle cells (FCs), including female-specific incomplete cytokinesis, as early as one day ofchinmoinhibition. In the ovary, FCs collectively migrate around the underlying germ cells to establish the elongated shape of the oocyte. Surprisingly, we find that FC-like soma inchinmo-depleted testes also engage this female-specific collective cell migration. Critically, migration of FC-like cells in the testis has the same molecular requirements as FC migration in the ovary. Depletion of the basement membrane protein Perlecan or adhesion protein Ecadherin significantly disrupts rotational migration in both the ovary andchinmo-depleted testes. Finally, we find that feminized soma non-autonomously alters sex identity of the associated XY germ cells, inducing expression of a protein required for early oocyte specification. Taken together, our work reveals a dramatic transformation of somatic cell behavior during the process of sex conversion and provides a powerful model to study soma-derived induction of oocyte identity.
The distribution of clade size in a coalescent diversification model
Authors: Song Yexuan , Colijn Caroline , MacPherson Ailene
Published: November 2024

Characterizing the patterns and determinants of biological diversity is a central aim of evolutionary biology. Doing so requires developing expectations for clade size, the relationship between the number of species in a clade and its age, for standard diversification models, such as the coalescent or birth-death process. These expectations are necessary for identifying diversity outliers, specious or depauperate clades in the macroevolutionary context or transmission clusters of particular or little public health concern in the epidemiological context, and for testing alternative diversification hypotheses. Here, we derive a closed-form expression for the distribution of clade sizes under the widely used Kingman coalescent diversification model and extend the results to allow the number of niches (the effective population size) to vary through time. This result complements analogous results for the birth-death model in that it provides expectations for the joint distribution of clade sizes for a case where diversification is strongly density-dependent.
Natural selection of synthetic gene drives for population suppression can favour an intermediate strength of drive
Authors: Beaghton PJ , Burt Austin
Published: November 2024

Synthetic gene drives are being investigated as tools to suppress pest populations, and it is important to understand how natural selection will act on variant drivers that may either arise byde novomutation or are intentionally released. In this study we extend previous spatially implicit stochastic models to examine the evolutionary dynamics of synthetic driving Y chromosomes in patchy environments when population size is responding dynamically to the spread of the driver, and derive conditions for the existence of an evolutionarily stable strategy (ESS) for drive strength. Under broad conditions an intermediate drive strength emerges as the ESS, capable of outcompeting both stronger and weaker variants. Additionally, we show how the intentional release of two drivers straddling the ESS can help stabilise population dynamics. Finally, inbreeding depression has the effect of expanding the range of conditions under which no intermediate ESS exists, with ever stronger drive being selected until the population is eliminated. These results provide insights into the expected evolutionary trajectories of gene drive systems, with important implications for the design and release of gene drives for pest and vector control.
An exploration of complex action stopping across multiple datasets: Insights into the mechanisms of action cancellation and re-programming
Authors: Salomoni Sauro Emerick , Weber Simon , Hinder Mark R
Published: November 2024

A long history of psychological experiments has utilised stop signal paradigms to assess action inhibition. Recent studies have investigated complex stopping behaviours, such as response-selective stopping where only one component of a bimanual action requires cancellation. A current emphasis has been to utilise electromyographical (EMG) recordings to assess the temporal dynamics of action inhibition at the level of the muscle, beyond those based solely on observable behavioural events. Here, we combine EMG and behavioural data from 17 cohorts of healthy younger and older adults yielding over 42,000 response-selective stopping trials, providing unique insights into this emerging field. Expanding from past research in this area, our robust single-trial EMG analyses permit detection of cancelled (partial) and response-generating EMG bursts in both hands, revealing substantial overlaps in the distributions of timing of action cancellation and re-programming. These findings are consistent with recent experimental and modelling evidence, suggesting that response-selective stopping involves two independent processes: a discrete bimanual stop and initiation of a new unimanual response. This overlap appears incompatible with the recent pause-then-cancel model, and more consistent with a broader 'pause-then-retune' account, where a slower process mediates any action updating, not just cancellation. Moreover, this independence means that cancellation can happen at any time during motor planning and execution, against the notion of an observable 'point of no return' in motor actions. We also discuss best practices for the analysis of EMG data and indicate how methodological aspects, such as choosing appropriate reference time points, can influence the outcomes and their interpretation.
Role of Non-Exponential Reversal times in Aggregation Models of Bacterial Populations
Authors: Batista Michael , Murphy Patrick , Igoshin Oleg A. , Perepelitsa Misha , Timofeyev Ilya
Published: November 2024

In this paper, we consider 1D agent-based and kinetic models of aggregation with reversals. In particular, we fit a Gamma distribution to represent the run times in myxobacteria and analyze numerically the importance of non-exponential reversal times. We demonstrate that non-exponential reversal times aid aggregation and result in tighter aggregates. We compare and contrast the behavior of agent-based and kinetic models, and also consider kinetic models with aggregation driven by chemotaxis. Thus, incorporating non-exponential reversal times into models of aggregation can be particularly important for reproducing experimental data, such as aggregate persistence and dispersal.
Drug Delivery Process Simulation - Quantifying the Conformation Dynamics of Paclitaxel and Cremophor EL
Authors: Uddin Mafiz , Coombe Dennis
Published: November 2024

Paclitaxel is a highly successful anti-neoplastic cancer drug. The first clinically successful paclitaxl-delivery method is a mixture with cremophor EL and ethanol, here termed the taxol micelle. Until now, molecular dynamics analysis has not been presented to quantify the structural and conformation properties of these drug molecules when interacting with each other to create this nonstandard micelle. Here we apply systematic molecular simulation and statistical analysis of paclitaxel and cremophor EL conformations based on all atom and coarse-grained approaches. The cremophor EL in the taxol micelle showed a clustering network in a 3D landscape where paclitaxel can be loaded at much higher than standard concentration with no aggregation. Paclitaxel particles within the cremophor EL cavities showed some oscillatory behaviour due to a repeated adsorption/desorption with the surrounding network. Paclitaxel conformations at the lowest energy state can be described when the side-chain phenyl rings are closer relative to the immobile core. Cremophor EL molecules reached the highest energy state when wings were fully spread and at the lowest energy state when wings were fully closed. The spiral shapes were observed to be the dominant species in the cremophor EL population. We then established reliable statistical correlations between molecular conformations and the energy states. Our reliable all atom and coarse-grained modelling approach can also be applied for effective drug design analysis using different drug delivery systems.

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