bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond planar: fish schools adopt ladder formations in 3D
Authors: Ko Hungtang , Girma Abigail , Zhang Yangfan , Pan Yu , Lauder George V , Nagpal Radhika 
Published: October 2024

AbstractThe coordinated movement of fish schools has long captivated researchers studying animal collective behavior. Classical literature from Weihs and Lighthill suggests that fish schools should favor planar diamond formations to increase hydrodynamic efficiency, inspiring a large body of work ranging from fluid simulations to hydrofoil experiments. However, whether fish schools actually adopt and maintain this idealized formation remains debated and unresolved. When fish schools are free to self-organize in three dimensions, what formations do they prefer? By tracking polarized schools of giant danios (Devario aequipinnatus) swimming continuously for ten hours, we demonstrate that fish rarely stay in a horizontal plane, and even more rarely, in the classical diamond formation. Of all fish pairs within four body-lengths from each other, only 25.2% are in the same plane. Of these, 54.6% are inline, 30.0% are staggered, and 15.4% are side-by-side. The diamond formation was observed in less than 0.1% of all frames. Notably, a “ladder formation” emerged as the most probable formation for schooling giant danios, appearing in 79% of all fish pairs and fish schools elongate at higher swimming speeds. These findings highlight the dynamic and three-dimensional nature of fish schools and suggest that hydrodynamic benefits may be obtained without requiring fixed positions. This research provides a foundation for future studies that examine the hydrodynamics and control of underwater collectives in 3D formations.
Autophagy, the Ubiquitin proteasome system, and the MAPK pathway control the temperature dependence of synaptic growth
Authors: De Leon Kevin , Marie Bruno 
Published: October 2024

AbstractThere is clear evidence that Earth’s temperature is rising at an unprecedented rate. While consequences on ecosystems are being extensively studied, little is known about the consequences of temperature on the nervous system of ectothermic animals. Here we used theDrosophilamodel NMJ to assess the effect of temperature on the synaptic growth of a phasic, and a tonic, motoneuron. We find that the tonic neuron’s synaptic size is not affected by temperature, however we do observe a temperature-dependent synaptic growth in the phasic neuron, which might be related to the increased motility observed previously at higher temperatures. We find that the level of autophagy activity changes with temperature and that autophagy genes are responsible for the temperature dependence of synaptic growth. We present evidence that this regulation could occur through the major synaptic growth regulator and ubiquitin ligase Highwire, and a pathway involving the Mitogen-Activated Protein Kinases. We present a new function for the MAPKKK, Wallenda and the MAPK P38b in directing the additional synaptic growth that takes place between 25°C and 29°C. This illustrates that temperature has different effects on a diverse population of neurons and that distinct genetic pathways are involved in regulating temperature driven changes.
Contextual Neural Dynamics During Time Perception in Primate Ventral Premotor Cortex
Authors: Díaz Héctor , Bayones Lucas , Alvarez Manuel , Andrade-Ortega Bernardo , Valero Sebastián , Zainos Antonio , Romo Ranulfo , Rossi-Pool Román 
Published: October 2024

AbstractUnderstanding how time perception adapts to cognitive demands remains a significant challenge. In some contexts, the brain encodes time categorically (as “long” or “short”), while in others, it encodes precise time intervals on a continuous scale. Although the ventral premotor cortex (VPC) is known for its role in complex temporal processes, such as speech, its specific involvement in time estimation remains underexplored. In this study, we investigated how the VPC processes temporal information during a time interval comparison task (TICT) and a time interval categorization task (TCT) in primates. We found a notable heterogeneity in neuronal responses associated with time perception across both tasks. While most neurons responded during time interval presentation, a smaller subset retained this information during the working memory periods. Population-level analysis revealed distinct dynamics between tasks: in TICT, population activity exhibited a linear and parametric relationship with interval duration, whereas in TCT, neuronal activity diverged into two distinct dynamics corresponding to the interval categories. During delay periods, these categorical or parametric representations remained consistent within each task context. This contextual shift underscores the VPC’s adaptive role in interval estimation and highlights how temporal representations are modulated by cognitive demands.Significance StatementThe neural representation of time has long intrigued neuroscientists, particularly how it adapts to cognitive demands. Depending on the task, the brain encodes time either categorically (“long” or “short”) or as precise intervals. While the ventral premotor cortex (VPC) is known for its role in temporal processes, its role in time estimation remains underexplored. Here, we examined how the VPC processes temporal information in primates during a time interval comparison task (TICT) and a categorization task (TCT). The VPC exhibited heterogeneous neuronal responses with distinct dynamics: a linear, parametric relationship in TICT and bifurcated dynamics in TCT. These representations remained consistent during delay periods, underscoring the VPC’s adaptive role in time interval estimation.
Warming treatments shift the temporal dynamics of diversity and composition of bacteria in wild blueberry soils
Authors: Alaba Oluwafemi A. , Ishaq Suzanne L. , Chen Yu-Ying , Calderwood Lily , Hao Jianjun , Zhang Yong-Jiang 
Published: October 2024

AbstractSoil bacterial communities are a crucial biological indicator of soil health and crop performance; however, their response to climate change remains poorly understood. In Maine, wild blueberry farms are experiencing unprecedented temperature changes, which may exacerbate microbial responses and potentially harm the crop. To elucidate the response of bacterial communities to warming during the growing season, we employed passive and active open-top chambers to simulate climate warming scenarios in wild blueberry fields. Warming treatments elevated atmospheric temperatures by 1.2 and 3.3 °C (passive and active warming), respectively, but did not affect soil temperatures. Nevertheless, soils in the active warming treatment exhibited significantly lower water content than ambient conditions. Overall, soil bacterial diversity and richness (June, July, and August data combined) under the warming (passive and active) treatments and ambient controls did not demonstrate significant differences after two years of experimental warming. However, significantly higher bacterial evenness and diversity under warming treatments were observed in the early growing season (June). Our study also reveals pronounced seasonal shifts in the evenness and diversity of bacteria in wild blueberry soil, suggesting that the variation in bacterial community structure may be more influenced by seasonal changes in temperature and plant activity during the growing season than by warming treatments. The increased bacterial evenness and diversity under warming treatments in June may be attributed to advanced plant phenology, indicating a potential future shift in seasonal dynamics of bacterial activity under global warming.
Analyzing Biodiversity in Protected vs. Unprotected Tide Pools
Authors: Chen Vicki , Campbell Rowan , Chirputkar Arohi , Tran Emma , Chaturvedi Parnika , Han Sally , Lu Amber , Chu Zoe , Erb Melody , Mehta Tejin , Bindal Vidya , Lee Isaac , Benson Andrew , Adams Connor T. 
Published: October 2024

AbstractThis study assessed the efficacy of marine protected areas (MPAs) by comparing tide pool biodiversity in Half Moon Bay, California between a protected site (Fitzgerald Marine Reserve) and an unprotected site (Maverick’s Beach). Samples were collected through random quadrat surveys. ImageJ and RStudio were used to analyze data through three methods utilizing the Simpson’s Diversity Index along with three metrics. The unprotected Maverick’s Beach displayed greater biodiversity through two metrics while the third did not find significant difference in biodiversity between sites. 30 unique species were present at each site with 43 species between both. These mixed findings prevent us from drawing definitive conclusions on the effectiveness of Half Moon Bay’s tide pool MPAs but suggest the MPA is less biodiverse. Potential explanations include the Intermediate Disturbance Hypothesis, lack of sample size, or that the MPA is not effective in maintaining biodiversity.
Cell cycle regulation of polymerase theta mediated end-joining underlies its sensitivity to loss of BLM-DNA2
Authors: McBrine Connor P. , Jensen Ryan B. , King Megan C. 
Published: October 2024

AbstractDNA double-strand breaks (DSBs) are predominantly resolved by the error-prone non-homologous end-joining (NHEJ) or high-fidelity homologous recombination (HR) DNA repair pathways. NHEJ involves minimal end-processing and drives direct ligation of the broken ends, while HR first requires a DSB resection step that degrades 5’ strands to generate 3’ ssDNA tails necessary for homology search. When HR fails, an alternative end-joining pathway involving polymerase theta can serve as a backup repair mechanism by annealing and ligating microhomologies present in ssDNA tails on either side of a resected DSB. Resection is the early step that commits a DSB to repair by HR, and is therefore considered a prerequisite for TMEJ as well. It has been proposed that the exonuclease EXO1 and the helicase/nuclease complex of BLM-DNA2 have redundant roles in resection, and therefore may both contribute to TMEJ. Here, we use a sensitive deep-sequencing approach to identify DSB repair outcomes at an endogenous locus in response to genetic and chemical perturbation of the resection machinery. While we observe that both EXO1 and BLM-DNA2 contribute to resection, our findings highlight a predominant role for BLM-DNA2 in facilitating TMEJ. However, careful cell cycle analysis revealed that BLM-DNA primarily contributes to TMEJ by ensuring normal progression to the G2/M transition, required for TMEJ to become activated. We propose that rather than direct, mechanistic roles in resection, the critical functions of BLM and DNA2 in genome replication largely account for their genetic contribution to efficient TMEJ.
Synergy betweencis-regulatory elements can render cohesin dispensable for distal enhancer function
Authors: Hansen Karissa L. , Adachi Annie S. , Braccioli Luca , Kadvani Smit , Boileau Ryan M. , Pokorny Bozhena , Shah Rini , Anderson Erika C. , Martinovic Moreno , Zhang Kaite , Carel Irié , Bonitto Kenya , Blelloch Robert , Fudenberg Geoffrey , de Wit Elzo , Nora Elphège P. 
Published: October 2024

AbstractEnhancers are critical genetic elements controlling transcription from promoters, but the mechanisms by which they convey regulatory information across large genomic distances remain elusive. Here, we engineered pluripotent stem cells in which cohesin loop extrusion can be inducibly disrupted without causing confounding cell cycle defects. While evident, transcriptional dysregulation was cell-type specific, and not all loci with distal enhancers depend equally on cohesin extrusion. Using comparative genome editing, we demonstrate that enhancer-promoter communication across as little as 20 kilobases can rely on cohesin. However, promoter-proximal regulatory elements can support long-range, cohesin-independent enhancer action – either upon disabling extrusion or across strong CTCF insulators. Finally, transcriptional dynamics and the emergence of new embryonic cell types in response to differentiation cues remained largely robust to disrupting cohesin extrusion. Beyond establishing novel experimental strategies to study cohesin functions in enhancer biology, our work provides mechanistic insight accounting for both cell type- and genomic context-specificity.
An Expanded Substrate Scope for Cross-Chiral Ligation Enables Efficient Synthesis of Long L-RNAs
Authors: Han Xuan , Sczepanski Jonathan T. 
Published: October 2024

ABSTRACTDespite the growing interest in mirror-image L-oligonucleotides, both as a robust nucleic acid analogue and as an artificial genetic polymer, their broader adoption in research and medicine remains hindered by challenges associated with the synthesis of long sequences, especially for L-RNA. Herein, we present a novel strategy for assembling long L-RNAs via the joining of two or more shorter fragments using cross-chiral ligase ribozymes together with new substrate activation chemistry. We show that 5′-monophosphorylated L-RNA, which is readily prepared by solid phase synthesis, can be activated by chemical attachment of a 5′-adenosine monophosphate (AMP) or diphosphate (ADP), yielding 5′-adenosyl (di-or tri-) phosphate L-RNA. The activation reaction is performed in mild aqueous conditions, proceeds efficiently with short or large L-RNA, and, yielding few biproducts, requires little or no further purification after activation. Importantly, both groups, when added to L-RNA, are compatible with ribozyme-mediated ligation, with the 5′-adenosyl triphosphate permitting rapid and efficient joining of multiple, long L-RNA strands. This is exemplified by the assembly of a 129-nt L-RNA molecule via a single cross-chiral ligation event. Overall, by relying on ribozymes that can be readily prepared byin vitrotranscription and L-RNA substrates that can be activated through simple chemistry, these methods are expected to make long L-RNAs more accessible to a wider range of researchers and facilitate the expansion of L-ON-based technologies.
APOE Protects Against Severe Infection withMycobacterium tuberculosisby Restraining Production of Neutrophil Extracellular Traps
Authors: Liu Dong , Mai Dat , Jahn Ana N. , Murray Tara A. , Aitchison John D. , Gern Benjamin H. , Urdahl Kevin B. , Aderem Alan , Diercks Alan H. , Gold Elizabeth S. 
Published: October 2024

AbstractWhile neutrophils are the predominant cell type in the lungs of humans with active tuberculosis (TB), they are relatively scarce in the lungs of most strains of mice that are used to study the disease. However, similar to humans, neutrophils account for approximately 45% of CD45+ cells in the lungs ofApoe-/-mice on a high-cholesterol (HC) diet following infection withMycobacterium tuberculosis(Mtb). We hypothesized that the susceptibility ofApoe-/-HC mice might arise from an unrestrained feed-forward loop in which production of neutrophil extracellular traps (NETs) stimulates production of type I interferons by pDCs which in turn leads to the recruitment and activation of more neutrophils, and demonstrated that depleting neutrophils, depleting plasmacytoid dendritic cells (pDCs), or blocking type I interferon signaling, improved the outcome of infection. In concordance with these results, we found that Mtb-infected inApoe-/-HC mice produce high levels of LTB4 and 12-HETE, two eicosanoids known to act as neutrophil chemoattractants and showed that blocking leukotriene B4 (LTB4) receptor signaling also improved the outcome of tuberculosis. While production of NETs has been associated with severe tuberculosis in other mouse models and in humans, a causative role for NETs in the pathology has not been directly established. We demonstrate that blocking the activation of peptidylarginine deiminase 4 (PAD4), an enzyme critical to NET formation, leads to fewer NETs in the lungs and, strikingly, completely reverses the hypersusceptibility ofApoe-/-HC mice to tuberculosis.
Early Postnatal Dysfunction of mPFC PV Interneurons in Shank3B−/−Mice
Authors: Shih Yi-Chun , Nelson Lars , Janeček Michael , Matarazzo Michael , Peixoto Rui T. 
Published: October 2024

AbstractMedial prefrontal cortex(mPFC)dysfunction is associated with cognitive and sensory abnormalities in individuals with autism spectrum disorder(ASD), yet the trajectory of mPFC circuit development in these conditions remains poorly understood. In this study, we investigated the postnatal maturation of glutamatergic connectivity and neuronal excitability in pyramidal neurons(PYR)and parvalbumin-positive interneurons(PVIN)in the mPFC of mice harboring deletions in SHANK3, a well-established genetic cause of autism associated with severe cognitive impairments and seizures. Our findings reveal early deficits in PVIN excitability that precede changes in the synaptic and intrinsic properties of PYR, resulting in impaired feedforward inhibition.In vivocalcium imaging demonstrated hypoactivity of PVIN in dorsal mPFC circuits during early postnatal development, characterized by reduced frequency of calcium transients. By adulthood, excitability phenotypes were reversed, with PVIN becoming hyperexcitable and PYR hypoexcitable. These results suggest that PVIN dysfunction in Shank3B−/−mice emerges during postnatal development and may represent a key pathogenic mechanism and potential therapeutic target in SHANK3-related disorders.
EASI-ORC: A Pipeline for the Efficient Analysis and Segmentation of smFISH Images for Organelle-RNA Colocalization Measurements in Yeast
Authors: Garin Shahar , Levavi Liav , Gerst Jeffrey E. 
Published: October 2024

AbstractAnalysis of single-molecule fluorescentin situhybridization (smFISH) images is an arduous and time-consuming task that is important to perform accurately in order to translate image data into a quantifiable format. This task becomes increasingly more difficult greater the experimental scope and number of images captured. Although smFISH is the gold standard for RNA localization measurements, there are no freely available, user-friendly applications for assaying messenger RNA localization to sub-cellular structures, like the endoplasmic reticulum (ER) or mitochondria). We have developed a pipeline that allows for the automated analysis of multiple smFISH images in yeast cells: EASI-ORC (EfficientAnalysis andSegmentation of smFISH Images forOrganelle-RNAColocalization). The EASI-ORC pipeline automates the segmentation of cells and sub-cellular structures (e.g.organelles), identifiesbona fidesmFISH signals, and measures the level of colocalization between an organelle and mRNA signals. Importantly, EASI-ORC works in a fast, accurate, and unbiased manner that is difficult to replicate manually. It also allows for the visualization of data filtering and outputs graphical representations of the colocalization data along with statistical analysis. EASI-ORC is based on existing ImageJ plugins and original scripts, thus, allowing free access and a relative ease of use. To circumvent any technical literacy issues, a step-by-step user guide is provided. EASI-ORC offers a robust solution for smFISH image analysis for both new and experienced researchers - one that saves time and effort, as well as providing more consistent overall measurements of RNA-organelle colocalization in yeast.
A post-mitoticin vitromurine as a model of muscle damage and repair
Authors: Galluccio Angelo , Maurotti Samantha , Noto Francesca Rita , Scionti Francesca , Pujia Carmelo , Mazza Elisa , Ferro Yvelise , Mare Rosario , Geirola Nadia , Scopacasa Bernadette , Candeloro Patrizio , Tirinato Luca , Sciacqua Angela , Pujia Arturo , Romeo Stefano , Montalcini Tiziana 
Published: October 2024

ABSTRACTSarcopenia is a degenerative condition characterized by the atrophy and functional decline of myofibers, resulting in disability. While the clinical risk factors are known, there is no validatedin vitromodel to understand the molecular mechanisms and identify therapeutics. To tackle this challenge, we generated anin vitropost-mitotic muscular system by differentiating mouse myoblast cells, namely C2C12. After 12 days of differentiation, cells were expressing physiological markers of myotubes and became self-contracting. Importantly, transcriptomic analyses demonstrated high similarity (r=0.70) when compared to primary human myotubes (HSkMC) providing evidence of resemblance to human cells. Next, we starved and incubated cells with dexamethasone and observed myotube shrinkage, oxidative stress, modification of anabolic, inflammatory, and catabolic markers recapitulating sarcopenia. Conversely, cell refeeding resulted in a recovery in the model with nutrient deprivation but not when incubated also with dexamethasone. In conclusion, we present a model of sarcopenia due to nutrient deprivation and corticosteroids. This model may allow more efficient and effective future research to identify therapeutics against sarcopenia in humans.
Soil pH influences the composition of bacteriophage communities infecting individual hosts
Authors: Lee Sungeun , Nicol Graeme W. , Hazard Christina 
Published: October 2024

AbstractBacteriophages (phages) can infect a range of hosts in highly diverse soil bacterial communities. However, selection of host communities across ecological gradients and co-evolutionary processes may influence both the distribution of phages and the susceptibility of individual hosts through virus interactions and local adaptation within distinct ecological niches. Metagenomic-based analyses have revealed that soil pH selects for distinct populations and community structures for both phage and hosts at local and global scales. However, whether contrasting soil pH represents a selective barrier for phages capable of infecting an individual host is unknown. To examine the influence of pH on individual host-virus interactions, two closely relatedBacillusstrains were isolated and characterized from pH 7.5 soil associated with a long-term contiguous pH gradient (pH 4.5 to 7.5). Phages infecting each strain were subsequently enriched from soils across the pH gradient (pH 4.5, 5.5, 6.5 and 7.5), enumerated using a plaque assay, and characterized via metagenomic analysis. Phages infecting each strain were cultivated from all soils but their community composition and abundance varied with pH. Phage populations infecting each of the two strains were distinct despite the close relatedness of the two hosts, indicating relatively narrow host ranges for each virus. These results suggest that while phage community structures vary substantially across an ecological gradient, soil pH alone does not represent a barrier for the distribution of phages capable of infecting an individual host.
Comparative Analysis of Lipid Nanoparticles in Pfizer-BioNTech and Moderna COVID-19 Vaccines: Insights from Molecular Dynamics Simulations
Authors: Biswal Malay Ranjan , Roy Sudip , Singh Jayant K 
Published: October 2024

AbstractCOVID-19 vaccines, such as Pfizer-BioNTech’s BNT162b and Moderna’s mRNA-1273, have demonstrated robust efficacy. However, direct comparisons of their delivery vehicles remain limited. Notably, BNT162b requires storage at -80°C, while mRNA-1273 is stored at -20°C. This discrepancy in storage temperatures may be influenced by differences in the structure and stability of the lipid nanoparticles (LNPs) used in these vaccines. Ionizable lipids, such as SM-102 in Moderna’s vaccine and ALC-0315 in Pfizer’s vaccine, play a crucial role in LNP stability and function, affecting endosomal escape, cellular uptake, and drug release. Understanding these variations is essential for optimizing vaccine delivery systems. In our study, we use molecular dynamics simulations with the coarse-grained Martini forcefield to compare the LNPs in Moderna and Pfizer’s COVID-19 vaccines, providing insights at an experimental scale. Our findings indicate that the ionizable lipid tail of BNT162b (ALC-0315) exhibits a higher degree of branching, resulting in a more bifurcated appearance compared to the structure of the ionizable lipids in mRNA-1273 (SM-102).