bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress-free state in human carotid arteries cannot be revealed without layer separation
Authors: Hrubanová Anna , Lisický Ondřej , Sochor Ondřej , Bednařík Zdeněk , Joukal Marek , Burša Jiří
Published: October 2024

Residual stresses are considered as a significant factor influencing the stress-states in arteries. These stresses are typically observed through opening angle of a radially cut artery segment, often regarded as a primary descriptor of their stress-free state. However, the experimental evidence regarding the stress-free states of different artery layers is scarce. In this study, two experimental protocols, each employing different layer-separating sequences, were performed on 17 human common carotid arteries; the differences between both protocols were found statistically insignificant. While the media exhibited opening behaviour (reduced curvature), a contrasting trend was observed for the adventitia curvature, indicating its closing behaviour. In addition to the different bending effect, length changes of both layers after separation were observed, namely shortening of the adventitia and elongation of the media. The results point out that not all the residual stresses are released after a radial cut but a significant portion of them is released only after the layer separation. Considering the different mechanical properties of layers, this may significantly change the stress distribution in arterial wall and should be considered in its biomechanical models.
Glycolysis inhibition functionally reprograms T follicular helper cells and reverses lupus
Authors: Elshikha Ahmed , Ge Yong , Choi Seung Chul , Park Yuk Pheel , Padilla Lauren , Zhu Yanan , Clapp William L. , Sobel Eric S. , Mohamadzadeh Mansour , Morel Laurence
Published: October 2024

Systemic lupus erythematosus (SLE) is an autoimmune disease in which the production of pathogenic autoantibodies depends on T follicular helper (TFH) cells. This study was designed to investigate the mechanisms by which inhibition of glycolysis with 2-deoxy-d-glucose (2DG) reduces the expansion of TFHcells and the associated autoantibody production in lupus-prone mice. Integrated cellular, transcriptomic, epigenetic and metabolic analyses showed that 2DG reversed the enhanced cell expansion and effector functions, as well as mitochondrial and lysosomal defects in lupus TFHcells, which include an increased chaperone-mediated autophagy induced by TLR7 activation. Importantly, adoptive transfer of 2DG-reprogrammed TFHcells protected lupus-prone mice from disease progression. Orthologs of genes responsive to 2DG in murine lupus TFHcells were overexpressed in the TFHcells of SLE patients, suggesting a therapeutic potential of targeting glycolysis to eliminate aberrant TFHcells and curb the production of autoantibodies inducing tissue damage.
Intratumoral CXCL12 Gradients Contextualize Tumor Cell Invasion, Migration and Immune Suppression in Breast Cancer
Authors: Anastasiadou Dimitra P. , Couturier Nicole , Goel Sakshi , Argyris Dimitrios G. , Vodopyanov Stepan , Rivera-Sanchez Luis , Gonzalez Edgar , Kreger Jesse , Griffen Anthony , Kazakov Abigail , Burt Joseph , Recoder Natasha , Duran Camille L. , Harney Allison S. , Quesnel Agathe , Filippou Panagiota S. , Lenis Vasileios P. , Shukla Suryansh , Entenberg David , Zintiridou Aliona , Chen Xiaoming , Eddy Robert J. , Oktay Maja H. , Condeelis John S. , Karagiannis Nikolaos S. , Briceno Andrea , Guzik Hillary , Alon Rotem , DesMarais Vera , Ioannou Giorgio , Gnjatic Sacha , Raynolds David. M. , Macedo Rodney , Reshef Ran , Gil-Henn Hava , MacLean Adam L. , Torres Evanthia Roussos , LaFave Lindsay M. , Lauvau Gregoire , Karagiannis George S.
Published: October 2024

Although the CXCL12/CXCR4 pathway has been prior investigated for its prometastatic and immuno- suppressive roles in the tumor microenvironment, evidence on the spatiotemporal regulation of these hallmarks has been lacking. Here, we demonstrate that CXCL12 forms a gradient specifically around cancer cell intravasation doorways, also known as Tumor Microenvironment of Metastasis (TMEM) doorways, thus facilitating the chemotactic translocation of prometastatic tumor cells expressing CXCR4 toward the perivascular TMEM doorways for subsequent entry into peripheral circulation. Fur- thermore, we demonstrate that the CXCL12-rich micro-environment around TMEM doorways may cre- ate immunosuppressive niches, whereby CD8+T cells, despite being attracted to these regions, often exhibit reduced effector functions, limiting their efficacy. While the CXCL12/CXCR4 pathway can mini- mally influence the overall composition of immune cell populations, it biases the distribution of CD8+T cells away from TMEM doorways, justifying its prior-established role as immunosuppressive factor for CD8+T cells. Our research suggests that the complex interactions between CXCL12 and the various tumor and immune cell types contributes not only to the completion of the initial steps of the metastatic cascade, but also offers an immunological “sanctuary” to prometastatic tumor cells homed around TMEM doorways. Overall, our study enhances our current understanding on the mechanisms, via which CXCL12 orchestrates tumor cell behavior and immune dynamics, potentially guiding future thera- peutic strategies to combat breast cancer metastasis and improve anti-tumor immunity.
Evolutionary genomics of two co-occurring congeneric fore reef coral species on Guam (Mariana Islands)
Authors: Torrado Héctor , Rios Dareon , Primov Karim , Burdick David R , Bentlage Bastian , Lemer Sarah , Combosch David
Published: October 2024

Population structure provides essential information for developing meaningful conservation plans. This is especially important in remote places, such as oceanic islands, where limited population sizes and genetic isolation can make populations more susceptible and self-dependent.

In this study, we assess and compare the relatedness, population genetics and molecular ecology of two sympatricAcroporaspecies,A. surculosa sensuRandall & Myers (1983) andA.cf.verweyiVeron & Wallace, 1984 around Guam, using genome-wide sequence data (ddRAD). We further contrast our findings with the results of a recent study on back reefA.cf.pulchra(Brook, 1891) to assess the impact of habitat, colony morphology and phylogenetic relatedness on these basic population genetic characteristics and generate testable hypotheses for future studies.

Both target species were found to have small effective population sizes, low levels of genetic diversity, and minimal population structure around Guam. Nonetheless,A.cf.verweyihad significantly higher levels of genetic diversity, some population structure as well as more clones, close relatives and putative loci under selection. Comparisons withA.cf.pulchraindicate a potentially significant impact by habitat on population structure and genetic diversity while colony morphology seems to significantly impact clonality.

This study revealed significant differences in the basic population genetic makeup of two sympatricAcroporaspecies on Guam. Our results suggest that colony morphology and habitat/ecology may have a significant impact on the population genetic make-up in reef corals, which could offer valuable insights for future management decisions in the absence of genetic data.
An Environmental Vulnerability Index framework supporting targeted public health interventions at the census tracts level
Authors: Anderson Lauren B. , Holm Rochelle H. , Black Caison , Biddle Donald J. , Chiu Weihsueh A. , Bhatnagar Aruni , Smith Ted
Published: October 2024

BACKGROUND

Analyzing and visualizing disparities in environmental risks can help in assessing place-based vulnerabilities and provide civic leaders and community members with essential data about promoting health equity and inform public health strategies. However, there is a lack of effective and integrative tools for evaluating census tract vulnerabilities.

OBJECTIVE

We investigated the adaption of a previously developed environmental vulnerability index to evaluate cumulative impacts of diverse stressors in Louisville Metro-Jefferson County, KY, with the goal of supporting multi-faceted targeted public health interventions at the census tract-level.

METHODS

We assessed countywide variability in vulnerability using Toxicological Prioritization Index interface across five domains with 32 indicators and modeled the effects of theoretical public health interventions.

RESULTS

Our findings suggest similarly vulnerable areas are not always geographically clustered. Higher vulnerability scores are observed along the western and central areas of the county with lower vulnerability scores in the central urban core and eastern regions. The index enabled the selection of the most at-risk census tracts for modeling targeted public health interventions to reduce cumulative environmental vulnerability.

SIGNIFICANCE

Environmental vulnerabilities are not invariant features of urban environments, rather the knowledge of these risks can guide the development and implementation of targeted solutions.

IMPACT STATEMENT

Targeted interventions to modify environmental conditions that are supportive of health can be developed and implemented locally with greater precision at the census tract level, yielding impactful outcomes.
Vasomotor Pulsation Becomes a Driver of Cerebrospinal Fluid and Electrophysiological Dynamics in Sleeping Human Brain
Authors: Väyrynen Tommi , Tuunanen Johanna , Helakari Heta , Elabasy Ahmed , Korhonen Vesa , Huotari Niko , Piispala Johanna , Kallio Mika , Nedergaard Maiken , Kiviniemi Vesa
Published: October 2024

Sleep is essential for maintaining brain tissue homeostasis, which is facilitated by enhanced cerebrospinal fluid (CSF) solute transport. Infra-slow (<0.1 Hz) vasomotion, CSF flow, and electrophysiological potential all increase during sleep, but their contributions as potential drivers of CSF flow in human brain remain unknown. To investigate this, we recorded the three signals in healthy volunteers across sleep-wake states using 10 Hz functional magnetic resonance imaging (fMRI BOLD), electroencephalography (DC-EEG), and functional near-infrared spectroscopy (fNIRS). We then analyzed the directed coupling patterns using phase transfer entropy (TE). In the awake state, electrophysiological potential and water concentration changes both predicted vasomotor waves across the brain, possibly reflecting functional hyperemia. During sleep, this coupling reversed, with vasomotor waves instead predicting electrical changes and CSF flow in cortical areas. Furthermore, we found that the amplitude of these dynamics increased during sleep, highlighting the critical role of physiological oscillations in sleep-associated brain fluid flow.
Microglia signals to fibroblasts and neural progenitor cells to control regenerative neurogenesis after spinal cord injury in zebrafish
Authors: Docampo-Seara Alberto , Cosacak M. Ilyas , Heilemann Kim , Kessel Friederike , Oprişoreanu Ana-Maria , Westphal Markus , Çark Özge , Zöller Daniela , Arnold Josi , Bretschneider Anja , Hnatiuk Alisa , Ninov Nikolay , Becker Catherina G. , Becker Thomas
Published: October 2024

Zebrafish, in contrast to mammals, regenerate neurons after spinal cord injury, but little is known about the control mechanisms of this process. Here we show that microglia are the main cell type to express the evolutionarily conserved signalling moleculesema4abin the injury site. Deletion ofsema4abdoubles the number of newly generated progenitor cells and neurons after spinal injury. Using scRNAseq of all lesion site cell types after gene disruption, we find thatsema4absupports the microglial activation state and promotes interactions with fibroblasts and neural progenitor cells. Mechanistically,sema4absignals throughplxn1a/breceptors on spinal progenitors and attenuates expression of the neurogenesis-promoting cytokinetgfb3in fibroblasts. Hence, microglia regulate neurogenesis viasema4abin successful spinal cord regeneration in zebrafish, which may be one of the mechanisms preventing regenerative neurogenesis in the mammalian spinal cord.

HIGHLIGHTS

- Microglia control signalling from fibroblasts in a spinal injury site

- Fibroblasts promote regenerative neurogenesis via Tgfb3 signalling

- scRNAseq reveals full complement ofsema4ab-dependent cell type interactions in a spinal injury site

-sema4abstabilises activation state of microglia after injury
AI-Driven Spatial Transcriptomics Unlocks Large-Scale Breast Cancer Biomarker Discovery from Histopathology
Authors: Shulman Eldad D. , Campagnolo Emma M. , Lodha Roshan , Stemmer Amos , Cantore Thomas , Ru Beibei , Chang Tian-Gen , Biswas Sumona , Dhruba Saugato Rahman , Wang Andrew , Paul Rohit , Kalisetty Sarath , Hu Tom , Nasrallah Maclean , Rajagopal Sheila , Sammut Stephen-John , Lipkowitz Stanley , Jiang Peng , Caldas Carlos , Knott Simon , Hoang Danh-Tai , Aldape Kenneth , Ruppin Eytan
Published: October 2024

Spatial transcriptomics (ST) is transforming our understanding of tumor heterogeneity by enabling high-resolution, location-specific mapping of gene expression across tumors and their microenvironment. However, the associated high cost of the assay has limited cohort size and hence large-scale biomarker discovery. Here we presentPath2Space, a deep learning approach that predicts spatial gene expression directly from histopathology slides. Trained on substantial breast cancer ST data, it robustly predicts the spatial expression of over 4,300 genes in independent validations, markedly outperforming existing ST predictors.Path2Spaceadditionally accurately infers cell-type abundances in the tumor microenvironment (TME) based on the inferred ST data. Applied to more than a thousand breast tumor histopathology slides from the TCGA,Path2Spacecharacterizes their TME on an unprecedented scale and identifies three new spatially-grounded breast cancer subgroups with distinct survival rates.Path2Space-inferred TME landscapes enable more accurate predictions of patients’ response to chemotherapy and trastuzumab directly from H&E slides than those obtained by existing established sequencing-based biomarkers.Path2Spacethus offers a transformative, fast and cost-effective approach to robustly delineate the TME directly from their histopathology slides, facilitating the development of spatially-grounded biomarkers to advance precision oncology.
Switch in parasitic and autotrophic-dominated protist assemblages coupled to seasonal oligotrophic-mesotrophic gradients in the sunlit layer of a subtropical marine ecosystem
Authors: Avrahami Yoav , Siano Raffaele , Rubin-Blum Max , Koplovitz Gil , Henry Nicolas , de Vargas Colomban , Frada Miguel J.
Published: October 2024

Protists are major functional players in the oceans. Time-resolved epipelagic protist successions remain poorly described in subtropical ecosystems, limiting current understanding of food web dynamics and responses to environmental changes in these major world-ocean regions. Here, we used amplicon sequencing data and their trait-based annotation to examine the seasonality of planktonic protists in the subtropical Gulf of Aqaba (northern Red Sea). Temperature and nutrients were identified as major drivers of succession. Marked seasonal shifts in protists were detected. The warm, stratified oligotrophic period spanning through spring and summer were dominated by heterotrophs, including parasitic Syndiniales. By contrast, nutrient influx during deep convective-mixing in winter triggered a progressive shift to photoautotrophic communities dominated by few chlorophyte genera. Ephemeral phytoplankton blooms were detected during the mixing-to-stratification transition. Deeper winter mixing resulted in larger blooms dominated by diatoms and coccolithophores relative to chlorophytes prevalent during shallower mixing. This illustrates the impact of mixing-depth in the development and compostion of blooms. Comparisons with oceanwide rDNA datasets indicate that the oligotrophic protist assemblages from the Gulf of Aqaba resemble those from warm, open-oceans. This work provides a detailed assessment of the seasonality in protist communities and dominant functional strategies in a coastal subtropical planktonic ecosystem.
The role of IAA and its transport in the complex streptophyte algaeChara braunii
Authors: Kurtović Katarina , Vosolsobě Stanislav , Nedvěd Daniel , Müller Karel , Dobrev Petre , Schmidt Vojtěch , Piszczek Piotr , Kuhn Andre , Smoljan Adrijana , Fisher Tom J. , Weijers Dolf , Friml Jiří , Bowman John L. , Petrášek Jan
Published: October 2024

The role of auxin indole-3-acetic acid (IAA), a phytohormone with numerous morphogenic functions, is now well-established in land plants. Although the role of IAA and its transport in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within Streptophytes. Among streptophyte algae,Chararepresents a genus with a considerable degree of complexity in body arrangement. This study investigates the auxin response and characterizes homologs of land plant PIN auxin efflux carriers inChara braunii. Through regeneration experiments, we observed that IAA significantly promotes elongation of thallus and side branch development upon thallus tip decapitation, indicating an effect on morphogenesis. We show that IAA is actively uptaken and metabolized by thallus cells and that this process is influenced by N-1-naphthylphthalamic acid (NPA). To elucidate the underlying mechanisms, we cloned and sequenced the most expressedChara brauniiPINs, CbPINa and CbPINc. Using epitope-specific antibodies, we showed their presence in the plasma membrane (PM) of vegetative internodal cells and generative antheridial cells. Functional tests in tobacco BY-2 cells, supported byin silicodocking of IAA and NPA to CbPINa and CbPINc, showed that PM-localized CbPINa interferes with auxin transport in contrast to ER-localized CbPINc. Finally, our phosphoproteome analysis indicated that IAA rapidly induces specific phosphorylation events, including RAF-like kinase phosphorylation, highlighting a potential role for IAA in fast signaling processes inChara braunii.Altogether, we provide new insights into IAA role inChara brauniimorphogenesis and suggest that while the canonical auxin transport mechanism may not be conserved, auxin still may likely play a role in rapid signaling pathways in this close relative of land plants.
Weaker neuroligin 2 – neurexin 1β interaction tethers membranes and signal synaptogenesis through clustering
Authors: Boyd Robbie , Jaqaman Khuloud , Wang Weiwei
Published: October 2024

Single-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules (SAMs) that are essential for the formation of functional synapses. Binding affinities vary by ∼ 1000 folds between arrays of NL and NRX subtypes, which contribute to chemical and spatial specificities. Current structures are obtained with truncated extracellular domains of NL and NRX and are limited to the higher-affinity NL1/4-NRX complexes. How NL-NRX interaction leads to functional synapses remains unknown. Here we report structures of full-length NL2 alone, and in complex with NRX1β in several conformations, which has the lowest affinity among major NL-NRX subtypes. We show how conformational flexibilities may help in adapting local membrane geometry, and reveal mechanisms underlying variations in NL-NRX affinities modulation. We further show that, despite lower affinity, NL2-NRX1β interaction alone is capable of tethering different lipid membranes in total reconstitution, and that NL2 and NRX1β cluster at inter-cellular junctions without the need of other synaptic components. In addition, NL2 combines with the master post-synaptic scaffolding protein gephyrin and clusters neurotransmitter receptors at cellular membrane. These findings suggest dual roles of NL2 - NRX1β interaction – both as mechanical tether, and as signaling receptors, to ensure correct spatial and chemical coordination between two cells to generate function synapses.
Deciphering stiffness-driven changes in colorectal cancer by proteomics
Authors: Cresens Charlotte , Montero-Calle Ana , Solís-Fernández Guillermo , Shaghaghi Behrad , Gerrits Lotte , Aytekin Samet , Kouwer Paul H. J. , Barderas Rodrigo , Rocha Susana
Published: October 2024

Tumor stiffening plays a pivotal role in cancer progression. Increased tumor stiffness, resulting from interactions between cancer cells and their surrounding microenvironment, alters the tumor’s mechanical properties and significantly impacts cancer growth and metastasis, the primary cause of cancer-related deaths. Despite the importance of tumor stiffness, systematic studies exploring its effect on proteomic profiles are limited. In this study, focused on colorectal cancer, we show that matrix stiffness significantly alters the expression of secreted proteins, while intracellular protein levels remain largely unaffected. Functional assays reveal that the changes in the secretome, driven by matrix stiffness, enhance cell migration, angiogenesis, and matrix remodeling, which collectively contribute to a more aggressive cancer phenotype. Our findings emphasize the critical role of matrix stiffness in driving colorectal cancer progression through changes in the secretome, offering valuable insights for the development of biomechanical cancer therapies.

Abstract Figure
Why do bats fly into cave doors? Inattentional blindness in echolocating animals
Authors: Finger Nikita M , Eveland Keegan E , Yin Xiaoyan , Moss Cynthia F
Published: October 2024

Echolocating bats can navigate complex 3D environments by integrating prior knowledge of spatial layouts and real-time sensory cues. This study demonstrates that inattentional blindness to sensory information undermines successful navigation in Egyptian fruit bats,Rousettus aegyptiacus, a species that has access to vision and echolocation to traverse natural environments. Bats flew over repeated trials to a perch at a fixed location in the light, allowing them to navigate using both vision and echolocation. The experiment was then repeated in the dark to exclude the bat’s use of vision. The perch was subsequently displaced by either 15 or 30 cm in one of six different directions (up, down, left, right, front, back). Echolocation behavior was recorded using a 25-channel microphone array, while flight paths were tracked using 13 motion capture cameras. The directional aim of echolocation clicks served as a metric for the bat’s spatial attention to locations in their environment. In the light, bats modified their flight paths to successfully land on a perch that was moved 15 cm but surprisingly, often failed to land on it when displaced by 30 cm. In the dark, bats often failed to land on the perch after it was moved by only 15 cm. Landing failures suggest that learned spatial priors invoked inattentional blindness to changes in the environment, which interfered with successful navigation. In both the light and dark, when bats failed to land on the perch at its new location, they directed their attention toward the original perch position. Performance differences in the light and dark suggest that the bat’s attentional spotlight may be narrower when it relies on echolocation than vision. To our knowledge, these findings provide the first evidence of inattentional blindness in a flying echolocating animal, demonstrating that spatial priors can dominate sensory processing during navigation.
The Circadian Isoform Landscape of Mouse Livers
Authors: Zee Alexander , Deng Dori Z.Q. , DiTacchio Luciano , Vollmers Christopher
Published: October 2024

The mammalian circadian clock is an autoregulatory feedback process that is responsible for homeostasis in mouse livers. These circadian processes are well understood at the gene-level, however, not well understood at the isoform-level. To investigate circadian oscillations at the isoform-level, we used the nanopore-based R2C2 method to create over 78 million highly-accurate, full-length cDNA reads for 12 RNA samples extracted from mouse livers collected at 2 hour intervals. To generate a circadian mouse liver isoform-level transcriptome, we processed these reads using the Mandalorion tool which identified and quantified 58,612 isoforms, 1806 of which showed circadian oscillations. We performed detailed analysis on the circadian oscillation of these isoforms, their coding sequences, and transcription start sites and compiled easy-to-access resources for other researchers. This study and its results add a new layer of detail to the quantitative analysis of transcriptomes.
Human TRPV4 engineering yields an ultrasound-sensitive actuator for sonogenetics
Authors: Zhao Lu , Xu Kevin , Talyzina Irina , Shi Jingyi , Li Shisheng , Yang Yaoheng , Zhang Shuming , Zheng Jie , Sobolevsky Alexander I. , Chen Hong , Cui Jianmin
Published: October 2024

Abstract

Sonogenetics offers non-invasive and cell-type specific modulation of cells genetically engineered to express ultrasound-sensitive actuators. Finding an ion channel to serve as sonogenetic actuator it critical for advancing this promising technique. Here, we show that ultrasound can activate human TRP channel hTRPV4. By screening different hTRPV4 variants, we identify a mutation F617L that increases mechano-sensitivity of this channel to ultrasound, while reduces its sensitivity to hypo-osmolarity, elevated temperature, and agonist. This altered sensitivity profile correlates with structural differences in hTRPV4-F617L compared to wild-type channels revealed by our cryo-electron microscopy analysis. We also show that hTRPV4-F617L can serve as a sonogenetic actuator for neuromodulation in freely moving mice. Our findings demonstrate the use of structure-guided mutagenesis to engineer ion channels with tailored properties of ideal sonogenetic actuators.
In vivo CRISPRi screen identified lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth
Authors: Kim Gyuhyeon , Siprashvili Zurab , Yang Xue , Meyers Jordan M. , Ji Andrew , Khavari Paul A. , Ducoli Luca
Published: October 2024

Cutaneous squamous cell carcinoma (cSCC) accounts for 20% of all skin cancer deaths globally, making it the second-highest subtype of skin cancer. The prevalence of cSCC in humans, as well as the poor capacity for an efficient prognosis, highlights the need to uncover alternative actors and mechanisms at the foundation of skin cancer development. Significant advances have been made to better understand some key factors in cSCC progression. However, little is known about the role of noncoding RNAs, particularly of a specific category called long noncoding RNA (lncRNA). By performing pseudobulk analysis of single-cell sequencing data from normal and cSCC human skin tissues, we determined a global portfolio of lncRNAs specifically expressed in keratinocyte subpopulations. Integration of CRISPR interference screens in vitro and the xenograft model identified several lncRNAs impacting the growth of cSCC cancer lines both in vitro and in vivo. Among these, we further validated LINC00704 and LINC01116 as proliferation-regulating lncRNAs in cSCC lines and potential biomarkers of cSCC progression. Taken together, our study provides a comprehensive signature of lncRNAs with roles in regulating cSCC progression.
Genetic instrumental variable framework for assessing relevance of in-vitro cellular phenotypes to organism-level phenotypes
Authors: Howe Laurence J , Aulchenko Yury , Cortes Adrian , Gordillo Jorge Esparza , Johnson Toby , Richardson Tom G , Sanseau Philippe , Scott Robert A , Seaton Daniel D
Published: October 2024

Gene perturbation screens (e.g. CRISPR-Cas9) assess the impact of gene disruption on cellular phenotypes (e.g., proliferation, anti-viral response, transcriptomics). Cellular phenotypes can be useful in-vitro models for understanding the aetiology of organism-level (in-vivo) phenotypes (e.g., anti-viral response in immune cells and infectious disease outcomes). However, demonstrating relevance between cellular and organism-level phenotypes is non-trivial.

If a cellular phenotype is relevant, then we should observe that perturbed genes impacting the cellular phenotype also impact the organism-level phenotype with mechanism-consistent directionality. We propose a framework, loss-of-function instrumental variable analysis (LoF-IV), to evaluate relevance between cellular and organism-level phenotypes using estimates of gene effects on cellular phenotypes from perturbation screens and estimates of gene effects on human-level phenotypes from loss-of-function burden tests.

Using data from four published genome-wide CRISPR-Cas9 screens and UK Biobank whole-genome sequence burden tests, we evaluated relevance of four in-vitro cellular phenotypes (chondrocyte proliferation, insulin content, adipocyte differentiation, lysosomal cholesterol accumulation) to human-level phenotypes. We found evidence that higher lysosomal cholesterol accumulation lowers LDL-cholesterol measured in human blood plasma (P = 0.0006), consistent with the known role of lysosomes in lipid biosynthesis. However, we did not find strong evidence for phenotypic relevance of the other cellular phenotypes, illustrating the complexities of developing disease-relevant in-vitro models. LoF-IV enables systematic evaluation of the relevance of cellular phenotypes to the human phenome informing assay prioritization and supporting novel hypothesis generation.
Generalization and extinction of platform-mediated avoidance in male and female rats
Authors: López-Moraga Alba , Luyten Laura , Beckers Tom
Published: October 2024

Background

Understanding the basis of anxiety-related disorders can be advanced by studying the fear learning mechanisms implicated in the transition from adaptive to maladaptive fear. Individuals with anxiety disorders typically exhibit impaired fear extinction, pervasive avoidance, and overgeneralization of fear. While most research has examined deviations in these fear learning characteristics in isolation, their potential interactions remain understudied. Here, we introduce a modification of the platform-mediated avoidance task and use it to chart avoidance, generalization, and extinction using a single procedure in male and female rats.

Results

In the first experiment, we demonstrated that male rats readily acquire avoidance, show a gradient of generalization in a two-day generalization test, and gradually reduce avoidance and fear responding under extinction. In the second experiment, female rats likewise exhibited successful avoidance learning, showed gradual generalization and extinction of defensive behaviors. Across both experiments, interesting sex differences emerged. The third experiment aimed at corroborating these sex differences but showed that they were subtler than expected from the prior separate experiments. Finally, we present an open-source automated system to facilitate the processing of DeepLabCut and SimBA output and obtain reliable results for scoring avoidance and freezing behavior.

Conclusions

The modified platform-mediated avoidance task can effectively probe avoidance, generalization, and extinction of fear in male and female rats in a single procedure. Our automated behavioral scoring approach offers researchers an efficient and reproducible method to quantify the defensive behaviors of avoidance, freezing and darting in rats.
Neutrophils exhibit distinct migration phenotypes that are regulated by transendothelial migration
Authors: Schwartz Amy B. , Kandasamy Adithan , del Álamo Juan C. , Yeh Yi-Ting
Published: October 2024

The extravasation of polymorphonuclear neutrophils (PMNs) is a critical component of the innate immune response that involves transendothelial migration (TEM) and interstitial migration. TEM-mediated interactions between PMNs and vascular endothelial cells (VECs) trigger a cascade of biochemical and mechanobiological signals whose effects on interstitial migration are currently unclear. To address this question, we cultured human VECs on a fibronectin-treated transwell insert to model the endothelium and basement membrane, loaded PMN-like differentiated HL60 (dHL-60) cells in the upper chamber of the insert, and collected the PMNs that crossed the membrane-supported monolayer from the lower chamber. The 3D chemotactic migration of the TEM-conditioned PMNs through collagen matrices was then quantified. Data collected from over 50,000 trajectories showed two distinct migratory phenotypes, i.e., a high-persistence phenotype and a low-persistence phenotype. These phenotypes were conserved across treatment conditions, and their existence was confirmed in human primary PMNs. The high-persistence phenotype was characterized by more straight trajectories and faster migration speeds, whereas the low-persistence one exhibited more frequent sharp turns and loitering periods. A key finding of our study is that TEM induced a phenotypic shift in PMNs from high-persistence migration to low-persistence migration. Changes in the relative proportion of high-persistence and low-persistence populations correlated with GRK2 expression levels. Inhibiting GRK2 hindered the TEM-induced shift in migratory phenotype and impaired the phagocytic function of PMNs. Overall, our study suggests that TEM-mediated GRK2 signaling primes PMNs for a migration phenotype better suited for spatial exploration and inflammation resolution. These observations provide novel insight into the biophysical impacts of TEM that priming PMNs is essential to conduct sentinel functions.
Human Astrocytes Synchronize Neural Organoid Networks
Authors: Patel Megh Dipak , Lavekar Sailee Sham , Jaisalmeria Ronak , Oji Suki , Jayasi Jazmine , Cvetkovic Caroline , Krencik Robert
Published: October 2024

Biological neural networks exhibit synchronized activity within and across interconnected regions of the central nervous system. Understanding how these coordinated networks are established and maintained may reveal therapeutic targets for neurodegeneration and neuromodulation. Here, we tested the influence of astrocytes upon synchronous network activity using human pluripotent stem cell-derived bioengineered neural organoids. This study revealed that astrocytes significantly increase activity within individual organoids and across long distances among numerous rapidly merged organoids via influencing synapses and bioenergetics. Treatment of amyloid protein inhibited synchronous activity during neurodegeneration, yet this can be rescued by propagating activity from neighboring networks. Altogether, this study identifies critical contributions of human astrocytes to biological neural networks and delivers a rapid, reproducible, and scalable model to investigate long-range functional communication of the nervous system in healthy and disease states.
Coordinated Division of Selective Stationary-Phase Yeast Cells Expands the Population Survivorship in Quiescence
Authors: Hsiao Kai-Ching , Lin Hsin-Ying , Hazbun Tony R. , Kuo Min-Hao
Published: October 2024

Budding yeast employs a variety of survival strategies in response to starvation, including pseudohyphal development, invasive growth, and sporulation. Here we report an innate pathway of “viability resurgence in quiescent time” (VRQT) by aged cultures to preserve and expand the population survivorship. Without additional nutrients, a few stationary-phase cells synchronously enter mitosis, increasing the population viability that does not likely result from mutations. VRQT is a population density-dependent collective behavior that can be triggered by quorum sensing aromatic alcohols. Genetic analyses demonstrate that VRQT is independent of many canonical pathways for cell growth, development, or stress responses. This community survival program allows yeast to proactively extend vitality amidst a common nutritional crisis. Wild strains isolated from clinical samples exhibit VRQT, suggesting that this survival mechanism must be considered when treating human infections.
Targeted mRNA delivery with bispecific antibodies that tether LNPs to cell-surface markers
Authors: Dietmair Bettina , Humphries James , Mercer Timothy R. , Thurecht Kristofer J. , Howard Christopher B. , Cheetham Seth W.
Published: October 2024

Efficient delivery of mRNA-LNPs to specific cell-types remains a major challenge in the widespread application of mRNA therapeutics. Conventional targeting approaches involve modifying the lipid composition or functionalising the surface of lipid nanoparticles (LNPs), which complicates manufacturing, alters nanoparticle size, charge and stealth, impacting their delivery and immunogenicity. Here we present a generalisable method for targeted mRNA-LNP delivery that uses bispecific antibodies (BsAbs) to form a bridge between LNPs and cell-surface markers. Instead of attaching the targeting agent to the nanocarrier, BsAbs are administered first, bind to surface proteins on target cells, and later retain unmodified LNPs in affected tissues. We demonstrate efficient and cell-type-specific delivery of mRNA-LNPs to epidermal growth factor receptor (EGFR), and folate hydrolase 1 (PSMA) positive cellsin vitroandin vivo. The flexibility of this technology, achieved by substitution of the cell-targeting region of the BsAbs, enables rapid development of next-generation targeted mRNA drugs.
HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization
Authors: Brennan Lucy , Kim Hyeong-Ku , Colmenares Serafin , Ego Tatum , Ryu Je-Kyung , Karpen Gary
Published: October 2024

Compartmentalization of the nucleus into heterochromatin and euchromatin is highly conserved across eukaryotes. Constitutive heterochromatin (C-Het) constitutes a liquid-like condensate that packages the repetitive regions of the genome through the enrichment of histone modification H3K9me3 and recruitment of its cognate reader protein Heterochromatin Protein-1 (HP1a). The ability for well-ordered nucleosome arrays and HP1a to independently form biomolecular condensates suggests that the emergent material properties of C-Het compartments may contribute to its functions such as force-buffering, dosage-dependent gene silencing, and selective permeability. Using anin vitroreconstitution system we directly assess the contributions of H3K9me3 and HP1a on the biophysical properties of C-Het. In the presence of HP1a, H3K9me3 (Me-) and unmodified (U-) chromatin form co-condensates composed of distinct, immiscible domains. These chromatin domains form spontaneously and are reversible. Independently of HP1a, H3K9me3 modifications are sufficient to increase linker-DNA length within chromatin arrays and slow chromatin condensate growth. HP1a increases the liquidity of chromatin condensates while dramatically differentiating the viscoelastic properties of Me-chromatin versus U-chromatin. Mutating key residues in HP1a show that HP1a interactions with itself and chromatin determine the relative interfacial tension between chromatin compartments, however the formation of condensates is driven by the underlying chromatin. These direct measurements map the energetic landscape that determines C-Het compartmentalization, demonstrating that nuclear compartmentalization is a spontaneous and energetically favorable process in which HP1a plays a critical role in establishing a hierarchy of affinities between H3K9me3-chromatin and unmodified-chromatin.

Highlights

⍰ HP1a is necessary and sufficient for heterochromatin compartmentalization.

⍰ Heterochromatin compartmentalization is reversible and proceeds through microphase-separation.

⍰ H3K9me3 is sufficient to change nucleosome-array dynamics and mesoscale material properties.

⍰ HP1a increases chromatin liquidity.

⍰ HP1a-chromatin interaction modes tune the interfacial tensions and morphologies of heterochromatin compartments.
Realistic photon-number resolution in Gaussian boson sampling
Authors: Yeremenko I. S. , Dmytruk M. A. , Semenov A. A.
Published: October 2024

Gaussian boson sampling (GBS) is a model of nonuniversal quantum computation that claims to demonstrate quantum supremacy with current technologies. This model entails sampling photocounting events from a multimode Gaussian state at the outputs of a linear interferometer. In this scheme, collision events—those with more than one photon for each mode—are infrequent. However, they are still used for validation purposes. Therefore, the limitation of realistic detectors to perfectly resolve adjacent photon numbers becomes pivotal. We derive a photocounting probability distribution in GBS schemes which is applicable for use with general detectors and photocounting techniques. This probability distribution is expressed in terms of functionals of the field-quadrature covariance matrix, e.g., Hafnian and Torontonian in the well-known special cases of photon-number-resolving and on-off detectors, respectively. Based on our results, we consider a GBS validation technique involving detectors with realistic photon-number resolution.

Published by the American Physical Society
2024
Effects of space charge force on the beam-beam mode coupling instability
Authors: Ohmi Kazuhito , Zhang Yuan
Published: October 2024

Recent e+e− colliders operate with very low emittance and high current. The space-charge tune shift is not negligible in tau-charm and B factories. The vertical space-charge tune shift is on the order of 0.02–0.1 and is comparable to the synchrotron tune and the beam-beam tune shift. The beam-beam mode coupling instability has been studied with and without vacuum environment impedance. The mode coupling is influenced by the space-charge force, which exhibits similar characteristics to the beam-beam force. The combined effect of beam-beam, space charge, and vacuum environment impedance is discussed within the framework of the mode coupling theory. Strong-strong beam-beam simulation, considering the space-charge force and the impedance, are conducted to validate the theory and to study general cases such as asymmetric colliders.

Published by the American Physical Society
2024
Measuring the impact of laser relative intensity noise on heterodyne interferometers using differential wavefront sensing
Authors: Wissel L. , Hewitson M. , Heinzel G.
Published: October 2024

Laser-intensity fluctuations cause undesired phase noise even in balanced heterodyne interferometers. However, in space missions in particular, such as LISA Pathfinder or LISA, direct measurements of these fluctuations at the relevant frequencies are often not available. Hence, it can be challenging to estimate their impact on the interference phase. To address this, we propose a new method for characterizing laser relative intensity noise (RIN) using differential wavefront sensing (DWS), with the latter being a well-established technique typically used for angular sensing and control. Unlike other methods, this approach does not require an additional reference interferometer and instead takes advantage of the inherent phase subtraction of DWS. This allows us to estimate the RIN value at the heterodyne frequency and its harmonic, relative to the sensor noise floor of the total measurement system. Moreover, it provides a strategy to identify the ideal set point for minimizing RIN couplings in DWS.

Published by the American Physical Society
2024
Hydrogen energy levels from the anomalous energy-momentum QED trace
Authors: Eides Michael I.
Published: October 2024

Energy levels of hydrogen are calculated as one-loop matrix elements of the QED energy-momentum tensor trace in the external field approximation. An explicit connection established between the one-loop trace diagrams and the standard Lamb shift one-loop diagrams. Our calculations provide an argument against inclusion of the anomalous trace contribution as a separate term in the decomposition of the QED quantum field Hamiltonian and serve as an illustration how the trace anomaly is realized in the bound state QED.

Published by the American Physical Society
2024
Anomalous and linear holographic hard wall models for light unflavored mesons
Authors: Costa-Silva Rafael A. , Boschi-Filho Henrique
Published: October 2024

In this work we consider anomalous and linear holographic hard wall (HW) models for light unflavored mesons inspired by the AdS/CFT correspondence. The anomalous dimensions depend on the logarithm of the spin S of the meson state and come from a semiclassical analysis of gauge/string duality. The anomalous HW model produces very good masses and good Regge trajectories for mesons compared with PDG data. Inspired by this anomalous HW model we also propose a phenomenological modification of the dimension of the boundary operators such that the model produces asymptotic linear Regge trajectories. Both anomalous HW models considered here present mass percentage deviations of less than 3%, when compared with PDG data.

Published by the American Physical Society
2024
Superresolution and analysis of three-dimensional velocity fields of underexpanded jets in different screech modes
Authors: Lee Chungil , Ozawa Yuta , Nagata Takayuki , Colonius Tim , Nonomura Taku
Published: October 2024

Time-resolved (TR), three-dimensional (3D) velocity fields of screeching, underexpanded jets are estimated using non-time-resolved particle image velocimetry and simultaneous TR microphone measurements. Specifically, we aim to reconstruct TR 3D velocity fluctuation fields associated with the A2, B, and C modes of a screeching jet using a linear regression model and to analyze screech dynamics of these modes. The linear regression model is constructed on the basis of a linear relationship between the velocity and acoustic fields. Three nozzle pressure ratios (NPRs) of 2.30, 2.97, and 3.40 are employed. The dominant azimuthal modes for three cases are investigated using azimuthal Fourier coefficients of the acoustic data obtained by the azimuthal array of eight microphones placed near the nozzle exit. The dominant azimuthal modes at NPRs of 2.30, 2.97, and 3.40 are m=0, 1, and 1, respectively. The first two proper orthogonal decomposition (POD) modes in these azimuthal modes are dominant at all NPRs and are associated with screech. 3D velocity fluctuation fields associated with screech are reconstructed from these leading POD modes of the acoustic data. The reconstructed 3D velocity fluctuation fields at NPRs of 2.97 and 3.40 exhibit two helical structures with opposite rotation directions. The present results demonstrate that, in the B mode, the flapping structure exhibits random clockwise and counterclockwise rotations over an extended time domain, while maintaining a consistent direction within short time domains. In addition, in the C mode, two helical structures with opposite rotation directions, as well as the flapping structure, are observed.

Published by the American Physical Society
2024