bluuebunny/crossref_metadata_2025 huggingface dataset:
Benefits of nature-based intervention in combating the impact of urbanization on psychopathology in industrialized societies
Authors: Wang Yuanyuan , Timms Franklin , Li Jiaqi , Yu Hui
Published: February 2024

Purpose of review

The assumption has been made that urbanization adversely affects mental health, primarily attributed to the lack of access to nature. Our objective is to examine whether nature-based interventions can reduce psychopathology within an urban setting.

Recent findings

Nature-based interventions are generally categorized as either physical or virtual. Physical interventions engage participants in various activities like passive exposure, outdoor swimming, or physical activities in natural environments. On the other hand, virtual interventions expose participants to visual, auditory, or even olfactory stimuli to simulate natural environments. While most interventions achieved some degree of success in enhancing overall well being, not all demonstrated a significant reduction in depression and anxiety.

The review identified a shortage of well designed and well implemented outdoor or virtual nature-based interventions. Longitudinal designs in physical nature-based interventions provided the strongest evidence for reducing anxiety and depression. Multisensory virtual nature-based interventions also show significant potential for alleviating anxiety and depression in urban dwellers. Conversely, brief nature-based interventions yielded inconsistent results in improving mental health. Urgent investment in high-quality interventions and research in this domain is imperative to inform policy and enhance overall mental health in urban settings.
Losing foreignness: Johann Sigismund Elsholtz on the meaning of plants in the pleasure gardens of Berlin
Authors: Wietecha Tracy
Published: February 2024

As a result of trade and commerce in global empires, plants from around the world could be found growing in gardens throughout Europe, including Germany. Johann Sigismund Elsholtz (1623–1688), a member of the Leopoldina scientific academy, would never personally travel to the Americas or Asia, but he had direct experience with plants from abroad under his care in the pleasure gardens of Berlin. Elsholtz composed several editions of a work that focused on the role of climate in growing a garden. For it was the climate, and not so much the soil, that posed the most significant challenge for the gardens he supervised, especially for the foreign plants. Curiously, Elsholtz's work is selective on which plants it categorizes as foreign; the category is also malleable, and proper acclimation of a plant was a first step for it no longer to be called foreign. In this paper, I explore the question of how plants lose their foreignness and take on a new, domestic meaning.
The roots of polarization in the individual reward system
Authors: Lefebvre Germain , Deroy Ophélia , Bahrami Bahador
Published: February 2024

Polarization raises concerns for democracy and society, which have expanded in the internet era where (mis)information has become ubiquitous, its transmission faster than ever, and the freedom and means of opinion expressions are expanding. The origin of polarization however remains unclear, with multiple social and emotional factors and individual reasoning biases likely to explain its current forms. In the present work, we adopt a principled approach and show that polarization tendencies can take root in biased reward processing of new information in favour of choice confirmatory evidence. Through agent-based simulations, we show that confirmation bias in individual learning is an independent mechanism and could be sufficient for creating polarization at group level independently of any additional assumptions about the opinions themselves,
a priori
beliefs about them, information transmission mechanisms or the structure of social relationship between individuals. This generative process can interact with polarization mechanisms described elsewhere, but constitutes an entrenched biological tendency that helps explain the extraordinary resilience of polarization against mitigating efforts such as dramatic informational change in the environment.
Quantitative characterization of cell niches in spatial atlases
Authors: Birk Sebastian , Bonafonte-Pardàs Irene , Feriz Adib Miraki , Boxall Adam , Agirre Eneritz , Memi Fani , Maguza Anna , Fan Rong , Castelo-Branco Gonçalo , Theis Fabian J. , Bayraktar Omer , Talavera-López Carlos , Lotfollahi Mohammad
Published: February 2024

Spatial omics allow us to identify and analyze communities of cells coordinating specific functions within a tissue. While these communities, defined as cell niches, are fundamentally shaped by interactions between spatially neighboring cells, we lack computational frameworks that can leverage spatial omics data to quantitatively characterize niches based on cell interaction events. To address this, we introduce NicheCompass, a graph deep learning method designed based on the principles of cellular communication. NicheCompass not only identifies cell niches, but also learns and informs about the signaling events shaping the identity of these niches. Unlike existing methods, it uniquely characterizes niches by quantifying their activity of spatial gene programs which represent diverse mechanisms of cell-cell communication and transcriptional regulation, thereby uncovering the underlying cellular processes constituting each niche. We showcase a comprehensive workflow encompassing data integration, niche identification, and functional interpretation, and demonstrate that, with its biologically informed design, NicheCompass outperforms existing methods. NicheCompass is broadly applicable to spatial transcriptomics data, which we illustrate by mapping the architecture of diverse tissues during mouse embryonic development, and delineating basal (KRT14) and luminal (KRT8) tumor niches in human breast cancer. We further introduce fine-tuning-based spatial reference mapping, revealing an SPP1+ macrophage-dominated tumor niche in non-small cell lung cancer patients. Additionally, we extend NicheCompass to multimodal spatial profiling of gene expression and chromatin accessibility, identifying and characterizing distinct white matter niches in the mouse brain. Finally, we apply NicheCompass to a whole mouse brain spatial atlas with 8.4 million cells demonstrating its scalability and ability to build foundational, interpretable spatial representations for entire organs. Overall, NicheCompass provides a novel approach to the challenge of identifying and analyzing niches, and suggests a more rigorous niche definition grounded in the quantitative characterization of underlying cellular processes.
Applying Multi-Theory Model (MTM) in Determining Intentions to Smoking Cessation among male Health Worker Smokers in Kabul, Afghanistan
Authors: Bashir Mousa , Shokravi Farkhondeh Amin , Kazem nezhad Anooshiravan
Published: February 2024

Introduction

Globally, smoking causes lung cancer and a wide range of acute and chronic diseases. A fourth-generation behavioral framework, the multi-theory model (MTM) of health behavior change was used to predict the initiation and maintenance of smoking cessation among health worker smokers.

Methods

By visiting different Health Centers, a convenience sample of male health worker smokers from west part of Kabul city, was invited to participate in this cross-sectional study. A valid and reliable 37-item MTM-based survey instrument was administered to the male participants who smoked. To explain smoking cessation behavior, stepwise multiple regressions were conducted. The entire value of the Cronbach alpha coefficient (α) of the subscales and the scale for the initiation of MTM variables was 0.80 and for the sustenance of MTM variables was 0.79.

Results

The study was completed by 170 participants. Participants were averaging 29.33 years of age (SD = 6.21). The average number of years smokers reported (SD = 4.7), was 5.6. Smoking cigarettes was the median (SD = 5.21), with 5.64 cigarettes consumed per day. Changes in the physical environment (+0.2225, P = 0.029) and behavioral confidence (+0.441, P = 0.014) were significant predictors of smoking cessation initiation. The intention to sustain smoking cessation behavior was significantly influenced by emotional transformation (β = 0.222,P= 0.017) and practicing for change (β = 0.217,P= 0.015).

Conclusions

There was moderate variance in smoking cessation behavior among health worker smokers in Kabul’s western part explained by two MTM constructs (behavioral confidence, physical environment) for initiation and two MTM constructs (emotional transformation, practicing for change) for maintenance. Smoking cessation behavior can be assessed using MTM both at the initiation and maintenance stages. It is important to develop future interventions using MTM constructs aiming to change smokers’ behavior in regard to quitting smoking.
What Does Large-scale Electrodermal Sensing Reveal?
Authors: McDuff Daniel , Thomson Seamus , Abdel-Ghaffar Samy , Galatzer-Levy Isaac R. , Poh Ming-Zher , Sunshine Jake , Barakat Andrew , Heneghan Conor , Sunden Lindsey
Published: February 2024

Electrodermal activity (EDA) is a physiological measure that is used to index sympathetic arousal in response to stressors and other perturbations. However, EDA is underutilized in real-world, population-level research and clinical practice because of a paucity of remote measurement capabilities on commodity devices. The current study examined the capabilities of continuous remote measurement of EDA at scale to quantify physiological changes in the context of diurnal and circadian rhythms, demographic differences, high arousal contexts such as public holidays and high arousal moments (e.g., the Super Bowl). We first demonstrated the accuracy of a novel EDA sensor developed for the Fitbit Sense 2 wearable device within a controlled, arousal-inducing experiment. We then retrospectively analyzed 10 million hours of continuous EDA data collected from over 16,000 people. We show that continuously sampledin-situEDA from Sense 2 has similar population-level diurnal patterns as those established from more tightly controlled in-lab experiments. Following this, variation of SCL across day of the week and season are presented. Finally, EDA dynamics occurring in response to commonly held stressful or exciting events such as Thanksgiving and the Super Bowl are described which we interpret as a natural experiment eliciting autonomic arousal.
Limiting Brownian Motion to Enhance Immunogold Phenotyping and Superimpose Optical and Non-Optical Single-EP Analyses
Authors: Nguyen Kim Truc , Rima Xilal Y. , Hisey Colin L. , Doon-Ralls Jacob , Nagaraj Chiranth K. , Reátegui Eduardo
Published: February 2024

Optical and non-optical techniques propelled the field of single extracellular particle (EP) research through phenotypic and morphological analyses, revealing the similarities, differences, and co-isolation of EP subpopulations. Overcoming the challenges of optical and non-optical techniques motivates the use of orthogonal techniques while analyzing extracellular particles (EPs), which require varying concentrations and preparations. Herein, we introduce the nano-positioning matrix (NPMx) technique capable of superimposing optical and non-optical modalities for a single-EP orthogonal analysis. The NPMx technique is realized by ultraviolet-mediated micropatterning to reduce the stochasticity of Brownian motion. While providing a systematic orthogonal measurement of a single EP via total internal reflection fluorescence microscopy and transmission electron microscopy, the NPMx technique is compatible with low-yield samples and can be utilized for non-biased electrostatic capture and enhanced positive immunogold sorting. The success of the NPMx technique thus provides a novel platform by marrying already trusted optical and non-optical techniques at a single-EP resolution.
Emodin modulates PI3K-AKT pathway to inhibit proliferation, invasion and induce apoptosis in glioma cells
Authors: Mir Ashaq Hussain , Banday Mujeeb Zafar , Aadil Fayeem , Ganie Shabir Ahmad , Haq Ehtishamul
Published: February 2024

Glioma is a type of tumor that begins in glial cells and occurs in the brain and spinal cord. Glioma forms a major health challenge worldwide. They are hard to treat, not only because of the deregulation in multiple signaling transduction pathways affecting various cellular processes but also because they are not contained in a well-defined mass with clear borders. One of the main pathways deregulated in glioma is PI3K-AKT and its associated downstream targets like NF-ĸB which affects different proteins/transcription factors influencing many aspects of gliomagenesis like epithelial to mesenchymal transition (EMT). A combination ofin-silicoandin-vitroapproaches targeted against specific catalytic isoform (p110δ) of Class IA PI3K with potent and selective inhibitors would maximize the chances of tumor regression. We adopted an in-silico approach to screen a range of natural molecules for a potent p110δ inhibitor and among them, “emodin” was found to be a potential candidate. In vitro, emodin treatment inhibits proliferation, induces apoptosis, modulates astrocytic phenotype, and decreases cell density of glioma cells. Emodin induces changes in the astrocytic phenotype of glioma cells to elongated form with rounded-off, shrunken-down morphology. Emodin was found to contribute to ROS production which leads to apoptosis of glioma cells. The apoptosis induced by emodin was confirmed by propidium iodide staining and ascertained by FACS analysis. We evaluated the effect of emodin on various proteins of PI3K-AKT and downstream targets. We found that emodin treatment decreases the expression of p-AKT, increases expression levels of Iĸ-B, inhibits nuclear translocation of NF-ĸB, and upregulates the phosphorylated form of GSK-3β. Changes at the molecular level of these proteins result in the inhibition/degradation of downstream proteins and transcription factors associated with the growth and proliferation of glioma cells. Inhibition of nuclear translocation of NF-ĸB also inhibits nuclear activation of various protumorigenic signaling pathway mediators involved in EMT such as N-cadherin, β-catenin, Claudin-1. These EMT markers promote invasion, proliferation, migration, and growth in glioma cells. Emodin treatment resulted in changed expression profiles of these EMT markers involved in promoting gliomagenesis. In essence these results suggest that in-vitro emodin treatment remarkably reduces the proliferation of glioma cells possibly targeting multiple pathways involved in tumor growth, proliferation, and development, supporting the rationale and relevance of using multipronged strategies for effective treatment of glioma.
Transcriptomic signature and pro-osteoclastic secreted factors of abnormal bone marrow stromal cells in fibrous dysplasia
Authors: Michel Zachary , Raborn Layne N. , Spencer Tiahna , Pan Kristen , Martin Daniel , Roszko Kelly L. , Wang Yan , Robey Pamela G. , Collins Michael T. , Boyce Alison M. , de Castro Diaz Luis Fernandez
Published: February 2024

Fibrous dysplasia (FD) is a mosaic skeletal disorder caused by somatic activating variants inGNAS, encoding for Gαs, which leads to excessive cAMP signaling in bone marrow stromal cells (BMSCs). Despite advancements in our understanding of FD pathophysiology, the effect of Gαsactivation in the BMSC transcriptome remains unclear, as well as how this translates into their local influence in the lesional microenvironment. In this study, we analyzed changes induced by Gαsactivation in BMSC transcriptome and performed a comprehensive analysis of their production of cytokines and other secreted factors. We performed RNAseq of cultured BMSCs from patients with FD and healthy volunteers, and from an inducible mouse model of FD, and combined their transcriptomic profiles to build a robust FD BMSC genetic signature. Pathways related to Gαsactivation, cytokine signaling, and extracellular matrix deposition were identified. In addition, a comprehensive profile of their secreted cytokines and other factors was performed to identify modulation of several key factors we hypothesized to be involved in FD pathogenesis. We also screened circulating cytokines in a collection of plasma samples from patients with FD, finding positive correlations of several cytokines to their disease burden score, as well as to one another and bone turnover markers. Overall, these data support a pro-inflammatory, pro-osteoclastic behavior of BMSCs bearing hyperactive Gαsvariants, and point to several cytokines and other secreted factors as possible therapeutic targets and/or circulating biomarkers for FD.
Extended blood stage sensitivity profiles ofPlasmodium vivaxto doxycycline and tafenoquine usingPlasmodium cynomolgias a model
Authors: Christensen Peter , Cinzah Rosy , Suwanarusk Rossarin , Chua Adeline Chiew Yen , Kaneko Osamu , Kyle Dennis E. , Aung Htin Lin , Matheson Jessica , Bifani Pablo , Rénia Laurent , Cook Gregory M. , Snounou Georges , Russell Bruce
Published: February 2024

TestingPlasmodium vivaxantimicrobial sensitivity is limited toex vivoschizont maturation assays, which precludes determining the IC50sof delayed action antimalarials such as doxycycline. UsingPlasmodium cynomolgias a model forP. vivax, we determined the physiologically significant delayed death effect induced by doxycycline (IC50(96h), 1401 ± 607 nM). As expected, IC50(96 h)to chloroquine (20.4 nM), piperaquine (12.6 µM) and tafenoquine (1424 nM) were not affected by extended exposure.
Integrative, Segregative, and Degenerate Harmonics of the Structural Connectome
Authors: Sipes Benjamin Snow , Nagarajan Srikantan , Raj Ashish
Published: February 2024

Unifying integration and segregation in the brain has been a fundamental puzzle in neuroscience ever since the conception of the "binding problem." Here, we introduce a framework that places integration and segregation within a continuum based on a fundamental property of the brain--its structural connectivity graph Laplacian harmonics and a new feature we term the gap-spectrum. This framework organizes harmonics into three regimes--integrative, segregative, and degenerate--that together account for various group-level properties. Integrative and segregative harmonics occupy the ends of the continuum, and they share properties such as reproducibility across individuals, stability to perturbation, and involve "bottom-up" sensory networks. Degenerate harmonics are in the middle of the continuum, and they are subject-specific, flexible, and involve "top-down" networks. The proposed framework accommodates inter-subject variation, sensitivity to changes, and structure-function coupling in ways that offer promising avenues for studying cognition and consciousness in the brain.
Expanding theBonnMusequence-indexed repository of transposon induced maize (Zea maysL.) mutations in dent and flint germplasm
Authors: Win Yan Naing , Stöcker Tyll , Du Xuelian , Brox Alexa , Pitz Marion , Klaus Alina , Schoof Heiko , Hochholdinger Frank , Marcon Caroline
Published: February 2024

TheBonnMuresource is a transposon-tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an activeMutator(Mu) line with dent (B73, Co125) and flint (DK105, EP1 and F7) germplasm, resulting in the generation of 8,064 mutagenizedBonnMuF2-families. Sequencing of theseMu-tagged families revealed 425,924 heritableMuinsertions affecting 36,612 (83%) of the 44,303 high-confidence gene models of maize (B73v5). On average, we observed 12Muinsertions per gene (425,924 total insertions/ 36,612 affected genes) and 53 insertions perBonnMuF2-family (425,924 total insertions/ 8,064 families).Muinsertions and photos of seedling phenotypes from segregatingBonnMuF2-families can be accessed through the Maize Genetics and Genomics Database (MaizeGDB). Downstream examination via the automated Mutant-seq Workflow Utility (MuWU) identified 94% of the germinal insertion sites in genic regions and only a small fraction of 6% inserting in non-coding intergenic sequences of the genome. Consistently,Muinsertions aligned with gene-dense chromosomal arms. In total, 42% of allBonnMuinsertions were located in the 5’ untranslated region (UTR) of genes, corresponding to accessible chromatin. Furthermore, for 38% of the insertions (163,843 of 425,924 total insertions)Mu1,Mu8andMuDRwere confirmed to be the causalMuelements. Our publicly accessible EuropeanBonnMuresource has archived insertions covering two major germplasm groups, thus facilitating both forward and reverse genetics studies.
Multi-ancestry tandem repeat association study of hair colour using exome-wide sequencing
Authors: Fazzari Victoria , Moo-Choy Ashley , Panoyan Mary Anne , Abbatangelo Cristina L , Polimanti Renato , Novroski Nicole MM , Wendt Frank R
Published: February 2024

Hair colour variation is influenced by hundreds of positions across the human genome but this genetic contribution has only been narrowly explored. Genome-wide association studies identified single nucleotide polymorphisms (SNPs) influencing hair colour but the biology underlying these associations is challenging to interpret. We report 16 tandem repeats (TRs) with effects on different models of hair colour plus two TRs associated with hair colour in diverse ancestry groups. Several of these TRs expand or contract amino acid coding regions of their localized protein such that structure, and by extension function, may be altered. We also demonstrate that independent of SNP variation, these TRs can be used to great an additive polygenic score that predicts darker hair colour. This work adds to the growing body of evidence regarding TR influence on human traits with relatively large and independent effects relative to surrounding SNP variation.
Inhibition of Protein Synthesis Attenuates Formation of Traumatic Memory and Normalizes Fear-induced c-Fos Expression in a Mouse Model of Posttraumatic Stress Disorder
Authors: Zamorina Tatyana A. , Ivashkina Olga I. , Toropova Ksenia A. , Anokhin Konstantin V.
Published: February 2024

Posttraumatic stress disorder (PTSD) is a debilitating psychosomatic condition characterized by impairment of brain fear circuits and persistence of exceptionally strong associative memories notoriously resistant to extinction. In this study, we investigated the neural and behavioral consequences of inhibiting protein synthesis, a process known to suppress the formation of conventional aversive memories, in an established animal model of PTSD based on contextual fear conditioning in mice. Control animals were subjected to the conventional fear conditioning task to evaluate the differential impact of protein synthesis inhibition on traumatic versus normal aversive memories. Utilizing c-Fos neural activity mapping, we found that the retrieval of PTSD and normal aversive memories produced activation of overlapping set of brain structures, though several specific areas, such as the infralimbic cortex and the paraventricular nucleus of the thalamus, exhibited heightened activation during induction of PTSD. Administration of protein synthesis inhibitor cycloheximide prior to PTSD induction disrupted the formation of traumatic memories, resulting in behavior that matched the behavior of mice with usual aversive memory. Concomitant with this behavioral shift was a normalization of brain c-Fos activation pattern matching the one observed in usual fear memory. Our findings demonstrate that inhibiting protein synthesis during traumatic experiences significantly impairs the development of PTSD in a mouse model. These data provide insights into the neural underpinnings of protein synthesis-dependent traumatic memory formation and open prospects for the development of new therapeutic strategies for prevention of PTSD.
Comparative Analysis of Gene Expression Analysis Methods for RNA In Situ Hybridization Images
Authors: Ariotta Valeria , Azzalini Eros , Canzonieri Vincenzo , Hautaniemi Sampsa , Bonin Serena
Published: February 2024

Gene expression analysis is pivotal in cancer research and clinical practice. While traditional methods lack spatial context, RNA in situ hybridization (RNA-ISH) is a powerful technique that retains spatial tissue information. Here, we investigated RNAscope score, RT-droplet digital PCR (RT-ddPCR), and automated QuantISH and QuPath in quantifying RNA-ISH expression values from formalin-fixed paraffin-embedded samples. We compared the methods using high-grade serous ovarian carcinoma samples, focusing onCCNE1,WFDC2, andPPIBgenes. Our findings demonstrate good concordance between automated methods and RNAscope, with RT-ddPCR showing less concordance. We conclude that QuantISH exhibits robust performance, even for low-expressed genes likeCCNE1, showcasing its modular design and enhancing accessibility as a viable alternative for gene expression analysis.
Mutant GNAS drives a pyloric metaplasia with tumor suppressive glycans in intraductal papillary mucinous neoplasia
Authors: Trinh Vincent Quoc-Huy , Ankenbauer Katherine E. , Torbit Sabrina M. , Liu Jiayue , Batardiere Maelle , Kumar Bhoj , Maurer H. Carlo , Revetta Frank , Chen Zhengyi , Kruse Angela , Judd Audra , Copeland Celina , Wong Jahg , Ben-Levy Olivia , Jarvis Brenda , Brown Monica , Brown Jeffrey W. , Das Koushik , Makino Yuki , Spraggins Jeffrey M. , Lau Ken S. , Azadi Parastoo , Maitra Anirban , Tan Marcus C.B. , DelGiorno Kathleen E.
Published: February 2024

BACKGROUND & AIMS

Intraductal Papillary Mucinous Neoplasms (IPMNs) are cystic lesions andbona fideprecursors for pancreatic ductal adenocarcinoma (PDAC). Recent studies have shown that pancreatic precancer is characterized by a transcriptomic program similar to gastric metaplasia. The aims of this study were to assay IPMN for pyloric markers, to identify molecular drivers, and to determine a functional role for this program in the pancreas.

METHODS

Pyloric marker expression was evaluated by RNA-seq and multiplex immunostaining in patient samples. Cell lines and organoids expressingKrasG12D+/-GNASR201Cunderwent RNA sequencing. A PyScenic-based regulon analysis was performed to identify molecular drivers, and candidates were evaluated by RNA-seq, immunostaining, and small interfering RNA knockdown. Glycosylation profiling was performed to identifyGNASR201C-driven changes. Glycan abundance was evaluated in patient samples.

RESULTS

Pyloric markers were identified in human IPMN.GNASR201Cdrove expression of this program as well as an indolent phenotype characterized by distinct glycosyltransferase changes. Glycan profiling identified an increase in LacdiNAcs and loss of pro-tumorigenic Lewis antigens. Knockdown of transcription factorsSpdeforCreb3l1or chitinase treatment reduced LacdiNAc deposition and reversed the indolent phenotype. LacdiNAc and 3’-sulfoLeA/Cabundance discriminated low from high grade patient IPMN.

CONCLUSION

GNASR201Cdrives an indolent phenotype in IPMN by amplifying a differentiated, pyloric phenotype through SPDEF/CREB3L1 which is characterized by distinct glycans. Acting as a glycan rheostat, mutantGNASelevates LacdiNAcs at the expense of pro-tumorigenic acidic Lewis epitopes, inhibiting cancer cell invasion and disease progression. LacdiNAc and 3’-Sulfo-LeA/Care mutually exclusive and may serve as markers of disease progression.
Rheological and Lipid Characterization of Minipig and Human Skin Tissue: A Comparative Study Across Different Locations and Depths
Authors: Mitra Harsa , Nonamaker Evelyn , Cordera Ria D. , Solorio Luis , Ardekani Arezoo M.
Published: February 2024

Understanding the rheology of minipig and human skin is crucial for enhancing drug delivery methods, particularly for injections. Despite many studies on skin’s viscoelasticity, especially the subcutaneous layer, comparative analyses across different clinical sites are scarce, as is data on the impact of hydration or lipid levels. This study employs shear rheology and lipid analysis to evaluate viscoelasticity and lipid content across three anatomical locations —breast, belly, and neck and three different depth layers in Yucatan minipigs. It reports on how viscoelastic properties change with frequency, time, and strain, noting strain-stiffening and shear-thinning at high strain amplitudes. Human male and female abdominal tissues are also compared to minipig tissues, highlighting distinct viscoelastic traits and lipid’s role in them. The findings suggest the existence of species, anatomical location, tissue depth, and sex-based rheological differences. We also concluded the minipig male tissue is a more accurate model for human male subcutaneous tissue than for females.
Comparative study of enriched dopaminergic neurons from siblings with Gaucher disease discordant for parkinsonism
Authors: Hertz Ellen , Perez Gani , Hao Ying , Rytel Krystyna , Ma Charis , Kirby Martha , Anderson Stacie , Wincovitch Stephen , Andersh Kate , Ahfeldt Tim , Blanchard Joel , Qi Yue Andy , Lopez Grisel , Tayebi Nahid , Sidransky Ellen , Chen Yu
Published: February 2024

Inducible pluripotent stem cells (iPSCs) derived from patient samples have significantly enhanced our ability to model neurological diseases. Comparative studies of dopaminergic (DA) neurons differentiated from iPSCs derived from siblings with Gaucher disease discordant for parkinsonism provides a valuable avenue to explore genetic modifiers contributing toGBA1-associated parkinsonism in disease-relevant cells. However, such studies are often complicated by the inherent heterogeneity in differentiation efficiency among iPSC lines derived from different individuals. To address this technical challenge, we devised a selection strategy to enrich dopaminergic (DA) neurons expressing tyrosine hydroxylase (TH). A neomycin resistance gene(neo)was inserted at the C-terminus of theTHgene following a T2A self-cleavage peptide, placing its expression under the control of theTHpromoter. This allows for TH+ DA neuron enrichment through geneticin selection. This method enabled us to generate comparable, high-purity DA neuron cultures from iPSC lines derived from three sisters that we followed for over a decade: one sibling is a healthy individual, and the other two have Gaucher disease (GD) withGBA1genotype N370S/c.203delC+R257X (p.N409S/c.203delC+p.R296X). Notably, the younger sister with GD later developed Parkinson disease (PD). A comprehensive analysis of these high-purity DA neurons revealed that although GD DA neurons exhibited decreased levels of glucocerebrosidase (GCase), there was no substantial difference in GCase protein levels or lipid substrate accumulation between DA neurons from the GD and GD/PD sisters, suggesting that the PD discordance is related to of other genetic modifiers.
Factors influencing the implementation of integrated screening for HIV, syphilis, and hepatitis B for pregnant women in Nepal: a qualitative study
Authors: Sabin Lucie , Haghparast-Bidgoli Hassan , Thapaliya Bibhu , Chand Obindra , Bhattarai Sanju , Arjyal Abriti , Saville Naomi
Published: February 2024

According to the Nepalese national guidelines, integrated screening for HIV, syphilis and hepatitis B should be offered free of charge to all pregnant women during their first antenatal visit. However, the screening uptake among pregnant women remains low in the country. Identifying factors influencing the implementation of integrated screening for HIV, syphilis, and hepatitis B is essential to increase uptake and prevent mother-to-child transmission. This study investigated the knowledge, attitude, and perceptions of pregnant women, their family members, healthcare workers and decision-makers on integrated antenatal screening. On the demand side, we conducted 26 semi-structured in-depth interviews with pregnant women, their husbands, and mothers-in-law in Kapilvastu and Kathmandu. On the supply side, we conducted 11 interviews with health workers involved in antenatal screening and local and national health system decision-makers. Data were analysed using a thematic content analysis. A combination of the social-ecological model and the WHO building blocks provided a theoretical framework for interpreting the data. The analysis showed that integrated antenatal screening for HIV, syphilis and hepatitis B in Nepal involved many stakeholders and was influenced by various factors. Barriers were mainly on the supply side, including a lack of resources, a shortage of healthcare workers and a lack of training. Husbands and in-laws also play an important role in the acceptance of screening by pregnant women, mainly in rural areas. Stigma and discrimination against people with sexually transmitted diseases were reported high in the communities, and knowledge of hepatitis B and syphilis was low. Improving integrated antenatal screening will require a multi-sectoral approach with greater engagement with communities through awareness programs and enhancement of the role of health posts. This study may be useful to inform decision-makers about the challenges and enable affecting integrated screening, to guide the design of targeted interventions to improve antenatal screening rates.
Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells
Authors: Soltys Volker , Peters Moritz , Su Dingwen , Kučka Marek , Chan Yingguang Frank
Published: February 2024

Gene regulation consists of several highly interconnected layers including gene expression and chromatin accessibility. To understand cell-type specific regulatory circuits, both of these processes therefore need to be profiled simultaneously at single-cell level. However, these joint measurements are challenging and current methodologies suffer from limited applicability. Here, we present easySHARE-seq, an elaboration of SHARE-seq, for the simultaneous measurement of ATAC- and RNA-seq in single cells. By streamlining the barcode design, easySHARE-seq libraries have a usable sequence of up to 300bp (+200%), making it suitable for e.g. investigation of allele-specific signals or variant discovery. Furthermore, easySHARE-seq libraries do not require a dedicated sequencing run thus saving costs. Lastly, recovery of transcripts per cell is substantially boosted (> +50%) while retaining high scalability and low cost. To showcase these changes, we generated joint profiles for 19,664 murine liver nuclei, identified cell types, exploited the multi-omic measurements to linkcis-regulatory elements to their target genes and investigated liver-specific micro-scale changes. easySHARE-seq produces high-quality multiomic data sets and is applicable to a wide range of study designs.
Ontogenetic variation in the marine foraging of Atlantic salmon functionally links genomic diversity with a major life history polymorphism
Authors: Aykanat Tutku , Jacobsen Jan Arge , Hindar Kjetil
Published: February 2024

The ecological role of heritable phenotypic variation in free-living populations remains largely unknown. Knowledge of the genetic basis of functional ecological processes can link genomic and phenotypic diversity, providing insight into polymorphism evolution and how populations respond to environmental changes. By quantifying the marine diet of Atlantic salmon, we assessed how foraging behavior changes along the ontogeny, and in relation to genetic variation in two loci with major effects on age at maturity (six6andvgll3). We used a two-component, zero-inflated negative binomial model to simultaneously quantify foraging frequency and foraging outcome, separately for fish and crustaceans diets. We found that older salmon forage for both prey types more actively (as evidenced by increased foraging frequency), but with a decreased efficiency (as evidenced by fewer prey in the diet), suggesting an age-dependent shift in foraging dynamics. Thevgll3locus was linked to age-dependent changes in foraging behavior: younger salmon withvgll3LL(the genotype associated with late maturation) tended to forage crustaceans more often than those withvgll3EE(the genotype associated with early maturation), whereas the pattern was reversed in older salmon.Vgll3LLgenotype was also linked to a marginal increase in fish acquisition, especially in younger salmon, whilesix6was not a factor explaining the diet variation. Our results suggest a functional role for marine feeding behavior linking genomic diversity atvgll3with age at maturity among salmon, with potential age-dependent trade-offs maintaining the genetic variation. A shared genetic basis between dietary ecology and age at maturity likely subjects Atlantic salmon populations to evolution induced by bottom-up changes in marine productivity.
Stochastic cell-intrinsic stem cell decisions control colony growth in planarians
Authors: Frankovits Tamar , Cherian Prakash Varkey , Yesharim Yarden , Dobler Simon , Wurtzel Omri
Published: February 2024

Stem cells contribute to organismal homeostasis by balancing division, self-renewal and differentiation. Elucidating the strategies by which stem cells achieve this balance is critical for understanding homeostasis, and for addressing pathogenesis associated with the disruption of this balance (e.g., cancer). Planarians, highly regenerative flatworms, use pluripotent stem cells called neoblasts to maintain and regrow organs. A single neoblast can rescue an entire animal depleted from stem cells and regenerate all cell lineages. How neoblast differentiation and clonal expansion are governed to produce all the required cell types is unclear. Here, we integrated experimental and computational approaches to develop a quantitative model revealing basic principles of clonal growth of individual neoblasts. By experimentally suppressing differentiation to major lineages, we elucidated the interplay between colony growth and lineage decisions. Our findings suggest that neoblasts select their progenitor lineage based on a cell-intrinsic fate distribution. Arresting differentiation into specific lineages disrupts neoblast proliferative capacity without inducing compensatory expression of other lineages. Our analysis of neoblast colonies is consistent with a cell-intrinsic decision model that can operate without memory or communication between neoblasts. This simple cell fate decision process breaks down in homeostasis, likely because of the activity of feedback mechanisms. Our findings uncover essential principles of stem cell regulation in planarians, which are distinct from those observed in many vertebrate models. These mechanisms enable robust production of diverse cell types and facilitate regeneration of missing tissues.
T6SS-associated Rhs toxin containers: Structural and functional insights into bacterial weaponry and self-protection
Authors: Kielkopf Claudia S. , Shneider Mikhail M. , Leiman Petr G. , Taylor Nicholas M.I.
Published: February 2024

Bacteria use the type VI secretion system (T6SS) to secrete a variety of toxins into pro- and eukaryotic cells via a machinery consisting of a contractile sheath and a rigid tube. Rearrangement hotspot (Rhs) proteins represent one of the most common T6SS-secreted effectors. The C-terminal toxin domain of Rhs proteins displays great functional diversity, while the large Rhs core is characterised by YD repeats. T6SS- associated Rhs proteins are attached to the VgrG spike protein, often via an N- terminal PAAR-repeat domain. Using X-ray crystallography, we here elucidate the Rhs core structures of PAAR- and VgrG-linked Rhs proteins fromSalmonella bongoriandAdvenella mimigardefordensis, respectively. The Rhs core forms a large container made up of β-sheets that has a negatively charged interior and encloses a large volume. The presence of the toxin domain ofS. bongoriPAAR-linked Rhs does not lead to ordered density in the Rhs container, suggesting the toxin domain is at least partially unfolded. Together with bioinformatics analysis showing that Rhs toxins predominantly act intracellularly, this suggests that the Rhs core domain functions two-fold, as safety feature for the producer cell and as delivery mechanism for the toxin domain. Our results strengthen our knowledge of Rhs structure and function.
Astrocytic RNA editing regulates the host immune response to alpha-synuclein
Authors: D’Sa Karishma , Choi Minee L. , Wagen Aaron Z. , Setó-Salvia Núria , Kopach Olga , Evans James R. , Rodrigues Margarida , Lopez-Garcia Patricia , Lachica Joanne , Clarke Benjamin E. , Singh Jaijeet , Ghareeb Ali , Bayne James , Grant-Peters Melissa , Garcia-Ruiz Sonia , Chen Zhongbo , Rodriques Samuel , Athauda Dilan , Gustavsson Emil K. , Taliun Sarah A. Gagliano , Toomey Christina , Reynolds Regina H. , Young George , Strohbuecker Stephanie , Warner Tom , Rusakov Dmitri A. , Patani Rickie , Bryant Clare , Klenerman David A. , Gandhi Sonia , Ryten Mina
Published: February 2024

RNA editing is a post transcriptional mechanism that targets changes in RNA transcripts to modulate innate immune responses. We report the role of astrocyte specific, ADAR1 mediated RNA editing in neuroinflammation in Parkinson’s disease. We generated hiPSC-derived astrocytes, neurons and co-cultures and exposed them to small soluble alpha-synuclein aggregates. Oligomeric alpha-synuclein triggered an inflammatory glial state associated with TLR activation, viral responses, and cytokine secretion. This reactive state resulted in loss of neurosupportive functions, and the induction of neuronal toxicity. Notably, interferon response pathways were activated leading to upregulation, and isoform switching of the RNA deaminase enzyme, ADAR1. ADAR1 mediates A-to-I RNA editing, and increases in RNA editing were observed in inflammatory pathways in cells, as well as in post-mortem human PD brain. Aberrant, or dysregulated, ADAR1 responses and RNA editing may lead to sustained inflammatory reactive states in astrocytes triggered by alpha-synuclein aggregation, and this may drive the neuroinflammatory cascade in Parkinson’s.
The intracellular Ca2+sensitivity of transmitter release from neocortical boutons
Authors: Bornschein Grit , Brachtendorf Simone , Eshra Abdelmoneim , Kraft Robert , Eilers Jens , Hallermann Stefan , Schmidt Hartmut
Published: February 2024

Synaptotagmin 1 (Syt1) and Syt2 are the main Ca2+sensors triggering synchronous release in the brain. The Ca2+-sensitivity of Syt2-triggered release has been studied in detail. However, for Syt1, the dominating isoform in the neocortex, quantitative detail is lacking. We measured the Ca2+-dependency of Syt1-triggered release at layer 5 pyramidal neuron synapses by laser photolysis of caged Ca2+. Syt1-triggered release had high Ca2+affinity and positive cooperativity (EC50, 20 μM; Hill coefficient, 3.57). It was steep in a dynamic range between ∼10 and ∼30 μM that was covered by action potential-evoked release. A kinetic model reveals significant differences to models of Syt2-triggered release. Our results suggest that Syt1 optimizes neocortical synapses for high reliability at moderate local Ca2+elevations and for high plastic controllability.
Adoptive transfer of mitochondrial antigen-specific CD8+T-cells in mice causes parkinsonism and compromises the dopamine system
Authors: Elemeery MN , Tchung A , Boulet S , Mukherjee S , Giguère N , Daudelin J-F , Even A , Hétu-Arbour R , Matheoud D , Stratton JA , Labrecque N , Trudeau L-E
Published: February 2024

The progressive dysfunction and degeneration of dopamine (DA) neurons of the ventral midbrain is linked to the development of motor symptoms in Parkinson’s disease (PD). Multiple lines of evidence suggest the implication of neuroinflammation and mitochondrial dysfunction as key drivers of neurodegenerative mechanisms in PD. Recent work has revealed that loss of the mitochondrial kinase PINK1 leads to enhanced mitochondrial antigen presentation (MitAP) by antigen-presenting cells (APCs), the amplification of mitochondrial antigen-specific CD8+T cells and the loss of DA neuron terminals markers in the brain in response to gut infection. However, whether mitochondrial antigen- specific T cells are involved in and/or sufficient to cause DA system dysfunction remains unclear. Here, we investigated the effect of mitochondrial autoimmunity by adoptively transferring mitochondrial peptide-specific CD8+T cells into wild-type (WT) and PINK1 KO mice. We find that this leads to L- DOPA-reversible motor impairment and to robust loss of DA neurons and axonal markers in the striatum in both PINK1 WT and KO mice. Our findings provide direct evidence of the pivotal role played by mitochondrial-specific CD8+T cell infiltration in the brain in driving PD-like pathology and the development of parkinsonism. Altogether, our data strongly support the hypothesis that MitAP and autoimmune mechanisms play a key role in the pathophysiological processes leading to PD.
Matching Excellence: ONT’s Rise to Parity with PacBio in Genome Reconstruction of Non-Model Bacterium with High GC Content
Authors: Soto-Serrano Axel , Li Wenwen , Panah Farhad M. , Hui Yan , Atienza Pablo , Fomenkov Alexey , Roberts Richard J. , Deptula Paulina , Krych Lukasz
Published: February 2024

Reconstruction of complete bacterial genomes is a vital aspect of microbial research, as it provides complex information about genetic content, gene ontology, and regulation. It has become a domain of 3rd generation, long-read sequencing platforms, as short-read technologies can deliver mainly fragmented genomes. PacBio platform can provide high-quality complete genomes, yet remains one of the most expensive sequencing strategies. Oxford Nanopore Technology (ONT) offers the advantage of producing the longest reads, being at the same time the most cost-effective option in terms of platform costs, as well as library preparation, and sequencing. However, ONTs error rate, although significantly reduced lately, still holds a certain level of distrust in the scientific community.

In recent years, hybrid assembly of Nanopore and Illumina data has been used to solve ONTs issue with error rate and has yielded the best results in terms of genome completeness, quality, and price. However, the latest advancements in Nanopore technology, including new flow cells (R10.4.1), new library preparation chemistry (V14) and duplex-mode, updated basecallers (Dorado v0.4.1), and the realization that sequencing in dark mode results in significantly increased throughput, have had a significant impact on the quality of generated data and, thus, the recovery of complete genomes by ONT sequencing alone.

In this study, we compared the data generated by ONT using three sequencing strategies (Native barcoding, RAPID barcoding, and custom-developed: BARSEQ) against PacBio and Illumina (NextSeq) as well as Illumina-ONT hybrid data. For this purpose, we employed three strains of the actinobacteriaPropionibacterium freudenreichii, whose genomes have been proven difficult to reconstruct due to high GC content, regions of repeated sequences and massive genome rearrangements.

Our data indicate that DNA libraries prepared with the native barcoding kit, sequenced with V14 chemistry on R10.4.1 flow cell, and assembled with Flye resulted in the reconstruction of complete genomes of overall quality highly similar to that of genomes reconstructed with PacBio. The highest level of quality can be achieved by hybrid assembly of data from the Native barcoding kit complemented with data from custom-developed BARSEQ, both sequenced on R10.4.1 flow cell. In conclusion, our results demonstrate that ONT can be used as a cost-effective sequencing strategy, without the need for complementing with other sequencing technologies, for the reconstruction of complete genomes of the highest quality.