bluuebunny/crossref_metadata_2025 huggingface dataset:
The Haemagglutinin Gene of Bovine Origin H5N1 Influenza Viruses Currently Retains an Avian Influenza Virus phenotype
Authors: Yang Jiayun , Qureshi Mehnaz , Kolli Reddy , Peacock Thomas P. , Sadeyen Jean-Remy , Carter Toby , Richardson Samuel , Daines Rebecca , Barclay Wendy S. , Brown Ian , Iqbal Munir
Published: September 2024

Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) has caused a panzootic affecting all continents except Australia, expanding its host range to several mammalian species. In March 2024, H5N1 HPAIV was first detected in dairy cattle and goats in the United States. Since then, over 230 dairy farms across 14 states have tested positive, with zoonotic infections reported among dairy workers. This raises concerns about the virus undergoing evolutionary changes in cattle that could enhance its zoonotic potential. The Influenza glycoprotein haemagglutinin (HA) facilitates entry into host cells through receptor binding and pH-induced fusion with cellular membranes. Adaptive changes in HA modulate virus-host cell interactions. This study compared the HA genes of cattle and goat H5N1 viruses with the dominant avian-origin clade 2.3.4.4b H5N1 in the United Kingdom, focusing on receptor binding, pH fusion, and thermostability. All the tested H5N1 viruses showed binding exclusively to avian-like receptors, with a pH fusion of 5.9, outside the pH range associated with efficient human airborne transmissibility (pH 5.0 to 5.5). We further investigated the impact of emerging HA substitutions seen in the ongoing cattle outbreaks, but saw little phenotypic difference, with continued exclusive binding to avian-like receptor analogues and pHs of fusion above 5.8. This suggests that the HA genes from the cattle and goat outbreaks do not pose an enhanced threat compared to circulating avian viruses. However, given the rapid evolution of H5 viruses, continuous monitoring and updated risk assessments remain essential to understanding virus zoonotic and pandemic risks.
The Neural Blueprint of Stress Susceptibility: Brain-wide neuronal activity associated with the consequences of stress
Authors: Dirven Bart C.J. , Negwer Moritz , Botan Andriana , Maas Riv , van Melis Lennart , Merjenburgh Sanne , van Rijn Rebecca , Grandjean Joanes , Homberg Judith R. , Kozicz Tamas , Henckens Marloes J.A.G.
Published: September 2024

Understanding the neurobiological mechanisms of stress susceptibility is key to advancing our insight into stress-related psychopathology like post-traumatic stress disorder (PTSD). Preclinical animal models however typically lack translationally relevant brain readouts. Here, we used a mouse model for severe stress, segregating mice into stress-susceptible and resilient groups. We analyzed and contrasted their whole-brain neuronal activity pre-, peri- and post-stress exposure and compared functional connectivity of the salience (SN), default mode (DMN) and executive control network (lateral cortical network (LCN) in rodents). We found that stress-susceptible mice exhibited pre-existing hyperactivity in the lateral orbital area, a potential risk factor for stress vulnerability, and heightened retrosplenial cortex activity peri- and post-stress, potentially contributing to maladaptive fear memory. Upon stress exposure, susceptible mice showed strong recruitment of visual and memory-related areas, whereas resilient mice displayed marked reductions in retrosplenial activity and increased activation in the agranular insula and ventral striatum. Observations of enhanced intra-SN and SN-DMN connectivity in susceptible mice mirrored those observed in individuals with PTSD. Moreover, susceptible mice displayed aberrant DMN-LCN network pre- and peri-stress. These findings highlight the importance of dynamic network interactions in stress susceptibility and suggest novel brain region targets for (early) intervention.
Specific growth rates and growth stoichiometries of Saccharomycotina yeasts on ethanol as sole carbon and energy substrate
Authors: Warmerdam Marieke , Vieira-Lara Marcel A. , Mans Robert , Daran Jean Marc , Pronk Jack T.
Published: September 2024

Emerging low-emission production technologies make ethanol an interesting substrate for yeast biotechnology, but information on growth rates and biomass yields of yeasts on ethanol is scarce. Strains of 52 Saccharomycotina yeasts were screened for growth on ethanol. The 21 fastest strains, among which representatives of the Phaffomycetales order were overrepresented, showed specific growth rates in ethanol-grown shake-flask cultures between 0.12 and 0.46 h-1. Seven strains were studied in aerobic, ethanol-limited chemostats (dilution rate 0.10 h-1).Saccharomyces cerevisiaeandKluyveromyces lactis, whose genomes do not encode Complex-I-type NADH dehydrogenases, showed biomass yields of 0.59 and 0.56 gbiomassg-1, respectively. Different biomass yields were observed among species whose genomes do harbour Complex-I genes:Phaffomyces thermotolerans(0.58 g g-1),Pichia ethanolica(0.59 g g-1),Saturnispora dispora(0.66 g g-1),Ogataea parapolymorpha(0.67 g g-1), andCyberlindnera jadinii(0.73 g g-1). The biomass yield ofC. jadinii, which also showed the highest biomass protein content of these yeasts, corresponded to 88% of the theoretical maximum achieved when growth is limited by assimilation rather than by energy availability. This study indicates that energy coupling of mitochondrial respiration and its regulation are key factors for selecting and improving yeast strains for ethanol-based processes.
Mapping herpesvirus-driven impacts on the cellular milieu and transcriptional profile of Kaposi sarcoma in patient-derived mouse models
Authors: Li Xiaofan , Ohler Zoë Weaver , Day Amanda , Bassel Laura , Grosskopf Anna , Afsari Bahman , Tagawa Takanobu , Custer Wendi , Mangusan Ralph , Lurain Kathryn , Yarchoan Robert , Ziegelbauer Joseph , Ramaswami Ramya , Krug Laurie T.
Published: September 2024

Kaposi sarcoma (KS) is defined by aberrant angiogenesis driven by Kaposi sarcoma herpesvirus (KSHV)-infected spindle cells with endothelial characteristics. KS research is hindered by rapid loss of KSHV infection upon explant culture of tumor cells. Here, we establish patient-derived KS xenografts (PDXs) upon orthotopic implantation of cutaneous KS biopsies in immunodeficient mice. KS tumors were maintained in 27/28 PDX until experimental endpoint, up to 272 days in the first passage of recipient mice. KSHV latency associated nuclear antigen (LANA)+ endothelial cell density increased by a mean 4.3-fold in 14/15 PDX analyzed by IHC at passage 1 compared to respective input biopsies, regardless of implantation variables and clinical features of patients. The Ki-67 proliferation marker colocalized with LANA more frequently in PDXs. Spatial transcriptome analysis revealed increased expression of viral transcripts from latent and lytic gene classes in the PDX. The expanded KSHV+ regions of the PDX maintained signature gene expression of KS tumors, with enrichment in pathways associated with angiogenesis and endothelium development. Cells with characteristics of tumor-associated fibroblasts derived from PDX were propagated for 15 passages. These fibroblast-like cells were permissive forde novoKSHV infection, and one lineage produced CXCL12, a cancer-promoting chemokine. Spatial analysis revealed that fibroblasts are a likely source of CXCL12 signaling to CXCR4 that was upregulated in KS regions. The reproducible expansion of KSHV-infected endothelial cells in PDX from multiple donors and recapitulation of a KS tumor gene signature supports the application of patient-derived KS mouse models for studies of pathogenesis and novel therapies.

One Sentence Summary

Tumor virus-driven expansion of endothelial cells with a transcriptional signature of Kaposi sarcoma in a large cohort of patient-derived xenografts provides a platform to discover cell communications within the tumor microenvironment.
A novel degenerate primer set for eDNA metabarcoding of amphibians, turtles and fish
Authors: Rodgers Torrey W. , Olson John R. , Hawkins Charles P , Mock Karen E.
Published: October 2024

Metabarcoding of environmental DNA (eDNA) has revolutionized the detection of aquatic species across large geographic scales. However, the effectiveness of eDNA metabarcoding across taxa is marker-dependent, often requiring multiple markers to detect divergent taxonomic groups. Here, we introduce a novel metabarcoding marker designed to simultaneously detect amphibians, turtles, and fish from eDNA samples. We initially optimized this marker to match species from central and southern California, USA, and conducted validation on 525 field-collected eDNA samples from central California, while also testing an existing published amphibian marker from the literature. Additionally, we assessed the global applicability of the marker within-silicoanalysis through comparison with 11,350 amphibian, turtle, and fish mitochondrial genomes downloaded from GenBank. Field validation demonstrated the markers robustness in detecting aquatic vertebrates, outperforming the published marker in sensitivity, particularly for turtles and fish. In-silico evaluation demonstrated the potential for global use of this marker, indicating broad applicability for amplifying eDNA from amphibians, turtles, and fish worldwide. Our findings highlight the utility of this novel marker for monitoring of aquatic vertebrate communities, with implications for conservation, management, and ecological research.
Active morphodynamics of intracellular organelles in the trafficking pathway
Authors: Rautu S. Alex , Morris Richard G. , Rao Madan
Published: October 2024

From the Golgi apparatus to endosomes, organelles in the endomembrane system exhibit complex and varied morphologies that are often related to their function. Such membrane-bound organelles operate far from equilibrium due to directed fluxes of smaller trafficking vesicles; the physical principles governing the emergence and maintenance of these structures have thus remained elusive. By understanding individual fission and fusion events in terms of active mechano-chemical cycles, we show how such trafficking manifests at the hydrodynamic scale, resulting not only in fluxes of material— such as membrane area and encapsulated volume— but also in active stresses that drive momentum transfer between an organelle and its cytosolic environment. Due to the fluid and deformable nature of the bounding membrane, this gives rise to novel physics, coupling nonequilibrium forces to organelle composition, morphology and hydrodynamic flows. We demonstrate how both stable compartment drift and ramified sac-like morphologies, each reminiscent of Golgi-cisternae, emerge naturally from the same underlying nonequilibrium dynamics of fission and fusion.
Single cell variation and rapid emergence of phenotypic heterogeneity in cell lines- a cautionary tale for devotees of CRISPR-Cas9
Authors: Bradley Hayley , Barr John N , Stacey Martin
Published: September 2024

The use and publication of research utilising CRISPR/cas9 in gene editing and knock outs (KOs) within cell lines is now widespread and has proved extremely powerful in the interrogation of gene function. However, the potential of experimental artefacts resulting from the need to generate single cell clones post gene-manipulation has been somewhat overlooked. In this study, we show that the commonly used pulmonary cell line A549 displays significant heterogeneity in terms of their gene expression, and that individual cells from a population exhibit dramatically different susceptibility to viral infection from a range of viruses including respiratory syncytial virus (RSV), influenza A virus (IAV), Hazara virus (HAZV), lymphocytic choriomeningitis virus (LCMV) and Bunyamwera virus (BUNV). Moreover, we demonstrate the rapid re-emergence of phenotypic heterogeneity even after cloning. These results demonstrate the need for caution in interpreting results from CRISPR screens and CRISPR-KO validation studies, especially in the study of viral infection.
Activation of group I mGluRs is required for heterosynaptic priming of long-term potentiation in mouse hippocampus
Authors: Koek Laura A. , Sanderson Thomas M. , Georgiou John , Collingridge Graham L.
Published: September 2024

Metaplasticity involves changes in the state of neurons or synapses that influence their ability to generate synaptic plasticity. One form of heterosynaptic metaplasticity, known as synaptic tagging and capture (STC), has been intensively studied but the underlying mechanisms are not fully understood. In experiments using hippocampal slices prepared from C57BL/6J mice, we have examined the role of group I metabotropic glutamate receptors (mGluRs) in STC. We used a version of STC where a strong theta-burst stimulus (TBS), delivered to one set of Schaffer collateral-commissural pathway inputs to CA1, preceded a weak TBS delivered to a second independent set of inputs. We observed that, firstly, dual inhibition of mGluR1 and mGluR5, using YM 298198 and MTEP respectively, did not affect a form of protein synthesis-independent LTP (LTP1), but substantially inhibited a form of protein synthesis-dependent LTP (LTP2). Secondly, these inhibitors prevented the small heterosynaptic potentiation, which is often associated with LTP2. Thirdly, STC was abolished when these antagonists were applied either during the strong (priming) TBS or during the subsequent weak TBS at the independent pathway. It is proposed that the activation of group I mGluRs serves as a trigger for local protein synthesis both during the strong and weak TBS and, as such, are an integral part of the STC process. STC is involved in associative learning and memory, a cognitive function that is disrupted in many brain disorders including Alzheimer’s disease.
Millisecond-scale motor coding precedes sensorimotor learning in songbirds
Authors: Pascual Leila May M. , Vusirikala Aanya , Nemenman Ilya M. , Sober Samuel J. , Pasek Michael
Published: September 2024

A key goal of the nervous system in young animals is to learn motor skills. Songbirds learn to sing as juveniles, providing a unique opportunity to identify the neural correlates of skill acquisition. Prior studies have shown that spike rate variability in vocal motor cortex decreases substantially during song acquisition, suggesting a transition from rate-based neural control to the millisecond-precise motor codes known to underlie adult vocal performance. By distinguishing how the ensemble of spike patterns fired by cortical neurons (the “neural vocabulary”) and the relationship between spike patterns and song acoustics (the “neural code”) change during song acquisition, we quantified how vocal control changes across learning in juvenile Bengalese finches. We found that despite the expected drop in rate variability (a learning-related change in spike vocabulary), the precision of the neural code in the youngest singers is the same as in adults, with 1–2 ms variations in spike timing transduced into quantifiably different behaviors. In contrast, fluctuations in firing rates on longer timescales fail to affect the motor output in both juvenile and adult animals. The consistent presence of millisecond-scale motor coding during changing levels of spike rate and behavioral variability suggests that learning-related changes in cortical activity reflect the brain’s changing its spiking vocabulary to better match the underlying motor code, rather than a change in the precision of the code itself.
Context-Dependent Interaction Between Goal-Directed and Habitual Control Under Time Pressure
Authors: Frölich Sascha , Wagner Ben J. , Smolka Michael N. , Kiebel Stefan J.
Published: October 2024

Habits are an important aspect of human behaviour. Habits are reflexive, inflexible, and fast, in contrast to goal-directed behaviour which is reflective, flexible, and slow. Current theories assume that habits and goal-directed actions are controlled by two separate but interacting systems. However, it is not clear how these two systems interact when actions must be made under time pressure. Here we use a task which induces habitual behaviour in the form of action sequences, while concurrently requiring participants to perform goal-directed actions that are either congruent or incongruent with the habit. This task thus allows for concurrent measurement of both goal-directed and habitual behaviour, thereby permitting a nuanced analysis of the interaction between these two control modes. Using computational modelling, we find that models where the influence of the habit depends on the number of repetitions, explain participant behaviour better than models that assume the habit to be constant. We further show that roughly half of the participants modulate their use of the habit depending on the context, i.e. they selectively inhibit the habit’s influence when it is incongruent to their explicit goals, but not when both are congruent and the influence of the habit is adaptive. Additional drift-diffusion modelling of choice and reaction time data shows that proactive control is mobilized in the congruent task context whereas reactive control is mobilized in the incongruent task context. The present study thus indicates that habitual control is context-dependent and can be adaptively deployed via proactive and reactive control, rather than being a fixed or isolated mechanism.
Concentration dependent CsrA regulation of theuxuBtranscript leads to development of post-transcriptional BANDPASS Filter
Authors: Rojano-Nisimura Alejandra M. , Simmons Trevor R. , Lukasiewicz Alexandra J. , Buchser Ryan , Ruzek Josie S. , Avila Jacqueline L. , Contreras Lydia M.
Published: October 2024

Post-transcriptional control systems offer new avenues to design synthetic circuits that offer reduced burden and less synthetic regulatory components compared to transcriptionally based tools. Herein, we repurpose a newly identified post-transcriptional interaction between theuxuBleader sequence and theE. coliCsrA regulatory protein to design a biological post-transcriptional BANDPASS filter. In this work, we characterizethe uxuBmRNA as heterogenous target of the Carbon Storage Regulatory A (CsrA) protein, where the protein can both activate and repressuxuBactivity depending on its intracellular concentration. We leverage this interaction to implement a novel strategy of regulation within the 5’UTR of an mRNA. Specifically, we report a hierarchical binding strategy that may be leveraged by CsrA withinuxuBto result in a dose- dependent response in regulatory outcomes. In our semi-synthetic circuit, theuxuBmRNA leader sequence is used as a scaffold that is fused to a gene of interest, which allows the circuit to transition between ON/OFF states based on a range of free native concentration of the CsrA regulatory protein. Notably, this system exerts regulation comparable to previously developed transcriptional BANDPASS filters while reducing the number of circuit components and can be used in concert with additional controlled circuits to achieve complex multi-signal control. We anticipate that future characterization of native regulatory RNA-protein systems will allow for development of more complex RNP-based circuits for synthetic biology applications.

Abstract Figure
Sex differences in colonic inflammation are driven by epithelial-specific expression of estrogen receptor alpha
Authors: Pereda Guillermo A. , Kocinski Adrian D. , Broncano Alyssia V. , McNeer Sarah K. , Raymond Michelle L. , Ziats Nicholas P. , Breau Keith A. , Burclaff Joseph , Magness Scott T. , Goodman Wendy A.
Published: October 2024

Background & Aims

Inflammatory bowel disease (IBD) patients exhibit altered expression of nuclear estrogen receptors alpha and beta (ERα, ERβ) and G-protein coupled estrogen receptor 1 (GPER1). We previously showed that deletion of ERα protects against intestinal damage selectively in female mice; however, the mechanisms conferring sex-specific protection are poorly understood. The goal of this study was to compare ERα- and ERβ-specific mechanisms contributing to intestinal epithelial function in males and females.

Methods

Expression of ERα, ERβ, and GPER1 was evaluated in colonocytes from wild-type (WT) male and female mice. Intestinal epithelial cell (IEC)-specific ERα and ERβ knockout mice were developed and challenged with dextran sulfate sodium (DSS). Colonic organoids were used to identify estrogen-dependent and -independent effects on cellular growth, differentiation, and transcriptional regulation in WT, ERα-KO, and ERβ-KO IECs.

Results

Colonic IECs showed significant expression of ERα, ERβ, and GPER1 as well as Cyp19A1, which catalyzes production of 17β-estradiol (estrogen). Female mice lacking ERα specifically in colonic IECs showed protection from DSS-induced injury, whereas males showed increased pathology. Organoids derived from male ERα-KO mice showed enhanced proliferation and decreased expression of key functional genes even without exogenous estrogen; however, colonoids derived from female ERα-KO mice transcriptional analysis showed a protective gene signature. These findings reveal that deletion of ERα differentially contributes to enhanced barrier function and resistance to inflammation in females, but to dysfunctional hyper-proliferation in males.

Conclusions

ERα signaling within IECs drives opposing sex-dependent effects on the development, regenerative capacity, and inflammatory susceptibility of the intestinal epithelium.
Direct and Indirect Regulation of SIX1+EYA Transcriptional Activity by PA2G4, MCRS1, and SOBP
Authors: Jourdeuil Karyn , Gafurova Jasmina , Ben-Mayor Ashley , Moody Sally A. , Tavares Andre L. P.
Published: October 2024

Branchio-oto-renal (BOR) syndrome is an autosomal dominant condition characterized by variable craniofacial malformations, hearing loss and in some patients, renal dysfunction. Recently, a clinical study showed that patients with mutations causative of BOR also present with craniosynostosis, indicating that this could be an undiagnosed feature of BOR. Approximately half of all patients presenting with BOR have a variant in eitherSIX1or its activating co-factorEYA1. The genes underlying BOR in the other 50% of patients remain unknown. To date, most studies on the role of SIX1 in the inner ear have focused on its role in the placode-based development of the sensorineural epithelia (cochlear and vestibular organs), as sensorineural hearing loss has long term effects on human health and development. The role of SIX1 in the neural crest cells (NCCs) of the first pharyngeal (a.k.a., mandibular) arch, which will give rise to the upper and lower jaws as well as the middle ear ossicles which may be affected in patients with BOR, is less well understood. To that end, we examine herein the role of three proteins that have been identified inXenopus laevisas SIX1 co-factors to determine whether their function as regulators of SIX1+EYA transcriptional activity is conserved in mouse and begin to elucidate their function in the NCCs of the mandibular arch. Our data reveal that SIX1 is co-expressed with PA2G4, MCRS1, and SOBP within the oral domain of the mandibular arch, although each has a very distinct expression pattern. We further demonstrate that MCRS1 and SOBP arebona fideSIX1 co-factors that can repress SIX1+EYA transcriptional activity. PA2G4, on the other hand, does not bind to SIX1 in the mouse but can indirectly enhance the transcriptional activity of the SIX1+EYA transcriptional complex. Further, we show that both MCRS1 and SOBP are also able to translocate EYA to the nucleus via direct (i.e., SOBP) or indirect (i.e., MCRS1) mechanisms. We also show that later, during development of the mandible and incisors that SOBP is co-expressed with SIX1 within these anlagen, confirming the biological relevance of these transcriptional complexes in craniofacial bone formation and within the derivatives of the mandibular NCCs. This study, therefore, highlights the complexity of SIX1+EYA transcriptional regulation suggesting that there are multiple, and potentially redundant, mechanisms in place to ensure precise levels of SIX1+EYA transcriptional activity during craniofacial development.
Aladyn Individual: Bayesian Hierarchical Dynamic Genetic Modeling of Comorbidity Progression
Authors: Urbut Sarah , Ding Yi , Jiang Xilin , Hornsby Whitney , Gusev Alexander , Natarajan Pradeep , Parmigiani Giovanni
Published: October 2024

Early identification of high-risk individuals through the analysis of their unique disease trajectories has a strong potential to support efficient prevention and clinical management across a range of chronic conditions. In this paper we present a novel approach for dynamic modeling of the evolution of chronic disease risks over time, incorporating individual genetic predispositions. Our approach uses a hierarchical Bayesian topic model including Gaussian Processes to capture age effects. It accounts for genetic predisposition through a time-warping function and topic-dependent genetic scores, enabling both simultaneous learning and updated predictions of complex comorbidity patterns, inclusive of genomic and non-genomic effects. We systematically compare to previous approaches and provide detailed simulations athttps://bookdown.org/sarahmurbut/dynamic_ehr/andhttps://surbut.shinyapps.io/dynamic_ehr.

Impact Statement

Our model significantly advances healthcare for aging populations by facilitating the early identification of high-risk individuals through the analysis of their unique disease trajectories within complex comorbidity patterns. Existing models are limited in their capacity to manage diverse comorbidity patterns, particularly those that are time-dependent. We introduce an approach leveraging Bayesian hierarchical modeling to concurrently learn population-level patterns and provide updated real-time predictions across 350 diseases, thereby uncovering and forecasting intricate comorbidity patterns. This methodology paves the way for preventive measures and targeted interventions that enhance health outcomes, mitigate late-stage disease burdens, and foster healthier aging. Furthermore, our model incorporates genetic influences via a genetic predisposition parameter to estimate the lifetime risk of specific diseases and disorders, alongside a time-warping function to facilitate personalized predictions of disease trajectories.
R2DT: a comprehensive platform for visualising RNA secondary structure
Authors: McCann Holly , Meade Caeden D. , Williams Loren Dean , Petrov Anton S. , Johnson Philip Z. , Simon Anne E. , Hoksza David , Nawrocki Eric P. , Chan Patricia P. , Lowe Todd M. , Ribas Carlos Eduardo , Sweeney Blake A. , Madeira Fábio , Anyango Stephen , Appasamy Sri Devan , Deshpande Mandar , Varadi Mihaly , Velankar Sameer , Zirbel Craig L. , Naiden Aleksei , Jossinet Fabrice , Petrov Anton I.
Published: October 2024

RNA secondary (2D) structure visualisation is an essential tool for understanding RNA function. R2DT is a software package designed to visualise RNA 2D structures in consistent, recognisable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms (SNPs) or SHAPE reactivities. It also offers a new template-free mode allowing visualisation of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualisations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualisation, accessible athttps://r2dt.bio.
Iterative sacrificial 3D printing and polymer casting to create complex vascular grafts and multi-compartment bioartificial organs
Authors: Brassard Jonathan A. , Dharmaraj Saleth Sidharthan , Orimi Hamid Ebrahimi , Vdovenko Daria , Rioux Yannick , Wang Hanwen , Champion Kurtis , Lemaire Florent , Moeun Brenden N. , Zhao Jia , Liang Shenghui , Kieffer Timothy J. , Tchervenkov Jean I. , Soulez Gilles , Bégin-Drolet André , Ruel Jean , Leask Richard L. , Paraskevas Steven , Hoesli Corinne A.
Published: October 2024

Several emerging strategies to engineer artificial organs employ 3D printing to create vascular templates to provide nutrients and oxygen to immobilized cells. Significant challenges emerge when considering clinical implementation such as immune rejection of allogeneic cell sources, as well as achieving adequate perfusion and integration with endogenous vasculature. We propose a method by which cell-laden hydrogels are molded around ready-made polymeric vascular templates created via 3D printing to create human-scale artificial organs with internal vasculature. We applied this technique to create bioartificial pancreas systems with up to 9 internal flow channels via sacrificial carbohydrate glass 3D printing, porogen-loaded polycarbonate polyurethane dip-coating, followed by casting cell-laden hydrogels around the vascular templates. We optimized porogen size and concentration to maximise the porosity of our scaffolds without compromising mechanical properties, resulting in suture retention strength and compliance respectively matching commercial vascular grafts and native vessels. Bioreactor perfusion studies showed survival and maturation of stem cell derived pancreatic islets without significant differences to traditional suspension culture protocols. Insulin response dynamics were rapid in response to a glucose challenge at the perfusion inlet. Transplantation of the devices as iliac arteriovenous shunts in nondiabetic pigs confirmed safety and patency. These results show promise for the development of an implantable vascularized pancreas for the treatment of type 1 diabetes and demonstrate how bioartificial organs with engineered vascular geometries can be designed for translational applications.
Quantitative phase imaging with temporal kinetics predicts hematopoietic stem cell diversity
Authors: Yogo Takao , Iwamoto Yuichiro , Becker Hans Jiro , Kimura Takaharu , Sugiyama-Finnis Ayano , Yokomizo Tomomasa , Suda Toshio , Ota Sadao , Yamazaki Satoshi
Published: October 2024

Innovative identification technologies for hematopoietic stem cells (HSCs) have advanced the frontiers of stem cell biology. However, most analytical techniques capture only a single snapshot, disregarding the temporal context. A comprehensive understanding of the temporal heterogeneity of HSCs necessitates live-cell, real-time and non-invasive analysis. Here, we developed a prediction system for HSC diversity by integrating single-HSC ex vivo expansion technology with quantitative phase imaging (QPI)-driven machine learning. By analyzing single-cell kinetics with QPI, we discovered previously undetectable diversity among HSCs that snapshot analysis fails to capture. Our QPI-driven algorithm quantitatively evaluates the stemness of individual HSCs and incorporates temporal information to significantly improve prediction accuracy. This platform marks a paradigm shift from “identification” to “prediction”, enabling us to forecast HSC status by analyzing their past temporal kinetics.
Liver Sinusoidal Endothelial Cells and Laminin dictate cholangiocytes’ fate in chronic liver disease
Authors: Manco Rita , Moliterni Camilla , Neirynck Gauthier , De Rudder Maxime , Picalausa Corinne , Ducor Leana , Fraga Montserrat , Lemaigre Frédéric , Sempoux Christine , Dili Alexandra , Leclercq Isabelle A.
Published: October 2024

In chronic liver disease (CLD), hepatocyte senescence limits conventional regeneration, prompting an alternative regeneration mechanism through transdifferentiation of reactive cholangiocytes (or ductular reaction cells - DRs). Yet, this alone is insufficient to avoid liver failure and transplantation, highlighting the importance of a deeper understanding of the mechanism. We focused on the DRs microenvironment. We identified laminin as a crucial component of the extracellular matrix to maintain DRs in a biliary phenotype, preventing their differentiation into hepatocytes. Liver sinusoidal endothelial cells (LSEC) are the cells regulating laminin degradation around DRs. By preventing LSEC capillarization during CLD, we enhanced DR differentiation into hepatocytes. We also demonstrated this causality in human samples. This is the first time that a mechanism for DR-driven regeneration has been described.
Electromagnetic Stimulated Anisotropic Hydrogels for Guided Neuronal Morphogenesis
Authors: Jensen Bjarke Nørrehvedde , Tong Tong , Skovborg Grith , Zhang Yuge , Müller Christoph , Matthiesen Cecillie Linneberg , Eschen Jens Toft , Elbæk Kirstine Juul , Wang Yuting , Pallesen Lone Tjener , Seliktar Dror , Dong Mingdong , Vægter Christian Bjerggaard , Korshøj Anders Rosendal , Chen Menglin
Published: October 2024

While electrical circuits are a fundamental part of neural activity, the soft microstructural extracellular environment plays a vital role in driving the morphogenesis of neurons. To leverage this, we combine a wireless electromagnetic neural stimulation system with anisotropic GelMA hydrogels to promote and guide neural morphogensis. We show that oriented GelMA hydrogels support anisotropic growth of dorsal root ganglion as potential peripheral neural guide conduit and promote the formation of hippocampal neurospheres networking along the fiber direction. The central nervous system has limited regeneration due to glial scar formation, the presence of the perineuronal network, and limited upregulation of growth-associated genes post traumatic injuries. The system was further tested on human cortical brain tissue where hydrogel microfilaments promoted neurite outgrowth in a white-matter-mimicking manner between two pieces of brain slices, opening the possibility of central neural tissue regeneration.
Treatment with carnosic acid attenuates the secretion of pro-inflammatory mast cell mediators following IL-33 activation
Authors: Crozier Robert W.E. , Masi Jordan T. , MacNeil Adam J.
Published: October 2024

IL-33 is an alarmin cytokine, released upon cellular damage, that has gained significant attention as a regulator of inflammation in several pathologies, including allergy. Once released, IL-33 binds to and activates its cognate receptor ST2, leading to the activation of the classical inflammatory Myddosome signalosome in an array of cells, including mast cells. Our group has recently identified the polyphenol carnosic acid (CA), as a potent regulator of mast cell activation in the context of allergic inflammation. Due to the key role IL-33 plays in the enhancement of allergies and other mast cell-associated diseases, we sought to determine the inhibitory potential of CA in a model of IL-33-mediated mast cell activation. Bone marrow-derived mast cells were stimulated with IL-33 under potentiation of SCF and treated with CA in the presence or absence of an allergen co-stimulation. Here, it was determined that treatment with CA led to a reduction in early ROS production, which translated into a significant impairment in the release of pro-inflammatory cytokines IL-6, IL-13, TNF and chemokines CCL1, CCL2 and CCL3. Surprisingly however, it was determined that CA treatment increased signaling through Akt and NFκB protein phosphorylation, leading to increased gene expression ofIL6, IL13,andCCL3as well as increased intracellular concentrations of IL-6 and CCL3. Taken together, our data suggests treatment with CA impairs the release mechanisms of pro-inflammatory mediators following IL-33 activation, warranting further investigation into the versatile biological activity of CA toward advance our understanding of CA as a potential anti-inflammatory therapeutic.
Impact of early-life respiratory syncytial virus infection on cell type-specific airway DNA methylation
Authors: McKennan Chris , Newcomb Dawn C. , Berdnikovs Sergejs , Gebretsadik Tebeb , Ma Siyuan , Bacharier Leonard B. , Seibold Max A. , Anderson Larry J. , Gern James E. , Ober Carole , Hartert Tina
Published: October 2024

Rationale

Infection with respiratory syncytial virus (RSV) in early-life is associated with subsequent childhood respiratory disorders, but the mechanism for this association is unknown. We hypothesized that RSV-mediated alteration in airway DNA methylation (DNAm) may play a role.

Objectives

Investigate the impact of early-life RSV infection on airway DNAm.

Methods

Our study population consisted of children from the INSPIRE population-based birth cohort. Early-life infection with RSV was defined as infection not requiring clinical illness before age one year, ascertained through active and passive surveillance. Methylation was measured in DNA from nasal airway epithelial cells (NAECs) at ages two years (n=88) and six years (n=539). Bulk gene expression in NAECs was available in a subset of participants at age two years (n=54).In silicocell type deconvolution was used to infer cell type-specific associations in suprabasal, ciliated, and “other” cell types.

Measurements and Main Results

We identified 164 CpGs in ciliated cells and seven CpGs in suprabasal cells whose cell type-specific DNAm at age two years was associated with early-life RSV infection. The seven associations in suprabasal cells were still present at age six years and the directions of association replicated inin vitroinfection of epithelial cells with RSV in air liquid interface cultures. DNAm levels at four of the seven CpGs identified in suprabasal cells correlated with the expression of their nearest genes in suprabasal cells, which included genes previously implicated in asthma-related diseases. The DNAm levels of these four CpGs and the expression of their nearest genes in suprabasal cells at age two years were also associated with recurrent wheezing at age four years.

Conclusions

We demonstrate epigenetic changes in airway progenitor cells of children who have had RSV infection in the first year of life are conserved over time, associated with subsequent wheeze, have functional relevance, and replicate inin vitroinfection in ALI cultures. Our study is the first to show that early-life RSV infection, as opposed to severe illness, alters DNAm levels at functionally and clinically relevant loci.
Integrating geospatial tools in mapping forest fire severity and burned areas in the Western Usambara Mountain Forests, Lushoto, Tanzania
Authors: Mkiwa Braison P. , Mauya Ernest W. , Jonas Justo N. , Mbeyale Gimbage E.
Published: October 2024

Despite the numerous negative effects of tropical forest fires in Tanzania, the causes and effects remain insufficiently documented. This study aimed to develop an integrated approach of using geospatial tools and socio-economic data to assess and map forest fire burn severity in West Usambara Mountain Forests. Three approaches including Participatory Rural Appraisal (PRA), satellite image analysis, and direct observation were used to generate information on spatial and temporal forest fire severity. Findings revealed that agricultural activities (44.5%) and charcoal production (21.1%) are the primary causes of these fires. Burn severity maps were created using the differenced Normalized Burned Ratio (dNBR) index, and the combined high and low severity areas ranged from 32.120% to 20.31%. The differenced Normalized Difference Vegetation Index (dNDVI) maps showed the combined high and low severity areas of 36.30% to 21.10% of the total study sites respectively. Post-fire NDVI time series analyses revealed a sharp decrease from 0.21 to 0.36 in all burned areas, indicating significant vegetation loss. Therefore, this study demonstrated the potential of integrating Remote Sensing and Socio-economic aspects highlighting the need for improved forest fire management through sustainable practices that balance economic and ecological considerations, offering insights that can be upscaled to other forest areas for effective management.
Amyloid Beta Pathology Accelerates Alterations in the Visual Pathway of the 5xFAD Mouse
Authors: McCool Shaylah , Smith Jennie C. , Sladek Asia , Fan Shan , Van Hook Matthew J.
Published: October 2024

Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by the formation of amyloid beta plaques and neurofibrillary tangles that leads to decreased quality of life due to behavioral, motor, and cognitive impairments. Due to the widespread pathological nature of AD, many brain regions are affected by amyloid beta plaques including regions important for vision such as the lateral geniculate nucleus (LGN) of the thalamus which is critical for relaying signals from the retina to the primary visual cortex. Using a wide range of techniques including electrophysiological approaches,in vivoandex vivoimaging methods, and immunohistochemistry in a mouse model with progressing amyloidosis (5xFAD), the goal of this study was to determine whether AD-like pathology disrupts neuronal and synaptic structure and function in the visual system.In vivoelectroretinogram recordings revealed photoreceptor dysfunction in the 6- and 9-month-old 5xFAD mice, while optical coherence tomography indicated no changes in retinal thickness. In the dorsolateral geniculate nucleus (dLGN), the rodent homolog of the primate LGN, we identified decreased densities of retinal ganglion cell axon terminals and fewer thalamocortical (TC) neuron cell bodies. No detectable deficits in excitatory synaptic function or TC neuron dendritic structure were seen in the dLGN, and reflexive visual behavior was also found to be normal in the 5xFAD mice. These results indicate relatively modest amyloid-triggered dysfunction in these stages of the visual system suggesting that amyloid beta plaque formation may play only a small role in the visual system dysfunction seen in AD patients. These results may also point to potential compensatory mechanisms that preserve function of visual pathways in the 5xFAD visual system.
Topographic organization of bidirectional connections between the cingulate region (infralimbic area and anterior cingulate area, dorsal part) and the interbrain (diencephalon) of the adult male rat
Authors: Negishi Kenichiro , Montes Laura P. , Navarro Vanessa I. , Soto Arzate Lidice , Oliveros Cindy , Khan Arshad M.
Published: October 2024

The medial prefrontal cortex [cingulate region (Brodmann, 1909)(CNG)] in the rat is a connectionally and functionally diverse structure. It harbors cerebral nuclei that use long-range connections to promote adaptive changes to ongoing behaviors. The CNG is often described across functional and anatomical gradients, a dorsal-ventral gradient being the most prominent. Topographic organization is a general feature of the nervous system, and it is becoming clear that such spatial arrangements can reflect connectional, functional, and cellular differences. Portions of the CNG are known to form reciprocal connections with cortical areas and thalamus; however, these connectional features have not been described in detail or mapped to standardized rat brain atlases. Here, we used co-injected anterograde (Phaseolus vulgarisleucoagglutinin) and retrograde (cholera toxin B subunit) tracers throughout the CNG to identify zones of reciprocal connectivity in the diencephalon [orinterbrain (Baer, 1837)(IB)]. Tracer distributions were observed using a Nissl-based atlas-mapping approach that facilitates description of topographic organization. This draft report describes CNG connections of theinfralimbic area (Rose & Woolsey, 1948)(ILA) andthe anterior cingulate area, dorsal part (Krettek & Price, 1977)(ACAd) throughout the IB. We found that corticothalamic connections are predominantly reciprocal, and that ILA and ACAd connections tended to be spatially segregated with minimal overlap. In thehypothalamus (Kuhlenbeck, 1927), we found dense and specific ILA-originating terminals in the followingBrain Maps 4.0 atlas territories:dorsal region (Swanson, 2004)(LHAd) andsuprafornical region (Swanson, 2004)(LHAs) of thelateral hypothalamic area (Nissl, 1913),parasubthalamic nucleus (Wang & Zhang, 1995)(PSTN),tuberal nucleus, terete part (Petrovich et al., 2001)(TUte), and an ill-defined dorsal cap of themedial mammillary nucleus (Gudden, 1881)(MM). We discuss these findings in the context of feeding behaviors.
Electrical Impedance Spectroscopy as a Tool to Detect the Epithelial to Mesenchymal Transition in Prostate Cancer Cells
Authors: Crowell Lexi L. , Henriquez Luis A. , Tran Mary , Adams Tayloria N.G.
Published: October 2024

Prostate cancer (PCa) remains a significant health threat, with chemoresistance and recurrence posing major challenges despite advances in treatment. The epithelial to mesenchymal transition (EMT), a biochemical process where cells lose epithelial features and gain mesenchymal traits, is linked to chemoresistance and metastasis. Electrical impedance spectroscopy (EIS), a novel label-free electrokinetic technique, offers promise in detecting cell phenotype changes. In this study, we employed EIS to detect EMT in prostate cancer cells (PCCs). PC3, DU145, and LNCaP cells were treated with an EMT induction media for five days. EIS characterization revealed unique impedance spectra correlating with metastatic potential, distinguishing DU145 EMT+ and EMT-cells, and LNCaP EMT+ and EMT-cells (in combination with dielectrophoresis), with comparisons made to epithelial and mesenchymal controls. These changes were supported by shifts in electrical signatures, morphological, and protein expression, including downregulation of E-cadherin and upregulation of vimentin. No phenotype change was observed in PC3 cells, which maintained a mesenchymal phenotype. EMT+ cells were also distinguishable from mixtures of EMT+ and EMT-cells. This study demonstrates key advancements: application of EIS and dielectrophoresis for label-free EMT detection in PCCs, characterization of cell electrical signature after EMT, and EIS sensitivity to EMT transitions. Detecting EMT in PCa is important to the development of more effective treatments and overcoming the challenges of chemoresistance.
A Large Scale Multi-dataset Investigation of Brain Metastases Distribution Based on Primary Cancer Type
Authors: Lyu Qing , Yuan Hongyu , Lin Zhen , Barcus Richard , Hudson Jeremy , Jiang Yuming , Kim Jeongchul , Whitlow Christopher T
Published: October 2024

Brain metastases (BM) present a significant clinical challenge, characterized by poor prognosis and high morbidity. Previous research has demonstrated heterogeneous distribution patterns of BMs depending on the primary tumor type. This study aims to further investigate the distribution patterns of BMs. Utilizing three public datasets and one private dataset, we analyzed 1,344 patients with a total of 9,431 identified BMs, categorizing them into lung, breast, melanoma, kidney cancer, and other groups. Our findings indicate that lung cancer BMs predominantly localize in the cerebellum, as well as the frontal, temporal, occipital, and parietal lobes. Breast cancer BMs are commonly found in the cerebellum, frontal, occipital, and temporal lobes, while melanoma BMs are most frequently located in the occipital, temporal, and frontal lobes. Kidney cancer BMs, less studied in existing literature, primarily affect the frontal and temporal lobes. Additionally, we explored the relationship between BM volume and tumor type, revealing that lung and breast cancer BMs are more likely to have smaller tumor volumes compared to melanoma and kidney cancer BMs. These findings confirm and expand upon previous research, offering new insights into the distribution and characteristics of kidney cancer BMs.