bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of the terminal airspaces in the Gray short-tailed opossum (Monodelphis domestica) – 3 D reconstruction by microcomputed tomography
Authors: Ferner Kirsten
Published: September 2023

Marsupials are born with structurally immature lungs when compared to eutherian mammals. The Gray short-tailed opossum (Monodelphis domestica) is born at the late canalicular stage of lung development. Despite the high degree of immaturity, the lung is functioning as respiratory organ, however supported by the skin for gas exchange during the first postnatal days. Consequently, the majority of lung development takes place in ventilated functioning state during the postnatal period.

X-ray computed tomography (µCT) was used to three-dimensionally reconstruct the terminal airspaces in order to reveal the timeline of lung morphogenesis. In addition, lung and air space volume as well as surface area were determined to assess the functional relevance of the structural changes in the developing lung. The development of the terminal air spaces was examined in 35 animals from embryonic day 13, during the postnatal period (neonate to 57 days) and in adults. At birth, the lung ofM. domesticaconsists of few large terminal air spaces, which are poorly subdivided and open directly from short lobar bronchioles. During the first postnatal week the number of smaller terminal air spaces increases and numerous septal ridges indicate a process of subdivision, attaining the saccular stage by 7 days. The 3 D reconstructions of the terminal air spaces demonstrated massive increases in air sac number and architectural complexity during the postnatal period. Between 28 and 35 days alveolarization started. Respiratory bronchioles, alveolar ducts and a typical acinus developed. With alveolarization the volume of the air spaces and the surface area for gas exchange increased markedly. The structural transformation from large terminal sacs to the final alveolar lung in the Gray short-tailed opossum follows similar patterns as described in other marsupial and placental mammals. The processes involved in sacculation and alveolarization during lung development seem to be highly conservative within mammalian evolution.
Evaluating and Improving Health Equity and Fairness of Polygenic Scores
Authors: Zhang Tianyu , Klei Lambertus , Liu Peng , Chouldechova Alexandra , Roeder Kathryn , G’Sell Max , Devlin Bernie
Published: September 2023

Polygenic scores (PGS) are quantitative metrics for predicting phenotypic values, such as human height or disease status. Some PGS methods require only summary statistics of a relevant genome-wide association study (GWAS) for their score. One such method is Lassosum, which inherits the model selection advantages of Lasso to select a meaningful subset of the GWAS single nucleotide polymorphisms as predictors from their association statistics. However, even efficient scores like Lassosum, when derived from European-based GWAS, are poor predictors of phenotype for subjects of non-European ancestry; that is, they have limited portability to other ancestries. To increase the portability of Lassosum, when GWAS information and estimates of linkage disequilibrium are available for both ancestries, we propose Joint-Lassosum. In the simulation settings we explore, Joint-Lassosum provides more accurate PGS compared with other methods, especially when measured in terms of fairness. Like all PGS methods, Joint-Lassosum requires selection of predictors, which are determined by data-driven tuning parameters. We describe a new approach to selecting tuning parameters and note its relevance for model selection for any PGS. We also draw connections to the literature on algorithmic fairness and discuss how Joint-Lassosum can help mitigate fairness-related harms that might result from the use of PGS scores in clinical settings. While no PGS method is likely to be universally portable, due to the diversity of human populations and unequal information content of GWAS for different ancestries, Joint-Lassosum is an effective approach for enhancing portability and reducing predictive bias.
Antifungal efficacy of natural antiseptic products againstCandida auris
Authors: Wu Wing-Gi , Luk Kristine Shik , Hung Mei-Fan , Tsang Wing-Yi , Lee Kin-Ping , Lam Bosco Hoi-Shiu , Cheng Ka-Lam , Cheung Wing-Sze , Tang Hau-Ling , To Wing-Kin
Published: September 2023

Candida aurisis an emerging fungal pathogen responsible for healthcare associated infections and outbreaks with high mortality around the world. It readily colonizes the skin, nares, respiratory and urinary tract of hospitalized patients, and such colonization may lead to invasiveCandidainfection in susceptible patients. However, there is no recommended decolonization protocol forC. aurisby international health authorities. The aim of this study is to evaluate the susceptibility ofC. auristo commonly used synthetic and natural antiseptic products using an in vitro, broth microdilution assay. Synthetic antiseptics including chlorhexidine, povidone-iodine, and nystatin were shown to be fungicidal againstC. auris. Among the natural antiseptics tested, tea tree oil and manuka oil were both fungicidal againstC. aurisat concentrations less than or equal to 1.25% (v/v). Manuka honey inhibitedC. aurisat 25% (v/v) concentrations. Among the commercial products tested, manuka body wash and mouthwash were fungicidal againstC. aurisat concentrations less than or equal to 0.39% (w/v) and 6.25% (v/v) of products as supplied for use, respectively, while tea tree body wash and MedihoneyTMwound gel demonstrated fungistatic properties. In conclusion, this study demonstrated good in vitro antifungal efficacy of tea tree oil, manuka oil, manuka honey, and commercially available antiseptic products containing these active ingredients. Future studies are warranted to evaluate the effectiveness of these antiseptic products in clinical settings.
Identification of Genetic Suppressors for a Berardinelli-Seip Congenital Generalized Lipodystrophy Type 2 (BSCL2) Pathogenic Variant inC. elegans
Authors: Bai Xiaofei , Smith Harold E. , Golden Andy
Published: September 2023

Maintaining the metabolic homeostasis of fatty acids is crucial for human health. Excess fatty acids are stored in lipid droplets (LDs), the primary energy reservoir that helps regulate fat and lipid homeostasis in nearly all cell types. Seipin (BSCL2), a conserved endoplasmic reticulum protein, plays a critical role in LD biogenesis and regulating LD morphology. Pathogenic variants of seipin are associated with multiple human genetic diseases, including Berardinelli-Seip Congenital Generalized Lipodystrophy Type 2 (BSCL2). However, the cellular and molecular mechanisms by which dysfunctional seipin leads to these diseases remain unclear. To model BSCL2 disease, we generated an orthologousBSCL2pathogenic variantseip-1(A185P)using CRISPR/Cas9 genome editing inCaenorhabditis elegans. This variant led to severe developmental and cellular defects, including embryonic lethality, impaired eggshell formation, and abnormally enlarged LDs. We set out to identify genetic determinants that could suppress these defective phenotypes in theseip-1(A185P)mutant background. To this end, we conducted an unbiased chemical mutagenesis screen to identify genetic suppressors that restore embryonic viability in theseip-1(A185P)mutant background. A total of five suppressor lines were isolated and recovered from the screen. The defective phenotypes ofseip-1(A185P), including embryonic lethality and impaired eggshell formation, were significantly suppressed in each suppressor line. Two of the five suppressor lines also alleviated the enlarged LDs in the oocytes. We then mapped a suppressor candidate gene,R05D3.2(renamed aslmbr-1), which is an ortholog of humanLMBR1(limb development membrane protein 1). The CRISPR/Cas9 editedlmbr-1suppressor alleles,lmbr-1(Ser647Phe)andlmbr-1(Pro314Leu), both significantly suppressed embryonic lethality and defective eggshell formation in theseip-1(A185P)background. The newly identified suppressor lines offer valuable insights into potential genetic interactors and pathways that may regulate seipin in the lipodystrophy model.
Synthetic control of actin polymerization and symmetry breaking in active protocells
Authors: Razavi Shiva , Wong Felix , Abubaker-Sharif Bedri , Matsubayashi Hideaki T. , Nakamura Hideki , Sandoval Eduardo , Robinson Douglas N. , Chen Baoyu , Liu Jian , Iglesias Pablo A. , Inoue Takanari
Published: September 2023

Non-linear biomolecular interactions on the membranes drive membrane remodeling that underlies fundamental biological processes including chemotaxis, cytokinesis, and endocytosis. The multitude of biomolecules, the redundancy in their interactions, and the importance of spatiotemporal context in membrane organization hampers understanding the physical principles governing membrane mechanics. A minimal, in vitro system that models the functional interactions between molecular signaling and membrane remodeling, while remaining faithful to cellular physiology and geometry is powerful yet remains unachieved. Here, inspired by the biophysical processes underpinning chemotaxis, we reconstituted externally-controlled actin polymerization inside giant unilamellar vesicles, guiding self-organization on the membrane. We show that applying undirected external chemical inputs to this system results in directed actin polymerization and membrane deformation that are uncorrelated with upstream biochemical cues, indicating symmetry breaking. A biophysical model of the dynamics and mechanics of both actin polymerization and membrane shape suggests that inhomogeneous distributions of actin generate membrane shape deformations in a non-linear fashion, a prediction consistent with experimental measurements and subsequent local perturbations. The active protocellular system demonstrates the interplay between actin dynamics and membrane shape in a symmetry breaking context that is relevant to chemotaxis and a suite of other biological processes.
Orthogonality of sensory and contextual categorical dynamics embedded in a continuum of responses from the second somatosensory cortex
Authors: Bayones Lucas , Zainos Antonio , Alvarez Manuel , Romo Ranulfo , Franci Alessio , Rossi-Pool Román
Published: September 2023

How does the brain simultaneously process signals that bring complementary information, like raw sensory signals and their transformed counterparts, without any disruptive interference? Contemporary research underscores the brain’ ss adeptness in using decorrelated responses to reduce such interference. Both neurophysiological findings and artificial neural networks (ANNs) support the notion of orthogonal representation for signal differentiation and parallel processing. Yet, where, and how raw sensory signals are transformed into more abstract representations remains unclear. Using a temporal pattern discrimination task (TPDT) in trained monkeys, we revealed that the second somatosensory cortex (S2) efficiently segregates faithful and transformed neural responses into orthogonal subspaces. Importantly, S2 population encoding for transformed signals, but not for faithful ones, disappeared during a non-demanding version of the task, which suggests that signal transformation and their decoding from downstream areas are only active on-demand. A mechanistic computation model points to gain modulation as a possible biological mechanism for the observed context-dependent computation. Furthermore, individual neural activities that underlie the orthogonal population representations exhibited a continuum of responses, with no well-determined clusters. These findings advocate that the brain, while employing a continuum of heterogeneous neural responses, splits population signals into orthogonal subspaces in a context-dependent fashion to enhance robustness, performance, and improve coding efficiency.

SIGNIFICANCE STATEMENT

An important function of the brain is turning sensation into perception. Yet, how this function is implemented remains unknown. Current research, insights from artificial neural networks, highlights using of orthogonal representations as an effective means to transform sensory signals into perceptual signals while separating and simultaneously processing the two information streams. Neuronal recordings in S2 while trained monkeys performed the TPDT, revealed that this function is implemented at the population level. While S2 encodes sensory information independently of context, the encoding of categorical information, like task parameters, is only performed when the task demands it. Such distinct and flexible organization, enriched by a spectrum of neural activities, reflects the brain’s efficiency, resilience, and overall purpose for solving cognitive tasks.
Local adaptation of a marine diatom is governed by genome-wide changes in diverse metabolic processes
Authors: Pinseel Eveline , Ruck Elizabeth C. , Nakov Teofil , Jonsson Per R. , Kourtchenko Olga , Kremp Anke , Pinder Matthew I.M. , Roberts Wade R. , Sjöqvist Conny , Töpel Mats , Godhe Anna , Hahn Matthew W. , Alverson Andrew J.
Published: September 2023

Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics data with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experiment that has played out over the past 8,000 years in one of the world’s largest brackish water bodies: the colonization of the Baltic Sea by the marine diatomSkeletonema marinoi. To this end, we used a novel approach for protist population genomics, combining target capture of the entire nuclear genome with pooled sequencing, and showed that the method performs well on both cultures and single cells. Genotype-environment association analyses identified >3,000 genes with signals of selection in response to major environmental gradients in the Baltic Sea, which apart from salinity, include marked differences in temperature and nutrient availability. Locally adapted genes were related to diverse metabolic processes, including signal transduction, cell cycle, DNA methylation, and maintenance of homeostasis. The locally adapted genes showed significant overlap with salinity-responsive genes identified in a laboratory common garden experiment, suggesting the Baltic salinity gradient is a major factor driving local adaptation ofS. marinoi. Altogether, our data show that local adaptation of phytoplankton to complex coastal environments, which are characterized by a multitude of environmental gradients, is driven by intricate changes in diverse metabolic pathways and functions.
Ketone supplementation dampens subjective and objective responses to alcohol in rats and humans
Authors: Li Xinyi , Shi Zhenhao , Todaro Dustin , Pond Timothy , Byanyima Juliana , Vesslee Sianneh , Reddy Rishika , Reddy Nanga Ravi Prakash , Kass Gabriel , Ramchandani Vijay , Kranzler Henry R. , Vendruscolo Janaina C.M. , Vendruscolo Leandro F. , Wiers Corinde E.
Published: September 2023

Previous preclinical and human studies have shown that high-fat ketogenic diet and ketone supplements (KS) are efficacious in reducing alcohol craving, alcohol consumption, and signs of alcohol withdrawal. However, the effects of KS on alcohol sensitivity are unknown. In this single-blind, cross-over study, 10 healthy participants (3 females) were administered a single, oral dose of a KS (25 g of ketones from D-β-hydroxybutyric acid and R-1,3-butanediol) or placebo 30 min prior to an oral alcohol dose (0.25 g/kg for women; 0.31 g/kg for men). Assessments of breath alcohol concentration (BrAC) and blood alcohol levels (BAL) and responses on the Drug Effect Questionnaire were repeatedly obtained over 180 min after alcohol consumption. In a parallel preclinical study, 8 Wistar rats (4 females) received an oral gavage of KS (0.42 g ketones/kg), water, or the sweetener allulose (0.58 g/kg) followed 15 min later by an oral alcohol dose (0.8 g/kg). BAL were monitored for 240 min after alcohol exposure. In humans, the intake of KS prior to alcohol significantly blunted BrAC and BAL, reduced ratings of alcohol liking and wanting, and increased disliking for alcohol. In rats, KS reduced BAL more than either allulose or water. In conclusion, KS altered physiological and subjective responses to alcohol in both humans and rats and the effects were likely not mediated by the sweetener allulose present in the KS drink. Therefore, KS could potentially reduce the intoxicating and rewarding effects of alcohol and thus be a novel intervention for treating alcohol use disorder.
The representational geometry of emotional states in basolateral amygdala
Authors: O’Neill Pia-Kelsey , Posani Lorenzo , Meszaros Jozsef , Warren Phebe , Schoonover Carl E. , Fink Andrew J.P. , Fusi Stefano , Salzman C. Daniel
Published: September 2023

Sensory stimuli associated with aversive outcomes cause multiple behavioral responses related to an animal’s evolving emotional state, but neural mechanisms underlying these processes remain unclear. Here aversive stimuli were presented to mice, eliciting two responses reflecting fear and flight to safety: tremble and ingress into a virtual burrow. Inactivation of basolateral amygdala (BLA) eliminated differential responses to aversive and neutral stimuli without eliminating responses themselves, suggesting BLA signals valence, not motor commands. However, two-photon imaging revealed that neurons typically exhibited mixed selectivity for stimulus identity, valence, tremble and/or ingress. Despite heterogeneous selectivity, BLA representational geometry was lower-dimensional when encoding valence, tremble and safety, enabling generalization of emotions across conditions. Further, tremble and valence coding directions were orthogonal, allowing linear readouts to specialize. Thus BLA representational geometry confers two computational properties that identify specialized neural circuits encoding variables describing emotional states: generalization across conditions, and readouts lacking interference from other readouts.
Caveolin-1 Autonomously Regulates Hippocampal Neurogenesis Via Mitochondrial Dynamics
Authors: Stephen Terilyn K. L. , Cofresi Luis Aponte , Quiroz Elvis , Owusu-Ansah Kofi , Ibrahim Yomna , Qualls Ellis , Marshall Jeffery , Li Wenping , Shetti Aashutosh , Bonds Jacqueline A , Minshall Richard D. , Cologna Stephanie M. , Lazarov Orly
Published: September 2023

The mechanisms underlying adult hippocampal neurogenesis (AHN) are not fully understood. AHN plays instrumental roles in learning and memory. Understanding the signals that regulate AHN has implications for brain function and therapy. Here we show that Caveolin-1 (Cav-1), a protein that is highly enriched in endothelial cells and the principal component of caveolae, autonomously regulates AHN. Conditional deletion of Cav-1 in adult neural progenitor cells (nestin +) led to increased neurogenesis and enhanced performance of mice in contextual discrimination. Proteomic analysis revealed that Cav-1 plays a role in mitochondrial pathways in neural progenitor cells. Importantly, Cav-1 was localized to the mitochondria in neural progenitor cells and modulated mitochondrial fission-fusion, a critical process in neurogenesis. These results suggest that Cav-1 is a novel regulator of AHN and underscore the impact of AHN on cognition.
ER mediates spatial regulation of lysosome-endosome interactionsviamotion switch at junction sites
Authors: Li Wenjing , Qiu Mengxuan , Zhang Yudong , Guo Yuanhao , Yang Yutong , Hu Junjie , Yang Ge
Published: September 2023

Membrane-bound intracellular organelles engage in extensive direct interactions through membrane contact or fusion to work together for vital physiological functions. However, how their interactions are regulated is unclear. Lysosomes, for example, interact with ER and endosomes through membrane contact or fusion/fission to receive macromolecular cargos for recycling and degradation. The interactions are thought to be spatially regulated because participating lysosomes and endosomes must be positioned in close proximity. But the mechanism of spatial regulation is unknown. In this study, we examined how individual lysosomes and endosomes move along the endoplasmic reticulum (ER) network and found primarily two modes of movement. In the fast mode they explore different regions. In the slow mode they often pause and become confined near ER junctions to come near each other for interactions. The pause and confinement of lysosomes and endosomes occur in ER regions with elevated network density and connectivity and are mediated by condensation of the actin cytoskeleton, in which the VAP-STARD3-YWHAH pathway plays a key role. Together, these results reveal that ER mediates spatial regulation of lysosome-endosome interactions. Other organelles such as lipid droplets and peroxisomes are also found to pause near ER junctions. Overall, our findings suggest a general ER-mediated mechanism for spatial regulation of organelle interactions.
Perisaccadic and Attentional Remapping of Receptive Fields in Lateral Intraparietal Area and Frontal Eye Fields
Authors: Wang Xiao , Zhang Cong , Yang Lin , Jin Min , Goldberg Michael E. , Zhang Mingsha , Qian Ning
Published: September 2023

The nature and function of perisaccadic receptive-field (RF) remapping have been controversial. We used a delayed saccade task to reduce previous confounds and examined the remapping time course in areas LIP and FEF. In the delay period, the RF shift direction turned from the initial fixation to the saccade target. In the perisaccadic period, RFs first shifted toward the target (convergent remapping) but around the time of saccade onset/offset, the shifts became predominantly toward the post-saccadic RF locations (forward remapping). Thus, unlike forward remapping that depends on the corollary discharge (CD) of the saccade command, convergent remapping appeared to follow attention from the initial fixation to the target. We modelled the data with attention-modulated and CD-gated connections, and showed that both sets of connections emerged automatically in neural networks trained to update stimulus retinal locations across saccades. Our work thus unifies previous findings into a mechanism for transsaccadic visual stability.
A potential acoustic role for CFTR ion channel in conductive hearing loss
Authors: Liyanage Pramodha , Mun Kyu-Shik , Carraro Gianni , Ogden Herbert Luke , Huang Yunjie , Lee Jesun , Ramananda Yashaswini , Stripp Barry R , Arora Kavisha , Salomonis Nathan , Hunter Lisa L. , Naren Anjaparavanda P.
Published: September 2023

Loss-of-function mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF). The middle ear and eustachian tube could be adversely affected in CF. In this study, we provide evidence of the role of CFTR function in conductive hearing. We developed an in-situ model to determine CFTR dependent fluid secretion in the middle ear using native mouse auditory capsule. A unique middle ear-on-a-chip was developed to address the functional and molecular basis of conductive hearing impairment. Using single-cell transcriptomics, middle ear cell composition and the associated transcriptomic signature were compared between CF and WT groups. A specialized subset of epithelial cells expressed CFTR with an overlapping signature with secretory epithelial cells. Genes related to ciliogenesis, hearing and ossification were significantly altered in CF mice middle ear. Our data suggest that CF middle ear may be at higher risk for conductive hearing loss.
Cross-reactive macaque antibodies targeting marburgvirus glycoprotein induced by multivalent immunization
Authors: Janus Benjamin M. , Wang Ruixue , Cleveland Thomas E. , Metcalf Matthew C. , Lemmer Aaron C. , Class Kenneth , Fuerst Thomas R. , Ofek Gilad
Published: September 2023

We utilized B cells from a Rhesus macaque immunized with a multivalent prime-boost regimen of filovirus antigens to isolate a novel panel of marburgvirus glycoprotein (GP)-specific monoclonal antibodies (mAbs). A heterologous marburgvirus GP probe was used to sort for B cells with cross-marburgvirus reactive breadth. 33 mAbs belonging to 28 unique lineages were expressed and experimentally characterized. Antibody specificities were assessed by binding competition and overlapping pepscan analyses, and were found to map to a previously characterized protective region on GP2 and a cross-filovirus reactive region on GP1, among others. A third of the lineages targeted the predicted receptor binding region (RBR), including two lineages with potent Marburg pseudovirus neutralization that were structurally analyzed and confirmed to recognize this region. Our study describes the discovery and characterization of a diverse panel of antibodies against marburgvirus GP induced by multivalent immunization and provides candidate immunotherapeutics for further study and development.

Author Summary

Marburgviruses were the first filoviruses characterized to emerge in humans in 1967, and have led to multiple outbreaks since then with average case fatality rates of ∼50%. Although a vaccine and monoclonal antibody countermeasures have been approved for clinical use against the related Ebola viruses, these are ineffective against marburgviruses or other filoviruses. As such, gaps exist in the clinical toolkit against filoviruses, in particular marburgviruses. Here, we isolated and characterized a novel panel of monoclonal antibodies directed against the marburgvirus surface glycoprotein from an immunized Rhesus macaque. We utilized an antibody isolation method that ensured broad antibody recognition across multiple marburgvirus isolates. Functional and structural analyses revealed that roughly half of the antibodies in the panel mapped to regions on the glycoprotein shown previously to protect from infection, including the receptor binding domain and a protective region on the membrane-anchoring subunit, while a quarter of the antibodies did not fall into any known binding competition group indicating potential novel specificities. Our study advances the understanding of marburgvirus glycoprotein antigenicity and furthers efforts to develop candidate antibody countermeasures against these lethal viruses.
Signature-Informed Selection Detection: A Novel Method for Multi-Locus Wright-Fisher Models with Recombination
Authors: Xu Yuehao , Khoo Sherman , Futschik Andreas , Dutta Ritabrata
Published: September 2023

Abstract

In this manuscript, we present an innovative Bayesian framework tailored for the inference of the selection coefficients in multi-locus Wright-Fisher models. Utilizing a signature kernel score, our approach offers an innovative solution for approximating likelihoods by extracting informative signatures from the trajectories of haplotype frequencies. Moreover, within the framework of a generalized Bayesian posterior, we derive the scoring rule posterior, which we then pair with a Population Monte Carlo (PMC) algorithm to obtain posterior samples for selection coefficients. This powerful combination enables us to infer selection dynamics efficiently even in complex high-dimensional and temporal data settings. We show that our method works well through extensive tests on both simulated and real-world data. Notably, our approach effectively detects selection not just in univariate, but also in multivariate Wright-Fisher models, including 2-locus and 3-locus models with recombination. Our proposed novel technique contributes to a better understanding of complex evolutionary dynamics.
Whole mount multiplexed visualization of DNA, mRNA, and protein in plant-parasitic nematodes
Authors: Sperling Alexis L. , Eves-van den Akker Sebastian
Published: September 2023

Background

Plant-parasitic nematodes compromise the agriculture of a wide variety of the most common crops worldwide. Obtaining information on the fundamental biology of these organisms and how they infect the plant has been restricted by the ability to visualize intact nematodes using small molecule stains, antibodies, orin situhybridization. Consequently, there is limited information available about the internal composition of the nematodes or the biology of the effector molecules they use to reprogram their host plant.

Results

We present the Sperling prep -a whole mount method for nematode preparation that enables staining with small molecules, antibodies, orin situhybridization chain reaction. This method does not require specialized apparatus and utilizes typical laboratory equipment and materials. By dissociating the strong cuticle and interior muscle layers, we enabled entry of the small molecule stains into the tissue. After permeabilization, small molecule stains can be used to visualize the nuclei with the DNA stain DAPI and the internal structures of the digestive tract and longitudinal musculature with the filamentous actin stain phalloidin. The permeabilization even allows entry of larger antibodies, albeit with lower efficiency. Finally, this method works exceptionally well within situHCR. Using this method, we have visualized effector transcripts specific to the dorsal gland and the subventral grand of the sugar beet cyst nematode,Heterodera schachtii, multiplexed in the same nematode.

Conclusion

We were able to visualize the internal structures of the nematode as well as key effector transcripts that are used during plant infection and parasitism. Therefore, this method provides an important toolkit for studying the biology of plant-parasitic nematodes.
Activity-dependent development of the body’s touch receptors
Authors: Santiago Celine , Sharma Nikhil , Africawala Nusrat , Siegrist Julianna , Handler Annie , Tasnim Aniqa , Anjum Rabia , Turecek Josef , Lehnert Brendan P. , Renauld Sophia , Nolan-Tamariz Michael , Iskols Michael , Magee Alexandra R. , Paradis Suzanne , Ginty David D.
Published: September 2023

We report a role for activity in the development of the primary sensory neurons that detect touch. Genetic deletion of Piezo2, the principal mechanosensitive ion channel in somatosensory neurons, caused profound changes in the formation of mechanosensory end organ structures and altered somatosensory neuron central targeting. Single cell RNA sequencing ofPiezo2conditional mutants revealed changes in gene expression in the sensory neurons activated by light mechanical forces, whereas other neuronal classes were less affected. To further test the role of activity in mechanosensory end organ development, we genetically deleted the voltage-gated sodium channel Nav1.6 (Scn8a) in somatosensory neurons throughout development and found thatScn8amutants also have disrupted somatosensory neuron morphologies and altered electrophysiological responses to mechanical stimuli. Together, these findings indicate that mechanically evoked neuronal activity acts early in life to shape the maturation of the mechanosensory end organs that underlie our sense of gentle touch.
Differential effects of aneuploidy on growth and differentiation in human intestinal stem cells
Authors: Johnson Blake A. , Liu Albert Z. , Bi Tianhao , Dong Yi , Li Taibo , Zhou Dingjingyu , Narkar Akshay , Wu Yufei , Sun Sean X. , Larman Tatianna C. , Zhu Jin , Li Rong
Published: September 2023

Aneuploidy, a near ubiquitous genetic feature of tumors, is a context-dependent driver of cancer evolution; however, the mechanistic basis of this role remains unclear. Here, by inducing heterogeneous aneuploidy in non-transformed human colon organoids (colonoids), we investigate how the effects of aneuploidy on cell growth and differentiation may promote malignant transformation. Single-cell RNA sequencing reveals that the gene expression signature across over 100 unique aneuploid karyotypes is enriched with p53 responsive genes. The primary driver of p53 activation is karyotype complexity. Complex aneuploid cells with multiple unbalanced chromosomes activate p53 and undergo G1 cell-cycle arrest, independent of DNA damage and without evidence of senescence. By contrast, simple aneuploid cells with 1-3 chromosomes gained or lost continue to proliferate, demonstrated by single cell tracking in colonoids. Notably, simple aneuploid cells exhibit impaired differentiation when niche factors are withdrawn. These findings suggest that while complex aneuploid cells are eliminated from the normal epithelium due to p53 activation, simple aneuploid cells can escape this checkpoint and may contribute to niche factor-independent growth of cancer-initiating cells.
Engineering antigen-specific tolerance to an artificial protein hydrogel
Authors: Rapp Peter B. , Baccile Joshua A. , Galimidi Rachel P. , Vielmetter Jost
Published: September 2023

Artificial protein hydrogels are an emerging class of biomaterials with numerous prospective applications in tissue engineering and regenerative medicine. These materials are likely to be immunogenic due their frequent incorporation of novel amino acid sequence domains, which often serve a functional role within the material itself. We engineered injectable “self” and “non-self” artificial protein hydrogels which were predicted to have divergent immune outcomesin vivoon the basis of their primary amino acid sequence. Following implantation in mouse, the non-self gels raised significantly higher anti-gel antibody titers than the corresponding self gels. Prophylactic administration of a fusion antibody targeting the non-self hydrogel epitopes to DEC-205, an endocytic receptor involved in Treginduction, fully suppressed the elevated antibody titer against the non-self gels. These results suggest that the clinical immune response to artificial protein biomaterials, including those that contain highly antigenic sequence domains, can be tuned through the induction of antigen-specific tolerance.
High-resolution dissection of human cell type-specific enhancers incisandtransactivities
Authors: Wang Meng , Yang Xiaoxu , Wu Qixi
Published: September 2023

The spatiotemporal specific gene expression is regulated by cell type-specific regulatory elements including enhancers, silencers and insulators etc. The massively parallel reporter assay (MPRA) methods like STARR-seq facilitate the systematic study of DNA sequence intrinsic enhancer activities in a large scale. However, when applied to human cells, it remains challenging to identify and quantify cell type-specific active enhancers in the genome-wide scale with high-resolution, due to the large size of human genome. In this study, we selected the H3K4me1 associated dinucleosome with the linker DNA sequences as candidate enhancer sequences in two different human cell lines and performed ChIP-STARR-seq to quantify the cell type-specific enhancer activities with high-resolution in a genome-wide scale. Furthermore, we investigated how the activity landscape of enhancer repository would change when transferred from native cells (cisactivity) to another cell lines (transactivity). Using ChIP-STARR-seq of the candidate enhancers in native cells and another type of cells, we obtained enhancerscisactivity maps andtransactivity maps in two different cell lines. Thecisandtransactivity maps enabled us to identify cell type-specific active enhancers, with enrichment of motifs of differentially expressed TFs. Comparisons between thecisandtransactivity maps revealed general consistent regulatory property with different levels of activity in the two cell types, suggesting the sequence intrinsic regulatory properties keep similar in different type of cells. This study provides a new perspective of sequence intrinsic enhancer activities in different types of cells.
Interactions with a phage gene underlie costs of a β-lactamase
Authors: Lai Huei-Yi , Cooper Tim F.
Published: September 2023

The fitness cost of an antibiotic resistance gene (ARG) can differ across host strains creating refuges that allow maintenance of an ARG in the absence of direct selection for its resistance phenotype. Despite the importance of such ARG-host interactions for predicting ARG dynamics, the basis of ARG fitness costs and their variability between hosts are not well understood. We determined the genetic basis of a host-dependent cost of a β-lactamase,blaTEM-116*, that conferred a significant cost in oneEscherichia colistrain but was close to neutral in 11 otherEscherichia spp.strains. Selection of ablaTEM-116*encoding plasmid in the strain in which it initially had a high cost resulted in rapid and parallel compensation to that cost through mutations in a P1 phage gene,relAP1. When the wildtyperelAP1gene was added to a strain in which it was not present and in whichblaTEM-116*was neutral, it caused the ARG to become costly. Thus,relAP1is both necessary and sufficient to explainblaTEM-116*costs in at least some host backgrounds. To our knowledge, these findings represent the first demonstrated case of the cost of an ARG being influenced by a genetic interaction with a phage gene. The interaction between a phage gene and a plasmid-borne ARG highlights the complexity of selective forces determining the maintenance and spread of ARGs, and, by extension, encoding phage and plasmids, in natural bacterial communities.
Hand2 represses non-cardiac cell fates through chromatin remodeling atcis-regulatory elements
Authors: Komatsu Valerie , Cooper Brendon , Yim Paul , Chan Kira , Gong Wesley , Wheatley Lucy , Rohs Remo , Fraser Scott E. , Trinh Le A.
Published: September 2023

Developmental studies have revealed the importance of the transcription factor Hand2 in cardiac development. Hand2 promotes cardiac progenitor differentiation and epithelial maturation, while repressing other tissue types. The mechanisms underlying the promotion of cardiac fates are far better understood than those underlying the repression of alternative fates. Here, we assess Hand2-dependent changes in gene expression and chromatin remodeling in cardiac progenitors of zebrafish embryos. Cell-type specific transcriptome analysis shows a dual function for Hand2 in activation of cardiac differentiation genes and repression of pronephric pathways. We identify functionalcis-regulatory elements whose chromatin accessibility are increased inhand2mutant cells. These regulatory elements associate with non-cardiac gene expression, and drive reporter gene expression in tissues associated with Hand2-repressed genes. We find that functional Hand2 is sufficient to reduce non-cardiac reporter expression in cardiac lineages. Taken together, our data support a model of Hand2-dependent coordination of transcriptional programs, not only through transcriptional activation of cardiac and epithelial maturation genes, but also through repressive chromatin remodeling at the DNA regulatory elements of non-cardiac genes.
Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised Blood-Brain Barrier integrity
Authors: Bassi Ivan , Grunspan Moshe , Hen Gideon , Ravichandran Kishore A. , Moshe Noga , Safriel Stav R. , Chen Amitai , Ruiz de Almodovar Carmen , Yaniv Karina
Published: September 2023

The neurovascular unit (NVU) is a complex structure comprising neurons, glia, and pericytes that interact with specialized endothelial cells to maintain cerebral homeostasis and blood-brain barrier (BBB) integrity. Alterations to NVU formation and function can lead to serious forms of cerebrovascular disease, including cerebral small vessel diseases (CSVDs), a range of pathological changes of cerebral capillaries within the white matter contributing to BBB dysfunction and demyelination.

Despite the growing recognition of the pivotal roles played by neuro-vascular and glia-vascular interfaces in NVU formation and functioning, CSVD research has mainly focused on characterizing pericyte and EC dysfunction, leaving our understanding of the contribution of non-vascular cells of the brain parenchyma limited.

Here, we use a novel zebrafish mutant to delve into the intricate interplay among NVU components and demonstrate how the compromised specification of a progenitor cell population sets off a cascade of events, ultimately leading to severe cerebrovascular abnormalities. The mutation affects Scavenger Receptor B2 (scarb2)/Lysosomal Membrane Protein 2 (limp2), a highly conserved protein residing in the membrane of late endosomes and lysosomes. We find Scarb2 to be predominantly expressed in Radial Glia Cells (RGCs), a multipotent cell giving rise to neurons and glia in both zebrafish and mammals. Through live imaging and genetic manipulations, we identify impaired Notch3 signaling in RGCs and their glial progeny as the primary consequence of Scarb2a depletion and show that this disruption causes excessive neurogenesis at the expense of glial cell differentiation. We further pinpoint compromised acidification of the endolysosomal compartment in mutant cells as the underlying cause of disrupted Notch3 processing, linking for the first time Notch3 defects in non-vascular cells of the brain parenchyma to CSVD phenotypes.

Given the evolutionary conservation of SCARB2 expression and the remarkable recapitulation of CSVD phenotypes,scarb2mutants provide a promising framework for investigating the mechanisms governing Notch3 processing in non-vascular cells and their involvement in the onset of CSVD.
Development and implementation barriers of a new patient‐reported measure: The Radiation therapy‐related Inconvenience Questionnaire (RIQ)
Authors: Shunmugasundaram Chindhu , Sundaresan Puma , White Kate , King Madeleine T , Milross Chris , Rodd Lucinda , Fuller Matthew , Rutherford Claudia
Published: September 2023

Introduction

Radiation therapy (RT) can benefit approximately 50% of cancer patients and contribute to 40% of all cancer cures, yet its utilisation in cancer is low globally. Several factors contribute to this including perceived inconvenience related to accessing and utilising RT. To quantitatively assess the latter, a new tool – the Radiation therapy‐related Inconvenience Questionnaire (RIQ) – was developed. This study aimed to pre‐test the RIQ and explore barriers and facilitators to implementing it in routine clinical practice and clinical trials.

Methods

Semi‐structured cognitive interviews were conducted with patients undertaking RT, recruited via three hospitals to examine content validity, acceptability, and comprehensibility of the RIQ. Interviews identified inconsistencies, relevance, and clarity of items. Semi‐structured interviews with healthcare professionals involved in the delivery of care to individuals undertaking RT explored barriers and facilitators to routine usage. Thematic analysis was used to identify themes.

Results

Patients (N = 15) identified problems in content, instructions, layout, length, and response options; consequently, 25 items were revised and eight removed, resulting in a final 29‐item questionnaire. Clinicians identified staff‐ and patient‐specific barriers to implementing RIQ in clinical practice. Perceived facilitators included the following: (a) workplace factors, (b) mode of administration, and (c) imparting knowledge.

Conclusion

This study demonstrated acceptability and comprehensibility of the 29‐item RIQ amongst cancer patients undertaking RT and treating clinicians. The next phase will evaluate the RIQ's measurement properties in a larger clinical study. The barriers and facilitators identified can guide future implementation of RIQ in clinical practice and clinical trials.
Interventional management of malignant bone tumours
Authors: Cazzato Roberto Luigi , Garnon Julien , Jennings Jack William , Gangi Afshin
Published: September 2023

In the last few decades, interventional radiology (IR) has significantly increased its role in the management of bone tumours including bone metastases (BM) that represent the most common type of tumour involving the bone. The current IR management of BM is based on the ‘palliative‐curative’ paradigm and relies on the use of consolidative (i.e. osteplasty, osteosynthesis) and/or ablation (i.e. cryoablation, radiofrequency ablation, electrochemotherapy) techniques. The present narrative review will overview the current role of IR for the management of BM.
The percutaneous management of pulmonary metastases
Authors: de Baere Thierry , Bonnet Baptiste , Tselikas Lambros , Deschamps Frederic
Published: September 2023

Local treatment of lung metastases has been in the front scene since late 90s when an international registry of thoracic surgery reported a median overall survival of 35 months in resected patients versus 15 months in non‐resected patients. Today, other local therapies are available for patients with oligometastatic lung disease, including image guided thermal ablation, such as ablation, microwave ablation, and cryoablation. Image‐guided ablation is increasingly offered, and now recommended in guidelines as option to surgery. Today, the size of the target tumour remains the main driver of success and selection of patients with limited tumour size allowing for local tumour control in the range of 90% in most recent and larger series targeting lung metastases up to 3.5 cm. Overall survival exceeding five‐years in large series of thermal ablation for lung metastases from colorectal origin are align with outcome of same patients treated with surgical resection. Moreover, thermal ablation in such population allows for one‐year chemotherapy holidays in all comers and over 18 months in lung only metastatic patients, allowing for improved patient quality of life and preserving further lines of systemic treatment when needed. Tolerance of thermal ablation is excellent and better than surgery with no lost in respiratory function, allowing for repeated treatment when needed. In the future, it is likely that practice of lung surgery for small oligometastatic lung disease will decrease, and that minimally invasive techniques will replace surgery in such indications. Randomized study will be difficult to obtain as demonstrated by discontinuation of many studies testing the hypothesis of surgery versus observation, or surgery versus SBRT.
Private health care, cancer, and the vulnerable middle class in Kenya
Authors: Prince Ruth J.
Published: September 2023

A novel terrain of health care is emerging in Kenya at the intersection of a cancer epidemic, expanding medical and health insurance markets, the continued evisceration of public health care, and a middle class that can raise funds from credit, loans, and social networks. As middle‐class cancer patients and their families navigate these landscapes, they find themselves vulnerable both to the “ordinary crisis” of public health care undermined by austerity and neglect, and to an extractive medical marketplace offering state‐of‐the‐art treatment that is just within, or just beyond, financial reach. To analyze this, I build on Lauren Berlant's concept of cruel optimism, which captures how precarity is not only grounded in economic realities but also tied to hopes and expectations that always remain unfulfilled, creating constant anxiety and exhaustion. Further, I examine the double binds of cancer treatment and the entanglements between medical, health, and economic precarities, as families are drawn into private health care while the state disinvests in public services.