bluuebunny/crossref_metadata_2025 huggingface dataset:
Drug interaction mapping with proximity dependent enzyme recruiting chimeras
Authors: Venable John D , Vashisht Ajay A , Rayatpisheh Shima , Lajiness James P , Phillips Dean P , Brock Ansgar
Published: September 2022

Proximity dependent labeling using engineered enzymes has been used extensively to identify protein-protein interactions, and map protein complexesin-vitroandin-vivo. Here, we extend the use of engineered promiscuous biotin ligases to the identification of small molecule protein targets. Chimeric bi-functional chemical probes (“recruiters”) are used to effectively recruit tagged biotin ligases for proximity dependent labeling of target and target interactors. The broad applicability of this approach is demonstrated with probes developed from a multi-kinase inhibitor, a bromodomain targeting moiety, and an FKBP targeting molecule. While complementary to traditional chemo-proteomic strategies such as photo-affinity labeling (PAL), and activity-based protein profiling (ABPP), this approach is a useful addition to the target ID toolbox with opportunities for tunability based on the inherent labeling efficiencies of different engineered enzymes and control over the enzyme cellular localization.
HB-EGF Promotes Horizontal Basal Cell Proliferation and Olfactory Sensory Neuron Regeneration in the Zebrafish Olfactory Epithelium
Authors: Sireci Siran , Kocagöz Yigit , Alkiraz Aysu Sevval , Güler Kardelen , Dokuzluoglu Zeynep , Balcioglu Ecem , Demirler Mehmet Can , Fuss Stefan Herbert
Published: September 2022

Maintenance and regeneration of the zebrafish olfactory epithelium (OE) are supported by distinct progenitor cell populations that occupy discrete stem cell niches and respond to different tissue conditions. Globose basal cells (GBCs) reside at the inner and peripheral margins of the sensory OE and are constitutively active to replace sporadically dying olfactory sensory neurons (OSNs). In contrast, horizontal basal cells (HBCs) are more uniformly distributed across the tissue, including basal layers of the sensory region, and are selectively activated by acute injury conditions that affect the morphological integrity of the OE. Here we show that expression of the heparin-binding epidermal growth factor-like growth factor (HB-EGF) is strongly and transiently upregulated in response to OE injury and signals through the EGF receptor (EGFR), which is expressed by HBCs. Exogenous stimulation of the OE with recombinant HB-EGF promotes HBC expansion and OSN neurogenesis within the sensory OE, resembling the tissue response to injury. In contrast, pharmacological inhibition of HB-EGF shedding, HB-EGF availability, and EGFR signaling strongly attenuate or delay injury-induced HBC activity and OSN restoration without affecting maintenance neurogenesis by GBCs. Thus, HB-EGF/EGFR signaling appears to be a critical component of a complex signaling network that controls HBC activity and, consequently, repair neurogenesis in the zebrafish OE.
Influenza A virus reassortment is strain dependent
Authors: Taylor Kishana Y. , Agu Ilechukwu , José Ivy , Mäntynen Sari , Campbell A.J. , Mattson Courtney , Chou Tsui-wen , Zhou Bin , Gresham David , Ghedin Elodie , Díaz Muñoz Samuel L.
Published: September 2022

RNA viruses can exchange genetic material during coinfection, an interaction that creates novel strains with implications for viral evolution and public health. Influenza A viral genetic exchange occurs when genome segments from distinct strains reassort in coinfection. Predicting potential reassortment between influenza strains is a longstanding goal. Experimental coinfection studies have shed light on factors that limit or promote reassortment. However, determining the reassortment potential between diverse Influenza A strains has remained an elusive goal. To fill this gap, we developed a high throughput genotyping approach to quantify reassortment among a diverse panel of human influenza virus strains, encompassing 41 years of epidemics, multiple geographic locations, and both circulating human subtypes A/H1N1 and A/H3N2. We found that the reassortment rate (proportion of reassortants) is an emergent property of a pair of strains where strain identity is a predictor of the reassortment rate. We show little evidence that antigenic subtype drives reassortment as intersubtype (H1N1xH3N2) and intrasubtype reassortment rates were, on average, similar. Instead, our data suggest that certain strains bias the reassortment rate up or down, independently of the coinfecting partner. We also observe that viral productivity is an emergent property of coinfections and that it is not correlated to reassortment rate, thus affecting the total number of reassortant progeny produced. Assortment of individual segments among progeny, and pairwise segment combinations within progeny, were not random and generally favored homologous combinations. This outcome was not related to strain similarity or shared subtype. Reassortment rate was closely correlated to both the proportion of unique genotypes and the proportion of progeny with heterologous pairwise segment combinations. We provide experimental evidence that viral genetic exchange is potentially an individual social trait subject to natural selection, which implies the propensity for reassortment is not evenly shared among strains. This study highlights the need for research incorporating diverse strains to discover the traits that shift the reassortment potential as we work towards the goal of predicting influenza virus evolution resulting from segment exchange.
The assembly of wild natural isolates define neuronal integrity and life history traits of co-inhabiting C. elegans
Authors: Urquiza-Zurich Sebastian , Garcia-Angulo Victor Antonio , Burdisso Paula , Palominos M. Fernanda , Fernandez-Hubeid Lucia , Castillo Juan Pablo , Calixto Andrea
Published: September 2022

Bacterivore nematodes are the most abundant animals in the biosphere, largely contributing to global biogeochemistry. The effect of environmental microbes as source of associated microbiota and natural diet on their life history traits of nematodes is likely to impact the general health of the biosphere. Caenorhabditis elegans is a unique model to study the behavioral and physiological outputs of different available microbial diets. Nonetheless, most studies are on monoaxenic cultures of laboratory bacteria while the effect of natural microbiota isolates has only recently started to be reported. Here, we quantified physiological, phenotypical and behavioral traits of worms feeding on two bacteria that co-isolated with wild nematodes and tested how combinations of these isolates with other bacteria affected the traits measured. These bacteria were identified as a putative novel species of Stenotrophomonas denominated Stenotrophomonas sp. Iso1 and a strain of Bacillus pumilus designated Iso2. The isolates induced distinctive behaviors and development patterns that changed in mixes of the two bacteria and/or the pathogen Salmonella enterica. Focusing on the degeneration rate of the touch circuit of C. elegans we show that B. pumilus alone is protective while the mix with Stenotrophomonas sp. is degenerative. The analysis of the metabolite content of each isolate and their combination identified NAD+ as potentially neuroprotective. In vivo supplementation shows that NAD+ restores neuroprotection to the mixes and also to individual non-protective bacteria. The results highlight the need to study the physiological effects of bacteria resembling native diets in a multicomponent scenario rather than using single isolates.

Importance

The behavioral decisions of animals depend on their microbiota. In nature it is unknown how this interaction affects the health of the biosphere. To study how the nematode-bacteria relationship impacts the life history traits of these animals, we isolated bacteria found in association with wild nematodes and tested their influence as single species and consortia, in the life history traits of the model C. elegans. We identify metabolites from wild bacteria that change these traits. The bacteria isolated were identified a Stenotrophomonas sp and a B. pumilus. We find that all traits depend on the biota composition. For example, B. pumilus is neuroprotective to degenerating neurons of the touch circuit of C. elegans needed to sense and escape from predators in the wild. The co-culture with Stenotrophomonas sp. eliminates the protection. We identified NAD+ as the metabolite lost in the mix, and show that NAD+ by itself is neuroprotective.
Label-based meta-analysis of functional brain dysconnectivity across mood and psychotic disorders
Authors: Grot Stéphanie , Smine Salima , Potvin Stéphane , Darcey Maëliss , Pavlov Vilena , Genon Sarah , Nguyen Hien , Orban Pierre
Published: September 2022

BACKGROUND

Psychiatric diseases are increasingly conceptualized as brain network disorders. Hundreds of resting-state functional magnetic resonance imaging (rsfMRI) studies have revealed patterns of functional brain dysconnectivity in disorders such as major depression disorder (MDD), bipolar disorder (BD) and schizophrenia (SZ). Although these disorders have been mostly studied in isolation, there is mounting evidence of shared neurobiological alterations across disorders.

METHODS

To uncover the nature of the relatedness between these psychiatric disorders, we conducted an innovative meta-analysis of past functional brain dysconnectivity findings obtained separately in MDD, BD and SZ. Rather than relying on a classical coordinate-based approach at the voxel level, our procedure extracted relevant neuroanatomical labels from text data and reported findings at the whole brain network level. Data were drawn from 428 rsfMRI studies investigating MDD (158 studies, 7429 patients / 7414 controls), BD (81 studies, 3330 patients / 4096 patients) and/or SZ (223 studies, 11168 patients / 11754 controls). Permutation testing revealed commonalities and specificities in hypoconnectivity and hyperconnectivity patterns across disorders.

RESULTS

Among 78 connections within or between 12 cortico-subcortical networks, hypoconnectivity and hyperconnectivity patterns of higher-order cognitive (default-mode, fronto-parietal, cingulo-opercular) networks were similarly observed across the 3 disorders. By contrast, dysconnectivity of lower-order (somatomotor, visual, auditory) networks in some cases differed between disorders, notably dissociating SZ from BD and MDD.

CONCLUSIONS

Our label-based meta-analytic approach allowed a comprehensive inclusion of prior studies. Findings suggest that functional brain dysconnectivity of higher-order cognitive networks is largely transdiagnostic in nature while that of lower-order networks may best discriminate mood and psychotic disorders, thus emphasizing the relevance of motor and sensory networks to psychiatric neuroscience.
Regulating the timing of enhancer transitions is key to defining sharp boundaries of Fushi tarazu expression in the Drosophila embryo
Authors: Birnie Anthony , Plat Audrey , Bothma Jacques P.
Published: September 2022

Coordinating the action of different enhancers is crucial to correctly specify cell fate decisions during development. Yet it remains poorly understood how the activity of multiple enhancers is choregraphed in time. To shed light on this question we used new live imaging approaches to quantify transcription and protein expression in single cells of Drosophila melanogaster embryos. We employed these tools to dissect the regulation of Fushi tarazu (Ftz), a transcription factor expressed in a series of stripes by two distinct enhancers: autoregulatory and zebra. The anterior edges of the Ftz stripes are sharply defined and specify essential signaling centers. Here, we determined the time at which each boundary cell commits to either a high-Ftz or low-Ftz fate using dynamic features of time-resolved Ftz protein traces. By following the activity of each enhancer individually, we showed that the autoregulatory enhancer does not establish this fate choice. Instead, it perpetuates the decision defined by zebra. This is contrary to the prevailing view that autoregulation drives the fate decision by causing bi-stable Ftz expression. Furthermore, we showed that the autoregulatory enhancer is not activated based on a Ftz concentration threshold, but through a timing-based mechanism. We hypothesize that this is regulated by a set of pioneer-like transcription factors, which have recently been shown to act as timers in the embryo. Our work provides new insight into the genetic mechanisms that directly regulate the dynamics of gene regulatory networks, and supports the emerging view that this regulation is vital for reliable cell fate specification.
Real-Time Spatial Registration for 3D Human Atlas
Authors: Chen Lu , Teng Dejun , Zhu Tian , Kong Jun , Herr Bruce W. , Bueckle Andreas , Borner Katy , Wang Fusheng
Published: September 2022

Abstract

The human body is made up of about 37 trillion cells (adults). Each cell has its own unique role and is affected by its neighboring cells and environment. The NIH Human BioMolecular Atlas Program (HuBMAP) aims at developing a 3D atlas of human body consisting of organs, vessels, tissues to singe cells with all 3D spatially registered in a single 3D human atlas using tissues obtained from normal individuals across a wide range of ages. A critical step of building the atlas is to register 3D tissue blocks in real-time to the right location of a human organ, which itself consists of complex 3D substructures. The complexity of the 3D organ model, e.g., 35 meshes for a typical kidney, poses a significant computational challenge for the registration. In this paper, we propose a comprehensive framework TICKET (TIssue bloCK rEgisTration) for tissue block registration for 3D human atlas, including (1) 3D mesh pre-processing, (2) spatial queries on intersection relationship and (3) intersection volume computation between organs and tissue blocks. To minimize search space and computation cost, we develop multi-level indexing on both the anatomical structure level and mesh level, and utilize OpenMP for parallel computing. Considering cuboid based shape of the tissue block, we propose an efficient voxelization-based method to estimate the intersection volume. Our experiments demonstrate that the proposed framework is practical and efficient. TICKET is now integrated into the HuBMAP CCF registration portal [1].
Characterization of membrane vesicles inAlteromonas macleodiiindicates potential roles in their copiotrophic lifestyle
Authors: Fadeev Eduard , Bastos Cécile Carpaneto , Hennenfeind Jennifer , Biller Steven J , Sher Daniel , Wietz Matthias , Herndl Gerhard J
Published: September 2022

Bacterial membrane vesicles (MVs) are likely abundant in the oceans. Based on observations from non-marine bacteria, MVs are involved in a range of physiological processes and play important roles in interactions between microbial cells. In this study we characterized MV production of six different strains ofAlteromonas macleodii, a cosmopolitan marine bacterium.A. macleodiistrains produced MVs at rates of up to 30 MVs cell-1generation-1. The produced MVs had high morphological diversity that could potentially define their functional roles. Proteomic characterization revealed that MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs were harboring hydrolytic enzymes. Taken together, our results suggest that in the largely oligotrophic oceans,A. macleodiiMVs may support its growth through generation of extracellular “hotspots” that facilitate access to essential substrates. This study provides an important basis for further investigation of the ecological relevance of MVs in heterotrophic marine bacteria.
Sharing GWAS summary statistics results in more citations: evidence from the GWAS catalog
Authors: Reales Guillermo , Wallace Chris
Published: September 2022

Genome-wide association studies (GWAS) have been a crucial tool in genomics and an example of applied reproducible science principles for almost two decades.1 Their output, summary statistics, are especially suited for sharing, which in turn enables new hypothesis testing and scientific discovery. However, GWAS summary statistics sharing rates have been historically low due to a lack of incentives and strong data sharing mandates, privacy concerns and standard guidelines.2 Albeit imperfect, citations are a key metric to evaluate the research impact. We hypothesised that data sharing might benefit authors through increased citation rates and investigated this using GWAS catalog3 data. We found that sharers get on average ~75% more citations, independently of journal of publication and impact factor, and that this effect is sustained over time. This work provides further incentivises authors to share their GWAS summary statistics in standard repositories, such as the GWAS catalog.
High-resolution analysis of individualDrosophila melanogasterlarvae within groups uncovers inter- and intra-individual variability in locomotion and its neurogenetic modulation
Authors: Thane Michael , Paisios Emmanouil , Stöter Torsten , Krüger Anna-Rosa , Gläß Sebastian , Dahse Anne-Kristin , Scholz Nicole , Gerber Bertram , Lehmann Dirk J. , Schleyer Michael
Published: September 2022

Neuronally orchestrated muscular movement and locomotion are defining faculties of multicellular animals. Due to its numerically simple brain and neuromuscular system and its genetic accessibility, the larva of the fruit flyDrosophila melanogasteris an established model to study these processes at tractable levels of complexity. However, although the faculty of locomotion clearly pertains to the individual animal, present studies of locomotion in larvalDrosophilamostly use group assays and measurements aggregated across individual animals. The alternative is to measure animals one at a time, an extravagance for larger-scale analyses. In principle or in practice, this in particular rules out grasping the inter- and intra-individual variability in locomotion and its genetic and neuronal determinants. Here we present the IMBA (Individual Maggot Behaviour Analyser) for tracking and analysing the behaviour of individual larvae within groups. Using a combination of computational modelling and statistical approaches, the IMBA reliably resolves individual identity across collisions. It does not require specific hardware and can therefore be used in non-expert labs. We take advantage of the IMBA first to systematically describe the inter- and intra-individual variability in free, unconstrained locomotion in wild-type animals. We then report the discovery of a novel, complex locomotion phenotype of a mutant lacking an adhesion-type GPCR. The IMBA further allows us to determine, at the level of individual animals, the modulation of locomotion across repeated activations of dopamine neurons. Strikingly, IMBA can also be used to analyse ‘silly walks’, that is patterns of locomotion it was not originally designed to investigate. This is shown for the transient backward locomotion induced by brief optogenetic activation of the brain-descending ‘mooncrawler’ neurons, and the variability in this behaviour. Thus, the IMBA is an easy-to-use toolbox allowing an unprecedentedly rich view of the behaviour and behavioural variability of individualDrosophilalarvae, with utility in multiple biomedical research contexts.
The structure of monkeypox virus 2’-O-ribose methyltransferase VP39 in complex with sinefungin provides the foundation for inhibitor design
Authors: Silhan Jan , Klima Martin , Chalupska Dominika , Kozic Jan , Boura Evzen
Published: September 2022

Monkeypox is an emerging, rapidly spreading disease with pandemic potential. It is caused by the monkeypox virus (MPXV), a dsDNA virus from the Poxviridae family, that replicates in the cytoplasm and must encode for its own RNA processing machinery including the capping machinery. Here, we present the crystal structure of its 2’-O-RNA methyltransferase (MTase) VP39 in complex with the pan-MTase inhibitor sinefungin. A comparison of this 2’-O RNA MTase with enzymes from unrelated ssRNA viruses (SARS-CoV-2 and Zika) reveals a surprisingly conserved sinefungin binding mode implicating that a single inhibitor could be used against unrelated viral families.
MHC class I and MHC class II reporter mice enable analysis of immune oligodendroglia in mouse models of multiple sclerosis
Authors: Harrington Em P , Catenacci Riley B , Smith Matthew D , Heo Dongeun , Miller Cecilia E , Meyers Keya R , Glatzer Jenna , Bergles Dwight E , Calabresi Peter A
Published: September 2022

Oligodendrocytes and their progenitors upregulate MHC pathways in response to inflammation, but the frequency of this phenotypic change is unknown and the features of these immune oligodendroglia are poorly defined. We generated MHC class I and II transgenic reporter mice to define their dynamics in response to inflammatory demyelination, providing a means to monitor MHC activation in diverse cell types in living mice and define their roles in aging, injury and disease.
Decoding Age-specific Changes in Brain Functional Connectivity Using a Sliding-window Based Clustering Method
Authors: Zhang Aiying , Pagliaccio David , Marsh Rachel , Lee Seonjoo
Published: September 2022

Functional magnetic resonance imaging (fMRI) permits detailed study of human brain function. Understanding the age-specific development of neural circuits in the typically developing brain may help us generate new hypotheses for developmental psychopathologies. Functional connectivity (FC), defined as the statistical associations between two brain regions, has been widely used in estimating functional networks from fMRI data. Previous research has shown that the evolution of FC does not follow a linear trend, particularly from childhood to young adulthood. Thus, this work aims to detect the nuanced FC changes with age from the non-linear curves and identify age-period-specific FC development patterns. We proposed a sliding-window based clustering approach to identify refined age interval of FC development. We used resting-state fMRI (rs-fMRI) data from the human connectome project-development (HCP-D), which recruited children, adolescents, and young adults aged from 5 to 21 years. Our analyses revealed different developmental patterns of resting-state FC by sex. In general, females matured earlier than males, but males had a faster development rate during age 100 -120 months. We identified four developmental phases: network construction in late childhood, segregation and integration construction in adolescence, network pruning in young adulthood, and a unique phase in males -- U-shape development. In addition, we investigated the sex effect on the slopes of FC-age correlation. Males had higher slopes during late childhood and young adulthood. These results inform trajectories of normal FC development, information that can in the future be used to pinpoint when development might go awry in neurodevelopmental disorders.

Highlight

Propose a novel sliding-window-based framework to identify refined age intervals of functional connectivity (FC) development.

Identify four developmental phases: network construction in late childhood, segregation and integration in adolescence, network pruning in young adulthood, and a unique phase in males -- U-shape development.

Characterize the representative FC pattern for each developmental phase based on global network statistics, modular connectivity, and hub ROIs.

Reveal sex differences in developmental timing, rate, and patterns of resting-state FC.
Characterising stationary and dynamic effective connectivity changes in the motor network during and after tDCS
Authors: Calzolari Sara , Jalali Roya , Fernández-Espejo Davinia
Published: September 2022

The exact mechanisms behind the effects of transcranial direct current stimulation (tDCS) at a network level are still poorly understood, with most studies to date focusing on local (cortical) effects and changes in motor-evoked potentials or BOLD signal. Here, we explored stationary and dynamic effective connectivity across the motor network at rest in two experiments where we applied tDCS over the primary motor cortex (M1-tDCS) or the cerebellum (cb-tDCS) respectively. Two cohorts of healthy volunteers (n = 21 and n = 22) received anodal, cathodal, and sham tDCS sessions (counterbalanced) during 20 minutes of resting-state functional magnetic resonance imaging (fMRI). We used spectral Dynamic Causal Modelling (DCM) and hierarchical Parametrical Empirical Bayes (PEB) to analyse data after (compared to a pre-tDCS baseline) and during stimulation. We also implemented a novel dynamic (sliding windows) DCM/PEB approach to model the nature of network reorganisation across time. In both experiments we found widespread effects of tDCS that extended beyond the targeted area and modulated effective connectivity between cortex, thalamus, and cerebellum. These changes were characterised by unique nonlinear temporal fingerprints across connections and polarities. Our results challenged the classic notion of anodal and cathodal tDCS as excitatory and inhibitory respectively, as well as the idea of a cumulative effect of tDCS over time. Instead, they described a rich set of changes with specific spatial and temporal patterns. Our work provides a starting point for advancing our understanding of network-level tDCS effects and optimise its cognitive and clinical applications.
Wild red deer (Cervus elaphus) do not play a role as vectors or reservoirs of SARS-CoV-2 in northeastern Poland
Authors: Krupińska Martyna , Borkowski Jakub , Goll Aleksander , Nowicka Joanna , Baranowicz Karolina , Bourret Vincent , Strandin Tomas , Mäki Sanna , Kant Ravi , Sironen Tarja , Grzybek Maciej
Published: September 2022

Several studies reported a high prevalence of SARS-CoV-2 among white-tailed deer in North America. Monitoring cervids in all regions to better understand SARS-CoV-2 infection and circulation in other deer populations has been urged. To evaluate deer exposure to SARS-CoV-2 in Poland, we sampled 90 reed deer individuals shot by hunters in five hunting districts in northeastern Poland. Serum and nasopharyngeal swabs were collected, and then the Immunofluorescent Assay (IFA) to detect anti-SARS-CoV-2 antibodies was performed as well as real-time PCR with reverse transcription for direct virus detection. No positive samples were detected. There is no evidence of spillover of SARS-CoV-2 from the human to deer population in Poland.
Intrinsic neural timescales in the temporal lobe support an auditory processing hierarchy
Authors: Cusinato Riccardo , Alnes Sigurd L. , van Maren Ellen , Boccalaro Ida , Ledergerber Debora , Adamantidis Antoine , Imbach Lukas L. , Schindler Kaspar , Baud Maxime O. , Tzovara Athina
Published: September 2022

During rest, intrinsic neural dynamics manifest at multiple timescales, which progressively increase along visual and somatosensory hierarchies. Theoretically, intrinsic timescales are thought to facilitate processing of external stimuli at multiple stages. However, direct links between timescales at rest and sensory processing, as well as translation to the auditory system are lacking. Here, we used intracranial electroencephalography in humans to show that in the auditory network, intrinsic neural timescales progressively increase, while the spectral slope flattens, from temporal to entorhinal cortex, hippocampus, and amygdala. Within the neocortex, intrinsic timescales exhibit spatial gradients that follow the temporal lobe anatomy. Crucially, intrinsic timescales at rest can explain the latency of auditory responses: as intrinsic timescales increase, so do the single-electrode response onset and peak latencies. Our results suggest that the human auditory network exhibits a repertoire of intrinsic neural dynamics, which manifest in cortical gradients with millimeter resolution and may provide a variety of temporal windows to support auditory processing.
Effect of Nonlinear Hyperelastic Property of Arterial Tissues on the Pulse Wave Velocity based on the Unified-Fiber-Distribution (UFD) Model
Authors: Dong Hai , Liu Minliang , Woodall Julia , Leshnower Bradley , Gleason Rudolph L.
Published: September 2022

Pulse wave velocity (PWV) is a key, independent risk factor for future cardiovascular events. The Moens-Korteweg equation describes the relation between PWV and the stiffness of arterial tissue with an assumption of isotopic linear elastic property of the arterial wall. However, the arterial tissue exhibits highly nonlinear and anisotropic mechanical behaviors. There is a limited study regarding the effect of arterial nonlinear and anisotropic properties on the PWV. In this study, we investigated the impact of the arterial nonlinear hyperelastic properties on the PWV, based on our recently developed unified-fiber-distribution (UFD) model. The UFD model considers the fibers (embedded in the matrix of the tissue) as a unified distribution, which expects to be more physically consistent with the real fiber distribution than existing models that separate the fiber distribution into two/several fiber families. With the UFD model, we fitted the measured relation between the PWV and blood pressure which obtained a good accuracy. We also modeled the aging effect on the PWV based on observations that the stiffening of arterial tissue increases with aging, and the results agree well with experimental data. In addition, we did parameter studies on the dependence of the PWV on the arterial properties of fiber initial stiffness, fiber distribution, and matrix stiffness. The results indicate the PWV increases with increasing overall fiber component in the circumferential direction. The dependences of the PWV on the fiber initial stiffness, and matrix stiffness are not monotonic and change with different blood pressure. The results of this study could provide new insights into arterial property changes and disease information from the clinical measured PWV data.
Iterative immunostaining combined with expansion microscopy and image processing reveals nanoscopic network organization of nuclear lamina
Authors: Mäntylä Elina , Montonen Toni , Azzari Lucio , Mattola Salla , Hannula Markus , Vihinen-Ranta Maija , Hyttinen Jari , Vippola Minnamari , Foi Alessandro , Nymark Soile , Ihalainen Teemu O.
Published: September 2022

Investigation of nuclear lamina architecture relies on super-resolved microscopy. However, epitope accessibility, labeling density, and detection precision of individual molecules pose challenges within the molecularly crowded nucleus. We developed iterative indirect immunofluorescence (IT–IF) staining approach combined with expansion microscopy (ExM) and structured illumination microscopy to improve super-resolution microscopy of subnuclear nanostructures like lamins. We prove that ExM is applicable in analyzing highly compacted nuclear multiprotein complexes such as viral capsids and provide technical improvements to ExM method including 3D-printed gel casting equipment. We show that in comparison to conventional immunostaining, IT-IF results in a higher signal-to-background –ratio and a mean fluorescence intensity by improving the labeling density. Moreover, we present a signal processing pipeline for noise estimation, denoising, and deblurring to aid in quantitative image analyses and provide this platform for the microscopy imaging community. Finally, we show the potential of signal-resolved IT–IF in quantitative super-resolution ExM imaging of nuclear lamina and reveal nanoscopic details of the lamin network organization - a prerequisite for studying intranuclear structural co-regulation of cell function and fate. (Words: 175)
Strong Ethanol- and Frequency-Dependent Ecological Interactions in a Community of Wine-Fermenting Yeasts
Authors: Lax Simon , Gore Jeff
Published: September 2022

Natural wine fermentation is carried out by the complex consortia of microorganisms native to grapes and winery equipment, rather than by inoculation with industrial yeast strains. While this diversity of yeasts can result in an increased repertoire of wine flavors and aromas, it can also result in the inhibition of Saccharomyces cerevisiae, which is uniquely able to withstand the high ethanol and low resource conditions in the end stages of fermentation. Understanding how yeast species interact with each other within the wine-fermenting community, and disentangling the importance of these ecological interactions from the environmental impacts on growth rates, is key to developing synthetic communities that can provide the sensory benefits of natural fermentation while lowering the risk of stuck ferments. While numerous studies have characterized the dynamics of experimental fermentations, carried out by both synthetic and natural communities, it is difficult to infer ecological interactions from transient population dynamics. Here, we co-culture all pairwise combinations of five commonly isolated wine-fermenting yeasts at various ethanol concentrations. We show that these pairwise outcomes are a strong function of ethanol concentration, with frequency-dependent bistable interactions common at low alcohol and an increasingly transitive competitive hierarchy developing as alcohol increases. We also show that these pairwise outcomes are predictive of five-species community outcomes, and that frequency dependence in pairwise interactions can propagate to alternative states in the full community, highlighting the importance of species abundance as well as composition. We also observe that monoculture growth rates as a function of ethanol are only weakly predictive of competitive success, highlighting the need to incorporate ecological interactions when designing synthetic communities for optimal fermentation performance.
The Developmental Profile of Visual Cortex Astrocytes
Authors: Watanabe Airi , Guo Connie , Sjöström Per Jesper
Published: September 2022

Though once thought of as passive support cells for neurons, it is now clear that astrocytes signal via calcium (Ca2+) to trigger gliotransmission that impacts surrounding neurons and synapses. We therefore investigated how astrocytes in layer-5 (L5) mouse visual cortex mature electrophysiologically and morphologically over postnatal days (P) 3 – 30 and how these relate to changes in spontaneous Ca2+ events. Across this age range, resting membrane potential increased, and input resistance decreased. Astrocytes also revealed different membrane responses to voltage steps: notably, membrane responses became more passive with age. Two-photon (2p) imaging of dye-loaded patched cells and confocal imaging revealed that gap-junction coupling increased starting around P7. Morphological reconstructions revealed increased branch density but also shorter branches after P20, suggesting that astrocyte branches may get pruned as dense tiling is established. Finally, we visualized spontaneous Ca2+ transients with 2p microscopy and found that Ca2+ events decorrelated, became more frequent as well as briefer with age. As astrocytes mature, spontaneous Ca2+ activity thus changes from relatively cell-wide, synchronous waves to local transients. Several astrocyte properties were stably mature from ~P15 onwards, although morphology continued to develop further. Our findings provide a descriptive foundation of astrocyte maturation, useful for the study of astrocytic impact on visual cortex critical period plasticity.
Pollen contamination and mating structure in maritime pine (Pinus pinasterAit.) clonal seed orchards revealed by SNP markers
Authors: Bouffier Laurent , Debille Sandrine , Alazard Pierre , Raffin Annie , Pastuszka Patrick , Trontin Jean-François
Published: September 2022

Maritime pine (Pinus pinasterAit.) is a major forest tree species in south-western Europe. In France, an advanced breeding program for this conifer species has been underway since the early 1960s. Open-pollinated seed orchards currently supply more than 90% of maritime pine seedlings for plantation forestry. However, pollen contamination and mating structure have been poorly studied in such seed orchards whereas they could impact genetic gains and diversity. We analyzed these features in three maritime pine clonal seed orchards. We addressed biological (tree genotype, age, flowering phenology) and environmental factors (vicinity with external pollen sources, orchard structure, soil type, climatic conditions) that are expected to determine the genetic composition of seed lots. Genetic analyses were based on an optimized set of 60 SNP markers and performed on 2,552 seedlings with Cervus software (likelihood inference methodology).

Pollen contamination rates were highly variable between seed lots (from 20 to 96%), with a mean value of 50%. Interpretative factors included the distance between the seed orchard and external pollen sources, rain during the pollination period, seed orchard age, soil conditions and seed parent identity. All parental genotypes from the seed orchards contributed to the offspring as pollen parents, but differences in paternal reproductive success were detected. Finally, the overall self-fertilization rate was estimated at 5.4%, with considerable variability between genotypes (from 0% to 26%). These findings are useful to formulate recommendations for seed orchard management (seed orchard location, soil and climate optimal conditions, minimum age for commercial seed lots harvesting) and for identifying new research perspectives (exploring links between pollen contamination and climatic data, genetic control of flowering traits).
A Multivariate Approach to Understanding the Genetic Overlap between Externalizing Phenotypes and Substance Use Disorders
Authors: Poore Holly E. , Hatoum Alexander , Mallard Travis T. , Sanchez-Roige Sandra , Waldman Irwin D. , Palmer Abraham A. , Harden K. Paige , Barr Peter B. , Dick Danielle M.
Published: September 2022

Substance use disorders (SUDs) are phenotypically and genetically correlated with each other and with other psychological traits characterized by behavioral undercontrol, termed externalizing phenotypes. In this study, we used Genomic Structural Equation Modeling to explore the shared genetic architecture among six externalizing phenotypes and four SUDs used in two previous multivariate GWAS of an externalizing and an addiction risk factor, respectively. Using a preregistered set of criteria, we first evaluated the performance of five confirmatory factor analytic models, including a common factor model, alternative parameterizations of two-factor structures, and a bifactor model. We used a combination of model fit, factor reliability, and model characteristics to adjudicate among the models. We next explored the genetic correlations between factors identified in these models and other relevant psychological traits. We found that a common factor model, in which all externalizing phenotypes and SUDs were influenced by a single dimension of genetic risk best characterized the relationships among our phenotypes. Although two two-factor models also performed well, we found that the factors in those models were very highly correlated with each other (rgS > .87) and similarly genetically correlated with external criteria, suggesting they did not represent meaningfully distinct dimensions. Results from this study can be used to inform future efforts to characterize genetic liability for broad externalizing as well as specific externalizing phenotypes.
Permittivity-Based Microparticle Classification by the Integration of Impedance Cytometry and Microwave Resonators
Authors: Tefek Uzay , Sari Burak , Hanay Mehmet S.
Published: September 2022

Permittivity of microscopic particles can be used as a classification parameter for applications in materials and environmental sciences. However, directly measuring the permittivity of individual microparticles has proven to be challenging due to the convoluting effect of particle size on capacitive signals. To overcome this challenge, we built a sensing platform to independently obtain both the geometric and electric size of a particle, by combining impedance cytometry and microwave resonant sensing in a microfluidic chip. This way the microwave signal, which contains both permittivity and size effects, can be normalized by the size information provided by impedance cytometry to yield an intensive parameter that depends only on permittivity. The technique allowed us to differentiate between polystyrene and soda lime glass microparticles — below 22 microns in diameter— with more than 94% accuracy, despite their similar sizes and electrical characteristics. The technique offers a potential route for targeted applications such as environmental monitoring of microplastic pollution or quality control in pharmaceutical industry.
YAP/TAZ inactivation with simvastatin attenuates glucocorticoid-induced human trabecular meshwork cell dysfunction
Authors: Yoo Hannah , Singh Ayushi , Li Haiyan , Strat Ana N. , Bagué Tyler , Ganapathy Preethi S. , Herberg Samuel
Published: September 2022

Purpose

Impairment of the trabecular meshwork (TM) is the principal cause of increased outflow resistance in the glaucomatous eye. Yes-associated protein (YAP) and transcriptional coactivator with PDZ binding motif (TAZ) are emerging as potential mediators of TM cell/tissue dysfunction. Furthermore, YAP/TAZ activity was recently found to be controlled by the mevalonate pathway in non-ocular cells. Clinically-used statins block the mevalonate cascade and were shown to improve TM cell pathobiology; yet, the link to YAP/TAZ signaling was not investigated. In this study, we hypothesized that YAP/TAZ inactivation with simvastatin attenuates glucocorticoid-induced human TM (HTM) cell dysfunction.

Methods

Primary HTM cells were seeded atop or encapsulated within bioengineered extracellular matrix (ECM) hydrogels. Dexamethasone was used to induce a pathologic phenotype in HTM cells in the absence or presence of simvastatin. Changes in YAP/TAZ activity, actin cytoskeletal organization, phospho-myosin light chain levels, hydrogel contraction/stiffness, and fibronectin deposition were assessed.

Results

Simvastatin potently blocked pathologic YAP/TAZ nuclear localization/activity, actin stress fiber formation, and myosin light chain phosphorylation in HTM cells. Importantly, simvastatin co-treatment significantly attenuated dexamethasone-induced ECM contraction/stiffening and extracellular fibronectin deposition. Sequential treatment was similarly effective but did not match clinically-used Rho kinase inhibition.

Conclusions

YAP/TAZ inactivation with simvastatin attenuates HTM cell pathobiology in a tissue-mimetic ECM microenvironment. Our data may help explain the association of statin use with a reduced risk of developing glaucoma via indirect YAP/TAZ inhibition as a proposed regulatory mechanism.
Genome-wide co-essentiality analysis inMycobacterium tuberculosisreveals an itaconate defense enzyme module
Authors: Jinich Adrian , Nazia Sakila Z. , Tellez Andrea V. , Wu Amy M. , Almada-Monter Ricardo , Smith Clare M. , Rhee Kyu
Published: September 2022

Genome-wide random mutagenesis screens using transposon sequencing (TnSeq) have been a cornerstone of functional genetics inMycobacterium tuberculosis(Mtb), helping to define gene essentiality across a wide range of experimental conditions. Here, we harness a recently compiled TnSeq database to identify pairwise correlations of gene essentiality profiles (i.e. co-essentiality analysis) across theMtbgenome and reveal clusters of genes with similar function. We describe selected modules identified by our pipeline, review the literature supporting their associations, and propose hypotheses about novel associations. We focus on a cluster of seven enzymes for experimental validation, characterizing it as an enzymatic arsenal that helpsMtbcounter the toxic effects of itaconate, a host-derived antibacterial compound. We extend the use of these correlations to enable prediction of protein complexes by designing a virtual screen that ranks potentially interacting heterodimers from co-essential protein pairs. We envision co-essentiality analysis will help accelerate gene functional discovery in this important human pathogen.
Substrate stiffness engineered to replicate disease conditions influence senescence and fibrotic responses in primary lung fibroblasts
Authors: Blokland Kaj E.C. , Nizamoglu Mehmet , Habibie Habibie , Borghuis Theo , Schuliga Michael , Melgert Barbro N. , Knight Darryl A. , Brandsma Corry-Anke , Pouwels Simon D. , Burgess Janette K.
Published: September 2022

In idiopathic pulmonary fibrosis (IPF) there is excessive ECM deposition, increased stiffness and ultimately destruction of lung parenchyma. IPF presents mainly in the elderly, implying that senescence, a hallmark of ageing, contributes to disease progression. Several studies have reported that IPF is characterised by increased senescence and accumulating evidence suggests that structural changes, such as increased stiffness may contribute to senescence. This study therefore investigated if increased tissue stiffness could modulate markers of senescence and/or fibrosis in primary lung fibroblasts. Using hydrogels representing healthy and fibrotic stiffnesses, we cultured primary fibroblasts from non-diseased lung tissue on top of these hydrogels for up to seven days before assessing senescence and fibrosis markers. Fibroblasts cultured on stiff (±15kPa) hydrogels showed higher Yes-associated protein-1 (YAP) nuclear translocation compared to soft hydrogels. When looking at senescence-associated proteins we also found higher secretion of receptor activator of nuclear factor kappa-B ligand (RANKL) but no change in transforming growth factor-β1 (TGF-β1) or connective tissue growth factor (CTGF) expression and higher decorin protein deposition on stiff matrices. With respect to genes associated with fibrosis, fibroblasts on stiff hydrogels compared to soft had higher expression of smooth muscle alpha (α)-2 actin (ACTA2), collagen (COL) 1A1andfibulin-1(Fbln1) and higher Fbln1 protein deposition after seven days. Our results show that exposure of lung fibroblasts to fibrotic stiffness activates genes and secreted factors that are part of fibrotic responses and part of the senescence-associated secretory profile (SASP). This overlap may contribute to the creation of a feedback loop whereby fibroblasts create a perpetuating cycle reinforcing disease progression in IPF.