bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell Dynamic Mechanics Regulates Large-spatial Isotropic Matrix Modeling with Computational Simulations
Authors: Ouyang Mingxing , Hu Yanling , Chen Weihui , Li Hui , Ji Yingbo , Qiu Linshuo , Zhu Linlin , Ji Baohua , Bu Bing , Deng Linhong
Published: November 2022

Tissues are often isotropic and heterogeneous organizations, which developmental processes are coordinated by cells and extracellular matrix modeling. Cells have the capability of modeling matrix in distance, however, the biophysical mechanism is largely unknown. We investigated underlying mechanism of large collagen I (COL) fibrillary modeling by cell mechanics with designed arrays of cell clusters. By incorporating dynamic contractions, Molecular Dynamics simulations yielded highly matching isotropic outcomes with observed COL clustering in experiments from variable geometrical arrays without spatial limitation. Further designed single polygons from triangles to hexagons resulted in predicted structural assembly which showed maintained spatial balance. Cell cytoskeletal integrity (actin filaments, microtubules), actomyosin contractions, and endoplasmic reticulum calcium channels were essential for remote fiber inductions, while membrane mechanosensitive integrin and Piezo showed coordinative role in regulating the fiber assembly. The study provides new insights on cell mechanics-induced isotropic matrix modeling with dynamic large-spatial scales and the associated cellular mechanism. The assembled biomechanical scaffolds with pre-designs may lead to applications in micro-tissue engineering. This work implicates heterogeneous tissue structures maybe partially derived from isotropic cell mechanics.
Antigen presentation by discrete class I molecules on brain endothelium dynamically regulates T-cell mediated neuropathology in experimental cerebral malaria
Authors: Fain CE , Zheng J , Jin F , Ayasoufi K , Wu Y , Lilley MT , Dropik AR , Wolf DM , Rodriguez RC , Aibaidula A , Tritz ZP , Bouchal SM , Pewe LL , Urban SL , Chen Y , Chang S , Hansen MJ , Kachergus JM , Shi J , Thompson EA , Harty JT , Parney IF , Sun J , Wu LJ , Johnson AJ
Published: November 2022

CD8 T cell engagement of brain vasculature is a putative mechanism of neuropathology in human cerebral malaria. To define contributions of brain endothelial cell MHC class I antigen-presentation to CD8 T cells in establishing this pathology, we developed novel H-2KbLoxP and H-2DbLoxP mice crossed with Cdh5-Cre mice to achieve targeted deletion of discrete class I molecules on brain endothelium. Using thePlasmodium bergheiANKA model of experimental cerebral malaria (ECM), we observe that H-2Kband H-2Dbregulate distinct patterns of disease onset, CD8 T cell infiltration, targeted cell death, and regional blood-brain barrier (BBB) disruption. Strikingly, ablation of H-2Kbor H-2Dbfrom brain endothelial cells resulted in reduced CD8 T cell activation, attenuated T cell interaction with brain vasculature, lessened targeted cell death, preserved BBB integrity, and prevented ECM and the death of the animal. These data demonstrate that interactions of CD8 T cells with discrete MHC class I molecules on brain endothelium regulate development of ECM neuropathology. Therefore, targeting MHC class I interactions therapeutically may hold potential for treatment of cases of severe malaria.
Unique features of the arterial Blood-Brain Barrier
Authors: Bell Batia , Anzi Shira , Sasson Esther , Ben-Zvi Ayal
Published: November 2022

CNS vasculature differs from vascular networks of peripheral organs by its ability to tightly control selective material exchange across capillary barriers. Capillary permeability is mostly defined by unique cellular components of the endothelium. While capillaries are extensively investigated, the barrier properties of larger vessels are understudied. Here, we investigate barrier properties of CNS arterial walls. Using tracer challenges and various imaging modalities, we discovered that at the mouse cortex, the arterial barrier does not reside at the classical level of the endothelium. The arterial wall’s unique permeability acts bi-directionally; CSF substances travel along the glymphatic path and can penetrate from the peri-vascular space through arteriolar walls towards the lumen. We found that caveolae vesicles in arteriole endothelial and smooth-muscle cells are functional transcytosis machinery components, and that a similar mechanism is evident in the human brain. Our discoveries highlight vascular heterogeneity investigations as a potent approach to uncover new barrier mechanisms.
An iterative search algorithm to identify oscillatory dynamics in neurophysiological time series
Authors: Beck Amanda M. , He Mingjian , Gutierrez Rodrigo G. , Hotan Gladia C. , Purdon Patrick L.
Published: November 2022

Neural oscillations have long been recognized for their mechanistic importance in coordinating activity within and between brain circuits. Co-occurring broad-band, non-periodic signals are also ubiquitous in neural data and are thought to reflect the characteristics of populationlevel neuronal spiking activity. Identifying oscillatory activity distinct from broadband signals is therefore an important, yet surprisingly difficult, problem in neuroscience. Commonly-used bandpass filters produce spurious oscillations when applied to broad-band noise and may be illinformed by canonical frequency bands. Curve-fitting procedures have been developed to identify peaks in the power spectrum distinct from broadband noise. Unfortunately, these ad hoc methods are prone to overfitting and are difficult to interpret in the absence of generative models to formally represent oscillatory behavior. Here we present a novel method to identify and characterize neural oscillations distinct from broad-band noise. First, we propose a new conceptual construct that makes clear, from a dynamical systems perspective, when oscillations are present or not. We then use this construct to develop generative models for neural oscillations. We show through extensive analyses of simulated and human EEG data that our approach identifies oscillations and their characteristics far more accurately than widely used methods, achieving near-perfect recovery of the number of oscillations when the SNR exceeds a very modest threshold. We also show that our method can automatically identify subject-level variations in frequency to overcome the limitations of fixed canonical frequency bands. Finally we demonstrate how our method can extract clinically-relevant neurophysiological features with greater statistical efficiency other established methods.
Mineral phase analysis of various marine-species shells and skeletons collected in Japan: Implications for marine biominerals
Authors: Mitsuguchi Takehiro , Minakata Keiji , Sugihara Kaoru , Hiraoka Masanori , Yoshida Masa-aki , Saito-Kokubu Yoko
Published: November 2022

Mineral phase analysis was performed, using X-ray diffractometry (XRD), for marine-organism shell/skeleton samples of 146–148 extant species of the following 10 phyla (18 classes) collected in Japan: Rhodophyta (Florideophyceae), Foraminifera (Globothalamea and Tubothalamea), Porifera (Hexactinellida), Cnidaria (Anthozoa and Hydrozoa), Bryozoa (Gymnolaemata), Brachiopoda (Lingulata and Rhynchonellata), Mollusca (Bivalvia, Cephalopoda, Gastropoda and Polyplacophora), Annelida (Polychaeta), Arthropoda (Cirripedia), and Echinodermata (Asteroidea, Crinoidea and Echinoidea). Some of the species were analyzed for each specific part of their shells/skeletons. Almost all the samples exhibited any of calcite, aragonite or their mixed phase, predominantly depending on their taxonomy and shell/skeletal structures. For samples containing significant amounts of calcite, the MgCO3wt % of calcite has been determined from their XRD data, which ranges from ∼0 to ∼15 wt % and indicates clear inter-taxonomic differences. Low MgCO3values (∼0–4 wt %) are observed for Rhynchonellata, Bivalvia, Gastropoda and Cirripedia; intermediate values (∼4–8 wt %) for Cephalopoda; high values (∼8–15 wt %) for Florideophyceae, Globothalamea, Tubothalamea, Polychaeta, Asteroidea and Crinoidea; low-to-high values for Gymnolaemata; intermediate-to-high values for Anthozoa and Echinoidea. These MgCO3data show broad trends mostly consistent with general phylogenetic evolution (i.e. very similar patterns for each phylogenetic group). Distinct within-individual variability of the MgCO3content is found for regular Echinoidea species (i.e. their teeth and spines have lower MgCO3values than the other skeletal parts). Correlation of the MgCO3content with seawater temperature is also examined/discussed for most of the above calcite-containing classes. In order to interpret our XRD-based observations of various marine-species shells/skeletons, detailed discussions are presented by comparing with previous studies and also by using knowledge of taxonomy, shell/skeletal structures, habitats, living modes and so on. The comprehensive dataset and discussions will provide useful implications for biomineralization studies.
Copper-independent lysosomal localization of the Wilson disease protein ATP7B
Authors: Maji Saptarshi , Pirozzi Marinella , Ruturaj  , Pandey Raviranjan , Ghosh Tamal , Das Santanu , Gupta Arnab
Published: November 2022

In hepatocytes, the Wilson disease protein ATP7B resides on trans-Golgi network and traffics to peripheral lysosomes to export excess intracellular copper through lysosomal exocytosis. We found that in basal copper or even upon copper chelation, a significant amount of ATP7B persists in endolysosomal compartment of hepatocytes but not in non-hepatic cells. These ATP7B-harboring lysosomes lie in close proximity of ∼10nm to the TGN. ATP7B constitutively distributes itself between the sub-domain of the TGN with a lower pH and the TGN-proximal lysosomal compartments. Presence of ATP7B on TGN-Lysosome colocalizing sites upon Golgi disruption suggested possible exchange of ATP7B directly between the TGN and its proximal lysosomes. Manipulating lysosomal positioning significantly alters the localization of ATP7B in the cell. Contrary to previous understanding, we found that upon copper chelation in a copper-replete hepatocyte, ATP7B is not retrieved back to TGN from peripheral lysosomes; rather, ATP7B recycles to these TGN-proximal lysosomes to initiate the next cycle of copper transport. We report a hitherto unknown copper-independent lysosomal localization of ATP7B and the importance of TGN-proximal lysosomes but not TGN as the terminal acceptor organelle of ATP7B in its retrograde pathway.

Synopsis

Excess copper is toxic to the cell. In hepatocytes, the Wilson disease protein ATP7B has been reported to recycle between the trans-Golgi network and lysosomes to export copper in elevated copper conditions. We, for the first time, show that a large fraction of ATP7B constitutively resides on the lysosome and rather, the position of the lysosome shifts from TGN-proximal to the peripheral region of the cell in high copper to facilitate ATP7B-mediated lysosomal exocytosis of copper.
Simulations reveal high efficiency and confinement of a population suppression CRISPR toxin-antidote gene drive
Authors: Zhu Yutong , Champer Jackson
Published: November 2022

Though engineered gene drives hold great promise for spreading through and eventually suppressing populations of disease vectors or invasive species, complications such as resistance alleles and spatial population structure can prevent their success. Additionally, most forms of suppression drives, such as homing drives or driving Y chromosomes, will generally spread uncontrollably between populations with even small levels of migration. The previously proposed CRISPR-based toxin-antidote system called TADE suppression drive could potentially address the issue of confinement and resistance alleles. However, it is a relatively weak form of drive compared to homing drives, which might make it particularly vulnerable to spatial population structure. In this study, we investigate TADE suppression drive using individual-based simulations in continuous space. We find that the drive is actually more confined in continuous space than in panmictic populations, even in its most efficient form with a low cleavage rate in embryos from maternally deposited Cas9. Furthermore, the drive performed well in continuous space scenarios if the initial release requirements were met, suppressing the populations in a timely manner without being severely affected by chasing, a phenomenon in which wild-type individuals avoid the drive by recolonizing empty areas. At higher embryo cut rates, the drive loses its ability to propagate on its own, but a single, widespread release can often still induce rapid population collapse. Thus, if TADE suppression gene drives can be successfully constructed, they may play an important role in control of disease vectors and invasive species when stringent confinement to target populations is desired.
COVID-19 primary series and booster vaccination and potential for immune imprinting
Authors: Chemaitelly Hiam , Ayoub Houssein H. , Tang Patrick , Coyle Peter V. , Yassine Hadi M. , Thani Asmaa A. Al , Al-Khatib Hebah A. , Hasan Mohammad R. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Butt Adeel A. , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J.
Published: November 2022

Laboratory science evidence suggests possibility of immune imprinting, a negative impact for vaccination on subsequent protective immunity against SARS-CoV-2 infection. We investigated differences in incidence of SARS-CoV-2 reinfection in the cohort of persons who had a primary omicron infection, but different vaccination histories using matched, national, retrospective, cohort studies. Adjusted hazard ratio (AHR) for incidence of reinfection, factoring also adjustment for differences in testing rate, was 0.43 (95% CI: 0.39-0.49) comparing history of two-dose vaccination to no vaccination, 1.47 (95% CI: 1.23-1.76) comparing history of three-dose vaccination to two-dose vaccination, and 0.57 (95% CI: 0.48-0.68) comparing history of three-dose vaccination to no vaccination. Divergence in cumulative incidence curves increased markedly when incidence was dominated by BA.4/BA.5 and BA.2.75* omicron subvariant. History of primary-series vaccination enhanced immune protection against omicron reinfection, but history of booster vaccination compromised protection against omicron reinfection. These findings do not undermine the short-term public health utility of booster vaccination.

Teaser

History of booster vaccination showed lower protection against omicron reinfection than history of two-dose vaccination.
Different helminth parasites show contrasting relationships with age in a wild ungulate
Authors: Albery Gregory F , Morris Sean , Morris Alison , Kenyon Fiona , McBean David , Pemberton Josephine M , Nussey Daniel H , Firth Josh A
Published: November 2022

As animals age they often exhibit substantial physiological and behavioural changes that can drive changes in infection status over the lifespan. Generally, immunosenescence is expected to lead to greater infection in older individuals, but this process could be confounded or counteracted by changes in behaviour, selective disappearance of certain individuals, or a range of immune processes. Here, we uncover contrasting age-related patterns of infection across three different helminth parasites in wild adult red deer (Cervus elaphus). Counts of strongyle nematodes (order: Strongylida) increased with age, while counts of liver fluke (Fasciola hepatica) and tissue worm (Elaphostrongylus cervi) decreased. These relationships could not be explained by selective disappearance of certain individuals or changes in behaviour, suggesting that immune changes could be responsible. Additionally, we found a positive relationship between social connectedness and strongyle infection, implying that previously documented age-related decreases in social behaviour may minimise exposure, reducing the negative effects of immunosenescence. These findings demonstrate that burdens of different parasites can show contrasting changes over an individual’s lifespan depending on a complex suite of intrinsic and extrinsic factors.
Inter-leaflet Organization of Membrane Nanodomains: What Can(not) Be Resolved by FRET?
Authors: Chmelová Barbora , Davidović David , Šachl Radek
Published: November 2022

Plasma membranes as well as their simplified model systems show an inherent nanoscale heterogeneity. As a result of strong interleaflet interactions, these nanoheterogeneities (called here lipid nanodomains) can be found in perfect registration (i.e.nanodomains in the inner leaflet are registered with the nanodomains in the outer leaflet). Alternatively, they might be inter-leaflet independent, anti-registered or located asymmetrically in one bilayer leaflet only. To distinguish these scenarios from each other appears to be an experimental challenge. In this work, we analyzed the potential of Förster resonance energy transfer (FRET) to characterize inter-leaflet organization of nanodomains. We generatedin-silicotime-resolved fluorescence decays for a large set of virtual as well as real donor/acceptor pairs distributed over the bilayer containing registered, independent, anti-registered or asymmetrically distributed nanodomains. In this way, we were able to identify conditions that gave satisfactory or unsatisfactory resolution. Overall, FRET appears as a robust method that - when using D/A pairs with good characteristics - yields otherwise difficult-to-reach characteristics of membrane lipid nanodomains.

STATEMENT OF SIGNIFICANCE

This work first explores the potential of Förster resonance energy transfer (FRET) to characterize inter-leaflet nanodomain coupling and then shows how a FRET experiment can designed to achieve optimal resolution towards nanodomain coupling. Importantly, the analysis identifies as the most critical the following parameters fundamentally affecting the resolution of FRET: the Förster radius and its value related to the inter-layer distance at which donors and acceptors in the opposing membrane leaflets are separated from each other and the donor and acceptor partition coefficients characterizing their distribution between the domain and nondomain region. By setting these parameters correctly, FRET allows for the characterization of inter-leaflet nanodomain organization with unprecedented detail.
The alphaherpesvirus conserved pUS10 is important for natural infection and its expression is regulated by the conservedHerpesviridaeprotein kinase (CHPK)
Authors: Ponnuraj Nagendraprabhu , Akbar Haji , Arrington Justine V. , Spatz Stephen J. , Nagarajan Balaji , Desai Umesh R. , Jarosinski Keith W.
Published: November 2022

ConservedHerpesviridaeprotein kinases (CHPK) are conserved among all members of theHerpesviridae. Herpesviruses lacking CHPK propagate in cell culture at varying degrees, depending on the virus and cell culture system. CHPK is dispensable for Marek’s disease herpesvirus (MDV) replication in cell culture and experimental infection in chickens; however, CHPK—particularly its kinase activity—is essential for horizontal transmission in chickens, also known as natural infection. To address the importance of CHPK during natural infection in chickens, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics of samples collected from live chickens. Comparing modification of viral proteins in feather follicle epithelial (FFE) cells infected with wildtype or a CHPK-null virus, we identified the US10 protein (pUS10) as a potential target for CHPKin vivo. When expression of pUS10 was evaluated in cell culture and in FFE skin cells duringin vivoinfection, pUS10 was severely reduced or abrogated in cells infected with CHPK mutant or CHPK-null viruses, respectively, indicating a potential role for pUS10 in transmission. To test this hypothesis, US10 was deleted from the MDV genome, and the reconstituted virus was tested for replication, horizontal transmission, and disease induction. Our results showed that removal of US10 had no effect on the ability of MDV to transmit in experimentally infected chickens, but disease induction in naturally infected chickens was significantly reduced. These results show CHPK is necessary for pUS10 expression both in cell culture and in the host, and pUS10 is important for disease induction during natural infection.

Author Summary

Marek’s disease herpesvirus (MDV) is an important pathogen in the poultry industry. Current vaccines reduce disease but do not protect chickens from infection. Understanding natural infection provides vital information for developing potential therapies to protect against Marek’s disease, while also providing a robust natural virus-host model to study herpesvirus pathogenesis. The conservedHerpesviridaeprotein kinase (CHPK) of MDV is essential for the initiation of natural infection, and we identified the virion protein US10 as a potential target for CHPK during natural infection. Our results showed that MDV CHPK was required for expression of pUS10 in both cell culture and in chickens. Although MDV lacking pUS10 replicated and spread in experimentally infected chickens, it was less virulent implicating an important role of pUS10 in natural infection of the host. These results emphasize the importance of studying specific viral proteins and their functions during infection of the natural host.
Duplication and sub-functionalisation characterise diversification of opsin genes in the Lepidoptera
Authors: Kuwalekar Muktai , Deshmukh Riddhi , Baral Saurav , Padvi Ajay , Kunte Krushnamegh
Published: November 2022

Gene duplication is a vital process for evolutionary innovation. Functional diversification of duplicated genes is best explored in multicopy gene families such as histones, hemoglobin, and opsins. Rhodopsins are photo-sensitive proteins that respond to different wavelengths of light and contribute to diverse visual adaptations across insects. While there are several instances of gene duplications in opsin lineages, the functional diversification of duplicated copies and their ecological significance is properly characterised only in a few insect groups. We examined molecular and structural evolution that underlies diversification and sub-functionalisation of four opsin genes and their duplicated copies across 132 species of the diverse insect order—Lepidoptera. Opsins have largely evolved under purifying selection with few residues showing signs of episodic and pervasive diversifying selection. Although these do not affect overall protein structures of opsins, substitutions in key amino acids in the chromophore-binding pocket of duplicated copies might cause spectral sensitivity shifts leading to sub-functionalisation or neofunctionalisation. Duplicated copies of opsins also exhibit developmental stage-specific expression inPapilio polytes, suggesting functional partitioning during development. Together, altered spectral sensitivities owing to key substitutions and differential expression of duplicated copies across developmental stages might enable enhanced colour perception and improved discrimination across wavelengths in this highly visual insect group.
Prospective isolation according to melanin pigment content of melanoma cells with heterogeneous potentials for disease propagation
Authors: Fedele Clare , Kuser-Abali Gamze , Rossi Ralph , Zhao Peinan , Li Jason , Szeto Pacman , Zhang YouFang , Wong Nick , Andrews Miles , Shackleton Mark
Published: November 2022

Functional variation between cancer cells (intra-tumoral heterogeneity) poses a major challenge to treating and managing cancer patients. Melanomas are typically composed of cancer cells with heterogeneous content of melanin pigment. Pigment production is a hallmark of normal melanocytic differentiation, however the functional consequences of melanin production in melanoma cells remains poorly understood owing to a lack of experimental approaches for detection of pigment in unfixed cells. Here, we describe a novel flow cytometric method for high purity separation of viable melanoma cells based on their content of melanin pigment, exploiting the infrared light scattering properties of melanin. By fluorescence-activated cell sorting, we show that melanoma cells with low-pigment content (LPCs) in culture and in patient tumors are far more abundant than high-pigment cells (HPCs), and have substantially increased potentials for colony formation in vitro and for tumor formation in vivo. RNAseq analysis revealed activation of P53 in HPCs associated with perturbed cell cycling, whereas LPCs displayed upregulation of MYC-associated transcription and activated ribosome biogenesis. The latter was reduced by topoisomerase 2 beta targeting with CX-5461, which also induced senescent HPC phenotypes and irreversible loss of clonogenic activity. These data illuminate an ‘inverted pyramid’ hierarchical model of melanoma cell propagation wherein abundant LPCs frequently renew their own malignant potential to propagate disease, but also rarely generate HPCs that lose this ability in a manner that may be promoted as an anti-melanoma strategy.
Ultrastructural effects of sleep and wake on the parallel fiber synapses of the cerebellum
Authors: Loschky Sophia S , Spano Giovanna Maria , Marshall William , Schroeder Andrea , Nemec Kelsey Marie , Schiereck Shannon Sandra , de Vivo Luisa , Bellesi Michele , Banningh Sebastian Weyn , Tononi Giulio , Cirelli Chiara
Published: November 2022

Multiple evidence in rodents shows that the strength of excitatory synapses in the cerebral cortex and hippocampus is greater after wake than after sleep. The widespread synaptic weakening afforded by sleep is believed to keep the cost of synaptic activity under control, promote memory consolidation, and prevent synaptic saturation, thus preserving the brain’s ability to learn day after day. The cerebellum is highly plastic and the Purkinje cells, the sole output neurons of the cerebellar cortex, are endowed with a staggering number of excitatory parallel fiber synapses. However, whether these synapses are affected by sleep and wake is unknown. Here we used serial block face scanning electron microscopy to obtain the full 3D reconstruction of more than 7,000 spines and their parallel fiber synapses in the mouse posterior vermis. We find that most Purkinje cell spines carry a synapse, but some do not. The latter, which we call “naked” spines, are ∼5% of all spines after wake but grow to ∼10% of all spines after sleep. Further analysis shows that the changes in the number of naked synapses with wake and sleep can be accounted for by a change in the number of “branched” synapses, which are housed in two or more spines sharing the same neck. Thus, during sleep branched spines may lose one or more synapses or convert to single spines, while the opposite changes occur after wake. Because branched synapses almost always contact different parallel fibers, these results also suggest that during wake, coincidences of firing over parallel fibers may translate into the formation of synapses converging on the same branched spine, which may be especially effective at driving the soma of Purkinje cells. Sleep, on the other hand, may promote the pruning of branched synapses that were formed due to spurious coincidences.
Safety margin evaluations for transtympanic laser stimulation of the cochlea from the outer ear in Mongolian gerbils (Meriones unguiculatus)
Authors: Okamoto Aya , Uenaka Miku , Ito Yuki , Miyasaka Tomohiro , Toda Koji , Hiryu Shizuko , Kobayasi Kohta I. , Tamai Yuta
Published: November 2022

Infrared laser cochlear stimulation has been suggested as an alternative to traditional auditory prostheses. Previous research has mainly examined the short-term effects of laser stimulation, but to effectively use this technique, it is necessary to study whether prolonged laser exposure can safely and sustainably induce cochlear responses. This study assessed the effect of laser-induced cochlear damage using classically-conditioned Mongolian gerbils. The white noise was presented as a conditioned stimulus, and reward licking was recorded as a conditioned response. After training, the subject’s cochlea was exposed to a continuous pulsed laser for 15 h. The licking rate drastically decreased after the exposure of 26.4 W/cm2, while it did not change after 6.6 W/cm2or weaker. These findings showed, for the first time, that the safety margin of long-term, at least several hours, cochlear laser stimulation exists and will contribute to the safe and effective delimitation of laser parameters in future research.
Sleep waves in a large-scale corticothalamic model constrained by activities intrinsic to neocortical networks and single thalamic neurons
Authors: Dervinis Martynas , Crunelli Vincenzo
Published: November 2022

Aim

Many biophysical and non-biophysical models have been able to reproduce the corticothalamic activities underlying different EEG sleep rhythms but none of them included the known ability of neocortical networks and single thalamic neurons to generate some of these waves intrinsically.

Methods

We built a large-scale corticothalamic model with a high fidelity in anatomical connectivity consisting of a single cortical column and first- and higher-order thalamic nuclei. The model is constrained by different neocortical excitatory and inhibitory neuronal populations eliciting slow (<1 Hz) oscillations and by thalamic neurons generating sleep waves when isolated from the neocortex.

Results

Our model faithfully reproduces all EEG sleep waves and the transition from a desynchronized EEG to spindles, slow (<1 Hz) oscillations and delta waves by progressively increasing neuronal membrane hyperpolarization as it occurs in the intact brain. Moreover, our model shows that slow (<1 Hz) waves most often start in a small assembly of thalamocortical neurons though occasionally they originate in cortical layer 5. Moreover, thalamocortical neuron input increases the frequency of slow (<1 Hz) waves compared to those generated by isolated cortical networks.

Conclusion

Our simulations challenge current mechanistic understanding of the temporal dynamics of sleep wave generation and suggest testable predictions.
Reduced acetylation of TFAM promotes bioenergetic dysfunction in the failing heart
Authors: Zhang Manling , Feng Ning , Thapa Dharendra , Stoner Michael W. , Manning Janet R. , McTiernan Charles F. , Yang Xue , Peng Zishan , Jurczak Michael J. , Guimaraes Danielle , Shiva Sruti , Kaufman Brett A. , Sack Michael N. , Scott Iain
Published: November 2022

General Control of Amino-Acid Synthesis 5-like 1 (GCN5L1) was previously identified as a key regulator of protein lysine acetylation in mitochondria. Subsequent studies demonstrated that GCN5L1 regulates the acetylation status and activity of mitochondrial fuel substrate metabolism enzymes. However, the role of GCN5L1 in response to chronic hemodynamic stress is largely unknown. Here, we show that cardiomyocyte-specific GCN5L1 knockout mice (cGCN5L1 KO) display exacerbated pressure overload-induced heart failure progression following transaortic constriction (TAC). Mitochondrial DNA and mitochondrial electron transport chain protein levels were decreased in cGCN5L1 KO hearts after TAC, and isolated neonatal cardiomyocytes with reduced GCN5L1 expression had lower bioenergetic output in response to hypertrophic stress. Loss of GCN5L1 expression led to a decrease in the acetylation status of mitochondrial transcription factor A (TFAM) after TACin vivo, which was linked to a reduction in mtDNA levelsin vitro. Together, these data suggest that GCN5L1 may protect from hemodynamic stress by maintaining mitochondrial bioenergetic output.

Highlights

Reduced GCN5L1 expression in the failing heart promotes contractile dysfunction

Mitochondrial DNA (mtDNA) levels are reduced in cardiomyocyte-specific GCN5L1 knockout mice following hemodynamic stress

GCN5L1 knockdown reduces, and GCN5L1 overexpression increases, bioenergetic output in hypertrophic cardiomyocytes

GCN5L1-mediated acetylation of TFAM promotes increased mtDNA levels
Aging impairs astrocytes in the human cerebral cortex
Authors: Popov Alexander , Brazhe Nadezda , Morozova Kseniia , Yashin Konstantin , Bychkov Maxim , Nosova Olga , Sutyagina Oksana , Brazhe Alexey , Parshina Evgenia , Li Li , Medyanik Igor , Korzhevskii Dmitry E , Shenkarev Zakhar , Lyukmanova Ekaterina , Verkhratsky Alexei , Semyanov Alexey
Published: November 2022

How aging affects cellular components of the human brain active milieu remains largely unknown. We analyzed astrocytes and neurons in the neocortical access tissue of younger (22 - 50 years) and older (51 - 72 years) adult patients who underwent glioma resection. Aging decreased the amount of reduced mitochondrial cytochromes in astrocytes but not neurons. The total amount of protein was decreased in astrocytes and increased in neurons. Aged astrocytes showed morphological dystrophy quantified by the decreased length of branches, decreased volume fraction of leaflets, and shrinkage of the anatomical domain. Dystrophy correlated with the loss of gap junction coupling between astrocytes and increased input resistance. Aging was accompanied by the upregulation of glial fibrillary acidic protein (GFAP) and downregulation of membrane-cytoskeleton linker Ezrin associated with leaflets. No significant changes in neuronal excitability or spontaneous inhibitory postsynaptic signaling were observed. Thus, brain aging is associated with the impaired morphological presence and mitochondrial malfunction of astrocytes, but not neurons.
Rab8, Rab11, and Rab35 coordinate lumen and cilia formation during Zebrafish Left-Right Organizer development
Authors: Aljiboury Abrar A. , Ingram Eric , Krishnan Nikhila , Ononiwu Favour , Pal Debadrita , Manikas Julie , Taveras Christopher , Hall Nicole A. , Da Silva Jonah , Freshour Judy , Hehnly Heidi
Published: November 2022

An essential process duringDanio rerio’sleft-right organizer (Kupffer’s Vesicle, KV) development is for the majority of developing KV cells to form a motile cilium that extend into the KV lumen. Left-right beating of motile cilia within the KV lumen directs fluid flow to establishment the embryo’s left-right axis. However, when KV cells start to form cilia and how cilia formation is coordinated with KV lumen formation has not been examined. We identified that nascent KV cells form cilia at their centrosomes at random intracellular positions that then move towards a forming apical membrane containing cystic fibrosis transmembrane conductance regulator (CFTR). Using optogenetic clustering approaches, we found that Rab35 positive membranes recruit Rab11 to modulate CFTR delivery to the apical membrane, which is required for lumen opening, and subsequent cilia extension into the lumenal cavity. Once the intracellular cilia reach the CFTR positive apical membrane, Arl13b-positive cilia extend and elongate in a Rab8 dependent manner into the forming lumen once the lumen reaches an area of 300 μm2. These studies demonstrate the need to acutely coordinate Rab8, Rab11, and Rab35-mediated membrane trafficking events to ensure appropriate timing in lumen and cilia formation during KV development.
DAT Val559 Mice Exhibit Compulsive Behavior Under Devalued Reward Conditions Accompanied by Cellular and Pharmacological Changes
Authors: Stewart Adele , Davis Gwynne L. , Areal Lorena B. , Rabil Maximilian J. , Tran Vuong , Mayer Felix P. , Blakely Randy D.
Published: November 2022

Identified across multiple psychiatric disorders, the dopamine (DA) transporter (DAT) Ala559Val substitution triggers non-vesicular, anomalous DA efflux (ADE), perturbing DA neurotransmission and behavior. We have shown that DAT Val559 mice display a waiting impulsivity and changes in cognitive performance associated with enhanced reward motivation. Here, utilizing a within-subject, lever-pressing paradigm designed to bias the formation of goal-directed or habitual behavior, we demonstrate that DAT Val559 mice modulate their nose-poke behavior appropriately to match context, but demonstrate a perseverative checking behavior. Although DAT Val559 mice display no issues with the cognitive flexibility required to acquire and re-learn a visual pairwise discrimination task, devaluation of reward evoked habitual reward seeking in DAT Val559 mutants in operant tasks regardless of reinforcement schedule. The direct DA agonist apomorphine also elicits locomotor stereotypies in DAT Val559, but not WT mice. Our observation that dendritic spine density is increased in the dorsal medial striatum (DMS) of DAT Val559 mice speaks to an imbalance in striatal circuitry that might underlie the propensity of DAT Val559 mutants to exhibit compulsive behaviors when reward is devalued. Thus, DAT Val559 mice represent a model for dissection of how altered DA signaling perturbs circuits that normally balance habitual and goal-directed behaviors.
Quantitative live cell imaging of a tauopathy model enables the identification of a polypharmacological drug candidate that restores physiological microtubule regulation
Authors: Pinzi Luca , Conze Christian , Bisi Nicolo , Torre Gabriele Dalla , Monteiro-Abreu Nanci , Trushina Nataliya I. , Soliman Ahmed , Krusenbaum Andrea , Dolouei Maryam Khodaei , Hellwig Andrea , Christodoulou Michael S. , Passarella Daniele , Bakota Lidia , Rastelli Giulio , Brandt Roland
Published: November 2022

Tauopathies such as Alzheimer’s disease are characterized by the aggregation and increased phosphorylation of the microtubule-associated protein tau. The pathological changes in tau are closely linked to neurodegeneration, making tau a prime candidate for intervention. However, the multiple facets of tau function and the lack of cellular tauopathy models that could support mechanism-based drug development hampers progress. Here we report the development of a live-cell imaging approach to quantitatively monitor pathological changes of human tau as it interacts with axonal microtubules. We show that a full-length aggregation-prone tau construct exhibits reduced interaction with microtubules as it increasingly aggregates. Through chemoinformatic analyses, we identified 2-phenyloxazole (PHOX) derivatives as putative polypharmacological small molecules that inhibit tau aggregation and modulate tau phosphorylation. We found that PHOX15 restores the physiological microtubule interaction of aggregation-prone tau in neurons and inhibits the first phase of tau aggregationin vitro. Furthermore, we report that PHOX15 inhibits the tau kinases GSK3β and Cdk5, alters the kinome activity of model neurons, and reduces tau phosphorylation at disease-relevant sites. Molecular dynamics simulations highlight cryptic channel-like pockets crossing tau protofilaments and indicate that the binding of PHOX15 in one of the channels reduces the protofilament’s ability to adopt a PHF-like conformation. The data show that our imaging approach provides a useful tool for identifying compounds that modulate tau-microtubule interaction in axons. We demonstrate that a polypharmacological approach to simultaneously treat tau aggregation and tau phosphorylation is able to restore physiological microtubule regulation, identifying PHOX15 as a promising drug candidate to counteract tau-induced neurodegeneration.
A new polymodal gating model of the proton-activated chloride channel
Authors: Zhao Piao , Tang Cheng , Yang Yuqin , Xiao Zhen , Perez-Miller Samantha , Zhang Heng , Luo Guoqing , Liu Hao , Li Yaqi , Liao Qingyi , Yang Fan , Dong Hao , Khanna Rajesh , Liu Zhonghua
Published: November 2022

The proton-activated chloride (PAC) channel plays critical roles in ischemic neuron death, but its activation mechanisms remain elusive. Here, we interrogated PAC channel gating using its unique bidirectional modulator C77304 as a pharmacological probe. C77304 activated the PAC channel by acting on its proton gating, while simultaneously inhibiting channel activity at higher doses, through interaction with two modulatory sites with different affinities and state-dependence. Excitingly, we revealed that PAC undergoes intrinsic proton gating-independent voltage activation, which was defined by an ion-flux gating mechanism. Scanning-mutagenesis and molecular dynamics simulation confirmed that E181, E257, and E261 in human PAC form the primary proton sensors, as alanine mutations eliminated the channel’s proton gating while sparing the voltage-dependent gating. This proton sensing mechanism was basically conserved among orthologous PAC channels. Collectively, our data unveils the polymodal gating and proton sensing mechanisms in the PAC channel which may inspire potential drug development.
Phase leads between oscillatory visual stimuli induce a salience illusion
Authors: Stauch Benjamin J. , Psarou Eleni , Roese Rasmus , Fries Pascal
Published: November 2022

Neuronal populations often engage in oscillations, and corresponding theories and computational models propose that this affects their impact on other neurons. Specifically, when two neuronal populations oscillating at similar frequencies compete for impact, the phase-leading one might have an advantage by providing inputs to target neurons earlier. Here, we provide direct empirical support by driving visual neuronal responses with oscillating stimuli. We superimposed two orthogonal grating stimuli of temporally oscillating intensities, whose phase relations were precisely controlled. The leading stimulus was perceived as oscillating more intensely. This held for phase leads of a few milliseconds, and for each participant and almost every trial. Thus, we found a strong perceptual illusion directly predicted by theories on the functional role of oscillations for neuronal interactions.
A novel anti-cancer therapy with nuclear export inhibitor Selinexor in combination with oncolytic myxoma virus
Authors: Rahman Masmudur M. , van Oosterom Fleur , Enow Junior Ayuk , Hossain Maksuda , Gutierrez-Jensen Ami D. , Cashen Mackenzie , Everts Anne , Lowe Kenneth , Kilbourne Jacquelyn , Daggett-Vondras Juliane , Karr Timothy L. , McFadden Grant
Published: November 2022

Oncolytic viruses exploited for cancer therapy are developed to selectively infect, replicate, and kill cancer cells to stop tumor growth. However, in some cancer cells, oncolytic viruses are often limited in completing their full replication cycle, making progeny virions, and/or spread in the tumor bed due to the heterogeneous cell types within the tumor bed. Here we report that nuclear export pathway regulates oncolytic myxoma virus (MYXV) infection and cytoplasmic viral replication in a subclass of human cancer cell types where virus replication is restricted. Inhibition of CRM1/XPO-1 nuclear export pathway with nuclear export inhibitors can overcome this restriction by trapping restriction factors in the nucleus and allow significantly enhanced virus replication and killing of human cancer cells. Furthermore, knockdown of CRM1/XPO-1 significantly enhanced MYXV replication in restrictive human cancer cells and reduced the formation of anti-viral granules associated with RNA helicase DHX9. Bothin vitroandin vivo, we demonstrate that the approved CRM1 inhibitor drug Selinexor enhances the replication of MYXV and cell killing of diverse human cancer cells. In the xenograft tumor model in NSG mice, combination therapy with Selinexor plus MYXV significantly reduced tumor burden and enhanced the survival of animals. Additionally, we performed global scale proteomic analysis of nuclear and cytosolic proteins in human cancer cells to identify the host and viral proteins that are upregulated or downregulated by different treatments. These results for the first time indicate that Selinexor in combination with oncolytic MYXV can be used as potential new anti-cancer therapy
Neotelomere formation by human telomerase
Authors: Kinzig Charles G. , Zakusilo George , Takai Kaori K. , de Lange Titia
Published: November 2022

The maintenance of genome integrity requires that telomerase action be limited to telomeres and not convert DSBs into neotelomeres. Using the breakpoint sequence from an apparent germline neotelomere formation event, we developed an assay to detect and quantify telomeric repeat addition at Cas9-programmed DSBs in human cells. The data show that telomerase can add telomeric repeats to DSBs and that this process can generate functional neotelomeres. Neotelomere formation is increased when telomerase is overexpressed, suggesting that in most human cells, low (or absent) telomerase activity limits the deleterious effects of de novo telomere addition. We show that neotelomere formation at DSBs is inhibited by long-range resection and the accompanying activation of ATR signaling. Our findings reveal that telomerase can cause genome instability by generating neotelomeres at DSBs. We propose that neotelomere formation can promote tumorigenesis by ending detrimental breakage-fusion-bridge cycles in cancer cells whose genome alterations engender dicentric chromosomes.
Intermediate Gray Matter Interneurons in the Lumbar Spinal Cord Play a Critical and Necessary Role in Coordinated Locomotion
Authors: Kuehn Naëmi , Schwarz Andreas , Beretta Carlo Antonio , Schwarte Yvonne , Schmitt Francesca , Motsch Melanie , Weidner Norbert , Puttagunta Radhika
Published: November 2022

Locomotion is a complex task involving excitatory and inhibitory circuitry in spinal gray matter. While genetic knockouts examine the function of unique spinal interneuron (SpIN) subtypes, the phenotype of combined premotor interneuron loss remains to be explored. We modified a kainic acid lesion to damage intermediate gray matter (laminae V-VII) in the lumbar spinal enlargement (spinal L2-L4) in female rats. A thorough, tailored behavioral evaluation revealed deficits in gross hindlimb function, skilled walking, coordination, balance and gait two-weeks post-injury. Using a Random Forest algorithm, we combined these behavioral assessments into a highly predictive binary classification system which strongly correlated with structural deficits in the rostro-caudal axis. Machine-learning quantification confirmed interneuronal damage to laminae V-VII in spinal L2-L4 correlates with hindlimb dysfunction. White matter damage and lower motoneuron loss did not correlate with behavioral deficits. Animals do not regain lost sensorimotor function three months after injury, indicating that natural recovery of the spinal cord cannot compensate for loss of laminae V-VII neurons. As spinal cord injuries are often located at spinal enlargements, this research lays the groundwork for new neuroregenerative therapies to replace these lost neuronal pools vital to sensorimotor function.

Highlights

Functional deficits in coordination, balance, rhythmic walking and gait follow two weeks after a lumbar (L2-L4) intermediate (V-VII) gray matter spinal cord injury in rats

Deficits correlate with neuronal loss in laminae V-VII in spinal levels L2-L4 but do not correlate with lower motoneuron loss or white matter damage nor do animals show signs of sensory dysfunction due to spinal cord injury

Coordination deficits remain after three months, indicating that natural recovery cannot compensate for this interneuronal loss

Newly developed machine-learning models non-invasively fully classify injured animals by functional readouts equivalent to time-intensive endpoint histological analysis