bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractIn 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.SynopsisExcess 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

AbstractThough 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

AbstractLaboratory 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.TeaserHistory 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

AbstractAs 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

ABSTRACTPlasma 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 SIGNIFICANCEThis 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

AbstractConservedHerpesviridaeprotein 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 SummaryMarek’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

AbstractGene 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

ABSTRACTFunctional 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

ABSTRACTMultiple 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

AbstractInfrared 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

ABSTRACTAimMany 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.MethodsWe 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.ResultsOur 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.ConclusionOur 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

SummaryGeneral 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.HighlightsReduced GCN5L1 expression in the failing heart promotes contractile dysfunctionMitochondrial DNA (mtDNA) levels are reduced in cardiomyocyte-specific GCN5L1 knockout mice following hemodynamic stressGCN5L1 knockdown reduces, and GCN5L1 overexpression increases, bioenergetic output in hypertrophic cardiomyocytesGCN5L1-mediated acetylation of TFAM promotes increased mtDNA levels