bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of potassium ion channels reduces Semliki Forest virus genome replication
Authors: Russell Tristan , O’Brien Caoimhe , Gangotia Disha , Fulford Stefanie , Kenny Roísín , Alkhamees Abdullah , Premchand-Branker Shonnette , Fragkoudis Rennos , Barry Gerald 
Published: May 2023

AbstractIntroductionSemliki forest virus(SFV) is a model virus used to investigate the Alphavirus genus, which includes human pathogens Chikungunya virus and Ross River virus. Viruses harness cellular machinery to facilitate various steps of their replicative cycles. Ion channels are one group of cellular proteins required for the efficient replication of some viruses, including Influenza A viruses, Ebola virus and members of theBetacoronavirusgenus. This study focussed on understanding SFV’s requirement for functional ion channels during replication.MethodsThe effect of ion channel inhibitors onin vitroSFV infections was measured to investigate the contribution of ion channels in its replication cycle.ResultsIn vitroSFV infections carried out in the presence or absence of different ion channel inhibitors showed broad-range K+channel inhibitors reproducibly attenuated virus replication and reduced its cytotoxicity in two mammalian cell lines. These broad-range K+channel inhibitors disrupted an early, post-entry step causing a delay or reduction in SFV protein and RNA synthesis. Screens using inhibitors of specific K+channel families showed that two-pore domain K+channel (2pK) inhibitors attenuated SFV replication. Confocal microscopy revealed decreased detection of dsRNA and SFV protein in the presence of inhibitor but no change in RNA and protein colocalisation, which would indicate disruption of replication complexes. Broad-range K+and 2pK inhibitors decreased viral RNA replication and transcription from the subgenomic promoter.ConclusionsK+channel inhibitors attenuatein vitroSFV replication by inhibiting an early, post-entry step of virus replication, potentially RNA synthesis.ImportanceNo antiviral therapies have been approved for clinical use against diseases caused by members of the Alphavirus genus. Work presented in this manuscript shows for the first time that SFV genome replication and virus induced cytotoxicity can be reducedin vitroby treating infected cells with K+channel inhibitors. This work provides the basis for investigating the effectiveness of K+channel inhibitors against other alphaviruses bothin vitro and in vivoand, because many ion channel inhibiting drugs are already in clinical use, rapid repurposing against alphavirus infections would be possible.
Ascidian embryonic cells with properties of neural-crest cells and neuromesodermal progenitors of vertebrates
Authors: Ishida Tasuku , Satou Yutaka 
Published: May 2023

SummaryNeural-crest cells and neuromesodermal progenitors (NMPs) are multipotent cells that are important for development of vertebrate embryos. In embryos of ascidians, which are the closest invertebrate relatives of vertebrates, several cells located at the border between the neural plate and the epidermal region have neural-crest-like properties; hence, the last common ancestor of ascidians and vertebrates may have had ancestral cells similar to neural-crest cells. However, these ascidian neural-crest-like cells do not produce cells that are commonly of mesodermal origin. Here, we showed that a cell population located in the lateral region of the neural plate has properties resembling those of vertebrate neural-crest cells and NMPs. Among them, cells withTbx6-relatedexpression contribute to muscle near the tip of the tail region, and cells withSox1/2/3expression give rise to the nerve cord. These observations and cross-species transcriptome comparisons indicate that these cells have properties like those of NMPs. Meanwhile, transcription factor genesDlx.b,Zic-r.b, andSnai,which are reminiscent of a gene circuit in vertebrate neural-crest cells, are involved in activation ofTbx6-related.b. Thus, the last common ancestor of ascidians and vertebrates may have had cells with properties of neural-crest cells and NMPs, and such ancestral cells may have produced cells commonly of ectodermal and mesodermal origins.
Analysis of cortical cell polarity by imaging flow cytometry
Authors: Jespersen Jesper Huitfeld , Harazin Andras , Bohn Anja Bille , Christensen Anni , Lorentzen Esben , Lorentzen Anna 
Published: May 2023

AbstractMetastasis is the main cause of cancer-related death and therapies specifically targeting metastasis are highly needed. Cortical cell polarity (CCP) is a pro-metastatic property of circulating tumor cells (CTCs) affecting their ability to exit blood vessels and form new metastases that constitutes a promising point of attack to prevent metastasis. However, conventional fluorescence microscopy on single cells and manual quantification of CCP are time-consuming and unsuitable for screening of regulators. In this study, we developed an imaging flow cytometry (IFC)-based method for high-throughput screening of factors affecting CCP in melanoma cells. The artificial intelligence (AI)-supported analysis method we developed is highly reproducible, accurate, and orders of magnitude faster than manual quantification. Additionally, this method is flexible and can be adapted to include additional cellular parameters. In a small-scale pilot experiment using polarity-, cytoskeleton-or membrane-affecting drugs, we demonstrate that our workflow provides a straightforward and efficient approach for screening factors affecting CCP in cells in suspension and provide insights into the specific function of these drugs in this cellular system. The method and workflow presented here will facilitate large-scale studies to reveal novel cell-intrinsic as well as systemic factors controlling CCP during metastasis.
Alterations in the preneoplastic breast microenvironment ofBRCA1/2mutation carriers revealed by spatial transcriptomics
Authors: Caputo Anthony , Vipparthi Kavya , Bazeley Peter , Downs-Kelly Erinn , McIntire Patrick , Ni Ying , Hu Bo , Keri Ruth A. , Karaayvaz Mihriban 
Published: May 2023

AbstractBreast cancer is the most common cancer in females, affecting one in every eight women and accounting for the majority of cancer-related deaths in women worldwide. Germline mutations in theBRCA1andBRCA2genes are significant risk factors for specific subtypes of breast cancer.BRCA1mutations are associated with basal-like breast cancers, whereasBRCA2mutations are associated with luminal-like disease. There are currently few chemoprevention strategies available forBRCA1/2mutation carriers, and irreversible prophylactic mastectomy is the primary option. Designing chemo-preventive strategies requires an in-depth understanding of the physiological processes underlying tumor initiation. Here, we employ spatial transcriptomics to investigate defects in mammary epithelial cell differentiation accompanied by distinct microenvironmental alterations in preneoplastic breast tissues fromBRCA1/2mutation carriers and normal breast tissues from non-carrier controls. We uncovered spatially defined receptor-ligand interactions in these tissues for the investigation of autocrine and paracrine signaling. We discovered that β1-integrin-mediated autocrine signaling inBRCA2-deficient mammary epithelial cells differs fromBRCA1-deficient mammary epithelial cells. In addition, we found that the epithelial-to-stromal paracrine signaling in the breast tissues ofBRCA1/2mutation carriers is greater than in control tissues. More integrin-ligand pairs were differentially correlated inBRCA1/2-mutant breast tissues than non-carrier breast tissues with more integrin receptor-expressing stromal cells. These results reveal alterations in the communication between mammary epithelial cells and the microenvironment inBRCA1andBRCA2mutation carriers, laying the foundation for designing innovative breast cancer chemo-prevention strategies for high-risk patients.
Revealing the Oligomerization of Channelrhodopsin-2 in the Cell Membrane using Photo-Activated Localization Microscopy
Authors: Bestsennaia Ekaterina , Maslov Ivan , Balandin Taras , Alekseev Alexey , Yudenko Anna , Shamseye Assalla Abu , Zabelskii Dmitrii , Baumann Arnd , Catapano Claudia , Karathanasis Christos , Gordeliy Valentin , Heilemann Mike , Gensch Thomas , Borshchevskiy Valentin 
Published: May 2023

AbstractMicrobial rhodopsins are retinal membrane proteins that found a broad application in optogenetics. The oligomeric state of rhodopsins is important for their functionality and stability. Of particular interest is the oligomeric state in the cellular native membrane environment. Fluorescence microscopy provides powerful tools to determine the oligomeric state of membrane proteins directly in cells. Among these methods is quantitative photoactivated localization microscopy (qPALM) allowing the investigation of molecular organization at the level of single protein clusters. Here, we apply qPALM to investigate the oligomeric state of the first and most used optogenetic tool Channelrhodopsin-2 (ChR2) in the plasma membrane of eukaryotic cells. ChR2 appeared predominantly as a dimer in the cell membrane and did not form higher oligomers. The disulfide bonds between Cys34 and Cys36 of adjacent ChR2 monomers were not required for dimer formation and mutations disrupting these bonds resulted in only partial monomerization of ChR2. The monomeric fraction increased when the total concentration of mutant ChR2 in the membrane was low. The dissociation constant was estimated for this partially monomerized mutant ChR2 as 2.2±0.9 proteins/μm2. Our findings are important for understanding the mechanistic basis of ChR2 activity as well as for improving existing and developing future optogenetic tools.
Environment and taxonomy shape the genomic signature of prokaryotic extremophiles
Authors: Millán Arias Pablo , Butler Joseph , Randhawa Gurjit S. , Soltysiak Maximillian P. M. , Hill Kathleen A. , Kari Lila 
Published: May 2023

ABSTRACTThis study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental component in the genomic signature of microbial extremophiles. Both supervised and unsupervised machine learning algorithms were used to analyze genomic signatures, each computed as thek-mer frequency vector of a 500 kbp DNA fragment arbitrarily selected to represent a genome. Computational experiments classified/clustered genomic signatures extracted from a curated dataset of ∼700 extremophile (temperature, pH) bacteria and archaea genomes, at multiple scales of analysis, 1 ≤k≤6. The supervised learning resulted in high accuracies for taxonomic classifications at 2 ≤k≤6, and medium to medium-high accuracies for environment category classifications of the same datasets at 3 ≤k≤6. Fork= 3, our findings were largely consistent with amino acid compositional biases and codon usage patterns in coding regions, previously attributed to extreme environment adaptations. The unsupervised learning of unlabelled sequences identified several exemplars of hyperthermophilic organisms with large similarities in their genomic signatures, in spite of belonging to different domains in the Tree of Life.
Future movement plans interact in sequential arm movements
Authors: Kashefi Mehrdad , Reschechtko Sasha , Ariani Giacomo , Shahbazi Mahdiyar , Tan Alice , Diedrichsen Jörn , Pruszynski J. Andrew 
Published: May 2023

AbstractReal world actions often comprise of a series of movements that cannot be entirely planned before initiation. When these actions are executed rapidly, the planning of multiple future movements needs to occur simultaneously with the ongoing action. How the brain solves this task remains unknown. Here we address this question with a new sequential arm reaching paradigm that manipulates how many future reaches are available for planning while controlling execution of the ongoing reach. We show that participants plan at least two future reaches simultaneously with an ongoing reach. Further, the planning processes of the two future reaches are not independent of one another. Evidence that the planning processes interact is two-fold. First, correcting for a visual perturbation of the ongoing reach target is slower when more future reaches are planned. Second, the curvature of the current reach is modified based on the next reach only when their planning processes temporally overlap. These interactions between future planning processes may enable smooth production of sequential actions by linking individual segments of a long sequence at the level of motor planning.
Morphogenesis inTrypanosoma cruziepimastigotes proceeds via a highly asymmetric cell division
Authors: Campbell Paul C. , Graffenried Christopher L. de 
Published: May 2023

AbstractTrypanosoma cruziis a protist parasite that is the causative agent of Chagas’ disease, a neglected tropical disease endemic to the Americas.T. cruzicells are highly polarized and undergo morphological changes as they cycle within their insect and mammalian hosts. Work on related trypanosomatids has described cell division mechanisms in several life-cycle stages and identified a set of essential morphogenic proteins that serve as markers for key events during trypanosomatid division. Here, we use Cas9-based tagging of morphogenic genes, live-cell imaging, and expansion microscopy to study the cell division mechanism of the insect-resident epimastigote form ofT. cruzi,which represents an understudied trypanosomatid morphotype. We find thatT. cruziepimastigote cell division is highly asymmetric, producing one daughter cell that is significantly smaller than the other. Daughter cell division rates differ by 4.9 h, which may be a consequence of this size disparity. Many of the morphogenic proteins identified inT. bruceihave altered localization patterns inT. cruziepimastigoes, which may reflect fundamental differences in the cell division mechanism of this life cycle stage, which widens and shortens the cell body to accommodate the duplicated organelles and cleavage furrow rather than elongating the cell body along the long axis of the cell, as is the case in life-cycle stages that have been studied inT. brucei. This work provides a foundation for further investigations ofT. cruzicell division and shows that subtle differences in trypansomatid cell morphology can alter how these parasites divide.Author SummaryTrypanosoma cruzicauses Chagas’ disease, which is among the most neglected of tropical diseases, affecting millions of people in South and Central America along with immigrant populations around the world.T. cruziis related to other important pathogens such asTrypanosoma bruceiandLeishmania spp,which have been the subject of molecular and cellular characterizations that have provided an understanding of how these organisms shape their cells and undergo division. Work inT. cruzihas lagged due to an absence of molecular tools for manipulating the parasite and the complexity of the original published genome; these issues have recently been resolved. Building on work inT. brucei, we have studied the localization of key cell cycle proteins and quantified changes in cell shape during division in an insect-resident form ofT. cruzi. This work has uncovered unique adaptations to the cell division process inT. cruziand provides insight into the range of mechanisms this family of important pathogens can employ to colonize their hosts.
A hierarchical Bayesian brain parcellation framework for fusion of functional imaging datasets
Authors: Zhi Da , Shahshahani Ladan , Nettekoven Caroline , Pinho Ana Lúısa , Bzdok Danilo , Diedrichsen Jörn 
Published: May 2023

AbstractOne important barrier in the development of complex models of human brain organization is the lack of a large and comprehensive task-based neuro-imaging dataset. Therefore, current atlases of functional brain organization are mainly based on single and homogeneous resting-state datasets. Here, we propose a hierarchical Bayesian framework that can learn a probabilistically defined brain parcellation across numerous task-based and resting-state datasets, exploiting their combined strengths. The framework is partitioned into a spatial arrangement model that defines the probability of a specific individual brain parcellation, and a set of dataset-specific emission models that defines the probability of the observed data given the individual brain organization. We show that the framework optimally combines information from different datasets to achieve a new population-based atlas of the human cerebellum. Furthermore, we demonstrate that, using only 10 min of individual data, the framework is able to generate individual brain parcellations that outperform group atlases.
Gut physiology of rainbow trout (Oncorhynchus mykiss) is influenced more by short-term fasting followed by refeeding than by feeding fishmeal-free diets
Authors: Frohn Laura , Peixoto Diogo , Terrier Frédéric , Costas Benjamin , Bugeon Jérôme , Cartier Christel , Richard Nadège , Pinel Karine , Skiba-Cassy Sandrine 
Published: May 2023

ABSTRACTSupplementing a fishmeal-free diet with yeast extract improves rainbow trout (Oncorhynchus mykiss) growth performance and modulates the hepatic and intestinal transcriptomic response. These effects are often observed in the long term, but are not well documented after short periods of fasting. Fasting for a few days is a common practice in fish farming, especially before handling the fish, such as for short sorting, tank transfers and vaccinations. In the present study, rainbow trout were subjected to a four-day fast and then refed, for eight days, a conventional diet containing fishmeal (control diet) or alternative diets composed of terrestrial animal by-products supplemented or not with a yeast extract. During the refeeding period alone, most of the parameters considered did not differ significantly in response to the different feeds. Only the expression of claudin-15 was upregulated in fish fed the yeast-supplemented diet compared to the control diet. Conversely, fasting followed by refeeding significantly influenced most of the parameters analyzed. In the proximal intestine, the surface area of villi significantly increased and the density of goblet cell tended to decrease during refeeding. Although no distinct plasma immune response or major signs of gut inflammation were observed, some genes involved in the structure, complement pathway, antiviral functions, coagulation and endoplasmic reticulum stress response of the liver and intestine were significantly regulated by refeeding after fasting. These results indicate that short-term fasting, as commonly practiced in fish farming, significantly alters the physiology of the liver and intestine regardless of the composition of the diet.
Differential early-life survival underlies the adaptive significance of temperature-dependent sex determination in a long-lived reptile
Authors: Bock Samantha , Loera Yeraldi , Johnson Josiah , Smaga Christopher , Haskins David Lee , Tuberville Tracey , Singh Randeep , Rainwater Thomas , Wilkinson Philip , Parrott Benjamin B 
Published: May 2023

AbstractMany ectotherms rely on temperature cues experienced during development to determine offspring sex. The first descriptions of temperature-dependent sex determination (TSD) were made over 50 years ago, yet an understanding of its adaptive significance remains elusive, especially in long-lived taxa.One novel hypothesis predicts that TSD should be evolutionarily favored when two criteria are met – (a) incubation temperature influences annual juvenile survival and (b) sexes mature at different ages. Under these conditions, a sex-dependent effect of incubation temperature on offspring fitness arises through differences in age at sexual maturity, with the sex that matures later benefiting disproportionately from temperatures that promote juvenile survival.The American alligator (Alligator mississippiensis) serves as an insightful model in which to test this hypothesis, as males begin reproducing nearly a decade after females. Here, through a combination of artificial incubation experiments and mark-recapture approaches, we test the specific predictions of the survival-to-maturity hypothesis for the adaptive value of TSD by disentangling the effects of incubation temperature and sex on annual survival of alligator hatchlings across two geographically distinct sites.Hatchlings incubated at male-promoting temperatures consistently exhibited higher survival compared to those incubated at female-promoting temperatures. This pattern appears independent of hatchling sex, as females produced from hormone manipulation at male-promoting temperatures exhibit similar survival to their male counterparts.Additional experiments show that incubation temperature may affect early-life survival primarily by affecting the efficiency with which maternally transferred energy resources are used during development.Results from this study provide the first explicit empirical support for the adaptive value of TSD in a crocodilian and point to developmental energetics as a potential unifying mechanism underlying persistent survival consequences of incubation temperature.
BAP1 deficient human and mouse uveal melanomas up-regulate a shared EMT pathway
Authors: Farag Roula , Jain Fagun , Longakit Anne Nathalie , Luty Amy , Van Raamsdonk Catherine D. 
Published: May 2023

SUMMARYMonosomy 3 is a negative indicator for uveal melanoma (UM). A key tumor suppressor on chromosome 3 is the deubiquitinaseBAP1, which usually has a second hit in cases with monosomy 3. Here, we investigated the role ofBap1loss in the GNAQQ209Lmouse UM model. We found that heterozygousBap1mutations increased the proportion of lung lesions reaching an unusually large size and permitted the growth of liver lesions. Comparison of RNAseq data from mouse and human UM identified a set of 270 genes differentially expressed in the same direction whenBAP1is mutant. The most significant pathway in this gene set was Epithelial to Mesenchymal Transition (EMT). The expression of five apical junction complex genes known to be down-regulated in association with EMT was very significantly correlated with survival in human UM patients. Activation of EMT throughBap1deficiency could increase melanoma plasticity and adaptation to new microenvironments.