bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of tWO novel primers for THE promising amplification of the mitogenomic Cytochrome c Oxidase subunit I (COI) barcoding region in Artemia aff. sinica (Branchiopoda, Anostraca)
Authors: Asem Alireza , Fu Chun-Zheng , Yang Ning , Eimanifar Amin , Cao Ying , Wang Pei-Zheng , Shen Chun-Yang 
Published: May 2022

ABSTRACTDue to the lack of a taxonomic key for the identification of Artemia species, molecular markers have been increasingly used for phylogenetic studies. The mtCOI marker is a regularly considered marker for the molecular systematics of Artemia populations. The proposed universal and specific primers have mostly failed to amplify the Artemia aff. sinica mtCOI marker, and on the whole, the successfully amplified products of the PCR were inefficient, primarily through the representation of poly-peak or incomplete sequences. We presumed that if a forward primer could be developed regarding the joint regions of the last part of the previous gene (tRNATyr) and the beginning of the target gene mtCOI, the sequence could be relevant to the target-sequence of mtCOI. Thus, here, we describe a new set of primers, which could be used to amplify the mtCOI barcoding region of Artemia aff. sinica Cai, 1989, with a high performance of sequencing. The new primer set worked well also for other Artemia bisexual species, as well as for parthenogenetic populations. It is recommended that joint regions between the previous/next gene(s) and the target marker, could be aimed at when designing specific primers for other markers and taxa.
Cell cycle independent role of cyclin D3 in host restriction of SARS-CoV-2 infection
Authors: Gupta Ravi K. , Mlcochova Petra 
Published: May 2022

AbstractThe COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents a great threat to human health. The interplay between the virus and host plays a crucial role in successful virus replication and transmission. Understanding host-virus interactions is essential for development of new COVID-19 treatment strategies. Here we show that SARS-CoV-2 infection triggers redistribution of cyclin D1 and cyclin D3 from the nucleus to the cytoplasm, followed by its proteasomal degradation. No changes to other cyclins or cyclin dependent kinases were observed. Further, cyclin D depletion was independent from SARS-CoV-2 mediated cell cycle arrest in early S phase or S/G2/M phase. Cyclin D3 knockdown by small interfering RNA specifically enhanced progeny virus titres in supernatants. Finally, cyclin D3 co-immunoprecipitated with SARS-CoV-2 Envelope and Membrane proteins. We propose that cyclin D3 inhibits virion assembly and is depleted during SARS-CoV-2 infection to restore efficient assembly and release of newly produced virions.
Single-cell RNA sequencing reveals molecular features of postnatal maturation in the murine retinal pigment epithelium
Authors: Pandey Ravi S. , Krebs Mark P. , Bolisetty Mohan T. , Charette Jeremy R. , Naggert Jürgen K. , Robson Paul , Nishina Patsy M. , Carter Gregory W. 
Published: May 2022

AbstractTranscriptomic analysis of the mammalian retinal pigment epithelium (RPE) aims to identify cellular networks that influence ocular development, maintenance, function, and disease. However, available evidence points to RPE cell heterogeneity in the native tissue, which adds complexity to transcriptomic analysis. Here, to assess cell heterogeneity, we performed single-cell RNA sequencing of RPE cells from two young adult male C57BL/6J mice. Following quality control to ensure robust transcript identification limited to cell singlets, we detected 13,858 transcripts among 2,667 and 2,846 RPE cells, respectively. Dimensional reduction by principal component analysis and uniform manifold approximation and projection revealed six distinct cell popu-lations. All clusters expressed transcripts typical of RPE cells; the smallest (C1, containing 1–2% of total cells) exhibited hallmarks of stem and/or progenitor cells. Placing C1–6 along a pseudotime axis suggested a relative decrease in melanogenesis and stem/progenitor gene expression, and a corresponding increase in visual cycle gene expression upon RPE maturation. K-means testing of all detected transcripts identified additional expression patterns that may advance understanding of RPE stem/pro-genitor cell maintenance and the evolution of cellular metabolic networks during development. This work provides new insights into the transcriptome of the mouse RPE and a baseline for identifying experimentally induced transcriptional changes in future studies of this tissue.
Discovery of diverse human BH3-only and non-native peptide binders of pro-apoptotic BAK indicate that activators and inhibitors use a similar binding mode and are not distinguished by binding affinity or kinetics
Authors: Aguilar Fiona , Yu Stacey , Grant Robert A. , Swanson Sebastian , Ghose Dia , Su Bonnie G. , Sarosiek Kristopher A. , Keating Amy E. 
Published: May 2022

ABSTRACTApoptosis is a programmed form of cell death important for the development and maintenance of tissue homeostasis. The BCL-2 protein family controls key steps in apoptosis, dysregulation of which can lead to a wide range of human diseases. BCL-2 proteins comprise three groups: anti-apoptotic proteins, pro-apoptotic proteins, and BH3-only proteins. BAK is one of two pro-apoptotic proteins, and previous work has shown that binding of certain BH3-only proteins such as truncated BID (tBID), BIM, or PUMA to BAK leads to mitochondrial outer membrane permeabilization, the release of cytochrome c, and ultimately cell death. This process, referred to asactivation, involves the BH3-stimulated conversion of BAK from monomer to dimer and then to oligomers that promote membrane disruption. Crystal structures of putative intermediates in this pathway, crosslinking data, andin vitrofunctional tests have provided insights into the activation event, yet the sequence-function relationships that make some but not all BH3-only proteins function as activators remain largely unexamined. In this work, we used computational protein design, yeast surface-display screening of candidate BH3-like peptides, and structure-based energy scoring to identify ten new binders of BAK that span a large sequence space. Among the new binders are two peptides from human proteins BNIP5 and PXT1 that promote BAK activation in liposome assays and induce cytochrome-c release from mitochondria, expanding current views of how BAK-mediated cell death may be triggered in cells. High-resolution crystal structures and binding experiments revealed a high degree of similarity in binding geometry, affinity, and association kinetics between peptide activators and inhibitors, including peptides described previously and those identified in this work. We propose a model for BAK activation that is based on differential engagement of BAK monomers vs. the BAK activation transition state that integrates our observations with previous reports of BAK binders, activators, and inhibitors.
Comparative and longitudinal analysis of axial and retinal biometry in prospective models of hyperopia
Authors: Pinkney Jai , Gogna Navdeep , Collin Gayle B. , Stone Lisa , Krebs Mark P. , Naggert Juergen K. , Nishina Patsy M. 
Published: May 2022

Structured AbstractPurposeTo quantify changes in axial and retinal biometry in aging hyperopic mouse models.MethodsFundus photographs and ocular biometric measurements from Mfrprd6, Prss56glcr4, Adipor1tm1Dgen, C1qtnf5tm1.1(KOMP)Vlcg and Prss56em2(IMPC)J homozygotes and C57BL/6J control mice were ascertained longitudinally up to one year of age. Parameters including axial length (AL), central corneal thickness (CCT), anterior chamber depth (ACD), lens thickness (LT), outer nuclear layer thickness (ONLT), retinal thickness (RT), vitreous chamber depth (VCD) and posterior length (PL) were measured using Spectral Domain-Optical Coherence Tomography imaging. Mixed-model analysis of variance and factorial analysis of covariance, using body size as a covariate, followed by post-hoc analysis was performed to identify significant strain differences.ResultsStrain specific changes in axial and retinal biometry along with significant effects of age, sex and body size on AL were noted. Mfrprd6, Prss56glcr4, Adipor1tm1Dgen and Prss56em2(IMPC)J homozygotes had significantly shorter AL than controls. While a comparable decrease in PL was observed in Mfrprd6, Prss56glcr4, and Adipor1tm1Dgen homozygotes, the decrease was attributed to changes in different posterior components from each mutant. Mfrprd6 and Adipor1tm1Dgen homozygotes developed regularly sized fundus spots across the ocular globe, which differed from the large bright spots seen in aged Prss56glcr4 and Prss56em2(IMPC)J homozygotes. While ONLT of C1qtnf5tm1.1(KOMP)Vlcg mice was less than controls, AL and fundus images appeared normal.ConclusionsThis study highlights differences in contributions of ocular components to AL among hyperopic mouse models with decreased AL. Understanding the mechanisms through which these proteins function, will help to elucidate their role in controlling ocular growth.
Skeletal muscle cells derived from induced pluripotent stem cells: A platform for limb girdle muscular dystrophies
Authors: Bruge Céline , Geoffroy Marine , Benabidès Manon , Pellier Emilie , Gicquel Evelyne , Dhiab Jamila , Hoch Lucile , Richard Isabelle , Nissan Xavier 
Published: May 2022

AbstractLimb girdle muscular dystrophies (LGMD), caused by mutations in 29 different genes, are the fourth most prevalent group of genetic muscle diseases, leading to progressive weakness and atrophy of the skeletal muscles. Although the link between LGMD and their genetic origins has been determined, LGMD still represent an unmet medical need. In this paper, we describe a platform for modeling LGMD based on the use of human induced pluripotent stem cells (hiPSC). Thanks to the self-renewing and pluripotency properties of hiPSC, this platform provides an alternative and renewable source of skeletal muscle cells (skMC) to primary, immortalized or overexpressing cells. We report that skMC derived from hiPSC express the majority of the genes and proteins causing LGMD. As a proof of concept, we demonstrate the importance of this cellular model for studying LGMDR9 by evaluating disease-specific phenotypes in skMC derived from hiPSC obtained from four patients.
Locating causal hubs of memory consolidation in spontaneous brain network
Authors: Li Zengmin , Athwal Dilsher , Lee Hsu-Lei , Sah Pankaj , Opazo Patricio , Chuang Kai-Hsiang 
Published: May 2022

SUMMARYMemory consolidation after learning involves spontaneous, brain-wide network reorganization during rest and sleep, but how this is achieved is still poorly understood. Current theory suggests that the hippocampus is pivotal for reshaping the connectivity. Here we identify that a different set of spontaneous networks and their hubs are instrumental in consolidating memory during post-learning rest. We found that two types of spatial memory training invoke distinct functional connections, but a network of the sensory cortex and subcortical areas is common for both tasks. Furthermore, learning increased brain-wide network integration, with the prefrontal, striatal and thalamic areas being influential for this network-level reconfiguration. Chemogenetic suppression of each hub identified after learning resulted in retrograde amnesia, confirming the behavioral significance. These results demonstrate the causal and functional roles of resting-state network hubs in memory consolidation and suggest a distributed network beyond the hippocampus subserving this process.
MuSiC2: cell type deconvolution for multi-condition bulk RNA-seq data
Authors: Fan Jiaxin , Lyu Yafei , Zhang Qihuang , Wang Xuran , Li Mingyao , Xiao Rui 
Published: May 2022

ABSTRACTCell type composition of intact bulk tissues can vary across samples. Deciphering cell type composition and its changes during disease progression is an important step towards understanding disease pathogenesis. To infer cell type composition, existing cell type deconvolution methods for bulk RNA-seq data often require matched single-cell RNA-seq (scRNA-seq) data, generated from samples with similar clinical conditions, as reference. However, due to the difficulty of obtaining scRNA-seq data in diseased samples, only limited scRNA-seq data in matched disease conditions are available. Using scRNA-seq reference to deconvolve bulk RNA-seq data from samples with different disease conditions may lead to biased estimation of cell type proportions. To overcome this limitation, we propose an iterative estimation procedure, MuSiC2, which is an extension of MuSiC [1], to perform deconvolution analysis of bulk RNA-seq data generated from samples with multiple clinical conditions where at least one condition is different from that of the scRNA-seq reference. Extensive benchmark evaluations indicated that MuSiC2 improved the accuracy of cell type proportion estimates of bulk RNA-seq samples under different conditions as compared to the traditional MuSiC [1] deconvolution. MuSiC2 was applied to two bulk RNA-seq datasets for deconvolution analysis, including one from human pancreatic islets and the other from human retina. We show that MuSiC2 improves current deconvolution methods and provides more accurate cell type proportion estimates when the bulk and single-cell reference differ in clinical conditions. We believe the condition-specific cell type composition estimates from MuSiC2 will facilitate downstream analysis and help identify cellular targets of human diseases.
A sequential two-step priming scheme reproduces diversity in synaptic strength and short-term plasticity
Authors: Lin Kun-Han , Taschenberger Holger , Neher Erwin 
Published: May 2022

AbstractGlutamatergic synapses display variable strength and diverse short-term plasticity (STP), even for a given type of connection. Using non-negative tensor factorization (NTF) and conventional state modelling, we demonstrate that a kinetic scheme consisting of two sequential and reversible steps of release-machinery assembly and a final step of synaptic vesicle (SV) fusion reproduces STP and its diversity among synapses. Analyzing transmission at calyx of Held synapses reveals that differences in synaptic strength and STP are not primarily caused by variable fusion probability (pfusion) but determined by the fraction of docked synaptic vesicles equipped with a mature release machinery. Our simulations show, that traditional quantal analysis methods do not necessarily report pfusion of SVs with a mature release machinery but reflect both pfusion and the distribution between mature and immature priming states at rest. Thus, the approach holds promise for a better mechanistic dissection of the roles of presynaptic proteins in the sequence of SV docking, two-step priming and fusion and suggests a mechanism for activity-induced redistribution of synaptic efficacy.
Comparative brain structure and the neural network features of cuttlefish and squid
Authors: Chung Wen-Sung , Galan Alejandra L. , Kurniawan Nyoman D. , Justin Marshall N. 
Published: May 2022

AbstractCuttlefishes, like their octopus cousins, are masters of camouflage by control of body pattern and skin texture to blend in with their surroundings for prey ambush and threat avoidance. Aside from significant progress on the cuttlefish visual perception and communication, a growing number of studies have focused on their behavioural neurobiology and the remarkably rapid and apparently cognitively complex reactions to novel challenges such as spatial learning to solve maze tasks and vertebrate-like cognitive capabilities (e.g. object recognition, number sense and episodic-like memory). Despite intense interest of cuttlefish, much of our knowledge of its neuroanatomy and links to behaviour and ecology comes from one temperate species, the European common cuttlefish, Sepia officinalis. Here we present the first detailed comparison of neuroanatomical features between the tropical cuttlefish and squid and describe differences in basic brain and wiring anatomy using MRI-based techniques and conventional histology. Furthermore, comparisons amongst nocturnal and diurnal cuttlefish species suggest that the characteristic neuroanatomical features infer interspecific variation in visual capabilities, the importance of vision relative to the less utilised chemosensory system and clear links with life modes (e.g. diurnal vs nocturnal), ecological factors (e.g. living depth and ambient light condition) as well as to an extent, phylogeny. These findings link brain heterogeneity to ecological niches and lifestyle, feeding hypotheses around evolutionary history and provide a timely, new technology update to older literature.
“Centrosome Amplification promotes cell invasion via cell-cell contact disruption and Rap-1 activation”
Authors: Prakash Anu , Paunikar Shishir , Webber Mark , McDermott Emma , Vellanki Sri H. , Thompson Kerry , Dockery Peter , Jahns Hanne , Brown James A.L. , Hopkins Ann M. , Bourke Emer 
Published: May 2022

ABSTRACTCentrosome amplification (CA) is a prominent feature of human cancers linked to genomic instability and tumourigenesisin vivo. CA is observed as early as pre-malignant metaplasia, with CA incidence increasing as the disease progresses from dysplasia to neoplasia. However, the mechanistic contributions of CA to tumourigenesis (tumour architecture and remodelling) are poorly understood.Using non-tumourigenic breast cells (MCF10A), we demonstrate that CA induction (by CDK1 inhibition or PLK4 overexpression) alone increased both cell migration, invasion and Extracellular Matrix (ECM) remodeling. Mechanistically, CA induction activated small GTPase Rap-1. We demonstrated the key role of Rap-1 mediated signalling in CA induced tumourigenesis through Rap-1 inhibition (using GGTI-298) which blocked CA-induced migration, invasion and ECM attachment.CA induction in a long-term MCF10A cell culture system disrupted epithelial cell-cell junction integrity, via dysregulation of expression and subcellular localisation of cell junction proteins (ZO-1, Occludin, JAM-A & β-catenin). At the ultrastructural level, CA significantly inhibited apical junctional complex formation, as visualized by transmission electron microscopy. CA induction in the luminal A breast cancer cell line MCF7 revealed similar trends in cell junction disruption. Furthermore, CA induction in MCF10A elevated expression of integrin β-3, matrix metalloprotease MMP1 and MMP13 facilitating the observed ECM attachment, degradation and cell invasion phenotype.In vivovalidation using a Chicken Embryo xenograft model, showed CA positive (CA+) MCF10A cells invaded into the chicken mesodermal layer, characterised by inflammatory cell infiltration and a marked focal reaction between chorioallantoic membrane and cell graft. This reaction was inhibited by pre-treatment of CA+ MCF10A cells with GGTI-298. Interestingly, in metastatic breast cancer cells with high levels of endogenous CA (triple negative cell line MDA-MB-231) inhibition of this CA-signalling pathway (using PLK4 inhibitor Centrinone B) abrogated their metastatic capacityin vitro. This demonstrates dual roles for CA signalling, for initiating and maintaining the CA-induced metastatic phenotype.Here, we demonstrated that CA induction in normal non-tumourigenic cells acts through Rap-1-dependent signaling to confer early pro-tumourigenic changes promoting tumour progression, mediated by ECM disruption, and altered cell-cell contacts. These insights reveal that in normal cells, CA induction alone (without additional pro-tumorigenic alterations) is sufficient to induce tumourigenesis and CA-mediated signaling supports a metastatic phenotype.StatementCentrosome amplification alone drives early tumourigenic change in normal breast epithelial cells
Automated design of gene circuits with optimal mushroom-bifurcation behaviour
Authors: Otero-Muras Irene , Perez-Carrasco Ruben , Banga Julio R. , Barnes Chris P. 
Published: May 2022

AbstractRecent advances in synthetic biology are enabling exciting technologies, including the next generation of biosensors, the rational design of cell memory, modulated synthetic cell differentiation and generic multi-functional bio-circuits. These novel applications require the design of gene circuits leading to sophisticated behaviours and functionalities. At the same time, designs need to be kept minimal to avoid compromising cell viability. Bifurcation theory of dynamical systems provides powerful tools to address complex nonlinear dynamics and multifunctionality, linking model topology and kinetic parameters with circuit behaviour. However, the challenge of incorporating bifurcation analysis to automated design has not been accomplished so far. In this work we present an optimisation-based method for the automated forward design of synthetic gene circuits with specified bifurcation diagrams, allowing us to find minimal topologies optimizing the required functionalities and taking into account additional requirements and/or context specifications. We apply the method to design of gene circuits exhibiting the so called mushroom bifurcation, a relatively unexplored multi-functional behaviour of particular relevance for developmental biology. Using the results of the optimisation analysis we explore the capabilities of the resulting circuits for possible applications in advanced biosensors, memory devices, and synthetic cell differentiation.
Brain Activity During Constraint Relaxation in the Insight Problem-Solving Process: An fNIRS Study
Authors: Ohkuma Reiji , Kurihara Yuto , Takahashi Toru , Osu Rieko 
Published: May 2022

AbstractPeople solve insight problems that they encounter daily with a sudden sense of ‘aha!’ to reach a solution. Chunk decomposition, which decomposes the factors of the problem, and constraint relaxation, which manipulates filters to organize the information necessary to solve the problem, are important in insight problem-solving. Although there have been many studies on brain activity during chunk decomposition, few have examined brain activity during constraint relaxation. Particularly, no study has observed the changes over time due to constraint relaxation during insight problem-solving. This study used a slot machine task as an insight problem to measure brain activity using functional Near-Infrared Spectroscopy (fNIRS), and eye movements to estimate constraint relaxation. The results showed that the right dorsolateral prefrontal cortex (DLPFC) and right superior temporal gyrus (STG) were activated over time in participants in whom constraint relaxation was induced. The right inferior temporal gyrus (ITG) of participants who were able to solve the insight problem after constraint relaxation was also activated. The analysis of brain activity during constraint relaxation in insight problem-solving may be useful for advancing research on the ‘aha!’ phenomenon and creativity.