bluuebunny/crossref_metadata_2025 huggingface dataset:
Cancer stem cell-derived extracellular vesicles preferentially target MHC-II– macrophages and PD1+ T cells in the tumor microenvironment
Authors: Gonzalez-Callejo P. , Guo Z. , Ziglari T. , Claudio N.M. , Oshimori N. , Seras-Franzoso J. , Pucci F.
Published: May 2022

Immunotherapy is an approved treatment option for head and neck squamous cell carcinoma (HNSCC). However, the response rate to immune checkpoint blockade is only 13% for recurrent HNSCC, highlighting the urgent need to better understand tumor-immune interplay, with the ultimate goal of improving patient outcomes. HNSCC present high local recurrence rates and therapy resistance that can be attributed to the presence of cancer stem cells (CSC) within tumors. CSC exhibit singular properties that enable them to avoid immune detection and eradication. The immune cell types that directly engage with CSC to allow immune escape and cancer recurrence are still unknown. Here, we genetically engineered CSC-derived extracellular vesicles (EVs) to perform sortase-mediated in vivo proximity labeling. We identified specific immune cell subsets recruited into the CSC niche. We demonstrated that unmanipulated CSC-EVs preferentially target MHC-II– macrophages and PD1+ T cells, and that such EV-mediated intercellular communication between CSC and these immune cells contributed to the observed spatial interactions and niche sharing. These results suggest that combination therapies targeting CSC, tumor macrophages and PD1 may synergize and lower local recurrence rates in HNSCC patients.
Lhx9 haploinsufficiency alters transcription in the adult mouse ovary, causing subfertility and abnormal epithelium
Authors: Workman Stephanie , Wilson Megan J.
Published: May 2022

Understanding the molecular pathways that underpin ovarian development and function is vital for improving the research approaches to investigating fertility. Despite a significant improvement in our knowledge of molecular activity in the ovary, many questions remain unanswered in the quest to understand factors influencing fertility and ovarian pathologies such as cancer. Here we present an investigation into the expression and function of developmental transcription factor LIM Homeobox 9 (LHX9) in the adult mouse ovary. We have characterised Lhx9 expression in several cell types of the mature ovary across follicle stages. To elucidate the function of this expression, we carried out an investigation of ovarian anatomy and transcription in a Lhx9+/- knockout mouse model displaying subfertility. Despite a lack of gross anatomical differences between genotypes, RNA-sequencing found that 90 genes were differentially expressed between Lhx9+/- and Lhx9+/+ mice. Gene ontology analyses revealed a downregulation of genes with major roles in ovarian steroidogenesis and an upregulation of genes with implications for ovarian cancer. Analysis of the ovarian epithelium revealed Lhx9+/- mice have a disorganised epithelial phenotype and a significant increase in epithelial marker gene expression. These results provide an analysis of Lhx9 in the adult mouse ovary and a new candidate for fertility research and ovarian epithelial cancer.

Summary sentence

Lhx9 haploinsufficient mice are subfertile with altered expression of steroid genes in the adult ovary and abnormal ovarian surface epithelium.
Hemodynamic transient and functional connectivity follow structural connectivity and cell type over the brain hierarchy
Authors: Chuang Kai-Hsiang , Huang Helena H , Gerdekoohi Shabnam Khorasani , Li Zengmin , Athwal Dilsher
Published: May 2022

The neural circuit of the brain is organized as a hierarchy of functional units with wide-ranging connections that support information flow and functional connectivity. Studies using magnetic resonance imaging (MRI) indicate a moderate coupling between structural and functional connectivity at the system level. However, how do connections of different directions (feedforward and feedback) and regions with different excitatory and inhibitory (E/I) neurons shape the hemodynamic activity and functional connectivity over the hierarchy are unknown. Here, we used functional MRI to detect optogenetic-evoked and resting-state activities over a somatosensory pathway in the mouse brain in relation to axonal projection and E/I distribution. Using a highly sensitive ultrafast imaging, we identified extensive activation in regions up to the third order of axonal projections following optogenetic excitation of the ventral posteriomedial nucleus of the thalamus. The evoked response and functional connectivity correlated with feedforward projections more than feedback projections and weakened with the hierarchy. The hemodynamic response exhibited regional and hierarchical differences, with slower and more variable responses in high-order areas and bipolar response predominantly in the contralateral cortex. Importantly, the positive and negative parts of the hemodynamic response correlated with E/I neuronal densities, respectively. Furthermore, resting-state functional connectivity was more associated with E/I distribution whereas stimulus-evoked effective connectivity followed structural wiring. These findings indicate that the structure-function relationship is projection-, cell-type- and hierarchy-dependent. Hemodynamic transients could reflect E/I activity and the increased complexity of hierarchical processing.

Significance Statement

The neural circuit of the brain is organized as a hierarchy of functional units with complicated feedforward and feedback connections to selectively enhance (excitation) or suppress (inhibit) information from massive sensory inputs. How brain activity is shaped by the structural wiring and excitatory and inhibitory neurons is still unclear. We characterize how brain-wide hemodynamic responses reflect these structural constituents over the hierarchy of a somatosensory pathway. We find that functional activation and connectivity correlate with feedforward connection strengths and neuronal distributions. This association subsides with hierarchy due to slower and more variable hemodynamic responses, reflecting increased complexity of processing and neuronal compositions in high-order areas. Our findings indicate that hemodynamics follow the hierarchy of structural wiring and neuronal distribution.
Molecular dynamics of spike variants in the locked conformation: RBD interfaces, fatty acid binding and furin cleavage sites
Authors: Shoemark Deborah K. , Oliveira A. Sofia F. , Davidson Andrew D. , Berger Imre , Schaffitzel Christiane , Mulholland Adrian J.
Published: May 2022

Since December 2019 the SARS-CoV-2 virus has infected billions of people around the world and caused millions of deaths. The ability for this RNA virus to mutate has produced variants that have been responsible for waves of infections across the globe. The spike protein on the surface of the SARS-CoV-2 virion is responsible for cell entry in the infection process. Here we have studied the spike proteins from the Original, Alpha (B.1.1.7), Delta (B1.617.2), Delta-plus (B1.617.2-AY1), Omicron BA.1 and Omicron BA.2 variants. Using models built from cryo-EM structures with linoleate bound (6BZ5.pdb) and the N-terminal domain from 7JJI.pdb, each is built from the first residue, with missing loops modelled and 45 disulphides per trimer. Each spike variant was modified from the same Original model framework to maximise comparability. Three replicate, 200 ns atomistic molecular dynamics simulations were performed for each case. (These data also provide the basis for further, non-equilibrium molecular dynamics simulations, published elsewhere.) The analysis of our equilibrium molecular dynamics reveals that sequence variation at the closed receptor binding domain interface particularly for Omicron BA.2 has implications for the avidity of the locked conformation, with potential effects on Omicron BA.1 and Delta-plus. Linoleate binding has a mildly stabilizing effect on furin cleavage site motions in the Original and Alpha variants, but has no effect in Delta, Delta-plus and slightly increases motions at this site for Omicron BA.1, but not BA.2, under these simulation conditions.
The SARS-CoV-2 cellular receptor ACE2 is expressed in oropharyngeal cells and is modulated in vitro by the bacterial lysate Lantigen B
Authors: Pizzimenti Caterina , D’Agostino Antonella , Pirrello Paola , Ruiba Alessia , Melioli Giovanni
Published: May 2022

Angiotensin-converting enzyme2 (ACE2) is the main cell surface receptor of the SARS-CoV-2 spike protein and is expressed in a variety of cell types, including cells of the respiratory tract. A bacterial lysate used for the prophylaxis of respiratory infections (OM-85), was recently shown to downregulate the expression of ACE2 in epithelial cells, suggesting its possible role as a prophylaxis of the onset of COVID19. Another bacterial lysate (Lantigen B, administered sublingually) is used in the prophylaxis of recurrent respiratory tract infections. It contains antigens obtained by chemical lysis from the most representative microbes of the respiratory tract. In this in vitro study, the capacity of Lantigen B to decrease ACE2 in human oropharyngeal cells was evaluated. The study was carried out in 40 healthy donors undergoing oropharyngeal swab for routine SARS-CoV-2 detection. Cells were treated in vitro with a 1:2 of Lantigen B. ACE2 expression was evaluated using a fluorescent anti-ACE2 monoclonal antibody and flow cytometry. A reduction in the number of positive cells was observed in 72% of the patients, while a modulation of ACE2 expression was observed in 62% of the samples. As a control, the expression of the CD54 rhinovirus receptor in the same cells was unaffected. To evaluate the functional effects of down regulation, in a subset of samples, the same oropharynx cells were incubated with Lantigen B and infected with wild-type SARS-CoV-2. After 24 hours, viral RNA, as assessed by rt-PCR, was significantly lower in samples treated with Lantigen B. In conclusion, this study demonstrates that Lantigen B, at a pharmacological dose, modulates the expression of the main SARS-CoV-2 receptor in oropharyngeal cells, and reduces viral yield. This activity could be synergistic with other approaches (vaccination and therapy) by reducing the number of potentially infected cells and thus reducing the effects of SARS-CoV-2 infection.
MegaBayesianAlphabet: Mega-scale Bayesian Regression methods for genome-wide prediction and association studies with thousands of traits
Authors: Qu Jiayi , Runcie Daniel , Cheng Hao
Published: May 2022

Large-scale phenotype data are expected to increase the accuracy of genome-wide prediction and the power of genome-wide association analyses. However, genomic analyses of high-dimensional, highly correlated data are challenging. We developed MegaBayesianAlphabet to simultaneously analyze genetic variants underlying thousands of traits using the flexible priors of the Bayesian Alphabet family. As a demonstration, we implemented the BayesC prior in the R package MegaLMM and applied it to both simulated and real data sets. Our analyses show that the resulting model MegaBayesC can effectively use high-dimensional phenotypic data to improve the accuracy of genetic value prediction, the reliability of marker discovery, and the accuracy of marker effect size estimation in genome-wide analyses.
Evolution towards small colony variants of pandemic multidrug resistant ST131 Escherichia coli isolates from a 10-year bone infection
Authors: Li Fengyang , Lüthje Petra , Shafeeq Sulman , Ahl Marcus , Trcek Janja , Lacosta Analucia Diaz , Özenci Volkan , Ullberg Måns , Åkerlund Börje , Römling Ute
Published: May 2022

Background

Chronic wounds are usually challenging to treat due to underlying medical conditions of the individual and as they readily become infected by microorganisms due to the failure of mechanical and physiological first line innate immune responses. We report here the characterization of host adaptation of five E. coli genomes including three E. coli ST131 genomes that occurred concomitantly with Enterococcus faecalis from a 10-year chronic wound infection after a foot fracture during the 2004 tsunami.

Methods

The five E. coli strains were characterized by various microbiological and genomic approaches. Microbiological methods were antimicrobial resistance, growth in different media and biofilm formation. Genomic methods were determination of the genome sequence by PacBio RSII and Illumina sequencing. Phylogenetic analyses and genome alterations such as single nucleotide polymorphisms, deletion and rearrangements that led to pseudogenes and chromosomal inversions were documented. Relevant selected metabolic and physiological pathways were analyzed for integrity.

Finding

Strains of two initially present sequence types, including the highly antimicrobial resistant ST405 clone, were subsequently replaced by isolates of the ubiquitous ST131 clone. The three E. coli ST131 strains showed a heavily host-adapted genome with a high number of pseudogenes and a large chromosomal inversion compared to ST131 reference strains. Furthermore, two of three E. coli ST131 isolates were small colony variants with its genetic basis in multiple genome alterations including pseudogenes and deletions in the pathway for heme biosynthesis. Pseudogene analysis indicated also the three ST131 strains to be mutator strains. Although enhanced capability of biofilm formation of the ST131 isolates was indicated by the agar plate assay, the a liquid culture biofilm assay did not display pronounced biofilm formation suggesting unconventional modes of biofilm formation.

Interpretation

ST131 clone members, which originally appeared as commensal strains can cause urinary tract and blood stream infections and are ubiquitously found in the environment including waste water and in animals. ST131 strains have presumably been already acquired from the environment on occurrence of the initial foot fracture and can persist in wounds showing an outmost genome plasticity and adaptability which might causing the chronic infection. Although co-infection with E. faecalis might have supported chronicity, these findings indicate that in individuals with underlying metabolic diseases wound infection by ST131 E. coli isolates can be a health risk.

Funding

This work was partially funded by ALF.
A task-general connectivity model reveals variation in convergence of cortical inputs to functional regions of the cerebellum
Authors: King Maedbh , Shahshahani Ladan , Ivry Richard , Diedrichsen Jörn
Published: May 2022

While resting-state fMRI studies have provided a broad picture of the connectivity between human neocortex and cerebellum, the degree of convergence of cortical inputs onto cerebellar circuits remains unknown. Does each cerebellar region receive input from a single cortical area or convergent inputs from multiple cortical areas? Here we use task-based fMRI data to build a range of cortico-cerebellar connectivity models, each allowing for a different degree of convergence. We compared these models by their ability to predict cerebellar activity patterns for novel Task Sets. Models that allow some degree of convergence provided the best predictions, arguing for convergence of multiple cortical inputs onto single cerebellar voxels. Importantly, the degree of convergence varied across the cerebellum with the highest convergence observed in areas linked to language, working memory, and social cognition. These findings suggest important differences in the way that functional subdivisions of the cerebellum support motor and cognitive function.

Highlights

Models of cortico-cerebellar connectivity are quantified using task-based fMRI

Convergent rather than sparse inputs best characterize cortico-cerebellar connectivity

Cerebellar areas linked to cognition receive high convergence of cortical inputs

Models successfully generalize to new tasks and new participants
Multi-tasking Deep Network for Tinnitus Classification and Severity Prediction from Multimodal Structural Images
Authors: Lin Chieh-Te , Ghosh Sanjay , Hinkley Leighton B. , Dale Corby L. , Souza Ana , Sabes Jennifer H. , Hess Christopher P. , Adams Meredith E. , Cheung Steven W. , Nagarajan Srikantan S.
Published: May 2022

Subjective tinnitus is an auditory phantom perceptual disorder without an objective biomarker. Fast and efficient diagnostic tools will advance clinical practice by detecting or confirming the condition, tracking change in severity, and monitoring treatment response. Motivated by evidence of subtle anatomical or functional morphological information in magnetic resonance images (MRI) of the brain, we examined data-driven machine learning methods for joint tinnitus classification (tinnitus or no tinnitus) and tinnitus severity prediction. We propose a deep multi-task multi-modal framework for joint functionalities using structural MRI (sMRI) data. To leverage cross-information multimodal neuroimaging data, we integrated two modalities of 3-dimensional sMRI - T1 weighted (T1w) and T2 weighted (T2w) images. To explore the key components in the MR images that drove task performance, we segmented both T1w and T2w images into three different components - cerebrospinal fluid (CSF), grey matter (GM) and white matter (WM), and examined performance of each segmented image. Results demonstrate that our multimodal framework capitalizes on the information across both modalities (T1w and T2w) for the joint task of tinnitus classification and severity prediction. Our model outperforms existing learning-based and conventional methods in terms of accuracy, sensitivity, specificity, and negative predictive value.
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

Due 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

The 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

Transcriptomic 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

Apoptosis 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 Abstract

Purpose

To quantify changes in axial and retinal biometry in aging hyperopic mouse models.

Methods

Fundus 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.

Results

Strain 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.

Conclusions

This 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

Limb 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

Memory 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

Cell 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

Glutamatergic 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

Cuttlefishes, 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

Centrosome 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.

Statement

Centrosome 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

Recent 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

People 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.
Stiffness of primordial germ cells is required for their extravasation in avian embryos
Authors: Saito Daisuke , Tadokoro Ryosuke , Nagasaka Arata , Yoshino Daisuke , Teramoto Takayuki , Mizumoto Kanta , Funamoto Kenichi , Kidokoro Hinako , Miyata Takaki , Tamura Koji , Takahashi Yoshiko
Published: May 2022

During metastasis intravascularly circulating cancer cells undergo extravasation, which frequently takes place in vascular capillary beds 1–3. It remains poorly understood how the extravasation in the capillary beds is regulated. To address this question, chicken primordial germ cells (PGCs) serve as a powerful model since they circulate in blood stream and extravasate at a specific site of capillary bed near the forming gonad 4–6. The extravasation consists of two steps, the intravascular arrest of cells and their subsequent transmigration through the endothelial lining. We here demonstrate with live imaging at a single cell level in vivo that the arrest of PGCs is predominantly governed by occlusion at a narrow path in the capillary bed. In addition, this occlusion is enabled by a hightened stiffness of the PGCs, revealed by atomic force microscopy indentation analyses. The PGCs’ stiffness is regulated by actin polymerization: inhibition of the actin function causes not only a failure of PGC occlusion in the capillary bed, but also a failure of PGC colonization in the gonads at later stages. Following the occlusion, PGCs reset their stiffness to soften in order to squeeze through the endothelial lining as they transmigrate. The discovery of F-actin-mediated stiffness in pre-extravasating cells provides a model for understanding of dynamic mechanism by which other cells, including metastasizing cancer cells, extravasate in capillary beds.
Chemoenzymatic fluorescence labeling of intercellularly contacting cells using lipidated sortase A
Authors: Yamaguchi Satoshi , Ikeda Ryosuke , Umeda Yuki , Kosaka Takahiro , Yamahira Shinya , Okamoto Akimitsu
Published: May 2022

Methods to label intercellular contact attract particular attention due to their potential in cell biological and medical applications through analysis of intercellular communications. In this study, a simple and versatile method for chemoenzymatically labeling the intercellularly contacting cell was developed by using a cell-surface anchoring reagent of poly(ethylene glycol)(PEG)-lipid conjugate. The surfaces of each cell in cell pairs of interest were efficiently decorated with sortase A (SrtA) and triglycine peptide that were lipidated with PEG-lipid, respectively. In the mixture of the two cell populations, the triglycine-modified cells were enzymatically labeled with a fluorescent labeling reagent by contacting with the SrtA-modified cells both on the substrate and in cell suspensions. Such selective labeling of the contacting cells was confirmed by confocal microscopy and flow cytometry. The results show a proof of principle that the present method is a promising tool for selective visualization and quantification of the intercellularly contacting cells among cell mixtures in cell-cell communication analysis.
Molecular architecture of the C. elegans centriole
Authors: Woglar Alexander , Pierron Marie , Schneider Fabian Zacharias , Jha Keshav , Busso Coralie , Gönczy Pierre
Published: May 2022

Uncovering organizing principles of organelle assembly is a fundamental pursuit in the life sciences. C. elegans was key in identifying evolutionary conserved components governing assembly of the centriole organelle. However, localizing these components with high precision has been hampered by the minute size of the worm centriole, thus impeding understanding of underlying assembly mechanisms. Here, we used Ultrastructure Expansion coupled with STimulated Emission Depletion microscopy (U-Ex-STED), as well as electron microscopy (EM) and tomography (ET), to decipher the molecular architecture of the worm centriole. Achieving an effective lateral resolution of ∼14 nm, we localize centriolar and PeriCentriolar Material (PCM) components in a comprehensive manner with utmost spatial precision. We uncovered that the procentriole assembles from a location on the centriole margin characterized by SPD-2 and ZYG-1 accumulation. Moreover, we found that SAS-6 and SAS-5 are present in the nascent procentriole, with SAS-4 and microtubules recruited thereafter. We registered U-Ex-STED and EM data using the radial array of microtubules, thus allowing us to map each centriolar and PCM protein to a specific ultrastructural compartment. Importantly, we discovered that SAS-6 and SAS-4 exhibit a radial symmetry that is offset relative to microtubules, leading to a chiral centriole ensemble. Furthermore, we establish that the centriole is surrounded by a region from which ribosomes are excluded and to which SAS-7 localizes. Overall, our work uncovers the molecular architecture of the C. elegans centriole in unprecedented detail and establishes a comprehensive framework for understanding mechanisms of organelle biogenesis and function.
Sampling biases obscure the early diversification of the largest living vertebrate group
Authors: Henderson Struan , Dunne Emma M. , Giles Sam
Published: May 2022

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet their spatiotemporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of potential biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends and apply richness estimation techniques to a recently-assembled occurrence database for Palaeozoic ray-finned fishes. We reconstruct patterns of local richness of Palaeozoic actinopterygians, alongside sampling standardised estimates of ‘global’ diversity. We identify substantial fossil record biases, such as geographic bias in the sampling of actinopterygian occurrences centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the abundance distributions of occurrences, reflecting past taxonomic practices and historical biases in sampling. Increasing sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the ‘global’ dataset may identify accurate local diversity trends.
The effect of sociality on competitive interactions among birds
Authors: Berberi Ilias , Miller Eliot T. , Dakin Roslyn
Published: May 2022

Sociality can provide many benefits, including increased foraging success, reproductive opportunities, and defence against predation. How does sociality influence the dominance hierarchies of ecological competitors? Here, we address this question using a large citizen science dataset of competitive interactions among birds foraging at backyard feeders, representing a network of over 55,000 interactions among 68 common species. We first show that species differ in average group size (the number of conspecifics observed together) as a fundamental measure of sociality. When analyzing heterospecific competition, we find that sociality is inversely related to dominance. On average, a single individual from a solitary species is more likely to displace a size-matched opponent than a single individual from a social species. Yet, we find that social species gain an increase in their competitive advantage when in the presence of their conspecifics, which may occur as a result of dynamics within their groups. Finally, we show that more social species have relatively fewer dominance interactions with heterospecifics, and more with conspecifics. Overall, these results demonstrate that sociality can influence competition in ecological networks. More social species have decreased competitive ability as individuals, but they may gain competitive ability in groups.