bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Regulatory Role for the Circadian Clock Protein TOC1 via RNA binding
Authors: Li Yi , Chang Yong-Gang , Nagel Dawn H. , Chen Tingjian , Rugnone Matias L , LiWang Andy , Kay Steve A. 
Published: May 2020

AbstractThe circadian clock enables plants to predict daily changes of external signals and synchronize them with internal processes, conferring enhanced fitness and growth vigor. The first describedArabidopsiscircadian clock protein is TIMING OF CAB EXPRESSION 1 (TOC1), which functions in a transcriptional feedback loop with two myb transcription factors, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). Previous studies have shown that TOC1 is a DNA-binding transcriptional repressor ofCCA1andLHY. However, the DNA motifs enriched amongst TOC1 targets share weak sequence similarity and lack consensus, suggesting that TOC1 regulates the expression of its targets through a novel mechanism. Here we show that the TOC1 protein binds directly to RNA via its conserved CCT domain. Using in vitro RNA selection, we identified an RNA motif that is recognized by the TOC1-CCT domain. The TOC1-CCT domain binds to this RNA sequence with nanomolar affinity determined by quantitative electrophoretic mobility shift assays (EMSAs) and isothermal titration calorimetry (ITC). NMR experiments showed that two CCT fragments, CCT533-547and CCT550-565, use basic residues to bind the RNA motif. Mutational analysis confirmed that lysyl and arginyl residues bind to RNA in a cooperative manner. Furthermore, transiently expressed wildtype and mutant TOC1 in protoplasts demonstrated that RNA binding activity of TOC1 is required for its function as a transcriptional repressor in vivo. Our results reveal a novel regulatory mechanism for TOC1 through RNA binding, suggesting that TOC1 might play key roles as a multi-function protein.
An inhalation anaesthesia approach for neonatal mice allowing streamlined stereotactic injection in the brain
Authors: Ho Hinze , Fowle Adam , Coetzee Marisa , Greger Ingo H. , Watson Jake F. 
Published: May 2020

AbstractInvestigating brain function requires tools and techniques to visualise, modify and manipulate neuronal tissue. One powerful and popular method is intracerebral injection of customised viruses, allowing expression of exogenous transgenes. This technique is a standard procedure for adult mice, and is used by laboratories worldwide. Use of neonatal animals in scientific research allows investigation of developing tissues, and enables long-term study of cell populations. However, procedures on neonatal mice are more challenging, due to the lack of reliable methods and apparatus for anaesthesia of these animals. Here, we report an inhalation-based protocol for anaesthesia of neonatal (P0-2) mice, and present a custom 3D-printed apparatus for maintenance of anaesthesia during surgical procedures. This approach significantly enhances animal welfare and facilitates wider and simpler use of neonatal rodents in scientific research. Our optimised method of anaesthesia enables a rapid method of stereotactic injection in neonatal mice for transduction of brain tissue. We demonstrate this procedure for targeted labelling of specific brain regions, andin vivomodification of tissue prior to organotypic culture. This anaesthetic approach can be readily employed by any laboratory, and will enable safer use of neonatal rodents across a diverse spectrum of scientific disciplines.HighlightsDevelopment of inhalation-based anaesthesia for early postnatal (P0-2) mice3D-printed mould allows anaesthetic maintenance for neonatal surgeryImproved mouse welfare through reliable neonatal inhalation anaesthesiaRapid procedure for brain transduction of mouse litter in under 2 hours
Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media
Authors: Rajput Akanksha , Poudel Saugat , Tsunemoto Hannah , Meehan Michael , Szubin Richard , Olson Connor A. , Seif Yara , Lamsa Anne , Dillon Nicholas , Vrbanac Alison , Sugie Joseph , Dahesh Samira , Monk Jonathan M. , Dorrestein Pieter C. , Knight Rob , Pogliano Joe , Nizet Victor , Feist Adam M. , Palsson Bernhard O. 
Published: May 2020

AbstractHealthcare-associated methicillin-resistantStaphylococcus aureus(HA-MRSA) USA100 strains are of major concern due to their evolving antibiotic resistant. They are resistant to a broad class of antibiotics like macrolides, aminoglycosides, fluoroquinolones, and many more. The selection of appropriate antibiotic susceptibility examination media is very important. Thus, we use bacteriological (CA-MHB) as well as physiological (R10LB) media to determine the effect of vancomycin on USA100 strains. The study includes the profiling behaviour of HA-MRSA USA100 D592 and D712 strains in the presence of vancomycin through various high-throughput assays. The US100 D592 and D712 strains were characterized at sub-inhibitory concentrations through growth curves, RNA sequencing, bacterial cytological profiling, and exo-metabolomics high throughput experiments. The study reveals the vancomycin resistance behavior of USA100 strains in dual media conditions using wide-ranging experiments.
Development of a vaccine against the newly emerging COVID-19 virus based on the receptor binding domain displayed on virus-like particles
Authors: Zha Lisha , Zhao Hongxin , Mohsen Mona O. , Hong Liang , Zhou Yuhang , Li Zehua , Chen Hongquan , Liu Xuelan , Chang Xinyue , Zhang Jie , Li Dong , Wu Ke , Vogel Monique , Bachmann Martin F , Wang Junfeng 
Published: May 2020

AbstractThe ongoing coronavirus COVID-19 pandemic is caused by a new coronavirus (SARS-CoV-2) with its origin in the city of Wuhan in China. From there it has been rapidly spreading to many cities inside and outside China. Nowadays more than 33 millions with deaths surpassing 1 million have been recorded worldwide thus representing a major health issue. Rapid development of a protective vaccine against COVID-19 is therefore of paramount importance. Here we demonstrated that recombinantly expressed receptor binding domain (RBD) of the spike protein homologous to SARS binds to ACE2, the viral receptor. Higly repetitive display of RBD on immunologically optimized virus-like particles derived from cucumber mosaic virus (CuMVTT) resulted in a vaccine candidate that induced high levels of specific antibodies in mice which were able to block binding of spike protein to ACE2 and potently neutralized COVID-19 virusin vitro.
Extracting transition rates in single-particle tracking using analytical diffusion distribution analysis
Authors: Vink Jochem N.A. , Brouns Stan J.J. , Hohlbein Johannes 
Published: May 2020

AbstractSingle-particle tracking is an important technique in the life sciences to understand the kinetics of biomolecules. Observed diffusion coefficientsin vivo, for example, enable researchers to determine whether biomolecules are moving alone, as part of a larger complex or are bound to large cellular components such as the membrane or chromosomal DNA. A remaining challenge has been to retrieve quantitative kinetic models especially for molecules that rapidly interchange between different diffusional states. Here, we present analytic diffusion distribution analysis (anaDDA), a framework that allows extracting transition rates from distributions of observed diffusion coefficients. We show that theoretically predicted distributions accurately match simulated distributions and that anaDDA outperforms existing methods to retrieve kinetics especially in the fast regime of 0.1-10 transitions per imaging frame. AnaDDA does account for the effects of confinement and tracking window boundaries. Furthermore, we added the option to perform global fitting of data acquired at different frame times, to allow complex models with multiple states to be fitted confidently. Previously, we have started to develop anaDDA to investigate the target search of CRISPR-Cas complexes. In this work, we have optimized the algorithms and reanalysed experimental data of DNA polymerase I diffusing in liveE. coli. We found that long-lived DNA interaction by DNA polymerase are more abundant upon DNA damage, suggesting roles in DNA repair. We further revealed and quantified fast DNA probing interactions that last shorter than 10 ms. AnaDDA pushes the boundaries of the timescale of interactions that can be probed with single-particle tracking and is a mathematically rigorous framework that can be further expanded to extract detailed information about the behaviour of biomolecules in living cells.
Bayesian combination of mechanistic modeling and machine learning (BaM3): improving personalized tumor growth predictions
Authors: Mascheroni Pietro , Savvopoulos Symeon , Alfonso Juan Carlos López , Meyer-Hermann Michael , Hatzikirou Haralampos 
Published: May 2020

AbstractIn clinical practice, a plethora of medical examinations are conducted to assess the state of a patient’s pathology producing a variety of clinical data. However, exploiting these data faces the following challenges: (C1) we lack the knowledge of the mechanisms involved in regulating these data variables, and (C2) data collection is sparse in time since it relies on patient’s clinical presentation. (C1) implies that only a small subset of the relevant variables can be modeled by virtue of mathematical modeling. This limitation allows models to be effective in analyzing the qualitative dynamics of the system, but limits their predictive accuracy. On the other hand, statistical learning methods are well-suited for quantitative reproduction of data, but they do not provide mechanistic understanding of the investigated problem. Moreover, due to (C2) any algorithm is challenged in learning the corresponding disease dynamics. Herein, we propose a novel method, based on the Bayesian coupling of mathematical modeling and machine learning (BaM3), aiming at improving individualized predictions by addressing the aforementioned challenges. As a proof of concept, we evaluate the proposed method on a synthetic dataset for brain tumor growth and analyze its performance in predicting two major clinical outputs, namely tumor burden and infiltration. The BaM3method results in improved predictions in almost all simulated patients, especially for those with a late clinical presentation. In addition, we test the proposed methodology in two settings dealing with real patient cohorts. In both cases, namely cancer growth in chronic lymphocytic leukemia and ovarian cancer, BaM3predictions show excellent agreement with reported clinical data.
Integrated neural dynamics for behavioral decisions and attentional control in the prefrontal cortex
Authors: Erez Yaara , Kadohisa Mikiko , Petrov Philippe , Sigala Natasha , Buckley Mark J. , Kusunoki Makoto , Duncan John 
Published: May 2020

ABSTRACTComplex neural dynamics in the prefrontal cortex contribute to context-dependent decisions and attentional competition. To analyze these dynamics, we apply demixed principal component analysis to activity of a primate prefrontal cell sample recorded in a cued target detection task. The results track dynamics of cue and object coding, feeding into movements along a target present-absent decision axis in a low-dimensional subspace of population activity. For a single stimulus, object and cue coding are seen mainly in the contralateral hemisphere. Later, a developing decision code in both hemispheres may reflect interhemispheric communication. With a target in one hemifield and a competing nontarget in the other, each hemisphere initially encodes the contralateral object, but finally, decision coding is dominated by the task-relevant target. These findings further suggest that exchange of information between hemispheres plays a key role when attentional competition resolves. Tracking complex neural events in a low-dimensional activity subspace illuminates integration of neural codes towards task-appropriate behavior, comprising a building block of learned task structure in the prefrontal cortex.AUTHOR SUMMARYFlexible adaptive processing of information is integral for everyday goal-directed behavior. To unravel dynamic representation of task-relevant information, we analyzed population activity of a primate prefrontal cell sample in a cued target detection task. In a low-dimensional neural subspace, with separate axes for cue, object identity and decision, trajectories showed initial coding of cue and object in the contralateral hemisphere, followed by coding of the behavioral decision across both hemispheres. With target and nontarget stimuli in opposite hemifields, the data suggest initial coding of the contralateral object in each hemisphere. Object coding is then rapidly shut off for the nontarget, and followed by bilateral coding of the target decision. The results bring detailed insight into task structure and information flow within and between the two frontal lobes as a decision is made and attentional competition is resolved.
Detect Genomic G-Quadruplexes in Living Animal Cells with a Tiny Artificial Protein Probe
Authors: Zheng Ke-wei , Zhang Jia-yu , He Yi-de , Gong Jia-yuan , Wen Cui-jiao , Chen Juan-nan , Hao Yu-hua , Tan Zheng 
Published: May 2020

ABSTRACTG-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the biological role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. We engineered a 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technology, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123,000 G4 peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ~70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
Nanoscale imaging of bacterial infections by sphingolipid expansion microscopy
Authors: Götz Ralph , Kunz Tobias C. , Fink Julian , Solger Franziska , Schlegel Jan , Seibel Jürgen , Kozjak-Pavlovic Vera , Rudel Thomas , Sauer Markus 
Published: May 2020

AbstractExpansion microscopy (ExM) enables super-resolution imaging of proteins and nucleic acids on conventional microscopes. However, imaging of details of the organization of lipid bilayers by light microscopy remains challenging. We introduce an azide- and amino-modified sphingolipid ceramide, which upon incorporation into membranes can be labeled by click chemistry and linked into hydrogels, followed by 4x to 10x expansion. Confocal and structured illumination microscopy (SIM) enabled imaging of sphingolipids and their interactions with proteins in the membrane of intracellular organelles with a spatial resolution of 10-20 nm. Because sphingolipids accumulated efficiently in pathogens we used sphingolipid ExM to investigate bacterial infections of human HeLa229 cells byNeisseria gonorrhoeae, Chlamydia trachomatisandSimkania negevensiswith a resolution so far only provided by electron microscopy. In particular, sphingolipid ExM allowed us to visualize the inner and outer membrane of intracellular bacteria and determine their distance to 27.6 ± 7.7 nm.
Cancer-associated hypersialylated MUC1 drives the differentiation of monocytes into macrophages with a pathogenic phenotype
Authors: Beatson Richard , Graham Rosalind , Freile Fabio Grundland , Cozzetto Domenico , Kannambath Shichina , Pfeifer Ester , Woodman Natalie , Owen Julie , Nuamah Rosamond , Mandel Ulla , Pinder Sarah , Gillett Cheryl , Noll Thomas , Bouybayoune Ihssane , Taylor-Papadimitriou Joyce , Burchell Joy M. 
Published: May 2020

AbstractThe tumour microenvironment plays a crucial role in the growth and progression of cancer and the presence of tumour-associated macrophages (TAMs) is associated with poor prognosis. Recent studies show that TAMs show transcriptomic, phenotypic, functional and geographical diversity. Here we show that a sialylated tumour-associated glycoform of the mucin MUC1, MUC1-ST, through the engagement of Siglec-9 can specifically and independently induce the differentiation of monocytes into TAMs with a unique phenotype. These TAMs can recruit and maintain neutrophils, inhibit the function of T cells, degrade basement membrane allowing for invasion, are inefficient at phagocytosis, and can induce plasma clotting. This novel macrophage phenotype is enriched in the stroma at the edge of breast cancer nests and their presence is associated with poor prognosis in breast cancer patients.
Myosin 10 and a Cytoneme-Localized Ligand Complex Promote Morphogen Transport
Authors: Hall Eric T. , Stewart Daniel P. , Dillard Miriam , Wagner Ben , Sykes April , Temirov Jamshid , Cheney Richard E. , Mori Motomi , Robinson Camenzind G. , Ogden Stacey K. 
Published: May 2020

SummaryMorphogens function in concentration-dependent manners to instruct cell fate during tissue patterning. Molecular mechanisms by which these signaling gradients are established and reinforced remain enigmatic. The cytoneme transport model posits that specialized filopodia extend between morphogen-sending and responding cells to ensure that appropriate signal activation thresholds are achieved across developing tissues. How morphogens are transported along and deployed from cytonemes is not known. Herein we show that the actin motor Myosin 10 promotes cytoneme-based transport of Sonic Hedgehog (SHH) morphogen to filopodial tips, and that SHH movement within cytonemes occurs by vesicular transport. We demonstrate that cytoneme-mediated deposition of SHH onto receiving cells induces a rapid signal response, and that SHH cytonemes are promoted by a complex containing a ligand-specific deployment protein and associated co-receptor.One-Sentence summaryCytoneme-based delivery of the Sonic Hedgehog activation signal is promoted by Myosin 10 and BOC/CDON co-receptor function.
Lack of astrocytic glycogen alters synaptic plasticity but not seizure susceptibility
Authors: Duran Jordi , Brewer M. Kathryn , Hervera Arnau , Gruart Agnès , del Rio Jose Antonio , Delgado-García José M. , Guinovart Joan J. 
Published: May 2020

ABSTRACTBrain glycogen is mainly stored in astrocytes. However, recent studies bothin vitroandin vivoindicate that glycogen also plays important roles in neurons. By conditional deletion of glycogen synthase (GYS1), we previously developed a mouse model entirely devoid of glycogen in the central nervous system (GYS1Nestin-KO). These mice displayed altered electrophysiological properties in the hippocampus and increased susceptibility to kainate-induced seizures. To understand which of these functions is related to astrocytic glycogen, in the present study we generated a mouse model in which glycogen synthesis is eliminated specifically in astrocytes (GYS1Gfap-KO). Electrophysiological recordings of awake behaving mice revealed alterations in input/output curves and impaired long-term potentiation, similar, but to a lesser extent, to those obtained with GYS1Nestin-KOmice. Surprisingly, GYS1Gfap-KOmice displayed no change in susceptibility to kainate-induced seizures as determined by fEPSP recordings and video monitoring. These results confirm the importance of astrocytic glycogen in synaptic plasticity.
Pretreatment of aged mice with retinoic acid restores alveolar regeneration via upregulation of reciprocal PDGFRA signaling
Authors: Gokey Jason J. , Snowball John , Green Jenna , Waltamath Marion , Spinney Jillian J. , Black Katharine E. , Hariri Lida P. , Xu Yan , Perl Anne-Karina T. 
Published: May 2020

AbstractObjectivesIdiopathic Pulmonary Fibrosis (IPF) primarily affects the aged population and is characterized by failure of alveolar regeneration leading to loss of alveolar type 1 cells (AT1). Aged mouse models of lung repair have demonstrated that regeneration fails with increased age. Mouse and rat lung repair models have shown retinoic acid (RA) treatment can restore alveolar regeneration. Herein we seek to determine the signaling mechanisms by which RA treatment prior to injury supports alveolar differentiation.DesignPartial pneumonectomy (PNX) lung injury model and next generation sequencing of sorted cell populations are used to uncover molecular targets regulating alveolar repair.In-vitroorganoids generated from Mouse or IPF patient epithelial cells co-cultured with young, aged, or RA pretreated murine mesenchyme are used to test potential targets.Main outcome measurementsKnown alveolar epithelial cell differentiation markers, including HOPX and AGER for AT1 cells are used to assess outcome of treatments.ResultsGene expression analysis of sorted fibroblasts and epithelial cells isolated from lungs of young, aged, and RA treated aged mice predicted increased PDGFA signaling that coincided with regeneration and alveolar epithelial differentiation. Addition of PDGFA induced AT1 and AT2 alveolar differentiation in both mouse and human IPF lung organoids generated with aged fibroblasts and PDGFA monoclonal antibody blocked AT1 cell differentiation in organoids generated with young murine fibroblasts.ConclusionsOur data support the concept that reciprocal PDGFA signaling activates regenerative fibroblasts that support alveolar epithelial cell differentiation and repair, providing a potential therapeutic strategy to influence the pathogenesis of IPF.Key QuestionWhich epithelial-mesenchymal crosstalk pathways are activated by RA pretreatment of aged lungs that support realveolarization after partial pneumonectomy surgery?Bottom LineIncreased PDGFA/PDGFRA signaling in aged lungs promotes regenerative activation of interstitial matrixfibroblast which is required for AT2 to AT1 differentiation and alveolar regeneration.Read OnIn-vitroand in-vivo analysis demonstrated that PDGFA signaling supports alveolar matrixfibroblast and AT1 epithelial cell differentiation, both necessary for alveolar regeneration in aged lungs.
An estimator of the Opportunity for Selection that is independent of mean fitness
Authors: Waples Robin S. 
Published: May 2020

AbstractVariation among individuals in number of offspring (fitness,k) sets an upper limit to the evolutionary response to selection. This constraint is quantified by Crow’s Opportunity for Selection (I), which is the variance in relative fitness. Crow’sIhas been widely used but remains controversial because it depends on mean offspring number in a sample. Here I used a generalized Wright-Fisher model that allows for unequal probabilities of producing offspring to evaluate behavior of Crow’sIand related indices under a wide range of sampling scenarios. Analytical and numerical results are congruent and show that rescaling the sample varianceto its expected value at a fixedremoves dependence ofIon mean offspring number, but the result still depends on choice of. A new index is introduced,, which makesÎindependent of samplewithout the need for variance rescaling. ΔIhas a straightforward interpretation as the component of variance in relative fitness that exceeds that expected under a null model of random reproductive success. ΔIcan be used to directly compare estimates of the Opportunity for Selection for samples from different studies, different sexes, and different life stages.