bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmembrane signalling by a bionic receptor: biological input and output, chemical mechanism of signal transduction
Authors: Løvschall Kaja B. , Monge Pere , Nielsen Line F. , Stevanovic Sandra , Walther Raoul , Zelikin Alexander N. 
Published: July 2021

AbstractSignal transduction through sealed biological membranes is among the most important evolutionary achievements. Herein, we focus on the development of artificial signal transduction mechanisms and engineer a bionic receptor with capacity of transduction of biological signals across biological membranes using tools of chemistry. The bionic receptor described in this work exhibits similarity with the natural counterpart in the most essential characteristics: in having an exofacial ligand for signal capture, in being membrane anchored, and in featuring a releasable secondary messenger molecule, which performs enzyme activation in the endo volume. The main difference with the natural receptors is that signal transduction across the lipid bilayer was performed using the tools of organic chemistry, namely a self-immolative linker. The highest novelty of our work is that the artificial signalling cascade designed herein achieved transmembrane activation of enzymatic activity, as is the hallmark of activity by natural signalling receptors.
Green self-immolative polymer: molecular antenna to collect and propagate the signal for zymogen activation
Authors: Montasell Mireia Casanovas , Monge Pere , Carmali Sheiliza , Dias Loiola Livia Mesquita , Andersen Dante Guldbrandsen , Løvschall Kaja Borup , Søgaard Ane Bretschneider , Kristensen Maria Merrild , Pütz Jean Maurice , Zelikin Alexander N. 
Published: July 2021

AbstractChemical zymogens of three different types were established herein around protein cysteinome, in each case converting the protein thiol into a disulfide linkage: zero length Z0, polyethylene glycol based ZPEG, and ZLA that features a fast-depolymerizing fuse polymer. The latter was a polydisulfide based on a naturally occurring water-soluble lipoic acid. Three zymogen designs were applied to cysteinyl proteases and a kinase and in each case, enzymatic activity was successfully masked in full and reactivated by small molecule reducing agents. However, only ZLA could be reactivated by protein activators, demonstrating that the macromolecular fuse escapes the steric bulk created by the protein globule, collects activation signal in solution, and relays it to the enzyme active site. This afforded first-in-class chemical zymogens that are activated via protein-protein interactions. For ZLA, we also document a “chain transfer” bioconjugation mechanism and a unique zymogen exchange reaction between two proteins.
A comprehensive collection of transcriptome data to support life cycle analysis of the poplar rust fungus Melampsora larici-populina
Authors: Guerillot Pamela , Morin Emmanuelle , Kohler Annegret , Louet Clémentine , Duplessis Sébastien 
Published: July 2021

AbstractMelampsora larici-populina is an obligate biotrophic plant pathogen responsible for the poplar rust disease. This fungus belongs to the taxonomical order Pucciniales and exhibits a complex heteroecious and macrocyclic life cycle, i.e. it has the capacity to infect two unrelated host plants, larch and poplar, and to form five distinct spore types through the year. The M. larici-populina genome has been sequenced and annotated in 2011 and since, different transcriptomic analyses were conducted at different stages with oligoarrays and later on with RNA-Seq covering most of its life cycle. Here, we collected published transcriptome data for the poplar rust fungus, transposed them for the version 2 of the genome now available at the Joint Genome Institute Mycocosm website and performed normalization of different oligoarray datasets on one hand, and of RNA-Seq on the other hand. We report a comprehensive normalized dataset for this fungus, made available for the community, which allows life cycle transcriptomics analysis.
Miniature inverted-repeat transposable elements drive rapid microRNA diversification in angiosperms
Authors: Guo Zhonglong , Kuang Zheng , Tao Yihan , Wang Haotian , Wan Miaomiao , Hao Chen , Shen Fei , Yang Xiaozeng , Li Lei 
Published: July 2021

AbstractMicroRNAs (miRNAs) are rapidly evolving endogenous small RNAs programing organism function and behavior. Although models for miRNA origination have been proposed based on sporadic cases, the genomic mechanisms driving swift diversification of the miRNA repertoires in plants remain elusive. Here, by comprehensively analyzing 20 phylogenetically representative plant species, we identified miniature inverted-repeat transposable elements (MITEs) as the predominant genomic sources for de novo miRNAs in angiosperms. Our data illustrated a transposition-transcription process whereby properly sized MITEs transposed into active genic regions could be converted into new miRNAs, termed MITE-miRNAs, in as few as 20 generations. We showed that this molecular domestication mechanism leads to a possible evolutionary arms race between the MITEs and the host genomes that rapidly and continuously changes the miRNA repertoires. We found that the MITE-miRNAs are selected for targeting genes associated with plant adaptation and habitat expansion, thereby constituting a genomic innovation potentially underlying angiosperm megadiversity.
Distinct mechanisms underlie H2O2 sensing in C. elegans head and tail
Authors: Quintin Sophie , Aspert Théo , Ye Tao , Charvin Gilles 
Published: July 2021

AbstractEnvironmental oxidative stress threatens cellular integrity and should therefore be avoided by living organisms. Yet, relatively little is known about environmental oxidative stress perception. Here, using microfluidics, we showed that like I2 pharyngeal neurons, the tail phasmid PHA neurons function as oxidative stress sensing neurons in C. elegans, but display different responses to H2O2 and light. We uncovered that different but related receptors, GUR-3 and LITE-1, mediate H2O2 signaling in I2 and PHA neurons. Still, the peroxiredoxin PRDX-2 is essential for both, and might promote H2O2-mediated receptor activation. Our work demonstrates that C. elegans can sense a broad range of oxidative stressors using partially distinct H2O2 signaling pathways in head and tail sensillae, and paves the way for further understanding of how the integration of these inputs translates into the appropriate behavior.Graphical abstract
The robustness of a simple dynamic model of island biodiversity to geological and eustatic change
Authors: Neves Pedro Santos , Lambert Joshua W. , Valente Luis , Etienne Rampal S. 
Published: July 2021

AbstractAimBiodiversity on islands is affected by various geo-physical processes and sea-level fluctuations. Oceanic islands (never connected to a landmass) are initially vacant with diversity accumulating via colonisation and speciation, followed by a decline as islands shrink. Continental islands have species upon formation (when disconnected from the mainland) and may have transient land-bridge connections. Theoretical predictions for the effects of these geo-processes on rates of colonisation, speciation and extinction have been proposed, but methods of phylogenetic inference assume only oceanic island scenarios without accounting for island ontogeny, sea-level changes or past landmass connections. Here, we analyse to what extent ignoring geodynamics affects the inference performance of a phylogenetic island model, DAISIE, when confronted with simulated data that violate its assumptions.LocationSimulation of oceanic and continental islands.MethodsWe extend the DAISIE simulation model to include: area-dependent rates of colonisation and diversification associated with island ontogeny and sea-level fluctuations, and continental islands with biota present upon separation from the mainland, and shifts in rates to mimic temporary land-bridges. We quantify the error made when geo-processes are not accounted for by applying DAISIE’s inference method to geodynamic simulations.ResultsWe find that the robustness of the model to dynamic island area is high (error is small) for oceanic islands and for continental islands that have been separated for a long time, suggesting that, for these island types, it is possible to obtain reliable results when ignoring geodynamics. However, for continental islands that have been recently or frequently connected, robustness of DAISIE is low, and inference results should not be trusted.Main conclusions: This study highlights that under a large proportion of island biogeographic geo-scenarios (oceanic islands and ancient continental fragments) a simple phylogenetic model ignoring geodynamics is empirically applicable and informative. However, recent connection to the continent cannot be ignored, requiring development of a new inference model.
Resiniferatoxin hampers the nocifensive response ofCaenorhabditis elegansto noxious heat, and pathway analysis revealed that the Wnt signaling pathway is involved
Authors: Ben Salem Jennifer , Nkambeu Bruno , Arvanitis Dina N , Beaudry Francis 
Published: July 2021

AbstractResiniferatoxin (RTX) is a metabolite extracted fromEuphorbia resinifera. RTX is a potent capsaicin analog with specific biological activities resulting from its agonist activity with the transient receptor potential channel vanilloid subfamily member 1 (TRPV1). RTX has been examined as a pain reliever, and more recently, investigated for its ability to desensitize cardiac sensory fibers expressing TRPV1 to improve chronic heart failure (CHF) outcomes using validated animal models.Caenorhabditis elegans(C. elegans) expresses orthologs of vanilloid receptors activated by capsaicin, producing antinociceptive effects. Thus, we usedC. elegansto characterize the antinociceptive properties and performed proteomic profiling to uncover specific signaling networks. After exposure to RTX, wild-type (N2) and mutantC. eleganswere placed on petri dishes divided into quadrants for heat stimulation. The thermal avoidance index was used to phenotype each testedC. elegansexperimental group. The data revealed for the first time that RTX can hamper the nocifensive response ofC. elegansto noxious heat (32°C – 35°C). The effect was reversed 6 h after RTX exposure. Additionally, we identified the RTX target, theC. eleganstransient receptor potential channel OCR-3. The proteomics and pathway enrichment analysis results suggest that Wnt signaling is triggered by the agonistic effects of RTX onC. elegansvanilloid receptors.
AGO1 regulates pericentromeric regions in mouse embryonic stem cells
Authors: Müller Madlen , Fäh Tara , Schaefer Moritz , Hermes Victoria , Luitz Janina , Stalder Patrick , Arora Rajika , Ngondo Richard Patryk , Ciaudo Constance 
Published: July 2021

ABSTRACTArgonaute proteins (AGOs), that play an essential role in cytosolic post-transcriptional gene silencing, have been also reported to function in nuclear processes like transcriptional activation or repression, alternative splicing and, chromatin organization. As most of these studies have been conducted in human cancer cell lines, the relevance of AGOs nuclear functions in the context of mouse early embryonic development remains uninvestigated. Here, we examined a possible role of the AGO1 protein on the distribution of constitutive heterochromatin in mouse Embryonic Stem Cells (mESCs). We observed a specific redistribution of the repressive histone mark H3K9me3 and the heterochromatin protein HP1α, away from pericentromeric regions upon Ago1 depletion. Furthermore, we demonstrated that major satellite transcripts are strongly upregulated in Ago1_KO mESCs and that their levels are partially restored upon AGO1 rescue. We also observed a similar redistribution of H3K9me3 and HP1α in Drosha_KO mESCs, suggesting a role for microRNAs (miRNAs) in the regulation of heterochromatin distribution in mESCs. Finally, we showed that specific miRNAs with complementarity to major satellites can partially regulate the expression of these transcripts.Summary blurbDepletion of AGO1 in mESCs leads to a redistribution of H3K9me3 and HP1α away from pericentromeric regions and is accompanied by an upregulation of major satellites transcripts.
Low affinity integrin states have faster binding kinetics than the high affinity state
Authors: Li Jing , Yan Jiabin , Springer Timothy A. 
Published: July 2021

AbstractIntegrin conformational ensembles contain two low-affinity states, bent-closed and extended-closed, and an active, high-affinity, extended-open state. It is widely thought that integrins must be activated before they bind ligand; however, one model holds that activation follows ligand binding. As ligand-binding kinetics are not only rate limiting for cell adhesion but also have important implications for the mechanism of activation, we measure them here for integrins α4β1 and α5β1 and show that the low-affinity states bind substantially faster than the high-affinity state. On and off-rate measurements are similar for integrins on cell surfaces and ectodomain fragments. Although the extended-open conformation’s on-rate is ∼20-fold slower, its off-rate is ∼25,000-fold slower, resulting in a large affinity increase. The tighter ligand-binding pocket in the open state may slow its on-rate. These kinetic measurements, together with previous equilibrium measurements of integrin conformational state affinity and relative free energy on intact cells, are key to a definitive understanding of the mechanism of integrin activation.
EXPRESSION OF A SECRETABLE, CELL-PENETRATING CDKL5 PROTEIN ENHANCES THE EFFICACY OF AAV VECTOR-MEDIATED GENE THERAPY FOR CDKL5 DEFICIENCY DISORDER
Authors: Medici Giorgio , Tassinari Marianna , Galvani Giuseppe , Bastianini Stefano , Gennaccaro Laura , Loi Manuela , Mottolese Nicola , Alvente Sara , Berteotti Chiara , Sagona Giulia , Lupori Leonardo , Baggett Helen Rappe , Zoccoli Giovanna , Giustetto Maurizio , Muotri Alysson , Pizzorusso Tommaso , Nakai Hiroyuki , Trazzi Stefania , Ciani Elisabetta 
Published: July 2021

ABSTRACTNo therapy is currently available for CDKL5 (cyclin-dependent kinase-like 5) deficiency disorder (CDD), a severe neurodevelopmental disorder caused by mutations in the CDKL5 gene. Although delivery of a wild-type copy of the mutated gene to cells represents the most curative approach for a monogenic disease, proof-of-concept studies highlight significant efficacy caveats for brain gene therapy. Herein, we used a secretable TATk-CDKL5 protein to enhance the efficiency of a gene therapy for CDD. We found that, although AAVPHP.B_Igk-TATk-CDKL5 and AAVPHP.B_CDKL5 vectors had similar brain infection efficiency, the AAVPHP.B_Igk-TATk-CDKL5 vector led to a higher CDKL5 protein replacement due to secretion and transduction of the TATk-CDKL5 protein into the neighboring cells. Importantly, Cdkl5 KO mice treated with the AAVPHP.B_Igk-TATk-CDKL5 vector showed a behavioral and neuroanatomical improvement in comparison with vehicle-treated Cdkl5 KO mice or Cdkl5 KO mice treated with the AAVPHP.B_CDKL5 vector, indicating that a gene therapy based on a secretable recombinant TATk-CDKL5 protein is more effective at compensating Cdkl5-null brain defects than gene therapy based on the expression of the native CDKL5.
EMDA: A Python package for Electron Microscopy Data Analysis
Authors: Warshamanage Rangana , Yamashita Keitaro , Murshudov Garib N. 
Published: July 2021

AbstractAn open-source Python library EMDA for cryo-EM map and model manipulation is presented with a specific focus on validation. The use of several functionalities in the library is presented through several examples. The utility of local correlation as a metric for identifying map-model differences and unmodeled regions in maps, and how it is used as a metric of map-model validation is demonstrated. The mapping of local correlation to individual atoms, and its use to draw insights on local signal variations are discussed. EMDA’s likelihood-based map overlay is demonstrated by carrying out a superposition of two domains in two related structures. The overlay is carried out first to bring both maps into the same coordinate frame and then to estimate the relative movement of domains. Finally, the map magnification refinement in EMDA is presented with an example to highlight the importance of adjusting the map magnification in structural comparison studies.
Quantitative Profiling of Adaptation to Cyclin E Overproduction
Authors: Limas Juanita C. , Littlejohn Amiee N. , House Amy M. , Kedziora Katarzyna M. , Mouery Brandon L. , Ma Boyang , Fleifel Dalia , Walens Andrea , Aleman Maria M. , Dominguez Daniel , Cook Jeanette Gowen 
Published: July 2021

ABSTRACTCyclin E/CDK2 drives cell cycle progression from G1 to S phase. Cyclin E overproduction is toxic to mammalian cells, although the gene encoding cyclin E (CCNE1) is overexpressed in some cancers. To gain insight into how cancer cells tolerate high cyclin E, we extensively characterized non-transformed epithelial cells throughout a time course of chronic cyclin E overproduction. Cells overproducing human cyclin E, but not cyclin D or cyclin A, briefly experienced truncated G1 phases, then endured a transient period of DNA replication origin underlicensing, replication stress, and severely impaired proliferation. Individual cells displayed substantial intercellular heterogeneity in cell cycle dynamics and CDK activity. Each phenotype improved rapidly despite maintaining high cyclin E-associated activity. Transcriptome analysis revealed that adapted cells downregulated a cohort of G1-regulated genes. Withdrawing cyclin E induction only partially reversed the intermediate licensing phenotype of adapted cells indicating that adaptation is at least partly independent of mutations. This study provides evidence that mammalian cyclin E/CDK inhibits origin licensing by an indirect mechanism through premature S phase onset and provides further insight into the relationship between CDK activity and licensing in mammals. It serves as an example of specific oncogene adaptation that may recapitulate molecular changes during tumorigenesis.
Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance
Authors: Abrams Melanie B. , Chuong Julie N. , AlZaben Faisal , Dubin Claire A. , Skerker Jeffrey M. , Brem Rachel B. 
Published: July 2021

ABSTRACTDecades of successes in statistical genetics have revealed the molecular underpinnings of traits as they vary across individuals of a given species. But standard methods in the field can’t be applied to divergences between reproductively isolated taxa. Genome-wide reciprocal hemizygosity mapping (RH-seq), a mutagenesis screen in an inter-species hybrid background, holds promise as a method to accelerate the progress of interspecies genetics research. Here we describe an improvement to RH-seq in which mutants harbor barcodes for cheap and straightforward sequencing after selection in a condition of interest. As a proof of concept for the new tool, we carried out genetic dissection of the difference in thermotolerance between two reproductively isolated budding yeast species. Experimental screening identified dozens of candidate loci at which variation between the species contributed to the thermotolerance trait. Hits were enriched for mitosis genes and other housekeeping factors, and among them were multiple loci with robust sequence signatures of positive selection. Together, these results shed new light on the mechanisms by which evolution solved the problems of cell survival and division at high temperature in the yeast clade, and they illustrate the power of the barcoded RH-seq approach.
Interstitial and cerebrospinal fluid exchanging process revealed by phase alternate labeling with null recovery MRI
Authors: Li Anna M. , Xu Jiadi 
Published: July 2021

AbstractPurposeTo develop Phase Alternate LAbeling with Null recovery (PALAN) MRI methods for the quantification of interstitial to cerebrospinal fluid flow (ICF) and cerebrospinal to interstitial fluid flow (CIF) in the brain.MethodIn both T1-PALAN and apparent diffusion coefficient (ADC)-PALAN MRI methods, the cerebrospinal fluid (CSF) signal was nulled, while the residual interstitial fluid (ISF) was labeled by alternating the phase of pulses. ICF was extracted from the difference between the recovery curves of CSF with and without labeling. Similarly, CIF was measured by the T2-PALAN MRI method by labeling CSF, which took advance of the significant T2 difference between CSF and parenchyma.ResultsBoth T1-PALAN and ADC-PALAN observed a rapid occurrence of ICF at 67±56 ms and 13±2 ms interstitial fluid transit times, respectively. ICF signal peaked at 1.5 s for both methods. ICF was 1153±270 ml/100ml/min with T1-PALAN in the third and lateral ventricles, which was higher than 891±60 ml/100ml/min obtained by ADC-PALAN. The results of the T2-PALAN suggested the ISF exchanging from ependymal layer to the parenchyma was extremely slow.ConclusionThe PALAN methods are suitable tools to study ISF and CSF flow kinetics in the brain.
Structure and function of the ROR2 cysteine-rich domain in vertebrate noncanonical WNT5A signaling
Authors: Griffiths Samuel C. , Tan Jia , Wagner Armin , Blazer Levi , Adams Jarret J. , Srinivasan Srisathya , Moghisaei Shayan , Sidhu Sachdev S. , Siebold Christian , Ho Hsin-Yi Henry 
Published: July 2021

AbstractThe receptor tyrosine kinase ROR2 mediates noncanonical WNT5A signaling to orchestrate tissue morphogenetic processes, and dysfunction of the pathway causes Robinow syndrome, Brachydactyly B and metastatic diseases. The domain(s) and mechanisms required for ROR2 function, however, remain unclear. We solved the crystal structure of the extracellular cysteine-rich (CRD) and Kringle (Kr) domains of ROR2 and found that, unlike other CRDs, the ROR2 CRD lacks the signature hydrophobic pocket that binds lipids/lipid-modified proteins, such as WNTs, suggesting a novel mechanism of ligand reception. Functionally, we showed that the ROR2 CRD, but not other domains, is required and minimally sufficient to promote WNT5A signaling, and Robinow mutations in the CRD and the adjacent Kr impair ROR2 secretion and function. Moreover, using function-activating and -perturbing antibodies against the Frizzled (FZ) family of WNT receptors, we demonstrate the involvement of FZ in WNT5A-ROR signaling. Thus, ROR2 acts via its CRD to potentiate the function of a receptor super-complex that includes FZ to transduce WNT5A signals.