bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small molecule chaperones facilitate the folding of long non-coding RNA G
Authors: Lejault Pauline , Prudent Louis , Terrier Michel-Pierre , Perreault Jean-Pierre 
Published: April 2023

AbstractRNA G-quadruplexes (rG4) have recently emerged as major regulatory elements in both mRNA and non-coding RNA. To investigate the biological roles of the rG4 structures, chemists have developed a variety of highly specific and potent ligands. All these ligands bind to the rG4 by staking on their top, and the specificity of binding is demonstrated in comparison to other structures such as duplex or three-way junctions. It remains unclear whether rG4-ligands merely stabilize fully formed rG4 structures, or if they actively participate in the folding of the rG4 structure through their association with an unfolded RNA sequence. In order to access the innate steps of ligand-rG4 association and mechanisms, robustin vitrotechniques, including FRET, electrophoretic mobility shift assay and reverse transcriptase stalling assays, were used to examine the capacity of five well-known G4 ligands to induce rG4 structures derived from either long non-coding RNAs of from synthetic RNAs. It was found that both PhenDC3 and PDS induce rG4 formation in unfolded single RNA strands. This discovery has important implications for the interpretation of RNA-seq experiments. Overall,in vitrodata that can assist biochemists in selecting the optimal G4-ligands for their RNA cellular experiments are presented, while also considering the effects induced by these ligands of the rG4.Abstract FigureGraphical abstractA schematic representation of the potential structures that may arise from unfolded RNA that is rich in G nucleotides. rG4 can be stabilized by K+either with or without G4 ligand and can be induced by a molecular chaperone in the presence of Li+.
Dynein-Powered Cell Locomotion Guides Metastasis of Breast Cancer
Authors: Tagay Yerbol , Kheirabadi Sina , Ataie Zaman , Singh Rakesh K. , Prince Olivia , Nguyen Ashley , Zhovmer Alexander S. , Ma Xuefei , Sheikhi Amir , Tsygankov Denis , Tabdanov Erdem D. 
Published: April 2023

ABSTRACTMetastasis is a principal cause of death in cancer patients, which remains an unresolved fundamental and clinical problem. Conventionally, metastatic dissemination is linked to the actomyosin-driven cell locomotion. However, locomotion of cancer cells often does not strictly line up with the measured actomyosin forces. Here, we identify a complementary mechanism of metastatic locomotion powered by the dynein-generated forces. These forces that arise within a non-stretchable microtubule network drive persistent contact guidance of migrating cancer cells along the biomimetic collagen fibers. We also show that dynein-powered locomotion becomes indispensable during invasive 3D migration within a tissue-like luminal network between spatially confining hydrogel microspheres. Our results indicate that the complementary contractile system of dynein motors and microtubules is always necessary and in certain instances completely sufficient for dissemination of metastatic breast cancer cells. These findings advance fundamental understanding of cell locomotion mechanisms and expand the spectrum of clinical targets against metastasis.
The ENCODE Uniform Analysis Pipelines
Authors: Hitz Benjamin C. , Lee Jin-Wook , Jolanki Otto , Kagda Meenakshi S. , Graham Keenan , Sud Paul , Gabdank Idan , Seth Strattan J. , Sloan Cricket A. , Dreszer Timothy , Rowe Laurence D. , Podduturi Nikhil R. , Malladi Venkat S. , Chan Esther T. , Davidson Jean M. , Ho Marcus , Miyasato Stuart , Simison Matt , Tanaka Forrest , Luo Yunhai , Whaling Ian , Hong Eurie L. , Lee Brian T. , Sandstrom Richard , Rynes Eric , Nelson Jemma , Nishida Andrew , Ingersoll Alyssa , Buckley Michael , Frerker Mark , Kim Daniel S , Boley Nathan , Trout Diane , Dobin Alex , Rahmanian Sorena , Wyman Dana , Balderrama-Gutierrez Gabriela , Reese Fairlie , Durand Neva C. , Dudchenko Olga , Weisz David , Rao Suhas S. P. , Blackburn Alyssa , Gkountaroulis Dimos , Sadr Mahdi , Olshansky Moshe , Eliaz Yossi , Nguyen Dat , Bochkov Ivan , Shamim Muhammad Saad , Mahajan Ragini , Aiden Erez , Gingeras Tom , Heath Simon , Hirst Martin , James Kent W. , Kundaje Anshul , Mortazavi Ali , Wold Barbara , Cherry J. Michael 
Published: April 2023

AbstractThe Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of theHomo sapiensandMus musculusgenomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and availableviathe ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL;https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environmentsviaCromwell. Access to the pipelines and dataviathe cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.Database URL:https://www.encodeproject.org/
Optogenetic control of medaka behavior with channelrhodopsin
Authors: Seki Takahide , Takeuchi Hideaki , Ansai Satoshi 
Published: April 2023

AbstractOptogenetics enables the manipulation of neural activity with high spatiotemporal resolution in genetically defined neurons. The method is widely used in various model animals in the neuroscience and physiology fields. Channelrhodopsins are robust tools for optogenetic manipulation, but they have not yet been used for studies in medaka. In the present study, we used the CRISPR/Cas9-mediated knock-in approach to establish a transgenic medaka strain expressing theChloromonas oogamachannelrhodopsin (CoChR) in theISL LIM homeobox 1(isl1) locus. We demonstrated that light stimuli elicited specific behavioral responses such as bending or turning locomotion in the embryos and pectoral fin movements in the larvae and adults. The response probabilities and intensities of these movements could be controlled by adjusting the intensity, duration, or wavelength of each light stimulus. Furthermore, we demonstrated that the pectoral fin movements in the adult stage could be elicited using a laser pointer to irradiate only the hindbrain region. Our results indicate that CoChR allows for manipulation of medaka behaviors by activating targeted neurons, which will further our understanding of the detailed neural mechanisms of social behaviors in medaka.
TALLSorts: a T-cell acute lymphoblastic leukaemia subtype classifier using RNA-seq expression data
Authors: Gu Allen , Schmidt Breon , Lonsdale Andrew , Brown Lauren M. , Sadras Teresa , Ekert Paul G. , Oshlack Alicia 
Published: April 2023

AbstractT-cell acute lymphoblastic leukaemia (T-ALL) is an aggressive and heterogenous haematological malignancy affecting both children and adults. T-ALL subtype identification is an emerging area of active research, with several recent studies proposing potential subtypes based on transcriptomic and genomic analyses. Here we present TALLSorts, a machine-learning bioinformatic tool which classifies T-ALL samples by using bulk RNA sequencing (RNA-seq) data. Trained on four international cohorts totalling 264 samples, TALLSorts exhibits excellent accuracy when tested on holdout and independent test sets. TALLSorts is publicly available for use and will be constantly updated as the field of T-ALL classification further develops.
The Cauchy Process on Phylogenies: a Tractable Model for Pulsed Evolution
Authors: Bastide Paul , Didier Gilles 
Published: April 2023

AbstractPhylogenetic comparative methods use random processes, such as the Brownian Motion, to model the evolution of continuous traits on phylogenetic trees. Growing evidence for non-gradual evolution motivated the development of complex models, often based on Lévy processes. However, their statistical inference is computationally intensive, and currently relies on approximations, high dimensional sampling, or numerical integration. We consider here the Cauchy Process (CP), a particular pure-jump Lévy process in which the trait increment along each branch follows a centered Cauchy distribution with a dispersion proportional to its length. In this work, we derive an exact algorithm to compute both the joint probability density of the tip trait values of a phylogeny under a CP, and the ancestral trait values and branch increments posterior densities in quadratic time. A simulation study shows that the CP generates patterns in comparative data that are distinct from any Gaussian process, and that Restricted Maximum Likelihood (REML) parameter estimates and root trait reconstruction are unbiased and accurate for trees with 200 tips or less. The CP has only two parameters but is rich enough to capture complex pulsed evolution. It can reconstruct posterior ancestral trait distributions that are multimodal, reflecting the uncertainty associated with the inference of the evolutionary history of a trait from extant taxa only. Applied on empirical datasets taken from the Evolutionary Ecology and Virology literature, the CP suggests nuanced scenarios for the body size evolution of Greater Antilles Lizards and for the geographical spread of the West Nile Virus epidemics in North America, both consistent with previous studies using more complex models. The method is efficiently implemented in C with an R interface in package cauphy, that is open source and freely available online. Cauchy process, Phylogenetic Comparative Methods, Evolutionary jumps, Quantitative traits, Phylogeography
RhoB promotesSalmonellasurvival by regulating autophagy
Authors: Kirchenwitz Marco , Halfen Jessica , von Peinen Kristin , Prettin Silvia , Kollasser Jana , Brakebusch Cord , Rottner Klemens , Steffen Anika , Stradal Theresia E.B. 
Published: April 2023

AbstractSalmonella entericaserovar Typhimurium manipulates cellular Rho GTPases for host cell invasion by effector protein translocation via the Type III Secretion System (T3SS). The two Guanine nucleotide exchange (GEF) mimicking factors SopE and –E2 and the inositol phosphate phosphatase (PiPase) SopB activate the Rho GTPases Rac1, Cdc42 and RhoA, thereby mediating bacterial invasion.S.Typhimurium lacking these three effector proteins are largely invasion-defective. Type III secretion is crucial for both early and later phases of the intracellular life ofS.Typhimurium. Here we investigated whether and how the small GTPase RhoB, known to localize on endomembrane vesicles and at the invasion site ofS.Typhimurium, contributes to bacterial invasion and to subsequent steps relevant forS.Typhimurium lifestyle.We show that RhoB is significantly upregulated within hours ofSalmonellainfection. This effect depends on the presence of the bacterial effector SopB, but does not require its phosphatase activity. Our data reveal that SopB and RhoB bind to each other, and that RhoB localizes on early phagosomes of intracellularS.Typhimurium. Whereas both SopB and RhoB promote intracellular survival ofSalmonella, RhoB is specifically required forSalmonella-induced upregulation of autophagy. Finally, in the absence of RhoB, vacuolar escape and cytosolic hyper-replication ofS.Typhimurium is diminished. Our findings thus uncover a role for RhoB inSalmonella-induced autophagy, which supports intracellular survival of the bacterium and is promoted through a positive feedback loop by theSalmonellaeffector SopB.
Spinal motoneurons respond aberrantly to serotonin in a rabbit model of cerebral palsy
Authors: Reedich E. J. , Genry L.T. , Steele P.R. , Avila E. Mena , Dowaliby L. , Drobyshevsky A. , Manuel M. , Quinlan K. A. 
Published: April 2023

AbstractCerebral palsy (CP) is caused by a variety of factors that damage the developing central nervous system. Impaired motor control, including muscle stiffness and spasticity, is the hallmark of spastic CP. Rabbits that experience hypoxic-ischemic (HI) injuryin utero(at 70-80% gestation) are born with muscle stiffness, hyperreflexia, and, as recently discovered, increased serotonin (5-HT) in the spinal cord. To determine whether serotonergic modulation of spinal motoneurons (MNs) contributes to motor deficits, we performedex vivowhole cell patch clamp in neonatal rabbit spinal cord slices at postnatal day (P) 0-5. HI MNs responded to application of α-methyl 5-HT (a 5-HT1/5-HT2receptor agonist) and citalopram (a selective 5-HT reuptake inhibitor) with hyperpolarization of persistent inward currents and threshold voltage for action potentials, reduced maximum firing rate, and an altered pattern of spike frequency adaptation while control MNs did not exhibit any of these responses. To further explore the differential sensitivity of MNs to 5-HT, we performed immunohistochemistry for inhibitory 5-HT1Areceptors in lumbar spinal MNs at P5. Fewer HI MNs expressed the 5-HT1Areceptor compared to age-matched controls. This suggests many HI MNs lack a normal mechanism of central fatigue mediated by 5-HT1Areceptors. Other 5-HT receptors (including 5-HT2) are likely responsible for the robust increase in HI MN excitability. In summary, by directly exciting MNs, the increased concentration of spinal 5-HT in HI rabbits can cause MN hyperexcitability, muscle stiffness, and spasticity characteristic of CP. Therapeutic strategies that target serotonergic neuromodulation may be beneficial to individuals with CP.Key pointsAfter prenatal hypoxia-ischemia (HI), neonatal rabbits that show hypertonia are known to have higher levels of spinal serotoninWe tested responsivity of spinal motoneurons (MNs) in neonatal control and HI rabbits to serotonin using whole cell patch clampMNs from HI rabbits showed a more robust excitatory response to serotonin than control MNs, including hyperpolarization of the persistent inward current and threshold for action potentials, larger post-inhibitory rebound, and less spike frequency adaptationBased on immunohistochemistry of lumbar MNs, fewer HI MNs express inhibitory 5HT1Areceptors than control MNs, which could account for the more robust excitatory response of HI MNs.These results suggest that after HI injury, the increased serotonin could trigger a cascade of events leading to muscle stiffness and altered motor unit development
Statistical analysis of a Potts glass model of cortical dynamics
Authors: Ryom Kwang Il , Treves Alessandro 
Published: April 2023

AbstractWe introduce, in a previously studied Potts model of long-range cortical interactions, a differentiation between a frontal and a posterior subnetwork. “Frontal” units, representing patches of anterior cortex, are endowed with a higher numberSof attractor states, in keeping with the larger number of local synaptic contacts of neurons there, than in occipital cortex. A thermodynamic analysis and computer simulations confirm that disorder leads to glassy properties and slow dynamics but, surprisingly, the frontal network, which would be slower if isolated, becomes faster than the posterior network when interacting with it. From an abstract, drastically simplified model we take some steps towards approaching a neurally plausible one, and find that the speed inversion effect is basically preserved.
SPATIO-TEMPORAL DYNAMICS OF EARLY SOMITE SEGMENTATION IN THE CHICKEN EMBRYO
Authors: Maia-Fernandes Ana Cristina , Martins-Jesus Ana , Pais-de-Azevedo Tomás , Magno Ramiro , Duarte Isabel , Andrade Raquel P. 
Published: April 2023

ABSTRACTDuring vertebrate embryo development, the body is progressively segmented along the anterior-posterior (A-P) axis early in development. The rate of somite formation is controlled by the somitogenesis embryo clock (EC), which was first described as gene expression oscillations ofhairy1(hes4) in the presomitic mesoderm of chick embryos with 15-20 somites. Here, the EC displays the same periodicity as somite formation, 90 min, whereas the posterior-most somites (44-52) only arise every 150 minutes, matched by a corresponding slower pace of the EC. Evidence suggests that the rostral-most somites are formed faster, however, their periodicity and the EC expression dynamics in these early stages are unknown. In this study, we used time-lapse imaging of chicken embryos from primitive streak to somitogenesis stages with high temporal resolution (3-minute intervals). We measured the length between the anterior-most and the last formed somitic clefts in each captured frame and developed a simple algorithm to automatically infer both the length and time of formation of each somite. We found that the occipital somites (up to somite 5) form at an average rate of 75 minutes, while somites 6 onwards are formed approximately every 90 minutes. We also assessed the expression dynamics ofhairy1using half-embryo explants cultured for different periods of time. This showed that EChairy1expression is highly dynamic prior to somitogenesis and assumes a clear oscillatory behaviour as the first somites are formed. Importantly, usingex ovoculture and live-imaging techniques, we showed that thehairy1expression pattern recapitulates with the formation of each new pair of somites, indicating that somite segmentation is coupled with EC oscillations since the onset of somitogenesis.HighlightsTime of early somite formation can be inferred from sequential length measurementsThe cranial-most somites are formed faster than trunk somitesOscillations ofhairy1expression are temporally coupled with early somite formationGRAPHICAL ABSTRACT
Synthetic microbial sensing and biosynthesis of amaryllidaceae alkaloids
Authors: d’Oelsnitz Simon , Diaz Daniel , Acosta Daniel , Schechter Mason , Minus Matthew , Howard James , Loy James , Do Hannah , Alper Hal S. , Ellington Andrew D. 
Published: April 2023

AbstractA major challenge to achieving industry-scale biomanufacturing of therapeutic alkaloids is the slow process of biocatalyst engineering. Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are complex plant secondary metabolites with recognized therapeutic value. Due to their difficult synthesis they are regularly sourced by extraction and purification from low-yielding plants, including the wild daffodilNarcissus pseudonarcissus. Engineered biocatalytic methods have the potential to stabilize the supply chain of amaryllidaceae alkaloids. Here, we propose a highly efficient biosensor-AI technology stack for biocatalyst development, which we apply to engineer amaryllidaceae alkaloid production inEscherichia coli. Directed evolution is used to develop a highly sensitive (EC50= 20 uM) and specific biosensor for the key amaryllidaceae alkaloid branchpoint 4-O’Methylnorbelladine. A machine learning model (MutComputeX) was subsequently developed and used to generate activity-enriched variants of a plant methyltransferase, which were rapidly screened with the biosensor. Functional enzyme variants were identified that yielded a 60% improvement in product titer, 17-fold reduced remnant substrate, and 3-fold lower off-product regioisomer formation.
Chromatin conformation dynamics during CD4+ T cell activation implicates autoimmune disease-associated genes and regulatory elements
Authors: Pahl Matthew C. , Sharma Prabhat , Thomas Rajan M. , Thompson Zachary , Mount Zachary , Pippin James , Morawski Peter A. , Su Chun , Campbell Daniel J. , Grant Struan F.A. , Wells Andrew D. 
Published: April 2023

ABSTRACTGenome-wide association studies (GWAS) have identified hundreds of genetic signals associated with autoimmune disease. The majority of these signals are located in non-coding regions and likely impactcis-regulatory elements (cRE). Because cRE function is dynamic across cell types and states, profiling the epigenetic status of cRE across physiological processes is necessary to characterize the molecular mechanisms by which autoimmune variants contribute to disease risk. We localized risk variants from 15 autoimmune GWAS to cRE active during TCR-CD28 costimulation of naïve human CD4+ T cells. To characterize how dynamic changes in gene expression correlate with cRE activity, we measured transcript levels, chromatin accessibility, and promoter-cRE contacts across three phases of naive CD4+ T cell activation using RNA-seq, ATAC-seq, and HiC. We identified ∼1,200 protein-coding genes physically connected to accessible disease-associated variants at 423 GWAS signals, at least one-third of which are dynamically regulated by activation. From these maps, we functionally validated a novel stretch of evolutionarily conserved intergenic enhancers whose activity is required for activation-inducedIL2gene expression in human and mouse, and is influenced by autoimmune-associated genetic variation. The set of genes implicated by this approach are enriched for genes controlling CD4+ T cell function and genes involved in human inborn errors of immunity, and we pharmacologically validated eight implicated genes as novel regulators of T cell activation. These studies directly show how autoimmune variants and the genes they regulate influence processes involved in CD4+ T cell proliferation and activation.
Non-equilibrium antigen recognition in acute infections
Authors: Morán-Tovar Roberto , Lässig Michael 
Published: April 2023

AbstractThe immune response to an acute primary infection is a coupled process of antigen proliferation, molecular recognition by naive B-cells, and their subsequent proliferation and antibody shedding. Here we show B-cells can efficiently recognise new antigens by a tuned kinetic proofreading mechanism, where the number of proofreading steps and the characteristic rate of each step are set by the complexity of the immune repertoire. This process produces potent, specific and fast recognition of antigens, maintaining a spectrum of genetically distinct B-cell lineages as input for affinity maturation. We show that the proliferation-recognition dynamics of a primary infection can me mapped onto a generalised Luria-Delbrück process, akin to the dynamics of the classic fluctuation experiment. We derive the resulting statistics of the activated immune repertoire: antigen binding affinity, expected size, and frequency of active B-cell clones are related by power laws. Their exponents depend on the antigen and B-cell proliferation rate, the number of proofreading steps, and the lineage density of the naive repertoire. Empirical data of mouse immune repertoires are found to be consistent with activation involving at least three proofreading steps. Our model predicts key clinical characteristics of acute infections. The primary immune response to a given antigen is strongly heterogeneous across individuals; few elite responders are distinguished by early activation of high-affinity clones. Conversely, ageing of the immune system, by reducing the density of naive clones, degrades potency and speed of pathogen recognition.