bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultra-Rapid Somatic Variant Detection via Real-Time Threshold Sequencing
Authors: Wadden Jack , Newell Brandon , Bugbee Joshua , Dickson Robert P. , Koschmann Carl , Blaauw David , Narayanasamy Satish , Das Reetuparna 
Published: May 2021

AbstractMolecular markers are becoming increasingly important for cancer diagnosis, proper clinical trial enrollment, and even surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform. In this work, we present Threshold Sequencing, a methodology for designing protocols for targeted variant detection on real-time sequencers with a minimal time to result. Threshold Sequencing analytically identifies a time-optimal threshold to stop target amplification and begin sequencing. To further reduce diagnostic time, we explore targeted Loop-mediated Isothermal Amplification (LAMP) and design a LAMP-specific bioinformatics tool—LAMPrey—to process sequenced LAMP product. LAMPrey’s concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Coupled with time-optimized DNA extraction and library preparation, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes.
Dissection of N-, O- and glycosphingolipid glycosylation changes in PaTu-S pancreatic adenocarcinoma cells upon TGF-β challenge
Authors: Zhang Jing , Zhang Zejian , Holst Stephanie , Blöchl Constantin , Madunic Katarina , Wuhrer Manfred , ten Dijke Peter , Zhang Tao 
Published: May 2021

AbstractPancreatic ductal adenocarcinoma (PDAC) is characterized by poor prognosis and high mortality. Transforming growth factor-β (TGF-β) plays a key role in tumor progression, which is often associated with aberrant glycosylation. How PDAC cells respond to TGF-β and the role of glycosylation therein is, however, not well known. Here, we investigated the TGF-β-mediated response and glycosylation changes in SMAD4-deficient PaTu-8955S (PaTu-S) cell line. PaTu-S cells responded to TGF-β by upregulating SMAD2 phosphorylation and target gene expression. TGF-β induced expression of the mesenchymal marker N-cadherin, but did not significantly affect epithelial marker E-cadherin expression. The differences of N-glycans, O-glycans and glycosphingolipid (GSL) glycans in PaTu-S cells with TGF-β stimulation were examined. TGF-β treatment primarily induced N-glycome aberrations involving elevated levels of branching, core fucosylation, and sialylation in PaTu-S cells, in line with TGF-β-induced changes in the expression of glycosylation-related genes. In addition, we observed differences in O- and GSL-glycosylation profiles after TGF-β treatment, including lower levels of sialylated Tn antigen, and neoexpression of globosides. Furthermore, SOX4 expression was upregulated upon TGF-β stimulation, and its depletion blocked the TGF-β-induced N-glycomic changes. Thus, our study provides a mechanism by which TGF-β-induced N-glycosylation changes in SOX4 dependent and SMAD4 independent manner in pancreatic cancer cells. Our results open up avenues to study the relevance of glycosylation in TGF-β signaling in SMAD4 inactivated PDAC.
Processing of Pain by the Developing Brain: Evidence of Differences Between Adolescent and Adult Females
Authors: Tong Han , Maloney Thomas C. , Payne Michael F. , King Christopher D. , Ting Tracy V. , Kashikar-Zuck Susmita , Coghill Robert C. , López-Solà Marina 
Published: May 2021

AbstractAdolescence is a sensitive period for both brain development and the emergence of chronic pain particularly in females. However, the brain mechanisms supporting pain perception during adolescence remain unclear. This study compares perceptual and brain responses to pain in female adolescents and adults to characterize pain processing in the developing brain. Thirty adolescent (ages 13-17) and thirty adult (ages 35-55) females underwent a functional MRI scan involving acute experimental pain. Participants received 12 ten-second noxious pressure stimuli which were applied to the left thumbnail at 2.5 and 4 kg/cm2, and rated pain intensity and unpleasantness on a visual analogue scale. We found a significant group-by-stimulus intensity interaction on pain ratings. Compared to adults, adolescents reported greater pain intensity and unpleasantness in response to 2.5 kg/cm2, but not 4 kg/cm2. Adolescents showed greater medial-lateral prefrontal cortex (PFC) and supramarginal gyrus activation in response to 2.5 kg/cm2, and greater medial PFC and rostral anterior cingulate responses to 4 kg/cm2. Adolescents showed augmented pain-evoked responses in the Neurologic Pain Signature and greater activation in the default mode (DMN) and ventral attention (VAN) networks. Also, the amygdala and associated regions played a stronger role in predicting pain intensity in adolescents, and activity in DMN and VAN regions more strongly mediated the relationship between stimulus intensity and pain ratings. This study provides the first evidence of augmented pain-evoked brain responses in healthy female adolescents involving regions important for nociceptive, affective and cognitive processing, in line with their augmented sensitivity to low-intensity noxious stimuli.
Septin function tunes lipid kinase activity and phosphatidylinositol 4,5 bisphosphate turnover during G-protein coupled PLC signaling in vivo
Authors: Kumari Aastha , Ghosh Avishek , Kolay Sourav , Raghu Padinjat 
Published: May 2021

AbstractThe hydrolysis of phosphatidylinositol 4,5− bisphosphate [PI(4,5)P2] at the plasma membrane by receptor activated phospholipase C (PLC) activity is a conserved mechanism of signal transduction. Given the low abundance of PI(4,5)P2 at the plasma membrane, its hydrolysis needs to be coupled to lipid resynthesis to ensure continued PLC activity during receptor activation. However, the mechanism by which PI(4,5)P2 depletion during signalling is coupled to its resynthesis remains unknown. PI(4,5)P2 synthesis is catalyzed by lipid kinase activity and the phosphorylation of phosphatidylinositol 4 phosphate (PI4P) by phosphatidylinositol 4 phosphate 5 kinase (PIP5K) is the final step in this process. In Drosophila photoreceptors, sensory transduction of photon absorption is transduced into PLC activity leading to an electrical response to light. During this process, PI(4,5)P2 is resynthesized by a PIP5K activity but the mechanism by which the activity of this enzyme is coupled to PLC signalling is not known. In this study, we identify a unique protein isoform of dPIP5K, dPIP5KL that is both necessary and sufficient to mediate PI(4,5)P2 synthesis during phototransduction. The activity of dPIP5KLin vitro is enhanced by depletion of PNUT, a non-redundant subunit of the septin family of GTP binding proteins and in vivo, depletion of pnut rescues the effect of dPIP5KL depletion on the light response and PI(4,5)P2 resynthesis during PLC signalling. Lastly we find that depletion of Septin Interacting Protein 1 (Sip1), previously shown to bind PNUT, phenocopies the effect of dPIP5KL depletion in vivo. Thus, our work defines a septin 7 and Sip1 mediated mechanism through which PIP5K activity is coupled to ongoing PLC mediated PI(4,5)P2 depletion.
Loss of imprinting of the Igf2-H19 ICR1 enhances placental endocrine capacity via sex-specific alterations in signalling pathways in the mouse
Authors: Aykroyd Bethany R. L. , Tunster Simon J. , Sferruzzi-Perri Amanda N. 
Published: May 2021

AbstractImprinting control region (ICR1) controls the expression of the Igf2 and H19 genes in a parent-of-origin specific manner. Appropriate expression of the Igf2-H19 locus is fundamental for normal fetal development, yet the importance of ICR1 in the placental production of hormones that promote maternal nutrient allocation to the fetus is unknown. To address this, we used a novel mouse model to selectively delete ICR1 in the endocrine junctional zone (Jz) of the mouse placenta (Jz-ΔICR1). The Jz-ΔICR1 mice exhibit increased Igf2 and decreased H19 expression specifically in the Jz. This was accompanied by an expansion of Jz endocrine cell types due to enhanced rates of proliferation and increased expression of pregnancy-specific glycoprotein 23 in the placenta of both fetal sexes. However, changes in the endocrine phenotype of the placenta were related sexually-dimorphic alterations to the abundance of IGF2 receptors and downstream signalling pathways (PI3K-AKT and MAPK). There was no effect of Jz-ΔICR1 on the expression of targets of the H19 embedded miR-675 or on fetal weight. Our results demonstrate that ICR1 controls placental endocrine capacity via sex-dependant changes in signalling.Summary statementImprinting at Igf2-H19 ICR1 regulates endocrine cell formation and function via sexually-dimorphic changes in PI3K-AKT and MAPK signalling in the mouse.
Pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification
Authors: Weeder Benjamin R. , Wood Mary A. , Li Ellysia , Nellore Abhinav , Thompson Reid F. 
Published: May 2021

AbstractProteasomal cleavage is a key component in protein turnover, as well as antigen presentation and subsequent immune response. Herein we present pepsickle, an open-source tool for proteasomal cleavage prediction with better in vivo prediction performance (AUC) and computational speed than current models available in the field, and with the ability to predict sites based on both constitutive and immunoproteasome profiles. Post-hoc filtering of predicted patient neoepitopes using pepsickle significantly enriches for immune-responsive epitopes and may represent a significant opportunity to improve current epitope prediction and vaccine development pipelines.
Structure-Function Relationships of the Vertebral Endplate
Authors: Wu Yuanqiao , Loaiza Johnfredy , Banerji Rohin , Blouin Olivia , Morgan Elise F. 
Published: May 2021

AbstractBackgroundAlthough deformation and fracture of the vertebral endplate have been implicated in spinal conditions such as vertebral fracture and disc degeneration, few biomechanical studies of this structure are available. The goal of this study was to quantify the mechanical behavior of the vertebral endplate.MethodsEight-five rectangular specimens were dissected from the superior and/or inferior central endplates of human lumbar spine segments L1-L4. Micro-computed tomography (μCT) imaging, four-point-bend testing, and ashing were performed to quantify the apparent elastic modulus and yield stress (modulus and yield stress, respectively, of the porous vertebral endplate), tissue yield stress (yield stress of the tissue of the vertebral endplate, excluding pores), ultimate strain, fracture strain, bone volume fraction (BV/TV), bone mineral density (BMD), and various measures of tissue density and composition (tissue mineral density, ash fraction, and ash density). Regression was used to assess the dependence of mechanical properties on density and composition.ResultsWide variations in elastic and failure properties, and in density and tissue composition, were observed. BMD and BV/TV were good predictors of many of the apparent-level mechanical properties, including modulus, yield stress, and in the case of the inferior vertebral endplate, failure strains. Similar values of the mechanical properties were noted between superior and inferior vertebral endplates. In contrast to the dependence of apparent stiffness and strength on BMD and BV/TV, none of the mechanical properties depended on any of the tissue-level density measurements.ConclusionThe dependence of many of the mechanical properties of the vertebral endplate on BV/TV and BMD suggests possibilities for non-invasive assessment of how this region of the spine behaves during habitual and injurious loading. Further study of the non-mineral components of the endplate tissue is required to understand how the composition of this tissue may influence the overall mechanical behavior of the vertebral endplate.
Herpetologists’ Conservation Research Focus Drives Their Intentions to Participate in Future Public Engagement
Authors: Hecht Kirsten A , Stofer Kathryn A. , Monroe Martha , Klarenberg Geraldine , Nickerson Max A. 
Published: May 2021

AbstractPublic Engagement with Science (PES) is a popular topic in the science community due to general concerns about public support for science, attitudes toward science, and changes in scientific funding requirements. PES may be especially relevant in conservation disciplines as the public plays an important role in conservation practice. Herpetofauna specifically stand to benefit, as PES activities can help improve attitudes and conservation behavior of participants toward uncharismatic species. We assessed the current scope of herpetologists’ PES activities and investigated factors associated with their participation in PES. We used a closed-ended question survey distributed via the listservs of four American herpetological organizations. Herpetologists’ intentions to engage at least 10 hours in the next 12 months significantly differed between herpetologists with high and low conservation research focuses, but hours of engagement in the past 12 months was not significantly different among these groups. Despite most responding herpetologists having limited formal training, time, resources, and institutional support, many participated in a variety of PES activities, often utilizing partnerships and their own resources. Sampled herpetologists rarely evaluated their PES activities or considered publishing about their engagement activities. Some respondents expressed unease with the idea of message framing. Respondents were interested in evaluation training and providing accessible opportunities, and grant funds were the most likely interventions to increase herpetologists’ participation in PES. These results provide reference data and insight into the public engagement practices and needs of practicing herpetologists and conservation scientists.Author statementWe informed participants of their rights and protections as approved by University of Florida IRB201800258. None of the authors have conflicts of interest related to this research. Funding for the research was provided by a Roger Conant Grant from the Society for the Study of Amphibians and Reptiles (SSAR). SSAR had no role in interpretation of data, the writing of the report, or the decision to submit the article for publication.
Soil chemistry determines whether defensive plant secondary metabolites promote or suppress herbivore growth
Authors: Hu Lingfei , Wu Zhenwei , Robert Christelle A.M. , Ouyang Xiao , Züst Tobias , Mestrot Adrien , Xu Jianming , Erb Matthias 
Published: May 2021

AbstractSpecialized metabolites mediate important interactions in both the rhizosphere and the phyllosphere. How this compartmentalized multifunctionality influences plant-environment interactions is unknown. Here, we investigated how the dual role of maize benzoxazinoids as leaf defenses and root siderophores shapes the interaction between maize and a major global insect pest, the fall armyworm. We find that benzoxazinoids suppress fall armyworm growth in soils with low bioavailable iron but enhance growth in soils with higher bioavailable iron. Manipulation experiments confirm that benzoxazinoids suppress herbivore growth under iron-deficient conditions but enhance herbivore growth when iron is present in its free form. This reversal of the protective effect of benzoxazinoids is not associated with major changes in plant primary metabolism. Plant defense activation is modulated by the interplay between soil iron and benzoxazinoids but does not explain fall armyworm performance. Instead, increased iron supply to the fall armyworm by benzoxazinoids in the presence of free iron enhances larval performance. This work identifies soil chemistry as a decisive factor for the impact of plant secondary metabolites on herbivore growth. It also demonstrates how the multifunctionality of plant secondary metabolites drives interactions between abiotic and biotic factors, with major consequences for plant health in variable environments.
Functional alterations in cortical processing of speech in glioma-infiltrated cortex
Authors: Aabedi Alexander A. , Lipkin Benjamin , Kaur Jasleen , Kakaizada Sofia , Reihl Sheantel , Young Jacob S. , Lee Anthony T. , Krishna Saritha , Chang Edward F. , Brang David , Hervey Jumper Shawn L. 
Published: May 2021

AbstractRecent developments in the biology of malignant gliomas have demonstrated that glioma cells interact with neurons through both paracrine signaling and electrochemical synapses. Glioma-neuron interactions consequently modulate the excitability of local neuronal circuits, and it is unclear the extent to which glioma-infiltrated cortex can meaningfully participate in neural computations. For example, gliomas may result in a local disorganization of activity that impedes the transient synchronization of neural oscillations. Alternatively, glioma-infiltrated cortex may retain the ability to engage in synchronized activity, in a manner similar to normal-appearing cortex, but exhibit other altered spatiotemporal patterns of activity with subsequent impact on cognitive processing. Here, we use subdural electrocorticography to sample both normal-appearing and glioma-infiltrated cortex during speech. We find that glioma-infiltrated cortex engages in synchronous activity during task performance in a manner similar to normal-appearing cortex, but recruits a diffuse spatial network. On a temporal scale, we show that glioma-infiltrated cortex has lower capacity for information encoding when performing nuanced tasks such as speech production of monosyllabic versus polysyllabic words. As a result, temporal decoding strategies for distinguishing monosyllabic from polysyllabic words were feasible for signals arising from normal-appearing cortex, but not from glioma-infiltrated cortex. These findings inform our understanding of cognitive processing in chronic disease states and have implications for neuromodulation and prosthetics in patients with malignant gliomas.Significance StatementAs gliomas proliferate, they infiltrate healthy brain tissue. Often, patients with such tumors in the language areas of the brain develop aphasia. Understanding how gliomas interact with normal neural circuits is critical for developing neuroprostheses that restore speech. Recent evidence demonstrates that glioma cells interact synaptically with neurons, and thus can modulate neural circuits. However, it is unclear the extent to which glioma-infiltrated cortex participates in cognitive processing. Using electrocorticography to record both glioma-infiltrated and normal-appearing cortex during speech, we found that glioma-infiltrated cortex is capable of coordinated neural responses, but has reduced capacity for information encoding. Instead, glioma-infiltrated cortex recruits a broader network of cortical regions during speech, which may represent a compensatory mechanism with implications for future neuroprostheses.
Joint inference of migration and reassortment patterns for viruses with segment genomes
Authors: Stolz Ugnė , Stadler Tanja , Müller Nicola F. , Vaughan Timothy G. 
Published: May 2021

AbstractThe structured coalescent allows inferring migration patterns between viral sub-populations from genetic sequence data. However, these analyses typically assume that no genetic recombination process impacted the sequence evolution of pathogens. For segmented viruses, such as influenza, that can undergo reassortment this assumption is broken. Reassortment reshuffles the segments of different parent lineages upon a coinfection event, which means that the shared history of viruses has to be represented by a network instead of a tree. Therefore, full genome analyses of such viruses is complex or even impossible. While this problem has been addressed for unstructured populations, it is still impossible to account for population structure, such as induced by different host populations, while also accounting for reassortmentWe address this by extending the structured coalescent to account for reassortment and present a framework for investigating possible ties between reassortment and migration (host jump) events. This method can accurately estimate sub-population dependent effective populations sizes, reassortment and migration rates from simulated data. Additionally, we apply the new model to avian influenza A/H5N1 sequences, sampled from two avian host types, Anseriformes and Galliformes. We contrast our results with a structured coalescent without reassortment inference, which assumes independently evolving segments. This reveals that taking into account segment reassortment and using sequencing data from several viral segments for joint phylodynamic inference leads to different estimates for effective population sizes, migration and clock rates.This new model is implemented as the Structured Coalescent with Reassortment (SCoRe) package for BEAST 2.5 and is available at https://github.com/jugne/SCORE.
Condensin-driven loop extrusion on supercoiled DNA
Authors: Kim Eugene , Gonzalez Alejandro Martin , Pradhan Biswajit , van der Torre Jaco , Dekker Cees 
Published: May 2021

AbstractCondensin, a structural maintenance of chromosomes (SMC) complex, has been shown to be a molecular motor protein that organizes chromosomes by extruding loops of DNA. In cells, such loop extrusion is challenged by many potential conflicts, e.g., the torsional stresses that are generated by other DNA-processing enzymes. It has so far remained unclear how DNA supercoiling affects loop extrusion. Here, we use time-lapse single-molecule imaging to study condensin-driven DNA loop extrusion on supercoiled DNA. We find that condensin binding and DNA looping is stimulated by positive supercoiled DNA where it preferentially binds near the tips of supercoiled plectonemes. Upon loop extrusion, condensin collects all nearby plectonemes into a single supercoiled loop that is highly stable. Atomic force microscopy imaging shows that condensin generates supercoils in the presence of ATP. Our findings provide insight into the topology-regulated loading and formation of supercoiled loops by SMC complexes and clarify the interplay of loop extrusion and supercoiling.
Calcium dependence of neurotransmitter release at a high fidelity synapse
Authors: Eshra Abdelmoneim , Schmidt Hartmut , Eilers Jens , Hallermann Stefan 
Published: May 2021

AbstractThe Ca2+-dependence of the recruitment, priming, and fusion of synaptic vesicles are fundamental parameters controlling neurotransmitter release and synaptic plasticity. Despite intense efforts, these important steps in the synaptic vesicles’ cycle remain poorly understood because disentangling recruitment, priming, and fusion of vesicles is technically challenging. Here, we investigated the Ca2+-sensitivity of these steps at cerebellar mossy fiber synapses, which are characterized by fast vesicle recruitment mediating high-frequency signaling. We found that the basal free Ca2+ concentration (<200 nM) critically controls action potential-evoked release, indicating a high-affinity Ca2+ sensor for vesicle priming. Ca2+ uncaging experiments revealed a surprisingly shallow and non-saturating relationship between release rate and intracellular Ca2+ concentration up to 50 μM. Sustained vesicle recruitment was Ca2+-independent. Finally, quantitative mechanistic release schemes with five Ca2+ binding steps incorporating rapid vesicle recruitment via parallel or sequential vesicle pools could explain our data. We thus show that co-existing high and low-affinity Ca2+ sensors mediate recruitment, priming, and fusion of synaptic vesicles at a high-fidelity synapse.