bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibitory Gating of Coincidence-Dependent Sensory Binding in Secondary Auditory Cortex
Authors: Kline Amber M. , Aponte Destinee A. , Tsukano Hiroaki , Giovannucci Andrea , Kato Hiroyuki K 
Published: May 2021

AbstractIntegration of multi-frequency sounds into a unified perceptual object is critical for recognizing syllables in speech. This “feature binding” relies on the precise synchrony of each component’s onset timing, but little is known regarding its neural correlates. We find that multi-frequency sounds prevalent in vocalizations, specifically harmonics, preferentially activate the mouse secondary auditory cortex (A2), whose response deteriorates with shifts in component onset timings. The temporal window for harmonics integration in A2 was broadened by inactivation of somatostatin-expressing interneurons (SOM cells), but not parvalbumin-expressing interneurons (PV cells). Importantly, A2 has functionally connected subnetworks of neurons encoding harmonic, but not inharmonic sounds. These subnetworks are stable across days and exist prior to experimental harmonics exposure, suggesting their formation during development. Furthermore, A2 inactivation impairs performance in a discrimination task for coincident harmonics. Together, we propose A2 as a locus for harmonic integration, which may form the circuit basis for vocal processing.
The BH3-only protein NOXA serves as an independent predictor of breast cancer patient survival and defines susceptibility to microtubule targeting agents
Authors: Karbon Gerlinde , Haschka Manuel D. , Hackl Hubert , Soratroi Claudia , Rocamora-Reverte Lourdes , Parson Walther , Fiegl Heidelinde , Villunger Andreas 
Published: May 2021

AbstractBreast cancer (BC) treatment frequently involves microtubule-targeting agents (MTAs), such as paclitaxel, that arrest cells in mitosis. Sensitivity to MTAs is defined by a subset of pro- and anti-apoptotic BCL2 family proteins controlling mitochondrial apoptosis. Here, we aimed to determine their prognostic value in primary tumour samples from 92 BC patients. Our analysis identified high NOXA/PMAIP mRNA expression levels as an independent prognostic marker for improved relapse-free survival (RFS) and overall survival (OS) in multivariate analysis in BC patients, independent of their molecular subtype. Analysis of available TCGA datasets of 1060 BC patients confirmed our results and added a clear predictive value of NOXA mRNA levels for patients who received MTA-based therapy. In this TCGA cohort, 122 patients received MTA-treatment and high NOXA mRNA levels correlated with their progression-free interval (PFI) and OS. Our follow-up analyses in a panel of BC cell lines of different molecular subtypes identified NOXA protein expression as a key determinant of paclitaxel sensitivity in triple-negative breast cancer (TNBC) cells. Moreover, we noted highest additive effects between paclitaxel and chemical inhibition of BCLX, but not BCL2 or MCL1, documenting dependence of TNBC cells on BCLX for survival and paclitaxel sensitivity, defined by NOXA expression levels.
Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity
Authors: McBride Cameron D. , Del Vecchio Domitilla 
Published: May 2021

AbstractThe design of genetic circuits typically relies on characterization of constituent modules in isolation to predict the behavior of modules’ composition. However, it has been shown that the behavior of a genetic module changes when other modules are in the cell due to competition for shared resources. In order to engineer multi-module circuits that behave as intended, it is thus necessary to predict changes in the behavior of a genetic module when other modules load cellular resources. Here, we introduce two characteristics of circuit modules: the demand for cellular resources and the sensitivity to resource loading. When both are known for every genetic module in a circuit library, they can be used to predict any module’s behavior upon addition of any other module to the cell. We develop an experimental approach to measure both characteristics for any circuit module using a resource sensor module. Using the measured resource demand and sensitivity for each module in a library, the outputs of the modules can be accurately predicted when they are inserted in the cell in arbitrary combinations. These resource competition characteristics may be used to inform the design of genetic circuits that perform as predicted despite resource competition.
Female mice exhibit a more sensitive automated squint response to pain induced by CGRP and amylin
Authors: Rea Brandon J. , Sowers Levi P. , Davison Abigail L. , Fairbanks Aaron M. , Wattiez Anne-Sophie , Poolman Pieter , Kardon Randy H. , Russo Andrew F. 
Published: May 2021

ABSTRACTWe developed an automated squint assay using both black C57BL/6J and white CD1 mice that measured the interpalpebral fissure area between the upper and lower eyelids as an objective quantification of pain. In C57BL/6J mice, we observed a squint response to increasing doses of a migraine trigger, the neuropeptide CGRP, including a significant response in female mice at a dose below detection by the manual grimace scale. Using the automated software, both C57BL/6J and CD1 mice lacked a detectable photic blink response. The CGRP-related peptide amylin induced squinting behavior in female mice, but not males. These data demonstrate that an automated squint assay can be used as an objective, real-time continuous-scale measure of pain that provides higher precision and real-time analysis compared to manual grimace assessments.
Expression of putative effectors of different Xylella fastidiosa subspecies/strains reveals recognition and defense activation in various model plants
Authors: Sertedakis Matthaios , Kotsaridis Konstantinos , Tsakiri Dimitra , Dominguez-Ferreras Ana , Ntoukakis Vardis , Sarris Panagiotis F. 
Published: May 2021

SUMMARYThe re-emergence of Gram-negative bacterium Xylella fastidiosa in Europe in 2013 impelled the scientific community to discover novel strategies for crop protection. The wide host range of Xylella indicates the existence of yet not characterized pathogenic mechanisms to overcome plant defenses. The recent uprising accuracy of a variety of bioinformatics tools, with the ability to predict the function of putative microbial protein represent a useful approach for understanding which of these proteins are associated with pathogens virulence. In this study we collected a number of putative effectors from two X. fastidiosa strains: Temecula1 and CoDiRo and the subspecies (ssp.) Sandyi Ann-1. We designed an in-planta Agrobacterium based expression system that drives the expressed proteins to the cell apoplast, in order to investigate their ability to activate defense in various model plants. Furthermore, we organized the resulted proteins according to their sequential and structural similarities via the I-TASSER online tool. We identified that various X. fastidiosa proteins were able to differentially elicit cell death-like phenotypes in Nicotiana tabacum, N. sylvestris and N. benthamiana. These proteins are members of different enzymatic groups: a) hydrolases/hydrolases inhibitors, b) serine proteases and c) metal transferases. Collectively, we identified structurally similar proteins that were able to differentially elicit cell death-like phenotypes in different cultivars of the same species. Our findings provide the bases for further studies on the mechanisms that underlie host-defense activation by X. fastidiosa putative effectors, as well as, pathogens adaptation in susceptible hosts.
Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages
Authors: Meeske Alexander J , Johnson Matthew C. , Hille Logan T. , Kleinstiver Benjamin P. , Bondy-Denomy Joseph 
Published: May 2021

AbstractCRISPR systems are prokaryotic adaptive immune systems that use RNA-guided Cas nucleases to recognize and destroy foreign genetic elements, like bacteriophages and plasmids. To overcome CRISPR immunity, phages have evolved diverse families of anti-CRISPR proteins (Acrs), each of which inhibits the nucleic acid binding or cleavage activities of specific Cas protein families. Recently, Lin et al. (2020) described the discovery and characterization of 7 different Acr families (AcrVIA1-7) that inhibit type VI-A CRISPR systems, which use the nuclease Cas13a to perform RNA-guided RNA cleavage. In this Matters Arising article, we detail several inconsistencies that question the results reported in the Lin et al. (2020) study. These include inaccurate bioinformatics analyses, as well as reported experiments involving bacterial strains that are impossible to construct. The authors were unable to provide their published strains with which we might reproduce their experiments. We independently tested the Acr sequences described in Lin et al. (2020) in two different Cas13 inhibition assays, but could not detect anti-CRISPR activity. Taken together, our data and analyses prompt us to question the claim that AcrVIA1-7 reported in Lin et al. are bona fide type VI anti-CRISPR proteins.
Identifying and Classifying Goals For Scientific Knowledge
Authors: Boguslav Mayla R. , Salem Nourah M. , White Elizabeth K. , Leach Sonia M. , Hunter Lawrence E. 
Published: May 2021

AbstractMotivationScience progresses by posing good questions, yet work in biomedical text mining has not focused on them much. We propose a novel idea for biomedical natural language processing: identifying and characterizing thequestionsstated in the biomedical literature. Formally, the task is to identify and characterizeignorance statements, statements where scientific knowledge is missing or incomplete. The creation of such technology could have many significant impacts, from the training of PhD students to ranking publications and prioritizing funding based on particular questions of interest. The work presented here is intended as the first step towards these goals.ResultsWe present a novel ignorance taxonomy driven by the role ignorance statements play in the research, identifying specific goals for future scientific knowledge. Using this taxonomy and reliable annotation guidelines (inter-annotator agreement above 80%), we created a gold standard ignorance corpus of 60 full-text documents from the prenatal nutrition literature with over 10,000 annotations and used it to train classifiers that achieved over 0.80 F1 scores.AvailabilityCorpus and source code freely available for download athttps://github.com/UCDenver-ccp/Ignorance-Question-Work. The source code is implemented in Python.ContactMayla.Boguslav@CUAnshcutz.edu
Genetic Variation as a Long-Distance Modulator of RAD21 Expression in Humans
Authors: Schierding William , Horsfield Julia A. , O’Sullivan Justin 
Published: May 2021

AbstractMutations and changes in expression in RAD21 are common across cancers types and outside of cancer can result in cohesinopathy. As such, exploration of variants that modify RAD21 enhancer activity, across the genome, may also provide insights into mechanisms by which distinct variants impact healthy human development and disease. We searched 42,953,834 genomic variants for a spatial-eQTL association with the transcription of RAD21. We identified 123 significant associations (FDR < 0.05), which are local (cis) or long-distance (trans) regulators of RAD21 expression. The 123 variants co-regulate a further seven genes, enriched for having Sp2 transcription factor binding sites in their promoter regions. The Sp2 transcription factor and six of the seven genes had previously been associated with cancer onset, progression, and metastasis. Our results suggest that genome-wide variation in non-coding regions impacts on RAD21 transcript levels in addition to other genes, which then could impact on oncogenesis and the process of ubiquitination. This identification of distant co-regulation of oncogenes represents a strategy for discovery of novel genetic regions which impact cancer onset and a potential for diagnostics.
Fitness Landscapes Reveal Context-dependent Benefits of Oviposition Choice
Authors: Ravi Kumar Vrinda , Agavekar Gaurav , Agashe Deepa 
Published: May 2021

ABSTRACTResource choice behaviour has enormous fitness consequences and can drive niche expansion. However, individual behavioural choices are often mediated by context, determined by past experience. Are such context-dependent behaviours adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition choice reflects distinct, context-specific local fitness peaks. Manipulating female egg allocation in a habitat containing optimal and suboptimal resource patches, we measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviours (i.e., combinations of fecundity and resource preference). Females from different age and competition contexts exhibit distinct behaviours which optimize different fitness components that are linked in a tradeoff. With increasing age and prior exposure to competition, they produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naïve females produce many slow-developing offspring, beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioural optimality and offers predictive power in novel contexts.Preprint available at - https://www.biorxiv.org/content/10.1101/2021.05.27.445916v1.fullCitation - Vrinda Ravi Kumar, Gaurav Agavekar, Deepa Agashe; bioRxiv 2021.05.27.445916; doi: https://doi.org/10.1101/2021.05.27.445916
Production of human translation-competent lysates using dual centrifugation
Authors: Gurzeler Lukas-Adrian , Ziegelmüller Jana , Mühlemann Oliver , Karousis Evangelos D. 
Published: May 2021

ABSTRACTProtein synthesis is a central process in gene expression and the development of efficient in vitro translation systems has been the focus of scientific efforts for decades. The production of translation-competent lysates originating from human cells or tissues remains challenging, mainly due to the variability of cell lysis conditions. Here we present a robust and fast method based on dual centrifugation that allows for detergent-free cell lysis under controlled mechanical forces. We optimized the lysate preparation to yield cytoplasm-enriched extracts from human cells that efficiently translate mRNAs in a cap-dependent as well as in an IRES-mediated way. Reduction of the phosphorylation state of eIF2α using recombinant GADD34 and 2-aminopurine considerably boosts the protein output, reinforcing the potential of this method to produce recombinant proteins from human lysates.
Distinct Neural Representations of Decision Uncertainty in Metacognition and Mentalizing
Authors: Jiang Shaohan , Wang Sidong , Wan Xiaohong 
Published: May 2021

AbstractMetacognition and mentalizing are both associated with meta-level mental state representations. Specifically, metacognition refers to monitoring one’s own cognitive processes, while mentalizing refers to monitoring others’ cognitive processes. However, this self-other dichotomy is insufficient to delineate the two high-level mental processes. We here used functional magnetic resonance imaging (fMRI) to systematically investigate the neural representations of different levels of decision uncertainty in monitoring different targets (the current self, the past self, and others) performing a perceptual decision-making task. Our results reveal diverse formats of intrinsic mental state representations of decision uncertainty in mentalizing, separate from the associations with external information. External information was commonly represented in the right inferior parietal lobe (IPL) across the mentalizing tasks. However, the meta-level mental states of decision uncertainty attributed to others were uniquely represented in the dorsomedial prefrontal cortex (dmPFC), rather than the temporoparietal junction (TPJ) that also equivalently represented the object-level mental states of decision inaccuracy attributed to others. Further, the object-level and meta-level mental states of decision uncertainty, when attributed to the past self, were represented in the precuneus and the lateral frontopolar cortex (lFPC), respectively. In contrast, the dorsal anterior cingulate cortex (dACC) consistently represented both decision uncertainty in metacognition and estimate uncertainty during monitoring the different mentalizing processes, but not the inferred decision uncertainty in mentalizing. Hence, our findings identify neural signatures to clearly delineate metacognition and mentalizing and further imply distinct neural computations on the mental states of decision uncertainty during metacognition and mentalizing.
Integrating digital and field surveillance to complement efforts to manage epidemic diseases of livestock: African swine fever as a case study
Authors: Tizzani Michele , Muñoz-Gómez Violeta , De Nardi Marco , Paolotti Daniela , Muñoz Olga , Ceschi Piera , Viltrop Arvo , Capua Ilaria 
Published: May 2021

AbstractThe SARS-CoV-2 pandemic has unveiled the importance of stakeholders and ordinary citizens in managing infectious disease emergencies. Efficient management of infectious diseases requires a top-down approach which must be complemented with a bottom-up response to be effective. Here we investigate a novel approach to surveillance for transboundary animal diseases using African Swine fever as a model. We were able to collect data at a population level on information-seeking behavior and at a local level through a targeted questionnaire-based survey to relevant stakeholders such as farmers and veterinary authorities. Our study shows how information-seeking behavior and resulting public attention during an epidemic, can be addressed through novel data streams from digital platforms such as Wikipedia. We also bring evidence on how field surveys aimed at local workers (e.g. farmers) and public authorities remain a crucial tool to assess more in-depth preparedness and awareness among front-line actors. We conclude that they should be used in combination to maximize the outcome of surveillance and prevention activities for selected transboundary animal diseases.
Abiotic factors modulate interspecies competition mediated by the type VI secretion system effectors inVibrio cholerae
Authors: Tang Ming-Xuan , Pei Tong-Tong , Wang Zeng-Hang , Luo Han , Wang Xing-Yu , Dong Tao G. 
Published: May 2021

AbstractVibrio cholerae, the etiological pathogen of cholera, relies on its type VI secretion system (T6SS) as an effective weapon to survive in highly competitive communities. The anti-bacterial and anti-eukaryotic functions of T6SS depend on its secreted effectors that target multiple essential cellular processes. However, the mechanisms that account for effector diversity and different effectiveness during interspecies competition remain elusive. Here, we report that environmental cations and temperature play a key role in dictating effector-mediated competition ofVibrio cholerae. We found thatV. choleraecould employ its cell-wall-targeting effector TseH to outcompete the otherwise resistantEscherichia coliand theV. choleraeimmunity deletion mutantΔtsiHwhen Ca2+and Mg2+were supplemented. TheE. coliΔphoQmutant was more sensitive to TseH-mediated killing during competition, suggesting the metal-sensing PhoPQ two-component system is protective toE. colifrom TseH activity. Using transcriptome analysis, we found multiple stress response systems, including acid stress response, oxidative stress response, and osmotic stress response, were activated inE. coliexpressing TseH in comparison withE. coliexpressing the inactive mutant TseHH64A. The membrane-targeting lipase effector TseL also exhibited reduced killing againstE. coliwhen divalent cations were removed. In addition, competition analysis ofE. coliwithV. choleraesingle-effector active strains reveals a temperature-dependent susceptibility ofE. colito effectors, VasX, VgrG3, and TseL. These findings suggest that abiotic factors, thatV. choleraefrequently encounters in natural habitats, play a crucial role in dictating the competitive fitness conferred by the type VI secretion system in complex multispecies communities.
hei-tag: a highly efficient tag to boost targeted genome editing
Authors: Thumberger Thomas , Tavhelidse Tinatini , Gutierrez-Triana Jose Arturo , Medert Rebekka , Cornean Alex , Welz Bettina , Freichel Marc , Wittbrodt Joachim 
Published: May 2021

AbstractPrecise, targeted genome editing by CRISPR/Cas9 is key for basic research and translational approaches in model and non-model systems1. While active in all species tested so far, editing efficiencies still leave room for improvement. To reach its target, the bacterial Cas9 needs to be efficiently shuttled into the nucleus as attempted by fusion of nuclear localization signals (NLSs) to the Cas9 protein2. Additional domains such as FLAG- or myc-tags are added for immediate detection or straight-forward purification3. To avoid steric hinderance impacting on activity, amino acid linkers are employed connecting Cas9 and additional domains.We present the ‘hei-tag (high efficiency-tag)’, boosting the activity of the wide variety of CRISPR/Cas genome editing tools. The addition of the hei-tag to Cas9 or a C-to-T base editor dramatically enhances the respective targeting efficiency in model systems ranging from fish to mammals, including tissue culture applications. This allows to instantly upgrade existing and potentially highly adapted systems as well as establish novel highly efficient tools.
The 3-phosphoinositide-dependent protein kinase 1 is an essential upstream activator of protein kinase A in malaria parasites
Authors: Hitz Eva , Wiedemar Natalie , Passecker Armin , Brancucci Nicolas M. B. , Vakonakis Ioannis , Mäser Pascal , Voss Till S. 
Published: May 2021

AbstractCyclic AMP (cAMP) signalling is crucial for the propagation of asexual malaria blood stage parasites. Recent work on Plasmodium falciparum demonstrated that phosphorylation of the invasion ligand AMA1 by the catalytic subunit of cAMP-dependent protein kinase A (PfPKAc) is an essential step during parasite invasion into red blood cells. However, the exact mechanisms regulating PfPKAc activity are only partially understood and PfPKAc function has not been extensively studied in gametocytes, the sexual blood stage forms that are essential for malaria transmission. By studying a conditional PfPKAc knockdown mutant, we confirm the essential role for PfPKAc in erythrocyte invasion and demonstrate that PfPKAc is involved in regulating gametocyte deformability. Interestingly, we observed that the conditional overexpression of PfPKAc also caused a profound lethal phenotype by preventing intra-erythrocytic parasite multiplication. Whole genome sequencing of parasites selected to tolerate increased PfPKAc expression levels identified missense mutations exclusively in the gene encoding the putative parasite orthologue of 3-phosphoinositide-dependent protein kinase-1 (PfPDK1). Using targeted mutagenesis, we show that PfPDK1 is essential for PfPKAc activation, most likely by phosphorylating T189 in the PfPKAc activation loop. In summary, our results corroborate the importance of tight regulation of PfPKA signalling for parasite survival and identify PfPDK1 as a crucial upstream regulator in this pathway and potential new drug target.