bluuebunny/crossref_metadata_2025_split huggingface dataset:
An optimized retroviral toolbox for overexpression and genetic perturbation of primary lymphocytes
Authors: van der Donk Lieve EH , van der Spek Jet , van Duivenvoorde Tom , ten Brink Marieke S , Geijtenbeek Teunis BH , Kuijl Coenraad P , van Heijst Jeroen WJ , Ates Louis S 
Published: January 2021

AbstractGenetic manipulation of primary lymphocytes is crucial for both clinical purposes and fundamental research. Despite their broad use, we encountered a paucity of data on systematic comparison and optimization of retroviral vectors, the workhorses of genetic modification of primary lymphocytes. Here, we report the construction and validation of a versatile range of retroviral expression vectors. These vectors can be used for the knockdown or overexpression of genes of interest in primary human and murine lymphocytes, in combination with a wide choice of selection and reporter strategies. By streamlining the vector backbone and insert design, these publicly available vectors allow easy interchangeability of the independent building blocks, such as different promoters, fluorescent proteins, surface markers and antibiotic resistance cassettes. We validated these vectors and tested the optimal promoters for in vitro and in vivo overexpression and knockdown of the murine T cell antigen receptor. By publicly sharing these vectors and the data on their optimization, we aim to facilitate genetic modification of primary lymphocytes for researchers entering this field.
Measuring arterial pulsatility with Dynamic Inflow MAgnitude Contrast (DIMAC)
Authors: Whittaker Joseph R. , Fasano Fabrizio , Venzi Marcello , Liebig Patrick , Gallichan Daniel , Murphy Kevin 
Published: January 2021

AbstractThe pulsatility of blood flow through cerebral arteries is clinically important, as it is intrinsically associated with cerebrovascular health. In this study we outline a new MRI approach to measuring the real-time pulsatile flow in cerebral arteries, which is based on the inflow phenomenon associated with fast gradient-recalled-echo acquisitions. Unlike traditional phase-contrast techniques, this new method, which we dubDynamicInflowMagnitudeContrast (DIMAC), does not require velocity-encoding gradients as sensitivity to flow velocity is derived purely from the inflow effect. We achieved this using a highly accelerated single slice EPI acquisition with a very short TR (15 ms) and a 90° flip angle, thus maximizing inflow contrast. We simulate the spoiled GRE signal in the presence of large arteries and perform a sensitivity analysis to demonstrate that in the regime of high inflow contrast it shows much greater sensitivity to flow velocity over blood volume changes. We support this theoretical prediction within-vivodata collected in two separate experiments designed to demonstrate the utility of the DIMAC signal contrast. We perform a hypercapnia challenge experiment in order to experimentally modulate arterial tone within subjects, and thus modulate the arterial pulsatile flow waveform. We also perform a thigh-cuff release challenge, designed to induce a transient drop in blood pressure, and demonstrate that the continuous DIMAC signal captures the complex transient change in the pulsatile and non-pulsatile components of flow. In summary, this study proposes a new role for a well-established source of MR image contrast and demonstrates its potential for measuring both steady-state and dynamic changes in arterial tone.HighlightsWe present a novel method for measuring pulsatility of cerebral arteries.The inflow effect on fast GRE imaging can be exploited to yield a flow velocity dependent signal.We measure pulsatile flow through cerebral arteries dynamically on a beat-to-beat basis.We use physiological challenges to demonstrate sensitivity to dynamic and steady-state changes in vascular tone.
Understanding the holobiont: crosstalk between gut microbiota and mitochondria during endurance
Authors: Mach Núria , Moroldo Marco , Rau Andrea , Lecardonnel Jérôme , Moyec Laurence Le , Robert Céline , Barrey Eric 
Published: January 2021

ABSTRACTEndurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of the intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the gut-mitochondria crosstalk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of theLachnospiraceaefamily, especiallyEubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted onPPARγ,theFRX-CREBaxis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis therefore appears to be a potential strategy to enhance athletic performance.
Joint development recovery on resumption of embryonic movement following paralysis
Authors: Rolfe Rebecca A. , O’Callaghan David Scanlon , Murphy Paula 
Published: January 2021

AbstractFetal activityin uterois a normal part of pregnancy and reduced or absent movement can lead to long-term skeletal defects such as Fetal Akinesia Deformation Sequence (FADS), joint dysplasia and arthrogryposis. A variety of animal models with decreased or absent embryonic movements show a consistent set of developmental defects providing insight into the aetiology of congenital skeletal abnormalities. At developing joints defects include reduced joint interzones with frequent fusion of cartilaginous skeletal rudiments across the joint. At the spine defects include shortening and a spectrum of curvature deformations. An important question, with relevance to possible therapeutic interventions for human conditions, is the capacity for recovery with resumption of movement following short term immobilisation. Here we use the well-established chick model to compare the effects of sustained immobilisation from embryonic day (E) 4-10 to two different recovery scenarios: (i) natural recovery from E6 until E10 and (ii) the addition of hyperactive movement stimulation during the recovery period. We demonstrate partial recovery of movement and partial recovery of joint development under both recovery conditions, but no improvement in spine defects. The joints examined (elbow, hip and knee) showed better recovery in hindlimb than forelimb, with hyperactive mobility leading to greater recovery in the knee and hip. The hip joint showed the best recovery with improved rudiment separation, tissue organisation and commencement of cavitation. This work demonstrates that movement post paralysis can partially-recover specific aspects of joint development which could inform therapeutic approaches to ameliorate the effects of human fetal immobility.Summary StatementThe study reveals that embryonic movement post paralysis can partially-recover specific aspects of joint development, which could inform therapeutic approaches to ameliorate the effects of restricted fetal movementin utero.
Targeting conserved sequences circumvents the evolution of resistance in a viral gene drive against human cytomegalovirus
Authors: Walter Marius , Perrone Rosalba , Verdin Eric 
Published: January 2021

AbstractGene drives are genetic systems designed to efficiently spread a modification through a population. They have been designed almost exclusively in eukaryotic species, and especially in insects. We recently developed a CRISPR-based gene drive system in herpesviruses that relies on similar mechanisms and could efficiently spread into a population of wildtype viruses. A common consequence of gene drives in insects is the appearance and selection of drive-resistant sequences that are no longer recognized by CRISPR-Cas9. Here, we analyze in cell culture experiments the evolution of resistance in a viral gene drive against human cytomegalovirus. We report that after an initial invasion of the wildtype population, a drive-resistant population is positively selected over time and outcompetes gene drive viruses. However, we show that targeting evolutionary conserved sequences ensures that drive-resistant viruses acquire long-lasting mutations and are durably attenuated. As a consequence, and even though engineered viruses don’t stably persist in the viral population, remaining viruses have a replication defect, leading to a long-term reduction of viral levels. This marks an important step toward developing effective gene drives in herpesviruses, especially for therapeutic applications.
The neural basis of effort valuation: A meta-analysis of functional magnetic resonance imaging studies
Authors: Lopez-Gamundi Paula , Yao Yuan-Wei , Chong Trevor T-J. , Heekeren Hauke R. , Herrero Ernest Mas , Pallares Josep Marco 
Published: January 2021

AbstractChoosing how much effort to expend is a critical for everyday decisions. While effort-based decision-making is altered in common psychopathologies and many neuroimaging studies have been conducted to examine how effort is valued, it remains unclear where the brain processes effort-related costs and integrates them with rewards. Using meta-analyses of combined maps and coordinates of functional magnetic resonance imaging (fMRI) studies (total N = 22), we showed that raw effort demands consistently activated the pre-supplementary motor area (pre-SMA). In contrast, the net value of effortful reward consistently activated regions, such as the ventromedial prefrontal cortex (vmPFC) and ventral striatum (VS), that have been previously implicated in value integration in other cost domains. The opposite activation patterns of the pre-SMA and vmPFC imply a double dissociation of these two regions, in which the pre-SMA is involved in pure effort cost representation and the vmPFC in net value integration. These findings advance our understanding of the neural basis of effort-related valuation and reveal potential brain targets to treat motivation-related disorders.
Human gut bacteria produce TH17-modulating bile acid metabolites
Authors: Paik Donggi , Yao Lina , Zhang Yancong , Bae Sena , D’Agostino Gabriel D. , Kim Eunha , Franzosa Eric A. , Avila-Pacheco Julian , Bisanz Jordan E. , Rakowski Christopher K. , Vlamakis Hera , Xavier Ramnik J. , Turnbaugh Peter J. , Longman Randy S. , Krout Michael R. , Clish Clary B. , Huttenhower Curtis , Huh Jun R. , Devlin A. Sloan 
Published: January 2021

AbstractThe microbiota plays a pivotal role in gut immune homeostasis. Bacteria influence the development and function of host immune cells, including T helper cells expressing interleukin-17a (TH17 cells). We previously reported that the bile acid metabolite 3-oxolithocholic acid (3-oxoLCA) inhibits TH17 cell differentiation1. While it was suggested that gut-residing bacteria produce 3-oxoLCA, the identity of such bacteria was unknown. Furthermore, it was not clear whether 3-oxoLCA and other immunomodulatory bile acids are associated with gut inflammatory pathologies in humans. Using a high-throughput screen, we identified human gut bacteria and corresponding enzymes that convert the secondary bile acid lithocholic acid into 3-oxoLCA as well as the abundant gut metabolite isolithocholic acid (isoLCA). Like 3-oxoLCA, isoLCA suppressed TH17 differentiation by inhibiting RORγt (retinoic acid receptor-related orphan nuclear receptor γt), a key TH17 cell-promoting transcription factor. Levels of both 3-oxoLCA and isoLCA and the 3α-hydroxysteroid dehydrogenase (3α-HSDH) genes required for their biosynthesis were significantly reduced in patients with inflammatory bowel diseases (IBD). Moreover, levels of these bile acids were inversely correlated with expression of TH17 cell-associated genes. Overall, our data suggest that bacterially produced TH17 cell-inhibitory bile acids may reduce the risk of autoimmune and inflammatory disorders such as IBD.
Selective modulation of population dynamics during neuroprosthetic skill learning
Authors: Zippi Ellen L. , You Albert K. , Ganguly Karunesh , Carmena Jose M. 
Published: January 2021

AbstractLearning to control a brain-machine interface (BMI) is associated with the emergence of coordinated neural dynamics in populations of neurons whose activity serves as direct input to the BMI decoder (direct subpopulation). While previous work shows differential modification of firing rate modulation in this population relative to a population whose activity was not directly input to the BMI decoder (indirect subpopulation), little is known about how learning-rated changes in cortical population dynamics within these groups compare. To investigate this, we monitored both direct and indirect subpopulations as two macaque monkeys learned to control a BMI. We found that while the combined population increased coordinated neural dynamics, this coordination was primarily driven by changes in the direct subpopulation while the indirect subpopulation remained relatively stable. These findings indicate that motor cortex refines cortical dynamics throughout the entire network during learning, with a more pronounced effect in ensembles causally linked to behavior.
Strong and tunable anti-CRISPR/Cas9 activity of AcrIIA4 in plants
Authors: Calvache Camilo , Vazquez-Vilar Marta , Selma Sara , Uranga Mireia , Daròs José Antonio , Orzáez Diego 
Published: January 2021

AbstractThis study describes the strong anti-CRISPR activity of the bacterial AcrIIA4 protein inNicotiana benthamiana, a model plant used as molecular farming platform. The results demonstrate that AcrIIA4 abolishes site-directed mutagenesis in leaves when transiently co-expressed with CRISPR/Cas9. We also show that AcrIIA4 represses CRISPR/dCas9-based transcriptional activation (CRISPRa) of both reporter and endogenous genes in a highly efficient, dose-dependent manner. Furthermore, the fusion of an auxin degron to AcrIIA4 results in auxin-regulated activation of a downstream reporter gene. The strong anti-Cas9 activity of AcrIIA4 reported here opens new possibilities for customized control of gene editing and gene expression in plants.
Low light intensity delays vegetative phase change inArabidopsis thaliana
Authors: Xu Mingli , Hu Tieqiang , Poethig R. Scott 
Published: January 2021

AbstractPlants that develop under low intensity light (LL) often display a phenotype known as the “shade tolerance syndrome (STS)”. This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development inArabidopsis thaliana. We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase the expression of the master regulators of vegetative phase change, miR156 and miR157, and a decrease in the expression of their SPL targets. Exogenous sucrose partially corrected the effect of LL on seedling development and miR156 expression. Our results suggest that the response of Arabidopsis to LL is mediated by an increase in miR156/miR157 expression and by factors that repress SPL gene expression independently of miR156/miR157, and is caused in part by a decrease in carbohydrate production. The effect of LL on vegetative phase change does not require the photoreceptors and transcription factors responsible for the shade avoidance syndrome, implying that light intensity and light quality regulate rosette development by different pathways.
Proton-gated coincidence detection is a common feature of GPCR signaling
Authors: Kapolka Nicholas J. , Rowe Jacob B. , Taghon Geoffrey J. , Morgan William M. , O’Shea Corin R. , Isom Daniel G. 
Published: January 2021

AbstractThe evolutionary expansion of G protein-coupled receptors (GPCRs) has produced a rich diversity of transmembrane sensors for many physical and chemical signals. In humans alone, over 800 GPCRs detect stimuli such as light, hormones, and metabolites to guide cellular decision making primarily using intracellular G protein signaling networks. This diversity is further enriched by GPCRs that function as molecular logic gates capable of discerning multiple inputs to transduce cues encoded in complex, context-dependent signals. Here, we show that many GPCRs are switch-like Boolean-gated coincidence detectors that link proton (H+) binding to GPCR signaling. Using a panel of 28 receptors, covering 280 individual GPCR-Gα coupling combinations, we show that H+gating both positively and negatively modulates and controls GPCR signaling. Notably, these observations extend to all modes of GPCR pharmacology including ligand efficacy, potency, and cooperativity. Additionally, we show that GPCR antagonism and constitutive activity are regulated by H+gating and report the discovery of a new acid sensor, the adenosine A2a receptor (ADORA2A), which can be activated solely by acidic pH. Together, these findings establish a new paradigm for GPCR biology and pharmacology in acidified microenvironments such as endosomes, synapses, tumors, and ischemic vasculature.
Systematically quantifying morphological features reveals constraints on organoid phenotypes
Authors: Beck Lauren E. , Lee Jasmine , Coté Christopher , Dunagin Margaret C. , Lukonin Ilya , Salla Nikkita , Chang Marcello K. , Hughes Alex J. , Mornin Joseph D. , Gartner Zev J. , Liberali Prisca , Raj Arjun 
Published: January 2021

AbstractOrganoids recapitulate complex 3D organ structures and represent a unique opportunity to probe the principles of self-organization. While we can alter an organoid’s morphology by manipulating the culture conditions, the morphology of an organoid often resembles that of its original organ, suggesting that organoid morphologies are governed by a set of tissue-specific constraints. Here, we establish a framework to identify constraints on an organoid’s morphological features by quantifying them from microscopy images of organoids exposed to a range of perturbations. We apply this framework to Madin-Darby Canine Kidney cysts and show that they obey a number of constraints taking the form of scaling relationships or caps on certain parameters. For example, we found that the number, but not size, of cells increases with increasing cyst size. We also find that these constraints vary with cyst age and can be altered by varying the culture conditions. We observed similar sets of constraints in intestinal organoids. This quantitative framework for identifying constraints on organoid morphologies may inform future efforts to engineer organoids.
Speech-like sounds dominate the human infant vocal landscape
Authors: Oller D. Kimbrough , Ramsay Gordon , Bene Edina , Long Helen L. , Griebel Ulrike 
Published: January 2021

AbstractEarly human infant vocalization is viewed as forming not only a critical foundation for vocal learning of language, but also a crucial realm of communication affecting emotional and social development. Although speech-like sounds are rare or absent in other ape infants, they share distress sounds (shrieks and cries) and laughter with humans, forming a potential basis for especially informative cross-species comparisons as well as potential insights regarding usage and learning of vocal sounds. A fundamental need to make such comparisons possible is empirical research to document frequency of occurrence of vocalizations of various types in natural environments.The present work focuses on laughter in the human infant, a topic that has been viewed by many as a key factor in social development for humans and other apes. Yet we know of no research quantifying frequency of occurrence of human infant laughter in natural environments across the first year. In the past two decades it has been shown that the predominant vocalizations of the human infant are “protophones”, the precursor sounds to speech. Longitudinal research has indicated unambiguously that protophones outnumber cries by a factor of at least five based on data from random-sampling of all-day recordings across the whole first year. The present work expands on the prior reports by reporting data showing that human infant laughter occurs even more rarely than cry in all-day recordings. Yet laughter is clearly a salient and important aspect of social development. We reason about the dominance of protophones in the infant vocal landscape in light of their role in illuminating human vocal learning and the origin of language.
Variance misperception under skewed empirical noise statistics explains overconfidence in the visual periphery
Authors: Winter Charles J. , Peters Megan A. K. 
Published: January 2021

AbstractPerceptual confidence typically corresponds to accuracy. However, observers can be overconfident relative to accuracy, termed ‘subjective inflation’. Inflation is stronger in the visual periphery relative to central vision, especially under conditions of peripheral inattention. Previous literature suggests inflation stems from errors in estimating noise, i.e. ‘variance misperception’. However, despite previous Bayesian hypotheses about metacognitive noise estimation, no work has systematically explored how noise estimation may critically depend on empirical noise statistics which may differ across the visual field, with central noise distributed symmetrically but peripheral noise positively skewed. Here we examined central and peripheral vision predictions from five Bayesian-inspired noise-estimation algorithms under varying usage of noise priors, including effects of attention. Models that failed to optimally estimate noise exhibited peripheral inflation, but only models that explicitly used peripheral noise priors -- but used them incorrectly -- showed increasing peripheral inflation under increasing peripheral inattention. Further, only one model successfully captured previous empirical results which showed a selective increase in confidence in incorrect responses under performance reductions due to inattention accompanied by no change in confidence in correct responses; this was the model that implemented Bayesian estimation of peripheral noise, but using an (incorrect) symmetric rather than the correct positively skewed peripheral noise prior. Our findings explain peripheral inflation, especially under inattention, and suggest future experiments that might reveal the noise expectations used by the visual metacognitive system.SignificancePerceptual confidence can dissociate from accuracy in peripheral visual perception, a phenomenon known as peripheral inflation. No previous model has considered how this phenomenon may arise from metacognitive noise estimation which depends on empirical noise statistics. Here we simulate Bayesian-inspired noise estimation algorithms to show that the system’s erroneous beliefs about distributions of noise in the visual periphery can explain the occurrence of peripheral inflation, including how inflation varies with attentional manipulations in surprising ways. Our results explain why peripheral inflation occurs by positing a new Bayesian metacognitive noise estimation mechanism, paving the way for future psychophysical studies.