bluuebunny/crossref_metadata_2025_split huggingface dataset:
IER5, a DNA-damage response gene, is required for Notch-mediated induction of squamous cell differentiation
Authors: Pan Li , Lemieux Madeleine E. , Thomas Tom , Rogers Julia M. , Lee Winston , Johnson Carl , Sholl Lynette , South Andrew P. , Marto Jarrod A. , Adelmant Guillaume O. , Blacklow Stephen C. , Aster Jon C. 
Published: April 2020

AbstractNotch signaling regulates normal squamous cell proliferation and differentiation and is frequently disrupted in squamous cell carcinomas, in which Notch is a key tumor suppressive pathway. To identify the direct targets of Notch that produce these phenotypes, we introduced a conditional Notch transgene into squamous cell carcinoma cell lines, which respond to Notch activation in 2D culture and in organoid cultures by undergoing differentiation. RNA-seq and ChIP-seq analyses show that in squamous cells Notch activates a context-specific program of gene expression that depends on lineage-specific regulatory elements, most of which lie in long- range enhancers. Among the direct Notch target genes are multiple DNA damage response genes, includingIER5, which is regulated by Notch through several enhancer elements. We show thatIER5is required for Notch-induced differentiation in squamous carcinoma cells and in TERT-immortalized keratinocytes. Its function is epistatic toPPP2R2A, which encodes the B55αsubunit of PP2A, and IER5 interacts with B55αin cells and in purified systems. These results show that Notch and DNA-damage response pathways converge in squamous cells and that some components of these pathways promote differentiation, which may serve to eliminate DNA-damaged cells from the proliferative pool in squamous epithelia. Crosstalk involving Notch and PP2A may enable Notch signaling to be tuned and integrated with other pathways that regulate squamous differentiation. Our work also suggests that squamous cell carcinomas remain responsive to Notch signaling, providing a rationale for reactivation of Notch as a therapeutic strategy in these cancers.ImpactOur findings highlight context-specific crosstalk between Notch, DNA damage response genes, and PP2A, and provide a roadmap for understanding how Notch induces the differentiation of squamous cells.
Strain background, species frequency and environmental conditions are important in determining population dynamics and species co-existence betweenPseudomonas aeruginosaandStaphylococcus aureus
Authors: Niggli Selina , Kümmerli Rolf 
Published: April 2020

AbstractBacterial communities in the environment and in infections are typically diverse, yet we know little about the factors that determine interspecies interactions. Here, we apply concepts from ecological theory to understand how biotic and abiotic factors affect interaction patterns between the two opportunistic human pathogensPseudomonas aeruginosaandStaphyloccocus aureus, which often co-occur in polymicrobial infections. Specifically, we conducted a series of short- and long-term competition experiments betweenP. aeruginosaPAO1 (as our reference strain) and three differentS. aureusstrains (Cowan I, 6850, JE2) at three starting frequencies and under three environmental (culturing) conditions. We found that the competitive ability ofP. aeruginosastrongly depended on the strain background ofS. aureus, wherebyP. aeruginosadominated against Cowan I and 6850, but not against JE2. In the latter case, both species could end up as winners depending on conditions. Specifically, we observed strong frequency-dependent fitness patterns, including positive frequency dependence, whereP. aeruginosacould dominate JE2 only when common, but not when rare. Finally, changes in environmental (culturing) conditions fundamentally altered the competitive balance between the two species, in a way thatP. aeruginosadominance increased when moving from shaken to static environments. Altogether, our results highlight that ecological details can have profound effects on the competitive dynamics between co-infecting pathogens, and determine whether two species can co-exist or invade each others’ populations from rare. Moreover, our findings might parallel certain dynamics observed in chronic polymicrobial infections.ImportanceBacterial infections are frequently caused by more than one species and such polymicrobial infections are often considered more virulent and more difficult to treat than the respective monospecies infections.Pseudomonas aeruginosaandStaphyloccocus aureusare among the most important pathogens in polymicrobial infections and their co-occurrence is linked to worse disease outcome. There is great interest in understanding how these two species interact with each other and what the consequences for the host are. While previous studies have mainly looked at molecular mechanisms implicated in interactions betweenP. aeruginosaandS. aureus, here we show that ecological factors such as strain background, species frequency and environmental conditions are important elements determining population dynamics and species co-existence patterns. We propose that the uncovered principles may also play major roles in infections, and therefore proclaim that an integrative approach combining molecular and ecological aspects is required to fully understand polymicrobial infections.
The lemur baseline: How lemurs compare to monkeys and apes in the Primate Cognition Test Battery
Authors: Fichtel Claudia , Dinter Klara , Kappeler Peter M. 
Published: April 2020

ABSTRACTPrimates have relatively larger brains than other mammals even though brain tissue is energetically costly. Comparative studies of variation in cognitive skills allow testing of evolutionary hypotheses addressing socioecological factors driving the evolution of primate brain size. However, data on cognitive abilities for meaningful interspecific comparisons are only available for haplorhine primates (great apes, Old- and New World monkeys) although strepsirrhine primates (lemurs and lorises) serve as the best living models of ancestral primate cognitive skills, linking primates to other mammals. To begin filling this gap, we tested members of three lemur species (Microcebus murinus, Varecia variegata, Lemur catta) with the Primate Cognition Test Battery, a comprehensive set of experiments addressing physical and social cognitive skills that has previously been used in studies of haplorhines. We found no significant differences in cognitive performance among lemur species and, surprisingly, their average performance was not different from that of haplorhines in many aspects. Specifically, lemurs’ overall performance was inferior in the physical domain but matched that of haplorhines in the social domain. These results question a clear-cut link between brain size and cognitive skills, suggesting a more domain-specific distribution of cognitive abilities in primates, and indicate more continuity in cognitive abilities across primate lineages than previously thought.
FORCAST: a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments
Authors: Elrick Hillary , Nelakuditi Viswateja , Clark Greg , Brudno Michael , Ramani Arun K. , Nutter Lauryl M.J. 
Published: April 2020

AbstractCas-mediated genome editing has enabled researchers to perform mutagenesis experiments with relative ease. Effective genome editing requires tools for guide RNA selection, off-target prediction, and genotyping assay design. While independent tools exist for these functions, there is still a need for a comprehensive platform to design, view, evaluate, store, and catalogue guides and their associated primers. The Finding Optimizing and Reporting Cas Targets (FORCAST) application integrates existing open source tools such as JBrowse, Primer3, BLAST, bwa, and Silica to create a complete allele design and quality assurance pipeline. FORCAST is a fully integrated software that allows researchers performing Cas-mediated genome editing to generate, visualize, store, and share information related to guides and their associated experimental parameters. It is available from a public GitHub repository and as a Docker image, for ease of installation and portability.
Neuronal complexity is attenuated in chronic migraine and restored by HDAC6 inhibition
Authors: Bertels Zachariah , Singh Harinder , Dripps Isaac , Siegersma Kendra , Tipton Alycia F , Witkowski Wiktor , Sheets Zoie , Shah Pal , Conway Catherine , Petukhova Valentina , Karumudi Bhargava , Petukhov Pavel A. , Baca Serapio M. , Rasenick Mark M , Pradhan Amynah A 
Published: April 2020

AbstractMigraine is the third most prevalent disease worldwide but the mechanisms that underlie migraine chronicity are poorly understood. Cytoskeletal flexibility is fundamental to neuronal-plasticity and is dependent on dynamic microtubules. Histone-deacetylase-6 (HDAC6) decreases microtubule dynamics by deacetylating its primary substrate, α-tubulin. We use validated models of migraine to show that HDAC6-inhibition is a promising migraine treatment and reveal an undiscovered cytoarchitectural basis for migraine chronicity. The human migraine trigger, nitroglycerin, produced chronic migraine-associated pain and decreased neurite growth in headache-processing regions, which were reversed by HDAC6 inhibition. Cortical spreading depression (CSD), a physiological correlate of migraine aura, also decreased cortical neurite growth, while HDAC6-inhibitor restored neuronal complexity and decreased CSD. Importantly, a calcitonin gene-related peptide receptor antagonist also restored blunted neuronal complexity induced by nitroglycerin. Our results demonstrate that disruptions in neuronal cytoarchitecture are a feature of chronic migraine, and effective migraine therapies might include agents that restore microtubule/neuronal plasticity.
Tgfbr2 in dental pulp cells guides sensory innervation in developing teeth
Authors: Barkley Courtney , Serra Rosa , Nguyen Kevin , Peters Sarah B. 
Published: April 2020

AbstractTransforming growth factor β (TGFβ) plays an important role in tooth morphogenesis and mineralization. Our laboratory established a mouse model in which Tgfbr2 was conditionally deleted in the dental pulp (DP) mesenchyme using an Osterix promoter-driven Cre recombinase (Tgfbr2cko). These mice survived postnatally, but had significant defects in bones and teeth, including reduced mineralization and short roots. H&E staining revealed reduced axon-like structures in the mutant mice. Reporter imaging demonstrated that Osterix-Cre activity was localized within the tooth and was active in the DP and derivatives, but not in neurons. Previous research has established that paracrine signals from the dental pulp attract trigeminal axons toward and into the tooth during postnatal development, yet very little is known about the signals that regulate tooth innervation. Immunofluorescent staining for a neuronal marker, β3 tubulin, was performed on serial cryosections from control and mutant molars at two different postnatal stages. Confocal imaging and pixel quantification of β3 tubulin demonstrated reduced innervation in P7 and P24 Tgfbr2ckofirst molars compared to controls, indicating that the signals necessary to promote neurite outgrowth were disrupted by Tgfbr2 deletion. Quantitative real time PCR showed that the mRNA expression levels of several neuronal genes were reduced. Lastly, trigeminal neurons were co-cultured atop Transwell filters overlying primary Tgfbr2f/fDP cells. Tgfbr2 in the DP was deleted with an adenovirus expressing Cre recombinase. Confocal imaging of axons through the filter pores showed increased axonal sprouting from neurons cultured in the presence of Tgfbr2-positive DP cells compared to neurons cultured alone. Further, axon sprouting was reduced when Tgfbr2 was knocked down in the DP cells. These results indicate that Tgfbr2 in the DP mesenchyme regulates paracrine signals that guide sensory innervation of the tooth.Note: A list of abbreviations is included in the appendix.
Genomic regions linked to soft sweeps approximate neutrality when inferring population history from site pattern frequencies
Authors: Harris Nathan S. , Rogers Alan R. 
Published: April 2020

ABSTRACTRecent studies have suggested that selection is widespread throughout the genome and largely uncompensated for in inferences of population history. To address this potential issue, we estimated site pattern frequencies for neutral and selection associated areas of the genome. There are notable differences in these frequencies between neutral regions and those affected by selection. However, these differences have relatively small effects when inferring population history.
Hyperexcitability and loss of feedforward inhibition in theFmr1KO lateral amygdala
Authors: Guthman E. Mae , Svalina Matthew N. , Cea-Del Rio Christian A. , Kushner J. Keenan , Baca Serapio M. , Restrepo Diego , Huntsman Molly M. 
Published: April 2020

SummaryFragile X Syndrome (FXS) is a neurodevelopmental disorder characterized by intellectual disability, autism spectrum disorders (ASDs), and anxiety disorders. The disruption in the function of theFMR1gene results in a range of alterations in cellular and synaptic function. Previous studies have identified dynamic alterations in inhibitory neurotransmission in early postnatal development in the amygdala of the mouse model of FXS. Yet little is known how these changes alter microcircuit development and plasticity in the lateral amygdala (LA). Using whole-cell patch clamp electrophysiology, we demonstrate that principal neurons (PNs) in the LA exhibit hyperexcitability with a concomitant increase in the synaptic strength of excitatory synapses in the BLA. Further, reduced feed-forward inhibition appears to enhance synaptic plasticity in the FXS amygdala. These results demonstrate that plasticity is enhanced in the amygdala of the juvenileFmr1KO mouse and that E/I imbalance may underpin anxiety disorders commonly seen in FXS and ASDs.
Simplicity in numbers: Implications of diversity for the community Bioturbation Potential (BPc)
Authors: Neumann Andreas , Wrede Alexa 
Published: April 2020

AbstractThe mobility of particles and solutes within aquatic sediment is substantially impacted by faunal bioturbation activities such as bioirrigation and sediment reworking. The non-quantitative community bioturbation potential (BPc) aims to estimate the potential of a given benthic community for bioturbation activities, based on the functional traits of the species within that community. We argue that in sufficiently diverse communities, the characteristics of individual species, expressed as traits scores, average each other out, and approach a universal constant. This enables to derive a simpler community bioturbation potential (BPs), which may be applied in cases when taxonomic expertise or trait data are not available. As a proof of concept, we evaluated a dataset of 84 benthos assemblages, and found a high degree of agreement of full BPc and simplified BPs.
T2 heterogeneity provides a sensitive measure of early tumor response to radiotherapy
Authors: Tomaszewski Michal R. , Dominguez-Viqueira William , Ortiz Antonio , Shi Yu , Costello James R. , Enderling Heiko , Rosenberg Stephen A. , Gillies Robert J. 
Published: April 2020

AbstractPurposeExternal beam radiotherapy (XRT) is a widely used cancer treatment, yet responses vary dramatically between patients. These differences are not accounted for in clinical practice, in part due to a lack of sensitive biomarkers of early response. In this work, we test the hypothesis that quantification of intratumor heterogeneity is a sensitive and robust biomarker of early response to XRT. A novel Magnetic Resonance Imaging (MRI) approach is proposed, utilizing histogram analysis of clinically-used T2 relaxation measurements to assess early changes in the tumor heterogeneity following irradiation in murine models of pancreatic cancer, indicative of radiotherapy response.Methods and MaterialsDynamic Magnetic Resonance T2 relaxation imaging was performed every 72h following 10 Gy dose XRT in two murine models of pancreatic cancer. Proposed biomarker of radiotherapy response was compared with tumor growth kinetics, and biological validation was performed through quantitative histology analysis.ResultsQuantification of tumor T2 interquartile range (IQR) as a measure of histogram width showed excellent sensitivity for detection of XRT-induced tumor changes as early as 72h after treatment, outperforming whole tumor T2 and Diffusion weighted MRI metrics. This response was observed both in quantitative T2 maps and in T2-weighted images that are routine in clinical practice. Histological comparison revealed the T2 IQR provides a measure of spatial heterogeneity in tumor cell density, related to radiation-induced necrosis. The early IQR changes were found to presage subsequent tumor volume changes in two distinct pancreatic models, suggesting promise for treatment response prediction. The metric showed excellent test-retest robustness.ConclusionsOur preclinical findings indicate that spatial heterogeneity analysis of T2 MRI can provide a sensitive and readily translatable method for early radiotherapy response assessment in pancreatic cancer. We propose that this will be useful in adaptive radiotherapy, specifically in MRI-guided treatment paradigms.
Rapid and cost-effective development of stable clones for the production of anti-Ebola monoclonal antibodies in HEK293T cells
Authors: González-González Everardo , Palestino-Díaz Iñaki , López-Pacheco Felipe , Márquez-Ipiña Alan Roberto , Lara-Mayorga Itzel Montserrat , Trujillo-de Santiago Grissel , Alvarez Mario Moisés 
Published: April 2020

AbstractThe Ebola virus (EBOV) disease has caused serious and recurrent epidemics in recent years, resulting in a fatality rate of nearly 50%. The most effective experimental therapy against the EBOV is the use of monoclonal antibodies (mAbs). In this work, we describe the development of HEK293T cells engineered for the transient and stable expression of mAb13C6, a neutralizing anti-EBOV monoclonal antibody. We transfected the HEK293T cells with a tricistronic vector to produce the heavy and the light chain of the antibody 13C6 and intracellular Green Fluorescent Protein (GFP) using Lipofectamine 3000. We then selected the transfected cells using puromycin pressure, dilution cloning, and cloning disks. This integrated strategy generated mAb-producing cells in 7 days with a transient expression of ∼1 mg/L. Stable pools were produced after 4 weeks, with expression levels of ∼0.8 mg/L. Stable clones with expression levels of ∼1.8 mg/L were obtained within 10 weeks. The produced antibodies exhibited the expected functionality; they recognized the GP glycoprotein of the Ebola virus in both ELISA assays and cell binding experiments using HEK293T cells engineered to express the EBOV GP at their membrane surface. By the combined use of GFP and the set of selection techniques here described, we drastically reduced the time from transfection to stable clone generation without resorting to costly equipment. In outbreaks or emergencies, this platform can significantly shorten the development of new biopharmaceuticals and vaccines.
Changing color and intensity of LED lighting across the day impacts on human circadian physiology, sleep, visual comfort and cognitive performance
Authors: Stefani O. , Freyburger M. , Veitz S. , Basishvili T. , Meyer M. , Weibel J. , Kobayashi K. , Shirakawa Y. , Cajochen C. 
Published: April 2020

ABSTRACTWe examined whether dynamic light across a scheduled 16-h waking day influences cognitive performance, visual comfort, melatonin secretion, sleepiness and sleep under strictly controlled laboratory conditions of 49-h duration.Participants spent the first 5-h in the evening under standard lighting, followed by an 8-h nocturnal sleep episode at habitual bedtimes. Thereafter volunteers either woke up with static daylight LED (100 lux and 4000 Kelvin) or with a dynamic daylight LED that changed color (2700 – 5000 Kelvin) and intensity (0 - 100 lux) across the scheduled 16-h waking day. This was followed by an 8-h nocturnal treatment sleep episode at habitual bedtimes. Thereafter, volunteers spent another 12-h either under static or dynamic light during scheduled wakefulness.Under dynamic light, evening melatonin levels were less suppressed 1.5hours prior to usual bedtime, and participants felt less vigilant in the evening compared to static light. Sleep latency was significantly shorter in both the baseline and treatment night compared to the static light condition while sleep structure, sleep quality, cognitive performance and visual comfort did not significantly change. Our results support the recommendation of using blue-depleted light and low illuminances in the late evening, which can be achieved by a dynamically changing daylight LED solution.
Targeted delivery of acid alpha-glucosidase corrects skeletal muscle phenotypes in Pompe disease mice
Authors: Baik Andrew D. , Calafati Philip T. , Aaron Nina A. , Mehra Antonia , Moller-Tank Sven , Miloscio Lawrence , Wang Lili , Praggastis Maria , Birnbaum Matthew S. , Pan Cheryl , Brydges Susannah , Mujica Alejandro , Barbounis Peter , Gale Nicholas W. , Li Ning , Kyratsous Christos A. , Schoenherr Christopher J. , Murphy Andrew J. , Economides Aris N. , Cygnar Katherine D. 
Published: April 2020

AbstractLysosomal diseases are a class of genetic disorders predominantly caused by loss of lysosomal hydrolases, leading to lysosomal and cellular dysfunction. Enzyme Replacement Therapy (ERT), where recombinant enzyme is given intravenously, internalized by cells, and trafficked to the lysosome, has been applied to treat several lysosomal diseases. However, current ERT regimens do not correct disease phenotypes in all affected organs because the biodistribution of enzyme uptake does not match that of the affected cells and tissues that require the enzyme. We present here targeted ERT, an approach that utilizes antibody-enzyme fusion proteins to target the enzyme to specific tissues. The antibody moiety recognizes transmembrane proteins involved in lysosomal trafficking and that are also preferentially expressed in those cells most affected in disease. Using Pompe disease (PD) as an example, we show that targeted ERT is superior to ERT in treating the skeletal muscle phenotypes of PD mice.
Heritability estimates of antler and body traits in white-tailed deer (Odocoileus virginianus) from genomic-relatedness matrices
Authors: Jamieson Aidan , Anderson Spencer J , Fuller Jérémie , Côté Steeve D , Northrup Joseph M , Shafer Aaron BA 
Published: April 2020

AbstractEstimating heritability (h2) is required to predict the response to selection and is useful in species that are managed or farmed using trait information. Estimatingh2in free-ranging populations is challenging due to the need for pedigrees; genomic-relatedness matrices (GRMs) circumvent this need and can be implemented in nearly any system where phenotypic and SNP data are available. We estimated the heritability of five body and three antler traits in a free-ranging population of white-tailed deer (Odocoileus virginianus) on Anticosti Island, Quebec, Canada. We generated GRMs from >10,000 SNPs: dressed body mass and peroneus muscle mass had moderateh2values of 0.49 and 0.56, respectively. Heritability in male-only antler features ranged from 0.00 to 0.51 and had high standard errors. We explored the influence of minor allele frequency and data completion filters onh2: GRMs derived from fewer SNPs had reducedh2estimates and the relatedness coefficients significantly deviated from those generated with more SNPs. As a corollary, we discussed limitations to the application of GRMs in the wild, notably how skewed GRMs increase variance aroundh2estimates. This is the first study to estimateh2on a free-ranging population of white-tailed deer and should be informative for breeding designs and management.