bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Long Lost Key Opens an Ancient Lock:DrosophilaMyb Causes a Synthetic Multivulval Phenotype in Nematodes
Authors: Vorster Paul J. , Goetsch Paul , Wijeratne Tilini U. , Guiley Keelan Z. , Andrejka Laura , Tripathi Sarvind , Larson Braden J. , Rubin Seth M. , Strome Susan , Lipsick Joseph S. 
Published: October 2019

ABSTRACTThe five-protein MuvB core complex (LIN9/Mip130, LIN37/Mip40, LIN52, LIN54/Mip120, and LIN53/p55CAF1/RBBP4) has been highly conserved during the evolution of animals. This nuclear complex interacts with proteins encoded by theRBtumor suppressor gene family and its associated E2F-DP transcription factors to form DREAM complexes that repress the expression of genes that regulate cell cycle progression and cell fate. The MuvB core complex also interacts with proteins encoded by theMyboncogene family to form the Myb-MuvB complexes that activate many of the same target genes. We show that animal-typeMybgenes and proteins are present in Bilateria, Cnidaria, and Placozoa, the latter including some of the simplest known animal species. However, bilaterian nematode worms appear to have lost their animal-typeMybgenes hundreds of millions of years ago. Nevertheless, the amino acids in the LIN9 and LIN52 proteins that directly interact with the MuvB-binding domains of human B-Myb andDrosophilaMyb are conserved inC. elegans. Here we show that, despite greater than 500 million years since their last common ancestor, theDrosophila melanogasterMyb protein can bind to the nematode LIN9 and LIN52 family proteinsin vitroand can cause a synthetic multivulval (synMuv) phenotypein vivo. This phenotype is similar to that caused by loss-of-function mutations inC. eleganssynMuvB class genes including those that encode homologs of the MuvB core, RB, E2F, and DP. Furthermore, amino acid substitutions in the MuvB-binding domain ofDrosophilaMyb that disrupt its functionsin vitroandin vivoalso disrupt its activity inC. elegans. We speculate that nematodes and other animals may contain another protein that can bind to LIN9 and LIN52 in order to activate transcription of genes repressed by DREAM complexes.
The PRR14 heterochromatin tether encodes modular domains that mediate and regulate nuclear lamina targeting
Authors: Dunlevy Kelly L. , Medvedeva Valentina , Wilson Jade E. , Hoque Mohammed , Pellegrin Trinity , Maynard Adam , Kremp Madison M. , Wasserman Jason S. , Poleshko Andrey , Katz Richard A. 
Published: October 2019

AbstractA large fraction of epigenetically silent heterochromatin is anchored to the nuclear periphery via “tethering proteins” that function to bridge heterochromatin and the nuclear membrane or nuclear lamina. We identified previously a human tethering protein, PRR14, that binds heterochromatin through an N-terminal domain, but the mechanism and regulation of nuclear lamina association remained to be investigated. Here we identify a centrally located, evolutionarily conserved PRR14 nuclear lamina binding domain (LBD) that is both necessary and sufficient for positioning of PRR14 at the nuclear lamina. We also show that PRR14 associates dynamically with the nuclear lamina, and provide evidence that such dynamics are regulated through phosphorylation of the LBD. We also show that the evolutionary conserved PRR14 C-terminal Tantalus domain encodes a PP2A phosphatase recognition site that regulates PRR14 nuclear lamina association. The overall findings demonstrate a heterochromatin anchoring mechanism whereby the PRR14 tether simultaneously binds heterochromatin and the nuclear lamina through two modular domains. Furthermore, the identification of a modular LBD may provide an engineering strategy for delivery of cargo to the nuclear lamina.
A method for rapid selection of randomly induced mutations in a gene of interest using CRISPR/Cas9 mediated activation of gene expression
Authors: Ng William A. , Ma Andrew , Chen Molly , Reed Bruce H. 
Published: October 2019

AbstractWe have developed a CRISPR/Cas9 based method for isolating randomly induced recessive lethal mutations in a gene of interest (GOI) by selection within the F1 progeny of a single genetic cross. Our method takes advantage of the ability to overexpress a GOI using CRISPR/Cas9 mediated activation of gene expression. In essence, the screening strategy is based upon the idea that if overexpression of a wild type allele can generate a phenotype, then overexpression of a newly induced loss-of-function allele will lack this phenotype. As a proof-of-principle, we used this method to select EMS induced mutations of the Drosophila genehindsight(hnt). From approximately 45,000 F1 progeny we recovered 8 new EMS induced loss-of-functionhntalleles that we characterized as an allelic series of hypomorphic mutations. This new method can, in theory, be used to recover randomly induced point mutants in a GOI and can be applied to any circumstance where CRISPR/Cas9 mediated activation of gene expression is associated with lethality or a visible phenotype.
Proximate Predictors of Variation in Egg Rejection Behavior by Hosts of Avian Brood Parasites
Authors: Abolins-Abols Mikus , Hauber Mark E. 
Published: October 2019

AbstractThe rejection of parasitic eggs by hosts of avian brood parasites is one of the most common and effective defenses against parasitism. Despite its adaptive significance, egg rejection often shows substantial intraspecific variation: some individuals are more likely to remove or abandon parasitic eggs than others. Understanding variation in egg rejection requires that we study factors linked to both the ability to perceive parasitic eggs, as well as factors that may influence the rejection of a foreign egg once it has been recognized. Here we asked what cognitive, physiological, and life-history factors explained variation in the rejection of model eggs by American Robin Turdus migratorius females. We found that the probability of egg rejection was related to the clutch size at the time of parasitism: in support of Weber’s law, females with fewer eggs were more likely to reject the model eggs. In turn, females with greater mass and higher corticosterone levels were less likely to reject eggs, and egg rejection probability was negatively related to incubation progress. Our data thus suggest that proximate predictors of an individual’s egg rejection behavior include components of the nest’s perceptual environment, life-history factors, as well as the physiological state of the animal. However, much of the variation in the responses of robins to the model eggs remained unexplained. Future experiments should aim to understand the causal roles of these and other factors in generating within- and among-individual variation in the rejection of parasitic eggs.
Pathway Commons: 2019 Update
Authors: Rodchenkov Igor , Babur Ozgun , Luna Augustin , Aksoy Bulent Arman , Wong Jeffrey V. , Fong Dylan , Franz Max , Siper Metin Can , Cheung Manfred , Wrana Michael , Mistry Harsh , Mosier Logan , Dlin Jonah , Wen Qizhi , O’Callaghan Caitlin , Li Wanxin , Elder Geoffrey , Smith Peter T. , Dallago Christian , Cerami Ethan , Gross Benjamin , Dogrusoz Ugur , Demir Emek , Bader Gary D. , Sander Chris 
Published: October 2019

ABSTRACTPathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g., metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (1) tools to search this comprehensive resource, (2) a download site offering integrated bulk sets of pathway data (e.g., tables of interactions and gene sets), (3) reusable software libraries for working with pathway information in several programming languages (Java, R, Python, and Javascript), and (4) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4,794 detailed human biochemical processes (i.e., pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.
Long-term alterations in brain and behavior after postnatal Zika virus infections in infant macaques
Authors: Raper Jessica , Kovacs-Balint Zsofia , Mavigner Maud , Gumber Sanjeev , Burke Mark W. , Habib Jakob , Mattingly Cameron , Fair Damien , Earl Eric , Feczko Eric , Styner Martin , Jean Sherrie M. , Cohen Joyce K. , Suthar Mehul S. , Sanchez Mar M. , Alvarado Maria C. , Chahroudi Ann 
Published: October 2019

AbstractConsidering the impact that Zika virus (ZIKV) infection has on the fetal nervous system and given that the postnatal period is also a time of rapid brain growth, it is important to understand the potential neurobehavioral consequences of ZIKV infection during infancy. Postnatal ZIKV infection in a rhesus macaque (RM) model resulted in long-term behavioral, motor, and cognitive changes, including increased emotional reactivity, decreased social contact, loss of balance, and deficits in visual recognition memory at one year of age. Structural and functional MRI showed that ZIKV-infected infant RMs had persistent enlargement of lateral ventricles, smaller volumes and altered functional connectivity between brain areas important for socioemotional behavior, cognitive, and motor function (e.g. amygdala, hippocampus, cerebellum). Neuropathological changes corresponded with neuroimaging results and were consistent with the behavioral and memory deficits. Overall, this study demonstrates that postnatal ZIKV infection of infants in this model has long lasting neurodevelopmental consequences.
A flexible network of Vimentin intermediate filaments promotes the migration of amoeboid cancer cells through confined environments
Authors: Tudor Sara M. , Lavenus Sandrine B. , Logue Jeremy S. 
Published: October 2019

AbstractThe spread of tumor cells to distant sites is promoted by their ability to switch between mesenchymal and amoeboid (bleb-based) migration. Because of this, inhibitors of metastasis must account for each motility mode. To this end, here we determine the precise role of the Vimentin intermediate filament system in regulating the migration of amoeboid human cancer cells. Vimentin is a classic marker of epithelial to mesenchymal transition and is therefore, an ideal target for a metastasis inhibitor. However, the role of Vimentin in amoeboid migration has not been determined. Since amoeboid, leader bleb-based migration occurs in confined spaces and Vimentin is known to be a major determinant of cell mechanical properties, we hypothesized that a flexible Vimentin network is required for fast amoeboid migration. This was tested using our PDMS slab-based approach for the confinement of cells, RNAi, over-expression, pharmacological treatments, and measurements of cell stiffness. In contrast to Vimentin RNAi, inducing the bundling of Vimentin was found to inhibit fast amoeboid migration and proliferation. Importantly, these effects were independent of changes in actomyosin contractility. Collectively, our data supports a model whereby the perturbation of cell mechanical properties by Vimentin bundling inhibits the invasive properties of cancer cells.
Visualization and Analysis of Whole Depot Adipose Tissue Neural Innervation
Authors: Willows Jake W. , Blaszkiewicz Magdalena , Lamore Amy , Borer Samuel , Dubois Amanda L. , Garner Emma , Breeding William P. , Tilbury Karissa B. , Khalil Andre , Townsend Kristy L. 
Published: October 2019

SummaryLittle is known about the diversity and function of adipose tissue nerves due, in part, to the inability to effectively visualize the various nerve subtypes residing within these tissues. The tools currently available for researchers to image and quantify adipose tissue innervation are limited and dependent on optical clearing techniques and light sheet microscopy. Here we present a method of tissue processing that uses mechanical force to compress tissue to decrease tissue thickness in the z-axis by expanding it in the x and y-axes whilst leaving cells intact. This has been combined with autofluorescence quenching techniques to permit intact whole tissues to be mounted on slides and imaged on any microscope, with a complementary means to perform whole tissue neurite density quantification. We have included examples of how this technique can be used to further our current knowledge of adipose-nerve communication by characterizing the nerves, nerve-subtypes, and neurovascular interactions within subcutaneous white adipose tissue in mice.
Breeding at higher latitude as measured by stable isotope is associated with higher photoperiod threshold and delayed reproductive development in a songbird
Authors: Singh D. , Reed S.R. , Kimmitt A.A. , Alford K. A. , Ketterson E.D. 
Published: October 2019

AbstractMany organisms time reproduction to photoperiod, a constant from year to year. Predicting how anthropogenic change will influence future timing demands greater knowledge of the current role of photoperiod. We held two closely related bird populations in a common environment. One population is resident; the other winters in sympatry with the resident population but migrates north prior to reproducing. We increased photoperiod gradually and measured preparation for migration and reproduction, using feather stable isotopes to estimate breeding latitude. We predicted population differences in the minimum stimulatory day length to elicit a response (CPP, critical photoperiod) and co-variation between CPP and distance migrated. We found clear population differences in CPP and greater CPP in longer distance migrants. We conclude that current geographic variation in reproductive timing has a genetic or early developmental basis and recommend that future research focus on how anthropogenic changes will interact with CPP to adjust timing of reproduction and migration.
Optogenetic modulation of TDP-43 oligomerization fast-forwards ALS-related pathologies in the spinal motor neurons
Authors: Asakawa Kazuhide , Handa Hiroshi , Kawakami Koichi 
Published: October 2019

AbstractCytoplasmic aggregation of TDP-43 characterizes degenerating neurons in most cases of amyotrophic lateral sclerosis (ALS), yet the mechanisms and cellular outcomes of TDP-43 pathology remain largely elusive. Here, we develop an optogenetic TDP-43 variant (opTDP-43), whose multimerization status can be modulated in vivo through external light illumination. Using the translucent zebrafish neuromuscular system, we demonstrate that short-term light stimulation reversibly induces cytoplasmic opTDP-43 mislocalization, but not aggregation, in the spinal motor neuron, leading to an axon outgrowth defect associated with myofiber denervation. In contrast, opTDP-43 forms pathological aggregates in the cytoplasm after longer-term illumination and seeds non-optogenetic TDP-43 aggregation. Furthermore, we find that an ALS-linked mutation in the intrinsically disordered region (IDR) exacerbates the light-dependent opTDP-43 toxicity on locomotor behavior. Together, our results propose that IDR-mediated TDP-43 oligomerization triggers both acute and long-term pathologies of motor neurons, which may be relevant to the pathogenesis and progression of ALS.
Thermodynamic destabilization informs pathogenicity assessment of a variant of uncertain significance in cardiac myosin binding protein C
Authors: Pricolo Maria Rosaria , Herrero-Galán Elías , Mazzaccara Cristina , Losi Maria Angela , Alegre-Cebollada Jorge , Frisso Giulia 
Published: October 2019

ABSTRACTIn the era of Next Generation Sequencing (NGS), genetic testing for inherited disorders identifies an ever-increasing number of variants whose pathogenicity remains unclear. These variants of uncertain significance (VUS) limit the reach of genetic testing in clinical practice. The VUS for Hypertrophic Cardiomyopathy (HCM), the most common familial heart disease, constitute over 60% of entries for missense variants shown in ClinVar database. We have studied a novel VUS (c.1809T>G-p.I603M) in the most frequently mutated gene in HCM, MYBPC3, which codes for cardiac myosin-binding protein C (cMyBPC). Our determinations of pathogenicity integrate bioinformatics evaluation and functional studies of RNA splicing and protein thermodynamic stability. In silico prediction and mRNA analysis indicated no alteration of RNA splicing induced by the variant. At the protein level, the p.I603M mutation maps to the C4 domain of cMyBPC. Although the mutation does not perturb much the overall structure of the C4 domain, the stability of C4 I603M is severely compromised as detected by circular dichroism and differential scanning calorimetry experiments. Taking into account the highly destabilizing effect of the mutation in the structure of C4, we propose reclassification of variant p.I603M as likely pathogenic. Looking into the future, the workflow described here can be used to refine the assignment of pathogenicity of variants of uncertain significance in MYBPC3.
Availability of Zinc Impacts Interactions BetweenStreptococcus sanguinisandPseudomonas aeruginosain Co-culture
Authors: Li Kewei , Gifford Alex , Hampton Thomas , O’Toole George A. 
Published: October 2019

ABSTRACTAirway infections associated with cystic fibrosis (CF) are polymicrobial. We reported previously that clinical isolates ofP. aeruginosapromote the growth of a variety of streptococcal species. To explore the mechanistic basis of this interaction, we performed a genetic screen to identify mutants ofStreptococcus sanginuisSK36 whose growth was no longer enhanced byP. aeruginosaPAO1. Mutations in zinc uptake systems ofS. sanginuisSK36 reduced growth of these strains by 1-3 log compared to wild-typeS. sanginuisSK36 when grown in coculture withP. aeruginosaPA01, while exogenous zinc (0.1-10 μm) rescued the coculture defect of zinc uptake mutants ofS. sanginuisSK36. Zinc uptake mutants ofS. sanginuisSK36 had no obvious growth defect in monoculture. Consistent with a competition for zinc driving coculture dynamics,S. sanginuisSK36 grown in coculture withP. aeruginosashowed increased expression of zinc uptake genes compared toS. sanginuisgrown alone. Strains ofP. aeruginosaPAO1 defective in zinc transport also supported more robust growth byS. sanginuiscompared to coculture with wild-typeP. aeruginosaPAO1. An analysis of 118 CF sputum samples revealed that total zinc levels varied from ~5-145 μM. At relatively low zinc levels,PseudomonasandStreptococcuswere found in approximately equal abundance; at higher zinc levels, we observed an increasing relative abundance ofPseudomonasand decline ofStreptococcus, perhaps as a result of increasing zinc toxicity. Together, our data indicate that the relative abundance of these microbes in the CF airway may be impacted by zinc levels.IMPORTANCEPolymicrobial infections in CF likely impact patient health, but the mechanism(s) underlying such interactions are poorly understood. Here we show that interactions betweenPseudomonasandStreptococcusare modulated by zinc availability using anin vitromodel system, and clinical data are consistent with this model. Together with previous studies, our work supports a role for metal homeostasis as a key factor driving microbial interactions.
Label-free characterization of Amyloid-β-plaques and associated lipids in brain tissues using stimulated Raman scattering microscopy
Authors: Schweikhard Volker , Baral Andrea , Krishnamachari Vishnu , Hay William C. , Fuhrmann Martin 
Published: October 2019

ABSTRACTThe brains of patients with neurodegenerative diseases such as Alzheimer’s Disease (AD) often exhibit pathological alterations that involve abnormal aggregations of proteins and lipids. Here, we demonstrate that high-resolution, label-free, chemically-specific imaging using Stimulated Raman Scattering Microscopy (SRS) provides novel insights into the biophysical properties and biochemical composition of such pathological structures. In brain slices of a mouse model of AD, SRS reveals large numbers of Amyloid-β plaques that commonly form a characteristic, three-dimensional core-shell structure, with a fibrillar proteinaceous core surrounded by a halo-like shell of lipid-rich deposits. SRS spectroscopic imaging allows for a clean, label-free visualization of the misfolded (β-sheet) Amyloid-β content in the plaque core. Surrounding lipid-rich deposits are found to contain comparatively high concentrations of membrane lipids (sphingomyelin, phosphatidylcholine), but lower levels of cholesterol than healthy white matter structures. Overall, the SRS spectra of plaque-associated lipids closely resemble those of nearby neurites, with the notable difference of a higher degree of lipid unsaturation compared to healthy brain structures. We hypothesize that plaque-associated lipid deposits may result from neuritic dystrophy associated with AD, and that the observed increased levels of unsaturation could help identify the kinds of pathological alterations taking place. Taken together, our results highlight the potential of Stimulated Raman Scattering microscopy to contribute to a deeper understanding of neurodegenerative diseases.
CDK8 and CDK19 kinases have non-redundant oncogenic functions in hepatocellular carcinoma
Authors: Bacevic Katarina , Prieto Susana , Caruso Stefano , Camasses Alain , Dubra Geronimo , Ursic-Bedoya José , Lozano Anthony , Butterworth Jacqueline , Zucman-Rossi Jessica , Hibner Urszula , Fisher Daniel , Gregoire Damien 
Published: October 2019

AbstractHepatocellular carcinoma (HCC) is a common cancer with high mortality. The limited therapeutic options for advanced disease include treatment with Sorafenib, a multi-kinase inhibitor whose targets include the Mediator kinase CDK8. Since CDK8 has reported oncogenic activity in Wnt-dependent colorectal cancer, we investigated whether it is also involved in HCC. We find that CDK8 and its paralogue CDK19 are significantly overexpressed in HCC patients, where high levels correlate with poor prognosis. Liver-specific genetic deletion of CDK8 in mice is well supported and protects against chemical carcinogenesis. Deletion of either CDK8 or CDK19 in hepatic precursors had little effect on gene expression in exponential cell growth but prevented oncogene-induced transformation. This phenotype was reversed by concomitant deletion of TP53. These data support important and non-redundant roles for mediator kinases in liver carcinogenesis, where they genetically interact with the TP53 tumor suppressor.