bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of pyrazolo[1,5-a]pyrimidines lead to the identification of a highly selective casein kinase 2 inhibitor
Authors: Krämer Andreas , Kurz Christian Georg , Berger Benedict-Tilman , Celik Ibrahim Ethem , Knapp Stefan , Hanke Thomas 
Published: June 2020

ABSTRACTCasein kinase 2 (CK2) is a constitutively expressed serine/threonine kinase that has a large diversity of cellular substrates. Thus, CK2 has been associated with a plethora of regulatory functions and dysregulation of CK2 has been linked to disease development in particular to cancer. The broad implications in disease pathology makes CK2 an attractive target. To date, the most advanced CK2 inhibitor is silmitasertib, which has been investigated in clinical trials for treatment of various cancers, albeit several off-targets for silmitasertib have been described. To ascertain the role of CK2 inhibition in cancer, other disease and normal physiology the development of a selective CK2 inhibitor would be highly desirable. In this study we explored the pyrazolo[1,5-a]pyrimidine hinge-binding moiety for the development of selective CK2 inhibitors. Optimization of this scaffold, which included macrocyclization, led toIC20(31) a compound that displayed highin vitropotency for CK2 (KD= 12 nM) and exclusive selectivity for CK2. X-ray analysis revealed a canonical type-I binding mode forIC20. However, the polar carboxylic acid moiety that is shared by many CK2 inhibitors including silmitasertib was required for potency and reduced somewhat cellular activity. In summary,IC20represents a highly selective and potent inhibitor of CK2, which can be used as a tool compound to study CK2 biology and potential new applications for the treatment of diseases.NotesThe authors declare no conflict of interest.TOC Figure / Graphical Abstract
Contrasting hierarchical and multiple-demand accounts of frontal lobe functional organisation during task-switching
Authors: Daws Richard E. , Soreq Eyal , Li Yuqi , Sandrone Stefano , Hampshire Adam 
Published: June 2020

AbstractThere is an unresolved discrepancy between popular hierarchical and multiple-demand perspectives on the functional organisation of the human frontal lobes. Here, we tested alternative predictions of these perspectives with a novel fMRI switching paradigm. Each trial involved switching attention between stimuli, but at different levels of difficulty and abstraction. As expected, increasing response times were evident when comparing low-level perceptual switching to more abstract dimension, rule and task-switching. However, there was no evidence of an abstraction hierarchy within the prefrontal cortex (PFC). Nor was there recruitment of additional anterior PFC regions under increased switching demand. Instead, switching activated a widespread network of frontoparietal and cerebellar regions. Critically, the activity within PFC sub-regions uniformly increased with behavioural switch costs. We propose that both perspectives have some validity, but neither is complete. Too many studies have reported dissociations within MD for this volume to be functionally uniform, and the recruitment of more anterior regions with increased general difficulty cannot explain those results. Conversely, whilst reproducible evidence for a hierarchical functional organisation has been reported, this cannot be explained in terms of abstraction of representation or reconfigurationper se, because those interpretations generalise poorly to other task contexts.
Modified Vaccinia Ankara Based SARS-CoV-2 Vaccine Expressing Full-Length Spike Induces Strong Neutralizing Antibody Response
Authors: Routhu Nanda Kishore , Gangadhara Sailaja , Cheedarla Narayanaiah , Shiferaw Ayalnesh , Rahman Sheikh Abdul , Sahoo Anusmita , Shi Pei-Yong , Menachery Vineet D. , Floyd Katharine , Fischinger Stephanie , Atyeo Caroline , Alter Galit , Suthar Mehul S. , Amara Rama Rao 
Published: June 2020

AbstractThere is a great need for the development of vaccines for preventing SARS-CoV-2 infection and mitigating the COVID-19 pandemic. Here, we developed two modified vaccinia Ankara (MVA) based vaccines which express either a membrane anchored full-length spike protein (MVA/S) stabilized in a prefusion state or the S1 region of the spike (MVA/S1) which forms trimers and is secreted. Both immunogens contained the receptor-binding domain (RBD) which is a known target of antibody-mediated neutralization. Following immunizations with MVA/S or MVA/S1, both spike protein recombinants induced strong IgG antibodies to purified full-length SARS-CoV-2 spike protein. The MVA/S induced a robust antibody response to purified RBD, S1 and S2 whereas MVA/S1 induced an antibody response to the S1 region outside of the RBD region. Both vaccines induced an antibody response in the lung and that was associated with induction of bronchus-associated lymphoid tissue. MVA/S but not MVA/S1 vaccinated mice generated robust neutralizing antibody responses against SARS-CoV-2 that strongly correlated with RBD antibody binding titers. Mechanistically, S1 binding to ACE-2 was strong but reduced following prolonged pre-incubation at room temperature suggesting confirmation changes in RBD with time. These results demonstrate MVA/S is a potential vaccine candidate against SARS-CoV-2 infection.
I-KCKT allows dissection-free RNA profiling of adultDrosophilaintestinal progenitor cells
Authors: Buddika Kasun , Xu Jingjing , Ariyapala Ishara S. , Sokol Nicholas S. 
Published: June 2020

AbstractThe adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. Here, we describe a new proximity-based profiling method that relies upon a GAL4 driver, termedintestinal-kickout-GAL4(I-KCKT-GAL4), exclusively expressed in intestinal progenitor cells. This method used UV cross-linked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven byI-KCKT-GAL4. When applied to the general mRNA-binder, poly(A)-binding protein, the RNA profile obtained by this method identified 98.8% of transcripts found after progenitor cell sorting, and had low background noise despite being derived from whole animal lysate. We also mapped the targets of the more selective RNA binder, Fragile Mental Retardation Protein, using enhanced CLIP, and report for the first time its binding motif in Drosophila cells. This method will therefore enable the RNA profiling of wildtype and mutant intestinal progenitor cells from intact flies exposed to normal and altered environments, as well as the identification of RNA-protein interactions critical for stem cell function.Summary StatementWe report a dissection-free method to identify proximity-based RNA-protein interactions in anin vivostem cell population, enabling molecular analysis of these cells at unprecedented speed and resolution.
LI Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects
Authors: Parikh Saurin Bipin , Coelho Nelson Castilho , Carvunis Anne-Ruxandra 
Published: June 2020

ABSTRACTMicrobial growth characteristics have long been used to investigate fundamental questions of biology. Colony-based high-throughput screens enable parallel fitness estimation of thousands of individual strains using colony growth as a proxy for fitness. However, fitness estimation is complicated by spatial biases affecting colony growth, including uneven nutrient distribution, agar surface irregularities, and batch effects. Analytical methods that have been developed to correct for these spatial biases rely on the following assumptions: i) that fitness effects are normally distributed, and ii) that most genetic perturbations lead to minor changes in fitness. Although reasonable for many applications, these assumptions are not always warranted and can limit the ability to detect small fitness effects. Beneficial fitness effects, in particular, are notoriously difficult to detect under these assumptions. Here, we developed the linear interpolation-based detector (LI Detector) framework to enable sensitive colony-based screening without making prior assumptions about the underlying distribution of fitness effects. The LI Detector uses a grid of reference colonies to assign a relative fitness value to every colony on the plate. We show that the LI Detector is effective in correcting for spatial biases and equally sensitive towards increase and decrease in fitness. LI Detector offers a tunable system that allows the user to identify small fitness effects with unprecedented sensitivity and specificity. LI Detector can be utilized to develop and refine gene-gene and gene-environment interaction networks of colony-forming organisms, including yeast, by increasing the range of fitness effects that can be reliably detected.
A collection of programs for one-dimensional Ising analysis of linear repeat proteins with point substitutions
Authors: Marold Jacob D. , Sforza Kevin , Geiger-Schuller Kathryn , Aksel Tural , Klein Sean , Petersen Mark , Poliakova-Georgantas Ekaterina , Barrick Doug 
Published: June 2020

AbstractA collection of programs is presented to analyze the thermodynamics of folding of linear repeat proteins using a 1D Ising model to determine intrinsic folding and interfacial coupling free energies. Expressions for folding transitions are generated for a series of constructs with different repeat numbers and are globally fitted to transitions for these constructs. These programs are designed to analyze Ising parameters for capped homopolymeric consensus repeat constructs as well as heteropolymeric constructs that contain point substitutions, providing a rigorous framework for analysis of the effects of mutation on intrinsic and directional (i.e., N- versus C-terminal) interfacial coupling free-energies. A bootstrap analysis is provided to estimate parameter uncertainty as well as correlations among fitted parameters. Rigorous statistical analysis is essential for interpreting fits using the complex models required for Ising analysis of repeat proteins, especially heteropolymeric repeat proteins. Programs described here are available athttps://github.com/barricklab-at-jhu/Ising_programs.
Regional gene expression patterns are associated with task-specific brain activation during reward and emotion processing measured with functional MRI
Authors: Komorowski Arkadiusz , Vidal Ramon , Singh Aditya , Murgaš Matej , Pena-Centeno Tonatiuh , Gryglewski Gregor , Kasper Siegfried , Wiltfang Jens , Lanzenberger Rupert , Goya-Maldonado Roberto 
Published: June 2020

AbstractThe spatial relationship between gene expression profiles and neural response patterns known to be altered in neuropsychiatric disorders, e.g. depression, can guide the development of more targeted therapies. Here, we estimated the correlation between human transcriptome data and two different brain activation maps measured with functional magnetic resonance imaging (fMRI) in healthy subjects. Whole-brain activation patterns evoked during an emotional face recognition task were associated with topological mRNA expression of genes involved in cellular transport. In contrast, fMRI activation patterns related to the acceptance of monetary rewards were associated with genes implicated in neuronal development, synapse regulation, and gene transcription. An overlap of these genes with risk genes from major depressive disorder genome-wide associations studies revealed the involvement of the master regulators TCF4 and MEF2C. These results were further validated by means of meta-analytic fMRI data. Overall, the identification of stable relationships between spatial gene expression profiles and fMRI data may reshape the prospects for imaging transcriptomics studies.
Two-Photon Microperimetry: A media opacity-independent retinal function assay
Authors: Wei Ang , Mehta Urmi V. , Palczewska Grazyna , Palma Anton M. , Hussey Vincent M. , Hoffmann Luke E. , Diep Anna , Nguyen Kevin , Le Bryan , Chang Steven Yone-Shun , Browne Andrew W. 
Published: June 2020

AbstractHumans perceive light in the visible portion of electromagnetic radiation. However, visible light is scattered and attenuated by optical media opacities. Because all conventional visual function tests rely on visible light, test results are reduced in patients with optical media opacities like corneal scars, cataracts, and vitreous hemorrhages. Infrared (IR) light has greater penetrance through tissue than visible light. Two-photon IR visual stimulation, a recently pioneered technology, should enable testing of retinal visual function and produce results that are less susceptible to media opacities. The effects of simulated media opacities on visual performance in young healthy volunteers and the change in visual function in healthy phakic patients of two age ranges (20-40 and 60-80-year-old) were studied using conventional testing and 2-photon infrared visual stimulation. All subjects completed visual function testing using cone contrast threshold (CCT) testing, conventional microperimetry, visible light microperimetry from a novel device (2PM-Vis), and infrared 2-photon microperimetry (2PM-IR). Retinal sensitivity measured by 2PM-IR demonstrated lower variability than all other devices relying on visible spectrum stimuli. Retinal sensitivity decreased proportionally with the transmittance of light through each filter. CCT scores and retinal sensitivity decreased with age in all testing modalities. Visible spectrum testing modalities demonstrated larger test result differences between young and old patient cohorts; this difference was inversely proportional to the wavelength of the visual function test. 2PM-IR mitigates media opacities which may mask small differences in retinal sensitivity when tested with conventional visual function testing devices.One Sentence SummaryTwo photon infrared visual function testing produces results that are less susceptible to media opacities than conventional tests.
Activation of the Crtc2/Creb1 transcriptional network in skeletal muscle enhances weight loss during intermittent fasting
Authors: Bruno Nelson E. , Nwachukwu Jerome C. , Srinivasan Sathish , Hawkins Richard , Sturgill David , Hager Gordon L. , Hurst Stephen , Sheu Shey-Shing , Conkright Michael D. , Nettles Kendall W. 
Published: June 2020

AbstractThe Creb-Regulated Transcriptional Coactivator (Crtc) family of transcriptional coregulators drive Creb1-mediated transcription effects on metabolism in many tissues, but the in vivo effects of Crtc2/Creb1 transcription on skeletal muscle metabolism are not known. Skeletal muscle-specific overexpression of Crtc2 (Crtc 2 mice) induced greater mitochondrial activity, metabolic flux capacity for both carbohydrates and fats, improved glucose tolerance and insulin sensitivity, and increased oxidative capacity, supported by upregulation of key metabolic genes. Crtc2 overexpression led to greater weight loss during alternate day fasting (ADF), selective loss of fat rather than lean mass, supported by maintenance of higher energy expenditure during the fast. ADF downregulated most of the mitochondrial electron transport genes, and other regulators of mitochondrial function, that were substantially reversed by Crtc2-driven transcription. Glucocorticoids acted with AMPK to drive atrophy and mitophagy, which was reversed by Crtc2/Creb1 signaling. Crtc2/Creb1-mediated signaling coordinates metabolic adaptations in skeletal muscle that explain how Crtc2/Creb1 regulates metabolism and weight loss.
Coordinate transcriptional and post-transcriptional repression of pro-differentiation genes maintains intestinal stem cell identity
Authors: Buddika Kasun , Huang Yi-Ting , Ariyapala Ishara S. , Griffith Alex Butrum- , Norrell Sam A. , O’Connor Alex M. , Patel Viraj K. , Rector Samuel A. , Slovan Mark , Sokolowski Mallory , Kato Yasuko , Nakamura Akira , Sokol Nicholas S. 
Published: June 2020

SummaryThe role of Processing bodies (P-bodies), key sites of post-transcriptional control, in adult stem cells remains poorly understood. Here, we report that adult Drosophila intestinal stem cells, but not surrounding differentiated cells such as absorptive Enterocytes (ECs), harbor P-bodies that containDrosophilaorthologs of mammalian P-body components DDX6, EDC3, EDC4 and LSM14A/B. A targeted RNAi screen in intestinal progenitor cells identified 39 previously known and 64 novel P-body regulators, includingPatr-1, a gene necessary for P-body assembly. Loss ofPatr-1-dependent P-bodies leads to a loss of stem cells that is associated with inappropriate translation and expression of EC-fate genenubbin. Transcriptomic analysis of progenitor cells identifies a cadre of such weakly transcribed pro-differentiation transcripts that are elevated after P-body loss. Altogether, this study identifies a coordinated P-body dependent, translational and transcriptional repression program that maintains a defined set ofin vivostem cells in a state primed for differentiation.Graphical abstractHighlightsDrosophila intestinal progenitor cells contain constitutive and ultrastructurally organized P-bodies.A P-body regulatorPatr-1is required for intestinal progenitor cell maintenance.Enterocyte (EC) genes such asnubbinare weakly transcribed but not translated in intestinal progenitors.P-bodies repress EC gene translation to promote stem cell maintenance.
Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations
Authors: Ghorbani Mahdi , Brooks Bernard R. , Klauda Jeffery B. 
Published: June 2020

AbstractThe novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion’s surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of RBD/ACE2 complex. It is found that most of the naturally-occurring mutations to the RBD either strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This may have implications for high human-to-human transmission of coronavirus in regions where these mutations have been found as well as any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in-silico Ala-scanning and long-timescale MD simulations, highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become more infectious.
Full-length isoform transcriptome of developing human brain provides new insights into autism
Authors: Chau Kevin , Zhang Pan , Urresti Jorge , Amar Megha , Pramod Akula Bala , Chen Jiaye , Thomas Amy , Corominas Roser , Lin Guan Ning , Iakoucheva Lilia M. 
Published: June 2020

SummaryAlternative splicing plays important role in brain development, however its global contribution to human neurodevelopmental diseases (NDD) has not been fully investigated. Here, we examined the relationships between full-length splicing isoforms expression in the brain andde novoloss-of-function mutations identified in the patients with NDDs. We analyzed the full-length isoform transcriptome of the developing human brain and observed differentially expressed isoforms and isoform co-expression modules undetectable by gene-level analyses. These isoforms were enriched in loss-of-function mutations and microexons, co-expressed with a unique set of partners, and had higher prenatal expression. We experimentally tested the impact of splice site mutations in five NDD risk genes, includingSCN2A,DYRK1AandBTRC,and demonstrated exon skipping. Furthermore, our results suggest that the splice site mutation inBTRCreduces translational efficiency, likely impacting Wnt signaling through impaired degradation of β-catenin. We propose that functional effect of mutations associated with human diseases should be investigated at the isoform-rather than the gene-level resolution.HighlightsDifferential isoform expression analysis of the human brain transcriptome reveals neurodevelopmental processes and pathways undetectable by differential gene expression analyses.Splicing isoforms impacted by neurodevelopmental disease (NDD) risk mutations exhibit higher prenatal expression, are enriched in microexons and are involved in neuronal-related functions.Isoform co-expression network analysis identifies modules with splicing and synaptic functions that are enriched in NDD mutations.Splice site mutations impacting NDD risk genes cause exon skipping and produce novel isoforms with altered biological properties.Functional impact of mutations should be investigated at the full-length isoform-level rather than the gene-level resolution
Quantifying Color Vision Changes Associated with Cataracts Using Cone Contrast Thresholds
Authors: Mehta Urmi , Diep Anna , Nguyen Kevin , Le Bryan , Yuh Clara , Frambach Caroline , Doan John , Wei Ang , Palma Anton M. , Farid Marjan , Garg Sumit , Kedhar Sanjay , Wade Matthew , Marshall Kailey A. , Jameson Kimberly A. , Kenney M. Cristina , Browne Andrew W. 
Published: June 2020

AbstractPurposeThe cone contrast threshold (CCT) test quantified color vision changes in subjects of all ages and those undergoing cataract surgery.MethodsTwenty-four healthy volunteers from two cohort studies performed CCT using best corrected visual acuity, filters, mydriasis, and pinhole correction. Retrospective cross-sectional study of patients seen in eye clinics evaluated the relationship between age and color vision, and age and lens status in 355 eyes. Lastly, 25 subjects performed CCT before and after cataract surgery.ResultsCCT scores were most reliable in the non-mydriatic condition without pinhole correction. Progressively dense brown filters produced small but significant reductions in S-cone sensitivity. Linear regression analysis of phakic subjects showed a decline for all cone classes with age. Rate of decline was greater for S-cones (slope (95% CI) = −1.09 (−1.23, 0.94)) than M-cones (slope (95% CI) = −0.80 (−0.95, −0.66)) and L-cones (slope (95% CI) = −0.66 (−0.81, - 0.52)). CCT scores increased for S-cones but reduced for L- and M-cones in pseudophakic subjects compared to phakic patients. CCT scores after cataract surgery increased for S-cones, M-cones, and L-cones by 33.0 (p<0.001), 24.9 (p=0.001), and 22.0 (p=0.008).ConclusionsCCT assessment allows for clinically practical quantitation of color and contrast vision improvement after cataract surgery and aging patients who note poor vision despite good visual acuity.Translational RelevanceCCT testing, historically used in research, is now a clinically practical tool to evaluate age and cataract related changes in color and contrast vision and routinely quantify vision beyond black and white visual acuity testing.