bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interleukin-12 elicits a non-canonical response in B16 melanoma cells to enhance survival
Authors: Byrne-Hoffman C. N. , Deng W. , McGrath O. , Wang P. , Rojanasakul Y. , Klinke D. J. 
Published: April 2019

AbstractOncogenesis rewires signaling networks to confer a fitness advantage to malignant cells. For instance, the B16F0 melanoma cell model creates a cytokine sink for Interleukin-12 (IL-12) to deprive neighboring cells of this important anti-tumor immune signal. While a cytokine sink provides an indirect fitness advantage, does IL-12 provide an intrinsic advantage to B16F0 cells? Functionally, stimulation with IL-12 enhanced B16F0 cell survival but not normal Melan-A melanocytes that were challenged with a cytotoxic agent. To identify a mechanism, we assayed the phosphorylation of proteins involved in canonical IL-12 signaling, STAT4, and cell survival, Akt. In contrast to T cells that exhibited a canonical response to IL-12 by phosphorylating STAT4, IL-12 stimulation of B16F0 cells predominantly phosphorylated Akt. Mechanistically, the differential response in B16F0 cells is explained by both ligand-dependent and ligand-independent aspects to initiate PI3K-AKT signaling upon IL12RB2 homodimerization. Namely, IL-12 promotes IL12RB2 homodimerization with low affinity and IL12RB2 overexpression promotes homodimerization via molecular crowding on the plasma membrane. Collectively, the data suggest that B16F0 cells shifted the intra-cellular response to IL-12 from engaging immune surveillance to favoring cell survival. Identifying how signaling networks are rewired in model systems of spontaneous origin can inspire therapeutic strategies in humans.Statement of SignificanceWhile Interleukin-12 is a key cytokine that promotes anti-tumor immunity, thinking of cancer as an evolutionary process implies that an immunosuppressive tumor microenvironment could arise during oncogenesis by interfering with endogenous anti-tumor immune signals, like IL-12. Previously, we found that B16F0 cells, a cell line derived from a spontaneous melanoma, interrupts this heterocellular signal by sequestering IL-12, which provides an indirect fitness advantage. Here, we report that B16F0 cells gain an intrinsic advantage by rewiring the canonical response to IL-12 to instead initiate PI3K-AKT signaling, which promotes cell survival. The data suggest a model where overexpressing one component of the IL-12 receptor, IL12RB2, enables melanoma cells to shift the functional response via both IL-12-mediated and molecular crowding-based IL12RB2 homodimerization.
Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
Authors: Venkatasubramanian Meenakshi , Chetal Kashish , Atluri Gowtham , Salomonis Nathan 
Published: April 2019

ABSTRACTThe rapid proliferation of single-cell RNA-Sequencing (scRNA-Seq) technologies has spurred the development of diverse computational approaches to detect transcriptionally coherent populations. While the complexity of the algorithms for detecting heterogeneity have increased, most existing algorithms require significant user-tuning, are heavily reliant on dimensionality reduction techniques and are not scalable to ultra-large datasets. We previously described a multi-step algorithm, Iterative Clustering and Guide-gene selection (ICGS), which applies intra-gene correlation and hybrid clustering to uniquely resolve novel transcriptionally coherent cell populations from an intuitive graphical user interface. Here, we describe a new iteration of ICGS that outperforms state-of-the-art scRNA-Seq detection workflows when applied to well-established benchmarks. This approach combines multiple complementary subtype detection methods (HOPACH, sparse-NMF, cluster “fitness”, SVM) to resolve rare and common cell-states, while minimizing differences due to donor or batch effects. Using data from the Human Cell Atlas, we show that the PageRank algorithm effectively down samples ultra-large scRNA-Seq datasets, without losing extremely rare or transcriptionally similar distinct cell-types and while recovering novel transcriptionally unique cell populations. We believe this new approach holds tremendous promise in reproducibly resolving hidden cell populations in complex datasets.HighlightsICGS2 outperforms alternative approaches in small and ultra-large benchmark datasetsIntegrates multiple solutions for cell-type detection with supervised refinementScales effectively to resolve rare cell-states from ultra-large datasets using PageRank sampling with a low memory footprintIntegrated into AltAnalyze to enable sophisticated and automated downstream analysis
Identification of novel key biomarkers in Simpson-Golabi-Behmel Syndrome: Evidence from bioinformatics analysis
Authors: Mustafa Mujahed I. , Abdelmoneim Abdelrahman H. , Elfadol Nafisa M. , Murshed Naseem S. , Mohammed Zainab O. , Hassan Mohamed A. 
Published: April 2019

AbstractBackgroundThe Simpson-Golabi-Behmel Syndrome (SGBS) or overgrowth Syndrome is a rare inherited X-linked condition characterized by pre- and postnatal overgrowth. The aim of the present study is to identify functional non-synonymous SNPs of GPC3 gene using various in silico approaches. These SNPs are supposed to have a direct effect on protein stability through conformation changes.Material and methodsThe SNPs were retrieved from the Single Nucleotide Polymorphism database (dbSNP) and further used to investigate a damaging effect using SIFT, PolyPhen, PROVEAN, SNAP2, SNPs&GO, PHD-SNP and P-mut, While we used I-mutant and MUPro to study the effect of SNPs on GPC3 protein structure. The 3D structure of human GPC3 protein is not available in the Protein Data Bank, so we used RaptorX to generate a 3D structural model for wild-type GPC3 to visualize the amino acids changes by UCSF Chimera. For biophysical validation we used project HOPE. Lastly we run conservational analysis by BioEdit and Consurf web server respectively.Resultsour results revealed three novel missense mutations (rs1460413167, rs1295603457 and rs757475450) that are found to be the most deleterious which effect on the GPC3 structure and function.ConclusionThis present study could provide a novel insight into the molecular basis of overgrowth Syndrome.
Studying early embryogenesis in the flatwormMaritigrella crozieriindicates a unique modification of the spiral cleavage program in polyclad flatworms
Authors: Girstmair Johannes , Telford Maximilian J. 
Published: April 2019

AbstractBackgroundSpiral cleavage is a conserved early developmental mode found in several phyla of Lophotrochozoans with highly diverse adult body plans. While the cleavage pattern has clearly been broadly conserved, it has also undergone many modifications in various taxa. The precise mechanisms of how different adaptations have altered the ancestral spiral cleavage pattern is an important ongoing evolutionary question and adequately answering this question requires obtaining a broad developmental knowledge of different spirally cleaving taxa.In flatworms (Platyhelminthes), the spiral cleavage program has been lost or severely modified in most taxa. Polyclad flatworms, however, have retained the pattern up to the 32-cell stage. Here we study early embryogenesis of the cotylean polyclad flatwormMaritigrella crozierito investigate how closely this species follows the canonical spiral cleavage pattern and to discover any potential deviations from it.ResultsUsing live imaging recordings and 3D reconstructions of embryos, we give a detailed picture of the events that occur during spiral cleavage inM. crozieri. We suggest, contrary to previous observations, that the 4-cell stage is a product of unequal cleavages. We show that that the formation of third and fourth micromere quartets are accompanied by strong blebbing events; blebbing also accompanies the formation of micromere 4d. We find an important deviation from the canonical pattern of cleavages with clear evidence that micromere 4d follows an atypical cleavage pattern, so far exclusively found in polyclad flatworms.ConclusionsOur findings highlight that early development inM. crozierideviates in several important aspects from the canonical spiral cleavage pattern. We suggest that some of our observations extend to polyclad flatworms in general as they have been described in both suborders of the Polycladida, the Cotylea and Acotylea.
Activation of a Protein Kinase Via Asymmetric Allosteric Coupling of Structurally Conserved Signaling Modules
Authors: Hao Yuxin , England Jeneffer , Belluci Luca , Paci Emanuele , Hodges H. Courtney , Taylor Susan S. , Maillard Rodrigo A. 
Published: April 2019

AbstractCyclic nucleotide binding (CNB) domains are universally conserved signaling modules that regulate the activities of diverse protein functions. Yet, the structural and dynamic features that enable the cyclic nucleotide binding signal to allosterically regulate other functional domains remain unknown. We use force spectroscopy and molecular dynamics to monitor in real time the pathways of signals transduced by cAMP binding in protein kinase A (PKA). Despite being structurally conserved, we find that the response of the folding energy landscape to cAMP is domain-specific, resulting in unique but mutually coordinated regulatory tasks: one CNB domain initiates cAMP binding and cooperativity, while the other triggers inter-domain interactions that lock the active conformation. Moreover, we identify a new cAMP-responsive switch, whose stability and conformation depends on cAMP occupancy. Through mutagenesis and nucleotide analogs we show that this dynamic switch serves as a signaling hub, a previously unidentified role that amplifies the cAMP binding signal during the allosteric activation of PKA.
Centromere clustering stabilizes meiotic homolog pairing
Authors: Hatkevich Talia , Boudreau Vincent , Rubin Thomas , Maddox Paul S. , Huynh Jean-René , Sekelsky Jeff 
Published: April 2019

ABSTRACTDuring meiosis, each chromosome must selectively pair and synapse with its own unique homolog to enable crossover formation and subsequent segregation. How homolog pairing is maintained in early meiosis to ensure synapsis occurs exclusively between homologs is unknown. We aimed to further understand this process by utilizing a uniqueDrosophilameiotic mutant,Mcm5A7. We found thatMcm5A7mutants are proficient in homolog pairing at meiotic onset yet fail to maintain pairing as meiotic synapsis ensues, causing seemingly-normal synapsis between non-homologous loci. This pairing defect corresponds with a reduction of SMC1-dependent centromere clustering at meiotic onset. Overexpressing SMC1 in this mutant significantly restores centromere clustering, homolog pairing, and crossover formation. These data indicate that the initial meiotic pairing of homologs is not sufficient to yield synapsis between exclusively between homologs and provide a model in which meiotic homolog pairing must be stabilized by SMC1-dependent centromere clustering to ensure proper synapsis.
The coordinate actions of calcineurin and Hog1 mediate the response to cellular stress through multiple nodes of the cell cycle network
Authors: Leech Cassandra M. , Flynn Mackenzie J. , Arsenault Heather E. , Ou Jianhong , Liu Haibo , Zhu Lihua Julie , Benanti Jennifer A. 
Published: April 2019

SummaryUpon exposure to environmental stressors, cells transiently arrest the cell cycle while they adapt and restore homeostasis. A challenge for all cells is to distinguish between diverse stress signals and coordinate the appropriate adaptive response with cell cycle arrest. Here we investigate the role of the stress-activated phosphatase calcineurin (CN) in this process and show that CN utilizes multiple pathways to control the cell cycle. Upon activation, CN inhibits transcription factors (TFs) that regulate the G1/S transition through activation of the stress-activated MAPK Hog1. In contrast, CN inactivates G2/M TFs through a combination of Hog1-dependent and -independent mechanisms. These findings demonstrate that CN and Hog1 act in a coordinated manner at multiple nodes of the cell cycle-regulatory network to rewire gene expression and arrest cells in response to stress. Our results suggest that crosstalk between CN and stress-activated MAPKs helps cells tailor their adaptive responses to specific stressors.
Regardless of the deposition pathway, aminoacid 31 in histone variant H3 is essential at gastrulation in Xenopus
Authors: Sitbon David , Boyarchuk Ekaterina , Almouzni Geneviève 
Published: April 2019

AbstractThe closely related replicative H3 and non-replicative H3.3 variants show specific requirement during development in vertebrates. Whether it involves distinct mode of deposition or unique roles once incorporated into chromatin remains unclear. To disentangle the two aspects, we took advantage of the Xenopus early development combined with chromatin assays. Our previous work showed that in Xenopus, depletion of the non-replicative variant H3.3 impairs development at gastrulation, without compensation through provision of the replicative variant H3.2. We systematically mutated H3.3 at each four residues that differ from H3.2 and tested their ability to rescue developmental defects. Surprisingly, all H3.3 mutated variants functionally complemented endogenous H3.3, regardless of their incorporation pathways, except for one residue. This particular residue, the serine at position 31 in H3.3, gets phosphorylated onto chromatin in a cell cycle dependent manner. While the alanine substitution failed to rescue H3.3 depletion, a phosphomimic residue sufficed. We conclude that the time of gastrulation reveals a critical importance of the H3.3S31 residue independently of the variant incorporation pathway. We discuss how this single evolutionary conserved residue conveys a unique property for this variant in vertebrates during cell cycle and cell fate commitment.
Phosphatase PP2C6 negatively regulates phosphorylation status of Pti1b kinase, a regulator of flagellin-triggered immunity in tomato
Authors: Giska Fabian , Martin Gregory B. 
Published: April 2019

AbstractPlant immune responses, including the production of reactive oxygen species (ROS), are triggered when pattern recognition receptors (PRR) become activated upon detection of microbe-associated molecular patterns (MAMPs). Receptor-like cytoplasmic kinases are key components of PRR-dependent signaling pathways. In tomato two such kinases, Pti1a and Pti1b, are important positive regulators of the plant immune response. However, it is unknown how these kinases control plant immunity at the molecular level, and how their activity is regulated. To investigate these issues, we used mass spectrometry to search for interactors of Pti1b in Nicotiana benthamiana leaves and identified a protein phosphatase, PP2C6. An in vitro pull-down assay and in vivo split luciferase complementation assay verified this interaction. Pti1b was found to autophosphorylate on threonine-233 and this phosphorylation was abolished in the presence of PP2C6. An arginine-to-cysteine substitution at position 240 in the Arabidopsis MARIS kinase was previously reported to convert it into a constitutive-active form. The analogous substitution in Pti1b made it resistant to PP2C6 phosphatase activity, although it still interacted with PP2C6. Treatment of N. benthamiana leaves with the MAMP flg22 induced threonine phosphorylation of Pti1b. Expression of PP2C6, but not a phosphatase-inactive variant of this protein, in N. benthamiana leaves greatly reduced ROS production in response to treatment with MAMPs flg22 or csp22. The results indicate that PP2C6 acts as a negative regulator by dephosphorylating the Pti1b kinase, thereby interfering with its ability to activate plant immune responses.
A study of psychological pain in substance use disorder and its relationship to treatment outcome
Authors: Mee Steven , Bunney Blynn G , Fujimoto Ken , Penner John , Seward Garrett , Bunney William E , Reist Christopher 
Published: April 2019

ABSTRACTSubstance Use Disorder (SUD) is a major public health concern affecting an estimated 22.5 million individuals in the United States. The primary aim of this study was to characterize psychological pain in a cohort of patients participating in outpatient substance abuse treatment. A secondary aim was to determine the relationships between pre-treatment assessments of psychological pain, depression, anxiety and hopelessness with treatment retention time and completion rates. Data was analyzed from 289 patients enrolled in an outpatient community drug treatment clinic that provides mental healthcare to the underserved. A previously determined threshold score on the Mee-Bunney Psychological Pain Assessment Scale (MBP) was utilized to group patients into high and low-moderate scoring subgroups. The higher pain group reported increased levels of anxiety, hopelessness and depression compared to those in the low-moderate pain group. Additionally, patients scoring in the higher psychological pain group exhibited reduced retention times in treatment and more than two-fold increased odds of dropout relative to patients with lower pre-treatment levels of psychological pain. Among all assessments, the correlation between psychological pain and treatment retention time was strongest. To our knowledge, this is the first study to demonstrate that psychological pain is an important construct that correlates with relevant clinical outcomes in substance abuse treatment. Further, pre-treatment screening for psychological pain may be of benefit in identifying higher-risk patients in need of targeted additional clinical resources to improve treatment retention and completion rates.
Identification of flowering-time genes in mast flowering plants usingde novotranscriptomic analysis
Authors: Samarth  , Lee Robyn , Song Jason , Macknight Richard , Jameson Paula E. 
Published: April 2019

AbstractMast flowering is synchronised highly variable flowering by a population of perennial plants over a wide geographical area. High seeding years are seen as a threat to native and endangered species due to high predator density caused by the abundance of seed. An understanding of the molecular pathways that influence masting behaviour in plants could provide better prediction of a forthcoming masting season and enable conservation strategies to be deployed. In this study, a high-throughput large-scale RNA-sequencing was performed on two masting plant species,Celmisia lyallii(Asteraceae), andChionochloa pallens(Poaceae) to develop a reference transcriptome for functional and molecular analysis. An average total of 33 million 150 base-paired reads, for both species, were assembled using the Trinity pipeline, resulting in 151,803 and 348,649 transcripts respectively forCelmisiaandChionochloa. The two datasets generated were blasted against the publicly available databases, TAIR, Swiss-Prot, non-redundant protein (nr), KEGG and COG for unigene annotations. On average, 56% of the unigenes were finally annotated with gene descriptions mapped to known protein sequences for both the species. Gene ontology analysis was then performed on the assembled reference transcriptomes, categorising the transcripts on the basis of putative biological processes, molecular function, and cellular localisation. A total of 543 transcripts fromCelmisiaand 470 transcripts fromChionochloawere also mapped to unique flowering-time proteins identified in Arabidopsis, suggesting the conservation of the flowering network in these wild alpine plants, growing in natural field conditions. These genes can further be analysed to understand the molecular regulation of the reproductive phase transition in the masting plants.
Butterfly abundance declines over 20 years of systematic monitoring in Ohio, USA
Authors: Wepprich Tyson , Adrion Jeffrey R. , Ries Leslie , Wiedmann Jerome , Haddad Nick M. 
Published: April 2019

AbstractSevere insect declines make headlines, but they are rarely based on systematic monitoring outside of Europe. We estimate the rate of change in total butterfly abundance and the population trends for 81 species using 21 years of systematic monitoring in Ohio, USA. Total abundance is declining at 2% per year, resulting in a cumulative 33% reduction in butterfly abundance. Three times as many species have negative population trends compared to positive trends. The rate of total decline and the proportion of species in decline mirror those documented in three comparable long-term European monitoring programs. Multiple environmental changes such as climate change, habitat degradation, and agricultural practices may contribute to these declines in Ohio and shift the makeup of the butterfly community by benefiting some species over others. Our analysis of life-history traits associated with population trends shows an impact of climate change, as species with northern distributions and fewer annual generations declined more rapidly. However, even common and invasive species associated with human-dominated landscapes are declining, suggesting widespread environmental causes for these trends. Declines in common species, although they may not be close to extinction, will have an outsized impact on the ecosystem services provided by insects. These results from the most extensive, systematic insect monitoring program in North America demonstrate an ongoing defaunation in butterflies that on an annual scale might be imperceptible, but cumulatively has reduced butterfly numbers by a third over 20 years.
A stealth adhesion factor contributes toVibrio vulnificuspathogenicity: Flp pili play roles in host invasion, survival in the blood stream and resistance to complement activation
Authors: Duong–Nu Tra–My , Jeong Kwangjoon , Kim Soo Young , Tan Wenzhi , Puth Sao , Lee Kwang Ho , Lee Shee Eun , Rhee Joon Haeng 
Published: April 2019

AbstractThe tad operons encode the machinery required for adhesive Flp (fimbrial low-molecular-weight protein) pili biogenesis.Vibrio vulnificus, an opportunistic pathogen, harbors three distincttadloci. Among them, onlytad1locus was highly upregulated inin vivogrowing bacteria compared toin vitroculture condition. To understand the pathogenic roles of the threetadloci during infection, we constructed single, double and triple tad loci deletion mutants. Interestingly, only theΔtad123triple mutant cells exhibited significantly decreased lethality in mice. Ultrastructural observations revealed short, thin filamentous projections disappeared on theΔtad123mutant cells. Since the pilin was paradoxically non-immunogenic, a V5 tag was fused to Flp to visualize the pilin protein by using immunogold EM and immunofluorescence microscopy. TheΔtad123mutant cells showed attenuated host cell adhesion, delayed RtxA1 exotoxin secretion and subsequently impaired translocation across the intestinal epithelium compared to wild type, which could be partially complemented with each wild type operon. TheΔtad123mutant was susceptible to complement-mediated bacteriolysis, predominantly via the alternative pathway, suggesting stealth hiding role of the Tad pili. Taken together, all threetadloci cooperate to confer successful invasion ofV. vulnificusinto deeper tissue and evasion from host defense mechanisms, ultimately resulting in septicemia.Author SummaryTo understand the roles of the three Tad operons in the pathogenesis ofV. vulnificusinfection, we constructed mutant strain with single, double and triple Tad loci deletions. Employing a variety of mouse infection models coupled with molecular genetic analyses, we demonstrate here that all three Tad operons are required forV. vulnificuspathogenicity as the cryptic pili contribute to host cell and tissue invasion, survival in the blood, and resistance to complement activation.