bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stochastic model of BKPy Virus replication and assembly
Authors: Stiegelmeyer Suzy M. , Jeffers-Francis Liesl K. , Giddings Morgan C. , Webster-Cyriaque Jennifer 
Published: August 2019

AbstractBK Polyomavirus (BKPyV), belongs to the same family as SV40 and JC Virus and has recently been associated with both Sjögrens Syndrome and HIV associated Salivary Gland Disease. BKPyV was previously only known for causing the rejection of kidney transplants. As such, BKPyV infection of salivary gland cells implicates oral transmission of the virus. BKPyV replicates slowly in salivary gland cells, producing infectious virus after 72-96 hours. However, it remains unclear how this virus infects or replicates within salivary gland cells, blocking the development of therapeutic strategies to inhibit the virus. Thus, an intracellular, computational model using agent-based modeling was developed to model BKPyV replication within a salivary gland cell. In addition to viral proteins, we modeled host cell machinery that aids transcription, translation and replication of BKPyV. The model has separate cytosolic and nuclear compartments, and represents all large molecules such as proteins, RNAs, and DNA as individual computer “agents” that move and interact within the simulated salivary gland cell environment. An application of the Boids algorithm was implemented to simulate molecular binding and formation of BKPyV virions and BKPyV virus-like particles (VLPs). This approach enables the direct study of spatially complex processes such as BKPyV virus self-assembly, transcription, and translation. This model reinforces experimental results implicating the processes that result in the slow accumulation of viral proteins. It revealed that the slow BKPyV replication rate in salivary gland cells might be explained by capsid subunit accumulation rates. BKPyV particles may only form after large concentrations of capsid subunits have accumulated. In addition, salivary gland specific transcription factors may enable early region transcription of BKPyV.
Enzyme-free synthesis of natural phospholipids in water
Authors: Liu Luping , Zou Yike , Bhattacharya Ahanjit , Zhang Dongyang , Lang Susan Q. , Houk K. N. , Devaraj Neal K. 
Published: August 2019

AbstractAll living organisms synthesize phospholipids as the primary constituent of their cell membranes. While phospholipids can spontaneously self-assemble in water to form membrane-bound vesicles, their aqueous synthesis requires pre-existing membrane-embedded enzymes. This limitation has led to models in which the first cells used simpler types of membrane building blocks and has hampered integration of phospholipid synthesis into artificial cells. Here we demonstrate that a combination of ion pairing and self-assembly of reactants allows high-yielding synthesis of cellular phospholipids in water. Acylation of 2-lysophospholipids using cationic thioesters occurs in mildly alkaline solutions resulting in the formation of cell-like membranes. A variety of membrane-forming natural phospholipids can be synthesized. Membrane formation takes place in water from natural alkaline sources, such as soda lakes and hydrothermal oceanic vents. When formed vesicles are transferred to more acidic solutions, electrochemical proton gradients are spontaneously established and maintained.
Brain wiring and supragranular-enriched genes linked to protracted human frontal cortex development
Authors: Hendy Jasmine P. , Takahashi Emi , van der Kouwe Andre J. , Charvet Christine J. 
Published: August 2019

AbstractThe human frontal cortex is unusually large compared with many other species. The expansion of the human frontal cortex is accompanied by both connectivity and transcriptional changes. Yet, the developmental origins generating variation in frontal cortex circuitry across species remain unresolved. Nineteen genes, which encode filaments, synapse, and voltage-gated channels (e.g., NEFH, SYT2, VAMP1) are especially enriched in the supragranular layers of the cerebral cortex in humans relative to mice. The increased expression of these genes suggests enhanced cortico-cortical projections emerging from layer III in humans. We confirm that the expression of these supragranular-enriched genes is preferentially expressed in frontal cortex layer III in humans relative to mice. We demonstrate a concomitant expansion in cortico-cortical pathways projecting within the frontal cortex white matter in humans with diffusion MR tractography. To identify developmental sources of such variation, we compare frontal cortical white matter growth and developmental trajectories of transcriptional profiles of supragranular-enriched genes in humans and mice. We also use temporal changes in gene expression during postnatal development to control for variation in developmental schedules across species. The growth of the frontal cortex white matter and transcriptional profiles of supragranular genes are both protracted in humans relative to the timing of other transformations. These findings demonstrate that an expansion of projections emerging from the human frontal cortex is achieved by extending the duration of cortical circuitry development. Integrating RNA sequencing with neuroimaging level phenotypes is an effective strategy to assess deviations in developmental programs leading to variation in connections across species.
Practical Aspects of Phylogenetic Network Analysis Using PhyloNet
Authors: Cao Zhen , Liu Xinhao , Ogilvie Huw A. , Yan Zhi , Nakhleh Luay 
Published: August 2019

AbstractPhylogenetic networks extend trees to enable simultaneous modeling of both vertical and horizontal evolutionary processes. PhyloNet is a software package that has been under constant development for over 10 years and includes a wide array of functionalities for inferring and analyzing phylogenetic networks. These functionalities differ in terms of the input data they require, the criteria and models they employ, and the types of information they allow to infer about the networks beyond their topologies. Furthermore, PhyloNet includes functionalities for simulating synthetic data on phylogenetic networks, quantifying the topological differences between phylogenetic networks, and evaluating evolutionary hypotheses given in the form of phylogenetic networks.In this paper, we use a simulated data set to illustrate the use of several of PhyloNet’s functionalities and make recommendations on how to analyze data sets and interpret the results when using these functionalities. All inference methods that we illustrate are incomplete lineage sorting (ILS) aware; that is, they account for the potential of ILS in the data while inferring the phylogenetic network. While the models do not include gene duplication and loss, we discuss how the methods can be used to analyze data in the presence of polyploidy.The concept of species is irrelevant for the computational analyses enabled by PhyloNet in that species-individuals mappings are user-defined. Consequently, none of the functionalities in PhyloNet deals with the task of species delimitation. In this sense, the data being analyzed could come from different individuals within a single species, in which case population structure along with potential gene flow is inferred (assuming the data has sufficient signal), or from different individuals sampled from different species, in which case the species phylogeny is being inferred.
ER reorganization and intracellular retention of CD58 are functionally independent properties of the human cytomegalovirus ER resident glycoprotein UL148
Authors: Nguyen Christopher C. , Domma Anthony J. , Zhang Hongbo , Kamil Jeremy P. 
Published: August 2019

ABSTRACTThe human cytomegalovirus (HCMV) endoplasmic reticulum (ER)-resident glycoprotein UL148 is posited to play roles in immune evasion and regulation of viral cell tropism. UL148 prevents cell surface presentation of the immune cell costimulatory ligand CD58 while promoting maturation and virion incorporation of glycoprotein O, a receptor binding subunit for an envelope glycoprotein complex involved in entry. Meanwhile, UL148 activates the unfolded protein response (UPR) and causes large-scale reorganization of the ER. In an effort to determine whether the seemingly disparate effects of UL148 are related or discrete, we generated charged-cluster-to-alanine (CCTA) mutants of six charged clusters within the UL148 ectodomain, and compared them against wildtype UL148, in the context of recombinant viruses and in ectopic expression, assaying for effects on ER remodeling and CD58 surface presentation. Two mutants, targeting charged clusters spanning residues 79-83 (CC3) and 133-136 (CC4), respectively, retained the potential to impede CD58 presentation, and did so to an extent comparable to wildtype. Of the six mutants, only CC3 retained the capacity to reorganize the ER, showing a partial phenotype. Wildtype UL148 accumulates in a detergent-insoluble form during infection. However, all six CCTA mutants were fully soluble, which may imply a relationship between insolubility and organelle remodeling. Additionally, we found that the chimpanzee cytomegalovirus UL148 homolog suppresses CD58 presentation but fails to reorganize the ER, while the homolog from rhesus cytomegalovirus shows neither activity. Collectively, our findings illustrate varying degrees of functional divergence between homologous primate cytomegalovirus immunevasins and suggest that ER reorganization is unique to HCMV UL148.IMPORTANCEIn myriad examples, viral gene products cause striking effects on cells, such as activation of stress responses. It can be challenging to decipher how such effects contribute to the biological roles of the proteins. The HCMV glycoprotein UL148 retains CD58 within the ER, thereby preventing it from reaching the cell surface where it functions to stimulate cell-mediated antiviral responses. Intriguingly, UL148 also triggers the formation of large, ER-derived membranous structures, and activates the UPR, a set of signaling pathways involved in adaptation to ER stress. We demonstrate that the potential of UL148 to reorganize the ER and to retain CD58 are separable by mutagenesis and possibly, by evolution, since chimpanzee cytomegalovirus UL148 retains CD58 but does not remodel the ER. Our findings imply that ER reorganization contributes to other roles of UL148, such as modulation of alternative viral glycoprotein complexes that govern the virus’ ability to infect different cell types.
Evolution of linkage and genome expansion in protocells
Authors: Szilágyi András , Péter Kovács Viktor , Szathmáry Eörs , Santos Mauro 
Published: August 2019

AbstractChromosomes are likely to have followed unlinked genes in early evolution. Genetic linkage reduces the assortment load and intragenomic conflict in reproducing protocell models to the extent that chromosomes can go to fixation even if chromosomes suffer from a replicative disadvantage, relative to unlinked genes, proportional to their length. Here we show that chromosomes spread within protocells even if recurrent deleterious mutations affecting replicating genes (as ribozymes) are taken into account. Dosage effect selects for optimal genomic composition within protocells that carries over to the genic composition of emerging chromosomes. Lacking an accurate segregation mechanism protocells continue to benefit from the stochastic corrector principle (group selection of early replicators), but now at the chromosome level. A remarkable feature of this process is the appearance of multigene families (in optimal genic proportions) on chromosomes. An added benefit of chromosome formation is an increase in the selectively maintainable genome size (number of different genes), primarily due to the marked reduction of the assortment load. This result complements the established benefit conferred by chromosomes on protocells allowing for the fixation of highly specific and efficient enzymes.
A systematic survey of PRMT interactomes reveals key roles of arginine methylation in the global control of RNA splicing and translation
Authors: Wei Huan-Huan , Fan Xiao-Juan , Hu Yue , Tian Xiao-Xu , Guo Meng , Fang Zhao-Yuan , Wu Ping , Gao Shuai-Xin , Peng Chao , Yang Yun , Wang Zefeng 
Published: August 2019

AbstractThousands of proteins undergo arginine methylation, a widespread post-translational modification catalyzed by various protein arginine methyltransferases (PRMTs). However, a full picture of the catalytic network for each PRMT is lacking and the global understanding of their biological roles remains limited. Here we systematically identified interacting proteins for all human PRMTs and demonstrated that they are functionally important for mRNA splicing and translation. We showed that the interactomes of human PRMTs are significantly overlapped with the known methylarginine containing proteins, and different PRMTs are functionally complementary with a high degree of overlap in their substrates and high similarities between their putative methylation motifs. Importantly, arginine methylation is significantly enriched in RNA binding proteins involved in regulating RNA splicing and translation, and inhibition of PRMTs leads to global alteration of alternative splicing and suppression of translation. In particular, ribosomal proteins are pervasively modified with methylarginine, and mutations on their methylation sites suppress ribosome assembly, translation, and eventually cell growth. Collectively, our study provides a novel global view of different PRMT networks and uncovers critical functions of arginine methylation in the regulation of mRNA splicing and translation.
Galactose-modified duocarmycin prodrugs as senolytics
Authors: Guerrero Ana , Guiho Romain , Herranz Nicolás , Uren Anthony , Withers Dominic J. , Martínez-Barbera Juan Pedro , Tietze Lutz F. , Gil Jesús 
Published: August 2019

SUMMARYSenescence is a stable growth arrest that impairs the replication of damaged, old or preneoplastic cells, therefore contributing to tissue homeostasis. Senescent cells accumulate during ageing and are associated with diseases, such as cancer, fibrosis and many age-related pathologies. Recent evidence suggests that the selective elimination of senescent cells can be effective on the treatment of many of these senescence-associated diseases. A universal characteristic of senescent cells is that they display elevated activity of the lysosomal β-galactosidase this has been exploited as a marker for senescence (senescence-associated β-galactosidase activity). Consequently, we hypothesised that galactose-modified cytotoxic prodrugs will be preferentially processed by senescent cells, resulting in their selective killing. Here, we show that different galactose-modified duocarmycin (GMD) derivatives preferentially kill senescent cells. GMD prodrugs induce selective apoptosis of senescent cells in a lysosomal β-galactosidase (GLB1)-dependent manner. GMD prodrugs can eliminate a broad range of senescent cells in culture, and treatment with a GMD prodrug enhances the elimination of bystander senescent cells that accumulate upon whole body irradiation or doxorubicin treatment of mice. Moreover, taking advantage of a mouse model of human adamantinomatous craniopharyngioma (ACP), we show that treatment with a GMD pro-drug result selectively reduced the number of β-catenin-positive preneoplastic senescent cells, what could have therapeutic implications. In summary, the above results show that galactose-modified duocarmycin prodrugs behave as senolytics, suggesting that they could be used to treat a wide range of senescence-related pathologies.
Molecular Basis for G-protein-Coupled Receptor (GPCR) Activation and Biased Signalling at the Platelet Thrombin Receptor Proteinase Activated Receptor-4 (PAR4)
Authors: Thibeault Pierre E. , LeSarge Jordan C. , Arends D’Arcy , Fernandes Michaela , Chidiac Peter , Stathopulos Peter B. , Luyt Leonard G. , Ramachandran Rithwik 
Published: August 2019

AbstractProteinase Activated Receptor-4 (PAR4) is a member of the proteolytically-activated PAR family of G-Protein-coupled Receptors (GPCRs). PARs are activated following proteolytic cleavage of the receptor N-terminus by enzymes such as thrombin, trypsin, and cathepsin-G to reveal the receptor-activating motif termed the tethered ligand. The tethered ligand binds intramolecularly to the receptor and triggers receptor signalling and cellular responses. In spite of this unusual mechanism of activation, PARs are fundamentally peptide receptors and can also be activated by exogenous application of short synthetic peptides derived from the tethered ligand sequence. In order to gain a better understanding of the molecular basis for PAR4-dependent signalling, we examined signalling responses to a library of peptides derived from the canonical PAR4 activating peptide (PAR4-AP), AYPGKF-NH2. We examined peptide residues involved in activation of the Gαq/11-coupled calcium signalling pathway, β-arrestin recruitment, and mitogen-activated protein kinase pathway activation. The peptideN-methyl-alanine-YPGKF-NH2was identified as a compound that is a poor activator of PAR4-dependent calcium signalling but was fully competent in recruiting β-arrestin-1 and -2. In order to gain a better understanding of the ligand-binding pocket, we usedin silicodocking to identify key residues involved in PAR4 interaction with AYPGKF-NH2. The predicted interactions were verified by site-directed mutagenesis and analysis of calcium signalling and β-arrestin-1/-2 recruitment following proteolytic activation (with thrombin) or activation with the synthetic agonist peptide (AYPGKF-NH2). We determined that a key extracellular loop-2 aspartic acid residue (Asp230) is critical for signalling following both proteolytic and peptide activation of PAR4. Finally, we investigated platelet aggregation in response to AyPGKF-NH2(a peptide with D-tyrosine in position two) which is unable to activate calcium signalling, and AYPGRF-NH2a peptide that is equipotent to the parental peptide AYPGKF-NH2for calcium signalling but is more potent at recruiting β-arrestins. We found that AyPGKF-NH2fails to activate platelets while AYPGRF-NH2causes a platelet aggregation response that is greater than that seen with the parental peptide and is comparable to that seen with thrombin stimulation. Overall, these studies uncover molecular determinants for agonist binding and signalling through a non-canonically activated GPCR and provide a template for development of small molecule modulators of PAR4.
Ongoing repair of migration-coupled DNA damage allows stem cells to reach wound sites
Authors: Sahu Sounak , Sridhar Divya , Abnave Prasad , Kosaka Nobuyoshi , Dattani Anish , Thompson James M. , Hill Mark A. , Aboobaker A. Aziz 
Published: August 2019

AbstractThe impact of mechanical stress during cell migration may be a previously unappreciated source of genome instability [1–3], but to what extent this happens in vivo remains unknown. Here we consider an in vivo system where the adult stem cells of planarian flatworms are required to migrate to a distal wound site [4]. We observe a relationship between adult stem cell migration and ongoing DNA damage and repair during tissue regeneration. Migrating planarian stem cells undergo changes in nuclear shape and increased levels of DNA damage. Increased DNA damage levels resolve once stem cells reach the wound site and stop migrating. Stem cells in which DNA damage is induced prior to wounding take longer to initiate migration suggesting migration activity is sensitive to DNA damage. Migrating stem cells populations are more sensitive to further DNA damage than stationary stem cells, providing evidence that levels of migration-coupled-DNA-damage (MCDD) are significant. RNAi mediated knockdown of DNA repair pathway components blocks normal stem cell migration, confirming that DNA repair pathways are required to allow successful migration to a distal wound site. Together these lines of evidence demonstrate that migration leans to DNA damage in vivo and requires DNA repair mechanisms. Our findings reveal that migration of stem cells represents an unappreciated source of damage, that could be a significant source of mutations in animals during development or during long term tissue homeostasis.
In vitrohepatitis C virus infection and hepatic choline metabolism
Authors: Odai Kaelan Gobeil , O’Dwyer Conor , Steenbergen Rineke , Shaw Tyler A. , Renner Tyler M. , Ghorbani Peyman , Rezaaifar Mojgan , Han Shauna , Langlois Marc-André , Crawley Angela M. , Russell Rodney S. , Pezacki John P. , Tyrrell D. Lorne , Fullerton Morgan D. 
Published: August 2019

AbstractCholine is an essential nutrient required for normal neuronal and muscular development, as well as homeostatic regulation of hepatic metabolism. In the liver, choline is incorporated into the main eukaryotic phospholipid, phosphatidylcholine (PC) and can enter one carbon metabolism via mitochondrial oxidation. Hepatitis C virus (HCV) is a hepatotropic positive-strand RNA virus that similar to other positive-strand RNA viruses can impact phospholipid metabolism. In the current study we sought to interrogate the link between choline transport and early HCV infection. Namely, we aimed to investigate how HCV modulates markers of choline metabolism followingin vitroinfection, while subsequently assessing how the inhibition of choline uptake and metabolism upon concurrent HCV infection may alter early viral replication. Finally, we assessed whether these parameters were consistent between cells cultured in fetal bovine serum (FBS) or human serum (HS), conditions known to differentially affectin vitroHCV infection. We observed that choline transport in FBS-cultured Huh7.5 cells is facilitated by the intermediate affinity transporter choline transporter-like family (CTL), and that CTL1 expression and the incorporation of choline into PC is diminished in 24 h infected FBS-cultured cells. Reciprocally, limiting the availability of choline for PC synthesis resulted in increased HCV replication at this early stage. In chronically HS-cultured Huh7.5 cells, there were no differences in the expression of choline transporters upon HCV infection or alterations to viral replication when choline transport was inhibited compared to control treatments. However, inhibiting choline uptake and metabolism in this system significantly impaired the production of infectious virions in HS-cultured cells. These results suggest that in addition to a known role of choline kinase, the transport of choline, potentially via CTL1, might also represent an important and regulated process during HCV infection.Abstract Figure
Interpretable Machine Learning for Perturbation Biology
Authors: Yuan Bo , Shen Ciyue , Luna Augustin , Korkut Anil , Marks Debora S. , Ingraham John , Sander Chris 
Published: August 2019

AbstractSystematic perturbation of cells followed by comprehensive measurements of molecular and phenotypic responses provides an informative data resource for constructing computational models of cell biology. Models that generalize well beyond training data can be used to identify combinatorial perturbations of potential therapeutic interest. Major challenges for machine learning on large biological datasets are to find global optima in an enormously complex multi-dimensional solution space and to mechanistically interpret the solutions. To address these challenges, we introduce a hybrid approach that combines explicit mathematical models of dynamic cell biological processes with a machine learning framework, implemented in Tensorflow. We tested the modeling framework on a perturbation-response dataset for a melanoma cell line after drug treatments. The models can be efficiently trained to accurately describe cellular behavior, as tested by cross-validation. Even though completely data-driven and independent of prior knowledge, the resultingde novonetwork models recapitulate some known interactions. The main predictive application is the identification of combinatorial candidates for cancer therapy. The approach is readily applicable to a wide range of kinetic models of cell biology.