bluuebunny/crossref_metadata_2025_split huggingface dataset:
μ Opioid Receptors Modulate Action Potential Kinetics and Firing Frequency in Neocortical Interneurons
Authors: Dutkiewicz Adrian P , Morielli Anthony D. 
Published: November 2020

ABSTRACTThe endogenous opioid system of the cerebral cortex is an important feature of antinociception and reward valuation through its modulation of inhibitory neocortical interneurons. Dysregulation of this system, through disease or drugs, disrupts the reward system and contributes to eating and mood disorders, impulsive actions, and addiction. Impulsive behaviors can be induced experimentally through infusion of the μ opioid receptor specific agonist [D-Ala2, N-Me-Phe4, Gly5-ol]-Enkephalin (DAMGO) into the frontal cortex in animal models. The mechanism involves increased potassium channel function, which suppresses neocortical interneuron activity. However, much of the data on the effect of this receptor on ion channels have been derived from noncortical μORs, and the identity and effects of the ion channels that the μOR targets in neocortical neurons have not been thoroughly investigated. Based on previous experiments by other labs, we hypothesized that the μOR could activate α-dendrotoxin (αDTX) sensitive channels (Kv1.1, Kv1.2, and Kv1.6 subunits) to exert its inhibitory effects in cortical interneurons. This, in turn, is expected to confer a variety of effects on passive and active electrical properties of the cell. We performed patch-clamp electrophysiology to examine the electrophysiological effects of μORs in cultured neocortical interneurons. We found that a range of features among the 54 membrane and action potential properties we analyzed were modulated by μORs, including action potential kinetics and frequency. The Kv1.1, Kv1.2, and Kv1.6 inhibitor αDTX reversed some effects on action potential frequency, but not effects on their kinetics. Therefore, μORs in neocortical interneurons influence αDTX-sensitive channels, as well as other channels, to modulate action potential kinetics and firing properties.
Dynamics of gene expression and chromatin marking during cell state transition
Authors: Borsari Beatrice , Abad Amaya , Klein Cecilia C. , Nurtdinov Ramil , Esteban Alexandre , Palumbo Emilio , Ruiz-Romero Marina , Sanz María , Correa Bruna R. , Johnson Rory , Pérez-Lluch Sílvia , Guigó Roderic 
Published: November 2020

SummaryWe have monitored the transcriptomic and epigenomic status of cells at twelve time-points during the transdifferentiation of human pre-B cells into macrophages. Using this data, we have investigated some fundamental questions regarding the role of chromatin in gene expression. We have found that, over time, genes are characterized by a limited number of chromatin states (combinations of histone modifications), and that, consistently, chromatin changes over genes tend to occur in a coordinated manner. We have observed strong association between these changes and gene expression only at the time of initial gene activation. Activation is preceded by H3K4me1 and H3K4me2, and followed in a precise order by most other histone modifications. Further changes in gene expression, comparable or even stronger than those at initial activation, occur without associated changes in histone modifications. The data generated here constitutes, thus, a unique resource to investigate transcriptomic and epigenomic dynamics during a differentiation process.
Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus
Authors: Dalvie Neil C. , Brady Joseph R. , Crowell Laura E. , Tracey Mary Kate , Biedermann Andrew M. , Kaur Kawaljit , Hickey John M. , Kristensen D. Lee , Bonnyman Alexandra , Rodriguez-Aponte Sergio A. , Whittaker Charles A. , Bok Marina , Vega Celina , Mukhopadhyay Tarit , Joshi Sangeeta B. , Volkin David B. , Parreño Viviana , Love Kerry R. , Love J. Christopher 
Published: November 2020

AbstractBackgroundVaccines comprising recombinant subunit proteins are well-suited to low-cost and high-volume production for global use. The design of manufacturing processes to produce subunit vaccines depends, however, on the inherent biophysical traits presented by an individual antigen of interest. New candidate antigens typically require developing custom processes for each one and may require unique steps to ensure sufficient yields without product-related variants.ResultsWe describe a holistic approach for the molecular design of recombinant protein antigens—considering both their manufacturability and antigenicity—informed by bioinformatic analyses such as RNA-seq, ribosome profiling, and sequence-based prediction tools. We demonstrate this approach by engineering the product sequences of a trivalent non-replicating rotavirus vaccine (NRRV) candidate to improve titers and mitigate product variants caused by N-terminal truncation, hypermannosylation, and aggregation. The three engineered NRRV antigens retained their original antigenicity and immunogenicity, while their improved manufacturability enabled concomitant production and purification of all three serotypes in a single, end-to-end perfusion-based process using the biotechnical yeast Komagataella phaffii.ConclusionsThis study demonstrates that molecular engineering of subunit antigens using advanced genomic methods can facilitate their manufacturing in continuous production. Such capabilities have potential to lower the cost and volumetric requirements in manufacturing vaccines based on recombinant protein subunits.
Convergent consequences of parthenogenesis on stick insect genomes
Authors: Jaron Kamil S. , Parker Darren J. , Anselmetti Yoann , Tran Van Patrick , Bast Jens , Dumas Zoé , Figuet Emeric , François Clémentine M. , Hayward Keith , Rossier Victor , Simion Paul , Robinson-Rechavi Marc , Galtier Nicolas , Schwander Tanja 
Published: November 2020

AbstractThe shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generatedde novoreference genomes for five independently evolved parthenogenetic species in the stick insect genusTimemaand their closest sexual relatives. Using these references in combination with population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity, and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, supporting the view that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Contrary to studies of non-recombining genome portions in sexual species, genomes of parthenogenetic species do not accumulate transposable elements (TEs), likely because successful parthenogens derive from sexual ancestors with inactive TEs. Because we are able to conduct replicated comparisons across five species pairs, our study reveals, for the first time, how animal genomes evolve in the absence of sex in natural populations, providing empirical support for the negative consequences of parthenogenetic reproduction as predicted by theory.
Multiple latent clustering model for the inference of RNA life-cycle kinetic rates from sequencing data
Authors: Mastrantonio Gianluca , Bibbona Enrico , Furlan Mattia 
Published: November 2020

SummaryWe here propose a hierarchical Bayesian model to infer RNA synthesis, processing, and degradation rates from sequencing data, based on an ordinary differential equation system that models the RNA life cycle. We parametrize the latent kinetic rates, that rule the system, with a novel functional form, and estimate their parameters through 6 Dirichlet process mixture models. Owing to the complexity of this approach, we are able to simultaneously perform inference, clustering and model selection. We apply our method to investigate transcriptional and post-transcriptional responses of murine fibroblasts to the activation of proto-oncogene Myc. Our approach uncovers simultaneous regulations of the rates, which had not previously been observed in this biological system.
KIR2DL4genetic diversity in a Brazilian population sample: implications for transcription regulation and protein diversity in samples with different ancestry backgrounds
Authors: Weiss Emiliana , Andrade Heloisa S. , Lara Juliana Rodrigues , Souza Andreia S. , Paz Michelle A. , Lima Thálitta H. A. , Porto Iane O. P. , Silva Nayane dos S. B. , Castro Camila F. Bannwart , Grotto Rejane M. T. , Donadi Eduardo A. , Mendes-Junior Celso T. , Castelli Erick C. 
Published: November 2020

AbstractKIR2DL4 is an important immune modulator expressed in Natural Killer cells, being HLA-G its main ligand. We characterizeKIR2DL4gene diversity considering the promoter, all exons, and all introns, in a highly admixed Brazilian population sample using massively parallel sequencing. We also introduce a molecular method to amplify and sequence the completeKIR2DL4gene. To avoid mapping bias and genotype errors commonly observed in gene families, we have developed a bioinformatic pipeline designed to minimize mapping, genotyping, and haplotyping errors. We have applied this method to survey the variability of 220 samples from the State of São Paulo, southeastern Brazil. We have also compared theKIR2DL4genetic diversity in Brazilian samples with the previously reported by the 1000Genomes consortium.KIR2DL4presents high linkage disequilibrium throughout the gene, with coding sequences associated with specific promoters. There were few, but divergent, promoter haplotypes. We have also detected many newKIR2DL4sequences, all with nucleotide exchanges in introns and encoding previously described proteins. Exons 3 and 4, which encode the external domains, were the most variable ones. The ancestry background influencesKIR2DL4allele frequencies and must be considered for association studies regardingKIR2DL4.
Recruitment of CTCF to anFtoenhancer is responsible for transgenerational inheritance of obesity
Authors: Jung Yoon Hee , Wang Hsiao-Lin V. , Ruiz Daniel , Grandi Fiorella C. , Bixler Brianna J. , Linsenbaum Hannah , Xiang Jian-Feng , Forestier Samantha , Shafik Andrew M. , Jin Peng , Corces M. Ryan , Corces Victor G. 
Published: November 2020

AbstractTransgenerational transmission of epiphenotypes is poorly understood. Here we show that exposure of pregnant mouse F0 females to BPA results in obesity in the F2 progeny due to increased food intake and leptin resistance. This epiphenotype can be transmitted up to the F6 generation and disappears in F7. Analyses of chromatin accessibility in sperm of the F1-F6 generations reveals alterations in the binding of CTCF at two enhancers of theFtogene in obese but not control animals that correlates with transmission of obesity. Deletion of the CTCF site inFtoresults in mice that fail to become obese when exposed to BPA. TheseFtoenhancers show increased interactions in sperm of obese mice with theIrx3andIrx5genes, which are involved in the differentiation of appetite controlling AgRP/NPY neurons. Single-nucleus and immunofluorescence analyses in the arcuate nucleus of the hypothalamus suggest that exposure to BPA results in expansion of the number of orexigenic AgRP neurons. This expansion correlates with increased accessibility of theFtoproximal enhancer in radial glia-like neural stem cells (RG-NSCs), which give rise to AgRP/NPY neurons, and in mature oligodendrocytes. The results provide a molecular mechanism for transgenerational inheritance in mammals and suggest that both genetic and epigenetic alterations ofFtocan lead to the same phenotypic outcomes.
High-Grade Serous Ovarian Tumor Cells Modulate NK Cell Function to Create an Immune-Tolerant Microenvironment
Authors: Gonzalez Veronica D. , Huang Ying-Wen , Chen Shih-Yu , Delgado-Gonzalez Antonio , Donoso Kenyi , Gentles Andrew , Sachs Karen , Porpiglia Ermelinda , Fantl Wendy J. 
Published: November 2020

SummaryTubo-ovarian high-grade serous cancer (HGSC) is unresponsive to immune checkpoint blockade despite significant frequencies of exhausted T cells. Here we applied mass cytometry to uncover decidual-like (dl)-NK cell subpopulations (CD56+CD9+CXCR3+KIR+CD3-CD16-) in chemo-naïve HGSC tumors that correlated with both tumor and transitioning epithelial-mesenchymal cell abundance. We showed different combinatorial expression patterns of ligands for activating and inhibitory NK receptors within the three HGSC tumor cell compartments; epithelial (E), transitioning epithelial-mesenchymal (EV) and mesenchymal (vimentin-expressing cells, V) with a more inhibitory ligand phenotype in V cells. When co-cultured with HGSC cell lines the NK-92 cell line acquired CD9 from tumor cells by trogocytosis with a resultant reduction in both anti-tumor cytokine production and cytotoxicity. Critically, a CD9 blocking antibody restored the killing activity of CD9+-NK-92 cells. These findings identify previously unrecognized mechanisms of immune suppression in HGSC. Furthermore, since CD9 is widely expressed in HGSC tumors it represents an important new therapeutic target with immediate relevance for NK immunotherapy.
Quantifying biofilm propagation on chemically modified surfaces
Authors: Halsted Michelle C. , Bible Amber N. , Morrell-Falvey Jennifer L. , Retterer Scott T. 
Published: November 2020

AbstractConditions affecting biofilm formation differ among bacterial species and this presents a challenge to studying biofilms in the lab. This work leverages functionalized silanes to control surface chemistry in the study of early biofilm propagation, quantified with a semi-automated image processing algorithm. These methods support the study ofPantoeasp. YR343, a gram-negative bacterium isolated from the poplar rhizosphere. We found thatPantoeasp. YR343 does not readily attach to hydrophilic surfaces but will form biofilms with a “honeycomb” morphology on hydrophobic surfaces. Our image processing algorithm described here was used to quantify this honeycomb morphology over time and displayed a logarithmic behavior in the propagation of the honeycomb biofilm. This methodology was repeated with a flagella-deficientfliRmutant ofPantoeasp. YR343 which resulted in reduced surface attachment. Quantifiable differences betweenPantoeaWT and ΔfliRbiofilm morphologies were captured by the image processing algorithm, further demonstrating the insight gained from these methods.
Comparative biochemistry of four polyester (PET) hydrolases
Authors: Bååth Jenny Arnling , Borch Kim , Jensen Kenneth , Brask Jesper , Westh Peter 
Published: November 2020

AbstractThe potential of bioprocessing in a circular plastic economy has strongly stimulated research in enzymatic degradation of different synthetic resins. Particular interest has been devoted to the commonly used polyester, poly(ethylene terephthalate) (PET), and a number of PET hydrolases have been described. However, a kinetic framework for comparisons of PET hydrolases (or other plastic degrading enzymes) acting on the insoluble substrate, has not been established. Here, we propose such a framework and test it against kinetic measurements on four PET hydrolases. The analysis provided values of kcatand KM, as well as an apparent specificity constant in the conventional units of M−1s−1. These parameters, together with experimental values for the number of enzyme attack sites on the PET surface, enabled comparative analyses. We found that the PET hydrolase fromIdeonella sakaiensiswas the most efficient enzyme at ambient conditions, and that this relied on a high kcatrather than a low KM. Moreover, both soluble and insoluble PET fragments were consistently hydrolyzed much faster than intact PET. This suggests that interactions between polymer strands slow down PET degradation, while the chemical steps of catalysis and the low accessibility associated with solid substrate were less important for the overall rate. Finally, the investigated enzymes showed a remarkable substrate affinity, and reached half the saturation rate on PET, when the concentration of attack sites in the suspension was only about 50 nM. We propose that this is linked to nonspecific adsorption, which promotes the nearness of enzyme and attack sites.
Caenorhabditis ElegansJunctophilin has Tissue-Specific Functions and Regulates Neurotransmission with Extended-Synaptotagmin
Authors: Piggott Christopher A. , Wu Zilu , Nurrish Stephen , Xu Suhong , Kaplan Joshua M. , Chisholm Andrew D. , Jin Yishi 
Published: November 2020

AbstractThe junctophilin family of proteins tether together plasma membrane (PM) and endoplasmic reticulum (ER) membranes, and couple PM- and ER-localized calcium channels. Understandingin vivofunctions of junctophilins is of great interest for dissecting the physiological roles of ER-PM contact sites. Here, we show that the soleC. elegansjunctophilin JPH-1 localizes to discrete membrane contact sites in neurons and muscles and has important tissue-specific functions.jph-1null mutants display slow growth and development due to weaker contraction of pharyngeal muscles, leading to reduced feeding. In the body wall muscle, JPH-1 co-localizes with the PM-localized EGL-19 voltage-gated calcium channel and ER-localized UNC-68/RyR calcium channel, and is required for animal movement. We also find an unexpected cell non-autonomous effect ofjph-1in axon regrowth after injury. In neurons, JPH-1 co-localizes with the membrane contact site protein Extended-SYnaptoTagmin 2 (ESYT-2) and modulates neurotransmission. Interestingly,jph-1andesyt-2null mutants display mutual suppression in their response to aldicarb, suggesting that JPH-1 and ESYT-1 have antagonistic roles in neuromuscular synaptic transmission. Our genetic double mutant analysis also reveals thatjph-1functions in overlapping pathways with two PM-localized voltage-gated calcium channels,egl-19andunc-2,andunc-68/RyRfor animal health and development. Finally, we show thatunc-68/RyRis required for JPH-1 localization to ER-PM puncta. Our data demonstrate important roles for junctophilin in cellular physiology, and also provide insights into how junctophilin functions together with other calcium channelsin vivo.
Age-Associated Insolubility of Parkin in Human Midbrain is Linked to Redox Balance and Sequestration of Reactive Dopamine Metabolites
Authors: Tokarew Jacqueline M. , El-Kodsi Daniel N. , Lengacher Nathalie A. , Fehr Travis K. , Nguyen Angela P. , Shutinoski Bojan , O’Nuallain Brian , Jin Ming , Khan Jasmine M. , Ng Andy C. H. , Li Juan , Jiang Qiubo , Zhang Mei , Wang Liqun , Sengupta Rajib , Barber Kathryn R. , Tran An , Zandee Stephanie , Dong Xiajun , Scherzer Clemens R. , Prat Alexandre , Tsai Eve , Takanashi Masashi , Hattori Nobutaka , Chan Jennifer A. , Zecca Luigi , West Andrew B. , Holmgren Arne , Puente Lawrence , Shaw Gary S. , Toth Gergely , Woulfe John M. , Taylor Peggy , Tomlinson Julianna J. , Schlossmacher Michael G. 
Published: November 2020

AbstractThe mechanisms by which parkin protects the adult human brain from Parkinson disease remain incompletely understood. We hypothesized that parkin cysteines participate in redox reactions, which are reflected in its posttranslational modifications. We found that in human control brain, including theS. nigra, parkin is largely insoluble after age 40 years, which is linked to its oxidation,e.g.,at Cys95 and Cys253. In mice, oxidative stress increases posttranslational modifications at parkin cysteines and reduces its solubility. Oxidation of recombinant parkin also promotes insolubility and aggregate formation, but in parallel, lowers hydrogen peroxide (H2O2). This thiol-based redox activity is diminished by parkin point mutants,e.g.,p.C431F and p.G328E. Intriguingly, in parkin-deficient human brain H2O2concentrations are elevated. Inprkn-null mice, H2O2levels are dysregulated under oxidative stress conditions, such as acutely by MPTP-toxin exposure or chronically due to a second genetic hit. In dopamine toxicity studies, wild-type parkin, but not disease-linked mutants, protects human dopaminergic M17 cells, in part through lowering H2O2. Parkin also neutralizes reactive, electrophilic dopamine metabolites via adduct formation, which occurs foremost at primate-specific Cys95. Further, wild-type but not p.C95A-mutant parkin augments melanin formation. In sections of normal, adult human midbrain, parkin specifically co-localizes with neuromelanin pigment, frequently within LAMP-3/CD63+lysosomes. We conclude that oxidative modifications of parkin cysteines are associated with protective outcomes, which include the reduction of H2O2, conjugation of reactive dopamine metabolites, sequestration of radicals within insoluble aggregates, and increased melanin formation. The loss of these redox effects may augment oxidative stress in dopamine producing neurons of mutantPRKNallele carriers, thereby contributing to neurodegeneration.
Rapid benchmarking: the case of a multinational dairy company
Authors: Malik Rubab , Mann Robin , Knapman Rebecca 
Published: November 2020

PurposeThe purpose of the study is to investigate and document a new approach to best practice benchmarking called rapid benchmarking. Rapid benchmarking is defined by the authors as an approach to dramatically shorten the typical length of time to conduct a successful best practice benchmarking project.Design/methodology/approachThe methodology involved a case study exploration of a multinational dairy company's best practice benchmarking approach using structured interviews and data collection to examine the speed and results achieved through its benchmarking approach and whether it was justified in naming it as rapid benchmarking. A comparison of the speed of the dairy company's approach was undertaken against 24 other organisations that had utilised the same benchmarking methodology (TRADE Best Practice Benchmarking). In addition, a literature review was undertaken to search for other cases of rapid benchmarking and compare rapid benchmarking with other rapid improvement approaches.FindingsThe findings revealed that the approach used by the dairy company was unique, with best practices being identified and action plans signed off for deployment within a five-day period (far quicker than the average time of 211 days reported by other organisations). Key success factors for rapid benchmarking were found to be allocating five dedicated days for the benchmarking team to spend on the project, identifying the right team members for the project, obtaining sponsorship support for the project and providing intensive facilitation support through a benchmarking facilitator.Research limitations/implicationsOnly one company was found to use a rapid benchmarking approach; therefore, the findings are from one case study. The depth of analysis presented was restricted due to commercial sensitivity.Practical implicationsThe rapid benchmarking approach is likely to be of great interest to practitioners, providing them with a new way of finding solutions and best practices to address challenges that need to be solved quickly or with minimal expense. For organisations that have been using benchmarking for many years, the research will enable them to re-evaluate their own benchmarking approach and consider if rapid benchmarking could be used for some projects, particularly for internal benchmarking where it is easier to apply.Originality/valueThis research is the first to identify and document a rapid benchmarking approach and the first to provide a detailed analysis of the length of time it takes to undertake best practice benchmarking projects (and each stage of a benchmarking project).