bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimal effects ofspargel(PGC-1α) overexpression in aDrosophilamitochondrial disease model
Authors: George Jack , Jacobs Howard T. 
Published: January 2019

ABSTRACTPGC-1α and its homologues have been proposed to act as master regulators of mitochondrial biogenesis in animals. Most relevant studies have been conducted in mammals, where interpretation is complicated by the fact that there are three partially redundant members of the gene family. InDrosophila, only a single PGC-1α homologue,spargel(srl), is present in the genome. Here we analyzed the effects ofsrloverexpression on phenotype and on gene expression intko25t, a recessive bang-sensitive mutant with a global defect in oxidative phosphorylation, resulting in a deficiency of mitochondrial protein synthesis. In contrast to previous reports, we found only minimal effects of substantial overexpression ofsrlthroughout development, on the expression of a representative set of both mtDNA- and nuclear-encoded OXPHOS- related transcripts, both intko25tmutant flies and heterozygous controls. Sex and genetic background appeared to influence the expression of the tested genes, butsrloverexpression ortko25titself did not have clear-cut or systematic effects thereon. These studies provide no support to the concept of spargel as a global regulator of mitochondrial biogenesis.Summary blurboverexpression ofspargel, the fly PGC-1α homologue proposed as a mitochondrial biogenesis regulator, has minimal effects on the phenotype oftko25t, considered a fly model for mitochondrial disease
Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations
Authors: Fulco Charles P. , Nasser Joseph , Jones Thouis R. , Munson Glen , Bergman Drew T. , Subramanian Vidya , Grossman Sharon R. , Anyoha Rockwell , Patwardhan Tejal A. , Nguyen Tung H. , Kane Michael , Doughty Benjamin , Perez Elizabeth M. , Durand Neva C. , Stamenova Elena K. , Aiden Erez Lieberman , Lander Eric S. , Engreitz Jesse M. 
Published: January 2019

AbstractMammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but it remains unclear which enhancers regulate which genes. Here we describe an experimental approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome, and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. A simple equation based on a mechanistic model for enhancer function performed remarkably well at predicting the complex patterns of regulatory connections we observe in our CRISPR dataset. This Activity-by-Contact (ABC) model involves multiplying measures of enhancer activity and enhancer-promoter 3D contacts, and can predict enhancer-gene connections in a given cell type based on chromatin state maps. Together, CRISPRi-FlowFISH and the ABC model provide a systematic approach to map and predict which enhancers regulate which genes, and will help to interpret the functions of the thousands of disease risk variants in the noncoding genome.
High-pass filtering artifacts in multivariate classification of neural time series data
Authors: van Driel Joram , Olivers Christian N.L. , Fahrenfort Johannes J. 
Published: January 2019

0.AbstractBackgroundTraditionally, EEG/MEG data are high-pass filtered and baseline-corrected to remove slow drifts. Minor deleterious effects of high-pass filtering in traditional time-series analysis have been well-documented, including temporal displacements. However, its effects on time-resolved multivariate pattern classification analyses (MVPA) are largely unknown.New MethodTo prevent potential displacement effects, we extend an alternative method of removing slow drift noise – robust detrending – with a procedure in which we mask out all cortical events from each trial. We refer to this method astrial-masked robust detrending.ResultsIn both real and simulated EEG data of a working memory experiment, we show that both high-pass filtering and standard robust detrending create artifacts that result in the displacement of multivariate patterns into activity silent periods, particularly apparent in temporal generalization analyses, and especially in combination with baseline correction. We show that trial-masked robust detrending is free from such displacements.Comparison with Existing Method(s)Temporal displacement may emerge even with modest filter cut-off settings such as 0.05 Hz, and even in regular robust detrending. However, trial-masked robust detrending results in artifact-free decoding without displacements. Baseline correction may unwittingly obfuscate spurious decoding effects and displace them to the rest of the trial.ConclusionsDecoding analyses benefits from trial-masked robust detrending, without the unwanted side effects introduced by filtering or regular robust detrending. However, for sufficiently clean data sets and sufficiently strong signals, no filtering or detrending at all may work adequately. Implications for other types of data are discussed, followed by a number of recommendations.
Crosslinking Proteomics Indicates Effects of Simvastatin on the TLR2 interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade
Authors: Mostafa Kamal Abu Hena , Aloor Jim J. , Fessler Michael B. , Chowdhury Saiful M. 
Published: January 2019

AbstractToll-like receptor 2 (TLR2) is a pattern recognition receptor that, upon ligation by microbial molecules, interacts with other proteins to initiate pro-inflammatory responses by the cell. Statins (hydroxymethylglutaryl coenzyme A reductase inhibitors), drugs widely prescribed to reduce hypercholesterolemia, are reported to have both pro- and anti-inflammatory effects upon cells. Some of these responses are presumed to be driven by effects on signaling proteins at the plasma membrane, but the underlying mechanisms remain obscure. We reasoned that profiling the effect of statins on the repertoire of TLR2-interacting proteins might provide novel insights into the mechanisms by which statins impact inflammation. In order to study the TLR2 interactome, we designed a co-immunoprecipitation (IP)-based cross-linking proteomics study. A hemagglutinin (HA)-tagged-TLR2 transfected HEK293 cell line was utilized to precipitate the TLR2 interactome upon cell exposure to the TLR2 agonist Pam3CSK4 and simvastatin, singly and in combination. To stabilize protein interactors, we utilized two different chemical cross-linkers with different spacer chain lengths. Proteomic analysis revealed important combinatorial effects of simvastatin and Pam3CSK4 on the TLR2 interactome. After stringent data filtering, we identified alpha-centractin (ACTR1A), an actin-related protein and subunit of the dynactin complex, as a potential interactor of TLR2. The interaction was validated using biochemical methods. RNA interference studies revealed an important role for ACTR1A in induction of pro-inflammatory cytokines. Taken together, we report that statins remodel the TLR2 interactome, and we identify ACTR1A, a part of the dynactin complex, as a novel regulator of TLR2-mediated immune signaling pathways.
Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole
Authors: Yesbolatova Aisha , Natsume Toyoaki , Hayashi Ken-ichiro , Kanemaki Masato T. 
Published: January 2019

AbstractControlling protein expression using a degron is drawing more attention because the protein of interest can be rapidly depleted in a reversible manner. We pioneered the development of the auxin-inducible degron (AID) technology by transplanting a plant-specific degradation pathway to non-plant cells. In human cells expressing an E3 ligase component, OsTIR1, it is possible to degrade a degron-fused protein with a half-life of 15–45 min in the presence of the phytohormone auxin. We reported previously the generation of human HCT116 mutants in which the C terminus of endogenous proteins was fused with the degron by CRISPR–Cas9-based knock-in. Here, we show new plasmids for N-terminal tagging and describe a detailed protocol for the generation of AID mutants of human HCT116 and DLD1 cells. Moreover, we report the use of an OsTIR1 inhibitor, auxinole, to suppress leaky degradation of degron-fused proteins. The addition of auxinole is also useful for rapid re-expression after depletion of degron-fused proteins. These improvements enhance the utility of AID technology for studying protein function in living human cells.
Seascape genetics at its finest: dispersal patchiness within a well-connected population
Authors: Schunter C. , Pascual M. , Raventos N. , Garriga J. , Garza J.C. , Bartumeus F. , Macpherson E. 
Published: January 2019

ABSTRACTDispersal is a main determining factor of population structure and variation. In the marine habitat, well-connected populations with large numbers of reproducing individuals are common but even so population structure can exist on a small-scale. Variation in dispersal between populations or over time is often associated to both environmental and genetic variation. Nonetheless, detecting structure and dispersal variation on a fine-scale within marine populations still remains a challenge. Here we propose and use a novel approach of combining a clustering model, early-life history trait information from fish otoliths, spatial coordinates and genetic markers to detect very fine-scale dispersal patterns. We collected 1573 individuals (946 adults and 627 juveniles) of the black-faced blenny across a small-scale (2km) coastline as well as at a larger-scale area (<50kms). A total of 178 single nucleotide polymorphism markers were used to evaluate relatedness patterns within this well-connected population. Local retention and/or dispersal varied across the 2km coastline with higher frequency of SHORT-range disperser adults; representing local recruitment; towards the southwest of the area. An inverse pattern was found for juveniles, showing an increase of SHORT-range dispersers towards the northeast. This reveals a complex but not full genetic mixing and suggests oceanic/coastal circulation as the main driver of this fine-scale chaotic genetic patchiness within this otherwise homogeneous population. When focusing on the patterns within one recruitment season, we found large differences in temperatures (from approx. 17oC to 25oC) as well as pelagic larval duration (PLD) for juveniles from the beginning of the season and the end of the season. We were able to detect fine-scale differences in HIGH-range juvenile dispersers, representing distant migrants, depending on whether they were born at the beginning of the season, hence, with a longer PLD, or at the end of the reproductive season. The ability to detect such fine-scale dispersal patchiness will aid in our understanding of the underlying mechanisms of population structuring and chaotic patchiness in a wide range of species even with high potential dispersal abilities.
Regulation and dynamics of force transmission at individual cell-matrix adhesion bonds
Authors: Tan Steven J. , Chang Alice C. , Miller Cayla M. , Anderson Sarah M. , Prahl Louis S. , Odde David J. , Dunn Alexander R. 
Published: January 2019

AbstractIntegrin-based adhesion complexes link the cytoskeleton to the extracellular matrix (ECM) and are central to the construction of multicellular animal tissues. How biological function emerges from the 10s-1000s of proteins present within a single adhesion complex has remained unclear. We used fluorescent molecular tension sensors to visualize force transmission by individual integrins in living cells. These measurements revealed an underlying functional modularity in which integrin class controlled adhesion size and ECM ligand specificity, while the number and type of connections between integrins and F-actin determined the force per individual integrin. In addition, we found that most integrins existed in a state of near-mechanical equilibrium, a result not predicted by existing models of cytoskeletal force transduction. A revised model that includes reversible crosslinks within the F-actin network accounts for this result, and suggests how cellular mechanical homeostasis can arise at the molecular level.
Evolution of life cycles and reproductive traits: insights from the brown algae
Authors: Heesch Svenja , Serrano-Serrano Martha , Luthringer Rémy , Peters Akira F. , Destombe Christophe , Cock J. Mark , Valero Myriam , Roze Denis , Salamin Nicolas , Coelho Susana 
Published: January 2019

ABSTRACTBrown algae are characterized by a remarkable diversity of life cycles, sexual systems, and reproductive modes, and these traits seem to be very labile across the whole group. This diversity makes them ideal models to test existing theories on the evolution of alternation between generations, and to examine correlations between life cycle and reproductive life history traits. In this study, we investigate the dynamics of trait evolution for four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assign states to up to 70 species in a multi-gene phylogeny of brown algae, and use maximum likelihood and Bayesian analyses of correlated evolution, taking phylogeny into account, to test for correlations between life history traits and sexual systems, and to investigate the sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth may evolve because it allows the complementation of deleterious mutations, and that haploid sex determination is ancestral in relation to diploid sex determination. However, the idea that increased zygotic and diploid growth is associated with increased sexual dimorphism is not supported by our analysis. Finally, it appears that in the brown algae isogamous species evolved from anisogamous ancestors.
Proteolytic program-dependent functions are impaired in INF2-mediated focal segmental glomerulosclerosis
Authors: Subramanian Balajikarthick , Chun Justin , Perez Chandra , Yan Paul , Stillman Isaac , Higgs Henry , Alper Seth L. , Schlondorff Johannes , Pollak Martin R. 
Published: January 2019

AbstractRegulation of the actin cytoskeleton is critical for normal glomerular podocyte structure and function. Altered regulation of the podocyte cytoskeleton can lead to proteinuria, reduced kidney filtration function and focal segmental glomerulosclerosis (FSGS). Mutations in inverted formin 2 (INF2), a member of the formin family of actin regulatory proteins, are the most common cause of autosomal dominant FSGS. INF2 is a multi-domain protein regulated by interaction between its N-terminal Diaphanous Inhibitory Domain (DID) and its C-terminal Diaphanous Auto-regulatory Domain (DAD). Although many aspects of the INF2 DID-DAD interaction are understood, it remains unclear why disease-causing mutations are restricted to the DID and how these mutations cause human disease. Here we report a proteolytic cleavage in INF2 that liberates the INF2 N-terminal DID to function independently of the INF2 C-terminal fragment containing the DAD domain. N-terminal DID region epitopes are differentially localized to podocyte foot process structures in normal glomeruli. This N-terminal fragment localization is lost in INF2-mediated FSGS, whereas INF2 C-terminal fragment epitopes localize to the podocyte cell body in both normal and disease conditions. INF2 cleavage is mediated by cathepsin proteases. In cultured podocytes, the wild-type INF2 N-terminal fragment localizes to membrane regions and promotes cell spreading, while these functions are impaired in a disease-associated INF2 mutant R218Q in the DID. These features are dependent on INF2-cleavage, with accompanying interaction of INF2 N-fragment with mDIA1. Our data suggest a unique cellular function of the DID dependent on INF2 cleavage and help explain the altered localization of FSGS-associated INF2 mutant polypeptides.
Assessing metadata and curation quality: a case study from the development of a third-party curation service at Springer Nature
Authors: Grant Rebecca , Smith Graham , Hrynaszkiewicz Iain 
Published: January 2019

AbstractSince 2017, the publisher Springer Nature has provided an optional Research Data Support service to help researchers deposit and curate data that support their peer-reviewed publications. This service builds on a Research Data Helpdesk, which since 2016 has provided support to authors and editors who need advice on the options available for sharing their research data. In this paper we describe a short project which aimed to facilitate an objective assessment of metadata quality, undertaken during the development of a third-party curation service for researchers (Research Data Support). We provide details on the single-blind user-testing which was undertaken, and the results gathered during this experiment. We also briefly describe the curation services which have been developed and introduced following an initial period of testing and piloting. This paper will be presented at the International Digital Curation Conference 2019, and has been submitted to the International Journal of Digital curation.
Genomes of a major nosocomial pathogenEnterococcus faeciumare shaped by adaptive evolution of the chromosome and plasmidome
Authors: Arredondo-Alonso S , Top J , Schürch AC , McNally A , Puranen S , Pesonen M , Pensar J , Marttinen P , Braat JC , Rogers MRC , van Schaik W , Kaski S , Corander J , Willems RJL 
Published: January 2019

AbstractEnterococcus faeciumis a gut commensal of many mammals but is also recognized as a major nosocomial human pathogen, as it is listed on the WHO global priority list of multi-drug resistant organisms. Previous research has suggested that nosocomial strains have multiple zoonotic origins and are only distantly related to those involved in human commensal colonization. Here we present the first comprehensive population-wide joint genomic analysis of hospital, commensal and animal isolates using both short- and long-read sequencing techniques. This enabled us to investigate the population plasmidome, core genome variation and genome architecture in detail, using a combination of machine learning, population genomics and genome-wide co-evolution analysis. We observed a high level of genome plasticity with large-scale inversions and heterogeneous chromosome sizes, collectively painting a high-resolution picture of the adaptive landscape ofE. faecium,and identified plasmids as the main indicator for host-specificity. Given the increasing availability of long-read sequencing technologies, our approach could be widely applied to other human and animal pathogen populations to unravel fine-scale mechanisms of their evolution.
Towards an “assayome” for binary interactome mapping
Authors: Choi Soon Gang , Olivet Julien , Cassonnet Patricia , Vidalain Pierre-Olivier , Luck Katja , Lambourne Luke , Spirohn Kerstin , Lemmens Irma , Santos Mélanie Dos , Demeret Caroline , Jones Louis , Rangarajan Sudharshan , Bian Wenting , Coutant Eloi P. , Janin Yves L. , Werf Sylvie van der , Rivas Javier De Las , Tavernier Jan , Twizere Jean-Claude , Hao Tong , Hill David E. , Vidal Marc , Calderwood Michael A. , Jacob Yves 
Published: January 2019

ABSTRACTComplementary assays are required to comprehensively map complex biological entities such as genomes, proteomes and interactome networks. However, how various assays can be optimally combined to approach completeness while maintaining high precision often remains unclear. Here, we propose the concept of an “assayome” for binary protein-protein interaction (PPI) mapping as an optimal combination of assays and/or assay versions that maximizes detection of true positive interactions, while avoiding detection of random protein pairs. We engineered a novel NanoLuc two-hybrid (N2H) system that integrates 12 different versions differing by protein expression systems and tagging configurations. The resulting N2H assayome recovers as many PPIs as 10 distinct assays combined. Thus, to further improve PPI mapping, developing alternative versions of existing assays might be as productive as designing completely new assays. Our assayome concept should be applicable to systematic mapping of other biological landscapes.
Antigen-specific humoral immune responses by CRISPR/Cas9-edited B cells
Authors: Hartweger Harald , McGuire Andrew T. , Horning Marcel , Taylor Justin J. , Dosenovic Pia , Yost Daniel , Gazumyan Anna , Seaman Michael S. , Stamatatos Leonidas , Jankovic Mila , Nussenzweig Michel C. 
Published: January 2019

AbstractA small number of HIV-1 infected individuals develop broadly neutralizing-antibodies to the virus (bNAbs). These antibodies are protective against infection in animal models. However, they only emerge 1 - 3 years after infection, and show a number of highly unusual features including exceedingly high levels of somatic mutations. It is therefore not surprising that elicitation of protective immunity to HIV-1 has not yet been possible. Here we show that mature, primary mouse and human B cells can be editedin vitrousing CRISPR/Cas9 to express mature bNAbs from the endogenousIghlocus. Moreover, edited B cells retain the ability to participate in humoral immune responses. Immunization with cognate antigen in wild type mouse recipients of edited B cells elicits bNAb titers that neutralize HIV-1 at levels associated with protection against infection. This approach enables humoral immune responses that may be difficult to elicit by traditional immunization.One-sentence summaryB cells edited by CRISPR/Cas9 to produce antibodies participate in humoral immune reactions and secrete neutralizing serum titers of anti-HIV bNAbs.
A Chemokine-Fusion Vaccine Targeting Immature Dendritic Cells Elicits Elevated Antibody Responses to Malaria Sporozoites in Infant Macaques
Authors: Luo Kun , Gordy James T. , Zavala Fidel , Markham Richard B. 
Published: January 2019

AbstractInfants and young children are the groups at greatest risk for severe disease resulting from Plasmodium falciparum infection. We previously demonstrated in mice that a protein vaccine composed of the chemokine macrophage inflammatory protein 3α genetically fused to the minimally truncated circumsporozoite protein of P. falciparum (MCSP) elicits high concentrations of specific antibody and significant reduction of liver sporozoite load in a mouse model system. In the current study, a squalene based adjuvant (AddaVax, InvivoGen, San Diego, Ca) equivalent to the clinically approved MF59 (Seqiris, Maidenhead, UK) elicited greater antibody responses in mice than the previously employed adjuvant polyinosinic:polycytidylic acid, ((poly(I:C), InvivoGen, San Diego, Ca) and the clinically approved Aluminum hydroxide gel (Alum, Invivogen, San Diego, Ca) adjuvant. Use of the AddaVax adjuvant also expanded the range of IgG subtypes elicited by mouse vaccination. Sera passively transferred into mice from MCSP/AddaVax immunized one and six month old macaques significantly reduced liver sporozoite load upon sporozoite challenge. Protective antibody concentrations attained by passive transfer in the mice were equivalent to those observed in infant macaques 18 weeks after the final immunization. The efficacy of this vaccine in a relevant non-human primate model indicates its potential usefulness for the analogous high risk human population.