bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between schizophrenia polygenic score and psychotic symptoms in Alzheimer’s disease: meta-analysis of 11 cohort studies
Authors: Creese Byron , Vassos Evangelos , Bergh Sverre , Athanasiu Lavinia , Johar Iskandar , Rongve Arvid , Medbøen Ingrid Tøndel , Da Silva Miguel Vasconcelos , Aakhus Eivind , Andersen Fred , Bettella Francesco , Braekhus Anne , Djurovic Srdjan , Paroni Giulia , Proitsi Petroula , Saltvedt Ingvild , Seripa Davide , Stordal Eystein , Fladby Tormod , Aarsland Dag , Andreassen Ole A. , Ballard Clive , Selbaek Geir ,   on behalf of the AddNeuroMed consortium and the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2019

Background

Psychosis (delusions and hallucinations) is common in Alzheimer’s disease (AD) and associated with worse clinical outcomes including accelerated cognitive decline and shorter time to nursing home admission. Atypical antipsychotics have limited efficacy which, along with emerging genomic research, suggests some overlapping mechanisms with other disorders characterized by psychosis, like schizophrenia. In this study, we tested whether polygenic risk score (PRS) for schizophrenia was associated with psychotic symptoms in AD.

Methods

Schizophrenia PRS was calculated using Psychiatric Genomics Consortium data at 10 GWAS p-value thresholds (PT) in 3,173 AD cases from 11 cohort studies. Association between PRS and AD psychosis status was tested by logistic regression in each cohort individually and the results meta-analyzed.

Results

The schizophrenia PRS was associated with psychosis in AD at an optimumPTof The strongest association was for delusions where a one standard deviation increase in PRS was associated with a 1.17-fold increased risk (95% CI: 1.07-1.3; p=0.001).

Conclusion

These new findings point towards psychosis in AD – and particularly delusions – sharing some genetic liability with schizophrenia, and support a transdiagnostic view of psychotic symptoms across the lifespan.
Minimal effects ofspargel(PGC-1α) overexpression in aDrosophilamitochondrial disease model
Authors: George Jack , Jacobs Howard T.
Published: January 2019

PGC-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 blurb

overexpression 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

Mammalian 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.

Background

Traditionally, 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 Method

To 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.

Results

In 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.

Conclusions

Decoding 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

Toll-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

Controlling 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

Dispersal 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

Integrin-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

Brown 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.
Quantifying the Confidence in fMRI-based Language Lateralisation through Laterality Index Deconstruction
Authors: Wegrzyn Martin , Mertens Markus , Bien Christian G. , Woermann Friedrich G. , Labudda Kirsten
Published: January 2019

In epilepsy patients, language lateralisation is an important part of the presurgical diagnostic process. Using task-based fMRI, language lateralisation can be determined by visual inspection of activity patterns or by quantifying the difference in left- and right-hemisphere activity using variations of a basic formula [(L-R)/(L+R)]. However, the values of this laterality index (LI) depend on the choice of activity thresholds and regions of interest. The diagnostic utility of the LI also depends on how its continuous values are translated into categorical decisions about a patient’s language lateralisation. Here, we analysed fMRI data from 712 epilepsy patients who performed a verbal fluency task. Each fMRI data set was evaluated by a trained human rater as depicting left-sided, right-sided, or bilateral lateralisation or as being inconclusive. We used data-driven methods to define the activity thresholds and regions of interest used for LI computation and to define a classification scheme that allowed us to translate the LI values into categorical decisions. By deconstructing the LI into measures of laterality (L-R) and strength (L+R), we also modelled the relationship between activation strength and conclusiveness of a data set. In a held-out data set, predictions reached 91% correct when using only conclusive data and 82% when inconclusive data were included. Although only trained on human evaluations of fMRIs, the approach generalised to the prediction of language Wada test results, allowing for significant above-chance accuracies. Compared against different existing methods of LI-computation, our approach improved the identification of inconclusive cases and increased the accuracy with which decisions for the remaining data could be made. We discuss how this approach can support clinicians in assessing fMRI data on a single-case level, deciding whether lateralisation can be determined with sufficient certainty or whether additional information is needed.
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

Regulation 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

Since 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

Enterococcus 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

Complementary 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

A 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 summary

B 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

Infants 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.
Loss of one Engrailed1 allele enhances induced α-synucleinopathy
Authors: Chatterjee Diptaman , Sanchez Daniel Saiz , Quansah Emmanuel , Rey Nolwen L , George Sonia , Becker Katelyn , Madaj Zachary , Steiner Jennifer A , Ma Jiyan , Escobar Galvis Martha L , Kordower Jeffrey H , Brundin Patrik
Published: January 2019

Background:

Parkinson’s disease (PD) is a synucleinopathy that has multiple neuropathological characteristics, with nigrostriatal dopamine system degeneration being a core feature. Current models of PD pathology typically fail to recapitulate several attributes of the pathogenic process and neuropathology. We aimed to define the effects of combining a mouse model exhibiting multiple PD-like changes with intrastriatal injections of α-synuclein (α-syn) pre-formed fibrils (PFFs) aggregates. We employed the heterozygous Engrailed 1 (En1+/-) mouse that features several pathophysiological hallmarks of clinical PD. Objective: To test the hypothesis that the neuropathological changes in the En1+/- mice will promote formation of α-syn aggregates following intrastriatal injections of pathogenic human α-syn PFFs. Methods: We unilaterally injected PFFs into the striata of 1 month-old En1+/- and control wild-type mice and euthanized animals at 3 months for post-mortem analysis. Results: Using immunohistochemistry and unbiased stereology, we established that PFF-injected En1+/- mice exhibited a near-threefold increase in pS129-α-syn-positive neurons in the substantia nigra compared to PFF-injected wild-type mice. The PFF-injected En1+/- mice also displayed significant increases in pS129-α-syn-positive neurons in the amygdala and ventral tegmental area; regions of known PD pathology with projections to the striatum. Additionally, we observed amplified pS129-α-syn-positive aggregation in En1+/- mice in multiple cortical regions. Conclusions: Following intrastriatal injection of PFFs, absence of an En1 allele leads to additional aggregation of pathological α-syn, potentially due to En1-loss mediated nigrostriatal impairment. We propose that further development of this double-hit model could be predictive of pre-clinical therapeutic potential and success for PD than existing mouse models.
Lupin (Lupinus sp.) seeds exert anthelmintic activity associated with their alkaloid content
Authors: Dubois O. , Allanic C. , Charvet C. L. , Guégnard F. , Février H. , Théry-Koné I. , Cortet J. , Koch C. , Bouvier F. , Fassier T. , Marcon D. , Magnin-Robert J.B. , Peineau N. , Courtot E. , Huau C. , Meynadier A. , Enguehard-Gueiffier C. , Neveu C. , Boudesocque-Delaye L. , Sallé G.
Published: January 2019

The growing expansion range of drug resistant parasitic nematode populations threatens the sustainability of ruminant farming worldwide. In this context, nutraceuticals, i.e. feed that would both fulfil dietary requirements while ensuring parasite control, would contribute to increase farming sustainability in developed and low resource settings. In this study, we characterized the anthelmintic potential of lupin seed extracts against major ruminant trichostrongylids, i.e. H. contortus and T. circumcincta. Our observations showed that total seed extracts from commercially available lupin varieties significantly inhibited larval migration. This anthelmintic effect was sustained on multidrug resistant field isolate and across parasite species and was mediated by the seed alkaloid content. Analytical chemistry revealed a set of four lupanine and sparteine-derivatives with anthelmintic activity and electrophysiology assays on recombinant nematode acetylcholine receptors suggested an antagonistic mode of action for lupin alkaloids. While commercial lupin seeds did not exert direct anthelmintic effect in H. contortus infected lupin-fed ewes and goats, it significantly dampened blood production losses suffered by goats. Lupin seed extracts hence provide a working basis for the development of novel anthelmintic compounds able to break drug resistance in the field, while they could be used to increase the resilience of infected dairy ruminants.
Exploring Environmental Coverages of Species: A New Variable Selection Methodology for Rulesets from the Genetic Algorithm for Ruleset Prediction
Authors: Yang Anni , Gomez Juan Pablo , Blackburn Jason K.
Published: January 2019

Variable selection for, and determination of variable importance within, species distribution models (SDMs) remain an important area of research with continuing challenges. Most SDM algorithms provide normally exhaustive searches through variable space, however, selecting variables to include in models is a first challenge. The estimation of the explanatory power of variables and the selection of the most appropriate variable set within models can be a second challenge. Although some SDMs incorporate the variable selection rubric inside the algorithms, there is no integrated rubric to evaluate the variable importance in the Genetic Algorithm for Ruleset Production (GARP). Here, we designed a novel variable selection methodology based on the rulesets generated from a GARP experiment. The importance of the variables in a GARP experiment can be estimated based on the consideration of the prevalence of each environmental variable in the dominant presence rules of the best subset of models and its coverage. We tested the performance of this variable selection method based on simulated species with both weak and strong responses to simulated environmental covariates. The variable selection method generally performed well during the simulations with over 2/3 of the trials correctly identifying most covariates. We then predict the distribution of Bacillus anthracis (the bacterium that causes anthrax) in the continental United States (US) and apply our variable selection procedure as a real-world example. We found that the distribution of B. anthracis was primarily determined by organic content, soil pH, calcic vertisols, vegetation, sand fraction, elevation, and seasonality in temperature and moisture.
Targeted Cleavage and Polyadenylation of RNA by CRISPR-Cas13
Authors: Anderson Kelly M. , Poosala Pornthida , Lindley Sean R. , Anderson Douglas M.
Published: January 2019

Post-transcriptional cleavage and polyadenylation of messenger and long noncoding RNAs is coordinated by a supercomplex of ~20 individual proteins within the eukaryotic nucleus1,2. Polyadenylation plays an essential role in controlling RNA transcript stability, nuclear export, and translation efficiency3–6. More than half of all human RNA transcripts contain multiple polyadenylation signal sequences that can undergo alternative cleavage and polyadenylation during development and cellular differentiation7,8. Alternative cleavage and polyadenylation is an important mechanism for the control of gene expression and defects in 3’ end processing can give rise to myriad human diseases9,10. Here we show that fusion of catalytically dead Cas13 to a single mammalian polyadenylation factor, Nudix hydrolase 21 (NUDT21), allows for site-specific CRISPR-Cas13-guided cleavage and polyadenylation of RNA in mammalian cells. This approach, which we namedPostscriptr, can be utilized for the non-genomic manipulation of gene expression and may have potential future therapeutic applications for treating human RNA processing diseases.
Benzoate-TolerantEscherichia coliStrains from Experimental Evolution Lose the Gad Regulon, Multi-Drug Efflux Pumps, and Hydrogenases
Authors: Moore Jeremy P. , Li Haofan , Engmann Morgan L. , Bischof Katarina M. , Kunka Karina S. , Harris Mary E. , Tancredi Anna C. , Ditmars Frederick S. , Basting Preston J. , George Nadja S. , Bhagwat Arvind A. , Slonczewski Joan L.
Published: January 2019

Benzoate, a partial uncoupler of the proton motive force (PMF), selects for sensitivity to chloramphenicol and tetracycline inEscherichia coliK-12. Genetic mechanisms of increased benzoate tolerance and decreased drug resistance were analyzed in strains isolated from experimental evolution with benzoate. Transcriptomes showed reversal of benzoate-dependent regulation, including the Gad regulon for acid resistance and multi-drug resistance (MDR). Benzoate-evolved strains knocked down the nitrate reductasenarHJand the acid-consuming hydrogenase Hyd-3, but upregulated OmpF and other porins that admit nutrients and antibiotics. Mutations were found affecting many genes of aromatic catabolism such asfolDandadd. Several candidate genes from benzoate-evolved strains had a role in benzoate tolerance. Growth with benzoate or salicylate was increased by deletion of the Gad activatorariR, or by deletion of theslp-gadXacid fitness island encoding Gad regulators and the MDR pump MdtEF. Benzoate growth was also increased by deletion of MDR componentemrA, the RpoS post-transcriptional regulatorcspC, or the adenosine deaminaseadd. Growth in chloramphenicol with benzoate was decreased by a point mutation in the RNA polymerase alpha-subunitrpoA, which appeared in one chloramphenicol-sensitive benzoate-evolved strain. Growth in chloramphenicol was also decreased by deletion of Mar activatorrob, or ofrfaY(lipopolysaccharide biosynthesis). Hydrogenase Hyd-3 deletion increased benzoate tolerance. Overall, long-term culture in the presence of benzoate or salicylate favors loss of MDR efflux pumps and of hydrogenases that generate a futile cycle of PMF; and favors upregulation of large-hole porins that increase uptake of fermentable nutrients and of antibiotics.

IMPORTANCE

Benzoate is a common food preservative, and salicylate is the active form of aspirin. InE. coli, benzoate derivatives upregulate multiple regulons that export antibiotics and other toxic products, and downregulate large outer-membrane porins that allow antibiotic influx. But benzoate or salicylate exposure causes energy stress by depleting the proton motive force. In the absence of antibiotics, long-term benzoate exposure selects against energy-spending systems such as multi-drug efflux pumps and the proton-consuming hydrogenase. Selection favors upregulation of porins that admit fermentable substrates but also allow entry of antibiotics. Thus, evolution with benzoate requires a tradeoff for antibiotic sensitivity. Benzoate and salicylate are naturally occurring plant signal molecules that may influence the evolution of microbiomes in plants and in animal digestive tracts. Effects on hydrogenase activity may be relevant to the biotechnology of hydrogen production.
BOLD signatures of sleep
Authors: Song Chen , Boly Melanie , Tagliazucchi Enzo , Laufs Helmut , Tononi Giulio
Published: January 2019

Sleep can be distinguished from wake by changes in brain electrical activity, typically assessed using electroencephalography (EEG). The hallmark of non-rapid-eye-movement sleep are two major EEG events: slow waves and spindles. Here we sought to identify possible signatures of sleep in brain hemodynamic activity, using simultaneous fMRI-EEG. We found that, during the transition from wake to sleep, blood-oxygen-level-dependent (BOLD) activity evolved from a mixed-frequency pattern to one dominated by two distinct oscillations: a low-frequency (~0.05Hz) oscillation prominent in light sleep and a high-frequency (~0.17Hz) oscillation in deep sleep. The two BOLD oscillations correlated with the occurrences of spindles and slow waves, respectively. They were detectable across the whole brain, cortically and subcortically, but had different regional distributions and opposite onset patterns. These spontaneous BOLD oscillations provide fMRI signatures of basic sleep processes, which may be employed to study human sleep at spatial resolution and brain coverage not achievable using EEG.

HIGHLIGHTS

spontaneous BOLD oscillations differentiate sleep from wake

low-frequency BOLD oscillation tracks sleep spindles

high-frequency BOLD oscillation tracks sleep slow waves

BOLD oscillations provide fMRI signatures of key sleep processes
Tumor-Intrinsic Response to IFNγ Shapes the Tumor Microenvironment and Anti-PD-1 Response in NSCLC
Authors: Bullock Bonnie L. , Kimball Abigail K. , Poczobutt Joanna M. , Li Howard Y. , Kwak Jeff W. , Neuwelt Alexander J. , Johnson Amber M. , Kleczko Emily , Kaspar Rachael , Hopp Katharina , Schenk Erin , Weiser-Evans Mary C. M. , Clambey Eric T. , Nemenoff Raphael A.
Published: January 2019

Targeting PD-1/ PD-L1 is only effective in ~20% of lung cancer patients, but determinants of this response are poorly defined. We previously observed differential responses of two murine K-Ras lung cancer cell lines to anti-PD-1 therapy: CMT167 tumors were eliminated while LLC tumors were resistant. The goal of this study was to define mechanism(s) mediating this difference. RNA-Seq analysis of cancer cells recovered from lung tumors revealed that CMT167 cells induced an IFNγ signature that was absent in LLC cells. Silencing Ifngr1 in CMT167 resulted in tumors resistant to IFNγ and anti-PD-1 therapy. Conversely, LLC cells had high basal expression of Socs1, an inhibitor of IFNγ. Silencing Socs1 increased response to IFNγ in vitro and sensitized tumors to anti-PD-1. This was associated with a reshaped TME, characterized by enhanced T cell infiltration and enrichment of PD-L1 high myeloid cells. These studies demonstrate that targeted enhancement of tumor-intrinsic IFNγ signaling can induce of cascade of changes associated with increased therapeutic vulnerability.

Mechanisms regulating response to anti-PD-1 therapy in lung cancer are not well defined. This study, using orthotopic immunocompetent mouse models of lung cancer, demonstrates that intrinsic sensitivity of cancer cells to IFNγ determines anti-PD-1 responsiveness through alterations in the tumor microenvironment.
Computational Geometric Tools for Modeling Inherent Variability in Animal Behavior
Authors: Stamps Matthew T. , Go Soo , Mathuru Ajay S.
Published: January 2019

ABSTRACT

A fundamental challenge for behavioral neuroscientists is to represent inherent variability among animals accurately without compromising the ability to quantify differences between conditions. We developed two new methods that apply curve and shape alignment techniques to address this issue. As a proof-of-concept we applied these methods to compare normal or alarmed behavior in pairs of medaka (Oryzias latipes). The curve alignment method we call Behavioral Distortion Distance (BDD) revealed that alarmed fish display less predictable swimming over time, even if individuals incorporate the same action patterns like immobility, sudden changes in swimming trajectory, or changing their position in the water column. The Conformal Spatiotemporal Distance (CSD) technique on the other hand revealed that, in spite of the unpredictability, alarmed individuals share an overall swim pattern, possibly accounting for the widely held notion of “stereotypy” in alarm responses. More generally, we propose that these new applications of known computational geometric techniques are useful in combination to represent, compare, and quantify complex behaviors consisting of common action patterns that differ in duration, sequence, or frequency.
Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models
Authors: Rasmussen David A. , Stadler Tanja
Published: January 2019

Beneficial and deleterious mutations cause fitness to vary among individuals in a population, which natural selection can then act upon to drive adaptive evolution. Non-neutral mutations can likewise cause fitness to vary among lineages in a phylogeny and thereby shape its branching structure. While standard phylogenetic models do not allow mutations to feedback and shape tree topology, birth-death models can account for this feedback by letting the fitness of lineages vary depending on their type. To date though, these multi-type birth-death models have only been applied to cases where a lineage’s fitness is determined by a single evolving character state and have not been extended to model sequence evolution across multiple sites. We introduce an extension of the multi-type birth-death model, the marginal fitness birth-death model, that tracks sequence evolution at multiple sites and how the fitness of a lineage depends on its genotype across all sites. This approach remains computationally tractable even for many evolving sites because it tracks the genotype of a lineage probabilistically in an approximate manner, and then marginalizes over all possible genotypes to determine the expected fitness of a lineage. Although approximate, we show that we can accurately estimate the fitness of a lineage and even site-specific mutational fitness effects from the branching pattern of a phylogeny. To demonstrate the power of this approach, we apply it to estimate the host population level fitness effects of mutations previously identified to increase the infectivity of Ebola virus in human cell lines during the 2013-16 epidemic in West Africa.
Prefrontal oscillations modulate the propagation of neuronal activity required for working memory
Authors: Sherfey Jason S. , Ardid Salva , Miller Earl K. , Hasselmo Michael E. , Kopell Nancy J.
Published: January 2019

Cognition involves using attended information, maintained in working memory (WM), to guide action. During a cognitive task, a correct response requires flexible, selective gating so that only the appropriate information flows from WM to downstream effectors that carry out the response. In this work, we used biophysically-detailed modeling to explore the hypothesis that network oscillations in prefrontal cortex (PFC), leveraging local inhibition, can independently gate responses to items in WM. The key role of local inhibition was to control the period between spike bursts in the outputs, and to produce an oscillatory response no matter whether the WM item was maintained in an asynchronous or oscillatory state. We found that the WM item that induced an oscillatory population response in the PFC output layer with the shortest period between spike bursts was most reliably propagated. The network resonant frequency (i.e., the input frequency that produces the largest response) of the output layer can be flexibly tuned by varying the excitability of deep layer principal cells. Our model suggests that experimentally-observed modulation of PFC beta-frequency (15-30 Hz) and gamma-frequency (30-80 Hz) oscillations could leverage network resonance and local inhibition to govern the flexible routing of signals in service to cognitive processes like gating outputs from working memory and the selection of rule-based actions. Importantly, we show for the first time that nonspecific changes in deep layer excitability can tune the output gate’s resonant frequency, enabling the specific selection of signals encoded by populations in asynchronous or fast oscillatory states. More generally, this represents a dynamic mechanism by which adjusting network excitability can govern the propagation of asynchronous and oscillatory signals throughout neocortex.