bluuebunny/crossref_metadata_2025 huggingface dataset:
Regressive Sin Taxes, with an Application to the Optimal Soda Tax*
Authors: Allcott Hunt , Lockwood Benjamin B , Taubinsky Dmitry
Published: May 2019

A common objection to “sin taxes”—corrective taxes on goods that are thought to be overconsumed, such as cigarettes, alcohol, and sugary drinks—is that they often fall disproportionately on low-income consumers. This paper studies the interaction between corrective and redistributive motives in a general optimal taxation framework and delivers empirically implementable formulas for sufficient statistics for the optimal commodity tax. The optimal sin tax is increasing in the price elasticity of demand, increasing in the degree to which lower-income consumers are more biased or more elastic to the tax, decreasing in the extent to which consumption is concentrated among the poor, and decreasing in income effects, because income effects imply that commodity taxes create labor supply distortions. Contrary to common intuitions, stronger preferences for redistribution can increase the optimal sin tax, if lower-income consumers are more responsive to taxes or are more biased. As an application, we estimate the optimal nationwide tax on sugar-sweetened beverages, using Nielsen Homescan data and a specially designed survey measuring nutrition knowledge and self-control. Holding federal income tax rates constant, our estimates imply an optimal federal sugar-sweetened beverage tax of 1 to 2.1 cents per ounce, although optimal city-level taxes could be as much as 60% lower due to cross-border shopping.
‘Action Not Words’: The Conservative Party, Public Opinion and ‘Scientific’ Politics, c.1945–70
Authors: Lockwood Charles
Published: May 2019

From the late 1950s, Conservative research and policy thinkers underwent a conscious intellectual adjustment, which had profound implications for how the party conceived the relationship between politicians and the public during Edward Heath’s period as Conservative leader after 1965. In response to contemporaneous debates regarding ‘modernization’, and as a result of their engagement with the emergent social sciences, a new generation of Conservatives tended to repudiate the party’s traditional preference for idealist and organicist philosophical assumptions in favour of a rationalistic approach to political administration. Their preoccupation with economic management was concomitant of their loss of faith in the formative role of rhetorical and moral appeals in shaping public opinion. This article, by focusing on debates within the party’s research and political apparatus—the Conservative Research Department, the Conservative Political Centre and Swinton College—will contend that, far from being the last gasp of a post-war consensual Conservatism, Heath’s period as leader marked a relatively unique period in the party’s history, in which the conception of the nature of political leadership held by those at the top of the party differed from the conception held by both their predecessors and successors.
Organism-wide single-cell transcriptomics of long-livedC. elegans daf-2-/-mutants reveals tissue-specific reprogramming of gene expression networks
Authors: Preston Jessica L. , Stiffler Nicholas , Weitzman Maggie
Published: May 2019

A critical requirement for a systems-level understanding of complex biological processes such as aging is the ability to directly characterize interactions between cells and tissues within a multicellular organism.C. elegansnematodes harboring mutations in the insulin-like receptordaf-2exhibit dramatically-increased lifespans. To identify tissue-specific biochemical mechanisms regulating aging plasticity, we single-cell sequenced 3’-mRNA libraries generated from seven populations of whole day-one adult wild-type anddaf-2-/-worms using the 10x ChromiumV1™platform. The age-synchronized samples were bioinformatically merged into a single aligned dataset containing 40,000 age-synchronized wild-type anddaf-2-/-cellular transcriptomes partitioned into 101 clusters, using unsupervised machine-learning algorithms to identify common cell types. Here we describe the basic features of the adultC. eleganssingle-cell transcriptome and summarize functional alterations observed in the gene expression profiles of long-liveddaf-2-/-worms. Comprehensive methods and datasets are provided. This is the first study to directly quantify cell-specific differential gene expression between two age-synchronized, genetically-distinct populations of multicellular organisms. This novel approach answers fundamental questions regarding tissue-specific regulation of gene expression and helps to establish a foundation for a comprehensiveC. eleganssingle-cell gene expression atlas.
Evolutionary loss of foot muscle during development with characteristics of atrophy and no evidence of cell death
Authors: Tran Mai P. , Tsutsumi Rio , Erberich Joel M. , Chen Kevin D. , Flores Michelle D. , Cooper Kimberly L.
Published: May 2019

Many species that run or leap across sparsely vegetated habitats, including horses and deer, evolved the severe reduction or complete loss of foot muscles as skeletal elements elongated and digits were lost, and yet the developmental mechanisms remain unknown. Here, we report the natural loss of foot muscles in the bipedal jerboa,Jaculus jaculus. Although adults have no muscles in their feet, newborn animals have muscles that rapidly disappear soon after birth. We were surprised to find no evidence of apoptotic or necrotic cell death during stages of peak myofiber loss, countering well-supported assumptions of developmental tissue remodeling. We instead see hallmarks of muscle atrophy, including an ordered disassembly of the sarcomere associated with upregulation of the E3 ubiquitin ligases,MuRF1andAtrogin-1. We propose that the natural loss of muscle, which remodeled foot anatomy during evolution and development, involves cellular mechanisms that are typically associated with disease or injury.
Analysis of Risk Factor Domains in Psychosis Patient Health Records
Authors: Holderness Eben , Miller Nicholas , Cawkwell Philip , Bolton Kirsten , Pustejovsky James , Meteer Marie , Hall Mei-Hua
Published: May 2019

Readmission after discharge from a hospital is disruptive and costly, regardless of the reason. However, it can be particularly problematic for psychiatric patients, so predicting which patients may be readmitted is critically important but also very difficult. Clinical narratives in psychiatric electronic health records (EHRs) span a wide range of topics and vocabulary; therefore, a psychiatric readmission prediction model must begin with a robust and interpretable topic extraction component. We created a data pipeline for using document vector similarity metrics to perform topic extraction on psychiatric EHR data in service of our long-term goal of creating a readmission risk classifier. We show initial results for our topic extraction model and identify additional features we will be incorporating in the future.
Human cytomegalovirus nuclear capsid motility is non-directed and independent of nuclear actin bundles
Authors: Flomm Felix , Borst Eva Maria , Günther Thomas , Reimer Rudolph , de Vries Laura , Schneider Carola , Grundhoff Adam , Grünewald Kay , Messerle Martin , Bosse Jens Bern-hard
Published: May 2019

Herpesvirus genome replication, capsid assembly and packaging take place in the host cell nucleus. Matured capsids leave the nucleus through a unique envelopment-de-envelopment process at the nuclear membranes called nuclear egress. How assembled and DNA-containing herpesvirus capsids reach the sites of nuclear egress is however still controversially discussed, as host chromatin that marginalizes during infection might constitute a major barrier. For alphaherpesviruses, previous work has suggested that nuclear capsids use active transport mediated by nuclear filamentous actin (F-actin). However, direct evidence for nuclear capsid motility on nuclear F-actin was missing. Our subsequent work did not detect nuclear F-actin associated with motile capsids, but instead found evidence for chromatin remodeling to facilitate passive capsid diffusion. A recent report described that human cyto-megalovirus, a betaherpesvirus, induces nuclear F-actin and that the motor protein myosin V localizes to these structures. Direct evidence of capsid recruitment to these structures and motility on them was however missing. In this study, we tested the functional role of HCMV-induced, nuclear actin assemblies for capsid transport. We did not observe transport events along nuclear F-actin. Instead, reproduction of nuclear F-actin was only possible using strong overexpression of the fluorescent marker LifeAct-mCherry-NLS. Also, two alternative fluo-rescent F-actin markers did not detect F-actin in HCMV-infected cells. Furthermore, single particle tracking of nuclear HCMV capsids showed no indication for active transport, which is in line with previous work on alphaherpesviruses.
Metabolic response to Parkinson’s disease recapitulated by the haploinsufficient phenotype of diploid yeast cells hemizygous for the adrenodoxin reductase gene
Authors: Dikicioglu Duygu , Coxon James W. M. T. , Oliver Stephen G.
Published: May 2019

Adrenodoxin reductase, a widely conserved mitochondrial P450 protein, catalyses essential steps in steroid hormone biosynthesis and is highly expressed in the adrenal cortex. The yeast adrenodoxin reductase homolog, Arh1p, is involved in cytoplasmic and mitochondrial iron homeostasis and is required for activity of enzymes containing an Fe-S cluster. In this paper, we investigated the response of yeast to the loss of a single copy ofARH1, an oxidoreductase of the mitochondrial inner membrane, which is among the few mitochondrial proteins that is essential for viability in yeast. The phenotypic, transcriptional, proteomic, and metabolic landscape indicated thatSaccharomyces cerevisiaesuccessfully adapted to this loss, displaying an apparently dosage-insensitive cellular response. However, a considered investigation of transcriptional regulation inARH1-impaired yeast highlighted that a significant hierarchical reorganisation occurred, involving the iron assimilation and tyrosine biosynthetic processes. The interconnected roles of the iron and tyrosine pathways, coupled with oxidative processes, are of interest beyond yeast since they are involved in dopaminergic neurodegeneration associated with Parkinson’s disease. The identification of similar responses in yeast suggest that this simple eukaryote could have potential as a model system for investigating the regulatory mechanisms leading to the initiation and progression of early disease responses in humans.
Functional divergence of Plexin B structural motifs in distinct steps ofDrosophilaolfactory circuit assembly
Authors: Guajardo Ricardo , Luginbuhl David J , Han Shuo , Luo Liqun , Li Jiefu
Published: May 2019

Plexins exhibit multitudinous, evolutionarily conserved functions in the development of nervous systems. However, how Plexins employ their diverse structural motifsin vivoto perform distinct roles in the stepwise assembly of neural circuits is unclear. Here, we systematically mutagenized structural motifs ofDrosophilaPlexin B (PlexB) and examined the function of these variants at multiple PlexB-mediated neurodevelopmental processes in olfactory receptor neurons: axon fasciculation, trajectory choice, and synaptic partner selection. We found that the extracellular Sema domain is essential for all three processes, the catalytic site of the intracellular RapGAP is engaged in none, and the intracellular GTPase-binding motifs are essential for trajectory choice and synaptic partner selection, but are dispensable for fasciculation. Moreover, extracellular PlexB cleavage serves as a regulatory mechanism of PlexB signaling. Thus, PlexB structural motifs have divergent roles in distinct steps of neural development, altogether contributing to the functional versatility of PlexB in neural circuit assembly.
Fighting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics
Authors: Khaledi Ariane , Weimann Aaron , Schniederjans Monika , Asgari Ehsaneddin , Kuo Tzu-Hao , Oliver Antonio , Cabot Gabriel , Kola Axel , Gastmeier Petra , Hogardt Michael , Jonas Daniel , Mofrad Mohammad R.K. , Bremges Andreas , McHardy Alice C. , Häussler Susanne
Published: May 2019

The growing importance of antibiotic resistance on clinical outcomes and cost of care underscores the need for optimization of current diagnostics. For a number of bacterial species antimicrobial resistance can be unambiguously predicted based on their genome sequence. In this study, we sequenced the genomes and transcriptomes of 414 drug-resistant clinical Pseudomonas aeruginosa isolates. By training machine learning classifiers on information about the presence or absence of genes, their sequence variation, and gene expression profiles, we generated predictive models and identified biomarkers of susceptibility or resistance to four commonly administered antimicrobial drugs. Using these data types alone or in combination resulted in high (0.8-0.9) or very high (>0.9) sensitivity and predictive values, where the relative contribution of the different categories of biomarkers strongly depended on the antibiotic. For all drugs except for ciprofloxacin, gene expression information substantially improved diagnostic performance. Our results pave the way for the development of a molecular resistance profiling tool that reliably predicts antimicrobial susceptibility based on genomic and transcriptomic markers. The implementation of a molecular susceptibility test system in routine clinical microbiology diagnostics holds promise to provide earlier and more detailed information on antibiotic resistance profiles of bacterial pathogens and thus could change how physicians treat bacterial infections.
The rapid regenerative response of a model sea anemone speciesExaiptasia pallidais characterised by tissue plasticity and highly coordinated cell communication
Authors: van der Burg Chloé A. , Pavasovic Ana , Gilding Edward K. , Pelzer Elise S. , Surm Joachim M. , Smith Hayden L. , Walsh Terence P. , Prentis Peter J.
Published: May 2019

Regeneration of a limb or tissue can be achieved through multiple different pathways and mechanisms. The sea anemoneExaiptasia pallidahas been observed to have excellent regenerative proficiency but this has not yet been described transcriptionally. In this study we examined the genetic expression changes during a regenerative timecourse and report key genes involved in regeneration and wound healing. We found that the major response was an early upregulation of genes involved in cellular movement and cell communication, which likely contribute to a high level of tissue plasticity resulting in the rapid regeneration response observed in this species. We find the immune system is only transcriptionally active in the first eight hours post-amputation and conclude, in accordance with previous literature, that the immune system and regeneration have an inverse relationship. Fifty-nine genes (3.8% of total) differentially expressed during regeneration were identified as having no orthologues in other species, indicating that regeneration inE. pallidamay rely on the activation of species-specific novel genes. Additionally, taxonomically-restricted novel genes, including species-specific novels, and highly conserved genes were identified throughout the regenerative timecourse, showing that both may work in concert to achieve complete regeneration. We conclude thatE. pallidabehaves similarly to other anemone species such asNematostella vectensisandCalliactis polypusbut with some notable novel differences.
Parental care shapes evolution of aposematism and provides lifelong protection against predators
Authors: Lindstedt C. , Boncoraglio G. , Cotter S.C. , Gilbert J.D.J. , Kilner R.M
Published: May 2019

Social interactions within species can modulate the response to selection and determine the extent of evolutionary change. Yet relatively little work has determined whether the social environment can influence the evolution of traits that are selected by interactions with other species - a major source of natural selection. Here we show that the amount of parental care received as an offspring can influence the expression, and potential evolution, of warning displays deployed against predators in adulthood. In theory, warning displays by prey are selected by predators for uniformity and to reliably advertise the extent to which individuals are chemically defended. However, the correlated evolution of intensity of the visual display and strength of the chemical defense is only possible if there is a genetic correlation between them. Adult burying beetlesNicrophorus vespilloidesbear bright orange elytral markings which advertise their chemical defenses. We experimentally manipulated the level of maternal care that individuals received when they were larvae and then measured the strength of the correlation between the component parts of the warning display when they reached adulthood. We found that under limited care individuals were smaller and produced less conspicuous warning displays. The underlying family (genetic) correlation between the visual display and the chemical defense was weaker in individuals that received little care as larvae. We conclude that parenting by burying beetles modulates the evolvability of aposematic defense, making correlated evolutionary change in signal intensity and chemical defense less likely when they restrict care to their young.

Significance Statement

Parental care can improve early offspring survival against predators. However, we have little knowledge of how its effects shape the evolution of predator-prey interactions later in the offspring’s life. We tested this with carrion beetles who provide care for offspring and who carry warning coloration to advertise to predators that they are chemically defended. We show that more parental care resulted in larger, more brightly coloured and chemically defended adult beetles. Furthermore, when parents had provided little care for their young we found weaker genetic correlations between warning signal salience and chemical defense. Over time, this could result in untrustworthy warning signals, which could render them ineffective against predators.
Constraints on somite formation in developing embryos
Authors: Juul Jonas S. , Jensen Mogens H. , Krishna Sandeep
Published: May 2019

Segment formation in vertebrate embryos is a stunning example of biological self-organisation. Here, we present an idealized model of the presomitic mesoderm (PSM) as a one-dimensional line of oscillators. We use the model to derive constraints that connect the size of somites, and the timing of their formation, to the growth of the PSM and the gradient of the somitogenesis clock period across the PSM. Our analysis recapitulates the observations made recently in ex-vivo cultures of mouse PSM cells, and makes predictions for how perturbations, such as increased Wnt levels, would alter somite widths. Finally, our model makes testable predictions for the shape of the phase profile and somite widths at different stages of PSM growth. In particular, we show that the phase profile is robustly concave when the PSM length is steady and slightly convex in an important special case when it is decreasing exponentially. In both cases, the phase profile scales with the PSM length; in the latter case, it scales dynamically. This has important consequences for the velocity of the waves that traverse the PSM and trigger somite formation, as well as the effect of errors in phase measurement on somite widths.
Consistency in macroscopic human brain responses to noisy time-varying visual inputs
Authors: Kitajo Keiichi , Sase Takumi , Mizuno Yoko , Suetani Hiromichi
Published: May 2019

It is an open question as to whether macroscopic human brain responses to repeatedly presented external inputs show consistent patterns across trials. We here provide experimental evidence that human brain responses to noisy time-varying visual inputs, as measured by scalp electroencephalography (EEG), show a signature of consistency. The results indicate that the EEG-recorded responses are robust against fluctuating ongoing activity, and that they respond to visual stimuli in a repeatable manner. This consistency presumably mediates robust information processing in the brain. Moreover, the EEG response waveforms were discriminable between individuals, and were invariant over a number of days within individuals. We reveal that time-varying noisy visual inputs can harness macroscopic brain dynamics and can manifest hidden individual variations.
Comparing statistical and mechanistic models to identify the drivers of mortality within a rear-edge beech population
Authors: Petit-Cailleux Cathleen , Davi Hendrik , Lefèvre François , Garrigue Joseph , Magdalou Jean-André , Hurson Christophe , Magnanou Elodie , Oddou-Muratorio Sylvie
Published: May 2019

Abstract

Since several studies have been reporting an increase in the decline of forests, a major issue in ecology is to better understand and predict tree mortality. The interactions between the different factors and the physiological processes giving rise tree mortality, as well as the inter-individual variability in mortality risk, still need to be better assessed.

This study investigates mortality in a rear-edge population of European beech (Fagus sylvaticaL.) using a combination of statistical and process-based modelling approaches. Based on a survey of 4323 adult beeches since 2002 within a natural reserve, we first used statistical models to quantify the effects of competition, tree growth, size, defoliation and fungi presence on mortality. Secondly, we used an ecophysiological process-based model (PBM) to separate out the different mechanisms giving rise to temporal and inter-individual variations in mortality by simulating depletion of carbon stocks, loss of hydraulic conductance and damage due to late frosts in response to climate.

The combination of all these simulated processes was associated with the temporal variations in the population mortality rate. The individual probability of mortality decreased with increasing mean growth, and increased with increasing crown defoliation, earliness of budburst, fungi presence and increasing competition, in the statistical model. Moreover, the interaction between tree size and defoliation was significant, indicating a stronger increase in mortality associated to defoliation in smaller than larger trees. Finally, the PBM predicted a higher conductance loss together with a higher level of carbon reserves for trees with earlier budburst, while the ability to defoliate the crown was found to limit the impact of hydraulic stress at the expense of the accumulation of carbon reserves.

We discuss the convergences and divergences obtained between statistical and process-based approaches and we highlight the importance of combining them to characterize the different processes underlying mortality, and the factors modulating individual vulnerability to mortality.
No effect of triple-pulse TMS medial to intraparietal sulcus on online correction for target perturbations during goal-directed hand and foot reaches
Authors: Marigold Daniel S. , Lajoie Kim , Heed Tobias
Published: May 2019

Posterior parietal cortex (PPC) is central to sensorimotor processing for goal-directed hand and foot movements. Yet, the specific role of PPC subregions in these functions is not clear. Previous human neuroimaging and transcranial magnetic stimulation (TMS) work has suggested that PPC lateral to the intraparietal sulcus (IPS) is involved in directing the arm, shaping the hand, and correcting both finger-shaping and hand trajectory during movement. The lateral localization of these functions agrees with the comparably lateral position of the hand and fingers within the motor and somatosensory homunculi along the central sulcus; this might suggest that, in analogy, (goal-directed) foot movements would be mediated by medial portions of PPC. However, foot movement planning activates similar regions for both hand and foot movement along the caudal-to-rostral axis of PPC, with some effector-specificity evident only rostrally, near the central regions of sensorimotor cortex. Here, we attempted to test the causal involvement of PPC regions medial to IPS in hand and foot reaching as well as online correction evoked by target displacement. Participants made hand and foot reaches towards identical visual targets. Sometimes, the target changed position 100-117 ms into the movement. We disturbed cortical processing over four positions medial to IPS with three pulses of TMS separated by 40 ms, both during trials with and without target displacement. We timed TMS to disrupt reach execution and online correction. TMS did not affect endpoint error, endpoint variability, or reach trajectories for hand or foot. While these negative results await replication with different TMS timing and parameters, we conclude that regions medial to IPS are involved in planning, rather than execution and online control, of goal-directed limb movements.
Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
Authors: Karst Søren M. , Ziels Ryan M. , Kirkegaard Rasmus H. , Sørensen Emil A. , McDonald Daniel , Zhu Qiyun , Knight Rob , Albertsen Mads
Published: May 2019

High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, we report a high-throughput amplicon sequencing approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies or Pacific Biosciences CCS sequencing, yielding high accuracy single-molecule consensus sequences of large genomic regions. Our approach generates amplicon and genomic sequences of >10,000 bp in length with a mean error-rate of 0.0049-0.0006% and chimera rate <0.022%.
Technical Note: Efficient and accurate estimation of genotype odds ratios in biobank-based unbalanced case-control studies
Authors: Dey Rounak , Lee Seunggeun
Published: May 2019

In genome-wide association studies (GWASs), genotype log-odds ratios (LORs) quantify the effects of the variants on the binary phenotypes, and calculating the genotype LORs for all of the markers is required for several downstream analyses. Calculating genotype LORs at a genome-wide scale is computationally challenging, especially when analyzing large-scale biobank data, which involves performing thousands of GWASs phenome-wide. Since most of the binary phenotypes in biobank-based studies have unbalanced (case : control = 1 : 10) or often extremely unbalanced (case : control = 1 : 100) case-control ratios, the existing methods cannot provide a scalable and accurate way to estimate the genotype LORs. The traditional logistic regression provides biased LOR estimates in such situations. Although the Firth bias correction method can provide unbiased LOR estimates, it is not scalable for genome-wide or phenome-wide scale association analyses typically used in biobank-based studies, especially when the number of non-genetic covariates is large. On the other hand, the saddlepoint approximation-based test (fastSPA), which can provide accurate p values and is scalable to analyse large-scale biobank data, does not provide the genotype LOR estimates as it is a score-based test. Here, we propose a scalable method based on score statistics, to accurately estimate the genotype LORs, adjusting for non-genetic covariates. Comparing to the Firth method, our proposed method reduces the computational complexity from O(nK2 + K3) to O(n), where n is the sample-size, and K is the number of non-genetic covariates. Our method is ~ 10x faster than the Firth method when 15 covariates are being adjusted for. Through extensive numerical simulations, we show that the proposed method is both scalable and accurate in estimating the genotype ORs in genome-wide or phenome-wide scale.
Next generation sequencing to investigate genomic diversity in Caryophyllales
Authors: Pucker Boas , Feng Tao , Brockington Samuel F.
Published: May 2019

Caryophyllales are a highly diverse and large order of plants with a global distribution. While some species are important crops like Beta vulgaris, many others can survive under extreme conditions. This order is well known for the complex pigment evolution, because the pigments anthocyanins and betalains occur with mutual exclusion in species of the Caryophyllales. Here we report about genome assemblies of Kewa caespitosa (Kewaceae), Macarthuria australis (Macarthuriaceae), and Pharnaceum exiguum (Molluginaceae) which are representing different taxonomic groups in the Caryophyllales. The availability of these assemblies enhances molecular investigation of these species e.g. with respect to certain genes of interest.
Tomato root transformation followed by inoculation with Ralstonia solanacearum for straightforward genetic analysis of bacterial wilt disease
Authors: Morcillo Rafael J. L. , Zhao Achen , Tamayo-Navarrete María I. , García-Garrido José M. , Macho Alberto P.
Published: May 2019

Ralstonia solanacearum is a devastating soil borne vascular pathogen that is able to infect a large range of plant species, causing an important threat to agriculture. However, the Ralstonia model is considerably under-explored in comparison to other models involving bacterial plant pathogens, such as Pseudomonas syringae in Arabidopsis. Research targeted to understanding the interaction between Ralstonia and crop plants is essential to develop sustainable solutions to fight against bacterial wilt disease, but is currently hindered by the lack of straightforward experimental assays to characterize the different components of the interaction in native host plants. In this scenario, we have developed an easy method to perform genetic analysis of Ralstonia infection of tomato, a natural host of Ralstonia. This method is based on Agrobacterium rhizogenes-mediated transformation of tomato roots, followed by Ralstonia soil-drenching inoculation of the resulting plants, containing transformed roots expressing the construct of interest. The versatility of the root transformation assay allows performing either gene overexpression or gene silencing mediated by RNAi. As a proof of concept, we used this method to show that RNAi-mediated silencing of SlCESA6 of tomato roots conferred resistance to Ralstonia. Here, we describe this method in detail, enabling genetic approaches to understand bacterial wilt disease in a relative short time and with small requirements of equipment and plant growth space.

A versatile method for tomato root transformation followed by inoculation with Ralstonia solanacearum to perform straightforward genetic analysis for the study of bacterial wilt disease.
Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection
Authors: Borg Constantina , Jahun Aminu S. , Thorne Lucy , Sorgeloos Frédéric , Bailey Dalan , Goodfellow Ian
Published: May 2019

Background

Murine norovirus (MNV) is widely used as a model for studying norovirus biology. While MNV isolates vary in their pathogenesis, infection of immunocompetent mice mostly results in persistent infection. The ability of a virus to establish a persistent infection is dependent on its ability to subvert or avoid the host immune response. Previously, we described the identification and characterization of virulence factor 1 (VF1) in MNV, and established that it acts as an innate immune antagonist. Here, we explore the role of VF1 during persistent MNV infection in an immunocompetent host.

Methods

Using reverse genetics, we generated VF1-knockout MNV-3 that contained a single or a triple termination codon inserted in the VF1 open reading frame.

Results

VF1-knockout MNV-3 replicated to comparable levels to the wildtype virus in tissue culture. Comparative studies between MNV-3 and an acute MNV-1 strain show that MNV-3 VF1 exerts the same functions as MNV-1 VF1, but with reduced potency. Mice infected with VF1-knockout MNV-3 showed significantly reduced replication kinetics during the acute phase of the infection, but viral loads rapidly reached the levels seen in mice infected with wildtype virus after phenotypic restoration of VF1 expression. Infection with an MNV-3 mutant that had three termination codons inserted into VF1, in which reversion was suppressed, resulted in consistently lower replication throughout a three-month persistent infection in mice, suggesting a role for VF1 in viral fitness in vivo.

Conclusion

Our results indicate that VF1 expressed by a persistent strain of MNV also functions to antagonise the innate response to infection. We found that VF1 is not essential for viral persistence, but instead contributes to viral fitness in mice. These data fit with the hypothesis that noroviruses utilise multiple mechanisms to avoid and/or control the host response to infection and that VF1 is just one component of this.
Parkinson’s disease: a systemic inflammatory disease accompanied by bacterial inflammagens
Authors: Adams Büin , Nunes J Massimo , Page Martin J , Roberts Timothy , Carr Jonathan , Nell Theo A , Kell Douglas B , Pretorius Etheresia
Published: May 2019

Parkinson’s disease (PD) is a well-known neurodegenerative disease. Recently, the role of gingipains fromPorphyromonas gingivaliswas implicated in Alzheimer’s disease. Here we present evidence of systemic inflammation, accompanied by hypercoagulation; we also show that ginipains fromP. gingivalisand its LPS may foster abnormal clotting, and that ginipains are present in PD blood, and thus that ginipain’s action on blood may be relevant to PD pathology. Bloods from both PD and healthy blood samples were analysed using thromboelastography (TEG), confocal and electron microscopies, and for cytokine and other circulating biomarkers. We also probed PD and healthy plasma clots with a polyclonal antibody for the bacterial protease, gingipain R1, fromP. gingivalis. Low concentrations of recombinant gingipain R1 were also added to purified fluorescent fibrinogen. TEG, fibrin(ogen) amyloid formation and platelet ultrastructure analysis confirmed profound hypercoagulation, while the biomarker analysis confirmed significantly increased levels of circulating proinflammatory cytokines. We provide evidence for the presence of the protease, gingipain R1 in PD blood, implicating inflammatory microbial cell wall products in PD.
The lottery of spermatogenesis
Authors: Kalirad Ata , Safdari Hadiseh , Sadeghi Mehdi
Published: May 2019

The causes of male infertility are yet to be fully understood. Here, we propose that male infertility can be partly attributed to the insufficiency of cytoplasmically-inherited proteins in sperms. Using a simple stochastic model of spermatogenesis, we show that in a range of parameters, the proportion of viable sperms can be reduced simply due to stochastic transmission of proteins from spermatogonia to spermatids.
Novel Small Molecules Targeting the Intrinsically Disordered Structural Ensemble of α-Synuclein Protect Against Diverse α-Synuclein Mediated Dysfunctions
Authors: Tóth Gergely , Neumann Thomas , Berthet Amandine , Masliah Eliezer , Spencer Brian , Tao Jiahui , Jobling Michael F. , Gardai Shyra J. , Bertoncini Carlos W. , Cremades Nunilo , Bova Michael , Ballaron Stephen , Chen Xiao-Hua , Mao Wenxian , Nguyen Phuong , Tabios Mariano C. , Tambe Mitali A. , Rochet Jean-Christophe , Junker Hans-Dieter , Schwizer Daniel , Sekul Renate , Ott Inge , Anderson John P. , Szoke Balazs , Hoffman Wherly , Christodoulou John , Yednock Ted , Agard David A. , Schenk Dale , McConlogue Lisa
Published: May 2019

The over-expression and aggregation of α-synuclein (αSyn) are linked to the onset and pathology of Parkinson’s disease. Native monomeric αSyn exists in an intrinsically disordered ensemble of interconverting conformations, which has made its therapeutic targeting by small molecules highly challenging. Nonetheless, here we successfully target the monomeric structural ensemble of αSyn and thereby identify novel drug-like small molecules that impact multiple pathogenic processes. Using a surface plasmon resonance high-throughput screen, in which monomeric αSyn is incubated with microchips arrayed with tethered compounds, we identified novel αSyn interacting drug-like compounds. Because these small molecules could impact a variety of αSyn forms present in the ensemble, we tested representative hits for impact on multiple αSyn malfunctions in vitro and in cells including aggregation and perturbation of vesicular dynamics. We thereby identified a compound that inhibits αSyn misfolding and is neuroprotective, multiple compounds that restore phagocytosis impaired by αSyn overexpression, and a compound blocking cellular transmission of αSyn. Our studies demonstrate that drug-like small molecules that interact with native αSyn can impact a variety of its pathological processes. Thus, targeting the intrinsically disordered ensemble of αSyn offers a unique approach to the development of small molecule research tools and therapeutics for Parkinson’s disease.
ClassifyMe: a field-scouting software for the identification of wildlife in camera trap images
Authors: Falzon G , Lawson C , Cheung K-W , Vernes K , Ballard GA , Fleming PJS , Glen AS , Milne H , Mather-Zardain AT , Meek PD
Published: May 2019

We presentClassifyMea software tool for the automated identification of animal species from camera trap images.ClassifyMeis intended to be used by ecologists both in the field and in the office. Users can download a pre-trained model specific to their location of interest and then upload the images from a camera trap to a laptop or workstation.ClassifyMewill identify animals and other objects (e.g. vehicles) in images, provide a report file with the most likely species detections and automatically sort the images into sub-folders corresponding to these species categories. False Triggers (no visible object present) will also be filtered and sorted. Importantly, theClassifyMesoftware operates on the user’s local machine (own laptop or workstation) not via internet connection. This allows users access to state-of-the-art camera trap computer vision softwarein situ, rather than only in the office. The software also incurs minimal cost on the end-user as there is no need for expensive data uploads to cloud services. Furthermore, processing the images locally on the users’ end-device allows them data control and resolves privacy issues surrounding transfer and third-party access to users’ datasets.
Transcript degradation and codon usage regulate gene expression in a lytic phage
Authors: Jack Benjamin R. , Boutz Daniel R. , Paff Matthew L. , Smith Bartram L. , Wilke Claus O.
Published: May 2019

Many viral genomes are small, containing only single- or double-digit numbers of genes and relatively few regulatory elements. Yet viruses successfully execute complex regulatory programs as they take over their host cells. Here, we propose that some viruses regulate gene expression via a carefully balanced interplay between transcription, translation, and transcript degradation. As our model system, we employ bacteriophage T7, whose genome of approximately 60 genes is well annotated and for which there is a long history of computational models of gene regulation. We expand upon prior modeling work by implementing a stochastic gene expression simulator that tracks individual transcripts, polymerases, ribosomes, and RNases participating in the transcription, translation, and transcript-degradation processes occurring during a T7 infection. By combining this detailed mechanistic modeling of a phage infection with high throughput gene expression measurements of several strains of bacteriophage T7, evolved and engineered, we can show that both the dynamic interplay between transcription and transcript degradation, and between these two processes and translation, appear to be critical components of T7 gene regulation. Our results point to a generic gene regulation strategy that may have evolved in many other viruses. Further, our results suggest that detailed mechanistic modeling may uncover the biological mechanisms at work in both evolved and engineered virus variants.
Design of a genetic layered feedback controller in synthetic biological circuitry
Authors: Hu Chelsea Y. , Murray Richard M.
Published: May 2019

Feedback control is the key to achieve robust performances for many engineered systems. However, its application in biological contexts is still largely unexplored. In this work, we designed, analyzed and simulated a layered controller functioning at both molecular and populational levels. First, we used a minimal model of three states to represent a system where state A activates state B; state R is a by-product of state B that acts as a negative feedback regulating both state A, B, and sequentially R. We call the feedback applied to state B acisfeedback and the one applied to state A atransfeedback. Through stability analysis via linearization at equilibrium and sensitivity analysis at transient state, we found that thecisfeedback attenuates disturbances better but recovers slower; thetransfeedback recovers faster but has more dramatic responses to fluctuations; the layered feedback demonstrates both advantageous traits of the two single layers. Then we designed two versions of synthetic genetic circuits to implement the layered controller in living cells. One version with an sRNA as regulator R, the other with a transcription factor protein as the regulator R. The analysis and dynamical simulation of the models confirmed the analytical results from the minimal model. At the same time, we found that the protein regulated feedback controls have faster recovery speed but the RNA version has a stronger disturbance attenuation effect.
Rapid phenotypic and metabolomic domestication of wildPenicilliummolds on cheese
Authors: Bodinaku Ina , Shaffer Jason , Connors Allison B. , Steenwyk Jacob L. , Kastman Erik , Rokas Antonis , Robbat Albert , Wolfe Benjamin
Published: May 2019

Fermented foods provide novel ecological opportunities for natural populations of microbes to evolve through successive recolonization of resource-rich substrates. Comparative genomic data have reconstructed the evolutionary histories of microbes adapted to food environments, but experimental studies directly demonstrating the process of domestication are lacking for most fermented food microbes. Here we show that during the repeated colonization of cheese, phenotypic and metabolomic traits of wildPenicilliummolds rapidly change to produce mutants with properties similar to industrial cultures used to make Camembert and other bloomy rind cheeses. Over a period of just a few weeks, populations of wildPenicilliumstrains serially passaged on cheese resulted in the reduction or complete loss of pigment, spore, and mycotoxin production. Mutants also had a striking change in volatile metabolite production, shifting from production of earthy or musty volatile compounds (e.g. geosmin) to fatty and cheesy volatiles (e.g. 2-nonanone, 2-undecanone). RNA-sequencing demonstrated a significant decrease in expression of 356 genes in domesticated mutants, with an enrichment of many secondary metabolite production pathways in these downregulated genes. By manipulating the presence of neighboring microbial species and overall resource availability, we demonstrate that the limited competition and high nutrient availability of the cheese environment promote rapid trait evolution ofPenicilliummolds.

IMPORTANCE

Industrial cultures of filamentous fungi are used to add unique aesthetics and flavors to cheeses and other microbial foods. How these microbes adapted to live in food environments is generally unknown as most microbial domestication is unintentional. Our work demonstrates that wild molds closely related to the starter culturePenicillium camembertican readily lose undesirable traits and quickly shift toward producing desirable aroma compounds. In addition to experimentally demonstrating a putative domestication pathway forP. camemberti, our work suggests that wildPenicilliumisolates could be rapidly domesticated to produce new flavors and aesthetics in fermented foods.
Polylactic acid, a sustainable, biocompatible, transparent substrate material for Organ-On-Chip, and Microfluidic applications
Authors: Ongaro Alfredo E. , Giuseppe Davide Di , Kermanizadeh Ali , Crespo Allende Miguelez , Mencatti Arianna , Ghibelli Lina , Mancini Vanessa , Wlodarczyk Krystian L. , Hand Duncan P. , Martinelli Eugenio , Stone Vicki , Howarth Nicola , Carrubba Vincenzo La , Pensabene Virginia , Kersaudy-Kerhoas Maïwenn
Published: May 2019

Organ-on-chips are miniaturised devices aiming at replacing animal models for drug discovery, toxicology and studies of complex biological phenomena. The field of Organ-On-Chip has grown exponentially, and has led to the formation of companies providing commercial Organ-On-Chip devices. Yet, it may be surprising to learn that the majority of these commercial devices are made from Polydimethylsiloxane (PDMS), a silicone elastomer that is widely used in microfluidic prototyping, but which has been proven difficult to use in industrial settings and poses a number of challenges to experimentalists, including leaching of uncured oligomers and uncontrolled adsorption of small compounds. To alleviate these problems, we propose a new substrate for organ-on-chip devices: Polylactic Acid (PLA). PLA is a material derived from renewable resources, and compatible with high volume production technologies, such as microinjection moulding. PLA can be formed into sheets and prototyped into desired devices in the research lab. In this article we uncover the suitability of Polylactic acid as a substrate material for Microfluidic cell culture and Organ-on-a-chip applications. Surface properties, biocompatibility, small molecule adsorption and optical properties of PLA are investigated and compared with PDMS and other reference polymers.

Significance

Organ-On-Chip (OOC) technology is a powerful and emerging tool that allows the culture of cells constituting an organ and enables scientists, researchers and clinicians to conduct more physiologically relevant experiments without using expensive animal models. Since the emergence of the first OOC devices 10 years ago, the translation from research to market has happened relatively fast. To date, at least 28 companies are proposing body and tissue on-a chip devices. The material of choice in most commercial organ-on-chip platforms is an elastomer, Polydymethyloxane (PDMS), commonly used in microfluidic R&D. PDMS is however subject to poor reproducibility, and absorbs small molecule compounds unless treated. In this study we show that PLA overcomes all the drawbacks related to PDMS: PLA can be prototyped in less than 45 minutes from design to test, is transparent, not autofluorescent, and biocompatible. PLA-based microfluidic platforms have the potential to transform the OOC industry as well as to provide a sustainable alternative for future Lab-On-Chip and point-of-care devices.
Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation
Authors: Yukawa Masashi , Jagannathan Sajjeev , Kartashov Andrey V. , Chen Xiaoting , Weirauch Matthew T. , Barski Artem
Published: May 2019

Activation of T cells is dependent on organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naïve T cells within 5 hours of activation. These newly open regions were strongly enriched for the AP-1 motif, and indeed, ChIP-seq demonstrated AP-1 binding at more than 70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation, was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1–dependent elements with risk loci for multiple immune diseases, including multiple sclerosis, inflammatory bowel disease and allergic disease. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.