bluuebunny/crossref_metadata_2025 huggingface dataset:
HCPro Suppression of Callose Deposition Contributes to Strain-Specific Resistance Against Potato Virus Y
Authors: Chowdhury Rawnaq N. , Lasky Danny , Karki Hari , Zhang Zongying , Goyer Aymeric , Halterman Dennis , Rakotondrafara Aurélie M.
Published: September 2019

Potato virus Y (PVY; Potyviridae) is a continuing challenge for potato production owing to the increasing popularity of strain-specific resistant cultivars. Hypersensitive resistance (HR) is one type of plant defense responses to restrict virus spread. In many potato cultivars, such as cultivar Premier Russet (PR), local necrosis at the site of infection protects against the most common PVYO strain, but the HR often fails to restrain necrotic strains, which spread systemically. Here, we established the role of callose accumulation in the strain-specific resistance responses to PVY infection. We first uncovered that PVY, independent of the strain, is naturally capable of suppressing pathogenesis-related callose formation in a susceptible host. Such activity can be dissociated from viral replication by the transient expression of the viral-encoded helper component proteinase (HCPro) protein, identifying it as the pathogen elicitor. However, unlike the necrotic strain, PVYO and its corresponding HCPro are unable to block callose accumulation in resistant PR potatoes, in which we observed an abundance of callose deposition and the inability of the virus to spread. The substitution of eight amino acid residues within the HCPro C-terminal region that differ between PVYO and PVYN strains and were previously shown to be responsible for eliciting the HR response, are sufficient to restore the ability of HCProO to suppress callose accumulation, despite the resistant host background, in line with a new viral function in pathogenicity.
Temporal Dynamics of Wheat Blast Epidemics and Disease Measurements Using Multispectral Imagery
Authors: Gongora-Canul C. , Salgado J. D. , Singh D. , Cruz A. P. , Cotrozzi L. , Couture J. , Rivadeneira M. G. , Cruppe G. , Valent B. , Todd T. , Poland J. , Cruz C. D.
Published: September 2019

Wheat blast is a devastating disease caused by the Triticum pathotype of Magnaporthe oryzae. M. oryzae Triticum is capable of infecting leaves and spikes of wheat. Although symptoms of wheat spike blast (WSB) are quite distinct in the field, symptoms on leaves (WLB) are rarely reported because they are usually inconspicuos. Two field experiments were conducted in Bolivia to characterize the change in WLB and WSB intensity over time and determine whether multispectral imagery can be used to accurately assess WSB. Disease progress curves (DPCs) were plotted from WLB and WSB data, and regression models were fitted to describe the nature of WSB epidemics. WLB incidence and severity changed over time; however, the mean WLB severity was inconspicuous before wheat began spike emergence. Overall, both Gompertz and logistic models helped to describe WSB intensity DPCs fitting classic sigmoidal shape curves. Lin’s concordance correlation coefficients were estimated to measure agreement between visual estimates and digital measurements of WSB intensity and to estimate accuracy and precision. Our findings suggest that the change of wheat blast intensity in a susceptible host population over time does not follow a pattern of a monocyclic epidemic. We have also demonstrated that WSB severity can be quantified using a digital approach based on nongreen pixels. Quantification was precise (0.96 < r> 0.83) and accurate (0.92 < ρ > 0.69) at moderately low to high visual WSB severity levels. Additional sensor-based methods must be explored to determine their potential for detection of WLB and WSB at earlier stages.
The role of Ap2a2 in PPARα‐mediated regulation of lipolysis in adipose tissue
Authors: Montgomery Magdalene K. , Bayliss Jacqueline , Keenan Stacey , Rhost Sarah , Ting Stephen B. , Watt Matthew J.
Published: September 2019

Adipose tissue plays a major role in the regulation of systemic metabolic homeostasis, with the AP2 adaptor complex being important in clathrin‐mediated endocytosis (CME) of various cell surface receptors, including glucose transporter 4, the insulin receptor, and β‐adrenergic receptors (ARs). One of the AP2 subunits, adaptor‐related protein complex 2, α2 subunit (Ap2a2), has recently been identified as a peroxisome proliferator‐activated receptor (PPAR)α target gene. The effects of PPARα on the AP2 adaptor complex and CME are unknown. We generated adipocyte‐specific Ap2a2 knockout mice and investigated their metabolism when fed a standard chow or high‐fat diet, without and with supplementation with the PPARα‐agonist WY‐14643 (WY). Although Ap2a2 deletion had only minor effects on glycaemic control, it led to substantial impairment in β‐adrenergic activation of lipolysis, as evidenced by a loss of cAMP response, PKA activation, and glycerol/fatty acid release. These differences were related to increased cell surface localization of the β2‐ and β3‐ARs. Lipolytic defects were accompanied by impaired WY‐mediated loss of fat mass and whole‐body fat oxidation. This study demonstrates a novel role for PPARα in β‐adrenergic regulation of adipose tissue lipolysis and for adipose tissue in supplying adequate substrate to other peripheral tissues to accommodate the increase in systemic fatty acid oxidation that occurs upon treatment with PPARα agonists.—Montgomery, M. K., Bayliss, J., Keenan, S., Rhost, S., Ting, S. B., Watt, M. J. The role of Ap2a2 in PPARα‐mediated regulation of lipolysis in adipose tissue. FASEB J. 33, 13267–13279 (2019). www.fasebj.org
Viral infection causes sex-specific changes in fruit fly social aggregation behaviour
Authors: Siva-Jothy Jonathon A. , Vale Pedro F.
Published: September 2019

Host behavioural changes following infection are common and could be important determinants of host behavioural competence to transmit pathogens. Identifying potential sources of variation in sickness behaviours is therefore central to our understanding of disease transmission. Here, we test how group social aggregation and individual locomotor activity vary between different genotypes of male and female fruit flies (Drosophila melanogaster) following septic infection withDrosophilaC virus (DCV). We find genetic-based variation in both locomotor activity and social aggregation, but we did not detect an effect of DCV infection on fly activity or sleep patterns within the initial days following infection. However, DCV infection caused sex-specific effects on social aggregation, as male flies in most genetic backgrounds increased the distance to their nearest neighbour when infected. We discuss possible causes for these differences in the context of individual variation in immunity and their potential consequences for disease transmission.
Migratory flight on the Pacific Flyway: strategies and tendencies of wind drift compensation
Authors: Newcombe Patrick B. , Nilsson Cecilia , Lin Tsung-Yu , Winner Kevin , Bernstein Garrett , Maji Subhransu , Sheldon Daniel , Farnsworth Andrew , Horton Kyle G.
Published: September 2019

Applications of remote sensing data to monitor bird migration usher a new understanding of magnitude and extent of movements across entire flyways. Millions of birds move through the western USA, yet this region is understudied as a migratory corridor. Characterizing movements in the Pacific Flyway offers a unique opportunity to study complementary patterns to those recently highlighted in the Atlantic and Central Flyways. We use weather surveillance radar data from spring and autumn (1995–2018) to examine migrants' behaviours in relation to winds in the Pacific Flyway. Overall, spring migrants tended to drift on winds, but less so at northern latitudes and farther inland from the Pacific coastline. Relationships between winds and autumn flight behaviours were less striking, with no latitudinal or coastal dependencies. Differences in the preferred direction of movement (PDM) and wind direction predicted drift patterns during spring and autumn, with increased drift when wind direction and PDM differences were high. We also observed greater total flight activity through the Pacific Flyway during the spring when compared with the autumn. Such complex relationships among birds’ flight strategies, winds and seasonality highlight the variation within a migration system. Characterizations at these scales complement our understanding of strategies to clarify aerial animal movements.
Thermodynamic properties of atrial fibrillation cryoablation: a model-based approach to improve knowledge on energy delivery
Authors: Giaretto Valter , Ballatore Andrea , Passerone Claudio , Desalvo Paolo , Matta Mario , Saglietto Andrea , De Salve Mario , Gaita Fiorenzo , Panella Bruno , Anselmino Matteo
Published: September 2019

The objective of this study is to describe a suitable model of atrial fibrillation cryoablation thermodynamic properties. Three different thermal loads were applied to a cylindrical copper element simulating the cryoprobe, thermally coupled with a Peltier stack producing the freezing effect, and in contact with a bovine liver sample. Thermal events occurring inside the samples were measured using mirror image technique. Heat subtracted flux during ice formation and minimum temperature measured at probe–tissue interface were, respectively, 1.33 W cm
−2
and −27.8°C for Sample#0, 1.88 W cm
−2
and −35.6°C for Sample#1 and 1.82 W cm
−2
and 1.44 W cm
−2
before and after the ice trigger, respectively, and −29.3°C for Sample#2. Ice trigger temperature was around −8.5°C for Sample#0 and Sample#2, and −10.4°C for Sample#1. In all the investigated samples, ice front penetration was proportional to the square root of time and its velocity depended on the heat flux subtracted. The fraction of the useful energy spent for ice formation was less than 60% for Sample#0, and about 80% for Sample#1 and for Sample#2, before the reduction of the removed heat flux. Freezing time exceeding a cut-off, according to the heat subtracted flux, does not improve the procedure effectiveness and is detrimental to the surrounding tissues.
Martyrs made in the sky: the
Zénith
balloon tragedy and the construction of the French Third Republic's first scientific heroes
Authors: De Oliveira Patrick Luiz Sullivan
Published: September 2019

Following the balloon's invention in 1783, the French greeted the technology with enthusiasm, speculating extensively about its potential scientific and practical applications. However, the lack of progress in navigating against the winds discredited ballooning, and in the following decades it became the domain of spectacular forms of entertainment and of swindlers trying to defraud public subscriptions. All of this changed after the 1870–1871 Franco-Prussian War, during which balloons were used to breach the siege of Paris. This essay explores how the aeronautical community, led by the recently established Société Française de Navigation Aérienne, mobilized the memory of the war to transform the balloon into a symbol of a heroic republican science. Paramount in that process was the
Zénith
's 1875 high-altitude ascent that killed two aeronauts—Joseph Crocé-Spinelli and Théodore Sivel. The tragedy reverberated beyond France's scientific community, and through popular acclaim the two aeronauts became the Third Republic's first scientific martyrs, anticipating the eventual apotheoses of figures like Claude Bernard and Louis Pasteur. The ballooning revival in the last third of the century helped strengthen the association between France and aeronautics, thus setting the stage for the country to acquire a central position in the field by the early twentieth century.
Evaluating John Theophilus Desaguliers' Newtonianism: the case of waterwheel knowledge in
A course of experimental philosophy
Authors: Morris Andrew M. A.
Published: September 2019

John Theophilus Desaguliers (1683–1744) was a French-born English Huguenot who made his name as a public lecturer in London and a demonstrator at the Royal Society, writing a very popular introduction to Isaac Newton's natural philosophy, the two-volume
A course of experimental philosophy
(1734–1744). This paper looks at the influence of three French natural philosophers, Edme Mariotte (1620–1684), Antoine Parent (1666–1716) and Bernard Forest de Bélidor (1698–1761), on the account of waterwheel functioning in the second volume of that work. The aim of the paper is to show that, although Desaguliers demonstrated a commitment to Newton's work, his own natural philosophical objectives also led him to borrow ideas from natural philosophers outside Newton's direct sphere of influence. To do this I shall give an account of what Desaguliers appropriated from Newton's
Principia
, how it fitted in with his own project and how he also made use of other natural philosophers' theories in his discussion of fluid mechanics. This will hopefully result in a more nuanced conception of Desaguliers' ‘Newtonianism’ that takes into account the diverse sources and influences in his work.
Label-free sensitive detection of influenza virus using PZT discs with a synthetic sialylglycopolymer receptor layer
Authors: Erofeev Alexander S. , Gorelkin Petr V. , Kolesov Dmitry V. , Kiselev Gleb A. , Dubrovin Evgeniy V. , Yaminsky Igor V.
Published: September 2019

We describe rapid, label-free detection of Influenza A viruses using the first radial mode of oscillations of lead zirconate titanate (PZT) piezoelectric discs with a 2 mm radius and 100 µm thickness fabricated from a piezoelectric membrane. The discs are modified with a synthetic sialylglycopolymer receptor layer, and the coated discs are inserted in a flowing virus suspension. Label-free detection of the virus is achieved by monitoring the disc radial mode resonance frequency shift. Piezo transducers with sialylglycopolymer sensor layers exhibited a long lifetime, a high sensitivity and the possibility of regeneration. We demonstrate positive, label-free detection of Influenza A viruses at concentrations below 10
5
virus particles per millilitre. We show that label-free, selective, sensitive detection of influenza viruses by home appliances is possible in principle.
Low connectivity between shallow, mesophotic and rariphotic zone benthos
Authors: Stefanoudis Paris V. , Rivers Molly , Smith Struan R. , Schneider Craig W. , Wagner Daniel , Ford Helen , Rogers Alex D. , Woodall Lucy C.
Published: September 2019

Worldwide coral reefs face catastrophic damage due to a series of anthropogenic stressors. Investigating how coral reefs ecosystems are connected, in particular across depth, will help us understand if deeper reefs harbour distinct communities. Here, we explore changes in benthic community structure across 15–300 m depths using technical divers and submersibles around Bermuda. We report high levels of floral and faunal differentiation across depth, with distinct assemblages occupying each depth surveyed, except 200–300 m, corresponding to the lower rariphotic zone. Community turnover was highest at the boundary depths of mesophotic coral ecosystems (30–150 m) driven largely by taxonomic turnover and to a lesser degree by ordered species loss (nestedness). Our work highlights the biologically unique nature of benthic communities in the mesophotic and rariphotic zones, and their limited connectivity to shallow reefs, thus emphasizing the need to manage and protect deeper reefs as distinct entities.
Phylogenetic and kinematic constraints on avian flight signals
Authors: Berg K. S. , Delgado S. , Mata-Betancourt A.
Published: September 2019

Many birds vocalize in flight. Because wingbeat and respiratory cycles are often linked in flying vertebrates, birds in these cases must satisfy the respiratory demands of vocal production within the physiological limits imposed by flight. Using acoustic triangulation and high-speed video, we found that avian vocal production in flight exhibits a largely phasic and kinematic relationship with the power stroke. However, the sample of species showed considerable flexibility, especially those from lineages known for vocal plasticity (songbirds, parrots and hummingbirds), prompting a broader phylogenetic analysis. We thus collected data from 150 species across 12 avian orders and examined the links between wingbeat period, flight call duration and body mass. Overall, shorter wingbeat periods, controlling for ancestry and body mass, were correlated with shorter flight call durations. However, species from vocal learner lineages produced flight signals that, on average, exceeded multiple phases of their wingbeat cycle, while vocal non-learners had signal periods that were, on average, closer to the duration of their power stroke. These results raise an interesting question: is partial emancipation from respiratory constraints a necessary step in the evolution of vocal learning or an epiphenomenon? Our current study cannot provide the answer, but it does suggest several avenues for future research.
Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes
Authors: Gaboriau Théo , Albouy Camille , Descombes Patrice , Mouillot David , Pellissier Loïc , Leprieur Fabien
Published: September 2019

We develop a spatially explicit model of diversification based on palaeohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the ‘time-area’, ‘tropical niche conservatism’, ‘ecological limits’ and ‘evolutionary speed’ hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating biodiversity patterns.
GWAS including 82,707 subjects identifies functional coding variant in OPRM1 gene associated with opioid use disorder
Authors: Zhou Hang , Rentsch Christopher T. , Cheng Zhongshan , Kember Rachel L. , Nunez Yaira Z. , Tate Janet P. , Dao Cecilia , Xu Ke , Polimanti Renato , Farrer Lindsay A. , Justice Amy C. , Kranzler Henry R. ,   the VA Million Veteran Program, Gelernter Joel
Published: September 2019

One way to address the current crisis in opioid use is to improve our understanding of the biological mechanisms of opioid use disorder (OUD). We completed a primary GWAS of electronic health record-defined OUD in European-ancestry participants in the Million Veteran Program (MVP) sample, which included 8,529 affected subjects and 71,200 opioid-exposed controls. In the MVP alone, there were no genome-wide significant (GWS) associations. We then subjected the MVP and additional OUD GWAS results from the Yale-Penn and SAGE samples to meta-analysis (in total, 10,544 OUD cases and 72,163 opioid-exposed controls). A functional coding variant (rs1799971, encoding Asn40Asp) in OPRM1 (mu opioid receptor gene, the main biological target for opioid drugs) reached GWS (p=1.51×10−8); then replicated in two independent samples (each at p<0.05). The final meta-analyzed p-value for this variant in all samples was 7.81×10−10. SNP-based heritability of OUD was 11.3%. OUD was genetically correlated with 83 traits, including multiple substance use traits, psychiatric illnesses, cognitive performance, and others. Mendelian Randomization revealed possible causal effects on OUD risk from tobacco smoking, major depression, neuroticism, and cognitive performance. Despite the inclusion of data from the MVP, discovery of a significant association depended on including other purpose-collected samples as well. Recruitment of additional opioid dependent subjects for future studies – especially of non-European ancestry – is a crucial next step.
Automated Processing and Statistical Analysis of NMR spectra obtained from Arabidopsis thaliana Extracts
Authors: Mäkelä Valtteri , Vaahtera Lauri , Helminen Jussi , Koskela Harri , Brosché Mikael , Kilpeläinen Ilkka , Heikkinen Sami
Published: September 2019

To cope with vast amounts of data produced by metabolomic and mixture analysis using NMR, the employed analysis techniques and tools are very important. In this paper, we demonstrate quantitative 1H and 2D-JRES NMR analysis of Arabidopsis thaliana extracts utilizing our ImatraNMR and SimpeleNMR software to automate the processing the spectra, extracting data, and perform statistical analysis of the results. Metabolomes of four different strains of Arabidopsis thaliana are analyzed under control conditions and during acute ozone exposure. Key differences are identified between accessions Col-0 and Cvi-0 (epithionitriles, iberin nitrile) and ozone damage associated metabolite(s) can be identified. Sample stability is also addressed.
Automated Gene Data Integration with Databio
Authors: Reid Robert W , Ferrier Jacob W , Jay Jeremy J
Published: September 2019

Databio is capable of providing fast and accurate annotation of gene-oriented data sets, coupled with an integrated identifier conversion service to empower downstream data mining and computational analysis. Databio is enabled by fast real-time data structures applied to over 137 million unique identifiers, and uses automated heuristics to permit accurate data provenance without highly specialized knowledge and bioinformatics training.

Availability and Implementation

Freely available on the web at https://datab.io/. Source code and binaries are freely available for download at https://github.com/joiningdata/databio/, implemented in Go and supported on Linux, Windows, and macOS.
iSeqQC: A Tool for Expression-Based Quality Control in RNA Sequencing
Authors: Kumar Gaurav , Ertel Adam , Feldman George , Kupper Joan , Fortina Paolo
Published: September 2019

Quality Control in any high-throughput sequencing technology is a critical step, which if overlooked can compromise the data. A number of methods exist to identify biases during sequencing or alignment, yet not many tools exist to interpret biases due to outliers or batch effects. Hence, we developed iSeqQC, an expression-based QC tool that detects outliers either produced by batch effects due to laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers. It can be utilized either through command-line (Github: https://github.com/gkumar09/iSeqQC) or web-interface (http://cancerwebpa.jefferson.edu/iSeqQC). iSeqQC is a fast, light-weight, expression-based QC tool that detects outliers by implementing various statistical approaches.
Stat2 loss disrupts damage signalling and is protective in acute pancreatitis
Authors: Heath Helen , Britton Gary , Kudo Hiromi , Renney George , Ward Malcolm , Hutchins Robert , Foster Graham R. , Goldin Robert , Alazawi William
Published: September 2019

Severity of sterile inflammation, as seen in acute pancreatitis, is determined by damage-sensing receptors, signalling cascades and cytokine production. Stat2 is a type I interferon signalling mediator that also has interferon-independent roles in murine lipopolysaccharide-induced NF-κB-mediated sepsis. However its role in sterile inflammation is unknown. We hypothesised that Stat2 determines severity of non-infective inflammation in the pancreas.

Wild type (WT) and Stat2−/− mice were injected intraperitoneally with cerulein or L-arginine. Specific cytokine-blocking antibodies were used in some experiments. Pancreata and blood were harvested 1h and 24h after the final dose of cerulein and up to 96h post L-arginine. Whole-tissue phosphoproteomic changes were assessed using label-free mass spectrometry. Tissue-specific Stat2 effects were studied in WT/Stat2−/− bone-marrow chimera and using Cre-lox recombination to delete Stat2 in pancreatic and duodenal homeobox 1(Pdx1)-expressing cells.

Stat2−/− mice were protected from cerulein- and L-arginine-induced pancreatitis. Protection was independent of type I interferon signalling. Stat2−/− mice had lower cytokine levels including TNFα and IL-10 and reduced NF-kB nuclear localisation in pancreatic tissue compared to WT. Inhibition of TNFα improved (inhibition of IL-10 worsened) cerulein-induced pancreatitis in WT but not Stat2−/− mice. Phosphoproteomics showed down-regulation of mitogen-activated protein kinase (MAPK) mediators but accumulation of Ser412-phosphorylated Tak1. Stat2 deletion in Pdx1-expressing acinar cells (Stat2flox/Pdx1-cre) reduced pancreatic TNFα expression, but not histological injury or serum amylase. WT/Stat2−/− bone-marrow chimera were protected from pancreatitis irrespective of host or recipient genotype.

Stat2 loss results in disrupted signalling in pancreatitis, upstream of NF-κB in non-acinar and/or bone marrow derived cells.
Functional connectivity between the entorhinal and posterior cingulate cortices associated with navigation impairment following path integration in at-genetic-risk Alzheimer’s disease
Authors: Coughlan Gillian , Zhukovsky Peter , Puthusseryppady Vaisakh , Gillings Rachel , Minihane Anne-Marie , Cameron Donnie , Hornberger Michael
Published: September 2019

Navigation processes mediated selectively by the entorhinal cortex (EC) may be impaired in individuals with suspected preclinical Alzheimer’s disease (AD), but the clinical utility of navigation tests to detect such impairments remains to be established. In a sample of 64 individuals (32 e3e3 and 32 e3e4), we tested whether an existing paradigm, the Virtual Supermarket Test (VST), can reliably detect the presence or absence of the APOE e4 allele which accelerates amyloid plaque deposition in the brain. The present study assessed four major navigational processes that are subserved by functionally specialised cell groups located in AD vulnerable regions including the EC and examined the relationship between navigation process and regional functional connectivity (FC) given FC is a marker early AD-related tau seeding. While heading direction and spatial memory were unaffected by at-risk AD, clear altered navigational strategies following path integration were found on the VST in the e3e4 group. The APOE-sensitive VST measure correctly classified 77% of the APOE cohort. Including resting-state FC between the EC and the posterior cingulate cortex, a correlate of the path integration deficit in the APOE e4 group, the classification model increased the accuracy to 85%. Our findings show that at-genetic-risk AD selectively impairs path integration and biases self-reported spatial locations away from the centre and towards the boundary of a virtual environment. Importantly, this impairment is associated with reduced FC between the EC and the posterior cingulate cortex, which in turn informs the neurobiological mechanisms of at-genetic-risk of AD.
Modulation of peptidoglycan synthesis by recycled cell wall tetrapeptides
Authors: Hernández Sara B. , Dörr Tobias , Waldor Matthew K. , Cava Felipe
Published: September 2019

The bacterial cell wall is made of peptidoglycan (PG), a polymer that is essential for maintenance of cell shape and survival. During growth, bacteria remodel their PG, releasing fragments that are predominantly re-internalized by the cell, where they are recycled for synthesis of new PG. Although the PG recycling pathway is widely conserved, its components are not essential and its roles in cell wall homeostasis are not well-understood. Here, we identified LdcV, aVibrio choleraeL,D-carboxypeptidase that cleaves the terminal D-Alanine from recycled murotetrapeptides. In the absence ofldcV, recycled tetrapeptides accumulated in the cytosol, leading to two toxic consequences for the cell wall. First, incorporation of tetrapeptide-containing PG precursors into the cell wall led to reduction in D,D-cross-linkage between stem peptides, diminishing PG integrity. Second, tetrapeptide accumulation led to a decrease in canonical UDP-pentapeptide precursors, reducing PG synthesis. Thus, LdcV and the recycling pathway promote optimal cell wall assembly and composition. Furthermore, Ldc substrate preference for murotetrapeptides containing canonical (D-Alanine) vs. non-canonical (D-Methionine) D-amino acids is conserved, suggesting that accumulation of tetrapeptide recycling intermediates may modulate PG homeostasis in environments enriched in non-canonical-muropeptides via substrate competition.
Muntjac chromosome evolution and architecture
Authors: Mudd Austin B. , Bredeson Jessen V. , Baum Rachel , Hockemeyer Dirk , Rokhsar Daniel S.
Published: September 2019

Abstract

Despite their recent divergence, muntjac deer show striking karyotype differences. Here we describe new chromosome-scale genome assemblies for the Chinese and Indian muntjacs,Muntiacus reevesi(2n=46) andMuntiacus muntjak(2n=6/7), and analyze their evolution and architecture. We identified six fusion events shared by both species relative to the cervid ancestor and therefore present in the muntjac common ancestor, six fusion events unique to theM. reevesilineage, and twenty-six fusion events unique to theM. muntjaklineage. One of theseM. muntjakfusions reverses an earlier fission in the cervid lineage. Although comparative Hi-C analysis revealed differences in long-range genome contacts and A/B compartment structures, we discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. A small number of genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype. Analysis of muntjac genomes reveals new insights into this unique case of rapid karyotype evolution and the resulting biological variation.
A large-scale chemical-genetic strategy to design antimicrobial combination chemotherapy forMycobacterium tuberculosis
Authors: Johnson Eachan O , Office Emma , Kawate Tomohiko , Orzechowski Marek , Hung Deborah T
Published: September 2019

The efficacies of all antibiotics against tuberculosis are eventually eroded by resistance. New strategies to discover drugs or drug combinations with higher barriers to resistance are needed. Previously, we reported the application of a large-scale chemical-genetic interaction screening strategy called PROSPECT to the discovery of newMycobacterium tuberculosisinhibitors, which resulted in identification of the small molecule BRD-8000, an inhibitor of a novel target, EfpA. Leveraging the chemical genetic interaction profile of BRD-8000, we identified BRD-9327, another, structurally distinct small molecule EfpA inhibitor. We show that the two compounds are synergistic and display collateral sensitivity because of their distinct modes of action and resistance mechanisms. High-level resistance to one increases the sensitivity to and reduces the emergence of resistance to the other. Thus, the combination of BRD-9327 and BRD-8000 represents a proof-of-concept for the novel strategy of leveraging chemical-genetics in the design of antimicrobial combination chemotherapy in which mutual collateral sensitivity is exploited.
Clinical severity in Fanconi anemia correlates with residual function of FANCB missense variants
Authors: Jung Moonjung , Ramanagoudr-Bhojappa Ramanagouda , van Twest Sylvie , Rosti Rasim Ozgur , Murphy Vincent , Tan Winnie , Donovan Frank X. , Lach Francis P. , Kimble Danielle C. , Jiang Caroline S. , Vaughan Roger , Mehta Parinda , Pierri Filomena , Doufour Carlo , Auerbach Arleen D. , Deans Andrew J. , Smogorzewska Agata , Chandrasekharappa Settara C.
Published: September 2019

Fanconi anemia (FA) is the most common genetic cause of bone marrow failure, and is caused by inherited pathogenic variants in any of 22 genes. Of these, onlyFANCBis X-linked. We describe a cohort of 19 children withFANCBvariants, from 16 families of the International Fanconi Anemia Registry (IFAR). Those withFANCBdeletion or truncation demonstrate earlier than average onset of bone marrow failure, and more severe congenital abnormalities compared to a large series of FA individuals in the published reports. This reflects the indispensable role of FANCB protein in the enzymatic activation of FANCD2 monoubiquitination, an essential step in the repair of DNA interstrand crosslinks. ForFANCBmissense variants, more variable severity is associated with the extent of residual FANCD2 monoubiquitination activity. We used transcript analysis, genetic complementation, and biochemical reconstitution of FANCD2 monoubiquitination to determine the pathogenicity of each variant. Aberrant splicing and transcript destabilization was associated with two missence variants. Individuals carrying missense variants with drastically reduced FANCD2 monoubiquitination in biochemical and/or cell-based assays showed earlier onset of hematologic disease and shorter survival. Conversely, variants with near-normal FANCD2 monoubiquitination were associated with more favorable outcome. Our study reveals a genotype-phenotype correlation within the FA-B complementation group of FA, where severity is linked to the extent of residual FANCD2 monoubiquitination.

KEY POINTS

X-linkedFANCBpathogenic variants predominantly cause acute, early onset bone marrow failure and severe congenital abnormalities

Biochemical and cell-based assays with patient variants reveal functional properties of FANCB that associate with clinical severity
Golgi-localized PAQR4 mediates Anti-apoptotic Ceramidase Activity in Breast Cancer
Authors: Pedersen Line , Panahandeh Pouda , Siraji Muntequa Ishtiaq , Knappskog Stian , Lønning Per Eystein , Zhu Qingzhang , Gordillo Ruth , Scherer Philipp E. , Molven Anders , Teigen Knut , Halberg Nils
Published: September 2019

The metabolic network of sphingolipids plays important roles in cancer biology. Prominent sphingolipids include ceramides and sphingosine-1-phosphate that regulate multiple aspects of growth, apoptosis and cellular signaling. Although many significant enzymatic regulators of the sphingolipid pathway have been described in detail, the list is currently incomplete. Here, we applied a systemic approach to identify and molecularly define progestin and adipoQ receptor family member IV (PAQR4) as a Golgi-localized ceramidase. We find PAQR4 to be ∼5 fold upregulated in breast cancer compared to matched control tissue and that its overexpression correlate with disease-specific survival rates in breast cancer. PAQR4 is a seven transmembrane protein, and depletion of PAQR4 leads to cellular apoptosis through accumulation of ceramides. Our findings establish PAQR4 as Golgi-localized ceramidase required for cellular growth in breast cancer.
Naturally Occurring Shorter and Tumor-associated Mutant RNF167 Variants Facilitates Lysosomal Exocytosis and Plasma Membrane Resealing
Authors: Nair Sreeja V. , Narendradev Nikhil Dev , Nambiar Rithwik P. , Kumar Rakesh , Srinivasula Srinivasa M.
Published: September 2019

Lysosomal exocytosis and resealing of damaged plasma membrane play critical roles in physiological and pathological processes, including, restoration of cellular homeostasis and tumor invasion. However, to-date, only a few regulatory molecules of these biological processes have been identified. Moreover, no mutations in any of the known regulators of lysosomal exocytosis in primary tumors of patients have been characterized. Here we demonstrate that RNF167, a lysosomal associated ubiquitin ligase, negatively regulates lysosomal exocytosis by inducing perinuclear clustering of lysosomes. Importantly, we also characterized a set of novel natural mutations in RNF167, which are commonly found in diverse tumor types. We found that RNF167-K97N mutant, unlike the wild-type, localizes in the cytoplasm and does not promote perinuclear lysosomal clustering and that cells expressing RNF167-K97N exhibit dispersed lysosomes, increased exocytosis, and enhanced plasma membrane repair. Interestingly, these functional features of RNF167-K97N were shared with a naturally occurring short version of RNF167, i.e. isoform b. In brief, the results presented here reveal a novel role of RNF167 as well as its natural variants, RNF167-K97N and RNF167-b as an upstream regulator of lysosomal exocytosis and plasma membrane resealing which might play an important role in organelle dynamics or tumor progression or both.
Fluctuation-Based Super-Resolution Traction Force Microscopy
Authors: Stubb Aki , Laine Romain F. , Guzmán Camilo , Henriques Ricardo , Jacquemet Guillaume , Ivaska Johanna
Published: September 2019

Cellular mechanics play a crucial role in tissue morphogenesis and homeostasis and are often misregulated in disease. Traction force microscopy (TFM) is one of the key methods that has enabled researchers to study fundamental aspects of mechanobiology; however, the power of TFM is limited by poor resolution and low throughput. Here, we propose a simplified protocol and imaging strategy, relying on super-resolution microscopy enabled by fluorophore fluctuation analysis, to enhance the output of TFM, by increasing both bead density as well as the accuracy of bead tracking in TFM gels. Our analysis pipeline can be used on either camera-based confocal or widefield microscopes and is fully compatible with available TFM analysis software. In addition, we demonstrate that our workflow can be used to gain biologically relevant information and is suitable for long-term live measurement of traction forces even in light-sensitive cells. Finally, we propose that our strategy could be used to considerably simplify the implementation of TFM screens. Our streamlined protocol can be performed with minimal hardware and software investment, and has the potential to standardize high-resolution TFM.
SCAR FORMATION AND DECREASED CARDIAC FUNCTION FOLLOWING ISCHEMIA/REPERFUSION INJURY IN 1-MONTH-OLD SWINE
Authors: Agnew Emma J , Velayutham Nivedhitha , Ortiz Gabriela Matos , Alfieri Christina M , Moore Victoria , Riggs Kyle W , Baker R. Scott , Gibson Aaron M , Ponny Sithara Raju , Alsaied Tarek , Zafar Farhan , Yutzey Katherine E
Published: September 2019

Studies in mice show a brief neonatal period of cardiac regeneration with minimal scar formation. Less is known about reparative mechanisms in large mammals. A transient cardiac injury approach (ischemia/reperfusion, IR) was used in weaned postnatal day (P)30 pigs, to assess regenerative repair in young large mammals. Female and male P30 pigs were subjected to cardiac ischemia (1 hour) by occlusion of the left anterior descending artery followed by reperfusion, or to sham operation. Following IR, myocardial damage occurred, with cardiac ejection fraction significantly decreased 2 hours post-ischemia. No improvement or worsening of cardiac function to the 4 week study end-point was observed. Histology demonstrated cardiomyocyte (CM) cell cycling at 2-months-of-age in multinucleated CMs in both sham-operated and IR pigs. Regional scar formation and inflammation in the epicardial region proximal to injury were observed 4 weeks post-IR. Sex differences were found, suggestive of females creating a greater fibrotic response with worse cardiac function, highlighting the importance of representing both sexes in cardiac injury studies. Together, our results describe an effective novel cardiac injury model in P30 swine, at a time when CMs are still cycling. Pigs subjected to IR show myocardial damage with a prolonged decrease in cardiac function, formation of a small, regional scar with increased inflammation. These data demonstrate that P30 pigs do not regenerate myocardium, even in the presence of CM mitotic activity, but form a scar after transient IR injury.

NEW & NOTEWORTHY

Here, we report for the first time ischemia/reperfusion (IR) cardiac injury in 1-month-old (P30) pigs. This model of IR injury highlights lack of cardiac regeneration, even in the presence of cardiomyocyte (CM) cell cycling in young swine. An effective injury approach is described for use in large mammals to investigate cardiac function, CM cell cycling, extracellular matrix (ECM) remodeling, and gene expression changes, while highlighting the importance of studying both sexes.
Neural Mechanisms for Executive Control of Speed-Accuracy Tradeoff
Authors: Reppert Thomas R. , Heitz Richard P. , Schall Jeffrey D.
Published: September 2019

The balance of speed with accuracy requires error detection and performance adaptation. To date, neural concomitants of these processes have been investigated only with noninvasive measures. To provide the first neurophysiological description, macaque monkeys performed visual search under cued speed accuracy tradeoff (SAT). Monkeys changed SAT emphasis immediately after a cued switch while neuron discharges were sampled in medial frontal cortex area supplementary eye field (SEF). A multiplicity of SEF neurons signaled production of choice errors and timing errors. Modulation of SEF activity after choice errors predicted production of un-rewarded corrective saccades. Modulation of activity after timing errors signaled reward prediction error. Adaptation of performance during SAT of visual search was accomplished through pronounced changes in neural state from before search array presentation until after reward delivery. These results contextualize previous findings using noninvasive measures, complement neurophysiological findings in visuomotor structures, endorse the role of medial frontal cortex as a critic relative to the actor instantiated in visuomotor structures, and extend our understanding of the distributed neural mechanisms of SAT.

HIGHLIGHTS

Medial frontal cortex enables post-error adjustment during SAT

Choice and timing errors were signaled by partially overlapping neural pools

Medial frontal cortex can proactively modulate visuomotor processes

Medial frontal cortex is to visuomotor circuits as critic to actor
Food-borne mycotoxin hazards in the Kenyan market-a retrospective study
Authors: Kibugu James Karuku , Mburu David , Munga Leonard Karongo , Kurgat Richard , Mukasa Bernard , Lusweti Fransisca Naliaka , Grace Delia , Lindahl Johanna
Published: September 2019

Mycotoxin contamination data (n=1818) in feed and food from major laboratories were categorized into hazardous and non-hazardous using contaminants regulatory limits, analyzed by logistic regression and chi-square test to identify potential health hazards. Feeds were most contaminated, with 64% and 39% having total aflatoxin (AFT) levels above Kenyan and American standards respectively. Peanuts, the most contaminated food, had 61% and 47% of samples failing Kenyan and American AFT standards respectively. By European standards, wheat had highest AFT contamination rate of 84%. Half of baby foods sampled had AFT level above Kenyan and European standards. Maize had failure rates of 20% (Kenyan standard), 14% (American standard) and 25% (European standard) for AFT. We observed high frequency of mycotoxins (AFT, aflatoxin M1, zearalenone, T-2 toxin, ochratoxin A, fumonisins, deoxynivalenol) and AFT hazards with significantly (p<0.001) higher failure rates in wheat, peanuts, mycotoxin hazards in dairy products in that order (European standard). Failure rates were significantly (p<0.001) higher in feed ingredients (p<0.01), baby foods (p<0.05), maize (p<0.001), fodder (p<0.05) for mycotoxins, and compound feeds, peanuts, wheat (p<0.001), feed ingredients, baby foods (p<0.01), maize (p<0.001), fodder (0.01), in that order, for AFT (American standard). Fail rates were significantly higher for mycotoxins in compound feeds, feed ingredients, peanuts, wheat, baby foods, maize (p<0.001), herbal health drink (p<0.01), and for AFT in compound feeds, feed ingredients, peanuts, wheat (p<0.001), baby foods (p<0.01), herbal health drink (p<0.05), maize (p<0.001) in that order (Kenyan standard). High frequency of mycotoxin and AFT hazards in maize, baby foods, herbal health drink and aflatoxin M1 in dairy products was noted. Detection by different laboratories varied significantly (p<0.001). Health and economic implications of this and limitations of current food safety standards are discussed. Humans and animals in Kenya are chronically exposed to mycotoxin hazards that require constant surveillance and strict regulation.
Unpacking the Allee effect: determining individual-level mechanisms that drive global population dynamics
Authors: Fadai Nabil T. , Johnston Stuart T. , Simpson Matthew J.
Published: September 2019

We present a solid theoretical foundation for interpreting the origin of Allee effects by providing the missing link in understanding how local individual-based mechanisms translate to global population dynamics. Allee effects were originally proposed to describe population dynamics that cannot be explained by exponential and logistic growth models. However, standard methods often calibrate Allee effect models to match observed global population dynamics without providing any mechanistic insight. By introducing a stochastic individual-based model, with proliferation, death, and motility rates that depend on local density, we present a modelling framework that translates particular global Allee effects to specific individual-based mechanisms. Using data from ecology and cell biology, we unpack individual-level mechanisms implicit in an Allee effect model and provide simulation tools for others to repeat this analysis.
AKrüppel-like factor 1(KLF1) mutation associated with severe congenital dyserythropoietic anemia alters its DNA-binding specificity
Authors: Kulczynska Klaudia , Bieker James J , Siatecka Miroslawa
Published: September 2019

Krüppel-like factor 1 (KLF1/EKLF) is a transcription factor that globally activates genes involved in erythroid cell development. Various mutations are identified in the human KLF1 gene. The E325K mutation causes congenital dyserythropoietic anemia (CDA) type IV, characterized by severe anemia and non-erythroid-related symptoms. The CDA mutation is in the second zinc finger of KLF1 at a position functionally involved in its interactions with DNA. The molecular parameters of how CDA-KLF1 exerts its biological effects have not been addressed. Here, using an in vitro selection strategy we determined the preferred DNA-binding site for CDA-KLF1. Binding to the deduced consensus sequence is supported by in vitro gel shifts and by in vivo functional reporter gene studies. Two significant changes compared to WT binding are observed: G is selected as the middle nucleotide and the 3’-portion of the consensus sequence is more degenerate. As a consequence CDA-KLF1 did not bind the WT consensus sequence. However, activation of ectopic sites is promoted. Continuous activation of WT target genes occurs if they fortuitously contain the novel CDA site nearby. Our findings provide a molecular understanding of how a single mutation in the KLF1 zinc finger exerts an effects on erythroid physiology in CDA type IV.