bluuebunny/crossref_metadata_2025 huggingface dataset:
Streptococcus pyogenes evades adaptive immunity through specific IgG glycan hydrolysis
Authors: Naegeli Andreas , Bratanis Eleni , Karlsson Christofer , Shannon Oonagh , Kalluru Raja , Linder Adam , Malmström Johan , Collin Mattias
Published: May 2019

Streptococcus pyogenes (Group A streptococcus; GAS) is a human pathogen causing diseases from uncomplicated tonsillitis to life-threatening invasive infections. GAS secretes EndoS, an endoglycosidase that specifically cleaves the conserved N-glycan on IgG antibodies. In vitro, removal of this glycan impairs IgG effector functions, but its relevance to GAS infection in vivo is unclear. Using targeted mass spectrometry, we characterized the effects of EndoS on host IgG glycosylation during the course of infections in humans. Substantial IgG glycan hydrolysis occurred at the site of infection and systemically in the severe cases. We demonstrated decreased resistance to phagocytic killing of GAS lacking EndoS in vitro and decreased virulence in a mouse model of invasive infection. This is the first described example of specific bacterial IgG glycan hydrolysis during infection and thereby verifies the hypothesis that EndoS modifies antibodies in vivo. This mechanisms of immune evasion could have implications for treatment of severe GAS infections and for future efforts at vaccine development.
Multi-Rees algebras and toric dynamical systems
Authors: Cox David , Lin Kuei-Nuan , Sosa Gabriel
Published: May 2019

This paper explores the relation between multi-Rees algebras and ideals that arise in the study of toric dynamical systems from the theory of chemical reaction networks.
On the structure of ideals and multipliers: A unified approach
Authors: Mbekhta Mostafa , Neufang Matthias
Published: May 2019

We study the structure of one-sided ideals in a Banach algebra

A

\mathcal {A}

. We find very general conditions under which any left (right) ideal is of the form

A

q

\mathcal {A} q

(

q

A

q \mathcal {A}

) for some idempotent right (left) multiplier on

A

\mathcal {A}

. We further show that a large class of one-sided multipliers can be realized as a product of an invertible and an idempotent multiplier. Applying our results to algebras over locally compact quantum groups and

C
∗

C^*

-algebras, we demonstrate that our approach generalizes and unifies various theorems from abstract harmonic analysis and operator algebra theory. In particular, we generalize results of Bekka (and Reiter), Berglund, Forrest, and Lau–Losert. We also deduce the Choquet–Deny theorem for compact groups as an application of our approach. Moreover, we answer, for a certain class of measures on a compact group, a question of Ülger which, in the abelian case, goes back to Beurling (1938).
Employment Quality: An Overlooked Determinant of Workers’ Health and Well-being?
Authors: Vanroelen Christophe
Published: May 2019

In the past four decades, high-income countries have seen a thorough socio-economic restructuring with important implications for the jobs of many workers, including health- and safety-related aspects. Much attention has been paid to psychosocial risks related to intrinsic features of contemporary work tasks, while the occupational health and safety consequences of ‘new’ conditions and relations of employment have remained neglected. This relative neglect is unjustified given the disrupting nature of many contemporary forms of employment. In this commentary, I introduce the concept of ‘employment quality’ as a novel approach towards measuring employment-related OHS risks. Employment quality involves a ‘typological approach’ towards employment arrangements, identifying five employment types in European labour markets, showing a distinct profile in terms of health-related employment characteristics. Moreover, these types align with segmented labour market theory, have a clear socio-economic profile, and show strong associations with workers’ self-reported health.
Do patients with anomalous origin of the left coronary artery benefit from an early repair of the mitral valve?
Authors: Weixler Viktoria H M , Zurakowski David , Baird Christopher W , Guariento Alvise , Piekarski Breanna , del Nido Pedro J , Emani Sitaram
Published: May 2019

OBJECTIVES

The aim of this study was to determine mid-term outcomes of patients with anomalous origin of the left coronary artery from the pulmonary artery undergoing coronary repair only (group A) or simultaneous mitral valve repair (group B).

METHODS

Patients with anomalous origin of the left coronary artery from the pulmonary artery who underwent surgery from 2000 to 2017 were reviewed. Mitral regurgitation (MR) grade (none, mild, moderate, severe), left ventricular (LV) function [ejection fraction (EF): <40%, 40–50%, >50%] and LV Z-scores (long axis) were assessed preoperatively and at last visit. Outcomes were compared within/between the groups using the Wilcoxon signed-rank test.

RESULTS

Of 58 patients (67% women; median age 4.4 months), 39 patients were in group A (67%) and 19 patients in group B (33%). The median hospital stay (11 days, interquartile range 5–18) and average follow-up time (2.6 ± 0.5 years) did not differ significantly between the groups (P > 0.05). Four patients in group A (10.3%) underwent mitral valve reintervention. The median MR grade differed significantly between the groups preoperatively (2 vs 3, P < 0.001) but not at the last visit (2 vs 2, P = 0.88); both groups improved significantly (P = 0.021, P < 0.001). EF grade (<40%, 40–50%, >50%) did not differ significantly between the groups at baseline (group A: 38%/23%/38% vs group B: 58%/10%/32%, P = 0.32) or at last visit (group A: 18%/15%/67% vs group B: 26%/16%/58%, P = 0.75); both groups improved significantly (P = 0.004, P = 0.014). The mean LV Z-scores for groups A and B were 3.1 ± 0.5 and 4.5 ± 0.6 before surgery (P < 0.05) and 1.5 ± 0.3 and 2.7 ± 0.6 at last visit (P = 0.77).

CONCLUSIONS

The repair of anomalous origin of the left coronary artery from the pulmonary artery is associated with improvement in MR, EF and LV dimensions. However, in cases of ≥moderate MR, the risk of mitral valve reintervention may be higher in patients undergoing coronary transfer only.
The low return to English fluency during the Age of Mass Migration☆
Authors: Ward Zachary
Published: May 2019

English skills are highly valuable for today’s immigrants, but has this always been the case? I estimate the premium for English fluency and the rate of language acquisition in the early 20th century US using new linked data on over two hundred thousand immigrants. Few early 20th century immigrants arrived with English proficiency, yet many acquired language skills rapidly after arrival. Based on individual fixed effects, acquiring English fluency was associated with a small upgrade in occupational income. The results suggest that English fluency was less important for economic assimilation in the early 20th century than in recent decades.
A novel six-phage cocktail reducesPectobacterium atrosepticumsoft rot infection in potato tubers under simulated storage conditions
Authors: Carstens Alexander Byth , Djurhuus Amaru Miranda , Kot Witold , Hansen Lars Hestbjerg
Published: May 2019

Pectobacterium atrosepticum is a species of plant pathogenic bacteria responsible for significant losses in potato production worldwide. Pectobacterium atrosepticum can cause blackleg disease on potato stems as well as the tuber disease termed potato soft rot. Methods for the effective control of these diseases are limited and are primarily based on good agricultural practices. Bacteriophages, viruses of bacteria, could be used as an alternative, environmentally friendly, control measure. Here, we describe the isolation and characterization of 29 phages virulent to P. atrosepticum. The phages belong to 12 different species based on a 95% sequence identity cut-off. Furthermore, based on sequence diversity and propagation results, we selected six of these phages to form a phage cocktail. The phages in the cocktail was tested on a number of P. atrosepticum strains in order to determine their host range. The phages was found to lyse 93% of the tested strains. The cocktail was subsequently tested for its effectiveness in combatting potato soft rot under simulated storage conditions. Use of the phage cocktail reduced both disease incidence and disease severity by 61% and 64%, respectively, strongly indicating that phage biocontrol has the potential to reduce the economic impact of soft rot in potato production.
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
Authors: Nicholls Samuel M , Quick Joshua C , Tang Shuiquan , Loman Nicholas J
Published: May 2019

Background

Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition.

Findings

We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning.

Conclusions

We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.
Postexposure Administration of a Yersinia pestis Live Vaccine for Potentiation of Second-Line Antibiotic Treatment Against Pneumonic Plague
Authors: Zauberman Ayelet , Gur David , Levy Yinon , Aftalion Moshe , Vagima Yaron , Tidhar Avital , Chitlaru Theodor , Mamroud Emanuelle
Published: May 2019

Pneumonic plague, caused by Yersinia pestis, is a rapidly progressing contagious disease. In the plague mouse model, a single immunization with the EV76 live attenuated Y. pestis strain rapidly induced the expression of hemopexin and haptoglobin in the lung and serum, both of which are important in iron sequestration. Immunization against a concomitant lethal Y. pestis respiratory challenge was correlated with temporary inhibition of disease progression. Combining EV76-immunization and second-line antibiotic treatment, which are individually insufficient, led to a synergistic protective effect that represents a proof of concept for efficient combinational therapy in cases of infection with antibiotic-resistant strains.
Diagnosis and Management of Rhabdomyolysis in the Absence of Creatine Phosphokinase: A Medical Record Review
Authors: Chandel Abhimanyu , Brusher Kara , Hall Victoria , Howard Robin S , Clark Paul A
Published: May 2019

Introduction

Rhabdomyolysis is often encountered in austere environments where the diagnosis can be challenging due to the expense or unavailability of creatine phosphokinase (CPK) testing. CPK concentration ≥5,000 U/L has previously been found to be a sensitive marker for progression to renal failure. This study sought to propose a model utilizing an alternate biomarker to allow for the diagnosis and monitoring of clinically significant rhabdomyolysis in the absence of CPK.

Materials and Methods

We performed a retrospective chart review of 77 patients admitted to a tertiary medical center with a primary diagnosis of rhabdomyolysis. A linear regression model with aspartate aminotransferase (AST) as the independent variable was developed and used to predict CPK ≥5,000 U/L on admission and CPK values on subsequent hospital days. The study was approved and monitored by the Institutional Review Board at Walter Reed National Military Medical Center.

Results

Ln(AST) explained over 80% of the variance in ln(CPK) (adjusted R2 = 0.802). The diagnostic accuracy to predict CPK ≥5,000 U/L was high (AUC 0.959; 95% CI: 0.921–0.997, P < 0.001). A cut point of AST ≥110 U/L in our study population had a 97.1% sensitivity and an 85.7% specificity for the detection of a CPK value ≥5,000 U/L. The agreement between actual CPK and predicted CPK for subsequent days of hospitalization was fair with an intraclass correlation coefficient of 0.52 (95% CI: 0.38–0.63). The developed model based on day 1 data tended to overpredict CPK values on subsequent hospital days.

Conclusions

We propose a threshold concentration of AST that has an excellent sensitivity for detecting CPK concentration ≥5,000 U/L on day of admission in a patient population with a diagnosis of rhabdomyolysis. A formula with a fair ability to predict CPK levels based on AST concentrations on subsequent hospital days was also developed.
Mosquito and human hepatocyte infections with Plasmodium ovale curtisi and Plasmodium ovale wallikeri
Authors: Kristan Mojca , Thorburn Samuel G , Hafalla Julius C , Sutherland Colin J , Oguike Mary C
Published: May 2019

Background

Human ovale malaria is caused by the two closely related species, Plasmodium ovale curtisi and P. ovale wallikeri. Both species are known to relapse from quiescent hepatic forms months or years after the primary infection occurred. Although some studies have succeeded in establishing mosquito transmission for ovale malaria, none have specifically described transmission and human hepatocyte infection of both sibling species.

Methods

Here we describe a simplified protocol for successful transmission of both P. ovale curtisi and P. ovale wallikeri to Anopheles coluzzii mosquitoes and streamlined monitoring of infection using sensitive parasite DNA detection, by loop-activated amplification, in blood-fed mosquitoes.

Results

In one experimental infection with P. ovale curtisi and one with P. ovale wallikeri, viable sporozoites were isolated from mosquito salivary glands and used to successfully infect cultured human hepatocytes.

Conclusions

This protocol provides a method for the utilisation of pretreatment clinical blood samples from ovale malaria patients, collected in EDTA, for mosquito infection studies and generation of the hepatic life cycle stages of P. ovale curtisi and P. ovale wallikeri. We also demonstrate the utility of loop-activated amplification as a rapid and sensitive alternative to dissection for estimating the prevalence of infection in Anopheles mosquitoes fed with Plasmodium-infected blood.
Untargeted Metabolomics Based on GC-MS and Chemometrics: A New Tool for the Early Diagnosis of Strawberry Anthracnose Caused byColletotrichum theobromicola
Authors: Dai Tan , Chang Xunian , Hu Zhihong , Liang Li , Sun Mingyou , Liu Pengfei , Liu Xili
Published: May 2019

To prevent the spread of anthracnose in strawberry plants and characterize the metabolic changes occurring during plant–pathogen interactions, we developed a method for the early diagnosis of disease based on an analysis of the metabolome by gas chromatography-mass spectrometry. An examination of the metabolic profile revealed 189 and 202 total ion chromatogram peaks for the control and inoculated plants, respectively. A partial least squares discriminant analysis (PLS-DA) model was conducted for the reliable and accurate discrimination between healthy and diseased strawberry plants, even in the absence of disease symptoms (e.g., early stages of infection). ANOVA (analysis of variance) and orthogonal partial least squares analysis (OPLS) identified 20 metabolites as tentative biomarkers of Colletotrichum theobromicola infection (e.g., citric acid, d-xylose, erythrose, galactose, gallic acid, malic acid, methyl α-galactopyranoside, phosphate, and shikimic acid). At least some of these potential biomarkers may be applicable for the early diagnosis of anthracnose in strawberry plants. Moreover, these metabolites may be useful for characterizing pathogen infections and plant defense responses. This study confirms the utility of metabolomics research for developing diagnostic tools and clarifying the mechanism underlying plant–pathogen interactions. Furthermore, the data presented herein may be relevant for developing new methods for preventing anthracnose in strawberry seedlings cultivated under field conditions.
Liberibacter crescens Is a Cultured Surrogate for Functional Genomics of Uncultured Pathogenic ‘Candidatus Liberibacter’ spp. and Is Naturally Competent for Transformation
Authors: Jain M. , Cai L. , Fleites L. A. , Munoz-Bodnar A. , Davis M. J. , Gabriel D. W.
Published: May 2019

‘Candidatus Liberibacter’ spp. are uncultured insect endosymbionts and phloem-limited bacterial plant pathogens associated with diseases ranging from severe to nearly asymptomatic. ‘Ca. L. asiaticus’, causal agent of Huanglongbing or citrus “greening,” and ‘Ca. L. solanacearum’, causal agent of potato zebra chip disease, respectively threaten citrus and potato production worldwide. Research on both pathogens has been stymied by the inability to culture these agents and to reinoculate into any host. Only a single isolate of a single species of Liberibacter, Liberibacter crescens, has been axenically cultured. L. crescens strain BT-1 is genetically tractable to standard molecular manipulation techniques and has been developed as a surrogate model for functional studies of genes, regulatory elements, promoters, and secreted effectors derived from the uncultured pathogenic Liberibacters. Detailed, step-by-step, and highly reproducible protocols for axenic culture, transformation, and targeted gene knockouts of L. crescens are described. In the course of developing these protocols, we found that L. crescens is also naturally competent for direct uptake and homology-guided chromosomal integration of both linear and circular plasmid DNA. The efficiency of natural transformation was about an order of magnitude higher using circular plasmid DNA compared with linearized fragments. Natural transformation using a replicative plasmid was obtained at a rate of approximately 900 transformants per microgram of plasmid, whereas electroporation using the same plasmid resulted in 6 × 104 transformants. Homology-guided marker interruptions using either natural uptake or electroporation of nonreplicative plasmids yielded 10 to 12 transformation events per microgram of DNA, whereas similar interruptions using linear fragments via natural uptake yielded up to 34 transformation events per microgram of DNA.
Evidence for convergent evolution of ultrasonic hearing in toothed whales (Cetacea: Odontoceti)
Authors: Racicot Rachel A. , Boessenecker Robert W. , Darroch Simon A. F. , Geisler Jonathan H.
Published: May 2019

Toothed whales (Cetacea: Odontoceti) are the most diverse group of modern cetaceans, originating during the Eocene/Oligocene transition approximately 38 Ma. All extant odontocetes echolocate; a single origin for this behaviour is supported by a unique facial source for ultrasonic vocalizations and a cochlea adapted for hearing the corresponding echoes. The craniofacial and inner ear morphology of Oligocene odontocetes support a rapid (less than 5 Myr) early evolution of echolocation. Although some cranial features in the stem odontocetes
Simocetus
and
Olympicetus
suggest an ability to generate ultrasonic sound, until now, the bony labyrinths of taxa of this grade have not been investigated. Here, we use µCT to examine a petrosal of a taxon with clear similarities to
Olympicetus avitus
. Measurements of the bony labyrinth, when added to an extensive dataset of cetartiodactyls, resulted in this specimen sharing a morphospace with stem whales, suggesting a transitional inner ear. This discovery implies that either the lineage leading to this
Olympicetus
­-like taxon lost the ability to hear ultrasonic sound, or adaptations for ultrasonic hearing evolved twice, once in xenorophids and again on the stem of the odontocete crown group. We favour the latter interpretation as it matches a well-documented convergence of craniofacial morphology between xenorophids and extant odontocetes.
A more principled use of the
p
-value? Not so fast: a critique of Colquhoun’s argument
Authors: Arandjelović Ognjen
Published: May 2019

The usefulness of the statistic known as the
p
-value, as a means of quantifying the strength of evidence for the presence of an effect from empirical data has long been questioned in the statistical community. In recent years, there has been a notable increase in the awareness of both fundamental and practical limitations of the statistic within the target research fields and especially biomedicine. In this article, I analyse the recently published article (Colquhoun 2017
R. Soc. open sci.
4
, 171085 (
doi:10.1098/rsos.171085
)) which, in summary, argues that with a better understanding and thus more appropriate use of the statistic, many of the aforementioned limitations can be addressed. In particular, I demonstrate that the (often implicit) premises of this counterargument are questionable, in some cases arguably inconsistent, and that therefore the counterargument provides little if any justification for the continued use of the
p
-value. Additionally, my analysis should help researchers seeking to interpret their empirical data by illustrating the nuanced nature and the multiplicity of statistical, methodological and epistemological issues which must be considered in this process.
Using 3D modelling and printing to study avian cognition from different geometric dimensions
Authors: Yang Canchao , Liang Wei , Møller Anders Pape
Published: May 2019

Studying animal cognition is meaningful because it helps us understand how animals adapt to the natural environment. Many birds build nests, clean their nests and reject foreign objects from their nests, which provide an optimal opportunity for studying their cognition toward foreign objects in nests. However, hand-made models used in previous studies have many deficiencies that considerably constrain our capacity to understand the evolution of avian cognition of foreign objects because they are unquantifiable and dependent on different features. We established a 3D modelling and printing method to manipulate one geometric dimension of a model while controlling for others, which allowed us to investigate avian cognition for different dimensions independently. Here we introduce this method, conduct an empirical study as an example, and discuss its applications to further studies.
Preparation of aminated chitosan microspheres by one-pot method and their adsorption properties for dye wastewater
Authors: Meng Jian , Cui Jianlan , Yu Siyuan , Jiang Hui , Zhong Congshan , Hongshun Ji
Published: May 2019

Polyamine chelating adsorbents have a good removal effect on dye wastewater. In this study, small molecule triethylenetetramine and macromolecular poly(ethylene imine) were selected as aminated reagent, and two kinds of aminated chitosan microspheres, TETA-CTSms and PEI-CTSms, were obtained by emulsion cross-linking method. The microspheres were fully characterized by FTIR, SEM, XRD, EDS and TGA. EDS results showed that the N content of the PEI-CTSms and TETA-CTSms microspheres increased significantly after the cross-linking reaction and can reach 5.7 wt% and 7.3 wt%, respectively. Adsorption experiments confirmed that TETA-CTSms and PEI-CTSms showed greater adsorption characteristics for anionic dye reactive yellow (RY) in aqueous solutions compared with CTSms, and the adsorption capacity per unit area was increased by 39.11% and 88.56%, respectively. The adsorption capacity of aminated microspheres for RY decreased with the increase of pH. The adsorption kinetics conformed to the pseudo-second-order model, and the adsorption process was in accordance with the Langmuir isotherm model. The negative value of Δ
G
confirmed that the adsorption process was spontaneous, and the dye adsorption was a multiple process dominated by chemical chelating and physical adsorption.
The variability of song variability in zebra finch (Taeniopygia guttata) populations
Authors: Lansverk Allison L. , Schroeder Katie M. , London Sarah E. , Griffith Simon C. , Clayton David F. , Balakrishnan Christopher N.
Published: May 2019

Birdsong is a classic example of a learned social behaviour. Song behaviour is also influenced by genetic factors, and understanding the relative contributions of genetic and environmental influences remains a major goal. In this study, we take advantage of captive zebra finch populations to examine variation in a population-level song trait: song variability. Song variability is of particular interest in the context of individual recognition and in terms of the neuro-developmental mechanisms that generate song novelty. We find that the Australian zebra finchTaeniopygia guttata castanotis(TGC) maintains higher song diversity than the Timor zebra finchT. g. guttata(TGG) even after experimentally controlling for early life song exposure, suggesting a genetic basis to this trait. Although wild-derivedTGCwere intermediate in song variability between domesticatedTGCpopulations andTGG, the difference between domesticated and wildTGCwas not statistically significant. The observed variation in song behaviour among zebra finch populations represents a largely untapped opportunity for exploring the mechanisms of social behaviour.
Adaptive responses and local stressor mitigation drive coral resilience in warmer, more acidic oceans
Authors: Jury Christopher P. , Toonen Robert J.
Published: May 2019

Coral reefs have great biological and socioeconomic value, but are threatened by ocean acidification, climate change and local human impacts. The capacity for corals to adapt or acclimatize to novel environmental conditions is unknown but fundamental to projected reef futures. The coral reefs of Kāne‘ohe Bay, Hawai‘i were devastated by anthropogenic insults from the 1930s to 1970s. These reefs experience naturally reduced pH and elevated temperature relative to many other Hawaiian reefs which are not expected to face similar conditions for decades. Despite catastrophic loss in coral cover owing to human disturbance, these reefs recovered under low pH and high temperature within 20 years after sewage input was diverted. We compare the pH and temperature tolerances of three dominant Hawaiian coral species from within Kāne‘ohe Bay to conspecifics from a nearby control site and show that corals from Kāne‘ohe are far more resistant to acidification and warming. These results show that corals can have different pH and temperature tolerances among habitats and understanding the mechanisms by which coral cover rebounded within two decades under projected future ocean conditions will be critical to management. Together these results indicate that reducing human stressors offers hope for reef resilience and effective conservation over coming decades.
The cost of chemical defence: the impact of toxin depletion on growth and behaviour of cane toads (
Rhinella marina
)
Authors: Blennerhassett Ryann A. , Bell-Anderson Kim , Shine Richard , Brown Gregory P.
Published: May 2019

Many animals capable of deploying chemical defences are reluctant to use them, suggesting that synthesis of toxins imposes a substantial cost. Typically, such costs have been quantified by measuring the elevation in metabolic rate induced by toxin depletion (i.e. during replenishment of toxin stores). More generally, we might expect that toxin depletion will induce shifts in a broad suite of fitness-relevant traits. In cane toads (
Rhinella marina
), toxic compounds that protect against predators and pathogens are stored in large parotoid (shoulder) glands. We used correlational and experimental approaches in field and laboratory settings to investigate impacts of toxin depletion on growth rate and behaviour in cane toads. In free-ranging toads, larger toxin stores were associated with smaller gonads and livers, suggesting energetic trade-offs between toxin production and both reproduction and energy metabolism. Experimental removal of toxin (by manually squeezing parotoid glands) reduced rates of growth in body mass in both captive and free-ranging toads. Radio tracking demonstrated that de-toxined toads dispersed more slowly than did control toads. Given that toxin stores in cane toads take several months to fully replenish, deploying toxin to repel a predator may impose a substantial cost, explaining why toads use toxin only as a final line of defence.
FreeHi-C: high fidelity Hi-C data simulation for benchmarking and data augmentation
Authors: Zheng Ye , Keleş Sündüz
Published: May 2019

Ability to simulate realistic high-throughput chromatin conformation (Hi-C) data is foundational for developing and benchmarking statistical and computational methods for Hi-C data analysis. We propose FreeHi-C, a data-driven Hi-C simulator for simulating and augmenting Hi-C datasets. FreeHi-C employs a non-parametric strategy for estimating interaction distribution of genome fragments from a given sample and simulates Hi-C reads from interacting fragments. Data from FreeHi-C exhibit higher fidelity to the biological Hi-C data compared with other tools in its class. FreeHi-C not only enables benchmarking a wide range of Hi-C analysis methods but also boosts the precision and power of differential chromatin interaction detection methods while preserving false discovery rate control through data augmentation.
OTUB1 is a key regulator of RIG-I dependent immune signalling and is targeted for proteasomal degradation by influenza A NS1
Authors: Jahan Akhee Sabiha , Biquand Elise , Muñoz-Moreno Raquel , Le Quang Agathe , Mok Chris Ka-Pun , Wong Ho Him , Teo Qi Wen , Doak Sophie , Chin Alex W. H. , Poon Leo Lit Man , te Velthuis Artejan , García-Sastre Adolfo , Demeret Caroline , Sanyal Sumana
Published: May 2019

Deubiquitylases (DUBs) regulate critical signaling pathways at the intersection of host innate immunity and viral pathogenesis. Although RIG-I activation is heavily dependent on ubiquitylation, DUBs that regulate this pathway have not been identified. Using a ubiquitin C-terminal electrophile, we profiled DUBs that function during influenza A virus (IAV) infection, and isolated OTUB1 as a key regulator of RIG-I dependent antiviral responses. OTUB1 was interferon-inducible, and interacted with RIG-I, viral PB2 and NS1. Upon infection, OTUB1 relocalised from the nucleus to mitochondrial membranes, and activated the RIG-I signaling complex via hydrolysis of K48 polyubiquitin chains and by forming a repressive complex with UBCH5c. Using a reconstituted system composed of in vitro translated [35S]IRF3, purified RIG-I, mitochondrial membranes and cytosol expressing OTUB1 variants, we recapitulated the mechanism of OTUB1-dependent RIG-I activation. A wide range of IAV NS1 proteins triggered proteasomal degradation of OTUB1, thereby antagonizing the RIG-I signaling cascade and antiviral responses.

Highlights

OTUB1 is induced during influenza A virus infections in an IFN-I dependent manner

OTUB1 regulates the RIG-I complex by hydrolysing K48-linked polyubiquitin chains and by sequestering UBCH5c to prevent K48 polyubiquitylation

Optimal K63 versus K48 polyubiquitin chain concentrations determine RIG-I activation

Influenza NS1 targets OTUB1 for proteasomal degradation
SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with unparalleled generalization performance
Authors: Kim Hui Kwon , Kim Younggwang , Lee Sungtae , Min Seonwoo , Bae Jung Yoon , Choi Jae Woo , Park Jinman , Jung Dongmin , Yoon Sungroh , Kim Hyongbum Henry
Published: May 2019

We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing sgRNA-encoding and target sequence pairs. Deep learning-based training on this large data set of SpCas9-induced indel frequencies led to the development of a SpCas9-activity predicting model named DeepSpCas9. When tested against independently generated data sets (our own and those published by other groups), DeepSpCas9 showed unprecedentedly high generalization performance. DeepSpCas9 is available athttp://deepcrispr.info/DeepCas9.
Frustration and Fidelity in Influenza Genome Assembly
Authors: Farheen Nida , Thattai Mukund
Published: May 2019

The genome of the influenza virus consists of eight distinct single-stranded RNA segments, each encoding proteins essential for the viral life cycle. When the virus infects a host cell these segments must be replicated and packaged into new budding virions. The viral genome is assembled with remarkably high fidelity: experiments reveal that most virions contain precisely one copy of each of the eight RNA segments. Cell-biological studies suggest that genome assembly is mediated by specific reversible and irreversible interactions between the RNA segments and their associated proteins. However, the precise inter-segment interaction network remains unresolved. Here we computationally predict that tree-like irreversible interaction networks guarantee high-fidelity genome assembly, while cyclic interaction networks lead to futile or frustrated off-pathway products. We test our prediction against multiple experimental datasets. We find that tree-like networks capture the nearest-neighbor statistics of RNA segments in packaged virions, as observed by EM tomography. Just eight tree-like networks (of a possible 262,144) optimally capture both the nearest-neighbor data as well as independently measured RNA-RNA contact propensities. These eight do not include the previously-proposed hub-and-spoke and linear networks. Rather, each predicted network combines hub-like and linear features, consistent with evolutionary models of interaction gain and loss.
Adrenergic-melatonin heteroreceptor complexes are key in controlling ion homeostasis and intraocular eye pressure and their disruption contributes to hypertensive glaucoma
Authors: Alkozi Hanan Awad , Navarro Gemma , Aguinaga David , Reyes-Resina Irene , Sanchez-Naves Juan , Perez de Lara Maria J , Franco Rafael , Pintor Jesus
Published: May 2019

Melatonin regulates intraocular pressure (IOP) whose increase leads to glaucoma and eye nerve degeneration. Aiming at elucidating the role of melatonin receptors in humour production and IOP maintenance, we here demonstrate that glaucoma correlates with disassembly of α1-adrenergic/melatonin receptor functional units in cells producing the aqueous humour. Remarkably, α1-adrenoceptor-containing complexes do not coupled to the cognate Gq protein and, hence, phenylephrine activation of these receptors does not lead to Ca2+ mobilization. Functional complexes are significantly decreased in models of glaucoma and, more importantly, in human samples of glaucoma patients (GP). In such glaucomatous conditions phenylephrine produces, via α1-adrenoceptor activation, an increase in cytoplasmic [Ca2+] that is detrimental in glaucoma. The results led to hypothesize that using melatonin, a hypotensive agent, plus blockade of α1-adrenergic receptors may normalize pressure in glaucoma. Remarkably, co-instillation of melatonin and prazosin, a α1-adrenergic receptor antagonist, results in long-term decreases in IOP in a well-established animal model of glaucoma. The findings are instrumental to understand the physiological function of melatonin in the eye and its potential to address eye pathologies by targeting melatonin receptors and their complexes.
High throughput Characterization ofKCNB1variants Associated with Developmental and Epileptic Encephalopathy
Authors: Kang Seok Kyu , Vanoye Carlos G. , Misra Sunita N. , Echevarria Dennis M. , Calhoun Jeffrey D. , O’Connor John B. , Fabre Katarina L. , McKnight Dianalee , Demmer Laurie , Goldenberg Paula , Grote Lauren E. , Thiffault Isabelle , Saunders Carol , Strauss Kevin A. , Torkamani Ali , van der Smagt Jasper , van Gassen Koen , Carson Robert P. , Diaz Jullianne , Leon Eyby , Jacher Joseph E. , Hannibal Mark C. , Litwin Jessica , Friedman Neil R. , Schreiber Allison , Lynch Bryan , Poduri Annapurna , Marsh Eric D. , Goldberg Ethan M. , Millichap John J. , George Alfred L. , Kearney Jennifer A.
Published: May 2019

Pathogenic variants inKCNB1, encoding the voltage-gated potassium channel Kv2.1, are associated with developmental and epileptic encephalopathies (DEE). Previous functional studies on a limited number ofKCNB1variants indicated a range of molecular mechanisms by which variants affect channel function, including loss of voltage sensitivity, loss of ion selectivity, and reduced cell-surface expression. We evaluated a series of 17KCNB1variants associated with DEE or neurodevelopmental disorder (NDD) to rapidly ascertain channel dysfunction using high-throughput functional assays. Specifically, we investigated the biophysical properties and cell-surface expression of variant Kv2.1 channels expressed in heterologous cells using high-throughput automated electrophysiology and immunocytochemistry-flow cytometry. Pathogenic variants exhibited diverse functional defects, including altered current density and shifts in the voltage-dependence of activation and/or inactivation, as homotetramers or when co-expressed with wild-type Kv2.1. Quantification of protein expression also identified variants with reduced total Kv2.1 expression or deficient cell-surface expression.

Our study establishes a platform for rapid screening of functional defects ofKCNB1variants associated with DEE and other NDDs, which will aid in establishingKCNB1variant pathogenicity and may enable discovery of targeted strategies for therapeutic intervention based on molecular phenotype.
Development of a high-throughput γ-H2AX assay based on imaging flow cytometry
Authors: Lee Younghyun , Wang Qi , Shuryak Igor , Brenner David J. , Turner Helen C.
Published: May 2019

Background

Measurement of γ-H2AX foci formation in cells provides a sensitive and reliable method for quantitation of the radiation-induced DNA damage response. The objective of the present study was to develop a rapid, high-throughput γ-H2AX assay based on imaging flow cytometry (IFC) using the ImageStream®X Mk II (ISX MKII) platform to evaluate DNA double strand break (DSB) repair kinetics in human peripheral blood cells after exposure to ionizing irradiation.

Methods

The γ-H2AX protocol was optimized for small volumes (100 µl) of blood in Matrix™ 96-tube format and blood cell lymphocytes were identified and captured by ISX INSPIRE™ software and analyzed by Data Exploration and Analysis Software.

Results

Presented here are: 1) dose response curves based on γ-H2AX fluorescence intensity and foci number, 2) measurements of DNA repair kinetics up to 24 h after exposure to 4 Gy γ rays and, 3) a mathematical approach for modeling DNA DSB rejoining kinetics using two key parameters a) rate of γ-H2AX decay, and b) yield of residual unrepaired breaks.

Conclusions

The results indicate that the IFC-based γ-H2AX protocol may provide a practical, high-throughput and inexpensive platform for measurements of individual global DSB repair capacity and facilitate the prediction of precision medicine concepts.
Somatosensory-Motor Dysconnectivity Spans Multiple Transdiagnostic Dimensions of Psychopathology
Authors: Kebets Valeria , Holmes Avram J. , Orban Csaba , Tang Siyi , Li Jingwei , Sun Nanbo , Kong Ru , Poldrack Russell A. , Yeo B.T. Thomas
Published: May 2019

Background

There is considerable interest in a dimensional transdiagnostic approach to psychiatry. Most transdiagnostic studies have derived factors based only on clinical symptoms, which might miss possible links between psychopathology, cognitive processes and personality traits. Furthermore, many psychiatric studies focus on higher-order association brain networks, thus neglecting the potential influence of huge swaths of the brain.

Methods

A multivariate data-driven approach (partial least squares; PLS) was utilized to identify latent components linking a large set of clinical, cognitive and personality measures to whole-brain resting-state functional connectivity (RSFC) patterns across 224 participants. The participants were either healthy (N=110) or diagnosed with bipolar disorder (N=40), attention-deficit/hyperactivity disorder (N=37), schizophrenia (N=29) or schizoaffective disorder (N=8). In contrast to traditional case-control analyses, the diagnostic categories were not utilized in the PLS analysis, but were helpful for interpreting the components.

Results

Our analyses revealed three latent components corresponding to general psychopathology, cognitive dysfunction and impulsivity. Each component was associated with a unique whole-brain RSFC signature and shared across all participants. The components were robust across multiple control analyses and replicated using independent task functional magnetic resonance imaging data from the same participants. Strikingly, all three components featured connectivity alterations within the somatosensory-motor network, and its connectivity with subcortical structures and cortical executive networks.

Conclusions

We identified three distinct dimensions with dissociable (but overlapping) whole-brain RSFC signatures across healthy individuals and individuals with psychiatric illness, providing potential intermediate phenotypes that span across diagnostic categories. Our results suggest expanding the focus of psychiatric neuroscience beyond higher-order brain networks.
Branched-Chain Amino Acid Metabolic Reprogramming Orchestrates Drug Resistance to EGFR Tyrosine Kinase Inhibitors
Authors: Wang Yuetong , Zhang Jian , Ren Shengxiang , Sun Dan , Huang Hsin-Yi , Wang Hua , Jin Yujuan , Li Fuming , Zheng Chao , Yang Liu , Deng Lei , Jiang Zhonglin , Jiang Tao , Han Xiangkun , Hou Shenda , Guo Chenchen , Li Fei , Gao Dong , Qin Jun , Gao Daming , Chen Luonan , Wong Kwok-Kin , Li Cheng , Hu Liang , Zhou Caicun , Ji Hongbin
Published: May 2019

Drug resistance is a significant hindrance to effective cancer treatment. Although resistance mechanisms of epidermal growth factor receptor (EGFR)-mutant cancer cells to lethal EGFR tyrosine kinase inhibitors (TKI) treatment have been investigated intensively, how cancer cells orchestrate adaptive response under sublethal drug challenge remains largely unknown. Here we find that 2-hour sublethal TKI treatment elicits a transient drug-tolerant state in EGFR-mutant lung cancer cells. Continuous sublethal treatment reinforces this tolerance and eventually establishes long-term TKI resistance. This adaptive process involves H3K9 demethylation-mediated epigenetic upregulation of branched-chain amino acid aminotransferase 1 (BCAT1) and subsequent metabolic reprogramming, which promotes TKI resistance through attenuating reactive oxygen species (ROS) accumulation. Combinational treatment with TKI and ROS-inducing reagents overcomes this drug resistance in preclinical mouse models. Clinical information analyses support the correlation of BCAT1 expression with EGFR TKI response. Collectively, our findings reveal the importance of epigenetically regulated BCAT1-engaged metabolism reprogramming in TKI resistance in lung cancer.

HIGHLIGHTS

Sublethal EGFR TKI treatment induces transient drug-tolerant state and long-term resistance in EGFR-mutant lung cancer cells

Epigenetically regulated BCAT1-mediated metabolic reprogramming orchestrates EGFR TKI-induced drug resistance

Combinational treatment with TKI and ROS-inducing agents overcomes the drug resistance induced by EGFR TKI treatment
A role for theSaccharomyces cerevisiaeABCF protein New1 during translation termination
Authors: Kasari Villu , Pochopien Agnieszka A. , Margus Tõnu , Murina Victoriia , Zhou Yang , Nissan Tracy , Graf Michael , Nováček Jiří , Atkinson Gemma C. , Johansson Marcus J.O. , Wilson Daniel N. , Hauryliuk Vasili
Published: May 2019

Translation on the ribosome is controlled by numerous accessory proteins and translation factors. In the yeastSaccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related ABCF ATPase, New1, is encoded by a non-essential gene with a cold sensitivity and ribosome assembly defect knock-out phenotype. Since the exact molecular function of New1 is unknown, it is unclear if the ribosome assembly defect is direct, i.e. New1 is abona fideribosome assembly factor, or indirect, for instance due to a defect in protein synthesis. To investigate this, we employed a combination of yeast genetics, cryo-electron microscopy (cryo-EM) and ribosome profiling (Ribo-Seq) to interrogate the molecular function of New1. Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3. The structure of the ATPase-deficient (EQ2) New1 mutant locked on the 80S ribosome reveals that New1 binds analogously to the ribosome as eEF3. Finally, Ribo-Seq analysis revealed that loss of New1 leads to ribosome queuing upstream of 3’-terminal lysine and arginine codons, including those genes encoding proteins of the cytoplasmic translational machinery. Our results suggest that New1 is a translation factor that fine-tunes the efficiency of translation termination.
Membrane insertion of soluble CLIC1 into active chloride channels is triggered by specific divalent cations
Authors: Varela Lorena , Hendry Alex C. , Medina-Carmona Encarnacion , Cantoni Diego , Ortega-Roldan Jose L.
Published: May 2019

The CLIC family of proteins display the unique feature of altering their structure from a soluble form to a membrane-bound chloride channel. CLIC1, a member of this family, can be found in the cytoplasm or in nuclear, ER and plasma membranes, with membrane overexpression linked to tumour proliferation. The molecular switch promoting CLIC1 membrane insertion has been related to environmental factors, but still remains unclear. Here, we use solution NMR studies to confirm that both the soluble and membrane bound forms are in the same oxidation state. Our data from fluorescence assays and chloride efflux assays indicate that Ca2+and Zn2+trigger association to the membrane into active chloride channels. We use fluorescence microscopy to confirm that an increase of the intracellular Ca2+leads to re-localisation of CLIC1 to both plasma and internal membranes. Finally, we show that soluble CLIC1 adopts an equilibrium of oligomeric species, and Ca2+/Zn2+mediated membrane insertion promotes the formation of a tetrameric assembly. Thus, our results identify Ca2+and Zn2+binding as the molecular switch promoting CLIC1 membrane insertion.

SIGNIFICANCE STATEMENT

CLIC1, a member of the CLIC family of proteins, is expressed as a soluble protein in cells but can insert in the membrane forming a chloride channel. This chloride channel form is upregulated in different types of cancers including glioblastoma and promote tumour invasiveness and metastasis. The factors promoting CLIC1 membrane insertion nor the mechanism of this process are yet understood. Here, we use a combination of solution NMR, biophysics and fluorescence microscopy to identify Ca2+and Zn2+binding as the switch to promote CLIC1 insertion into the membrane to form active chloride channels. We also provide a simple mechanism how such transition to the membrane occurs. Such understanding will enable subsequent studies on the structure of the chloride channel form and its inhibition.