bluuebunny/crossref_metadata_2025 huggingface dataset:
The adaptive response to long-term nitrogen starvation inEscherichia colirequires the breakdown of allantoin
Authors: Switzer Amy , Burchell Lynn , McQuail Josh , Wigneshweraraj Sivaramesh
Published: April 2020

Bacteria initially respond to nutrient starvation by eliciting large-scale transcriptional changes. The accompanying changes in gene expression and metabolism allow the bacterial cells to effectively adapt to the nutrient starved state. How the transcriptome subsequently changes as nutrient starvation ensues is not well understood. We used nitrogen (N) starvation as a model nutrient starvation condition to study the transcriptional changes inEscherichia coliexperiencing long-term N starvation. The results reveal that the transcriptome of N starvedE. coliundergoes changes that are required to maximise chances of viability and to effectively recover growth when N starvation conditions become alleviated. We further reveal that, over time, N starvedE. colicells rely on the degradation of allantoin for optimal growth recovery when N becomes replenished. This study provides insights into the temporally coordinated adaptive responses that occur inE. coliexperiencing sustained N starvation.

IMPORTANCE

Bacteria in their natural environments seldom encounter conditions that support continuous growth. Hence, many bacteria spend the majority of their time in states of little or no growth due to starvation of essential nutrients. To cope with prolonged periods of nutrient starvation, bacteria have evolved several strategies, primarily manifesting themselves through changes in how the information in their genes is accessed. How these coping strategies change over time under nutrient starvation is not well understood and this knowledge is not only important to broaden our understanding of bacterial cell function, but also to potentially find ways to manage harmful bacteria. This study provides insights into how nitrogen starvedEscherichia colibacteria rely on different genes during long term nitrogen starvation.
Mathematical Model of Muscle Wasting in Cancer Cachexia
Authors: Farhang-Sardroodi Suzan , Wilkie Kathleen P.
Published: April 2020

Cancer cachexia is a debilitating condition characterized by an extreme loss of skeletal muscle mass which negatively impacts patient’s quality of life, reduces their ability to sustain anticancer therapies, and increases the risk of mortality. Recent discoveries have identified the myostatin/activin-ActRIIB pathway as critical to muscle wasting by inducing satellite cell quiescence and increasing muscle-specific ubiquitin ligases responsible for atrophy. Remarkably, pharmacological blockade of the ActRIIB pathway has shown to reverse muscle wasting and prolong the survival time of tumor-bearing animals. To explore the implications of this signaling pathway and potential therapeutic targets in cachexia, we construct a novel mathematical model of muscle tissue subjected to tumor-derived cachexic factors. The model formulation tracks the intercellular interactions between cancer, satellite cell, and muscle cell populations. The model is parameterized by fitting to colon-26 mouse model data, and analysis provides insight into tissue growth in healthy, cancerous, and post-treatment conditions. Model predictions suggest that cachexia fundamentally alters muscle tissue health, as measured by the stem cell ratio, and this is only partially recovered by anti-cachexia treatment. Our mathematical findings suggest that the activation and proliferation of satellite cells, after blocking the myostatin/activin B pathway, is required to partially recover cancer-induced muscle loss.
Prioritization of SARS-CoV-2 epitopes using a pan-HLA and global population inference approach
Authors: Campbell Katie M. , Steiner Gabriela , Wells Daniel K. , Ribas Antoni , Kalbasi Anusha
Published: April 2020

SARS-CoV-2 T cell response assessment and vaccine development may benefit from an approach that considers the global landscape of the human leukocyte antigen (HLA) proteins. We predicted the binding affinity between 9-mer and 15-mer peptides from the SARS-CoV-2 peptidome for 9,360 class I and 8,445 class II HLA alleles, respectively. We identified 368,145 unique combinations of peptide-HLA complexes (pMHCs) with a predicted binding affinity less than 500nM, and observed significant overlap between class I and II predicted pMHCs. Using simulated populations derived from worldwide HLA frequency data, we identified sets of epitopes predicted in at least 90% of the population in 57 countries. We also developed a method to prioritize pMHCs for specific populations. Collectively, this public dataset and accessible user interface (Shiny app:https://rstudio-connect.parkerici.org/content/13/) can be used to explore the SARS-CoV-2 epitope landscape in the context of diverse HLA types across global populations.
DNA Encoded Glycan Libraries as a next-generation tool for the study of glycan-protein interactions
Authors: Kondengaden Shukkoor M. , Zhang Jiabin , Zhang Huajie , Parameswaran Aishwarya , Kondengadan Shameer M. , Pawar Shrikant , Puthengot Akhila , Sunderraman Rajshekhar , Song Jing , Polizzi Samuel J. , Wen Liuqing , Wang Peng George
Published: April 2020

Interactions between glycans and glycan-binding proteins (GBPs) mediate diverse cellular functions, and therefore are of diagnostic and therapeutic significance. Current leading strategies for studying glycan-GBP interactions require specialized knowledge and instrumentation. In this study, we report a strategy for studying glycan-GBP interactions that uses PCR, qPCR and next-generation sequencing (NGS) technologies that are more routinely accessible. Our headpiece conjugation-code ligation (HCCL) strategy couples glycans with unique DNA codes that specify glycan sugar moieties and glycosidic linkages when sequenced. We demonstrate the technology by synthesizing a DNA encoded glycan library of 50 biologically relevant glycans (DEGL-50) and probing interactions against 25 target proteins including lectins and antibodies. Data show glycan-GPB interactions in solution that are consistent with lower content, lower throughput ELISA assays. Data further demonstrate how monovalent and multivalent headpieces can be used to increase glycan-GPB interactions and enrich signals while using smaller sample sizes. The flexibility of our modular HCCL strategy has potential for producing large glycan libraries, facilitating high content-high throughput glycan binding studies, and increasing access to lower cost glyco-analyses.

Abstract Figure
The effects of transcranial direct current stimulation on corticospinal and cortico-cortical excitability and response variability: conventional versus high-definition montages
Authors: Pellegrini Michael , Zoghi Maryam , Jaberzadeh Shapour
Published: April 2020

Response variability following transcranial direct current stimulation (tDCS) highlights need for exploring different tDCS electrode montages. This study compared corticospinal excitability (CSE), cortico-cortical excitability and intra-individual variability following conventional and HD anodal (a-tDCS) and cathodal (c-tDCS) tDCS. Fifteen healthy young males attended four sessions at least one-week apart: conventional a-tDCS, conventional c-tDCS, HD-a-tDCS, HD-c-tDCS. TDCS was administered (1mA, 10-minutes) over the primary motor cortex (M1), via 6×4cm active and 7×5cm return electrodes (conventional tDCS) and 4×1 ring-electrodes 3.5cm apart in ring formation around M1 (HD-tDCS). For CSE, twenty-five single-pulse transcranial magnetic stimulation (TMS) peak-to-peak motor evoked potentials (MEP) were recorded at baseline, 0-minutes and 30-minutes post-tDCS. For cortico-cortical excitability, twenty-five paired-pulse MEPs with 3-millisecond (ms) inter-pulse interval (IPI) and twenty-five at 10ms assessed short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF) respectively. MEP standardised z-values standard deviations represented intra-individual variability. No significant differences were reported in CSE between conventional and HD a-tDCS, but significant differences between conventional and HD c-tDCS 0-minutes post-tDCS. Intra-individual variability was significantly reduced in conventional tDCS compared to HD-tDCS for a-tDCS (0-minutes) and c-tDCS (30-minutes). No significant changes were reported in SICI and ICF. These novel findings highlight current technical issues with HD-tDCS, suggesting future tDCS studies should utilise conventional tDCS to minimise intra-individual variability, ensuring tDCS after-effects are true changes in CSE and cortico-cortical excitability.
Diversification or collapse of self-incompatibility haplotypes as a rescue process
Authors: Harkness Alexander , Goldberg Emma E. , Brandvain Yaniv
Published: April 2020

In angiosperm self-incompatibility systems, pollen with an allele matching the pollen recipient at the self-incompatibility locus is rejected. Extreme allelic polymorphism is maintained by frequency-dependent selection favoring rare alleles. However, two challenges limit the spread of a new allele (a tightly linked haplotype in this case) under the widespread “collaborative non-self recognition” mechanism. First, there is no obvious selective benefit for pollen compatible with non-existent stylar incompatibilities, which themselves cannot spread if no pollen can fertilize them. However, a pistil-function mutation complementary to a previously neutral pollen mutation may spread if it restores self-incompatibility to a self-compatible intermediate. Second, we show that novel haplotypes can drive elimination of existing ones with fewer siring opportunities. We calculate relative probabilities of increase and collapse in haplotype number given the initial collection of incompatibility haplotypes and the population gene conversion rate. Expansion in haplotype number is possible when population gene conversion rate is large, but large contractions are likely otherwise. A Markov chain model derived from these expansion and collapse probabilities generates a stable haplotype number distribution in the realistic range of 10–40 under plausible parameters. However, smaller populations might lose many haplotypes beyond those lost by chance during bottlenecks.
Lessons and considerations for the creation of universal primers targeting non-conserved, horizontally mobile genes
Authors: Brown Damon C. , Turner Raymond J.
Published: April 2020

Effective and accurate primer design is an increasingly important skill as the use of PCR-based diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been successfully designed for highly conserved core genes such as 16S rRNA and characteristic genes such asdsrABanddnaJ, primer sets for mobile, accessory genes such as multidrug resistance efflux pumps (MDREP) have not been explored. Here, we describe an approach to create universal primer sets for select MDREP genes chosen from five superfamilies (SMR, MFS, MATE, ABC and RND) identified in a model community of six members(Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putidaandThauera aromatica).Using sequence alignments andin silicoPCR analyses, a new approach for creating universal primers sets targeting mobile, non-conserved genes has been developed and compared to more traditional approaches used for highly conserved genes. A discussion of the potential shortfalls of the primer sets designed this way are described. The approach described here can be adapted to any unique gene set and aid in creating a wider, more robust library of primer sets to detect less conserved genes and improve the field of PCR-based screening research.

Importance

Increasing use of molecular detection methods, specifically PCR and qPCR, requires utmost confidence in the results while minimizing false positives and negatives due to poor primer designs. Frequently, these detection methods are focused on conserved, core genes which limits their applications. These screening methods are being used in various industries for specific genetic targets or key organisms such as viral or infectious strains, or characteristic genes indicating the presence of key metabolic processes. The significance of this work is to improve primer design approaches to broaden the scope of detectable genes. The use of the techniques explored here will improve detection of non-conserved genes through unique primer design approaches. Additionally, the approaches here highlight additional, important information which can be gleaned during thein silicophase of primer design which will improve our gene annotations based on sequence homologies.
Tamoxifen repurposing to combat infections by multidrug-resistant Gram-negative bacilli
Authors: Miró-Canturri Andrea , Ayerbe-Algaba Rafael , del Toro Raquel , Pachón Jerónimo , Smani Younes
Published: April 2020

The development of new strategic therapies for multidrug-resistant bacteria, like the use of non-antimicrobial approaches and/or drugs repurposing to be used as monotherapies or in combination with clinically relevant antibiotics, has become an urgent need. A therapeutic alternative for infections by multidrug-resistant Gram-negative bacilli (MDR-GNB) is immune system modulation to improve the infection clearance. We showed that immunocompetent mice infected byAcinetobacter baumannii, Pseudomonas aeruginosaorEscherichia coliin peritoneal sepsis models and treated with tamoxifen at 80 mg/kg/d for three days reduced the release of MCP-1 and its signalling pathway IL-18 and phosphorylated ERK1/2. This reduction of MCP-1 induced the reduction of migration of inflammatory monocytes and neutrophils from bone marrow to blood. Indeed, the treatment with tamoxifen in murine peritoneal sepsis models reduced the bacterial load in tissues and blood; and increased the mice survival from 0% to 60-100%. Tamoxifen treatment of neutropenic mice infected by these pathogens increased mice survival up to 20-60%. Furthermore, susceptibility and time-kill assays showed that the metabolites of tamoxifen, N-desmethyltamoxifen, hydroxytamoxifen and endoxifen, the three together exhibited MIC90values of 16 mg/L and were bactericidal against clinical isolates ofA. baumanniiandE. coli. This antimicrobial activity of tamoxifen metabolites parallels’ an increased membrane permeability ofA. baumanniiandE. coliwithout affecting their outer membrane proteins profiles. Together, these data showed that tamoxifen present a therapeutic efficacy against MDRA. baumannii, P. aeruginosaandE. coliin experimental models of infections and can be repurposed as new treatment for GNB infections.

Importance

Antimicrobial resistance in Gram-negative bacilli (GNB) is a global health treat. Drug repurposing, a novel approach involving the search of new indications for FDA approved drugs is gaining interest. Among them, we found the anti-cancer drug tamoxifen, which presents very promising therapeutic efficacy. The current study showed that tamoxifen presents activity in animal models of infection with MDRAcinetobacter baumannii, Pseudomonas aeruginosaandEscherichia coliby modulating the traffic of innate immune system cells and the antibacterial activity presented by its three major metabolites producedin vivoagainst these GNB. Our results offer a new candidate to be repurposed to treat severe infections caused by these pathogens.
S100A8/A9 modulates inflammatory collateral tissue damage during intraperitoneal origin systemic candidiasis
Authors: Shankar Madhu , Uwamahoro Nathalie , Holmberg Sandra , Niemiec Maria Joanna , Roth Johannes , Vogl Thomas , Urban Constantin F.
Published: April 2020

Peritonitis is a leading cause of severe sepsis in surgical intensive care units, as over 70% of patients diagnosed with peritonitis develop septic shock. A critical role of the immune system is to return to homeostasis after combating infection. S100A8/A9 (calprotectin) is an antimicrobial, pro-inflammatory protein complex often used as a biomarker for diagnosis of disease activities in many inflammatory disorders. Here we describe the role of S100A8/A9 on inflammatory collateral tissue damage (ICTD).

We performed anin vivo Candida albicansdisseminated peritonitis mouse model using WT and S100A9-deficient mice and stimulated primary macrophages with recombinant S100A8/A9 in the presence or absence of the compound paquinimod, a specific inhibitor of S100A9. In addition, the effects on ICTD and fungal clearance were investigated. S100A9-deficient mice developed less ICTD than wildtype mice. Restoration of S100A8/A9 in S100A9 knockout mice resulted in increased ICTD and fungal clearance comparable to wildtype levels. Treatment with paquinimod abolished ICTD.

The data indicated that S100A8/A9 controls ICTD levels and host antimicrobial modulation at a systemic level during intra-abdominal candidiasis (IAC).
Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network
Authors: Abbas Asmaa , Abdelsamea Mohammed M. , Medhat Gaber Mohamed
Published: April 2020

Chest X-ray is the first imaging technique that plays an important role in the diagnosis of COVID-19 disease. Due to the high availability of large-scale annotated image datasets, great success has been achieved using convolutional neural networks (CNNs) for image recognition and classification. However, due to the limited availability of annotated medical images, the classification of medical images remains the biggest challenge in medical diagnosis. Thanks to transfer learning, an effective mechanism that can provide a promising solution by transferring knowledge from generic object recognition tasks to domain-specific tasks. In this paper, we validate and adapt a deepCNN, called Decompose, Transfer, and Compose (DeTraC), for the classification of COVID-19 chest X-ray images.DeTraCcan deal with any irregularities in the image dataset by investigating its class boundaries using a class decomposition mechanism. The experimental results showed the capability ofDeTraCin the detection of COVID-19 cases from a comprehensive image dataset collected from several hospitals around the world. High accuracy of 95.12% (with a sensitivity of 97.91%, and a specificity of 91.87%) was achieved byDeTraCin the detection of COVID-19 X-ray images from normal, and severe acute respiratory syndrome cases.
Demand for hospitalization services for COVID-19 patients in Brazil
Authors: Castro Marcia C. , de Carvalho Lucas Resende , Chin Taylor , Kahn Rebecca , França Giovanny V. A. , Macário Eduardo Marques , de Oliveira Wanderson Kleber
Published: April 2020

COVID-19 is now a pandemic and many of the affected countries face severe shortages of hospital resources. In Brazil, the first case was reported on February 26. As the number of cases grows in the country, there is a concern that the health system may become overwhelmed, resulting in shortages of hospital beds, intensive care unit beds, and mechanical ventilators. The timing of shortage is likely to vary geographically depending on the observed onset and pace of transmission observed, on the availability of resources, and on the actions implemented. Here we consider the daily number of cases reported in municipalities in Brazil to simulate twelve alternative scenarios of the likely timing of shortage, based on parameters consistently reported for China and Italy, on rates of hospital occupancy for other health conditions observed in Brazil in 2019, and on assumptions of allocation of patients in public and private facilities. Results show that hospital services could start to experience shortages of hospital beds, ICU beds, and ventilators in early April, the most critical situation observed for ICU beds. Increasing the allocation of beds for COVID-19 (in lieu of other conditions) or temporarily placing all resources under the administration of the state delays the anticipated start of shortages by a week. This suggests that solutions adopted by the Brazilian government must aim at expanding the available capacity (e.g., makeshift hospitals), and not simply prioritizing the allocation of available resources to COVID-19.
Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR primer-probe sets
Authors: Vogels Chantal B.F. , Brito Anderson F. , Wyllie Anne L. , Fauver Joseph R. , Ott Isabel M. , Kalinich Chaney C. , Petrone Mary E. , Casanovas-Massana Arnau , Muenker M. Catherine , Moore Adam J. , Klein Jonathan , Lu Peiwen , Lu-Culligan Alice , Jiang Xiaodong , Kim Daniel J. , Kudo Eriko , Mao Tianyang , Moriyama Miyu , Oh Ji Eun , Park Annsea , Silva Julio , Song Eric , Takahashi Takehiro , Taura Manabu , Tokuyama Maria , Venkataraman Arvind , Weizman Orr-El , Wong Patrick , Yang Yexin , Cheemarla Nagarjuna R. , White Elizabeth B. , Lapidus Sarah , Earnest Rebecca , Geng Bertie , Vijayakumar Pavithra , Odio Camila , Fournier John , Bermejo Santos , Farhadian Shelli , Dela Cruz Charles S. , Iwasaki Akiko , Ko Albert I. , Landry Marie L. , Foxman Ellen F. , Grubaugh Nathan D.
Published: April 2020

The recent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt clinical and public health interventions. Currently, several quantitative reverse-transcription polymerase chain reaction (qRT-PCR) assays are being used by clinical, research, and public health laboratories. However, it is currently unclear if results from different tests are comparable. Our goal was to evaluate the primer-probe sets used in four common diagnostic assays available on the World Health Organization (WHO) website. To facilitate this effort, we generated RNA transcripts to be used as assay standards and distributed them to other laboratories for internal validation. We then used (1) RNA transcript standards, (2) full-length SARS-CoV-2 RNA, (3) pre-COVID-19 nasopharyngeal swabs, and (4) clinical samples from COVID-19 patients to determine analytical efficiency and sensitivity of the qRT-PCR primer-probe sets. We show that all primer-probe sets can be used to detect SARS-CoV-2 at 500 virus copies per reaction, except for the RdRp-SARSr (Charité) confirmatory primer-probe set which has low sensitivity. Our findings characterize the limitations of currently used primer-probe sets and can assist other laboratories in selecting appropriate assays for the detection of SARS-CoV-2.
Specialisation and plasticity in a primitively social insect
Authors: Patalano S. , Alsina A. , Gregorio-Rodriguez C. , Bachman M. , Dreier S. , Hernando-Herraez I. , Nana P. , Balasubramanian S. , Sumner S. , Reik W. , Rulands S.
Published: April 2020

Biological systems not only have the remarkable capacity to build and maintain complex spatio-temporal structures in noisy environments, they can also rapidly break up and rebuild such structures. How such systems can simultaneously achieve both robust specialisation and plasticity is poorly understood. Here we use primitive societies ofPolisteswasps as a model system where we experimentally perturb the social structure by removing the queen and follow the re-establishment of the social steady state over time. We combine a unique experimental strategy correlating time-resolved measurements across vastly different scales with a theoretical approach. We show thatPolistesintegrates antagonistic processes on multiple scales to distinguish between extrinsic and intrinsic perturbations and thereby achieve both robust specialisation and rapid plasticity. The long-term stability of the social structure relies on dynamic DNA methylation which controls transcriptional noise. Such dynamics provide a general principle of how both specialization and plasticity can be achieved in biological systems.

One Sentence Summary

A primitive social insect simultaneously achieves specialisation and plasticity by integrating antagonistic dynamics on different scales.

Highlights

We employ a unique experimental approach correlating dynamics of societies, individuals, and epigenetic gene regulation

A social insect simultaneously achieves specialisation and plasticity by integrating antagonistic processes on different spatial scales

Regulation of population-level noise by DNA methylation ensures long-term stability of phenotypic specialisation
A way to break bones? The weight of intuitiveness
Authors: Vettese D. , Stavrova T. , Borel A. , Marin J. , Moncel M.-H. , Arzarello M. , Daujeard C.
Published: April 2020

During the Middle Paleolithic period, bone marrow extraction was an essential source of fat nutrients for hunter-gatherers especially throughout cold and dry seasons. This is attested by the recurrent findings of percussion marks in osteological material from anthropized archaeological levels. Among them some showed indicators that the marrow extraction process was part of a butchery cultural practice, meaning that the inflicted fracturing gestures and techniques were recurrent, standardized and counter-intuitive i.e. culturally influenced. In order to assess the weight of the counter-intuitive factor in the percussion mark pattern distribution, we carried out an experiment that by contrast focuses on the intuitive approach of fracturing bones to extract marrow, involving individual without experience in this activity.

We wanted to evaluate the influence of bone morphology and the individuals’ behaviour on the distribution of percussion marks. Twelve experimenters broke 120 limb bones, a series of 10 bones per individual. During the experiment, information concerning the fracture of the bones as well as individual behaviour was collected and was subsequently compared to data from the laboratory study of the remains. Then, we applied an innovative GIS (Geographic Information System) method to analyze the distribution of percussion marks to highlight recurrent patterns. Results show that in spite of all the variables there is a high similarity in the distribution of percussion marks which we consider as intuitive patterns. The factor influenced the distribution for the humerus, radius-ulna and tibia series is the bone morphology, while for the femur series individual behaviour seems to have more weight in the distribution. To go further in the subject we need to compare the intuitive models with the distributions of percussion marks registered in fossil assemblages. Thus, it would be possible to propose new hypotheses on butchering practices based on the results presented in this work.
Experiments on localization accuracy with non-individual and individual HRTFs comparing static and dynamic reproduction methods
Authors: Oberem Josefa , Richter Jan-Gerrit , Setzer Dorothea , Seibold Julia , Koch Iring , Fels Janina
Published: April 2020

Binaural reproduction can be used in listening experiments under real-life conditions to achieve a high realism and good reproducibility. In recent years a clear trend to more individual reproduction can be observed as the ability to measure individual head-related-transfer-functions (HRTFs) is becoming more widespread. The question of the accuracy and reproduction methods needed for a realistic playback however has not been sufficiently answered. To evaluate an appropriate approach for binaural reproduction via headphones different head-related-transfer-functions (HRTFs) and reproduction methods were compared in this paper. In a listening test eleven explicitly trained participants were asked to localize eleven sound sources positioned in the right hemisphere using the proximal pointing method. Binaural stimuli based on individually measured HRTFs were compared to those of an artificial head in a static reproduction of stimuli and in three dynamic reproduction methods of different resolutions (5°, 2.5° and 1°). Unsigned errors in azimuth and elevation as well as front-back-confusions and in-head-localization were observed. Dynamic reproduction of any resolution applied turned out fundamental for a reduction of undesired front-back-confusions and in-head-localization. Individually measured HRTFs showed a smaller effect on localization accuracy compared to the influence of dynamic sound reproduction. They were mainly observed to reduce the front-back-confusion rate.
High levels of frataxin overexpression leads to mitochondrial and cardiac toxicity in mouse models
Authors: Belbellaa Brahim , Reutenauer Laurence , Messaddeq Nadia , Monassier Laurent , Puccio Hélène
Published: April 2020

Friedreich ataxia (FA) is currently an incurable inherited mitochondrial disease caused by reduced levels of frataxin (FXN). Cardiac dysfunction is the main cause of premature death in FA. AAV-mediated gene therapy constitutes a promising approach for FA, as demonstrated in cardiac and neurological mouse models. While the minimal therapeutic level of FXN protein to be restored and biodistribution have recently been defined for the heart, it is unclear if FXN overexpression could be harmful. Indeed, depending on the vector delivery route and dose administrated, the resulting FXN protein level could reach very high levels in the heart, cerebellum, or in off-target organs such as the liver. The present study demonstrates safety of FXN cardiac overexpression up to 9-fold the normal endogenous level, but significant toxicity to the mitochondria and heart above 20-fold. We show gradual severity with increasing FXN overexpression, ranging from subclinical cardiotoxicity to left ventricle dysfunction. This appears to be driven by impairment of mitochondria respiratory chain, ultrastructure and homeostasis, which lead to myofilaments alteration, cell death and fibrosis. Overall, this study underlines the need, during the development of gene therapy approaches, to consider appropriately vector potency, long term safety and biomarkers to monitor such events.
Brain-wide structural and functional disruption in mice with oligodendrocyte specificNf1deletion is rescued by inhibition of NOS
Authors: Asleh Jad , Shofty Ben , Cohen Nadav , Kavushansky Alexandra , López-Juárez Alejandro , Constantini Shlomi , Ratner Nancy , Kahn Itamar
Published: April 2020

Neurofibromin gene (NF1) mutation causes Neurofibromatosis type 1 (NF1), a disorder in which brain white matter deficits identified by neuroimaging are common, yet of unknown cellular etiology. In mice,Nf1loss in adult oligodendrocyte causes myelin decompaction, and increases oligodendrocyte nitric oxide (NO) levels. Nitric oxide synthase (NOS) inhibitors rescue this pathology. Whether oligodendrocyte pathology is sufficient to affect brainwide structure and account for NF1 imaging findings is unknown. Here, we show thatNf1gene inactivation in adult oligodendrocytes (Plp-Nf1fl/+mice) results in a motor coordination deficit. Magnetic resonance imaging in awake mice shows that fractional anisotropy is reduced in Plp-Nf1fl/+corpus callosum and that interhemispheric functional connectivity in motor cortex is also reduced, consistent with disrupted myelin integrity. Further, NOS-specific inhibition rescued both measures. These results demonstrate that oligodendrocyte defects account for aspects of brain dysfunction in NF1, which can be identified by neuroimaging and ameliorated by NOS inhibition.

Significance statement

This study assesses the effects of myelin decompaction on motor behavior and brain-wide structural and functional connectivity, and the effect of nitric oxide synthase (NOS) inhibition by N-nitro-L-arginine methyl ester (L-NAME) on these imaging measures. We report that inducible oligodendrocyte-specific inactivation of theNf1gene, which causes myelin decompaction, results in reduced motor coordination. Using diffusion-based MRI we show reduced myelin integrity and using functional MRI we show reduced functional connectivity in awake passive mice. L-NAME administration results in rescue of the pathology at the mesoscopic level using imaging procedures that can be directly applied to humans to study treatment efficacy in clinical trials.
“A negative feedback loop mediated by the NR4A family of nuclear hormone receptors restrains expansion of B cells that receive signal one in the absence of signal two”
Authors: Tan Corey , Hiwa Ryosuke , Mueller James L. , Vykunta Vivasvan , Hibiya Kenta , Noviski Mark , Huizar John , Brooks Jeremy , Garcia Jose , Heyn Cheryl , Li Zhongmei , Marson Alexander , Zikherman Julie
Published: April 2020

Ag stimulation (signal 1) triggers B cell activation and proliferation, and primes B cells to recruit, engage, and respond to T cell help (signal 2). However, failure to receive signal 2 within a defined window of time results in an abortive round of proliferation, followed by anergy or apoptosis. Although the molecular basis of T cell help has been extensively dissected, the mechanisms that restrain Ag-stimulated B cells, and enforce dependence upon co-stimulation, are incompletely understood.Nr4a1-3encode a small family of orphan nuclear receptors that are rapidly induced by B cell receptor (BCR) stimulation, yet little is known about their function in humoral immune responses. Here we use germline and conditional loss-of-function mouse models to show thatNr4a1andNr4a3play partially redundant roles to restrain both the survival and proliferation of B cells that receive signal 1 in the absence of co-stimulatory signals, and do so in part by repressing expression of BATF and consequently c-MYC. Correspondingly, Ab responses to TI-2 immunogens are enhanced in the absence ofNr4a1, but are unaltered in response to immunogens that incorporate co-stimulatory signals. Unexpectedly, we also identify a role for the NR4A family in restraining B cell access to T cell help by repressing expression of the T cell chemokines CCL3/4, as well as CD86 and ICAM1, and show that this is relevant under conditions of competition for limiting T cell help. Our studies collectively reveal a novel negative feedback loop mediated by the NR4A family that increases B cell dependence upon T cell help and restrains strongly Ag-activated B cell clones from monopolizing limiting amounts of T cell help. We speculate that this imposes B cell tolerance and dampens immunodominance to facilitate preservation of clonal diversity during an immune response.
A Mendelian randomization study of glycemic and anthropometric traits and Parkinson’s disease
Authors: Grover Sandeep , Graf Ricarda , Klein Christine , Brüggemann Norbert , König Inke R. , Greco M Fabiola Del , Sharma Manu
Published: April 2020

Background

Impaired glucose and obesity are frequently observed in patients with Parkinson’s disease (PD), although it is unclear whether the impairment precedes or results from the neurodegeneration.

Objective

We aimed to assess whether glycemic and anthropometric traits can influence the risk of PD in 33,674 cases and 449,056 healthy controls using the Mendelian randomization (MR) framework.

Methods

We investigated causality with a two-sample MR approach in the European population to compute effect estimates with summary statistics from available discovery meta-analyses of genome-wide association studies (GWAS) on glycemic and anthropometric traits.

Results

We considered a threshold of p-value=0.0038 as significant after accounting for multiple testing, and p-value<0.05 was considered to be a suggestive evidence for a potential association. We observed a protective effect of waist-hip ratio (WHR) on PD (Inverse variance-weighted (IVW): ORIVW=0.735; 95%CI= 0.622–0.868; p-value=0.0003; I2index=22.0%; MR-Egger intercept p-value=0.1508; Cochran Q test p-value=0.0003). The association was further retained after the exclusion of overlapping UK biobank (UKB) samples between the WHR and PD datasets (ORIVW=0.791; 95%CI=0.659–0.950; p-value=0.012; I2index=13.0%; MR-Egger intercept p-value=0.733; Cochran Q test p-value=0.035). The sensitivity analysis provided suggestive evidence of an increased risk of PD on fasting glucose (FG) (βIVW=0.0188; 95%CI=0.0062–0.0313, p-value=0.0055; I2index=0.0%; MR-Egger intercept p-value=0.0957; Cochran Q test p-value=0.4555) and protective effect of PD on T2D (Weighted median effect: ORWME=0.946; 95%CI=0.9290.983; p-value=0.0051; Weighted mode effect: ORMBE=0.943; 95%CI=0.904–0.983; p-value=0.0116).

Conclusions

Our results showed that central or abdominal obesity may be protective against PD development, independent of glucose levels.
mtDNAcombine: tools to combine sequences from multiple studies
Authors: Miller Eleanor F. , Manica Andrea
Published: April 2020

Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing mtDNA data for Bayesian Skyline Plot demographic reconstructions.
Colonizations drive host shifts, diversification of preferences and expansion of herbivore diet breadth
Authors: Singer Michael C , Parmesan Camille
Published: April 2020

Dynamics of herbivorous insect diet breadth are important in generation of novel pests, biological control of weeds and as indicators of global change impacts. But what forces and events drive these dynamics? Here we present evidence for a novel scenario: that specialization increases in persistent populations, but that, at the species level, this trend is countered by effects of colonizations. Colonizations cause host shifts, which are followed by non-adaptive evolutionary expansions of diet breadth, adding transitory hosts during adaptation to the principal novel host.

We base this thesis on long-term study of 15 independently-evolving populations of Edith’s Checkerspot butterfly, eight of which used fewer host genera in recent censuses than in the 1980’s, while none used more - a significant increase in specializaton. At the same time, two extintion/recolonization events were followed by temporary expansions of diet breadth. Behavioural experiments showed that these expansions were driven by within-population diversification of individual oviposition preferences. These results may explain an old puzzle: a significant negative association between population-level diet breadth and mtDNA diversity. Populations with fewer mtDNA haplotypes had broader diets, suggesting that diet breadth increases in younger, recently-colonized populations.

A recent global meta-analysis of butterfly diets, using biogeographic data, explains latitudinal patterns of diet breadth by showing that poleward range expansions have caused reduced specialization. This implies broad applicability of our results, which provide a plausible mechanism for the latitudinal trends: colonizations at expanding range margins would increase population-level diet breadths, while population persistence in range interiors would facilitate increasing specialization.
Biological characterization of Euscelidius variegatus iflavirus 1
Authors: Ottati Sara , Persico Alberto , Rossi Marika , Bosco Domenico , Vallino Marta , Abbà Simona , Molinatto Giulia , Palmano Sabrina , Balestrini Raffaella , Galetto Luciana , Marzachì Cristina
Published: April 2020

Virus-based biocontrol technologies represent sustainable alternatives to pesticides and insecticides. Phytoplasmas are prokaryotic plant pathogens causing severe losses to crops worldwide. Novel approaches are needed since insecticides against their insect vectors and rogueing of infected plants are the only available strategies to counteract phytoplasma diseases. A new iflavirus, named EVV-1, has been described in the leafhopper phytoplasma vectorEuscelidius variegatus, raising the potential to use virus-based application strategies against phytoplasma disease. Here transmission routes of EVV-1 are characterized, and localization within the host reveals the mechanism of insect tolerance to virus infection. Both vertical and horizontal transmission of EVV-1 occur and vertical transmission was more efficient. The virus is systemic and occurs in all life-stages, with the highest loads measured in ovaries and first to third instar nymphs. The basic knowledge gained here on the biology of the virus is crucial for possible future application of iflaviruses as biocontrol agents.
The MPS1 kinase NTE region has helical propensity and preferred conformations towards the TPR domain
Authors: Hiruma Yoshitaka , Matsoukas Minos-Timotheos , Touw Wouter G. , Spyroulias Georgios , Kops Geert J.P.L. , Ubbink Marcellus , Perrakis Anastassis
Published: April 2020

The mitotic spindle assembly checkpoint (SAC) ensures accurate segregation of chromosomes by preventing onset of anaphase until all chromosomes are properly attached to spindle microtubules. The Monopolar spindle 1 (MPS1) kinase is one of the SAC components, localizing at unattached kinetochores by an N-terminal localization module. This module comprises a flexible NTE module and the TPR domain, which we previously characterized for their contribution to kinetochore binding. Here we discuss the conformations of the highly flexible NTE with respect to the TPR domain, using paramagnetic NMR. The distance restraints derived from paramagnetic relaxation enhancements (PREs) show that the mobile NTE can be found in proximity of a large but specific part of the surface area of the TPR domain. To sample the conformational space of the NTE in the context of the NTE-TPR module, we used theab initioRosetta approach supplemented by paramagnetic NMR restraints. We find that many NTE residues have a propensity to form helical structures and that the module localizes at the convex surface of the TPR domain. This work demonstrates the highly dynamic nature of the interactions between the NTE and TPR domains and it shows that the convex rather than the canonical concave TPR surface mediates interactions, leading to the auto-inhibition that the TPR exerts upon the NTE region in the context of SAC signaling.
Deubiquitylase UCHL3 drives error correction at kinetochores and chromosome segregation independent of spindle assembly checkpoint
Authors: Jerabkova Katerina , Liao Yongrong , Kleiss Charlotte , Fournane Sadek , Durik Matej , Agote-Arán Arantxa , Brino Laurent , Sedlacek Radislav , Sumara Izabela
Published: April 2020

Equal segregation of chromosomes during mitosis ensures euploidy of daughter cells. Defects in this process may result in imbalance in chromosomal composition and cellular transformation. Two surveillance pathways, the spindle assembly checkpoint (SAC) and the error-correction (EC), exist at kinetochores that monitor microtubule attachment and faithful segregation of chromosomes at the metaphase to anaphase transition. However, the molecular understanding of the interplay between EC and SAC signaling remains limited. Here we describe a role of deubiquitylase UCHL3 in the regulation of EC pathway during mitosis. Downregulation or inhibition of UCHL3 leads to improper attachments of chromosomes to spindle microtubules and to chromosome alignment defects during metaphase. Frequent segregation errors during anaphase and consequently aneuploidy is also observed upon inactivation of UCHL3. Surprisingly, UCHL3 is not involved in SAC signaling as both recruitment of SAC proteins to kinetochores and timely anaphase onset are not perturbed in UCHL3-deficient cells. Mechanistically, UCHL3 interacts with and deubiquitylates the mitotic kinase Aurora B known to drive both SAC and EC signaling. UCHL3 promotes interaction of Aurora B with MCAK, important EC factor but does not regulate Aurora B binding to other interacting partners or subcellular localization of Aurora B. Our results thus suggest that UCHL3-mediated deubiquitylation functionally separates EC from SAC signaling during mitosis and is critical for maintenance of euploidy in human cells.
CO2enhances the ability ofCandida albicansto form biofilms, overcome nutritional immunity and resist antifungal treatment
Authors: Pentland Daniel R. , Mühlschlegel Fritz A. , Gourlay Campbell W.
Published: April 2020

C. albicansis the predominant fungal pathogen of humans and frequently colonises medical devices, such as voice prosthesis, as a biofilm. It is a dimorphic yeast that can switch between yeast and hyphal forms in response to environmental cues, a property that is essential during biofilm establishment and maturation. One such cue is the elevation of CO2levels, as observed in exhaled breath.. However, despite the clear medical relevance, the effects of CO2onC. albicansbiofilm growth has not been investigated to date. Here, we show that physiologically relevant CO2elevation enhances each stage of theC. albicansbiofilm forming process;from attachment through to maturation and dispersion.. The effects of CO2are mediated via the Ras/cAMP/PKA signalling pathway and the central biofilm regulators Efg1, Brg1, Bcr1 and Ndt80. Biofilms grown under elevated CO2conditions also exhibit increased azole resistance, tolerance to nutritional immunity and enhanced glucose uptake to support their rapid growth. These findings suggest thatC. albicanshas evolved to utilise the CO2signal to promote biofilm formation within the host. We investigate the possibility of targeting CO2activated processes and propose 2-Deoxyglucose as a drug that may be repurposed to preventC. albicansbiofilm formation on medical airway management implants. We thus characterise the mechanisms by which CO2promotesC. albicansbiofilm formation and suggest new approaches for future preventative strategies.
Integration of behavioral and biological variables using penalized regression: an application to the maternal immune activation model of autism
Authors: Paraschivescu Cristina , Barbosa Susana , Lorivel Thomas , Glaichenhaus Nicolas , Davidovic Laetitia
Published: April 2020

Maternal immune activation (MIA) during pregnancy increases the odds of developing neuropsychiatric disorders such as autism spectrum disorder (ASD) later in life. In pregnant mice, MIA can be induced by injecting the viral mimic polyinosinic:polycytidylic acid (poly(I:C) to pregnant dams resulting in altered fetal neurodevelopmental and behavioral changes in their progeny. Although the murine MIA model has been extensively studied worldwide, the underlying mechanisms have only been partially elucidated. Furthermore, the murine MIA model suffers from lack of reproducibility, at least in part because it is highly influenced by subtle changes in environmental conditions. In human studies, multivariable (MV) statistical analysis is widely used to control for covariates including sex, age, exposure to environmental factors and many others. We reasoned that animal studies in general, and studies on the MIA model in particular, could therefore benefit from MV analyzes to account for complex phenotype interactions and high inter-individual variability. Here, we used a dataset consisting of 26 variables collected on 67 male pups during the course of several independent experiments on the MIA model. We then analyzed this dataset using penalized regression to identify variables associated within uteroexposure to MIA. In addition to confirming the association between some previously described biological variables and MIA, we identified new variables that could play a role in neurodevelopment alterations. Aside from providing new insights into variable interactions in the MIA model, this study highlights the importance of extending the use of MV statistics to animal studies.