bluuebunny/crossref_metadata_2025 huggingface dataset:
Mixing and matching methylotrophic enzymes to design a novel methanol utilization pathway inE. coli
Authors: De Simone A. , Vicente C.M. , Peiro C. , Gales L. , Bellvert F. , Enjalbert B. , Heux S.
Published: April 2020

One-carbon (C1) compounds, such as methanol, have recently gained attention as alternative low-cost and non-food feedstocks for microbial bioprocesses. Considerable research efforts are thus currently focused on the generation of synthetic methylotrophs by transferring methanol assimilation pathways into established bacterial production hosts. In this study, we used an iterative combination of dry and wet approaches to design, implement and optimize this metabolic trait in the most common chassis,E. coli. Throughin silicomodeling, we designed a new route that “mixed and matched” two methylotrophic enzymes: a bacterial methanol dehydrogenase (Mdh) and a dihydroxyacetone synthase (Das) from yeast. To identify the best combination of enzymes to introduce intoE. coli, we built a library of 266 pathway variants containing different combinations of Mdh and Das homologues and screened it using high-throughput13C-labeling experiments. The highest level of incorporation, 22% of labeled methanol carbon into the multi-carbon compound PEP, was obtained using a variant composed of a Mdh fromA. gerneriand a codon-optimized version ofP. angustaDas. Finally, the activity of this new synthetic pathway was further improved by engineering strategic metabolic targets identified using omics and modelling approaches. The final synthetic strain had 1.5 to 5.9 times higher methanol assimilation in intracellular metabolites and proteinogenic amino acids than the starting strain did. Broadening the repertoire of methanol assimilation pathways is one step further toward synthetic methylotrophy inE. coli.
Spectral graph theory efficiently characterises ventilation heterogeneity in lung airway networks
Authors: Whitfield Carl A. , Latimer Peter , Horsley Alex , Wild Jim M. , Collier Guilhem J. , Jensen Oliver E.
Published: April 2020

This paper introduces a linear operator for the purposes of quantifying the spectral properties of transport within resistive trees, such as airflow in lung airway networks. The operator, which we call the Maury matrix, acts only on the terminal nodes of the tree and is equivalent to the adjacency matrix of a complete graph summarising the relationships between all pairs of terminal nodes. We show that the eigenmodes of the Maury operator have a direct physical interpretation as the relaxation, or resistive, modes of the network. We apply these findings to both idealised and image-based models of ventilation in lung airway trees and show that the spectral properties of the Maury matrix characterise the flow asymmetry in these networks more concisely than the Laplacian modes, and that eigenvector centrality in the Maury spectrum is closely related to the phenomenon of ventilation heterogeneity caused by airway narrowing or obstruction. This method has applications in dimensionality reduction in simulations of lung mechanics, as well as for characterisation of models of the airway tree derived from medical images.
Genome-wide identification, characterization, and expression analysis of the monovalent cation-proton antiporter superfamily in maize, and functional analysis of its role in salt tolerance
Authors: Kong Mengsi , Luo Meijie , Li Jingna , Feng Zhen , Zhang Yunxia , Song Wei , Zhang Ruyang , Wang Ronghuan , Wang Yuandong , Zhao Jiuran , Tao Yongsheng , Zhao Yanxin
Published: April 2020

Na+, K+and pH homeostasis are important for plant life and they are controlled by the monovalent cation proton antiporter (CPA) superfamily. The roles ofZmCPAsin salt tolerance are not fully elucidated. In this study, we identified 35ZmCPAscomprising 13 Na+/H+exchangers (ZmNHXs), 16 cation/H+exchanger (ZmCHXs), and 6 K+efflux antiporters (ZmKEAs). All ZmCPAs have transmembrane domains and maize protoplasts transient expression showed that ZmNHX5 and ZmCHX17 localized to cell membrane system.ZmCHXswere specifically highly expressed in anthers, whileZmNHXsandZmKEAsshowed high expression in various tissues.ZmNHX5andZmKEA2were up-regulated in maize seedlings under both NaCl and KCl stresses. Yeast complementation experiments revealed the roles ofZmNHX5, ZmKEA2in NaCl tolerance. Analyses of the maize mutants further validated the salt tolerance functions ofZmNHX5andZmKEA2. Our study highlights comprehensive information ofZmCPAsand provides new gene targets for salt tolerance maize breeding.
Macroevolutionary Stability Predicts Interaction Patterns of Species in Seed Dispersal Networks
Authors: Burin Gustavo , Guimaraes Paulo R. , Quental Tiago B.
Published: April 2020

Assessing deep-time mechanisms affecting the assembly of ecological networks is key to understanding biodiversity changes on broader time scales. We combined analyses of diversification rates with interaction network descriptors from 468 bird species belonging to 29 seed-dispersal networks to show that bird species that contribute most to the network structure of plant-frugivorous interactions belong to lineages that show higher macroevolutionary stability. This association is stronger in warmer, wetter, less seasonal environments. We infer that the macroevolutionary sorting mechanism acts through the regional pool of species by sorting species based on the available relative differences in diversification rates, rather than absolute rates. Our results illustrate how the interplay between interaction patterns and diversification dynamics may shape the organization and long-term dynamics of ecological networks.
Selective enhancement of low-gamma activity by tACS improves phonemic processing and reading accuracy in dyslexia
Authors: Marchesotti Silvia , Nicolle Johanna , Merlet Isabelle , Arnal Luc H. , Donoghue John P. , Giraud Anne-Lise
Published: April 2020

The phonological deficit in dyslexia is associated with altered low-gamma oscillatory function in left auditory cortex, but a causal relationship between oscillatory function and phonemic processing has never been established. After confirming a deficit at 30 Hz with electroencephalography (EEG), we applied 20 minutes of transcranial alternating current stimulation (tACS) to transiently restore this activity in adults with dyslexia. The intervention significantly improved phonological processing and reading accuracy as measured immediately after tACS. The effect was selective to 30 Hz stimulation, and proportional to dyslexia severity. Importantly, we observed that the focal intervention on the left auditory cortex also decreased 30 Hz activity in the right superior temporal cortex, resulting in reinstating a left dominance for the oscillatory response, as present in controls. These findings formally establish a causal role of neural oscillations in phonological processing, and offer solid neurophysiological grounds for a potential correction of low-gamma anomalies, and for alleviating of the phonological deficit in dyslexia.
Multiple evolutionary origins and losses of tooth complexity in squamates
Authors: Lafuma Fabien , Corfe Ian J. , Clavel Julien , Di-Poï Nicolas
Published: April 2020

Teeth act as tools for acquiring and processing food and so hold a prominent role in vertebrate evolution1,2. In mammals, dental-dietary adaptations rely on tooth shape and complexity variations controlled by cusp number and pattern – the main features of the tooth surface3,4. Complexity increase through cusp addition has dominated the diversification of many mammal groups3,5-9. However, studies of Mammalia alone don’t allow identification of patterns of tooth complexity conserved throughout vertebrate evolution. Here, we use morphometric and phylogenetic comparative methods across fossil and extant squamates (“lizards” and snakes) to show they also repeatedly evolved increasingly complex teeth, but with more flexibility than mammals. Since the Late Jurassic, six major squamate groups independently evolved multiple-cusped teeth from a single-cusped common ancestor. Unlike mammals10,11, reversals to lower cusp numbers were frequent in squamates, with varied multiple-cusped morphologies in several groups resulting in heterogenous evolutionary rates. Squamate tooth complexity evolved in correlation with dietary change – increased plant consumption typically followed tooth complexity increases, and the major increases in speciation rate in squamate evolutionary history are associated with such changes. The evolution of complex teeth played a critical role in vertebrate evolution outside Mammalia, with squamates exemplifying a more labile system of dental- dietary evolution.
multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets
Authors: Bhagwat Aditya M , Graumann Johannes , Wiegandt Rene , Bentsen Mette , Kuenne Carsten , Preussner Jens , Braun Thomas , Looso Mario
Published: April 2020

Targeting the coding genome to introduce single nucleotide deletions/insertions via Crispr/Cas9 technology has become a standard procedure in recent years. It has quickly spawned a multitude of methods such as Prime Editing, Crispr/Cas9 assisted APEX proximity labeling of proteins, or homology directed repair (HDR), for which supporting bioinformatic tools are, however, lagging behind. New applications often require specific guide-RNA (gRNA) design functionality, and a generic gRNA design tool is critically missing. Here we review gRNA designer software and introduce multicrispr, an R based tool intended to design individual gRNAs as well as gRNA libraries targeting many genomic loci in parallel. The package is easy to use, detects, scores and filters gRNAs on both efficiency and specificity, visualizes and aggregates results per target or Crispr/Cas9 sequence, and finally returns both genomic ranges as well as sequences of preferred, off target-free gRNAs. In order to be generic, multicrispr defines and implements agenomic arithmetics frameworkas a basis for facile adaptation to techniques yet to arise. Its performance and new gRNA design concepts such astarget set specific filteringfor gRNA libraries render multicrispr the tool of choice when dealing with screening-like approaches.
Traveling fronts in self-replicating persistent random walks with multiple internal states
Authors: Ishihara Keisuke , George Ashish B. , Cornelius Ryan , Korolev Kirill S.
Published: April 2020

Self-activation coupled to a transport mechanism results in traveling waves that describe polymerization reactions, forest fires, tumor growth, and even the spread of epidemics. Diffusion is a simple and commonly used model of particle transport. Many physical and biological systems are, however, better described by persistent random walks that switch between multiple states of ballistic motion. So far, traveling fronts in persistent random walk models have only been analyzed in special, simplified cases. Here, we formulate the general model of reaction-transport processes in such systems and show how to compute the expansion velocity for arbitrary number of states. For the two-state model, we obtain a closed-form expression for the velocity and report how it is affected by different transport and replication parameters. We also show that nonzero death rates result in a discontinuous transition from quiescence to propagation. We compare our results to a recent observation of a discontinuous onset of propagation in microtubule asters and comment on the universal nature of the underlying mechanism.
Neonicotinoids Disrupt Circadian Rhythms and Sleep in Honey Bees
Authors: Tackenberg Michael C. , Giannoni-Guzmán Manuel A. , Doll Caleb A. , Agosto-Rivera José L. , Broadie Kendal , Moore Darrell , McMahon Douglas G.
Published: April 2020

Honey bees are critical pollinators in ecosystems and agriculture, but their numbers have significantly declined. Declines in pollinator populations are thought to be due to multiple factors including habitat loss, climate change, increased vulnerability to disease and parasites, and pesticide use. Neonicotinoid pesticides are agonists of insect nicotinic cholinergic receptors, and sub-lethal exposures are linked to reduced honey bee hive survival. Honey bees are highly dependent on circadian clocks to regulate critical behaviors, such as foraging orientation and navigation, time-memory for food sources, sleep, and learning/ memory processes. Because circadian clock neurons in insects receive light input through cholinergic signaling we tested for effects of neonicotinoids on honey bee circadian rhythms and sleep. Neonicotinoid ingestion by feeding over several days results in neonicotinoid accumulation in the bee brain, disrupts circadian rhythmicity in many individual bees, shifts the timing of behavioral circadian rhythms in bees that remain rhythmic, and impairs sleep. Neonicotinoids and light input act synergistically to disrupt bee circadian behavior, and neonicotinoids directly stimulate wake-promoting clock neurons in the fruit fly brain. Neonicotinoids disrupt honey bee circadian rhythms and sleep, likely by aberrant stimulation of clock neurons, to potentially impair honey bee navigation, time-memory, and social communication.
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
Authors: Cao Yuming , Guo Zhiru , Vangala Pranitha , Donnard Elisa , Liu Ping , McDonel Patrick , Ordovas-Montanes Jose , Shalek Alex K. , Finberg Robert W. , Wang Jennifer P. , Garber Manuel
Published: April 2020

Influenza virus infections are major causes of morbidity and mortality. Research using cultured cells, bulk tissue, and animal models cannot fully capture human disease dynamics. Many aspects of virus-host interactions in a natural setting remain unclear, including the specific cell types that are infected and how they and neighboring bystander cells contribute to the overall antiviral response. To address these questions, we performed single-cell RNA sequencing (scRNA-Seq) on cells from freshly collected nasal washes from healthy human donors and donors diagnosed with acute influenza during the 2017-18 season. We describe a previously uncharacterized goblet cell population, specific to infected individuals, with high expression of MHC class II genes. Furthermore, leveraging scRNA-Seq reads, we obtained deep viral genome coverage and developed a model to rigorously identify infected cells that detected influenza infection in all epithelial cell types and even some immune cells. Our data revealed that each donor was infected by a unique influenza variant and that each variant was separated by at least one unique non-synonymous difference. Our results demonstrate the power of massively-parallel scRNA-Seq to study viral variation, as well as host and viral transcriptional activity during human infection.
The role of gene expression on human sexual dimorphism: too early to call
Authors: Porcu Eleonora , Claringbould Annique , Lepik Kaido ,   BIOS Consortium, Richardson Tom G. , Santoni Federico A. , Franke Lude , Reymond Alexandre , Kutalik Zoltán
Published: April 2020

The genetic underpinning of sexual dimorphism is very poorly understood. The prevalence of many diseases differs between men and women, which could be in part caused by sex-specific genetic effects. Nevertheless, only a few published genome-wide association studies (GWAS) were performed separately in each sex. The reported enrichment of expression quantitative trait loci (eQTLs) among GWAS–associated SNPs suggests a potential role of sex-specific eQTLs in the sex-specific genetic mechanism underlying complex traits.

To explore this scenario, we performed a genome-wide analysis of sex-specific whole blood RNA-seq eQTLs from 3,447 individuals. Among 9 million SNP-gene pairs showing sex-combined associations, we found 18 genes with significant sex-specificcis-eQTLs (FDR 5%). Our phenome-wide association study of the 18 top sex-specific eQTLs on >700 traits unraveled that these eQTLs do not systematically translate into detectable sex-specific trait-associations. Power analyses using real eQTL- and causal effect sizes showed that millions of samples would be necessary to observe sex-specific trait associations that are fully driven by sex-specificcis-eQTLs. Compensatory effects may further hamper their detection. In line with this observation, we confirmed that the sex-specific trait-associations detected so far are not driven by sex-specificcis-eQTLs.
Identifying Neural Signatures Mediating Behavioral Symptoms and Psychosis Onset: High-Dimensional Whole Brain Functional Mediation Analysis
Authors: Chén Oliver Y. , Cao Hengyi , Phan Huy , Nagels Guy , Reinen Jenna M. , Gou Jiangtao , Qian Tianchen , Di Junrui , Prince John , Cannon Tyrone D. , de Vos Maarten
Published: April 2020

Along the pathway from behavioral symptoms to the development of psychotic disorders sits the multivariate mediating brain. The functional organization and structural topography of large-scale neural mediators among patients with brain disorders, however, are not well understood. Here, we design a high-dimensional brain-wide functional mediation framework to investigate brain regions that intermediate between baseline behavioral symptoms and future conversion to full psychosis among individuals at clinical high risk (CHR). Using resting-state functional magnetic resonance imaging (fMRI) data from 263 CHR subjects, we extract anαbrain atlas and aβbrain atlas: the former underlines brain areas associated with prodromal symptoms and the latter highlights brain areas associated with disease onset. In parallel, we identify thePmediators and theNmediators that respectively facilitate or protect against developing brain disorders among subjects with more severe behavioral symptoms and quantify the effect of each neural mediator on disease development. Taken together, theα-βatlases and theP-Nmediators paint a brain-wide picture of neural markers that are potentially regulating behavioral symptoms and the development of psychotic disorders and highlight a statistical framework that is useful to uncover large-scale intermediating variables in a regulatory biological organization.
Analysis of SARS-CoV-2 Antibodies in COVID-19 Convalescent Blood using a Coronavirus Antigen Microarray
Authors: de Assis Rafael R. , Jain Aarti , Nakajima Rie , Jasinskas Algis , Felgner Jiin , Obiero Joshua M. , Adenaiye Oluwasanmi , Tai Sheldon , Hong Filbert , Norris Philip J. , Stone Mars , Simmons Graham , Bagri Anil , Schreiber Martin , Buser Andreas , Holbro Andreas , Battegay Manuel , Hosimer Philip , Noesen Charles , Milton Donald K. ,   Prometheus Study Group, Davies D. Huw , Contestable Paul , Corash Laurence M. , Busch Michael P. , Felgner Philip L. , Khan Saahir
Published: April 2020

The current practice for diagnosis of COVID-19, based on SARS-CoV-2 PCR testing of pharyngeal or respiratory specimens in a symptomatic patient at high epidemiologic risk, likely underestimates the true prevalence of infection. Serologic methods can more accurately estimate the disease burden by detecting infections missed by the limited testing performed to date. Here, we describe the validation of a coronavirus antigen microarray containing immunologically significant antigens from SARS-CoV-2, in addition to SARS-CoV, MERS-CoV, common human coronavirus strains, and other common respiratory viruses. A comparison of antibody profiles detected on the array from control sera collected prior to the SARS-CoV-2 pandemic versus convalescent blood specimens from virologically confirmed COVID-19 cases demonstrates near complete discrimination of these two groups, with improved performance from use of antigen combinations that include both spike protein and nucleoprotein. This array can be used as a diagnostic tool, as an epidemiologic tool to more accurately estimate the disease burden of COVID-19, and as a research tool to correlate antibody responses with clinical outcomes.
Vesicular GABA-transporter neurons in the zona incerta are maximally active during non rapid-eye movement (NREM) and rapid-eye movement (REM) sleep
Authors: Blanco-Centurion Carlos , Luo SiWei , Vidal-Ortiz Aurelio , Shiromani Priyattam J.
Published: April 2020

Sleep and wake are opposing behavioral states controlled by the activity of specific neurons. The neurons responsible for sleep/wake control have not been fully identifed due to the lack ofin-vivohigh throughput technology. We use the deep-brain calcium (Ca2+) imaging method to identify activity of hypothalamic neurons expressing the vesicular GABA transporter (vGAT), a marker of GABAergic neurons. vGAT-cre mice (n=5) were microinjected with rAAV-FLEX-GCaMP6Minto the lateral hypothalamus and 21d later the Ca2+influx in vGAT neurons (n=372) was recorded in freely-behaving mice during waking (W), NREM and REM sleep. Post-mortem analysis revealed the lens tip located in the zona incerta/lateral hypothalamus (ZI-LH) and the change in fluorescence of neurons in the field of view was as follows: 54.9% of the vGAT neurons had peak fluorescence during REM sleep (REM-max), 17.2% were NREM-max, 22.8% were wake-max while 5.1% were both wake+REM max. Thus, three quarters of the recorded vGAT neurons in the ZI-LH were most active during sleep. In the NREM-max group Ca2+fluorescence anticipated the initiation of NREM sleep onset and remained high throughout sleep (NREM and REM sleep). In the REM-max neurons Ca2+fluorescence increased before the onset of REM sleep and stayed elevated during the episode. Activation of the vGAT NREM-max neurons in the zona incerta and dorsal lateral hypothalamus would inhibit the arousal neurons to initiate and maintain sleep.
Social groups with diverse personalities mitigate physiological stress in a songbird
Authors: Vágási Csongor I. , Fülöp Attila , Osváth Gergely , Pap Péter L. , Pénzes Janka , Benkő Zoltán , Lendvai Ádám Z. , Barta Zoltán
Published: April 2020

Social groups often consist of diverse phenotypes, including personality types, and this diversity is known to affect the functioning of the group as a whole. Social selection theory proposes that group composition (i.e. social environment) also influences the performance of individual group members. However, the effect of group behavioural composition on group members remains largely unexplored, and it is still contentious whether individuals benefit more in a social environment with homogeneous or diverse behavioural composition. We experimentally formed groups of house sparrowsPasser domesticuswith high and low diversity of personality (exploratory behaviour), and found that their physiological state (body condition, physiological stress and oxidative damage) improved with increasing group-level diversity of personality. These findings demonstrate that group personality composition affects the condition of group members and individuals benefit from social heterosis (i.e. associating with a diverse set of behavioural types). This aspect of the social life can play a key role in affiliation rules of social animals and might explain the evolutionary coexistence of different personalities in nature.
Volatiles defenses of AmazonAztecaants (repellent ants)
Authors: Jardine Kolby J. , de O. Piva Luani R. , Rodrigues Tayana B. , Spanner Gustavo C. , Rodrigues Jardel R. , Menezes Valdiek S. , Sampaio Israel , Oliveira Daniela C. , Gimenez Brunon O. , Higuchi Niro , Chambers Jeffrey
Published: April 2020

Aztecaants are widely distributed in the neotropics and have been utilized as natural insect repellent for centuries.Aztecaoils provide natural defense against herbivores in mutualistic interactions between ants and their host trees. While chemical characterization of oil secretions revealed a composition dominated by iridoids and ketones, the volatile emissions fromAztecaants, and therefore the active gas-phase semiochemicals, remain uncharacterized. In this study, we determined the composition of volatile emissions from a sample of anAztecaant nest near the Rio Negro in the central Amazon. We foundAztecaemissions were composed of a blend of methyl cyclopentyl and methyl cyclopentenyl based volatiles previously identified inAztecaoil extracts as potent alarm pheromones. The ketone 6-methyl-5-hepten-2-one, which also waspreviously identified as a major component of theAztecaoil, was found to be the dominant volatile emitted. For the first time, we report emissions of the highly volatile ketones 2,3-butadione and acetoin from theAztecanest. Our study has important implications for the better understanding of the ecology and defense strategies ofAztecaants in herbivore defense and provides a base for future commercial applications involvingAztecaant essential oils as natural insect repellents.
Deletion of the mitochondrial matrix protein cyclophilin-D prevents parvalbumin interneuron dysfunction and cognitive deficits in a mouse model of NMDA hypofunction
Authors: Phensy Aarron , Lindquist Kathy L. , Lindquist Karen A. , Bairuty Dania , Gauba Esha , Guo Lan , Tian Jing , Du Heng , Kroener Sven
Published: April 2020

Redox dysregulation and oxidative stress are final common pathways in the pathophysiology of a variety of psychiatric disorders, including schizophrenia. Oxidative stress causes dysfunction of GABAergic parvalbumin-positive interneurons (PVI), which are crucial for the coordination of neuronal synchrony during sensory- and cognitive-processing. Mitochondria are the main source of reactive oxygen species (ROS) in neurons and they control synaptic activity through their roles in energy production and intracellular calcium homeostasis. We have previously shown that in male mice transient blockade of NMDA receptors during development (subcutaneous injections of 30 mg/kg ketamine (KET) on postnatal days 7, 9, and 11) results in long-lasting alterations in synaptic transmission and reduced parvalbumin expression in the adult prefrontal cortex (PFC), contributing to a behavioral phenotype that mimics multiple symptoms associated with schizophrenia. These changes correlate with oxidative stress and impaired mitochondrial function in both PVI and pyramidal cells. Here, we show that genetic deletion (Ppif-/-) of the mitochondrial matrix protein cyclophilin D (CypD) prevents perinatal KET-induced increases in ROS and the resulting deficits in PVI function, and changes in excitatory and inhibitory synaptic transmission in the PFC. Deletion of CypD also prevented KET-induced behavioral deficits in cognitive flexibility, social interaction, and novel object recognition. Taken together, these data highlight how mitochondrial activity may play an integral role in modulating PVI-mediated cognitive processes.

Significance Statement

Mitochondria are important modulators of oxidative stress and cell function, yet how mitochondrial dysfunction affects cell activity and synaptic transmission in psychiatric illnesses is not well understood. NMDA receptor blockade with ketamine during development causes oxidative stress, dysfunction of parvalbumin-positive interneurons (PVI), and long-lasting physiological and behavioral changes. Here we show that mice deficient for the mitochondrial matrix protein cyclophilin D show robust protection from PVI dysfunction following perinatal NMDAR-blockade. Mitochondria serve as an essential node for a number of stress-induced signaling pathways and our experiments suggest that failure of mitochondrial redox regulation can contribute to PVI dysfunction.
Recycling old drugs: cardiac glycosides as therapeutics to target barrier inflammation of the vasculature, meninges and choroid plexus
Authors: Jansson Deidre , Dieriks Victor Birger , Rustenhoven Justin , Smyth Leon C.D. , Scotter Emma , Aalderink Miranda , Feng Sheryl , Johnson Rebecca , Schweder Patrick , Mee Edward , Heppner Peter , Turner Clinton , Curtis Maurice , Faull Richard , Dragunow Mike
Published: April 2020

Neuroinflammation is a key component of virtually all neurodegenerative diseases; preceding neuronal loss and associating directly with cognitive impairment. Neuroinflammatory signals can originate and be amplified at barrier tissues such as brain vasculature, surrounding meninges and the choroid plexus. We designed a high-throughput screening system to target inflammation in cells of the blood-brain barrier (primary human pericytes and endothelia) and microglia enabling us to target human disease-specific inflammatory modifiers. Screening an FDA-approved drug library we identified digoxin and lanatoside C, members of the cardiac glycoside family as inflammatory modulating drugs that work in blood-brain barrier cells. A novelex vivoassay of leptomeningeal and choroid plexus explants further confirmed that these drugs maintain their function in 3D cultures of brain border tissues. While current therapeutic strategies for the treatment of neurodegenerative diseases are missing the mark in terms of targets, efficacy and translatability, our innovative approach usingin vitroandex vivohuman barrier cells and tissues to target neuroinflammatory pathways is a step forward in drug development and testing, and brings us closer to translatable treatments for human neurodegenerative disease.

One Sentence Summary

We have identified cardiac glycosides as powerful regulators of neuroinflammatory pathways in brain-barrier tissues such as vasculature, meninges and choroid plexus.
Bio-Node – Bioinformatics in the Cloud
Authors: Spreen Yannick , Miller Maximilian
Published: April 2020

Motivation: The applicability and reproducibility of bioinformatics methods and results often depend on the structure and software architecture of their development. Exponentially growing data sets require ever more optimization and performance with conventional computing capacities lacking this process. This creates a large overhead for software development in a research area which is primarily interested in solving complex biological problems rather than developing new, performant software solutions. In pure computer science, new structures in the field of web development have produced more efficient processes for container-based software solutions. The advantages of these structures have rarely been explored in a broader scientific scale. This is also the case with the trend of migrating computations from on premise resources to the cloud. Results: We created Bio-Node, a new platform for large scale bio data analysis utilizing cloud compute resources (publicly available at https://bio-node.de). Bio-Node enables building complex workflows using a sophisticated web interface. We applied Bio-Node to implement bioinformatic workflows for rapid metagenome function annotation. We further developed "Auto-Clustering", a workflow that automatically extracts the most suited clustering parameters for specific data types and subsequently enables to optimally segregate unknown samples of the same type. Compared to existing methods and approaches Bio-Node improves performance and costs of bioinformatics data analyses while providing an easier and faster development process with focus on reproducibility and reusability.
Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci
Authors: Hong Ted , Parameswaran Sreeja , Donmez Omer , Miller Daniel , Forney Carmy , Lape Michael , Ribeiro Mariana Saint Just , Liang Jun , Edsall Lee E. , Magnusen Albert , Miller William , Chepelev Iouri , Harley John B. , Zhao Bo , Kottyan Leah C. , Weirauch Matthew T.
Published: April 2020

The interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein-Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we demonstrated that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders. To further examine the mechanistic roles played by EBNA2 at these loci on a genome-wide scale, we globally examined gene expression, chromatin accessibility, chromatin looping, and EBNA2 binding, in a B cell line that was 1) uninfected, 2) infected with a strain of EBV lacking EBNA2, or 3) infected with a strain that expresses EBNA2. We identified >400 EBNA2-dependent differentially expressed human genes and >5,000 EBNA2 binding events in the human genome. ATAC-seq analysis revealed >2,000 regions in the human genome with EBNA2-dependent chromatin accessibility, and HiChIP-seq data revealed >1,700 regions where EBNA2 altered chromatin looping interactions. Importantly, autoimmune genetic risk loci were highly enriched at the sites of these EBNA2-dependent chromatin-altering events. We present examples of autoimmune risk genotype-dependent EBNA2 events, nominating genetic risk mechanisms for autoimmune risk loci such asZMIZ1. Taken together, our results reveal important interactions between host genetic variation and EBNA2-driven disease mechanisms. Further, our study highlights a critical role for EBNA2 in rewiring human gene regulatory programs through rearrangement of the chromatin landscape and nominates these interactions as components of genetic mechanisms that influence the risk of multiple autoimmune diseases.
Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression
Authors: Vanderpool Dan , Minh Bui Quang , Lanfear Robert , Hughes Daniel , Murali Shwetha , Harris R. Alan , Raveendran Muthuswamy , Muzny Donna M. , Gibbs Richard A. , Worley Kim C. , Rogers Jeffrey , Hahn Matthew W.
Published: April 2020

Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here we present new reference genome assemblies for three Old World Monkey species:Colobus angolensis ssp. palliatus(the black and white colobus),Macaca nemestrina(southern pig-tailed macaque), andMandrillus leucophaeus(the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.
Girls gone wild: Social isolation induces hyperactivity and exploration in aged female mice
Authors: Sullens D. Gregory , Gilley Kayla , Jensen Kendall , Sekeres Melanie J.
Published: April 2020

The likelihood of experiencing social isolation increases later in life, particularly for females. It remains unknown how late-life social isolation impacts cognition and affective behavior in aged mice. We assessed the impact of late-life social isolation in 18-month old female mice. One month of single-housing did not lead to robust depressive-like symptomology, altered social interaction behavior, or sensitivity to context fear acquisition or memory. Rather, isolation increased hyperactivity and exploration, and reduced anxiety-like behavior in the open field and elevated plus maze, findings that have been similarly observed in young female and male mice following early-life isolation. These findings suggest that hyperactivity is a robust behavior following social isolation across the lifespan.
Tuning Hsp104 specificity to selectively detoxify α-synuclein
Authors: Mack Korrie L. , Kim Hanna , Jackrel Meredith E. , Lin JiaBei , DeNizio Jamie E. , Yan Xiaohui , Chuang Edward , Tariq Amber , Cupo Ryan R. , Castellano Laura M. , Caldwell Kim A. , Caldwell Guy A. , Shorter James
Published: April 2020

Hsp104 is an AAA+ protein disaggregase that solubilizes and reactivates proteins trapped in aggregated states. We have engineered potentiated Hsp104 variants to mitigate toxic misfolding of α-synuclein, TDP-43, and FUS implicated in fatal neurodegenerative disorders. Though potent disaggregases, these enhanced Hsp104 variants lack substrate specificity, and can have unfavorable off-target effects. Here, to lessen off-target effects, we engineer substrate-specific Hsp104 variants. By altering Hsp104 pore loops that engage substrate, we disambiguate Hsp104 variants that selectively suppress α-synuclein toxicity but not TDP-43 or FUS toxicity. Remarkably, α-synuclein-specific Hsp104 variants emerge that mitigate α-synuclein toxicity via distinct ATPase-dependent mechanisms, involving α-synuclein disaggregation or detoxification of α-synuclein conformers without disaggregation. Importantly, both types of α-synuclein-specific Hsp104 variant reduce dopaminergic neurodegeneration in aC. elegansmodel of Parkinson’s disease more effectively than non-specific variants. We suggest that increasing the substrate specificity of enhanced disaggregases could be applied broadly to tailor therapeutics for neurodegenerative disease.
Chikungunya virus infection impairs the function of osteogenic cells
Authors: Roy Enakshi , Shi Wen , Duan Bin , Reid St Patrick
Published: April 2020

Chikungunya virus (CHIKV) is a positive-sense, single-stranded RNA virus, spread by theAedesspecies (sp.) mosquitoes. Chikungunya virus (CHIKV) causes a condition characterized by high fever, headache, rash, and joint pain. Recent investigations reveal presence of bone lesions and erosive arthritis in the joints of CHIKV infected patients, indicating an association of bone pathology with CHIKV infection. However, the molecular mechanism underlying CHIKV-induced bone pathology remains poorly defined. Bone marrow derived mesenchymal stem cells (BMSCs) contribute to bone homeostasis by differentiating into osteogenic cells which later mature to form the bone. Disruption of osteogenic differentiation and function of BMSCs lead to bone pathologies. Studies show that virus infections can alter the properties and function of BMSCs. However, to date, pathogenesis of CHIKV infection in this context has not been studied. In the current study, we investigated the susceptibility of BMSCs and osteogenic cells to CHIKV and studied the effect of infection on these cells. To our knowledge, for the first time we report that CHIKV can productively infect BMSCs and osteogenic cells. We also observed a decreased gene expression of the major regulator of osteogenic differentiation, RUNX2 in CHIKV infected osteogenic cells. Furthermore, impaired functional properties of osteogenic cells i.e. decreased production and activity of alkaline phosphatase (ALP) and matrix mineralization were observed in the presence of CHIKV infection. Thus, we conclude that CHIKV likely impairs osteogenic differentiation of BMSCs indicating a possible role of BMSCs in altering bone homeostasis during CHIKV infection.

Importance

Presently, no vaccines or treatment options are available for CHIKV infection. Joint pain is one of the major concerns. Although studies have shown an association between bone pathology and infection, the molecular pathogenesis in context of bone pathology is poorly defined. Here, we demonstrate for the first time that BMSCs and BMSC-derived osteogenic cells are susceptible to CHIKV infection and infection likely alters function of the osteogenic cells. This study highlights altered osteogenic differentiation as a possible mechanism for causing the bone pathology observed in CHIKV pathogenesis.
Spt5 phosphorylation and the Rtf1 Plus3 domain promote Rtf1 function through distinct mechanisms
Authors: Chen Jennifer J. , Mbogning Jean , Hancock Mark A. , Majdpour Dorsa , Madhok Manan , Nassour Hassan , Dallagnol Juliana C. , Pagé Viviane , Chatenet David , Tanny Jason C.
Published: April 2020

Rtf1 is a conserved RNA polymerase II (RNAPII) elongation factor that promotes co-transcriptional histone modification, RNAPII transcript elongation, and mRNA processing. Rtf1 function requires phosphorylation of Spt5, an essential RNAPII processivity factor. Spt5 is phosphorylated within its C-terminal domain (CTD) by cyclin-dependent kinase 9 (Cdk9), catalytic component of positive transcription elongation factor b (P-TEFb). Rtf1 recognizes phosphorylated Spt5 (pSpt5) through its Plus3 domain. Since Spt5 is a unique target of Cdk9, and Rtf1 is the only known pSpt5-binding factor, the Plus3/pSpt5 interaction is thought to be a key Cdk9-dependent event regulating RNAPII elongation. Here we dissect Rtf1 regulation by pSpt5 in the fission yeastSchizosaccharomyces pombe. We demonstrate that the Plus3 domain of Rtf1 (Prf1 inS. pombe) and pSpt5 are functionally distinct, and that they act in parallel to promote Prf1 function. This alternate Plus3 domain function involves an interface that overlaps with the pSpt5 binding site and that can interact with single-stranded nucleic acid or with the Polymerase Associated Factor (PAF) Complexin vitro. We further show that the C-terminal region of Prf1, which also interacts with PAF, has a similar parallel function with pSpt5. Our results elucidate unexpected complexity underlying Cdk9-dependent pathways that regulate transcription elongation.
Comprehensive database of secondary metabolites from cyanobacteria
Authors: Jones Martin R. , Pinto Ernani , Torres Mariana A. , Dörr Fabiane , Mazur-Marzec Hanna , Szubert Karolina , Tartaglione Luciana , Dell’Aversano Carmela , Miles Christopher O. , Beach Daniel G. , McCarron Pearse , Sivonen Kaarina , Fewer David P. , Jokela Jouni , Janssen Elisabeth M.-L.
Published: April 2020

Cyanobacteria form harmful mass blooms in freshwater and marine environments around the world. A range of secondary metabolites has been identified from cultures of cyanobacteria and biomass collected from cyanobacterial bloom events. A comprehensive database is necessary to correctly identify cyanobacterial metabolites and advance research on their abundance, persistence and toxicity in natural environments. We consolidated open access databases and manually curated missing information from the literature published between 1970 and March 2020. The result is the database CyanoMetDB, which includes more than 2000 entries based on more than 750 literature references. This effort has more than doubled the total number of entries with complete literature metadata and structural composition (SMILES codes) compared to publicly available databases to this date. Over the past decade, more than one hundred additional secondary metabolites have been identified yearly. We organized all entries into structural classes and conducted substructure searches of the provided SMILES codes. This approach demonstrated, for example, that 65% of the compounds carry at least one peptide bond, 57% are cyclic compounds, and 30% carry at least one halogen atom. Structural searches by SMILES code can be further specified to identify structural motifs that are relevant for analytical approaches, research on biosynthetic pathways, bioactivity-guided analysis, or to facilitate predictive science and modeling efforts on cyanobacterial metabolites. This database facilitates rapid identification of cyanobacterial metabolites from toxic blooms, research on the biosynthesis of cyanobacterial natural products, and the identification of novel natural products from cyanobacteria.
Stability of the vaginal microbiota during pregnancy and its importance for early infant colonization
Authors: Mortensen Martin S. , Rasmussen Morten A. , Stokholm Jakob , Brejnrod Asker D. , Balle Christina , Thorsen Jonathan , Krogfelt Karen A. , Bisgaard Hans , Sørensen Søren J.
Published: April 2020

Early life microbiota has been linked to the development of chronic inflammatory diseases. It has been hypothesized that maternal vaginal microbiota is an important initial seeding source and therefore can have lifelong effects on disease risk. To understand maternal vaginal microbiota’s role in seeding the child’s microbiota and the extent of delivery mode-dependent transmission, we studied 700 mother-child dyads from the COPSAC2010 cohort.

The maternal vaginal microbiota was evaluated in the third trimester and compared with the children’s fecal and airway microbiota.

The vaginal samples displayed known stable community state types and only 1:6 changed over time. Only one OTU was significantly transferred to children’s fecal compartment, but an inflated number had positive transfer odds. A few taxonomic families showed early transfer enrichment to vaginally-born children, indicating vertical transfer, while half of the observed transfer effects were delivery mode independent enrichment with attenuating strength over time, indicating a common reservoir.
Reanalysis of Genome Sequences of tomato accessions and its wild relatives: Development of tomato genomic variation (TGV) database integrating SNPs and INDELs polymorphisms
Authors: Gupta Prateek , Dholaniya Pankaj Singh , Devulapalli Sameera , Tawari Nilesh Ramesh , Sreelakshmi Yellamaraju , Sharma Rameshwar
Published: April 2020

Motivation

Facilitated by technological advances and expeditious decrease in the sequencing costs, whole-genome sequencing (WGS) is increasingly implemented to uncover variations in cultivars/accessions of many crop plants. In tomato (Solanum lycopersicum), the availability of the genome sequence, followed by the resequencing of tomato cultivars and its wild relatives, has provided a prodigious resource for the improvement of traits. A high-quality genome resequencing of 84 tomato accessions and wild relatives generated a dataset that can be used as a resource to identify agronomically important alleles across the genome. Converting this dataset into a searchable database, including information about the influence of SNPs on protein function, provides valuable information about the genetic variations. The database will assist in searching for functional variants of a gene for introgression into tomato cultivars.

Results

A recent release of better-quality tomato genome reference assembly SL3.0, and new annotation ITAG3.2 of SL3.0, dropped 3,857 genes, added 4,900 novel genes, and updated 20,766 genes. Using the above version, we remapped the data from the tomato lines resequenced under the “100 Tomato Genome ReSequencing Project” on new tomato genome assembly SL3.0 and made an online searchable Tomato Genomic Variations (TGV) database. The TGV contains information about SNPs and InDels and expands it by functional annotation of variants with new ITAG3.2 using SIFT4G software. This database with search function assists in inferring the influence of SNPs on the function of a target gene. This database can be used for selecting SNPs, which can be potentially deployed for improving tomato traits.

Availability and Implementation

TGV is freely available athttp://psd.uohyd.ac.in/tgv.

Contact

rameshwar.sharma@gmail.com