bluuebunny/crossref_metadata_2025 huggingface dataset:
Precise characterization of somatic complex structural variations from paired long-read sequencing data with nanomonsv
Authors: Shiraishi Yuichi , Koya Junji , Chiba Kenichi , Okada Ai , Arai Yasuhito , Saito Yuki , Shibata Tatsuhiro , Kataoka Keisuke
Published: July 2020

We present our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. The current version of nanomonsv includes two detection modules, Canonical SV module, and Single breakend SV module. Using paired long-read sequencing data from three cancer and their matched lymphoblastoid lines, we demonstrate that Canonical SV module can identify somatic SVs that can be captured by short-read technologies with higher precision and recall than existing methods. In addition, we have developed a workflow to classify mobile element insertions while elucidating their in-depth properties, such as 5’ truncations, internal inversions, as well as source sites for 3’ transductions. Furthermore, Single breakend SV module enables the detection of complex SVs that can only be identified by long-reads, such as SVs involving highly-repetitive centromeric sequences, and LINE1- and virus-mediated rearrangements. In summary, our approaches applied to cancer long-read sequencing data can reveal various features of somatic SVs and will lead to a better understanding of mutational processes and functional consequences of somatic SVs.
Signatures of optimal codon usage predict metabolic ecology in budding yeasts
Authors: LaBella Abigail Leavitt , Opulente Dana A. , Steenwyk Jacob , Hittinger Chris Todd , Rokas Antonis
Published: July 2020

Reverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically-relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism (GAL) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in theGALpathway is positively correlated with quantitative growth on galactose, suggesting thatGALcodon optimization reflects increased capacity to grow on galactose. Optimal codon usage in theGALpathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage ofGALgenes is greater than 85% of all genes in the major human pathogenCandida albicans(CUG-Ser1 clade) and greater than 75% of genes in the dairy yeastKluyveromyces lactis(family Saccharomycetaceae). We further find a correlation between optimization in the thiamine biosynthesis andGALpathways. As a result, optimal codon usage in thiamine biosynthesis genes is also associated with dairy ecological niches in Saccharomycetaceae, which may reflect competition with co-occurring microbes for extracellular thiamine. This work highlights the potential of codon optimization as a tool for gaining insights into the metabolic ecology of microbial eukaryotes. Doing so may be especially illuminating for studying fungal dark matter—species that have yet to be cultured in the lab or have only been identified by genomic material.
Orally Administered Exosomes Alleviate Mouse Contact Dermatitis through Delivering miRNA-150 to Antigen-Primed Macrophages Targeted by Exosome-Surface Antibody Light Chains
Authors: Nazimek Katarzyna , Bryniarski Krzysztof , Ptak Wlodzimierz , Kormelink Tom Groot , Askenase Philip W.
Published: July 2020

We previously discovered suppressor T cell-derived, antigen (Ag)-specific exosomes inhibiting mouse hapten-induced contact sensitivity effector T cells by targeting antigen-presenting cells (APCs). These suppressive exosomes acted Ag-specifically due to a coating of antibody free light chains (FLC) from Ag-activated B1a cells. Current studies aimed at determining if similar immune tolerance could be induced in cutaneous delayed-type hypersensitivity (DTH) to the protein Ag (ovalbumin, OVA). Intravenous administration of a high dose of OVA-coupled, syngeneic erythrocytes induced CD3+CD8+suppressor T cells producing suppressive, miRNA-150-carrying exosomes, also coated with B1a cell-derived, OVA-specific FLC. Simultaneously, OVA-immunized B1a cells produced exosome subpopulation, originally coated with Ag-specific FLC, that could be rendered suppressive by in vitro association with miRNA-150. Importantly, miRNA-150-carrying exosomes from both suppressor T cells and B1a cells efficiently induced prolonged DTH suppression after single systemic administration into actively immunized mice, with the strongest effect observed after oral administration. Current studies also showed that OVA-specific FLC on suppressive exosomes bind OVA peptides, suggesting that exosome-coating FLC target APCs by binding to Ag-major histocompatibility complexes. This renders APCs able to inhibit DTH effector T cells. Thus, our studies described a novel immune tolerance mechanism mediated by FLC-coated, Ag-specific, miRNA-150-carrying exosomes that are particularly effective after oral administration.
Evidence for spreading seizure as a cause of theta-alpha activity electrographic pattern in stereo-EEG seizure recordings
Authors: Sip Viktor , Scholly Julia , Guye Maxime , Bartolomei Fabrice , Jirsa Viktor
Published: July 2020

Intracranial electroencephalography is a standard tool in clinical evaluation of patients with focal epilepsy. Various early electrographic seizure patterns differing in frequency, amplitude, and waveform of the oscillations are observed. The pattern most common in the areas of seizure propagation is the so-called theta-alpha activity (TAA), whose defining features are oscillations in theθ–αrange and gradually increasing amplitude. A deeper understanding of the mechanism underlying the generation of the TAA pattern is however lacking. In this work we evaluate the hypothesis that the TAA patterns are caused by seizures spreading across the cortex. To do so, we perform simulations of seizure dynamics on detailed patient-derived cortical surfaces using the spreading seizure model as well as reference models with one or two homogeneous sources. We then detect the occurrences of the TAA patterns both in the simulated stereo-electroencephalographic signals and in the signals of recorded epileptic seizures from a cohort of fifty patients, and we compare the features of the groups of detected TAA patterns to assess the plausibility of the different models. Our results show that spreading seizure hypothesis is qualitatively consistent with the evidence available in the seizure recordings, and it can explain the features of the detected TAA groups best among the examined models.
Visual Feedback Weakens the Augmentation of Perceived Stiffness by Artificial Skin Stretch
Authors: Farajian Mor , Kossowsky Hanna , Leib Raz , Nisky Ilana
Published: July 2020

Tactile stimulation devices are gaining popularity in haptic science and technology – they are lightweight, low-cost, can be easily made wearable, and do not suffer from instability during closed loop interactions with users. Applying tactile stimulation in the form of stretching the skin of the fingerpads, concurrently with kinesthetic force feedback, has been shown to augment the perceived stiffness during interactions with elastic objects. However, all of the studies to date have investigated the perceptual augmentation effects of artificial skin-stretch in the absence of visual feedback. We investigated how visual displacement feedback affects the augmentation of perceived stiffness caused by the skin-stretch. We used a forced-choice paradigm stiffness discrimination task with four different conditions: force feedback, force feedback with artificial skin-stretch, force and visual feedback, and force and visual feedback with artificial skin-stretch. We found that visual displacement feedback weakens the skin-stretch induced perceptual augmentation and improves the stiffness discrimination sensitivity.
Characterization of two novel proteins involved in mitochondrial DNA anchoring
Authors: Amodeo Simona , Hoffmann Anneliese , Fradera-Sola Albert , Bregy Irina , Baudouin Hélène , Haenni Beat , Zuber Benoît , Butter Falk , Ochsenreiter Torsten
Published: July 2020

Trypanosoma bruceiis a single celled eukaryotic parasite in the group of the Excavates.T. bruceicells harbor a single mitochondrion with a singular mitochondrial genome, that consists of a unique network of thousands of interwoven circular DNA molecule copies and is termed the kinetoplast DNA (kDNA). To ensure proper inheritance of the kDNA to the daughter cells the genome is linked to the basal body, the master organizer of the cell cycle in trypanosomes. The structure connecting the basal body and kDNA is termed the tripartite attachment complex (TAC). Using a combination of proteomics and RNAi (depletomics) we test the current model of hierarchical TAC assembly and identify TbmtHMG44 and Tb927.11.16120 as novel candidates of a structure that connects the TAC to the kDNA. Both proteins localize in the region of the unilateral filaments between TAC102 and the kDNA and depletion of each leads to a strong kDNA loss phenotype. TbmtHMG44 and Tb927.11.16120 stably associate with extracted flagella, even after DNase treatment however they do require the kDNA for initial assembly. Furthermore we demonstrate that recombinant Tb927.11.16120 is a DNA binding protein and thus a promising candidate to link the TAC to the kDNA.
Factors of sex and age dictate the regulation of GABAergic activity by corticotropin-releasing factor receptor 1 in the medial sub-nucleus of the central amygdala
Authors: Rouzer Siara Kate , Diaz Marvin R.
Published: July 2020

Adolescents are phenotypically characterized with hyper-sensitivity to stress and inappropriate response to stress-inducing events. Despite behavioral distinctions from adults, investigations of developmental shifts in the function of stress peptide corticotrophin-releasing factor (CRF) are generally limited. Rodent models have determined that CRF receptor 1 (CRFR1) activation within the central amygdala is associated with a stress response and induces increased GABAergic synaptic neurotransmission within adult males. To investigate age-specific function of this system, we performed whole-cell patch clamp electrophysiology in brain slices from naive adolescent (postnatal days (P) 40-49) and adult (>P70) male and female Sprague Dawley rats to assess GABAergic activity in the medial central amygdala (CeM). Our results indicate a dynamic influence of age and sex on neuronal excitability within this region, as well as basal spontaneous and miniature (m) inhibitory post-synaptic currents (IPSCs) in the CeM. In addition to replicating prior findings of CRFR1-regulated increases in mIPSC frequency in adult males, we found that the selective CRFR1 agonist, Stressin-1,attenuatedmIPSC frequency in adolescent males, at a concentration that did not affect adult males. Importantly, this age-specific distinction was absent in females, as Stressin-1 attenuated mIPSC frequency in both adolescent and adult females. Finally, only adult males exhibited an increase in mIPSC frequency in response to the CRF1R antagonist, NBI 35965, suggestive of tonic CRFR1 activation in the CeM of adult males. Together, these data emphasize the robust influence of age and sex on neurophysiological function of a brain region involved in the production of the stress response.
Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information
Authors: López M.E. , Cádiz M.I. , Rondeau E.B. , Koop B.F. , Yáñez J.M.
Published: July 2020

Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection known as selection signatures or selective sweeps have been traced in the genomes of many animal livestock species by exploiting variations in linkage disequilibrium patterns and/or reduction of genetic diversity.

Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subject to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes suchanapc2,alad,chp2andmynthat have been previously associated with body weight in Atlantic salmon orsec24dandrobo1that have been associated with disease resistance toPiscirickettsia salmonisin coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.
Computational investigation of protein photoinactivation by molecular hyperthermia
Authors: Kang Peiyuan , Xie Chen , Fall Oumar , Randrianalisoa Jaona , Qin Zhenpeng
Published: July 2020

To precisely control protein activity in a living system is a challenging yet long-pursued objective in biomedical sciences. Recently we have developed a new approach named molecular hyperthermia (MH) to photoinactivate protein activity of interest without genetic modification. MH utilizes nanosecond laser pulse to create nanoscale heating around plasmonic nanoparticles to inactivate adjacent protein in live cells. Here we use a numerical model to study important parameters and conditions for MH to efficiently inactivate proteins in nanoscale. To quantify the protein inactivation process, the impact zone is defined as the range where proteins will be inactivated by nanoparticle localized heating. Factors that reduce the MH impact zone include stretching the laser pulse duration, temperature-dependent thermal conductivity (versus constant properties), and non-spherical nanoparticle geometry. In contrast, the impact zone is insensitive to temperature-dependent material density and specific heat, as well as thermal interface resistance based on reported data. The low thermal conductivity of cytoplasm increases the impact zone. Different proteins with various Arrhenius kinetic parameters have significantly different impact zones. This study provides guidelines to design the protein inactivation process in MH.
Efficiency of a Randomized Confirmatory Basket Trial Design Constrained to Control the False Positive Rate by Indication
Authors: He Linchen , Ren Yuru , Chen Han , Guinn Daphne , Parashar Deepak , Chen Cong , Yuan Shuai Sammy , Korostyshevskiy Valeriy , Beckman Robert A.
Published: July 2020

PURPOSE

Molecular oncology determines biomarker-defined niche indications. Basket trials pool histologic indications sharing molecular pathophysiology, potentially improving development efficiency. Currently basket trials have been confirmatory only for exceptional therapies. Our previous randomized basket design may be generally suitable in the resource-intensive confirmatory phase, maintains high power, and provides nearlyk-fold increased efficiency forkindications, but controls false positives for the pooled result only. Since false positive control by indications (FWER) may sometimes be required, we now simulate a variant of this basket design controlling FWER at 0.025k, the total FWER ofkseparate randomized trials.

METHODS

The previous design eliminated indications at an interim analysis, conducting a final pooled analysis of remaining indications. To control FWER, we rechecked individual indications at a prospectively defined level of statistical significance after any positive pooled result. We simulated this modified design under numerous scenarios varying design parameters. Only designs controlling FWER and minimizing estimation bias were allowable.

RESULTS

Sequential analyses (interim, pooled, and post-individual tests)) result in cumulative power losses. Optimal performance results whenk= 3,4. We report efficiency (expected # true positives/expected sample size) relative tokparallel studies, at 90% power (“uncorrected”) or at the power achieved in the basket trial (“corrected”, because conventional designs could also increase efficiency by sacrificing power). Efficiency and power (percentage active indications identified) improve with higher percentage of initial indications active. Up to 92% uncorrected and 38% corrected efficiency improvement is possible, with power ≈ 60%.

CONCLUSIONS

Even under FWER control, randomized confirmatory basket trials substantially improve development efficiency. Initial indication selection is critical. The design is particularly attractive when enrollment challenges preclude full powering of individual indications.
Post-mitotic Prox1 expression controls the final specification of cortical VIP interneuron subtypes
Authors: Stachniak Tevye Jason , Kastli Rahel , Hanley Olivia , Argunsah Ali Özgür , Karayannis Theofanis
Published: July 2020

Neuronal identity is controlled in multiple developmental steps by key transcription factors that determine the unique properties of a cell. During embryogenesis, the transcription factor Prox1 has been shown to regulate VIP interneuron migration, survival, and as a result, circuit integration. Here, we explore the role of Prox1 as a regulator of genetic programs that guide the final specification of VIP interneuron subtypes in early post-natal life. Using in-vitro electrophysiology we find that post-natal removal of Prox1 differentially affects the synaptic integration of VIP bipolar and multipolar subtypes.

RNA sequencing reveals that one of the downstream targets of Prox1 is the postsynaptic protein Elfn1, a constitutive regulator of presynaptic release probability. Genetic, pharmacological and electrophysiological experiments demonstrate that knocking out Prox1 reduces Elfn1 function in VIP multipolar but not in bipolar cells. Thus, in addition to the activity-dependent and contextual processes that finalize developmental trajectories, genetic programs engaged by Prox1 control the differentiation and connectivity of VIP interneuron subtypes.
Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2
Authors: Ou Tianling , Mou Huihui , Zhang Lizhou , Ojha Amrita , Choe Hyeryun , Farzan Michael
Published: July 2020

Hydroxychloroquine, used to treat malaria and some autoimmune disorders, potently inhibits viral infection of SARS coronavirus (SARS-CoV-1) and SARS-CoV-2 in cell-culture studies. However, human clinical trials of hydroxychloroquine failed to establish its usefulness as treatment for COVID-19. This compound is known to interfere with endosomal acidification necessary to the proteolytic activity of cathepsins. Following receptor binding and endocytosis, cathepsin L can cleave the SARS-CoV-1 and SARS-CoV-2 spike (S) proteins, thereby activating membrane fusion for cell entry. The plasma membrane-associated protease TMPRSS2 can similarly cleave these S proteins and activate viral entry at the cell surface. Here we show that the SARS-CoV-2 entry process is more dependent than that of SARS-CoV-1 on TMPRSS2 expression. This difference can be reversed when the furin-cleavage site of the SARS-CoV-2 S protein is ablated. We also show that hydroxychloroquine efficiently blocks viral entry mediated by cathepsin L, but not by TMPRSS2, and that a combination of hydroxychloroquine and a clinically-tested TMPRSS2 inhibitor prevents SARS-CoV-2 infection more potently than either drug alone. These studies identify functional differences between SARS-CoV-1 and -2 entry processes, and provide a mechanistic explanation for the limitedin vivoutility of hydroxychloroquine as a treatment for COVID-19.

Author Summary

The novel pathogenic coronavirus SARS-CoV-2 causes COVID-19 and remains a threat to global public health. Chloroquine and hydroxychloroquine have been shown to prevent viral infection in cell-culture systems, but human clinical trials did not observe a significant improvement in COVID-19 patients treated with these compounds. Here we show that hydroxychloroquine interferes with only one of two somewhat redundant pathways by which the SARS-CoV-2 spike (S) protein is activated to mediate infection. The first pathway is dependent on the endosomal protease cathepsin L and sensitive to hydroxychloroquine, whereas the second pathway is dependent on TMPRSS2, which is unaffected by this compound. We further show that SARS-CoV-2 is more reliant than SARS coronavirus (SARS-CoV-1) on the TMPRSS2 pathway, and that this difference is due to a furin cleavage site present in the SARS-CoV-2 S protein. Finally, we show that combinations of hydroxychloroquine and a clinically tested TMPRSS2 inhibitor work together to effectively inhibit SARS-CoV-2 entry. Thus TMPRSS2 expression on physiologically relevant SARS-CoV-2 target cells may bypass the antiviral activities of hydroxychloroquine, and explain its lack ofin vivoefficacy.
Chemotherapeutic Nanoparticles Accumulate in the Female Reproductive System during Ovulation Affecting Fertility and Anticancer Activity
Authors: Poley Maria , Shammai Yael , Kaduri Maya , Koren Lilach , Adir Omer , Shklover Jeny , Shainsky Janna , Ben-Aharon Irit , Zinger Assaf , Schroeder Avi
Published: July 2020

Throughout the female menstrual cycle, physiological changes occur that affect the biodistribution of nanoparticles within the reproductive system. This can have positive or negative effects. We demonstrate a 2-fold increase in nanoparticle accumulation in the ovaries during female mouse ovulation compared to the non-ovulatory stage following intravenous administration. Accumulation in the reproductive system is favored by nanoparticles smaller than 100 nm. Chemotherapeutic nanoparticles administered during ovulation increased ovarian toxicity and decreased short-term and long-term fertility when compared to the free drug. Breast cancer treated with nanomedicines during ovulation results in higher drug accumulation in the reproductive system rather than at the site of the tumor, reducing treatment efficacy. Conversely, ovarian cancer treatment was improved by enhanced nanoparticle accumulation in the ovaries during ovulation. Our findings suggest that the menstrual cycle should be considered when designing and implementing nanotherapeutics for females.
Sparsification of AP firing in adult-born hippocampal granule cells via voltage-dependent α5-GABAAreceptors
Authors: Lodge Meredith , Hernandez Maria-Clemencia , Schulz Jan M. , Bischofberger Josef
Published: July 2020

GABA can depolarize immature neurons close to the action potential (AP) threshold in development and adult neurogenesis. Nevertheless, GABAergic synapses effectively inhibit AP firing in newborn granule cells of the adult hippocampus as early as 2 weeks post mitosis. The underlying mechanisms are largely unclear. Here we analyzed GABAergic inputs in newborn 2- to 4-week-old hippocampal granule cells mediated by soma-targeting parvalbumin (PV) and dendrite-targeting somatostatin (SOM) interneurons. Surprisingly, both interneuron subtypes activate α5-subunit containing GABAAreceptors (α5-GABAARs) in young neurons, showing a nonlinear voltage dependence with increasing conductance around the AP threshold. By contrast, in mature cells, PV interneurons mediate linear GABAergic synaptic currents lacking α5-subunits, while SOM-interneurons continue to target nonlinear α5-GABAARs. Computational modelling shows that the voltage-dependent amplification of α5-GABAAR opening in young neurons is crucial for inhibition of AP firing to generate balanced and sparse firing activity, even with depolarized GABA reversal potentials.
Decadal changes in fire frequencies shift tree communities and functional traits
Authors: Pellegrini Adam F. A. , Refsland Tyler , Averill Colin , Terrer César , Staver A. Carla , Brockway Dale G. , Caprio Anthony , Clatterbuck Wayne , Coetsee Corli , Haywood James D. , Hobbie Sarah E. , Hoffmann William A. , Kush John , Lewis Tom , Moser W. Keith , Overby Steven T. , Patterson Bill , Peay Kabir G. , Reich Peter B. , Ryan Casey , Sayer Mary Anne S. , Scharenbroch Bryant C. , Schoennagel Tania , Smith Gabriel R. , Stephan Kirsten , Swanston Chris , Turner Monica G. , Varner J. Morgan , Jackson Robert B.
Published: July 2020

Global change has resulted in chronic shifts in fire regimes, increasing fire frequency in some regions and decreasing it in others. Predicting the response of ecosystems to changing fire frequencies is challenging because of the multi-decadal timescales over which fire effects emerge and the variability in environmental conditions, fire types, and plant composition across biomes. Here, we address these challenges using surveys of tree communities across 29 sites that experienced multi-decadal alterations in fire frequencies spanning ecosystems and environmental conditions. Relative to unburned plots, more frequently burned plots had lower tree basal area and stem densities that compounded over multiple decades: average fire frequencies reduced basal area by only 4% after 16 years but 57% after 64 years, relative to unburned plots. Fire frequency had the largest effects on basal area in savanna ecosystems and in sites with strong wet seasons. Analyses of tree functional-trait data across North American sites revealed that frequently burned plots had tree communities dominated by species with low biomass nitrogen and phosphorus content and with more efficient nitrogen acquisition through ectomycorrhizal symbioses (rising from 85% to nearly 100%). Our data elucidate the impact of long-term fire regimes on tree community structure and composition, with the magnitude of change depending on climate, vegetation type, and fire history. The effects of widespread changes in fire regimes underway today will manifest in decades to come and have long-term consequences for carbon storage and nutrient cycling.
A normative account of choice history effects in mice and humans
Authors: Lopez-Yepez Junior Samuel , Martin Juliane , Hulme Oliver , Kvitsiani Duda
Published: July 2020

Choice history effects describe how future choices depend on the history of past choices. Choice history effects are typically framed as a bias rather than an adaptive phenomenon because the phenomenon generally degrades reward rates in experimental tasks. How-ever, in natural habitats, choices made in the past constrain choices that can be made in the future. For foraging animals, the probability of obtaining a reward in a given patch depends on the degree to which the animals have exploited the patch in the past. One problem with many experimental tasks that show choice history effects is that such tasks artificially decouple choice history from its consequences in regard to reward availability over time. To circumvent this, we used a variable interval (VI) reward schedule that reinstates a more natural contingency between past choices and future reward availability. By manipulating first- and second-order statistics of the environment, we dissociated choice history, reward history, and reaction times. We found that choice history effects reflect the growth rate of the reward probability of the unchosen option, reward history effects reflect environmental volatility, and reaction time reflects overall reward rate. By testing in mice and humans, we show that the same choice history effects can be generalized across species and that these effects are similar to those observed in optimal agents. Furthermore, we develop a new reinforcement learning model that explicitly incorporates choice history over multiple timescales into the decision process, and we examine its predictive adequacy in accounting for the associated behavioral data. We show that this new variant, known as the double trace model, has a higher predictive adequacy of choice data, in addition to better reward harvesting efficiency in simulated environments. Finally, we show that the choice history effects emerge in optimal models of foraging in habitats with diminishing returns, thus linking this phenomenon to a wider class of optimality models in behavioral ecology. These results suggests that choice history effects may be adaptive for natural contingencies between consumption and reward availability. This concept lends credence to a normative account of choice history effects that extends beyond its description as a bias.
Fast Whole-Genome Phylogeny of the COVID-19 Virus SARS-CoV-2 by Compression
Authors: Cilibrasi Rudi L. , Vitányi Paul M.B.
Published: July 2020

We analyze the whole genome phylogeny and taxonomy of the SARS-CoV-2 virus using compression. This is a new fast alignment-free method called the “normalized compression distance” (NCD) method. It discovers all effective similarities based on Kolmogorov complexity. The latter being incomputable we approximate it by a good compressor such as the modern zpaq. The results comprise that the SARS-CoV-2 virus is closest to the RaTG13 virus and similar to two bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat-SL-CoVZC4. The similarity is quantified and compared with the same quantified similarities among the mtDNA of certain species. We treat the question whether Pangolins are involved in the SARS-CoV-2 virus. The compression method is simpler and possibly faster than any other whole genome method, which makes it the ideal tool to explore phylogeny.
Beclin-1-mediated activation of autophagy improves proximal and distal urea cycle disorders
Authors: Soria Leandro R. , Perocheau Dany P. , De Sabbata Giulia , De Angelis Angela , Bruno Gemma , Polishchuk Elena , Gurung Sonam , Paris Debora , Cuomo Paola , Motta Andrea , Orford Michael , Eaton Simon , Waddington Simon , Settembre Carmine , Muro Andrés F. , Baruteau Julien , Brunetti-Pierri Nicola
Published: July 2020

Urea cycle disorders (UCD) are inherited defects in clearance of waste nitrogen with high morbidity and mortality. Novel and more effective therapies for UCD are needed. Studies in mice with constitutive activation of autophagy unraveled Beclin-1 asdruggablecandidate for therapy of hyperammonemia. Next, we investigated efficacy of cell penetrating autophagy inducing Tat-Beclin-1 (TB-1) peptide for therapy of the two most common UCD, namely ornithine transcarbamylase (OTC) and argininosuccinate lyase (ASL) deficiencies. TB-1 reduced urinary orotic acid and hyperammonemia, and improved survival under protein-rich diet inspf-ashmice, a model of OTC deficiency (proximal UCD). InAslNeo/Neomice, a model of ASL deficiency (distal UCD), TB-1 increased ureagenesis, reduced argininosuccinate, and improved survival. Moreover, it alleviated hepatocellular injury and decreased both cytoplasmic and nuclear glycogen accumulation inAslNeo/Neomice. In conclusion, Beclin-1-dependent activation of autophagy improved biochemical and clinical phenotypes of proximal and distal defects of the urea cycle.
Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Authors: Lind Abigail L. , Pollard Katherine S.
Published: July 2020

Background

Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded.

Results

Here we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3,713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastid genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes inArabidopsisleaf samples, many of which are not identifiable from public protein databases.

Conclusions

EukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes.
Cell type-specific immune dysregulation in severely ill COVID-19 patients
Authors: Yao Changfu , Bora Stephanie A , Parimon Tanyalak , Zaman Tanzira , Friedman Oren A , Palatinus Joseph A , Surapaneni Nirmala S , Matusov Yuri P , Chiang Giuliana Cerro , Kassar Alexander G , Patel Nayan , Green Chelsi ER , Aziz Adam W , Suri Harshpreet , Suda Jo , Lopez Andres A , Martins Gislaine A , Stripp Barry R , Gharib Sina A , Goodridge Helen S , Chen Peter
Published: July 2020

Coronavirus disease 2019 (COVID-19) has quickly become the most serious pandemic since the 1918 flu pandemic. In extreme situations, patients develop a dysregulated inflammatory lung injury called acute respiratory distress syndrome (ARDS) that causes progressive respiratory failure requiring mechanical ventilatory support. Recent studies have demonstrated immunologic dysfunction in severely ill COVID-19 patients. To further delineate the dysregulated immune response driving more severe clinical course from SARS-CoV-2 infection, we used single-cell RNA sequencing (scRNAseq) to analyze the transcriptome of peripheral blood mononuclear cells (PBMC) from hospitalized COVID-19 patients having mild disease (n = 5), developing ARDS (n = 6), and recovering from ARDS (n = 6). Our data demonstrated an overwhelming inflammatory response with select immunodeficiencies within various immune populations in ARDS patients. Specifically, their monocytes had defects in antigen presentation and deficiencies in interferon responsiveness that contrasted the higher interferon signals in lymphocytes. Furthermore, cytotoxic activity was suppressed in both NK and CD8 lymphocytes whereas B cell activation was deficient, which is consistent with the delayed viral clearance in severely ill COVID-19 patients. Finally, we identified altered signaling pathways in the severe group that suggests immunosenescence and immunometabolic changes could be contributing to the dysfunctional immune response. Our study demonstrates that COVID-19 patients with ARDS have an immunologically distinct response when compared to those with a more innocuous disease course and show a state of immune imbalance in which deficiencies in both the innate and adaptive immune response may be contributing to a more severe disease course in COVID-19.
Local structure of DNA toroids reveals curvature-dependent intermolecular forces
Authors: Barberi Luca , Livolant Françoise , Leforestier Amélie , Lenz Martin
Published: July 2020

In viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helices. Here we use cryo electron microscopy to shed light on the interaction between highly curved helices. We find that the spacing between DNA helices in spermine-induced DNA toroidal condensates depends on their location within the torus, consistent with a mathematical model based on the competition between electrostatic interactions and the bending rigidity of DNA. We use our model to infer the characteristics of the interaction potential, and find that its equilibrium spacing strongly depends on the curvature of the filaments. In addition, the interaction is much softer than previously reported in bulk samples using different salt conditions. Beyond viruses and cells, our characterization of the interactions governing DNA-based dense structures could help develop robust designs in DNA nanotechnologies.
NF-kappa-B activation unveils the presence of inflammatory hotspots in human gut xenografts
Authors: Nissim-Eliraz Einat , Nir Eilam , Marsiano Noga , Yagel Simcha , Shpigel Nahum Y.
Published: July 2020

The single-epithelial cell layer of the gut mucosa serves as an essential barrier between the host and luminal microflora and plays a major role in innate immunity against invading pathogens. Nuclear factor kB (NF-κB), a central component of the cellular signaling machinery, regulates immune response and inflammation. NF-κB proteins are activated by signaling pathways downstream to microbial recognition receptors and cytokines receptors. Highly regulated NF-κB activity in intestinal epithelial cells (IEC) is essential for normal gut homeostasis; dysregulated activity has been linked to a number of disease states, including inflammatory bowel diseases (IBD) such as Crohn’s Disease (CD). Our aim was to visualize and quantify spatial and temporal dynamics of NF-κB activity in steady state and inflamed human gut. Lentivirus technology was used to transduce the IEC of human gut xenografts in SCID mice with a NF-κB luminescence reporter system. NF-κB signaling was visualized and quantified using low resolution, intravital imaging of the whole body and high resolution, immunofluorescence microscopic imaging of the tissues. We show that NF-κB is activated in select subset of IEC with low “leaky” NF-κB activity. These unique inflammatory epithelial cells are clustered in the gut into discrete hotspots of NF-κB activity that are visible in steady state and selectively activated by systemic LPS and human TNFα or luminal bacteria. The presence of inflammatory hotspots in the normal and inflamed gut might explain the patchy mucosal lesions characterizing CD and thus could have important implications for diagnosis and therapy.
Niche and local geography shape the pangenome of wastewater- and livestock-associatedEnterobacteriaceae
Authors: Shaw Liam P. , Chau Kevin K. , Kavanagh James , AbuOun Manal , Stubberfield Emma , Gweon H. Soon , Barker Leanne , Rodger Gillian , Bowes Mike J. , Hubbard Alasdair T. M. , Pickford Hayleah , Swann Jeremy , Gilson Daniel , Smith Richard P. , Hoosdally Sarah J. , Sebra Robert , Brett Howard , Peto Tim E. A. , Bailey Mark J. , Crook Derrick W. , Read Daniel S. , Anjum Muna F. , Walker A. Sarah , Stoesser Nicole
Published: July 2020

Escherichia coliand otherEnterobacteriaceaeare highly diverse species with ‘open’ pangenomes1,2, where genes move intra- and inter-species via horizontal gene transfer3. These species can cause clinical infections4,5as well as persist environmentally6,7. Environmental populations have been suggested as important reservoirs of antimicrobial resistance (AMR) genes. However, as most analyses focus on clinical isolates8,9, the pangenome dynamics of natural populations remain understudied, particularly the role of plasmids. Here, we reconstructed near-complete genomes for 828Enterobacteriaceae, including 553Escherichiaspp. and 275 non-Escherichiaspecies with 2,293 circularised plasmids in total, collected from nineteen locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30km radius at three timepoints over the course of a year. We find different dynamics for the chromosomal and plasmid-borne components of the pangenome, showing that plasmids have a higher burden of both AMR genes and insertion sequences, and AMR plasmids show evidence of being under stronger selective pressure. Focusing onE. coli, we observe that plasmid dynamics are more strongly dominated by niche and local geography, rather than phylogeny or season. Our results highlight the diversity of the AMR reservoir in these species and niches, and the importance of local strategies for controlling the emergence and spread of AMR.
The effect of absent blood flow on the zebrafish cerebral and trunk vasculature
Authors: Kugler Elisabeth , Snodgrass Ryan , Bowley George , Plant Karen , Serbanovic-Canic Jovana , Evans Paul C. , Chico Timothy , Armitage Paul
Published: July 2020

The role of blood flow is complex and context-dependent. In this study, we quantify the effect of the lack of blood flow on vascular development and compare its impact in two vascular beds, namely the cerebral and trunk vasculature, using zebrafish as preclinical model. We performed this by analysing vascular topology, endothelial cell number, apoptosis, and inflammatory response in animals with normal blood flow or absent blood flow. We find that absent blood flow reduced vascular area and endothelial cell number significantly in both examined vascular beds, but the effect is more severe in the cerebral vasculature. Similarly, while stereotypic vascular patterning in the trunk is maintained, intra-cerebral vessels show altered patterning. Absent blood flow lead to an increase in non-EC-specific apoptosis without increasing tissue inflammation, as quantified by cerebral immune cell numbers and nitric oxide. In conclusion, blood flow is essential for cellular survival in both the trunk and cerebral vasculature, but particularly intra-cerebral vessels are affected by the lack of blood flow, suggesting that responses to blood flow differ between these two vascular beds.

Key points

We here use zebrafish as a model to quantitatively assess the impact of the lack of blood flow in development and compare its impact in two vascular beds, namely the cerebral to trunk vasculature.

In both vascular beds, vascular growth and endothelial cell number are reduced by lack of blood flow, with increasing effect size from 2-5 days post fertilisation.

Examination of vascular patterning shows that while stereotypic patterning in the trunk is preserved, the intra-cerebral vasculature patterning is altered.

We found non-EC-specific cell death to be increased in both vascular beds, with a larger effect size in the brain, but that this cell death occurs without triggering tissue inflammation.
Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1
Authors: Ruegenberg Sabine , Mayr Felix A.M.C. , Miethe Stephan , Atanassov Ilian , Baumann Ulrich , Denzel Martin S.
Published: July 2020

The hexosamine pathway (HP) is a key anabolic pathway whose product uridine 5’-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc) is an essential precursor for all glycosylation processes in mammals. It modulates the ER stress response, is implicated in cancer and diabetes, and HP activation extends lifespan inCaenorhabditis elegans. The highly conserved glutamine fructose-6-phosphate amidotransferase 1 (GFAT-1) is the first and rate-limiting HP enzyme. GFAT-1 activity is modulated through UDP-GlcNAc feedback inhibition and by kinase signaling, including Ser205 phosphorylation by protein kinase A (PKA). The consequence and molecular mechanism of GFAT-1 phosphorylation, however, remains poorly understood. Here, we identify the GFAT-1 R203H substitution that elevates UDP-GlcNAc levels inC. elegans, leading to ER stress resistance. In human GFAT-1, the R203H substitution interfered with both UDP-GlcNAc inhibition and PKA-mediated Ser205 phosphorylation. Of note, Ser205 phosphorylation had two discernible effects: It lowered baseline GFAT-1 activity and abolished UDP-GlcNAc feedback inhibition. Thus, GFAT-1 phosphorylation by PKA uncoupled the feedback loop of the HP and, depending on UDP-GlcNAc availability, phosphorylation by PKA results in lower or enhanced GFAT-1 activityin vivo. Mechanistically, our data indicate that the relative positioning of the two GFAT-1 domains might be affected by phosphorylation and we propose a model how Ser205 phosphorylation modulates the activity and feedback inhibition of GFAT-1.
Genomic epidemiology and evolution ofEscherichia coliin wild animals
Authors: Murphy Robert , Palm Martin , Mustonen Ville , Warringer Jonas , Farewell Anne , Moradigaravand Danesh , Parts Leopold
Published: July 2020

Escherichia coliis a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenic and antimicrobial resistance inE. colimay emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensalE. coliwithin wild hosts and the epidemiological links betweenE. coliin non-human hosts andE. coliin humans is still scarce. In this study, we analysed the whole genome sequencing data of a collection of 119 commensalE. colirecovered from the guts of 68 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures ofE. colicolonizing wild animals and the phylogeny, taxonomy and ecological and physiological attributes of the host species, with distantly relatedE. colioften colonizing the same or similar host species and distantly related host species often hosting closely relatedE. coli. We found no evidence for recent transmission ofE. coligenomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present inE. coliof wild animals, including virulence factors characteristic for Shiga toxin-producingE. coli(STEC) and atypical enteropathogenicE. coli(aEPEC), where several isolates from wild hosts harboured the locus of enterocyte effacement (LEE) pathogenicity island. Moreover,E. coliin wild animal hosts often harboured known antibiotic resistance determinants, including against ciprofloxacin, aminoglycosides, tetracyclines and beta-lactams, with some determinants present in multiple, distantly relatedE. colilineages colonizing very different host animals. We conclude that although the genome pools ofE. colicolonizing wild animal and human gut are well separated, they share virulence and antibiotic resistance genes andE. coliunderscoring that wild animals could serve as reservoirs forE. colipathogenicity in human and livestock infections.

Importance

Escherichia coliis a clinically importance bacterial species implicated in human and livestock associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock and wild animals. Although wild animals are recognized to serve as potential reservoirs for pathogenicE. colistrains, the knowledge of the population structure ofE. coliin wild hosts is still scarce. In this study we used the fine resolution of whole genome sequencing to provide novel insights into the evolution ofE. coligenomes within a broad range of wild animal species (including mammals and birds), the co-evolution ofE. colistrains with their hosts and the genetics of pathogenicity ofE. colistrains in wild hosts. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and necessitate the inclusion of non-human hosts in the surveillance programs forE. coliinfections.