bluuebunny/crossref_metadata_2025 huggingface dataset:
The Mechanism of Vesicle Solubilization by the Detergent Sodium Dodecyl Sulfate
Authors: Juan-Colás José , Dresser Lara , Morris Katie , Lagadou Hugo , Ward Rebecca H. , Burns Amy , Tear Steve , Johnson Steven , Leake Mark C. , Quinn Steven D.
Published: June 2020

Membrane solubilization by sodium dodecyl sulfate (SDS) is indispensable for many established biotech-nological applications, including viral inactivation and protein extraction. Although the ensemble thermo-dynamics have been thoroughly explored, the underlying molecular dynamics have remained inaccessible, owing to major limitations of traditional measurement tools. Here, we integrate multiple advanced biophysical approaches to gain multi-angle insight into the time-dependence and fundamental kinetic steps associated with the solubilization of single sub-micron sized vesicles in response to SDS. We find that the accumulation of SDS molecules on in-tact vesicles triggers biphasic solubilization kinetics comprising an initial vesicle expansion event followed by rapid lipid loss and micellization. Our findings support a general mechanism of detergent-induced membrane solubilization and we expect the framework of correlative biophysical technologies presented here will form a general platform for elucidating the complex kinetics of membrane perturbation induced by a wide variety of surfactants and disrupting agents.
Neuropilin-1 is a host factor for SARS-CoV-2 infection
Authors: Daly James L. , Simonetti Boris , Antón-Plágaro Carlos , Kavanagh Williamson Maia , Shoemark Deborah K. , Simón-Gracia Lorena , Klein Katja , Bauer Michael , Hollandi Reka , Greber Urs F. , Horvath Peter , Sessions Richard B. , Helenius Ari , Hiscox Julian A. , Teesalu Tambet , Matthews David A. , Davidson Andrew D. , Cullen Peter J. , Yamauchi Yohei
Published: June 2020

SARS-CoV-2 is the causative agent of COVID-19, a coronavirus disease that has infected more than 6.6 million people and caused over 390,000 deaths worldwide1,2. The Spike (S) protein of the virus forms projections on the virion surface responsible for host cell attachment and penetration. This viral glycoprotein is synthesized as a precursor in infected cells and, to be active, must be cleaved to two associated polypeptides: S1 and S2(3,4). For SARS-CoV-2 the cleavage is catalysed by furin, a host cell protease, which cleaves the S protein precursor at a specific sequence motif that generates a polybasic Arg-Arg-Ala-Arg (RRAR) C-terminal sequence on S1. This sequence motif conforms to the C-end rule (CendR), which means that the C-terminal sequence may allow the protein to associate with cell surface neuropilin-1 (NRP1) and neuropilin-2 (NRP2) receptors5. Here we demonstrate using immunoprecipitation, site-specific mutagenesis, structural modelling, and antibody blockade that, in addition to engaging the known receptor ACE2, S1 can bind to NRP1 through the canonical CendR mechanism. This interaction enhances infection by SARS-CoV-2 in cell culture. NRP1 thus serves as a host factor for SARS-CoV-2 infection, and provides a therapeutic target for COVID-19.
High quality single amplicon sequencing method for illumina platforms using ‘N’ (0-10) spacer primer pool without PhiX spik-in
Authors: Naik Tejali , Sharda Mohak , Pandit Awadhesh
Published: June 2020

Illumina sequencing platform requires base diversity in initial 11 cycles for efficient cluster identification and color matrix estimation. This limitation yields low quality data for amplicon libraries having homogeneous base composition. Spike-in of PhiX library ensures base diversity but overall reduces the number of sequencing reads for data analysis. To overcome such low diversity issues during amplicon sequencing on illumina platforms we developed high throughput single amplicon sequencing method by introducing ‘N’ spacers in target gene amplification primers that are pooled for simple handling. We evaluated the efficiency of ‘N’ spacer primers by targeting bacterial 16S V3-V4 region, demonstrating heterogonous base library construction. Addition of ‘N’ spacer causes sequencing frame shift at every base that leads to base diversity and produces heterogenous high quality reads within single amplicon library. We have written a python script “MetReTrim” to trim the heterogenous ‘N’ spacers from the pre-processed reads. This method terminates the need for PhiX spike-in and allows for multiplexing of multiple samples, greatly reducing the overall cost and yields improved sequence quality.
Individual differences in theta-band oscillations in a spatial memory network revealed by EEG predict rapid place learning
Authors: Bauer Markus , Buckley Matthew G. , Bast Tobias
Published: June 2020

Spatial memory has been closely related to the medial temporal lobe (MTL), and theta-oscillations are thought to play a key role. However, it remains difficult to investigate medio-temporal lobe (MTL) activation related to spatial memory with non-invasive electrophysiological methods in humans.

Here, we combined the virtual delayed-matching-to-place (DMP) task, reverse-translated from the watermaze DMP task in rats, with high-density electroencephalography (EEG) recordings. Healthy young volunteers performed this computerised task in a virtual circular arena, which contained a hidden target whose location moved to a new place every four trials, allowing the assessment of rapid memory formation.

Using behavioural measures as predictor variables for source reconstructed frequency specific EEG power, we found that inter-individual differences in ‘search preference’ during ‘probe trials’, a measure of 1-trial place learning known from rodent studies to be particularly hippocampus dependent, correlated predominantly with distinct theta-band oscillations (approx. 7 Hz), particularly in the right temporal lobe, the right striatum and inferior occipital cortex or cerebellum. Notably, this pattern was found with very high consistency during both encoding and retrieval/expression, but not in control analyses and could not be explained by motor confounds. Alpha-activity in sensorimotor and parietal cortex contralateral to the hand used for navigation also correlated with search preference, which likely reflected movement-related factors associated with task performance.

Relating inter-individual differences in ongoing brain activity to behaviour in a continuous rapid place learning task that is suitable for a variety of populations, we could demonstrate that memory related theta-band activity in temporal lobe can be measured with EEG recordings, revealing a presumed network of MTL, striatum and cerebellum and/or inferior occipital cortex that may interact through theta oscillations. This approach holds great potential for further studies investigating the interactions within this network during encoding and retrieval, as well as neuromodulatory impacts and age-related changes.
Abiotic treatment to common bean plants results in an altered endophytic seed microbiome
Authors: Bintarti A. Fina , Kearns Patrick J. , Sulesky-Grieb Abby , Shade Ashley
Published: June 2020

There has been a growing interest in the seed microbiome due to its important role as an end and starting point of plant microbiome assembly that can have consequences for plant health. However, the effect of abiotic conditions on the seed microbial community remains unknown. We performed a pilot study in a controlled growth chamber to investigate how the endophytic seed microbiome of the common bean(Phaseolus vulgaris L.(var. Red Hawk)) was altered under abiotic treatments relevant for crop management with changing climate. Bean plants were subjected to one of three treatments: 66% water withholding to simulate mild drought, 50% Hoagland nutrient solution to simulate fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene amplicon sequencing and ITS1 amplicon sequencing of the endophytic DNA to assess seed bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed microbiome structure was high while alpha diversity was low, with tens of taxa present. Water withholding and nutrient addition altered the seed microbiome structure for bacterial/archaeal communities as compared to the control, and each treatment resulted in a distinct microbiome structure. There were no statistically supported differences in the fungal microbiome across treatments. While we discuss several limitations of this study, the promising results suggest that further investigation is needed to better understand abiotic or stress-induced changes in the seed microbiome, the mechanisms that drive those changes, and their implications for the health and stress responses of the next plant generation.

Importance

Seed microbiome members initiate the assembly of plant-associated microbial communities, but the environmental drivers of endophytic seed microbiome composition are unclear. Here, we exposed plants to short-term drought and fertilizer treatments during early vegetative growth and quantified the microbiome composition of the seeds that were ultimately produced. We found that seeds produced by plants stressed by water limitation or receiving nutrient addition had statistically different endophytic bacterial/archaeal microbiome compositions from each other and from seeds produced by control plants. This work suggests that the abiotic experience of a parental plant can influence the composition of its seed microbiome, with unknown consequences for the next plant generation.
CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells
Authors: Darvish Shafighi Shadi , Kiełbasa Szymon M , Sepúlveda-Yáñez Julieta , Monajemi Ramin , Cats Davy , Mei Hailiang , Menafra Roberta , Kloet Susan , Veelken Hendrik , van Bergen Cornelis A.M. , Szczurek Ewa
Published: June 2020

Background

Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells. The confidence of the cell-to-clone mapping can be increased by accounting for additional measurements. Follicular lymphoma, a malignancy of mature B cells that continuously acquire mutations in parallel in the exome and in B-cell receptor loci, presents a unique opportunity to align exome-derived mutations with B-cell receptor clonotypes as an independent measure for clonal evolution.

Results

Here, we propose CACTUS, a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell RNA sequencing data to map single cells to given imperfect genotypes of tumor clones. We apply CACTUS to two follicular lymphoma patient samples, integrating three measurements: whole exome sequencing, single cell RNA sequencing, and B-cell receptor sequencing. CACTUS outperforms a predecessor model by confidently assigning cells and B-cell receptor clonotypes to the tumor clones.

Conclusions

The integration of independent measurements increases model certainty and is the key to improving model performance in the challenging task of charting the genotype-to-phenotype maps in tumors. CACTUS opens the avenue to study the functional implications of tumor heterogeneity, and origins of resistance to targeted therapies.
An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time
Authors: Abley Katie , Formosa-Jordan Pau , Tavares Hugo , Chan Emily , Leyser Ottoline , Locke James C.W.
Published: June 2020

Genetically identical plants growing in the same conditions can display heterogeneous phenotypes. Whether this phenotypic variability is functional and the mechanisms behind it are unclear. Here we use Arabidopsis seed germination time as a model system to examine phenotypic variability. We show extensive variation in seed germination time variability between Arabidopsis accessions, and use a multi-parent recombinant inbred population to identify two loci involved in this trait. Both loci include genes implicated in ABA signalling that could contribute to seed germination variability. Modelling reveals that the GA/ABA bistable switch underlying germination can amplify variability and account for the effects of these two loci on germination distributions. The model predicts the effects of modulating ABA and GA levels, which we validate genetically and by exogenous addition of hormones. We confirm that germination variability could act as a bet hedging strategy, by allowing a fraction of seeds to survive lethal stress.
Novel allergen discovery through comprehensivede novotranscriptomic analyses of 5 shrimp species
Authors: Karnaneedi Shaymaviswanathan , Huerlimann Roger , Johnston Elecia B. , Nugraha Roni , Ruethers Thimo , Taki Aya C. , Kamath Sandip D. , Wade Nicholas M. , Jerry Dean R. , Lopata Andreas L.
Published: June 2020

Shellfish allergy affects up to 2% of the world’s population and persists for life in most patients. The diagnosis of a shellfish allergy, in particular shrimp, is however often challenging due to the similarity of allergenic proteins in other invertebrates. Despite the clinical importance, the complete allergen repertoire of allergy-causing shrimps remains unclear. Here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. The transcriptomes were assembledde novofrom raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). Trinity was used to assemble the transcriptome, and Transrate and BUSCO applied to verify the assembly. Blast search with the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. Salmon was utilised to measure their relative abundance, demonstrating sarcoplasmic calcium-binding protein, arginine kinase and myosin light chain as highly abundant allergens. In addition, the analyses revealed up to 40 unreported allergens in different shrimp species, including heat shock protein (HSP), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase A, and glyceraldehyde-3-phosphate dehydrogenase (G3PD). Multiple sequence alignment, conducted in Jalview 2.1 with Clustal Omega, demonstrated high homology with allergens from other invertebrates including mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable genomic resource for investigating shellfish allergens, comparing invertebrate allergens and developing improved diagnostics and novel immunotherapeutics for food allergy.
Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2
Authors: Zhang Rongxin , Ke Xiao , Gu Yu , Liu Hongde , Sun Xiao
Published: June 2020

The Coronavirus Disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) quickly become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about G-quadruplexes on the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes both in the positive and negative-sense viral stands. The identified potential G-quadruplexes exhibits similar features to the G-quadruplexes detected in the human transcriptome. Within some bat and pangolin related beta coronaviruses, the G-quartets rather than the loops are under heightened selective constraints. We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. Further analysis revealed that the SARS-CoV-2 SUD-like sequence is almost conserved among 16,466 SARS-CoV-2 samples. And the SARS-CoV-2 SUDcore-like dimer displayed similar electrostatic potential pattern to the SUD dimer. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, we hope our fundamental research could provide new insights for the SARS-CoV-2 drug discovery.
Post-Translational Modifications Soften Vimentin Intermediate Filaments
Authors: Kraxner Julia , Lorenz Charlotta , Menzel Julia , Parfentev Iwan , Silbern Ivan , Denz Manuela , Urlaub Henning , Schwappach Blanche , Köster Sarah
Published: June 2020

The mechanical properties of biological cells are determined by the cytoskeleton, a composite biopolymer network consisting of microtubules, actin filaments and intermediate filaments (IFs). By differential expression of cytoskeletal proteins, modulation of the network architecture and interactions between the filaments, cell mechanics may be adapted to varying requirements on the cell. Here, we focus on the intermediate filament protein vimentin and introduce post-translational modifications as an additional, much faster mechanism for mechanical modulation. We study the impact of phosphorylation on filament mechanics by recording force-strain curves using optical traps. Partial phosphorylation softens the filaments. We show that binding of the protein 14–3–3 to phosphorylated vimentin IFs further enhances this effect and speculate that in the cell 14–3–3 may serve to preserve the softening and thereby the altered cell mechanics. We explain our observation by the additional charges introduced during phosphorylation.
ANANSE: An enhancer network-based computational approach for predicting key transcription factors in cell fate determination
Authors: Xu Quan , Georgiou Georgios , Frölich Siebren , van der Sande Maarten , Veenstra Gert Jan C. , Zhou Huiqing , van Heeringen Simon J.
Published: June 2020

Proper cell fate determination is largely orchestrated by complex gene regulatory networks centered around transcription factors. However, experimental elucidation of key transcription factors that drive cellular identity is currently often intractable. Here, we present ANANSE (ANalysisAlgorithm forNetworksSpecified byEnhancers), a network-based method that exploits enhancer-encoded regulatory information to identify the key transcription factors in cell fate determination. As cell type-specific transcription factors predominantly bind to enhancers, we use regulatory networks based on enhancer properties to prioritize transcription factors. First, we predict genome-wide binding profiles of transcription factors in various cell types using enhancer activity and transcription factor binding motifs. Subsequently, applying these inferred binding profiles, we construct cell type-specific gene regulatory networks, and then predict key transcription factors controlling cell fate transitions using differential networks between cell types. This method outperforms existing approaches in correctly predicting major transcription factors previously identified to be sufficient for trans-differentiation. Finally, we apply ANANSE to define an atlas of key transcription factors in 18 normal human tissues. In conclusion, we present a ready-to-implement computational tool for efficient prediction of transcription factors in cell fate determination and to study transcription factor-mediated regulatory mechanisms. ANANSE is freely available athttps://github.com/vanheeringen-lab/ANANSE.
A novel in-cell ELISA assay allows rapid and automated quantification of SARS-CoV-2 to analyse neutralizing antibodies and antiviral compounds
Authors: Schöler Lara , Le-Trilling Vu Thuy Khanh , Eilbrecht Mareike , Mennerich Denise , Anastasiou Olympia E. , Krawczyk Adalbert , Herrmann Anke , Dittmer Ulf , Trilling Mirko
Published: June 2020

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the most pressing medical and socioeconomic challenge. Constituting important correlates of protection, determination of virus-neutralizing antibodies (NAbs) is indispensable for convalescent plasma selection, vaccine candidate evaluation, and immunity certificates. In contrast to standard serology ELISAs, plaque reduction neutralization tests (PRNTs) are laborious, time-consuming, expensive, and restricted to specialized laboratories. To replace microscopic counting-based SARS-CoV-2 PRNTs by a novel assay exempt from genetically modified viruses, which are inapplicable in most diagnostics departments, we established a simple, rapid, and automated SARS-CoV-2 neutralization assay employing an in-cell ELISA (icELISA) approach.

After optimization of various parameters such as virus-specific antibodies, cell lines, virus doses, and duration of infection, SARS-CoV-2-infected cells became amenable as direct antigen source for quantitative icELISA. Using commercially available nucleocapsid protein-specific antibodies, viral infection could easily be quantified in human and highly permissive Vero E6 cells by icELISA. Antiviral agents such as human sera containing NAbs or antiviral interferons dose-dependently reduced the SARS-CoV-2-specific signal. Applying increased infectious doses, the icNT was superior to PRNT in discriminating convalescent sera with high from those with intermediate neutralizing capacities.

The SARS-CoV-2 icELISA test allows rapid (<48h in total, read-out in seconds) and automated quantification of virus infection in cell culture to evaluate the efficacy of NAbs as well as antiviral drugs, using reagents and equipment present in most routine diagnostics departments. We propose the icELISA and the icNT for COVID-19 research and diagnostics.
Stability of Begomoviral pathogenicity determinant βC1 is modulated by mutually antagonistic SUMOylation and SIM interactions
Authors: Nair Ashwin , Chatterjee Kiran Sankar , Jha Vikram , Das Ranabir , Shivaprasad P. V.
Published: June 2020

To successfully invade new hosts, to break host resistance as well as to move within and between plant cells, viruses and their satellites have evolved a coordinated network of protein interactions. βC1 protein encoded by specific geminiviral satellites acts as a key pathogenicity determinant. βC1 from diverse viruses undergo multiple post-translational modifications (PTMs) such as ubiquitination and phosphorylation. However, the relevance of these and other layers of PTMs in host-geminiviral interactions has not been fully understood. Here we identified the significance of a novel layer of PTMs in Synedrella yellow vein clearing virus (SyYVCV) encoded βC1 protein having well conserved SUMOylation and SUMO-interacting motifs (SIMs). We observed that SyYVCV βC1 undergoes SUMOylation in host plants as a defensive strategy against ubiquitin mediated degradation. On the contrary, SIMs encoded in βC1 mediate degradation of βC1. Both these PTMs are also essential for the function of βC1 protein since SIM and SUMOylation motif mutants failed to promote pathogenicity and viral replicationin vivo. In addition, SUMOylation in different motifs of βC1 led to functionally distinct outcomes, regulating the stability and function of the βC1 protein, as well as increased global SUMOylation of host proteins. Our results indicate the presence of a novel mechanism mediating a fine balance between defence and counter-defence in which a SIM site is competitively sought for degradation and as a counter defense, βC1 undergoes SUMOylation to escape from its degradation.

Summary Statement

βC1 viral protein has evolved counter-defensive strategies to perturb host protein degradation pathways
Ontogeny, species identity and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)
Authors: Brown Joel J. , Rodríguez-Ruano Sonia M. , Poosakkannu Anbu , Batani Giampiero , Schmidt Justin O. , Roachell Walter , Zima Jan , Hypša Václav , Nováková Eva
Published: June 2020

Background

Kissing bugs (Triatominae) are blood-feeding insects best known as the vectors ofTrypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their biology and bacterial symbiosis remains surprisingly understudied. While previous investigations revealed generally low individual complexity but high among-individual variability of the triatomine microbiomes, any consistent microbiome determinants have not yet been identified across multiple Triatominae species.

Methods

To obtain a more comprehensive view of triatomine microbiomes, we investigated the host-microbiome relationship of fiveTriatomaspecies sampled from white-throated woodrat (Neotoma albigula) nests in multiple locations across the USA. We applied optimized 16S rRNA gene metabarcoding with a novel 18S rRNA gene blocking primer to a set of 170T. cruzinegative individuals across all six instars.

Results

Triatomine gut microbiome composition is strongly influenced by three principal factors: ontogeny, species identity, and the environment. The microbiomes are characterised by significant loss in bacterial diversity throughout ontogenetic development. First instars possess the highest bacterial diversity while adult microbiomes are routinely dominated by a single taxon. Primarily, the bacterial genusDietziadominates late-stage nymphs and adults ofT. rubida, T. protracta, andT. lecticularia, but is not present in the phylogenetically more distantT. gerstaeckeriandT. sanguisuga.Species-specific microbiome composition, particularly pronounced in early instars, is further modulated by locality-specific effects. In addition, pathogenic bacteria of the genusBartonella, acquired from the vertebrate hosts, are an abundant component ofTriatomamicrobiomes.

Conclusion

Our study is the first to demonstrate deterministic patterns in microbiome composition among all life stages and multipleTriatomaspecies. We hypothesize that triatomine microbiome assemblages are produced by species- and life stage-dependent uptake of environmental bacteria and multiple indirect transmission strategies that promote bacterial transfer between individuals. Altogether, our study highlights the complexity of Triatominae symbiosis with bacteria and warrant further investigation to understand microbiome function in these important vectors.
Magnetocontrolled protein membranes for cell cultures co-cultivation
Authors: Minin A. , Tiuchai M. , Rodionov S. , Blatov I. , Zubarev I.
Published: June 2020

Investigation of cells and tissues in vitro systems is an attempt to simplify the very complex interactions between the various cell types from multicellular organisms. Monolayer cell cultures with single cell type do not allow to show all the possible paracrine interactions between various types of cells. To analyze intercellular inter-actions, it is possible to use systems that co-cultivate several cell types. This article proposes a new cell co-cultivation system based on levitation in the magnetic field in the culture medium of a magnetic protein membrane with cells. The developed system of co-cultivation of cells can be made in any laboratory of available reagents and have a low manufacturing cost.
Introgression fromOryza meridionalisinto domesticated riceOryza sativaresults in shoot-based iron tolerance
Authors: Wairich Andriele , de Oliveira Ben Hur Neves , Wu Lin-Bo , Murugaiyan Varunseelan , Margis-Pinheiro Marcia , Fett Janette Palma , Ricachenevsky Felipe Klein , Frei Michael
Published: June 2020

Iron (Fe) toxicity is one of the most common mineral disorders affecting rice (Oryza sativa) production in flooded lowland fields.Oryza meridionalisis endemic from Northern Australia and grows in regions with Fe rich soils, making it a candidate for use in adaptive breeding. Aiming to understand tolerance mechanisms in rice, we screened a population of interspecific introgression lines (IL) from a cross betweenO. sativaandO. meridionalisfor the identification of QTLs contributing to Fe toxicity tolerance. Six putative QTLs were identified. A line carrying one introgression fromO. meridionalison chromosome 9 associated with one QTL was highly tolerant despite very high shoot Fe concentrations. Physiological, biochemical, ionomic and transcriptomic analyses showed that the IL tolerance could partly be explained by Fe retention in the leaf sheath and culm. We constructed the interspecific hybrid genomein silicofor transcriptomic analysis, and identified differentially regulated introgressed genes fromO. meridionalisthat could be involved in shoot-based Fe tolerance, such as metallothioneins, glutathione S-transferases and transporters from ABC and MFS families. This is the first work to demonstrate that introgressions ofO. meridionalisinto theO. sativagenome can confer increased tolerance to excess Fe.

Highlight

We identified QTLs associated with iron tolerance derived fromO. meridionalis, and characterized their physiological basis inO. sativa.
Assessing SARS-CoV-2 spatial phylogenetic structure: Evidence from RNA and protein sequences
Authors: Jones Leandro R. , Manrique Julieta M.
Published: June 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent RNA virus that spread around the planet in about 4 months. The consequences of this rapid dispersion are under investigation. In this work, we analyzed thousands of genomes and protein sequences from Africa, America, Asia, Europe, and Oceania. We show that the virus is a complex of slightly different variants that are unevenly distributed on Earth, and demonstrate that SARS-CoV-2 phylogeny is spatially structured. Remarkably, the virus phylogeographic patterns were associated with ancestral amino acidic mutations. We hypothesize that geographic structuring is the result of founder effects occurring as a consequence of, and local evolution occurring after, long-distance dispersal. Based on previous studies, the possibility that this could significantly affect the virus phenotype is not remote.
Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity
Authors: Youngblut Nicholas D. , de la Cuesta-Zuluaga Jacobo , Reischer Georg H. , Dauser Silke , Schuster Nathalie , Walzer Chris , Stalder Gabrielle , Farnleitner Andreas H. , Ley Ruth E.
Published: June 2020

Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 5596 metagenome-assembled genomes from the gut metagenomes of 180 predominantly wild animal species representing 5 classes, in addition to 14 existing animal gut metagenome datasets. The MAGs comprised 1522 species-level genome bins (SGBs); most of which were novel at the species, genus, or family levels, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1986 diverse biosynthetic gene clusters; only 23 clustered with any MIBiG database references. Gene-based assembly revealed tremendous gene diversity, much of it host- or environment-specific. Our MAG and gene datasets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to the vertebrate gut.

Importance

Microbiome studies on a select few mammalian species (e.g.,humans, mice, and cattle) have revealed a great deal of novel genomic diversity in the gut microbiome. However, little is known of the microbial diversity in the gut of other vertebrates. We studied the gut microbiome of a large set of mostly wild animal species consisting of mammals, birds, reptiles, amphibians, and fish. Unfortunately, we found that existing reference databases commonly used for metagenomic analyses failed to capture the microbiome diversity among vertebrates. To increase database representation, we applied advanced metagenome assembly methods to our animal gut data and to many public gut metagenome datasets that had not been used to obtain microbial genomes. Our resulting genome and gene cluster collections comprised a great deal of novel taxonomic and genomic diversity, which we extensively characterized. Our findings substantially expand what is known of microbial genomic diversity in the vertebrate gut.
Irreversible sterility of workers and high-volume egg production by queens in the stingless beeTetragonula carbonaria
Authors: Bulle Bueno Francisco Garcia , Gloag Rosalyn , Latty Tanya , Ronai Isobel
Published: June 2020

Social insect reproduction is characterised by a division of labour. Typically, the queen is the sole reproductive female in the colony and the female workers are non-reproductive. However, in the majority of social insect species the workers are only facultatively sterile and remain capable of laying eggs under some conditions, such as when the queen dies. The Australian stingless beeTetragonula carbonariais noteworthy as workers never lay eggs, even if a colony loses its queen. Here we describe the reproductive anatomy ofT. carbonariaworkers (deactivated ovaries), virgin queens (semi-activated ovaries), and mated queens (activated ovaries).T. carbonariamated queens have high-volume egg production compared to other female insects as each of their eight ovarioles (filaments of the ovary) produces approximately 40 eggs per day. We then conduct the first experimental test of absolute worker sterility in the social insects. Using a controlled microcolony environment, we investigate whether the reproductive capacity of adult workers can be rescued by manipulating the workers’ social environment (separating them from a queen) and diet (feeding them unrestricted highly nutritious honey bee royal jelly), both conditions which cause ovary activation in bee species where workers are facultatively sterile. The ovaries ofT. carbonariaworkers that are queenless and fed royal jelly remain non-functional, indicating they are irreversibly sterile and that ovary degeneration is fixed prior to adulthood. We suggest thatT. carbonariamight have evolved absolute worker sterility because colonies under natural conditions are unlikely to ever be queenless.
Pan-Cancer analysis of somatic mutations in miRNA genes
Authors: Urbanek-Trzeciak Martyna Olga , Galka-Marciniak Paulina , Nawrocka Paulina Maria , Kowal Ewelina , Szwec Sylwia , Giefing Maciej , Kozlowski Piotr
Published: June 2020

miRNAs are considered important players in oncogenesis, serving either as oncomiRs or suppressormiRs. Although the accumulation of somatic alterations is an intrinsic aspect of cancer development and many important cancer-driving mutations have been identified in protein-coding genes, the area of functional somatic mutations in miRNA genes is heavily understudied. Here, based on analysis of the whole-exome sequencing of over 10,000 cancer/normal sample pairs deposited within the TCGA repository, we identified and characterized over 10,000 somatic mutations in miRNA genes and showed that some of the genes are overmutated in Pan-Cancer and/or specific cancers. Nonrandom occurrence of the identified mutations was confirmed by a strong association of overmutated miRNA genes with KEGG pathways, most of which were related to specific cancer types or cancer-related processes. Additionally, we showed that mutations in some of the overmutated genes correlate with miRNA expression, cancer staging, and patient survival. Our results may also be the first step (form the basis and provide the resources) in the development of computational and/or statistical approaches/tools dedicated to the identification of cancer-driver miRNA genes.
Rapid purification and metabolomic profiling of synaptic vesicles from mammalian brain
Authors: Chantranupong Lynne , Saulnier Jessica L. , Wang Wengang , Jones Drew R. , Pacold Michael E. , Sabatini Bernardo L.
Published: June 2020

Neurons communicate by the activity-dependent release of small-molecule neurotransmitters packaged into synaptic vesicles (SVs). Although many molecules have been identified as neurotransmitters, technical limitations have precluded a full metabolomic analysis of synaptic vesicle content. Here, we present a workflow to rapidly isolate SVs and to interrogate their metabolic contents at a high-resolution using mass spectrometry. We validated the enrichment of glutamate in SVs of primary cortical neurons using targeted polar metabolomics. Unbiased and extensive global profiling of SVs isolated from these neurons revealed that the only detectable polar metabolites they contain are the established neurotransmitters glutamate and GABA. Finally, we adapted the approach to enable quick capture of SVs directly from brain tissue and determined the neurotransmitter profiles of diverse brain regions in a cell-type specific manner. The speed, robustness, and precision of this method to interrogate SV contents will facilitate novel insights into the chemical basis of neurotransmission.
A unifying framework disentangles genetic, epigenetic, and stochastic sources of drug-response variability in anin vitromodel of tumor heterogeneity
Authors: Hayford Corey E. , Tyson Darren R. , Robbins C. Jack , Frick Peter L. , Quaranta Vito , Harris Leonard A.
Published: June 2020

Tumor heterogeneity is a primary cause of treatment failure and acquired resistance in cancer patients. Even in cancers driven by a single mutated oncogene, variability of targeted therapy response is observed. Additional genetic mutations can only partially explain this variability, leading to consideration of non-genetic factors, such as “stem-like” and “mesenchymal” phenotypic states, as critical contributors to tumor relapse and resistance. Here, we show that both genetic and non-genetic factors contribute to targeted drug-response variability in an experimental tumor heterogeneity model based on multiple versions and clonal sublines of PC9, the archetypal EGFR-mutant non-small cell lung cancer cell line. We observe significant drug-response variability across PC9 cell line versions, among sublines, and within sublines. To disentangle genetic, epigenetic, and stochastic components underlying this variability, we adopt a theoretical framework whereby distinct genetic states give rise to multiple epigenetic “basins of attraction”, across which cells can transition driven by stochastic factors such as gene expression noise and asymmetric cell division. Using mutational impact analysis, single-cell differential gene expression, and semantic similarity of gene ontology terms to connect genomics and transcriptomics, we establish a baseline of genetic differences explaining drug-response variability across PC9 cell line versions. In contrast, with the same approach, we conclude that in all but one of the clonal sublines, drug-response variability is due to epigenetic rather than genetic differences. Finally, using a clonal drug-response assay and stochastic simulations, we attribute drug-response variability within sublines to intracellular stochastic fluctuations and confirm that one subline likely contains a genetic resistance mutation that emerged in the absence of selective pressures. We propose that a theoretical framework deconvolving the complex interplay among genetic, epigenetic, and stochastic sources of intratumoral heterogeneity will lead to novel therapeutic strategies to combat tumor relapse and resistance.
Accuracy of a battery-powered portable capnometer in neonates
Authors: Hirakawa Eiji , Ibara Satoshi
Published: June 2020

End-tidal CO2measurement (EtCO2) is useful for confirmation of successful tracheal intubation and ensuring adequate ventilation. There are two types of EtCO2detector, i.e., single-use-only devices and capnometers. Although portable capnometers are widely used for resuscitation, there have been no reports regarding their clinical utility in neonates. Here, the correspondence between EtCO2level determined using a battery-powered portable capnometer and arterial CO2(PaCO2) was investigated using paired data obtained simultaneously from 26 neonates weighing 1262 ± 589 g at examination on mechanical ventilation. EtCO2level and PaCO2showed a strong correlation (r = 0.839,P< 0.001), and the correlation equation was: EtCO2= 0.8 × PaCO2+ 1.1. Therefore, EtCO2readings obtained with a battery-powered portable capnometer were likely to be underestimated. This became more pronounced with decreasing infant body weight at examination as the net difference in measurements of PaCO2and EtCO2was significantly positively correlated with infant body weight at examination (r = 0.451,P< 0.001). The observations presented here may be helpful in the use of battery-powered portable capnometers in neonates requiring controlled ventilation with tracheal intubation.
Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics
Authors: Carbo Ellen C. , Buddingh Emilie P. , Karelioti Evita , Sidorov Igor , Feltkamp Mariet C.W. , von dem Borne Peter A. , Verschuuren Jan J.G.M. , Kroes Aloys C.M. , Claas Eric C.J. , de Vries Jutte J.C.
Published: June 2020

Metagenomic sequencing is a powerful technique that enables detection of the full spectrum of pathogens present in any specimen in a single test. Hence, metagenomics is increasingly being applied for detection of viruses in clinical cases with suspected infections of unknown etiology and a large number of relevant potential causes. This is typically the case in patients presenting with encephalitis, in particular when immunity is impaired by underlying disorders.

In this study, viral metagenomics has been applied to a cohort of hematological patients with encephalitis of unknown origin.

Since viral loads in cerebrospinal fluid of patients with encephalitis are generally low, the technical performance of a metagenomic sequencing protocol enriched by capture probes targeting all known vertebrate viral sequences was studied. Subsequently, the optimized viral metagenomics protocol was applied to a cohort of hematological patients with encephalitis of unknown origin.

Viral enrichment by capture probes increased the viral sequence read count of metagenomics on cerebrospinal fluid samples 100 – 10.000 fold, compared to unenriched metagenomic sequencing.

In five out of 41 (12%) hematological patients with encephalitis, a virus was detected by viral metagenomics which had not been detected by current routine diagnostics. BK polyomavirus, hepatitis E virus, human herpes virus-6 and Epstein Barr virus were identified by this unbiased metagenomic approach.

This study demonstrated that hematological patients with encephalitis of unknown origin may benefit from early viral metagenomics testing as a single step approach.

Highlights

A metagenomics protocol employing virus capture probes was validated and retrospectively applied to 41 hematological adult and pediatric patients presenting with encephalitis of unknown aetiology

Viral enrichment by capture probes increased sensitivity of viral metagenomics on cerebrospinal fluid samples 100 – 10.000 fold, compared to unenriched metagenomic sequencing

In 12% of hematological patients with encephalitis of unknown origin, a virus was detected by viral metagenomics, which was not found by routine diagnostics

Viral metagenomics represents a valuable addition to the diagnostics repertoire for hematological patients with suspected CNS infection
Multi-particle cryo-EM refinement withMvisualizes ribosome-antibiotic complex at 3.7 Å inside cells
Authors: Tegunov Dimitry , Xue Liang , Dienemann Christian , Cramer Patrick , Mahamid Julia
Published: June 2020

Cryo-electron microscopy (cryo-EM) enables macromolecular structure determinationin vitroandin situ. In addition to aligning individual particles, accurate registration of sample motion and 3D deformation during exposures is crucial for achieving high resolution. Here we describeM, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and improves the results of structure determination.Mprovides a unified optimization framework for bothin vitroframe series andin situtomographic tilt series data. We show that tilt series data can provide the same resolution as frame series, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION,Mimproves upon previous methods, and resolves a 70S ribosome bound to an antibiotic inside bacterial cells at a nominal resolution of 3.7 Å. Thus, computational tools are now available to resolve structures from tomographicin situcryo-EM data at residue level.
Cycling cancer persister cells arise from lineages with distinct transcriptional and metabolic programs
Authors: Oren Yaara , Tsabar Michael , Cabanos Heidie F. , Cuoco Michael S. , Zaganjor Elma , Thakore Pratiksha I. , Tabaka Marcin , Fulco Charles P , Hurvitz Sara A. , Slamon Dennis J. , Lahav Galit , Hata Aaron , Brugge Joan S. , Regev Aviv
Published: June 2020

Non-genetic mechanisms have recently emerged as important drivers of therapy failure in cancer (Salgia and Kulkarni, 2018), where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment (Vallette et al., 2019). While most cancer persisters, like their bacterial counterparts, remain arrested in the presence of drug, a rare subset of cancer persisters can re-enter the cell cycle under constitutive drug treatment (Sharma et al., 2010). Little is known about the non-genetic mechanisms that enable cancer persisters to maintain proliferative capacity in the presence of drug. Here, using time-lapse imaging, we found that cycling persisters emerge early in the course of treatment of EGFR-mutant lung cancer cells with the EGFR inhibitor osimertinib. To study this rare, transiently-resistant, proliferative persister population we developed Watermelon, a new high-complexity expressed barcode lentiviral library for simultaneous tracing each cell’s clonal origin, proliferative state, and transcriptional state. Analysis of Watermelon-transduced PC9 cells demonstrated that cycling and non-cycling persisters arise from different pre-existing cell lineages with distinct transcriptional and metabolic programs. The proliferative capacity of persisters is associated with an upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation in specific subpopulations of tumor cells. Mitigating oxidative stress or blocking metabolic reprograming significantly alters the fraction of cycling persister cells. In human tumors, programs associated with cycling persisters were induced in malignant cells in response to multiple tyrosine kinase inhibitors. The Watermelon system enabled the identification of rare persister lineages, that are preferentially poised through specific gene programs to proliferate under drug pressure, thus exposing new vulnerabilities that can be targeted to delay or even prevent disease recurrence.