bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serial femtosecond and serial synchrotron crystallography yield data of equivalent quality: a systematic comparison
Authors: Mehrabi P. , Bücker R. , Bourenkov G. , Ginn H.M. , von Stetten D. , Müller-Werkmeister H.M. , Kuo A. , Morizumi T. , Eger B.T. , Ou W.-L. , Oghbaey S. , Sarracini A. , Besaw J.E. , Paré-Labrosse O. , Meier S. , Schikora H. , Tellkamp F. , Marx A. , Sherrell D.A. , Axford D. , Owen R. , Ernst O.P. , Pai E.F. , Schulz E.C. , Miller R.J.D. 
Published: August 2020

AbstractFor the two proteins myoglobin (MB) and fluoroacetate dehalogenase (FAcD), we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of crystals, the same sample delivery device, as well as the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins reasonable data statistics can be obtained with approximately 5000 room temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that diffraction quality is rather linked to the properties of the crystals than to the radiation source. Time-resolved experiments can therefore be conducted at the source that best matches the desired time-resolution.
An ERF transcription factor from Brassica oleracea: a new member of the emerging pathogenicity hub in plant-Xanthomonas interactions
Authors: Zlobin Nikolay , Lebedeva Marina , Monakhova Yuliya , Ustinova Vera , Taranov Vasiliy 
Published: August 2020

Summary- TAL effectors (TALEs), which induce the expression of specific plant genes to promote infection, are the main pathogenic determinants of different Xanthomonas bacteria. However, investigation of TALEs fromXanthomonas campestrispv.campestris, which causes black rot disease of crucifers, is in its infancy.- In this study, we used PCR-based amplification in conjunction with SMRT amplicon sequencing to identify TALE genes in severalXanthomonas campestrispv.campestrisstrains and performed computational prediction in conjunction with RT-PCR-based analysis to identify their target genes inBrassica oleracea.- Transcription factor from the AP2/ERF family was predicted to be putative target gene for the conserved TALEs present in multipleXanthomonas campestrispv.campestrisstrains. Its expression dramatically increased upon leaf inoculation with strains harbouring such TALEs.- Several members of the AP2/ERF factor family from different plant species were identified as targets of TALEs from various Xanthomonas species, which suggests that they constitute a new pathogenicity hub in plant-Xanthomonas interactions.
Sphagnumpeat moss thermotolerance is modulated by the microbiome
Authors: Carrell Alyssa A. , Lawrence Travis J. , Cabugao Kristine Grace M. , Carper Dana L. , Pelletier Dale A. , Jawdy Sara , Grimwood Jane , Schmutz Jeremy , Hanson Paul J. , Shaw A. Jonathan , Weston David J. 
Published: August 2020

AbstractSphagnumpeat mosses is a major genus that is common to peatland ecosystems, where the species contribute to key biogeochemical processes including the uptake and long-term storage of atmospheric carbon. Warming threatensSphagnummosses and the peatland ecosystems in which they reside, potentially affecting the fate of vast global carbon stores. The competitive success ofSphagnumspecies is attributed in part to their symbiotic interactions with microbial associates. These microbes have the potential to rapidly respond to environmental change, thereby helping their host plants survive under changing environmental conditions. To investigate the importance of microbiome thermal origin on host plant thermotolerance, we mechanically separated the microbiome fromSphagnumplants residing in a whole-ecosystem warming study, transferred the component microbes to germ-free plants, and exposed the new hosts to temperature stress. Although warming decreased plant photosynthesis and growth in germ-free plants, the addition of a microbiome from a thermal origin that matched the experimental temperature completely restored plants to their pre-warming growth rates. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure, including the composition of key cyanobacteria symbionts, in a manner that induced the plant heat shock response, especially the Hsp70 family and jasmonic acid production. The plant heat shock response could be induced even without warming, suggesting that the warming-origin microbiome provided the host plant with thermal preconditioning. Together, our findings show that the microbiome can transmit thermotolerant phenotypes to host plants, providing a valuable strategy for rapidly responding to environmental change.
Forebrain projection neurons target functionally diverse respiratory control areas in the midbrain, pons and medulla oblongata
Authors: Trevizan-Baú Pedro , Dhingra Rishi R. , Furuya Werner I. , Stanić Davor , Mazzone Stuart B. , Dutschmann Mathias 
Published: August 2020

AbstractEupnea is generated by neural circuits located in the ponto-medullary brainstem, but can be modulated by higher brain inputs which contribute to volitional control of breathing and the expression of orofacial behaviors, such as vocalization, sniffing, coughing and swallowing. Surprisingly, the anatomical organization of descending inputs that connect the forebrain with the brainstem respiratory network remains poorly defined. We hypothesized that descending forebrain projections target multiple distributed respiratory control nuclei across the neuraxis. To test our hypothesis, we made discrete unilateral microinjections of the retrograde tracer Cholera toxin subunit B (CT-B) in the midbrain periaqueductal gray (PAG), the pontine Kölliker-Fuse nucleus (KFn), the medullary Bötzinger complex (BötC), pre-Bötzinger complex (pre-BötC) or caudal midline raphé nuclei. We quantified the regional distribution of retrogradely-labeled neurons in the forebrain 12-14 days post-injection. Overall, our data reveals that descending inputs from cortical areas predominantly target the PAG and KFn. Differential forebrain regions innervating the PAG (prefrontal, cingulate cortices, and lateral septum) and KFn (rhinal, piriform, and somatosensory cortices) imply that volitional motor commands for vocalization are specifically relayed via the PAG, while the KFn may receive commands to coordinate breathing with other orofacial behaviors (e.g. sniffing, swallowing). Additionally, we observed that the limbic or autonomic (interoceptive) systems are connected to broadly distributed downstream bulbar respiratory networks. Collectively, these data provide a neural substrate to explain how volitional, state-dependent, and emotional modulation of breathing is regulated by the forebrain.
Somatic deficiency causes reproductive parasitism in a fungus
Authors: Grum-Grzhimaylo Alexey A. , Bastiaans Eric , van den Heuvel Joost , Millanes Cristina Berenguer , Debets Alfons J.M. , Aanen Duur K. 
Published: August 2020

AbstractSome multicellular organisms can fuse because mergers potentially provide mutual benefits. However, experimental evolution in the fungusNeurospora crassahas demonstrated that free fusion of mycelia favours cheater lineages, but the mechanism and evolutionary dynamics of dishonest exploitation are unknown. Here we show, paradoxically, that all convergently evolved cheater lineages have similar fusion deficiencies. These mutants are unable to initiate fusion but retain access to wild-type mycelia that fuse with them. This asymmetry reduces cheater-mutant contributions to somatic substrate-bound hyphal networks, but increases representation of their nuclei in the aerial reproductive hyphae. Cheaters only benefit when relatively rare and likely impose genetic load reminiscent of germline senescence. We show that the consequences of somatic fusion can be unequally distributed among fusion partners, with the passive non-fusing partner profiting more. We discuss how our findings may relate to the extensive variation in fusion frequency of fungi found in nature.
Whole-animal connectome and cell-type complement of the three-segmentedPlatynereis dumeriliilarva
Authors: Verasztó Csaba , Jasek Sanja , Gühmann Martin , Shahidi Réza , Ueda Nobuo , Beard James David , Mendes Sara , Heinz Konrad , Bezares-Calderón Luis Alberto , Williams Elizabeth , Jékely Gáspár 
Published: August 2020

AbstractNervous systems coordinate effectors across the body during movements. We know little about the cellular-level structure of synaptic circuits for such body-wide control. Here we describe the whole-body synaptic connectome and cell-type complement of a three-segmented larva of the marine annelidPlatynereis dumerilii. We reconstructed and annotated over 1,500 neurons and 6,500 non-neuronal cells in a whole-body serial electron microscopy dataset. The differentiated cells fall into 180 neuronal and 90 non-neuronal cell types. We analyse the modular network architecture of the entire nervous system and describe polysynaptic pathways from 428 sensory neurons to four effector systems – ciliated cells, glands, pigment cells and muscles. The complete somatic musculature and its innervation will be described in a companion paper. We also investigated intersegmental differences in cell-type complement, descending and ascending pathways, and mechanosensory and peptidergic circuits. Our work provides the basis for understanding whole-body coordination in annelids.
T-bet fate mapping identifies a novel ILC1-ILC2 subsetin vivo
Authors: Schroeder J-H , Garrido-Mesa N , Zabinski T , Gallagher AL , Campbell L , Roberts LB , Stolarczyk E , Beattie G , Lo JW , Iseppon A , Heliodoro C Moreira , Reis R , Jenner RG , Lavender P , Howard JK , Grencis RK , Helmby H , Neves J F , Lord GM 
Published: August 2020

ABSTRACTInnate lymphoid cells (ILC) play a critical role in regulating immune responses at mucosal surfaces. Various subsets exist resembling T cell lineages defined by the expression of specific transcription factors. Thus, T-bet is expressed in ILC1 and Th1 cells. In order to further understand the functional roles of T-bet in ILC, we generated a fate-mapping mouse model that permanently marks cells and their progeny that are expressing, or have ever expressed T-bet. Here we have identified and characterised a novel ILC with characteristics of ILC1 and ILC2 that are “fate-mapped” for T-bet expression and arise early in neonatal life prior to establishment of a mature microbiome. These ILC1-ILC2 cells are critically dependent on T-bet and are able to express type 1 and type 2 cytokines at steady state, but not in the context of inflammation. These findings refine our understanding of ILC lineage regulation and stability and have important implications for the understanding of ILC biology at mucosal surfaces.SUMMARYInnate lymphoid cells (ILC) play a critical role in regulating immune responses at mucosal surfaces. Three distinct ILC groups have been described according to expression of subset defining transcription factors and other markers. In this study we characterize a novel ILC subset with characteristics of group 1 and group 2 ILCin vivo.
Ectopic histone clipping in the mouse model of progressive myoclonus epilepsy
Authors: Daura Eduard , Tegelberg Saara , Yoshihara Masahito , Jackson Christopher , Simonetti Francesca , Aksentjeff Katri , Ezer Sini , Hakala Paula , Katayama Shintaro , Kere Juha , Lehesjoki Anna-Elina , Joensuu Tarja 
Published: August 2020

ABSTRACTWe establish cystatin B (CSTB) as a regulator of histone H3 tail clipping in murine neural progenitor cells (NPCs) and provide evidence suggesting that epigenetic dysregulation contributes to the early pathogenesis in brain disorders associated with deficient CSTB function. We show that NPCs undergo regulated cleavage of the N-terminal tail of histone H3 at threonine 22 (H3T22) transiently upon induction of differentiation. CSTB-deficient NPCs present premature activation of H3T22 clipping during self-renewal mediated by increased activity of cathepsins L and B. During differentiation, the proportion of immature committed neurons undergoing H3T22 clipping is significantly higher in CSTB-deficient than in wild-type NPCs, with no observable decline within 12 days post-differentiation. CSTB-deficient NPCs exhibit significant transcriptional changes highlighting altered expression of nuclear-encoded mitochondrial genes. These changes are associated with significantly impaired respiratory capacity of differentiating NPCs devoid of CSTB. Our data expand the mechanistic understanding of diseases associated with CSTB deficiency.
Suppression without inhibition: How retinal computation contributes to saccadic suppression
Authors: Idrees Saad , Baumann Matthias-Philipp , Korympidou Maria M. , Schubert Timm , Kling Alexandra , Franke Katrin , Hafed Ziad M. , Franke Felix , Münch Thomas A. 
Published: August 2020

AbstractVisual perception remains stable across saccadic eye movements, despite the concurrent strongly disruptive visual flow. This stability is partially associated with a reduction in visual sensitivity, known as saccadic suppression, which already starts in the retina with reduced ganglion cell sensitivity. However, the retinal circuit mechanisms giving rise to such suppression remain unknown. Here, we describe these mechanisms using electrophysiology in mouse, pig, and macaque retina, 2-photon calcium imaging, computational modeling, and human psychophysics. We find that sequential stimuli, such as those that naturally occur during saccades, trigger three independent suppressive mechanisms in the retina. The main suppressive mechanism is triggered by contrast-reversing sequential stimuli and originates within the receptive field center of ganglion cells. It does not involve inhibition or other known suppressive mechanisms such as saturation or adaptation. Instead, it relies on temporal filtering of the inherently slow response of cone photoreceptors coupled with downstream nonlinearities. Two further mechanisms of suppression are present predominantly in ON ganglion cells and originate in the receptive field surround, highlighting a novel disparity between ON and OFF ganglion cells. The mechanisms uncovered here likely play a role in shaping the retinal output following eye movements and other natural viewing conditions where sequential stimulation is ubiquitous.
Functional and druggability analysis of the SARS-CoV-2 proteome
Authors: Cavasotto Claudio N. , Sánchez Lamas Maximiliano , Maggini Julián 
Published: August 2020

AbstractThe infectious coronavirus disease (COVID-19) pandemic, caused by the coronavirus SARS-CoV-2, appeared in December 2019 in Wuhan, China, and has spread worldwide. As of today, more than 22 million people have been infected, with almost 800,000 fatalities. With the purpose of contributing to the development of effective therapeutics, this work provides an overview of the viral machinery and functional role of each SARS-CoV-2 protein, and a thorough analysis of the structure and druggability assessment of the viral proteome. All structural, non-structural, and accessory proteins of SARS-CoV-2 have been studied, and whenever experimental structural data of SARS-CoV-2 proteins were not available, homology models were built based on solved SARS-CoV structures. Several potential allosteric or protein-protein interaction druggable sites on different viral targets were identified, knowledge that could be used to expand current drug discovery endeavors beyond the cysteine proteases and the polymerase complex. It is our hope that this study will support the efforts of the scientific community both in understanding the molecular determinants of this disease and in widening the repertoire of viral targets in the quest for repurposed or novel drugs against COVID-19.
Evidence for a role of phenotypic mutations in virus adaptation
Authors: Luzon-Hidalgo Raquel , Risso Valeria A. , Delgado Asuncion , Andrés-Leon Eduardo , Ibarra-Molero Beatriz , Sanchez-Ruiz Jose M. 
Published: August 2020

SUMMARYViruses interact extensively with the host molecular machinery, but the underlying mechanisms are poorly understood. Bacteriophage T7 recruits the small protein thioredoxin of theE. colihost as an essential processivity factor for the viral DNA polymerase. We challenged the phage to propagate in a host in which thioredoxin had been extensively modified to hamper its recruitment. The virus adapted to the engineered host without losing the capability to propagate in the original host, but no genetic mutations were fixed in the thioredoxin binding domain of the viral DNA polymerase. Virus adaptation correlated with mutations in the viral RNA polymerase, supporting that promiscuous thioredoxin recruitment was enabled by phenotypic mutations caused by transcription errors. These results point to a hitherto unknown mechanism of virus adaptation that may play a role in crossspecies transmission. We propose that phenotypic mutations may generally contribute to the capability of viruses to evade antiviral strategies.
Hematopoietic lineages diverge within the stem cell compartment
Authors: Morcos Mina N. F. , Li Congxin , Munz Clara M. , Greco Alessandro , Dressel Nicole , Reinhardt Susanne , Dahl Andreas , Becker Nils B. , Roers Axel , Höfer Thomas , Gerbaulet Alexander 
Published: August 2020

AbstractHematopoietic stem cells (HSCs) produce a highly diverse array of cell lineages. To assay hematopoietic differentiation with minimal experimental perturbation, non-invasive methods for heritable labeling1–3or barcoding4–7of HSCsin vivohave recently been developed and used to study lineage fate of HSCs in physiological conditions. However, the differentiation pathways leading from HSCs to mature cells remain controversial8, with suggested models ranging from gradual lineage restriction in a branching cascade of progenitors to HSCs already making ultimate lineage decisions. Here we show, by iterating HSC fate-mapping, mitotic history tracking, single-cell RNA-sequencing and computational inference, that the major differentiation routes to megakaryocytes, erythro-myeloid cells and lymphocytes split within HSCs. We identify the hitherto elusive self-renewing source of physiological hematopoiesis as an HSC subpopulation co-expressing high levels of Sca-1 and CD201. Downstream, HSCs reduce Sca-1 expression and enter into either thrombopoiesis or erythro-myelopoiesis, or retain high Sca-1 levels and the ability to generate lymphocytes. Moreover, we show that a distinct population of CD48−/lomegakaryocyte progenitors links HSCs to megakaryocytes. This direct thrombopoiesis pathway is independent of the classical pathway of megakaryocyte differentiation via multipotent progenitors and becomes the dominant platelet production line upon enhanced thrombopoietin signaling. Our results define a hierarchy of self-renewal and lineage decisions within HSCs in native hematopoiesis. Methodologically, we provide a blueprint for mapping physiological differentiation pathways of stem cells and probing their regulation.
A sort-seq approach to the development of single fluorescent protein biosensors
Authors: Koberstein John N. , Stewart Melissa L. , Mighell Taylor L. , Smith Chadwick B. , Cohen Michael S. 
Published: August 2020

AbstractThe utility of single fluorescent protein biosensors (SFPBs) in biological research is offset by the difficulty in engineering these tools. SFPBs generally consist of three basic components: a circularly permuted fluorescent protein, a ligand-binding domain, and a pair of linkers connecting the two domains. In the absence of predictive methods for biosensor engineering, most designs combining these three components will fail to produce allosteric coupling between ligand binding and fluorescence emission. Methods to construct libraries of biosensor designs with variations in the site of GFP insertion and linker sequences have been developed, however, our ability to construct new variants has exceeded our ability to test them for function. Here, we address this challenge by applying a massively parallel assay termed “sort-seq” to the characterization of biosensor libraries. Sort-seq combines binned fluorescence-activated cell sorting, next-generation sequencing, and maximum likelihood estimation to quantify the dynamic range of many biosensor variants in parallel. We applied this method to two common biosensor optimization tasks: choice of insertion site and optimization of linker sequences. The sort-seq assay applied to a maltose-binding protein domain-insertion library not only identified previously described high-dynamic-range variants but also discovered new functional insertion-sites with diverse properties. A sort-seq assay performed on a pyruvate biosensor linker library expressed in mammalian cell culture identified linker variants with substantially improved dynamic range. Machine learning models trained on the resulting data can predict dynamic range from linker sequence. This high-throughput approach will accelerate the design and optimization of SFPBs, expanding the biosensor toolbox.
Defining the early stages of intestinal colonisation by whipworms
Authors: Duque-Correa María A. , Goulding David , Rodgers Faye H. , Cormie Claire , Rawlinson Kate , Gillis J. Andrew , Bancroft Allison J. , Bennett Hayley M. , Lotkowska Magda , Reid Adam J. , Speak Anneliese , Scott Paul , Redshaw Nicholas , McCarthy Catherine , Brandt Cordelia , Sharpe Catherine , Ridley Caroline , Moya Judit Gali , Carneiro Claudia M. , Starborg Tobias , Hayes Kelly S. , Holroyd Nancy , Sanders Mandy , Thornton David J. , Grencis Richard K. , Berriman Matthew 
Published: August 2020

AbstractWhipworms are large metazoan parasites that inhabit distinct multi-intracellular epithelial burrows described as syncytial tunnels, in the large intestine of their hosts. How first-stage larvae invade host epithelia and establish infection remains unclear. Here, we investigate early infection events both usingTrichuris murisinfections of mice and murine caecaloids, the firstin-vitrosystem for whipworm infection. We show that larvae degrade the mucus layers to access epithelial cells. In early syncytial tunnels, larvae are completely intracellular but woven through multiple live enterocytes and goblet cells. We also use single cell RNA sequencing for the first time to describe the mouse caecum. From infected caeca, the transcriptome data reveal the progression of infection results in cell damage and an expansion of enterocytes with a type-I interferon (IFN) signature, characterised by the expression ofIsg15, instigating the host immune response to the whipworm and tissue repair. Our results unravel intestinal epithelium invasion by whipworms and reveal new specific interactions between the host and the parasite that allow the whipworm to establish its multi-intracellular niche.
A home and rescue gene drive efficiently spreads and persists in populations
Authors: Kandul Nikolay P. , Liu Junru , Bennett Jared B. , Marshall John M. , Akbari Omar S. 
Published: August 2020

AbstractHoming based gene drives, engineered using CRISPR/Cas9, have been proposed to spread desirable genes into target populations. However, spread of such drives can be hindered by the accumulation of resistance alleles. To overcome this significant obstacle, we engineer an inherently confinable population modificationHome-and-Rescue (HomeR) drive inDrosophila melanogasterthat, by creative design, limits the accumulation of such alleles. We demonstrate that HomeR can achieve nearly ∼100% transmission enabling it to spread and persist at genotypic fixation in several multi-generational population cage experiments, underscoring its long term stability and drive potential. Finally, we conduct mathematical modeling determining HomeR can outperform contemporary gene drive architectures for population modification over wide ranges of fitness and transmission rates. Given its straightforward design, HomeR could be universally adapted to a wide range of species.