bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Normal Levels of Urine and Plasma Free Glycosaminoglycans in Adults
Authors: Bratulic Sinisa , Limeta Angelo , Maccari Francesca , Galeotti Fabio , Volpi Nicola , Levin Max , Nielsen Jens , Gatto Francesco 
Published: May 2021

AbstractPlasma and urine glycosaminoglycans (GAGs) are long linear sulfated polysaccharides recognized as potential non-invasive biomarkers for several diseases. However, owing to the analytical complexity associated with the measurement of GAG concentration and disaccharide composition, the so-called GAGome, a reference study of the normal healthy GAGome is currently missing. Here, we prospectively enrolled 308 healthy adults and analyzed their urine and plasma free GAGomes using a standardized ultra-high-performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (UHPLC-MS/MS) method together with comprehensive demographic and blood chemistry biomarker data. Of 25 blood chemistry biomarkers, we mainly observed weak correlations between the free GAGome and creatinine in urine, and hemoglobin or erythrocyte counts in plasma. We found higher free GAGome concentration – but not composition - in males. Partitioned by gender, we established reference intervals for all detectable free GAGome features in urine and plasma. We carried out a transference analysis in healthy individuals from two distinct geographical sites, including the Lifelines Cohort Study, which validated the reference intervals in urine. Our study is the first large-scale determination of normal plasma and urine free GAGomes reference intervals and represents a critical resource for physiology and biomarker research.
Different individual-level responses of great black-backed gulls (Larus marinus) to shifting local prey availability
Authors: Maynard Laurie D. , Gulka Julia , Jenkins Edward , Davoren Gail K. 
Published: May 2021

AbstractTo grow, survive and reproduce under anthropogenic-induced changes, individuals must respond quickly and favourably to the surrounding environment. A species that feeds on a wide variety of prey types (i.e. generalist diet) may be comprised of generalist individuals, specialist individuals that feed on different prey types, or a combination of the two. If individuals within a population respond differently to an environmental change, population-level responses may not be detectable. By tracking foraging movements of eight great black-backed gulls (Larus marinus), a generalist species, we compared group-level and individual-level responses to an increase in prey biomass (capelin; Mallotus villosus) during the breeding season in coastal Newfoundland, Canada. As hypothesized, shifts in prey availability resulted in significantly different individual responses in foraging behaviour and space use, which was not detectable when data from individuals were combined. Some individuals maintained similar foraging areas, foraging trip characteristics (e.g., trip length, duration) and habitat use with increased capelin availability, while others shifted foraging areas and habitats resulting in either increased or decreased trip characteristics. We show that individual specialization can be non-contextual in some gulls, whereby these individuals continuously use the same feeding strategy despite significant change in prey availability conditions. Findings also indicate high response diversity among individuals to shifting prey conditions that a population- or group-level study would not have detected, emphasizing the importance of examining individual-level strategies for future diet and foraging studies on generalist species.
Linking animal migration and ecosystem processes: data-driven simulation of propagule dispersal by migratory herbivores
Authors: Somveille Marius , Ellis-Soto Diego 
Published: May 2021

AbstractAnimal migration is a key process underlying active subsidies and species dispersal over long distances, which affects the connectivity and functioning of ecosystems. Despite much research describing patterns of where animals migrate, we still lack a framework for quantifying and predicting how animal migration affects ecosystem processes.In this study, we aim to integrate animal movement behavior and ecosystem functioning by developing a predictive modeling framework that can inform ecosystem management and conservation. Our framework models individual-level migration trajectories between populations’ seasonal ranges as well as the resulting dispersal and fate of propagules carried by the migratory animals, and it can be calibrated using empirical data at every step of the modeling process.As a case study, we applied our framework to model the spread of guava seeds, Psidium guajava, by a population of migratory Galapagos tortoises, Chelonoidis porteri, across Santa Cruz Island. Galapagos tortoises are large herbivores that transport seeds and nutrients across the island, while Guava is one of the most problematic invasive species in the Galapagos archipelago.Our model is able to predict the pattern of spread of guava seeds alongside tortoises’ downslope migration range, and it identified areas most likely to see germination success and establishment. Our results show that Galapagos tortoises’ seed dispersal may particularly contribute to guava range expansion on Santa Cruz Island, due to both long gut retention time and tortoise’s long-distance migration across vegetation zones. In particular, we predict that tortoises are dispersing a significant amount of guava seeds into the Galapagos National Park, which has important consequences for the native flora.The flexibility and modularity of our framework allows for the integration of multiple data sources. It also allows for a wide range of applications to investigate how migratory animals affect ecosystem processes, including propagule dispersal but also other processes such as nutrient transport across ecosystems. Our framework is also a valuable tool for predicting how animal-mediated propagule dispersal can be affected by environmental change. These different applications can have important conservation implications for the management of ecosystems that include migratory animals.
Interrogation of cancer gene dependencies reveals novel paralog interactions of autosome and sex chromosome encoded genes
Authors: Köferle Anna , Schlattl Andreas , Hörmann Alexandra , Spreitzer Fiona , Popa Alexandra , Thatikonda Venu , Puchner Teresa , Oberndorfer Sarah , Wieshofer Corinna , Corcokovic Maja , Reiser Christoph , Wöhrle Simon , Popow Johannes , Pearson Mark , Mair Barbara , Neumüller Ralph A. 
Published: May 2021

AbstractGenetic networks are characterized by extensive buffering. During tumour evolution, disruption of these functional redundancies can createde novovulnerabilities that are specific to cancer cells. In this regard, paralog genes are of particular interest, as the loss of one paralog gene can render tumour cells dependent on a remaining paralog. To systematically identify cancer-relevant paralog dependencies, we searched for candidate dependencies using CRISPR screens and publicly available loss-of-function datasets. Our analysis revealed >2,000 potential candidate dependencies, several of which were subsequently experimentally validated. We provide evidence thatDNAJC15-DNAJC19, FAM50A-FAM50BandRPP25-RPP25Lare novel cancer relevant paralog dependencies. Importantly, our analysis also revealed unexpected redundancies between sex chromosome genes. We show that chrX- and chrY- encoded paralogs, as exemplified byZFX-ZFY, DDX3X-DDX3YandEIF1AX-EIF1AY, are functionally linked so that tumour cell lines from male patients with Y-chromosome loss become exquisitely dependent on the chrX-encoded gene. We therefore propose genetic redundancies between chrX- and chrY- encoded paralogs as a general therapeutic strategy for human tumours that have lost the Y-chromosome.
Afferent connections of cytoarchitectural area 6M and surrounding cortex in the marmoset: putative homologues of the supplementary and pre-supplementary motor areas
Authors: Bakola Sophia , Burman Kathleen J. , Bednarek Sylwia , Chan Jonathan M. , Jermakow Natalia , Worthy Katrina H. , Majka Piotr , Rosa Marcello G.P. 
Published: May 2021

AbstractCortical projections to the caudomedial frontal cortex were studied using retrograde tracers in marmosets. We tested the hypothesis that cytoarchitectural area 6M includes homologues of the supplementary and pre-supplementary motor areas (SMA and preSMA) of other primates. We found that, irrespective of the injection sites’ location within 6M, over half of the labeled neurons were located in motor and premotor areas. Other connections originated in prefrontal area 8b, ventral anterior and posterior cingulate areas, somatosensory areas (3a and 1-2), and areas on the rostral aspect of the dorsal posterior parietal cortex. Although the origin of afferents was similar, injections in rostral 6M received higher percentages of prefrontal afferents, and fewer somatosensory afferents, compared to caudal injections, compatible with differentiation into SMA and preSMA. Injections rostral to 6M (area 8b) revealed a very different set of connections, with increased emphasis in prefrontal and posterior cingulate afferents, and fewer parietal afferents. The connections of 6M were also quantitatively different from those of M1, dorsal premotor areas, and cingulate motor area 24d. These results show that the cortical motor control circuit is conserved in simian primates, indicating that marmosets can be valuable models for studying movement planning and control.
Plasmodiophora brassicae infection threshold – how many resting spores are required for infection of canola (Brassica napus)
Authors: Zahr Kher , Yang Yalong , Sarkes Alian , Dijanovic Snezana , Fu Heting , Harding Michael W. , Feindel David , Feng Jie 
Published: May 2021

AbstractClubroot, caused by Plasmodiophora brassicae, is an important disease of canola and other brassica crops. Improved understanding of host and pathogen biology is frequently useful in guiding management strategies. In order to better understand infection thresholds, seven-day old seedlings of canola cultivar Westar were inoculated with serially diluted concentrations of P. brassicae resting spores. Controlled soil and plant inoculation assays were performed and the plants maintained in a greenhouse for 42 days and clubroot disease severity evaluated visually. Clubroot symptoms were observed in soils containing as low as one spore/mL soil and on plants inoculated with as few as ≤ 100 resting spores. These thresholds were lower than any previously reported. The results indicated the importance of highly sensitive detection methods for P. brassicae diagnosis and quantification methods for clubroot risk prediction in soils. Furthermore, these results highlighted the low probability of obtaining P. brassicae single spore isolates.
Morpho-functional characterization of the endo-lysosomal system by high-throughput correlative light-electron microscopy
Authors: van der Beek Jan , de Heus Cecilia , Liv Nalan , Klumperman Judith 
Published: May 2021

AbstractRab5, EEA1 and APPL1 are frequently used in fluorescence microscopy to mark early endosomes, whereas Rab7 is used as marker for late endosomes and lysosomes. However, since these proteins localize poorly in immuno-electron microscopy, systematic studies on their ultrastructural distributions are lacking. Here we address this gap by presenting a quantitative, high-throughput, on-section correlative light-electron microscopy (CLEM) approach using the sensitivity of fluorescence microscopy to infer label to hundreds of organelles classified by ultrastructure. We show that Rab5 predominantly marks small, endocytic vesicles and early endosomes. EEA1 co-localizes with Rab5 on especially early endosomes, but unexpectedly also labels Rab5-negative late endosomes and even lysosomes. APPL1 is restricted to small Rab5-positive, vesicular profiles without any visible content or ultrastructural marks. Rab7 primarily labels late endosomes and lysosomes. Our studies reveal the first ultrastructural distribution of key endosomal proteins at their endogenous levels and introduce CLEM as sensitive alternative for quantitative immuno-EM.
Molecular basis for PICS-mediated piRNA biogenesis and cell division
Authors: Wang Xiaoyang , Zeng Chenming , Liao Shanhui , Zhu Zhongliang , Zhang Jiahai , Tu Xiaoming , Feng Xuezhu , Guang Shouhong , Xu Chao 
Published: May 2021

AbstractBy incorporating two mutually exclusive factors, PID-1 and TOST-1, C. elegans PICS complex plays important roles in piRNA biogenesis, chromosome segregation and cell division, respectively. We firstly mapped the interaction network between PICS subunits. By solving the several complex structures, including those of TOFU-6/PICS-1, ERH-2/PICS-1, and ERH-2/TOST-1, we uncover the mechanisms underlying the interactions between PICS subunits. Our biochemical experiment demonstrates that PICS exists as an octamer consisting of two copies of each subunits. Combining structural analyses with mutagenesis experiments, we identified residues of PICS subunits that are critical for maintaining intact PICS complex in vitro. Furthermore, using genetics, cell biology and imaging experiments, we found that those mutants impairing the in vitro interaction network within PICS, also lead to abnormal dysfunction PICS in vivo, including mislocalization of PICS, and reduced levels of piRNAs or abnormal chromosome segregation and cell division. Therefore, our work provides structural insights into understanding the PICS-mediated piRNA biogenesis and cell division.
Processing of the Ribosomal Ubiquitin-Like Fusion Protein FUBI-eS30/FAU is Required for 40S Maturation and Depends on USP36
Authors: van den Heuvel Jasmin , Ashiono Caroline , Gillet Ludovic , Dörner Kerstin , Wyler Emanuel , Zemp Ivo , Kutay Ulrike 
Published: May 2021

SummaryIn humans and other holozoan organisms, the ribosomal protein eS30 is synthesized as a fusion protein with the ubiquitin-like protein FUBI. However, FUBI is not part of the mature 40S ribosomal subunit and cleaved off by an as-of-yet unidentified protease. How FUBI-eS30 processing is coordinated with 40S subunit maturation is unknown. To study the mechanism and importance of FUBI-eS30 processing, we expressed non-cleavable mutants in human cells, which affected late steps of cytoplasmic 40S maturation, including the maturation of 18S rRNA and recycling of late-acting ribosome biogenesis factors. Differential affinity purification of wild-type and non-cleavable FUBI-eS30 mutants identified the deubiquitinase USP36 as a candidate FUBI-eS30 processing enzyme. Depletion of USP36 by RNAi or CRISPRi indeed impaired FUBI-eS30 processing and moreover, purified USP36 cut FUBI-eS30 in vitro. Together, these data demonstrate the functional importance of FUBI-eS30 cleavage and identify USP36 as a novel protease involved in this process.
The Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase
Authors: Weber Ryan , McCullagh Martin 
Published: May 2021

AbstractThe COVID-19 pandemic has demonstrated the need to develop potent and transferable therapeutics to treat coronavirus infections. Numerous antiviral targets are being investigated, but non-structural protein 13 (nsp13) stands out as a highly conserved and yet under studied target. Nsp13 is a superfamily 1 (SF1) helicase that translocates along and unwinds viral RNA in an ATP dependent manner. Currently, there are no available structures of nsp13 from SARS-CoV-1 or SARS-CoV-2 with either ATP or RNA bound presenting a significant hurdle to the rational design of therapeutics. To address this knowledge gap, we have built models of SARS-CoV-2 nsp13 in Apo, ATP, ssRNA and ssRNA+ATP substrate states. Using 30 μs of Gaussian accelerated molecular dynamics simulation (at least 6 μs per substrate state), these models were confirmed to maintain substrate binding poses that are similar to other SF1 helicases. A gaussian mixture model and linear discriminant analysis structural clustering protocol was used to identify key aspects of the ATP-dependent RNA translocation mechanism. Namely, four RNA-nsp13 structures are identified that exhibit ATP-dependent populations and support the inch-worm mechanism for translocation. These four states are characterized by different RNA-binding poses for motifs Ia, IV and V and suggest a powerstroke–like motion of domain 2A relative to domain 1A. This structural and mechanistic insight of nsp13 RNA translocation presents novel targets for the further development of antivirals.
A framework to identify antigen-expanded T Cell Receptor (TCR) clusters within complex repertoires
Authors: Ceglia Valentina , Kelley Erin J , Boyle Annalee S , Levy Yves , Zurawski Gerard , Altin John A 
Published: May 2021

AbstractCommon approaches for monitoring T cell responses are limited in their multiplexity and sensitivity. In contrast, deep sequencing of the T Cell Receptor (TCR) repertoire offers a global view whose theoretical sensitivity is limited only by the depth of available sampling. However, assignment of antigen specificities within TCR repertoires has become a bottleneck. Here, we combine antigen-driven expansion, deep TCR sequencing and a novel analysis framework to show that homologous ‘Clusters of Expanded TCRs (CETs)’ can be confidently identified without cell isolation, and assigned to antigen against a background of non-specific clones. We show that clonotypes within each CET respond to the same epitope, and that protein antigens stimulate multiple CETs reactive to constituent peptides. Finally, we demonstrate the personalized assignment of antigen-specificity to rare clones within fully-diverse unexpanded repertoires. The method presented here may be used to monitor T cell responses to vaccination and immunotherapy with high fidelity.
ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler
Authors: Rueca Martina , Giombini Emanuela , Messina Francesco , Bartolini Barbara , Di Caro Antonino , Capobianchi Maria R. , Gruber Cesare E. M. 
Published: May 2021

AbstractEarly sequencing and quick analysis of SARS-CoV-2 genome are contributing to understand the dynamics of COVID19 epidemics and to countermeasures design at global level. Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession, harboring multiple deletions and amino acid changing mutations. To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here we propose an easy-to-use SARS-CoV-2 genome Assembler: the ESCA pipeline. Results showed that ESCA can perform high quality genome assembly from IonTor-rent and Illumina raw data, and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility to compare assembled genomes of multi sample runs through an easy table format.Script and manuals are available on GitHub: https://github.com/cesaregruber/ESCA
Cap-dependent translation initiation monitored in living cells
Authors: Gandin Valentina , English Brian P. , Freeman Melanie , Leroux Louis-Philippe , Preibisch Stephan , Walpita Deepika , Jaramillo Maritza , Singer Robert H. 
Published: May 2021

AbstractDespite extensive biochemical, genetic, and structural studies, a complete understanding of mRNA translation initiation is still lacking. Imaging methodologies able to resolve the binding dynamics of translation factors at single-cell and single-molecule resolution are necessary to fully elucidate regulation of this paramount process. We fused tags suitable for live imaging to eIF4E, eIF4G1 and 4E-BP1 without affecting their function. We combined Fluorescence Correlation Spectroscopy (FCS) and Single-Particle Tracking (SPT) to interrogate the binding dynamics of initiation factors to the 5’cap. Both FCS and SPT were able to detect eIF4E:eIF4G1 binding to the mRNA in the cytoplasm of proliferating cells and neuronal processes. Upon inhibition of phosphorylation by mTOR, 4E-BP1:eIF4E complexes rapidly dissociated from the 5’cap followed by eIF4G1 dissociation. Imaging of the binding dynamics of individual translation factors in living cells revealed the temporal regulation of translation at unprecedented resolution.
Coordinated regulation of CB1 cannabinoid receptors and anandamide metabolism stabilizes network activity during homeostatic downscaling
Authors: Ye Michael , Monroe Sarah K. , Gay Sean M. , Armstrong Michael L. , Youngstrom Diane E. , Urbina Fabio L. , Gupton Stephanie L. , Reisdorph Nichole , Diering Graham H. 
Published: May 2021

AbstractNeurons express overlapping homeostatic mechanisms to regulate synaptic function and network properties in response to perturbations of neuronal activity. Endocannabinoids (eCBs) are bioactive lipids synthesized in the post-synaptic compartments to regulate synaptic transmission, plasticity, and neuronal excitability primarily through retrograde activation of pre- synaptic cannabinoid receptor type 1 (CB1). The eCB system is well-situated to regulate neuronal network properties and coordinate pre- and post-synaptic activity. However, the role of the eCB system in homeostatic adaptations to neuronal hyperactivity is unknown. To address this issue, we used western blot and targeted lipidomics to measure adaptations in eCB system to bicuculline (BCC)-induced chronic hyperexcitation in mature (>DIV21) cultured rat cortical neurons, and used multielectrode array recording and live-cell imaging of glutamate dynamics to test the effects of pharmacological manipulations of eCB on network activities. We show that BCC-induced chronic hyperexcitation triggers homeostatic downscaling and a coordinated adaptation to enhance tonic eCB signaling. Hyperexcitation triggers first the downregulation of fatty acid amide hydrolase (FAAH), the lipase that degrades the eCB anandamide, then an accumulation of anandamide and related metabolites, and finally a delayed upregulation of surface and total CB1. Additionally, we show that BCC-induced downregulation of surface AMPA-type glutamate receptors (AMPARs) and upregulation of CB1 occur through independent mechanisms. Finally, we show that endocannabinoids support baseline network activities before and after downscaling and is engaged to suppress network activities during adaptation to hyperexcitation. We discuss the implications of our findings in the context of downscaling and homeostatic regulation of oscillatory network activities.Significance statementNeurons are remarkably resilient to perturbations in network activities thanks to the expression of overlapping homeostatic adaptations. In response to network hyperactivity or silencing, neurons respond through regulating excitatory and inhibitory post-synaptic neurotransmitter receptors density, probability of pre-synaptic neurotransmitter release, and/or membrane excitability. The endocannabinoid system is a prominent signaling pathway at many synapses that is known to be involved in multiple forms of short- and long-term synaptic plasticity. Here we find that components of the endocannabinoid system are upregulated in response to chronic hyperexcitation of cultured cortical neurons, and that endocannabinoid signaling is required to maintain network activity but also suppresses network events during hyperexcitation. This work supports a novel tonic homeostatic function for the endocannabinoid system in neurons.