bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stable QTL for malate levels in ripe fruit and their transferability acrossVitisspecies
Authors: Reshef Noam , Karn Avinash , Manns David C. , Mansfield Anna Katharine , Cadle-Davidson Lance , Reisch Bruce , Sacks Gavin L. 
Published: December 2020

AbstractMalate is a major contributor to the sourness of grape berries (Vitisspp.) and their products, such as wine. Excessive malate at maturity, commonly observed in wildVitisgrapes, is detrimental to grape and wine quality and complicates the introgression of valuable disease resistance and cold hardy genes through breeding. This study investigated an interspecificVitisfamily that exhibited strong and stable variation in malate at ripeness for five years and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit in the last year of study. Genotyping was performed using transferable rhAmpSeq haplotype markers, based on theVitiscollinear core genome. Three significant QTL for ripe fruit malate on chromosomes 1, 7, and 17, accounted for over two-fold and 6.9 g/L differences in ripe fruit malate, and explained 40.6% of the phenotypic variation. QTL on chromosomes 7 and 17 were stable in all and in three out of five years, respectively. Variation in pre-veraison malate was the major contributor to variation in ripe fruit malate (39%) and their associated QTL overlapped on chromosome 7, indicating a common genetic basis. However, use of transferable markers on a closely relatedVitisfamily did not yield a common QTL across families. This suggests that diverse physiological mechanisms regulate the levels of this key metabolite in theVitisgenus, a conclusion supported by a review of over a dozen publications from the past decade, showing malate-associated genetic loci on all 19 chromosomes.
Mono-ubiquitination of Rabphilin 3A by UBE3A serves a non-degradative function
Authors: Trezza Rossella Avagliano , Punt A. Mattijs , Mientjes Edwin , van den Berg Marlene , Zampeta F. Isabella , de Graaf Ilona J. , van der Weegen Yana , Demmers Jeroen A. A. , Elgersma Ype , Distel Ben 
Published: December 2020

AbstractAngelman syndrome (AS) is a severe neurodevelopmental disorder caused by brain-specific loss of UBE3A, an E3 ubiquitin protein ligase. A substantial number of possible ubiquitination targets of UBE3A have been identified, although evidence of being direct UBE3A substrates is often lacking. Here we identified the synaptic protein Rabphilin-3a (RPH3A), an effector of the RAB3A small GTPase involved in axonal vesicle priming and docking, as a ubiquitination target of UBE3A. We found that the UBE3A and RAB3A binding sites on RPH3A partially overlap, and that RAB3A binding to RPH3A interferes with UBE3A binding. We confirmed previous observations that RPH3A levels are critically dependent on RAB3A binding but, rather surprisingly, we found that the reduced RPH3A levels in the absence of RAB3A are not mediated by UBE3A. Indeed, while we found that RPH3A is ubiquitinated in a UBE3A-dependent manner in mouse brain, UBE3A mono-ubiquitinates RPH3A and does not facilitate RPH3A degradation. Moreover, we found that an AS-linked UBE3A missense mutation in the UBE3A region that interacts with RPH3A, abrogates the interaction with RPH3A. In conclusion, our results identify RPH3A as a novel target of UBE3A and suggest that UBE3A-dependent ubiquitination of RPH3A serves a non-degradative function.
Remdesivir is a delayed translocation inhibitor of SARS CoV-2 replication in vitro
Authors: Bravo Jack P. K. , Dangerfield Tyler L. , Taylor David W. , Johnson Kenneth A. 
Published: December 2020

AbstractRemdesivir is a nucleoside analog approved by the FDA for treatment of COVID-19. Here, we present a 3.9-Å-resolution cryoEM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of three copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of three bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs.
Mutational and biophysical robustness in a pre-stabilized monobody
Authors: Chandler Peter G. , Tan Li Lynn , Porebski Benjamin T. , Green James S. , Riley Blake T. , Broendum Sebastian S. , Hoke David E. , Falconer Robert J. , Munro Trent P. , Buckle Malcolm , Jackson Colin J. , Buckle Ashley M. 
Published: December 2020

AbstractThe fibronectin type III (FN3) monobody domain is a promising non-antibody scaffold which features a less complex architecture than an antibody while maintaining analogous binding loops. We previously developed FN3Con, a hyper-stable monobody derivative with diagnostic and therapeutic potential. Pre-stabilization of the scaffold mitigates the stability-function trade-off commonly associated with evolving a protein domain towards biological activity. Here, we aimed to examine if the FN3Con monobody could take on antibody-like binding to therapeutic targets, while retaining its extreme stability. We targeted the first of the Adnectin derivative of monobodies to reach clinical trials, which was engineered by directed evolution for binding to the therapeutic target VEGFR2; however, this function was gained at the expense of large losses in thermostability and increased oligomerisation. In order to mitigate these losses, we grafted the binding loops from Adnectin-anti-VEGFR2 (CT-322) onto the pre-stabilized FN3Con scaffold to produce a domain that successfully bound with high affinity to the therapeutic target VEGFR2. This FN3Con-anti-VEGFR2 construct also maintains high thermostability, including remarkable long-term stability, retaining binding activity after 2 years of storage at 36 °C. Further investigations into buffer excipients doubled the presence of monomeric monobody in accelerated stability trials. These data suggest that loop grafting onto a pre-stabilized scaffold is a viable strategy for the development of monobody domains with desirable biophysical characteristics, and is therefore well-suited to applications such as the evolution of multiple paratopes or shelf-stable diagnostics and therapeutics.
Lactate Accelerates Mouse ES Cell Differentiation Towards the XEN Lineage
Authors: Gatie Mohamed I. , Cooper Tyler T. , Lajoie Gilles A. , Kelly Gregory M. 
Published: December 2020

SummaryMetabolism plays a crucial role for cell survival and function; however, recent evidence has implicated it in regulating embryonic development. The inner cell mass undergoes orchestrated cellular divisions resulting in the formation of embryonic stem cells and extraembryonic endoderm (XEN) cells. Concomitantly, changes in the metabolic profile occurs during development and are well-documented in the embryonic lineages. However, a comprehensive multi-omics analysis of these features in XEN cells remains lacking. We observed that feeder-free XEN cells exhibited high sensitivity to glycolytic inhibition in addition to maintaining elevated intra- and extracellular lactate levels. XEN cells maintain high lactate levels by increased LDHA activity and re-routing pyruvate away from the mitochondria. Importantly, exogenous lactate supplementation or promoting intracellular lactate accumulation enhances XEN differentiationin vitro. Our results highlight how lactate contributes to XEN differentiation in the mammalian embryo and may serve to enhance reprogramming efficiency of cells used for regenerative medicine.HighlightsFeeder-free XEN cells exhibit high sensitivity to glycolytic inhibitionDistinct transcriptomic, proteomic and metabolomic profile exists between feeder-free ES and XEN cellsElevated intracellular and extracellular lactate is observed in feeder-free XEN cellsLactate enhances feeder-free XEN differentiationin vitro
SOCIODEMOGRAPHIC CHARACTERISTICS AND COVID-19 TESTING RATES: SPATIO-TEMPORAL PATTERNS AND IMPACT OF TEST ACCESSIBILITY IN SWEDEN
Authors: Kennedy Beatrice , Varotsis Georgios , Hammar Ulf , Nguyen Diem , Carrasquilla Germán D. , van Zoest Vera , Kristiansson Robert S. , Fitipaldi Hugo , Dekkers Koen F. , Daivadanam Meena , Martinell Mats , Björk Jonas , Fall Tove 
Published: December 2020

ABSTRACTBackgroundDiagnostic testing is essential for disease surveillance and test-trace-isolate efforts. Here, we aimed to investigate if residential area sociodemographic characteristics and test accessibility were associated with COVID-19 testing rates.MethodsWe included information on 421 542 patient-initiated COVID-19 PCR tests from Uppsala County in Sweden from 24 June, 2020 to 9 February, 2022. Using Poisson regression analyses, we investigated whether the Care Need Index (CNI; median 1.0, IQR 0.8, 1.4), a composite measure of sociodemographic factors used in Sweden to allocate primary healthcare resources, was associated with aggregated COVID-19 daily testing rates after adjustments for community transmission. We further assessed if distance to the nearest testing station influenced testing. Lastly, we performed a difference-in-difference analysis of the opening of a testing station targeting a disadvantaged neighbourhood.ResultsWe observed that CNI, i.e. primary healthcare need, was negatively associated with COVID-19 testing rates in inhabitants aged 5-69 years. More pronounced differences were noted across younger age groups and in Uppsala City, with test rate ratios in children (5-14 years) ranging from 0.56 (95% CI 0.47-0.66) to 0.88 (95% CI 0.81-0.95) across the three pandemic waves. Longer distance to testing station was linked to lower testing rates, foremost in less densely populated areas. Furthermore, the opening of the targeted testing station was associated with increased testing, including twice as high testing rates in individuals aged 70-105, supporting an intervention effect.ConclusionsEnsuring accessible testing across all residential areas constitutes a promising tool to decrease differences and inequalities in testing.
Development of a Rapid Point-Of-Care Test that Measures Neutralizing Antibodies to SARS-CoV-2
Authors: Lake Douglas F. , Roeder Alexa J. , Kaleta Erin , Jasbi Paniz , Pfeffer Kirsten , Koelbel Calvin , Periasamy Sivakumar , Kuzmina Natalia , Bukreyev Alexander , Grys Thomas E. , Wu Liang , Mills John R , McAulay Kathrine , Gonzalez-Moa Maria , Seit-Nebi Alim , Svarovsky Sergei 
Published: December 2020

AbstractBackgroundAfter receiving a COVID-19 vaccine, most recipients want to know if they are protected from infection and for how long. Since neutralizing antibodies are a correlate of protection, we developed a lateral flow assay (LFA) that measures levels of neutralizing antibodies from a drop of blood. The LFA is based on the principle that neutralizing antibodies block binding of the receptor-binding domain (RBD) to angiotensin-converting enzyme 2 (ACE2).MethodsThe ability of the LFA was assessed to correctly measure neutralization of sera, plasma or whole blood from patients with COVID-19 using SARS-CoV-2 microneutralization assays. We also determined if the LFA distinguished patients with seasonal respiratory viruses from patients with COVID-19. To demonstrate the usefulness of the LFA, we tested previously infected and non-infected COVID-19 vaccine recipients at baseline and after first and second vaccine doses.ResultsThe LFA compared favorably with SARS-CoV-2 microneutralization assays with an area under the ROC curve of 98%. Sera obtained from patients with seasonal coronaviruses did not show neutralizing activity in the LFA. After a single mRNA vaccine dose, 87% of previously infected individuals demonstrated high levels of neutralizing antibodies. However, if individuals were not previously infected only 24% demonstrated high levels of neutralizing antibodies after one vaccine dose. A second dose boosted neutralizing antibody levels just 8% higher in previously infected individuals, but over 63% higher in non-infected individuals.ConclusionsA rapid, semi-quantitative, highly portable and inexpensive neutralizing antibody test might be useful for monitoring rise and fall in vaccine-induced neutralizing antibodies to COVID-19.
The Gradient Clusteron: A model neuron that learns via dendritic nonlinearities, structural plasticity, and gradient descent
Authors: Moldwin Toviah , Kalmenson Menachem , Segev Idan 
Published: December 2020

AbstractSynaptic clustering on neuronal dendrites has been hypothesized to play an important role in implementing pattern recognition. Neighboring synapses on a dendritic branch can interact in a synergistic, cooperative manner via the nonlinear voltage-dependence of NMDA receptors. Inspired by the NMDA receptor, the single-branch clusteron learning algorithm (Mel 1991) takes advantage of location-dependent multiplicative nonlinearities to solve classification tasks by randomly shuffling the locations of “under-performing” synapses on a model dendrite during learning (“structural plasticity”), eventually resulting in synapses with correlated activity being placed next to each other on the dendrite. We propose an alternative model, the gradient clusteron, or G-clusteron, which uses an analytically-derived gradient descent rule where synapses are “attracted to” or “repelled from” each other in an input- and location- dependent manner. We demonstrate the classification ability of this algorithm by testing it on the MNIST handwritten digit dataset and show that, when using a softmax activation function, the accuracy of the G-clusteron on the All-vs-All MNIST task (∼85%) approaches that of logistic regression (∼93%). In addition to the location update rule, we also derive a learning rule for the synaptic weights of the G-clusteron (“functional plasticity”) and show that a G-clusteron that utilizes the weight update rule can achieve ∼89% accuracy on the MNIST task. We also show that a G-clusteron with both the weight and location update rules can learn to solve the XOR problem from arbitrary initial conditions.
CERMEP-IDB-MRXFDG: A database of 37 normal adult human brain [18F]FDG PET, T1 and FLAIR MRI, and CT images available for research
Authors: Mérida Inés , Jung Julien , Bouvard Sandrine , Le Bars Didier , Lancelot Sophie , Lavenne Franck , Bouillot Caroline , Redouté Jérôme , Hammers Alexander , Costes Nicolas 
Published: December 2020

AbstractWe present a database of cerebral PET FDG and anatomical MRI for 37 normal adult human subjects (CERMEP-IDB-MRXFDG).Thirty-nine participants underwent [18F]FDG PET/CT and MRI, resulting in [18F]FDG PET, T1 MPRAGE MRI, FLAIR MRI, and CT images. Two participants were excluded after visual quality control. We describe the acquisition parameters, the image processing pipeline and provide participants’ individual demographics (mean age 38 ± 11.5 years, range 23-65, 20 women). Volumetric analysis of the 37 T1 MRIs showed results in line with the literature. A leave-one-out assessment of the 37 FDG images using Statistical Parametric Mapping (SPM) yielded a low number of false positives after exclusion of artefacts.The database is stored in three different formats, following the BIDS common specification: 1) DICOM (data not processed), 2) NIFTI (multimodal images coregistered to PET subject space), 3) NIFTI normalized (images normalized to MNI space).Bona fideresearchers can request access to the database via a short form.
Uneven protection of persistent giant kelp forest in the Northeast Pacific Ocean
Authors: Arafeh-Dalmau Nur , Cavanaugh Kyle C. , Possingham Hugh P. , Munguia-Vega Adrian , Montaño-Moctezuma Gabriela , Bell Tom W. , Cavanaugh Kate , Micheli Fiorenza 
Published: December 2020

AbstractIn most regions, the distribution of marine forests and the efficacy of their protection is unknown. We mapped the persistence of giant kelp forests across ten degrees of latitude in the Northeast Pacific Ocean and found that 7.7% of giant kelp is fully protected, with decreasing percentages from north to south. Sustainability goals should prioritize kelp mapping and monitoring, while protection and climate adaption targets should account for habitat dynamics.
DRAM1 requires PI(3,5)P2generation by PIKfyve to deliver vesicles and their cargo to endolysosomes
Authors: van der Vaart Michiel , Banducci-Karp Adrianna , Forn-Cuní Gabriel , Witt Philip M. M. , Willemse Joost J. , Sánchez Salomé Muñoz , Hosseini Rohola , Meijer Annemarie H. 
Published: December 2020

AbstractEndolysosomal vesicle trafficking and autophagy are crucial degradative pathways in maintenance of cellular homeostasis. The transmembrane protein DRAM1 is a potential therapeutic target that primarily localises to endolysosomal vesicles and promotes autophagy and vesicle fusion with lysosomes. However, the molecular mechanisms underlying DRAM1-mediated vesicle fusion events remain unclear. Using high-resolution confocal microscopy in the zebrafish model, we show that mCherry-Dram1 labelled vesicles interact and fuse with early endosomes marked by PI(3)P. Following these fusion events, early endosomes mature into late endosomes in a process dependent on the conversion of PI(3)P into PI(3,5)P2by the lipid kinase PIKfyve. Chemical inhibition of PIKfyve reduces the targeting of Dram1 to acidic endolysosomal vesicles, arresting Dram1 in multivesicular bodies, early endosomes, or non-acidified vesicles halted in their fusion with early endosomes. In conclusion, Dram1-mediated vesicle fusion requires the formation of PI(3,5)P2to deliver vesicles and their cargo to the degradative environment of the lysosome.
Extracting neuronal activity signals from microscopy recordings of contractile tissue: a cell tracking approach using B-spline Explicit Active Surfaces (BEAS)
Authors: Kazwiny Youcef , Pedrosa João , Zhang Zhiqing , Boesmans Werend , D’hooge Jan , Berghe Pieter Vanden 
Published: December 2020

AbstractCa2+imaging is a widely used microscopy technique to simultaneously study cellular activity in multiple cells. The desired information consists of cell-specific time series of pixel intensity values, in which the fluorescence intensity represents cellular activity. For static scenes, cellular signal extraction is straightforward, however multiple analysis challenges are present in recordings of contractile tissues, like those of the enteric nervous system (ENS). This layer of critical neurons, embedded within the muscle layers of the gut wall, shows optical overlap between neighboring neurons, intensity changes due to cell activity, and constant movement. These challenges reduce the applicability of classical segmentation techniques and traditional stack alignment and regions-of-interest (ROIs) selection workflows. Therefore, a signal extraction method capable of dealing with moving cells and is insensitive to large intensity changes in consecutive frames is needed.Here we propose a b-spline active contour method to delineate and track neuronal cell bodies based on local and global energy terms. We develop both a single as well as a double-contour approach. The latter takes advantage of the appearance of GCaMP expressing cells, and tracks the nucleus’ boundaries together with the cytoplasmic contour, providing a stable delineation of neighboring, overlapping cells despite movement and intensity changes. The tracked contours can also serve as landmarks to relocate additional and manually-selected ROIs. This improves the total yield of efficacious cell tracking and allows signal extraction from other cell compartments like neuronal processes. Compared to manual delineation and other segmentation methods, the proposed method can track cells during large tissue deformations and high-intensity changes such as during neuronal firing events, while preserving the shape of the extracted Ca2+signal. The analysis package represents a significant improvement to available Ca2+imaging analysis workflows for ENS recordings and other systems where movement challenges traditional Ca2+signal extraction workflows.
The effects of development and chronic oxidative stress on telomere length in an agricultural pest moth,Helicoverpa armigera
Authors: Apirajkamol Nonthakorn (Beatrice) , Walsh Tom K , McGaughran Angela 
Published: December 2020

AbstractTelomeres are repetitive sequences located at the end of chromosomes in eukaryotes that protect against loss of important sequences during the cell replication process. Telomere length (TL) shortens with every round of cell division. When a telomere becomes too short, cells can no longer proliferate and this triggers the cell apoptosis process. Apart from cell replication, the length of telomeres can be affected by factors such as sex, genetics, and stress levels. Oxidative stress in particular can cause damage to telomeres and telomere maintenance processes, resulting in TL shortening. This phenomenon occurs in humans and many vertebrates, especially endothermic species. However, the ways in which various stress types affect the TL of invertebrate species remains ambiguous.Here, we examined the effects of development and oxidative stress on TL in the invertebrate pest moth,Helicoverpa armigera. In the former case, we extracted genomic DNA from three developmental stages (1-day old egg, 4th instar, and first-day emerged moths) and measured TL by qPCR. In the latter, we chronically exposed individuals to paraquat – an organic herbicide that induces oxidative stress - and then measured TL as per our development methodology. In addition, we examined TL in a subset of published whole genome short-read sequencing data of caterpillars and moths using the software, Computel.In our experimental work, we found that TL inH. armigerawas significantly longer at the early stages of development and shortens in later stages. However, oxidative stress does not appear to shorten TL inH. armigerafollowing chronic exposure to paraquat. In our Computel analysis, we found that caterpillars had longer mean TL than moths but this difference was not significant due to the high variation among samples.Collectively, our research provides new data on TL in an underrepresented group, adding new insights into the progression of TL shortening with development and the effects of oxidative stress on TL, while also more generally highlighting the value of applying complementary approaches to TL measurement.
InSegtCone: Interactive Segmentation of crystalline Cones in compound eyes
Authors: Tichit Pierre , Zhou Tunhe , Kjer Hans Martin , Dahl Vedrana Andersen , Dahl Anders Bjorholm , Baird Emily 
Published: December 2020

AbstractUnderstanding the diversity of eyes is crucial to unravel how different animals use vision to interact with their respective environments. To date, comparative studies of eye anatomy are scarce because they often involve time-consuming or inefficient methods. X-ray micro-tomography is a promising high-throughput imaging technique that enables to reconstruct the 3D anatomy of eyes, but powerful tools are needed to perform fast conversions of anatomical reconstructions into functional eye models. We developed a computing method namedInSegtConeto automatically segment the crystalline cones in the apposition compound eyes of arthropods. Here, we describe the full auto-segmentation process, showcase its application to three different insect compound eyes and evaluate its performance. The auto-segmentation could successfully label the full individual shapes of 60%-80% of the crystalline cones, and is about as accurate and 250 times faster than manual labelling of the individual cones. We believe thatInSegtConecan be an important tool for peer scientists to enable extensive comparisons of the diversity of eyes and vision in arthropods.