bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sphingolipid changes in Parkinson L444P GBA mutation fibroblasts promote α-synuclein aggregation
Authors: Galvagnion Céline , Cerri Silvia , Schapira Anthony H.V. , Blandini Fabio , Di Monte Donato A. 
Published: November 2020

ABSTRACTIntraneuronal accumulation of aggregated α-synuclein is a pathological hallmark of Parkinson’s disease. Therefore, mechanisms capable of promoting α-synuclein deposition bear important pathogenetic implications. Mutations of the glucocerebrosidase 1 (GBA) gene represent a prevalent Parkinson’s disease risk factor. They are associated with loss of activity of a key enzyme involved in lipid metabolism, glucocerebrosidase, supporting a mechanistic relationship between abnormal α-synuclein-lipid interactions and the development of Parkinson pathology. In this study, the lipid membrane composition of fibroblasts isolated from control subjects, patients with idiopathic Parkinson’s disease (iPD) and Parkinson patients carrying the L444PGBAmutation (PD-GBA) was assayed using shotgun lipidomics. The lipid profile of PD-GBA fibroblasts differed significantly from that of control and iPD cells. It was characterized by an overall increase in sphingolipid levels. It also featured a significant change in the proportion of ceramide, sphingomyelin and hexosylceramide molecules with shorter and longer hydrocarbon chain length; levels of shorter-chain molecules were increased while the percent of longer-chain sphingolipids was decreased in PD-GBA lipid extracts. The extent of this shift was correlated to the degree of reduction of fibroblast glucocerebrosidase activity. In a second set of experiments, lipid extracts from control and PD-GBA fibroblasts were added to incubations of recombinant α-synuclein. The kinetics of α-synuclein aggregation, as assessed by the binding of thioflavin T to amyloid structures, was significantly accelerated after addition of PD-GBA extracts as compared to control samples. Amyloid fibrils collected at the end of these incubations contained lipids, indicating α-synuclein-lipid co-assembly. Lipids extracted from α-synuclein fibrils were also analysed by shotgun lipidomics. Data revealed that the lipid content of these fibrils was significantly enriched of shorter-chain sphingolipids. Taken together, findings of this study indicate that the L444PGBAmutation and consequent enzymatic loss are associated with a distinctly altered membrane lipid profile that provides a biological fingerprint of this mutation in Parkinson fibroblasts. This altered lipid profile, which includes an increased content of shorter-chain sphingolipids, could also be an indicator of increased risk for α-synuclein aggregate pathology. Shorter-chain molecules may act as preferred reactants during lipid-induced α-synuclein fibrillation.
Dilp8 controls a time window for tissue size adjustment inDrosophila
Authors: Boulan L. , Blanco-Obregon D. , El Marzkioui K. , Brutscher F. , Andersen D.S. , Colombani J. , Narasimha S. , Léopold P. 
Published: November 2020

ABSTRACTThe control of organ size mainly relies on precise autonomous growth programs. However, organ development is subject to random variations, called developmental noise, best revealed by the fluctuating asymmetry observed between bilateral organs. The developmental mechanisms ensuring bilateral symmetry in organ size are mostly unknown. InDrosophila, null mutations for the relaxin-like hormone Dilp8 increase wing fluctuating asymmetry, suggesting that Dilp8 plays a role in buffering developmental noise. Here we show that size adjustment of the wing primordia involves a peak of Dilp8 expression that takes place sharply at the end of juvenile growth. Wing size adjustment relies on a crossorgan communication involving the epidermis as the source of Dilp8. We identify ecdysone signaling as both the trigger for epidermaldilp8expression and its downstream target in the wing primordia, thereby establishing reciprocal feedback between the two hormones as a systemic mechanism controlling organ size precision. Our results reveal a hormone-based time window ensuring fine-tuning of organ size and bilateral symmetry.
Gain-of-function assay for SARS-CoV-2 Mproinhibition in living cells
Authors: Moghadasi Seyad Arad , Becker Jordan T. , Belica Christopher , Wick Chloe , Brown William L. , Harris Reuben S. 
Published: November 2020

AbstractThe main protease, Mpro, of SARS-CoV-2 is required to cleave the viral polyprotein into precise functional units for virus replication and pathogenesis. Here we demonstrate a quantitative reporter for Mprofunction in living cells, in which protease inhibition by genetic or chemical methods results in strong eGFP fluorescence. This robust gain-of-function system readily distinguishes between inhibitor potencies and can be scaled-up to high-throughput platforms for drug testing.
Acute ethanol stress induces sumoylation of conserved chromatin structural proteins inSaccharomyces cerevisiae
Authors: Bradley Amanda I. , Marsh Nicole M. , Borror Heather R. , Mostoller Kaitlyn E. , Gama Amber I. , Gardner Richard G. 
Published: November 2020

AbstractStress is a ubiquitous part of life that disrupts cellular function and, if unresolved, can irreparably damage essential biomolecules and organelles. All organisms can experience stress in the form of unfavorable environmental conditions including exposure to extreme temperatures, hypoxia, reactive oxygen species, alcohol, or shifts in osmolarity. To survive, organisms must sense these changes then react and adapt. One highly conserved adaptive response to stress is through protein sumoylation, which is a post-translational modification by thesmallubiquitin-likemodifier (SUMO) protein. In this study, we examine the effects of acute ethanol stress on protein sumoylation in the budding yeastSaccharomyces cerevisiae. Although ethanol induces protein sumoylation, the targets and roles of sumoylation are largely unknown. Here, we found that cells exhibit a transient sumoylation response after exposure of cells to ≤ 7.5% volume/volume ethanol. The response peaks at 15 minutes and resolves by 60 minutes, indicating that cells have an adaptive response to low concentrations of ethanol. By contrast, the sumoylation response becomes chronic at 10% ethanol stress with no resolution by 60 minutes. To identify key targets of ethanol-induced sumoylation, we performed mass spectrometry analyses and identified 18 proteins with increased sumoylation after acute ethanol exposure, with 15 identified as known chromatin-associated proteins. Two of these proteins are the chromatin structural proteins Smc5 and Smc6, which are sumoylated by the activity of the SUMO ligase Mms21. Ethanol-induced Smc5/6 sumoylation occurs during G1 and G2M phases of the cell cycle but is abrogated during S phase despite the fact that other proteins are sumoylated during this phase. Acute ethanol exposure leads to formation of Rad52 foci indicating DNA damage similar to that observed with the addition of methyl methanesulfonate (MMS), which is an alkylating agent that damages DNA. Whereas MMS exposure induces the intra-S phase DNA damage checkpoint as observed by Rad53 phosphorylation, ethanol exposure does not induce the intra-S phase checkpoint and prevents Rad53 phosphorylation when added with MMS. From these results, we propose that ethanol induces a structural change in chromatin, possibly through DNA damage, and this causes sumoylation of conserved chromatin-associated proteins, including Smc5 and Smc6.
Hyperoxia inhibits proliferation of retinal endothelial cells in Myc dependent manner
Authors: Singh Charandeep , Benos Andrew , Grenell Allison , Rao Sujata , Anand-Apte Bela , Sears Jonathan E. 
Published: November 2020

AbstractOxygen supplementation is necessary to prevent mortality of severely premature infants. However, the supraphysiological concentration of oxygen utilized in these infants simultaneously creates retinovascular growth attenuation and vasoobliteration that induces retinopathy of prematurity. Here, we report that hyperoxia regulates the cell cycle and retinal endothelial cell proliferation in a previously unknown Myc dependent manner which contributes to oxygen-induced retinopathy.
A plant lipocalin is required for retinal-mediatedde novoroot organogenesis
Authors: Dickinson Alexandra J. , Zhang Jingyuan , Luciano Michael , Wachsman Guy , Schnermann Martin , Dinneny José R. , Benfey Philip N. 
Published: November 2020

AbstractBranching of root systems enables the exploration and colonization of the soil environment. In Arabidopsis roots,de novoorganogenesis of lateral roots is patterned by an oscillatory mechanism called the root clock, which is dependent on metabolites derived from the β-carotene pathway1, 2. Retinoids are β-carotene-derived regulators of organogenesis in the animal kingdom. To determine if retinoids function in plant development, we conducted time-lapse imaging of a chemical reporter for retinoid binding proteins. We found that it oscillates with a comparable frequency to the root clock and accurately predicts sites of lateral root organogenesis. Exogenous application of retinal to wild-type plants is sufficient to induce root clock oscillations and lateral root organogenesis. A homology search yielded a potentialArabidopsishomolog, TEMPERATURE INDUCED LIPOCALIN (TIL) to vertebrate retinoid binding proteins. Genetic analysis indicates that TIL is necessary for normal lateral root development and atilmutant has decreased retinal sensitivity. TIL expression in a heterologous system conferred retinal binding activity, suggesting that it may directly interact with this molecule. Together, these results demonstrate an essential role for retinal and for plant retinal binding proteins in lateral root organogenesis.
Estimation of non-additive genetic variance in human complex traits from a large sample of unrelated individuals
Authors: Hivert Valentin , Sidorenko Julia , Rohart Florian , Goddard Michael E , Yang Jian , Wray Naomi R , Yengo Loic , Visscher Peter M 
Published: November 2020

AbstractNon-additive genetic variance for complex traits is traditionally estimated from data on relatives. It is notoriously difficult to estimate without bias in non-laboratory species, including humans, because of possible confounding with environmental covariance among relatives. In principle, non-additive variance attributable to common DNA variants can be estimated from a random sample of unrelated individuals with genome-wide SNP data. Here, we jointly estimate the proportion of variance explained by additive, dominanceand additive-by-additivegenetic variance in a single analysis model. We first show by simulations that our model leads to unbiased estimates and provide new theory to predict standard errors estimated using either least squares or maximum likelihood. We then apply the model to 70 complex traits using 254,679 unrelated individuals from the UK Biobank and 1.1M genotyped and imputed SNPs. We found strong evidence for additive variance (average across traits. In contrast, the average estimate ofacross traits was 0.001, implying negligible dominance variance at causal variants tagged by common SNPs. The average epistatic varianceacross the traits was 0.058, not significantly different from zero because of the large sampling variance. Our results provide new evidence that genetic variance for complex traits is predominantly additive, and that sample sizes of many millions of unrelated individuals are needed to estimate epistatic variance with sufficient precision.
Computationally-guided design and affinity improvement of a protein binder targeting a specific site on HER2
Authors: Kim Tae Yoon , Cha Jeong Seok , Kim Hoyoung , Choi Yoonjoo , Cho Hyun-Soo , Kim Hak-Sung 
Published: November 2020

AbstractA protein binder with a desired epitope and binding affinity is critical to the development of therapeutic agents. Here we present computationally-guided design and affinity improvement of a protein binder recognizing a specific site on domain IV of human epidermal growth factor receptor 2 (HER2). As a model, a protein scaffold composed of Leucine-rich repeat (LRR) modules was used. We designed protein binders which appear to bind a target site on domain IV using a computational method. Top 10 designs were expressed and tested with binding assays, and a lead with a low micro-molar binding affinity was selected. Binding affinity of the selected lead was further increased by two-orders of magnitude through mutual feedback between computational and experimental methods. The utility and potential of our approach was demonstrated by determining the binding interface of the developed protein binder through its crystal structure in complex with the HER2 domain IV.
B-1 lymphoid cells develop independently of Notch signaling during mouse embryonic development
Authors: Azevedo Nathalia , Bertesago Elisa , Ismailoglu Ismail , Kyba Michael , Kobayashi Michihiro , Ditadi Andrea , Yoshimoto Momoko 
Published: November 2020

AbstractThein vitrogeneration from pluripotent stem cells (PSCs) of different blood cell types, in particular those that are not replenished by hematopoietic stem cells (HSCs) like fetal-derived tissue-resident macrophages and innate-like lymphocytes, is of a particular interest. In order to succeed in this endeavor, a thorough understanding of the pathway interplay promoting lineage specification for the different blood cell types is needed. Notch signaling is essential for the HSC generation and their derivatives, but its requirement for tissue-resident immune cells is unknown. Using mouse embryonic stem cells (mESCs) to recapitulate murine embryonic development, we have studied the requirement for Notch signaling during the earliest B-lymphopoiesis and found thatRbpj-deficient mESCs are able to generate B-1 cells. Their Notch-independence was confirmed inex vivoexperiments usingRbpj-deficient embryos. In addition, we found that upregulation of Notch signaling was needed for the emergence of B-2 lymphoid cells. Taken together, these findings indicate that control of Notch signaling dosage is critical for the different B-cell lineage specification and provides pivotal information for theirin vitrogeneration from PSCs for therapeutic applications.
CGGBP1-dependent CTCF-binding sites restrict ectopic transcription
Authors: Patel Divyesh , Patel Manthan , Datta Subhamoy , Singh Umashankar 
Published: November 2020

AbstractBinding sites of the chromatin regulator protein CTCF function as important landmarks in the human genome. The recently characterized CTCF-binding sites at LINE-1 repeats depend on another repeat-regulatory protein CGGBP1. These CGGBP1-dependent CTCF-binding sites serve as potential barrier elements for epigenetic marks such as H3K9me3. Such CTCF-binding sites are associated with asymmetric H3K9me3 levels as well as RNA levels in their flanks. The functions of these CGGBP1-dependent CTCF-binding sites remain un-known. By performing targeted studies on candidate CGGBP1-dependent CTCF-binding sites cloned in an SV40 promoter-enhancer episomal system we show that these regions act as inhibitors of ectopic transcription from the SV40 promoter. CGGBP1-dependent CTCF-binding sites that recapitulate their genomic function of loss of CTCF binding upon CGGBP1 depletion and H3K9me3 asymmetry in immediate flanks are also the ones that show the strongest inhibition of ectopic transcription. By performing a series of strand-specific reverse transcription PCRs we demonstrate that this ectopic transcription results in the synthesis of RNA from the SV40 promoter in a direction opposite to the downstream reporter gene in a strand-specific manner. The unleashing of the bidirectionality of the SV40 promoter activity and a breach of the transcription barrier seems to depend on depletion of CGGBP1 and loss of CTCF binding proximal to the SV40 promoter. RNA-sequencing reveals that CGGBP1-regulated CTCF-binding sites act as barriers to transcription at multiple locations genomewide. These findings suggest a role of CGGBP1-dependent binding sites in restricting ectopic transcription.
Plasticity after cortical stroke involves potentiating responses of pre-existing circuits but not functional remapping to new circuits
Authors: Zeiger William A , Marosi Máté , Saggi Satvir , Noble Natalie , Samad Isa , Portera-Cailliau Carlos 
Published: November 2020

AbstractFunctional recovery after stroke is thought to be mediated by adaptive circuit plasticity, whereby surviving neurons assume the roles of those that died. This “remapping” hypothesis is based on human brain mapping studies showing apparent reorganization of cortical sensorimotor maps and animal studies documenting molecular and structural changes that could support circuit rewiring. However, definitive evidence of remapping is lacking, and other studies have suggested that maladaptive plasticity mechanisms, such as enhanced inhibition in peri-infarct cortex, might actually limit plasticity after stroke. Here we sought to directly test whether neurons can change their response selectivity after a stroke that destroys a single barrel (C1) within mouse primary somatosensory cortex. Using multimodal in vivo imaging approaches, including two-photon calcium imaging to longitudinally record sensory-evoked activity in peri-infarct cortex before and after stroke, we found no evidence to support the remapping hypothesis. In an attempt to promote plasticity via rehabilitation, we also tested the effects of forced use therapy by plucking all whiskers except the C1 whisker. Again, we failed to detect an increase in the number of C1 whisker-responsive neurons in surrounding barrels even 2 months after stroke. Instead, we found that forced use therapy potentiated sensory-evoked responses in a pool of surviving neurons that were already C1 whisker responsive by significantly increasing the reliability of their responses. Together, our results argue against the long-held theory of functional remapping after stroke, but support a plausible circuit-based mechanism for how rehabilitation may improve recovery of function.
Novelty Processing Depends on Medial Temporal Lobe Structures
Authors: Schomaker J. , Grouls M.M.E. , Rau E. , Hendriks M. , Colon A. , Meeter M. 
Published: November 2020

AbstractObjectivesThe goal of the present study was to identify the role of the medial temporal lobe (MTL) in the detection and later processing of novelty stimuli.MethodsTwenty-one epilepsy patients with unilateral MTL resection (10 left-sided; 11 right-sided) performed an adapted visual novelty oddball task. In this task two streams of stimuli were presented on the left and right of fixation while the patients’ electroencephalogram was measured. Patients responded to infrequent target stimuli, while ignoring frequent standard, and infrequent novel stimuli that could appear either contra- or ipsilateral to the resected side.ResultsNovelty detection, as indexed by the N2 ERP component elicited by novels, was not affected by the MTL resections. Later processing of novels, however, as indexed by the novelty P3 ERP component, was reduced for novels presented contra-versus ipsilateral to the resected side. Target processing, as indexed by the P3b, was unaffected.ConclusionsThe current results suggest that MTL structures play a role in novelty processing, but that the novelty signal may originate from a distinct neural source.
A Structural Ensemble of a Tau-Microtubule Complex Reveals Regulatory Tau Phosphorylation and Acetylation Mechanisms
Authors: Brotzakis Z. Faidon , Lindstedt Philip R. , Taylor Ross , Bernardes Gonçalo J. L. , Vendruscolo Michele 
Published: November 2020

AbstractTau is a microtubule-associated protein that regulates the stability of microtubules. The affinity of tau for microtubules is modulated by post-translational modifications, and the dysregulation of these events has been associated with the aberrant aggregation of tau in Alzheimer's disease and related tauopathies. Here, we use the metainference cryo-electron microscopy approach to determine an ensemble of structures representing the structure and dynamics of a tau-microtubule complex comprising an extended microtubule-binding region of tau (residues 202-395). We thus identify the ground state of the complex and a series of excited states of lower populations. An analysis of the interactions in these states of structures reveals positions in the tau sequence that are important to determine the overall stability of the tau-microtubule complex. This analysis leads to the identification of positions where phosphorylation and acetylation events have destabilising effects, which we validate by using site-specific post-translationally modified tau variants obtained by chemical mutagenesis. Taken together, these results illustrate how the simultaneous determination of ground and excited states of macromolecular complexes reveals functional and regulatory mechanisms.
Neuronal Activity-Dependent Accumulation of Arc in Astrocytes
Authors: Jiang Yuheng , VanDongen Antonius M.J. 
Published: November 2020

AbstractThe immediate-early gene Arc is a master regulator of synaptic plasticity and plays a critical role in memory consolidation. However, there has not been a comprehensive analysis of the itinerary of Arc protein, linking its function at different subcellular locations with corresponding time points after neuronal network activation. When cultured hippocampal neurons are treated with a combination of pharmacological agents to induce long term potentiation, they express high levels of Arc, allowing to study its spatiotemporal distribution. Our experiments show that neuronal activity-induced Arc expression was not restricted to neurons, but that its spatiotemporal dynamics involved a shift to astrocytes at a later timepoint. Specifically, astrocytic Arc is not due to endogenous transcription, but is dependent on the production of neuronal Arc and accumulates potentially via the recently reported intercellular transfer mechanism through Arc capsids. In conclusion, we found that Arc accumulates within astrocytes in a neuronal activity-dependent manner, which is independent of endogenous astrocytic Arc transcription, therefore highlighting the need to study the purpose of this pool of Arc, especially in learning and memory.
“Recalling hidden harms”: autistic experiences of childhood applied behavioural analysis (ABA)
Authors: McGill Owen , Robinson Anna 
Published: November 2020

Purpose
This paper aims to investigate the long-term impacts autistic adults experienced from childhood participation in the applied behavioural analysis (ABA).

Design/methodology/approach
Possible participants were recruited through advertisements on social media and autism and ABA organisations. Possible participants were given the choice between an online or face-to-face interview or an anonymised online questionnaire.

Findings
Reflections from 10 participants were indicative of a predominantly detrimental impact of ABA. Reflections gave rise to a core theme “recalling hidden harms of childhood experiences of ABA”. Outcomes are discussed in relation to the impact on autistic identity, current research and progressing understanding of the impacts of early intervention from the autistic perspective.

Research limitations/implications
The practical implications of ABA are discussed alongside recommendations for future practice and research with the involvement of autistic individuals within interventive processes.

Originality/value
This is the first paper to take an in-depth, qualitative approach to autistic experiences of ABA. The findings themselves are driven to conceptualise and give voice to the core impacts which carried through participants’ exploration and understanding of self.