bluuebunny/crossref_metadata_2025_split huggingface dataset:
A screen for sleep and starvation resistance identifies a wake-promoting role for the auxiliary channel unc79
Authors: Murakami Kazuma , Palermo Justin , Stanhope Bethany A. , Keene Alex C. 
Published: February 2021

AbstractThe regulation of sleep and metabolism are highly interconnected, and dysregulation of sleep is linked to metabolic diseases that include obesity, diabetes, and heart disease. Further, both acute and long-term changes in diet potently impact sleep duration and quality. To identify novel factors that modulate interactions between sleep and metabolic state, we performed a genetic screen for their roles in regulating sleep duration, starvation resistance, and starvation-dependent modulation of sleep. This screen identified a number of genes with potential roles in regulating sleep, metabolism or both processes. One such gene encodes the auxiliary ion channel UNC79, which was implicated in both the regulation of sleep and starvation resistance. Genetic knockdown or mutation ofunc79results in flies with increased sleep duration, as well as increased starvation resistance. Previous findings have shown thatunc79is required in pacemaker for 24-hour circadian rhythms. Here, we find thatunc79functions in the mushroom body, but not pacemaker neurons, to regulate sleep duration and starvation resistance. Together, these findings reveal spatially localized separable functions ofunc79in the regulation of circadian behavior, sleep, and metabolic function.
A transferrable and integrative type I-F Cascade for heterologous genome editing and transcription modulation
Authors: Xu Zeling , Li Yanran , Cao Huiluo , Si Meiru , Zhang Guangming , Woo Patrick CY , Yan Aixin 
Published: February 2021

ABSTRACTThe Class 1 type I CRISPR-Cas systems represent the most abundant and diverse CRISPR systems in nature. However, their applications for generic genome editing have been hindered by difficulties of introducing the class-specific, multi-component effectors in heterologous hosts for functioning. Here we established a transferrable Cascade system that enables stable integration and expression of a complete and highly active I-F Cascade in the notoriously recalcitrant and diverseP. aeruginosagenomes by conjugation. The transferred Cascade displayed substantially higher DNA interference activity and greater editing capacity than the Cas9 system in diverse genetic backgrounds, including removal of the large (21-kb) integrated cassette with efficiency and simplicity. An advanced λred-I-F system enabled editing in genotypes with poor homologous recombination capacity, clinical isolates lacking sequence information, and cells containing anti-CRISPR elements Acrs. Lastly, an ‘all-in-one’ I-F Cascade-mediated CRISPRi platform was developed for transcription modulation by simultaneous introduction of the Cascade and the mini-CRISPR array expressing desired crRNA in one-step. This study provides a framework for expanding the diverse type I Cascades for widespread, heterologous genome editing and establishment of editing techniques in non-model isolates of pathogens.
DNA damage-induced phosphorylation of histone H2A at serine 15 is linked to DNA end resection
Authors: Ahmad Salar , Côté Valérie , Côté Jacques 
Published: February 2021

ABSTRACTThe repair of DNA double-strand breaks (DSBs) occurs in chromatin and several histone post-translational modifications have been implicated in the process. Modifications of histone H2A N-terminal tail has also been linked to DNA damage response, through acetylation or ubiquitination of lysine residues that regulate repair pathway choice. Here, we characterize a new DNA damage-induced phosphorylation on chromatin, at serine 15 of H2A in yeast. We show that this SQ motif functions independently of the classical S129 C-terminal site (γH2A) and mutant mimicking constitutive phosphorylation increases cell sensitivity to DNA damage. H2AS129ph is induced by Tel1ATMand Mec1ATR, and loss of Lcd1ATRIPor Mec1 signaling decreases γH2A spreading distal to the DSB. In contrast, H2AS15ph is completely dependent on Lcd1ATRIP, indicating that this modification only happens when end resection is engaged. This is supported by an increase of RPA and a decrease in DNA signal near the DSB in theH2AS-15Ephosphomimic mutant, indicating higher resection. This serine is replaced by a lysine in mammals (H2AK15), which undergoes an acetyl-monoubiquityl switch to regulate binding of 53BP1 and resection. This regulation seems functionally conserved with budding yeast H2AS15 and 53BP1-homolog Rad9, using different post-translational modifications between organisms but achieving the same function.
“Susceptibility and risk of suffering SARS-COV-2 infection by demographic characteristics and pre-existing medical conditions among middle-aged and older adults in Tarragona, Spain: results from the COVID19 TARRACO Cohort Study, March-June 2020”
Authors: Satué-Gracia EM. , Vila-Córcoles A. , de Diego-Cabanes C. , Vila-Rovira A. , Torrente-Fraga C. , Gómez-Bertomeu F. , Hospital-Guardiola I. , Ochoa-Gondar O. , Martín-Luján F. 
Published: February 2021

SUMMARYObjectiveTo analyse susceptibility/risk of suffering COVID19 among adults with distinct underlying medical conditions.MethodsCohort study (population-based) including 79,083 people ≥50 years-old in Tarragona (Southern Catalonia, Spain). At study start (01/03/2020) baseline cohort characteristics (demographic, previous comorbidities, chronic medications and vaccinations’ history) were recorded. Primary outcome was laboratory-confirmed COVID19 incurred in cohort members throughout 01/03/2020-30/06/2020. Risk of suffering COVID19 was evaluated by Cox regression, estimating multivariable hazard ratios (HRs) adjusted for age/sex and previous comorbidities.ResultsAcross study period, 536 laboratory-confirmed COVID19 cases were observed (mean incidence: 39.5 cases per 100,000 persons-week). In multivariable-analysis, age/years (HR: 1.01; 95% CI: 1.00-1.02; p=0.050), nursing-home (HR: 20.19; 95% CI: 15.98-25.51; p<0.001), neurological disease (HR: 1.35; 95% CI: 1.03-1.77; p=0.029), taking diuretics (HR: 1.39; 95% CI: 1.10-1.75; p=0.006), antiplatelet (HR: 1.36; 95% CI: 1.05-1.76; p=0.021) and benzodiazepines (HR: 1.24; 95% CI:1.00-1.53; p=0.047) significantly increased risk; while smoking (HR: 0.57; 95%CI: 0.41-0.80; p=0.001), angiotensin converting enzyme inhibitors (HR: 0.78; 95% CI: 0.61-1.00; p=0.048), angiotensin II receptor blockers (HR: 0.70; 95%CI: 0.51-0.96; p=0.027) and statins (HR: 0.75; 95% CI: 0.58-0.96; p=0.025) were associated with reduced risk. Among non-institutionalised persons, cancer, renal and cardiac disease appeared also related to increased risk, whereas influenza vaccination was associated with reduced risk.ConclusionIn a setting with relatively low incidence of COVID19 across the first wave of pandemic period, age, nursing-home residence and multiple comorbidities appear predisposing for COVID19 among middle-aged/older adults. Conversely, statins, angiotensin-receptor blockers/inhibitors and influenza vaccination were related with decreased risk.
In vivooptogenetic stimulation of the primate retina activates the visual cortex after long-term transduction
Authors: Chaffiol Antoine , Provansal Matthieu , Joffrois Corentin , Blaize Kévin , Labernede Guillaume , Goulet Ruben , Burban Emma , Brazhnikova Elena , Duebel Jens , Pouget Pierre , Alain Sahel José , Picaud Serge , Gauvain Gregory , Arcizet Fabrice 
Published: February 2021

AbstractOver the last 15 years, optogenetics has changed fundamental research in neuroscience, and is now reaching toward therapeutic applications. Vision restoration strategies using optogenetics are now at the forefront of these new clinical opportunities. But applications to human patients suffering from retinal diseases leading to blindness rise important concerns on the long-term functional expression of optogenes and the efficient signal transmission to higher visual centers. Here we demonstrate in non-human primates, continued expression and functionality at the retina level ∼20 months after delivery of our construct. We also performedin-vivorecordings of visually evoked potentials in the primary visual cortex of anaesthetized animals. Using synaptic blockers, we isolated thein-vivocortical activation resulting from the direct optogenetic stimulation of primate retina.In conclusion, our work indicates long-term transgene expression and transmission of the signal generated in the macaque retina to the visual cortex, two important features for future clinical applications.
Plasmodium falciparumhydroxymethylbilane synthase does not house any cosynthase activity within the haem biosynthetic pathway
Authors: Scott Alan F. , Deery Evelyne , Lawrence Andrew D. , Warren Martin J. 
Published: February 2021

AbstractThe production of uroporphyrinogen III, the universal progenitor of macrocyclic, modified tetrapyrroles, is produced from aminolaevulinic acid (ALA) by a conserved pathway involving three enzymes: porphobilinogen synthase (PBGS), hydroxymethylbilane synthase (HmbS) and uroporphyrinogen III synthase (UroS). The gene encoding uroporphyrinogen III synthase has not yet been identified inPlasmodium falciparumbut it has been suggested that this activity is housed inside a bifunctional hybroxymethylbilane synthase (HmbS). In this present study it is demonstrated thatP. falciparumHmbS does not have uroporphyrinogen III synthase activity. This was demonstrated by the failure of a codon optimisedP. falciparum hemCgene, encoding HmbS, to compliment a definedE. coli hemD-mutant (SASZ31) deficient in uroporphyrinogen III synthase activity. Furthermore, HPLC analysis of the oxidsed reaction product from recombinant, purified HmbS showed that only uroporphyrin I could be detected (corresponding to hydroxymethylbilane production). No uroporphyrin III was detected, thus showing thatP. falciparumHmbS does not have UroS activity and can only catalyse the formation of hydroxymethylbilane from porphobilinogen.
Reversible blood-brain barrier opening utilizing the membrane active peptide melittinin vitroandin vivo
Authors: Linville Raleigh M. , Komin Alexander , Lan Xiaoyan , DeStefano Jackson G. , Chu Chengyan , Liu Guanshu , Walczak Piotr , Hristova Kalina , Searson Peter C. 
Published: February 2021

AbstractThe blood-brain barrier (BBB) tightly controls entry of molecules and cells into the brain, restricting the delivery of therapeutics. Blood-brain barrier opening (BBBO) utilizes reversible disruption of cell-cell junctions between brain microvascular endothelial cells to enable transient entry into the brain. Development of BBBO techniques has been hindered by a lack of physiological models forin vitrostudy. Here, we utilize anin vitrotissue-engineered microvessel model to demonstrate that melittin, a membrane active peptide present in bee venom, supports BBBO. From endothelial and neuronal viability studies, we identify the accessible concentration range for BBBO. We then use a tissue-engineered model of the human BBB to optimize dosing and elucidate the mechanism of opening. Melittin and other membrane active variants transiently increase paracellular permeability via disruption of cell-cell junctions. In mice, we demonstrate a minimum clinically effective intra-arterial dose of 3 μM·min melittin, which is reversible within one day and neurologically safe. Melittin-induced BBBO represents a novel platform for delivery of therapeutics into the brain.
A comparative study of genomic adaptations to low nitrogen availability in Genlisea aurea
Authors: Goldsborough Thibaut 
Published: February 2021

AbstractGenlisea aureais a carnivorous plant that grows on nitrogen-poor waterlogged sandstone plateaus and is thought to have evolved carnivory as an adaptation to very low nitrogen levels in its habitat. The carnivorous plant is also unusual for having one of the smallest genomes among flowering plants. Genomic DNA is known to have a high nitrogen content and yet, to the author’s knowledge, no published study has linked nitrogen starvation ofG. aureawith genome size reduction. This comparative study of the carnivorous plantG. aurea, the model organismArabidopsis thaliana(Brassicaceae) and the nitrogen fixingTrifolium pratense(Fabaceae) attempts to investigate whether the genome, transcriptome and proteome ofG. aureashowed evidence of adaptations to low nitrogen availability. It was found that althoughG. aurea’s genome, CDS and non-coding DNA were much lower in nitrogen than the genome ofT. pratenseandA. thalianathis was solely due to the length of the genome, CDS and non-coding sequences rather than the composition of these sequences.
A Human 3D neural assembloid model for SARS-CoV-2 infection
Authors: Wang Lu , Sievert David , Clark Alex E. , Federman Hannah , Gastfriend Benjamin D. , Shusta Eric , Palecek Sean P. , Carlin Aaron F. , Gleeson Joseph 
Published: February 2021

AbstractClinical evidence suggests the central nervous system (CNS) is frequently impacted by SARS-CoV-2 infection, either directly or indirectly, although mechanisms remain unclear. Pericytes are perivascular cells within the brain that are proposed as SARS-CoV-2 infection points1. Here we show that pericyte-like cells (PLCs), when integrated into a cortical organoid, are capable of infection with authentic SARS-CoV-2. Prior to infection, PLCs elicited astrocytic maturation and production of basement membrane components, features attributed to pericyte functions in vivo. While traditional cortical organoids showed little evidence of infection, PLCs within cortical organoids served as viral ‘replication hubs’, with virus spreading to astrocytes and mediating inflammatory type I interferon transcriptional responses. Therefore, PLC-containing cortical organoids (PCCOs) represent a new ‘assembloid’ model2that supports SARS-CoV-2 entry and replication in neural tissue, and PCCOs serve as an experimental model for neural infection.
Verbal Labels Facilitate Tactile Texture Discrimination in a Perceptual Learning Task
Authors: Arun Ishita , Lazar Leslee 
Published: February 2021

ABSTRACTThe influence of language on perceptual processes, referred to as the Whorfian hypothesis, has been a contentious issue. Cross-linguistic research and lab-based experiments have shown that verbal labels can facilitate perceptual and discriminatory processes, mostly in visual and auditory modalities. Here, we investigated whether verbal labels improve performance in a tactile texture discrimination task using natural textures. We also explored whether the grammatical category of these verbal labels plays a role in discrimination ability. In our experiments, we asked the participants to discriminate between pairs of textures presented to the fingertip after a five-day training phase. During the training phase, the tactile textures and English pseudowords were co-presented consistently in the congruent (experimental) condition and inconsistently in the incongruent (control) condition, allowing them to form implicit associations only in the former condition. The pseudoword verbal labels belonged to two grammatical categories, verb-like and noun-like. We found an improvement in the texture discrimination ability only for the congruent condition, irrespective of the grammatical category.
Synaptotagmin 7 is enriched at the plasma membrane through γ-secretase
processing to promote vesicle docking and control synaptic plasticity in mouse
hippocampal neurons
Authors: Vevea Jason D. , Kusick Grant F. , Chen Erin , Courtney Kevin C. , Watanabe Shigeki , Chapman Edwin R. 
Published: February 2021

Abstract
Synaptotagmin (SYT) 7 has emerged as key regulator of presynaptic function,
but its localization and precise function in the synaptic vesicle cycle remain
unclear. Here, we used iGluSnFR to optically and directly interrogate glutamate
release, at the single bouton level, in SYT7 KO dissociated mouse hippocampal
neurons. We analyzed asynchronous release, paired pulse facilitation, and
synaptic vesicle replenishment, and found that SYT7 contributes to each of these
processes to different degrees. ‘Zap-and-freeze’ electron microscopy revealed
that loss of SYT7 impairs the docking of synaptic vesicles after a stimulus and
the recovery of depleted synaptic vesicles after a stimulus train. To execute
these functions, SYT7 must be targeted to the plasma membrane via
γ-secretase-mediated cleavage of the amino terminus, followed by palmitoylation.
The complex sorting itinerary of SYT7 endows this
Ca2+-sensor with the ability to control crucial forms of
synaptic function and plasticity.

SYT7 mediated asynchronous release, paired pulse facilitation,
and synaptic vesicle replenishment was observed optically at
individual hippocampal synapses

Localization, trafficking, and stability of SYT7 is dependent on
processing by γ-secretase

Short term plasticity defects arise in SYT7KOs due to decreased
docking of synaptic vesicles after stimulation

SYT7 promotes paired-pulse facilitation and asynchronous release
via distinct mechanisms
Streptococcus pyogenesforms serotype and local environment-dependent inter-species protein complexes
Authors: Chowdhury Sounak , Khakzad Hamed , Ertürk Bergdahl Gizem , Lood Rolf , Ekstrom Simon , Linke Dirk , Malmström Lars , Happonen Lotta , Malmström Johan 
Published: February 2021

AbstractStreptococcus pyogenesis known to cause both mucosal and systemic infections in humans. In this study, we used a combination of quantitative and structural mass spectrometry techniques to determine the composition and structure of the interaction network formed between human plasma proteins and the surface of differentS. pyogenesserotypes. Quantitative network analysis revealed thatS. pyogenesform serotype-specific interaction networks that are highly dependent on the domain arrangement of the surface-attached M protein. Subsequent structural mass spectrometry analysis and computational modelling on one of the M proteins, M28 revealed that the network structure changes across different host microenvironments. We report that M28 binds secretory IgA via two separate binding sites with high affinity in saliva. During vascular leakage mimicked by increasing plasma concentrations in saliva, the binding of secretory IgA was replaced by binding of monomeric IgA and C4BP. This indicates that an upsurge of C4BP in the local microenvironment due to damage of the mucosal membrane drives binding of C4BP and monomeric IgA to M28. The results suggest thatS. pyogeneshas evolved to form microenvironment-dependent host-pathogen protein complexes to combat the human immune surveillance during both mucosal and systemic infections.
New exon ignites accelerated evolution of placental gene Nrk in the ancestral lineage of eutherians
Authors: Liu Guopeng , Zhang Chunxiao , Wang Yuting , Dai Guangyi , Liu Shu-Qun , Wang Wenshuai , Pan Yi-Hsuan , Ding Jianping , Li Haipeng 
Published: February 2021

AbstractAccelerated evolution is often driven by the interaction between environmental factors and genes. However, it remains unclear whether accelerated evolution can be ignited. Here, we focused on adaptive events during the emergence of chorioallantoic placenta. We scanned the chromosome X and identified eight accelerated regions in the ancestral lineage of eutherian mammals. Five of these regions (P = 5.61 × 10−11 ~ 9.03 × 10−8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Moreover, a eutherian-specific exogenous exon lack of splice variant was found to be conserved. Structure modelling of NRK suggests that the accelerated exons and the eutherian-specific exon could change the enzymatic activity of eutherian NRK. Since the eutherian-specific exon was surrounded by accelerated exons, it indicates that the accelerated evolution of Nrk may be ignited by the emergence of the new exon in the ancestral lineage of eutherian mammals. The new exon might shift the function of Nrk and provide a new fitness landscape for eutherian species to explore. Although multiple exons were accelerated in both of the Nrk catalytic and regulatory domains, positive selection can only be revealed on the regulatory domain if the branch specific nonsynonymous and synonymous rate test was performed by PAML. Thus, it may be important to detect accelerated evolution when studying positive selection on coding regions. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection. Identifying positively selected placental genes provides insights into how eutherian mammals gain benefits from the invasive chorioallantoic placenta to form one of the most successful groups among terrestrial vertebrates.
Nse5/6 inhibits the Smc5/6 ATPase to facilitate DNA substrate selection
Authors: Taschner Michael , Basquin Jérôme , Steigenberger Barbara , Schaefer Ingmar , Soh Young-Min , Basquin Claire , Lorentzen Esben , Räschle Markus , Scheltema Richard A. , Gruber Stephan 
Published: February 2021

AbstractEukaryotic cells employ three SMC complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo-complex. We found that the Nse5/6 sub-complex strongly inhibited the Smc5/6 ATPase by preventing productive ATP binding. This inhibition was relieved by plasmid DNA binding but not by short linear DNA, while opposing effects were observed without Nse5/6. We uncovered two binding sites for Nse5/6 on Smc5/6, based on an Nse5/6 crystal structure and cross-linking mass spectrometry data. One binding site is located at the Smc5/6 arms and one at the heads, the latter likely exerting inhibitory effects on ATP hydrolysis. Cysteine cross-linking demonstrated that the interaction with Nse5/6 anchored the ATPase domains in a non-productive state, which was destabilized by ATP and DNA. Under similar conditions, the Nse4/3/1 module detached from the ATPase. Altogether, we show how DNA substrate selection is modulated by direct inhibition of the Smc5/6 ATPase by Nse5/6.
Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing
Authors: Johnson Samantha T. , Chu Yongjun , Liu Jing , Corey David R. 
Published: February 2021

ABSTRACTTNRC6 is a scaffolding protein that bridges interactions between small RNAs, argonaute (AGO) protein, and effector proteins to control gene expression. There are three paralogs in mammalian cells,TNRC6A, TNRC6B, and TNRC6C. These paralogs have ~40% amino acid sequence identity and the extent of their unique or redundant functions is unclear. Here, we use knockout cell lines, enhanced crosslinking immunoprecipitation (eCLIP), and high-throughput RNA sequencing (RNAseq) to explore the roles of TNRC6 paralogs in RNA-mediated control of gene expression. We find that that the paralogs are largely functionally redundant and changes in levels of gene expression are well-correlated with those observed inAGOknockout cell lines. Splicing changes observed inAGOknockout cell lines are observed inTNRC6knockout cells. These data further define the roles of the TNRC6 isoforms as part of the RNA interference (RNAi) machinery.