bluuebunny/crossref_metadata_2025 huggingface dataset:
Origin and evolution of the cannabinoid oxidocyclase gene family
Authors: van Velzen Robin , Schranz M. Eric
Published: December 2020

Cannabisis an ancient crop representing a rapidly increasing legal market, especially for medicinal purposes. Medicinal and psychoactive effects ofCannabisrely on specific terpenophenolic ligands named cannabinoids. Recent whole-genome sequencing efforts have uncovered variation in multiple genes encoding the final steps in cannabinoid biosynthesis. However, the origin, evolution, and phylogenetic relationships of these cannabinoid oxidocyclase genes remain unclear. To elucidate these aspects we performed comparative genomic analyses ofCannabis, related genera within the Cannabaceae family, and selected outgroup species. Results show that cannabinoid oxidocyclase genes originated in theCannabislineage from within a larger gene expansion in the Cannabaceae family. Localization and divergence of oxidocyclase genes in theCannabisgenome revealed two main syntenic blocks, each comprising tandemly repeated cannabinoid oxidocyclase genes. By comparing these blocks with those in genomes from closely related species we propose an evolutionary model for the origin, neofunctionalization, duplication, and diversification of cannabinoid oxidocycloase genes. Based on phylogenetic meta-analyses, we propose a comprehensive classification of three main clades and seven subclades that is intended to aid unequivocal referencing and identification of cannabinoid oxidocyclase genes. Our data suggest that cannabinoid oxidocyclase gene copy number variation may have less functional relevance than previously thought. Instead, we propose that cannabinoid phenotype is primarily determined by presence/absence of single-copy genes. Increased sampling acrossCannabis’native geographic range is likely to uncover additional cannabinoid oxidocyclase gene sequence variation.

Significance statement

Cannabisgenome sequencing efforts have revealed extensive cannabinoid oxidocyclase gene variation. However, phylogenetic relationships and evolution of these genes remains unclear. Our meta analysis of currently available data reveals that these genes comprise three main clades and seven subclades that originated throughCannabis-specific gene duplication and divergence. Our new conceptual and evolutionary framework serves as a reference for future description and functional analyses of cannabinoid oxidocyclases.
Leveraging selective hippocampal vulnerability among Alzheimer’s disease subtypes reveals a novel tau binding partner SERPINA5
Authors: Crist Angela M. , Hinkle Kelly M. , Wang Xue , Moloney Christina M. , Matchett Billie J. , Labuzan Sydney A. , Frankenhauser Isabelle , Azu Nkem O. , Liesinger Amanda M. , Lesser Elizabeth R. , Serie Daniel J. , Quicksall Zachary S. , Patel Tulsi A. , Carnwath Troy P. , DeTure Michael , Tang Xiaojia , Petersen Ronald C. , Duara Ranjan , Graff-Radford Neill R. , Allen Mariet , Carrasquillo Minerva M. , Li Hu , Ross Owen A. , Ertekin-Taner Nilufer , Dickson Dennis W. , Asmann Yan W. , Carter Rickey E. , Murray Melissa E.
Published: December 2020

Selective vulnerability is a central concept to the myriad of devastating neurodegenerative disorders. Although hippocampus and cortex are selectively vulnerable in Alzheimer’s disease (AD), the degree of involvement lies along a spectrum that we previously defined as AD subtypes revealing distinct clinical correlates. To operationalize heterogeneity of disease spectrum, we classified corticolimbic patterns of neurofibrillary tangles to capture extreme and representative phenotypes. We combined bulk RNA sequencing with digital pathology to examine hippocampal vulnerability in AD. Using a multidisciplinary approach, we uncovered disease-relevant hippocampal gene expression changes. Biological relevance was prioritized using machine learning and several levels of human validation. This resulted in five genes highly predictive of neuropathologically diagnosed AD:SERPINA5, RYBP, SLC38A2, FEM1B, andPYDC1. Deeper investigation revealed SERPINA5 to be a novel tau binding partner that may represent a “tipping point” in the dynamic maturity of neurofibrillary tangles. Our study highlights the importance of embracing heterogeneity of the human brain to yield promising gene candidates as exampled bySERPINA5.
Sensitive detection of DNA contamination in tumor samples via microhaplotypes
Authors: Whitty Brett , Thompson John F.
Published: December 2020

Low levels of sample contamination with other human DNAs can have disastrous effects on the accurate identification of somatic variation in tumor samples. Detection of sample contamination in DNA is often based on low frequency variants that indicate if more than a single source of DNA is present. This strategy works with standard DNA samples but can be problematic in solid tumor FFPE samples because there are often huge variations in allele frequency (AF) due to copy number changes arising from gains and losses across the genome. The variable AFs make detection of contamination challenging. To avoid this, we counted microhaplotypes to assess sample contamination. Microhaplotypes are sets of variants on the same sequencing read that can be unambiguously phased. Instead of measuring AF, the number of microhaplotypes is determined. Contamination detection becomes based on fundamental genomic properties, linkage disequilibrium (LD) and the diploid nature of human DNA, rather than variant frequencies. We optimized microhaplotype panel content and selected 164 SNV sets located in regions already being sequenced within a cancer panel. Thus, contamination detection uses existing sequence data. LD data from the 1000 Genomes Project is used to make the panel ancestry agnostic, providing the same sensitivity for contamination detection with samples from individuals of African, East Asian, and European ancestry. Detection of 1% contamination with no matching normal sample is possible. The methods described here can also be extended to other DNA mixtures such as forensic and non-invasive prenatal testing samples where DNA mixes can be similarly detected. The microhaplotype method allows sensitive detection of DNA contamination in FFPE tumor and other samples when deep coverage with Illumina or other high accuracy NGS is used.
A versatile toolkit for molecular QTL mapping and meta-analysis at scale
Authors: Quick Corbin , Guan Li , Li Zilin , Li Xihao , Dey Rounak , Liu Yaowu , Scott Laura , Lin Xihong
Published: December 2020

Molecular QTLs (xQTLs) are widely studied to identify functional variation and possible mechanisms underlying genetic associations with diseases. Larger xQTL sample sizes are critical to help identify causal variants, improve predictive models, and increase power to detect rare associations. This will require scalable and accurate methods for analysis of tens of thousands of molecular traits in large cohorts, and/or from summary statistics in meta-analysis, both of which are currently lacking. We developed APEX (All-in-one Package for Efficient Xqtl analysis), an efficient toolkit for xQTL mapping and meta-analysis that provides (a) highly optimized linear mixed models to account for relatedness and shared variation across molecular traits; (b) rapid factor analysis to infer latent technical and biological variables from molecular trait data; (c) fast and accurate trait-level omnibus tests that incorporate prior functional weights to increase statistical power; and (d) compact summary data files for flexible and accurate joint analysis of multiple variants (e.g., joint/conditional regression or Bayesian finemapping) without individual-level data in meta-analysis. We applied the methods to data from three LCL eQTL studies and the UK Biobank. APEX is open source:https://corbinq.github.io/apex.
Paternal leakage of organelles can improve adaptation to changing environments
Authors: Radzvilavicius Arunas , Johnston Iain G.
Published: December 2020

Sexual eukaryotes have diverse mechanisms preventing the biparental inheritance of mitochondria and plastids, and reducing the coexistence of dissimilar organelle DNA (heteroplasmy). Nevertheless, paternal leakage often occurs in plants, fungi, protists and animals, and this leaves the possibility that heteroplasmy can in some contexts be advantageous. Theoretical models developed in the past revealed that maternal inheritance improves selection against deleterious mitochondrial mutations, but none of them have explained the observed variation in the extent of paternal leakage. Here we show that paternal leakage regulated by nuclear loci can evolve to maintain advantageous organelle diversity in fluctuating environments. Strict maternal inheritance reduces organelle variance within the cell, but this loss of diversity can be detrimental when environments are shifting rapidly. Our model reveals that high levels of paternal leakage can evolve in these types of rapidly changing environments and that strict maternal inheritance evolves only when the environment is changing slowly.

Data

Matlab/Octave implementation of the model is available atHttps://github.com/StochasticBiology/PaternalLeakageEvolution.
Apoptosis is a generator of Wnt-dependent regeneration and homeostatic cell renewal in the ascidianCiona
Authors: Jeffery William R. , Goricki Spela
Published: December 2020

Body regeneration is unilateral in the ascidianCiona intestinalis: severed basal body parts can regenerate distal structures, such as the siphons and neural complex, but severed distal body parts do not replace basal structures. Regeneration involves the activity of adult stem cells in vasculature of the branchial sac, which are induced to proliferate and produce migratory progenitor cells for the replacement of missing tissues and organs. Branchial sac-derived stem cells also replenish continuously recycling cells lining the pharyngeal fissures during homeostatic growth. Apoptosis at injury sites is an early and transient event of regeneration and occurs continuously in the pharyngeal fissures during homeostatic growth. Treatment of amputated animals with caspase 1 inhibitor, caspase 3 inhibitor, or the pan-caspase inhibitor Z-VAD-FMK blocked apoptosis, prevented regeneration, and suppressed the growth and function of the branchial sac. A pharmacological screen and inhibitory siRNA treatments indicated that regeneration and homeostatic growth require canonical Wnt signaling. Furthermore, exogenously supplied recombinant Wnt3a protein rescued both caspase-blocked regeneration and normal branchial sac growth. As determined by EdU pulse-chase studies, inhibition of apoptosis did not affect branchial sac stem cell proliferation but instead prevented the survival of progenitor cells. After bisection across the mid-body, apoptosis at the injury site occurred in the regenerating basal fragments, but not in the non-regenerating distal fragments, although both fragments contain a large portion of the branchial sac, suggesting that apoptosis is unilateral at the wound site and the presence of branchial sac stem cells is insufficient for regeneration. The results show that apoptosis-dependent Wnt signaling mediates regeneration and homeostatic growth by promoting progenitor cell survival inCiona.
Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2
Authors: Nouailles Geraldine , Wyler Emanuel , Pennitz Peter , Postmus Dylan , Vladimirova Daria , Kazmierski Julia , Pott Fabian , Dietert Kristina , Mülleder Michael , Farztdinov Vadim , Obermayer Benedikt , Wienhold Sandra-Maria , Andreotti Sandro , Höfler Thomas , Sawitzki Birgit , Drosten Christian , Sander Leif Erik , Suttorp Norbert , Ralser Markus , Beule Dieter , Gruber Achim Dieter , Goffinet Christine , Landthaler Markus , Trimpert Jakob , Witzenrath Martin
Published: December 2020

In COVID-19, the immune response largely determines disease severity and is key to therapeutic strategies. Cellular mechanisms contributing to inflammatory lung injury and tissue repair in SARS-CoV-2 infection, particularly endothelial cell involvement, remain ill-defined. We performed detailed spatiotemporal analyses of cellular and molecular processes in SARS-CoV-2 infected Syrian hamsters. Comparison of hamster single-cell sequencing and proteomics with data sets from COVID-19 patients demonstrated inter-species concordance of cellular and molecular host-pathogen interactions. In depth vascular and pulmonary compartment analyses (i) supported the hypothesis that monocyte-derived macrophages dominate inflammation, (ii) revealed endothelial inflammation status and T-cell attraction, and (iii) showed that CD4+ and CD8+ cytotoxic T-cell responses precede viral elimination. Using the Syrian hamster model of self-limited moderate COVID-19, we defined the specific roles of endothelial and epithelial cells, among other myeloid and non-myeloid lung cell subtypes, for determining the disease course.
Task specificity in mouse parietal cortex
Authors: Lee Julie J , Krumin Michael , Harris Kenneth D , Carandini Matteo
Published: December 2020

Parietal cortex is implicated in a variety of behavioral processes, but it is unknown whether and how individual neurons participate in multiple tasks. We trained head-fixed mice to perform two visual decision tasks involving a steering wheel or a virtual T-maze, and recorded from the same parietal neurons during the two. Neurons that were active during the T-maze task were typically inactive during the steering-wheel task, and vice versa. Recording from the same neurons in the same apparatus without task stimuli yielded the same specificity as in the task, suggesting that task specificity depends on physical context. To confirm this, we trained some mice in a third task combining the steering wheel with the visual environment of the T-maze. This hybrid task engaged the same neurons as the steering-wheel task. Thus, participation by neurons in mouse parietal cortex is task-specific, and this specificity is determined by physical context.
Analysis of Circuits for Dosage Control in Microbial Populations
Authors: Walton Sophie J. , Clamons Samuel E. , Murray Richard M.
Published: December 2020

Designing genetic circuits to control the behaviors of microbial populations is an ongoing challenge in synthetic biology. Here we analyze circuits which implement dosage control by controlling levels of a global signal in a microbial population in face of varying cell density, growth rate, and environmental dilution. We utilize the Lux quorum sensing system to implement dosage control circuits, and we analyze the dynamics of circuits using both simplified analytical analysis andin silicosimulations. We demonstrate that strong negative feedback through inhibiting LuxI synthase expression along with AiiA degradase activity results in circuits with fast response times and robustness to cell density and dilution rate. We find that degradase activity yields robustness to variations in population density for large population sizes, while negative feedback to synthase production decreases sensitivity to dilution rates.
Different SP1 binding dynamics at individual genomic loci in human cells
Authors: Hasegawa Yuko , Struhl Kevin
Published: December 2020

Using a tamoxifen-inducible time-course ChIP-seq approach, we show that the ubiquitous transcription factor SP1 has different binding dynamics at its target sites in the human genome that are not correlated with SP1 occupancy levels at those sites. While ~70% of SP1 binding sites are located in promoter regions, loci with slow SP1 binding turnover are enriched in enhancer and Polycomb-repressed regions. Unexpectedly, SP1 sites with fast turnover times tend to have higher quality and more copies of the SP1 sequence motif. Different co-binding factors associate near SP1 binding sites depending on their binding kinetics and on their location at promoters or enhancers. For example, NFY and FOS are preferentially associated near promoter-bound SP1 sites with fast turnover, whereas DNA motifs of ETS and homeodomain proteins are preferentially observed at sites with slow turnover. At promoters but not enhancers, proteins involved in sumoylation and PML bodies associate more strongly with slow SP1 binding sites than with the fast-binding sites. The speed of SP1 binding turnover is not associated with nucleosome occupancy, and it is not necessarily coupled to higher transcriptional activity. These results with SP1 are in contrast from those of human TBP, indicating that there is no common mechanism affecting transcription factor binding kinetics.
A robust and automated algorithm that uses single-channel spike sorting to label multi-channel Neuropixels data
Authors: Zhang Zheng , Constandinou Timothy G.
Published: December 2020

This paper describes preliminary work towards an automated algorithm for labelling Neuropixel data that exploits the fact that adjacent recording sites are spatially oversampled. This is achieved by combining classical single channel spike sorting with spatial spike grouping, resulting in an improvement in both accuracy and robustness. This is additionally complemented by an automated method for channel selection that determines which channels contain high quality data. The algorithm has been applied to a freely accessible dataset, produced by Cortex Lab, UCL. This has been evaluated to have a accuracy of over 77% compared to a manually curated ground truth.
The molecular framework of heterophylly inCallitriche palustrisL. differs from that in other amphibious plants
Authors: Koga Hiroyuki , Kojima Mikiko , Takebayashi Yumiko , Sakakibara Hitoshi , Tsukaya Hirokazu
Published: December 2020

Heterophylly refers to the development of different leaf forms in a single plant depending on the environmental conditions. It is often observed in amphibious aquatic plants that can grow under aerial and submerged conditions. Although heterophylly is well recognized in aquatic plants, the associated developmental mechanisms and the molecular basis remain unclear. In this study, we analyzed heterophyllous leaf formation in an aquatic plant,Callitriche palustris, to clarify the underlying developmental and molecular mechanisms. Morphological analyses revealed extensive cell elongation and the rearrangement of cortical microtubules in the elongated submerged leaves ofC. palustris. Our observations also suggested that gibberellin, ethylene, and abscisic acid regulate the formation of submerged leaves. However, the perturbation of one or more of the hormones was insufficient to induce the formation of submerged leaves under aerial conditions. Finally, we analyzed gene expression changes during aerial and submerged leaf development and narrowed down the candidate genes controlling heterophylly via transcriptomic comparisons, including a comparison with a closely related terrestrial species. We revealed that the molecular mechanism regulating heterophylly inC.palustrisis associated with hormonal changes and diverse transcription factor gene expression profiles, suggesting differences from the corresponding mechanisms in previously investigated amphibious plants.
RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes
Authors: Agret Clément , Chateau Annie , Droc Gaetan , Sarah Gautier , Ruiz Manuel , Mancheron Alban
Published: December 2020

Background

As the cost of DNA sequencing decreases, high-throughput sequencing technologies become increasingly accessible to many laboratories. Consequently, new issues emerge that require new algorithms, including tools for indexing and compressing hundred to thousands of complete genomes.

Results

This paper presents RedOak, a reference-free and alignment-free software package that allows for the indexing of a large collection of similar genomes. RedOak can also be applied to reads from unassembled genomes, and it provides a nucleotide sequence query function. This software is based on ak-mer approach and has been developed to be heavily parallelized and distributed on several nodes of a cluster. The source code of our RedOak algorithm is available athttps://gite.lirmm.fr/doccy/RedOak.

Conclusions

RedOak may be really useful for biologists and bioinformaticians expecting to extract information from large sequence datasets.
A comprehensive library of fluorescent constructs of SARS-CoV-2 proteins and their initial characterization in different cell types
Authors: Miserey-Lenkei Stéphanie , Trajkovic Katarina , D'Ambrosio Juan Martìn , Patel Amanda J , Čopič Alenka , Mathur Pallavi , Schauer Kristine , Goud bruno , Albanèse Véronique , Gautier Romain , Subra Melody , Kovacs David , Barelli Hélène , Antonny Bruno
Published: December 2020

Comprehensive libraries of plasmids for SARS-CoV-2 proteins with various tags (e.g. Strep, HA, Turbo) are now available. They enable the identification of numerous potential protein-protein interactions between the SARS-CoV-2 virus and host proteins. To facilitate further cellular investigations, notably by imaging techniques, we present here a large library of SARS CoV-2 protein constructs fused with green and red fluorescent proteins and their initial characterization in various human cell lines including lung epithelial cell models (A549, BEAS-2B), as well as in budding yeast. The localization of a few SARS-CoV-2 proteins matches their proposed interactions with host proteins. These include the localization of Nsp13 to the centrosome, Orf3a to late endosomes, and Orf9b to mitochondria.
Honeybee gut microbiota modulates host behaviors and neurological processes
Authors: Zhang Zijing , Mu Xiaohuan , Cao Qina , Shi Yao , Hu Xiaosong , Zheng Hao
Published: December 2020

Honeybee is a highly social insect with a reach behavioral repertoire and is a versatile model for neurobiological research. The honeybee gut microbiota is composed of a limited number of bacterial phylotypes that play an important role in host health. However, it remains unclear whether the microbiota can shape brain profiles and behaviors. Here, we revealed that the gut microbiota is requisite for the olfactory learning and memory ability of honeybees and alters the level of neurotransmitters in the brain. Transcriptomic and proteomic analysis showed distinctive gene expression and protein signatures for gnotobiotic bees associated with different gut bacteria. Specifically, genes related to olfactory functions and labor division are most upregulated. Moreover, differentially spliced genes in the brains of colonized bees largely overlapped with the datasets for human autism. The circulating metabolome profiles identified that different gut species regulated specific module of metabolites in the host hemolymph. Most altered metabolites are involved in the amino acid and glycerophospholipid metabolism pathways for the production of neuroactive compounds. Finally, antibiotic treatment disturbed the gut community and the nursing behavior of worker bees under field conditions. The brain transcripts and gut metabolism was also greatly interfered in treated bees. Collectively, we demonstrate that the gut microbiota regulates honeybee behaviors, brain gene transcription, and the circulating metabolism. Our findings highlight the contributions of honeybee gut microbes in the neurological processes with striking parallels to those found in other animals, thus providing a promising model to understand the host-microbe interactions via the gut-brain axis.
Dopamine D1 receptor-expressing neurons activity is essential for locomotor and sensitizing effects of a single injection of cocaine
Authors: Nakamura Yukari , Longueville Sophie , Nishi Akinori , Hervé Denis , Girault Jean-Antoine , Nakamura Yuki
Published: December 2020

D1 dopamine receptors play an important role in the effects of cocaine. Here we investigated the role of neurons which express these receptors (D1-neurons) in the acute locomotor effects of cocaine and the locomotor sensitization observed after a second injection of this drug. We inhibited D1-neurons using double transgenic mice conditionally expressing the inhibitory Gi-coupleddesigner receptor exclusively activated by designer drugs(Gi-DREADD) in D1-neurons. Chemogenetic inhibition of D1-neurons by a low dose of clozapine (0.1 mg/kg) decreased the induction ofFosin striatal neurons. It diminished the basal locomotor activity and acute hyper-locomotion induced by cocaine (20 mg/kg). Clozapine 0.1 mg/kg had no effect by itself and did not alter cocaine effects in non-transgenic mice. Inhibition of D1-neurons during the first cocaine administration reduced the sensitization of the locomotor response in response to a second cocaine administration ten days later. At day 11, inhibition of D1-neurons by clozapine stimulation of Gi-DREADD, prevented the expression of the sensitized locomotor response, whereas at day 12, in the absence of clozapine and D1-neurons inhibition, all mice displayed a sensitized response to cocaine. These results show that chemogenetic inhibition of D1-neurons decreases spontaneous and cocaine-induced locomotor activity. It blunts the induction and prevents the expression of sensitization in a two-injection protocol of sensitization but does not alter established sensitization. Our study further supports the central role of D1-neurons in mediating the acute locomotor effects of cocaine and its sensitization.
Alternative promoter usage modulates miRNA-guided translation inhibition of a m6A reader in phosphate starvation
Authors: Reis Rodrigo Siqueira , Deforges Jules , Clúa Joaquín , Poirier Yves
Published: December 2020

Alternative transcription start sites (TSSs) are widespread in eukaryotes. In plants, light, development and tissue regulate selective usage of several TSSs, producing transcripts with distinct 5′UTR as well as shorter protein isoforms with distinct subcellular localization or activity. However, the function of non-coding transcripts generated by alternative TSSs is still largely unknown. We show that phosphate availability regulates numerous alternative TSSs, including a non-coding alternative TSS (ALTECT4) associated withECT4, encoding a N6-methyladenosine (m6A) reader. We found thatECT4harbors a cleavage-resistant miR826b target site at its 3’UTR, also present inALTECT4. In the absence ofALTECT4, miR826b guides translation inhibition ofECT4. Phosphate deficiency triggers specific and robust expression ofALTECT4, counteracting miR826b inhibition of its targets, includingECT4. The role ofALTECT4as a miR826b antagonist shows that it acts incisto regulate translation of the m6A reader ECT4, and this function might be shared among other non-coding transcripts generated by alternative TSS.
Predicting speech from a cortical hierarchy of event-based timescales
Authors: Schmitt Lea-Maria , Erb Julia , Tune Sarah , Rysop Anna , Hartwigsen Gesa , Obleser Jonas
Published: December 2020

How can anticipatory neural processes structure the temporal unfolding of context in our natural environment? We here provide evidence for a neural coding scheme that sparsely updates contextual representations at the boundary of events and gives rise to a hierarchical, multi-layered organization of predictive language comprehension. Training artificial neural networks to predict the next word in a story at five stacked timescales and then using model-based functional MRI, we observe a sparse, event-based “surprisal hierarchy”. The hierarchy evolved along a temporo-parietal pathway, with model-based surprisal at longest timescales represented in inferior parietal regions. Along this hierarchy, surprisal at any given timescale gated bottom-up and top-down connectivity to neighbouring timescales. In contrast, surprisal derived from a continuously updated context influenced temporo-parietal activity only at short timescales. Representing context in the form of increasingly coarse events constitutes a network architecture for making predictions that is both computationally efficient and semantically rich.
A recombinant protein SARS-CoV-2 candidate vaccine elicits high-titer neutralizing antibodies in macaques.
Authors: Baisa Gary , Rancour David , Mansfield Keith , Burns Monika , Martin Lori , Cunha Daise , Fischer Jessica , Muecksch Frauke , Hatziioannou Theodora , Bieniasz Paul , Schomburg Frtiz , Luke Kimberly
Published: December 2020

Vaccines that generate robust and long-lived protective immunity against SARS-CoV-2 infection are urgently required. We assessed the potential of vaccine candidates based on the SARS-CoV-2 spike in cynomolgus macaques (M. fascicularis) by examining their ability to generate spike binding antibodies with neutralizing activity. Antigens were derived from two distinct regions of the spike S1 subunit, either the N-terminal domain (NTD) or an extended C-terminal domain containing the receptor-binding domain (RBD) and were fused to the human IgG1 Fc domain. Three groups of 2 animals each were immunized with either each antigen, alone or in combination. The development of antibody responses was evaluated through 20 weeks post-immunization. A robust IgG response to the spike protein was detected as early as 2 weeks after immunization with either protein and was maintained for over 20 weeks. Sera from animals immunized with antigens derived from the RBD were able to prevent binding of soluble spike proteins to the ACE2 receptor, shown by in vitro binding assays, while sera from animals immunized with the NTD alone lacked this activity. Crucially, sera from animals immunized with the RBD but not the NTD had potent neutralizing activity against SARS-CoV-2 pseudotyped virus, with titers in excess of 10,000, greatly exceeding that typically found in convalescent humans. Neutralizing activity persisted for more than 20 weeks. These data support the utility of spike subunit-based antigens as a vaccine for use in humans.
Disablingde novoDNA methylation in embryonic stem cells allows an illegitimate fate trajectory
Authors: Kinoshita Masaki , Li Meng Amy , Barber Michael , Mansfield William , Dietmann Sabine , Smith Austin
Published: December 2020

Genome remethylation is essential for mammalian development but specific reasons are unclear. Here we examined embryonic stem (ES) cell fate in the absence ofde novoDNA methyltransferases. We observed that ES cells deficient for bothDnmt3aandDnmt3bare rapidly eliminated from chimaeras. On further investigation we found that in vivo and in vitro the formative pluripotency transition is derailed towards production of trophoblast. This aberrant trajectory is associated with failure to suppress activation ofAscl2. Ascl2encodes a bHLH transcription factor expressed in placenta. Misexpression ofAscl2in ES cells provokes transdifferentiation to trophoblast-like cells. Conversely,Ascl2deletion rescues formative transition ofDnmt3a/bmutants and improves contribution to chimaeric epiblast. Thus,de novoDNA methylation safeguards against ectopic activation ofAscl2. However,Dnmt3a/b-deficient cells remain defective in ongoing embryogenesis. We surmise that multiple developmental transitions may be secured by DNA methylation silencing potentially disruptive genes.

SIGNIFICANCE STATEMENT

Mammalian DNA is widely modified by methylation of cytosine residues. This modification is added to DNA during early development. If methylation is prevented, the embryo dies by mid-gestation with multiple abnormalities. In this study we found that stem cells lacking the DNA methylation enzymes do not differentiate efficiently into cell types of the embryo and are diverted into producing placental cells. This switch in cell fate is driven by a transcription factor, Ascl2, which should only be produced in placenta. In the absence of DNA methylation, theAscl2gene is mis-expressed. Removing Ascl2 redirects embryonic fate but not full differentiation potential, suggesting that methylation acts at multiple developmental transitions to restrict activation of disruptive genes.
Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome length and individualization
Authors: Choppakatla Pavan , Dekker Bastiaan , Cutts Erin E. , Vannini Alessandro , Dekker Job , Funabiki Hironori
Published: December 2020

DNA loop extrusion by condensins and decatenation by DNA topoisomerase II (topo II) are thought to drive mitotic chromosome compaction and individualization. Here, we reveal that the linker histone H1.8 antagonizes condensins and topo II to shape mitotic chromosome organization. In vitro chromatin reconstitution experiments demonstrate that H1.8 inhibits binding of condensins and topo II to nucleosome arrays. Accordingly, H1.8 depletion in Xenopus egg extracts increased condensins and topo II levels on mitotic chromatin. Chromosome morphology and Hi-C analyses suggest that H1.8 depletion makes chromosomes thinner and longer through shortening the average loop size and reducing the DNA amount in each layer of mitotic loops. Furthermore, excess loading of condensins and topo II to chromosomes by H1.8 depletion causes hyper-chromosome individualization and dispersion. We propose that condensins and topo II are essential for chromosome individualization, but their functions are tuned by the linker histone to keep chromosomes together until anaphase.
A global map of the impact of deletion of Post-Translational Modification sites in genetic diseases
Authors: Vellosillo Perceval , Minguez Pablo
Published: December 2020

Background

There are >200 protein post-translational modification (PTMs) types described in eukaryotes, having diverse species conservation levels, proteome coverage, number of high-throughput experiments and functional roles. From a clinical perspective, a number of diseases have been associated to deregulated PTM sites and missense rare variants are globally enriched in PTMs. We hypothesize that some genetic diseases may be caused by the deregulation of particular functions produced by the removal of a specific PTM type by genomic variants.

Results

We collected >320,000 human PTMs of 59 types and cross them with >4M missense DNA variants annotated with pathogenic predictions and disease associations. We report >1.74M PTM-variant concurrences in >16,500 proteins that an enrichment analysis distributed in 217 pairwise significant associations between 18 PTM types and 150 genetic diseases. Around 23% of these associations are already described in the literature, 34% have partial evidences based on single variants, related diseases or regulatory evidences, and 43% are novel. Removal of acetylation presents the highest effect, still low studied PTM types like S-glutathionylation or S-nitrosylation show relevance. A network of PTM types and phenotypes associations is also discussed. Using pathogenicity predictions we identified potential PTM sites to produce particular diseases if genomic variants remove them.

Conclusions

Our results show an important impact of PTM removal producing genetic diseases and phenotypes that is PTM type specific. We describe for the first time a general scenario of PTM types and genetic diseases direct associations, many of them novel, that provides new capacities to understand and diagnose these disorders.
A Distributed Circuit for Associating Environmental Context to Motor Choice in Retrosplenial Cortex
Authors: Franco Luis M. , Goard Michael J.
Published: December 2020

During navigation, animals often use recognition of familiar environmental contexts to guide motor action selection. The retrosplenial cortex (RSC) receives inputs from both visual cortex and subcortical regions required for spatial memory, and projects to motor planning regions. However, it is not known whether RSC is important for associating familiar environmental contexts with specific motor actions. Here, we test this possibility by developing a task in which trajectories are chosen based on the context. We find that mice exhibit differential pre-decision activity in RSC, and that optogenetic suppression of RSC activity impairs task performance. Individual RSC neurons encode a range of task variables, often multiplexed with distinct temporal profiles. However, the responses are spatiotemporally organized, with task variables represented along a posterior-to-anterior gradient along RSC during the behavioral performance, consistent with histological characterization. These results reveal an anatomically-organized retrosplenial cortical circuit for associating environmental contexts to appropriate motor outputs.
CTCF is a Barrier for Totipotent-like Reprogramming
Authors: Olbrich Teresa , Vega-Sendino Maria , Tillo Desiree , Wu Wei , Zolnerowich Nicholas , Tran Andy D. , Domingo Catherine N. , Franco Mariajose , Markiewicz-Potoczny Marta , Pegoraro Gianluca , FitzGerald Peter C. , Kruhlak Michael J. , Lazzerini-Denchi Eros , Nora Elphege P. , Nussenzweig Andre , Ruiz Sergio
Published: December 2020

Totipotent cells have the ability of generating embryonic and extra-embryonic tissues1,2. Interestingly, a rare population of cells with totipotent-like potential was identified within ESC cultures3. These cells, known as 2 cell (2C)-like cells, arise from ESC and display similar features to those found in the totipotent 2 cell embryo2-4. However, the molecular determinants of 2C-like conversion have not been completely elucidated. Here, we show that CTCF is a barrier for 2C-like reprogramming. Indeed, forced conversion to a 2C-like state by DUX expression was associated with DNA damage at a subset of CTCF binding sites. Endogenous or DUX-induced 2C-like ESC showed decreased CTCF enrichment at known binding sites, suggesting that acquisition of a totipotent-like state is associated with a highly dynamic chromatin architecture. Accordingly, depletion of CTCF in ESC efficiently promoted spontaneous and asynchronous conversion to a totipotent-like state. This phenotypic reprogramming was reversible upon restoration of CTCF levels. Furthermore, we showed that transcriptional activation of the ZSCAN4 cluster was necessary for successful 2C-like reprogramming. In summary, we revealed the intimate relation between CTCF and totipotent-like reprogramming.
Probabilistic discrimination of relative stimulus features in mice
Authors: Lyamzin Dmitry R , Aoki Ryo , Abdolrahmani Mohammad , Benucci Andrea
Published: December 2020

Understanding how the brain computes choice from sensory information is a central question in perceptual decision-making research. From a behavioral perspective, paradigms suitable to study perceptual decision-making condition choice on invariant properties of the stimuli, thus decoupling stimulus-specific information from decision-related variables. From a neural perspective, powerful tools for the dissection of brain circuits are needed, which suggests the mouse as a suitable animal model. However, whether and how mice can perform an invariant visual discrimination task has not yet been fully established. Here, we show that mice can solve a complex orientation discrimination task where the choices are decoupled from the orientation of individual stimuli. Moreover, we demonstrate a discrimination acuity of at least 6°, challenging the common belief that mice are poor visual discriminators. We reached these conclusions by introducing a novel probabilistic choice model that explained behavioral strategies in (n = 40) mice and identified unreported dimensions of variation associated with the circularity of the stimulus space. Furthermore, the model showed a dependence of history biases on task engagement, demonstrating behavioral sensitivity to the availability of cognitive resources. In conclusion, our results reveal that mice are capable of decoupling decision-relevant information from stimulus-specific information, thus demonstrating they are a useful animal model for studying neural representation of abstract learned categories in perceptual decision-making research.
Voltage-clamp fluorometry analysis of structural rearrangements of ATP-gated channel P2X2 upon hyperpolarization
Authors: Andriani Rizki Tsari , Kubo Yoshihiro
Published: December 2020

The gating of the ATP-activated channel P2X2 has been shown to be dependent not only on [ATP] but also on membrane voltage, despite the absence of a canonical voltage-sensor domain. We aimed to investigate the structural rearrangements of the rat P2X2 during ATP- and voltage-dependent gating by voltage-clamp fluorometry technique. We observed fast and linearly voltage-dependent fluorescence intensity (F) changes at Ala337 and Ile341 in the TM2 domain, which could be due to the electrochromic effect, reflecting the presence of a converged electric field here. We also observed slow and voltage-dependent F changes at Ala337, which reflect the structural rearrangements. Furthermore, we identified that the interaction between Ala337 in TM2 and Phe44 in TM1, located in close proximity in the ATP-bound open state, is critical for activation. Taken together, we propose that the voltage dependence of the interaction in the converged electric field underlies the voltage-dependent gating.
Discovery of synthetic lethal and tumor suppressive paralog pairs in the human genome
Authors: Parrish Phoebe C. R. , Thomas James D. , Kamlapurkar Shriya , Gabel Austin , Bradley Robert K. , Berger Alice H.
Published: December 2020

CRISPR knockout screens have accelerated the discovery of important cancer genetic dependencies. However, traditional CRISPR-Cas9 screens are limited in their ability to assay the function of redundant or duplicated genes. Paralogs in multi-gene families constitute two-thirds of the protein-coding genome, so this blind spot is the rule, not the exception. To overcome the limitations of single gene CRISPR knockout screens, we developedpairedguide RNAs forParalog gENetic interaction mapping (pgPEN), a pooled CRISPR/Cas9 approach which targets over a thousand duplicated human paralogs in single knockout and double knockout configurations. We applied pgPEN to two cell lineages and discovered that over 10% of human paralogs exhibit synthetic lethality in at least one cellular context. We recovered known synthetic lethal paralogs such asMAP2K1/MAP2K2, important drug targets such asCDK4/CDK6, and numerous other synthetic lethal pairs such asCCNL1/CCNL2.In addition, we identified ten tumor suppressive paralog pairs whose compound loss promotes cell growth. These findings identify a large number of previously unidentified essential gene families and nominate new druggable targets for oncology drug discovery.

Highlights

Comprehensive genetic interaction mapping of 1,030 human duplicated paralogs using a dual targeting CRISPR/Cas9 approach

Duplicated paralogs are highly enriched for genetic interactions

Synthetic lethal paralogs includeCCNL1/CCNL2, CDK4/CDK6, andGSK3A/GSK3B

Tumor suppressor paralog pairs includeCDKN2A/CDKN2BandFBXO25/FBXO32
Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer's model
Authors: Clarke Michael F , Reinitz Felicia , Chen Elizabeth , Nicolis di Robilant Benedetta , Chuluun Bayarsaikhan , Antony Jane , Jones Robert C , Gubbi Neha , Kolluru Sai Saroja , Qian Dalong , Piltti Katja , Monje Michelle , Anderson Aileen , Heller H. Craig , Quake Stephen R.
Published: December 2020

Alzheimers disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify an earlier targetable phenotype. Utilizing a mouse model of AD and human fetal cells harboring mutant amyloid precursor protein, we show cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it the earliest defect in the evolution of disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. Reduction of USP16 led to decreased expression of senescence gene Cdkn2a and mitigated aberrant regulation of the BMP pathway, a previously unknown function of USP16. Thus, we reveal USP16 as a novel target in an AD model that can both ameliorate the NPC defect and rescue memory and learning through its regulation of both Cdkn2a and BMP signaling.
In-depth characterization of denitrifier communities across different soil ecosystems in the tundra
Authors: Pessi Igor S. , Viitamäki Sirja , Virkkala Anna-Maria , Eronen-Rasimus Eeva , Delmont Tom O. , Marushchak Maija E. , Luoto Miska , Hultman Jenni
Published: December 2020

Background

In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra.

Results

We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23.

Conclusions

By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.
Oligomerization of the Human Adenosine A2AReceptor is Driven by the Intrinsically Disordered C-terminus
Authors: Nguyen Khanh D. Q. , Vigers Michael , Sefah Eric , Seppälä Susanna , Hoover Jennifer P. , Schonenbach Nicole S. , Mertz Blake , O’Malley Michelle A. , Han Songi
Published: December 2020

G protein-coupled receptors (GPCRs) have long been shown to exist as oligomers with functional properties distinct from those of the monomeric counterparts, but the driving factors of GPCR oligomerization remain relatively unexplored. In this study, we focus on the human adenosine A2Areceptor (A2AR), a model GPCR that forms oligomers bothin vitroandin vivo. Combining experimental and computational approaches, we discover that the intrinsically disordered C-terminus of A2AR drives the homo-oligomerization of the receptor. The formation of A2AR oligomers declines progressively and systematically with the shortening of the C-terminus. Multiple interaction sites and types are responsible for A2AR oligomerization, including disulfide linkages, hydrogen bonds, electrostatic interactions, and hydrophobic interactions. These interactions are enhanced by depletion interactions along the C-terminus, forming a tunable network of bonds that allow A2AR oligomers to adopt multiple interfaces. This study uncovers the disordered C-terminus as a prominent driving factor for the oligomerization of a GPCR, offering important guidance for structure-function studies of A2AR and other GPCRs.