bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic analysis of sugar metabolism reveals the mechanisms of action of synthetic sugar analogs
Authors: van Scherpenzeel Monique , Conte Federica , Büll Christian , Ashikov Angel , Hermans Esther , Willems Anke , van Tol Walinka , Kragt Else , Moret Ed E. , Heise Torben , Langereis Jeroen D. , Rossing Emiel , Zimmermann Michael , Rubio-Gozalbo M. Estela , de Jonge Marien I. , Adema Gosse J. , Zamboni Nicola , Boltje Thomas , Lefeber Dirk J.
Published: September 2020

Synthetic sugar analogs are widely applied in metabolic oligosaccharide engineering (MOE) and as novel drugs to interfere with glycoconjugate biosynthesis. However, mechanistic insights on their exact metabolism in the cell and over time are mostly lacking. We developed sensitive ion-pair UHPLC-QqQ mass spectrometry methodology for analysis of sugar metabolites in organisms and in model cells and identified novel low abundant nucleotide sugars in human cells, such as ADP-glucose and UDP-arabinose, and CMP-sialic acid (CMP-NeuNAc) in Drosophila. Dynamic tracing of propargyloxycarbonyl (Poc) labeled analogs, commonly used for MOE, revealed that ManNPoc is metabolized to both CMP-NeuNPoc and UDP-GlcNPoc. Finally, combined treatment of B16-F10 melanoma cells with antitumor compound 3Fax-NeuNAc and13C-labeled GlcNAc revealed that endogenous CMP-NeuNAc levels started to decrease before a subsequent decrease of ManNAc 6-phosphate was observed. This implicates 3Fax-NeuNAc first acts as a substrate for cytosolic CMP-sialic acid synthetase and subsequently its product CMP-3Fax-NeuNAc functions as a feed-back inhibitor for UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase. Thus, dynamic analysis of sugar metabolites provides key insights into the time-dependent metabolism of synthetic sugars, which is important for the rational design of analogs with optimized effects.
The 5α-reductase inhibitor finasteride reduces opioid self-administration
Authors: Bosse Gabriel D. , Cadeddu Roberto , Floris Gabriele , Farero Ryan D. , Vigato Eva , Lee Suhjung J. , Zhang Tejia , Gaikwad Nilesh W. , Keefe Kristen A. , Philips Paul E.M. , Bortolato Marco , Peterson Randall T.
Published: September 2020

Opioid use disorder (OUD) has become a leading cause of death in the US, yet current therapeutic strategies remain highly inadequate. To identify novel potential treatments for OUD, we screened a targeted selection of over 100 drugs, using a recently developed opioid self-administration assay in zebrafish. This paradigm showed that finasteride, a steroidogenesis inhibitor approved for the treatment of benign prostatic hyperplasia and androgenetic alopecia, reduced self-administration of multiple opioids without affecting locomotion or feeding behavior. These findings were confirmed in rats; furthermore, finasteride did not interfere with the antinociceptive effect of opioids in rat models of neuropathic pain. Steroidomic analyses of the brains of fish treated with finasteride revealed a significant increase in dehydroepiandrosterone sulfate (DHEAS). Treatment with precursors of DHEAS reduced opioid self-administration in zebrafish, in a fashion akin to the effects of finasteride. Our results highlight the importance of steroidogenic pathways as a rich source of therapeutic targets for OUD and point to the potential of finasteride as a new option for this disorder.
LOX-1+immature neutrophils predict severe COVID-19 patients at risk of thrombotic complications
Authors: Combadiere Béhazine , Adam Lucille , Quentric Paul , Rosenbaum Pierre , Dorgham Karim , Bonduelle Olivia , Parizot Christophe , Sauce Delphine , Mayaux Julien , Luyt Charles-Edouard , Boissonnas Alexandre , Amoura Zahir , Pourcher Valérie , Miyara Makoto , Gorochov Guy , Guihot Amélie , Combadière Christophe
Published: September 2020

Rational

Lymphopenia and neutrophil/lymphocyte ratio may have prognostic value in coronavirus disease 2019 (COVID-19) severity.

Objective

We sought to investigate the representation of neutrophil subsets in severe and critical COVID-19 patients based on Intensive Care Units (ICU) and non-ICU admission.

Methods

We developed a multi-parametric neutrophil profiling strategy based on known neutrophil markers to distinguish COVID-19 phenotypes in critical and severe patients.

Results

Our results showed that 80% of ICU patients develop strong myelemia with CD10−CD64+immature neutrophils. Cellular profiling revealed two distinct neutrophil subsets expressing either the lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) or the Interleukin-3 receptor alpha (CD123), both significantly overrepresented in ICU patients compared to non-ICU patients. The proportion of LOX-1-expressing immature neutrophils positively correlated with clinical severity, with the cytokine storm (IL-1β, IL-6, IL-8, TNFα), and with intravascular coagulation. Importantly, high proportions of LOX-1+-immature neutrophils are associated with high risks of severe thrombosis.

Conclusions

Together these data suggest that point of care enumeration of LOX-1-immature neutrophils might help distinguish patients at risk of thrombosis complication and most likely to benefit from intensified anticoagulant therapy.
The maternal foam plug constitutes a reservoir for the desert locust’s bacterial symbionts
Authors: Lavy Omer , Gophna Uri , Ayali Amir , Gihaz Shalev , Fishman Ayelet , Gefen Eran
Published: September 2020

A hallmark of the desert locust’s ancient and deserved reputation as a devastating agricultural pest is that of the long-distance, multi-generational migration of locust swarms to new habitats. The bacterial symbionts that reside within the locust gut comprise a key aspect of its biology, augmenting its immunity and having also been reported to be involved in the swarming phenomenon through the emission of attractant volatiles. However, it is still unclear whether and how these beneficial symbionts are transmitted vertically from parent to offspring. Using comparative 16S rRNA amplicon sequencing and direct experiments with engineered bacteria, we provide here evidence of the vertical transmission of locust gut bacteria. The females perform this activity by way of inoculation of the egg-pod’s foam plug, through which the larvae pass upon hatching. Furthermore, analysis of the biochemical structure of the foam revealed chitin to be its major component, along with immunity-related proteins such as lysozyme, which could be responsible for the inhibition of some bacteria in the foam while allowing other, more beneficial, strains to proliferate. Our findings reveal a potential vector for the transgenerational transmission of symbionts in locusts, which contributes to the locust swarm’s ability to invade and survive in new territories.
Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding
Authors: Scott Michael F. , Fradgley Nick , Bentley Alison R. , Brabbs Thomas , Corke Fiona , Gardner Keith A. , Horsnell Richard , Howell Phil , Ladejobi Olufunmilayo , Mackay Ian J. , Mott Richard , Cockram James
Published: September 2020

Background

Breeding has helped improve bread wheat yield significantly over the last century. Understanding the potential for future crop improvement depends on relating segregating genetic variation to agronomic traits.

Results

We bred NIAB Diverse MAGIC population, comprising over 500 recombinant inbred lines, descended from sixteen bread wheat varieties released between 1935-2004. We sequenced the founders’ exomes and promotors by capture. Despite being highly representative of North-West European wheat and capturing 73% of global polymorphism, we found 89% of genes contained no more than three haplotypes. We sequenced each line with 0.3x coverage whole-genome sequencing, and imputed 1.1M high-quality SNPs that were over 99% concordant with array genotypes. Imputation accuracy remained high at coverage as low as 0.076x, with or without the use of founder genomes as reference panels. We created a genotype-phenotype map for 47 traits over two years. We found 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Outside of these loci most traits are polygenic, as revealed by multi-locus shrinkage modelling.

Conclusions

Historically, wheat breeding has reshuffled a limited palette of haplotypes; continued improvement will require selection at dozens of loci of diminishing effect, as most of the major loci we mapped are known. Breeding to optimise one trait generates correlated trait changes, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break critical unfavourable trait-trait associations. Finally, low coverage whole genome sequencing of bread wheat populations is an economical and accurate genotyping strategy.
RBM20 phosphorylation on serine/arginine domain is crucial to regulate pre-mRNA splicing and protein shuttling in the heart
Authors: Sun Mingming , Jin Yutong , Zhu Chaoqun , Zhang Yanghai , Liss Martin , Gotthardt Michael , Ren Jun , Ge Ying , Guo Wei
Published: September 2020

Molecular and cellular mechanisms of mutations of splicing factors in heart function are not well understood. The splicing of precursor mRNA is dependent on an essential group of splicing factors containing serine-arginine (SR) domain(s) that are critical for protein-RNA and protein-protein interaction in the spliceosome assembly. Phosphorylation of SR domains plays a key role in splicing control and the distribution of splicing factors in the cell. RNA binding motif 20 (RBM20) is a splicing factor predominantly expressed in muscle tissues with the highest expression level in the heart. However, its phosphorylation status is completely unknown up-to-date. In this study, we identified sixteen amino acid residues that are phosphorylated by middle-down mass spectrometry. Four of them are located in the SR domain, and two out of the four residues, S638 and S640, play an essential role in splicing control and facilitate RBM20 shuttling from the nucleus to the cytoplasm. Re-localization of RBM20 promotes protein aggregation in the cytoplasm. We have also verified that SR-protein kinases (SRPKs), cdc2-like kinases (CLKs) and protein kinase B (PKB or AKT) phosphorylate S638 and S640. Mutations of S638A and S640G reduce RBM20 phosphorylation and disrupt the splicing. Taken together, we determine the phosphorylation status of RBM20 and provide the first evidence that phosphorylation on SR domain is crucial for pre-mRNA splicing and protein trafficking. Our findings reveal a new role of RBM20 via protein shuttling in cardiac function.
A transcriptomic taxonomy ofDrosophilacircadian neurons around the clock
Authors: Ma Dingbang , Przybylski Dariusz , Abruzzi Katharine C. , Schlichting Matthias , Li Qunlong , Long Xi , Rosbash Michael
Published: September 2020

Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs ofDrosophilacircadian neurons, we optimized a single cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. We suggest that these molecules orchestrate the temporal regulation of synapse formation and/or strength. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.
Transcriptomic responses and survival mechanisms of staphylococci to the antimicrobial skin lipid sphingosine
Authors: Chen Yiyun , Moran Josephine C. , Campbell-Lee Stuart , Horsburgh Malcolm J.
Published: September 2020

Sphingosines are antimicrobial lipids that form part of the innate barrier to skin colonisation by microbes. Sphingosine deficiencies can result in increased epithelial infections by bacteria includingStaphylococcus aureus. Recent studies have focused on the potential use of sphingosines as novel therapeutic agents, but there have been no investigations into sphingosine resistance or its potential mechanisms. We used RNA-Seq to identify the common D-sphingosine transcriptomic response of the transient skin coloniserS. aureusand the dominant skin coloniserS. epidermidis. A common D-sphingosine stimulon was identified that included downregulation of the SaeSR two-component system (TCS) regulon and upregulation of both the VraSR TCS and CtsR stress regulons. We show that the PstSCAB phosphate transporter, and VraSR offer intrinsic resistance to D-sphingosine. Further, we demonstrate increased sphingosine resistance in these staphylococci evolves readily through mutations in genes encoding the FarE-FarR efflux/regulator proteins. The ease of selecting mutants with resistance to sphingosine may impact upon staphylococcal colonisation of skin where the lipid is present and have implications with topical therapeutic applications.
Neural support of manual preference revealed by BOLD variations during right and left finger-tapping in a sample of 287 healthy adults balanced for handedness
Authors: Tzourio-Mazoyer Nathalie , Labache Loïc , Zago Laure , Hesling Isabelle , Mazoyer Bernard
Published: September 2020

Abstract

We have identified the brain areas involved in Manual Preference (MP) in 143 left-handers (LH) and 144 right-handers (RH)). First, we selected the pairs of homotopic regions of interest (hROIs) of the AICHA atlas with significant contralateral activation and asymmetry during the right-hand and the left-hand Finger-Tapping (FT) both in RH and LH. Thirteen hROIs were selected, including the primary and secondary sensorimotor, and premotor cortices, thalamus, dorsal putamen and cerebellar lobule IV. Both contralateral activations and ipsilateral deactivations (reversed for the cerebellum) were seen in primary motor and somatosensory areas, with stronger asymmetries when the preferred hand was used. Comparing the prediction of MP with different combinations of BOLD variations in these 13 hROIs, the differences between movement of the preferred hand versus that of the non-preferred hand within the contralateral and/or ipsilateral cortices of 11 hROIS performed best at explaining handedness distribution, Handedness is thus supported by: 1-between-hand variations of ipsilateral deactivations of hand primary sensorimotor and secondary somatosensory cortices and 2-variations in regions showing the same profile in left and right-handers during the right or left FT. The present study demonstrates that right and left-handedness are not based on mirrored organization of hand control areas.
Non-redundant functions of H2A.Z.1 and H2A.Z.2 in chromosome segregation and cell cycle progression
Authors: Sales-Gil Raquel , de Castro Ines J. , Amin Hasnat , Spanos Christos , Vinciotti Veronica , Rappsilber Juri , Sisu Cristina , Vagnarelli Paola
Published: September 2020

H2A.Z is a H2A-type histone variant essential for many aspects of cell biology ranging from gene expression to genome stability. From deuterostomes, H2A.Z evolved into two paralogues H2A.Z.1 and H2A.Z.2 that differ by only three amino acids and are encoded by different genes (H2AFZandH2AFVrespectively). Despite the importance of this histone variant in development and cellular homeostasis, very little is known about the individual functions of each paralogue in mammals. Here we investigated the distinct roles of two paralogues in cell cycle regulation. Using a specific siRNA approach for each paralogue in human cells, we unveiled non-redundant functions for H2A.Z.1 and H2A.Z.2 in cell division: H2A.Z.1 regulates the expression of important cell cycle genes (including Myc and Ki-67) and its depletion leads to a G1 arrest, whereas H2A.Z.2 is essential for centromere integrity and function, thus playing a key role in chromosome segregation.
Self-organisation and persistence of antibiotic resistance in evolving plasmid communities
Authors: Zwanzig Martin , Berger Uta
Published: September 2020

A key source of genetic variation of microbial populations are plasmids: extrachromosomal genetic elements that replicate autonomously and can be highly mobile between individual cells. Diverse plasmids were found in environmental samples and bacterial populations. Here we explore the mechanisms that help to preserve this gene pool as a fundamental basis for bacterial adaptation. An individual-based model of the plasmidome is presented and used to investigate how intra- and intercellular competition between diverse plasmid types affects the evolution of plasmid communities. It indicates the relative importance of stochastic and deterministic drivers of plasmid persistence both under neutral conditions and when the environment selects for specific plasmid-encoded traits such as antibiotic resistance for a certain period of time. We found that evolving plasmid communities exhibit a cyclical dynamics that contributes to the maintenance of plasmid diversity and the persistence of costly plasmid-mediated antibiotic resistance after stopped abiotic selection.
The piRNA pathway sustains adult neurogenesis by reducing protein synthesis and cellular senescence
Authors: Gasperini C. , Tuntevski K. , Pelizzoli R. , Lo Van A. , Mangoni D. , Cossu R.M. , Pascarella G. , Bianchini P. , Bielefeld P. , Scarpato M. , Pons-Espinal M. , Sanges R. , Diaspro A. , Fitzsimons C.P. , Carninci P. , Gustincich S. , De Pietri Tonelli D
Published: September 2020

Adult Neural progenitor cells (aNPCs) ensure lifelong neurogenesis in the mammalian hippocampus. Proper regulation of aNPC fate entails important implications for brain plasticity and healthy aging. Piwi proteins and the small noncoding RNAs interacting with them (piRNAs) are best known in gonads as repressors of transposons. Here, we show that Piwil2 (Mili) and piRNAs are abundant in aNPCs of the postnatal mouse hippocampus and demonstrate that this pathway is essential for proper neurogenesis. Particularly, depleting the piRNA pathway in aNPCs impaired neurogenesis, increased senescence and accordingly the generation of reactive glia. Moreover, this manipulation primarily elevated 5S ribosomal RNA, SINEB1 and mRNAs encoding ribosomal proteins and regulators of translation, resulting in higher polysome density and protein synthesis upon differentiation. Our results provide evidence of an essential role for the piRNA pathway in maintaining homeostasis to sustain neural stem cell fate, underpinning its possible involvement in brain plasticity and successful aging.
Performing Parentage Analysis for Polysomic Inheritances Based on Allelic Phenotypes
Authors: Huang Kang , Huber Gwendolyn , Ritland Kermit , Dunn Derek W. , Li Baoguo
Published: September 2020

Polyploidy poses several problems for parentage analysis. We present a new polysomic inheritance model for parentage analysis based on genotypes or allelic phenotypes to solve these problems. The effects of five factors are simultaneously accommodated in this model: (i) double-reduction, (ii) null alleles, (iii) negative amplification, (iv) genotyping errors and (v) self-fertilization. To solve genotyping ambiguity (unknown allele dosage), we developed a new method to establish the likelihood formulas for allelic phenotype data and to simultaneously include the effects of our five chosen factors. We then evaluated and compared the performance of our new method with three established methods by using both simulated data and empirical data from the cultivated blueberry (Vaccinium corymbosum). We also developed and compared the performance of two additional estimators to estimate the geno-typing error rate and the sample rate. We make our new methods freely available in the software packagepolygene, athttp://github.com/huangkang1987/polygene.
Voltage-gated potassium channels ensure action potential shape fidelity in distal axons
Authors: Sabater Victoria Gonzalez , Rigby Mark , Burrone Juan
Published: September 2020

The initiation and propagation of the action potential (AP) along an axon allows neurons to convey information rapidly and across distant sites. Although AP properties have typically been characterised at the soma and proximal axon, the propagation of APs towards distal axonal domains of mammalian neurons remains limited. We used Genetically Encoded Voltage Indicators (GEVIs) to image APs simultaneously at different locations along the long axons of dissociated hippocampal neurons with sub-millisecond temporal resolution. We found that APs became sharper and showed remarkable fidelity as they traveled towards distal axons, even during a high frequency train. Blocking voltage-gated potassium channels (Kv) with 4-AP resulted in an increase in AP width in all compartments, which was stronger at distal locations and exacerbated during AP trains. We conclude that the higher levels of Kv channel activity in distal axons serves to sustain AP fidelity, conveying a reliable digital signal to presynaptic boutons.
The Detailed Organization of the Human Cerebellum Estimated by Intrinsic Functional Connectivity Within the Individual
Authors: Xue Aihuiping , Kong Ru , Yang Qing , Eldaief Mark C. , Angeli Peter , DiNicola Lauren M. , Braga Rodrigo M. , Buckner Randy L. , Yeo B.T. Thomas
Published: September 2020

Distinct regions of the cerebellum connect to separate regions of the cerebral cortex forming a complex topography. While key properties of cerebellar organization have been revealed in group-averaged data, in-depth study of individuals provides an opportunity to discover functional-anatomical features that emerge at a higher spatial resolution. Here functional connectivity MRI was used to examine the cerebellum of two intensively-sampled individuals (each scanned across 31 MRI sessions). Connectivity to somatomotor cortex showed the expected crossed laterality and inversion of the body maps between the anterior and posterior lobes. A surprising discovery was connectivity to the primary visual cortex along the vermis with evidence for representation of the central field. Within the hemispheres, each individual displayed a hierarchical progression from the inverted anterior lobe somatomotor map through to higher-order association zones. The hierarchy ended near Crus I/II and then progressed in reverse order through to the upright somatomotor map in the posterior lobe. Evidence for a third set of networks was found in the most posterior extent of the cerebellum. Detailed analysis of the higher-order association networks around the Crus I/II apex revealed robust representations of two distinct networks linked to the default network, multiple networks linked to cognitive control, as well as a separate representation of a language network. While idiosyncratic spatial details emerged between subjects, each of these networks could be detected in both individuals, and small seed regions placed within the cerebellum recapitulated the full extent of the spatially-specific cerebral networks. The observation of multiple networks in juxtaposed regions at the Crus I/II apex confirms the importance of this zone to higher-order cognitive function and reveals new organizational details.
Electrical match between initial segment and somatodendritic compartment for action potential backpropagation in retinal ganglion cells
Authors: Goethals Sarah , Sierksma Martijn C. , Nicol Xavier , Réaux-Le Goazigo Annabelle , Brette Romain
Published: September 2020

The action potential of most vertebrate neurons initiates in the axon initial segment (AIS), and is then transmitted to the soma where it is regenerated by somatodendritic sodium channels. For successful transmission, the AIS must produce a strong axial current, so as to depolarize the soma to the threshold for somatic regeneration. Theoretically, this axial current depends on AIS geometry and Na+conductance density. We measured the axial current of mouse RGCs using whole-cell recordings with post-hoc AIS labeling. We found that this current is large, implying high Na+conductance density, and carries a charge that co-varies with capacitance so as to depolarize the soma by ~30 mV. Additionally, we observed that the axial current attenuates strongly with depolarization, consistent with sodium channel inactivation, but temporally broadens so as to preserve the transmitted charge. Thus, the AIS appears to be organized so as to reliably backpropagate the axonal action potential.
Evolutionary dynamics of transposable elements in bdelloid rotifers
Authors: Nowell Reuben W. , Wilson Christopher G. , Almeida Pedro , Schiffer Philipp H. , Fontaneto Diego , Becks Lutz , Rodriguez Fernando , Arkhipova Irina R. , Barraclough Timothy G.
Published: September 2020

Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates where males are thus far unknown. Contrary to expectations, we find a diverse range of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms, but we report that bdelloids share a large and unusual expansion of genes involved in RNAi-mediated TE suppression. This suggests that enhanced cellular defence mechanisms might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.
DMA-tudor interaction modules control the specificity ofin vivocondensates
Authors: Courchaine Edward M. , Barentine Andrew E.S. , Straube Korinna , Bewersdorf Joerg , Neugebauer Karla M.
Published: September 2020

Biomolecular condensation is a widespread mechanism of cellular compartmentalization. Because the ‘survival of motor neuron protein’ (SMN) is required for the formation of three different membraneless organelles (MLOs), we hypothesized that at least one region of SMN employs a unifying mechanism of condensation. Unexpectedly, we show here that SMN’s globular tudor domain was sufficient for dimerization-induced condensationin vivo, while its two intrinsically disordered regions (IDRs) were not. The condensate-forming property of the SMN tudor domain required binding to its ligand, dimethylarginine (DMA), and was shared by at least seven additional tudor domains in six different proteins. Remarkably, asymmetric versus symmetric DMA determined whether two distinct nuclear MLOs – gems and Cajal bodies – were separate or overlapping. These findings show that the combination of a tudor domain bound to its DMA ligand – DMA-tudor – represents a versatile yet specific interaction module that regulates MLO assembly and defines their composition.
Mouse fertilization triggers a conserved transcription program in one-cell embryos
Authors: Asami Maki , Lam Brian Y. H. , Hoffmann Martin , Suzuki Toru , Lu Xin , VerMilyea Matthew D. , Yoshida Naoko , Ma Marcella K. , Rainbow Kara , Braun Stefanie , Patwary Nina , Yeo Giles S. H. , Klein Christoph A. , Perry Anthony C. F.
Published: September 2020

Following fertilization, the new embryo reprograms parental genomes to begin transcription (embryonic genome activation, EGA). EGA is indispensable for development, but its dynamics, profile or when it initiates in vertebrates are unknown. We here characterize the onset of transcription in mouse one-cell embryos. Precise embryo staging eliminated noise to reveal a cascading program ofde novotranscription initiating within six hours of fertilization. This immediate EGA (iEGA) utilized canonical promoters, produced spliced transcripts, was distinctive and predominantly driven by the maternal genome. Expression represented pathways not only associated with embryo development but with cancer. In human one-cell embryos, hundreds of genes were up-regulated days earlier than thought, with conservation to mouse iEGA. These findings provide a functional basis for epigenetic analysis in early-stage embryos and illuminate networks governing totipotency and other cell-fate transitions.

One Sentence Summary

Fertilization instates transcription in mouse and human one-cell embryos far sooner than thought and is programmed.
Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil)
Authors: Naslavsky Michel S. , Scliar Marilia O. , Yamamoto Guilherme L. , Wang Jaqueline Yu Ting , Zverinova Stepanka , Karp Tatiana , Nunes Kelly , Ceroni José Ricardo Magliocco , de Carvalho Diego Lima , da Silva Simões Carlos Eduardo , Bozoklian Daniel , Nonaka Ricardo , Silva Nayane dos Santos Brito , da Silva Souza Andreia , de Souza Andrade Heloísa , Passos Marília Rodrigues Silva , Castro Camila Ferreira Bannwart , Mendes-Junior Celso T. , Mercuri Rafael L. V. , Miller Thiago L. A. , Buzzo Jose Leonel , Rego Fernanda O. , Araújo Nathalia M , Magalhães Wagner CS , Célia Mingroni-Netto Regina , Borda Victor , Guio Heinner , Barreto Mauricio L , Lima-Costa Maria Fernanda , Horta Bernardo L , Tarazona-Santos Eduardo , Meyer Diogo , Galante Pedro A. F. , Guryev Victor , Castelli Erick C. , Duarte Yeda A. O. , Passos-Bueno Maria Rita , Zatz Mayana
Published: September 2020

As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enabled identifying ~2,000 novel mobile element insertions, nearly 5Mb of genomic segments absent from human genome reference, and over 140 novel alleles from HLA genes. We reclassified and curated nearly four hundred variant's pathogenicity assertions in genes associated with dominantly inherited Mendelian disorders and calculated the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observed that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS.
Antibody potency, effector function and combinations in protection from SARS-CoV-2 infectionin vivo
Authors: Schäfer Alexandra , Muecksch Frauke , Lorenzi Julio C. C. , Leist Sarah R. , Cipolla Melissa , Bournazos Stylianos , Schmidt Fabian , Gazumyan Anna , Baric Ralph S. , Robbiani Davide F. , Hatziioannou Theodora , Ravetch Jeffrey V. , Bieniasz Paul D. , Nussenzweig Michel C. , Sheahan Timothy P.
Published: September 2020

SARS-CoV-2, the causative agent of COVID-19, is responsible for over 24 million infections and 800,000 deaths since its emergence in December 2019. There are few therapeutic options and no approved vaccines. Here we examine the properties of highly potent human monoclonal antibodies (hu-mAbs) in a mouse adapted model of SARS-CoV-2 infection (SARS-CoV-2 MA).In vitroantibody neutralization potency did not uniformly correlate within vivoactivity, and some hu-mAbs were more potent in combinationin vivo. Analysis of antibody Fc regions revealed that binding to activating Fc receptors is essential for optimal protection against SARS-CoV-2 MA. The data indicate that hu-mAb protective activity is dependent on intact effector function and thatin vivotesting is required to establish optimal hu-mAb combinations for COVID-19 prevention.
Zika virus alters centrosome organization to suppress the innate immune response
Authors: Kodani Andrew , Knopp Kristeene A. , Di Lullo Elizabeth , Retallack Hanna , Kriegstein Arnold R. , DeRisi Joseph L. , Reiter Jeremy F.
Published: September 2020

Zika virus (ZIKV) is a flavivirus transmitted via mosquitoes and sex to cause congenital neurodevelopmental defects, including microcephaly. Inherited forms of microcephaly (MCPH) are associated with disrupted centrosome organization. Similarly, we found that ZIKV infection disrupted centrosome organization. ZIKV infection disrupted the organization of centrosomal proteins including CEP63, a MCPH-associated protein. The ZIKV nonstructural protein NS3 bound CEP63, and expression of NS3 was sufficient to alter centrosome architecture and CEP63 localization. Loss of CEP63 suppressed ZIKV-induced centrosome disorganization, indicating that ZIKV requires CEP63 to disrupt centrosome organization. ZIKV infection or loss of CEP63 decreased the centrosomal localization and stability of TANK-binding kinase 1 (TBK1), a regulator of the innate immune response. ZIKV infection or loss of CEP63 also increased the centrosomal accumulation of the CEP63 interactors, Mindbomb1 (MIB1) and DTX4, ubiquitin ligases that respectively activate and degrade TBK1. Therefore, we propose that ZIKV NS3 binds CEP63 to increase centrosomal DTX4 localization and destabilization of TBK1, thereby tempering the innate immune response. In addition to identifying a mechanism by which CEP63 controls the innate immune responses in ZIKV infection, we propose that the altered centrosomal organization caused by altered CEP63 function may contribute to ZIKV-associated microcephaly.
Identifying HIV-1 RNA splice variant protein interactomes using HyPR-MSSV
Authors: Knoener Rachel A. , Evans Edward L. , Becker Jordan T. , Scalf Mark , Benner Bayleigh E. , Sherer Nathan M. , Smith Lloyd M.
Published: September 2020

HIV-1 generates unspliced (US), partially spliced (PS), and completely spliced (CS) classes of RNAs; each playing distinct roles in viral replication. Elucidating their host protein “interactomes” is crucial to understanding virus-host interplay. Here, we present HyPR-MSSVfor isolation of US, PS, and CS transcripts from a single population of infected CD4+ T-cells and mass spectrometric identification of theirin vivoprotein interactomes. Analysis revealed 212 proteins differentially associated with the unique RNA classes; including, preferential association of regulators of RNA stability with US- and PS-transcripts and, unexpectedly, mitochondria-linked proteins with US-transcripts. Remarkably, >80 of these factors screened by siRNA knock-down impacted HIV-1 gene expression. Fluorescence microscopy confirmed several to co-localize with HIV-1 US RNA and exhibit changes in abundance and/or localization over the course of infection. This study validates HyPR-MSSVfor discovery of viral splice variant protein interactomes and provides an unprecedented resource of factors and pathways likely important to HIV-1 replication.
Wetland birds in the northern prairie pothole region may show sensitivity to agriculture
Authors: Daniel Jody , Polan Heather , Rooney Rebecca C
Published: September 2020

Wetland losses in the Northern Prairie Pothole Region (NPPR) are largely attributed to agriculture. Since land-use is known to influence bird habitat selection, bird community composition is likely sensitive to the extent of neighboring agricultural activity. We determined which local and landscape habitat variables are most predictive of wetland bird assemblage occurrence in southern Alberta. We:1) identified distinct bird assemblages with a cluster analysis, 2) identified which species were indicative of these assemblages using an indicator species analysis and 3) predicted which bird assemblage would occur in a wetland with a classification and regression tree. Avian assemblages were more loosely defined and had few indicator species. Importantly, assemblages were specific to the natural region in which the wetland occurred. Also, landscapes with higher agricultural activity generally supported waterfowl and shorebirds, likely because agricultural activities excluded wetland-dependent birds that nest in upland habitat. Though waterfowl and shorebirds show poor sensitivity to surrounding landscape composition, edge-nesting wetland avifauna may make good indicators of ecological integrity.
Neural interactions in developing rhythmogenic spinal networks: Insights from computational modeling
Authors: Shevtsova Natalia A. , Ha Ngoc T. , Rybak Ilya A. , Dougherty Kimberly J.
Published: September 2020

The mechanisms involved in generation of rhythmic locomotor activity in the mammalian spinal cord remain poorly understood. These mechanisms supposedly rely on both intrinsic properties of constituting neurons and interactions between them. A subset of Shox2 neurons was found to contribute to generation of spinal locomotor activity, but the possible cellular basis for rhythmic bursting in these neurons remains unknown. Ha and Dougherty (2018) recently revealed the presence of bidirectional electrical coupling between Shox2 neurons in neonatal spinal cords, which can be critically involved in neuronal synchronization and generation of populational bursting. Gap junctional connections found between functionally-related Shox2 interneurons decrease with age, possibly being replaced by increasing interactions through chemical synapses. Here, we developed a computational model of a heterogeneous population of neurons sparsely connected by electrical or/and chemical synapses and investigated the dependence of frequency of populational bursting on the type and strength of neuronal interconnections. The model proposes a mechanistic explanation for emergence of a synchronized rhythmic activity in the neuronal population and provides insights into the mechanisms of the locomotor rhythm generation.
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)
Authors: McGrath J. Mitchell (Mitch) , Funk Andrew , Galewski Paul , Ou Shujun , Townsend Belinda , Davenport Karen , Daligault Hajnalka , Johnson Shannon , Lee Joyce , Hastie Alex , Darracq Aude , Willems Glenda , Barnes Steve , Liachko Ivan , Sullivan Shawn , Koren Sergey , Phillippy Adam , Wang Jie , Liu Tiffany , Pulman Jane , Childs Kevin , Yocum Anastasia , Fermin Damian , Mutasa-Göttgens Effie , Stevanato Piergiorgio , Taguchi Kazunori , Dorn Kevin
Published: September 2020

A contiguous assembly of the inbred ‘EL10’ sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short read error correction. The EL10.1 assembly was 540 Mb, of which 96.7% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNAseq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals drawn from EL10 progeny and three unrelated germplasm accessions, producing estimates from 633 to 875 Mb/1C. Read depth mapping with short-read whole genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.
Network Modeling and Inference of Peroxisome Proliferator-Activated Receptor Pathway in High fat diet-linked Obesity
Authors: Vundavilli Haswanth , Tripathi Lokesh P. , Datta Aniruddha , Mizuguchi Kenji
Published: September 2020

Systems biology aims to understand how holistic systems theory can be used to explain the observable living system characteristics, and mathematical modeling tools have been successful in understanding the intricate relationships underlying cellular functions. Lately, researchers have been interested in understanding molecular mechanisms underlying obesity, which is a major health concern worldwide and has been linked to several diseases. Various mechanisms such as peroxisome proliferator-activated receptors (PPARs) are known to modulate obesity-induced inflammation and its consequences. In this study, we have modeled the PPAR pathway using a Bayesian model and inferred the sub-pathways that are potentially responsible for the activation of the output processes that are associated with high fat diet (HFD)-induced obesity. We examined a previously published dataset from a study that compared gene expression profiles of 40 mice maintained on HFD against 40 mice fed with chow diet (CD). Our simulations have highlighted that GPCR and FATCD36 sub-pathways were aberrantly active in HFD mice and are therefore favorable targets for anti-obesity strategies. We further cross-validated our observations with experimental results from the literature. We believe that mathematical models such as those presented in the present study can help in inferring other pathways and deducing significant biological relationships.
Antibody interference by a non-neutralizing antibody abrogates humoral protection againstPlasmodiumliver stage
Authors: Vijayan Kamalakannan , Chandrasekaran Ramyavardhanee , Trakhimets Olesya , Brown Samantha L. , Dambrauskas Nicholas , Zuck Meghan , Visweswaran Ganesh Ram R. , Watson Alexander , Raappana Andrew , Carbonetti Sara , Kelnhofer-Millevolte Laurel , Glennon Elizabeth K.K. , Postiglione Rachel , Sather D. Noah , Kaushansky Alexis
Published: September 2020

Both subunit and attenuated whole sporozoite vaccination strategies againstPlasmodiuminfection have shown promising initial results in malaria-naïve westerners but exhibited less efficacy in malaria-exposed individuals in endemic areas. It has been hypothesized that preexisting immunity to malaria represents a significant roadblock to the development of a protective vaccine. Here, we demonstrate proof-of-concept that non-neutralizing antibodies (nNAb) can directly interfere with protective anti-PyCSP humoral responses. We developed and characterized a novel monoclonal antibody, RAM1, against theP. yoeliisporozoite major surface antigen, circumsporozoite protein (CSP). Unlike the canonicalPyCSP repeat domain binding and neutralizing antibody (NAb) 2F6, RAM1 does not inhibit sporozoite traversal or entry of hepatocytesin vitro. Though 2F6 and RAM1 bind non-overlapping regions of the CSP-repeat domain, pretreatment with RAM1 abrogated 2F6’s capacity to block sporozoite traversal and invasionin vitro. Importantly, RAM1 reduced the efficacy of the polyclonal humoral response against CSPin vivo,paralleling the observed reduced efficacy of RTS,S in malaria-exposed populations. Taken together, our data demonstrate the interference of non-neutralizing antibodies with the efficacy of NAbs and may impact the efficacy of anti-CSP vaccines in malaria-exposed individuals.
A rigorous method for integrating multiple heterogeneous databases in genetic studies
Authors: Bukszár József , van den Oord Edwin JCG
Published: September 2020

The large number of existing databases provides a freely available independent source of information with a considerable potential to increase the likelihood of identifying genes for complex diseases. We developed a flexible framework for integrating such heterogeneous databases into novel large scale genetic studies and implemented the methods in a freely-available, user-friendly R package called MIND. For each marker, MIND computes the posterior probability that the marker has effect in the novel data collection based on the information in all available data. MIND 1) relies on a very general model, 2) is based on the mathematical formulas that provide us with the exact value of the posterior probability, and 3) has good estimation properties because of its very efficient parameterization. For an existing data set, only the ranks of the markers are needed, where ties among the ranks are allowed. Through simulations, cross-validation analyses involving 18 GWAS, and an independent replication study of 6,544 SNPs in 6,298 samples we show that MIND 1) is accurate, 2) outperforms marker selection for follow up studies based onp-values, and 3) identifies effects that would otherwise require replication of over 20 times as many markers.

AUTHOR SUMMARY

The large number of existing databases provides a freely available independent source of information with a considerable potential to increase the likelihood of identifying genes for complex diseases. We developed a flexible framework for integrating such heterogeneous databases into novel large scale genetic studies and implemented the methods in a freely-available, user-friendly R package called MIND. For each marker, MIND computes an estimate of the (posterior) probability that the marker has effect in the novel data collection based on the information in all available data. For an existing data set, only the ranks of the markers are needed to be known, where ties among the ranks are allowed. MIND 1) relies on a realistic model that takes confounding effects into account, 2) is based on the mathematical formulas that provide us with the exact value of the posterior probability, and 3) has good estimation properties because of its very efficient parameterization. Simulation, validation, and a replication study in independent samples show that MIND is accurate and greatly outperforms marker selection without using existing data sets.
Ubiquitylome Analysis Reveals a Central Role for the Ubiquitin-Proteasome System in Plant Innate Immunity
Authors: Ma Xiyu , Zhang Chao , Kim Do Young , Huang Yanyan , He Ping , Vierstra Richard D. , Shan Libo
Published: September 2020

Protein ubiquitylation profoundly expands proteome functionality and diversifies cellular signaling processes, with recent studies providing ample evidence for its importance to plant immunity. To gain a proteome-wide appreciation of ubiquitylome dynamics during immune recognition, we employed a two-step affinity enrichment protocol based on a 6His-tagged ubiquitin (Ub) variant coupled with high sensitivity mass spectrometry to identifyArabidopsisproteins rapidly ubiquitylated upon plant perception of the microbe-associated molecular pattern (MAMP) peptide flg22. The catalog from two-week-old seedlings treated for only 30 minutes with flg22 contained nearly 1,000 conjugates, 150 Ub footprints, and all seven types of Ub linkages, and included previously uncharacterized conjugates of immune components, such as RECEPTOR-LIKE KINASE 1 (RKL1) shown to negatively regulate plant immunity.In vivoubiquitylation assays confirmed modification of several candidates upon immune elicitation, and revealed distinct modification patterns and dynamics for key immune components, including poly- and monoubiquitylation, as well as induced or reduced levels of ubiquitylation. Gene ontology and network analyses of the collection also uncovered rapid modification of the Ub-proteasome system itself, suggesting a critical auto-regulatory loop necessary for an effective MAMP-triggered immune response and subsequent disease resistance. Included targets were UBIQUITIN-CONJUGATING ENZYME 13 (UBC13) and proteasome component REGULATORY PARTICLE NON-ATPASE SUBUNIT 8b (RPN8b), whose subsequent biochemical and genetic analyses implied negative roles in immune elicitation. Collectively, our proteomic analyses further strengthened the connection between ubiquitylation and flg22-based immune signaling, identified novel components and pathways regulating plant immunity, and increased the database of ubiquitylated substrates in plants.

One-sentence summary

Proteome-wide catalogs of ubiquitylated proteins revealed a rapid engagement of the ubiquitin-proteasome system in Arabidopsis innate immunity.