bluuebunny/crossref_metadata_2025 huggingface dataset:
Testosterone and longevity in men and women: A Mendelian randomization study in the UK Biobank
Authors: Schooling CM , Zhao JV
Published: June 2020

Background

After decades of rising life expectancy, life expectancy in the developed West is currently stagnated and remains shorter in men than women. Very well-established evolutionary biology theory suggests that lifespan trades off against reproductive success, possibly sex-specifically. We examined whether a key driver of reproductive success, testosterone, affected lifespan using a Mendelian randomization study of longevity in the UK Biobank to obtain unbiased estimates, along with control exposures.

Methods

We applied published genetic instruments for testosterone to obtain inverse variance weighted estimates of associations with longevity, proxied by survival to (i.e., age at) recruitment, in 167020 men and 194174 women. We similarly obtained estimates for smoking initiation, and absorbate, a marker of vitamin C metabolism, because. We also conducted sensitivity analysis.

Results

Overall testosterone was associated with poorer survival (0.10 years younger at recruitment per effect size of testosterone, 95% confidence interval (CI) 0.004 to 0.20). As expected, smoking initiation was also associated with poorer survival (0.37 years younger, 95% CI 0.25 to 0.50), but not absorbate (0.01 years younger, 95% CI −0.09 to 0.11). Sensitivity analysis generally gave a similar interpretation

Conclusions

Consistent, with well-established theory, testosterone reduced longevity. Several aspects of a healthy lifestyle (such as a low animal fat diet) and several widely used medications (such as statins, metformin, dexamethasone and possibly aspirin) happen to modulate testosterone. Explicitly designing interventions sex-specifically based on these insights might be a means of addressing stagnating life expectancy and sexual disparities in life expectancy.
Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study
Authors: Lemey Philippe , Hong Samuel , Hill Verity , Baele Guy , Poletto Chiara , Colizza Vittoria , O’Toole Áine , McCrone John T. , Andersen Kristian G. , Worobey Michael , Nelson Martha I. , Rambaut Andrew , Suchard Marc A.
Published: June 2020

Spatiotemporal bias in genome sequence sampling can severely confound phylogeographic inference based on discrete trait ancestral reconstruction. This has impeded our ability to accurately track the emergence and spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Despite the availability of unprecedented numbers of SARS-CoV-2 genomes on a global scale, evolutionary reconstructions are hindered by the slow accumulation of sequence divergence over its relatively short transmission history. When confronted with these issues, incorporating additional contextual data may critically inform phylodynamic reconstructions. Here, we present a new approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2, while also including global air transportation data. We demonstrate that including travel history data for each SARS-CoV-2 genome yields more realistic reconstructions of virus spread, particularly when travelers from undersampled locations are included to mitigate sampling bias. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations in the analyses. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts. Although further research is needed to fully examine the performance of our travel-aware phylogeographic analyses with unsampled diversity and to further improve them, they represent multiple new avenues for directly addressing the colossal issue of sample bias in phylogeographic inference.
A nanoluciferase SARS-CoV-2 for rapid neutralization testing and screening of anti-infective drugs for COVID-19
Authors: Xie Xuping , Muruato Antonio E. , Zhang Xianwen , Lokugamage Kumari G. , Fontes-Garfias Camila R. , Zou Jing , Liu Jianying , Ren Ping , Balakrishnan Mini , Cihlar Tomas , Tseng Chien-Te K. , Makino Shinji , Menachery Vineet D. , Bilello John P. , Shi Pei-Yong
Published: June 2020

A high-throughput platform would greatly facilitate COVID-19 serological testing and antiviral screening. Here we report a nanoluciferase SARS-CoV-2 (SARS-CoV-2-Nluc) that is genetically stable and replicates similarly to the wild-type virus in cell culture. We demonstrate that the optimized reporter virus assay in Vero E6 cells can be used to measure neutralizing antibody activity in patient sera and produces results in concordance with a plaque reduction neutralization test (PRNT). Compared with the low-throughput PRNT (3 days), the SARS-CoV-2-Nluc assay has substantially shorter turnaround time (5 hours) with a high-throughput testing capacity. Thus, the assay can be readily deployed for large-scale vaccine evaluation and neutralizing antibody testing in humans. Additionally, we developed a high-throughput antiviral assay using SARS-CoV-2-Nluc infection of A549 cells expressing human ACE2 receptor (A549-hACE2). When tested against this reporter virus, remdesivir exhibited substantially more potent activity in A549-hACE2 cells compared to Vero E6 cells (EC500.115 vs 1.28 μM), while this difference was not observed for chloroquine (EC501.32 vs 3.52 μM), underscoring the importance of selecting appropriate cells for antiviral testing. Using the optimized SARS-CoV-2-Nluc assay, we evaluated a collection of approved and investigational antivirals and other anti-infective drugs. Nelfinavir, rupintrivir, and cobicistat were identified as the most selective inhibitors of SARS-CoV-2-Nluc (EC500.77 to 2.74 μM). In contrast, most of the clinically approved antivirals, including tenofovir alafenamide, emtricitabine, sofosbuvir, ledipasvir, and velpatasvir were inactive at concentrations up to 10 μM. Collectively, this high-throughput platform represents a reliable tool for rapid neutralization testing and antiviral screening for SARS-CoV-2.
Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes
Authors: Zhou Tongqing , Teng I-Ting , Olia Adam S. , Cerutti Gabriele , Gorman Jason , Nazzari Alexandra , Shi Wei , Tsybovsky Yaroslav , Wang Lingshu , Wang Shuishu , Zhang Baoshan , Zhang Yi , Katsamba Phinikoula S. , Petrova Yuliya , Banach Bailey B. , Fahad Ahmed S. , Liu Lihong , Acevedo Sheila N. Lopez , Madan Bharat , de Souza Matheus Oliveira , Pan Xiaoli , Wang Pengfei , Wolfe Jacy R. , Yin Michael , Ho David D. , Phung Emily , DiPiazza Anthony , Chang Lauren , Abiona Olubukula , Corbett Kizzmekia S. , DeKosky Brandon J. , Graham Barney S. , Mascola John R. , Misasi John , Ruckwardt Tracy , Sullivan Nancy J. , Shapiro Lawrence , Kwong Peter D.
Published: June 2020

Biotin-labeled molecular probes, comprising specific regions of the SARS-CoV-2 spike, would be helpful in the isolation and characterization of antibodies targeting this recently emerged pathogen. To develop such probes, we designed constructs incorporating an N-terminal purification tag, a site-specific protease-cleavage site, the probe region of interest, and a C-terminal sequence targeted by biotin ligase. Probe regions included full-length spike ectodomain as well as various subregions, and we also designed mutants to eliminate recognition of the ACE2 receptor. Yields of biotin-labeled probes from transient transfection ranged from ∼0.5 mg/L for the complete ectodomain to >5 mg/L for several subregions. Probes were characterized for antigenicity and ACE2 recognition, and the structure of the spike ectodomain probe was determined by cryo-electron microscopy. We also characterized antibody-binding specificities and cell-sorting capabilities of the biotinylated probes. Altogether, structure-based design coupled to efficient purification and biotinylation processes can thus enable streamlined development of SARS-CoV-2 spike-ectodomain probes.
A whole-cortex probabilistic diffusion tractography connectome
Authors: Rosen Burke Q. , Halgren Eric
Published: June 2020

The WU-Minn Human Connectome Project (HCP) is a publicly-available dataset containing state-of-art structural, functional, and diffusion-MRI for over a thousand healthy subjects. While the planned scope of the HCP included an anatomical connectome, resting-state functional-MRI forms the bulk of the HCP’s current connectomic output. We address this by presenting a full-cortex connectome derived from probabilistic diffusion tractography and organized into the HCP-MMP1.0 atlas. Probabilistic methods and large sample sizes are preferable for whole-connectome mapping as they increase the fidelity of traced low-probability connections. We find that overall, connection strengths are lognormally distributed and decay exponentially with tract length, that connectivity reasonably matches macaque histological tracing in homologous areas, that contralateral homologs and left-lateralized language areas are hyperconnected, and that hierarchical similarity influences connectivity. We compare the diffusion-MRI connectome to existing resting-state fMRI and cortico-cortico evoked potential connectivity matrices and find that it is more similar to the latter. This work helps fulfill the promise of the HCP and will make possible comparisons between the underlying structural connectome and functional connectomes of various modalities, brain states, and clinical conditions.

Significance Statement

The tracts between cortical parcels can be estimated from diffusion MRI, but most studies concentrate on only the largest connections. Here we present an atlas, the largest and most detailed of its kind, showing connections among all cortical parcels. Connectivity is relatively enhanced between frontotemporal language areas and homologous contralateral locations. We find that connectivity decays with fiber tract distance more slowly than predicted by brain volume and that structural and stimulation-derived connectivity are more similar to each other than to resting-state functional MRI correlations. The connectome presented is publicly available and organized into a commonly used scheme for defining brain areas in order to enable ready comparison to other brain imaging datasets of various modalities.
MRBLES 2.0: High-throughput generation of chemically functionalized spectrally and magnetically-encoded hydrogel beads using a simple single-layer microfluidic device
Authors: Feng Yinnian , White Adam K. , Hein Jamin B. , Appel Eric A. , Fordyce Polly M.
Published: June 2020

Widespread adoption of bead-based multiplexed bioassays requires the ability to easily synthesize encoded microspheres and conjugate analytes of interest to their surface. Here, we present a simple method (MRBLEs 2.0) for efficient high-throughput generation of microspheres with ratiometric barcode lanthanide encoding (MRBLEs) bearing functional groups for downstream bioconjugation. Bead production in MRBLEs 2.0 relies on manual mixing of lanthanide/polymer mixtures (each of which comprises a unique spectral code) followed by droplet generation using single-layer, parallel flow-focusing devices and off-chip batch polymerization of droplets into beads. To streamline downstream analyte coupling, MRBLEs 2.0 crosslinks copolymers bearing functional groups on the bead surface simultaneously during bead generation. Using the MRBLEs 2.0 pipeline, we generate monodisperse MRBLEs containing 48 distinct well-resolved spectral codes in high-throughput (>150,000/min and can be boosted to 450,000/min). We further demonstrate the efficient conjugation of oligonucleotides and entire proteins to carboxyl MRBLEs and biotin to amino MRBLEs. Finally, we show that MRBLEs can also be magnetized via simultaneous incorporation of magnetic nanoparticles with only a minor decrease in the potential code space. We anticipate that MRBLEs 2.0 can be directly applied towards a wide variety of downstream assays from basic biology to diagnostics and other translational research.
From local resynchronization to global pattern recovery in the zebrafish segmentation clock
Authors: Uriu Koichiro , Liao Bo-Kai , Oates Andrew C. , Morelli Luis G.
Published: June 2020

Rhythmic spatial gene expression patterns termed the segmentation clock regulate vertebrate body axis segmentation during embryogenesis. The integrity of these patterns requires local synchronization between neighboring cells by Delta-Notch signaling and its inhibition results in defective segment boundaries. The oscillating tissue deforms substantially throughout development, but whether such tissue-scale morphogenesis complements local synchronization during pattern generation and segment formation is not understood. Here, we investigate pattern recovery in the zebrafish segmentation clock by washing out a Notch inhibitor, allowing resynchronization at different developmental stages, and analyzing the recovery of normal segments. Although from previous work no defects are expected after recovery, we find that washing out at early stages causes a distinctive intermingling of normal and defective segments, suggesting unexpectedly large fluctuations of synchrony before complete recovery. To investigate this recovery behavior, we develop a new model of the segmentation clock combining key ingredients motivated by prior experimental observations: coupling between neighboring oscillators, a frequency profile, a gradient of cell mixing, tissue length change, and cell advection pattern. This model captures the experimental observation of intermingled normal and defective segments through the formation of persistent phase vortices of the genetic oscillators. Experimentally observed recovery patterns at different developmental stages are predicted by temporal changes of tissue-level properties, such as tissue length and cell advection pattern in the model. These results suggest that segmental pattern recovery occurs at two scales: local pattern formation and transport of these patterns through tissue morphogenesis, highlighting a generic mechanism of pattern dynamics within developing tissues.

SIGNIFICANCE

Interacting genetic oscillators can generate a coherent rhythm and a tissue-level pattern from an initially desynchronized state. Using experiment and theory we study resynchronization and pattern recovery of the zebrafish segmentation clock, which makes the embryonic body segments. Experimental perturbation of intercellular signaling with an inhibitor results in intermingled normal and defective segments. According to theory, this behavior may be caused by persistent local vortices scattered in the tissue during pattern recovery. Full pattern recovery follows dynamic global properties, such as tissue length and advection pattern, in contrast to other genetic oscillators in a static tissue such as circadian clocks. Our work highlights how dynamics of tissue level properties may couple to biochemical pattern formation in tissues and developing embryos.
Amino Sugars Reshape Interactions betweenStreptococcus mutansandStreptococcus gordonii
Authors: Chen Lulu , Walker Alejandro R. , Burne Robert A. , Zeng Lin
Published: June 2020

Amino sugars, particularly glucosamine (GlcN) and N-acetylglucosamine (GlcNAc), are abundant carbon and nitrogen sources that are continually supplied in host secretions and in the diet to the biofilms colonizing the human oral cavity. Evidence is emerging that these amino sugars provide ecological advantages to beneficial commensals over oral pathogens and pathobionts. Here, we performed transcriptome analysis onStreptococcus mutansandStreptococcus gordoniigrowing in single-species or dual-species cultures with glucose, GlcN or GlcNAc as the primary carbohydrate source. Compared to glucose, GlcN caused drastic transcriptomic shifts in each bacterium when they were cultured alone. Likewise, co-cultivation in the presence of GlcN yielded transcriptomic profiles that were dramatically different than the single-species results from GlcN-grown cells. In contrast, GlcNAc elicited only minor changes in the transcriptome of either organism in single- and dual-species cultures. Interestingly, genes involved in pyruvate metabolism were among the most significantly affected by GlcN in both species, and these changes were consistent with measurements of pyruvate in culture supernates. Differing from a previous report, growth ofS. mutansalone with GlcN inhibited expression of multiple operons required for mutacin production. Co-cultivation withS. gordoniiconsistently increased the expression byS. mutansof two manganese transporter operons (sloandmntH) and decreased expression of mutacin genes. Conversely,S. gordoniiappeared to be less affected by the presence ofS. mutans, but did show increases in genes for biosynthetic processes in the co-cultures. In conclusion, amino sugars profoundly alter the interactions between a pathogenic and commensal streptococcus by reprogramming central metabolism.

IMPORTANCE

Carbohydrate metabolism is central to the development of dental caries. A variety of sugars available to dental microorganisms influence the development of caries by affecting the physiology, ecology, and pathogenic potential of tooth biofilms. Using two well-characterized oral bacteria, one pathogen (Streptococcus mutans) and one commensal (Streptococcus gordonii) in a RNA deep-sequencing analysis, we studied the impact of two abundant amino sugars on bacterial gene expression and interspecies interactions. The results indicated large-scale remodeling of gene expression induced by GlcN in particular, affecting bacterial energy generation, acid production, protein synthesis, and release of antimicrobial molecules. Our study provides novel insights into how amino sugars modify bacterial behavior, information that will be valuable in the design of new technologies to detect and prevent oral infectious diseases.
Epstein-Barr virus tegument protein BGLF2 in exosomes released from virus-producer cells assistsde novoinfection
Authors: Sato Yoshitaka , Yaguchi Masahiro , Okuno Yusuke , Ishimaru Hanako , Ozaki Somi , Suzuki Takeshi , Inagaki Tomoki , Umeda Miki , Watanabe Takahiro , Fujimuro Masahiro , Murata Takayuki , Kimura Hiroshi
Published: June 2020

Viruses must adapt to the environment of their host cells to establish infection and persist. Diverse mammalian cells, including virus-infected cells, secrete extracellular vesicles such as exosomes containing proteins and miRNAs, and use these vesicles to mediate intercellular communications. However, the roles of exosomes in viral infection remain unclear. Here we screened viral proteins to identify those responsible for the exosome-mediated upregulation of Epstein-Barr virus (EBV) infection. We found BGLF2 protein encapsulated in exosomes, which were released from EBV-infected cells. BGLF2 protein is a tegument protein that exists the space between the envelope and the nucleocapsid, and it is released into the cytoplasm shortly after infection. BGLF2 protein-containing exosomes enhanced viral gene expression and repressed innate immunity, thereby assisting the EBV infection. In summary, the EBV tegument protein BGLF2 is encapsulated not only encapsulated in viral particles, but also in exosomes secreted from infected cells. Therefore, BGLF2 may play a crucial role in establishing EBV latent infection.
A novelEnterococcus faecalisheme transport regulator (FhtR) is a heme sensor in the gastrointestinal tract
Authors: Saillant Vincent , Lipuma Damien , Ostyn Emeline , Joubert Laetitia , Boussac Alain , Guerin Hugo , Brandelet G. , Arnoux P. , Lechardeur Delphine
Published: June 2020

Enterococcus faecalisis a commensal Gram-positive pathogen found in the intestines of mammals, and is also a leading cause of severe infections occurring mainly among antibiotic-treated dysbiotic hospitalized patients. Like most intestinal bacteria,E. faecalisdoes not synthesize heme. Nevertheless, environmental heme can improveE. faecalisfitness by activating respiration metabolism and a catalase that limits hydrogen peroxide stress. Since free heme also generates redox toxicity, its intracellular levels need to be strictly controlled. Here, we describe a unique transcriptional regulator, FhtR, (FaecalishemetransportRegulator), which manages heme homeostasis by controlling an HrtBA-like efflux pump (named HrtBAEf). We show that FhtR, by managing intracellular heme concentration, regulates the functional expression of the heme dependent catalase A (KatA), thus participating in heme detoxification. The biochemical features of FhtR binding to DNA, and its interactions with heme that induce efflux, are characterized. The FhtR-HrtBAEfsystem is shown to be relevant in a mouse intestinal model. We further show that FhtR senses heme from blood and hemoglobin but also from crossfeeding byEscherichia coli. These findings bring to light the central role of FhtR heme sensing in response to heme fluctuations within the gastrointestinal tract, which allow this pathogen to limit heme toxicity while ensuring expression of an oxidative defense system.

Importance

Enterococcus faecalis, a normal, harmless colonizer of the human intestinal flora can cause severe infectious diseases in immunocompromised patients, particularly those that have been heavily treated with antibiotics. Therefore, it is important to understand the factors that promote its resistance and its virulence. Here, we report a new mechanism used byE. faecalisto detect the concentration of heme, an essential but toxic metabolite that is present in the intestine.E. faecalisneeds to scavenge this molecule to respire and fight stress generated by oxydants. Heme sensing triggers the synthesis of a heme efflux pump that balances the amount of heme inside the bacteria. With this mechanism,E. faecaliscan use heme without suffering from its toxicity.
Inter-session repeatability of markerless motion capture gait kinematics
Authors: Kanko Robert M. , Laende Elise , Selbie W. Scott , Deluzio Kevin J.
Published: June 2020

The clinical uptake and influence of gait analysis has been hindered by inherent flaws of marker-based motion capture systems, which have long been the standard method for the collection of gait data including kinematics. Markerless motion capture offers an alternative method for the collection of gait kinematics that presents several practical benefits over marker-based systems. This work aimed to determine the reliability of lower limb gait kinematics from video based markerless motion capture using an established experimental protocol for testing reliability. Eight healthy adult participants performed three sessions of five over-ground walking trials in their own self-selected clothing, separated by an average of 8.5 days, while eight synchronized and calibrated cameras recorded video. 3D pose estimates from the video data were used to compute lower limb joint angles. Inter-session variability, inter-trial variability, and the variability ratio were used to assess the reliability of the gait kinematics. Relative to repeatability studies based on marker-based motion capture, inter-trial variability was slightly greater than previously reported for some angles, with an average across all joint angles of 2.2°. Inter-session variability was smaller on average than previously reported, with an average across all joint angles of 2.5°. Variability ratios were all smaller than those previously reported with an average of 1.2, indicating that the multi-session protocol increased the total variability of joint angles by only 20% of the inter-trial variability. These results indicate that gait kinematics measured using markerless tracking were less affected by multi-session protocols compared to marker-based motion capture.
Defining compartmentalized stem and progenitor populations with distinct cell division frequency in the ocular surface epithelium
Authors: Ishii Ryutaro , Yanagisawa Hiromi , Sada Aiko
Published: June 2020

Adult tissues contain label-retaining cell (LRC)s, which are relatively slow-cycling and considered to represent a unique property of tissue stem cell (SC)s. In the ocular surface epithelium, LRCs are detected in the limbus, a boundary between cornea and conjunctiva, and the fornix of the conjunctiva; however, the character of LRCs and identity of SCs remain unclear due to lack of appropriate molecular markers. Here we show that the ocular surface epithelium accommodates spatially distinct stem/progenitor populations with different cell division frequency. By combining EdU pulse-chase analysis and lineage tracing with three CreER transgenic mouse lines: Slc1a3CreER, Dlx1CreERand K14CreER, we detect distinct dynamics of epithelial SCs in the cornea and conjunctiva. In the limbus, long-lived SCs are labeled with Slc1a3CreERand they either migrate centripetally toward the central cornea or laterally expand their clones within the limbal region. In the central cornea, cells are mostly non-LRCs, labeled by Dlx1CreERand K14CreER, and the number of clones declines after a short period of time with rare long-lasting clones, suggesting their properties as short-lived progenitor cells. In the conjunctival epithelium, which consists of bulbar, fornix and palpebral conjunctiva, each territory is regenerated by compartmentalized, distinct SC populations without migrating one region to another. The severe damage of the cornea leads to the cancellation of SC compartments, causing conjunctivalization of the eye, whereas milder limbal injury induces a rapid increase of laterally-expanding clones in the limbus. Taken together, our work provides lineage tracing tools of the eye and defines compartmentalized, multiple SC/progenitor populations in homeostasis and their behavioral changes in response to injury.
Monomeric amyloid β-peptide (1-42) significantly populates compact fibril-like conformations
Authors: Barz Bogdan , Buell Alexander K. , Nath Soumav
Published: June 2020

The aggregation of the amyloid β (Aβ) peptide is a major hallmark of Alzheimer’s disease. This peptide can aggregate into oligomers, proto-fibrils, and mature fibrils, which eventually assemble into amyloid plaques. The peptide monomers are the smallest assembly units, and play an important role in most of the individual processes involved in amyloid fibril formation, such as primary and secondary nucleation and elongation. The structure of the Aβ monomer has been shown to be very dynamic and mostly disordered, both in experimental and in computational studies, similar to a random coil. This structural state of the monomer contrasts with the very stable and well defined structural core of the amyloid fibrils. An important question is whether the monomer can adopt transient fibril-like conformations in solution and what role such conformations might play in the aggregation process. Here we use enhanced and extensive molecular dynamics simulations to study the Aβ42 monomer structural flexibility with different force fields, water models and salt concentrations. We show that the monomer behaves as a random coil under different simulation conditions. Importantly, we find a conformation with the N-terminal region structured very similarly to that of recent experimentally determined fibril models. This is to the best of our knowledge the first monomeric structural ensemble to show such a similarity with the fibril structure.
Molecular signaling pathways underlying schizophrenia
Authors: Tiihonen Jari , Koskuvi Marja , Lähteenvuo Markku , Trontti Kalevi , Ojansuu Ilkka , Vaurio Olli , Cannon Tyrone D. , Lönnqvist Jouko , Therman Sebastian , Suvisaari Jaana , Cheng Lesley , Tanskanen Antti , Taipale Heidi , Lehtonen Šárka , Koistinaho Jari
Published: June 2020

The molecular pathophysiological mechanisms underlying schizophrenia have remained unknown, and no treatment exists for primary prevention. Studies using stem cell-derived neurons have investigated differentially expressed genes (DEGs) and GO and KEGG pathways between patients and controls, but not analyzed data-driven causal molecular pathways involved. We used Ingenuity Pathway Analysis (IPA) to analyze canonical and causal pathways in two different datasets, including patients from Finland and USA. The most significant findings in canonical pathway analysis were observed for glutamate receptor signaling, hepatic fibrosis, and glycoprotein 6 (GP6) pathways in the Finnish dataset, and GP6 and hepatic fibrosis pathways in the US dataset. In data-driven causal pathways,ADCYAP1, ADAMTS, andCACNAgenes were involved in the majority of the top 10 pathways differentiating patients and controls in both Finnish and US datasets. In contrast, no dopamine-specific genes were consistently involved. Results from a Finnish nation-wide database showed that the risk of schizophrenia relapse was 41% lower among first-episode patients during the use of losartan, the master regulator of anADCYAP1, ADAMTS, andCACNA-related pathway, compared to those time periods when the same individual did not use the drug. This association was not attributable to general adherence to drug treatments. The results from the two independent datasets suggest that the GP6 signaling pathway, and theADCYAP1, ADAMTS, andCACNA-related purine, oxidative stress, and glutamatergic signaling pathways are primary pathophysiological alterations in schizophrenia among patients with European ancestry. While no reproducible dopaminergic alterations were observed, the results imply that agents such as losartan, and ADCYAP1/PACAP -deficit alleviators, such as metabotropic glutamate 2/3 agonist MGS0028 and 5-HT7 antagonists – which have shown beneficial effects in an experimentalAdcyap1-/-mouse model for schizophrenia – could be potential treatments before the full manifestation of illness involving dopaminergic abnormalities.
Perturbed DNA methylation by sustained overexpression of Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death in mice
Authors: Ravel-Godreuil Camille , Massiani-Beaudoin Olivia , Mailly Philippe , Prochiantz Alain , Joshi Rajiv L. , Fuchs Julia
Published: June 2020

Heterochromatin disorganization is a key hallmark of aging and DNA methylation state is currently the main molecular predictor of chronological age. The most frequent neurodegenerative diseases like Parkinson disease and Alzheimer’s disease are age-related but how the aging process and chromatin alterations are linked to neurodegeneration is unknown. Here, we investigated the consequences of viral overexpression ofGadd45b, a multifactorial protein involved in active DNA demethylation, in the midbrain of wild-type mice.Gadd45boverexpression induces global and stable changes in DNA methylation, particularly on gene bodies of genes related to neuronal functions. DNA methylation changes were accompanied by perturbed H3K9me3-marked heterochromatin and increased DNA damage. ProlongedGadd45bexpression resulted in dopaminergic neuron degeneration accompanied by altered expression of candidate genes related to heterochromatin maintenance, DNA methylation or Parkinson disease.Gadd45boverexpression rendered midbrain dopaminergic neurons more vulnerable to acute oxidative stress. Heterochromatin disorganization and DNA demethylation resulted in derepression of mostly young LINE-1 transposable elements, a potential source of DNA damage, prior toGadd45b-induced neurodegeneration. Our data implicate that alterations in DNA methylation and heterochromatin organization, LINE-1 derepression and DNA damage can represent important contributors in the pathogenic mechanisms of dopaminergic neuron degeneration with potential implications for Parkinson disease.
Hapln1borganizes the ECM to modulatekitsignaling and control developmental hematopoiesis in zebrafish
Authors: Mahony Christopher B. , Pasche Corentin , Braunersreuther Vincent , Savvides Savvas N. , de Agostini Ariane , Bertrand Julien Y.
Published: June 2020

During early vertebrate development, hematopoietic stem cells (HSCs) are produced from a hemogenic endothelium located in the dorsal aorta, before they migrate to a transient niche where they expand, the fetal liver and the caudal hematopoietic tissue (CHT), in mammals and zebrafish, respectively. In zebrafish, previous studies have shown that the extracellular matrix (ECM) around the aorta needs to be degraded to allow HSCs to leave the aortic floor and reach blood circulation. However, the role of the ECM components in HSC specification has never been addressed. We show here thathapln1b, a key component of the ECM is specifically expressed in hematopoietic sites in the zebrafish embryo. Gain- and loss-of-function experiments all resulted in the absence of HSCs in the early embryo, showing thathapln1bis required, at the correct level, to specify HSCs in the hemogenic endothelium. Furthermore, we show that the expression ofhapln1bis necessary to maintain the integrity of the ECM through its link domain. In addition, by combining functional analyses and computer modelling, we show thatkitlgbinteracts with the ECM, to specify HSCs. Overall, we have demonstrated that the ECM is an integral component of the microenvironment as it mediates specific cytokine signaling that is required for normal HSC specification.
Monoclonal anti-AMP-antibodies reveal broad and diverse AMPylation patterns in cancer cells
Authors: Höpfner Dorothea , Fauser Joel , Kaspers Marietta S. , Pett Christian , Hedberg Christian , Itzen Aymelt
Published: June 2020

AMPylation is a post-translational modification that modifies amino acid side chains with adenosine monophosphate (AMP). Recent progress in the field reveals an emerging role of AMPylation as a universal regulatory mechanism in infection and cellular homeostasis, however, generic tools to study AMPylation are required. Here, we describe three monoclonal anti-AMP antibodies (mAbs) from mouse which are capable of protein backbone independent recognition of AMPylation, in denatured (Western Blot) as well as native (ELISA, IP) applications, thereby outperforming previously reported tools. These antibodies are highly sensitive and specific for AMP modifications, highlighting their potential as tools for new target identification, as well as for validation of known targets. Interestingly, applying the anti-AMP mAbs to various cancer cell lines reveals a previously undescribed broad and diverse AMPylation pattern. In conclusion, the anti-AMP mABs will aid the advancement of understanding AMPylation and the spectrum of modified targets.
Defining the lineage of thermogenic perivascular adipose tissue
Authors: Angueira Anthony R. , Sakers Alexander P. , Cheng Lan , Shrestha Rojesh , Okada Chihiro , Batmanov Kirill , Susztak Katalin , Seale Patrick
Published: June 2020

Brown adipose tissue can expend large amounts of energy and thus increasing its amount or activity is a promising therapeutic approach to combat metabolic disease. In humans, major deposits of brown fat cells are found intimately associated with large blood vessels, corresponding to perivascular adipose tissue (PVAT). However, the cellular origins of PVAT are poorly understood. Here, we applied single cell transcriptomic analyses,ex vivoadipogenesis assays, and genetic fate mappingin vivoto determine the identity of perivascular adipocyte progenitors. We found that thoracic PVAT initially develops from a fibroblastic lineage, comprising progenitor cells (Pdgfra+;Ly6a+;Pparg−) and preadipocytes (Pdgfra+;Ly6a−;Pparg+). Progenitors and preadipocytes in PVAT shared transcriptional similarity with analogous cell types in white adipose tissue, pointing towards a conserved adipose cell lineage hierarchy. Interestingly, the aortic adventitia of adult animals contained a novel population of adipogenic smooth muscle cells (Myh11+;Pdgfra−;Pparg+) possessing the capacity to generate adipocytesin vitroandin vivo. Taken together, these studies define distinct populations of fibroblastic and smooth muscle progenitor cells for thermogenic PVAT, providing a crucial foundation for developing strategies to augment brown fat activity.
Systemic analysis of putative SARS-CoV-2 entry and processing genes in cardiovascular tissues identifies a positive correlation of BSG with age in endothelial cells
Authors: Ahmetaj-Shala Blerina , Vaja Ricky , Atanur Santosh S , George Peter M. , Kirkby Nicholas S. , Mitchell Jane A.
Published: June 2020

COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly spread throughout the world with unprecedented global healthcare and socio-economic consequences. There is now an established secondary syndrome of COVID-19 characterised by thrombosis, vascular dysfunction and hypertension, seen in those most severely affected. Advancing age in adults is the single most significant risk factor for hospitalisation and death with COVID-19. In light of the cardiovascular/thrombotic sequalae associated with severe COVID-19 disease and the overwhelming risk that increased age carries, in this study, our aim was to obtain mechanistic insight by interrogating gene expression profiles in cardiovascular tissues and cells. Our focus was on the two putative receptors for SARS-CoV-2,ACE2andBSGalong with a selected range of genes thought to be involved in virus binding/processing. In this study we have made four important observations: (i)Cardiovascular tissues and/or endothelial cells express the required genes for SARS-CoV-2 infection, (ii) SASR-CoV-2 receptor pathways,ACE2/TMPRSS2andBSG/PPIB(A) polarise to lung/epithelium and vessel/endothelium respectively, (iii) expression of SARS-CoV-2 host genes are, on the whole, relatively stable with age and (iv) notable exceptions wereACE2which decreases with age in some tissues andBSGwhich increases with age in endothelial cells. Our data support the idea that that BSG is the dominate pathway utilised by SARS-CoV-2 in endothelial cells and are the first to demonstrate a positive correlation with age. We suggest BSG expression in the vasculature is a critical driver which explains the heightened risk of severe disease and death observed in those >40 years of age. Since BSG is utilised by other pathogens our findings have implications beyond the current pandemic. Finally, because BSG is functions in a range of cardiovascular diseases and fibrosis, our observations may have relevance to our understanding of the diseases associated with aging.
Genetic Diversity and Genomic Epidemiology of SARS-COV-2 in Morocco
Authors: Badaoui Bouabid , Sadki Khalid , Talbi Chouhra , Driss Salah , Tazi Lina
Published: June 2020

COVID-A9 is an infection disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), declared as a pandemic due to its rapid expansion worldwide. In this study we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 using 22 virus genome sequences reported by three different laboratories in Morocco till the date 07/06/2020 as well as (40366) virus genomes from all around the world.

The SARS-CoV-2 genomes from Moroccan patients revealed 62 mutations of which 30 were missense mutations. The mutations Spike_D614G and NSP12_P323L were present in all the 22 analyzed sequences, followed by N_G204R and N_R203K which occurred in 9 among the 22 sequences. The mutations NSP10_R134S, NSP15_D335N, NSP16_I169L, NSP3_L431H, NSP3_P1292L and Spike_V6F occurred one time in our sequences with no record in other sequence worldwide. These mutations should be investigated to figure out their potential effects on all around the world virulence. Phylogenetic analyses revealed that Moroccan SARS-CoV-2 genomes included 9 viruses pertaining to clade 20A, 9 to clade 20B and 2 to clade 20C. This finding suggest that the epidemic spread in Morocco did not show a predominant SARS-CoV-2 route. For multiple and unrelated introductions of SARS-CoV-2 into Morocco via different routes have occurred, giving rise to the diversity of virus genomes in the country. Furthermore, very likely, the SARS-CoV-2 virus circulated in cryptic way in Morocco starting from the fifteen January before the discovering of the first case the second of March.
Identification of a novel LysR-type transcriptional regulator inStaphylococcus aureusthat is crucial for secondary tissue colonization during metastatic bloodstream infection
Authors: Groma Michaela , Horst Sarah , Das Sudip , Huettel Bruno , Klepsch Maximilian , Rudel Thomas , Medina Eva , Fraunholz Martin
Published: June 2020

Staphylococcus aureusis a common cause of bacteremia that can lead to severe complications once the bacteria exit the bloodstream and establish infection into secondary organs. Despite its clinical relevance, little is known about the bacterial factors facilitating the development of these metastatic infections. Here, we used aS. aureustransposon mutant library coupled to transposon insertion sequencing (Tn-Seq) to identify genes that are critical for efficient bacterial colonization of secondary organs in a murine model of metastatic bloodstream infection. Our transposon screen identified a LysR-type transcriptional regulator (LTTR), which was required for efficient colonization of secondary organs such as the kidneys in infected mice. The critical role of LTTR in secondary organ colonization was confirmed using an isogenic mutant deficient in the expression of LTTR. To identify the set of genes controlled by LTTR, we used aS. aureusstrain carrying the LTTR gene in an inducible expression plasmid. Gene expression analysis upon induction of LTTR showed increased transcription of genes involved in branched chain amino-acid biosynthesis, a methionine sulfoxide reductase and a copper transporter as wells as decreased transcription of genes coding for urease and components of pyrimidine nucleotides. Furthermore, we show that transcription of LTTR is repressed by glucose, induced under microaerobic conditions, and required trace amounts of copper ions. Our data thus pinpoints LTTR as an important element that enable a rapid adaptation ofS. aureusto the changing host microenvironment.
Structure of core fungal endobiome inUlmus minor: patterns within the tree and across genotypes differing in tolerance to Dutch elm disease
Authors: Macaya-Sanz David , Witzell Johanna , Collada Carmen , Gil Luis , Martin Juan Antonio
Published: June 2020

Plants harbour a diverse fungal community with complex symbiotic interactions and significant roles in host physiology. However, the cues that steer the composition and structure of this community are poorly understood. Trees are useful models for assessing these factors because their large size and long lifespan give these ecosystems time and space to evolve and mature. Investigation of well-characterised pathosystems such as Dutch elm disease (DED) can reveal links between endomycobiome and pathogens. We examined the endophytic mycobiome across the aerial part of a landmark elm tree to identify structural patterns within plant hosts, highlighting not only commonalities but also the effect of local infections in some branches of the crown. We used a common garden trial of trees with varying levels of genotypic susceptibility to DED to identify associations between susceptibility and endomycobiome. Three families of yeasts were linked to higher DED tolerance: Buckleyzymaceae, Herpotrichiellaceae and Tremellaceae. Surveying a natural population with a gradient of vitality, we found some taxa enriched in declining trees. By combining all surveys and adding a further study in a distant natural population, we found evidence of aU. minorcore mycobiome, pervasive within the tree and ubiquitous across locations, genotypes and health status.
Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses
Authors: Andreatta Massimo , Corria-Osorio Jesus , Müller Sören , Cubas Rafael , Coukos George , Carmona Santiago J.
Published: June 2020

Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary technology for characterizing the heterogeneity of cell populations. However, robust reference atlases that can be used to systematically interpret cellular states across studies and diseases are currently lacking. Here, we generated the first cross-study T cell atlases for cancer and viral infection and developed a novel algorithm, ProjecTILs, that enables the projection of new scRNA-seq data onto these reference atlases. ProjecTILs accurately predicted the effects of multiple perturbations, including the ablation of immunoregulatory targets controlling T cell differentiation, such asTox,Ptpn2,miR-155andRegnase-1, and suggested novel gene programs that were altered in these cells. Moving beyond mouse models, we used ProjecTILs to conduct a meta-analysis of human tumor-infiltrating T lymphocytes (TILs), revealing a remarkable conservation of TIL subtypes between human and mouse and across cancer types. Clonotype analysis supported a model in which rare human tumor-specific effector-memory (EM)-like CD8 TILs that resemble blood-circulating EM cells, differentiate into proliferative terminal exhausted/dysfunctional effector TILs through a progenitor subtype that upregulates the exhaustion master regulatorTOX. Our novel computational method allows exploring the effect of human and murine T cell perturbations (e.g.as the result of therapy or genetic engineering) in terms of reference cellular states, altered genetic programs and clonotype structure, revealing mechanisms of action behind immunotherapies and opening opportunities for their improvement.
Nanoparticle Tracking Analysis: A powerful tool for characterizing magnetosome preparations
Authors: Fernández-Castané Alfred , Li Hong , Joseph Stephan , Ebeler Moritz , Franzreb Matthias , Bracewell Daniel G. , Overton Tim W. , Thomas Owen R.T.
Published: June 2020

Nanoparticle Tracking Analysis (NTA) has been employed to measure the particle concentration and size distribution of magnetosomes extracted and purified fromMagnetospirillum gryphiswaldenseMSR-1, and then exposed to probe ultrasonication for various times, or 1% (w/v) sodium dodecyl sulphate (SDS) for 1 h. Particle concentration increased 3.7-fold over the first 15 min of ultrasonication (from 2 × 108to >7.3 × 108particles mL−1), but fell steeply to ~3.6 × 108particles mL−1after 20 min. NTA of untreated magnetosome preparation confirmed a wide particle distribution dominated by larger species (D[1,0] = 312 nm; Dn50= 261 nm; mode = 243 nm) with no particles in the size range of isolated single magnetosomes. After 5 min of ultrasonication the whole particle size distribution shifted to smaller size (D[1,0] = 133 nm; Dn50= 99 nm; mode = 36 nm, corresponding to individual magnetosomes), but longer treatment times (15 and 20 min) reversed the previous transition; all characteristic numbers of the particle size distributions increased and very few small particles were detected. Side-by-side comparison of NTA and TEM sizing data revealed remarkable similarity at low ultrasonication times, with both showing single magnetosomes accounted for ~30% population after 5 min. Exposure of magnetosomes to SDS resulted in a ~3-fold increase in particle concentration to 5.8 × 108particles mL−1, narrowing of the size distribution and gross elimination of particles below 60 nm. We conclude that NTA is a rapid cost-effective technique for measuring particle number, size distribution and aggregation state of magnetosomes in solution, but requires further work to improve its resolving power.