bluuebunny/crossref_metadata_2025 huggingface dataset:
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
Authors: Orchard Peter , Manickam Nandini , Varshney Arushi , Rai Vivek , Kaplan Jeremy , Lalancette Claudia , Gallagher Katherine , Burant Charles F. , Parker Stephen C.J.
Published: July 2020

Background

Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases, mobility, and quality of life. It is composed of several different cell and muscle fiber types.

Results

Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 30,531 nuclei, representing 11 libraries, profiled in this study, and identify seven distinct cell types ranging in abundance from 63% (type II fibers) to 0.9% (muscle satellite cells) of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (∼3% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, and transcription factor motifs for creatinine levels and type 2 diabetes signals.

Conclusions

These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for investigating specific cell types and nominating causal GWAS SNPs and cell types.
S-nitrosoglutathione reductase deficiency causes aberrant placental S-nitrosylation and preeclampsia
Authors: Kulandavelu Shathiyah , Dulce Raul A , Murray Christopher I , Bellio Michael A , Fritsch Julia , Kanashiro-Takeuchi Rosemeire , Arora Himanshu , Paulino Ellena , Soetkamp Daniel , Balkan Wayne , Van Eyk Jenny E , Hare Joshua M
Published: July 2020

Preeclampsia (PE), a leading cause of maternal and fetal mortality and morbidity, is characterized by an increase in S-nitrosylated (SNO) proteins and reactive oxygen species (ROS), suggesting a pathophysiologic role for dysregulation in nitrosylation and nitrosative stress. Here we show that mice lacking S-nitrosoglutathione reductase (GSNOR−/−), a denitrosylase regulating protein S-nitrosylation, exhibit a PE phenotype, including hypertension, proteinuria, renal pathology, cardiac concentric hypertrophy, decreased placental vascularization, and fetal growth retardation. ROS, nitric oxide (NO) and peroxynitrite levels are elevated. Importantly, mass spectrometry reveals elevated placental SNO-amino acid residues inGSNOR−/−mice. Ascorbate reverses the phenotype except for fetal weight, reduces the difference in the S-nitrosoproteome, and identifies a unique set of SNO-proteins inGSNOR−/−mice. Therefore, deficiency of GSNOR creates dysregulation of placental S-nitrosylation and preeclampsia in mice, which can be rescued by ascorbate. These findings offer valuable insights and therapeutic implications for PE.

Abstract Figure

Graphical Abstract:

Dysregulation in nitrosylation contributes to nitroso-redox imbalance and nitrosative stress contributing to clinical features of PE including hypertension, proteinuria, concentric hypertrophy in the heart, decrease placental vascularization and fetal growth restriction. Antioxidant treatment rescued the PE-like phenotype in the mother.
6-Thioguanine blocks SARS-CoV-2 replication by inhibition of PLpro protease activities
Authors: Swaim Caleb D. , Perng Yi-Chieh , Zhao Xu , Canadeo Larissa A. , Harastani Houda H. , Darling Tamarand L. , Boon Adrianus C. M. , Lenschow Deborah J. , Huibregtse Jon M.
Published: July 2020

A recently emerged betacoronavirus, SARS-CoV-2, has led to a global health crisis that calls for the identification of effective therapeutics for COVID-19 disease. Coronavirus papain-like protease (PLpro) is an attractive drug target as it is essential for viral polyprotein cleavage and for deconjugation of ISG15, an antiviral ubiquitin-like protein. We show here that 6-Thioguanine (6-TG) inhibits SARS-CoV-2 PLpro-catalyzed viral polyprotein cleavage and ISG15 deconjugation in cells and inhibits replication of SARS-CoV-2 in Vero-E6 cells and Calu3 cells at submicromolar levels. As a well-characterized FDA-approved orally delivered drug, 6-TG represents a promising therapeutic for COVID-19 and other emerging coronaviruses.

One Sentence Summary

A repurposed drug that targets an essential enzymatic activity of SARS-CoV-2 represents a promising COVID-19 therapeutic.
RanDeL-seq: A high-throughput method to map viral cis- and trans-acting elements
Authors: Notton Timothy , Glazier Joshua J. , Saykally Victoria R. , Thompson Cassandra E. , Weinberger Leor S.
Published: July 2020

It has long been known that noncoding genomic regions can be obligateciselements acted uponin transby gene products. In viruses,ciselements regulate gene expression, encapsidation, and other maturation processes but mapping these elements relies on targeted iterative deletion or laborious prospecting for rare, spontaneously occurring mutants. Here, we introduce a method to comprehensively map viralcisandtranselements at single-nucleotide resolution by high-throughput random deletion. Variable-size deletions are randomly generated by transposon integration, excision, and exonuclease chewback, and then barcoded for tracking via sequencing (i.e.,Random-DeletionLibrarysequencing, RanDeL-seq). Using RanDeL-seq, we generated and screened >23,000 HIV-1 variants to generate a single-base resolution map of HIV-1’scisandtranselements. The resulting landscape recapitulated HIV-1’s knowncis-acting elements (i.e., LTR, Ψ, and RRE) and surprisingly indicated that HIV-1’s central DNA flap (i.e., central polypurine tract, cPPT to central termination sequence, CTS) is as critical as the LTR, Ψ, and RRE for long-term passage. Strikingly, RanDeL-seq identified a previously unreported ∼300bp region downstream of RRE extending to splice acceptor 7 that is equally critical for sustained viral passage. RanDeL-seq was also used to construct and screen a library of >90,000 variants of Zika virus (ZIKV). Unexpectedly, RanDeL-seq indicated that ZIKV’scis-acting regions are larger than the UTR termini, encompassing a large fraction of the non-structural genes. Collectively, RanDeL-seq provides a versatile framework for generating viral deletion mutants enabling discovery of replication mechanisms and development of novel antiviral therapeutics, particularly for emerging viral infections.

Importance

Recent studies have renewed interest in developing novel antiviral therapeutics and vaccines based on defective interfering particles (DIPs)—a subset of viral deletion mutant that conditionally replicate. Identifying and engineering DIPs requires that viralcis- andtrans-acting elements be accurately mapped. Here we introduce a high-throughput method (Random Deletion Library sequencing, RanDeL-seq) to comprehensively mapcis-andtrans-acting elements within a viral genome. RanDeL-seq identified essential cis elements in HIV, including the obligate nature of the once-controversial viral central poly-purine tract (cPPT) and identified a newcisregion proximal to the Rev responsive element (RRE). RanDeL-seq also identified regions of Zika virus required for replication and packaging. RanDeL-seq is a versatile and comprehensive technique to rapidly map cis and trans regions of a genome.
A model of population dynamics with complex household structure and mobility: implications for transmission and control of communicable diseases
Authors: Chisholm Rebecca H. , Crammond Bradley , Wu Yue , Bowen Asha C. , Campbell Patricia T. , Tong Steven Y. C. , McVernon Jodie , Geard Nicholas
Published: July 2020

Households are known to be high-risk locations for the transmission of communicable diseases. Numerous modelling studies have demonstrated the important role of households in sustaining both communicable diseases outbreaks and endemic transmission, and as the focus for control efforts. However, these studies typically assume that households are associated with a single dwelling and have static membership. This assumption does not appropriately reflect households in some populations, such as those in remote Australian Indigenous communities, which can be distributed across more than one physical dwelling, leading to the occupancy of individual dwellings changing rapidly over time. In this study, we developed an individual-based model of an infectious disease outbreak in communities with demographic and household structure reflective of a remote Australian Indigenous community. We used the model to compare the dynamics of unmitigated outbreaks, and outbreaks constrained by a household-focused prophylaxis intervention, in communities exhibiting fluid versus stable dwelling occupancy. Our findings suggest that fluid dwelling occupancy can lead to larger and faster outbreaks, interfere with the effectiveness of household-focused interventions, and may contribute to the considerable burden of communicable diseases in communities exhibiting this type of structure.
Macro-scale models for fluid flow in tumour tissues: impact of microstructure properties
Authors: Vaghi Cristina , Fanciullino Raphaelle , Benzekry Sebastien , Poignard Clair
Published: July 2020

Understanding the dynamics underlying fluid transport in tumour tissues is of fundamental importance to assess processes of drug delivery. Here, we analyse the impact of the tumour microscopic properties on the macroscopic dynamics of vascular and interstitial fluid flow by using formal asymptotic techniques.

Here, we obtained different macroscopic continuum models that couple vascular and interstitial flows. The homogenization technique allows us to derive two macroscale tissue models of fluid flow that take into account the microscopic structure of the vessels and the interstitial tissue. Different regimes were derived according to the magnitude of the vessel wall permeability and the interstitial hydraulic conductivity. Importantly, we provide an analysis of the properties of the models and show the link between them. Numerical simulations were eventually performed to test the models and to investigate the impact of the microstructure on the fluid transport.

Future applications of our models include their calibration with real imaging data to investigate the impact of the tumour microenvironment on drug delivery.
PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation
Authors: Aluru Neelakanteswar , Karchner Sibel I
Published: July 2020

Chemical modifications of proteins, DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs isN6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3’ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 hours starting from 72 hours post-fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (FDR 5%), respectively. The majority of the peaks were preferentially located around the 3’UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (e.g.,ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, foxi1). These results suggest thatenvironmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
A commercial autogenous injection vaccine protects ballan wrasse (Labrus bergylta, Ascanius) againstAeromonas salmonicida vapAtype V
Authors: Ramirez-Paredes J. Gustavo , Verner-Jeffreys D. , Papadopoulou A. , Monaghan S. J , Smith L. , Haydon D. , Wallis T. S. , Davie A. , Adams A. , Migaud H.
Published: July 2020

AtypicalAeromonas salmonicida(aAs) andVibrionaceaerelated species are bacteria routinely recovered from diseased ballan wrasse used as cleaner fish in Atlantic salmon farming. Autogenous multivalent vaccines formulated from these microorganisms are widely used by the industry to protect farmed wrasse despite limited experimental proof that they are primary pathogens. In this study, the components of a commercial multivalent injection wrasse vaccine were tested for infectivity, pathogenicity and virulence via intra peritoneal injection at pre-deployment size (25-50g) and the efficacy of the vaccine for protection against aAsassessed. Injection with 3.5×109, 8×1091.8×109and 5×109cfu/fish ofVibrio splendidus,V. ichthyoenteri,Aliivibrio logeiiandA. salmonicida, respectively, did not cause significant mortalities, lesions or clinical signs after a period of 14 days. IP injection with both aAsandPhotobacterium indicumsuccessfully reproduced the clinical signs and internal lesions observed during natural outbreaks of the disease. Differences in virulence (LD50at day 8-post infection of 3.6×106cfu/fish and 1.6×107cfu/fish) were observed for two aAs vapAtype V isolates. In addition, the LD50forPhotobacterium indicumwas 2.2×107cfu/fish. The autogenous vaccine was highly protective against the two aAs vapAtype V isolates after 700-degree days of immunisation. The RPSFINALvalues for the first isolate were 95 and 91% at 1×106cfu/fish and 1×107cfu/fish, respectively, and 79% at 1×107cfu/fish for the second isolate tested. In addition, significantly higher anti aAsseral antibodies (IgM), were detected by ELISA in vaccinated fish in contrast with control (mock vaccinated) fish. These results suggest wrasse can be effectively immunised and protected against aAsinfection by injection with oil adjuvanted vaccines prepared with inactivated homologous isolates. Further work should assess the efficacy of vaccination against other isolates that have proven to be pathogenic such as aAstype VI andPhotobacterium indicumand explore the feasibility of immersion vaccination. In addition, a full characterisation of aAsisolates within the samevapAtypes should be performed as differences in virulence betweenvapAtype V isolates were observed and partial genome analysis indicated small but potentially important genomic differences in these isolates.
Embryonic origin and serial homology of gill arches and paired fins in the skate (Leucoraja erinacea)
Authors: Sleight Victoria A. , Gillis J. Andrew
Published: July 2020

Paired fins are a defining feature of the jawed vertebrate body plan, but their evolutionary origin remains unresolved. Gegenbaur proposed that paired fins evolved as gill arch serial homologues, but this hypothesis is now widely discounted, owing largely to the presumed distinct embryonic origins of these structures from mesoderm and neural crest, respectively. Here, we use cell lineage tracing to test the embryonic origin of the pharyngeal and paired fin skeleton in the skate (Leucoraja erinacea). We find that while the jaw and hyoid arch skeleton derive from neural crest, and the pectoral fin skeleton from mesoderm, the gill arches are of dual origin, receiving contributions from both germ layers. We propose that gill arches and paired fins are serially homologous as derivatives of a continuous, dual-origin mesenchyme with common skeletogenic competence, and that this serial homology accounts for their parallel anatomical organization and shared responses to axial patterning signals.
Effects of prophylactic and therapeutic antimicrobial uses in small-scale chicken flocks
Authors: Van Cuong Nguyen , Kiet Bach Tuan , Phu Doan Hoang , Bich Van Nguyen Thi , Hien Vo Be , Thwaites Guy , Carrique-Mas Juan , Choisy Marc
Published: July 2020

Synopsis

Background

Antimicrobials are extensively used both prophylactically and therapeutically in poultry production. Despite this, there are little data on the effect of antimicrobial use (AMU) on disease incidence and mortality rate.

Objective

We investigated the relationships between AMU and disease and between AMU and mortality using data from a large (n=322 flocks) cohort of small-scale chicken flocks in the Mekong Delta, Vietnam, that were followed longitudinally from day-old to slaughter (5,566 observation weeks).

Methods

We developed a parameterized algorithm to categorize the observation weeks into ‘non-AMU’, ‘prophylactic AMU’ and ‘therapeutic AMU’. To evaluate the prophylactic AMU effect, we compared the frequencies of clinical signs in ‘non-AMU’ and ‘prophylactic AMU’ periods. To analyse therapeutic AMU, we compared mortality rates between the weeks of disease episodes before and after AMU. Analyses were stratified by clinical signs (4) and antimicrobial classes (13).

Results

Prophylactic AMU never reduced the probability of disease, some antimicrobial classes such as lincosamides, amphenicols and penicillins increased the risk. The risk of diarrhoea consistently increased with prophylactic AMU. Therapeutic AMU often had an effect on mortality but the pattern was inconsistent across the combinations of antimicrobial classes and clinical signs with 14/29 decreasing and 11/29 increasing the mortality rate. Lincosamides, methenamines and cephalosporins were the only three antimicrobial classes that always decreased the mortality rate when used therapeutically. Results were robust respective to the parameters values of the weeks categorization algorithm.

Conclusion

This information should help support policy efforts and interventions aiming at reducing AMU in animal production.
Increasing network stability towards large food webs
Authors: Veres Robert , László Zoltán
Published: July 2020

Stability is a key attribute of complex food webs that has been for a long time in the focus of studies. It remained an intriguing question how large and complex food webs are persisting if smaller and simple ones tend to be more stable at least from a mathematic perspective. Presuming that with the increasing size of food webs their stability also grows, we analyzed the relationship between number of nodes in food webs and their stability based on 450 food webs ranging from a few to 200 nodes. Our results show that stability increases non-linearly with food web size based both on return times after disturbance and on robustness calculated from secondary extinction rates of higher trophic levels. As a methodologic novelty we accounted for food web generation time in the return time calculation process. Our results contribute to the explanation of large and complex food web persistence: in spite of the fact that with increasing species number the stability of food webs decreases at small node numbers, there is a constant stability increase over a large interval of increasing food web size. Therefore, in food web stability studies, we stress the use of food web generation times.
Antimicrobial peptides signal need for sleep from peripheral wounds to the nervous system
Authors: Sinner Marina , Masurat Florentin , Ewbank Jonathan , Pujol Nathalie , Bringmann Henrik
Published: July 2020

Wounding triggers a protective innate immune response that includes the production of antimicrobial peptides and increased sleep. Little is known, however, about how peripheral wounds signal need for sleep to the nervous system. We found that duringC. eleganslarval molting, a tolloid/BMP-1-like protein promotes sleep through an epidermal innate immune pathway and the expression of more than a dozen antimicrobial peptide (AMP) genes. In the adult, epidermal injury activates innate immunity and turns up AMP production to trigger sleep. We show for one AMP, NLP-29, that it acts through the neuropeptide receptor NPR-12 in neurons that depolarize the sleep-active RIS neuron to induce sleep. Sleep in turn increases the chance of surviving injury. Thus, we found a novel mechanism by which peripheral wounds signal to the nervous system to increase protective sleep. Such a long-range somnogen signaling function of AMPs might also boost sleep in other animals including humans.

Highlights

- Gain-of-function mutation in the tolloid/BMP-1-like NAS-38 protein increases sleep

- NAS-38 activates innate immunity pathways to ramp up STAT-dependent antimicrobial peptide (AMP) expression

- Wounding increases sleep through the innate immune response and AMPs

- Antimicrobial peptides are long-range somnogens that act through neuronal neuropeptide receptors to depolarize a sleep-active neuron

- Sleep increases the chance to survive injury

Graphical Abstract
How to account for the uncertainty from standard toxicity tests in species sensitivity distributions: an example in non-target plants
Authors: Charles Sandrine , Wu Dan , Ducrot Virginie
Published: July 2020

This research aims to account for the uncertainty on 50% effective rates (ER50) in species sensitivity distribution (SSD) analyses and to study how including this uncertainty may influence the 5% Hazard Rate (HR5) estimation. We explored various endpoints (survival, emergence, shoot dry weight) for non-target plants from seven standard greenhouse studies that used different experimental approaches (vegetative vigour vs. seedling emergence) and applied seven herbicides at different growth stages. Firstly for each endpoint of each study, a three-parameter log-logistic model was fitted to experimental toxicity test data for each species under a Bayesian framework to get a posterior probability distribution for ER50. Then in order to account for the uncertainty on the ER50, we explored two censoring criteria to censor ER50taking the ER50distribution and the range of tested rates into account. Based on dose-response fitting results and censoring criteria, we considered input ER50values SSD analyses in three ways (only point estimates chosen as ER50medians, interval-censored ER50based on their 95% credible interval and censored ER50according to one of the two criteria), by fitting a log-normal distribution under a frequentist framework to get the three corresponding HR5estimates. We observed that SSD fitted reasonably well when there were at least six distinct ER50values. By comparing the three SSD curves and the three HR5estimates, we found that propagating the uncertainty from ER50and including censored data into the SSD analysis often leads to smaller point estimates of HR5, which is more conservative in a risk assessment context. In addition, we recommend not to focus solely on the point estimate of the HR5, but also to look at the precision of this estimate as depicted by the 95% confidence interval.
More than just a ticket canceller: The mitochondrial processing peptidase matures complex precursor proteins at internal cleavage sites
Authors: Friedl Jana , Knopp Michael R. , Groh Carina , Paz Eyal , Gould Sven B. , Boos Felix , Herrmann Johannes M.
Published: July 2020

Most mitochondrial proteins are synthesized in the cytosol as precursors that carry N-terminal presequences. After import into mitochondria, these targeting signals are cleaved off by the mitochondrial processing peptidase MPP, giving rise to shorter mature proteins. Using the mitochondrial tandem protein Arg5,6 as a model substrate, we demonstrate that MPP has an additional role in preprotein maturation, beyond the removal of presequences. Arg5,6 is synthesized as a polyprotein precursor that is imported into the mitochondrial matrix and subsequently separated into two distinct enzymes that function in arginine biogenesis. This internal processing is performed by MPP, which cleaves the Arg5,6 precursor both at its N-terminus and at an internal site between the Arg5 and Arg6 parts. The peculiar organization and biogenesis of Arg5,6 is conserved across fungi and might preserve the mode of co-translational subunit association of the arginine biosynthesis complex of the polycistronic arginine operon in prokaryotic mitochondrial ancestors. Putative MPP cleavage sites are also present at the junctions in other mitochondrial fusion proteins from fungi, plants and animals. Our data suggest that, in addition to its role as “ticket canceller” for the removal of presequences, MPP exhibits a second, widely conserved activity as internal processing peptidase for complex mitochondrial precursor proteins.
Molecular architecture of the developing mouse brain
Authors: La Manno Gioele , Siletti Kimberly , Furlan Alessandro , Gyllborg Daniel , Vinsland Elin , Langseth Christoffer Mattsson , Khven Irina , Johnsson Anna , Nilsson Mats , Lönnerberg Peter , Linnarsson Sten
Published: July 2020

The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions, and intrinsic genetic programs that result in the generation of likely more than a thousand distinct cell types. Therefore, a complete understanding of mammalian brain development requires systematic mapping of cell states covering the entire relevant spatiotemporal range. Here we report a comprehensive single-cell transcriptome atlas of mouse brain development spanning from gastrulation to birth. We identified almost a thousand distinct cellular states, including the initial emergence of the neuroepithelium, a rich set of region-specific secondary organizers and a complete developmental program for the functional elements of the brain and its enclosing membranes. We used the atlas to directly test the hypothesis that human glioblastoma reflects a return to a developmental cell state. In agreement, most aneuploid tumor cells matched embryonic rather than adult types, while karyotypically normal cells predominantly matched adult immune cell types.
Interleukin-3 is a predictive marker for severity and outcome during SARS-CoV-2 infections
Authors: Bénard Alan , Jacobsen Anne , Brunner Maximilian , Krautz Christian , Klösch Bettina , Swierzy Izabela , Naschberger Elisabeth , Birkholz Torsten , Castellanos Ixchel , Trufa Denis , Sirbu Horia , Vetter Marcel , Kremer Andreas E. , Hildner Kai , Hecker Andreas , Edinger Fabian , Tenbusch Matthias , Richter Enrico , Streeck Hendrik , Berger Marc M. , Brenner Thorsten , Weigand Markus A. , Swirski Filip K. , Schett Georg , Grützmann Robert , Weber Georg F.
Published: July 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a worldwide health threat. Here, we report that low plasma interleukin-3 (IL-3) levels were associated with increased severity and mortality during SARS-CoV-2 infections. IL-3 promoted the recruitment of antiviral circulating plasmacytoid dendritic cells (pDCs) into the airways by stimulating CXCL12 secretion from pulmonary CD123+epithelial cells. This study identifies IL-3 as a predictive disease marker and potential therapeutic target for SARS-CoV-2 infections.
Preparatory Suppression and Facilitation of Voluntary and Involuntary Responses to Loud Acoustic Stimuli in an Anticipatory Timing Task
Authors: Nguyen An T. , Tresilian James R. , Lipp Ottmar V. , Jacobs Le-Anne , Marinovic Welber
Published: July 2020

In this study, we sought to characterise the effects of intense sensory stimulation at different stages of preparation for an anticipated action on voluntary and involuntary behaviours. In our experiment, we presented unexpected loud acoustic stimuli (LAS) at four critical times during movement preparation to probe the state of the nervous system (Baseline, −1192 ms, −392 ms, and 0 ms relative to expected movement onset), and measured their effect on voluntary and involuntary motor actions (finger-press and eye-blink startle reflex, respectively).

Voluntary responses were largely facilitated by the LAS, leading to earlier and more forceful responses compared to Control and Baseline conditions. Notably, voluntary responses were significantly facilitated on trials where the LAS was presented early during preparation (−1192 ms). Eye-blink reflexes elicited by the LAS at −392 ms were significantly reduced and delayed compared to other time-points, indicating suppression of sub-cortical excitability. Despite being in a suppressive state, voluntary responses on these trials were still facilitated by the LAS.

The results provide insight into the mechanisms involved in preparing anticipatory actions. Induced activation can persist in the nervous system and can modulate subsequent actions for a longer time period than previously thought, highlighting that movement preparation is a continuously evolving process that is susceptible to external influence throughout the preparation period. Suppression of sub-cortical excitability shortly before movement onset is consistent with previous work showing corticospinal suppression which may be a necessary step before the execution of any voluntary response.
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
Authors: Riediger Matthias , Spät Philipp , Bilger Raphael , Voigt Karsten , Maček Boris , Hess Wolfgang R.
Published: July 2020

Regulatory sRNAs in photosynthetic cyanobacteria have been reported, but the lack of plausible RNA chaperones involved in this regulation appears enigmatic. Here, we analyzed the full ensemble of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) inSynechocystis6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished supporting a high quality of the approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include a YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. TheSynechocystisGrad-seq resource is available online athttps://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/, providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism.

One-sentence summary

We provide the first global analysis of a cyanobacterium using Grad-seq, providing a comprehensive resource for the in-depth analysis of the complexome in a photosynthetic organism.
Effects of practice on a mechanical horse with an online feedback on performing a sitting postural coordination
Authors: Baillet Héloïse , Leroy David , Vérin Eric , Delpouve Claire , Boulanger Jérémie , Benguigui Nicolas , Komar John , Thouvarecq Régis
Published: July 2020

The present research aims at quantifying the impact of practicing a new coordination pattern with an online visual feedback on the postural coordination performed on a mechanical horse. Forty-four voluntary participants were recruited in this study. They were randomly assigned to four practice groups based on i) with or without feedback (i.e., group 1, control, did not receive the feedback; group 2, 3 and 4 received an online feedback during practice) and ii) the specific trunk/horse coordination to target during practice (group 1, target coordination = 180° (without feedback); group 2, target coordination = 0°; group 3, target coordination = 90°; group 4, target coordination = 180°). All participants performed pre-, practice, post- and retention sessions. The pre-, post- and retention sessions consisted of four trials, with one trial corresponding to one specific target coordination to maintain between their own oscillations and the horse oscillations (spontaneous, 0°, 90°, and 180°). The practice phase was composed of three different sessions during which participants received an online feedback about the coordination between their own oscillations and the horse oscillations.

Results showed a significant change with practice in the trunk/horse coordination patterns which persisted even after one month (retention-test). However, all the groups did not show the same nature of change, evidenced by a high postural variability during post-test for 0° and 90° target coordination groups, in opposition to the 180° and spontaneous groups who showed a decrease in coordination variability for the 180° group. The coordination in anti-phase was characterized as spontaneously adopted by participants on the mechanical horse, explaining the ease of performing this coordination (compared to the 0° and 90° target coordination). The effect of online visual feedback appeared not only on the coordination pattern itself, but most importantly on its variability during practice, including concerning initially stable coordination patterns.
3 versus 7 Tesla Magnetic Resonance Imaging for parcellations of subcortical brain structures
Authors: Isaacs Bethany R , Mulder Martijn J , Groot Josephine M , van Berendonk Nikita , Lute Nicky , Bazin Pierre-Louis , Forstmann Birte U , Alkemade Anneke
Published: July 2020

7 Tesla (7T) magnetic resonance imaging holds great promise for improved visualization of the human brain for clinical purposes. To assess whether 7T is superior regarding localization procedures of small brain structures, we compared manual parcellations of the red nucleus, subthalamic nucleus, substantia nigra, globus pallidus interna and externa, created on a commonly used clinical anisotropic clinical 3T with an optimized isotropic (o)3T and standard 7T scan. While the clinical 3T MRI scan did not allow delineation of an anatomical plausible structure due to its limited spatial resolution, optimized 3T and 7T parcellations could be directly compared. We found that 7T outperformed theo3T MRI as reflected by higher Dice scores, which were used as a measurement of interrater agreement for manual parcellations on quantitative susceptibility maps. This increase in agreement was associated with higher contrast to noise ratios for smaller structures, but not for the larger globus pallidus segments. Additionally, control-analyses were performed to account for potential biases in manual parcellations by assessing semi-automatic parcellations. These results did not confirm increased Dice scores for 7T, although they revealed a higher consistency for structure volumes for 7T compared to optimized 3T, potentially indicative of more agreement with increased field strength. Together these results indicate the importance of the use of isotropic voxels with both 3T and 7T, and the potential for clinical applications.
Moistube™ Irrigation (MTI) Discharge Under Variable Evaporative Demand
Authors: Dirwai Tinashe Lindel , Senzanje Aidan. , Mabhaudhi Tafadzwanashe.
Published: July 2020

We investigated the conceptual capability of Moistube irrigation to discharge under zero applied positive pressure under varied climatic conditions by inducing an artificial evaporative demand (Ed) or negative pressure around moistube tubing. This was premised on the null hypothesis that an artificially inducedEdor negative pressure does not impact moistube discharge. Moistube tubing was enclosed in a 1 m long PVC conduit. A 20 l water reservoir placed on an electronic balance provided a continuous supply of water whilst a three-speed hot air blower facilitated the radiative factor and advection process. The procedure was conducted under varied climatic conditions of air velocities (ua) 1.2 m.s−1, 2.5 m.s−1, and 3.0 m.s−1and the experiment run times were 159 h, 134 h and 10 h, respectively. The average temperature (Tave) and relative humidity (RH) data forua= 1.2 m.s−1were 53°C and 7.31%, whilst forua= 2.5 m.s−1,Tavewas 56°C and RH = 7.19%, and forua= 3.0 m.s−1,Tavewas 63°C and RH = 6.16%. The experimental data was input into the four variable Penman-Monteith method to compute the evaporative demand (Ed). For each of the air velocities, the respectiveEdvalues obtained were 0.16, 0.31 and 0.36 mm.d−1. The Bowen ratios (r) were well below 1 (r< 1), which suggested a sufficient supply of moisture to evaporate. ForEd= 0.16 mm.d−1the vapour pressure deficit (VPD) was 113.08 mbars, whilst forEd= 0.31 mm.d−1and forEd= 0.36 mm.d−1the VPD were 129.93 mbars and 150.14 mbars, respectively. The recorded discharges (q) att= 10 hrs forEd= 0.16 mm.d−1was 7.67*10−3l.hr−1.m−1, whilst forEd= 0.31 mm.d−1q= 14.5*10−3l.hr−1.m−1, and forEd= 0.36 mm.d−1q= 20.8*10−3l.hr−1.m−1. The imposed negative pressure causes an exponential increase in moistube discharge, thus disproving the null hypothesis. The higher the evaporative demand the higher the discharge. This phenomenon allows moistube irrigation to be used for deficit irrigation purposes and allows irrigators to capitalize on realistic soil matric potential irrigation scheduling approach.
The gut microbiome influences host diet selection behavior
Authors: Trevelline Brian K. , Kohl Kevin D.
Published: July 2020

Diet selection is a fundamental aspect of animal behavior with numerous ecological and evolutionary implications. While the underlying mechanisms are complex, the availability of essential dietary nutrients can strongly influence diet selection behavior. The gut microbiome has been shown to metabolize many of these same nutrients, leading to the untested hypothesis that intestinal microbiota may influence diet selection. Here we show that germ-free mice colonized by gut microbiota from three rodent species with distinct foraging strategies differentially selected diets that varied in macronutrient composition. Specifically, we found that herbivore-conventionalized mice voluntarily selected a higher protein:carbohydrate ratio diet, while omnivore- and carnivore-conventionalized mice selected a lower P:C ratio diet. In support of the long-standing hypothesis that tryptophan – the essential amino acid precursor of serotonin – serves as a peripheral signal regulating diet selection, bacterial genes involved in tryptophan metabolism and plasma tryptophan availability prior to the selection trial were significantly correlated with subsequent voluntary carbohydrate intake. Finally, herbivore-conventionalized mice exhibited larger intestinal compartments associated with microbial fermentation, broadly reflecting the intestinal morphology of their donor species. Together, these results demonstrate that gut microbiome can influence host diet selection behavior, perhaps by mediating the availability of essential amino acids, thereby revealing a novel mechanism by which the gut microbiota can influence host foraging behavior.

SIGNIFICANCE

The behavior of diet choice or diet selection can have wide-reaching implications, scaling from individual animals to ecological and evolutionary processes. Previous work in this area has largely ignored the potential for intestinal microbiota to modulate these signals. This notion has been highly speculated for years but has not yet been explicitly tested. Here we show that germ-free mice colonized by differential microbiomes (from wild rodents with varying natural feeding strategies) exhibited significant differences in their voluntary dietary selection. Specifically, differences in voluntary carbohydrate selection were associated with plasma amino acid levels and bacterial genes involved in the metabolism of tryptophan. Together, these results demonstrate a role for the microbiome in host nutritional physiology and behavior.
Image-based pooled whole genome CRISPR screening for Parkin and TFEB subcellular localization
Authors: Kanfer Gil , Sarraf Shireen A. , Maman Yaakov , Baldwin Heather , Johnson Kory R. , Ward Michael E. , Kampmann Martin , Lippincott-Schwartz Jennifer , Youle Richard J.
Published: July 2020

Genome-wide CRISPR screens have transformed our ability to systematically interrogate human gene function, but are currently limited to a subset of cellular phenotypes. We report a novel pooled screening approach for a wider range of cellular and subtle subcellular phenotypes. Machine learning and convolutional neural network models are trained on the subcellular phenotype to be queried. Genome-wide screening then utilizes cells stably expressing dCas9 (CRISPRi), photoactivatable fluorescent protein (PA-mCherry), and a lentiviral guide RNA (gRNA) pool. Cells are screened by microscopy and classified by artificial intelligence (AI) algorithms, which precisely identify the genetically altered phenotype. Cells with the phenotype of interest are photoactivated, isolated via flow cytometry, and the gRNAs are identified by sequencing. A proof-of-concept screen accurately identified PINK1 as essential for Parkin recruitment to mitochondria. A genome-wide screen identified factors mediating TFEB relocation from the nucleus to the cytosol upon prolonged starvation. Twenty of the sixty-four hits called by the neural network model were independently validated, revealing new effectors of TFEB subcellular localization. This approach, AI-Photoswitchable Screening (AI-PS) offers a novel screening platform capable of classifying a broad range of mammalian subcellular morphologies, an approach largely unattainable with current methodologies at genome-wide scale.
A clinically-relevant polymorphism in the Na+/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position
Authors: Ruggiero Melissa J. , Malhotra Shipra , Fenton Aron W. , Swint-Kruse Liskin , Karanicolas John , Hagenbuch Bruno
Published: July 2020

Conventionally, most amino acid substitutions at important protein positions are expected to abolish function. However, in several soluble-globular proteins, we identified a class of non-conserved positions for which various substitutions produced progressive functional changes; we consider these evolutionary “rheostats”. Here, we report a strong rheostat position in the integral membrane protein, Na+/taurocholate cotransporting polypeptide (NTCP), at the site of a pharmacologically-relevant polymorphism (S267F). Functional studies were performed for all 20 substitutions (“S267X”) with three substrates (taurocholate, estrone-3-sulfate and rosuvastatin). The S267X set showed strong rheostatic effects on overall transport, and individual substitutions showed varied effects on transport kinetics (Kmand Vmax). However, the outcomes were substrate dependent, indicating altered specificity. To assess protein stability, we measured surface expression and used the Rosetta software suite to model structure and stability changes of S267X. Although buried near the substrate binding site, S267X substitutions were easily accommodated in the NTCP structure model. Across the modest range of changes, calculated stabilities correlated with surface-expression differences, but neither parameter correlated with altered transport. Thus, substitutions at rheostat position 267 had wide-ranging effects on the phenotype of this integral membrane protein. We further propose that polymorphic positions in other proteins might be locations of rheostat positions.
Evolution of sex hormone binding globulins reveals early gene duplication at the root of vertebrates
Authors: Guiguen Yann , Pasquier Jeremy , Fostier Alexis , Bobe Julien
Published: July 2020

Sex hormone-binding globulin (Shbg) is an important vertebrate blood carrier protein synthetized in the liver and involved in the transport and local regulation of sex steroids in target tissues. A novelshbg gene (shbgb)with a predominant ovarian expression was recently characterized. Being initially found only in salmonids, thisshbgbwas originally thought to result from the Salmonid-specific whole genome duplication. Using updated transcriptomic and genomic resources we identifiedShbgborthologs in non-salmonid teleosts (European eel, arowana), holosteans (spotted gar, bowfin), polypteriformes (reedfish), agnatha (sea lamprey) and in amphibians, and found that the classicalShbggene (Shbga) displays a predominant hepatic expression whereasShbgbhas a predominant gonadal expression. Together, these results indicate that these twoShgbgenes most likely originate from a whole genome duplication event at the root of vertebrate evolution, followed by numerous and independent losses and by tissue expression specialization ofShbgaandShbgbparalogs.

Highlights

Phylogeny, synteny and expression analyses shed new light on Shbg evolution in vertebrates.

Shbg diversity originates from a duplication event at the root of vertebrate evolution.

This duplication was followed by many independent losses ofShbgparalogs in vertebrates.

Shbgparalogs have acquired different tissue expression patterns.
Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission
Authors: Sapoval Nicolae , Mahmoud Medhat , Jochum Michael D. , Liu Yunxi , Leo Elworth R. A. , Wang Qi , Albin Dreycey , Ogilvie Huw , Lee Michael D. , Villapol Sonia , Hernandez Kyle M. , Berry Irina Maljkovic , Foox Jonathan , Beheshti Afshin , Ternus Krista , Aagaard Kjersti M. , Posada David , Mason Christopher E. , Sedlazeck Fritz , Treangen Todd J.
Published: July 2020

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.