bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling photosystem I as a complex interacting network
Authors: Montepietra D. , Bellingeri M. , Ross A. M. , Scotognella F. , Cassi D.
Published: November 2020

In this paper, we model the excitation energy transfer (EET) of photosystem I (PSI) of the common pea plant
Pisum sativum
as a complex interacting network. The magnitude of the link energy transfer between nodes/chromophores is computed by Forster resonant energy transfer (FRET) using the pairwise physical distances between chromophores from the PDB 5L8R (Protein Data Bank). We measure the global PSI network EET efficiency adopting well-known network theory indicators: the network efficiency (Eff) and the largest connected component (LCC). We also account the number of connected nodes/chromophores to P700 (CN), a new ad hoc measure we introduce here to indicate how many nodes in the network can actually transfer energy to the P700 reaction centre. We find that when progressively removing the weak links of lower EET, the Eff decreases, while the EET paths integrity (LCC and CN) is still preserved. This finding would show that the PSI is a resilient system owning a large window of functioning feasibility and it is completely impaired only when removing most of the network links. From the study of different types of chromophore, we propose different primary functions within the PSI system: chlorophyll
a
(CLA) molecules are the central nodes in the EET process, while other chromophore types have different primary functions. Furthermore, we perform nodes removal simulations to understand how the nodes/chromophores malfunctioning may affect PSI functioning. We discover that the removal of the CLA triggers the fastest decrease in the Eff, confirming that CAL is the main contributors to the high EET efficiency. Our outcomes open new perspectives of research, such comparing the PSI energy transfer efficiency of different natural and agricultural plant species and investigating the light-harvesting mechanisms of artificial photosynthesis both in plant agriculture and in the field of solar energy applications.
Interaction interface in the C-terminal parts of centriole proteins Sas6 and Ana2
Authors: Fatalska Agnieszka , Dzhindzhev Nikola S. , Dadlez Michal , Glover David M.
Published: November 2020

The centriole is a ninefold symmetrical structure found at the core of centrosomes and, as a basal body, at the base of cilia, whose conserved duplication is regulated by Plk4 kinase. Plk4 phosphorylates a single serine residue at the N-terminus of Ana2 to promote Ana2's loading to the site of procentriole formation. Four conserved serines in Ana2's STAN motif are then phosphorylated by Plk4, enabling Sas6 recruitment. Crystallographic data indicate that the coiled–coil domain of Ana2 forms a tetramer but the structure of full-length Ana2 has not been solved. Here, we have employed hydrogen–deuterium exchange coupled with mass spectrometry (HDX-MS) to uncover the conformational dynamics of Ana2, revealing the high flexibility of this protein with one rigid region. To determine the elusive nature of the interaction surfaces between Ana2 and Sas6, we have confirmed complex formation between the phosphomimetic form of Ana2 (Ana2-4D) and Sas6in vitroandin vivo. Analysis of this complex by HDX-MS identifies short critical regions required for this interaction, which lie in the C-terminal parts of both proteins. Mutational studies confirmed the relevance of these regions for the Ana2–Sas6 interaction. The Sas6 site required for Ana2 binding is distinct from the site required for Sas6 to bind Gorab and Sas6 is able to bind both these protein partners simultaneously.
Are post-error adjustments influenced by beliefs in free will? A failure to replicate Rigoni, Wilquin, Brass and Burle, 2013
Authors: Eben Charlotte , Chen Zhang , Cracco Emiel , Brass Marcel , Billieux Joël , Verbruggen Frederick
Published: November 2020

In this pre-registered study, we tried to replicate the study by Rigoni
et al.
2013
Cognition
127
, 264–269. In the original study, the authors manipulated the participants’ belief in free will in a between-subject design and subsequently measured post-error slowing (i.e. slower responses after an incorrect trial compared with a correct trial) as a marker of cognitive control. They found less post-error slowing in the group with reduced belief in free will (anti-free will group) compared with a control group in which belief in free will was not manipulated. In the present study, we used the same task procedure and the same free will manipulation (Crick text) in an attempt to replicate these findings. However, we used an online procedure and a larger sample size in order to address concerns about statistical power. Similar to the original study, we also used a questionnaire to measure beliefs in free will as an independent manipulation check. We found a difference in the scores on the questionnaire, thus a reduced belief in free will, after reading the Crick text. However, we did not find any difference in post-error slowing between the anti-free will and control groups. Our findings are in line with several other recent findings suggesting that the Crick text manipulation affects the participants’ self-reported belief in free will but not their behaviour. The present study can be considered a high-powered failed replication attempt.
The accelerating anuran: evolution of locomotor performance in cane toads (Rhinella marina, Bufonidae) at an invasion front
Authors: Hudson Cameron M. , Vidal-García Marta , Murray Trevor G. , Shine Richard
Published: November 2020

As is common in biological invasions, the rate at which cane toads (Rhinella marina) have spread across tropical Australia has accelerated through time. Individuals at the invasion front travel further than range-core conspecifics and exhibit distinctive morphologies that may facilitate rapid dispersal. However, the links between these morphological changes and locomotor performance have not been clearly documented. We used raceway trials and high-speed videography to document locomotor traits (e.g. hop distances, heights, velocities, and angles of take-off and landing) of toads from range-core and invasion-front populations. Locomotor performance varied geographically, and this variation in performance was linked to morphological features that have evolved during the toads' Australian invasion. Geographical variation in morphology and locomotor ability was evident not only in wild-caught animals, but also in individuals that had been raised under standardized conditions in captivity. Our data thus support the hypothesis that the cane toad's invasion across Australia has generated rapid evolutionary shifts in dispersal-relevant performance traits, and that these differences in performance are linked to concurrent shifts in morphological traits.
Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli
Authors: Pandey Anish , Humbert Maria Victoria , Jackson Alexandra , Passey Jade L. , Hampson David J. , Cleary David W. , La Ragione Roberto M. , Christodoulides Myron
Published: November 2020

The enteric, pathogenic spirochaete

Brachyspira pilosicoli

colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus

Brachyspira

. Our study revealed that an additional isolate that was unable to be species typed against any other

Brachyspira

lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the

B. pilosicoli

as random mutation (r/m=1.02). Comparative genomics has informed

Brachyspira

diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.
In Vitro Efficacy of “Essential Iodine Drops” Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2)
Authors: Zoltán Köntös
Published: November 2020

Background

Aerosolization of respiratory droplets is considered the main route of coronavirus disease 2019 (COVID-19). Therefore, reducing the viral load of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) shed via respiratory droplets is potentially an ideal strategy to prevent the spread of the pandemic. Thein vitrovirucidal activity of intranasal Povidone-Iodine (PVP-I) has been demonstrated recently to reduce SARS-CoV-2 viral titres. This study evaluated the virucidal activity of the aqueous solution of Iodine-V (a clathrate complex formed by elemental iodine and fulvic acid) as in Essential Iodine Drops (EID) with 200 μg elemental iodine/ml content against SARS-CoV-2 to ascertain whether it is a better alternative to PVP-I.

Methods

SARS-CoV-2 (USAWA1/2020 strain) virus stock was prepared by infecting Vero 76 cells (ATCC CRL-1587) until cytopathic effect (CPE). The virucidal activity of EID against SARS-CoV-2 was tested in three dilutions (1:1; 2:1 and 3:1) in triplicates by incubating at room temperature (22 ± 2°C) for either 60 or 90 seconds. The surviving viruses from each sample were quantified by a standard end-point dilution assay.

Results

EID (200 μg iodine/ml) after exposure for 60 and 90 seconds was compared to controls. In both cases, the viral titre was reduced by 99% (LRV 2.0). The 1:1 dilution of EID with virus reduced SARS-CoV-2 virus from 31,623 cell culture infectious dose 50% (CCCID50) to 316 CCID50within 90 seconds.

Conclusion

Substantial reductions in LRV by Iodine-V in EID confirmed the activity of EID against SARS-CoV-2 in vitro, demonstrating that Iodine-V in EID is effective at inactivating the virusin vitroand therefore suggesting its potential application intranasally to reduce SARS-CoV-2 transmission from known or suspected COVID-19 patients.
The hydroalcoholic extract ofUncaria tomentosa(Cat’s claw) inhibits the replication of novel coronavirus (SARS-CoV-2)in vitro
Authors: Yepes-Perez Andres F. , Herrera-Calderón Oscar , Flórez-Álvarez Lizdany , Zapata-Cardona María I. , Yepes Lina , Aguilar Wbeimar , Rugeles María T. , Zapata Wildeman
Published: November 2020

The coronavirus disease 2019 (COVID-19) has become a serious problem for public health since it was identified in the province of Wuhan (China) and spread around the world producing high mortality rates and economic losses. Nowadays, WHO recognizes traditional, complementary, and alternative medicine for treating COVID-19 symptoms. Therefore, we investigated the antiviral potential of the hydroalcoholic extract ofUncaria tomentosastem bark from Peru against SARS-CoV-2in vitro. The antiviral activity ofU. tomentosaagainst SARS-CoV-2in vitrowas assessed in Vero E6 cells using cytopathic effect (CPE) and plaque reduction assay. After 48h of treatment,U. tomentosashowed an inhibition of 92.7 % of SARS-CoV-2 at 25.0 µg/mL (p<0.0001) by plaque reduction assay on Vero E6 cells. In addition,U. tomentosa, induced a reduction of 98.6 % (p=0.02) and 92.7 % (p=0.03) in the CPE caused by SARS-CoV-2 on Vero E6 cells at 25 µg/mL and 12.5 µg/mL, respectively. The EC50calculated forU. tomentosaextract by plaque reduction assay was 6.6 µg/mL (4.89 – 8.85 µg/mL) for a selectivity index of 4.1. The EC50calculated forU. tomentosaextract by TCID50assay was 2.57 µg/mL (1.05 – 3.75 µg/mL) for a selectivity index of 10.54. These results showed thatU. tomentosaknown as Cat’s claw has antiviral effect against SARS-CoV-2 observed as a reduction in the viral titer and CPE after 48h of treatment on Vero E6 cells. Therefore, we hypothesized thatU. tomentosastem bark, could be promissory to the development of new therapeutic strategies against SARS-CoV-2.
Automatic fruit morphology phenome and genetic analysis: An application in the octoploid strawberry
Authors: Zingaretti L.M. , Monfort A. , Pérez-Enciso M.
Published: November 2020

Automatizing phenotype measurement is needed to increase plant breeding efficiency. Morphological traits are relevant in many fruit breeding programs, as appearance influences consumer preference. Often, these traits are manually or semi-automatically obtained. Yet, fruit morphology evaluation can be boosted by resorting to fully automatized procedures and digital images provide a cost-effective opportunity for this purpose. Here, we present an automatized pipeline for comprehensive phenomic and genetic analysis of morphology traits extracted from internal and external strawberry images. The pipeline segments, classifies and labels the images, extracts conformation features, including linear (area, perimeter, height, width, circularity, shape descriptor, ratio between height and width) and multivariate (Fourier Elliptical components and Generalized Procrustes) statistics. Internal color patterns are obtained using an autoencoder to smooth out the image. In addition, we develop a variational autoencoder to automatically detect the most likely number of underlying shapes. Bayesian modeling is employed to estimate both additive and dominant effects for all traits. As expected, conformational traits are clearly heritable. Interestingly, dominance variance is higher than the additive component for most of the traits. Overall, we show that fruit shape and color can be quickly and automatically evaluated and is moderately heritable. Although we study the strawberry species, the algorithm can be applied to other fruits, as shown in the GitHub repositoryhttps://github.com/lauzingaretti/DeepAFS.
Environmental vulnerability of the global ocean plankton community interactome
Authors: Chaffron S. , Delage E. , Budinich M. , Vintache D. , Henry N. , Nef C. , Ardyna M. , Zayed A.A. , Junger P.C. , Galand P.E. , Lovejoy C. , Murray A. , Sarmento H. ,   Tara Oceans coordinators, Acinas S. , Babin M. , Iudicone D. , Jaillon O. , Karsenti E. , Wincker P. , Karp-Boss L. , Sullivan M.B. , Bowler C. , de Vargas C. , Eveillard D.
Published: November 2020

Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles, and help regulate climate. Though global surveys are starting to reveal ecological drivers underlying planktonic community structure, and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here we leveragedTaraOceans sampling to infer a global ocean cross-domain plankton co-occurrence network –the community interactome– and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar), and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change, and forecasted most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios, while identifying plausible plankton bioindicators for ocean monitoring of climate change.
BABEL enables cross-modality translation between multi-omic profiles at single-cell resolution
Authors: Wu Kevin E. , Yost Kathryn E. , Chang Howard Y. , Zou James
Published: November 2020

Simultaneous profiling of multi-omic modalities within a single cell is a grand challenge for single-cell biology. While there have been impressive technical innovations demonstrating feasibility – for example generating paired measurements of scRNA-seq and scATAC-seq – wide-spread application of joint profiling is challenging due to the experimental complexity, noise, and cost. Here we introduce BABEL, a deep learning method that translates between the transcriptome and chromatin profiles of a single cell. Leveraging a novel interoperable neural network model, BABEL can generate scRNA-seq directly from a cell’s scATAC-seq, and vice versa. This makes it possible to computationally synthesize paired multi-omic measurements when only one modality is experimentally available. Across several paired scRNA-seq and scATAC-seq datasets in human and mouse, we validate that BABEL accurately translates between these modalities for individual cells. BABEL also generalizes well to new biological contexts not seen during training. For example, starting from scATAC-seq of patient derived basal cell carcinoma (BCC), BABEL generated scRNA-seq that enabled fine-grained classification of complex cell states, despite having never seen BCC data. These predictions are comparable to analyses of the experimental BCC scRNA-seq data. We further show that BABEL can incorporate additional single-cell data modalities, such as CITE-seq, thus enabling translation across chromatin, RNA, and protein. BABEL offers a powerful approach for data exploration and hypothesis generation.
Label-free lymphocytes reconstitution using side scatter for optimal T cell manufacturing
Authors: Wu Tongjin , Luah Yen Hoon , Luo Yongqiang , Womersley Howard John , Cheow Lih Feng
Published: November 2020

Lymphocyte biology research commonly involves purification of lymphocyte subpopulations by fluorescence-activated cell sorting (FACS) or immunomagnetic separation (IMS), both of which typically rely on antibody labeling of validated cell markers. Methods enabling label-free segregation of lymphocyte subpopulations would be invaluable with regard to less-perturbation, simplicity and cost-effectiveness. Here, we introduce TRuST, a label-free approach forTcellreconstitutionusingside-scatter (SSC). TRuST-sorted SSClowcells enrich for CD4+T and naïve T cells, while SSChighcells enrich for CD8+T, NK and differentiated T cells. Enrichment purity can be improved by computational gate design. SSClowcells have superior expansion capacity and generate more central memory precursors with naïve-resembling cytokine responses. Moreover, we find that both T cell differentiation status and CD4/CD8 T ratio in the starting cellular material are critical attributes predicting T cell product quality and quantity. TRuST presents an effective and reliable technique for label-free lymphocytes selection and reconstitution.
A longitudinal study of E. coli lineages and antimicrobial resistance in Ecuadorian children
Authors: Calderón Diana , Cárdenas Paúl A. , Graham Jay , Trueba Gabriel
Published: November 2020

The gastrointestinal tract (GIT) constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterized species in the gut ecosystem. Nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. Many intestinal E. coli lineages carry antimicrobial resistance and virulence genes, which have implications in disease and public health. In this one-year prospective study, a fresh fecal sample was obtained from 30 children longitudinally for one year (n = 82 fecal samples). From each stool sample, five Escherichia coli colonies were randomly selected to characterize their genotype and phenotypic antimicrobial resistance pattern (n = 405 E. coli isolates). We found that the most numerically dominant E. coli lineages in children’s intestines were transient colonizers, and phenotypic antimicrobial resistance varied significantly over time, however, ST131 a multi-drug resistant pathogen, and 3 additional STs persisted in a child’s intestine for 3 months or more.

IMPORTANCE

The length of residency and numeric dominance of antimicrobial-resistant E. coli may affect the extent to which an isolate contributes to the dissemination of antimicrobial resistance. We studied the persistence of numerically dominant and antimicrobial-resistant lineages of E. coli in the human intestine and found that E. coli lineages in the gut of children change rapidly over time.
Streptococcus suisinduces expression of cyclooxygenase-2 in porcine lung tissue
Authors: Dresen Muriel , Schenk Josephine , Berhanu Weldearegay Yenehiwot , Vötsch Désirée , Baumgärtner Wolfgang , Valentin-Weigand Peter , Nerlich Andreas
Published: November 2020

Streptococcus suisis a common pathogen colonising the respiratory tract of pigs. It can cause meningitis, sepsis and pneumonia leading to economic losses in the pig industry worldwide. Cyclooxygenase-2 (COX-2) and its metabolites play an important regulatory role in different biological processes like modulation of inflammation and immune activation. In this report we analysed the induction of COX-2 and the production of its metabolite prostaglandin E2(PGE2) in a porcine precision-cut lung slice (PCLS) model. Using Western blot analysis, we found a time-dependent induction of COX-2 in the infected tissue resulting in increased PGE2levels. Immunohistological analysis revealed a strong COX-2 expression in the proximity of the bronchioles between the ciliated epithelial cells and the adjacent alveolar tissue. The morphology, location and vimentin staining suggested that these cells are subepithelial bronchial fibroblasts. Furthermore, we showed that COX-2 expression as well as PGE2production was detected following infection with two prevalentS. suisserotypes and that the pore-forming toxin suilysin played an important role in this process. Therefore, this study provides new insights in the response of porcine lung cells toS. suisinfections and serves as a basis for further studies to define the role of COX-2 and its metabolites in the inflammatory response in porcine lung tissue during infection withS. suis.
Multi-omics Analysis of Dsup Expressing Human Cells Reveals Open Chromatin Architectural Dynamics Underyling Radioprotection
Authors: Westover Craig , Najjar Deena , Meydan Cem , Grigorev Kirill , Veling Mike T. , Chang Roger L , Chin Christopher , Butler Daniel , Afshin Evan E. , Silver Pamela A , Mason Christopher E.
Published: November 2020

Spaceflight has been documented to produce detrimental effects to physiology and genomic stability, partly a result of Galactic Cosmic Radiation (GCR). In recent years, extensive research into extremotolerant organisms has begun to reveal how they survive harsh conditions, such as ionizing radiation. One such organism is the tardigrade (Ramazzottius varieornatus) which can survive up to 5kGy of ionizing radiation and the vacuum of space. In addition to their extensive network of DNA damage response mechanisms, the tardigrade also possesses a unique damage suppressor protein (Dsup) that co-localizes with chromatin in both tardigrade and transduced human cells to protect against DNA damage from reactive oxygen species induced by ionizing radiation. While Dsup has been shown to confer human cells with increased radiotolerance; much of the mechanism of how it does this in the context of human cells remains unknown. Until now there is no knowledge yet of how introduction of Dsup into human cells can perturb molecular networks and if there are any systemic risks associated with foreign gene introduction. Here, we created a stable HEK293 cell line expressing Dsup, validated its radioprotective phenotype, and performed multi-omic analyses across different time points and doses of radiation to delineate molecular mechanism of the radioprotection and assess molecular network pertubations. Dsup expressing human cells showed an enrichment for pathways seen in cells overexpressing HMGN1, a chromosomal architectural protein that has a highly similar nucleosome binding motif. As HMGN1 binding to nucleosomes promotes a less transcriptionally repressed chromatin state, we further explored the hypothesis that Dsup could behave similarly via ATAC-seq analysis and discovered overall selective differential opening and closing of the chromatin landscape. Cut&Run analysis further revealed global increases in histone post translational modifications indicative of open chromatin and global decreases in repressive marks, with Dsup binding preferentially towards promoter regions marked by H3K27ac and H3K4me3. We further validated some of the enriched pathways via in-vitro assays and revealed novel phenotypes that Dsup confers to human cells such as reduction in apoptosis, increased cell proliferation, and increased cell adhesion properties. Our analysis provides evidence that the Dsup protein in the context of HEK293 cells may behave as a chromatin architectural protein and that in addition to its nucleosome shielding effect, may confer radio-resistance via chromatin modulation. These results provide future insight into mitigating some of the major challenges involved with long term spaceflight as well as understanding some of the molecular architectural underpinnings that lead to radioresistant cancer phenotypes back home.
Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2
Authors: Gultom Mitra , Licheri Matthias , Laloli Laura , Wider Manon , Strässle Marina , Steiner Silvio , Kratzel Annika , Thao Tran Thi Nhu , Stalder Hanspeter , Portmann Jasmine , Holwerda Melle , V’kovski Philip , Ebert Nadine , Stokar – Regenscheit Nadine , Gurtner Corinne , Zanolari Patrik , Posthaus Horst , Schuller Simone , Vicente – Santos Amanda , Moreira – Soto Andres , Corrales – Aguilar Eugenia , Ruggli Nicolas , Tekes Gergely , von Messling Veronika , Sawatsky Bevan , Thiel Volker , Dijkman Ronald
Published: November 2020

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally, and the number of cases continues to rise all over the world. Besides humans, the zoonotic origin, as well as intermediate and potential spillback host reservoirs of SARS-CoV-2 are unknown. To circumvent ethical and experimental constraints, and more importantly, to reduce and refine animal experimentation, we employed our airway epithelial cell (AEC) culture repository composed of various domesticated and wildlife animal species to assess their susceptibility to SARS-CoV-2. In this study, we inoculated well-differentiated animal AEC cultures of monkey, cat, ferret, dog, rabbit, pig, cattle, goat, llama, camel, and two neotropical bat species with SARS-CoV-2. We observed that SARS-CoV-2 only replicated efficiently in monkey and cat AEC culture models. Whole-genome sequencing of progeny virus revealed no obvious signs of nucleotide transitions required for SARS-CoV-2 to productively infect monkey and cat epithelial airway cells. Our findings, together with the previously reported human-to-animal spillover events warrants close surveillance to understand the potential role of cats, monkeys, and closely related species as spillback reservoirs for SARS-CoV-2.
Elevation of Gut-Derived p-Cresol During Spaceflight and its Effect on Drug Metabolism and Performance in Astronauts
Authors: Schmidt Michael A. , Meydan Cem , Schmidt Caleb M. , Afshinnekoo Ebrahim , Mason Christopher E.
Published: November 2020

Metabolites produced by enteric microbes may have important effects on astronauts on long-duration missions. The NASA Twins Study provided the most comprehensive multi-scale omics data to date from which to extract molecular features of potential clinical significance to spaceflight. From the multivariate data, we identified an elevation of the uremic toxinp-cresol, which is produced by gut microbial fermentation of dietary tyrosine.p-Cresol has adverse metabolic effects via depletion of the hepatic sulfur pool, which impacts metabolism of drugs, endogenous metabolites, and xenobiotics. Moreover,p-cresol reshapes gut microbial community structure by facilitating survival of species such as clostridia and inhibition of butyrate producers. Spaceflight may also impact the genes responsible for the metabolism ofp-cresol (e.g. SULT) and for the safe metabolism of common drugs used in space, such as acetaminophen (e.g. SULT, CYP4502E1, GST). Understandingp-cresol production and its related molecular networks in astronauts may lead to precision medicine advances that enhance astronaut safety and performance on long-duration missions.
Packed Like Sardines– How Surface Crowdedness Impacts Accessibility to Peptidoglycan ofStaphylococcus aureus
Authors: Ferraro Noel J. , Pires Marcos M.
Published: November 2020

Bacterial cell walls are essential barriers that protect bacteria against the onslaught of potentially lethal molecules from the outside. Small molecule therapeutics, proteins from bacterial foes, and host immune proteins must navigate past a dense layer of bacterial biomacromolecules (e.g., capsular proteins, teichoic acids, and anchored proteins) to reach the peptidoglycan (PG) layer of Gram-positive bacteria. A subclass of molecules (e.g., antibiotics with intracellular targets) must also permeate through the PG (in a molecular sieving manner) to reach the cytoplasmic membrane. In the case ofStaphylococcus aureus(S. aureus), teichoic acids are the major biopolymers that decorate bacterial cell surfaces. Despite the biological and therapeutic importance of surface accessibility, systematic analyses in live bacterial cells have been lacking. We describe a novel live cell fluorescence assay that reports on the permeability of molecules to and within the PG scaffold. The assay has robust reproducibility, is readily adoptable to any Gram-positive organism, and is compatible with high-throughput sample processing. Analysis of the factors controlling permeability toS. aureusand the methicillin resistant MRSA revealed that molecular flexibility plays a central role in molecular permeability. Moreover, teichoic acids impeded permeability of molecules of a wide range of sizes and chemical composition.
Benchmarking DNA isolation kits used in analyses of the urinary microbiome
Authors: Karstens Lisa , Siddiqui Nazema Y. , Zaza Tamara , Barstad Alecsander , Amundsen Cindy L. , Sysoeva Tatyana A.
Published: November 2020

The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples but non-significant differences in the number of reads recovered, alpha, or beta diversity. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. The Promega kit recovered fewer Gram positive bacteria compared to other kits. The Promega and DNeasy PowerSoil kits also appear to have some important biases towards over-representing certain Gram negative bacteria of biologic relevance within the urinary microbiome.
Coexpression reveals conserved mechanisms of transcriptional cell identity
Authors: Crow Megan , Suresh Hamsini , Lee John , Gillis Jesse
Published: November 2020

What makes a mouse a mouse, and not a hamster? The answer lies in the genome, and more specifically, in differences in gene regulation between the two organisms: where and when each gene is expressed. To quantify differences, a typical study will either compare functional genomics data from homologous tissues, limiting the approach to closely related species; or compare gene repertoires, limiting the resolution of the analysis to gross correlations between phenotypes and gene family size. As an alternative, gene coexpression networks provide a basis for studying the evolution of gene regulation without these constraints. By incorporating data from hundreds of independent experiments, meta-analytic coexpression networks reflect the convergent output of species-specific transcriptional regulation.

In this work, we develop a measure of regulatory evolution based on gene coexpression. Comparing data from 14 species, we quantify the conservation of coexpression patterns 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-specificity. Strikingly, we uncover deeply conserved patterns of gradient-like expression across cell types from both the animal and plant kingdoms. These results suggest that ancient genes contribute to transcriptional cell identity through mechanisms that are independent of duplication and divergence.
Cerebellar Contribution to Absence Epilepsy
Authors: Godlevsky Leonid S. , Pinyazhko Oleh R. , Poshyvak Olesya B.
Published: November 2020

The new aggregate data analyses revealed the earlier missing role played by the cerebellum long-term electrical stimulation in the absence epilepsy. Neurophysiologic data gained by authors favor that cerebellar serial deep brain stimulation (DBS) (100 Hz) causes the transformation of penicillin-induced cortical focal discharges into prolonged 3,5-3,75 sec oscillations resembling spike-wave discharges (SWD) in cats. Such SWDs were not organized in the form of bursts and persisted continuously after stimulation. Therefore the appearance of prolonged periods of SWD is regarded as a tonic cerebellar influence upon pacemaker of SWD and might be caused by the long-lasting DBS-induced increase of GABA-ergic extrasynaptic inhibition in forebrain networks. At the same time, cerebellar DBS high-frequency (100 Hz) suppressed bursts of SWD observed during the phase of stimulation. Different types of cerebellar DBS upon epileptic activity emphasized the absence seizure facilitation discussed with the reviewed data on optogenetic stimulation, neuronal activity of cerebellar structures, and functional magnetic resonance imaging data.
Comparison of three air samplers for the collection of four nebulized respiratory viruses
Authors: Kutter Jasmin S , de Meulder Dennis , Bestebroer Theo M , Mulders Ard , Fouchier Ron AM , Herfst Sander
Published: November 2020

Viral respiratory tract infections are a leading cause of morbidity and mortality worldwide. Unfortunately, the transmission routes and shedding kinetics of respiratory viruses remain poorly understood. Air sampling techniques to quantify infectious viruses in the air are indispensable to improve intervention strategies to control and prevent spreading of respiratory viruses. Here, the collection of infectious virus with the six-stage Andersen cascade impactor was optimized with semi-solid gelatin as collection surface. Subsequently, the collection efficiency of the cascade impactor, the SKC BioSampler, and an in-house developed electrostatic precipitator was compared. In an in-vitro setup, influenza A virus, human metapneumovirus, parainfluenza virus type 3 and respiratory syncytial virus were nebulized and the amount of collected infectious virus and viral RNA was quantified with each air sampler. Whereas only low amounts of virus were collected using the electrostatic precipitator, high amounts were collected with the BioSampler and cascade impactor. The BioSampler allowed straight-forward sampling in liquid medium, whereas the more laborious cascade impactor allowed size fractionation of virus-containing particles. Depending on the research question, either the BioSampler or the cascade impactor can be applied in laboratory and field settings, such as hospitals to gain more insight into the transmission routes of respiratory viruses.

Practical Implications

Respiratory viruses pose a continuous health threat, especially to vulnerable groups such as young children, immunocompromised individuals and the elderly. It is important to understand via which routes these viruses can transmit to and between individuals that are at risk. If we can determine the amount of a certain respiratory virus in the air, then this will help to predict the importance of transmission through the air for this virus. Most currently available air sampling devices have not been designed to collect infectious viruses from the air. Therefore, we here optimized and compared the performance of three air samplers for four different respiratory viruses.
Strong influence of vertebrate host phylogeny on gut archaeal diversity
Authors: Youngblut Nicholas D. , Reischer Georg H. , Dauser Silke , Walzer Chris , Stalder Gabrielle , Farnleitner Andreas H. , Ley Ruth E.
Published: November 2020

Commonly used 16S rRNA gene primers miss much of the archaeal diversity present in the vertebrate gut, leaving open the question of which archaea are host associated, the specificities of such associations, and the major factors influencing archaeal diversity. We applied 16S rRNA amplicon sequencing with Archaea-targeting primers to a dataset of 311 fecal/gut samples spanning 5 taxonomic classes (Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii) and obtained from mainly wild individuals (76% were wild). We obtained sufficient archaeal sequence data from 185 samples comprising 110 species that span all 5 classes. We provide evidence for novel Archaea-host associations, including Bathyarchaeia and Methanothermobacter — the latter of which was prevalent among Aves and enriched in higher body temperatures. Host phylogeny more strongly explained archaeal diversity than diet, while specific taxa were associated with each factor. Co-phylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last command ancestors of mammals and all host species. Archaea-Bacteria interactions seem to have a limited effect on archaeal diversity. These findings substantially expand on the paradigm of Archaea-vertebrate associations and the factors that explain those associations.

Significance

Archaea play key roles in the vertebrate gut such as promoting bacterial fermentation via consumption of waste products. Moreover, gut-inhabiting methanogenic Archaea in livestock are a substantial source of greenhouse gas production. Still, much is not known of the archaeal diversity in most vertebrates, especially since 16S rRNA sequence surveys often miss much of the archaeal diversity that is present. By applying Archaea-targeted gut microbiome sequencing to a large collection of diverse vertebrates, we reveal new Archaea-host associations such as a high prevalence of Methanothermobacter in birds. We also show that host evolutionary history explains archaeal diversity better than diet, and certain genera in one particular class of Archaea (Methanobacteria) were likely pervasive in the ancestral vertebrate gut.
Mixed-stock analysis in the age of genomics: Rapture genotyping enables evaluation of stock-specific exploitation in a freshwater fish population with weak genetic structure
Authors: Euclide Peter T. , MacDougall Tom , Robinson Jason M. , Faust Matthew D. , Wilson Chris C. , Chen Kuan-Yu , Marschall Elizabeth A. , Larson Wesley , Ludsin Stuart A.
Published: November 2020

Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple spawning stocks that are weakly differentiated. Freshwater fisheries exemplify this problem, with many harvested populations supported by multiple stocks of young evolutionary age that are isolated across small spatial scales. As a result, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing now offer the ability to discriminate among populations with weak population structure by providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We demonstrate the use of genomic data to conduct a mixed-stock analysis of Lake Erie’s commercial and recreational walleye (Sander vitreus) fisheries and estimate the relative harvest of weakly differentiated stocks (pairwiseFST< 0.01). We used RAD-capture (Rapture) to sequence and genotype individuals at 12,081 loci that had been previously determined to be capable of discriminating between western and eastern basin stocks with 95% reassignment accuracy, which was not possible in the past with microsatellite markers. Genetic assignment of 1,075 fish harvested from recreational and commercial fisheries in the eastern basin indicated that western basin stocks constituted the majority of individuals harvested during peak walleye fishing season (July – September). Composition of harvest changed seasonally, with eastern basin fish comprising much of the early season harvest (May – June). Clear spatial structure in harvest composition existed; more easterly sites contained more individuals of east basin origin than did westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the power of genomic data to facilitate mixed-stock analysis in exploited fish populations with weak population structure or limited existing genetic resources.
Alcohol use and cardiometabolic risk in the UK Biobank: a Mendelian randomization study
Authors: Lankester Joanna , Zanetti Daniela , Ingelsson Erik , Assimes Themistocles L.
Published: November 2020

Observational studies suggest alcohol use promotes the development of some adverse cardiometabolic traits but protects against others including outcomes related to coronary artery disease. We used Mendelian randomization to explore causal relationships between the degree of alcohol consumption and several cardiometabolic traits in the UK Biobank. We found carriers of theADH1BArg47His variant (rs1229984) reported a 26% lower amount of alcohol consumption compared to non-carriers. In our one-sample, two-stage least squares analyses of the UK Biobank using rs1229984 as an instrument, one additional drink/day was associated with statistically significant elevated level of systolic blood pressure (3.0 mmHg), body mass index (0.87 kg/m^2), waist circumference (1.3 cm), body fat percentage (1.7%), low-density lipoprotein levels in blood (0.16 mmol/L), and the risk of myocardial infarction (OR=1.50), stroke (OR=1.52), any cardiovascular disease (OR=1.43), and all-cause mortality (OR=1.41). Conversely, increasing use of alcohol was associated with reduced levels of triglycerides (−0.059 mmol/L) and HbA1C (−0.42 mmol/mol) in the blood, the latter possibly a consequence of a statistically elevated mean corpuscular volume amongADH1BArg47His carriers. Stratifications by sex and smoking revealed a pattern of more harm of alcohol use among men compared to women, but no consistent difference by smoking status. Men had an increased risk of heart failure (OR = 1.76), atrial fibrillation (OR = 1.35), and type 2 diabetes (OR = 1.31) per additional drink/day. Using summary statistics from external datasets in 2-sample analyses for replication, we found causal associations between alcohol and obesity, stroke, ischemic stroke, and type 2 diabetes. Our results are consistent with an overall harmful effect of alcohol on cardiometabolic health at all levels of use and suggest that even moderate alcohol use should not be promoted as a part of a healthy diet and lifestyle.
SARS-CoV-2 infection causes transient olfactory dysfunction in mice
Authors: Ye Qing , Zhou Jia , Yang Guan , Li Rui-Ting , He Qi , Zhang Yao , Wu Shu-Jia , Chen Qi , Shi Jia-Hui , Zhang Rong-Rong , Zhu Hui-Min , Qiu Hong-Ying , Zhang Tao , Deng Yong-Qiang , Li Xiao-Feng , Xu Ping , Yang Xiao , Qin Cheng-Feng
Published: November 2020

Olfactory dysfunction caused by SARS-CoV-2 infection represents as one of the most predictive and common symptoms in COVID-19 patients. However, the causal link between SARS-CoV-2 infection and olfactory disorders remains lacking. Herein we demonstrate intranasal inoculation of SARS-CoV-2 induces robust viral replication in the olfactory epithelium (OE), resulting in transient olfactory dysfunction in humanized ACE2 mice. The sustentacular cells and Bowman’s gland cells in OE were identified as the major targets of SARS-CoV-2 before the invasion into olfactory sensory neurons. Remarkably, SARS-CoV-2 infection triggers cell death and immune cell infiltration, and impairs the uniformity of OE structure. Combined transcriptomic and proteomic analyses reveal the induction of antiviral and inflammatory responses, as well as the downregulation of olfactory receptors in OE from the infected animals. Overall, our mouse model recapitulates the olfactory dysfunction in COVID-19 patients, and provides critical clues to understand the physiological basis for extrapulmonary manifestations of COVID-19.
ScalableIn VitroProduction of Defined Mouse Erythroblasts
Authors: Francis Helena S , Harold Caroline L , Beagrie Robert A , King Andrew J , Gosden Matthew E , Blayney Joseph W , Jeziorska Danuta M , Babbs Christian , Higgs Douglas R , Kassouf Mira T
Published: November 2020

Mouse embryonic stem cells (mESCs) can be manipulatedin vitroto recapitulate the process of erythropoiesis, during which multipotent cells undergo lineage specification, differentiation and maturation to produce erythroid cells. Although useful for identifying specific progenitors and precursors, this system has not been fully exploited as a source of cells to analyse erythropoiesis. Here, we establish a protocol in which characterised erythroblasts can be isolated in a scalable manner from differentiated embryoid bodies (EBs). Using transcriptional and epigenetic analysis, we demonstrate that this system faithfully recapitulates normal primitive erythropoiesis and fully reproduces the effects of natural and engineered mutations seen in primary cells obtained from mouse models. We anticipate this system to be of great value in reducing the time and costs of generating and maintaining mouse lines in a number of research scenarios.

Key Points

Scalable purification of primitive-like erythroid cells fromin vitrodifferentiated mESCs offers tractable tools for genetic studies

In vitroderived erythroid cells recapitulate wild type and engineered mutation phenotypes observed in primary cells obtained from mouse models
Electrophysiological analysis of healthy and dystrophic 3D bioengineered skeletal muscle tissues
Authors: Nguyen Christine T , Ebrahmi Majid , Gilbert Penney M , Stewart Bryan A
Published: November 2020

Recently, methods for creating three-dimensional (3D) human skeletal muscle tissues from myogenic cell lines have been reported. Bioengineered muscle tissues are contractile and respond to electrical and chemical stimulation. In this study we provide an electrophysiological analysis of healthy and dystrophic 3D bioengineered skeletal muscle tissues. We focus on Duchenne muscular dystrophy (DMD), a fatal muscle disorder involving the skeletal muscle system. Thedystrophingene, which when mutated causes DMD, encodes for the Dystrophin protein, which anchors the cytoskeletal network inside of a muscle cell to the extracellular matrix outside the cell. Here, we enlist a 3Din vitromodel of DMD muscle tissue, to evaluate an understudied aspect of DMD, muscle cell electrical properties uncoupled from presynaptic neural inputs. Our data shows that electrophysiological aspects of DMD are replicated in the 3D bioengineered skeletal muscle tissue model. Furthermore, we test a block co-polymer, poloxamer 188, and demonstrate capacity for improving the membrane potential in DMD muscle.Therefore, this study serves as the baseline for a newin vitromethod to examine potential therapies directed at muscular disorders.