bluuebunny/crossref_metadata_2025 huggingface dataset:
Halomonas azerbaijanica sp. nov., a halophilic bacterium isolated from Urmia Lake after the 2015 drought
Authors: Kazemi Elham , Tarhriz Vahideh , Amoozegar Mohammad Ali , Hejazi Mohammad Saeid
Published: December 2020

A novel, slightly halophilic bacterium, designated TBZ202T, was isolated from water of Urmia Lake, in the Azerbaijan region of north-west Iran. The strain was facultatively anaerobic, Gram-stain-negative, rod-shaped and motile. Colonies were creamy, circular, convex and shiny. It grew at NaCl concentrations of 0–12 % (w/v) (optimum 3–5 % w/v), at temperatures of 20–45 °C (optimum 30 °C) and at pH 5.0–10.0 (optimum pH 7.0). Based on the 16S rRNA gene sequence, strain TBZ202T belongs to the genus

Halomonas

in the

Halomonadaceae

and the most closely related species are

Halomonas gudaonensis

CGMCC 1.6133T (98.6 % similarity),

Halomonas ventosae

Al12T (96.8 %) and Halomonas rambilicola RS-16T (96.6%). The G+C content was 67.9 % and the digital DNA–DNA hybridization and average nucleotide identity values with

H. gudaonensis

were 35.8 and 83.8 %, respectively, indicating that the isolate differs from all species described. The major fatty acids were C18 : 1
ω7c, C16 : 0 and C16 : 1
ω7c. The only respiratory quinone detected was Q-9 and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and three unknown phospholipids. On the basis of a polyphasic taxonomic analysis, the isolate is considered to represent a novel species of the genus

Halomonas

, for which the name Halomonas azerbaijanica sp. nov. is proposed. The type strain is TBZ202T (=KCTC 62817T=CECT 9693T).
Pseudomonas allii sp. nov., a pathogen causing soft rot of onion in Japan
Authors: Sawada Hiroyuki , Fujikawa Takashi , Tsuji Mizue , Satou Mamoru
Published: December 2020

Six phytopathogenic bacterial strains, MAFF 301512, MAFF 301513, MAFF 301514T, MAFF 301515, MAFF 301516 and MAFF 301517, were isolated from soft rot lesions of onion (Allium cepa L.) in Japan. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. Analysis of their 16S rRNA gene sequences showed that they belong to the genus

Pseudomonas

, with the highest similarities to

Pseudomonas poae

DSM 14936T (99.86 %),

Pseudomonas simiae

OLiT (99.85 %),

Pseudomonas trivialis

DSM 14937T (99.79 %) and

Pseudomonas extremorientalis

KMM 3447T (99.79 %). Their genomic DNA G+C content was 60.9 mol% and the major fatty acids (>5 % of the total fatty acids) present were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c) and C17 : 0 cyclo. Phylogenetic and phylogenomic analyses based on the rpoD gene and whole genome sequences, respectively, demonstrated that the strains belong to the

Pseudomonas fluorescens

subgroup, but form a monophyletic and robust clade, with

Pseudomonas azotoformans

as their neighbour. Between the strains and

P. azotoformans

, the average nucleotide identity scores were 95.63–95.70 %, whereas the digital DNA–DNA hybridization scores of the strains against their closest relatives, including

P. azotoformans

, were 65.4 % or less, which are lower than the 70 % cut-off for prokaryotic species delineation. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity in onion and cellular fatty acid composition. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel

Pseudomonas

species, proposed to be named Pseudomonas allii sp. nov., with MAFF 301514T (=ICMP 23680T) being the type strain.
Mesobacillus harenae sp. nov., isolated from the sandy soil of a cold desert
Authors: Zhang Gaosen , Yang Ruiqi , Chen Tuo , Zhang Binglin , Yang Hui , Wu Xiukun , Gao Haining , Zhang Wei , Liu Guangxiu
Published: December 2020

A bacterial strain, designated Y40T, was isolated from sandy soil sampled on the Qinghai–Tibet Plateau. A polyphasic study confirmed the affiliation of the strain with the genus

Mesobacillus

. Strain Y40T was found to be an aerobic, Gram-stain-positive, motile and rod-shaped bacterium. The strain grew at 10–42 °C, pH 6–9 and with 0–2 % (w/v) NaCl. The diagnostic amino acid was meso-diaminopimeilic acid. MK7 was predominant menaquinone, and iso-C15:0, iso-C17:1 ω10c and anteiso-C15:0 were the major fatty acids. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content was 40.6 mol%. Based on he results of 16S rRNA gene sequence analysis, strain Y40T was phylogenetically closely related to

Mesobacillus zeae

JJ-247T and

Mesobacillus foraminis

CV53T, with similarities of 98.0 and 97.7 %, respectively. The average nucleotide identity (ANIb) values between strain Y40T and

Mesobacillus zeae

JJ-247T and

Mesobacillus foraminis

CV53T were 69.9 and 70.0 %, respectively. Based on the morphological, physiological, and chemotaxonomic data, it is proposed that strain Y40T (=CICC 24459T=JCM 32794T) should be classified into the genus

Mesobacillus

as Mesobacillus harenae sp. nov.
Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field
Authors: Raths Rachel , Peta Vincent , Bücking Heike
Published: December 2020

A Gram-negative, rod-shaped bacterium, strainDuganella callidaDN04T, was isolated from the soil of a maize field in North Carolina, USA. Based on the 16S rRNA gene sequence, the most similarDuganellaspecies areD. sacchariSac-22T,D. ginsengisoliDCY83T, andD. radicisSac-41Twith a 97.8, 97.6, or 96.9 % sequence similarity, respectively. We compared the biochemical phenotype of DN04TtoD. sacchariSac-22TandD. zoogloeoides115Tand other reference strains from different genera within the Oxalobacteraceae and while the biochemical profile of DN04Tis most similar toD. sacchariSac-22Tand otherDuganellaandMassiliastrains, there are also distinct differences. DN04Tcan for example utilize turanose, N-acetyl-d-glucosamine, inosine, andl-pyroglutamic acid. The four fatty acids found in the highest percentages were C15 : 0iso (24.6 %), C15 : 1isoG (19.4 %), C17 : 0iso3-OH (16.8 %), and summed feature 3 (C16:1⍵7c and/or C16:1⍵6c) (12.5 %). We also applied whole genome sequencing to determine if DN04Tis a novel species. The most similar AAI (average amino acid identity) score was 70.8 % (Massilia plicataNZ CP038026T), and the most similar ANI (average nucleotide identity) score was 84.8 % (D. radicisKCTC 22382T), which indicates that DN04Tis a novel species. The genome-to-genome-distance calculation (GGDC) revealed a DDH of 28.3 % toD. radicisKCTC 22382T, which is much lower than the new species threshold. Based on the morphological, phenotypic, and genomic differences, we proposeDuganella callidasp. nov. as a novel species within theDuganellagenus (type strain DN04T=NRRL B-65552T=LMG 31736T).
Detection of SARS-CoV-2 in saliva: implications for specimen transport and storage
Authors: Williams Eloise , Isles Nicole , Chong Brian , Bond Katherine , Yoga Yano , Druce Julian , Catton Mike , Ballard Susan A. , Howden Benjamin P. , Williamson Deborah A.
Published: December 2020

Saliva has recently been proposed as a suitable specimen for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Use of saliva as a diagnostic specimen may present opportunities for SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) testing in remote and low-resource settings. Determining the stability of SARS-CoV-2 RNA in saliva over time is an important step in determining optimal storage and transport times. We undertook an in vitro study to assess whether SARS-CoV-2 could be detected in contrived saliva samples. The contrived saliva samples comprised 10 ml pooled saliva spiked with gamma-irradiated SARS-CoV-2 to achieve a concentration of 2.58×104 copies ml SARS-CoV-2, which was subsequently divided into 2 ml aliquots comprising: (i) neat saliva; and a 1 : 1 dilution with (ii) normal saline; (iii) viral transport media, and (iv) liquid Amies medium. Contrived samples were made in quadruplicate, with two samples of each stored at either: (i) room temperature or (ii) 4 °C. SARS-CoV-2 was detected in all SARS-CoV-2 spiked samples at time point 0, day 1, 3 and 7 at both storage temperatures using the N gene RT-PCR assay and time point 0, day 1 and day 7 using the Xpert Xpress SARS-CoV-2 (Cepheid, Sunnyvale, USA) RT-PCR assay. The ability to detect SARS-CoV-2 in saliva over a 1 week period is an important finding that presents further opportunities for saliva testing as a diagnostic specimen for the diagnosis of SARS-CoV-2.
Individual variation underlying brain age estimates in typical development
Authors: Ball Gareth , Kelly Claire E , Beare Richard , Seal Marc L
Published: December 2020

Typical brain development follows a protracted trajectory throughout childhood and adolescence. Deviations from typical growth trajectories have been implicated in neurodevelopmental and psychiatric disorders. Recently, the use of machine learning algorithms to model age as a function of structural or functional brain properties has been used to examine advanced or delayed brain maturation in healthy and clinical populations. Termed ‘brain age’, this approach often relies on complex, nonlinear models that can be difficult to interpret. In this study, we use model explanation methods to examine the cortical features that contribute to brain age modelling on an individual basis.

In a large cohort of n=768 typically-developing children (aged 3-21 years), we build models of brain development using three different machine learning approaches. We employ SHAP, a model-agnostic technique to estimate sample-specific feature importance, to identify regional cortical metrics that explain errors in brain age prediction. We find that, on average, brain age prediction and the cortical features that explain model predictions are consistent across model types and reflect previously reported patterns of regional brain development. However, while several regions are found to contribute to brain age prediction, we find little spatial correspondence between individual estimates of feature importance, even when matched for age, sex and brain age prediction error. We also find no association between brain age error and cognitive performance in this typically-developing sample.

Overall, this study shows that, while brain age estimates based on cortical development are relatively robust and consistent across model types and preprocessing strategies, significant between-subject variation exists in the features that explain erroneous brain age predictions on an individual level.
Molecular characterization of projection neuron subtypes in the mouse olfactory bulb
Authors: Zeppilli Sara , Ackels Tobias , Attey Robin , Klimpert Nell , Ritola Kimberly D. , Boeing Stefan , Crombach Anton , Schaefer Andreas T. , Fleischmann Alexander
Published: December 2020

Projection neurons (PNs) in the mammalian olfactory bulb (OB) receive direct input from the nose and project to diverse cortical and subcortical areas. Morphological and physiological studies have highlighted functional heterogeneity, yet no molecular markers have been described that delineate PN subtypes. Here, we used viral injections into olfactory cortex and fluorescent nucleus sorting to enrich PNs for high-throughput single nucleus and bulk RNA deep sequencing. Transcriptome analysis and RNAin situhybridization identified three mitral and five tufted cell populations with characteristic transcription factor network topology and cell adhesion and excitability-related gene expression. Finally, by integrating bulk and snRNA-seq data we propose that different mitral cell populations selectively project to different regions of olfactory cortex. Together, we have identified potential molecular and gene regulatory mechanisms underlying PN diversity and provide new molecular entry points into studying the diverse functional roles of mitral and tufted cell subtypes.
CovidRiskCalc: An online app to calculate the risk of COVID infection in a gathering
Authors: Artzrouni Marc
Published: December 2020

CovidRiskCalc is an evidence based online app which calculates the risk of COVID-19 infection for a person coming into contact during a specific event/gathering with a group of individuals, some of whom may be infected (available at CovidRiskCalc.eu). The user is helped in providing a rough estimate of the COVID-19 prevalence rate in the group. She also inputs the size of the group, the number (and duration) of her contacts and the level of precautions (masks, social distancing, etc.). The app calculates the user’s risk of transmission in a single infected contact; her probability of infection during the entire event and the number of new infections within the group. Two numerical examples are given. The tool, designed for both professionals and the general public, thus quantifies the risks of infection in special populations (social gatherings, prisons, etc.), but also in general ones (stores, stadiums, etc.).
Associations between vaping and Covid-19: cross-sectional findings from the HEBECO study
Authors: Kale Dimitra , Herbec Aleksandra , Perski Olga , Jackson Sarah E , Brown Jamie , Shahab Lion
Published: December 2020

Aims

To explore i) associations between vaping and self-reported diagnosed/suspected Covid-19; ii) changes in vaping since Covid-19 and factors associated with these changes; iii) whether Covid-19 motivated current or recent ex-vapers to quit.

Methods

Cross-sectional online survey of 2791 UK adults recruited 30/04/2020–14/06/2020. Participants self-reported data on sociodemographic characteristics, diagnosed/suspected Covid-19, vaping status, changes in vaping and motivation to quit vaping since Covid-19.

Results

There were no differences in diagnosed/suspected Covid-19 between never, current and ex-vapers. Bayes factors indicated there was sufficient evidence to rule out small negative (protective) associations between vaping status and diagnosed/suspected Covid-19. Among current vapers (n=397), 9.7% (95% CI 6.8-12.6%) reported vaping less than usual since Covid-19, 42.0% (37.2-46.9%) reported vaping more, and 48.3% (43.4-53.2%) reported no change. In adjusted analyses, vaping less was associated with being female (aOR=3.40, 95% CI 1.73-6.71), not living with children (aOR=4.93, 1.15-21.08) and concurrent smoking (aOR=8.77, 3.04-25.64), while vaping more was associated with being younger (aOR=5.26, 1.37-20.0), living alone (aOR=2.08, 1.14-3.85), and diagnosed/suspected Covid-19 (aOR=4.72, 2.60-8.62). Of current vapers, 32.2% (95% CI 27.5-36.8%) were motivated to quit vaping since Covid-19, partly motivated by Covid-19, and 17.4%, (9.7-26.3%) of recent ex-vapers quit vaping due to Covid-19.

Conclusions

Among UK adults, self-reported diagnosed/suspected Covid-19 was not associated with vaping status. Half of current vapers changed their vaping consumption since Covid-19, with the majority reporting an increase, and a minority was motivated to quit due to Covid-19.

Registration

The analysis plan was pre-registered, and it is available at https://osf.io/6j8z3/

Highlights

No difference found in diagnosed/suspected Covid-19 between never, current and ex-vapers

Half of current vapers changed their vaping consumption since Covid-19

Motivation to quit vaping was partly related to Covid-19
Assessing the risk of vaccine-driven virulence evolution in SARS-CoV-2
Authors: Miller Ian F. , Metcalf C. Jessica E.
Published: December 2020

How might COVID-19 vaccines alter selection for increased SARS-CoV-2 virulence, or lethality? Framing current evidence surrounding SARS-CoV-2 biology and COVID-19 vaccines in the context of evolutionary theory indicates that prospects for virulence evolution remain uncertain. However, differential effects of vaccinal immunity on transmission and disease severity between respiratory compartments could select for increased virulence. To bound expectations for this outcome, we analyze an evo-epidemiological model. Synthesizing model predictions with vaccine efficacy data, we conclude that while vaccine driven virulence evolution remains a theoretical risk, it is unlikely to threaten prospects for herd immunity in immunized populations. Given that this event would nevertheless impact unvaccinated populations, virulence should be monitored to facilitate swift mitigation efforts.

Significance statement

Vaccines can provide personal and population level protection against infectious disease, but these benefits can exert strong selective pressures on pathogens. Virulence, or lethality, is one pathogen trait that can evolve in response to vaccination. We investigated whether COVID-19 vaccines could select for increased SARS-CoV-2 virulence by reviewing current evidence about vaccine efficacy and SARS-CoV-2 biology in the context of evolutionary theory, and subsequently analyzing a mathematical model. Our findings indicate that while vaccine-driven virulence evolution in SARS-CoV-2 is a theoretical risk, the consequences of this event would be limited for vaccinated populations. However, virulence evolution should be monitored, as the ramifications of a more virulent strain spreading into an under-vaccinated population would be more severe.
Variants in SARS-CoV-2 Associated with Mild or Severe Outcome
Authors: Voss Jameson D. , Skarzynski Martin , McAuley Erin M. , Maier Ezekiel J. , Gibbons Thomas , Fries Anthony C. , Chapleau Richard R.
Published: December 2020

Introduction

The coronavirus disease 2019 (COVID-19) pandemic is a global public health emergency causing a disparate burden of death and disability around the world. The molecular characteristics of the virus that predict better or worse outcome are largely still being discovered.

Methods

We downloaded 155,958 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from GISAID and evaluated whether variants improved prediction of reported severity beyond age and region. We also evaluated specific variants to determine the magnitude of association with severity and the frequency of these variants among the genomes.

Results

Logistic regression models that included viral genomic variants outperformed other models (AUC=0.91 as compared with 0.68 for age and gender alone; p<0.001). Among individual variants, we found 17 single nucleotide variants in SARS-CoV-2 have more than two-fold greater odds of being associated with higher severity and 67 variants associated with ≤ 0.5 times the odds of severity. The median frequency of associated variants was 0.15% (interquartile range 0.09%-0.45%). Altogether 85% of genomes had at least one variant associated with patient outcome.

Conclusion

Numerous SARS-CoV-2 variants have two-fold or greater association with odds of mild or severe outcome and collectively, these variants are common. In addition to comprehensive mitigation efforts, public health measures should be prioritized to control the more severe manifestations of COVID-19 and the transmission chains linked to these severe cases.
Risk Factors for Cerebral Palsy in Brazilian Children: A Case-Control Study
Authors: Peixoto Marcus Valerius da Silva , Duque Andrezza Marques , dos Santos Allan Dantas , Melo Almeida Lima Shirley Verônica , Nunes Ribeiro Caíque Jordan , Voci Silvia Maria , de Carvalho Susana , Antônio Prado Nunes Marco
Published: December 2020

Background

Cerebral palsy is the main cause of physical disability in childhood.

Objectives

This study analyzed prenatal and perinatal risk factors that contribute to cerebral palsy in Brazilian children.

Methods

A case-control study was conducted with 2- to 10-year-old children in the city of Aracaju, Sergipe, Brazil. The cases were population-based, selected from the Primary Health Care services. The controls were selected from the database of the Brazilian Live Births Information System. Controls were paired with cases by gender, year, and hospital of birth.

Results

A total of 570 participants (114 cases and 456 controls) were studied. Most of the participants were male, with bilateral spastic cerebral palsy. Among the prenatal factors examined, the presence of congenital anomalies was significantly different between cases and controls (OR = 54.28, [95% CI 12.55, 234.86]). The analysis of perinatal factors revealed significant differences between cases and controls in low birth weight (OR = 3.8, [95% CI 2.34, 6.16]), preterm birth (OR = 2.31, [95% CI 1.41, 3.80]), and low Apgar scores (OR = 14.73, [95% CI 5.27, 41.15]).

Conclusions

The main prenatal and perinatal factors associated with cerebral palsy in our population were congenital anomalies, low Apgar scores, low birth weight, and preterm birth. The perinatal period had more risk factors, demanding a deeper study of their causes and of possible preventive measures.
Imputed Gene Expression Risk Scores: A Functionally Informed Component of Polygenic Risk
Authors: Pain Oliver , Glanville Kylie P. , Hagenaars Saskia , Selzam Saskia , Fürtjes Anna , Coleman Jonathan R. I. , Rimfeld Kaili , Breen Gerome , Folkersen Lasse , Lewis Cathryn M.
Published: December 2020

Background

Integration of functional genomic annotations when estimating polygenic risk scores (PRS) can provide insight into aetiology and improve risk prediction. This study explores the predictive utility of gene expression risk scores (GeRS), calculated using imputed gene expression and transcriptome-wide association study (TWAS) results.

Methods

The predictive utility of GeRS was evaluated using 12 neuropsychiatric and anthropometric outcomes measured in two target samples: UK Biobank and the Twins Early Development Study (TEDS). GeRS were calculated based on imputed gene expression levels and TWAS results, using 53 gene expression-genotype panels, termed SNP-weight sets, capturing expression across a range of tissues. We compare the predictive utility of elastic net models containing GeRS within and across SNP-weight sets, and models containing both GeRS and PRS. We estimate the proportion of SNP-based heritability attributable tocis-regulated gene expression.

Results

GeRS significantly predicted a range of outcomes, with elastic net models combining GeRS across SNP-weight sets improving prediction. GeRS were less predictive than PRS, but models combining GeRS and PRS improved prediction for several outcomes, with relative improvements ranging from 0.3% for Height (p=0.023) to 4% for Rheumatoid Arthritis (p=5.9×10-8). The proportion of SNP-based heritability attributable tocis-regulated expression was modest for most outcomes, even when restricting GeRS to colocalised genes.

Conclusion

GeRS represent a component of PRS and could be useful for functional stratification of genetic risk. Only in specific circumstances can GeRS substantially improve prediction over PRS alone. Future research considering functional genomic annotations when estimating genetic risk is warranted.
Digging roots is easier with AI
Authors: Han Eusun , Smith Abraham George , Kemper Roman , White Rosemary , Kirkegaard John , Thorup-Kristensen Kristian , Athmann Miriam
Published: December 2020

The scale of root quantification in research is often limited by the time required for sampling, measurement and processing samples. Recent developments in Convolutional Neural Networks (CNN) have made faster and more accurate plant image analysis possible which may significantly reduce the time required for root measurement, but challenges remain in making these methods accessible to researchers without an in-depth knowledge of Machine Learning. We analyzed root images acquired from three destructive root samplings using the RootPainter CNN-software that features an interface for corrective annotation for easier use. Root scans with and without non-root debris were used to test if training a model, i.e., learning from labeled examples, can effectively exclude the debris by comparing the end-results with measurements from clean images. Root images acquired from soil profile walls and the cross-section of soil cores were also used for training and the derived measurements were compared with manual measurements. After 200 minutes of training on each dataset, significant relationships between manual measurements and RootPainter-derived data were noted for monolith (R2=0.99), profile wall (R2=0.76) and core-break (R2=0.57). The rooting density derived from images with debris was not significantly different from that derived from clean images after processing with RootPainter. Rooting density was also successfully calculated from both profile wall and soil core images, and in each case the gradient of root density with depth was not significantly different from manual counts. Our results demonstrate that the proposed approach using CNN can lead to substantial reductions in root sample processing workloads, increasing the potential scale of future root investigations.
ramr: an R package for detection of rare aberrantly methylated regions
Authors: Nikolaienko Oleksii , Lønning Per Eystein , Knappskog Stian
Published: December 2020

Motivation

With recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyse such events.

Results

We have developed a method (ramr) to identify aberrantly methylated DNA regions (AMRs).ramrcan be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics oframrand confirmed its applicability for analysis of large public data sets. Usingramrwe identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages.

Availability and implementation

The R package is freely available athttps://github.com/BBCG/ramr
Histone H4K20 methylation synchronizes cytoskeletal dynamics with cell cycle phases during epidermal differentiation
Authors: Angerilli Alessandro , Tait Janet , Berges Julian , Shcherbakova Irina , Schauer Tamas , Smialowski Pawel , Hsam Ohnmar , Mentele Edith , Nicetto Dario , Rupp Ralph A.W.
Published: December 2020

Histone tails are subject to various post-translational modifications, which play a fundamental role in altering chromatin accessibility. Although they are thought to regulate progression through development, the impact of the most abundant histone modification in vertebrates, i.e., histone H4 lysine 20 dimethylation (H4K20m2), has remained largely elusive. H4K20m2 arises from sequential methylation of new, unmodified histone H4 proteins, incorporated into chromatin during DNA replication, by the mono-methylating enzyme PR-SET7/KMT5A during G2/M phases, followed by conversion to the dimethylated state by SUV4-20H1 enzymes in the following G1/G0 phase. To address its function, we have blocked the deposition of this mark by depleting Xenopus embryos of SUV4-20H1/H2 methyltransferases, which convert H4K20 monomethylated to di- and tri-methylated states, respectively In the frog larval epidermis this results in a severe loss of cilia in multiciliated cells (MCC), a key component of all mucociliary epithelia. MCC precursor cells are correctly specified and amplify centrioles, but ultimately fail in ciliogenesis due to perturbation of cytoplasmic processes. Genome wide transcriptome profiling reveals that SUV4-20H1/H2 depleted ectodermal Animal Cap explants preferentially down-regulate the expression of several hundred cytoskeleton and cilium related genes as a consequence of persistent H4K20 monomethyl marks on postmitotic chromatin. Further analysis demonstrated that knockdown of SUV4-20H1 alone is sufficient to generate the MCC phenotype and that overexpression of the H4K20m1-specific histone demethylase PHF8 rescues the ciliogenic defect in significant, although partial, manner. Taken together, this indicates that the conversion of H4K20m1 to H4K20m2 by SUV4-20H1 is critical to synchronize cytoskeletal dynamics in concert with the cell cycle.
Cryptic β-lactamase evolution is driven by low β-lactam concentrations
Authors: Fröhlich Christopher , Gama João Alves , Harms Klaus , Hirvonen Viivi H.A. , Lund Bjarte Aarmo , van der Kamp Marc W. , Johnsen Pål Jarle , Samuelsen Ørjan , Leiros Hanna-Kirsti S.
Published: December 2020

Our current understanding of how low antibiotic concentrations shape the evolution of contemporary β-lactamases is limited. Using the wide-spread carbapenemase OXA-48, we tested the long-standing hypothesis that selective compartments with low antibiotic concentrations cause standing genetic diversity that could act as a gateway to develop clinical resistance. Here, we subjected Escherichia coli expressing blaOXA-48, on a clinical plasmid, to experimental evolution at sub-minimum inhibitory concentrations (sub-MIC) of ceftazidime. We identified and characterized seven single variants of OXA-48. Susceptibility profiles and dose-response curves showed that they increased resistance only marginally. However, in competition experiments at sub-MIC of ceftazidime, they showed strong selectable fitness benefits. Increased resistance was also reflected in elevated catalytic efficiencies towards ceftazidime. These changes are likely caused by enhanced flexibility of the Ω- and β5-β6 loops. In conclusion, low-level concentrations of β-lactams can drive the evolution of β-lactamases through cryptic phenotypes which may act as stepping-stones towards clinical resistance.
Combining Two Classes of Epigenetic Modifiers and Their Effect on Prostate Cancer Cells
Authors: Lodi Mudassir K. , Goliadze Ekaterine , Manjili Masoud H. , Guruli Georgi
Published: December 2020

The main objective of this experiment was to determine and study the effects of combining two epigenetic modifiers, 5-azacyticidine (5-AzaC) and SB939, on a RM-1 murine prostate cancer cell model. The effectiveness of this combination on prostate cancer cells has not been previously studied. The study was implemented on ex vivo cell models to gain a better understanding of the true effects of the combination therapy on prostate cancer cells. Two variations of the combination therapy were tested in this study, each with different concentrations of SB939 (100nm and 200nm).

To determine the effectivity of the combination therapy on prostate cancer cells, three factors were measured: cell proliferation, cancer testis antigen (CTA) expression, and apoptosis rate. To measure cell proliferation, a cell proliferation assay was conducted, and absorption rate was measured through a 450 nm wavelength. CTA expression was measured through a quantitative polymerase chain reaction (quant-PCR). For this study, the expression rates of five CTAs were measured (TEX15, CEP55, CCNA1, P1A, SPA17). Apoptosis rate was measured through an Annexin-V assay, in which two markers, Annexin-V and 7-AAD, were used.

We found that SB939 combined with 5-AzaC show highest efficacy compare to each drug alone in terms of inhibiting tumor cell proliferation, as well as inducing tumor cells apoptosis and enhancing tumor cell immunogenicity by the induction of the expression of CTAs. This combination proved to be effective in combating murine prostate cancer cells, and can potentially be effective within in vivo models due to its high toxicity to these cancer cells, and its ability to render prostate cancer more immunogenic.
Deep immune profiling reveals targetable mechanisms of immune evasion in checkpoint blockade-refractory glioblastoma
Authors: Simonds Erin F. , Lu Edbert D. , Liu Eric V. , Tamaki Whitney , Rancan Chiara , Stultz Jacob , Sinha Meenal , McHenry Lauren K. , Nasholm Nicole M. , Chuntova Pavlina , Sundström Anders , Genoud Vassilis , Shahani Shilpa A. , Wang Leo D. , Brown Christine E. , Walker Paul R. , Swartling Fredrik J. , Fong Lawrence , Okada Hideho , Weiss William A. , Hellström Mats
Published: December 2020

Background

Glioblastoma (GBM) is refractory to checkpoint blockade immunotherapy (CPI). We sought to determine to what extent this immune evasion is due to intrinsic properties of the tumor cells versus the specialized immune context of the brain, and if it can be reversed.

Methods

We used CyTOF mass cytometry to compare the tumor immune microenvironments (TIME) of human tumors that are generally CPI-refractory (GBM and sarcoma) or CPI-responsive (renal cell carcinoma), as well as mouse models of GBM that are CPI-responsive (GL261) or CPI-refractory (SB28). We further compared SB28 tumors grown intracerebrally versus subcutaneously to determine how tumor site affects TIME and responsiveness to dual CTLA-4/PD-1 blockade. Informed by these data, we explored rational immunotherapeutic combinations.

Results

CPI-sensitivity in human and mouse tumors was associated with increased T cells and dendritic cells, and fewer myeloid cells, in particular PD-L1+ tumor associated macrophages. The SB28 mouse model of GBM responded to CPI when grown subcutaneously but not intracerebrally, providing a system to explore mechanisms underlying CPI resistance in GBM. The response to CPI in the subcutaneous SB28 model required CD4 T cells and NK cells, but not CD8 T cells. Recombinant FLT3L expanded dendritic cells, improved antigen-specific T cell priming, and prolonged survival of mice with intracerebral SB28 tumors, but at the cost of increased Tregs. Targeting PD-L1 also prolonged survival, especially when combined with stereotactic radiation.

Conclusions

Our data suggest that a major obstacle for effective immunotherapy of GBM is the low antigenicity of the tumor cells coupled with poor antigen presentation in the brain, rather than intrinsic immunosuppressive properties of GBM tumor cells. Deep immune profiling identified dendritic cells and PD-L1+ tumor-associated macrophages as promising targetable cell populations, which was confirmed using therapeutic interventionsin vivo.

Graphical Abstract

In Brief

In mice and humans, tumors that were sensitive to checkpoint blockade had consistent immunological features. A mouse model of glioma that is refractory to checkpoint blockade was sensitized by increasing antigen presentation through a variety of approaches.
Localization, proteomics, and metabolite profiling reveal a putative vesicular transporter for UDP-glucose
Authors: Qian Cheng , Wu Zhaofa , Sun Rongbo , Yu Huasheng , Zeng Jianzhi , Rao Yi , Li Yulong
Published: December 2020

Vesicular neurotransmitter transporters (VNTs) mediate the selective uptake and enrichment of small molecule neurotransmitters into synaptic vesicles (SVs) and are therefore a major determinant of the synaptic output of specific neurons. To identify novel VNTs expressed on SVs (thus identifying new neurotransmitters and/or neuromodulators), we conducted localization profiling of 361 solute carrier (SLC) transporters tagging with a fluorescent protein in neurons, which revealed 40 possible candidates through comparison with a known SV marker. We parallelly performed proteomics analysis of immunoisolated SVs and identified 7 transporters in overlap. Ultrastructural analysis confirmed one of the transporters, SLC35D3, localized to SVs. Finally, by combining metabolite profiling with a radiolabeled substrate transport assay, we identified UDP-glucose as the principal substrate for SLC35D3. These results provide new insights into the functional role of SLC transporters in neurotransmission and improve our understanding of the molecular diversity of chemical transmitters.
Multimodal-Multisensory Experiments: Design and Implementation
Authors: Razavi Moein , Yamauchi Takashi , Janfaza Vahid , Leontyev Anton , Longmire-Monford Shanle , Orr Joseph
Published: December 2020

The human mind is multimodal. Yet most behavioral studies rely on century-old measures of behavior - task accuracy and latency (response time). Multimodal and multisensory analysis of human behavior creates a better understanding of how the mind works. The problem is that designing and implementing these experiments is technically complex and costly. This paper introduces versatile and economical means of developing multimodal-multisensory human experiments. We provide an experimental design framework that automatically integrates and synchronizes measures including electroencephalogram (EEG), galvanic skin response (GSR), eye-tracking, virtual reality (VR), body movement, mouse/cursor motion and response time. Unlike proprietary systems (e.g., iMotions), our system is free and open-source; it integratesPsychoPy, Unityand Lab Streaming Layer (LSL). The system embeds LSL insidePsychoPy/Unityfor the synchronization of multiple sensory signals - gaze motion, electroencephalogram (EEG), galvanic skin response (GSR), mouse/cursor movement, and body motion - with low-cost consumer-grade devices in a simple behavioral task designed byPsychoPyand a virtual reality environment designed byUnity. This tutorial shows a step-by-step process by which a complex multimodal-multisensory experiment can be designed and implemented in a few hours. When conducting the experiment, all of the data synchronization and recoding of the data to disk will be done automatically.
Acetylcholine as a trigger of the somatic exocytosis in Retzius neurons
Authors: Kazakova Tatiana A. , Suchalko Oleg N. , Ivanov Alexey D. , Alova Anna V. , Maksimov George V.
Published: December 2020

The redistribution of vesicles containing serotonin in leech neurons was studied using the fluorescent, scanning ion-conductance, and laser phase microscopy methods. During acetylcholine receptor (AChR) activation in Retzius neurons, the changes of Ca2+desorption, cellular stiffness and the cell optical phase difference (OPD) were established. It was found that the amplitude of OPD changes in the near-membrane area (membrane and near-membrane of the cytoplasm layers) increases upon AChR activation and this is, possibly, associated with the neurons vesicle redistribution. The decrease in the cell stiffness upon AChR activation suggests the crucial role of cytoskeleton for vesicle transport and release. Ca2+rise in the cytoplasm during AChR activation may regulate the mitochondrial recruitment to regions with high energy demand for vesicle trafficking.
Aspergillus fumigatusversus GenusAspergillus: Conservation, adaptive evolution and specific virulence genes
Authors: Gupta Shishir K , Srivastava Mugdha , Osmanoglu Özge , Xu Zhuofei , Brakhage Axel A , Dandekar Thomas
Published: December 2020

Aspergillusis an important fungal genus containing economically important species, as well as pathogenic species of animals and plants. Using eighteen fungal species of the genusAspergillus, we conducted a comprehensive investigation of conserved genes and their evolution. This also allows to investigate the selection pressure driving the adaptive evolution in the pathogenic speciesA. fumigatus.Among single-copy orthologs (SCOs) forA. fumigatusand the closely related speciesA. fischeri, we identified 122 versus 50 positively selected genes (PSGs), respectively. Moreover, twenty conserved genes of unknown function were established to be clearly positively selected and thus important for adaption.A. fumigatusPSGs interacting with human host proteins show over-representation of adaptive, symbiosis-related, immunomodulatory, and virulence related pathways such as the TGF-β pathway, insulin receptor signaling, IL1 pathway and interfering with phagosomal of GTPase signaling. Additionally, among the virulence factor coding genes, secretory and membrane protein coding genes in multi-copy gene families, 212 genes underwent positive selection and also suggest increased adaptation such as fungal immune evasion mechanisms (aspf2), siderophore biosynthesis (sidD), fumarylalanine production (sidE), stress tolerance (atfA) and thermotolerance (sodA). These genes presumably contribute to host adaptation strategies. Genes for the biosynthesis of gliotoxin are shared among all the close relatives ofA. fumigatusas ancient defense mechanism. Positive selection plays a crucial role in the adaptive evolution ofA. fumigatus. The genome-wide profile of PSGs provides valuable targets for further research on the mechanisms of immune evasion, for antimycotic targeting and understanding fundamental processes of virulence.
Construction and Analysis of Protein-Protein Interaction Network of Non-Alcoholic Fatty Liver Disease
Authors: Amanatidou Athina I. , Dedoussis George V.
Published: December 2020

Non-alcoholic fatty liver disease (NAFLD) is a disease with multidimensional complexities. Many attempts have been made over the years to treat this disease but its incidence is rising. For this reason, the need to identify and study new candidate proteins that may be associated with NAFLD is of utmost importance. Systems-based approaches such as the analysis of protein-protein interaction (PPI) network could lead to the discovery of new proteins associated with a disease that can then be translated into clinical practice. The aim of this study is to analyze the interaction network of human proteins associated with NAFLD as well as their experimentally verified interactors and to identify novel associations with other human proteins that may be involved in this disease. Computational analysis made it feasible to detect 77 candidate proteins associated with NAFLD, having high network scores. Furthemore, clustering analysis was performed to identify densely connected regions with biological significance in this network. Additionally, gene expression analysis was conducted to validate part of the findings of this research work. We believe that our research will be helpful in extending experimental efforts to address the pathogenesis and progression of NAFLD.
Lysosomal positioning regulates Rab10 phosphorylation at LRRK2-positive lysosomes
Authors: Kluss Jillian H. , Beilina Alexandra , Williamson Chad D. , Lewis Patrick A. , Cookson Mark R. , Bonet-Ponce Luis
Published: December 2020

Genetic variation at theLeucine-rich repeat kinase 2 (LRRK2)locus contributes to enhanced lifetime risk of familial and sporadic Parkinson’s disease. Previous data have demonstrated that recruitment to various membranes of the endolysosomal system results in LRRK2 activation. However, the mechanism(s) underlying LRRK2 activation at endolysosomal membranes and the cellular consequences of these events are still poorly understood. Here, we directed LRRK2 to lysosomes and early endosomes, triggering both LRRK2 autophosphorylation and phosphorylation of the direct LRRK2 substrates Rab10 and Rab12. However, when directed to the lysosomal membrane, pRab10 was restricted to perinuclear lysosomes, whereas pRab12 was visualized on both peripheral and perinuclear LRRK2-positive lysosomes, suggesting that lysosomal positioning provides additional regulation of LRRK2-dependent Rab phosphorylation. Anterograde transport of lysosomes to the cell periphery by increasing expression of ARL8B and SKIP or by knockdown of the motor adaptor protein JIP4 blocked recruitment and phosphorylation of Rab10 by LRRK2. Conversely, overexpression of the Rab7 effector protein RILP resulted in lysosomal clustering within the perinuclear area and increased LRRK2-dependent Rab10 recruitment and phosphorylation. The regulation of Rab10 phosphorylation in the perinuclear area depends on counteracting phosphatases, as knockdown of phosphatase PPM1H significantly increased pRab10 signal and lysosomal tubulation in the perinuclear region. Our novel findings suggest LRRK2 can be activated at multiple cellular membranes including lysosomes, and that lysosomal positioning further provides regulation of some Rab substrates likely via differential phosphatase activity in nearby cellular compartments.
Th17-skewed inflammation due to genetic deficiency of a cadherin stress sensor
Authors: Godsel Lisa M , Roth-Carter Quinn R , Koetsier Jennifer L , Tsoi Lam C , Broussard Joshua A , Fitz Gillian N , Lloyd Sarah M , Kweon Junghun , Huffine Amber L , Burks Hope E , Hegazy Marihan , Amagai Saki , Harms Paul W. , Johnson Jodi L , Urciuoli Gloria , Doglio Lynn T. , Swindell William R , Awatramani Rajeshwar , Sprecher Eli , Bao Xiaomin , Cohen-Barak Eran , Missero Caterina , Gudjonsson Johann E , Green Kathleen J
Published: December 2020

Desmoglein 1 (Dsg1) is a cadherin restricted to stratified tissues of terrestrial vertebrates, which serve as essential physical and immune barriers. Dsg1’s importance in epidermal integrity is underscored by genetic, autoimmune and bacterial toxin-mediated disorders interfering with Dsg1 function. Dsg1 loss-of-function mutations in humans result not only in skin lesions, but also multiple allergies, and isolated patient keratinocytes exhibit increased pro-allergic cytokine expression. However, the mechanism by which genetic deficiency of Dsg1 causes chronic inflammation is unknown. To determine the systemic response to Dsg1 loss, we deleted the three tandem Dsg1 genes in mice using CRISPR/Cas9. Whole transcriptome analysis of E18.5Dsg1−/−skin showed changes consistent with the observed aberrant differentiation and barrier impairment. Comparing epidermal transcriptomes from E18.5 Dsg1-deficient mice and humans with Dsg1 mutations revealed a shared psoriatic-like IL-17-skewed inflammatory signature and less so a pro-allergic IL-4/13 signature. Although the impaired intercellular adhesion observed inDsg1−/−mice resembles that resulting from autoimmune anti-Dsg1 pemphigus foliaceus antibodies, transcriptomic analysis of pemphigus skin lesions lacks a prominent IL-17 signature. Thus, beyond impairing the physical barrier, chronic loss of Dsg1 function through gene mutation results in a psoriatic-like inflammatory signature before birth, possibly predisposing to skin inflammation.
The genomic architecture of adaptation to larval malnutrition points to a trade-off with adult starvation resistance inDrosophila
Authors: Kawecki Tadeusz J. , Erkosar Berra , Dupuis Cindy , Hollis Brian , Stillwell R. Craig , Kapun Martin
Published: December 2020

Periods of nutrient shortage impose strong selection on animal populations. Experimental studies of genetic adaptation to nutrient shortage largely focus on resistance to acute starvation at adult stage; it is not clear how conclusions drawn from these studies extrapolate to other forms of nutritional stress. We studied the genomic signature of adaptation to chronic juvenile malnutrition in six populationsof Drosophila melanogasterevolved for 150 generations on an extremely nutrient-poor larval diet. Comparison with control populations evolved on standard food revealed repeatable genomic differentiation between the two set of population, involving >3,000 candidate SNPs forming >100 independently evolving clusters. The candidate genomic regions were enriched in genes implicated in hormone, carbohydrate, and lipid metabolism, including some with known effects on fitness-related life-history traits. Rather than being close to fixation, a substantial fraction of candidate SNPs segregated at intermediate allele frequencies in all malnutrition-adapted populations. This, together with patterns of among-population variation in allele frequencies and estimates of Tajima’sD, suggests that the poor diet results in balancing selection on some genomic regions. Our candidate genes for tolerance to larval malnutrition showed a high overlap with genes previously implicated in acute starvation resistance. However, adaptation to larval malnutrition in our study was associated with reduced tolerance to acute adult starvation. Thus, rather than reflecting synergy, the shared genomic architecture appears to mediate an evolutionary trade-off between tolerances to these two forms of nutritional stress.