bluuebunny/crossref_metadata_2025 huggingface dataset:
Tax Burdens in Japan and South Korea: Measurement Using Average Effective Tax Rates
Authors: PARK Sung Ho
Published: November 2019

Although tax policies in Japan and South Korea have notably changed over recent decades, few studies have thoroughly examined the nature of these changes. Building on the average effective tax rates developed by Mendoza et al. (1994) and OECD researchers (Carey and Tchilinguirian 2000; Carey and Rabesona 2003) and extending and revising their original data, this study analyzes the structure of tax burdens in these two countries over 1995–2015. In particular, it examines the scholarly claim that taxation in these countries has become increasingly neoliberal over recent decades. The author finds insufficient evidence to support fiscal neoliberalism as race-to-the-bottom cuts in public taxation. Future studies may conduct in-depth comparative and case analyses to better understand the nature of the new tax structure emerging in these countries.
Evaluation of lipid matrix microencapsulation for intestinal delivery of thymol in weaned pigs
Authors: Choi Janghan , Wang Lucy , Ammeter Emily , Lahaye Ludovic , Liu Song , Nyachoti Martin , Yang Chengbo
Published: November 2019

Essential oils (EO) are defined as plant-derived natural bioactive compounds, which can have positive effects on animal growth and health due to their antimicrobial and antioxidative properties. However, EO are volatile, can evaporate quickly, and be rapidly absorbed in the upper gastrointestinal tract. Also, due to their labile nature, the stability of EO during feed processing is often questionable, leading to variations in the final concentration in feed. Encapsulation has become one of the most popular methods of stabilizing EO during feed processing, storage, and delivery into the lower gut. The objectives of the present study were to 1) evaluate the stability of thymol microencapsulated in combination with organic acids in commercially available lipid matrix microparticles during the feed pelleting process and storage; 2) validate and demonstrate the slow release of thymol from the lipid matrix microparticles in a simulated pig gastric fluid (SGF) and a simulated pig intestinal fluid (SIF); and 3) evaluate in vivo release of thymol from the lipid matrix microparticles along the pig gut. The results showed that thymol concentration was not significantly different in the mash and pelleted feeds (P > 0.05). In the in vitro study, 26.04% thymol was released in SGF, and the rest of the thymol was progressively released in SIF until completion, which was achieved by 24 h. The in vivo study showed that 15.5% of thymol was released in the stomach, and 41.85% of thymol was delivered in the mid-jejunum section. Only 2.21% of thymol was recovered in feces. In conclusion, the lipid matrix microparticles were able to maintain the stability of thymol during a feed pelleting process and storage and allow a slow and progressive intestinal release of thymol in weaned pigs.
Specific Detection and Identification of Fusarium graminearum Sensu Stricto Using a PCR-RFLP Tool and Specific Primers Targeting the Translational Elongation Factor 1α Gene
Authors: Hafez Mohamed , Abdelmagid Ahmed , Adam Lorne R. , Daayf Fouad
Published: November 2019

Fusarium graminearum is a toxigenic plant pathogen that causes Fusarium head blight (FHB) disease on cereal crops. It has recently shown to have cross-pathogenicity on noncereals (i.e., Fusarium root rot [FRR] on soybean) in Canada and elsewhere. Specific detection and differentiation of this potent toxigenic, trichothecene-producing pathogen among other closely related species is extremely important for disease control and mycotoxin monitoring. Here, we designed a PCR restriction fragment length polymorphism protocol based on the DNA sequence of the translational elongation factor 1α (TEF1α) gene. A unique restriction site to the enzyme HpaII is only found in F. graminearum sensu stricto strains among different Fusarium strains in the F. graminearum species complex (FGSC) and other Fusarium spp. associated with FHB in cereals and FRR in soybean. Partial amplification of the TEF1α gene with newly designed primers mh1/mh2 generated a 459-bp PCR fragment. Restriction digestion of the generated fragments with the HpaII enzyme generated a unique restriction pattern that can rapidly and accurately differentiate F. graminearum sensu stricto among all other Fusarium spp. A primer pair (FgssF/FgssR) specific to F. graminearum sensu stricto also was designed and can distinguish F. graminearum sensu stricto from all other Fusarium spp. in the FGSC and other closely related Fusarium spp. involved in FHB and FRR. This finding will be very useful for the specific detection of F. graminearum sensu stricto for diagnostic purposes as well as for the accurate detection of this pathogen in breeding and other research purposes.
Succinate dehydrogenase deficiency in a chromaffin cell model retains metabolic fitness through the maintenance of mitochondrial NADH oxidoreductase function
Authors: Kľučková Katarína , Thakker Alpesh , Vettore Lisa , Escribano-Gonzalez Cristina , Hindshaw Rebecca L. , Tearle Jacqueline L. E. , Goncalves Judith , Kaul Baksho , Lavery Gareth G. , Favier Judith , Tennant Daniel A.
Published: November 2019

Mutations in succinate dehydrogenase (SDH) lead to the development of tumors in a restricted subset of cell types, including chromaffin cells and paraganglia. The molecular basis for this specificity is currently unknown. We show that loss of SDH activity in a chromaffin cell model does not perturb complex I function, retaining the ability to oxidize NADH within the electron transport chain. This activity supports continued oxidation of substrates within the tricarboxylic acid (TCA) cycle. However, due to the block in the TCA cycle at SDH, the high glutamine oxidation activity is only maintained through an efflux of succinate. We also show that although the mitochondria of SDH‐deficient cells are less active per se, their higher mass per cell results in an overall respiratory rate that is comparable with wild‐type cells. Finally, we observed that when their mitochondria are uncoupled, SDH‐deficient cells are unable to preserve their viability, suggesting that the mitochondrial metabolic network is unable to compensate when exposed to additional stress. We therefore show that in contrast to models of SDH deficiency based on epithelial cells, a chromaffin cell model retains aspects of metabolic “health,” which could form the basis of cell specificity of this rare tumor type.
An international multicenter examination of MOG antibody assays
Authors: Reindl Markus , Schanda Kathrin , Woodhall Mark , Tea Fiona , Ramanathan Sudarshini , Sagen Jessica , Fryer Jim , Mills John , Teegen Bianca , Mindorf Swantje , Ritter Nora , Krummrei Ulrike , Stöcker Winfried , Eggert Juliane , Flanagan Eoin P. , Ramberger Melanie , Hegen Harald , Rostasy Kevin , Berger Thomas , Leite Maria Isabel , Palace Jacqueline , Irani Sarosh R. , Dale Russell C. , Probst Christian , Probst Monika , Brilot Fabienne , Pittock Sean , Waters Patrick
Published: November 2019

Objectives

To compare the reproducibility of 11 antibody assays for IgG and IgM myelin oligodendrocyte glycoprotein antibodies (MOG-IgG, MOG-IgM) from five international centers.

Methods

The following samples were analyzed: MOG-IgG clearly positive sera (n=39), MOG-IgG low positive sera (n=39), borderline negative sera (n=13), clearly negative sera (n=40), and healthy blood donors (n=30). As technical controls, 18 replicates (9 MOG-IgG positive and 9 negative) were included. All samples and controls were re-coded, aliquoted, and distributed to the five testing centers which performed the following antibody assays: five live and one fixed immunofluorescence cell-based assays (CBA-IF, five MOG-IgG, one MOG-IgM), three live flow cytometry cell-based assays (FACS-CBA, all MOG-IgG), and two enzyme-linked immunosorbent assays (ELISA, both MOG-IgG).

Results

We found excellent agreement (96%) between the live CBAs for MOG-IgG for samples previously identified as clearly positive or negative from four different national testing centers. The agreement was lower with fixed CBA-IF (90%) and the ELISA showed no concordance with CBAs for detection of human MOG-IgG. All CBAs showed excellent inter-assay reproducibility. The agreement of MOG-IgG CBAs for borderline negative (77%) and particularly low positive (33%) samples was less good. Finally, most samples from healthy blood donors (97%) were negative for MOG-IgG in all CBAs.

Conclusion

Live MOG-IgG CBAs showed excellent agreement for high positive and very good agreement for negative samples at four international testing centers. Low positive samples were more frequently discordant than in similar assays for other autoantigens. Further research is needed to improve international standardization for clinical care.
Differential asthma risk following respiratory infection in children from three minority populations
Authors: Wohlford Eric M. , Borrell Luisa N. , Elhawary Jennifer R. , Plotkin Brian , Oh Sam S. , Nuckton Thomas J. , Eng Celeste , Salazar Sandra , LeNoir Michael A. , Meade Kelley , Farber Harold J. , Serebrisky Denise , Brigino-Buenaventura Emerita , Rodriguez-Cintron William , Kumar Rajesh , Thyne Shannon , Seibold Max A. , Rodriguez-Santana José R. , Burchard Esteban G.
Published: November 2019

Rationale

Severe early-life respiratory illnesses, particularly those caused by respiratory syncytial virus (RSV) and human rhinovirus (HRV), are strongly associated with the development of asthma in children. Puerto Rican children in particular have a strikingly high asthma burden, but prior studies of the potential associations between early-life respiratory illnesses and asthma in Puerto Rican and other minority populations have been limited.

Objectives

We sought to determine whether early-life respiratory illness was associated with asthma in Puerto Rican children relative to other minority children.

Methods

Using a logistic regression analysis, we examined the association between early-life respiratory illnesses (report of upper respiratory infection (URI), pneumonia, bronchitis, and bronchiolitis/RSV) within the first two years of life and physician-diagnosed asthma after the age of two in a large cohort of minority children.

Measurements and Main Results

Early-life respiratory illnesses were associated with greater asthma risk in Puerto Ricans relative to other racial/ethnic minority populations. Specifically, in Puerto Ricans, the odds was 6.15 (95% CI: 4.21-9.05) if the child reported at least one of the following respiratory illness: URI, pneumonia, bronchitis or bronchiolitis. The odds were also higher in Puerto Ricans when considering these conditions separately.

Conclusions

We observe population-specific associations between early-life respiratory illnesses and asthma, which was especially significant in Puerto Ricans. Taken together with the known high burden of RSV in Puerto Rico, our results may help explain the high burden of asthma in Puerto Ricans.
Brain functional network integrity sustains cognitive function despite atrophy in presymptomatic genetic frontotemporal dementia
Authors: Tsvetanov Kamen A. , Gazzina Stefano , Jones P. Simon , Swieten John van , Borroni Barbara , Sanchez-Valle Raquel , Moreno Fermin , Laforce Robert , Graff Caroline , Synofzik Matthis , Galimberti Daniela , Masellis Mario , Tartaglia Maria Carmela , Finger Elizabeth , Vandenberghe Rik , de Mendonça Alexandre , Tagliavini Fabrizio , Santana Isabel , Ducharme Simon , Butler Chris , Gerhard Alexander , Danek Adrian , Levin Johannes , Otto Markus , Frisoni Giovanni , Ghidoni Roberta , Sorbi Sandro , Rohrer Jonathan D. , Rowe James B.
Published: November 2019

INTRODUCTION

The presymptomatic phase of neurodegenerative disease can last many years, with sustained cognitive function despite progressive atrophy. We investigate this phenomenon in familial Frontotemporal dementia (FTD).

METHODS

We studied 121 presymptomatic FTD mutation carriers and 134 family members without mutations, using multivariate data-driven approach to link cognitive performance with both structural and functional magnetic resonance imaging. Atrophy and brain network connectivity were compared between groups, in relation to the time from expected symptom onset.

RESULTS

There were group differences in brain structure and function, in the absence of differences in cognitive performance. Specifically, we identified behaviourally-relevant structural and functional network differences. Structure-function relationships were similar in both groups, but coupling between functional connectivity and cognition was stronger for carriers than for non-carriers, and increased with proximity to the expected onset of disease.

DISCUSSION

Our findings suggest that maintenance of functional network connectivity enables carriers to maintain cognitive performance.
Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites
Authors: Perlinska Agata P. , Stasiulewicz Adam , Nawrocka Ewa K. , Kazimierczuk Krzysztof , Setny Piotr , Sulkowska Joanna I.
Published: November 2019

S-adenosylmethionine (SAM) is one of the most important enzyme substrates. It is vital for the function of various proteins, including large group of methyltransferases (MTs). Intriguingly, some bacterial and eukaryotic MTs, while catalysing the same reaction, possess significantly different topologies, with the former being a knotted one. Here, we conducted a comprehensive analysis of SAM conformational space and factors that affect its vastness. We investigated SAM in two forms: free in water (via NMR studies and explicit solvent simulations) and bound to proteins (based on all data available in the PDB). We identified structural descriptors – angles which show the major differences in SAM conformation between unknotted and knotted methyltransferases. Moreover, we report that this is caused mainly by a characteristic for knotted MTs tight binding site formed by the knot and the presence of adenine-binding loop. Additionally, we elucidate conformational restrictions imposed on SAM molecules by other protein groups in comparison to conformational space in water.

Author summary

The topology of a folded polypeptide chain has great impact on the resulting protein function and its interaction with ligands. Interestingly, topological constraints appear to affect binding of one of the most ubiquitous substrates in the cell, S-adenosylmethionine (SAM), to its target proteins. Here, we demonstrate how binding sites of specific proteins restrict SAM conformational freedom in comparison to its unbound state, with a special interest in proteins with non-trivial topology, including an exciting group of knotted methyltransferases. Using a vast array of computational methods combined with NMR experiments, we identify key structural features of knotted methyltransferases that impose unorthodox SAM conformations. We compare them with the characteristics of standard, unknotted SAM binding proteins. These results are significant for understanding differences between analogous, yet topologically different enzymes, as well as for future rational drug design.
Genome-wide association and functional analyses identify CASC20 and KIF26B as target loci in heterotopic ossification
Authors: Hatzikotoulas Konstantinos , Pickering George AE , Clark Matthew J , Felix-Ilemhenbhio Favour , Kocsy Klaudia , Simpson Jonathan , MacInnes Scott J , Koprulu Mine , Southam Lorraine , Bellantuono Ilaria , Baidžajevas Kajus , Young David A , Gartland Alison , Zeggini Eleftheria , Kiss-Toth Endre , Wilkinson J Mark
Published: November 2019

Heterotopic ossification (HO) is bone formation that occurs after trauma within tissues that do not normally have the property of ossification, resulting in pain and disability. The genetic architecture of HO remains unclear. In the first genome-wide association studies of this disease, we identify the human-only long non-coding RNA-encoding gene CASC20 as a robust, replicating susceptibility locus for HO and KIF26B as a potential severity locus. We find that both CASC20 and KIF26B are expressed in human bone. Both CASC20 and KIF26B expression is upregulated upon BMP2 induced osteogenic differentiation in primary human mesenchymal stem cells, followed by RUNX2 and OSTERIX upregulation and mineralised nodule formation. A CRISPR-Cas9 mediated knockout of Kif26b inhibits BMP2-induced Runx2, Sp7/Osterix, Col1A1, Alp, and Bglap/Osteocalcin expression in a murine myocyte model of osteogenic trans-differentiation, and prevents mineralised nodule formation. These studies provide the first insights into the heritable biology of common, complex HO.
Single-cell molecular profiling provides a high-resolution map of basophil and mast cell differentiation
Authors: Hamey Fiona K. , Lau Winnie W.Y. , Kucinski Iwo , Wang Xiaonan , Diamanti Evangelia , Wilson Nicola K. , Göttgens Berthold , Dahlin Joakim S.
Published: November 2019

Differentiation of hematopoietic stem and progenitor cells ensure a continuous supply of mature blood cells. Recent models of differentiation are represented as a landscape, in which individual progenitors traverse a continuum of multipotent cell states before reaching an entry point that marks lineage commitment. Basophils and mast cells have received little attention in these models and their differentiation trajectories are yet to be explored. Here, we have performed multicolor flow cytometry and high-coverage single-cell RNA sequencing analyses to chart the differentiation of hematopoietic progenitors into basophils and mast cells in mouse. Analysis of flow cytometry data reconstructed a detailed map of the differentiation, including a bifurcation of progenitors into two specific trajectories. Molecular profiling and pseudotime ordering of the single cells revealed gene expression changes during differentiation, with temporally separated regulation of mast cell protease genes. We validate that basophil and mast cell signature genes increased along the trajectories into their respective lineage, and we demonstrate how genes critical for each respective lineage are upregulated during the formation of the mature cells. Cell fate assays showed that multicolor flow cytometry and transcriptional profiling successfully predict the bipotent phenotype of a previously uncharacterized population of basophil-mast cell progenitor-like cells in mouse peritoneum. Taken together, we provide a detailed roadmap of basophil and mast cell development through a combination of molecular and functional profiling.
Genetic diversity of tilapia lake virus genome segment 1 from 2011 to 2019 and a newly validated semi-nested RT-PCR method
Authors: Taengphu Suwimon , Sangsuriya Pakkakul , Phiwsaiya Kornsunee , Debnath Partho Pratim , Delamare-Deboutteville Jerome , Mohan Chadag Vishnumurthy , Dong Ha Thanh , Senapin Saengchan
Published: November 2019

The gene of RNA viruses, encoding RNA-directed RNA polymerase (RdRp) is relatively conserved due to its crucial function in viral genome replication and transcription making it a useful target for genetic diversity study and PCR detection. In this study, we investigated the genetic diversity of 21 tilapia lake virus (TiLV) genome segment 1 sequences predictively coding for RdRp subunit P1. Those sequences were obtained from infected fish samples collected in Ecuador, Israel, Peru, and Thailand between 2011 and 2019 (nine sequences from this study and 12 sequences from GenBank). Primers were then designed from the highly conserved regions among all 21 TiLV segment 1 sequences and used in semi-nested RT-PCR condition optimization. The result revealed that all 21 TiLV segment 1 sequences showed 95.00-99.94 and 99.00-100% nucleotide and amino acid sequence identity, respectively. These isolates were phylogenically clustered into three separate genetic clades, called i) Israeli-2011 clade (containing of TiLV isolates from Israel collected in 2011, Ecuador, and Peru isolates), ii) monophyletic Israel-2012 clade (containing only TiLV isolates collected from Israel in 2012), and iii) Thai clade (containing only sequences obtained from Thailand isolates). The newly established PCR protocol was 100 times more sensitive than our previous segment 3-based protocol when comparatively assayed with RNA extracted from infected fish. The assay was also shown to be specific when tested against negative control samples, i.e. RNA extracted from clinical healthy tilapia and from bacterial and viral pathogens (other than TiLV) commonly found in aquatic animals. Validation experiment with RNA extracted from naturally infected fish specimens collected in 2013-2019 yielded positive test results for all samples tested, confirming that our newly designed primers and detection protocol against TiLV segment 1, have a potential application for detection of all current genetic variants of TiLV.
Winter in water: Differential responses and the maintenance of biodiversity
Authors: McMeans Bailey , McCann Kevin , Guzzo Matthew , Bartley Timothy , Bieg Carling , Blanchfield Paul , Fernandes Timothy , Giacomini Henrique , Middel Trevor , Rennie Michael , Ridgway Mark , Shuter Brian
Published: November 2019

The ecological consequences of winter in freshwater systems are an understudied but rapidly emerging research area. Here, we argue that winter periods of reduced temperature and light (and potentially oxygen and resources) could play an underappreciated role in mediating the coexistence of species. This may be especially true for temperate and subarctic lakes, where seasonal changes in the thermal environment might fundamentally structure species interactions. With climate change already shortening ice-covered periods on temperate and polar lakes, consideration of how winter conditions shape biotic interactions is urgently needed. Using freshwater fishes in northern temperate lakes as a case study, we demonstrate how physiological trait differences (e.g., thermal preference, light sensitivity) drive differential behavioral responses to winter among competing species. Specifically, some species have a higher capacity for winter activity than others. Existing and new theory is presented to argue that such differential responses to winter can promote species coexistence. Importantly, if winter is a driver of niche differences that weaken competition between relative to within species, then shrinking winter periods could threaten coexistence by tipping the scales in favor of certain sets of species over others.
Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms
Authors: Fu Xi , Li Yanling , Yuan Qianqian , Cai Gui-hong , Deng Yiqun , Zhang Xin , Norbäck Dan , Sun Yu
Published: November 2019

Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome surveys have not been conducted in hotel environments; thus, the composition and associated environmental factors are not clear. We presented the first continental-scale microbiome study of hotel rooms (n = 68) spanning large geographic regions. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified, but fungal taxa showed a local distribution compared with bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with high compositional similarity to previous samples from building and human nasopharynx environments. The abundance ofAspergilluswas negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbial dynamics and 16 indoor and outdoor environmental characteristics. Fungal β-diversity and quantity showed concordant variation and were associated with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea and visible mold, while α-diversity decreased with heavy traffic (95% CI: −127.05 to −0.25) and wall-to-wall carpet (95% CI: −47.60 to −3.82). Bacterial β-diversity was associated with latitude, quality of the interior and floor type, while α-diversity decreased with recent decoration (95% CI −179.00 to −44.55) and mechanical ventilation (95% CI: −136.71 to −5.12).

Importance

This is the first microbiome study to characterize microbial composition and associated environmental characteristics. In this study, we found concordant variation between microbial β-diversity and absolute quantity and discordant variation between β-diversity/quantity and α-diversity. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.
Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using VirusFISH
Authors: Castillo Yaiza M. , Sebastián Marta , Forn Irene , Grimsley Nigel , Yau Sheree , Moraru Cristina , Vaqué Dolors
Published: November 2019

One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. For this, techniques that enable the detection and quantification of virus–host interactions at the single-cell level are essential. With this goal in mind, we implemented VirusFISH (Virus Fluorescencein situHybridization) using as a model the marine picoeukaryoteOstreococcus tauriand its virus OtV5. VirusFISH allowed the visualization and quantification of the fraction of infected cells during an infection experiment. We were also able to quantify the abundance of free viruses released during cell lysis and assess the burst size of our non-axenic culture, because we could discriminate OtV5 from phages. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were produced between 8 and 24 h, propagating the infection. Nevertheless, the production of viral particles increased drastically after 24 h. The burst size for theO. tauri–OtV5 system was 7±0.4 OtV5 per cell, which was consistent with the estimated amount of viruses inside the cell prior to cell lysis. With this work we demonstrate that VirusFISH is a promising technique to study specific virus–host interactions in non-axenic cultures, and set the ground for its application in complex natural communities.
CtIP -mediated alternative mRNA splicing finetunes the DNA damage response
Authors: Prados-Carvajal Rosario , Rodríguez-Real Guillermo , Gutierrez-Pozo Gabriel , Huertas Pablo
Published: November 2019

In order to survive to the exposure of DNA damaging agents, cells activate a complex response that coordinates the cellular metabolism, cell cycle progression and DNA repair. Among many other events, recent evidence has described global changes in mRNA splicing in cells treated with genotoxic agents. Here, we explore further this DNA damage-dependent alternative splicing. Indeed, we show that both the splicing factor SF3B2 and the repair protein CtIP contribute to the global pattern of splicing both in cells treated or not to DNA damaging agents. Additionally, we focus on a specific DNA damage- and CtIP-dependent alternative splicing event of the helicase PIF1 and explore its relevance for the survival of cells upon exposure to ionizing radiation. Indeed, we described how the nuclear, active form of PIF1 is substituted by a splicing variant, named vPIF1, in a fashion that requires both the presence of DNA damage and CtIP. Interestingly, timely expression of vPIF1 is required for optimal survival to exposure to DNA damaging agents, but early expression of this isoform delays early events of the DNA damage response. On the contrary, expression of the full length PIF1 facilitates those early events, but increases the sensitivity to DNA damaging agents if the expression is maintained long-term.
Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes
Authors: Sanders Ashley D. , Meiers Sascha , Ghareghani Maryam , Porubsky David , Jeong Hyobin , van Vliet M. Alexandra C.C. , Rausch Tobias , Richter-Pechańska Paulina , Kunz Joachim B. , Jenni Silvia , Raeder Benjamin , Kinanen Venla , Zimmermann Jürgen , Benes Vladimir , Schrappe Martin , Mardin Balca R. , Kulozik Andreas , Bornhauser Beat , Bourquin Jean-Pierre , Marschall Tobias , Korbel Jan O.
Published: November 2019

Structural variation (SV), where rearrangements delete, duplicate, invert or translocate DNA segments, is a major source of somatic cell variation. It can arise in rapid bursts, mediate genetic heterogenity, and dysregulate cancer-related pathways. The challenge to systematically discover SVs in single cells remains unsolved, with copy-neutral and complex variants typically escaping detection. We developed single cell tri-channel-processing (scTRIP), a computational framework that jointly integrates read depth, template strand and haplotype phase to comprehensively discover SVs in single cells. We surveyed SV landscapes of 565 single cell genomes, including transformed epithelial cells and patient-derived leukemic samples, and discovered abundant SV classes including inversions, translocations and large-scale genomic rearrangements mediating oncogenic dysregulation. We dissected the ‘molecular karyotype’ of the leukemic samples and examined their clonal structure. Different from prior methods, scTRIP also enabled direct detection and discrimination of SV mutational processes in individual cells, including breakage-fusion-bridge cycles. scTRIP will facilitate studies of clonal evolution, genetic mosaicism and somatic SV formation, and could improve disease classification for precision medicine.
Convergence and divergence in anti-predator displays: A novel approach to quantitative behavioural comparison in snakes
Authors: Rabosky Alison R. Davis , Moore Talia Y. , Sánchez-Paredes Ciara M. , Westeen Erin P. , Larson Joanna G. , Sealey Briana A. , Balinski Bailey A.
Published: November 2019

Animals in nature use diverse strategies to evade or deter their predators, including many vivid behavioural displays only qualitatively described from field encounters with natural predators or humans. Within venomous snake mimicry, stereotyped anti-predator displays are suggested to be a critical component of the warning signal given by toxic models and thus under strong selection for independent convergence in mimetic species. However, no studies have systematically quantified variation in snake anti-predator displays across taxonomically broad clades to test how these behaviours evolve across species within a phylogenetic comparative methods framework. Here we describe a new, high-throughput approach for collecting and scoring snake anti-predator displays in the field that demonstrates both low observer bias and infinite extension across any species. Then, we show our method’s utility in quantitatively comparing the behaviour of 20 highly-divergent snake species from the Amazonian lowlands of Peru. We found that a simple experimental setup varying simulated predator cues was very successful in eliciting anti-predator displays across species and that high-speed videography captured a greater diversity of behavioural responses than described in the literature. We also found that although different display components evolve at different rates with complicated patterns of covariance, there is clear evidence of evolutionary convergence in anti-predator displays among distantly related elapid coral snakes and their colubrid mimics. We conclude that our approach provides new opportunity for analyses of snake behaviour, kinematics, and the evolution of anti-predator signals more generally, especially macroevolutionary analyses across clades with similarly intractable behavioural diversity.
Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch
Authors: Barbier Içvara , Carrasco Rubén Perez , Schaerli Yolanda
Published: November 2019

The formation of spatiotemporal patterns of gene expression is frequently guided by gradients of diffusible signaling molecules. The toggle switch subnetwork, composed of two cross-repressing transcription factors, is a common component of gene regulatory networks in charge of patterning, converting the continuous information provided by the gradient into discrete abutting stripes of gene expression. We present a synthetic biology framework to understand and characterize the spatiotemporal patterning properties of the toggle switch. To this end, we built a synthetic toggle switch controllable by diffusible molecules inEscherichia coli. We analyzed the patterning capabilities of the circuit by combining quantitative measurements with a mathematical reconstruction of the underlying dynamical system. The toggle switch can produce robust patterns with sharp boundaries, governed by bistability and hysteresis. We further demonstrate how the hysteresis, position, timing, and precision of the boundary can be controlled, highlighting the dynamical flexibility of the circuit.
Chronic viral infection promotes early germinal center exit of B cells and impaired antibody development
Authors: Staupe Ryan P. , Vella Laura A. , Manne Sasikanth , Giles Josephine R. , Meng Wenzhao , Herati Ramin Sedaghat , Khan Omar , Wu Jennifer E. , Baxter Amy E. , Prak Eline T. Luning , Wherry E. John
Published: November 2019

Chronic viral infections disrupt B cell responses leading to impaired affinity maturation and delayed control of viremia. Previous studies have identified early pre-germinal center (GC) B cell attrition but the impact of chronic infections on B cell fate decisions in the GC remains poorly understood. To address this question, we used single-cell transcriptional profiling of virus-specific GC B cells to test the hypothesis that chronic viral infection disrupted GC B cell fate decisions leading to suboptimal humoral immunity. These studies revealed a critical GC differentiation checkpoint that is disrupted by chronic infection, specifically at the point of dark zone re-entry. During chronic viral infection, virus-specific GC B cells were shunted towards terminal plasma cell (PC) or memory B cell (MBC) fates at the expense of continued participation in the GC. Early GC exit was associated with decreased B cell mutational burden and antibody quality. Persisting antigen and inflammation independently drove facets of dysregulation, with a key role for inflammation in directing premature terminal GC B cell differentiation and GC exit. Thus, these studies define GC defects during chronic viral infection and identify a critical GC checkpoint that is short-circuited, preventing optimal maturation of humoral immunity.
Brain coding of social network structure
Authors: Peer Michael , Hayman Mordechai , Tamir Bar , Arzy Shahar
Published: November 2019

To successfully navigate our social world, we keep track of other individuals’ relations to ourselves and to each other. But how does the brain encode this information? To answer this question, we mined participants’ social media (FacebookTM) profiles to objectively characterize the relations between individuals in their real-life social networks. Under fMRI, participants answered questions on each of these individuals. Using representational similarity analysis, we identified social network structure coding in the default-mode network (medial prefrontal, medial parietal and lateral parietal cortices). When regressing out subjective factors (ratings of personal affiliation, appearance and personality), social network structure information was uniquely found in the retrosplenial complex, a region implicated in spatial processing. In contrast, information on individuals’ personality traits and affiliation to the subjects was found in the medial prefrontal and parietal cortices, respectively. These findings demonstrate a cortical division between representation of structural, trait-based and self-referenced social knowledge.
Brain-Derived Extracellular Vesicles are Highly Enriched in the Prion Protein and Its C1 Fragment: Relevance for Cellular Uptake and Implications in Stroke
Authors: Brenna Santra , Altmeppen Hermann C. , Mohammadi Behnam , Rissiek Björn , Schlink Florence , Ludewig Peter , Failla Antonio Virgilio , Schneider Carola , Glatzel Markus , Puig Berta , Magnus Tim
Published: November 2019

Extracellular vesicles (EVs) are important means of intercellular communication and a potent tool for regenerative therapy. In ischemic stroke, transient blockage of a brain artery leads to a lack of glucose and oxygen in the affected brain tissue, provoking neuronal death by necrosis in the core of the ischemic region. The fate of neurons in the surrounding penumbra depends on the stimuli, including EVs, received during the following hours. A detailed characterization of such stimuli is crucial not only for understanding stroke pathophysiology but also for new therapeutic interventions.

In the present study, we characterize the EVs in mouse brain under physiological conditions and 24h after induction of transient ischemia in mice. We show that, in steady-state conditions, microglia are the main source of small EVs (sEVs) whereas after ischemia, the main EV population originates from astrocytes. Moreover, sEVs presented high amounts of the prion protein (PrP) which were increased after stroke. Conspicuously, sEVs were particularly enriched in a truncated PrP fragment (PrP-C1). Because of similarities between PrP-C1 and certain viral surface proteins, we studied the cellular uptake of brain-derived sEVs from mice lacking (PrP-KO) or containing PrP (WT). We show that PrP-KO-EVs are rapidly taken up by neurons and colocalize with lysosomes. Although eventually WT-EVs are also found in lysosomes, the amount taken up by neurons is significantly higher for PrP-KO-EVs. Likewise, microglia and astrocytes were also engulfing PrP-KO-sEVs more efficiently than WT-sEVs.

Our results provide information on the relative contribution of brain cell types to the sEV pool in mice and indicate that increased release of sEVs by astrocytes together with elevated levels of PrP in sEVs may play a role in intercellular communication at early stages after stroke. In addition, amounts of PrP (and probably PrP-C1) in brain sEVs seem to contribute to their cellular uptake.
The effect of a temperature-sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen
Authors: Bruneaux Matthieu , Ashrafi Roghaieh , Kronholm Ilkka , Laanto Elina , Örmälä-Odegrip Anni-Maria , Galarza Juan A. , Zihan Chen , Sumathi Mruthyunjay Kubendran , Ketola Tarmo
Published: November 2019

Viruses are key actors of ecosystems and have major impacts on global biogeochemical cycles. Prophages deserve particular attention as they are ubiquitous in bacterial genomes and can enter a lytic cycle when triggered by environmental conditions. We explored how temperature affects the interactions between prophages and other biological levels by using an opportunistic pathogen, the bacterium Serratia marcescens, that harbours several prophages and that had undergone an evolution experiment under several temperature regimes. We found that the release of one of the prophages was temperature-sensitive and malleable to evolutionary changes. We further discovered that the virulence of the bacterium in an insect model also evolved and was positively correlated with phage release rates. We determined through analysis of genetic and epigenetic data that changes in the outer cell wall structure possibly explain this phenomenon. We hypothezise that the temperature-dependent phage release rate acted as a selection pressure on S. marcescens and that it resulted in modified bacterial virulence in the insect host. Our study system illustrates how viruses can mediate the influence of abiotic environmental changes to other biological levels and thus be involved in ecosystem feedback loops.
Amplitude and timescale of metacommunity trait-lag response to climate change
Authors: Norberg Jon , Moor Helen
Published: November 2019

Climate change is altering the structure and functioning of communities1. Trait-based approaches are powerful predictive tools that allow consideration of changes in structure and functioning simultaneously2, 3. The realised biomass-weighted trait distribution of a community rests on the ecophysiology of individuals, but integrates local species interactions and spatial dynamics that feed back to ecosystem functioning. Consider a response trait that determines species performance (e.g. growth rate) as a function of an environmental variable (e.g. temperature). The change in this response trait’s distribution following directional environmental change integrates all factors contributing to the community’s response and directly reflects the community’s response capacity3.

Here we introduce the average regional community trait-lag (TLMC) as a novel measure of whole-metacommunity response to warming. We show that functional compensation (shifts in resident species relative abundances) confers initial response capacity to communities by reducing and delaying the initial development of a trait-lag. Metacommunity adaptive capacity in the long-term, however, was dependent on dispersal and species tracking of their climate niche by incremental traversal of the landscape. With increasing inter-patch distances, network properties of the functional connectivity network became increasingly more important, and may guide prioritisation of habitat for conservation.
Axonal mitochondria across species adjust in diameter depending on thickness of surrounding myelin
Authors: Ineichen Benjamin V , Zhu Keying , Carlström Karl E
Published: November 2019

In the central nervous system (CNS), axons and its surrounding myelin sheaths, generated by oligodendrocytes, greatly depend on each other, where oligodendrocytes provide axons with both trophic and metabolic support. Across spices, assessment of the axon-myelin ultrastructure is the key-approach to visualize de- and re-myelination of axons. However, this assessment omits to provide information on axonal homeostasis or how axon-myelin influence one another. Since mitochondria may adjust in size thus mirroring the intracellular physiological and metabolic status we applied this to myelinated axons in the CNS. We herein show that a large axonal mitochondria diameter correlates with thinner surrounding myelin sheaths across different CNS tracts and species, including human. We also show that the relation between axonal mitochondria diameter and surrounding myelin thickness is a valuable measurement to verify advanced remyelination in two commonly used experimental demyelinating models, namely the cuprizone and the lysolecithin (LPC) model. Lastly, we show that axonal mitochondria adjust in diameter in response to the thickness of the axonal surrounding myelin whereas the opposite adaption was absent. In summary, the link between axonal mitochondria diameter and surrounding myelin thickness provide insight on the axon-myelin relation both during homeostasis and pathological conditions. This link is also translational applicable and can thus contribute to a better understanding on how to study remyelination using experimental models.
Construction of light-activated neurotrophin receptors using the improved Light-Induced Dimerizer (iLID)
Authors: Hope Jen M. , Liu Aofei , Calvin Ghawayne J. , Cui Bianxiao
Published: November 2019

Receptor tyrosine kinases (RTKs) play crucial roles in human health, and their misregulation is implicated in disorders ranging from neurodegenerative disorders to cancers. The highly conserved mechanism of activation of RTKs makes them especially appealing candidates for control via optogenetic dimerization methods. This work offers a strategy for using the improved Light-Induced Dimer (iLID) system with a constructed tandem-dimer of its binding partner nano (tdnano) to build light-activatable versions of RTKs. In the absence of light, the iLID-RTK is cytosolic, monomeric and inactive. Under blue light, the iLID + tdnano system recruits two copies of iLID-RTK to tdnano, dimerizing and activating the RTK. We demonstrate that iLID opto-iTrkA and opto-iTrkB are capable of reproducing downstream ERK and Akt signaling only in the presence of tdnano. We further show with our opto-iTrkA that the system is compatible with multi-day and population-level activation of TrkA in PC12 cells. By leveraging genetic targeting of tdnano, we achieve RTK activation at a specific subcellular location even with whole-cell illumination, allowing us to confidently probe the impact of context on signaling outcome.
A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses
Authors: Geisen Stefan , Vaulot Daniel , Mahé Frédéric , Lara Enrique , de Vargas Colomban , Bass David
Published: November 2019

Protists – all eukaryotes besides fungi, animals, and plants - represent a major part of the taxonomic and functional diversity of eukaryotic life on the planet and drive many ecosystem processes. However, knowledge of protist communities and their diversity lags behind that of most other groups of organisms, largely due to methodological constraints. While protist communities differ markedly between habitats and biomes, they can be studied in very similar ways. Here we provide a guide to current molecular approaches used for studying protist diversity, with a particular focus on amplicon-based high-throughput sequencing (metabarcoding). We highlight that the choice of suitable primers artificially alters community profiles observed in metabarcoding studies. While there are no true ‘universal’ primers to target all protist taxa as a whole, we identify some primer combinations with a wide taxonomic coverage and provide detailed information on their properties. Although environmental protistan ecological research will probably shift towards PCR-free metagenomics or/and transcriptomic approaches in a near future, metabarcoding will remain the method of choice for in-depth community analyses and taxon inventories in biodiversity surveys and ecological studies, due its great cost-efficiency, sensitivity, and throughput. In this paper we provide a guide for scientists from a broad range of disciplines to implement protists in their ecological analyses.
Quantitative Phenotyping of Vascular Damage Caused by Fusarium Wilt Disease in Cowpea
Authors: Ndeve Arsenio D. , Roberts Philip A.
Published: November 2019

Assessment of the severity of Fusarium wilt disease in cowpea and other crops relies mainly on visual rating scales which are prone to errors, which can compromise the reproducibility of the data. Furthermore, the rating scales require considerable practical training and routine experience for reliable assessment. Two objective metrics, stem vascular discoloration length (%VDL) and number of Fusarium necrotic vessels (NFNV), for quantitative measurement of vascular damage incited by Fusarium oxysporum f. sp. tracheiphilum race 4 (Fot4) of cowpea, were compared and their utility as a measure of disease severity and potential usefulness in other crop pathosystems is proposed. The metrics were tested in seven F2 populations and one F2:3 population, segregating for wilt response, and inoculated with race Fot4 at the seedling stage. %VDL and NFNV were highly correlated with plant wilting for all populations (r = 0.51 – 0.93 and 0.52 – 0.94, respectively). Furthermore, the relationships between the variables were linear in all populations (R2 = 0.81 to 0.87 and 0.71 to 0.91), indicating that they can provide accurate and reliable measurement of severity of Fusarium wilt disease. Also, %VDL and NFNV were strongly correlated (r = 0.88 - 0.97) and demonstrated a linear relationship (R2 = 0.69 – 0.94). Analysis of goodness-of-fit in two F2 populations revealed that errors in measurement of vascular discoloration length can result in higher segregation distortion when compared to enumeration of necrotic vessels. However, both metrics were highly effective in accounting for the severity of vascular damage caused by Fusarium wilt disease.