bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractS-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 summaryThe 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

ABSTRACTHeterotopic 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

AbstractDifferentiation 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

AbstractThe 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.
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

AbstractCulture-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).ImportanceThis 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

ABSTRACTOne 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

AbstractIn 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

AbstractStructural 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

AbstractAnimals 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

AbstractThe 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

SUMMARYChronic 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-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

ABSTRACTExtracellular 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.