bluuebunny/crossref_metadata_2025 huggingface dataset:
The Cryo-EM structure of AAV2 Rep68 in complex with ssDNA reveals a malleable AAA+machine that can switch between oligomeric states
Authors: Santosh Vishaka , Musayev Faik , Jaiswal Rahul , Zárate-Pérez Francisco , Vandewinkel Bram , Dierckx Caroline , Endicott Molly , Sharifi Kamyar , Dryden Kelly , Henckaerts Els , Escalante Carlos R.
Published: June 2020

The adeno-associated virus (AAV) Rep proteins use a unique AAA+domain to catalyze DNA replication, transcription regulation, and genome packaging. Also, they mediate site-specific integration during a latent phase. To understand the mechanisms underlying AAV Rep function, we investigated the cryo-EM and X-ray structures of Rep68-ssDNA complexes. Surprisingly, Rep68 generates hybrid ring structures where the Origin-Binding-Domain (OBD) forms octameric rings while the helicase domain (HD) forms heptamers. Moreover, the binding to ATPγS promotes a large conformational change in the entire AAA+domain that leads the HD to form both heptamer and hexamers. The HD oligomerization is driven by an interdomain linker region that acts as a latch to ‘catch’ the neighboring HD subunit and is flexible enough to permit the formation of different stoichiometric ring structures. Overall, our studies show the structural basis of AAV Rep’s structural flexibility required to fulfill its multifunctional role during the AAV life cycle.
Glycopeptidomics Analysis of a Cell Line Model Revealing Pathogenesis and Potential Marker Molecules for the Early Diagnosis of Gastric MALT Lymphoma
Authors: Xiao Di , Meng Le , Xu Yanli , Zhang Huifang , Meng Fanliang , He Lihua , Zhang Jianzhong
Published: June 2020

Background

Gastric mucosa-associated lymphoma (GML) is a mature B cell tumor related toHelicobacter pylori(H.pylori) infection. The clinical manifestations of GML are not specific, so GML commonly escapes diagnosis or is misdiagnosed, leading to excessive treatment. The pathogenesis ofH.pylori-induced GML is not well understood and there are no molecular markers for early GML diagnosis.

Methods

Glycopeptidomics analyses of host cell lines (a BCG823 cell line, C823) and C823 cells infected byH. pyloriisolated from patients with GML (GMALT823), gastritis (GAT823), gastric ulcer (GAU823) and gastric cancer (GAC823) were carried out to clarify the host reaction mechanism against GML and identify potential molecular criteria for the early diagnosis of GML.

Findings

Thirty-three samples were analyzed and approximately 2000 proteins, 200 glycoproteins and 500 glycopeptides were detected in each sample. O-glycans were the dominant glycoforms in GMALT823 cells only. Four specific glycoforms in GMALT823 cells and 2 specific glycoforms in C823 and GMALT823 cells were identified. Eight specific glycopeptides of from 7 glycoproteins were found in GMALT823 cells; of these glycopeptides, 6 and 3 specific glycopeptides had high affinity for T cell epitopes and have conformational B cell epitopes, respectively.

Interpretation

The relationship between the predominant glycoforms of host cells and the development of host disease was determined, and the glycoproteins, glycosylation sites and glycoforms might be closely related to the formation of GML, which provides new insight into the pathogenic mechanisms ofH. pyloriinfection and suggests molecular indicators for the early diagnosis of GML.
PENGUINN: Precise Exploration of Nuclear G-quadruplexes Using Interpretable Neural Networks
Authors: Klimentova Eva , Polacek Jakub , Simecek Petr , Alexiou Panagiotis
Published: June 2020

G-quadruplexes (G4s) are a class of stable structural nucleic acid motifs that are known to play a role in a wide spectrum of genomic functions, such as DNA replication and transcription. The classical understanding of G4 structure points to four variable length guanine strands joined by variable length stretches of other nucleotides. Experiments using G4 immunoprecipitation and sequencing experiments have produced a high number of highly probable G4 forming genomic sequences. The expense and technical difficulty of experimental techniques highlights the need for computational approaches of G4 identification. Here, we present PENGUINN, a machine learning method based on Convolutional Neural Networks, that learns the characteristics of G4 sequences and accurately predicts G4s outperforming the state-of-the-art. We provide both a standalone implementation of the trained model, and a web application that can be used to evaluate sequences for their G4 potential.
Integer topological defects organize stresses driving tissue morphogenesis
Authors: Guillamat Pau , Blanch-Mercader Carles , Kruse Karsten , Roux Aurélien
Published: June 2020

Tissues acquire their function and shape via differentiation and morphogenesis. Both processes are driven by coordinating cellular forces and shapes at the tissue scale, but general principles governing this interplay remain to be discovered. Here, we report that self-organization of myoblasts around integer topological defects, namely spirals and asters, triggers localized differentiation and, when differentiation is inhibited, drives the growth of cylindrical multicellular protrusions. Both localized differentiation and growth require specific stress patterns. By analyzing the experimental velocity and orientation profiles through active gel theory, we show that integer topological defects can concentrate compressive stresses, which we measure by using deformable pillars. Altogether, we envision topological defects as mechanical organizational centers that control differentiation and morphogenesis to establish tissue architecture.
Ecological Differentiation Among Globally Distributed Lineages of the Rice Blast Fungus Pyricularia oryzae
Authors: Thierry Maud , Charriat Florian , Milazzo Joëlle , Adreit Henri , Ravel Sébastien , Cros-Arteil Sandrine , Borron Sonia , Sella Violaine , Kroj Thomas , Ioos Renaud , Fournier Elisabeth , Tharreau Didier , Gladieux Pierre
Published: June 2020

Many invasive fungal species coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. Here, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus (Pyricularia oryzae) covering a broad geographical range. We showed that the four lineages of P. oryzae were found in areas with different prevailing environmental conditions and types of rice grown, indicating niche separation. Pathogenicity tests revealed that specialization to rice subspecies contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong barriers to gene flow between these lineages. Our results demonstrate that the spread of a pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct invasive lineages.
Neuralized regulates a travelling wave of Epithelium-to-Neural Stem Cell morphogenesis inDrosophila
Authors: Shard Chloé , Luna-Escalante Juan , Schweisguth François
Published: June 2020

Many tissues are produced during development by specialized progenitor cells emanating from epithelia via an Epithelial-to-Mesenchymal Transition (EMT). Most studies have so far focused on cases involving single or isolated groups of cells. Here we describe an EMT-like process that requires tissue level coordination. This EMT-like process occurs along a continuous front in theDrosophilaoptic lobe neuroepithelium to produce neural stem cells (NSCs). We find that emerging NSCs remain epithelial and apically constrict before dividing asymmetrically to produce neurons. Apical constriction is associated with contractile myosin pulses and requires the E3 ubiquitin ligase Neuralized and RhoGEF3. Neuralized down-regulates the apical protein Crumbs via its interaction with Stardust. Disrupting the regulation of Crumbs by Neuralized led to defects in apical constriction and junctional myosin accumulation, and to imprecision in the integration of emerging NSCs into the transition front. Neuralized therefore appears to mechanically couple NSC fate acquisition with cell-cell rearrangement to promote smooth progression of the differentiation front.
A validated and interpretable predictive model of cruzain inhibitors
Authors: Rosas-Jimenez Jose G. , Garcia-Revilla Marco A. , Madariaga-Mazon Abraham , Martinez-Mayorga Karina
Published: June 2020

Chagas disease affects 8–11 million people worldwide, most of them living in Latin America. Moreover, migratory phenomenon have spread the infection beyond endemic areas. Efforts for the development of new pharmacological therapies are paramount, as the pharmacological profile of the two marketed drugs currently available, nifurtimox and benznidazole, needs to be improved. Cruzain, a parasitic cysteine protease, is one of the most attractive biological targets due to its roles in parasite survival and immune evasion. In this work, we generated Quantitative Structure-Activity Relationship linear models for the prediction of pIC50values of cruzain inhibitors. The statistical parameters for internal and external validation indicate high predictability with a cross-validated correlation coefficient ofand an external correlation coefficient of. The applicability domain is quantitatively defined, according to QSAR good practices, using the leverage method. A qualitative interpretation of the model is provided based on protein-ligand interactions obtained from docking studies and structural information codified in the molecular descriptors relevant to the QSAR model. The model described in this work will be valuable for the discovery of novel cruzain inhibitors.

Author summary

Chagas disease is a major health problem in Latin America. The disease involves a long-lasting silent phase that usually culminates in serious or fatal heart damage. Despite its prevalence, there are only two antichagas approved drugs available. Despite these drugs have been in the market for more than 50 years, significant undesirable side effects and modest effectiveness in the chronic phase are prevalent. The need of new drugs to treat this disease is evident. Cruzain is a vital protein for the survival ofTrypanosoma cruzi,the parasite causative of Chagas disease. Inhibition of this species-specific protein has been associated with improvements in pharmacological effects in animal models. Thus, blocking the activity of cruzain is an attractive approach for the development of antichagas agents. In this work, we present a validated mathematical model capable of predicting the cruzain inhibition value of a molecule from its chemical structure. This model can contribute to the identification of potential pharmacological alternatives against Chagas disease.
Nationwide survey on the barriers to converting turfgrass lawns to pollinator-friendly native wildflowers
Authors: Turley Nash E. , Hogan Joshua , Diehl Gloria J. , Stack Aaron C. , Sharanowski Barbara J.
Published: June 2020

The abundance and diversity of insect pollinators around the world is declining and habitat loss is a leading cause. Turfgrass lawns cover a vast area in North America and provide a great opportunity for habitat restoration to native wildflowers by the general public. Efforts to encourage the public to replace lawns with wildflowers could be improved by a better understanding of the thoughts and opinions of the public about lawns. We conducted a nationwide online survey to understand what barriers are most important in preventing people from converting a 6 x 6 ft portion of turfgrass lawn to native wildflowers. We also collected data on a variety of demographic factors to see if those influence survey responses. Over 3200 people took survey across the US. We found that ‘Maintenance time’ and ‘Not knowing what to do’ were the most important barriers to creating wildflower habitat. Age was the most important demographic factor impacting results with young people significantly more likely to select multiple barriers in the survey. For example, people aged 18-34 were 4.3 times more likely to indicate ‘Maintenance cost’ would prevent them from creating a wildflower plot than those age 65 or older. Those who had already created a wildflower plot, or those who were members in a native plant or pollinator organization were less likely to select barriers across the board, except for external barriers related to homeowners associations, neighbors, and local governments. This shows that these are persistent concerns even for those that are otherwise keen to create wildflower habitat. Our results suggest that outreach promoting pollinator-friendly native plant gardens should focus on clear and simple methods, small plots that will not take too much time and less likely to provoke neighbors or authority figures.
Sleep and circadian phenotype in people without cone-mediated vision
Authors: Spitschan Manuel , Garbazza Corrado , Kohl Susanne , Cajochen Christian
Published: June 2020

Background

Light exposure entrains the circadian clock through the intrinsically photosensitive retinal ganglion cells, which sense light in addition to the cones and rods. In congenital achromatopsia (ACHM; prevalence 1:30-50,000), the cone system is non-functional, resulting in severe light avoidance and photophobia at daytime light levels. How this condition affects circadian and neuroendocrine responses to light is not known.

Methods

In genetically confirmed ACHM patients (n=7; age 30-72 years; 6 women, 1 male), we examined survey-assessed sleep/circadian phenotype (PSQI, ESS, MEQ, MCTQ), self-reported visual function (NEI-VFQ-25), sensitivity to light (VLSQ-8) and use of spectral filters that modify chronic light exposure. In all but one patient, we measured rest-activity cycles using actigraphy over 3 weeks and measured the melatonin phase angle of entrainment using the dim-light melatonin onset (DLMO).

Results

ACHM patients experience a severely attenuated light-dark cycle due to severe light sensitivity and habitual use of filters to reduce retinal illumination. In aggregate, both MEQ and MCTQ indicated a tendency to late chronotype. We found regular rest-activity patterns in all patients and normal phase angles of entrainment in participants with a measurable DLMO.

Conclusions

Our results reveal that a functional cone system and exposure to daytime light intensities are not necessary for regular behavioural and hormonal entrainment, even when survey-assessed sleep and circadian phenotype indicated a tendency for a late chronotype and sleep problems in our ACHM cohort. Our results can be explained by an adaptation mechanism in circadian photoreception which adjusts to the range of habitual light exposures.
Sequence diversity and evolution of an iflavirus family associated with ticks
Authors: Daveu Romain , Hervet Caroline , Sigrist Louane , Sassera Davide , Jex Aaron , Labadie Karine , Aury Jean-Marc , Plantard Olivier , Rispe Claude
Published: June 2020

We studied a family of iflaviruses, a group of RNA viruses frequently found in arthropods, focusing on viruses associated with ticks. Our aim was to bring insight on the evolutionary dynamics of this group of viruses, which may interact with the biology of ticks. We explored systematicallyde novoRNA-Seq assemblies available for species of ticks which allowed to identify nine new genomes of iflaviruses. The phylogeny of virus sequences was not congruent with that of the tick hosts, suggesting recurrent host changes across tick genera along evolution. We identified five different variants with a complete or near-complete genome inIxodes ricinus.These sequences were closely related, which allowed a fine-scale estimation of patterns of substitutions: we detected a strong excess of synonymous mutations suggesting evolution under strong positive selection. ISIV, a sequence found in the ISE6 cell line ofIxodes scapularis,was unexpectedly nearidentical withI. ricinusvariants, suggesting a contamination of this cell line byI. ricinusmaterial. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.
Gaining comprehensive biological insight into chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis
Authors: Zhang Aidi , Fang Jing , Jiang Xiaohan , Wang Tengfei , Zhang Xiujun
Published: June 2020

Background

RNA editing is a post-transcriptional modification that complement variation at the DNA level. Until now, different RNA editing systems were found in the major eukaryotic lineages. However, the evolution trajectory in plant chloroplast remains unclear. To gain a better understanding of RNA editing in plant chloroplast, in this study, based on publicly available RNA-seq data across three plant lineages (fern, gymnosperm, and angiosperm), we provided a detailed analysis of RNA editing events in plant chloroplasts and discussed the evolution of RNA editing in land plants.

Results

There were a total of 5,389 editing sites located in leaf chloroplast identified across 21 plants after rigorous screening. We found that the cluster of RNA editing sites across 21 plants complied with the phylogenetic tree based on linked protein sequences approximately, and majority (∼ 95%) of the editing events resulted in non-synonymous codon changes, RNA editing occurred in second codon position was mainly the largest. Additionally, RNA editing caused an overall increase in hydrophobicity of the resulting proteins. The analyses also revealed that there is an uneven distribution of editing sites among species, genes, and codon positions, the average RNA editing extent varied among different plant species as well as genes. Finally, we found that the loss of editing sites along angiosperm evolution is mainly occurring by reduce of cytosines content, fern plants has the highest cytosine content, with the evolution of plants, cytosine were lost in RNA edited genes.

Conclusions

Many of the identified sites in our study have not been previously reported and represent a valuable data set for future research community. Our findings provide valuable information for evolution of RNA editing in plants.
Comprehensive characterization of internal and cuticle surface microbiota of laboratory-reared F1Anopheles albimanusoriginating from different sites
Authors: Dada Nsa , Benedict Ana Cristina , López Francisco , Lol Juan C. , Sheth Mili , Dzuris Nicole , Padilla Norma , Lenhart Audrey
Published: June 2020

Background

Research on mosquito-microbe interactions may lead to new tools for mosquito and mosquito-borne disease control. To date, such research has largely utilized laboratory-reared mosquitoes that typically lack the microbial diversity of wild populations. A logical progression in this area involves working under controlled settings using field-collected mosquitoes or, in most cases, their progeny. Thus, an understanding of how laboratory colonization affects the assemblage of mosquito microbiota would aid in advancing mosquito microbiome studies and their applications beyond laboratory settings.

Methods

Using high throughput 16S rRNA amplicon sequencing, we characterized the internal and cuticle surface microbiota of F1progeny of wild-caught adultAnopheles albimanusfrom four locations in Guatemala. A total of 132 late instar larvae and 135 2-5day old, non-blood-fed virgin adult females that were reared under identical laboratory conditions, were pooled (3 individuals/pool) and analyzed.

Results

Results showed geographical heterogeneity in both F1larval internal (p=0.001; pseudo-F= 9.53) and cuticle surface (p=0.001; pseudo-F= 8.51) microbiota, and only F1adult cuticle surface (p=0.001; pseudo-F= 4.5) microbiota, with a more homogenous adult internal microbiota (p=0.12; pseudo-F= 1.6) across collection sites. Overall, ASVs assigned toLeucobacter, Thorsellia, Chryseobacteriumand uncharacterizedEnterobacteriaceae, dominated F1larval internal microbiota, whileAcidovorax, Paucibacter, and uncharacterizedComamonadaceae, dominated the larval cuticle surface. F1adults comprised a less diverse microbiota compared to larvae, with ASVs assigned to the genusAsaiadominating both internal and cuticle surface microbiota, and constituting at least 70% of taxa in each microbial niche.

Conclusions

These results suggest that location-specific heterogeneity in filed mosquito microbiota can be transferred to F1progeny under normal laboratory conditions, but this may not last beyond the F1larval stage without adjustments to maintain field-derived microbiota. Our findings provide the first comprehensive characterization of laboratory-colonized F1An. albimanusprogeny from field-derived mothers. This provides a background for studying how parentage and environmental conditions differentially or concomitantly affect mosquito microbiome composition, and how this can be exploited in advancing mosquito microbiome studies and their applications beyond laboratory settings.
Ferrochelatase regulates retinal neovascularization
Authors: Sheik Pran Babu Sardar Pasha , White Darcy , Corson Timothy W.
Published: June 2020

Ferrochelatase (FECH) is the terminal enzyme in heme biosynthesis. We previously showed that FECH is required for endothelial cell growth in vitro and choroidal neovascularization in vivo. But FECH has not been explored in retinal neovascularization, which underlies diseases like proliferative diabetic retinopathy and retinopathy of prematurity. Here, we investigated the inhibition of FECH using genetic and chemical approaches in the oxygen-induced retinopathy (OIR) mouse model. In OIR mice, FECH expression is upregulated and co-localized with neovascular tufts. Partial loss-of-functionFechm1Pasmutant mice showed reduced retinal neovascularization and endothelial cell proliferation in OIR. An intravitreal injection of the FECH inhibitorN-methyl protoporphyrin had similar effects. Griseofulvin is an anti-fungal drug that inhibits FECH as an off-target effect. Strikingly, intravitreal griseofulvin blocked pathological tuft formation and revascularized areas of vasoobliteration faster than vehicle, suggesting potential as a FECH-targeting therapy. Ocular toxicity studies revealed that intravitreal injection of griseofulvin in adult mice does not disrupt retinal vasculature, function, or morphology. In sum, mutation and chemical inhibition ofFechreduces retinal neovascularization and promotes physiological angiogenesis, suggesting a dual effect on vascular repair upon FECH inhibition, without ocular toxicity. These findings suggest that FECH inhibitors could be repurposed to treat retinal neovascularization.
Microengineered 3D pulmonary interstitial mimetics highlight a critical role for matrix degradation in idiopathic pulmonary fibrosis
Authors: Matera Daniel L. , DiLillo Katarina M. , Smith Makenzee R. , Davidson Christopher D. , Parikh Ritika , Said Mohammed , Wilke Carole A. , Lombaert Isabelle M. , Arnold Kelly B. , Moore Bethany B. , Baker Brendon M.
Published: June 2020

Fibrosis is often untreatable and is characterized by aberrant tissue scarring from activated myofibroblasts. Although the extracellular matrix becomes increasingly stiff and fibrous during disease progression, how these physical cues impact myofibroblast differentiation in 3D is poorly understood. Here we describe a multicomponent hydrogel that recapitulates the 3D fibrous structure hallmark to the interstitial tissue regions where idiopathic pulmonary fibrosis (IPF) initiates. In contrast to findings on 2D hydrogels, myofibroblast differentiation in 3D was inversely correlated with hydrogel stiffness, but positively correlated with matrix fiber density. Employing a multi-step bioinformatics analysis of IPF patient transcriptomes andin vitropharmacologic screening, we identify matrix-metalloprotease activity to be essential for 3D but not 2D myofibroblast differentiation. Given our observation that compliant degradable 3D matrices amply support fibrogenesis, these studies demonstrate a departure from the established relationship between stiffness and myofibroblast differentiation in 2D, and provide a new 3D model for studying fibrosis.
A population-genomic approach for estimating selection on polygenic traits in heterogeneous environments
Authors: Gompert Zachariah
Published: June 2020

Strong selection can cause rapid evolutionary change, but temporal fluctuations in the form, direction and intensity of selection can limit net evolutionary change over longer time periods. Fluctuating selection could affect molecular diversity levels and the evolution of plasticity and ecological specialization. Nonetheless, this phenomenon remains understudied, in part because of analytical limitations and the general difficulty of detecting selection that does not occur in a consistent manner. Herein, I fill this analytical gap by presenting an approximate Bayesian computation (ABC) method to detect and quantify fluctuating selection on poly-genic traits from population-genomic time-series data. I propose a model for environment-dependent phenotypic selection. The evolutionary genetic consequences of selection are then modeled based on a genotype-phenotype map. Using simulations, I show that the proposed method generates accurate and precise estimates of selection when the generative model for the data is similar to the model assumed by the method. Performance of the method when applied to an evolve-and-resequence study of host adaptation in the cowpea seed beetle (Cal-losobruchus maculatus) was more idiosyncratic and depended on specific analytical choices. Despite some limitations, these results suggest the proposed method provides a powerful approach to connect causes of (variable) selection to traits and genome-wide patterns of evolution. Documentation and open source computer software (fsabc) implementing this method are available from GitHub (https://github.com/zgompert/fsabc.git).
The burden of rare protein-truncating genetic variants on human lifespan
Authors: Liu Jimmy Z. , Chen Chia-Yen , Tsai Ellen A. , Whelan Christopher D. , Sexton David , John Sally , Runz Heiko
Published: June 2020

Genetic predisposition is believed to contribute substantially to the age at which we die. Genome-wide association studies (GWAS) have implicated more than 20 genetic loci to phenotypes related to human lifespan1. However, little is known about how lifespan is impacted by gene loss-of-function. Through whole-exome sequencing of 238,239 UK Biobank participants, we assessed the relevance of protein-truncating variant (PTV) gene burden on individual and parental survival. We identified exome-wide (P<2.5e-6) significant associations betweenBRCA2, BRCA1, TET2, PPM1D, LDLR, EML2andDEDD2PTV-burden with human lifespan. Gene and gene-set PTV-burden phenome-wide association studies (PheWAS) further highlighted the roles of these genes in cancer and cardiovascular disease as relevant for overall survival. The overlap between PTV-burden and prior GWAS results was modest, underscoring the value of sequencing in well-powered cohorts to complement GWAS for identifying loci associated with complex traits and disease.
Cortical beta oscillations reflect the contextual gating of visual action feedback
Authors: Limanowski Jakub , Litvak Vladimir , Friston Karl
Published: June 2020

In sensorimotor integration, the brain needs to decide how its predictions should accommodate novel evidence by ‘gating’ sensory data depending on the current context. Here, we examined the oscillatory correlates of this process using magnetoencephalography (MEG). We used virtual reality to decouple visual (virtual) and proprioceptive (real) hand postures during a task requiring matching either modality’s grasping movements to a target oscillation. Thus, we rendered visual information either task-relevant or a (to-be-ignored) distractor. Under visuo-proprioceptive incongruence, occipital beta power decreased relative to congruence when vision was task-relevant but increased when it had to be ignored. Dynamic causal modelling (DCM) revealed that this interaction was best explained by diametrical, task-dependent changes in visual gain. These results suggest a crucial role for beta oscillations in sensorimotor integration; particularly, in the contextual gating (i.e., gain or precision control) of visual vs proprioceptive action feedback, depending on concurrent behavioral demands.
NON-AVIAN DINOSAUR EGGSHELL CALCITE CONTAINS ANCIENT, ENDOGENOUS AMINO ACIDS
Authors: Saitta Evan T. , Vinther Jakob , Crisp Molly K. , Abbott Geoffrey D. , Kaye Thomas G. , Pittman Michael , Bull Ian , Fletcher Ian , Chen Xinqi , Collins Matthew J. , Sakalauskaite Jorune , Mackie Meaghan , Dal Bello Federica , Dickinson Marc R. , Stevenson Mark A. , Donohoe Paul , Heck Philipp R. , Demarchi Beatrice , Penkman Kirsty E. H.
Published: June 2020

Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded. However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, thermally matured, sub-fossil, and ~3.8 Ma avian eggshell, as well as ~30 Ma calcitic mollusc opercula. Selective preservation of certain fully racemic amino acids, which do not racemise in-chain, along with similar concentrations of free versus total hydrolysable amino acids, likely suggests complete hydrolysis of original peptides. Liquid chromatography-tandem mass spectrometry supports this hypothesis by failing to detect any non-contamination peptide sequences from the Mesozoic eggshell. Pyrolysis-gas chromatography-mass spectrometry reveals pyrolysates consistent with amino acids as well as aliphatic hydrocarbon homologues that are not present in modern eggshell, suggestive of kerogen formation deriving from eggshell lipids. Raman spectroscopy yields bands consistent with various organic molecules, possibly including N-bearing molecules or geopolymers. These closed-system amino acids are possibly the most thoroughly supported non-avian dinosaur endogenous protein-derived constituents, at least those that have not undergone oxidative condensation with other classes of biomolecules. Biocrystal matrices can help preserve mobile organic molecules by trapping them (perhaps with the assistance of resistant organic polymers), but trapped organics are nevertheless prone to diagenetic degradation even if such reactions might be slowed in exceptional circumstances. The evidence for complete hydrolysis and degradation of most amino acids in the eggshell raises concern about the validity of reported polypeptide sequences from open-system non-avian dinosaur bone and other Mesozoic fossils.
Microplastics have shape- and polymer-dependent effects on soil processes
Authors: Lehmann Anika , Leifheit Eva F. , Gerdawischke Maurice , Rillig Matthias C.
Published: June 2020

Microplastics are a diverse and ubiquitous contaminant, a global change driver with potential to alter ecosystem properties and processes. Microplastic-induced effects in soils are manifold as microplastics differ in a variety of properties among which the shape is of special interest. Microplastic shapes can resemble natural forms or be dissimilar from natural objects. Our knowledge is limited regarding the impact of various microplastic shapes on soil processes. Therefore, we conducted this two-part research comprising a meta-analysis on published literature and a lab experiment focusing on microplastic shapes- and polymer-induced effects on soil aggregation and organic matter decomposition. We here focus on fibers, films, foams and fragments as microplastic shapes.

In the meta-analysis, we revealed a strong research focus on fibrous and particulate microplastic materials, with films and foams neglected.

Our experiment showed that microplastic shapes are important modulators of responses in soil aggregation and organic matter decomposition. Fibers, irrespective of their chemistry, negatively affected the formation of aggregates. This supported the shape dissimilarity hypothesis. However, for other shapes like foams and fragments, the polymer identity is clearly an important factor co-modulating the soil responses.

Further research is needed to generate a data-driven foundation to build on our developing mechanistic understanding of the importance and consequences of microplastic shapes added to our soils.
Identification of long regulatory elements in the genome ofPlasmodium falciparumand other eukaryotes
Authors: Menichelli Christophe , Guitard Vincent , Martins Rafael M. , Lèbre Sophie , Lopez-Rubio Jose-Juan , Lecellier Charles-Henri , Bréhélin Laurent
Published: June 2020

Long regulatory elements (LREs), such as CpG islands, polydA:dT tracts or AU-rich elements, are thought to play key roles in gene regulation but, as opposed to conventional binding sites of transcription factors, few methods have been proposed to formally and automatically characterize them. We present here a computational approach named DExTER dedicated to the identification of LREs and apply it to the analysis of the genomes of different eukaryotes includingP. falciparum. Our analyses show that all tested genomes contain several LREs that are somewhat conserved along evolution, and that gene expression can be predicted with surprising accuracy on the basis of these long regions only. Regulation by LREs exhibits very different behaviours depending on species and conditions. On Apicomplexa organisms, the process appears highly dynamic, with different LREs involved at different phases of their life cycle. For multicellular organisms, the same LREs are involved in all tissues, but a dynamic behavior is observed along embryonic development stages. InP. falciparum, whose genome is known to be strongly depleted of transcription factors, LREs appear to be of especially high importance, and our analyses show that they are involved in both transcriptomic and post-transcriptomic regulation mechanisms. Moreover, we demonstrated the biological relevance of one the LREs discovered by DExTER inP. falciparumusing anin vivoreporter assay. The source code (python) of DExTER is available at addresshttps://gite.lirmm.fr/menichelli/DExTER.
HiDRA-seq: High-Throughput SARS-CoV-2 Detection by RNA Barcoding and Amplicon Sequencing
Authors: Yángüez Emilio , White Griffin , Kreutzer Susanne , Opitz Lennart , Poveda Lucy , Sykes Timothy , Moccia Maria Domenica , Aquino Catharine , Schlapbach Ralph
Published: June 2020

The recent outbreak of a new coronavirus that causes a Severe Acute Respiratory Syndrome in humans (SARS-CoV-2) has developed into a global pandemic with over 6 million reported cases and more than 375,000 deaths worldwide. Many countries have faced a shortage of diagnostic kits as well as a lack of infrastructure to perform necessary testing. Due to these limiting factors, only patients showing symptoms indicating infection were subjected to testing, whilst asymptomatic individuals, who are widely believed to be responsible for the fast dispersion of the virus, were largely omitted from the testing regimes. The inability to implement high throughput diagnostic and contact tracing strategies has forced many countries to institute lockdowns with severe economic and social consequences. The World Health Organization (WHO) has encouraged affected countries to increase testing capabilities to identify new cases, allow for a well-controlled lifting of lockdown measures, and prepare for future outbreaks. Here, we propose HiDRA-seq, a rapidly implementable, high throughput, and scalable solution that uses NGS lab infrastructure and reagents for population-scale SARS-CoV-2 testing. This method is based on the use of indexed oligo-dT primers to generate barcoded cDNA from a large number of patient samples. From this, highly multiplexed NGS libraries are prepared targeting SARS-CoV-2 specific regions and sequenced. The low amount of sequencing data required for diagnosis allows the combination of thousands of samples in a sequencing run, while reducing the cost to approximately 2 CHF/EUR/USD per RNA sample. Here, we describe in detail the first version of the protocol, which can be further improved in the future to increase its sensitivity and to identify other respiratory viruses or analyze individual genetic features associated with disease progression.
Mucin granules are degraded in the autophagosome-lysosome pathway as a means of resolving airway mucous cell metaplasia
Authors: Sweeter JM , Kudrna K , Hunt K , Thomes P , Dickey BF , Brody SL , Dickinson JD
Published: June 2020

Exacerbations of muco-obstructive airway diseases such as COPD and asthma are associated with epithelial changes termed mucous cell metaplasia (MCM). The molecular pathways triggering MCM have been identified; however, the factors that regulate resolution are less well understood. We hypothesized that the autophagosome-lysosome pathway is required for resolution of MCM by degrading cytoplasmic mucins. We found increased intracellular levels of Muc5ac and Muc5b in autophagy-deficient mice. This difference was not due to defective mucin secretion. Instead, we found that Lamp1-labeled lysosomes surrounded mucin granules of mucous cells indicating that granules were being degraded. Using a model of resolution of mucous cell metaplasia in mice, we found increased lysosomal proteolytic activity that peaked in the days after inflammation. Autophagy-deficient mice had persistent accumulation of mucin granules that failed to decline due to reduced mucin degradation. We applied these findingsin vitroto human airway epithelial cells (AECs). Activation of autophagy by mTOR inhibition led to degradation of mucin granules in AECs. Our findings indicate that during peak and resolution phases of MCM, mucin granules can be degraded by autophagy. The addition of mucin degradation to the existing paradigm of production and secretion may more fully explain how the secretory cells handle excess amounts of cytoplasmic mucin and offers a therapeutic target to speed resolution of MCM in airway disease exacerbations.

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The use of CRISPR-Cas Selective Amplicon Sequencing (CCSAS) to reveal the eukaryotic microbiome of metazoans
Authors: Zhong Kevin Xu , Cho Anna , Deeg Christophe M. , Chan Amy M. , Suttle Curtis A.
Published: June 2020

Characterization of the eukaryotic microbiome is required to understand the role of microbial communities in health and disease. Such investigation relies on sequencing 18S ribosomal RNA genes (rDNA), which serve as taxonomic markers; however, this is compromised by contaminating host rDNA sequences. To overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rDNA sequences of the host. Validation shows that >96.5% of rDNA amplicons from ten model organisms were cleaved, while rDNA from protists and fungi were unaffected. In oyster spat, CCSAS resolved ∼8.5-fold more taxa, and several additional major phylogenetic groups when compared to the best available alternative approach. We designed taxon-specific sgRNA for ∼16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected because of methodological challenges.
Context-dependent functional compensation between Ythdf m6A readers
Authors: Lasman Lior , Krupalnik Vladislav , Geula Shay , Zerbib Mirie , Viukov Sergey , Mor Nofar , Aguilera Castrejon Alejandro , Mizrahi Orel , Shashank Sathe , Nachshon Aharon , Schneir Dan , Aigner Stefan , Shankar Archana , Mueller Jasmine , Stern-Ginossar Noam , Yeo Gene W , Novershtern Noa , Hanna Jacob H
Published: June 2020

The N6-methyladenosine (m6A) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay, translation and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is dynamically regulated by a set of writer, eraser and reader proteins. The YTH-domain family of proteins: Ythdf1, Ythdf2, and Ythdf3, are three homologous m6A binding proteins, which have different cellular functions. However, their sequence similarity and their tendency to bind the same targets suggest that they may have overlapping roles. We systematically knocked out (KO) the Mettl3 writer for each of the Ythdf readers and for the three readers together (triple-KO). We then estimated the effectin-vivo, in mouse gametogenesis and viability, andin-vitro, in mouse embryonic stem cells (mESCs). We show that in gametogenesis, Mettl3-KO severity is increased as the deletion occurs earlier in the process, and Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, possibly due to differences in readers’ expression, both in quantity and in spatial location. By knocking out the three readers together and systematically testing offspring genotypes, we have revealed a redundancy in the readers’ role during early development, a redundancy which is dosage-dependent. Additionally, we show that in mESCs there is compensation between the three readers, since the inability to differentiate and the significant effect on mRNA decay occur only in the triple-KO cells and not in the single KOs. Thus, we suggest a novel model for the Ythdf readers function. There is a dosage-dependent redundancy when all three readers are co-expressed in the same location in the cells.
Complex oxides – non-toxic pigments for anticorrosive coatings
Authors: Ziganshina Mayya , Stepin Sergey , Karandashov Sergey , Mendelson Veronika
Published: June 2020

Purpose

The purpose of this paper is to search for toxic anticorrosive pigments’ substitute in protective coatings is one of the important tasks that the specialists in the field of steel corrosion face.

Design/methodology/approach

One of the ways to solve the problem of metal corrosion is to use complex oxides as pigments, which are characterized as low-toxic compounds and possess the ability to inhibit corrosion.

Findings

In the production of ferrites, it is possible to use production waste as raw material, and that makes it possible to reduce the price of the resulting product and solve environmental problems simultaneously.

Originality/value

Permanent growth of world production is accompanied by the increasing environment corrosiveness, associated with the intensification of air, water basin and soil pollution by industrial waste. This, as well as the continuously increasing operated metal stock, has recently made the tendency of metals’ total loss from corrosion steadily increasing. All of this points to the importance of studying corrosion processes and the systematic and effective fight against metal corrosion.
The airplane trim system – new functionalities
Authors: Szczepanski Cezary , Krawczyk Mariusz , Zajdel Albert
Published: June 2020

Purpose

A standard automatic flight control system – autopilot – will become required equipment of the future aircraft, operating in the common sky. For a specific group of aircraft, they are too expensive and too energy-consuming solutions. This paper aims to present the concept of an automatic flight control system that overcomes those limitations.

Design/methodology/approach

The proposed automatic flight control system uses the trim tabs in all prime flight controlling surfaces: elevator, ailerons and rudder, for stabilizing and controlling the steady flights of an aircraft.

Findings

The results of an aeroplane flight controlled with the use of trim tabs simulation tests and remarks have been presented and discussed. The simulation was conducted in real-time hardware in the loop environment. The stabilization of the flight was achieved in performed test scenarios.

Originality/value

The possibility to control an aircraft with coordinated deflections of the trimming surfaces is a beneficial alternate to those currently used and can be recommended for use in the next-generation aircraft.
Latin American countries in the BRI: challenges and potential implications for economic development
Authors: Gonzalez Jauregui Juliana
Published: June 2020

Purpose

According to official statements, BRI is a Chinese call for global cooperation, based on five priorities: policy coordination, facilities connectivity, unimpeded trade, financial integration and people-to-people bonds. The purpose of this paper is, primarily, to describe and contextualize the official discourse of China's foreign policy toward Latin America, emphasizing on BRI. On that basis, the author aims to contrast official rhetoric with real facts, bringing problematic cases associated with implementing BRI in Asian and African developing countries, so as to discuss possible challenges that Latin America can encounter when implementing the initiative. Finally, the author evaluates potential implications of resembling the Chinese three-level scheme of development in the region and make suggestions on this subject.

Design/methodology/approach

In an effort to evaluate possible implications of BRI in Latin America, the paper describes and contextualizes Chinese foreign policy official rhetoric toward the region's countries. Based on that, the author brings to discussion Asian and African experiences in the implementation of the initiative and raise questions on controversial issues that Latin America could meet when enforcing BRI-related projects.

Findings

As a part of its new foreign and economic policies, China continues to strengthen its engagement with Latin American countries, enlarging its strategy though the promotion of BRI. If Latin American countries, through BRI, seek to replicate the Chinese three-level of development scheme, including domestic, regional and global scopes, certain controversial issues cannot be ignored in the design and implementation processes. Also, equal participation of Chinese and Latin American governments, societies and enterprises is decisive if the goal is to settle a long-term development scenario for the region.

Originality/value

The central thesis of this paper is that the implementation of BRI in Latin American countries could potentially replicate the Chinese three-level development proposal. To achieve such an ambitious goal, much depends on how Latin American countries define and enforce BRI projects. Full understanding of those challenges requires close attention to what the Chinese official rhetoric claims and what actually puts into practice in other developing countries already involved in BRI, so as to anticipate possible consequences for the region.