bluuebunny/crossref_metadata_2025_split huggingface dataset:
Africanized honey bees in Colombia exhibit high prevalence but low level of infestation ofVarroamites and low prevalence of pathogenic viruses
Authors: Tibatá Víctor Manuel , Sanchez Andrés , Young-Palmer Evan , Junca Howard , Solarte Victor Manuel , Madella Shayne , Ariza Fernando , Figueroa Judith , Corona Miguel 
Published: December 2020

AbstractThe global spread of the ectoparasitic miteVarroa destructorhas promoted the spread and virulence of highly infectious honey bee viruses. This phenomenon is considered the leading cause for the increased number of colony losses experienced by the mite-susceptible European honey bee populations in the Northern Hemisphere. Most of the honey bee populations in Central and South America are Africanized honey bees, which are considered more resistant toVarroacompared to European honey bees. However, the relationship betweenVarroalevels and spread of honey bee viruses in Africanized honey bees remains unknown. In this study, we determinedVarroaprevalence and infestation levels as well as the prevalence of seven major honey bee viruses in Africanized honey bees from three regions of Colombia. We found that althoughVarroaexhibited high prevalence (92%), its infestation levels were low (4.6%) considering that these populations never received acaricide treatments. We also detected four viruses in the three regions analyzed, but all hives were asymptomatic, and virus prevalence was considerably lower than those found in other countries with higher rates of mite-associated colony loss (DWV 19.88%, BQCV 17.39%, SBV 23.4 %, ABPV 10.56%). Our findings indicate that AHBs possess natural resistance toVarroathat does not prevent the spread of this parasite among their population, but restrains mite population growth and suppresses the prevalence and pathogenicity of mite-associated viruses.
Survival and growth of saprotrophic and mycorrhizal fungi in recalcitrant amine, amide and ammonium containing media
Authors: Stenholm Åke , Backlund Anders , Holmström Sara , Backlund Maria , Hedeland Mikael , Fransson Petra 
Published: December 2020

AbstractThe elimination of hazardous compounds in chemical wastes can be a complex and technically demanding task. In the search for environmental-friendly technologies, fungal mediated remediation and removal procedures are of concern. In this study, we investigated whether there are fungal species that can survive and grow on solely amine-containing compounds. One compound containing a primary amine group; 2-diethylaminoethanol, one compound with a primary amide group; 2,6-dichlorobenzamide (BAM), and a third compound containing a quaternary ammonium group; N3-trimethyl(2-oxiranyl)methanaminium chloride, were selected. The choice of these compounds was motivated by their excessive use in large scale manufacturing of protein separation media (2-diethylaminoethanol and the quaternary amine). 2,6-dichlorobenzamide, the degradation product of the herbicide 2,6-dichlorobenzonitrile (dichlobenil), was chosen since it is an extremely recalcitrant compound. Utilising part of the large fungal diversity in Northern European forests, a screening study using 48 fungal isolates from 42 fungal species, including saprotrophic and mycorrhizal fungi, was performed to test for growth responses to the chosen compounds. The ericoid mycorrhizal fungusRhizoscyphus ericaeshowed the best overall growth on 2-diethylaminoethanol and BAM in the 1-20 gL-1concentration range. A 3500% and 450% increase in biomass, respectively, was observed. For N3-trimethyl(2-oxiranyl)methanaminium chloride, the peak growth occurred at 1 gL-1. In a second experiment, including three of the most promising species (Laccaria laccata, Hygrophorus camarophyllusandRhizoscyphus ericae) from the screening experiment, a simulated process water containing 1.9% (w/v) 2-diethylaminoethanol and 0.8% (w/v) N3-trimethyl(2-oxiranyl)methanaminium chloride was used.Laccaria laccatashowed the best biomass growth increase (380%) relative to a growth control, while the growth increase forRhizoscyphus ericaeandH. camarophylluswere 292% and 136% respectively, showing that also mycorrhizal fungal species can use amine- and amide-containing substrates as nutrients. These results show the potential of certain fungal species to be used in alternative green wastewater treatment procedures.
Effects of Transport and Altitude on Hormones and Oxidative Stress Parameters in Sheep
Authors: Tozlu Çelık Hilal , Aslan Fatih Ahmet , Us Altay Diler , Kahvecı Metehan Eser , Konanç Kalbiye , Noyan Tevfik , Ayhan Sertaç 
Published: December 2020

AbstractWith this study, it was aimed to determine the stress effects that can be caused by transporting and altitude in sheep. Karayaka sheep were used in the study. The live weight of the sheep (n=30) while hungry was determined before transport and sea level. Average live weight was determined as 55.64 ± 4.66 kg. Blood samples were collected just before (sea level) and just after transport (1500 meters above sea level). Transportation distance was approximately 182 km and duration was 5 hours. According to the findings, cortisol was not affected by transport stress and altitude (p>0.05) and Triiyodotironin (T3) (p<0.039) and Tyrosine (T4) (p<0.000) were affected significantly. Malondialchehyche (MDA), which is one of the oxidative stress parameters, was significantly affected (p<0.039) and Protein Carbonyl (PC) values were not affected by transport and altitude (p>0.184). As a result of this study, it was determined that transportation and altitude in sheep causes stress. Stress-reducing measures should be taken in the exposure of sheep to altitude differences and in transportation. Antioxidant nutritional supplements should be made in order not to negatively affect the meat quality in sheep.
A new genome-wide method to identify genes with bimodal gene expression
Authors: Justino Josivan Ribeiro , Reis Clovis F. , Fonseca Andre Faustino , de Souza Sandro Jose , Stransky Beatriz 
Published: December 2020

AbstractA new method is presented to detect bimodality in gene expression data using the Gaussian Mixture Models to cluster samples in each mode. We have used the method to search for bimodal genes in data from 25 tumor types available from The Cancer Genome Atlas. The method identified 554 genes with bimodal gene expression, of which 46 were identified in more than one cancer type. To further illustrate the impact of the method, we show that 96 out of the 554 genes with bimodal expression patterns presented different prognosis when patients belonging to the two expression peaks are compared. The software to execute the method and the corresponding documentation are available athttps://github.com/LabBiosystemUFRN/Bimodality_Genes.
Principled simulation of agent-based models in epidemiology
Authors: Wu Sean L. , Dolgert Andrew J. , Lewnard Joseph A. , Marshall John M. , Smith David L. 
Published: December 2020

AbstractAfter more than a century of sustained work by mathematicians, biologists, epidemiologists, probabilists, and other experts, dynamic models have become a vital tool for understanding and describing epidemics and disease transmission systems. Such models fulfill a variety of crucial roles including data integration, estimation of disease burden, forecasting trends, counterfactual evaluation, and parameter estimation. These models often incorporate myriad details, from age and social structure to inform population mixing patterns, commuting and migration, and immunological dynamics, among others. This complexity can be daunting, so many researchers have turned to stochastic simulation using agent-based models. Developing agent-based models, however, can present formidable technical challenges. In particular, depending on how the model updates state, unwanted or even unnoticed approximations can be introduced into a simulation model. In this article, we present computational methods for approximating continuous time discrete event stochastic processes based on a discrete time step to speed up complicated simulations which also converges to the true process as the time step goes to zero. Our stochastic models is constructed via hazard functions, and only those hazards which are dependent on the state of other agents (such as infection) are approximated, whereas hazards governing dynamics internal to an agent (such as immune response) are simulated exactly. By partitioning hazards as being either dependent or internal, a generic algorithm can be presented which is applicable to many models of contagion processes, with natural areas of extension and optimization.Author summaryStochastic simulation of epidemics is crucial to a variety of tasks in public health, encompassing intervention evaluation, trend forecasting, and estimation of epidemic parameters, among others. In many situations, due to model complexity, time constraints, unavailability or unfamiliarity with existing software, or other reasons, agent-based models are used to simulate epidemic processes. However, many simulation algorithms aread hoc, which may introduce unwanted or unnoticed approximations. We present a method to build approximate, agent-based models from mathematical descriptions of stochastic epidemic processes which will improve simulation speed and converge to exact simulation techniques in limiting cases. The simplicity and generality of our method should be widely applicable to various problems in mathematical epidemiology and its connection to other methods developed in chemical physics should inspire future work and elaboration.
N-glycolylneuraminic acid binding of avian H7 influenza A viruses
Authors: Spruit Cindy M. , Zhu Xueyong , Broszeit Frederik , Han Alvin X. , van der Woude Roosmarijn , Bouwman Kim M. , Luu Michel M. T. , Russell Colin A. , Wilson Ian A. , Boons Geert-Jan , de Vries Robert P. 
Published: December 2020

AbstractInfluenza A viruses initiate infection by binding to glycans with terminal sialic acids present on the cell surface. Hosts of influenza A viruses variably express two major forms of sialic acid, N-acetylneuraminic acid (NeuAc) and N-glycolylneuraminic acid (NeuGc). NeuGc is produced in the majority of mammals including horses, pigs, and mice, but is absent in humans, ferrets, and birds. Intriguingly, the only known naturally occurring influenza A viruses that exclusively bind NeuGc are the extinct highly pathogenic equine H7N7 viruses. We determined the crystal structure of a representative equine H7 hemagglutinin (HA) in complex with its NeuGc ligand and observed a high similarity in the receptor-binding domain with an avian H7 HA. To determine the molecular basis for NeuAc and NeuGc specificity, we performed systematic mutational analyses, based on the structural insights, on two distant avian H7 HAs. We found that mutation A135E is key for binding α2,3-linked NeuGc but does not abolish NeuAc binding. Interestingly, additional mutations S128T, I130V, or a combination of T189A and K193R, converted from NeuAc to NeuGc specificity as determined by glycan microarrays. However, specific binding to NeuGc-terminal glycans on our glycan array did not always correspond with full NeuGc specificity on chicken and equine erythrocytes and tracheal epithelium sections. Phylogenetic analysis of avian and equine H7 HAs that investigated the amino acids at positions 128, 130, 135, 189, and 193 reveals a clear distinction between equine and avian residues. The highest variability in amino acids (four different residues) is observed at key position 135, of which only the equine glutamic acid leads to binding of NeuGc. The results demonstrate that avian H7 viruses, although genetically distinct from equine H7 viruses, can bind NeuGc after the introduction of two to three mutations, providing insights into the adaptation of H7 viruses to NeuGc receptors.Author summaryInfluenza A viruses cause millions of cases of severe illness and deaths annually. To initiate infection and replicate, the virus first needs to bind to a structure on the cell surface, like a key fitting in a lock. For influenza A virus, these ‘keys’ (receptors) on the cell surface are chains of sugar molecules (glycans). The terminal sugar on these glycans is often either N-acetylneuraminic acid (NeuAc) or N-glycolylneuraminic acid (NeuGc). Most influenza A viruses bind NeuAc, but a small minority binds NeuGc. NeuGc is present in species like horses, pigs, and mice, but not in humans, ferrets, and birds. Therefore, NeuGc binding could be a determinant of an Influenza A virus species barrier. Here, we investigated the molecular determinants of NeuGc specificity and the origin of viruses that bind NeuGc.
Disintegration promotes proto-spacer integration by the Cas1-Cas2 complex
Authors: Ma Chien-Hui , Javanmardi Kamyab , Finkelstein Ilya J. , Jayaram Makkuni 
Published: December 2020

Abstract‘Disintegration’—the reversal of transposon DNA integration at a target site—is regarded as an abortive off-pathway reaction. Here we challenge this view with a biochemical investigation of the mechanism of protospacer insertion by theStreptococcus pyogenesCas1-Cas2 complex, which is mechanistically analogous to DNA transposition. In supercoiled target sites, the predominant outcome is the disintegration of one-ended insertions that fail to complete the second integration event. In linear target sites, one-ended insertions far outnumber complete proto-spacer insertions. The second insertion event is most often accompanied by disintegration of the first, mediated either by the 3’-hydroxyl exposed during integration or by water. One-ended integration intermediates may mature into complete spacer insertions via DNA repair pathways that are also involved in transposon mobility. We propose that disintegration-promoted integration is functionally important in the adaptive phase of CRISPR-mediated bacterial immunity, and perhaps in other analogous transposition reactions.
Relationship between vestibular hair cell loss and deficits in two anti-gravity reflexes in the rat
Authors: Maroto Alberto F. , Barrallo-Gimeno Alejandro , Llorens Jordi 
Published: December 2020

AbstractThe tail-lift reflex and the air-righting reflex in rats are anti-gravity reflexes that depend on vestibular function. To begin identifying their cellular basis, this study examined the relationship between reflex loss and the graded lesions caused in the vestibular sensory epithelia by varying doses of an ototoxic compound. After ototoxic exposure, we recorded these reflexes using high speed video. The movies were used to obtain objective measures of the reflexes: the minimum angle formed by the nose, the back of the neck and the base of the tail during the tail-lift maneuver and the time to right in the air-righting test. The vestibular sensory epithelia were then collected from the rats and used to estimate the loss of type I (HCI), type II (HCII) and all hair cells (HC) in both central and peripheral parts of the crista, utricle, and saccule. As expected, tail-lift angles decreased, and air-righting times increased, while the numbers of HCs remaining in the epithelia decreased in a dose-dependent manner. The results demonstrated greater sensitivity of HCI compared to HCII to the IDPN ototoxicity, as well as a relative resiliency of the saccule compared to the crista and utricle. Comparing the functional measures with the cell counts, we observed that loss of the tail-lift reflex associates better with HCI than with HCII loss. In contrast, most HCI in the crista and utricle were lost before air-righting times increased. These data suggest that these reflexes depend on the function of non-identical populations of vestibular HCs.
Untangling structural factors and evolutionary drivers in nascent polyploids
Authors: de Carvalho Julie Ferreira , Stoeckel Solenn , Eber Frédérique , Lodé-Taburel Maryse , Gilet Marie-Madeleine , Trotoux Gwenn , Morice Jérôme , Falentin Cyril , Chèvre Anne-Marie , Rousseau-Gueutin Mathieu 
Published: December 2020

SUMMARYAllopolyploids have globally higher fitness than their diploid progenitors however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success.Using theBrassicamodel, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploidB. napusand systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors and polyploid formation type. We evaluated the evolution of meiotic behavior, fertility and identified rearrangements in S1 to S9 lineages, to explore the positive consequences of euploid selection onB. napusgenome stability.Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a quasi disappearance of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number strongly depended on the genetic background and cytoplasm donor.The combined use of both self-fertilisation and outcrossing as well as recurrent euploid selection, allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explainB. napusspeciation success.
Pathogen effector recognition-dependent association of NRG1 with EDS1 and SAG101 in TNL receptor immunity
Authors: Sun Xinhua , Lapin Dmitry , Feehan Joanna M. , Stolze Sara C. , Kramer Katharina , Dongus Joram A. , Rzemieniewski Jakub , Blanvillain-Baufumé Servane , Harzen Anne , Bautor Jaqueline , Derbyshire Paul , Menke Frank L. H. , Finkemeier Iris , Nakagami Hirofumi , Jones Jonathan D.G. , Parker Jane E. 
Published: December 2020

AbstractPlants utilise intracellular nucleotide-binding, leucine-rich repeat (NLR) immune receptors to detect pathogen effectors and activate local and systemic defence. NRG1 and ADR1 “helper” NLRs (RNLs), cooperate with enhanced disease susceptibility 1 (EDS1), senescence-associated gene 101 (SAG101) and phytoalexin-deficient 4 (PAD4) lipase-like proteins to mediate signalling from TIR domain NLR receptors (TNLs). However, the mechanism of RNL/EDS1-family protein cooperation is poorly understood. Here, we provide genetic and molecular evidence for exclusive EDS1/SAG101/NRG1 and EDS1/PAD4/ADR1 co-functions in TNL immunity. Using immunoprecipitation and mass spectrometry, we show effector recognition-dependent association of NRG1 with EDS1 and SAG101, but not PAD4. An EDS1-SAG101 complex associates with NRG1, and EDS1-PAD4 associates with ADR1, only in an immune-activated state. NRG1 requires an intact nucleotide-binding P-loop motif, and EDS1 a functional EP domain and its partner SAG101, for induced association and immunity. Thus, two distinct modules (NRG1/EDS1/SAG101 and ADR1/EDS1/PAD4) are required to execute TNL receptor defence signalling.
Arginine Methylation Regulates Ribosome CAR Function
Authors: Scopino Kristen , Dalgarno Carol , Nachmanoff Clara , Krizanc Daniel , Thayer Kelly M. , Weir Michael P. 
Published: December 2020

AbstractThe ribosome CAR interaction surface is hypothesized to provide a layer of translation regulation through hydrogen-bonding to the +1 mRNA codon that is next to enter the ribosome A site during translocation. The CAR surface consists of three residues, 16S/18S rRNA C1054, A1196 (E. coli16S numbering), and R146 of yeast ribosomal protein Rps3. R146 can be methylated by the Sfm1 methyltransferase which is downregulated in stressed cells. Through molecular dynamics analysis, we show here that methylation of R146 compromises the integrity of CAR by reducing the pi stacking of the R146 guanidinium group with A1196, leading to reduced CAR hydrogen-bonding with the +1 codon. We propose that ribosomes assembled under stressed conditions have unmethylated R146, resulting in elevated CAR/+1 codon interactions, which tunes translation levels in response to the altered cellular context.
Metastasis and cancer stem cell markers identify two colorectal cancer subtypes with different molecular and clinical features
Authors: Alsaihati Burair A. , Zhao Shaying 
Published: December 2020

AbstractColorectal cancer (CRC) is among the top prevalent cancer types with lethal outcome in the United States and worldwide. CRC inter-tumor heterogeneity highlights the importance of identifying molecular markers for meaningful classification and prognosis. The recently published Consensus Molecular Subtypes (CMS) represent a widely used molecular subtyping system of CRC. However, our analyses indicate that clear heterogeneity still exists in some CMSs. In this work, we demonstrate that both CMS2 and CMS4 are composed of two molecularly distinct subtypes. We named them S1 and S2, short for subtype 1 and subtype 2. Our results indicate that the two subtypes also differ clinically. Notably, S2 exhibits more frequent lymphatic invasion across CRCs and more frequent metastasis events within CMS2 patients.
Cadherin-11 dimerization multi-site kinetics: combined partial unfolding and strand-swapping
Authors: Koss Hans , Honig Barry , Shapiro Lawrence , Palmer Arthur G 
Published: December 2020

SummaryCadherin extracellular domain 1 (EC1) mediates homophilic dimerization in adherens junctions. Conserved Trp2 and Trp4 residues in type II cadherins anchor the EC1 A-strand intermolecularly in strand-swapped dimers. Herein, NMR spectroscopy is used to elucidate the roles of Trp2 and Trp4 in Cadherin-11 dimerization. The monomeric state, with the A-strand and Trp side chains packed intramolecularly, is in equilibrium with sparsely populated partially and fully A-strand-exposed states, in which Trp2 (and Trp4, respectively) side-chain packing is disrupted. Exchange kinetics between the major state and the partially (fully) A-strand-exposed state is slow-intermediate (intermediate-fast). A separate very fast process exchanges ordered and random-coil BC loop conformations with populations dependent on A-strand exposure and dimerization status. Additionally, very slow processes connect the folded A-strand-exposed conformation to partially unfolded states, which may represent additional domain-swapping intermediates. The dimerization mechanism of type II cadherins is revealed as coupled folding and strand-swapping.
Identification of Potential Antibody Epitopes in MMP-15
Authors: Gan Jessie , Eisen Cheryl , Smider Vaughn 
Published: December 2020

AbstractMonoclonal antibody therapy is a well-established cancer treatment paradigm that often targets cancers-pecific cell surface proteins. Matrix Metalloproteinase 15 (MMP-15) is a surface protein implicated in metastasis and angiogenesis, however it is not well characterized. Here we use bioinformatics tools to identify epitopes for drug or diagnostic targeting and elucidate features of this potentially important protein in metastatic processes. We identified conserved regions in MMP-15 as well as unique, variable peptide regions compared to other Membrane Type MMPs (MT-MMP). Conservation of catalytic and hemopexin domains in MMP-15 imply functional importance, however, their similarity to other MT-MMPs discourage use as target epitopes. Our analyses also identified an MMP-15 peptide that was highly divergent from other MMPs, suggesting that it may serve as an appropriate specific epitope for a specific antibody drug. Thus, we were able to elucidate features and potential unique epitopes of MMP-15 for use in further antibody discovery and targeting.