bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 6.5kb intergenic structural variation enhances P450-mediated resistance to pyrethroids in malaria vectors lowering bed net efficacy
Authors: Mugenzi Leon M.J. , Menze Benjamin D. , Tchouakui Magellan , Wondji Murielle J. , Irving Helen , Tchoupo Micareme , Hearn Jack , Weedall Gareth D. , Riveron Jacob M. , Cho-Ngwa Fidelis , Wondji Charles S. 
Published: May 2020

AbstractElucidating the complex evolutionary armory that mosquitoes deploy against insecticides is crucial to maintain the effectiveness of insecticide-based interventions. Here, we deciphered the role of a 6.5kb structural variation (SV) in driving cytochrome P450-mediated pyrethroid resistance in the malaria vector,Anopheles funestus. Whole genome pooled sequencing detected an intergenic 6.5kb SV between duplicated CYP6P9a/b P450s in pyrethroid resistant mosquitoes through a translocation event. Promoter analysis revealed a 17.5-fold higher activity (P<0.0001) for the SV-carrying fragment than the SV-free one. qRT-PCR expression profiling ofCYP6P9a/bfor each SV genotype supported its role as an enhancer since SV+/SV+ homozygote mosquitoes had significantly greater expression for both genes than heterozygotes SV+/SV- (1.7-2-fold) and homozygotes SV-/SV- (4-5-fold). Designing a PCR assay revealed a strong association between this SV and pyrethroid resistance (SV+/SV+ vs SV-/SV-; OR=2079.4,P=<0.001). The 6.5kb SV is present at high frequency in southern Africa (80-100%) but absent in East/Central/West Africa. Experimental hut trials revealed that homozygote SV mosquitoes had significantly greater chance to survive exposure to pyrethroid-treated Nets (OR 27.7; P < 0.0001) and to blood feed than susceptible. Furthermore, triple homozygote resistant (SV+/CYP6P9a_R/CYP6P9b_R) exhibit a higher resistance level leading to a far superior ability to survive exposure to nets than triple susceptible mosquitoes, revealing a strong additive effect. This study highlights the important role of structural variations in the development of insecticide resistance in malaria vectors and their detrimental impact on the effectiveness of pyrethroid-based nets.
Delay of gratification in non-human animals: A review of inter-specific variation in performance
Authors: Susini Irene , Safryghin Alexandra , Hillemann Friederike , Wascher Claudia A.F. 
Published: May 2020

AbstractThe ability to regulate and withhold an immediate behaviour in pursuit of a more preferred or valuable, albeit delayed, outcome is regarded as an important cognitive ability enabling adaptive decision-making in both social and asocial contexts. Abilities to cope with a delay in gratification have been investigated in a range of species using a variety of experimental paradigms. The present study attempts a first systematic evaluation of available experimental data from non-human animals, which is an essential basis for quantifying biological and non-biological factors (e.g.socio-ecologyversusexperimental design) affecting performance in delay of gratification tasks. Data were sourced from 52 separate studies, and a comprehensive overview of the available literature on delay of gratification in non-human animals is presented. We present data from 21 species, spanning across eight taxonomic order, with 1–9 species tested per taxonomic group. We highlight variation in experimental paradigms used to study delay of gratification abilities in non-human animals, both with regard to reward type or experimental setup, and discuss the implications for comparative analyses. We conclude that, at present, cross-species comparisons of delay of gratification abilities are hindered by a lack of consistency in experimental designs and low number of species tested across taxonomic orders. We hope to stimulate research on a more diverse set of species, and that future studies consider potential social and ecological factors that cause intra-specific variation in test performances, that is repeatedly seen across species.
Anin silicoapproach to identification, categorization and prediction of nucleic acid binding proteins
Authors: Xu Lei , Jiang Shanshan , Zou Quan 
Published: May 2020

AbstractThe interaction between proteins and nucleic acid plays an important role in many processes, such as transcription, translation and DNA repair. The mechanisms of related biological events can be understood by exploring the function of proteins in these interactions. The number of known protein sequences has increased rapidly in recent years, but the databases for describing the structure and function of protein have unfortunately grown quite slowly. Thus, improving such databases is meaningful for predicting protein-nucleic acid interactions. Furthermore, the mechanism of related biological events, such as viral infection or designing novel drug targets, can be further understood by understanding the function of proteins in these interactions. The information for each sequence, including its function and interaction sites, were collected and identified, and a database called PNIDB was built. The proteins in PNIDB were grouped into 27 classes, such as transcription, immune system, and structural protein, etc. The function of each protein was then predicted using a machine learning method. Using our method, the predictor was trained on labeled sequences, and then the function of a protein was predicted based on the trained classifier. The prediction accuracy achieved a score of 77.43% by 10-fold cross validation.Availability and ImplementationPNIDB is now fully working and can be freely accessed at:http://server.malab.cn/PNIDB/index.html. All the data are publicly available for non-commercial use, distribution, and reproduction in any medium.Contactzouquan@nclab.net
Microbe-dependent heterosis in maize
Authors: Wagner Maggie R. , Tang Clara , Salvato Fernanda , Clouse Kayla M. , Bartlett Alexandria , Sermons Shannon , Hoffmann Mark , Balint-Kurti Peter J. , Kleiner Manuel 
Published: May 2020

ABSTRACTHybrids account for nearly all commercially planted varieties of maize and many other crop plants, because crosses between inbred lines of these species produce F1 offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, calledheterosisor hybrid vigor, are not well understood despite over a century of intensive research (1). The leading hypotheses—which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)—have been able to explain some but not all of the observed patterns of heterosis (2, 3). However, possible ecological drivers of heterosis have largely been ignored. Here we show that heterosis of root biomass and germination in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions, but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclavedvs.live soil slurries in a growth chamber, and for plants grown in fumigatedvs.untreated soil in the field. Together, our results demonstrate a novel, ecological mechanism for heterosis whereby soil microbes generally impair the germination and early growth of inbred but not hybrid maize.
Evolution of symbiont transmission in conditional mutualisms in spatially and temporally variable environments
Authors: Brown Alexandra , Akçay Erol 
Published: May 2020

AbstractSymbiotic relationships affect the fitness and organismal function of virtually all organisms. In many cases, the fitness effects of symbiosis may be beneficial or harmful depending on the environment. The hosts of such symbionts are favored to acquire them only when the symbiont is beneficial. However, it is not clear whether such selection favors vertical or horizontal transmission, both, or neither. To address this question, we model the evolution of transmission mode in a conditional mutualism experiencing spatial and temporal environmental variation. We find that when symbionts affect host lifespan, but not fecundity, horizontal transmission can contain them to beneficial environments. Vertical transmission can produce symbiont containment when the environmental state is synchronized across locations. We also find an emergent trade-off between horizontal and vertical transmission, suggesting that physiological constraints are not required for the evolution of limits on the total amount of transmission.
Hypotheses and models linking epigenetic transgenerational effects to population dynamics: Exploring oscillations and applications to wildlife cycles
Authors: Juckett David 
Published: May 2020

AbstractEpigenetic transgenerational mechanisms underpin the imprinting of gamete origin during reproduction in mammals but are also hypothesized to transmit environmental exposures from parents to progeny in many life forms, which could have important consequences in population dynamics. Transgenerational hypotheses embody epigenetic alterations occurring in gametes, embryonic somatic cells, and embryonic primordial germ cells because most of the epigenome is erased and reconstituted during development. Four scenarios are described in this paper encompassing somatic and germline effects where each of these is either non-propagating or propagating in time. The non-propagating effects could result from environmental impulses such as toxicants, weather, epidemics, forest fires, etc. The propagating effects could result from continuous signals such as climate variations, food web abundances, population densities, predator numbers, etc. Focusing on the propagating mode, a population growth model is constructed incorporating the intrinsic delays associated with somatic or germline effects. Each exhibit oscillatory behavior over a wide range of the parameter space due to the inherent negative feedback of such delays. The somatic (maternal) model oscillates with a period of ∼6 generations while the germline (grandmaternal) model oscillates with a period of ∼10 generations. These models can be entrained by oscillatory external signals providing that the signals contain harmonic components near the intrinsic oscillations of the models. The 10-generation oscillation of the germline-effects model is similar to many wildlife cycles in mammals, bird, and insects. The possibility that such a transgenerational mechanism is a component of these wildlife cycles is discussed.
HybridMine: pipeline for allele inheritance and gene copy number prediction in industrial yeast hybrids
Authors: Timouma Soukaina , Schwartz Jean-Marc , Delneri Daniela 
Published: May 2020

ABSTRACTSaccharomyces pastorianusis an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavour profiles are now a major ambition and challenge in craft brewing and distilling industries. Genome-scale computational approaches are opening opportunities to model and predict favourable combination of traits for strain development. However, mining the genome of these complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. Moreover, no genome annotation for these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl and Bash programming languages and is available athttps://github.com/Sookie-S/HybridMine.
Benchmarking available bacterial promoter prediction tools: potentialities and limitations
Authors: Anzolini Cassiano Murilo Henrique , Silva-Rocha Rafael 
Published: May 2020

AbstractBackgroundThe promoter region is a key element required for the production of RNA in bacteria. While new high-throughput technology allows massive mapping of promoter elements, we still mainly relay on bioinformatic tools to predict such elements in bacterial genomes. Additionally, despite many different prediction tools have become popular to identify bacterial promoters, there is no systematic comparison of such tools.ResultsHere, we performed a systematic comparison between several widely used promoter prediction tools (BPROM, bTSSfinder, BacPP, CNNProm, IBBP, Virtual Footprint, IPro70-FMWin, 70ProPred, iPromoter-2L and MULTiPly) using well-defined sequence data sets and standardized metrics to determine how well those tools performed related to each other. For this, we used datasets of experimentally validated promoters fromEscherichia coliand a control dataset composed by randomly generated sequences with similar nucleotide distributions. We compared the performance of the tools using metrics such as specificity, sensibility, accuracy and Matthews Correlation Coefficient (MCC). We show that the widely used BPROM presented the worse performance among compared tools, while four tools (CNNProm, IPro70-FMWin, 70ProPreda and iPromoter-2L) offered high predictive power. From these, iPro70-FMWin exhibited the best results for most of the metrics used.ConclusionsTherefore, we exploit here some potentials and limitations of available tools and hope future works can be built upon our effort to systematically characterize such quite useful class of bioinformatics tools.
Immunodietica: interrogating the role of diet in autoimmune disease
Authors: Gershteyn Iosif M. , Burov Andrey A. , Miao Brenda Y. , Morais Vasco H. , Ferreira Leonardo M. R. 
Published: May 2020

AbstractDiet is an environmental factor in autoimmune disorders, where the immune system erroneously destroys one’s own tissues. Yet, interactions between diet and autoimmunity remain largely unexplored, particularly the impact of immunogenetics, one’s human leukocyte antigen (HLA) allele make-up, in this interplay. Here, we interrogated animals and plants for the presence of epitopes implicated in human autoimmune diseases. We mapped autoimmune epitope distribution across organisms and determined their tissue expression pattern. Interestingly, diet-derived epitopes implicated in a disease were more likely to bind to HLA alleles associated with that disease than to protective alleles, with visible differences between organisms with similar autoimmune epitope content. We then analyzed an individual’s HLA haplotype, generating a personalized heatmap of potential dietary autoimmune triggers. Our work uncovered differences in autoimmunogenic potential across food sources and revealed differential binding of diet-derived epitopes to autoimmune disease-associated HLA alleles, shedding light on the impact of diet on autoimmunity.
Sampling bias exaggerates a textbook example of a trophic cascade
Authors: Brice Elaine M. , Larsen Eric J. , MacNulty Daniel R. 
Published: May 2020

ABSTRACTUnderstanding how ecosystems respond to the loss and recovery of large predators is a major challenge because these free-living systems are difficult to sample properly. We show how an accepted practice of nonrandom sampling has confounded this understanding in a textbook system (Yellowstone National Park) where carnivore [Canis lupus(wolf)] recovery is often associated with a trophic cascade involving changes in herbivore [Cervus canadensis(elk)] behavior and density that promote plant regeneration. Long-term data indicate that a customary practice of sampling only the tallest young plants overestimated regeneration of overstory aspen (Populus tremuloides) by a factor of 3-8 compared to random sampling. Sampling only the tallest young plants favored plants taller than the preferred browsing height of elk and overlooked non-regenerating aspen stands. Our results demonstrate how seemingly minor departures from principled sampling can generate substantial misunderstandings about the strength of trophic cascades in response to large predator recovery.
The fully resolved genome ofBacillus thuringiensisHER1410 reveals acry-containing chromosome, two megaplasmids & an integrative plasmidial prophage
Authors: Lechuga Ana , Lood Cédric , Salas Margarita , Vera van Noort V. , Lavigne Rob , Redrejo-Rodríguez Modesto 
Published: May 2020

AbstractBacillus thuringiensisis the most used biopesticide in agriculture. Its entomopathogenic capacity stems from the possession of plasmid-borne insecticidal crystal genes (cry), traditionally used as discriminant taxonomic feature for that species. As such, crystal and plasmid identification are key to the characterization of this species. To date, about 600B. thuringiensisgenomes have been reported, but less than 5% have been resolved, while the other draft genomes are incomplete, precluding plasmid delineation. Here we present the complete genome ofBacillus thuringiensisHER1410, a strain closely related toB. thuringiensis entomocidusand a known host for a variety ofBacillusphages. The combination of short and long-reads techniques allowed fully resolving the genome and delineation of three plasmids. This enabled the accurate detection of an unusual location of a uniquecrygene,cry1Ba4,located in a genomic island near the chromosome replication origin. Two megaplasmids, pLUSID1 and pLUSID2 could be delineated: pLUSID1 (368kb), a likely conjugative plasmid involved in virulence, and pLUSID2 potentially related to the sporulation process. A smaller plasmidial prophage pLUSID3, with a dual lifestyle whose integration within the chromosome, causes the disruption of a flagellar key component. Finally, phylogenetic analysis located this strain within a clade comprising members from theB. thuringiensisserovarthuringiensisand other serovars and withB.cereus s. s.This highlights the intermingled taxonomy ofB. cereus sensu latogroup, where genomics alone does not support the present taxonomy betweenB. cereus s. s.andB. thuringiensisas species designation currently relies solely on the presence of entomocidal genes.ImportanceBacillus cereusgroup species have been extensively studied due to their economical and clinical relevance. This importance originally set the basis forB. cereusgroup members classification which are commonly based on phenotypical criteria. Sequencing era has shed light about genomic characterization of these species, showing their chromosomal genomic similarity and highlighting the role of mobile genetic elements, especially megaplasmids, in the classification and characterization of this group. However, only the 5% of the sequencedB. thuringiensisgenomes have been fully resolved. Thus, here we addressed efficiently the studyB. thuringiensisHER1410 genomic features by the use of a combination of short and long-reads sequencing. This methodology resulted in the high-quality assembly, which led to the identification of an uncommon location of acrygene close to the chromosomal origin, as well as three fully resolved extrachromosomal elements, two megaplasmids and an integrative plasmidial prophage.
N-linked glycan sites on the influenza NA head domain are required for efficient IAV incorporation and replication
Authors: Östbye Henrik , Gao Jin , Martinez Mira Rakic , Wang Hao , de Gier Jan-Willem , Daniels Robert 
Published: May 2020

ABSTRACTN-linked glycans commonly contribute to secretory protein folding, sorting and signaling. For enveloped viruses such as the influenza A virus (IAV), the addition of largeN-linked glycans can also prevent access to epitopes on the surface antigens hemagglutinin (HA or H) and neuraminidase (NA or N). Sequence analysis showed that in the NA head domain of H1N1 IAVs three N-linked glycosylation sites are conserved and that a fourth site is conserved in H3N2 IAVs. Variable sites are almost exclusive to H1N1 IAVs of human origin, where the number of head glycosylation sites first increased and then decreased over time. In contrast, variable sites exist in H3N2 IAVs of human and swine origin, where the number of head glycosylation sites has mainly increased over time. Analysis of IAVs carrying N1 and N2 mutants demonstrated that theN-linked glycosylation sites on the NA head domain are required for efficient virion incorporation and replication in cells or eggs. It also revealed that N1 stability is more affected by the head domain glycans, suggesting N2 is more amenable to glycan additions. Together, these results indicate that in addition to antigenicity, N-linked glycosylation sites can alter NA enzymatic stability and the NA amount in virions.
Covid-19 prevalence estimation by random sampling in the wider population - Optimal sample pooling under varying assumptions about true prevalence
Authors: Brynildsrud Ola 
Published: May 2020

ABSTRACTThe number of confirmed Covid-19 cases in a population is used as a coarse measurement for the burden of disease. However, this number depends heavily on the sampling intensity and the various test criteria used in different jurisdictions. A wide range of sources indicate that a large fraction of cases go undetected. Estimates of the true prevalence of Covid-19 can be made by random sampling in the wider population. Here we use simulations to explore confidence intervals of prevalence estimates under different sampling intensities and degrees of sample pooling.