bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationing of Labellum and Glossae Biomorphological characteristics of honeybee workers as breeding tool on honey collection potential ofApis melliferaL. honeybee colonies
Authors: Iqbal Aneela , Rafique Muhammad Khalid , Mahmood Rashid , Noreen Mamoona , Sarwar Ghulam , Ahmad Ishaq , Shahzad Anjum , Shah Muhammad Jahangir , Ahmed Agha Mushtaque , Lashari Muhammad Akbar 
Published: April 2021

ABSTRACTThis study focused on the correlation of honey collection Potential and the length and width of labellum and glossae in worker honey bees (Apis melliferaLigustica). Sixty honeybeeA. melliferaL. colonies were selected, among these 60 colonies, 3 worker bees were sampled from each colony total numbers of samples collected were 180 adult worker foraging bees. Fifteen colonies for each group were used to check the correlation of honey production with length of labellum, width of labellum, length of glossae and the width of glossae respectively. These worker bees were bought to the laboratory frozen, boiled, dissected and mounted on the slides. Measurements of the labellum length, labellum width, glossae length and glossae width were taken by the stereomicroscope with ocular micrometer at 0.8X magnification. Correlation values for the honey collectionand length and width of labellum and glossae were high and positive. These Results support the perception that worker bees with larger labellum and glossae have more ability for honey collection Potential. It is concluded that Biomorphological characters of labellum and glossae are significantly correlated with the honeycollection Potential inA. melliferaL.
Clinical Efficacy of Prebiotics and Glycosaminoglycans versus Placebo In Dogs with Food Responsive Enteropathy Receiving a Hydrolyzed Diet: A Pilot Study
Authors: Glanemann Barbara , Seo Yeon-Jung , Priestnall Simon L. , Garden Oliver A. , Kilburn L. , Rossoni-Serao M. , Segarra Sergi , Mochel Jonathan P. , Allenspach Karin 
Published: April 2021

AbstractInduction of remission is easily achieved with dietary treatment in dogs diagnosed with Food Responsive Chronic Enteropathy (FRD). Administration of prebiotics and glycosaminoglycans (GAGs) may improve epithelial cell integrity and therefore be useful as adjunct treatment. This study evaluated whether the relapse rate of FRD dogs that are switched back to a normal diet can be influenced using supplemental treatment with prebiotics and GAGs.A randomized, controlled clinical trial (RCCT) was performed in dogs diagnosed with FRD. Dogs were diagnosed based on clinical exclusion diagnosis, endoscopic biopsies showing predominantly lymphoplasmacytic infiltration, and response to dietary treatment. Dogs were randomized to be fed a combination of prebiotics and GAGs (group 1) or placebo (group 2) in addition to a hydrolyzed diet. At week 10, a second endoscopy was performed and dogs were switched back to normal diet. Relapse rate was monitored every 2 weeks after that until week 18.Statistical analysis was performed for each outcome (Canine Chronic Enteropathy Clinical Activity Index (CCECAI), clinicopathological data, endoscopic scoring, mWSAVA histological scoring index (mWSAVA), and number of relapses following switch to normal diet) using a linear mixed effects model for group comparison. Time, group, and their interactions were included as a fixed effect, whereas each dog was treated as a random effect.Of the 35 dogs enrolled into the clinical trial, 10 in each group reached the point of second endoscopy. A total of 13 dogs (n=8 in group 1 and n=5 in group 2) reached the trial endpoint of 18 weeks. After switching back to normal diet, none of the dogs in either group relapsed. No significant differences were found over time or between groups for CCECAI, endoscopy scoring and histological scoring. Although there was a clinical worsening in the placebo group after switching back to the original diet, this was not statistically significant (CCECAI p=0.58). Post-hoc power calculation revealed that 63 dogs per group would have been needed to detect statistically significant differences in CIBDAI between treatment groups. Standard dietary treatment induced rapid clinical response in all cases, however, additional supplementation with prebiotics and GAGs did not significantly improve clinical outcome within 4 months after switching back to normal diet. Since there are very few RCCT published in CE in dogs, this pilot study provides important power analyses for planning of further studies.
Identification of the combining abilityof grain yield and its components in hybrid barley populations based on topcross analysis
Authors: Gulmira Akhmedova , Laura Tokhetova , Serikbai Umirzakov , Ainur Demesinova , Ibadulla Tautenov , Serik Bekzhanov , Omarov Kali , Bakhytzhan Shayanbekova 
Published: April 2021

AbstractThe topcross method for assessing combining abilityis more economical and less laborious compared to diallel analysis, and also allows the breeder to obtain quite valuable information about the inbred material. In this research, the determination of the general (GCA) and specific (SCA) combining ability of barley (Hordeum vulgare L.) hybridsin two regions of Kazakhstan contrasting in soil and climatic conditions,the role of additive and non-additive genes in the determination of thetraits understudyhas beenrevealed. It is concluded thatthe predominance of additive gene interactions in the control of the traits understudyin theconditions of the Aral Sea region indicates the possibility of effective selection already in the F2generation, and in the piedmontzone of the Almaty region, due to the high determination of these traits by dominant genes, it is necessary to differentiate the populations of hybrids, starting from the first generation and further selection shall be carried out in several cycles until the achievement of homozygosity of loci carrying dominant genes. Consequently, the genetic contribution of the additive and non-additive effects of genes to the determination and inheritance of the studied traits significantly depends on the conditions of growing the genotypes of spring barley. Of greatest practical interest are the varieties Rihane, WI2291/Roho/WI2269 from the International Center ICARDA and the variety-tester Odessa 100 (Odessa Selection and Genetic Institute, Ukraine) with high GCA and SCA effects, little dependent on growing conditions, which are recommended to be used as reliable donors in breeding programs.
Investigation of Different Free Image Analysis Software for High-Throughput Droplet Detection
Authors: Sanka Immanuel , Bartkova Simona , Pata Pille , Smolander Olli-Pekka , Scheler Ott 
Published: April 2021

ABSTRACTDroplet microfluidics has revealed innovative strategies in biology and chemistry. This advancement has delivered novel quantification methods, such as digital droplet polymerase chain reaction (ddPCR) and antibiotic heteroresistance analysis tool. For droplet analysis, researchers often use imaging techniques. Unfortunately, the analysis of images may require specific tools or programming skills to produce the expected results. In order to address the issue, we explore the potential use of standalone freely available software to detect droplets. We select four most popular software and classify them into instinctive and objective types based on their operation logic. We test and evaluate the software’s i) ability to detect droplets, ii) accuracy and precision, and iii) overall user-friendliness. In our experimental setting we find the objective type of software is better suited for droplet detection. The objective type of software also has simpler workflow or pipeline, especially aimed for non-experienced user. In our case, CellProfiler™(CP) offers the most user-friendly experience for both single image and batch processing analysis.
De novo genome assembly and functional annotation forFusarium langsethiae
Authors: Zuo Ya , Verheecke-Vaessen Carol , Molitor Corentin , Medina Angel , Magan Naresh , Mohareb Fady 
Published: April 2021

AbstractMotivationFusarium langsethiaeis a T-2 and HT-2 mycotoxins producingFusariumspecies firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis inF. langsethiaeto help develop effective control strategies.ResultsTheF. langsethiaeassembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye; producing a genome assembly total length of 59Mb and N50 of 3.51Mb. A total of 19,336 coding genes were identified using RNA-Seq informedab-initiogene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene Ontology.Contactf.mohareb@cranfield.ac.ukData availabilityRaw sequence reads and assembled genome can be downloaded from: GenBank under the accession JAFFKB000000000
Elasticity of dense actin networks produces nanonewton protrusive forces
Authors: Jasnin Marion , Hervy Jordan , Balor Stéphanie , Bouissou Anais , Proag Amsha , Voituriez Raphaël , Maridonneau-Parini Isabelle , Baumeister Wolfgang , Dmitrieff Serge , Poincloux Renaud 
Published: April 2021

AbstractActin filaments assemble into force-generating systems involved in diverse cellular functions, including cell motility, adhesion, contractility and division. It remains unclear how networks of actin filaments, which individually generate piconewton forces, can produce forces reaching tens of nanonewtons. Here we use in situ cryo-electron tomography to unveil how the nanoscale architecture of macrophage podosomes enables basal membrane protrusion. We show that the sum of the actin polymerization forces at the membrane is not sufficient to explain podosome protrusive forces. Quantitative analysis of podosome organization demonstrates that the core is composed of a dense network of bent actin filaments storing elastic energy. Theoretical modelling of the network as a spring-loaded elastic material reveals that it exerts forces of up to tens of nanonewtons, similar to those evaluated experimentally. Thus, taking into account not only the interface with the membrane but also the bulk of the network, is crucial to understand force generation by actin machineries. Our integrative approach sheds light on the elastic behavior of dense actin networks and opens new avenues to understand force production inside cells.
Effect of imputation on gene network reconstruction from single-cell RNA-seq data
Authors: Ly Lam-Ha , Vingron Martin 
Published: April 2021

AbstractDespite the advances in single-cell transcriptomics the reconstruction of gene regulatory networks remains challenging. Both the large amount of zero counts in experimental data and the lack of a consensus preprocessing pipeline for single-cell RNA-seq data make it hard to infer networks from transcriptome data. Data imputation can be applied in order to enhance gene-gene correlations and facilitate downstream data analysis. However, it is unclear what consequences imputation methods have on the reconstruction of gene regulatory networks.To study this question, we evaluate the effect of imputation methods on the performance and structure of the reconstructed networks in different experimental single-cell RNA-seq data sets. We use state-of-the-art algorithms for both imputation and network reconstruction and evaluate the difference in results before and after imputation. We observe an inflation of gene-gene correlations that affects the predicted network structures and may decrease the performance of network reconstruction in general. Yet, within the modest limits of achievable results, we also make a recommendation as to an advisable combination of algorithms, while warning against the indiscriminate use of imputation before network reconstruction in general.
A phased genome assembly for allele-specific analysis in Trypanosoma brucei
Authors: Cosentino RO , Brink BG , Siegel TN 
Published: April 2021

AbstractMany eukaryotic organisms are diploid or even polyploid, i.e. they harbour two or more independent copies of each chromosome. Yet, to date most reference genome assemblies represent a mosaic consensus sequence in which the homologous chromosomes have been collapsed into one sequence. This procedure generates sequence artefacts and impedes analyses of allele-specific mechanisms. Here, we report the allele-specific genome assembly of the diploid unicellular protozoan parasite Trypanosoma brucei.As a first step, we called variants on the allele-collapsed assembly of the T. brucei Lister 427 isolate using short-read error-corrected PacBio reads. We identified 96 thousand heterozygote variants across the genome (average of 4.2 variants / kb), and observed that the variant density along the chromosomes was highly uneven. Several long (>100 kb) regions of loss-of-heterozigosity (LOH) were identified, suggesting recent recombination events between the alleles. By analysing available genomic sequencing data of multiple Lister 427 derived clones, we found that most LOH regions were conserved, except for some that were specific to clones adapted to the insect lifecycle stage. Surprisingly, we also found that some Lister 427 clones were aneuploid. We found evidence of trisomy in chromosome five (chr 5), chr 2, chr 6 and chr 7. Moreover, by analysing RNA-seq data, we showed that the transcript level is proportional to the ploidy, evidencing the lack of a general expression control at the transcript level in T. brucei.As a second step, to generate an allele-specific genome assembly, we used two powerful datatypes for haplotype reconstruction: raw long reads (PacBio) and chromosome conformation (Hi-C) data. With this approach, we were able to assign 99.5% of all heterozygote variants to a specific homologous chromosome, building a 66 Mb long T. brucei Lister 427 allele-specific genome assembly. Hereby, we identified genes with allele-specific premature termination codons and showed that differences in allele-specific expression at the level of transcription and translation can be accurately monitored with the fully phased genome assembly.The obtained reference-grade allele-specific genome assembly of T. brucei will enable the analysis of allele-specific phenomena, as well as the better understanding of recombination and evolutionary processes. Furthermore, it will serve as a standard to ‘benchmark’ much needed automatic genome assembly pipelines for highly heterozygous wild species isolates.
Bistable host-pathogen interaction explains varied infection outcomes
Authors: Yu Guozhi , Hu Yingying , Wang Shizhong , Han Xingfa , Du Xiaogang , Xu Huailiang , Zeng Xianyin , Steiner Ulrich , Rolff Jens 
Published: April 2021

ABSTRACTDeath or survival are the two outcomes of an infection. The development of an infection depends on multiple interplaying factors, including the temporal dynamic of host nutrition, immune response and pathogen proliferation, but how these factors collectively determine the outcome of an infection is less understood. To understand the underlying principle of infection, here, we took a systems approach by developing a simple mathematical model to understand multi-factored host-pathogen interaction. We find that nonlinear interactions feedback between host and pathogens resulting in two distinct trajectories of disease progression. We show that disease progression, measured by the pathogen load, responds in a bistable manner, by either proliferating or eventually being eliminated. We identified key processes accounting for bistability, including host’s resource assimilation, immune response and intrinsic noise. In addition, resource availability, immunity, and pathogen load at the onset of infection are also critical in determining the bistability. We then highlight, by discussing in the light of previous theoretical and experimental work, how our framework provides testable theories for host-pathogen interaction inside the host.
Structural basis for the ARF GAP activity and specificity of the C9orf72 complex
Authors: Su Ming-Yuan , Fromm Simon A. , Remis Jonathan , Toso Daniel B. , Hurley James H. 
Published: April 2021

AbstractMutation ofC9ORF72is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 forms a complex with SMCR8 and WDR41, which was reported to have GTPase activating protein activity toward ARF proteins, RAB8A, and RAB11A. We determined the cryo-EM structure of ARF1-GDP-BeF3-bound to C9orf72:SMCR8:WDR41. The SMCR8longinand C9orf72longindomains form the binding pocket for ARF1. One face of the C9orf72longindomain holds ARF1 in place, while the SMCR8longinpositions the catalytic finger Arg147 in the ARF1 active site. Mutations in interfacial residues of ARF1 and C9orf72 reduced or eliminated GAP activity. RAB8A GAP required ∼10-fold higher concentrations of the C9orf72 complex than for ARF1. These data support a specific function for the C9orf72 complex as an ARF GAP.
Changing microbial activities during low salinity acclimation in the brown algaEctocarpus subulatus
Authors: KleinJan Hetty , Caliafano Gianmaria , Aite Méziane , Fremy Enora , Frioux Clémence , Karimi Elham , Corre Erwan , Wichard Thomas , Siegel Anne , Boyen Catherine , Dittami Simon M. 
Published: April 2021

SummaryEctocarpus subulatusis one of the few brown algae found in river habitats. Its ability to tolerate freshwater is due, in part, to its uncultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grownE. subulatususing mild antibiotic treatments, which affected its ability to grow in low salinity. The acclimation to low salinity of fresh water-tolerant and intolerant holobionts was then compared. Salinity had a significant impact on bacterial gene expression as well as the expression of algae- and bacteria-associated viruses in all holobionts, albeit in different ways for each holobiont. On the other hand, gene expression of the algal host and metabolite profiles were affected almost exclusively in the fresh water intolerant holobiont. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, we identified vitamin K synthesis as one possible bacterial service missing specifically in the fresh water-intolerant holobiont in low salinity.We also noticed an increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a compound that regulates quorum sensing. This could have caused a shift in bacterial behavior in the intolerant holobiont, resulting in virulence or dysbiosis.Originality-Significance StatementThe importance of symbiotic microbes for the health and stress resistance of multicellular eukaryotes is widely acknowledged, but understanding the mechanisms underlying these interactions is challenging. They are especially difficult to separate in systems with one or more uncultivable components. We bridge the gap between fully controlled, cultivable model systems and purely environmental studies through the use of a multi-omics approach and metabolic models on experimentally modified “holobiont” systems. This allows us to generate two promising working hypotheses on the mechanisms by which uncultivated bacteria influence their brown algal host’s fresh water tolerance.
Retrotransposons as pathogenicity factors of the plant pathogenic fungusBotrytis cinerea
Authors: Porquier Antoine , Tisserant Constance , Salinas Francisco , Glassl Carla , Wange Lucas , Enard Wolfgang , Hauser Andreas , Hahn Matthias , Weiberg Arne 
Published: April 2021

AbstractBackgroundRetrotransposons are genetic elements inducing mutations in all domains of life. Despite their detrimental effect, retrotransposons become temporarily active during epigenetic reprogramming and cellular stress response, which may accelerate host genome evolution. In fungal pathogens, a positive role has been attributed to retrotransposons when shaping genome architecture and expression of genes encoding pathogenicity factors; thus, retrotransposons are known to influence pathogenicity.ResultsWe here uncovered a hitherto unknown role of fungal retrotransposons as being pathogenicity factors, themselves. Studying the aggressive fungal plant pathogenBotrytis cinerea, that is known to deliver some long-terminal repeat (LTR) deriving regulatory trans-species small RNAs (BcsRNAs) into plant cells to suppress host gene expression for infection we found that naturally occurring, less aggressiveB. cinereastrains possess considerably lower copy numbers of LTR retrotransposons and had lost retrotransposonBcsRNA production. By a transgenic proof-of-concept approach, we reconstituted retrotransposon expression in aBcsRNA-lackingB. cinereastrain, which resulted in enhanced aggressiveness in a retrotransposon andBcsRNA expression-dependent manner. Moreover, retrotransposon expression inB. cinerealed to suppression of plant defence-related genes during infection.ConclusionsWe propose that retrotransposons are pathogenicity factors that manipulate host plant gene expression by encoding trans-speciesBcsRNAs. Taken together, the novelty that retrotransposons are pathogenicity factors will have general impact on studies of host-microbe interactions and pathology.
Alpha oscillations reflect suppression of distractors with increased perceptual load
Authors: Gutteling Tjerk , Sillekens Lonieke , Lavie Nilli , Jensen Ole 
Published: April 2021

SummaryAttention serves an essential role in cognition and behaviour allowing us to focus on behaviourally-relevant objects while ignoring distraction. Perceptual load theory states that attentional resources are allocated according to the requirements of the task, i.e. its ‘load’. The theory predicts that the resources left to process irrelevant, possibly distracting stimuli, are reduced when the perceptual load is high. However, it remains unclear how this allocation of attentional resources specifically relates to neural excitability and suppression mechanisms. In this magnetoencephalography (MEG) study, we show that brain oscillations in the alpha band (8-13Hz) implement the suppression of distracting objects when the perceptual load is high. In parallel, high load increased neuronal excitability for target objects, as reflected by rapid frequency tagging. We suggest that the allocation of resources in tasks with high perceptual load is implemented by a gain increase for targets, complemented by distractor suppression reflected by alpha band oscillations closing the ‘gate’ for interference.