bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic- and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes
Authors: Peng Peng , Lu Yue , Bosma Tom N.P. , Nijenhuis Ivonne , Nijsse Bart , Shetty Sudarshan A. , Ruecker Alexander , Umanetc Aleksandr , Ramiro-Garcia Javier , Kappler Andreas , Sipkema Detmer , Smidt Hauke , Atashgahi Siavash 
Published: December 2019

AbstractChloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. The lack of CF removal in the abiotic control cultures without artificial electron donors indicated that the observed CF removal is a biotic process. Metabolite analysis with13C labelled CF in the sediment-free enrichment cultures (pH 8.5, salinity 5%) revealed that increasing the vitamin B12concentration from 0.04 to 4 μM enhanced CF removal, reduced DCM formation, and increased13CO2production, which is likely a product of CF oxidation. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected by quantitative PCR nor metagenomic analysis. Rather, members of the orderClostridiales, known to co-metabolically transform CF to DCM and CO2, were detected in the enrichment cultures. Genome-resolved metagenome analysis indicated that their genomes encode enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis that are known to be involved in co-metabolic CF transformation.ImportanceMore than 90% of the global CF emission to the atmosphere originates from natural sources, including saline environments such as salt lake sediments. However, knowledge about the microbial metabolism of CF in such extreme environments is lacking. Here we showed CF transformation potential in a hypersaline lake that was reported as a natural source of CF production. Application of interdisciplinary approaches of microbial cultivation, stable isotope labelling, and metagenomics aided in defining potential chloroform transformation pathways. This study indicates that microbiota may act as a filter to reduce CF emission from hypersaline lakes to the atmosphere, and expands our knowledge of halogen cycling in extreme hypersaline environments.
Parallel genomics uncover novel enterococcal-bacteriophage interactions
Authors: Chatterjee Anushila , Willett Julia L. E. , Nguyen Uyen Thy , Monogue Brendan , Palmer Kelli L. , Dunny Gary M. , Duerkop Breck A. 
Published: December 2019

AbstractBacteriophages (phages) have been proposed as alternative therapeutics for the treatment of multidrug resistant bacterial infections. However, there are major gaps in our understanding of the molecular events in bacterial cells that control how bacteria respond to phage predation. Using the model organismEnterococcus faecalis, we employed two distinct genomic approaches, transposon (Tn) library screening and RNA sequencing, to investigate the interaction ofE. faecaliswith a virulent phage. We discovered that a transcription factor encoding a LytR family response regulator controls the expression of enterococcal polysaccharide antigen (epa) genes that are involved in phage infection and bacterial fitness. In addition, we discovered that DNA mismatch repair mutants rapidly evolve phage adsorption deficiencies, underpinning a molecular basis forepamutation during phage infection. Transcriptomic profiling of phage infectedE. faecalisrevealed broad transcriptional changes influencing viral replication and progeny burst size. We also demonstrate that phage infection alters the expression of bacterial genes associated with intra and inter-bacterial interactions, including genes involved in quorum sensing and polymicrobial competition. Together our results suggest that phage predation has the potential to influence complex microbial behavior and may dictate how bacteria respond to external environmental stimuli. These responses could have collateral effects (positive or negative) on microbial communities such as the host microbiota during phage therapy.ImportanceWe lack fundamental understanding of how phage infection influences bacterial gene expression and consequently how bacterial responses to phage infection affect the assembly of polymicrobial communities. Using parallel genomic approaches, we have discovered novel transcriptional regulators and metabolic genes that influence phage infection. The integration of whole genome transcriptomic profiling during phage infection has revealed the differential regulation of genes important for group behaviors and polymicrobial interactions. Our work suggests that therapeutic phages could more broadly influence bacterial community composition outside of their intended host targets.
Neural bases of phonological and semantic processing in early childhood
Authors: Mathur Avantika , Schultz Douglas , Wang Yingying 
Published: December 2019

AbstractDuring the early period of reading development, children gain phonological (letter-to-sound mapping) and semantic knowledge (storage and retrieval of word meaning). Their reading ability changes rapidly, accompanied by their learning-induced brain plasticity as they learn to read. This study aims to identify the specialization of phonological and semantic processing in early childhood using a combination of univariate and multivariate pattern analysis. Nineteen typically developing children between the age of five to seven performed visual word-level phonological (rhyming) and semantic (related meaning) judgment tasks during functional magnetic resonance imaging (fMRI) scans. Our multivariate analysis showed that young children with good reading ability have already recruited the left hemispheric regions in the brain for phonological processing, including the inferior frontal gyrus (IFG), superior and middle temporal gyrus, and fusiform gyrus. Additionally, our multivariate results suggested that the sub-regions of the left IFG were specialized for different tasks. Our results suggest the left lateralization of fronto-temporal regions for phonological processing and bilateral activations of parietal regions for semantic processing during early childhood. Our findings indicate that the neural bases of reading have already begun to be shaped in early childhood for typically developing children, which can be used as a control baseline for comparison of children at-risk for reading difficulties.
Eco-evolutionary control of pathogens
Authors: Lässig Michael , Mustonen Ville 
Published: December 2019

AbstractControl can alter the eco-evolutionary dynamics of a target pathogen in two ways, by changing its population size and by directed evolution of new functions. Here we develop a fitness model of eco-evolutionary control that specifies a minimum leverage for successful control against the intrinsic dynamics of the pathogen. We apply this model to pathogen control by molecular antibody-antigen binding with a tunable level of antibodies. By analytical solution, we obtain a phase diagram of optimal control and show that an error threshold separates regimes of successful and futile control. Our analysis identifies few, independently measurable fitness parameters that predict the outcome of control. We show that optimal control strategies depend on mutation rate and population size of the pathogen, and we discuss how monitoring and computational forecasting affect the efficiency of control. We argue that these results carry over to more general systems and are elements of an emerging eco-evolutionary control theory.
SAFB2 enables the processing of suboptimal stem-loop structures in clustered primary miRNA transcripts
Authors: Hutter Katharina , Lohmüller Michael , Jukic Almina , Eichin Felix , Avci Seymen , Labi Verena , Hoser Simon M. , Hüttenhofer Alexander , Villunger Andreas , Herzog Sebastian 
Published: December 2019

SummaryMicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally silence most protein-coding genes in mammals. They are generated from primary transcripts containing single or multiple clustered stem-loop structures that are thought to be recognized and cleaved by the DGCR8/DROSHA Microprocessor complex as independent units. Contrasting this view, we here report an unexpected mode of processing of a bicistronic cluster of the miR-15 family, miR-15a-16-1. We find that the primary miR-15a stem-loop is a poor Microprocessor substrate and is consequently not processed on its own, but that the presence of the neighboring primary miR-16-1 stem-loop on the same transcript can compensate for this deficiency in cis. Using a CRISPR/Cas9 screen, we identify SAFB2 (scaffold attachment factor B2) as an essential co-factor in this miR-16-1-assisted pri-miR-15 cleavage, and describe SAFB2 as a novel accessory protein of DROSHA. Notably, SAFB2-mediated cluster assistance expands to other clustered pri-miRNAs including miR-15b, miR-92a and miR-181b, indicating a general mechanism. Together, our study reveals an unrecognized function of SAFB2 in miRNA processing and suggests a scenario in which SAFB2 enables the binding and processing of suboptimal DGCR8/DROSHA substrates in clustered primary miRNA transcripts.Highlightsthe primary miR-15a stem-loop structure per se is a poor Microprocessor substratecleavage of pri-miR-15a requires the processing of an additional miRNA stem-loop on the same RNAsequential pri-miRNA processing or “cluster assistance” is mediated by SAFB proteinsSAFB2 associates with the Microprocessor
Zbtb24 binding protects promoter activity by antagonizing DNA methylation in mESCs
Authors: Wu Haoyu , Leon Granado David San , Vukic Maja , Vonk Kelly K.D. , Breukel Cor , Chouaref Jihed , Laros Jeroen F.J. , Daxinger Lucia 
Published: December 2019

ABSTRACTDNA methylation is a key epigenetic modification essential for normal development. How particular factors control DNA methylation patterns and activity of a given locus is incompletely understood. The zinc finger protein Zbtb24 has been implicated in transcriptional activation/repression and the DNA methylation maintenance pathway. Here, using whole genome bisulfite sequencing in mouse embryonic stem cells, we report that besides a general trend towards DNA hypomethylation, many genomic sites gain methylation in the absence of Zbtb24 and they include promoters of actively transcribed genes. DNA hypomethylation is not generally associated with gene expression changes, suggesting that additional epigenetic safeguards are in place that ensure silencing of the affected loci. Remarkably, we identify a set of genes that is particularly susceptible to Zbtb24 occupancy. At these sites, Zbtb24 binding is not only required for gene activity but also required for maintaining the unmethylated state of the promoter.
New, easy, quick and efficient DNA replication timing analysis by high-throughput approaches
Authors: Hadjadj Djihad , Denecker Thomas , Guérin Eva , Kim Su-Jung , Fauchereau Fabien , Baldacci Giuseppe , Maric Chrystelle , Cadoret Jean-Charles 
Published: December 2019

AbstractDNA replication must be faithful and follow a well-defined spatio-temporal program closely linked to transcriptional activity, epigenomic marks, intra-nuclear structures, mutation rate and cell fate determination. Among the readouts of the DNA replication spatio-temporal program, replication timing (RT) analyses require complex, precise and time-consuming experimental procedures, and the study of large-size computer files. We improved the RT protocol to speed it up and increase its quality and reproducibility. Also, we partly automated the RT protocol and developed a user-friendly software: the START-R suite (Simple Tool for the Analysis of the Replication Timing based on R). START-R suite is an open source web application using an R script and an HTML interface to analyze DNA replication timing in a given cell line with microarray or deep-sequencing results. This novel approach can be used by every biologist without requiring specific knowledge in bioinformatics. It also reduces the time required for generating and analyzing simultaneously data from several samples. START-R suite detects constant timing regions (CTR) but also, and this is a novelty, it identifies temporal transition regions (TTR) and detects significant differences between two experimental conditions. The informatic global analysis requires less than 10 minutes.
Quantitative Analysis of Effects of a Single 60Co Gamma Ray Point Exposure on Time-Dependent Change in Locomotor Activity in Rats
Authors: Otani Keiko , Ohtaki Megu , Fujimoto Nariaki , Saimova Aisulu , Kairkhanova Ynkar , Uzbekov Darkhan , Chaizhunusova Nailya , Aukenov Nulran , Rakhypbekov Tolebay , Sato Hitoshi , Kawano Noriyuki , Hoshi Masaharu 
Published: December 2019

AbstractFatigue is one of the earliest nonspecific symptoms of radiation exposure in humans, but its etiology, mechanism, and dose dependency remain unexplained. Investigating initial behavioral changes caused by irradiation of animals might provide important information to aid understanding of early health effects of radiation exposure and clinical features of radiation injury. Although previous studies in rodents suggested that radiation exposure leads to reduced activity, detailed properties of the effects were unrevealed due to a lack of proper statistical analysis, which is needed to better elucidate details of changes in locomotor activity. Ten-week-old male Wistar rats were subjected to single point external whole-body irradiation with 60Co gamma rays at 0, 2.0, 3.5, and 5.0 Gy (4 rats per group). Infrared sensors were used to continuously record locomotor activity of each rat. Cumulative number of movements during the night was defined as “activity” for each day. A non-linear mixed effects model accounting for individual differences and daily fluctuation of activity was applied to analyze the rats’ longitudinal locomotor data. Despite a small number of animals per group, our statistical method successfully revealed characteristics of the changes in locomotor activity after radiation exposure, showing that 1) reduction in activity occurred immediately—and in a dose-dependent manner—after irradiation and 2) recovery to pre-irradiation levels required almost one week, with the same recovery rate in each dose group. In addition to improving our understanding of radiation effects on locomotor activity, this statistical framework should be useful to analyze other data with similar structure.
Investigating olfactory behaviors in adult zebrafish
Authors: Kermen Florence , Darnet Lea , Wiest Christoph , Palumbo Fabrizio , Bechert Jack , Uslu Ozge , Yaksi Emre 
Published: December 2019

ABSTRACTOdor-driven behaviors such as feeding, mating and predator avoidance are crucial for animal survival. While the zebrafish olfactory circuitry is well understood, a comprehensive description of odor-driven behaviors is needed to better relate olfactory computations to animal responses. Here, we used a medium-throughput setup to measure the swimming trajectories of 10 zebrafish in response to 17 ecologically relevant odors. By selecting appropriate locomotor metrics, we constructed ethograms systematically describing odor-induced changes in the swimming trajectory. We found that fish reacted to most odorants, using different behavioral programs and that combination of few relevant behavioral metrics enabled to capture most of the variance in these innate odor responses. We observed that monomolecular odors in similar chemical categories were weakly clustered based on the behavioral responses, likely because natural odors elicited stronger reactions than the monomolecular odors. Finally, we uncovered a previously undescribed intra and inter-individual variability of olfactory behaviors and suggest a small set of odors that elicit robust responses. In conclusion, our setup and results will be useful resources for future studies interested in characterizing olfactory responses in aquatic animals.
Unravelling ant-symbiont network topology across Europe
Authors: Parmentier Thomas , de Laender Frederik , Bonte Dries 
Published: December 2019

ABSTRACTLong-term associations between different species are key drivers in community composition in all ecosystems. Understanding the ecological and evolutionary drivers of these symbiotic associations is challenging because of the diversity of species and interaction types hosted in natural ecological networks. Here, we compiled the most complete database on natural ant-symbiont networks in Europe to identify the drivers of bipartite network topology. These ant-symbiont networks host an unrivalled diversity of symbiotic associations across the entire mutualism-antagonism continuum, of which the most diverse types of symbionts are (1) trophobionts: mutualistic aphids and scale insects (2) myrmecophiles: commensalistic and parasitic arthropods, and (3) social parasites: parasitic ant species. These diverse ant-symbiont networks provide a unique opportunity to tease apart ecological and evolutionary drivers. To do so, we dissected network topology and asked what determines host specificity and which host factors drive symbiont species richness and facilitate host switching for the different types of symbionts.We found an unexpectedly high number of 701 obligate symbionts associated with European ants. Symbiont type explained host specificity and the average relatedness of the targeted host species. Social parasites were associated with few, but phylogenetically highly related hosts, whereas trophobionts and myrmecophiles interacted with a higher number of hosts across a wider taxonomic distribution. Colony size, host range and habitat type predicted total symbiont richness, where ants hosts with larger colony size or larger distribution range contained more symbiont species. However, we found that different sets of host factors affected diversity in the different types of symbionts. Ecological factors, such as colony size, host range and niche width predominantly drive myrmecophile species richness, whereas evolutionary factors, such as host phylogeny and biogeography, mainly determine richness of mutualistic trophobionts and social parasites. Lastly, we found that hosts with a common biogeographic history support a more similar community of symbionts. Phylogenetic related hosts also shared more trophobionts and social parasites, but not myrmecophiles. Taken together, these results suggest that ecological and evolutionary processes drive host specificity and symbiont richness in large-scale ant-symbiont networks, but these drivers may shift in importance depending on the type of symbiosis. Our findings highlight the potential of well-characterized bipartite networks composed of different types of symbioses to identify candidate processes driving community composition.
Feature matrix normalization, transformation and calculation of ß-diversity in metagenomics: Theoretical and applied perspectives on your decisions
Authors: Poulsen Casper Sahl , Aarestrup Frank Møller , Brinch Christian , Ekstrøm Claus Thorn 
Published: December 2019

AbstractMicrobial metagenomics utilising next generation sequencing is a powerful experimental approach enabling detailed and potentially complete descriptions of the microbial world around and within us. Selecting how to perform feature data normalization, transformation and calculate ß-diversity is a critical step in the analysis of metagenomic data, but also a step for which a multitude of methods are available. Researchers need to have a broad overview and understand the many methods that exist in the field and the consequences from applying them. In this perspectives article, some of the most widely used metagenomic feature data normalizations, transformations and ß-diversity metrics are discussed in the context of multivariate visualizations. We provide a framework that other researchers can utilize to evaluate how robust their test data are when applying different normalizations, transformations and ß-diversity metrics, and visually compare the results of the methods. We constructed an in silico test dataset to evaluate the setup and clarify how the theoretical discussion is transferable to this data. We urge other researchers to implement their own test data, normalization, transformation, ß-diversity metric and visualization methods, in the hope that it will advance better decision making both in study design and analysis strategy.
Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress-adaptedArabidopsis halleri
Authors: Lee Gwonjin , Ahmadi Hassan , Quintana Julia , Syllwasschy Lara , Janina Nadežda , Preite Veronica , Anderson Justin E. , Pietzenuk Björn , Krämer Ute 
Published: December 2019

AbstractHeavy metal-rich toxic soils and ordinary soils are both natural habitats ofArabidopsis halleri. The molecular divergence underlying survival in sharply contrasting environments is unknown. Here we comparatively address metal physiology and transcriptomes ofA. hallerioriginating from the most highly heavy metal-contaminated soil in Europe, Ponte Nossa (Noss/IT), and from non-metalliferous (NM) soil. Noss exhibits enhanced hypertolerance and attenuated accumulation of cadmium (Cd), and transcriptomic Cd responsiveness is decreased, compared to plants of NM soil origin. Among the condition-independent transcriptome characteristics of Noss, the most highly overrepresented functional class of “meiotic cell cycle” comprises 21 transcripts with elevated abundance in vegetative tissues, in particularArgonaute 9(AGO9) and the synaptonemal complex transverse filament protein-encodingZYP1a/b. IncreasedAGO9transcript levels in Noss are accompanied by decreased long terminal repeat retrotransposon expression, and are shared by plants from milder metalliferous sites in Poland and Germany. Expression ofIron-regulated Transporter(IRT1) is very low and ofHeavy Metal ATPase 2(HMA2) strongly elevated in Noss, which can account for its specific Cd handling. In plants adapted to the most extreme abiotic stress, broadly enhanced functions comprise genes with likely roles in somatic genome integrity maintenance, accompanied by few alterations in stress-specific functional networks.