bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing
Authors: Bentlage Bastian , Collins Allen G. 
Published: November 2020

AbstractHigher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydriodolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.
3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex
Authors: Sabinina Vilma Jimenez , Hossain M. Julius , Hériché Jean-Karim , Hoess Philipp , Nijmeijer Bianca , Mosalaganti Shyamal , Kueblbeck Moritz , Callegari Andrea , Szymborska Anna , Beck Martin , Ries Jonas , Ellenberg Jan 
Published: November 2020

AbstractNuclear pore complexes (NPCs) are large macromolecular machines that mediate the traffic between the nucleus and the cytoplasm. In vertebrates, each NPC consists of ~1000 proteins, termed nucleoporins, and has a mass of over 100 MDa. While a pseudo-atomic static model of the central scaffold of the NPC has recently been assembled by integrating data from isolated proteins and complexes, many structural components still remain elusive due to the enormous size and flexibility of the NPC. Here, we explored the power of 3D super-resolution microscopy combined with computational classification and averaging to explore the 3D structure of the NPC in single human cells. We show that this approach can build the first integrated 3D structural map containing both central as well as peripheral NPC subunits with molecular specificity and nanoscale resolution. Our unbiased classification of over ten thousand individual NPCs indicates that the nuclear ring and the nuclear basket can adopt different conformations. Our approach opens up the exciting possibility to relate different structural states of the NPC to function in situ.
Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite
Authors: Lin Mao-Jan , Lin Yu-Chun , Chen Nae-Chyun , Luo Allen Chilun , Lai Sheng-Kai , Hsu Chia-Lang , Hsu Jacob Shujui , Chen Chien-Yu , Yang Wei-Shiung , Chen Pei-Lung 
Published: November 2020

ABSTRACTGenetic profiling of germline adaptive immune receptor repertoire (AIRR), including T cell receptor (TR) and immunoglobulin (IG), is imaginably relevant to numerous immune-related conditions, but currently insurmountable due to high genetic complexity. Our gAIRR Suite comprises three modules. gAIRR-seq, a probe capture-based targeted sequencing pipeline, profiles AIRR from individual DNA samples. gAIRR-call and gAIRR-annotate call alleles from gAIRR-seq reads and annotate whole-genome assemblies respectively. We gAIRR-seqed TRV and TRJ of seven Genome in a Bottle (GIAB) DNA samples with 100% accuracy, and discovered novel alleles. We also gAIRR-seqed and gAIRR-called a subject from both the peripheral blood mononuclear cells (PBMC) and oral mucosal cells. The calling results from these two cell types have a high concordance (99% for all known AIRR alleles). We gAIRR-annotated 36 genomes to cumulatively unearth 325 novel TRV alleles and 29 novel TRJ alleles. We could further profile the flanking sequences, including the recombination signal sequence (RSS). We validated two structural variants for HG002. We uncovered substantial conflicts of AIRR genes in references GRCh37 and GRCh38. The gAIRR Suite can potentially benefit future genetic study and clinical applications of various immune-related phenotypes.
Spurious regulatory connections dictate the expression-fitness landscape of translation termination factors
Authors: Lalanne Jean-Benoît , Parker Darren J. , Li Gene-Wei 
Published: November 2020

AbstractDuring steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts.HighlightsPrecision measurements enable multiscale expression-to-fitness mapping.RF depletion leads to imbalanced translation for co-transcribed gene pairs.Imbalanced translation induces unintended regulons to the detriment of cell fitness.Swapping a single stop codon rewires global susceptibility to RF perturbation.
Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley
Authors: Sharma Rajiv , Cockram James , Gardner Keith A. , Russell Joanne , Ramsay Luke , Thomas William TB , O’Sullivan Donal M. , Powell Wayne , Mackay Ian J. 
Published: November 2020

AbstractThe process of crop breeding over the last century has delivered new varieties with increased genetic gains, resulting in higher crop performance and yield. However in many cases, the underlying alleles and genomic regions that have underpinned this success remain unknown. This is due, in part, to the difficulty in generating sufficient phenotypic data on large numbers of historical varieties to allow such analyses to be undertaken. Here we demonstrate the ability to circumvent such bottlenecks by identifying genomic regions selected over 100 years of crop breeding using the age of a variety as a surrogate for yield. Using ‘environmental genome-wide association scans’ (EnvGWAS) on variety age in two of the world’s most important crops, wheat and barley, we found strong signals of selection across the genomes of our target crops. EnvGWAS identified 16 genomic regions in barley and 10 in wheat with contrasting patterns between spring and winter types of the two crops. To further examine changes in genome structure in wheat and barley over the past century, we used the same genotypic data to derive eigenvectors for deployment in EigenGWAS. This resulted in the detection of seven major chromosomal introgressions that contributed to adaptation in wheat. The deployment of both EigenGWAS and EnvGWAS based on variety age avoids costly phenotyping and will facilitate the identification of genomic tracts that have been under selection during plant breeding in underutilized historical cultivar collections. Our results not only demonstrate the potential of using historical cultivar collections coupled with genomic data to identify chromosomal regions that have been under selection but to also guide future plant breeding strategies to maximise the rate of genetic gain and adaptation in crop improvement programs.Significance Statement100 years of plant breeding have greatly improved crop adaptation, resilience, and productivity. Generating the trait data required for these studies is prohibitively expensive and can be impossible on large historical traits. This study reports using variety age and eigenvectors of the genomic relationship matrix as surrogate traits in GWAS to locate the genomic regions that have undergone selection during varietal development in wheat and barley. In several cases these were confirmed as associated with yield and other selected traits. The success and the simplicity of the approach means it can easily be extended to other crops with a recent recorded history of plant breeding and available genomic resources.
Characterisation and chemometric evaluation of 17 elements in ten seaweed species from Greenland
Authors: Kreissig Katharina Johanna , Hansen Lisbeth Truelstrup , Jensen Pernille Erland , Wegeberg Susse , Geertz-Hansen Ole , Sloth Jens J 
Published: November 2020

AbstractSeveral Greenland seaweed species have potential as foods or food ingredients, both for local consumption and export. However, knowledge regarding their content of beneficial and deleterious elements on a species specific and geographical basis is lacking. This study investigated the content of 17 elements (As, Ca, Cd, Cr, Cu, Fe, Hg, I, K, Mg, Mn, Na, Ni, P, Pb, Se and Zn) in 77 samples of ten species (Agarum clathratum, Alaria esculenta, Ascophyllum nodosum, Fucus distichus, Fucus vesiculosus, Hedophyllum nigripes, Laminaria solidungula, Palmaria palmata, Saccharina latissima and Saccharina longicruris). Element profiles differed between species but showed similar patterns within the same family. For five species, different thallus parts were investigated separately, and showed different element profiles. A geographic origin comparison of Fucus species indicated regional differences. The seaweeds investigated were especially good sources of macrominerals (K > Na > Ca > Mg) and trace minerals, such as Fe. Iodine contents were high, especially in macroalgae of the family Laminariaceae. None of the samples exceeded the EU maximum levels for Cd, Hg or Pb, but some exceeded the stricter French regulations, especially for Cd and I. In conclusion, these ten species are promising food items.
Spatial Suitability Modeling of Zoonosis: Implicated Risk Areas of B. anthracis and Trends under climate change Scenarios in Ethiopia
Authors: Yousuf Michael A , Asfaw Solomon , Mengistu Shimelis , Husen Mohammedsham 
Published: November 2020

AbstractThe causative agent of Anthrax B. anthracis has long been known to cause disease in animals and humans. Its worldwide distribution includes Ethiopia as an endemic country to the disease. The current study was aimed at identifying and developing risk maps, in areas that are suitable for the persistence of anthrax spores under climate change scenarios by using anthrax occurrence data and other predictor variables in MaxEnt model. A total of 158 occurrence locations were used as inputs along 10 current bioclimatic, future climatic grids and topographic covariates to develop a model and evaluate the individual contribution of each variable to the presence of B. anthracis in Ethiopia. It’s concluded that the most important variables limiting the distribution of B. anthracis in Ethiopia were Temperature, Precipitation, and Elevation. Under HADGEM2-ES future modeling scenarios except for RCP 8.5/2050 there is a decrease in areas of suitability from Current scenario under RCP 2.6/2050, RCP 2.6/2070, and RCP 8.5/2070. Subtle expansions of suitable areas are identified under RCP 2.6/2050 and RCP 2.6/2070 in the eastern parts of Ethiopia. However, there are small portions of southern areas that are expected to lose suitable habitats under all future scenarios. These findings could help health management authorities to formulate prevention and control strategies of anthrax in suitable areas under B. anthracis.
Biosynthesis of dihydroquercetin inEscherichia colifrom glycerol
Authors: Park Seon Young , Yang Dongsoo , Ha Shin Hee , Lee Sang Yup 
Published: November 2020

AbstractPhenylpropanoids are a group of diverse natural products derived from aromatic amino acids. Although their demands are high both as drugs and nutraceuticals, their production mainly depends on inefficient extraction from plants. To achieve sustainable production of phenylpropanoids, engineering model microorganisms suchas Escherichia colihas been sought, but most strains require supplementation of expensive precursors. Here, we report one-step production of a representative phenylpropanoid, dihydroquercetin (DHQ), from simple carbon sources inE. colifor the first time. The best DHQ producer strain capable of producing 239.4 mg/L of DHQ from glycerol was obtained by optimizing the biosynthetic pathway and engineering the signal peptide of cytochrome P450 (TT7) fromArabidopsis thaliana. The engineered plant P450 could produce a significantly higher titer of DHQ than a bacterial monooxygenase, showing the potential of employing plant P450s for the production of diverse natural products that has been previously difficult in bacterial hosts. This study will serve as a guideline for industrial production of pharmaceutically important yet complex natural products.
Fast and sensitive taxonomic assignment to metagenomic contigs
Authors: Mirdita M. , Steinegger M. , Breitwieser F. , Söding J. , Levy Karin E. 
Published: November 2020

SummaryMMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig’s taxonomic identity by weighted voting. Its fragment extraction step is suitable for the analysis of all domains of life. MMseqs2 taxonomy is 2-18x faster than state-of-the-art tools and also contains new modules for creating and manipulating taxonomic reference databases as well as reporting and visualizing taxonomic assignments.AvailabilityMMseqs2 taxonomy is part of the MMseqs2 free open-source software package available for Linux, macOS and Windows at https://mmseqs.com.Contacteli.levy.karin@gmail.com
Distinct role of nucleus accumbens D2-MSN projections to ventral pallidum in different phases of motivated behavior
Authors: Soares-Cunha Carina , Correia Raquel , Domingues Ana Verónica , Coimbra Bárbara , de Vasconcelos Nivaldo AP , Pinto Luísa , Sousa Nuno , Rodrigues Ana João 
Published: November 2020

AbstractThe nucleus accumbens (NAc) is a key region in motivated behaviors. NAc medium spiny neurons (MSNs) are divided into those expressing dopamine receptor D1 or D2. Classically, D1- and D2-MSNs have been described as having opposing roles in reinforcement but recent evidence suggests a more complex role for D2-MSNs.Here we show that optogenetic modulation of D2-MSN to ventral pallidum (VP) projections during different stages of motivated behavior has contrasting effects in motivation. Activation of D2-MSN-VP projections during a reward-predicting cue results in increased motivational drive, whereas activation at reward delivery results in decreased motivation; optical inhibition has the opposite behavioral effect. In addition, in a free choice instrumental task, animals prefer the lever that originates one pellet in opposition to pellet plus D2-MSN-VP optogenetic activation, and vice versa for optogenetic inhibition.In summary, D2-MSN-VP projections play different (and even opposing) roles in distinct phases of motivated behavior.
ninaDregulates cholesterol homeostasis from the midgut which protects against neurodegeneration
Authors: Soulé Stéphanie , Martin Jean-René 
Published: November 2020

SUMMARYCholesterol is crucial to maintain normal cellular function. In human, it has also been involved in various neurodegeneration processes, as Niemann-Pick and Alzheimer diseases. Recently, we have identified a small nucleolar RNA (jouvence) required in the epithelial cells of the gut (enterocytes), and showed that its overexpression extends lifespan. A transcriptomic analysis has revealed a deregulation of several genes injouvencemutants. Among them,ninaDencoding a mammalian homolog to class B Scavenger receptor is importantly upregulated. InDrosophila, ninaDis required for the uptake of the dietary carotenoid, used for the formation of rhodopsin. Here, we show thatjouvence-deleted flies are deficient in cholesterol-ester, as well as old flies present neurodegenerative lesions. RestoringninaDmRNA expression level in enterocytes restores the metabolic cholesterol-ester level, prevents neurodegeneration and extends lifespan, revealing a gut-brain axis. Our studies demonstrates thatninaDis a central regulator of cholesterol homeostasis and a longevity-promoting factor.
The Dutch Microbiome Project defines factors that shape the healthy gut microbiome
Authors: Gacesa R. , Kurilshikov A. , Vich Vila A. , Sinha T. , Klaassen M.A.Y. , Bolte L.A. , Andreu-Sánchez S. , Chen L. , Collij V. , Hu S. , Dekens J.A.M. , Lenters V.C. , Björk J.R. , Swarte J.C. , Swertz M.A. , Jansen B.H. , Gelderloos-Arends J. ,   Lifelines cohort study, Hofker M. , Vermeulen R.C.H. , Sanna S. , Harmsen H.J.M. , Wijmenga C. , Fu J. , Zhernakova A. , Weersma R.K. 
Published: November 2020

AbstractThe gut microbiome is associated with diverse diseases, but the universal signature of an (un)healthy microbiome remains elusive and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. To fill this gap, we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We then correlated this to 241 host and environmental factors, including physical and mental health, medication use, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is primarily shaped by environment and cohousing. Only ∼13% of taxa are heritable, which are enriched with highly prevalent and health-associated bacteria. By identifying 2,856 associations between microbiome and health, we find that seemingly unrelated diseases share a common signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, of which numerous early-life and current factors are particularly linked to the microbiome. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.
A spiking neural circuit model for learning multi-sensory integration
Authors: Song Deying , Niu Xueyan , Zhang Wen-Hao , Lee Tai Sing 
Published: November 2020

AbstractNeurons in visual and vestibular information integration areas of macaque brain such as medial superior temporal (MSTd) and ventral intraparietal (VIP) have been classified into congruent neurons and opposite neurons, which prefer congruent inputs and opposite inputs from the two sensory modalities, respectively. In this work, we propose a mechanistic spiking neural model that can account for the emergence of congruent and opposite neurons and their interactions in a neural circuit for multi-sensory integration. The spiking neural circuit model is adopted from an established model for the circuits of the primary visual cortex with little changes in parameters. The network can learn, based on the basic Hebbian learning principle, the correct topological organization and behaviors of the congruent and opposite neurons that have been proposed to play a role in multi-sensory integration. This work explore the constraints and the conditions that lead to the development of a proposed neural circuit for cue integration. It also demonstrates that such neural circuit might indeed be a canonical circuit shared by computations in many cortical areas.
Positive effects of crop diversity on productivity driven by changes in soil microbial composition
Authors: Stefan Laura , Hartmann Martin , Engbersen Nadine , Six Johan , Schöb Christian 
Published: November 2020

SummaryIntensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant–microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and functions, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (3 times larger) or soil moisture (3 times larger). Furthermore, these processes were context-dependent: in Spain, where soil resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes, thereby emphasizing the context-dependence of crop–microbe relationships.