bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing
Authors: Srivathsan Amrita , Hartop Emily , Puniamoorthy Jayanthi , Lee Wan Ting , Kutty Sujatha Narayanan , Kurina Olavi , Meier Rudolf 
Published: April 2019

ABSTRACTBackgroundMore than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted using detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such “molecular Operational Taxonomic Units” (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well equipped, well-funded molecular laboratories are not readily available in many biodiverse countries.ResultsWe here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyper-diverse fly family Phoridae (Diptera). We sequenced 7,059 specimens collected in a single Malaise trap in Kibale National Park, Uganda over the short period of eight weeks. We discovered >650 species which exceeded the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3,500 barcodes per flowcell. This was achieved by adopting 1D sequencing, re-sequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio: 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; >99% of specimens) and revealed that 90% of the putative species belong to a neglected, megadiverse genus (Megaselia). We demonstrate for oneMegaseliaspecies how the molecular data can guide the description of a new species (Megaselia sepsioidessp. nov.).ConclusionsWe document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 100,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.
Transcriptional profiling of Impatiens walleriana genes through different stages of downy mildew infection reveals novel genes involved in disease susceptibility
Authors: Suarez Stephanie , Naveed Zunaira Afzal , Ali Gul Shad 
Published: April 2019

AbstractImpatiens downy mildew is a highly destructive disease of Impatiens walleriana, and economically important bedding ornamental crop. This disease is caused by a recently emerged pathogen Plasmopara obducens. Since both the host and pathogen are relatively less studied, there are only a few genomic resources available for both I. walleriana and P. obducens. In this study, we have analyzed transcriptional changes in I. walleriana in response to P. obducens infection during different stages of disease development. Our main goal was to identify candidate genes that may be involved in I. walleriana susceptibility to P. obducens. Since the genome of I. walleriana is not available publicly, we constructed and optimized a de novo transcriptome assembly consisting of 73,022 transcripts. Differential expression analysis based on this optimized de novo transcriptome assembly revealed 3,000 to 4,500 differentially expressed transcripts (DETs) at 0 hr, 12 hr, 48 hr, 120 hr, and 240 hr time points after infection. Functional annotation of these DETs revealed that numerous plant stress responsive genes are activated and deactivated throughout the infection cycle. Genes in the calcium signaling pathways, receptor-like kinases (RLKs) including 10 disease resistance associated RLK transcripts, powdery mildew resistance genes (MLO), and many other plant stress related genes were predominantly differentially expressed in I. walleriana in response to P. obducens. Analyses reported here provides molecular insights into the disease susceptibility mechanism of the Impatiens downy mildew, and lays out a strong foundation for future studies aimed at improving downy mildew resistance in I. walleriana.
Neuromesodermal progenitors separate the axial stem zones while producing few single- and dual-fated descendants
Authors: Wood Timothy R. , Kyrsting Anders , Stegmaier Johannes , Kucinski Iwo , Kaminski Clemens F. , Mikut Ralf , Voiculescu Octavian 
Published: April 2019

AbstractMost embryos and regenerating tissues grow by the action of stem zones. Two epithelial stem zones drive axial elongation in amniotes: the mature organizer generates mesoderm, the neuralised ectoderm around it extends the neuraxis. Bipotential progenitors were also shown to exist. How are these stem cell populations organised and what controls the cell fate of bipotential progenitors? We use direct, in vivo imaging of these stem cells in the chick. We find that progenitors of single and dual fates are mingled in a small region between the specialised stem zones. Divergent tissue movements surround this region. When transplanted downstream of these flows, cells from the region of mixed fates adopt the molecular identity and behaviour of the target stem zone, irrespective of their normal fate. Thus, multipotent cells serve to separate the specialized stem zones, instead of a classical boundary. We propose their fate is determined extrinsically by morphogenetic shearing.
CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a
Authors: Martins-Santana Leonardo , de Paula Renato Graciano , Gomes Silva Adriano , Christian Borges Lopes Douglas , do Nascimento Silva Roberto , Silva-Rocha Rafael 
Published: April 2019

AbstractBackgroundTrichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Over the last decades, there have been a strong increase in the understanding of the regulatory network controlling cellulase-coding gene expression in response to a number of inducers and environmental signals. In this sense, the role of calcium and the Calcineurin-responsive protein (CRZ1) has been investigated in industrially relevant strains of T. reesei RUT-C30, but this system has not been investigated in wild-type reference strain of this fungus.ResultsHere, we investigated the role of CRZ1 and Ca2+ signaling in the fungus T. reesei QM6a. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reesei Δcrzl strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In particular, our data demonstrate that Ca2+ acts synergistically with CRZ1 to modulate gene expression, but also exerts CRZ1-independent regulatory role in gene expression in T. reesei, suggesting the existence of additional Ca2+ sensing mechanisms in this fungus.ConclusionsThis work presents new evidence on the regulatory role of CRZ1 and Ca2+ sensing in the regulation of cellulolytic enzymes in T. reesei, evidencing significant and previously unknown function of this Ca2+ sensing system in the control key transcriptional regulators (XYR1 and CRE1) and on the expression of genes related to sugar and Ca2+ transport. Taken together, the data obtained here provide new evidence on the regulatory network of T. reesei related to plant biomass deconstruction.
Feature-Specific Neural Reactivation during Episodic Memory
Authors: Bone Michael B. , Ahmad Fahad , Buchsbaum Bradley R. 
Published: April 2019

AbstractWhen recalling an experience of the past, many of the component features of the original episode may be, to a greater or lesser extent, reconstructed in the mind’s eye. There is strong evidence that the pattern of neural activity that occurred during an initial perceptual experience is recreated during episodic recall (neural reactivation), and that the degree of reactivation is correlated with the subjective vividness of the memory. However, while we know that reactivation occurs during episodic recall, we have lacked a way of precisely characterizing the contents—in terms of its featural constituents—of a reactivated memory. Here we present a novel approach, feature-specific informational connectivity (FSIC), that leverages hierarchical representations of image stimuli derived from a deep convolutional neural network to decode neural reactivation in fMRI data collected while participants performed an episodic recall task. We show that neural reactivation associated with low-level visual features (e.g. edges), high-level visual features (e.g. facial features), and semantic features (e.g. “terrier”) occur throughout the dorsal and ventral visual streams and extend into the frontal cortex. Moreover, we show that reactivation of both low- and high-level visual features correlate with the vividness of the memory, whereas only reactivation of low-level features correlates with recognition accuracy when the lure and target images are semantically similar. In addition to demonstrating the utility of FSIC for mapping feature-specific reactivation, these findings resolve the relative contributions of low- and high-level features to the vividness of visual memories, clarify the role of the frontal cortex during episodic recall, and challenge a strict interpretation the posterior-to-anterior visual hierarchy.
ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion
Authors: Hulstaert Niels , Sachsenberg Timo , Walzer Mathias , Barsnes Harald , Martens Lennart , Perez-Riverol Yasset 
Published: April 2019

AbstractThe field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analysed per experiment, as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastructures. Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Here, we presented ThermoRawFileParser, an open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML. To ensure the broadest possible availability, and to increase integration capabilities with popular workflow systems such as Galaxy or Nextflow, we have also built Conda and BioContainers containers around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools. Finally, we performed a benchmark of ThermoRawFileParser and msconvert to verify that the converted mzML files contain reliable quantitative results.
Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population
Authors: Marla Sandeep R. , Burow Gloria , Chopra Ratan , Hayes Chad , Olatoye Marcus O. , Felderhoff Terry , Hu Zhenbin , Raymundo Rubi , Perumal Ramasamy , Morris Geoffrey P. 
Published: April 2019

AbstractDissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (<15°) is generally lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) population to dissect the genetic architecture of early-season chilling tolerance in the tropical-origin cereal sorghum(Sorghum bicolor[L.] Moench). The NAM resource, developed from reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (>75,000 data points from ∼16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30–45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5–10 chilling tolerance loci explaining 20–41% of variation. Surprisingly, several of the major chilling tolerance loci co-localize precisely with the classical grain tannin (Tan1andTan2) and dwarfing genes (Dw1andDw3) that were under strong directional selection in the US during the 20th century. These findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM reveals why past chilling tolerance breeding was stymied and provides a path for genomics-enabled breeding of chilling tolerance.Article SummaryChilling sensitivity limits productivity of tropical-origin crops in temperate climates, and remains poorly understood at a genetic level. We developed a nested association mapping resource in sorghum, a tropical-origin cereal, to understand the genetic architecture of chilling tolerance. Linkage mapping of growth traits from early-planted field trials revealed several major chilling tolerance loci, including some colocalized with genes that were selected in the origin of US grain sorghum. These findings suggest chilling sensitivity was inadvertently selected during 20th century breeding, but can be bypassed using a better understanding of the underlying genetic architecture.DisclaimerMention of a trademark, warranty, proprietary product, or vendor does not constitute a guarantee by the USDA and does not imply approval or recommendation of the product to the exclusion of others that may be suitable. USDA is an equal opportunity provider and employer.
Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population
Authors: Silva Pereira Guilherme da , Gemenet Dorcus C. , Mollinari Marcelo , Olukolu Bode A. , Wood Joshua C. , Diaz Federico , Mosquera Veronica , Gruneberg Wolfgang J. , Khan Awais , Buell C. Robin , Yencho G. Craig , Zeng Zhao-Bang 
Published: April 2019

ABSTRACTIn developing countries, the sweetpotato,Ipomoea batatas(L.) Lam. (2n= 6x= 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population (‘Beauregard’×‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly predicted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every cM position. Multiple interval mapping was performed using our R package QTLPOLY and detected a total of 41 QTL, ranging from one to ten QTL per trait. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions allowed us to characterize additive allele effects as well as to compute QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.
Interspecies interactions in bacterial colonies are determined by physiological traits and the environment
Authors: Booth Sean C. , Rice Scott A. 
Published: April 2019

AbstractInterspecies interactions in bacterial biofilms have important impacts on the composition and function of communities in natural and engineered systems. To investigate these interactions, synthetic communities provide experimentally tractable systems. Agar-surface colonies are similar to biofilms and have been used for investigating the eco-evolutionary and biophysical forces that determine community composition and spatial distribution of bacteria. Prior work has focused on intraspecies interactions, using differently fluorescent tagged but identical or genetically modified strains of the same species. Here, we investigated how physiological differences determine the community composition and spatial distribution in synthetic communities of Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae. Using quantitative microscopic imaging, we found that interspecies interactions in multispecies colonies are influenced by type IV pilus mediated motility, extracellular matrix secretion, environmental parameters and the specific species involved. These results indicate that the patterns observable in mixed species colonies can be used to understand the mechanisms that drive interspecies interactions, which are dependent on the interplay between specific species’ physiology and environmental conditions.
Diverse conjugative elements silence natural transformation inLegionellaspecies
Authors: Durieux Isabelle , Ginevra Christophe , Attaiech Laetitia , Picq Kevin , Juan Pierre-Alexandre , Jarraud Sophie , Charpentier Xavier 
Published: April 2019

AbstractNatural transformation,i.e.the uptake of DNA and its stable integration in the chromosome, is a major mechanism of horizontal gene transfer and is common in bacteria. The vast majority of bacterial genomes carry the specific genes involved in natural transformation, yet only a fraction of species are deemed naturally transformable. This is typically explained by the inability of standard laboratory conditions to induce this phenotypic trait. However, even when the inducing conditions are known, large intraspecific variations have been reported. In this study, we investigated the conservation and distribution of natural transformability in the human pathogenLegionella pneumophila. Using a panel of 113 clinical isolates, we found that natural transformability is relatively conserved but shows large variations inconsistent with the phylogeny. By conducting a genome-wide association study (GWAS) we identified the conjugative plasmid pLPL as a source of these intraspecific variations. We further show that the plasmid inhibits transformation by simultaneously silencing the genes required for DNA uptake and recombination,comEC, comEA, comFandcomM. We identified a plasmid-encoded small RNA (sRNA), RocRp, as solely responsible for the silencing of natural transformation. RocRp is homologous to the highly conserved and chromosome-encoded RocR which controls the transient expression of the DNA uptake system. We show that RocRp can take over the function of RocR, by acting as a substitute, ensuring that the bacterial host of the conjugative plasmid does not become naturally transformable. Distinct homologs of this plasmid-encoded sRNA are found in diverse conjugative elements in otherLegionellaspecies, suggesting that silencing natural transformation is beneficial to these genetic elements. We propose that transformation-interfering factors are frequent genetic cargo of mobile genetic elements, accounting for intraspecific variations in natural transformation but also responsible for the apparent non-transformability of some species.
A doublecortin-domain protein of Toxoplasma and its orthologues bind to and modify the structure and organization of tubulin polymers
Authors: Leung Jacqueline M. , Nagayasu Eiji , Hwang Yu-Chen , Liu Jun , Pierce Phillip G. , Phan Isabelle Q. , Prentice Robin A. , Murray John M. , Hu Ke 
Published: April 2019

ABSTRACTTgDCX is a doublecortin-domain protein associated with the conoid fibers, a set of strongly curved non-tubular tubulin-polymers in Toxoplasma. TgDCX deletion impairs conoid structure and parasite invasion. TgDCX contains two tubulin-binding domains: a partial P25-alpha and the DCX/doublecortin domain. Orthologues are found in apicomplexans and their free-living relatives Chromera and Vitrella. We report that isolated TgDCX-containing conoid fibers retain their pronounced curvature, but loss of TgDCX destabilizes the fibers. We crystallized and determined the 3D-structure of the DCX-domain, which is similar to those of human doublecortin and well-conserved among TgDCX orthologues. However, the orthologues vary widely in targeting to the conoid in Toxoplasma and in modulating microtubule organization in Xenopus cells. Several orthologues bind to microtubules in Xenopus cells, but only TgDCX generates short, strongly curved microtubule arcs. EM analysis shows microtubules decorated with TgDCX bundled into rafts, often bordered on one edge by a “C”-shaped incomplete tube. A Chromera orthologue closely mimics TgDCX targeting in Toxoplasma and binds to microtubules in Xenopus cells, but does not generate arcs or “C”-shaped tubes, and fails to rescue the defects of the TgDCX-knockout parasite. These observations suggest that species-specific features of TgDCX enable it to generate strongly curved tubulin-polymers to support efficient host-cell invasion.