bluuebunny/crossref_metadata_2025_split huggingface dataset:
The monoplastidic bottleneck in algae and plant evolution
Authors: de Vries Jan , Gould Sven B. 
Published: February 2019

AbstractPlant and algae plastids evolved from the endosymbiotic integration of a cyanobacterium by a heterotrophic eukaryote. A consequence of their ancestry is that new plastids can only emerge through fission and vital to organelle and host co-evolution was the early synchronization of bacterial division with the host’s eukaryotic cell cycle. Most of the sampled algae, including multicellular macroalgae, house a single plastid per cell — or nucleus in case of coenocytic cells — and basal branching relatives of polyplastidic lineages are all monoplastidic. The latter is also true regarding embryophytes, as some non-vascular plants are monoplastidic at least at some stage of their life cycle. Here we synthesize recent advances regarding plastid division and associated proteins, including those of the peptidoglycan wall biosynthesis, across the diversity of phototrophic eukaryotes. Through the comparison of the phenotype of 131 species harbouring plastids of primary or secondary origin, we uncover that one prerequisite for an algae or plant to house multiple plastids per nucleus appears the loss of the genes MinD and MinE from the plastid genome. Housing a single plastid whose division is coupled to host cytokinesis appears a prerequisite of plastid emergence; escaping that monoplastidic bottleneck succeeded rarely and appears tied to evolving a complex morphology. Considering how little we know about the mechanisms that guarantee proper organelle (and genome) inheritance raises the peculiar possibility that a quality control checkpoint of plastid transmission remains to be explored and which is tied to understanding the monoplastidic bottleneck.
Prodomain-Growth Factor Swapping in the Structure of pro-TGF-β1
Authors: Zhao Bo , Xu Shutong , Dong Xianchi , Lu Chafen , Springer Timothy A. 
Published: February 2019

AbstractTransforming growth factor (TGF)-β is synthesized as a proprotein that dimerizes in the endoplasmic reticulum. After processing in the Golgi to cleave the N-terminal prodomain from the C-terminal growth factor (GF) domain in each monomer, pro-TGF-β is secreted and stored in latent complexes. It is unclear which prodomain and GF monomer are linked prior to proprotein convertase (PC) cleavage, and how much conformational change occurs following cleavage. We have determined a structure of pro-TGF-β1 with the PC cleavage site mutated, to mimic the structure of the TGF-β1 proprotein. Our structure demonstrates that the prodomain arm domain in one monomer is linked to the GF that interacts with the arm domain in the other monomer in the dimeric structure, i.e., the prodomain arm domain and GF domain in each monomer are swapped. Swapping has important implications for the mechanism of biosynthesis in the TGF-β family and is relevant to the mechanism for preferential formation of heterodimers over homodimers for some members of the TGF-β family. Our structure also provides comparisons between independent TGF-β1 crystal structures and between human and porcine pro-TGF-β1.
The Effect of Visual Capture Towards Subjective Embodiment Within the Full Body Illusion
Authors: Carey Mark , Crucianelli Laura , Preston Catherine , Fotopoulou Aikaterini 
Published: February 2019

AbstractTypically, multisensory illusion paradigms emphasise the importance of synchronous visuotactile integration to induce subjective embodiment towards another body. However, the extent to which embodiment is due to the ‘visual capture’ of congruent visuoproprioceptive information alone remains unclear. Thus, across two experiments (total N = 80), we investigated how mere visual observation of a mannequin body, viewed from a first-person perspective, influenced subjective embodiment independently from concomitant visuotactile integration. Moreover, we investigated whether slow, affective touch on participants’ own, unseen body (without concomitant touch on the seen mannequin) disrupted visual capture effects to a greater degree than fast, non-affective touch. In total, 40% of participants experienced subjective embodiment towards the mannequin body following mere visual observation, and this effect was significantly higher than conditions which included touch to participants own, unseen body. The velocity of the touch that participants received (affective/non-affective) did not differ in modulating visual capture effects. Furthermore, the effects of visual capture and perceived pleasantness of touch was not modulated by subthreshold eating disorder psychopathology. Overall, this study suggests that congruent visuoproprioceptive cues can be sufficient to induce subjective embodiment of a whole body, in the absence of visuotactile integration and beyond mere confabulatory responses.
Propidium iodide staining underestimates viability of adherent bacterial cells
Authors: Rosenberg Merilin , Azevedo Nuno F. , Ivask Angela 
Published: February 2019

AbstractCombining membrane impermeable DNA-binding stain propidium iodide (PI) with membrane-permeable DNA-binding counterstains is a widely used approach for bacterial viability staining. In this paper we show that PI staining of adherent cells in biofilms may significantly underestimate bacterial viability due to the presence of extracellular nucleic acids. We demonstrate that gram-positive Staphylococcus epidermidis and gram-negative Escherichia coli 24-hour initial biofilms on glass consist of 76 and 96% PI-positive red cells in situ, respectively, even though 68% the cells of either species in these aggregates are metabolically active. Furthermore, 82% of E. coli and 89% S. epidermidis are cultivable after harvesting. Confocal laser scanning microscopy (CLSM) revealed that this false dead layer of red cells is due to a subpopulation of double-stained cells that have green interiors under red coating layer which hints at extracellular DNA (eDNA) being stained outside intact membranes. Therefore, viability staining results of adherent cells should always be validated by an alternative method for estimating viability, preferably by cultivation.
Ozymandias: A biodiversity knowledge graph
Authors: Page Roderic D. M. 
Published: February 2019

AbstractEnormous quantities of biodiversity data are being made available online, but much of this data remains isolated in their own silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a “biodiversity knowledge graph” for the Australian fauna. These steps involved in constructing the graph are described, and examples its application are discussed. A web interface to the knowledge graph (called “Ozymandias”) is available at https://ozymandias-demo.herokuapp.com.
Genome of the parasitoid waspDiachasma alloeum, an emerging model for ecological speciation and transitions to asexual reproduction
Authors: Tvedte Eric S. , Walden Kimberly K.O. , McElroy Kyle E. , Werren John H. , Forbes Andrew A. , Hood Glen R. , Logsdon John M. , Feder Jeffrey L. , Robertson Hugh M. 
Published: February 2019

AbstractParasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the waspDiachasma alloeum(Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot flyRhagoletis pomonella(Diptera: Tephritidae) and a developing model for understanding how ecological speciation can “cascade” across trophic levels. Identification of gene content confirmed the overall quality of the draft genome, and we manually annotated ∼400 genes as part of this study, including those involved in oxidative phosphorylation, chemosensation, and reproduction. Through comparisons to model hymenopterans such as the European honeybeeApis melliferaand parasitoid waspNasonia vitripennis, as well as a more closely related braconid parasitoidMicroplitis demolitor, we identified a proliferation of transposable elements in the genome, an expansion of chemosensory genes inD. alloeumand other parasitoid wasps, and the maintenance of several key genes with known roles in sexual reproduction and sex determination. TheD. alloeumgenome will provide a valuable resource for comparative genomics studies in Hymenoptera as well as specific investigations into the genomic changes associated with ecological speciation and transitions to asexuality.
Efficient exact associative structure for sequencing data
Authors: Marchet Camille , Kerbiriou Mael , Limasset Antoine 
Published: February 2019

AbstractMotivationA plethora of methods and applications share the fundamental need to associate information to words for high throughput sequence analysis. Doing so for billions of k-mers is commonly a scalability problem, as exact associative indexes can be memory expensive. Recent works take advantage of overlaps between k-mers to leverage this challenge. Yet existing data structures are either unable to associate information to k-mers or are not lightweight enough.ResultsWe present BLight, a static and exact data structure able to associate unique identifiers to k-mers and determine their membership in a set without false positive, that scales to huge k-mer sets with a low memory cost. This index combines an extremely compact representation along with very fast queries. Besides, its construction is efficient and needs no additional memory. Our implementation achieves to index the k-mers from the human genome using 8GB of RAM (23 bits per k-mer) within 10 minutes and the k-mers from the large axolotl genome using 63 GB of memory (27 bits per k-mer) within 76 minutes. Furthermore, while being memory efficient, the index provides a very high throughput: 1.4 million queries per second on a single CPU or 16.1 million using 12 cores. Finally, we also present how BLight can practically represent metagenomic and transcriptomic sequencing data to highlight its wide applicative range.AvailabilityWe wrote the BLight index as an open source C++ library under the AGPL3 license available at github.com/Malfoy/BLight. It is designed as a user-friendly library and comes along with code usage samples.
Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update
Authors: Cruz-Morales Pablo , Orellana Camila A. , Moutafis George , Moonen Glenn , Rincon Gonzalo , Nielsen Lars K , Marcellin Esteban 
Published: February 2019

AbstractClostridiumis a large genus of obligate anaerobes belonging to theFirmicutesphylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined asClostridiales, which includes the classClostridia. Here we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to; (i) confirm that the group is composed of more than one genus (ii), detect major differences between pathogens classified as a single species within the group of authenticClostridiumspp. (sensu stricto), identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains and, (iv) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification ofClostridiumspecies hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria and highlights the importance of phylogenomics for taxonomic studies.
Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
Authors: Steenwyk Jacob L. , Opulente Dana A. , Kominek Jacek , Shen Xing-Xing , Zhou Xiaofan , Labella Abigail L. , Bradley Noah P. , Eichman Brandt F. , Čadež Neža , Libkind Diego , DeVirgilio Jeremy , Hulfachor Amanda Beth , Kurtzman Cletus P. , Hittinger Chris Todd , Rokas Antonis 
Published: February 2019

AbstractCell cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genusHanseniasporaexhibited very high evolutionary rates, low GC content, small genome sizes, and lower gene numbers. To better understandHanseniasporaevolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18 / 21 known species in the genus. Our phylogenomic analyses identify twoHanseniasporalineages, the fast-evolving lineage (FEL), which began diversifying ∼87 million years ago (mya), and the slow-evolving lineage (SEL), which began diversifying ∼54 mya. Remarkably, both lineages lost genes associated with the cell cycle and genome integrity, but these losses were greater in the FEL. For example, all species lost the cell cycle regulatorWHI5, and the FEL lost components of the spindle checkpoint pathway (e.g.,MAD1, MAD2) and DNA damage checkpoint pathway (e.g.,MEC3, RAD9). Similarly, both lineages lost genes involved in DNA repair pathways, including the DNA glycosylase geneMAG1, which is part of the base excision repair pathway, and the DNA photolyase genePHR1, which is involved in pyrimidine dimer repair. Strikingly, the FEL lost 33 additional genes, including polymerases (i.e.,POL4andPOL32) and telomere-associated genes (e.g.,RIF1, RFA3, CDC13, PBP2). Echoing these losses, molecular evolutionary analyses reveal that, compared to the SEL, the FEL stem lineage underwent a burst of accelerated evolution, which resulted in greater mutational loads, homopolymer instabilities, and higher fractions of mutations associated with the common endogenously damaged base, 8-oxoguanine. We conclude thatHanseniasporais an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell cycle and genome integrity genes and pathways, and may represent a novel system for studying cellular life without them.
Nanoscopic Clustering of Neuroligin-3 and Neuroligin-4X Regulates Growth Cone Organization and Size
Authors: Gatford Nicholas J. F. , Michael Deans P. J. , Duarte Rodrigo R.R. , Chennell George , Raval Pooja , Srivastava Deepak P. 
Published: February 2019

AbstractThe cell-adhesion proteins neuroligin-3 and neuroligin-4X (NLGN3/4X) have well described roles in synapse formation. NLGN3/4X are also expressed highly during neurodevelopment. However, the role these proteins play during this period is unknown. Here we show that NLGN3/4X localized to the leading edge of growth cones where itpromoted neuritogenesis in immature human neurons. Super-resolution microscopyrevealed that NLGN3/4X clustering induced growth cone enlargement and influenced actin filament organization. Critically, these morphological effects were not induced by Autism spectrum condition (ASC)-associated NLGN3/4X variants. Finally, actin regulators p21-activated kinase 1 (PAK1) and cofilin were found to be activated by NLGN3/4X and involved in mediating the effects of these adhesion proteins on actin filaments, growth cones, and neuritogenesis. These data reveal a novel role for NLGN3 and NLGN4X in the development of neuronal architecture, which may be altered in the presence of ASD-associated variants.
Neural activity during a simple reaching task in macaques is counter to gating and rebound in basal ganglia-thalamic communication
Authors: Schwab Bettina C. , Kase Daisuke , Zimnik Andrew , Rosenbaum Robert , Codianni Marcello G. , Rubin Jonathan E. , Turner Robert S. 
Published: February 2019

AbstractTask-related activity in the ventral thalamus, a major target of basal ganglia output, is often assumed to be permitted or triggered by changes in basal ganglia activity through gating- or rebound-like mechanisms. To test those hypotheses, we sampled single-unit activity from connected basal ganglia output and thalamic nuclei (globus pallidus-internus, GPi, and ventrolateral-anterior nucleus, VLa) in monkeys performing a reaching task. Rate increases were the most common peri-movement change in both nuclei. Moreover, peri-movement changes generally began earlier in VLa than in GPi. Simultaneously-recorded GPi-VLa pairs rarely showed short-timescale spike-to-spike correlations or slow across-trials covariations and both were equally positive and negative. Finally, spontaneous GPi bursts and pauses were both followed by small, slow reductions in VLa rate. These results appear incompatible with standard gating and rebound models. Still, gating or rebound may be possible in other physiological situations: Simulations show how GPi-VLa communication can scale with GPi synchrony and GPi-to-VLa convergence, illuminating how synchrony of basal ganglia output during motor learning or in pathological conditions may render this pathway effective. Thus, in the healthy state, basal ganglia-thalamic communication during learned movement is more subtle than expected, with changes in firing rates possibly being dominated by a common external source.
Assessment of Dried Blood Spots for DNA Methylation Profiling
Authors: Walker Rosie M. , MacGillivray Louise , McCafferty Sarah , Wrobel Nicola , Murphy Lee , Kerr Shona M. , Morris Stewart W. , Campbell Archie , McIntosh Andrew M. , Porteous David J. , Evans Kathryn L. 
Published: February 2019

AbstractBackgroundDNA methylation reflect health-related environmental exposures and genetic risk, providing insights into aetiological mechanisms and potentially predicting disease onset, progression and treatment response. An increasingly recognised need for large-scale, longitudinally-profiled samples collected world-wide has made the development of efficient and straightforward sample collection and storage procedures a pressing issue. An alternative to the low-temperature storage of EDTA tubes of venous blood samples, which are frequently the source of the DNA used in such studies, is to collect and store at room temperature blood samples using filter paper engineered for the purpose, such as Whatman FTA®cards. Our goal was to determine whether DNA stored in this manner can be used to generate DNA methylation profiles comparable to those generated using blood samples frozen in EDTA tubes.MethodsDNA methylation profiles were obtained from matched EDTA tube and Whatman FTA®card whole-blood samples from 62 Generation Scotland: Scottish Family Health Study participants using the Infinium HumanMethylation450 BeadChip. Multiple quality control procedures were implemented, the relationship between the two sample types assessed, and EWASs performed for smoking status, age and the interaction between these variables and sample storage method. Results: Dried blood spot (DBS) DNA methylation profiles were of good quality and DNA methylation profiles from matched DBS and EDTA tube samples were highly correlated (mean r = 0.991) and could distinguish between participants. EWASs replicated established associations for smoking and age, with no evidence for moderation by storage method.ConclusionsOur results support the use of Whatman FTA®cards for collecting and storing blood samples for DNA methylation profiling. This approach is likely to be particularly beneficial for large-scale studies and those carried out in areas where freezer access is limited. Furthermore, our results will inform consideration of the use of newborn heel prick DBSs for research use.
SyRI: identification of syntenic and rearranged regions from whole-genome assemblies
Authors: Goel Manish , Sun Hequan , Jiao Wen-Biao , Schneeberger Korbinian 
Published: February 2019

AbstractHere, we present SyRI, an efficient tool for genome-wide structural rearrangement identification from genome graphs, which are build up from pair-wise whole-genome alignments. Instead of searching for differences, SyRI starts by finding all co-linear regions between the genomes. As all remaining regions are SRs by definition, they just have to be classified as inversions, translocations, or duplications based on their positions in convoluted networks of repetitive alignments. Finally, SyRI reports local variations like SNPs and indels within syntenic and rearranged regions. We show SyRI’s broad applicability to multiple species and genetically validate the presence of ~100 translocations identified in Arabidopsis.
Oligoribonuclease functions as a diribonucleotidase to bypass a key bottleneck in RNA degradation
Authors: Kim Soo-Kyoung , Lormand Justin D. , Weiss Cordelia A. , Eger Karin A. , Turdiev Husan , Turdiev Asan , Winkler Wade C. , Sondermann Holger , Lee Vincent T. 
Published: February 2019

AbstractDegradation of RNA polymers is a multistep process catalyzed by specific subsets of RNases. In all cases, degradation is completed by exoribonucleases that recycle RNA fragments into nucleotide monophosphate. In γ-proteobacteria, a group of up to eight 3’-5’ exoribonucleases have been implicated in RNA degradation. Oligoribonuclease (Orn) is unique among them as its activity is required for clearing short RNA fragments, a function important for cellular fitness. However, the mechanistic basis for this substrate selectivity remained unclear. Here we show that Orn’s activity as a general exoribonuclease has been vastly overestimated by demonstrating that the enzyme exhibits a much narrower substrate preference for diribonucleotides. Co-crystal structures of Orn with substrates reveal an active site optimized for diribonucleotides that does not accommodate longer substrates. While other cellular RNases process oligoribonucleotides down to diribonucleotide entities, our functional studies demonstrate that Orn is the one and only diribonucleotidase that completes the final stage of the RNA degradation pathway. Together, these results indicate that Orn is a dedicated diribonucleotidase that clears the diribonucleotide pool that otherwise affects cellular physiology and viability.
Evidence for Similar Structural Brain Anomalies in Youth and Adult Attention-Deficit/Hyperactivity Disorder: A Machine Learning Analysis
Authors: Zhang-James Yanli , Helminen Emily C , Liu Jinru ,   The ENIGMA-ADHD Working Group, Franke Barbara , Hoogman Martine , Faraone Stephen V 
Published: February 2019

AbstractADHD affects 5% of children world-wide. Of these, two-thirds continue to have impairing symptoms of ADHD into adulthood. Although a large literature implicates structural brain differences in the pathophysiology of the disorder, it is not clear if adults with ADHD have similar neuroanatomical impairments as those seen in children with recent reports from the large ENIGMA-ADHD consortium finding structural abnormalities for children but not for adults. This paper uses deep learning neural network classification models to determine if there are neuroanatomical changes in the brains of children with ADHD that are also observed for adult ADHD, and vice versa. We found that structural MRI data can significantly separate ADHD from control participants for both children and adults. Consistent with the prior reports from ENIGMA-ADHD, prediction performance and effect sizes were better for the child than the adult samples. The model trained on adult samples significantly predicted ADHD in the child sample, suggesting that our model learned anatomical features that common to ADHD in childhood and adulthood. These results support the continuity of ADHD’s pathophysiology from childhood to adulthood. In addition, our work demonstrates a novel use of neural network classification models to test hypotheses about developmental continuity.