bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds
Authors: Cortona Andrea Del , Jackson Christopher J. , Bucchini François , Van Bel Michiel , D’hondt Sofie , Škaloud Pavel , Delwiche Charles F. , Knoll Andrew H. , Raven John A. , Verbruggen Heroen , Vandepoele Klaas , De Clerck Olivier , Leliaert Frederik 
Published: June 2019

AbstractThe Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focusses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations, with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that the unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified following recolonization of benthic environments that became increasingly available as sea ice retreated. An increased supply of nutrients and biotic interactions such as grazing pressure has likely triggered the independent evolution of macroscopic growth via different strategies, including both true multicellularity, and multiple types of giant celled forms.Significance StatementGreen seaweeds are important primary producers along coastlines worldwide, and likely played a key role in the evolution of animals. To understand their origin and diversification, we resolve key relationships among extant green algae using a phylotranscriptomic approach. We calibrate our tree using available fossil data, to reconstruct important evolutionary events such as transitions to benthic environments, and evolution of macroscopic growth. We estimate green seaweeds to have originated in the late Tonian/Cryogenian Period, followed by a marked Ordovician diversification of macroscopic forms. This ancient proliferation of green seaweeds likely modified shallow marine ecosystems, which set off an evolutionary arms race between ever larger seaweeds and grazers.
Targeting the Cx43 Carboxyl Terminal H2 Domain Preserves Left Ventricular Function Following Ischemia-Reperfusion Injury
Authors: Jiang Jingbo , Palatinus Joseph A. , He Huamei , Iyyathurai Jegan , Jourdan L. Jane , Hoagland Daniel , Bultynck Geert , Wang Zhen , Zhang Zhiwei , Schey Kevin , Poelzing Steven , McGowan Francis X. , Gourdie Robert G. 
Published: June 2019

ABSTRACTBackgroundαCT1 is a 25 amino acid therapeutic peptide incorporating the Zonula Occludens-1 (ZO-1)-binding domain of connexin43 (Cx43) that is currently in Phase III clinical testing for healing chronic skin wounds. In preclinical studies in mice, we reported that αCT1 reduces arrhythmias and improves ventricular function following cardiac injury, effects that were accompanied by increases in PKCε phosphorylation of Cx43 at serine 368 (pS368). In this study, we undertake a systematic characterization of the molecular mode-of-action of αCT1 in mitigating the effects of ischemia reperfusion injury on ventricular contractile function.Methods and ResultsTo determine the basis of αCT1-mediated increases in pS368 we undertook tandem mass spectrometry of reactants in an in vitro assay of PKCε phosphorylation, identifying an interaction between negatively charged amino acids in the αCT1 Asp-Asp-Leu-Glu-Iso sequence and positively charged lysines (Lys345, Lys346) in a short α-helical sequence (H2) within the Cx43 CT domain. In silico modeling provided further support of the specificity of this interaction, leading us to conclude that αCT1 has potential to directly interact with both Cx43 and ZO-1. Using surface plasmon resonance, thermal shift and phosphorylation assays, we characterized a series of αCT1 variant peptides, identifying sequences competent to interact with either ZO-1 PDZ2 or the Cx43 CT, but with limited or no ability to bind both polypeptides. Based on this analysis, it was found that only those peptides competent to interact with Cx43, but not ZO-1 alone, resulted in increased pS368 phosphorylation in vitro and in vivo. Moreover, in a mouse model of global ischemia reperfusion injury we determined that pre-ischemic infusion only with those peptides competent to bind Cx43 preserved left ventricular (LV) contractile function following injury. Interestingly, a short 9 amino acid (MW=1110) Cx43-binding variant of the original 25 amino acid αCT1 sequence demonstrated potent LV-protecting effects when infused either before or after ischemic injury.ConclusionsInteraction of αCT1 with the Cx43 CT, but not ZO-1 PDZ2, explains cardioprotection mediated by this therapeutic peptide. Pharmacophores targeting the Cx43 carboxyl terminus could provide a novel translational approach to preservation of ventricular function following ischemic injury.
Dynamic patterns of transcript abundance of transposable element families in maize
Authors: Anderson Sarah N , Stitzer Michelle C , Zhou Peng , Ross-Ibarra Jeffrey , Hirsch Cory D , Springer Nathan M 
Published: June 2019

AbstractTransposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes.
Cooperation mitigates diversity loss in a spatially expanding microbial population
Authors: Gandhi Saurabh , Korolev Kirill S. , Gore Jeff 
Published: June 2019

AbstractThe evolution and potentially even the survival of a spatially expanding population depends on its genetic diversity, which can decrease rapidly due to a serial founder effect. The strength of the founder effect is predicted to depend strongly on the details of the growth dynamics. Here, we probe this dependence experimentally using a single microbial species, Saccharomyces cerevisiae, expanding in multiple environments that induce varying levels of cooperativity during growth. We observe a drastic reduction in diversity during expansions when yeast grows non-cooperatively on simple sugars, but almost no loss of diversity when cooperation is required to digest complex metabolites. These results are consistent with theoretical expectations. When cells grow independently from each other, the expansion proceeds as a pulled wave driven by the growth at the low-density tip of the expansion front. Such populations lose diversity rapidly because of the strong genetic drift at the expansion edge. In contrast, diversity loss is substantially reduced in pushed waves that arise due to cooperative growth. In such expansions, the low-density tip of the front grows much more slowly and is often reseeded from the genetically diverse population core. Additionally, in both pulled and pushed expansions, we observe a few instances of abrupt changes in allele fractions due to rare fluctuations of the expansion front and show how to distinguish such rapid genetic drift from selective sweeps.Significance statementSpatially expanding populations lose genetic diversity rapidly because of the repeated bottlenecks formed at the front as a result of the serial founder effect. However, the rate of diversity loss depends on the specifics of the expanding population, such as its growth and dispersal dynamics. We have previously demonstrated that changing the amount of within-species cooperation leads to a qualitative transition in the nature of expansion from pulled (driven by migration at the low density tip) to pushed (driven by migration from the high density region at the front, but behind the tip). Here we demonstrate experimentally that pushed waves, which emerge in the presence of sufficiently strong cooperation, result in strongly reduced genetic drift during range expansions, thus preserving genetic diversity in the newly colonized region.
The somatic mutation landscape of the human body
Authors: García-Nieto Pablo E. , Morrison Ashby J. , Fraser Hunter B. 
Published: June 2019

ABSTRACTSomatic mutations in healthy tissues contribute to aging, neurodegeneration, and cancer initiation, yet remain largely uncharacterized. To gain a better understanding of their distribution and functional impacts, we leveraged the genomic information contained in the transcriptome to uniformly call somatic mutations from over 7,500 tissue samples, representing 36 distinct tissues. This catalog, containing over 280,000 mutations, revealed a wide diversity of tissuespecific mutation profiles associated with gene expression levels and chromatin states. We found pervasive negative selection acting on missense and nonsense mutations, except for mutations previously observed in cancer samples, which were under positive selection and were highly enriched in many healthy tissues. These findings reveal fundamental patterns of tissue-specific somatic evolution and shed light on aging and the earliest stages of tumorigenesis.
From plasmodesma geometry to effective symplasmic permeability through biophysical modelling
Authors: Deinum Eva E. , Mulder Bela M. , Benitez-Alfonso Yoselin 
Published: June 2019

AbstractRegulation of molecular transport via intercellular channels called plasmodesmata (PDs) is important for both coordinating developmental and environmental responses among neighbouring cells, and isolating (groups of) cells to execute distinct programs. Cell-to-cell mobility of fluorescent molecules and PD dimensions (measured from electron micrographs) are both used as methods to predict PD transport capacity (i.e., effective symplasmic permeability), but often yield very different values. Here, we build a theoretical bridge between both experimental approaches by calculating the effective symplasmic permeability from a geometrical description of individual PDs and considering the flow towards them. We find that a dilated central region has the strongest impact in thick cell walls and that clustering of PDs into pit fields strongly reduces predicted permeabilities. Moreover, our open source multi-level model allows to predict PD dimensions matching measured permeabilities and add a functional interpretation to structural differences observed between PDs in different cell walls.
Population Genomics of GII.4 Noroviruses Reveal Complex Diversification and New Antigenic Sites Involved in the Emergence of Pandemic Strains
Authors: Tohma Kentaro , Lepore Cara J. , Gao Yamei , Ford-Siltz Lauren A. , Parra Gabriel I. 
Published: June 2019

AbstractGII.4 noroviruses are a major cause of acute gastroenteritis. Their dominance has been partially explained by the continuous emergence of antigenically distinct variants. To gain insights on the mechanisms of viral emergence and population dynamics of GII.4 noroviruses, we performed large-scale genomics, structural, and mutational analyses of the viral capsid protein (VP1). GII.4 noroviruses exhibited a periodic replacement of predominant variants with accumulation of amino acid substitutions. Genomic analyses revealed (i) a large number (87%) of conserved residues; (ii) variable residues that map on the previously determined antigenic sites; and (iii) variable residues that map outside of the antigenic sites. Residues from the third pattern formed motifs on the surface of VP1, which suggested extensions of previously predicted and new uncharacterized antigenic sites. The role of two motifs (C and G) in the antigenic make-up of the GII.4 capsid protein was confirmed with monoclonal antibodies and carbohydrate blocking assays. Amino acid profiles from antigenic sites (A, C, D, E, and G) correlated with the circulation patterns of GII.4 variants, with two of them (C and G) containing residues (352, 357, 378) linked with the emergence of new GII.4 variants. Notably, the emergence of each variant was followed by a stochastic diversification with minimal changes at the antigenic sites that did not progress towards the next variant. This study provides a methodological framework for antigenic characterization of viruses, and expands our understanding of the dynamics of GII.4 noroviruses that could facilitate the design of cross-reactive vaccines.ImportanceNoroviruses are an important cause of viral gastroenteritis around the world. An obstacle delaying the development of norovirus vaccines is an inadequate understanding of the role of norovirus diversity in immunity. Using a population genomics approach, we identified new residues on the viral capsid protein (VP1) from GII.4 noroviruses, the predominant genotype, that appear to be involved in the emergence and antigenic topology of GII.4 variants. Careful monitoring of the substitutions in those residues involved in the diversification and emergence of new viruses could help in the early detection of future novel variants with pandemic potential. Therefore, this novel information on the antigenic diversification could facilitate GII.4 norovirus vaccine design.
TheSalixSmSPR1 Involved in Light-Regulated Cell Expansion by Modulating Microtubule Arrangement
Authors: Xiaoxia Liu , Jianguo Zhang , Jinkai Sui , Ying Luo , Guodong Rao 
Published: June 2019

AbstractLight signaling and cortical microtubule (MT) arrays are essential to the anisotropic growth of plant cells. Microtubule-associated proteins (MAPs) function as regulators that mediate plant cell expansion or elongation by altering the arrangements of the MT arrays. However, current understanding of the molecular mechanism of MAPs in relation to light to regulate cell expansion or elongation is limited. Here, we show that the microtubule-associated protein SPR1 is involved in light-regulated directional cell expansion by modulating microtubule elongation inSalix matsudana. Overexpression ofSmSPR1in Arabidopsis results in right-handed helical orientation of hypocotyls in dark-grown etiolated seedlings, whereas the phenotype of transgenic plants was indistinguishable from those of wild-type plants under light conditions. Phenotypic characterization of the transgenic plants showed reduced anisotropic growth and left-handed helical MT arrays in etiolated hypocotyl cells. Protein interaction assays revealed that SPR1, CSN5A (subunits of COP9 signalosome, a negative regulator of photomorphogenesis), and ELONGATED HYPOCOTYL 5 (HY5, a transcription factor that promotes photomorphogenesis) interacted with each otherin vivo. The phenotype of ArabidopsisAtSPR1-overexpressing transgenic lines was similar to that ofSmSPR1-overexpressing transgenic plants, and overexpression ofSalix SmSPR1can rescue thespr1mutant phenotype, thereby revealing the function of SPR1 in plants.HighlightFunction of microtubule-associated protein SPR1 is directly related to light, and crucial to the balance of tubulin polymerization
Mass evacuation and increases in long-term care benefits: lessons from the Fukushima nuclear disaster
Authors: Morita Tomohiro , Ando Michihito , Ohtsu Yui 
Published: June 2019

AbstractBackgroundThough mass evacuation may increase the need for long-term care (LTC) services, how the need for LTC services increases and how the public LTC system affects it is not well understood. We evaluated changes in public LTC benefits for the people living in the mandatory evacuation areas established after the 2011 Fukushima nuclear disaster and examined the roles of the universal LTC insurance system in Japan.MethodsIn order to evaluate the effect of the mandatory evacuation on LTC benefits, we examined the trends of LTC benefits in the Fukushima evacuation group and the nationwide non-evacuation group. We first decomposed per-elderly-individual benefits at the municipality level into the LTC certification rate and per-certified-individual benefits, and then implemented difference-in-differences analysis using these variables as outcomes.ResultsPer-elderly-individual benefits significantly increased from 2012 onward in the evacuation group, and this was explained by an increase in the certification rate rather than in per-certified-individual benefits. Increases in per-elderly-individual benefits and the certification rate in the post-disaster period were observed in all but the highest care level, and the corresponding outcomes for the highest care level decreased immediately after the disaster. We also found that the increase in the certification rate had been mostly realized by an increase in the number of certified individuals.ConclusionsThe increase in LTC benefits can be associated with the impact of the increase in the number of people newly certified to receive LTC benefits after the mandatory evacuation. In order to cope with the increase in utilization of long-term care and associated costs after disasters in aging societies, both formal long-term care services and social support for informal care for evacuees should be considered important.
An unexpected alternative splicing of SKU5-Similar3 in Arabidopsis
Authors: Zhou Ke 
Published: June 2019

ABSTRACTAlternative splicing largely enhanced the diversity of transcriptome and proteome in eukaryas. Along with technical development, more and more alternatively splicing was demonstrated. Here, we report an unexpected alternative splicing of SKU5-Similar 3 (SKS3) within a special splicing site in Arabidopsis. Based on bioinformatics database, SKS3 was predicted to be alternatively transcribed into two variants, SKS3.1 and SKS3.2, which encoded a GPI-anchored protein and a soluble secretory protein respectively. But, instead of SKS3.2, a novel variant, SKS3.3, which encoded a protein with transmembrane region at its C-terminus, was demonstrated based on our experimental data. Interestingly, it exhibited a different organ-specific expression pattern from SKS3.1, and its intron splicing site did not follow ‘GT-AG’ rule or any reported rules.
PRR14 Overexpression Promotes Cell Growth, Epithelial to Mesenchymal Transition and Metastasis of Colon Cancer via the AKT Pathway
Authors: Li Fangfang , Zhang Chundong , Fu Lijuan 
Published: June 2019

AbstractBackgroundPRR14 (Proline rich protein 14) was firstly identified for its ability to specify and localize heterochromatin during cell cycle progression. Aberrant expression of PRR14 is associated with the tumorigenesis and progression of lung cancer. However, its involvement in colon cancer remains unknown. Herein, we report the role of PRR14 in colon cancer.MethodsColon cancer tissue microarray was used to analyze and compare the expression of PRR14 among some clinicopathological characteristics of colon cancer. HCT116 and RKO cells were transfected with siRNA to downregulate PRR14 expression. The roles of PRR14 in proliferation, migration and invasion of the cell lines were determined using cell counting kit-8, colony formation assay, wound healing assay and transwell assays respectively. The expression of PRR14 was measured by using immunofluorescence, qRT- PCR and western blot.ResultsPRR14 was highly expressed in colon cancer tissues, and the expression level was correlated with tumor size, distant metastasis and Tumor Node Metastasis stages. Functional study revealed that downregulation of PRR14 inhibited colon cancer cells growth, migration and invasion. Furthermore, knockdown of PRR14 inhibited epithelial-mesenchymal transition (EMT) process, cell cycle-associated proteins expression and p-AKT level.ConclusionPRR14 may promote the progression and metastasis of colon cancer, and may be a novel prognostic and therapeutic marker for the disease.
Gluten-free Fish? Marine Carnivores Cobia (Rachycentron canadum) and European Sea Bass (Dicentrarchus labrax) Have Different Tolerances to Dietary Wheat Gluten
Authors: Larkin Mary E.M. , Watson Aaron M. , Place Allen R. 
Published: June 2019

AbstractIn developing more sustainable fishmeal-free diets for a broad range of fish species, a “one-size-fits-all” approach should not be presumed. The production of more ecologically sustainable aquaculture diets has increased the incorporation of plant-based protein sources such as wheat gluten. Here we show that wheat gluten at even less than 4% inclusion in a compound feed has a negative impact on growth and survivorship in juvenile cobia (Rachycentron canadum). In addition, plasma factors capable of binding wheat gluten were detected in the plasma of cobia fed diets containing this ingredient but not in wild cobia with no exposure to dietary wheat gluten. Furthermore, there is evidence that supplementary taurine partially mitigates the deleterious effects provoked by wheat gluten. Based on these results, we propose that wheat gluten should be added with caution to aquaculture diets intended for juvenile cobia and potentially other marine carnivores. After observing that dietary wheat gluten can cause deleterious effects in cobia, we sought to evaluate a possible effect in European sea bass (Dicentrarchus labrax), another large, carnivorous, marine species. There were no major effects in terms of growth rate, plasma biochemical parameters, or detectable induction of plasma IgM, IgT, or factors capable of binding gliadin in response to 4% dietary wheat gluten. However, plasma levels of taurine doubled and there were considerable changes to the intestinal microbiome. There was increased diversity of predominant taxonomic orders in the pyloric caeca, anterior, middle, and posterior intestinal sections of fish consuming wheat gluten. Despite these measurable changes, the data suggest that dietary inclusion of 4% wheat gluten is well tolerated by European sea bass in feed formulations. Together these findings underscore the need to evaluate tolerance to ingredients in aquaculture formulations on a species by species basis.