bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indication of a reduction in the cover of thin-leaved plants in Danish grasslands over an eight-year period
Authors: Damgaard Christian 
Published: August 2019

AbstractAcross four grassland habitat types, the cover of thin-leaved plants was found to decrease significantly, but generally only limited trait selection was observed on leaf traits (SLA and LDMC) in a study of an extensive Danish grassland vegetation dataset from an eight-year period. The mostly negative result of this study may partly be due to the relatively conservative analysis, where the continuous plant trait variables are used for grouping plant species into functional types, which are then treated as dependent variables. This procedure is in contrast to most other analyses of trait selection, where it is the community weighted mean of the traits that is used as the dependent variable. However, it is not the traits, but rather individual plants that are sampled and, consequently, it is important to consider the sampling of species abundance in the statistical modelling of plant traits. This misapprehension has not received sufficient proper attention in the plant trait literature.
Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid
Authors: Zander Mark , Lewsey Mathew G. , Clark Natalie M. , Yin Lingling , Bartlett Anna , Saldierna Guzmán J. Paola , Hann Elizabeth , Langford Amber E. , Jow Bruce , Wise Aaron , Nery Joseph R. , Chen Huaming , Bar-Joseph Ziv , Walley Justin W. , Solano Roberto , Ecker Joseph R. 
Published: August 2019

AbstractUnderstanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigate the signaling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA that spans from the activity of master and secondary-regulatory transcription factors, through gene expression outputs and alternative splicing to protein abundance changes, protein phosphorylation and chromatin remodeling. We integrated time series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enable us to predict previously unknown points of crosstalk from JA to other signaling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behavior, the general principles of which provide a framework for analysis of cross-regulation between other hormone and stress signaling pathways.
Syndecan-4 is required for VE-Cadherin trafficking during pathological angiogenesis
Authors: Rossi Giulia De , Vähätupa Maria , Cristante Enrico , Liyanage Sidath E. , May Ulrike , Pellinen Laura , Aittomäki Saara , Cordova Zuzet Martinez , Pesu Marko , Uusitalo-Järvinen Hannele , Bainbridge James W. , Järvinen Tero A.H. , Whiteford James R. 
Published: August 2019

AbstractNew blood vessel formation, or angiogenesis, is characteristic of chronic diseases such as cancer, rheumatoid arthritis and vision-threatening conditions. Vascular Endothelial growth factor (VEGFA) and its receptor VEGFR2 drive neovascularization and hyperpermeability in these pathologies. One consequence of VEGFR2 activation is decreased stability of endothelial cell (EC) junctions through internalization of VE-Cadherin, allowing re-arrangement of sprouting ECs. Evidence suggests roles for heparan sulfate proteoglycans in angiogenesis and we show that Syndecan-4 (SDC4) expression is upregulated during pathological angiogenesis and is required for efficient VE-Cadherin internalization. Angiogenic responses in both tumor and neovascular eye disease models are impaired in Syndecan-4 null mice (Sdc4-/-), as is dermal hyper-permeability response to VEGFA. We show SDC4 resides at EC junctions and interacts with VE-Cadherin, an association lost upon VEGFA-stimulation, and this is SDC4 phosphorylation-dependent. Finally, we show that pathological angiogenic responses can be inhibited in a model of age-related macular degeneration by targeting SDC4. This study identifies SDC4 as a key component of VE-Cadherin trafficking and, as such, a critical regulator of pathological angiogenesis and vascular permeability.
MarkedNeurospora crassastrains for competition experiments and Bayesian methods for fitness estimates
Authors: Kronholm Ilkka , Ormsby Tereza , McNaught Kevin J. , Selker Eric U. , Ketola Tarmo 
Published: August 2019

AbstractThe filamentous fungusNeurospora crassa, a model microbial eukaryote, has a life cycle with many features that make it suitable for studying experimental evolution. However, it has lacked a general tool for estimating relative fitness of different strains in competition experiments. To remedy this need, we constructedN. crassastrains that contain a modifiedcsr-1locus and developed an assay for detecting the proportion of the marked strain using a post PCR high resolution melting assay. DNA extraction from spore samples can be performed on 96-well plates, followed by a PCR step, which allows many samples to be processed with ease. Furthermore, we suggest a Bayesian approach for estimating relative fitness from competition experiments that takes into account the uncertainty in measured strain proportions. We show that there is a fitness effect of the mating type locus, as mating typemat ahas a higher competitive fitness thanmat A. Thecsr-1* marker also has a small fitness effect, but is still a suitable marker for competition experiments. As a proof of concept, we estimate the fitness effect of theqde-2mutation, a gene in the RNA interference pathway, and show that its competitive fitness is lower than what would be expected from its mycelial growth rate alone.
Transcriptome-based Analysis of Tomato Genotypes Resistant to Bacterial spot (Xanthomonas perforans)Race T4
Authors: Shi Rui , Panthee Dilip R. 
Published: August 2019

AbstractBacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato caused by multiple species ofXanthomonas. We performed the RNA-Seq analysis of three tomato lines with different level of resistance toXanthomonas perforansrace T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations.Analysis between inoculated and control samples revealed that resistant line PI 270443 had more DEGs (834), followed by susceptible line NC 714 (373), and intermediate line NC 1CELBR (154). Gene functional analysis based onGene Ontology(GO) terms revealed that more GO terms (51) were enriched for up-regulated DEGs in the resistant line PI 270443, and more down-regulated DEGs (67) were enriched in the susceptible line NC 714. The specific analysis for DEGs in biotic stress pathway using MapMan software showed more up-regulated biotic stress pathway DEGs (67) for PI 270443 compared to more down-regulated DEGs (125) for susceptible NC 714 line. One interesting feature was that resistant PI 270443 has three up-regulated DEGs for PR-protein, and susceptible line NC 714 has one down-regulated R gene, which is disease-related.Analysis of sequence variations called from RNA-Seq reads against the reference genome of susceptible Heinz 1706 showed that chr11 which has multiple reported resistance QTLs to BS race T4 is identical between two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR-resistance proteins with sequence variation between the resistant and susceptible tomato lines were identified near the knownRx4resistance gene on chr11. These findings may be useful for further molecular breeding of tomato.
Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution
Authors: Ostevik Kate L. , Samuk Kieran , Rieseberg Loren H. 
Published: August 2019

AbstractMapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous ad-hoc methods while being systematic, repeatable, and is applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolarisssp.petiolarisandH. petiolarisssp.fallax.Using syntR, and we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years – a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between 1 and 3 translocations involving only 8 of the 17 chromosomes. This non-random exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm thatHelianthushas an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.
Diversification of CORVET tethers facilitates transport complexity inTetrahymena thermophila
Authors: Sparvoli Daniela , Zoltner Martin , Field Mark C. , Turkewitz Aaron 
Published: August 2019

AbstractIn endolysosomal networks, two hetero-hexameric tethers called HOPS and CORVET are found widely throughout eukaryotes. The unicellular ciliateTetrahymena thermophilapossesses elaborate endolysosomal structures, but curiously both it and related protozoa lack the HOPS tether and several other trafficking genes while retaining the related CORVET complex.Tetrahymenaencodes multiple paralogs of most CORVET subunits, which assemble into six distinct complexes. Each complex has a unique subunit composition and, significantly, shows unique localization, indicating participation in distinct pathways. One pair of complexes differ by a single subunit (Vps8), but have late endosomal vs. recycling endosome locations. While Vps8 subunits are thus prime determinants for targeting and functional specificity, determinants exist on all subunits except Vps11. This unprecedented expansion and diversification of CORVET provides a potent example of tether flexibility, and illustrates how ‘backfilling’ following secondary losses of trafficking genes can provide a mechanism for evolution of new pathways.
Geometric purity, kinematic scaling and dynamic optimality in drawing movements beyond ellipses
Authors: Matic Adam , Gomez-Marin Alex 
Published: August 2019

AbstractDrawing movements have been shown to comply with a power law constraining local curvature and instantaneous speed. In particular, ellipses have been extensively studied, enjoying a 2/3 exponent. While the origin of such non-trivial relationship remains debated, it has been proposed to be an outcome of the least action principle whereby mechanical work is minimized along 2/3 power law trajectories. Here we demonstrate that such claim is flawed. We then study a wider range of curves beyond ellipses that can have 2/3 power law scaling. We show that all such geometries are quasi-pure with the same spectral frequency. We then numerically estimate that their dynamics produce minimum jerk. Finally, using variational calculus and simulations, we discover that equi-affine displacement is invariant across different kinematics, power law or otherwise. In sum, we deepen and clarify the relationship between geometric purity, kinematic scaling and dynamic optimality for trajectories beyond ellipses. It is enticing to realize that we still do not fully understand why we move our pen on a piece of paper the way we do.HighlightsSeveral curves beyond ellipses have power-law kinematics with 2/3 exponent.The curvature spectrum of each of such geometries is quasi-pure at frequency 2.Their dynamics are shown to comply with minimum of jerk.But the 2/3 power law is not an outcome of minimizing mechanical work.Yet, equi-affine displacement is invariant upon different kinematics.Graphical abstract“We must represent any change, any movement, as absolutely indivisible.” — Henri Bergson
A Nanoemulsion as an Effective Treatment Against Human Pathogenic Fungi
Authors: Garcia Alexis , Fan Yong Yi , Vellanki Sandeep , Huh Eun Young , Vanegas DiFernando , Wang Su He , Lee Soo Chan 
Published: August 2019

AbstractThe emergence of immunocompromising diseases such as HIV/AIDS or other immunosuppressive medical conditions have opened an opportunity for fungal infections to afflict patients globally. An increase antifungal drug resistant fungi have posed a serious threat to patients. Combining these circumstances with a limited variety of antifungal drugs available to treat patients has left us in a situation where we need to develop new therapeutic approaches that are less prone to development of resistance by pathogenic fungi. In this study we present the utilization of the nanoemulsion NB-201 to control human pathogenic fungi. We found that the NB-201 exhibited in vitro activity against C. albicans, including both planktonic growth and biofilms. Furthermore, treatments with NB-201 significantly reduced the fungal burden at the infection site and presented enhanced healing process after subcutaneous infections by multidrug resistant C. albicans in a murine host system. NB-201 also exhibited in vitro growth inhibition activity against other fungal pathogens, including Cryptococcus spp, Aspergillus fumigatus, and Mucorales. Due to the nature of the activity of this nanoemulsion, there is a minimized chance of drug resistance to develop, thus presents a novel treatment to control fungal wound or skin infections.
Saving large fish through harvest slots outperforms the classical minimum-length limit when the aim is to achieve multiple harvest and catch-related fisheries objectives
Authors: Ahrens Robert N. M. , Allen Micheal S. , Walters Carl , Arlinghaus Robert 
Published: August 2019

AbstractWe address the problem of optimal size-selective exploitation in an age-structured fish population model by systematically examining how density- and size-dependency in growth, mortality and fecundity affect optimal harvesting patterns when judged against a set of common fisheries objectives. Five key insights are derived. First, while minimum-length limits often maximize the biomass yield, exploitation using harvest slots (i.e., regulations that protect both immature and very large individuals) can generate within 95% of maximum yield, and harvest slots generally maximize the number of fish that are harvested. Second, density-dependence in growth and size-dependent mortality predict more liberal optimal size-limits than those derived under assumptions of no density and size-dependence. Third, strong density-dependence in growth maximizes the production of trophy fish in the catch only when some modest harvest is introduced; the same holds for numbers harvested, when the stock-recruitment function follows the Ricker-type. Fourth, the inclusion of size-dependent maternal effects on fecundity or egg viability has only limited effects on optimal size limits, unless the increase in fecundity with mass (“hyperallometry”) is very large. Extreme hyperallometry in fecundity also shifts the optimal size-limit for biomass yield from the traditional minimum-length limit to a harvest slot. Fifth, harvest slots generally provide the best compromises among multiple objectives. We conclude that harvest slots, or more generally dome-shaped selectivity to harvest, can outperform the standard minimum-length selectivity. The exact configuration of optimal size limits crucially depends on objectives, local fishing pressure, the stock-recruitment function and the density and size-dependency of growth, mortality and fecundity.
Lossless and Contamination-Free Digital PCR
Authors: Liao Peiyu , Jiang Mengcheng , Chen Zitian , Zhang Fangli , Sun Yue , Nie Jun , Du Meijie , Wang Jianbin , Fei Peng , Huang Yanyi 
Published: August 2019

AbstractThe realization of the vast potential of digital PCR (dPCR), to provide extremely accurate and sensitive measurements in the clinical setting, has thus far been hindered by challenges such as assay robustness and high costs. Existing popular dPCR platforms that target the clinic have not reached wide-spread adoption, due to problems with sample loss and risk of contamination during sample preparation, compartmentalization, and transfers; limitations of dynamic range and signal-to-noise in the result readout also restricts broad applications. Here we introduce a lossless and contamination-free dPCR technology termed CLEAR-dPCR, which addresses these challenges by completing the dPCR sample preparation, PCR reaction, and readout all in one tube. We achieve this by adjusting the refractive index of the aqueous PCR mix to make the emulsion optically transparent, and devised a light-sheet microscope to capture 3D images of the cleared emulsion for results readout. This approach demonstrates improved accuracy over existing dPCR platforms, and enables a greatly increased dynamic range to be comparable to that of real-time quantitative PCR (qPCR). CLEAR-dPCR is an easy to operate, sensitive and accurate dPCR platform that we envision will fulfill the potential of dPCR for routine use clinical diagnosis.
Flexible regions in the molecular architecture of Human fibrin clots structurally resolved by XL-MS and integrative structural modeling
Authors: Klykov Oleg , van der Zwaan Carmen , Heck Albert J.R. , Meijer Alexander B. , Scheltema Richard A. 
Published: August 2019

AbstractUpon activation, fibrinogen forms large fibrin biopolymers that coalesce into clots that assist in wound healing. Limited insights into their molecular architecture, due to the sheer size and insoluble character of fibrin clots, have however restricted our ability to develop novel treatments for clotting diseases. The so far resolved disparate structural details did provide insights into linear elongation; however, molecular details like the C-terminal domain of theα-chain, the heparin-binding domain on theβ-chain, and others involved in lateral aggregation are lacking. To illuminate these dark areas, we applied crosslinking mass spectrometry (XL-MS) to obtain biochemical evidence in the form of over 300 distance constraints and combined this with structural modeling. These restraints additionally define the interaction network of the clots and e.g. provide molecular details for the interaction with Human Serum Albumin (HSA). We were able to construct the models of fibrinogenα(excluding two highly flexible regions) andβ, confirm these models with known structural arrangements and map how the structure laterally aggregates to form intricate lattices together with fibrinogenγ. We validate the final model by mapping mutations leading to impaired clot formation. From a list of 22 mutations, we uncovered structural features for all, including a crucial role forβArg’196 in lateral aggregation. The resulting model will be invaluable for research on dysfibrinogenemia and amyloidosis, as it provides insights into the molecular mechanisms of thrombosis and bleeding disorders related to fibrinogen variants. The structure is provided in the PDB-DEV repository.
Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems
Authors: Jacobsen Thomas , Yi Gloria , Asafen Hadel Al , Jermusyk Ashley A. , Beisel Chase L. , Reeves Gregory T. 
Published: August 2019

ABSTRACTAdvancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in Drosophila embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5’ untranslated region (UTR) vs. 3’UTR) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.
Corrosion inhibition of aluminum by oxalate self-assembling monolayer
Authors: Satyabama P. , Rajendran Susai , Nguyen Tuan Anh 
Published: August 2019

PurposeThis paper aims to evaluate the inhibition efficiency (IE) of oxalate ions in controlling corrosion of aluminum at pH 10.Design/methodology/approachThe IE has been determined by the classical weight loss method. The corrosion behavior of aluminum was investigated by using potentiodynamic polarization and electrochemical impedance measurements. Ultra violet (UV)-visible and Fluorescence spectra have been used to analyze the film formed on the aluminum surface after immersion.FindingsThe maximum IE was 88 per cent, which was offered by a mixture of 250 ppm oxalate ions and 50 ppm [Zn2+]. Potentiodynamic polarization data revealed that the protective film was formed on the metal surface. UV-visible and Fluorescence spectra indicated the presence of Al3+−oxalate complex in the protective film formed on aluminum substrate after immersion in [OX]/[Zn2+] solution.Originality/valueThe findings of this work shed more light on the corrosion inhibition of aluminum by oxalate self-assembling monolayers.