bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baobab Diversity, Seed Germination and Early Growth
Authors: Egbadzor Kenneth F. 
Published: September 2019

AbstractThe diversity in baobab was studied on 75 trees located at Adaklu District and Ho and Hohoe Municipalities. Thirteen morphological traits were used in the characterisation based on Bioversity descriptors for baobab. GenStat edition 12 was used to analyse the diversity as well as germination and growth data. Group average hierarchical clustering with Jaccard similarity coefficient discriminated among most of the baobab trees. Clustering was not based on location although few trees that were not discriminated were from the same communities. The clustering can be used in selecting trees for further studies and domestication. Germination tests were conducted with soaked, boiled and sulphuric acid treated seeds. Only the sulphuric acid treated seeds had germination significantly higher than the control. More studies should be done to find easier way of breaking seed dormancy of baobab. There were significant differences in 100 seed weight, seed length and thickness among seeds from three different trees. However, there were no significant difference in seed width of the same sample. Seed size traits should be considered in selecting baobab for domestication because of the high variability revealed. Observation on seedling growth revealed less than 10 leaves in the first month and increased to about 20 in the fourth month. Growth in girth was 5mm and 8mm in the first and fourth months respectively. Seedling height of 17cm in the first month reached 40cm in four months. Information from this research is valuable for further work on domestication of baobab.
Gnrh1-induced responses are indirect in female medaka Fsh cells
Authors: Hodne Kjetil , Fontaine Romain , Ager-Wick Eirill , Weltzien Finn-Arne 
Published: September 2019

ABSTRACTReproductive function in vertebrates is stimulated by gonadotropin-releasing hormone (GnRH) that controls the synthesis and release of the two pituitary gonadotropins, follicle-stimulating hormone (FSH) and luteinizing hormone (LH). FSH and LH, which regulates different stages of gonadal development, are produced by two different cell types in the fish pituitary, in contrast to mammals and birds, thus allowing the investigation of their differential regulation. In the present work, we show by fluorescentin situhybridization that Lh cells in adult female medaka express Gnrh receptors, whereas Fsh cells do not. This is confirmed by patch clamp recordings and cytosolic Ca2+measurements on dispersed pituitary cells, where Lh cells, but not Fsh cells, respond to Gnrh1 by increased action potential frequencies and cytosolic Ca2+levels. In contrast, both Fsh and Lh cells are able to respond electrically and by elevating the cytosolic Ca2+levels to Gnrh1 in brain-pituitary tissue slices. Using Ca2+uncaging in combination with patch clamp recordings and cytosolic Ca2+measurements, we show that Fsh and Lh cells form homo- and heterotypic networks in the pituitary. Taken together, these results show that the effects of Gnrh1 on Fsh release in adult female medaka is indirect, likely mediated via Lh cells.
The structure of the iron-catecholate transporter Fiu suggests substrate import occurs via a 2-step mechanism
Authors: Grinter Rhys , Lithgow Trevor 
Published: September 2019

AbstractThe Ferric Iron Uptake (Fiu) transporter fromEscherichia colifunctions in the transport of iron-catecholate complexes across the bacterial outer membrane, providing the bacterium with iron which is an essential element for growth. Recently, it became clear that Fiu also represents a liability: its activity allows the import of antimicrobial compounds that have evolved to mimic catecholate. In this work we have determined the structure of Fiu and analyzed its function to address how Fiu and related transporters from other bacterial species can bind catecholate in a surface-exposed cavity. In addition, the crystal structure of Fiu reveals the presence of a large, selectively gated cavity in the interior of this transporter. This chamber is large enough to accommodate the Fiu substrate and may act to regulate substrate import. These data provide insight into the mechanism of substrate uptake by Fiu and related transporters identified inPseudomonas aeruginosaandAcinetobacter baumannii. As Fiu and its homologues are the targets of substrate mimicking antibiotics, these data will assist in the development of antibiotics that target these receptors for cell entry.
Canine sense of quantity: evidence for numerical ratio-dependent activation in parietotemporal cortex
Authors: Aulet Lauren S. , Chiu Veronica C. , Prichard Ashley , Spivak Mark , Lourenco Stella F. , Berns Gregory S. 
Published: September 2019

AbstractThe approximate number system, which supports the rapid estimation of quantity, emerges early in human development and is widespread across species. Neural evidence from both human and non-human primates suggests the parietal cortex as a primary locus of numerical estimation, but it is unclear whether the numerical competencies observed across non-primate species are subserved by similar neural mechanisms. Moreover, because studies with non-human animals typically involve extensive training, little is known about the spontaneous numerical capacities of non-human animals. To address these questions, we examined the neural underpinnings of number perception using awake canine functional magnetic resonance imaging. Dogs passively viewed dot arrays that varied in ratio and, critically, received no task-relevant training or exposure prior to testing. We found evidence of ratio-dependent activation, which is a key feature of the approximate number system, in canine parietotemporal cortex in the majority of dogs tested. This finding is suggestive of a neural mechanism for quantity perception that has been conserved across mammalian evolution.
LAB-AID (Laboratory Automated Interrogation of Data): an interactive web application for visualization of multi-level data from biological experiments
Authors: Kozic Zrinko , Booker Sam , Dando Owen , Hardingham Giles , Kind Peter 
Published: September 2019

AbstractA key step in understanding the results of biological experiments is visualization of the data. Many laboratory experiments contain a range of measurements that exist within a hierarchy of interdependence. An automated way to visualise and interrogate experimental data would: 1) lead to improved understanding of the results, 2) help to determine which statistical tests should be performed, and 3) easily identify outliers and sources of batch effects. Unfortunately, existing graphing solutions often demand expertise in programming, require considerable effort to import and examine such multi-level data, or are unnecessarily complex for the task at hand. Here we present LAB-AID (Laboratory Automated Interrogation of Data), an interactive tool specifically designed to automatically visualize and query hierarchical data resulting from biological experiments.
Magainin 2 and PGLa in Bacterial Membrane Mimics II: Membrane Fusion and Sponge Phase Formation
Authors: Kabelka Ivo , Pachler Michael , Prévost Sylvain , Letofsky-Papst Ilse , Lohner Karl , Pabst Georg , Vácha Robert 
Published: September 2019

ABSTRACTWe studied the synergistic mechanism of equimolar mixtures of magainin 2 (MG2a) and PGLa in phosphatidylethanolamine/phosphatidylglycerol mimics of Gram-negative cytoplasmic membranes. In a preceding paper [Pachler et al., Biophys. J. 2019 xxx], we reported on the early onset of parallel heterodimer formation of the two antimicrobial peptides already at low concentrations and the resulting defect formation in membranes. Here, we focus on the structures of the peptide/lipid aggregates occurring in the synergistic regime at elevated peptide concentrations. Using a combination of calorimetric, scattering, electron microscopic andin silicotechniques, we demonstrate that the two peptides, even if applied individually, transform originally large unilamellar vesicles into multilamellar vesicles, with a collapsed interbilayer spacing resulting from peptide induced adhesion. Interestingly, the adhesion does not lead to a peptide induced lipid separation of charged and charge neutral species. In addition to this behavior, equimolar mixtures of MG2a and PGLa formed surface-aligned fibril-like structures, which induced adhesion zones between the membranes and the formation of transient fusion stalks in molecular dynamics simulations and a coexisting sponge phase observed by small-angle X-ray scattering. The previously reported increased leakage of lipid vesicles of identical composition in the presence of MG2a/PGLa mixtures is therefore related to a peptide-induced cross-linking of bilayers.STATEMENT OF SIGNIFICANCEWe demonstrate that the synergistic activity of the antimicrobial peptides MG2a and PGLa correlates to the formation of surface-aligned fibril-like peptide aggregates, which cause membrane adhesion, fusion and finally the formation of a sponge phase.
A low dose of simvastatin enhanced the therapeutic efficacy of mesenchymal stem cell (MSC) transplantation in skin wound healing in diabetic mice associated with increases in pAkt, SDF-1, and angiogenesis
Authors: Sukpat Supakanda , Israsena Nipan , Wongphoom Jutamas , Ingrungruanglert Praewphan , Sim Tao Ming , Patumraj Suthiluk 
Published: September 2019

AbstractPurposeWe aimed to determine the possible mechanisms of underlying the effects of low dose simvastatin on enhancing the therapeutic efficacy of MSC transplantation in diabetic wound healing.MethodsBalb/c nude mice were divided into five groups:- control mice (CON), diabetic mice (DM), diabetic mice pretreated with low-dose simvastatin (DM+SIM), diabetic mice implanted with MSCs (DM+MSCs) and diabetic mice pretreated with low-dose simvastatin and implanted with MSCs (DM+MSCs+SIM). Seven days before wound induction, low dose simvastatin was orally administered to the DM+SIM and DM+MSCs+SIM groups. Eleven weeks after the induction of diabetes, all mice were given bilateral full-thickness excisional back skin wounds.ResultsBy comparing the DM+MSCs+SIM and DM+MSCs groups, the results showed that on day 14; the wound closure (%WC) and capillary vascularity (%CV) in the DM+MSCs+SIM group were significantly increased compared to those in the DM+MSCs group. In addition, by using immunohistochemical techniques, it was also shown that the expression of SDF-1, a chemotactic factor regulating the migration of stem cells, in the DM+SIM+MSCs group was increased compared with that in the DM+MSCs group. Furthermore, using phospho-Akt (S473) Pan Specific DuoSet IC ELISA (R&D Systems, USA) kits, the increased tissue Akt levels were found in the DM+SIM+MSCs group but not in the other groups.ConclusionsOur study suggests that a low dose of simvastatin enhanced the therapeutic efficacy of MSCs in diabetic wound healing, and this effect was associated with increases in pAkt levels, SDF-1 levels, and angiogenesis, and improved wound closure.
CNS Glycosylphosphatidylinositol Deficiency Results in Delayed White Matter Development, Ataxia, and Premature Death in a Novel Mouse Model
Authors: Lukacs Marshall , Stottmann Rolf W. 
Published: September 2019

AbstractThe Glycosylphosphatidylinositol (GPI) anchor is a post-translational modification added to approximately 150 different proteins to facilitate proper membrane anchoring and trafficking to lipid rafts. Biosynthesis and remodeling of the GPI anchor requires the activity of over twenty distinct genes. Defects in the biosynthesis of GPI anchors in humans leads to Inherited Glycosylphosphatidylinositol Deficiency (IGD). IGD patients display a wide range of phenotypes though the central nervous system (CNS) appears to be the most commonly affected tissue. A full understanding of the etiology of these phenotypes has been hampered by the lack of animal models due to embryonic lethality of GPI biosynthesis gene null mutants. Here we model IGD by genetically ablating GPI production in the CNS with a conditional mouse allele of phosphatidylinositol glycan anchor biosynthesis, class A (Piga) and Nestin-Cre. We find that the mutants do not have structural brain defects but do not survive past weaning. The mutants show progressive decline with severe ataxia consistent with defects in cerebellar development. We show the mutants have reduced myelination and defective Purkinje cell development. Surprisingly we found Piga was expressed in a fairly restricted pattern in the early postnatal brain consistent with the defects we observed in our model. Thus, we have generated a novel mouse model of the neurological defects of IGD which demonstrates a critical role for GPI biosynthesis in cerebellar and white matter development.
Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)
Authors: Bangs Max R. , Douglas Marlis R. , Chafin Tyler K. , Douglas Michael E. 
Published: September 2019

AbstractThe delimitation of species-boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life-histories co-distributed in the highly modified Colorado River (i.e., Flannelmouth Sucker,Catostomus latipinnis; Bluehead Sucker,C. Pantosteus discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction-site associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in Bluehead Sucker, supporting elevation ofC. P. virescensto species-status, and recognizingC. P. discobolus yarrowi(Zuni Bluehead Sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate Flannelmouth Sucker lineages as ESUs (Evolutionarily Significant Units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the alignment of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolationversussecondary contact.
Muscle function and homeostasis require macrophage-derived cytokine inhibition of AKT activity in Drosophila
Authors: Kierdorf Katrin , Hersperger Fabian , Sharrock Jessica , Vincent Crystal M. , Ustaoglu Pinar , Dou Jiawen , Gyoergy Attila , Groß Olaf , Siekhaus Daria E. , Dionne Marc S. 
Published: September 2019

AbstractUnpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK-STAT signaling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signaling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signaling activity in the absence of any immune challenge. Macrophages are the source of much of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal from macrophages to muscle that controls AKT activity and metabolic homeostasis.
A versatile bulk electrotransfection protocol for mouse embryonic fibroblast and iPS cells
Authors: Eghbalsaied Shahin , Hyder Iqbal , Kues Wilfried A. 
Published: September 2019

AbstractA square-wave pulsing protocol was developed using OptiMEM-GlutaMAX for high efficient transfection of mouse embryonic fibroblast (MEF) and induced pluripotency stem (iPS) cells. An electrotransfection efficiency of > 95% was repeated for both MEF and iPS cells using reporter-encoding plasmids. The protocol was very efficient for plasmid size ranging from 6.2 to 13.5 kb. A high rate of targeted gene knockout (> 95 %) was produced in Venus transgenic cells using indels formation. Targeted deletions in the Venus transgene were performed by co-electroporation of two gRNA-encoding plasmids. In conclusion, this plasmid electrotransfection protocol is straight-forward, cost-effective, and efficient for CRISPRing mouse primary cells.
Human microbiome sequences in the light of the Nubeam
Authors: Dai Hang , Guan Yongtao 
Published: September 2019

AbstractWe present Nubeam (nucleotide be a matrix) as a novel reference-free approach to analyze short sequencing reads. Nubeam represents nucleotides by matrices, transforms a read into a product of matrices, and based on which assigns numbers to reads. Nubeam capitalizes on the non-commutative property of matrix multiplication, such that different reads are assigned different numbers, and similar reads similar numbers. A sample, which is a collection of reads, becomes a collection of numbers that form an empirical distribution. We demonstrate that the genetic difference between samples can be quantified by the distance between empirical distributions. Nubeam can account for GC bias and nucleotide quality, and is computationally efficient; the K-mer method is a special case of Nubeam, but without those benefits. As a reference-free approach, Nubeam avoids reference bias and mapping bias and can work with organisms without reference genomes. Thus, Nubeam is ideal to analyze datasets from metagenomic whole-genome sequencing, where the amount of unmapped reads is substantial. When applied to human microbiome sequencing, Nubeam recapitulated findings made by mapping-based methods, and shed lights on contributions of unmapped reads. In particular, body habitats dominate clustering of unmapped pseudo-samples; there are more outliers in skin whole samples than the skin mapped pseudo-samples; and analysis of unmapped reads suggested that the sequencing depth is far from sufficient for urogenital samples.
Multiplexed Nanometric 3D Tracking of Microbeads using a FFT-Phasor Algorithm
Authors: Brouwer T. B. , Hermans N. , van Noort J. 
Published: September 2019

AbstractMany single-molecule biophysical techniques rely on nanometric tracking of microbeads to obtain quantitative information about the mechanical properties of biomolecules such as chromatin fibers. Their three-dimensional position can be resolved by holographic analysis of the diffraction pattern in wide-field imaging. Fitting this diffraction pattern to Lorentz Mie scattering theory yields the bead position with nanometer accuracy in three dimensions but is computationally expensive. Real-time multiplexed bead tracking therefore requires a more efficient tracking method. Here, we introduce 3D phasor tracking, a fast and robust bead tracking algorithm with nanometric localization accuracy in a z-range of over 10 µm. The algorithm is based on a 2D cross-correlation using Fast Fourier Transforms with computer-generated reference images, yielding a processing rate of up to 10.000 regions of interest per second. We implemented the technique in magnetic tweezers and tracked the 3D position of over 100 beads in real-time on a generic CPU. Its easy implementation, efficiency, and robustness can improve multiplexed biophysical bead tracking applications, especially where high throughput is required.SignificanceMicrobeads are often used in biophysical single-molecule manipulation experiments and accurately tracking their position in 3 dimensions is key for quantitative analysis. Holographic imaging of these beads allows for multiplexing bead tracking but image analysis can be a limiting factor. Here we present a 3D tracking algorithm based on Fast Fourier Transforms that is fast, has nanometric precision, is robust against common artifacts and is accurate over 10’s of micrometers. We show its real-time application for magnetic tweezers based force spectroscopy on more than 100 chromatin fibers in parallel, but we anticipate that many other bead-based biophysical essays can benefit from this simple and robust 3 phasor algorithm.
Lipids in xylem sap of woody plants across the angiosperm phylogeny
Authors: Schenk H. Jochen , Michaud Joseph M. , Mocko Kerri , Espino Susana , Melendres Tatiana , Roth Mary R. , Welti Ruth , Kaack Lucian , Jansen Steven 
Published: September 2019

AbstractLipids have been observed attached to lumen-facing surfaces of mature xylem conduits of several plant species, but there has been little research on their functions or effects on water transport, and only one lipidomic study of the xylem apoplast. Therefore, we conducted lipidomic analyses of xylem sap from woody stems of seven plants representing six major angiosperm clades, including basal magnoliids, monocots, and eudicots, to characterize and quantify phospholipids, galactolipids, and sulfolipids in sap using mass spectrometry. Locations of lipids in vessels ofLaurus nobiliswere imaged using TEM and confocal microscopy. Xylem sap contained the galactolipids di- and mono-galactosyldiacylglycerol (DGDG and MGDG), as well as all common plant phospholipids, but only traces of sulfolipids, with total lipid concentrations in extracted sap ranging from 0.18 to 0.63 nmol / mL across all seven species. Contamination of extracted sap from lipids in cut living cells was found to be negligible. Lipid composition of sap was compared to wood in two species and was largely similar, suggesting that sap lipids, including galactolipids, originate from cell content of living vessels. Seasonal changes in lipid composition of sap were observed for one species. Lipid layers coated all lumen-facing vessel surfaces ofLaurus nobilis, and lipids were highly concentrated in inter-vessel pits. The findings suggest that apoplastic, amphiphilic xylem lipids are a universal feature of angiosperms. The findings require a reinterpretation of the cohesion-tension theory of water transport to account for the effects of apoplastic lipids on dynamic surface tension and hydraulic conductance in xylem.