bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanical stress initiates and sustains the morphogenesis of wavy leaf epidermal cells
Authors: Bidhendi Amir J , Altartouri Bara , Gosselin Frédérick P. , Geitmann Anja 
Published: March 2019

Plant cell morphogenesis is governed by the mechanical properties of the cell wall and the resulting cell shape is intimately related to the respective specific function. Pavement cells covering the surface of plant leaves form wavy interlocking patterns in many plants. We use computational mechanics to simulate the morphogenetic process based on experimentally assessed cell shapes, growth dynamics, and cell wall chemistry. The simulations and experimental evidence suggest a multistep process underlying the morphogenesis of pavement cells during tissue differentiation. The mechanical shaping process relies on spatially confined, feedback-augmented stiffening of the cell wall in the periclinal walls, an effect that correlates with experimentally observed deposition patterns of cellulose and de-esterified pectin. We provide evidence for mechanical buckling of the pavement cell walls that can robustly initiate patternsde novoand may precede chemical and geometrical anisotropy.HighlightsA multistep mechano-chemical morphogenetic process underlies the wavy pattern of epidermal pavement cells.Microtubule polarization is preceded by an event that breaks mechanical isotropy in the cell wall.Mechanical models simulate the formation of wavy cell shapes, predict buckling of the cell walls and spatially confined variations in the mechanical properties of leaf epidermal cells.Stress/strain stiffening following the buckling of the cell walls constitutes a crucial element in a positive feedback loop forming interlocking pavement cells.Polarization of cortical microtubules, cellulose microfibrils, and de-esterified pectin occur at the necks of wavy pavement cells, matching thein silicoprediction of cell wall stiffening.
A hidden battle in the dirt: soil amoebae interactions withParacoccidioidesspp
Authors: Albuquerque Patrícia , Nicola André Moraes , Magnabosco Diogo Almeida Gomes , Derengowski Lorena da Silveira , Crisóstomo Luana Soares , Xavier Luciano Costa Gomes , de Oliveira Frazão Stefânia , Guilhelmelli Fernanda , de Oliveira Marco Antônio , Hurtado Fabián Andrés , de Melo Teixeira Marcus , Guimaraes Allan J. , Paes Hugo Costa , Bagagli Eduardo , Felipe Maria Sueli Soares , Casadevall Arturo , Silva-Pereira Ildinete 
Published: March 2019

AbstractParacoccidioidesspp. are thermodimorphic pathogenic fungi endemic to Latin America. Predation is believed to drive the evolution of virulence for soil saprophytes. We evaluated the presence of environmental amoeboid predators in soil from armadillo burrows whereParacoccidioideshad been previously detected and tested if interaction ofParacoccidioideswith amoebae increased fungal virulence. Nematodes, ciliates and amoebae – all potential predators of fungi – grew in cultures from soil samples. Microscopical observation and ITS sequencing identified the amoebae asAcanthamoebaspp,Allovahlkampfia spelaeaandVermamoeba vermiformis. These three amoebae efficiently ingested, killed and digestedParacoccidioidesspp. yeast cells, as did laboratory-adapted axenicAcanthamoeba castellanii. Sequential co-cultivation ofParacoccidioideswithA. castellaniiselected for phenotypical traits related to survival of the fungus within a natural predator as well as in murine macrophages and in vivo (Galleria mellonellaand mice). This increase in virulence is linked to the accumulation of cell wall alpha-glucans, polysaccharides that masks recognition of fungal molecular patterns by host pattern recognition receptors. Altogether, our results indicate thatParacoccidioidesinhabits a complex environment with multiple amoeboid predators that can exert selective pressure to guide the evolution of virulence traits.
Experimental Assessment of PCR Specificity and Copy Number for Reliable Data Retrieval in DNA Storage
Authors: Organick Lee , Chen Yuan-Jyue , Ang Siena Dumas , Lopez Randolph , Strauss Karin , Ceze Luis 
Published: March 2019

ABSTRACTSynthetic DNA has been gaining momentum as a potential storage medium for archival data storage1–9. Digital information is translated into sequences of nucleotides and the resulting synthetic DNA strands are then stored for later individual file retrieval via PCR7–9(Fig. 1a). Using a previously presented encoding scheme9and new experiments, we demonstrate reliable file recovery when as few as 10 copies per sequence are stored, on average. This results in density of about 17 exabytes/g, nearly two orders of magnitude greater than prior work has shown6. Further, no prior work has experimentally demonstrated access to specific files in a pool more complex than approximately 106unique DNA sequences9, leaving the issue of accurate file retrieval at high data density and complexity unexamined. Here, we demonstrate successful PCR random access using three files of varying sizes in a complex pool of over 1010unique sequences, with no evidence that we have begun to approach complexity limits. We further investigate the role of file size on successful data recovery, the effect of increasing sequencing coverage to aid file recovery, and whether DNA strands drop out of solution in a systematic manner. These findings substantiate the robustness of PCR as a random access mechanism in complex settings, and that the number of copies needed for data retrieval does not compromise density significantly.
The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data
Authors: Sze Marc A , Schloss Patrick D 
Published: March 2019

AbstractPCR amplification of 16S rRNA genes is a critical, yet under appreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represent their abundance in the original sample (i.e. bias). We compared the performance of high fidelity polymerases and varying number of rounds of amplification when amplifying a mock community and human stool samples. Although it was impossible to derive specific recommendations, we did observe general trends. Namely, using a polymerase with the highest possible fidelity and minimizing the number of rounds of PCR reduced the sequencing error rate, fraction of chimeric sequences, and bias. Evidence of bias at the sequence level was subtle and could not be ascribed to the fragments’ fraction of bases that were guanines or cytosines. When analyzing mock community data, the amount that the community deviated from the expected composition increased with rounds of PCR. This bias was inconsistent for human stool samples. Overall the results underscore the difficulty of comparing sequence data that are generated by different PCR protocols. However, the results indicate that the variation in human stool samples is generally larger than that introduced by the choice of polymerase or number of rounds of PCR.ImportanceA steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream data. We found that these choices can have a profound impact on the way that a microbial community is represented in the sequence data. The effects are relatively small compared to the variation in human stool samples, however, care should be taken to use polymerases with the highest possible fidelity and to minimize the number of rounds of PCR. These results also underscore that it is not possible to directly compare sequence data generated under different PCR conditions.
Polymer brush bilayer under stationary shear motion at linear response regime: A theoretical approach
Authors: Edwards Mike John 
Published: March 2019

AbstractStatistical mechanics is employed to tackle the problem of polymer brush bilayers under stationary shear motion. The article addresses, solely, the linear response regime in which the polymer brush bilayers behave very much similar to the Newtonian fluids. My approach to this long-standing problem split drastically from the work already published Kreer, T.,Soft Matter,12, 3479 (2016). It has been thought for many decades that the interpenetration between the brushes is source of the friction between the brush covered surfaces sliding over each other. Whiles, in the present article I strongly reject that idea. Instead, here, I show that structure of the whole system is responsible for friction between brush covered surfaces and the interpenetration is absolutely insignificant. Two simple reasons for that are the presence of ambient solvent and also flexibility of the chains. The results of this research would blow one’s mind about how the polymer brush bilayers respond at small shear rates.
Chronic Intermittent Ethanol and Lipopolysaccharide Exposure Differentially Alter Iba-1-Derived Microglia Morphology in the Prelimbic Cortex and Nucleus Accumbens Core
Authors: Siemsen BM , Landin JD , McFaddin JA , Hooker KN , Chandler LJ , Scofield MD 
Published: March 2019

AbstractAccumulating evidence has linked pathological changes associated with chronic alcohol exposure to neuroimmune signaling mediated by microglia. Prior characterization of the microglial structure-function relationship demonstrates that alterations in activity states occur concomitantly with reorganization of cellular architecture. Accordingly, gaining a better understanding of microglial morphological changes associated with ethanol exposure will provide valuable insight into how neuroimmune signaling may contribute to ethanol-induced reshaping of neuronal function. Here we have used Iba-1-staining combined with high-resolution confocal imaging and 3D reconstruction to examine microglial structure in the prelimbic (PL) cortex and nucleus accumbens (NAc) in male Long-Evans rats. Rats were either sacrificed at peak withdrawal following 14 days of exposure to chronic intermittent ethanol (CIE) or 48 hours after exposure to the immune activator lipopolysaccharide (LPS). LPS exposure resulted in dramatic structural reorganization of microglia in the PL cortex; including increased soma volume, overall cellular volume, and branching complexity. In comparison, CIE exposure was associated with a subtle increase in somatic volume and differential effects on microglia processes, which were largely absent in the NAc. These data reveal that microglial activation following a neuroimmune challenge with LPS or exposure to chronic alcohol exhibit distinct morphometric profiles and brain-region dependent specificity.
Functional arrays of human pluripotent stem cell-derived cardiac microtissues
Authors: Thavandiran Nimalan , Hale Christopher , Blit Patrick , Sandberg Mark L. , McElvain Michele E. , Gagliardi Mark , Sun Bo , Witty Alec , Graham George , Mcintosh May , Bakooshli Mohsen A. , Le Hon , Ostblom Joel , McEwen Samuel , Chau Erik , Prowse Andrew , Fernandes Ian , Gilbert Penney M. , Keller Gordon , Tagari Philip , Xu Han , Radisic Milica , Zandstra Peter W. , Nojima Dana , Vargas Hugo , Qu Yusheng , Motani Alykhan , Reagan Jeff 
Published: March 2019

ABSTRACTTo accelerate the cardiac drug discovery pipeline, we set out to develop a platform that would be amenable to standard multiwell-plate manipulations and be capable of quantifying tissue-level functions such as contractile force. We report a 96-well-based array of 3D human pluripotent stem cell (hPSC)-derived cardiac microtissues - termed Cardiac MicroRings (CaMiRi) - in custom printed multiwell plates capable of contractile force measurement. Within each well, two elastomeric microcantilevers are situated above a ramp. The wells are seeded with cell-laden collagen which, in response to the slope of the ramp, self-organizes around tip-gated microcantilevers to form contracting CaMiRi. The contractile force exerted by the CaMiRi is measured and calculated using the deflection of the cantilevers. Platform responses were robust and comparable across wells and we used it to determine an optimal tissue formulation. We validated contractile force response of CaMiRi using selected cardiotropic compounds with known effects. Additionally, we developed automated protocols for CaMiRi seeding, image acquisition, and analysis to enable measurement of contractile force with increased throughput. The unique tissue fabrication properties of the platform, and the consequent effects on tissue function, were demonstrated upon adding hPSC-derived epicardial cells to the system. This platform represents an open-source contractile force screening system useful for drug screening and tissue engineering applications.
Antigen structure affects cellular routing through DC-SIGN
Authors: Jarvis Cassie M. , Zwick Daniel B. , Grim Joseph C. , Prost Lynne R. , Alam Mohammad Murshid , Gardiner Jaye C. , Park Soyeong , Zimdars Laraine L. , Sherer Nathan M. , Kiessling Laura L. 
Published: March 2019

AbstractDendritic cell (DC) lectins mediate the recognition, uptake, and processing of antigens, but they can also be co-opted by pathogens for infection. These distinct activities depend upon the routing of antigens within the cell. Antigens directed to endosomal compartments are degraded and the peptides presented on MHC class II molecules thereby promoting immunity. Alternatively, HIV-1 can avoid degradation, as virus engagement with C-type lectin receptors (CLRs), such as DC-SIGN, results in trafficking to surface-accessible invaginated pockets. This process appears to enable infection of T cells intrans. We sought to explore whether antigen fate upon CLR-mediated internalization was affected by antigen physical properties. To this end, we employed the ring-opening metathesis polymerization to generate glycopolymers that each display multiple copies of mannoside ligand for DC-SIGN yet differ in length and size. The rate and extent of glycopolymer internalization depended upon polymer structure—longer polymers were internalized more rapidly and more efficiently than were shorter polymers. The trafficking, however, did not differ, and both short and longer polymers colocalized with transferrin-labeled early endosomes. To explore how DC-SIGN directs larger particles, such as pathogens, we induced aggregation of the polymers to access particulate antigens. Strikingly, these particulate antigens were diverted to the invaginated pockets that harbor HIV-1. Thus, antigen structure has a dramatic effect on DC-SIGN-mediated uptake and trafficking. These findings have consequences for the design of synthetic vaccines. Additionally, the results suggest new strategies for targeting DC reservoirs that harbor viral pathogens.Significance StatementDendritic cells (DCs) express cell-surface proteins (lectins) that bind to carbohydrates displayed on the surface of pathogens. The binding of pathogens to these lectins results in internalization to endosomal compartments where the pathogens are destroyed and an immune response is initiated. HIV-1 can subvert this process – lectin engagement routes HIV-1 to cellular compartments that allow the virus to evade destruction. We synthesized glycopolymers to test whether the size and physical properties of the antigens impact trafficking. Small polymers trafficked to endosomes, as expected. Alternatively, large particulate polymers localized in the non-endosomal compartments occupied by HIV. These data indicate that antigen structure affects routing by DC lectins. Our findings can be exploited to direct cargo to different compartments.
Digital removal of autofluorescence from microscopy images
Authors: Baharlou Heeva , Canete Nicolas P , Bertram Kirstie M , Sandgren Kerrie J , Cunningham Anthony L , Harman Andrew N , Patrick Ellis 
Published: March 2019

AbstractAutofluorescence is a long-standing problem that has hindered fluorescence microscopy image analysis. To address this, we have developed a method that identifies and removes autofluorescent signals from multi-channel images post acquisition. We demonstrate the broad utility of this algorithm in accurately assessing protein expression in situ through the removal of interfering autofluorescent signals.Availability and implementationhttps://ellispatrick.github.io/AFremoverContactellis.patrick@sydney.edu.auSupplementary informationSupplementary Figs. 1–13
PCH1 regulates light, temperature, and circadian signaling as a structural component of phytochrome B-photobodies inArabidopsis
Authors: Huang He , McLoughlin Katrice E. , Sorkin Maria L. , Burgie E. Sethe , Bindbeutel Rebecca K. , Vierstra Richard D. , Nusinow Dmitri A. 
Published: March 2019

AbstractThe phytochrome (phy) family of bilin-containing photoreceptors are major regulators of plant photomorphogenesis through their unique ability to photointerconvert between a biologically inactive red light-absorbing Pr state and an active far-red light­absorbing Pfr state. While the initial steps in Pfr signaling are unclear, an early event for the phyB isoform after photoconversion is its redistribution from the cytoplasm into subnuclear foci named photobodies (PBs) that dissipate after Pfr reverts back to Pr by far-red irradiation or by temperature-dependent non-photochemical reversion. Here we present evidence that PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) functions both as an essential structural component of phyB-containing PBs and as a direct regulator of thermal reversion that is sufficient to stabilize phyB as Pfrin vitro.By examining the genetic interaction between a constitutively active phyBY276H-YFP allele(YHB-YFP)and PCH1, we show that the loss of PCH1 prevents YHB from coalescing into PBs without affecting its nuclear localization, whereas overexpression of PCH1 dramatically increases PB levels. Loss of PCH1, presumably by impacting phyB-PB assembly, compromises a number of events elicited inYHB-YFPplants, including their constitutive photomorphogenic phenotype, red light-regulated thermomorphogenesis, and input of phyB into the circadian clock. Conversely, elevated levels of both phyB and PCH1 generate stable, yet far red-light reversible PBs that persisted for days. Collectively, our data demonstrate that the assembly of PCHl-containing PBs is critical for phyB signaling to multiple outputs, and suggest that altering PB dynamics could be exploited to modulate plant responses to light and temperature.SignificanceInArabidopsis, phytochrome B (phyB) perceives light and temperature signals to regulate various fundamental morphogenic processes in plants through its interconversion between its active Pfr and inactive Pr states. Upon photoconversion from Pr to Pfr, phyB forms subnuclear foci called photobodies, whose composition and molecular function(s) are unclear. We show here that the phyB-interacting protein PCH1 is a structural component of phyB-photobodies and protects Pfr from thermal reversion back to Pr thus helping maintain phyB signaling. Loss of PCH1 compromises photobody formation, which disrupts a number of downstream events including photo- and thermal perception and signaling into the circadian clock. These results demonstrate that forming PCHl-dependent phyB-photobodies is an essential step connecting light and temperature to controls on plant morphogenesis.
Modulation of coordinated activity across cortical layers by plasticity of inhibitory synapses onto layer 5 pyramidal neurons
Authors: Lourenço Joana , Stasi Angela Michela De , Deleuze Charlotte , Bigot Mathilde , Pazienti Antonio , Aguirre Andrea , Giugliano Michele , Ostojic Srdjan , Bacci Alberto 
Published: March 2019

AbstractIn the neocortex, synaptic inhibition shapes all forms of spontaneous and sensory-evoked activity. Importantly, inhibitory transmission is highly plastic, but the functional role of inhibitory synaptic plasticity is unknown. In the mouse barrel cortex, activation of layer 2/3 PNs elicited strong feed-forward perisomatic inhibition (FFI) onto layer 5 PNs. We found that FFI involving PV cells was strongly potentiated by postsynaptic PN burst firing. FFI plasticity modified PN excitation-to-inhibition (E/I) ratio, strongly modulated PN gain and altered information transfer across cortical layers. Moreover, our LTPi-inducing protocol modified the firing of layer 5 PNs and altered the temporal association of PN spikes to γ-oscillations both in vitro and in vivo. All these effects were captured by unbalancing the E/I ratio in a feed-forward inhibition circuit model. Altogether, our results indicate that activity-dependent modulation of perisomatic inhibitory strength effectively influences the participation of single principal cortical neurons to cognitive-relevant network activity.Impact StatementLong-term potentiation of feed-forward perisomatic inhibition effectively alters the computational properties of single layer 5 pyramidal neurons and their association to network activity.
Na/K-ATPase Activity and Ketone Body Metabolism in Long-term Diabetic Rats
Authors: Buxbaum Engelbert 
Published: March 2019

The long-term (34 weeks) effect of streptozotocin induced diabetes was assessed in Wistar rats.Na+/K+-ATPase activity was measured by ouabain inhibitable86Rb+-uptake into erythrocytes. No difference in the rate of Rb+-uptake, the Kmfor Rb+or the Kifor ouabain was detected between normal and diabetic rats. Thus, the change in Na+/K+-ATPase activity repeatedly described in short-term studies may not translate into a long term physiologically relevant change in ion flux through the sodium pump.Rats excrete ketone bodies mainly as β-hydroxybutyrate. This compound does not show up with nitroprusside sodium based test sticks, it can however be detected by coupled spectrophotometric assay with hydroxybutyrate dehydrogenase.Almost half of the diabetic animals reverted to a non-diabetic state during the experiment, followed by at least partial reversal of secondary diabetic damage.Abbreviations usedPKCProtein kinase CDAGDiacylglycerolEDTAEthylenediamine tetraacetic acidPIP3Phosphatidylinositol trisphosphatePBSPhosphate buffered salinei.p.intraperitonealHBAβ-hydroxybutyric acidSTZstreptozotocinEnzymes: Na+/K+-exchanging ATP-phosphohydrolase (Na+/K+-ATPase), E.C. 7.2.2.13; (R)-3-hydroxybutanoate:NAD+oxidoreductase [1.1.1.30] (β-hydroxybutyrate dehydro-genase)
Cryopreservation ofRosa hybridacv. Helmut Schmidt by PVS2 vitrification method usingin vitrofragmented explants (IFEs)
Authors: Mubbarakh Safiah Ahmad , Udain Jasim , James Jessica Jayanthi , Zakaria Rahmad , Subramaniam Sreeramanan 
Published: March 2019

AbstractThis is the first report on cryopreservation via PVS2 vitrification method on roses usingin vitrofragmented explants (IFEs) as the starting material. The aim of this study is to optimize the efficient plant recovery and regeneration system for cryopreservation ofRosa hybridacv. Helmut Schmidt using IFEs. Some important parameters have been optimized in this study are the effect of ascorbic acid (0.3 mM) examined separately and in combination at all steps in cryopreservation procedure (preculture, loading, unloading and growth recovery), loading type, loading duration, and PVS2 duration. The highest growth recovery of 43.33% was obtained when 3-4 mm size IFEs precultured on 0.25 M sucrose media supplemented with full-strength MS for one (1) day, followed by loading treatment supplemented with 1.5 M glycerol + 0.4 M sucrose + 5% DMSO + 0.3 mM ascorbic acid for 20 minutes, dehydration with PVS2 solution for 30 minutes and then treated with unloading solution supplemented with 1.2 M sucrose + 0.3 mM ascorbic acid for 20 minutes. This finding implies that long-term storage ofRosa Hybridacv. Helmut Schmidt by PVS2 vitrification method was successful with essential biomolecules.