bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective pollination of Aeschynanthus acuminatus (Gesneriaceae) by generalist passerines, in sunbird-absent East Asia
Authors: Chen Kai-Hsiu , Lu Jing-Yi , Wang Chun-Neng 
Published: November 2019

AbstractAeschynanthus (Gesneriaceae), a genus comprising approximately 160 species in subtropical Southeast Asia, has red, tubular flowers, typical of a sunbird pollination syndrome. A. acuminatus, the species that is distributed extending to the northern edge of the genus, where the specialized nectarivorous sunbirds are absent, possesses reddish-green flowers and a wide-open corolla tube, flowering time shifts from summer to winter and the species achieves high fruiting success. This atypical flower led us to investigate the pollination biology of this species. Three species of generalist passerines, Grey-cheeked Fulvetta (Alcippe morrisonia, Sylviidae), White-eared Sibia (Heterophasia auricularis, Leiothrichidae) and Taiwan Yuhina (Yuhina brunneiceps, Zosteropidae), were recorded visiting A. acuminatus flowers. Pollination effectiveness was quantified via conspecific pollen presence on stigmas and natural fruit set. The significantly high natural fruit set (60%) and conspecific pollen transfer rate (94%) indicate high reproductive success facilitated by the accurate pollen placement on the birds. The existence of copious (61 µL) and highly diluted (7%) hexose-dominant nectar, together with a major reflectance peak of corolla lobe in the long-wavelength red color spectrum, is consistent with the pollination syndrome of generalist passerines. The high pollination effectiveness of A. acuminatus due to the recruitment of generalist passerines as pollinators, and the specializations of floral traits to match generalist bird pollination, appear crucial in the successful colonization on islands such as Taiwan that lack specialized bird pollinators.
PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data
Authors: Zanardi Nicolò , Morini Martina , Tangaro Marco Antonio , Zambelli Federico , Bosco Maria Carla , Varesio Luigi , Eva Alessandra , Cangelosi Davide 
Published: November 2019

AbstractReverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and fast method to measure gene expression. Reproducibility of the analyses is the main limitation of RT-qPCR experiments. Galaxy is an open, web-based, genomic workbench for a reproducible, transparent, and accessible science. Our aim was developing a new Galaxy tool for the analysis of RT-qPCR expression data. Our tool was developed using Galaxy workbench version 19.01 and functions implemented in several R packages. We developed PIPE-T, a new Galaxy tool implementing a workflow, which offers several options for parsing, filtering, normalizing, imputing, and analyzing RT-qPCR data. PIPE-T requires two input files and returns seven output files. We tested the ability of PIPE-T to analyze RT-qPCR data on two example datasets available in the gene expression omnibus repository. In both cases, our tool successfully completed execution returning expected results. PIPE-T can be easily installed from the Galaxy main tool shed or from Docker. Source code, step-by-step instructions, and example files are available on GitHub to assist new users to install, execute, and test PIPE-T. PIPE-T is a new tool suitable for the reproducible, transparent, and accessible analysis of RT-qPCR expression data.
Growing a LaAlO3/SrTiO3 heterostructure on Ca2Nb3O10 nanosheets
Authors: Torren Alexander J. H. van der , Yuan Huiyu , Liao Zhaoliang , Elshof Johan E. ten , Koster Gertjan , Huijben Mark , Rijnders Guus J. H. M. , Hesselberth Marcel B. S. , Jobst Johannes , Molen Sense van der , Aarts Jan 
Published: November 2019

AbstractThe two-dimensional electron liquid which forms between the band insulators LaAlO3 (LAO) and SrTiO3 (STO) is a promising component for oxide electronics, but the requirement of using single crystal SrTiO3 substrates for the growth limits its applications in terms of device fabrication. It is therefore important to find ways to deposit these materials on other substrates, preferably Si, or Si-based, in order to facilitate integration with existing technology. Interesting candidates are micron-sized nanosheets of Ca2Nb3O10 which can be used as seed layers for perovskite materials on any substrate. We have used low-energy electron microscopy (LEEM) with in-situ pulsed laser deposition to study the subsequent growth of STO and LAO on such flakes which were deposited on Si. We can follow the morphology and crystallinity of the layers during growth, as well as fingerprint their electronic properties with angle resolved reflected electron spectroscopy. We find that STO layers, deposited on the nanosheets, can be made crystalline and flat; that LAO can be grown in a layer-by-layer fashion; and that the full heterostructure shows the signature of the formation of a conducting interface.
Association of Extracellular Vesicle Protein Cargo with Race and Clinical Markers of Mortality
Authors: Noren Hooten Nicole , McFarland Minna H. , Freeman David W. , Mode Nicolle A. , Ezike Ngozi , Zonderman Alan B. , Evans Michele K. 
Published: November 2019

AbstractDifferential mortality rates remain a significant health disparity in the United States, suggesting the need to investigate novel potential molecular markers associated with mortality. Extracellular vesicles (EVs), including exosomes, microvesicles and apoptotic bodies, are lipid-bound vesicles secreted by cells into the circulation. EVs mediate intercellular communication by shuttling functional signaling molecules as cargo. EV characteristics by race in the context of mortality risk factors have not been described. We isolated plasma EVs from a cross-sectional cohort of African Americans (AA) and whites and found no significant differences in EV size, distribution or concentration between race or by sex. However, EV cargo showed increased levels of phospho-p53, total p53, cleaved caspase 3, ERK1/2 and phospho-AKT in white individuals compared to AAs. phospho-IGF-1R levels were significantly higher in females compared to males. EV concentration was significantly associated with several clinical mortality risk factors: high-sensitivity C-reactive protein (hsCRP), homeostatic model assessment of insulin resistance (HOMA-IR), alkaline phosphatase, body mass index, waist circumference and pulse pressure. The association of EV proteins with mortality markers were dependent on race. These data suggest that EV cargo can differ by race and sex and is associated with mortality risk factors.
Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer
Authors: Orellana Luis H. , Hatt Janet K. , Iyer Ramsunder , Chourey Karuna , Hettich Robert L. , Spain Jim C. , Yang Wendy H. , Chee-Sanford Joanne C. , Sanford Robert A. , Löffler Frank E. , Konstantinidis Konstantinos T. 
Published: November 2019

AbstractTo what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3− g−1 dry soil d−1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3−) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.
Fetuin exhibits a strong affinity for plutonium and may facilitate its accumulation in the skeleton
Authors: Vidaud Claude , Miccoli Laurent , Brulfert Florian , Aupiais Jean 
Published: November 2019

AbstractAfter entering the blood, plutonium accumulates mainly in the liver and the bones. The mechanisms leading to its accumulation in bone are, however, completely unknown. We already know that another uptake pathway not involving the transferrin-mediated pathways is suspected to intervene in the case of the liver. Fetuin, a protein playing an important role in bone metabolism, is proposed as a potential transporter of Pu from serum to bone. For the first time, the binding constants of these two proteins (transferrin and fetuin) with tetravalent plutonium at physiological pH (pH 7.0) were determined by using capillary electrophoresis (CE) coupled with inductively coupled plasma mass spectrometry (ICP-MS). Their very close values (log10 KPuTf = 26.44 ± 0.28 and log10 KPuFet = 26.20 ± 0.24, respectively) suggest that transferrin and fetuin could compete to chelate plutonium, either in the blood or directly at bone surfaces in the case of Pu deposits. We performed competition reaction studies demonstrating that the relative distribution of Pu-protein complexes is fully explained by thermodynamics. Furthermore, considering the average concentrations of transferrin and fetuin in the blood, our calculation is consistent with the bio-distribution of Pu observed in humans.
Membrane directed expression in Escherichia coli of BBA57 and other virulence factors from the Lyme disease agent Borrelia burgdorferi
Authors: Robertson Karie E. , Truong Chloe D. , Craciunescu Felicia M. , Yang Jay-How , Chiu Po-Lin , Fromme Petra , Hansen Debra T. 
Published: November 2019

AbstractMembrane-embedded proteins are critical to the establishment, survival and persistence in the host of the Lyme disease bacterium Borrelia burgdorferi (Bb), but to date, there are no solved structures of transmembrane proteins representing these attractive therapeutic targets. All available structures from the genus Borrelia represent proteins expressed without a membrane-targeting signal peptide, thus avoiding conserved pathways that modify, fold and assemble membrane protein complexes. Towards elucidating structure and function of these critical proteins, we directed translocation of eleven expression-optimized Bb virulence factors, including the signal sequence, to the Escherichia coli membrane, of which five, BBA57, HtrA, BB0238, BB0323, and DipA, were expressed with C-terminal His-tags. P66 was also expressed using the PelB signal sequence fused to maltose binding protein. Membrane-associated BBA57 lipoprotein was solubilized by non-ionic and zwitterionic detergents. We show BBA57 translocation to the outer membrane, purification at a level sufficient for structural studies, and evidence for an α-helical multimer. Previous studies showed multiple critical roles of BBA57 in transmission, joint arthritis, carditis, weakening immune responses, and regulating other Bb outer surface proteins. In describing the first purification of membrane-translocated BBA57, this work will support subsequent studies that reveal the precise mechanisms of this important Lyme disease virulence factor.
A Simulated Microgravity Environment Causes a Sustained Defect in Epithelial Barrier Function
Authors: Alvarez Rocio , Stork Cheryl A. , Sayoc-Becerra Anica , Marchelletta Ronald R. , Prisk G. Kim , McCole Declan F. 
Published: November 2019

AbstractIntestinal epithelial cell (IEC) junctions constitute a robust barrier to invasion by viruses, bacteria and exposure to ingested agents. Previous studies showed that microgravity compromises the human immune system and increases enteropathogen virulence. However, the effects of microgravity on epithelial barrier function are poorly understood. The aims of this study were to identify if simulated microgravity alters intestinal epithelial barrier function (permeability), and susceptibility to barrier-disrupting agents. IECs (HT-29.cl19a) were cultured on microcarrier beads in simulated microgravity using a rotating wall vessel (RWV) for 18 days prior to seeding on semipermeable supports to measure ion flux (transepithelial electrical resistance (TER)) and FITC-dextran (FD4) permeability over 14 days. RWV cells showed delayed apical junction localization of the tight junction proteins, occludin and ZO-1. The alcohol metabolite, acetaldehyde, significantly decreased TER and reduced junctional ZO-1 localization, while increasing FD4 permeability in RWV cells compared with static, motion and flask control cells. In conclusion, simulated microgravity induced an underlying and sustained susceptibility to epithelial barrier disruption upon removal from the microgravity environment. This has implications for gastrointestinal homeostasis of astronauts in space, as well as their capability to withstand the effects of agents that compromise intestinal epithelial barrier function following return to Earth.
Radiosafe micro-computed tomography for longitudinal evaluation of murine disease models
Authors: Berghen Nathalie , Dekoster Kaat , Marien Eyra , Dabin Jérémie , Hillen Amy , Wouters Jens , Deferme Jasmine , Vosselman Thibault , Tiest Eline , Lox Marleen , Vanoirbeek Jeroen , De Langhe Ellen , Bogaerts Ria , Hoylaerts Marc , Lories Rik , Vande Velde Greetje 
Published: November 2019

AbstractImplementation of in vivo high-resolution micro-computed tomography (µCT), a powerful tool for longitudinal analysis of murine lung disease models, is hampered by the lack of data on cumulative low-dose radiation effects on the investigated disease models. We aimed to measure radiation doses and effects of repeated µCT scans, to establish cumulative radiation levels and scan protocols without relevant toxicity. Lung metastasis, inflammation and fibrosis models and healthy mice were weekly scanned over one-month with µCT using high-resolution respiratory-gated 4D and expiration-weighted 3D protocols, comparing 5-times weekly scanned animals with controls. Radiation dose was measured by ionization chamber, optical fiberradioluminescence probe and thermoluminescent detectors in a mouse phantom. Dose effects were evaluated by in vivo µCT and bioluminescence imaging read-outs, gold standard endpoint evaluation and blood cell counts. Weekly exposure to 4D µCT, dose of 540–699 mGy/scan, did not alter lung metastatic load nor affected healthy mice. We found a disease-independent decrease in circulating blood platelets and lymphocytes after repeated 4D µCT. This effect was eliminated by optimizing a 3D protocol, reducing dose to 180–233 mGy/scan while maintaining equally high-quality images. We established µCT safety limits and protocols for weekly repeated whole-body acquisitions with proven safety for the overall health status, lung, disease process and host responses under investigation, including the radiosensitive blood cell compartment.
Physiological strength electric fields modulate human T cell activation and polarisation
Authors: Arnold Christina E. , Rajnicek Ann M. , Hoare Joseph I. , Pokharel Swechha Mainali , Mccaig Colin D. , Barker Robert N. , Wilson Heather M. 
Published: November 2019

AbstractThe factors and signals driving T cell activation and polarisation during immune responses have been studied mainly at the level of cells and chemical mediators. Here we describe a physical driver of these processes in the form of physiological-strength electric fields (EFs). EFs are generated at sites where epithelium is disrupted (e.g. wounded skin/bronchial epithelia) and where T cells frequently are present. Using live-cell imaging, we show human primary T cells migrate directionally to the cathode in low strength (50/150 mV/mm) EFs. Strikingly, we show for the first time that EFs significantly downregulate T cell activation following stimulation with antigen-activated APCs or anti-CD3/CD28 antibodies, as demonstrated by decreased IL-2 secretion and proliferation. These EF-induced functional changes were accompanied by a significant dampening of CD4+ T cell polarisation. Expression of critical markers of the Th17 lineage, RORγt and IL-17, and the Th17 polarisation mediator phospho-STAT3 were reduced significantly, while STAT1, ERK and c-Jun phosphorylation were comparatively unaffected suggesting STAT3 modulation by EFs as one mechanism driving effects. Overall, we identify electrical signals as important contributors to the co-ordination and regulation of human T cell functions, paving the way for a new research area into effects of naturally occurring and clinically-applied EFs in conditions where control of T cell activity is paramount.
Regulation of protein kinase Cδ Nuclear Import and Apoptosis by Mechanistic Target of Rapamycin Complex-1
Authors: Layoun Antonio , Goldberg Alexander A. , Baig Ayesha , Eng Mikaela , Attias Ortal , Nelson Kristoff , Carella Alexandra , Amberber Nahomi , Fielhaber Jill A. , Joung Kwang-Bo , Schmeing T. Martin , Han Yingshan , Downey Jeffrey , Divangahi Maziar , Roux Philippe P. , Kristof Arnold S. 
Published: November 2019

AbstractInactivation of the protein complex ‘mechanistic target of rapamycin complex 1’ (mTORC1) can increase the nuclear content of transcriptional regulators of metabolism and apoptosis. Previous studies established that nuclear import of signal transducer and activator of transcription-1 (STAT1) requires the mTORC1-associated adaptor karyopherin-α1 (KPNA1) when mTORC1 activity is reduced. However, the role of other mTORC1-interacting proteins in the complex, including ‘protein kinase C delta’ (PKCδ), have not been well characterized. In this study, we demonstrate that PKCδ, a STAT1 kinase, contains a functional ‘target of rapamycin signaling’ (TOS) motif that directs its interaction with mTORC1. Depletion of KPNA1 by RNAi prevented the nuclear import of PKCδ in cells exposed to the mTORC1 inhibitor rapamycin or amino acid restriction. Mutation of the TOS motif in PKCδ led to its loss of regulation by mTORC1 or karyopherin-α1, resulting in increased constitutive nuclear content. In cells expressing wild-type PKCδ, STAT1 activity and apoptosis were increased by rapamycin or interferon-β. Those expressing the PKCδ TOS mutant exhibited increased STAT1 activity and apoptosis; further enhancement by rapamycin or interferon-β, however, was lost. Therefore, the TOS motif in PKCδ is a novel structural mechanism by which mTORC1 prevents PKCδ and STAT1 nuclear import, and apoptosis.
Association between impulsivity traits and body mass index at the observational and genetic epidemiology level
Authors: Meyre David , Mohamed Sebat , Gray Joshua C. , Weafer Jessica , MacKillop James , de Wit Harriet 
Published: November 2019

AbstractWe investigated the association between impulsivity related traits and BMI at the observational and genetic epidemiology level in a cross-sectional population of healthy young American-European adults. We studied 998 students and university staff of European ancestry recruited from Chicago (Illinois) and Athens (Georgia). We measured 14 impulsivity variables using three broad categories: impulsive choice, action and personality. Weight and height of participants were measured by research assistants. The single-nucleotide polymorphism (SNP) rs3751812 in the fat mass and obesity-associated (FTO) gene was genotyped using the Illumina PsychArray BeadChip platform. Within the three broad domains of impulsivity, 4 parameters (delay discounting of rewards area under the curve and average of k indexes, Conner’s continuous performance test, and negative urgency) were associated with BMI. The FTO rs3751812 minor allele T was associated with higher BMI. Of the 14 impulsivity variables, rs3751812 T was associated with more premeditation and perseverance, before and after adjusting for BMI. The association between FTO rs3751812 and BMI adjusted for premeditation remained significant, but disappeared after adjusting for perseverance and for both perseverance and premeditation traits. Our observational and genetic data indicate a complex pattern of association between impulsive behaviors and BMI in healthy young American-European adults.
Permeability of the small intestinal mucus for physiologically relevant studies: Impact of mucus location and ex vivo treatment
Authors: Macierzanka Adam , Mackie Alan R. , Krupa Lukasz 
Published: November 2019

AbstractThe small intestinal mucus is a complex colloidal system that coats the intestinal mucosa. It allows passage on nutrients/pharmaceuticals from the gut lumen towards the epithelium, whilst preventing it from direct contact with luminal microorganisms. Mucus collected from intestinal tissue is often used in studies looking at inter-mucosal transport of food particulates, drug carriers, etc. However, detaching the highly hydrated native mucus from the tissue and storing it frozen prior to use may disrupt its physiological microstructure, and thus selective barrier properties. Multiple-particle tracking experiments showed that microstructural organisation of native, jejunal mucus depends on its spatial location in the intestinal mucosa. The inter-villus mucus was less heterogeneous than the mucus covering villi tips in the pig model used. Collecting mucus from tissue and subjecting it to freezing and thawing did not significantly affect (P > 0.05) its permeability to model, sub-micron sized particles, and the microviscosity profile of the mucus reflected the overall profiles recorded for the native mucus in the tissue. This implies the method of collecting and storing mucus is a reliable ex vivo treatment for the convenient planning and performing of mucus-permeability studies that aim to mimic physiological conditions of the transport of molecules/particles in native mucus.
GaAs epilayers grown on patterned (001) silicon substrates via suspended Ge layers
Authors: Ballabio Andrea , Bietti Sergio , Scaccabarozzi Andrea , Esposito Luca , Vichi Stefano , Fedorov Alexey , Vinattieri Anna , Mannucci Cosimo , Biccari Francesco , Nemcsis Akos , Toth Lajos , Miglio Leo , Gurioli Massimo , Isella Giovanni , Sanguinetti Stefano 
Published: November 2019

AbstractWe demonstrate the growth of low density anti-phase boundaries, crack-free GaAs epilayers, by Molecular Beam Epitaxy on silicon (001) substrates. The method relies on the deposition of thick GaAs on a suspended Ge buffer realized on top of deeply patterned Si substrates by means of a three-temperature procedure for the growth. This approach allows to suppress, at the same time, both threading dislocations and thermal strain in the epilayer and to remove anti-phase boundaries even in absence of substrate tilt. Photoluminescence measurements show the good uniformity and the high optical quality of AlGaAs/GaAs quantum well structures realized on top of such GaAs layer.