bluuebunny/crossref_metadata_2025_split huggingface dataset:
Galectin-3 Induces a Pro-degradative/inflammatory Gene Signature in Human Chondrocytes, Teaming Up with Galectin-1 in Osteoarthritis Pathogenesis
Authors: Weinmann Daniela , Schlangen Karin , André Sabine , Schmidt Sebastian , Walzer Sonja M. , Kubista Bernd , Windhager Reinhard , Toegel Stefan , Gabius Hans-Joachim 
Published: December 2016

AbstractInflammatory chemo- and cytokines and matrix-degrading proteases underlie the progression of osteoarthritis (OA). Aiming to define upstream regulators for these disease markers, we pursued initial evidence for an upregulation of members of the adhesion/growth-regulatory galectin family. Immunohistochemical localization of galectin-3 (Gal-3) in sections of human cartilage with increasing levels of degeneration revealed a linear correlation reaching a chondrocyte positivity of 60%. Presence in situ was cytoplasmic, the lectin was secreted from OA chondrocytes in culture and binding of Gal-3 yielded lactose-inhibitable surface staining. Exposure of cells to the lectin led to enhanced gene expression and secretion of functional disease markers. Genome-wide transcriptomic analysis broadened this result to reveal a pro-degradative/inflammatory gene signature under the control of NF-κB. Fittingly, targeting this route of activation by inhibitors impaired the unfavourable response to Gal-3 binding, as also seen by shortening the lectin’s collagen-like repeat region. Gal-3’s activation profile overlaps with that of homodimeric galectin-1 (Gal-1) and also has distinctive (supplementing) features. Tested at subsaturating concentrations in a mixture, we found cooperation between the two galectins, apparently able to team up to promote OA pathogenesis. In summary, our results suggest that a network of endogenous lectins is relevant for initiating this process cascade.
Vibrational density of states and thermodynamics at the nanoscale: the 3D-2D transition in gold nanostructures
Authors: Carles R. , Benzo P. , Pécassou B. , Bonafos C. 
Published: December 2016

AbstractSurface enhanced Raman scattering (SERS) is generally and widely used to enhance the vibrational fingerprint of molecules located at the vicinity of noble metal nanoparticles. In this work, SERS is originally used to enhance the own vibrational density of states (VDOS) of nude and isolated gold nanoparticles. This offers the opportunity of analyzing finite size effects on the lattice dynamics which remains unattainable with conventional techniques based on neutron or x-ray inelastic scattering. By reducing the size down to few nanometers, the role of surface atoms versus volume atoms become dominant, and the “text-book” 3D-2D transition on the dynamical behavior is experimentally emphasized. “Anomalies” that have been predicted by a large panel of simulations at the atomic scale, are really observed, like the enhancement of the VDOS at low frequencies or the occurrence of localized modes at frequencies beyond the cut-off in bulk. Consequences on the thermodynamic properties at the nanoscale, like the reduction of the Debye temperature or the excess of the specific heat, have been evaluated. Finally the high sensitivity of reminiscent bulk-like phonons on the arrangements at the atomic scale is used to access the morphology and internal disorder of the nanoparticles.
Dual-seq transcriptomics reveals the battle for iron during Pseudomonas aeruginosa acute murine pneumonia
Authors: Damron F. Heath , Oglesby-Sherrouse Amanda G. , Wilks Angela , Barbier Mariette 
Published: December 2016

AbstractDetermining bacterial gene expression during infection is fundamental to understand pathogenesis. In this study, we used dual RNA-seq to simultaneously measure P. aeruginosa and the murine host’s gene expression and response to respiratory infection. Bacterial genes encoding products involved in metabolism and virulence were differentially expressed during infection and the type III and VI secretion systems were highly expressed in vivo. Strikingly, heme acquisition, ferric-enterobactin transport, and pyoverdine biosynthesis genes were found to be significantly up-regulated during infection. In the mouse, we profiled the acute immune response to P. aeruginosa and identified the pro-inflammatory cytokines involved in acute response to the bacterium in the lung. Additionally, we also identified numerous host iron sequestration systems upregulated during infection. Overall, this work sheds light on how P. aeruginosa triggers a pro-inflammatory response and competes for iron with the host during infection, as iron is one of the central elements for which both pathogen and host fight during acute pneumonia.
Efficient DNA–Polymer Coupling in Organic Solvents: A Survey of Amide Coupling, Thiol-Ene and Tetrazine–Norbornene Chemistries Applied to Conjugation of Poly(N-Isopropylacrylamide)
Authors: Wilks Thomas R. , O’Reilly Rachel K. 
Published: December 2016

AbstractA range of chemistries were explored for the efficient covalent conjugation of DNA to poly(N-isopropylacrylamide) (poly(NIPAM)) in organic solvents. Amide coupling and thiol–ene Michael addition were found to be ineffective for the synthesis of the desired products. However, the inverse electron-demand Diels–Alder (DAinv) reaction between tetrazine (Tz) and norbornene (Nb) was found to give DNA–polymer conjugates in good yields (up to 40%) in organic solvents (N,N-dimethylformamide, N,N-dimethylacetamide and N-methyl-2-pyrrolidone), and without the need for a catalyst. Methods for the synthesis of Tz-and Nb- functionalised DNA were developed, along with a post-polymerisation functionalisation strategy for the production of Tz-functionalised polymers.
Brown adipogenic potential of brown adipocytes and peri-renal adipocytes from human embryo
Authors: Wu Nan-Nan , Zhang Chuan-Hai , Lee Hyuek-Jong , Ma Yan , Wang Xin , Ma Xiao-Juan , Ma Wei , Zhao Dong , Feng Ying-Mei 
Published: December 2016

AbstractBoth brown adipocytes (BAC) and beige cells hold therapeutic potential for the treatment of metabolic disorders. Unfortunately, the amount and activity of these cells are limited in adults. Although BAC marker expression has been shown in peri-renal adipose tissues in children and adults, functional assessment is lacking. Furthermore, it is entirely unknown whether adipose progenitors are present in human embryo and able to give rise to BAC in situ during evolution. Therefore, adipose tissues in the interscapular and peri-renal regions were dissected from human embryo and subcutaneous white adipose tissues (sWAT) were obtained from an adult. After subjected to differentiation in vitro, adipocyte progenitors were detected present in all these adipose tissues. When stimulated for adipogenesis, differentiated adipocytes in the intercapular and peri-renal regions showed similar features: (1) induced BAC and beige cell marker expression including UCP1 and PRDM16 and comparable mitochondrion copy number; (2) similar gene expression patterns by RNA-Seq analysis; and (3) similar maximal oxygen consumption rates examined by respirometry. Nevertheless, stimulation of adipocyte progenitors in sWAT induces neither BAC and beige cell marker expression nor any change of oxygen consumption. In conclusion, peri-renal adipocyte progenitors in human embryo hold browning potential for BAC production.
Production of fluorescent dissolved organic matter in Arctic Ocean sediments
Authors: Chen Meilian , Kim Ji-Hoon , Nam Seung-Il , Niessen Frank , Hong Wei-Li , Kang Moo-Hee , Hur Jin 
Published: December 2016

AbstractLittle is known about the production of fluorescent dissolved organic matter (FDOM) in the anoxic oceanic sediments. In this study, sediment pore waters were sampled from four different sites in the Chukchi-East Siberian Seas area to examine the bulk dissolved organic carbon (DOC) and their optical properties. The production of FDOM, coupled with the increase of nutrients, was observed above the sulfate-methane-transition-zone (SMTZ). The presence of FDOM was concurrent with sulfate reduction and increased alkalinity (R2 > 0.96, p < 0.0001), suggesting a link to organic matter degradation. This inference was supported by the positive correlation (R2 > 0.95, p < 0.0001) between the net production of FDOM and the modeled degradation rates of particulate organic carbon sulfate reduction. The production of FDOM was more pronounced in a shallow shelf site S1 with a total net production ranging from 17.9 to 62.3 RU for different FDOM components above the SMTZ depth of ca. 4.1 mbsf, which presumably underwent more accumulation of particulate organic matter than the other three deeper sites. The sediments were generally found to be the sources of CDOM and FDOM to the overlying water column, unearthing a channel of generally bio-refractory and pre-aged DOM to the oceans.
Thiol-Capped Gold Nanoparticles Swell-Encapsulated into Polyurethane as Powerful Antibacterial Surfaces Under Dark and Light Conditions
Authors: Macdonald Thomas J. , Wu Ke , Sehmi Sandeep K. , Noimark Sacha , Peveler William J. , du Toit Hendrik , Voelcker Nicolas H. , Allan Elaine , MacRobert Alexander J. , Gavriilidis Asterios , Parkin Ivan P. 
Published: December 2016

AbstractA simple procedure to develop antibacterial surfaces using thiol-capped gold nanoparticles (AuNPs) is shown, which effectively kill bacteria under dark and light conditions. The effect of AuNP size and concentration on photo-activated antibacterial surfaces is reported and we show significant size effects, as well as bactericidal activity with crystal violet (CV) coated polyurethane. These materials have been proven to be powerful antibacterial surfaces against both Gram-positive and Gram-negative bacteria. AuNPs of 2, 3 or 5 nm diameter were swell-encapsulated into PU before a coating of CV was applied (known as PU-AuNPs-CV). The antibacterial activity of PU-AuNPs-CV samples was tested against Staphylococcus aureus and Escherichia coli as representative Gram-positive and Gram-negative bacteria under dark and light conditions. All light conditions in this study simulated a typical white-light hospital environment. This work demonstrates that the antibacterial activity of PU-AuNPs-CV samples and the synergistic enhancement of photoactivity of triarylmethane type dyes is highly dependent on nanoparticle size and concentration. The most powerful PU-AuNPs-CV antibacterial surfaces were achieved using 1.0 mg mL−1 swell encapsulation concentrations of 2 nm AuNPs. After two hours, Gram-positive and Gram-negative bacteria were reduced to below the detection limit (>4 log) under dark and light conditions.
Ionizing radiation from Chernobyl affects development of wild carrot plants
Authors: Boratyński Zbyszek , Arias Javi Miranda , Garcia Cristina , Mappes Tapio , Mousseau Timothy A. , Møller Anders P. , Pajares Antonio Jesús Muñoz , Piwczyński Marcin , Tukalenko Eugene 
Published: December 2016

AbstractRadioactivity released from disasters like Chernobyl and Fukushima is a global hazard and a threat to exposed biota. To minimize the deleterious effects of stressors organisms adopt various strategies. Plants, for example, may delay germination or stay dormant during stressful periods. However, an intense stress may halt germination or heavily affect various developmental stages and select for life history changes. Here, we test for the consequence of exposure to ionizing radiation on plant development. We conducted a common garden experiment in an uncontaminated greenhouse using 660 seeds originating from 33 wild carrots (Daucus carota) collected near the Chernobyl nuclear power plant. These maternal plants had been exposed to radiation levels that varied by three orders of magnitude. We found strong negative effects of elevated radiation on the timing and rates of seed germination. In addition, later stages of development and the timing of emergence of consecutive leaves were delayed by exposure to radiation. We hypothesize that low quality of resources stored in seeds, damaged DNA, or both, delayed development and halted germination of seeds from plants exposed to elevated levels of ionizing radiation. We propose that high levels of spatial heterogeneity in background radiation may hamper adaptive life history responses.
Unraveling gene expression profiles in peripheral motor nerve from amyotrophic lateral sclerosis patients: insights into pathogenesis
Authors: Riva Nilo , Clarelli Ferdinando , Domi Teuta , Cerri Federica , Gallia Francesca , Trimarco Amelia , Brambilla Paola , Lunetta Christian , Lazzerini Alberto , Lauria Giuseppe , Taveggia Carla , Iannaccone Sandro , Nobile-Orazio Eduardo , Comi Giancarlo , D’Antonio Maurizio , Martinelli-Boneschi Filippo , Quattrini Angelo 
Published: December 2016

AbstractThe aim of the present study is to investigate the molecular pathways underlying amyotrophic lateral sclerosis (ALS) pathogenesis within the peripheral nervous system. We analyzed gene expression changes in human motor nerve diagnostic biopsies obtained from eight ALS patients and seven patients affected by motor neuropathy as controls. An integrated transcriptomics and system biology approach was employed. We identified alterations in the expression of 815 genes, with 529 up-regulated and 286 down-regulated in ALS patients. Up-regulated genes clustered around biological process involving RNA processing and protein metabolisms. We observed a significant enrichment of up-regulated small nucleolar RNA transcripts (p = 2.68*10-11) and genes related to endoplasmic reticulum unfolded protein response and chaperone activity. We found a significant down-regulation in ALS of genes related to the glutamate metabolism. Interestingly, a network analysis highlightedHDAC2,belonging to the histone deacetylase family, as the most interacting node. While so far gene expression studies in human ALS have been performed in postmortem tissues, here specimens were obtained from biopsy at an early phase of the disease, making these results new in the field of ALS research and therefore appealing for gene discovery studies.
A method for high-throughput functional imaging of single cells within heterogeneous cell preparations
Authors: Neal Adam S. , Rountree Austin M. , Radtke Jared R. , Yin Jianzhu , Schwartz Michael W. , Hampe Christiane S. , Posner Jonathan D. , Cirulli Vincenzo , Sweet Ian R. 
Published: December 2016

AbstractFunctional characterization of individual cells within heterogeneous tissue preparations is challenging. Here, we report the development of a versatile imaging method that assesses single cell responses of various endpoints in real time, while identifying the individual cell types. Endpoints that can be measured include (but are not limited to) ionic flux (calcium, sodium, potassium and hydrogen), metabolic responsiveness (NAD(P)H, mitochondrial membrane potential), and signal transduction (H2O2 and cAMP). Subsequent to fluorescent imaging, identification of cell types using immunohistochemistry allows for mapping of cell type to their respective functional real time responses. To validate the utility of this method, NAD(P)H responses to glucose of islet alpha versus beta cells generated from dispersed pancreatic islets, followed by the construction of frequency distributions characterizing the variability in the magnitude of each individual cell responses were compared. As expected, no overlap between the glucose response frequency distributions for beta cells versus alpha cells was observed, thereby establishing both the high degree of fidelity and low rate of both false-negatives and false-positives in this approach. This novel method has the ability not only to resolve single cell level functional differences between cell types, but also to characterize functional heterogeneity within a given cell type.
Usefulness of CHA2DS2-VASc Scoring Systems for Predicting Risk of Perioperative Embolism in Patients of Cardiac Myxomas Underwent Surgical Treatment
Authors: Yin Liang , Wang Jing , Li Wei , Ling Xinyu , Xue Qian , Zhang Yufeng , Wang Zhinong 
Published: December 2016

AbstractCardiac myxomas are rare but manifested with risk of embolism and often cause unexpected symptoms or sudden death. We retrospectively collected the medical records of patients diagnosed of cardiac myxomas at the cardiac center of our university. Overall 465 patients were included in this study, patients in the embolism group had significantly higher CHA2DS2-VASc scores (P = 0.005). In embolic group, stroke was recorded in 110 (77.14%) patients, while embolic events in the limbs were observed in 10 (2.15%) and 9(1.93%) developed splenic infarction. Patients in embolism group had older age (P = 0.021) and higher BMI (P  <0.001) than those in non-embolism group. There was no significant difference between two groups in terms of time of mechanical ventilation (P = 0.065), ICU stay (P = 0.053), hospital stay (P = 0.071) and volume of drainage (P = 0.083), blood transfusions (P = 0.060) except that patients with embolic events had significantly higher incidence of postoperative atrial fibrillation (P = 0.032) and lower survival rate (P < 0.001). Furthermore, the CHA2DS2-VASc score was a significant predictor of embolism in patients with cardiac myxomas (P = 0.015; P = 0.003) and the Kaplan-Meier analysis obtained a higher rate of embolism in patients with higher stratification of CHA2DS2-VASc scores (P = 0.002). In conclusion, CHA2DS2-VASc scoring scheme was strongly predictive of stroke and embolic events in patients with cardiac myxomas.
Antibiotic free selection for the high level biosynthesis of a silk-elastin-like protein
Authors: Barroca Mário , Rodrigues Paulo , Sobral Rómulo , Costa M. Manuela R. , Chaves Susana R. , Machado Raul , Casal Margarida , Collins Tony 
Published: December 2016

AbstractSilk-elastin-like proteins (SELPs) are a family of genetically engineered recombinant protein polymers exhibiting mechanical and biological properties suited for a wide range of applications in the biomedicine and materials fields. They are being explored as the next generation of biomaterials but low productivities and use of antibiotics during production undermine their economic viability and safety. We have developed an industrially relevant, scalable, fed-batch process for the high level production of a novel SELP in E. coli in which the commonly used antibiotic selection marker of the expression vector is exchanged for a post segregational suicide system, the separate-component-stabilisation system (SCS). SCS significantly augments SELP productivity but also enhances the product safety profile and reduces process costs by eliminating the use of antibiotics. Plasmid content increased following induction but no significant differences in plasmid levels were discerned when using SCS or the antibiotic selection markers under the controlled fed-batch conditions employed. It is suggested that the absence of competing plasmid-free cells improves host cell viability and enables increased productivity with SCS. With the process developed, 12.8 g L−1 purified SELP was obtained, this is the highest SELP productivity reported to date and clearly demonstrates the commercial viability of these promising polymers.
ARN: Analysis and Visualization System for Adipogenic Regulation Network Information
Authors: Huang Yan , Wang Li , Zan Lin-sen 
Published: December 2016

AbstractAdipogenesis is the process of cell differentiation through which preadipocytes become adipocytes. Lots of research is currently ongoing to identify genes, including their gene products and microRNAs, that correlate with fat cell development. However, information fragmentation hampers the identification of key regulatory genes and pathways. Here, we present a database of literature-curated adipogenesis-related regulatory interactions, designated the Adipogenesis Regulation Network (ARN, http://210.27.80.93/arn/), which currently contains 3101 nodes (genes and microRNAs), 1863 regulatory interactions, and 33,969 expression records associated with adipogenesis, based on 1619 papers. A sentence-based text-mining approach was employed for efficient manual curation of regulatory interactions from approximately 37,000 PubMed abstracts. Additionally, we further determined 13,103 possible node relationships by searching miRGate, BioGRID, PAZAR and TRRUST. ARN also has several useful features: i) regulatory map information; ii) tests to examine the impact of a query node on adipogenesis; iii) tests for the interactions and modes of a query node; iv) prediction of interactions of a query node; and v) analysis of experimental data or the construction of hypotheses related to adipogenesis. In summary, ARN can store, retrieve and analyze adipogenesis-related information as well as support ongoing adipogenesis research and contribute to the discovery of key regulatory genes and pathways.
High maltose sensitivity of sweet taste receptors in the Japanese macaque (Macaca fuscata)
Authors: Nishi Emiko , Tsutsui Kei , Imai Hiroo 
Published: December 2016

AbstractTaste sensitivity differs among animal species depending on feeding habitat. To humans, sucrose is one of the sweetest natural sugars, and this trait is expected to be similar in other primates. However, previous behavioral tests have shown that some primate species have equal preferences for maltose and sucrose. Because sweet tastes are recognized when compounds bind to the sweet taste receptor Tas1R2/Tas1R3, we evaluated the responses of human and Japanese macaque Tas1R2/Tas1R3 to various natural sugars using a heterologous expression system. Human Tas1R2/Tas1R3 showed high sensitivity to sucrose, as expected; however, Japanese macaque Tas1R2/Tas1R3 showed equally high sensitivity to maltose and sucrose. Furthermore, Japanese macaques showed equally high sensitivity to sucrose and maltose in a two-bottle behavioral experiment. These results indicate that Japanese macaques have high sensitivity to maltose, and this sensitivity is directly related to Tas1R2/Tas1R3 function. This is the first molecular biological evidence that for some primate species, sucrose is not the most preferable natural sugar, as it is for humans.
Co-expression analysis and identification of fecundity-related long non-coding RNAs in sheep ovaries
Authors: Miao Xiangyang , Luo Qingmiao , Zhao Huijing , Qin Xiaoyu 
Published: December 2016

AbstractSmall Tail Han sheep, including the FecBBFecBB (Han BB) and FecB+ FecB+ (Han++) genotypes, and Dorset sheep exhibit different fecundities. To identify novel long non-coding RNAs (lncRNAs) associated with sheep fecundity to better understand their molecular mechanisms, a genome-wide analysis of mRNAs and lncRNAs from Han BB, Han++ and Dorset sheep was performed. After the identification of differentially expressed mRNAs and lncRNAs, 16 significant modules were explored by using weighted gene coexpression network analysis (WGCNA) followed by functional enrichment analysis of the genes and lncRNAs in significant modules. Among these selected modules, the yellow and brown modules were significantly related to sheep fecundity. lncRNAs (e.g., NR0B1, XLOC_041882, and MYH15) in the yellow module were mainly involved in the TGF-β signalling pathway, and NYAP1 and BCORL1 were significantly associated with the oxytocin signalling pathway, which regulates several genes in the coexpression network of the brown module. Overall, we identified several gene modules associated with sheep fecundity, as well as networks consisting of hub genes and lncRNAs that may contribute to sheep prolificacy by regulating the target mRNAs related to the TGF-β and oxytocin signalling pathways. This study provides an alternative strategy for the identification of potential candidate regulatory lncRNAs.