bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural changes induced by acidic pH in human apolipoprotein B-100
Authors: Fernández-Higuero José A. , Benito-Vicente Asier , Etxebarria Aitor , Milicua José Carlos G. , Ostolaza Helena , Arrondo José L. R. , Martín Cesar 
Published: November 2016

AbstractAcidification in the endosome causes lipoprotein release by promoting a conformational change in the LDLR allowing its recycling and degradation of LDL. Notwithstanding conformational changes occurring in the LDLR have expanded considerably, structural changes occurring in LDL particles have not been fully explored yet. The objectives of the present work were to study structural changes occurring in apoB100 by infrared spectroscopy (IR) and also LDL size and morphology by dynamic light scattering (DLS) and electron microscopy (EM) at both pH 7.4 and 5.0. We determined by IR that pH acidification from 7.4 to 5.0, resembling that occurring within endosomal environment, induces a huge reversible structural rearrangement of apoB100 that is characterized by a reduction of beta-sheet content in favor of alpha-helix structures. Data obtained from DLS and EM showed no appreciable differences in size and morphology of LDL. These structural changes observed in apoB100, which are likely implied in particle release from lipoprotein receptor, also compromise the apoprotein stability what would facilitate LDL degradation. In conclusion, the obtained results reveal a more dynamic picture of the LDL/LDLR dissociation process than previously perceived and provide new structural insights into LDL/LDLR interactions than can occur at endosomal low-pH milieu.
DDR1 promotes E-cadherin stability via inhibition of integrin-β1-Src activation-mediated E-cadherin endocytosis
Authors: Chen Hong-Ru , Yeh Yi-Chun , Liu Ching-Yi , Wu Yu-Ting , Lo Fang-Yu , Tang Ming-Jer , Wang Yang-Kao 
Published: November 2016

AbstractDiscoidin domain receptor 1 (DDR1), a receptor tyrosine kinase of collagen, is primarily expressed in epithelial cells. Activation of DDR1 stabilises E-cadherin located on the cell membrane; however, the detailed mechanism of DDR1-stabilised E-cadherin remains unclear. We performed DDR1 knockdown (Sh-DDR1) on Mardin-Darby canine kidney cells to investigate the mechanism of DDR1-stabilised E-cadherin. Sh-DDR1 decreased junctional localisation, increased endocytosis of E-cadherin, and increased physical interactions between E-cadherin and clathrin. Treatment of the dynamin inhibitor Dyngo 4a suppressed Sh-DDR1-induced E-cadherin endocytosis. In addition, the phosphorylation level of Src tyrosine 418 was increased in Sh-DDR1 cell junctions, and inhibition of Src activity decreased Sh-DDR1-induced E-cadherin endocytosis. To characterise the molecular mechanisms, blocking integrin β1 decreased Src activity and E-cadherin junctional localisation in Sh-DDR1 cells. Photoconversion results showed that inhibition of Src activity rescued E-cadherin membrane stability and that inhibition of integrin β1-Src signalling decreased stress fibres and rescued E-cadherin membrane stability in Sh-DDR1 cells. Taken together, DDR1 stabilised membrane localisation of E-cadherin by inhibiting the integrin β1-Src-mediated clathrin-dependent endocytosis pathway.
Detailed Analysis of Protein Topology of Extracellular Vesicles–Evidence of Unconventional Membrane Protein Orientation
Authors: Cvjetkovic Aleksander , Jang Su Chul , Konečná Barbora , Höög Johanna L. , Sihlbom Carina , Lässer Cecilia , Lötvall Jan 
Published: November 2016

AbstractExtracellular vesicles (EVs) are important mediators of intercellular communication that change the recipient cell by shuttling lipids, RNA, or protein cargo between cells. Here, we investigate the topology of the protein cargo found in EVs, as this topology can fundamentally influence the biological effects of EVs. A multiple proteomics approach, combining proteinase treatment and biotin tagging, shows that many proteins of cytosolic origin are localized on the surface of EVs. A detailed analysis of the EV proteome at the peptide level revealed that a number of EV membrane proteins are present in a topologically reversed orientation compared to what is annotated. Two examples of such proteins, SCAMP3 and STX4, were confirmed to have a reversed topology. This reversed typology was determined using flow cytometry and fluorescent microscopy with antibodies directed toward their cytoplasmic epitopes. These results describe a novel workflow to define the EV proteome and the orientation of each protein, including membrane protein topology. These data are fundamentally important to understanding the EV proteome and required to fully explain EV biogenesis as well as biological function in recipient cells.
Boreal earliest Triassic biotas elucidate globally depauperate hard substrate communities after the end-Permian mass extinction
Authors: Zatoń Michał , Niedźwiedzki Grzegorz , Blom Henning , Kear Benjamin P. 
Published: November 2016

AbstractThe end-Permian mass extinction constituted the most devastating biotic crisis of the Phanerozoic. Its aftermath was characterized by harsh marine conditions incorporating volcanically induced oceanic warming, widespread anoxia and acidification. Bio-productivity accordingly experienced marked fluctuations. In particular, low palaeolatitude hard substrate communities from shallow seas fringing Western Pangaea and the Tethyan Realm were extremely impoverished, being dominated by monogeneric colonies of filter-feeding microconchid tubeworms. Here we present the first equivalent field data for Boreal hard substrate assemblages from the earliest Triassic (Induan) of East Greenland. This region bordered a discrete bio-realm situated at mid-high palaeolatitude (>30°N). Nevertheless, hard substrate biotas were compositionally identical to those from elsewhere, with microconchids encrustingClaraiabivalves and algal buildups on the sea floor. Biostratigraphical correlation further shows that Boreal microconchids underwent progressive tube modification and unique taxic diversification concordant with changing habitats over time. We interpret this as a post-extinction recovery and adaptive radiation sequence that mirrored coeval subequatorial faunas, and thus confirms hard substrate ecosystem depletion as a hallmark of the earliest Triassic interval globally.
Identification of Novel HLA-A*0201-Restricted CTL Epitopes in Chinese Vitiligo Patients
Authors: Cui Tingting , Yi Xiuli , Guo Sen , Zhou Fubo , Liu Ling , Li Chunying , Li Kai , Gao Tianwen 
Published: November 2016

AbstractGeneralized vitiligo is an autoimmune disease characterized by melanocyte loss, which results in patchy depigmentation of skin and hair. Recent studies suggested the key role of CD8+T lymphocytes for mediating immune response in vitiligo through melanocyte differentiation antigens, including tyrosinase, gp100 and MelanA/Mart-1. However, the specific epitopes of these auto-antigens are still unknown. In our study, we predicted the possible HLA-A*0201-restricted nonapeptides overlaying the full-length amino acid sequences of these three known antigens and investigated the lymphocytes reactivity to these nonapeptides by Elispot assay. In addition, we evaluated the abilities of these nonapeptides to activate CD8+T cells. We screened out 5 possible epitopes originated from tyrosinase and gp100, numbered P28, P41, P112, P118 and P119. Among these 5 epitopes, notably, P28 and P119 played the dominant role in activating CTLs, with a significant increase in proliferation rate and Interferon-γ (IFN-γ) production of CD8+T cells. Nevertheless, antigen-specific T cell reactivity was not detected in MelanA/Mart-1 peptides. Our studies identified two novel epitopes originated from proteins of gp100 and tyrosinase, which may have implications for the development of immunotherapies for vitiligo.
Enterogenous bacterial glycolipids are required for the generation of natural killer T cells mediated liver injury
Authors: Wei Yingfeng , Zeng Benhua , Chen Jianing , Cui Guangying , Lu Chong , Wu Wei , Yang Jiezuan , Wei Hong , Xue Rufeng , Bai Li , Chen Zhi , Li Lanjuan , Iwabuchi Kazuya , Uede Toshimitsu , Van Kaer Luc , Diao Hongyan 
Published: November 2016

AbstractGlycolipids are potent activator of natural killer T (NKT) cells. The relationship between NKT cells and intestinal bacterial glycolipids in liver disorders remained unclear. We found that, in sharp contrast to specific pathogen-free (SPF) mice, germ-free (GF) mice are resistant to Concanavalin A (ConA)-induced liver injury. ConA treatment failed to trigger the activation of hepatic NKT cells in GF mice. These defects correlated with the sharply reduced levels of CD1d-presented glycolipid antigens in ConA-treated GF mice compared with SPF counterparts. Nevertheless, CD1d expression was similar between these two kinds of mice. The absence of intestinal bacteria did not affect the incidence of αGalCer-induced liver injury in GF mice. Importantly, we found the intestinal bacteria contain glycolipids which can be presented by CD1d and recognized by NKT cells. Furthermore, supplement of killed intestinal bacteria was able to restore ConA-mediated NKT cell activation and liver injury in GF mice. Our results suggest that glycolipid antigens derived from intestinal commensal bacteria are important hepatic NKT cell agonist and these antigens are required for the activation of NKT cells during ConA-induced liver injury. These finding provide a mechanistic explanation for the capacity of intestinal microflora to control liver inflammation.
Impaired T Cell-dependent Humoral Immune Response Associated with Juvenile-onset Recurrent Respiratory Papillomatosis Progression
Authors: Wu Xunyao , Wang Guoliang , Chen Xi , Zhang Jie , Zhao Jing , Wang Jun , Xiao Yang , Tai Jun , Wang Shengcai , Wang Guixiang , Wang Hua , Bai Lina , Gui Jingang , Ni Xin 
Published: November 2016

AbstractWhether humoral immunity plays a role in HPV type 6 or 11 virus-mediated Juvenile-onset Recurrent Respiratory Papillomatosis (JORRP) remains unknown. In the present study, serum total IgG level in 44 JORRP patients was significantly decreased compared with that in 40 healthy controls. Moreover, expanded CD3−CD19+ B cells with down-regulation of CD23, CD40, HLA-DR and up-regulation of CD86 expression were found in the peripheral blood of JORRP patients. Flow cytometry analysis of B-cell compartment showed that the frequency of both CD19+CD27hi plasma cells and CD19+CD27+ memory B cells were decreased in JORRP patients. Importantly, although the proportion of circulating CXCR5+PD1hi Tfh cells was not changed, the function of Tfh cells were greatly impaired with reduced ability of IL-21 secretion to promote B cell maturation. Association analysis by the Kaplan-Meier method revealed that IL-21 secreting Tfh cell was positively correlated to the CD27+ B cell subset frequency, the serum IgG level and the frequency of recurrence in JORRP patients, but negatively correlated to the percentage of IgD+CD27− B cell. We concluded that a reduced IL-21 secretion by Tfh cells may limit B cell maturation and antibody production in JORRP patients and Tfh cell-derived IL-21 might be associated with JORRP outcome in clinic.
Manipulation of zebrafish’s orientation using artificial cilia in a microchannel with actively adaptive wall design
Authors: Mani Karthick , Chang Chien Tsung-Chun , Panigrahi Bivas , Chen Chia-Yuan 
Published: November 2016

AbstractThe zebrafish is a powerful genetic model organism especially in the biomedical chapter for new drug discovery and development. The genetic toolbox which this vertebrate possesses opens a new window to investigate the etiology of human diseases with a high degree genetic similarity. Still, the requirements of laborious and time-consuming of contemporary zebrafish processing assays limit the procedure in carrying out such genetic screen at high throughput. Here, a zebrafish control scheme was initiated which includes the design and validation of a microfluidic platform to significantly increase the throughput and performance of zebrafish larvae manipulation using the concept of artificial cilia actuation. A moving wall design was integrated into this microfluidic platform first time in literature to accommodate zebrafish inside the microchannel from 1 day post-fertilization (dpf) to 6 dpf and can be further extended to 9 dpf for axial orientation control in a rotational range between 0 to 25 degrees at the minimum step of 2-degree increment in a stepwise manner. This moving wall feature was performed through the deflection of shape memory alloy wire embedded inside the microchannel controlled by the electrical waveforms with high accuracy.
Establishing Antibacterial Multilayer Films on the Surface of Direct Metal Laser Sintered Titanium Primed with Phase-Transited Lysozyme
Authors: Guan Binbin , Wang Haorong , Xu Ruiqing , Zheng Guoying , Yang Jie , Liu Zihao , Cao Man , Wu Mingyao , Song Jinhua , Li Neng , Li Ting , Cai Qing , Yang Xiaoping , Li Yanqiu , Zhang Xu 
Published: November 2016

AbstractDirect metal laser sintering is a technology that allows the fabrication of titanium (Ti) implants with a functional gradation of porosity and surface roughness according to three-dimensional (3D) computer data. The surface roughness of direct metal laser sintered titanium (DMLS-Ti) implants may provide abundant binding sites for bacteria. Bacterial colonization and subsequent biofilm formation can cause unsatisfactory cell adhesion and implant-related infections. To prevent such infections, a novel phase-transited lysozyme (PTL) was utilized as an initial functional layer to simply and effectively prime DMLS-Ti surfaces for subsequent coating with antibacterial multilayers. The purpose of the present study was to establish a surface with dual biological functionality. The minocycline-loaded polyelectrolyte multilayers of hyaluronic acid (HA) and chitosan (CS) formed via a layer-by-layer (LbL) self-assembly technique on PTL-functionalized DMLS-Ti were designed to inhibit pathogenic microbial infections while allowing the DMLS-Ti itself and the modified coatings to retain acceptable biocompatibility. The experimental results indicate that the DMLS-Ti and the hydrogel treated surfaces can inhibit early bacterial adhesion while completely preserving osteoblast functions. This design is expected to gain considerable interest in the medical field and to have good potential for applications in multifunctional DMLS-Ti implants.
Network motifs modulate druggability of cellular targets
Authors: Wu Fan , Ma Cong , Tan Cheemeng 
Published: November 2016

AbstractDruggability refers to the capacity of a cellular target to be modulated by a small-molecule drug. To date, druggability is mainly studied by focusing on direct binding interactions between a drug and its target. However, druggability is impacted by cellular networks connected to a drug target. Here, we use computational approaches to reveal basic principles of network motifs that modulate druggability. Through quantitative analysis, we find that inhibiting self-positive feedback loop is a more robust and effective treatment strategy than inhibiting other regulations, and adding direct regulations to a drug-target generally reduces its druggability. The findings are explained through analytical solution of the motifs. Furthermore, we find that a consensus topology of highly druggable motifs consists of a negative feedback loop without any positive feedback loops, and consensus motifs with low druggability have multiple positive direct regulations and positive feedback loops. Based on the discovered principles, we predict potential genetic targets in Escherichia coli that have either high or low druggability based on their network context. Our work establishes the foundation toward identifying and predicting druggable targets based on their network topology.
A scFv antibody targeting common oligomeric epitope has potential for treating several amyloidoses
Authors: Zha Jun , Liu Xiang-meng , Zhu Jie , Liu Shu-ying , Lu Shuai , Xu Peng-xin , Yu Xiao-lin , Liu Rui-tian 
Published: November 2016

AbstractOverproduction or poor clearance of amyloids lead to amyloid aggregation and even amyloidosis development. Different amyloids may interact synergistically to promote their aggregation and accelerate pathology in amyloidoses. Amyloid oligomers assembled from different amyloids share common structures and epitopes, and are considered the most toxic species in the pathologic processes of amyloidoses, which suggests that an agent targeting the common epitope of toxic oligomers could provide benefit to several amyloidoses. In this study, we firstly showed that an oligomer-specific single-chain variable fragment antibody, W20 simultaneously improved motor and cognitive function in Parkinson’s disease and Huntington’s disease mouse models, and attenuated a number of neuropathological features by reducing α-synuclein and mutant huntingtin protein aggregate load and preventing synaptic degeneration. Neuroinflammation and oxidative stressin vivowere also markedly inhibited. The proposed strategy targeting the common epitopes of amyloid oligomers presents promising potential for treating Parkinson’s disease, Huntington’s disease, Alzheimer’s disease, and other amyloidoses.
BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome
Authors: Shen Xueyan , Ngoh Si Yan , Thevasagayam Natascha May , Prakki Sai Rama Sridatta , Bhandare Pranjali , Tan Andy Wee Kiat , Tan Gui Quan , Singh Siddharth , Phua Norman Chun Han , Vij Shubha , Orbán László 
Published: November 2016

AbstractThe Asian seabass is an important marine food fish that has been cultured for several decades in Asia Pacific. However, the lack of a high quality reference genome has hampered efforts to improve its selective breeding. A 3D BAC pool set generated in this study was screened using 22 SSR markers located on linkage group 2 which contains a growth-related QTL region. Seventy-two clones corresponding to 22 FPC contigs were sequenced by Illumina MiSeq technology. We co-assembled the MiSeq-derived scaffolds from each FPC contig with error-corrected PacBio reads, resulting in 187 sequences covering 9.7 Mb. Eleven genes annotated within this region were found to be potentially associated with growth and their tissue-specific expression was investigated. Correlation analysis demonstrated that SNPs in ctsb, skp1 and ppp2ca can be potentially used as markers for selecting fast-growing fingerlings. Conserved syntenies between seabass LG2 and five other teleosts were identified. This study i) provided a 10 Mb targeted genome assembly; ii) demonstrated NGS of BAC pools as a potential approach for mining candidates underlying QTLs of this species; iii) detected eleven genes potentially responsible for growth in the QTL region; and iv) identified useful SNP markers for selective breeding programs of Asian seabass.
Improvement in the transport critical current density and microstructure of isotopic Mg11B2 monofilament wires by optimizing the sintering temperature
Authors: Qiu Wenbin , Jie Hyunseock , Patel Dipak , Lu Yao , Luzin Vladimir , Devred Arnaud , Somer Mehmet , Shahabuddin Mohammed , Kim Jung Ho , Ma Zongqing , Dou Shi Xue , Hossain Md. Shahriar Al 
Published: November 2016

AbstractSuperconducting wires are widely used in fabricating magnetic coils in fusion reactors. In consideration of the stability of 11B against neutron irradiation and lower induced radio-activation properties, MgB2 superconductor with 11B serving as boron source is an alternative candidate to be used in fusion reactor with severe irradiation environment. In present work, a batch of monofilament isotopic Mg11B2 wires with amorphous 11B powder as precursor were fabricated using powder-in-tube (PIT) process at different sintering temperature, and the evolution of their microstructure and corresponding superconducting properties was systemically investigated. Accordingly, the best transport critical current density (Jc) = 2 × 104 A/cm2 was obtained at 4.2 K and 5 T, which is even comparable to multi-filament Mg11B2 isotope wires reported in other work. Surprisingly, transport Jc vanished in our wire which was heat-treated at excessively high temperature (800 °C). Combined with microstructure observation, it was found that lots of big interconnected microcracks and voids that can isolate the MgB2 grains formed in this whole sample, resulting in significant deterioration in inter-grain connectivity. The results can be a constructive guide in fabricating Mg11B2 wires to be used as magnet coils in fusion reactor systems such as ITER-type tokamak magnet.
Pulse noise-hidden image reconstruction and visualization via stochastic resonance
Authors: Sun Qibing , Liu Hongjun , Huang Nan , Wang Zhaolu , Han Jing 
Published: November 2016

AbstractWe investigate the nanosecond pulse noise-hidden image reconstruction and visualization using stochastic resonance implemented by modulation instability. In particular, this dynamical stochastic resonance holds with coupling between the pulse incoherent noise and pulse coherent signal, and provides a substantial enhancement of the signal-to-noise ratio and cross-correlation. This means that the pulse noise-hidden image can be effectively reconstructed with high visibility and fidelity via stochastic resonance at appropriate system parameters. Such a simple and convenient method has potential applications in image processing under noisy environment.
Engineered Nanomedicine with Alendronic Acid Corona Improves Targeting to Osteosarcoma
Authors: Nguyen Tuyen Duong Thanh , Pitchaimani Arunkumar , Aryal Santosh 
Published: November 2016

AbstractWe engineered nanomedicine with the stealth corona made up of densely packed bone seeking ligand, alendronic acid. In a typical nanoconstruct, alendronic acid is conjugated with hydrophilic head moiety of phospholipid that has an ability to self-assemble with hydrophobic polymeric core through its hydrophobic long carbon-chain. Proposed nanomedicine has three distinct compartments namely; poly(l-lactic-co-glycolic acid) polymeric core acting as a drug reservoir and skeleton of the nanoconstruct, phospholipid monolayer covers the core acting as a diffusion barrier, and a densely packed alendronic acid corona acting as a stabilizer and targeting moiety. Thus engineered nanomedicine attain spherical entity with ~90 ± 6 nm having negative zeta potential, −37.7 ± 2 mV, and has an ability to load 7 ± 0.3 wt% of doxorubicin. In-vitro bone targeting efficiency of nanomedicine was studied using hydroxyapatite crystals as a bone model, and found significant accumulation of nanoparticle in the crystals. Moreover, cellular internalization studies with mouse osteosarcoma confirm the selectivity of nanomedicine when compared to its internalization in non-targeted mouse melanoma. This nanomedicine shows prolong stability in serum and deliver the drug into the cell exhibiting an IC50 of 3.7 μM. Given the strong interacting property of alendronic acid with bone, the proposed nanomedicine hold promises in delivering drug to bone microenvironment.