bluuebunny/crossref_metadata_2025_split huggingface dataset:
PEP-19 modulates calcium binding to calmodulin by electrostatic steering
Authors: Wang Xu , Putkey John A. 
Published: November 2016

AbstractPEP-19 is a small protein that increases the rates of Ca2+ binding to the C-domain of calmodulin (CaM) by an unknown mechanism. Although an IQ motif promotes binding to CaM, an acidic sequence in PEP-19 is required to modulate Ca2+ binding and to sensitize HeLa cells to ATP-induced Ca2+ release. Here, we report the NMR solution structure of a complex between PEP-19 and the C-domain of apo CaM. The acidic sequence of PEP-19 associates between helices E and F of CaM via hydrophobic interactions. This allows the acidic side chains in PEP-19 to extend toward the solvent and form a negatively charged surface that resembles a catcher’s mitt near Ca2+ binding loop III of CaM. The topology and gradients of negative electrostatic surface potential support a mechanism by which PEP-19 increases the rate of Ca2+ binding to the C-domain of CaM by ‘catching’ and electrostatically steering Ca2+ to site III.
Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances
Authors: Young Wayne , Moon Christina D. , Thomas David G. , Cave Nick J. , Bermingham Emma N. 
Published: November 2016

AbstractDietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets. The kittens fed kibbled diets had relatively higher abundances of Lactobacillus (>100-fold), Bifidobacterium (>100-fold), and Collinsella (>9-fold) than kittens fed canned diets. There were relatively few differences in the predicted microbiome functions associated with the pre-weaning diet. Post-weaning diet affected the abundance of functional gene groups. Genes involved in vitamin biosynthesis, metabolism, and transport, were significantly enriched in the metagenomes of kittens fed the canned diet. The impact of post-weaning diet on the metagenome in terms of vitamin biosynthesis functions suggests that modulation of the microbiome function through diet may be an important avenue for improving the nutrition of companion animals.
An anti-TNF-α antibody mimetic to treat ocular inflammation
Authors: Khalili Hanieh , Lee Richard W. , Khaw Peng T. , Brocchini Steve , Dick Andrew D. , Copland David A. 
Published: November 2016

AbstractInfliximab is an antibody that neutralizes TNF-α and is used principally by systemic administration to treat many inflammatory disorders. We prepared the antibody mimetic Fab-PEG-Fab (FpFinfliximab) for direct intravitreal injection to assess whether such formulations have biological activity and potential utility for ocular use. FpFinfliximab was designed to address side effects caused by antibody degradation and the presence of the Fc region. Surface plasmon resonance analysis indicated that infliximab and FpFinfliximab maintained binding affinity for both human and murine recombinant TNF-α. No Fc mediated RPE cellular uptake was observed for FpFinfliximab. Both Infliximab and FpFinfliximab suppressed ocular inflammation by reducing the number of CD45+ infiltrate cells in the EAU mice after a single intravitreal injection at the onset of peak disease. These results offer an opportunity to develop and formulate for ocular use, FpF molecules designed for single and potentially multiple targets using bi-specific FpFs.
Ultrasonic spray coating polymer and small molecular organic film for organic light-emitting devices
Authors: Liu Shihao , Zhang Xiang , Zhang Letian , Xie Wenfa 
Published: November 2016

AbstractUltrasonic spray coating process (USCP) with high material -utilization, low manufacture costs and compatibility to streamline production has been attractive in researches on photoelectric devices. However, surface tension exists in the solvent is still a huge obstacle to realize smooth organic film for organic light emitting devices (OLEDs) by USCP. Here, high quality polymer anode buffer layer and small molecular emitting layer are successfully realized through USCP by introducing extra-low surface tension diluent and surface tension control method. The introduction of low surface tension methyl alcohol is beneficial to the formation of poly (3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) films and brings obvious phase separation and improved conductivity to PEDOT:PSS film. Besides, a surface tension control method, in which new stable tension equilibrium is built at the border of wetting layer, is proposed to eliminate the effect of surface tension during the solvent evaporation stage of ultrasonic spray coating the film consists of 9,9-Spirobifluoren-2-yl-diphenyl-phosphine oxide doped with 10 wt% tris [2-(p -tolyl) pyridine] iridium (III). A smooth and homogenous small molecular emitting layer without wrinkles is successfully realized. The effectiveness of the ultrasonic spray coating polymer anode buffer layer and small molecular emitting layer are also proved by introducing them in OLEDs.
Hierarchical effects of pro-inflammatory cytokines on the post-influenza susceptibility to pneumococcal coinfection
Authors: Duvigneau Stefanie , Sharma-Chawla Niharika , Boianelli Alessandro , Stegemann-Koniszewski Sabine , Nguyen Van Kinh , Bruder Dunja , Hernandez-Vargas Esteban A. 
Published: November 2016

AbstractIn the course of influenza A virus (IAV) infections, a secondary bacterial infection frequently leads to serious respiratory conditions provoking high hospitalization and death tolls. Although abundant pro-inflammatory responses have been reported as key contributing factors for these severe dual infections, the relative contributions of cytokines remain largely unclear. In the current study, mathematical modelling based on murine experimental data dissects IFN-γ as a cytokine candidate responsible for impaired bacterial clearance, thereby promoting bacterial growth and systemic dissemination during acute IAV infection. We also found a time-dependent detrimental role of IL-6 in curtailing bacterial outgrowth which was not as distinct as for IFN-γ. Our numerical simulations suggested a detrimental effect of IFN-γ alone and in synergism with IL-6 but no conclusive pathogenic effect of IL-6 and TNF-α alone. This work provides a rationale to understand the potential impact of how to manipulate temporal immune components, facilitating the formulation of hypotheses about potential therapeutic strategies to treat coinfections.
Common variants in the PARL and PINK1 genes increase the risk to leprosy in Han Chinese from South China
Authors: Wang Dong , Zhang Deng-Feng , Feng Jia-Qi , Li Guo-Dong , Li Xiao-An , Yu Xiu-Feng , Long Heng , Li Yu-Ye , Yao Yong-Gang 
Published: November 2016

AbstractLeprosy is a chronic infectious and neurological disease caused by Mycobacterium leprae, an unculturable pathogen with massive genomic decay and dependence on host metabolism. We hypothesized that mitochondrial genes PARL and PINK1 would confer risk to leprosy. Thirteen tag SNPs of PARL and PINK1 were analyzed in 3620 individuals with or without leprosy from China. We also sequenced the entire exons of PARL, PINK1 and PARK2 in 80 patients with a family history of leprosy by using the next generation sequencing technology (NGS). We found that PARL SNP rs12631031 conferred a risk to leprosy (Padjusted = 0.019) and multibacillary leprosy (MB, Padjusted = 0.020) at the allelic level. rs12631031 and rs7653061 in PARL were associated with leprosy and MB (dominant model, Padjusted < 0.05) at the genotypic level. PINK1 SNP rs4704 was associated with leprosy at the genotypic level (Padjusted = 0.004). We confirmed that common variants in PARL and PINK1 were associated with leprosy in patients underwent NGS. Furthermore, PARL and PINK1 could physically interact with each other and were involved in the highly connected network formed by reported leprosy susceptibility genes. Together, our results showed that PARL and PINK1 genetic variants are associated with leprosy.
RETRACTED ARTICLE: Oncogenic transformation of human lung bronchial epithelial cells induced by arsenic involves ROS-dependent activation of STAT3-miR-21-PDCD4 mechanism
Authors: Pratheeshkumar Poyil , Son Young-Ok , Divya Sasidharan Padmaja , Wang Lei , Zhang Zhuo , Shi Xianglin 
Published: November 2016

AbstractArsenic is a well-documented human carcinogen. The present study explored the role of the onco-miR, miR-21 and its target protein, programmed cell death 4 (PDCD4) in arsenic induced malignant cell transformation and tumorigenesis. Our results showed that treatment of human bronchial epithelial (BEAS-2B) cells with arsenic induces ROS through p47phox, one of the NOX subunits that is the key source of arsenic-induced ROS. Arsenic exposure induced an upregulation of miR-21 expression associated with inhibition of PDCD4, and caused malignant cell transformation and tumorigenesis of BEAS-2B cells. Indispensably, STAT3 transcriptional activation by IL-6 is crucial for the arsenic induced miR-21 increase. Upregulated miR-21 levels and suppressed PDCD4 expression was also observed in xenograft tumors generated with chronic arsenic exposed BEAS-2B cells. Stable shut down of miR-21, p47phox or STAT3 and overexpression of PDCD4 or catalase in BEAS-2B cells markedly inhibited the arsenic induced malignant transformation and tumorigenesis. Similarly, silencing of miR-21 or STAT3 and forced expression of PDCD4 in arsenic transformed cells (AsT) also inhibited cell proliferation and tumorigenesis. Furthermore, arsenic suppressed the downstream protein E-cadherin expression and induced β-catenin/TCF-dependent transcription of uPAR and c-Myc. These results indicate that the ROS-STAT3-miR-21-PDCD4 signaling axis plays an important role in arsenic -induced carcinogenesis.
Solid-liquid density and spin crossovers in (Mg, Fe)O system at deep mantle conditions
Authors: Ghosh Dipta B. , Karki Bijaya B. 
Published: November 2016

AbstractThe low/ultralow-velocity zones in the Earth’s mantle can be explained by the presence of partial melting, critically depending on density contrast between the melt and surrounding solid mantle. Here, first-principles molecular dynamics simulations of (Mg, Fe) O ferropericlase in the solid and liquid states show that their densities increasingly approach each other as pressure increases. The isochemical density difference between them diminishes from 0.78 (±0.7) g/cm3 at zero pressure (3000 K) to 0.16 (±0.04) g/cm3 at 135 GPa (4000 K) for pure and alloyed compositions containing up to 25% iron. The simulations also predict a high-spin to low-spin transition of iron in the liquid ferropericlase gradually occurring over a pressure interval centered at 55 GPa (4000 K) accompanied by a density increase of 0.14 (±0.02) g/cm3. Temperature tends to widen the transition to higher pressure. The estimated iron partition coefficient between the solid and liquid ferropericlase varies from 0.3 to 0.6 over the pressure range of 23 to 135 GPa. Based on these results, an excess of as low as 5% iron dissolved in the liquid could cause the solid-liquid density crossover at conditions of the lowermost mantle.
Visualizing epithelial expression of EGFR in vivo with distal scanning side-viewing confocal endomicroscope
Authors: Duan Xiyu , Li Haijun , Zhou Juan , Zhou Quan , Oldham Kenn R. , Wang Thomas D. 
Published: November 2016

AbstractConfocal endomicroscopy is an emerging imaging technology that has recently been introduced into the clinic to instantaneously collect “optical biopsies” in vivo with histology-like quality. Here, we demonstrate a fast scanner located in the distal end of a side-viewing instrument using a compact lens assembly with numerical aperture of 0.5 to achieve a working distance of 100 μm and field-of-view of 300 × 400 μm2. The microelectromechanical systems (MEMS) mirror was designed based on the principle of parametric resonance and images at 5 frames per second. The instrument has a 4.2 mm outer diameter and 3 cm rigid length, and can pass through the biopsy channel of a medical endoscope. We achieved real time optical sections of NIR fluorescence with 0.87 μm lateral resolution, and were able to visualize in vivo binding of a Cy5.5-labeled peptide specific for EGFR to the cell surface of pre-cancerous colonocytes within the epithelium of dysplastic crypts in mouse colon. By performing targeted imaging with endomicroscopy, we can visualize molecular expression patterns in vivo that provide a biological basis for disease detection.
NF-kappaΒ-inducing kinase regulates stem cell phenotype in breast cancer
Authors: Vazquez-Santillan Karla , Melendez-Zajgla Jorge , Jimenez-Hernandez Luis Enrique , Gaytan-Cervantes Javier , Muñoz-Galindo Laura , Piña-Sanchez Patricia , Martinez-Ruiz Gustavo , Torres Javier , Garcia-Lopez Patricia , Gonzalez-Torres Carolina , Ruiz Victor , Avila-Moreno Federico , Velasco-Velazquez Marco , Perez-Tapia Mayra , Maldonado Vilma 
Published: November 2016

AbstractBreast cancer stem cells (BCSCs) overexpress components of the Nuclear factor-kappa B (NF-κB) signaling cascade and consequently display high NF-κB activity levels. Breast cancer cell lines with high proportion of CSCs exhibit high NF-κB-inducing kinase (NIK) expression. The role of NIK in the phenotype of cancer stem cell regulation is poorly understood. Expression of NIK was analyzed by quantitative RT-PCR in BCSCs. NIK levels were manipulated through transfection of specific shRNAs or an expression vector. The effect of NIK in the cancer stem cell properties was assessed by mammosphere formation, mice xenografts and stem markers expression. BCSCs expressed higher levels of NIK and its inhibition through small hairpin (shRNA), reduced the expression of CSC markers and impaired clonogenicity and tumorigenesis. Genome-wide expression analyses suggested that NIK acts on ERK1/2 pathway to exert its activity. In addition, forced expression of NIK increased the BCSC population and enhanced breast cancer cell tumorigenicity. The in vivo relevance of these results is further supported by a tissue microarray of breast cancer samples in which we observed correlated expression of Aldehyde dehydrogenase (ALDH) and NIK protein. Our results support the essential involvement of NIK in BCSC phenotypic regulation via ERK1/2 and NF-κB.
Knockout of Zebrafish Ovarian Aromatase Gene (cyp19a1a) by TALEN and CRISPR/Cas9 Leads to All-male Offspring Due to Failed Ovarian Differentiation
Authors: Lau Esther Shuk-Wa , Zhang Zhiwei , Qin Mingming , Ge Wei 
Published: November 2016

AbstractSexual or gonadal differentiation is a complex event and its mechanism remains elusive in teleosts. Despite its complexity and plasticity, the process of ovarian differentiation is believed to involve gonadal aromatase (cyp19a1a) in nearly all species studied. However, most data concerning the role of aromatase have come from gene expression analysis or studies involving pharmacological approaches. There has been a lack of genetic evidence for the importance of aromatase in gonadal differentiation, especially the timing when the enzyme starts to exert its effect. This is due to the lack of appropriate loss-of-function approaches in fish models for studying gene functions. This situation has changed recently with the development of genome editing technologies, namely TALEN and CRISPR/Cas9. Using both TALEN and CRISPR/Cas9, we successfully established three mutant zebrafish lines lacking the ovarian aromatase. As expected, all mutant fish were males, supporting the view that aromatase plays a critical role in directing ovarian differentiation and development. Further analysis showed that the ovarian aromatase did not seem to affect the formation of so-called juvenile ovary and oocyte-like germ cells; however, it was essential for further differentiation of the juvenile ovary into the true ovary.
Collagen cross-linking: insights on the evolution of metazoan extracellular matrix
Authors: Rodriguez-Pascual Fernando , Slatter David Anthony 
Published: November 2016

AbstractCollagens constitute a large family of extracellular matrix (ECM) proteins that play a fundamental role in supporting the structure of various tissues in multicellular animals. The mechanical strength of fibrillar collagens is highly dependent on the formation of covalent cross-links between individual fibrils, a process initiated by the enzymatic action of members of the lysyl oxidase (LOX) family. Fibrillar collagens are present in a wide variety of animals, therefore often being associated with metazoan evolution, where the emergence of an ancestral collagen chain has been proposed to lead to the formation of different clades. While LOX-generated collagen cross-linking metabolites have been detected in different metazoan families, there is limited information about when and how collagen acquired this particular modification. By analyzing telopeptide and helical sequences, we identified highly conserved, potential cross-linking sites throughout the metazoan tree of life. Based on this analysis, we propose that they have importantly contributed to the formation and further expansion of fibrillar collagens.
Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits
Authors: Hou Qiangchuan , Kwok Lai-Yu , Zheng Yi , Wang Lifeng , Guo Zhuang , Zhang Jiachao , Huang Weiqiang , Wang Yuxiang , Leng Li , Li Hui , Zhang Heping 
Published: November 2016

AbstractOur study combined 16S rRNA-pyrosequencing and whole genome sequencing to analyze the fecal metagenomes of the divergently selected lean (LL) and fat (FL) line chickens. Significant structural differences existed in both the phylogenic and functional metagenomes between the two chicken lines. At phylum level, the FL group had significantly less Bacteroidetes. At genus level, fourteen genera of different relative abundance were identified, with some known short-chain fatty acid producers (including Subdoligranulum, Butyricicoccus, Eubacterium, Bacteroides, Blautia) and a potentially pathogenic genus (Enterococcus). Redundancy analysis identified 190 key responsive operational taxonomic units (OTUs) that accounted for the structural differences between the phylogenic metagenome of the two groups. Four Cluster of Orthologous Group (COG) categories (Amino acid transport and metabolism, E; Nucleotide transport and metabolism, F; Coenzyme transport and metabolism, H; and Lipid transport and metabolism, I) were overrepresented in LL samples. Fifteen differential metabolic pathways (Biosynthesis of amino acids, Pyruvate metabolism, Nitrotoluene degradation, Lipopolysaccharide biosynthesis, Peptidoglycan biosynthesis, Pantothenate and CoA biosynthesis, Glycosaminoglycan degradation, Thiamine metabolism, Phosphotransferase system, Two-component system, Bacterial secretion system, Flagellar assembly, Bacterial chemotaxis, Ribosome, Sulfur relay system) were identified. Our data highlighted interesting variations between the gut metagenomes of these two chicken lines.
Lymphocytic Microparticles Modulate Angiogenic Properties of Macrophages in Laser-induced Choroidal Neovascularization
Authors: Tahiri Houda , Omri Samy , Yang Chun , Duhamel François , Samarani Suzanne , Ahmad Ali , Vezina Mark , Bussières Martin , Vaucher Elvire , Sapieha Przemyslaw , Hickson Gilles , Hammamji Karim , Lapointe Réjean , Rodier Francis , Tremblay Sophie , Royal Isabelle , Cailhier Jean-François , Chemtob Sylvain , Hardy Pierre 
Published: November 2016

AbstractPathological choroidal neovascularization (CNV) is the common cause of vision loss in patients with age-related macular degeneration (AMD). Macrophages possess potential angiogenic function in CNV. We have demonstrated that human T lymphocyte-derived microparticles (LMPs) exert a potent antiangiogenic effect in several pathological neovascularization models. In this study, we investigated the alteration of proangiogenic properties of macrophages by LMPs treatment in vitro and in vivo models. LMPs regulated the expression of several angiogenesis-related factors in macrophages and consequently stimulated their antiangiogenic effects evidenced by the suppression of the proliferation of human retinal endothelial cells in co-culture experiments. The involvement of CD36 receptor in LMPs uptake by macrophages was demonstrated by in vitro assays and by immunostaining of choroidal flat mounts. In addition, ex vivo experiments showed that CD36 mediates the antiangiogenic effect of LMPs in murine and human choroidal explants. Furthermore, intravitreal injection of LMPs in the mouse model of laser-induced CNV significantly suppressed CNV in CD36 dependent manner. The results of this study suggested an ability of LMPs to alter the gene expression pattern of angiogenesis-related factors in macrophages, which provide important information for a new therapeutic approach for efficiently interfering with both vascular and extravascular components of CNV.
Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer
Authors: Bernhart Stephan H. , Kretzmer Helene , Holdt Lesca M. , Jühling Frank , Ammerpohl Ole , Bergmann Anke K. , Northoff Bernd H. , Doose Gero , Siebert Reiner , Stadler Peter F. , Hoffmann Steve 
Published: November 2016

AbstractBivalent (poised or paused) chromatin comprises activating and repressing histone modifications at the same location. This combination of epigenetic marks at promoter or enhancer regions keeps genes expressed at low levels but poised for rapid activation. Typically, DNA at bivalent promoters is only lowly methylated in normal cells, but frequently shows elevated methylation levels in cancer samples. Here, we developed a universal classifier built from chromatin data that can identify cancer samples solely from hypermethylation of bivalent chromatin. Tested on over 7,000 DNA methylation data sets from several cancer types, it reaches an AUC of 0.92. Although higher levels of DNA methylation are often associated with transcriptional silencing, counter-intuitive positive statistical dependencies between DNA methylation and expression levels have been recently reported for two cancer types. Here, we re-analyze combined expression and DNA methylation data sets, comprising over 5,000 samples, and demonstrate that the conjunction of hypermethylation of bivalent chromatin and up-regulation of the corresponding genes is a general phenomenon in cancer. This up-regulation affects many developmental genes and transcription factors, including dozens of homeobox genes and other genes implicated in cancer. Thus, we reason that the disturbance of bivalent chromatin may be intimately linked to tumorigenesis.