bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient and reliable establishment of lymphoblastoid cell lines by Epstein-Barr virus transformation from a limited amount of peripheral blood
Authors: Omi Natsue , Tokuda Yuichi , Ikeda Yoko , Ueno Morio , Mori Kazuhiko , Sotozono Chie , Kinoshita Shigeru , Nakano Masakazu , Tashiro Kei 
Published: March 2017

AbstractLymphoblastoid cell lines (LCLs) transformed by Epstein-Barr virus (EBV) serve as an unlimited resource of human genomic DNA. The protocol that is widely used to establish LCLs involves peripheral blood mononuclear cell isolation by density gradient centrifugation, however, that method requires as much as 5 ml of peripheral blood. In this study, in order to provide a more simple and efficient method for the generation of LCLs, we developed a new protocol using hemolytic reaction to enrich white blood cells for EBV transformation and found that the hemolytic protocol successfully generated LCLs from a small volume (i.e., 0.1 ml) of peripheral blood. To assess the quality of genomic DNA extracted from LCLs established by the hemolytic protocol (LCL-hemolytic), we performed single nucleotide polymorphism (SNP) microarray genotyping using the GeneChip® 100 K Array Set (Affymetrix, Inc.). The concordances of the SNP genotyping resulting from genomic DNA from LCL-hemolytic (99.92%) were found to be as good as the technical replicate (99.90%), and Kappa statistics results confirmed the reliability. The findings of this study reveal that the hemolytic protocol is a simple and reliable method for the generation of LCLs, even from a small volume of peripheral blood.
Effects of the TLR4 signaling pathway on apoptosis of neuronal cells in diabetes mellitus complicated with cerebral infarction in a rat model
Authors: Li Chao , Che Li-He , Ji Tie-Feng , Shi Lei , Yu Jin-Lu 
Published: March 2017

AbstractThis study aims to explore the effects of the TLR4 signaling pathway on the apoptosis of neuronal cells in rats with diabetes mellitus complicated with cerebral infarction (DMCI). A DMCI model was established with 40 Sprague Dawley rats, which were assigned into blank, sham, DM + middle cerebral artery occlusion (MCAO) and DM + MCAO + TAK242 groups. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) content were measured. A TUNEL assay was applied for detecting cell apoptosis, and Western blotting was used for detecting the expression of TLR4, TNF-α, IL-1β and apoptosis-related proteins. Compared with the blank and sham groups, there was an increase in cell apoptosis, expression of Bcl-2, Bax, cleaved caspase-3, TNF-α, IL-1β and TLR4 proteins and MDA content and a decrease in SOD activity in the DM + MCAO and DM + MCAO + TAK242 groups. Compared with those in the DM + MCAO group, rats in the DM + MCAO + TAK242 group exhibited an increase in SOD activity and a decrease in cell apoptosis, expression of Bcl-2, Bax, cleaved caspase-3, TNF-α, IL-1β and TLR4 proteins and MDA content. Inhibition of the TLR4 signaling pathway reduces neuronal cell apoptosis and nerve injury to protect the brain.
Emergence of linguistic laws in human voice
Authors: Torre Iván González , Luque Bartolo , Lacasa Lucas , Luque Jordi , Hernández-Fernández Antoni 
Published: March 2017

AbstractLinguistic laws constitute one of the quantitative cornerstones of modern cognitive sciences and have been routinely investigated in written corpora, or in the equivalent transcription of oral corpora. This means that inferences of statistical patterns of language in acoustics are biased by the arbitrary, language-dependent segmentation of the signal, and virtually precludes the possibility of making comparative studies between human voice and other animal communication systems. Here we bridge this gap by proposing a method that allows to measure such patterns in acoustic signals of arbitrary origin, without needs to have access to the language corpus underneath. The method has been applied to sixteen different human languages, recovering successfully some well-known laws of human communication at timescales even below the phoneme and finding yet another link between complexity and criticality in a biological system. These methods further pave the way for new comparative studies in animal communication or the analysis of signals of unknown code.
Design and Functional Characterization of a Novel Abscisic Acid Analog
Authors: Han Xiaoqiang , Jiang Lun , Che Chuanliang , Wan Chuan , Lu Huizhe , Xiao Yumei , Xu Yanjun , Chen Zhongzhou , Qin Zhaohai 
Published: March 2017

AbstractThe phytohormone abscisic acid (ABA) plays a crucial role in mediating plant growth and development by recruiting genetically redundant ABA receptors. To overcome its oxidation inactivation, we developed a novel ABA analog named 2′,3′-benzo-iso-ABA (iso-PhABA) and studied its function and structural characterization with A. thaliana ABA receptors. The (+)-iso-PhABA form showed much higher ABA-like activities than (+)-ABA including inhibitory effects on the seed germination of lettuce and A. thaliana, wheat embryo germination and rice seedling elongation. The PP2C (protein phosphatases 2C) activity assay showed that (+)-iso-PhABA acted as a potent and selective ABA receptor agonist, which is preferred to PYL10. In some cases, (−)-iso-PhABA showed moderate to high activity for the PYL protein inhibiting PP2C activity, suggesting different mechanisms of action of iso-PhABA and ABA. The complex crystal structure of iso-PhABA with PYL10 was determined and elucidated successfully, revealing that (+)-iso-PhABA was better coordinated in the same binding pocket compared to (+)-ABA. Moreover, the detailed interaction network of iso-PhABA/PYL10 was disclosed and involves hydrogen bonds and multiple hydrophobic interactions that provide a robust framework for the design of novel ABA receptor agonists/antagonists.
A millisecond micro-RNA separation technique by a hybrid structure of nanopillars and nanoslits
Authors: Wu Qiong , Kaji Noritada , Yasui Takao , Rahong Sakon , Yanagida Takeshi , Kanai Masaki , Nagashima Kazuki , Tokeshi Manabu , Kawai Tomoji , Baba Yoshinobu 
Published: March 2017

AbstractA millisecond micro-RNA separation of a mixture of total RNA and genomic DNA, extracted from cultured HeLa cells, was successfully achieved using a hybrid structure of nanopillars and nanoslits contained inside a microchannel. The nanopillars, 250-nm in diameter and 100-nm in height, were fabricated with a 750-nm space inside the nanoslits, which were 100-nm in height and 25-μm in width; the nanopillars were then applied as a new sieve matrix. This ultra-fast technique for the separation of miRNA can be an effective pretreatment for semiconductor nanopore DNA sequencing, which has an optimum reading speed of 1 base/ms to obtain effective signal-to-noise ratio and discriminate each base by ion or tunneling current during the passage of nucleic acids.
Acid phosphatase 2 (ACP2) is required for membrane fusion during influenza virus entry
Authors: Lee Jihye , Kim Jinhee , Son Kidong , d’Alexandry d’Orengiani Anne-Laure Pham Humg , Min Ji-Young 
Published: March 2017

AbstractInfluenza viruses exploit host factors to successfully replicate in infected cells. Using small interfering RNA (siRNA) technology, we identified six human genes required for influenza A virus (IAV) replication. Here we focused on the role of acid phosphatase 2 (ACP2), as its knockdown showed the greatest inhibition of IAV replication. In IAV-infected cells, depletion of ACP2 resulted in a significant reduction in the expression of viral proteins and mRNA, and led to the attenuation of virus multi-cycle growth. ACP2 knockdown also decreased replication of seasonal influenza A and B viruses and avian IAVs of the H7 subtype. Interestingly, ACP2 depletion had no effect on the replication of Ebola or hepatitis C virus. Because ACP2 is known to be a lysosomal acid phosphatase, we assessed the role of ACP2 in influenza virus entry. While neither binding of the viral particle to the cell surface nor endosomal acidification was affected in ACP2-depleted cells, fusion of the endosomal and viral membranes was impaired. As a result, downstream steps in viral entry were blocked, including nucleocapsid uncoating and nuclear import of viral ribonucleoproteins. Our results established ACP2 as a necessary host factor for regulating the fusion step of influenza virus entry.
Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-ι
Authors: Jain Rinku , Choudhury Jayati Roy , Buku Angeliki , Johnson Robert E. , Prakash Louise , Prakash Satya , Aggarwal Aneel K. 
Published: March 2017

AbstractN1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-ι (Polι) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Polι is ~100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Polι bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a “foothold” and is largely disordered. Together, our kinetic and structural studies show how Polι maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.
Characterizing Biochar as Alternative Sorbent for Oil Spill Remediation
Authors: Silvani Ludovica , Vrchotova Blanka , Kastanek Petr , Demnerova Katerina , Pettiti Ida , Papini Marco Petrangeli 
Published: March 2017

AbstractBiochar (BC) was characterized as a new carbonaceous material for the adsorption of toluene from water. The tested BC was produced from pine wood gasification, and its sorption ability was compared with that of more common carbonaceous materials such as activated carbon (AC). Both materials were characterized in terms of textural features and sorption abilities by kinetic and equilibrium tests. AC and BC showed high toluene removal from water. Kinetic tests demonstrated that BC is characterized by faster toluene removal than AC is. Textural features demonstrated that the porosity of AC is double that of BC. Nevertheless, equilibrium tests demonstrated that the sorption ability of BC is comparable with that of AC, so the materials’ porosity is not the only parameter that drives toluene adsorption. The specific adsorption ability (mg sorbed m−2 of surface) of the BC is higher than that of AC: toluene is more highly sorbed onto the biochar surface. Biochar is furthermore obtained from biomaterial thermally treated for making energy; this also makes the use of BC economically and environmentally convenient compared with AC, which, as a manufactured material, must be obtained in selected conditions for this type of application.
Genetically-directed Sparse Neuronal Labeling in BAC Transgenic Mice through Mononucleotide Repeat Frameshift
Authors: Lu Xiao-Hong , Yang X. William 
Published: March 2017

AbstractMosaicism with Repeat Frameshift (MORF) allows a single Bacterial Artificial Chromosome (BAC) transgene to direct sparse labeling of genetically-defined neuronal populations in mice. The BAC transgene drives cell-type-specific transcription of an out-of-frame mononucleotide repeat that is placed between a translational start codon and a membrane-bound fluorescent protein lacking its start codon. The stochastic frameshift of the unstable repeat DNA in a subset of BAC-expressing neurons results in the in-frame translation of the reporter protein hence the sparse neuronal labeling. As a proof-of-concept, we generated D1-dopamine receptor (D1) BAC MORF mice that label about 1% striatal D1-expressing medium spiny neurons and allow visualization of their dendrites. These mice enable the study of D1-MSN dendrite development in wildtype mice, and its degeneration in a mouse model of Huntington’s disease.
Plasmalogen biosynthesis is spatiotemporally regulated by sensing plasmalogens in the inner leaflet of plasma membranes
Authors: Honsho Masanori , Abe Yuichi , Fujiki Yukio 
Published: March 2017

AbstractAlkenyl ether phospholipids are a major sub-class of ethanolamine- and choline-phospholipids in which a long chain fatty alcohol is attached at the sn-1 position through a vinyl ether bond. Biosynthesis of ethanolamine-containing alkenyl ether phospholipids, plasmalogens, is regulated by modulating the stability of fatty acyl-CoA reductase 1 (Far1) in a manner dependent on the level of cellular plasmalogens. However, precise molecular mechanisms underlying the regulation of plasmalogen synthesis remain poorly understood. Here we show that degradation of Far1 is accelerated by inhibiting dynamin-, Src kinase-, or flotillin-1-mediated endocytosis without increasing the cellular level of plasmalogens. By contrast, Far1 is stabilized by sequestering cholesterol with nystatin. Moreover, abrogation of the asymmetric distribution of plasmalogens in the plasma membrane by reducing the expression of CDC50A encoding a β-subunit of flippase elevates the expression level of Far1 and plasmalogen synthesis without reducing the total cellular level of plasmalogens. Together, these results support a model that plasmalogens localised in the inner leaflet of the plasma membranes are sensed for plasmalogen homeostasis in cells, thereby suggesting that plasmalogen synthesis is spatiotemporally regulated by monitoring cellular level of plasmalogens.
Controlling self-assembly of diphenylalanine peptides at high pH using heterocyclic capping groups
Authors: Martin Adam D. , Wojciechowski Jonathan P. , Robinson Andrew B. , Heu Celine , Garvey Christopher J. , Ratcliffe Julian , Waddington Lynne J. , Gardiner James , Thordarson Pall 
Published: March 2017

AbstractUsing small angle neutron scattering (SANS), it is shown that the existence of pre-assembled structures at high pH for a capped diphenylalanine hydrogel is controlled by the selection of N-terminal heterocyclic capping group, namely indole or carbazole. At high pH, changing from a somewhat hydrophilic indole capping group to a more hydrophobic carbazole capping group results in a shift from a high proportion of monomers to self-assembled fibers or wormlike micelles. The presence of these different self-assembled structures at high pH is confirmed through NMR and circular dichroism spectroscopy, scanning probe microscopy and cryogenic transmission electron microscopy.
Amplified centrosomes and mitotic index display poor concordance between patient tumors and cultured cancer cells
Authors: Mittal Karuna , Choi Da Hoon , Ogden Angela , Donthamsetty Shashi , Melton Brian D. , Gupta Meenakshi. V. , Pannu Vaishali , Cantuaria Guilherme , Varambally Sooryanarayana , Reid Michelle D. , Jonsdottir Kristin , Janssen Emiel A. M. , Aleskandarany Mohammad A. , Ellis Ian O. , Rakha Emad A. , Rida Padmashree C. G. , Aneja Ritu 
Published: March 2017

AbstractCentrosome aberrations (CA) and abnormal mitoses are considered beacons of malignancy. Cancer cell doubling times in patient tumors are longer than in cultures, but differences in CA between tumors and cultured cells are uncharacterized. We compare mitoses and CA in patient tumors, xenografts, and tumor cell lines. We find that mitoses are rare in patient tumors compared with xenografts and cell lines. Contrastingly, CA is more extensive in patient tumors and xenografts (~35–50% cells) than cell lines (~5–15%), although CA declines in patient-derived tumor cells over time. Intratumoral hypoxia may explain elevated CA in vivo because exposure of cultured cells to hypoxia or mimicking hypoxia pharmacologically or genetically increases CA, and HIF-1α and hypoxic gene signature expression correlate with CA and centrosomal gene signature expression in breast tumors. These results highlight the importance of utilizing low-passage-number patient-derived cell lines in studying CA to more faithfully recapitulate in vivo cellular phenotypes.
Geographical variation in morphology of Chaetosiphella stipae stipae Hille Ris Lambers, 1947 (Hemiptera: Aphididae: Chaitophorinae)
Authors: Wieczorek Karina , Bugaj-Nawrocka Agnieszka , Kanturski Mariusz , Miller Gary L. 
Published: March 2017

AbstractChaetosiphella stipae stipaeis a xerothermophilous aphid, associated with Palaearctic temperate steppe zones or dry mountain valleys, where there are grasses from the genusStipa. Its geographical distribution shows several populations that are spread from Spain, across Europe and Asia Minor, to Mongolia and China. Geographical variation in chaetotaxy and other morphological features were the basis to consider whether individuals from different populations are still the same species. Moreover, usingCh. stipae stipaeandStipaspecies occurrences, as well as climatic variables, we predict potential geographical distributions of the aphid and its steppe habitat. Additionally, forStipaspecies we projected current climatic conditions under four climate change scenarios for 2050 and 2070. While highly variable, our results of morphometric analysis demonstrates that allCh. stipae stipaepopulations are one very variable subspecies. And in view of predicted climate change, we expect reduction ofStipagrasslands. The disappearance of these ecosystems could result in stronger separation of the East-European and Asian steppes as well as European ‘warm-stage’ refuges. Therefore, the geographic morphological variability that we see today in the aphid subspeciesCh. stipae stipaemay in the future lead to speciation and creation of separate subspecies or species.
Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle
Authors: Guo Yuntao , Zhang Xiuxiu , Huang Wanlong , Miao Xiangyang 
Published: March 2017

AbstractMicroRNAs (miRNAs) are important post-transcriptional regulators involved in animal adipogenesis, however, their roles in bovine fat deposition remain poorly understood. In the present study, we conducted a comparative RNA sequencing to identify the key miRNAs involved in beef lipid accumulation by comparing the backfat small RNA samples between Wagyu (high intramuscular fat) and Holstein (moderate intramuscular fat) cattle. Fifteen miRNAs such as bta-miR-142-3p, bta-miR-379, bta-miR-196a, bta-miR-196b, bta-miR-30f and bta-miR-2887 were identified to have a higher expression level in Wagyu cattle compared with Holstein, whereas bta-miR-320a, bta-miR-874 and bta-miR-1247-3p had a lower expression level in Wagyu. Furthermore, a total of 1345 potential target genes of differentially expressed miRNAs were predicted using bioinformatics tools, in which PPARα and RXRα were known to play a critical role in adipocyte differentiation and lipid metabolism. In conclusion, the present study constructed a high-throughput RNA sequencing screen and successfully identified miRNAs such as bta-miR-874, bta-miR-320a and bta-miR-196b which may affect beef fat deposition. The present findings may provide a theoretical foundation for the utilization of beef cattle germplasm resources.
CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
Authors: Zhang Sijia , Wang Yihan , Chen Meijun , Sun Lulu , Han Jun , Elena V. Kazakova , Qiao Hong 
Published: March 2017

AbstractPapillary thyroid carcinoma (PTC) is the most common type of thyroid cancer, and its incidence rate is rapidly growing. It is necessary to understand the pathogenesis of PTC to develop effective diagnosis methods. Promoter methylation has been recognized to contribute to the alterations in gene expression observed in tumorigenesis. Our RNA-seq data identified 1191 differentially expressed mRNAs and 147 differentially expressed lncRNAs in PTC. Next, promoter methylation of these genes was detected by reduced representation bisulfite sequencing (RRBS) technology and comprehensively analyzed to identify differential methylation. In total, 14 genes (13 mRNAs and 1 lncRNA), in which methylation was intimately involved in regulating gene expression, were proposed as novel diagnostic biomarkers. To gain insights into the relationships among these 14 genes, a core co-function network was constructed based on co-expression, co-function and co-methylation data. Notably, CXCL12 was identified as an essential gene in the network that was closely connected with the other genes. These data suggested that CXCL12 down-regulation in PTC may be caused by promoter hypermethylation. Our study was the first to perform an RRBS analysis for PTC and suggested that CXCL12 may contribute to PTC development by methylation-mediated epigenetic regulation of gene expression.
Robustness and Uncertainties of the “Temperature and Greenness” Model for Estimating Terrestrial Gross Primary Production
Authors: Dong Jiaqi , Li Longhui , Shi Hao , Chen Xi , Luo Geping , Yu Qiang 
Published: March 2017

AbstractTerrestrial gross primary production (GPP) plays a vital role in offsetting anthropogenic CO2 emission and regulating global carbon cycle. Various remote sensing approaches for estimating GPP have attracted considerable scientific attentions, yet their robustness and uncertainties remain unclear. Here we evaluate the performance of the “temperature and greenness” (TG) model, a representative remote sensing model in estimating GPP, using the global FLUXNET GPP based on parameter sensitive analysis and optimization strategies. The results show that the minimum (xn) and optimum (xo) temperatures for photosynthesis are sensitive parameters but maximum temperature (xm) not. Optimized xn and xo differ largely from their defaults for more than half of 12 plant functional types (PFTs). Parameter optimization significantly improves the TG’s performance in forest ecosystems where temperature or solar radiation has significant contribution to GPP. For water-limited ecosystems where GPP are strongly dependent of EVI and EVI are sensitive to precipitation, parameter optimization has limited effects. These results imply that the TG model, and most likely for other kind of GPP models using same methodology, can’t be significantly improved for all PFTs through parameter optimization only, and other key climatic variables should be incorporated into the model for better predicting terrestrial ecosystem GPP.