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https://www.readbyqxmd.com/read/29345261/an-inert-3d-emulsification-device-for-individual-precipitation-and-concentration-of-amorphous-drug-nanoparticles
#1
T Lorenz, S Bojko, H Bunjes, A Dietzel
Nanosizing increases the specific surface of drug particles, leading to faster dissolution inside the organism and improving the bioavailability of poorly water-soluble drugs. A novel approach for the preparation of drug nanoparticles in water using chemically inert microfluidic emulsification devices is presented in this paper. A lithographic fabrication sequence was established, allowing fabrication of intersecting and coaxial channels of different depths in glass as is required for 3D flow-focusing. Fenofibrate was used as a model for active pharmaceutical ingredients with very low water solubility in the experiments...
January 18, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29343850/mirna-646-mediated-reciprocal-repression-between-hif-1%C3%AE-and-miip-contributes-to-tumorigenesis-of-pancreatic-cancer
#2
Yi Niu, Yan Jin, Shi-Chang Deng, Shi-Jiang Deng, Shuai Zhu, Yang Liu, Xiang Li, Chi He, Ming-Liang Liu, Zhu Zeng, Heng-Yu Chen, Jian-Xin Zhong, Zeng Ye, Chun-You Wang, Gang Zhao
Migration and invasion inhibitory protein (MIIP) is recently identified as an inhibitor in tumor development. However, the regulatory mechanism and biological contributions of MIIP in pancreatic cancer (PC) have been not elucidated. In this study, we demonstrated a negative feedback of MIIP and hypoxia-induced factor-1α (HIF-1α), which was mediated by a hypoxia-induced microRNA. Compared with paracarcinoma tissues, MIIP was downregulated in PC tissues. Overexpression of MIIP significantly impeded the proliferation and invasion of PC cells both in vitro and in mouse xenograft models...
January 18, 2018: Oncogene
https://www.readbyqxmd.com/read/29337851/transcriptional-regulation-by-cpg-sites-methylation-in-the-core-promoter-region-of-the-bovine-six1-gene-roles-of-histone-h4-and-e2f2
#3
Dawei Wei, Anning Li, Chunping Zhao, Hongbao Wang, Chugang Mei, Rajwali Khan, Linsen Zan
DNA methylation is a major epigenetic modification of the genome and has an essential role in muscle development. The SIX1 gene is thought to play a principal role in mediating skeletal muscle development. In the present study, we determined that bovine SIX1 expression levels were significantly higher in the fetal bovine group (FB) and in undifferentiated Qinchuan cattle muscle cells (QCMCs) than in the adult bovine group (AB) and in differentiated QCMCs. Moreover, a bisulfite sequencing polymerase chain reaction (BSP) analysis of DNA methylation levels showed that three CpG sites in the core promoter region (-216/-28) of the bovine SIX1 gene exhibited significantly higher DNA methylation levels in the AB and differentiated QCMCs groups...
January 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29335549/reconstructing-an-african-haploid-genome-from-the-18th-century
#4
Anuradha Jagadeesan, Ellen D Gunnarsdóttir, S Sunna Ebenesersdóttir, Valdis B Guðmundsdóttir, Elisabet Linda Thordardottir, Margrét S Einarsdóttir, Hákon Jónsson, Jean-Michel Dugoujon, Cesar Fortes-Lima, Florence Migot-Nabias, Achille Massougbodji, Gil Bellis, Luisa Pereira, Gísli Másson, Augustine Kong, Kári Stefánsson, Agnar Helgason
A genome is a mosaic of chromosome fragments from ancestors who existed some arbitrary number of generations earlier. Here, we reconstruct the genome of Hans Jonatan (HJ), born in the Caribbean in 1784 to an enslaved African mother and European father. HJ migrated to Iceland in 1802, married and had two children. We genotyped 182 of his 788 descendants using single-nucleotide polymorphism (SNP) chips and whole-genome sequenced (WGS) 20 of them. Using these data, we reconstructed 38% of HJ's maternal genome and inferred that his mother was from the region spanned by Benin, Nigeria and Cameroon...
January 15, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29331085/verification-of-dna-motifs-in-arabidopsis-using-crispr-cas9-mediated-mutagenesis
#5
Chenlong Li, Chen Chen, Huhui Chen, Suikang Wang, Xuemei Chen, Yuhai Cui
Transcription factors (TFs) and chromatin-modifying factors (CMFs) access chromatin by recognizing specific DNA motifs in their target genes. Chromatin Immunoprecipitation followed by next generation sequencing (ChIP-seq) has been widely used to discover the potential DNA binding motifs for both TFs and CMFs. Yet, an in vivo method for verifying DNA motifs captured by ChIP-seq is lacking in plants. Here, we describe the use of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) to verify DNA motifs in their native genomic context in Arabidopsis...
January 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29330416/virtual-genome-walking-across-the-32%C3%A2-gb-ambystoma-mexicanum-genome-assembling-gene-models-and-intronic-sequence
#6
Teri Evans, Andrew D Johnson, Matthew Loose
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330365/engineered-nanointerfaces-for-microfluidic-isolation-and-molecular-profiling-of-tumor-specific-extracellular-vesicles
#7
Eduardo Reátegui, Kristan E van der Vos, Charles P Lai, Mahnaz Zeinali, Nadia A Atai, Berent Aldikacti, Frederick P Floyd, Aimal H Khankhel, Vishal Thapar, Fred H Hochberg, Lecia V Sequist, Brian V Nahed, Bob S Carter, Mehmet Toner, Leonora Balaj, David T Ting, Xandra O Breakefield, Shannon L Stott
Extracellular vesicles (EVs) carry RNA, DNA, proteins, and lipids. Specifically, tumor-derived EVs have the potential to be utilized as disease-specific biomarkers. However, a lack of methods to isolate tumor-specific EVs has limited their use in clinical settings. Here we report a sensitive analytical microfluidic platform (EVHB-Chip) that enables tumor-specific EV-RNA isolation within 3 h. Using the EVHB-Chip, we achieve 94% tumor-EV specificity, a limit of detection of 100 EVs per μL, and a 10-fold increase in tumor RNA enrichment in comparison to other methods...
January 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29324422/assimilation-of-biophysical-neuronal-dynamics-in-neuromorphic-vlsi
#8
Jun Wang, Daniel Breen, Abraham Akinin, Frederic Broccard, Henry D I Abarbanel, Gert Cauwenberghs
Representing the biophysics of neuronal dynamics and behavior offers a principled analysis-by-synthesis approach toward understanding mechanisms of nervous system functions. We report on a set of procedures assimilating and emulating neurobiological data on a neuromorphic very large scale integrated (VLSI) circuit. The analog VLSI chip, NeuroDyn, features 384 digitally programmable parameters specifying for 4 generalized Hodgkin-Huxley neurons coupled through 12 conductance-based chemical synapses. The parameters also describe reversal potentials, maximal conductances, and spline regressed kinetic functions for ion channel gating variables...
December 2017: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/29324236/irf1-up-regulates-isg15-gene-expression-in-dsrna-stimulation-or-csfv-infection-by-targeting-nucleotides-487-to-325-in-the-5-flanking-region
#9
Xiao-Quan Li, Xiao Ning Li, Jing-Jing Liang, Xin-Bin Cai, Qian Tao, Yu-Xiao Li, Qing Qin, Su-Ping Xu, Ting Rong Luo
Interferon (IFN)-stimulated gene 15 (ISG15) encodes a ubiquitin-like protein that is heavily involved in immune response elicitation. As an important member of interferon regulatory factor (IRF) family, IRF1 can activate the expression of multiple genes, including the human optineurin gene (Sudhakar et al., 2013). In this study, a sequence in the promoter region of the optineurin gene was compared to the 5' flanking region of the porcine isg15 gene. Porcine IRF1 also possesses antiviral activity against several swine viruses (Li et al...
January 8, 2018: Molecular Immunology
https://www.readbyqxmd.com/read/29323174/large-scale-transcriptome-changes-in-the-process-of-long-term-visual-memory-formation-in-the-bumblebee-bombus-terrestris
#10
Li Li, Songkun Su, Clint J Perry, Maurice R Elphick, Lars Chittka, Eirik Søvik
Many genes have been implicated in mechanisms of long-term memory formation, but there is still much to be learnt about how the genome dynamically responds, transcriptionally, during memory formation. In this study, we used high-throughput sequencing to examine how transcriptome profiles change during visual memory formation in the bumblebee (Bombus terrestris). Expression of fifty-five genes changed immediately after bees were trained to associate reward with a single coloured chip, and the upregulated genes were predominantly genes known to be involved in signal transduction...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322784/bioinformatic-analysis-of-changes-in-rna-polymerase-ii-transcription-stimulated-by-estradiol-in-mcf7-cells
#11
J Wu, Y Cai, G Zhao
Estradiol (E2) is the most potent estrogen and RNA polymerase II (Pol II) regulates a great mass of gene expression. This study was designed to illustrate the mechanisms of estrogen-dependent human breast cancer (BC) through Pol II. ChIP-seq data, DNase-seq data and other sequencing data of human BC MCF-7 cells were downloaded from Gene Expression Omnibus database. Each of these datasets included one control and one E2 treated sample. Sequence alignment was performed and Pol II factor binding signal was determined...
2018: Neoplasma
https://www.readbyqxmd.com/read/29322780/signal-and-noise-in-fet-nanopore-devices
#12
William M Parkin, Marija Drndic
The combination of a nanopore with a local field-effect transistor (FET-nanopore), like a nanoribbon, nanotube, or nanowire, in order to sense single molecules translocating through the pore is promising for DNA sequencing at megahertz bandwidths. Previously, it was experimentally determined that the detection mechanism was due to local potential fluctuations that arise when an analyte enters a nanopore and constricts ion flow through it, rather than the theoretically proposed mechanism of direct charge coupling between the DNA and nanowire...
January 11, 2018: ACS Sensors
https://www.readbyqxmd.com/read/29322418/analysis-of-histone-modifications-in-acute-myeloid-leukaemia-using-chromatin-immunoprecipitation
#13
Benjamin J Shields, Andrew Keniry, Marnie E Blewitt, Matthew P McCormack
Chromatin Immunoprecipitation (ChIP) using antibodies specific for histone modifications is a powerful technique for assessing the epigenetic states of cell populations by either quantitative PCR (ChIP-PCR) or next generation sequencing analysis (ChIP-Seq). Here we describe the procedure for ChIP of histone marks in myeloid leukaemia cell lines and the subsequent purification of genomic DNA associated with repressive and activating histone modifications for further analysis. This procedure can be widely applied to a variety of histone marks to assess both activating and repressive modifications in the context of myeloid leukaemia...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321036/maternal-engineered-nanomaterial-inhalation-during-gestation-alters-the-fetal-transcriptome
#14
P A Stapleton, Q A Hathaway, C E Nichols, A B Abukabda, M V Pinti, D L Shepherd, C R McBride, J Yi, V C Castranova, J M Hollander, T R Nurkiewicz
BACKGROUND: The integration of engineered nanomaterials (ENM) is well-established and widespread in clinical, commercial, and domestic applications. Cardiovascular dysfunctions have been reported in adult populations after exposure to a variety of ENM. As the diversity of these exposures continues to increase, the fetal ramifications of maternal exposures have yet to be determined. We, and others, have explored the consequences of ENM inhalation during gestation and identified many cardiovascular and metabolic outcomes in the F1 generation...
January 10, 2018: Particle and Fibre Toxicology
https://www.readbyqxmd.com/read/29316949/ezh2-promotes-hepatocellular-carcinoma-progression-through-modulating-mir-22-galectin-9-axis
#15
Shaofei Chen, Jiarui Pu, Jie Bai, Yuping Yin, Ke Wu, Jiliang Wang, Xiaoming Shuai, Jinbo Gao, Kaixiong Tao, Guobin Wang, Hang Li
BACKGROUND: Recent studies have shown that interferon-γ (IFN-γ)-induced galectin-9 expression in Kupffer cells plays an essential role in modulatingthe microenvironment of hepatitis-associated hepatocellular carcinoma (HCC). However, whether or not IFN-γ induces galectin-9 expression in HCC cells, its biological role and regulatory mechanism in HCC development and progression are poorly defined. METHODS: Quantitative PCR and western blotting analysis were used to detect galectin-9 and EZH2 levels in HCC cell lines stimulated with IFN-γ...
January 9, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29315680/solexa-sequencing-and-custom-microrna-chip-reveal-repertoire-of-micrornas-in-mammary-gland-of-bovine-suffering-from-natural-infectious-mastitis
#16
Zhihua Ju, Qiang Jiang, Gang Liu, Xiuge Wang, Guojing Luo, Yan Zhang, Jibin Zhang, Jifeng Zhong, Jinming Huang
Identification of microRNAs (miRNAs), target genes and regulatory networks associated with innate immune and inflammatory responses and tissue damage is essential to elucidate the molecular and genetic mechanisms for resistance to mastitis. In this study, a combination of Solexa sequencing and custom miRNA chip approaches was used to profile the expression of miRNAs in bovine mammary gland at the late stage of natural infection with Staphylococcus aureus, a widespread mastitis pathogen. We found 383 loci corresponding to 277 known and 49 putative novel miRNAs, two potential mitrons and 266 differentially expressed miRNAs in the healthy and mastitic cows' mammary glands...
January 8, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29313085/a-long-non-coding-rna-inside-the-type-2-transglutaminase-gene-tightly-correlates-with-the-expression-of-its-transcriptional-variants
#17
Linda Minotti, Federica Baldassari, Marco Galasso, Stefano Volinia, Carlo M Bergamini, Nicoletta Bianchi
The long non-coding RNAs (lncRNAs) are matter of intense investigation as potential regulators of gene expression. In the case of the transglutaminase 2 gene (TGM2) the databases of genome sequence indicate location of a lncRNA (LOC107987281) within the first intron. This lncRNA is 1000 bp long, arises from 2 exons and starts few nucleotides 3' of the first splicing site of translated TGM2. We have analysed correlations between expression of LOC107987281 lncRNA and TGM2 mRNA by real-time PCR in K562 cell line untreated or treated with the anticancer drugs TPA (12-O-tetradecanoylphorbol-13-acetate), Docetaxel and Doxorubicin...
January 8, 2018: Amino Acids
https://www.readbyqxmd.com/read/29312534/the-pax8-cistrome-in-epithelial-ovarian-cancer
#18
Emily K Adler, Rosario I Corona, Janet M Lee, Norma Rodriguez-Malave, Paulette Mhawech-Fauceglia, Heidi Sowter, Dennis J Hazelett, Kate Lawrenson, Simon A Gayther
PAX8 is a lineage-restricted transcription factor that is expressed in epithelial ovarian cancer (EOC) precursor tissues, and in the major EOC histotypes. Frequent overexpression of PAX8 in primary EOCs suggests this factor functions as an oncogene during tumorigenesis, however, the biological role of PAX8 in EOC development is poorly understood. We found that stable knockdown of PAX8 in EOC models significantly reduced cell proliferation and anchorage dependent growth in vitro, and attenuated tumorigenicity in vivo...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29310299/millifluidic-chip-with-a-modular-design-used-as-a-sample-pretreatment-cartridge-for-flour-and-flour-food-products
#19
Yue Sun, Junchun Yuan, Jinling Pang, Xiaonan Li, Shumei Wang, Yongliang Zhou, Fang Xu, Paul C H Li, Shusen Jiang, Hong Chen
The integration of sample pretreatment remains one of the hurdles towards a rapid, automated micro total analytical system (µ-TAS) for real samples. In this paper, a modular design, which was used for sample preparation, has been developed as the polydimethylsiloxane (PDMS) millifluidic chips with channels at a millimeter level. Multiple functional units, including extraction, filtration, mixing and solid phase extraction (SPE), for sample pretreatment were integrated in one chip. In this chip, each functional unit was connected by pump tubings and one-way valves in series to form a fully automated system...
March 1, 2018: Talanta
https://www.readbyqxmd.com/read/29300409/concentrating-and-labeling-genomic-dna-in-a-nanofluidic-array
#20
Rodolphe Marie, Jonas N Pedersen, Kalim U Mir, Brian Bilenberg, Anders Kristensen
Nucleotide incorporation by DNA polymerase forms the basis of DNA sequencing-by-synthesis. In current platforms, either the single-stranded DNA or the enzyme is immobilized on a solid surface to locate the incorporation of individual nucleotides in space and/or time. Solid-phase reactions may, however, hinder the polymerase activity. We demonstrate a device and a protocol for the enzymatic labeling of genomic DNA arranged in a dense array of single molecules without attaching the enzyme or the DNA to a surface...
January 4, 2018: Nanoscale
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