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https://www.readbyqxmd.com/read/28436954/optimized-expression-based-microdissection-of-formalin-fixed-lung-cancer-tissue
#1
Markus Grafen, Thurid R Hofmann, Andreas H Scheel, Julia Beck, Alexander Emmert, Stefan Küffer, Bernhard C Danner, Ekkehard Schütz, Reinhardt Büttner, Andreas Ostendorf, Philipp Ströbel, Hanibal Bohnenberger
Analysis of specific DNA alterations in precision medicine of tumors is crucially important for molecular targeted treatments. Lung cancer is a prototypic example and one of the leading causes of cancer-related deaths worldwide. One major technical problem of detecting DNA alterations in tissue samples is cellular heterogeneity, that is, mixture of tumor and normal cells. Microdissection is an important tool to enrich tumor cells from heterogeneous tissue samples. However, conventional laser capture microdissection has several disadvantages like user-dependent selection of regions of interest (ROI), high costs for dissection systems and long processing times...
April 24, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28435053/in-depth-analysis-of-the-synaptic-plasma-membrane-proteome-of-small-hippocampal-slices-using-an-integrated-approach
#2
Rui Qiao, Shuiming Li, Mi Zhou, Penghui Chen, Zhao Liu, Min Tang, Jian Zhou
Comprehensive knowledge of the synaptic plasma membrane (SPM) proteome of a distinct brain region in a defined pathological state would greatly advance the understanding of the underlying biology of synaptic plasticity. The development of innovative approaches for studying the SPM proteome of small brain tissues is highly desired. This study presents a suitable protocol that integrates biotinylation-based affinity capture of cell surface-exposed proteins, isolation of synaptosomes, and biochemical extraction of SPM proteins from biotinylated hippocampal slices...
April 20, 2017: Neuroscience
https://www.readbyqxmd.com/read/28432530/an-integrated-microsystem-with-dielectrophoresis-enrichment-and-impedance-detection-for-detection-of-escherichia-coli
#3
Renjie Wang, Yi Xu, Haitao Liu, Jinlan Peng, Joseph Irudayaraj, Feiyun Cui
An integrated microsystem device with matched interdigitated microelectrode chip was fabricated for enrichment and detection of Escherichia coli O157:H7. The microsystem has integrated with positive dielectrophoresis (pDEP) enrichment and in situ impedance detection, whose total volume is only 3.0 × 10(-3) m(3), and could provide impedance testing voltages of 0 ~ 10 V, detection frequencies of 1 KHz ~ 1 MHz, DEP excitation signals with amplitude of 0 ~ 10 Vpp and frequencies of 1KHz ~ 1 MHz, which fully meets the demands of pDEP enrichment and impedance detection for bacteria...
June 2017: Biomedical Microdevices
https://www.readbyqxmd.com/read/28429065/rapid-electrochemical-quantification-of-salmonella-pullorum-and-salmonella-gallinarum-based-on-glucose-oxidase-and-antibody-modified-silica-nanoparticles
#4
Yiheng Luo, Wenchao Dou, Guangying Zhao
In this article, a facile and sensitive electrochemical method for quantification of Salmonella Pullorum and Salmonella Gallinarum (S. Pullorum and S. Gallinarum) was established by monitoring glucose consumption with a personal glucose meter (PGM). Antibody-functionalized magnetic nanoparticles (IgG-MNPs) were used to capture and enrich S. Pullorum and S. Gallinarum, and IgG-MNPs-S. Pullorum and IgG-MNPs-S. Gallinarum complexes were magnetically separated from a sample using a permanent magnet. The trace tag was prepared by loading polyclonal antibodies and high-content glucose oxidase on amino-functionalized silica nanoparticles (IgG-SiNPs-GOx)...
April 21, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28424352/chromatin-module-inference-on-cellular-trajectories-identifies-key-transition-points-and-poised-epigenetic-states-in-diverse-developmental-processes
#5
Sushmita Roy, Rupa Sridharan
Changes in chromatin state play important roles in cell fate transitions. Current computational approaches to analyze chromatin modifications across multiple cell types do not model how the cell types are related on a lineage or over time. To overcome this limitation, we have developed a method called CMINT (Chromatin Module INference on Trees), a probabilistic clustering approach to systematically capture chromatin state dynamics across multiple cell types. Compared to existing approaches, CMINT can handle complex lineage topologies, capture higher quality clusters, and reliably detect chromatin transitions between cell types...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28421179/synergy-based-bilateral-port-a-universal-control-module-for-tele-manipulation-frameworks-using-asymmetric-master-slave-systems
#6
Anais Brygo, Ioannis Sarakoglou, Giorgio Grioli, Nikos Tsagarakis
Endowing tele-manipulation frameworks with the capability to accommodate a variety of robotic hands is key to achieving high performances through permitting to flexibly interchange the end-effector according to the task considered. This requires the development of control policies that not only cope with asymmetric master-slave systems but also whose high-level components are designed in a unified space in abstraction from the devices specifics. To address this dual challenge, a novel synergy port is developed that resolves the kinematic, sensing, and actuation asymmetries of the considered system through generating motion and force feedback references in the hardware-independent hand postural synergy space...
2017: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/28420528/two-dimensional-gas-chromatography-with-electron-capture-detection-for-the-analysis-of-atmospheric-ozone-depleting-halocarbons
#7
Chang-Feng Ou-Yang, Hsi-Che Hua, Yu-Chieh Chou, Ming-Kai Teng, Wen-Tzu Liu, Jia-Lin Wang
This study is to develop a GC×GC method with electron capture detection (ECD) to analyze atmospheric halocarbons in the concentration range of parts per trillion by volume (pptv). To enrich atmospheric halocarbons a home-built thermal desorption (TD) device was coupled to the GC×GC-ECD. The technique of flow modulation was adopted using a Deans switch for GC×GC. Several column combinations of first and second dimensions were tested and the column set of DB-5×TG-1301 was found to show the best orthogonality for halocarbons...
April 4, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28419375/transcriptional-profiling-of-cholinergic-neurons-from-basal-forebrain-identifies-changes-in-expression-of-genes-between-sleep-and-wake-mrna-profiling-in-basal-forebrain-with-sleep-sleep-deprivation
#8
Elena V Nikonova, Jason DA Gilliland, Keith Q Tanis, Alexei A Podtelezhnikov, Alison M Rigby, Raymond J Galante, Eva M Finney, David J Stone, John J Renger, Allan I Pack, Christopher J Winrow
Study objective: To assess differences in gene expression in cholinergic basal forebrain cells between sleeping and sleep deprived mice sacrificed at the same time of day. Methods: Tg(ChAT-eGFP)86Gsat mice expressing eGFP under control of the choline acetyltransferase (Chat) promoter were utilized to guide laser capture of cholinergic cells in basal forebrain. mRNA expression levels in these cells were profiled using microarrays. Gene expression in eGFP(+) neurons was compared (1) to that in eGFP(-) neurons and to adjacent white matter, (2) between 7:00 am (lights on) and 7:00 pm (lights off), (3) between sleep deprived and sleeping animals at 0, 3, 6, 9 hrs from lights on...
April 13, 2017: Sleep
https://www.readbyqxmd.com/read/28419064/the-application-of-next-generation-sequencing-for-mutation-detection-in-autosomal-dominant-hereditary-hearing-impairment
#9
Nicolas Gürtler, Benno Röthlisberger, Katja Ludin, Christoph Schlegel, Anil K Lalwani
OBJECTIVE: Identification of the causative mutation using next-generation sequencing in autosomal-dominant hereditary hearing impairment, as mutation analysis in hereditary hearing impairment by classic genetic methods, is hindered by the high heterogeneity of the disease. PATIENTS: Two Swiss families with autosomal-dominant hereditary hearing impairment. INTERVENTION: Amplified DNA libraries for next-generation sequencing were constructed from extracted genomic DNA, derived from peripheral blood, and enriched by a custom-made sequence capture library...
April 17, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28417603/squamate-conserved-loci-sqcl-a-unified-set-of-conserved-loci-for-phylogenomics-and-population-genetics-of-squamate-reptiles
#10
Sonal Singhal, Maggie Grundler, Guarino Colli, Daniel L Rabosky
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches - anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) - and both approaches have proven useful for addressing questions in phylogenomics, phylogeography, and population genomics...
April 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28415132/genetic-alterations-in-mesiodens-as-revealed-by-targeted-ngs-and-gene-co-occurrence-network-analysis
#11
Young Youn Kim, Jihye Hwang, Hye-Sung Kim, Hee Jun Kwon, Sanguk Kim, Ji Hyun Lee, Jae Hoon Lee
OBJECTIVE: Mesiodens is the most common type of supernumerary tooth which includes a population prevalence of 0.15-1.9%. Alongside evidence that the condition is heritable, mutations in single genes have been reported in few human supernumerary tooth cases. Gene sequencing methods in tradition way are time-consuming and labor-intensive, whereas next generation sequencing and bioinformatics are cost-effective for large samples and target sizes. MATERIALS AND METHODS: We describe the application of a targeted next generation sequencing (NGS) and bioinformatics approach to samples from 17 mesiodens patients...
April 17, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28412036/rna-binding-proteins-revisited-the-emerging-arabidopsis-mrna-interactome
#12
REVIEW
Tino Köster, Claudius Marondedze, Katja Meyer, Dorothee Staiger
RNA-protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture - where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism...
April 12, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28411829/rapid-and-efficient-separation-of-glycoprotein-using-ph-double-responsive-imprinted-magnetic-microsphere
#13
Jingfan Xie, Guanqun Zhong, Changqun Cai, Chunyan Chen, Xiaoming Chen
As biomarkers of many diseases, glycoproteins are of great significance to clinical diagnostics. However, the determination of low abundant glycoproteins in complex biological samples without any pretreatment process is still a problem. In this study, a rapid and convenient separation method for highly efficient enrichment of glycoproteins is reported, based on pH double-responsive imprinted magnetic microspheres. Thin imprinted polymer shells were fabricated onto the surface of magnetic microspheres by free radical polymerization, using 2-(Dimethylamino) ethyl methacrylate as pH-sensitive monomer, 4-vinylphenylbronic acid as boronate affinity monomer, and ovalbumin (OVA) as template molecule...
July 1, 2017: Talanta
https://www.readbyqxmd.com/read/28411223/modified-bacteriophage-s16-long-tail-fiber-proteins-for-rapid-and-specific-immobilization-and-detection-of-salmonella-cells
#14
Jenna M Denyes, Matthew Dunne, Stanislava Steiner, Maximilian Mittelviefhaus, Agnes Weiss, Herbert Schmidt, Jochen Klumpp, Martin J Loessner
Bacteriophage-based assays and biosensors rival traditional antibody-based immunoassays for detection of low-level Salmonella contaminations. In this study, we harnessed the binding specificity of the long tail fiber (LTF) from bacteriophage S16 as an affinity molecule for immobilization, enrichment, and detection of Salmonella We demonstrate that paramagnetic beads (MBs) coated with recombinant gp37-gp38 LTF complexes (LTF-MBs) are highly effective tools for rapid affinity magnetic separation and enrichment of Salmonella Within 45 minutes, the LTF-MBs consistently captured over 95% of Salmonella Typhimurium cells from suspensions containing 10-10(5) CFU...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28407593/assessing-the-influence-of-ocean-acidification-to-marine-amphipods-a-comparative-study
#15
M C Passarelli, I Riba, A Cesar, F Serrano-Bernando, T A DelValls
CO2 increases in the ocean may occur both by the capacity of CO2 exchanges with its dissolved form between atmosphere and surface seawater as well by CO2 leaks during the carbon capture and storage (CCS) process. The decrease in seawater pH may result in a reduction in the concentration of both hydroxide and carbonate (OH(-) and CO3(2-)). The main aim of this work is to conduct an ecotoxicology comparative survey using two amphipod species from Europe and Brazil exposed to different acidification (CO2) scenarios...
April 10, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28405403/niche-partitioning-and-the-role-of-intraspecific-niche-variation-in-structuring-a-guild-of-generalist-anurans
#16
Carl S Cloyed, Perri K Eason
Intra-population niche differences in generalist foragers have captured the interest of ecologists, because such individuality can have important ecological and evolutionary implications. Few researchers have investigated how these differences affect the relationships among ecologically similar, sympatric species. Using stable isotopes, stomach contents, morphology and habitat preference, we examined niche partitioning within a group of five anurans and determined whether variation within species could facilitate resource partitioning...
March 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28405008/targeted-enrichment-and-sequencing-of-recent-endosymbiont-host-lateral-gene-transfers
#17
Julie C Dunning Hotopp, Barton E Slatko, Jeremy M Foster
Lateral gene transfer (LGT) from microbial symbionts to invertebrate animals is described at an increasing rate, particularly between Wolbachia endosymbionts and their diverse invertebrate hosts. We sought to assess the use of a capture system to cost-effectively sequence such LGT from the host genome. The sequencing depth of Illumina paired end data obtained with a Wolbachia capture system correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depleted B. malayi (p-value: <2e-16)...
April 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28403214/antibody-independent-capture-of-circulating-tumor-cells-of-non-epithelial-origin-with-the-apostream%C3%A2-system
#18
Priya Balasubramanian, Robert J Kinders, Shivaani Kummar, Vishal Gupta, David Hasegawa, Anoop Menachery, Scott M Lawrence, Lihua Wang, Katherine Ferry-Galow, Darren Davis, Ralph E Parchment, Joseph E Tomaszewski, James H Doroshow
Circulating tumor cells (CTCs) are increasingly employed for research and clinical monitoring of cancer, though most current methods do not permit the isolation of non-epithelial tumor cells. Furthermore, CTCs isolated with antibody-dependent methods are not suitable for downstream experimental uses, including in vitro culturing and implantation in vivo. In the present study, we describe the development, validation, and transfer across laboratories of a new antibody-independent device for the enrichment of CTCs from blood samples of patients with various cancer diagnoses...
2017: PloS One
https://www.readbyqxmd.com/read/28402395/mzml2isa-nmrml2isa-generating-enriched-isa-tab-metadata-files-from-metabolomics-xml-data
#19
Martin Larralde, Thomas N Lawson, Ralf J M Weber, Pablo Moreno, Kenneth Haug, Philippe Rocca-Serra, Mark R Viant, Christoph Steinbeck, Reza M Salek
Summary: Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28402103/patient-derived-airway-secretion-dissociation-technique-to-isolate-and-concentrate-immune-cells-using-closed-loop-inertial-microfluidics
#20
Hyunryul Ryu, Kyungyong Choi, Yanyan Qu, Taehong Kwon, Janet S Lee, Jongyoon Han
Assessment of airway secretion cells, both for research and clinical purposes, is a highly desired goal in patients with acute and chronic pulmonary diseases. However, lack of proper cell isolation and enrichment techniques hinder downstream evaluation and characterization of cells found in airway secretions. Here, we demonstrate a novel enrichment method to capture immune-related cells from clinical airway secretions using closed-loop separation of spiral inertial microfluidics (C-sep). By recirculating the output focusing stream back to the input reservoir and running continuously with a high flow processing rate, one can achieve optimal concentration, recovery and purity of airway immune cells from a large volume of diluent, which was not readily possible in the single-pass operation...
April 21, 2017: Analytical Chemistry
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