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https://www.readbyqxmd.com/read/28813625/detection-of-first-line-drug-resistance-mutations-and-drug-protein-interaction-dynamics-from-tuberculosis-patients-in-south-india
#1
Somanna Ajjamada Nachappa, Sumana M Neelambike, Chokkanna Amruthavalli, Nallur B Ramachandra
Diagnosis of drug-resistant tuberculosis predominantly relies on culture-based drug susceptibility testing, which take weeks to produce a result and a more time-efficient alternative method is multiplex allele-specific PCR (MAS-PCR). Also, understanding the role of mutations in causing resistance helps better drug designing. AIMS: To evaluate the ability of MAS-PCR in the detection of drug resistance and to understand the mechanism of interaction of drugs with mutant proteins in Mycobacterium tuberculosis...
August 16, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28813618/whole-exome-sequencing-identifies-novel-variants-for-tooth-agenesis
#2
N Dinckan, R Du, L E Petty, Z Coban-Akdemir, S N Jhangiani, I Paine, E H Baugh, A P Erdem, H Kayserili, H Doddapaneni, J Hu, D M Muzny, E Boerwinkle, R A Gibbs, J R Lupski, Z O Uyguner, J E Below, A Letra
Tooth agenesis is a common craniofacial abnormality in humans and represents failure to develop 1 or more permanent teeth. Tooth agenesis is complex, and variations in about a dozen genes have been reported as contributing to the etiology. Here, we combined whole-exome sequencing, array-based genotyping, and linkage analysis to identify putative pathogenic variants in candidate disease genes for tooth agenesis in 10 multiplex Turkish families. Novel homozygous and heterozygous variants in LRP6, DKK1, LAMA3, and COL17A1 genes, as well as known variants in WNT10A, were identified as likely pathogenic in isolated tooth agenesis...
August 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28812769/multiplex-coaxial-flow-focusing-for-producing-multicompartment-janus-microcapsules-with-tunable-material-compositions-and-structural-characteristics
#3
Qiang Wu, Chaoyu Yang, Guangli Liu, Wanghuai Xu, Zhiqiang Zhu, Ting Si, Ronald X Xu
We propose a simple but efficient multiplex coaxial flow focusing (MCFF) process for single-step fabrication of multicompartment Janus microcapsules (MJMs) in a wide range of operating parameters. The produced MJMs consist of a multicompartmental core-shell structure with material compositions tunable in individual shell and core compartments. Potential applications of such a MJM agent are demonstrated in both benchtop and in vitro experiments. For the benchtop experiment, magnetic nanoparticles are loaded into one of the shell compartments and photopolymerized under ultraviolet light for controlled alignment and rotation of the microcapsules in a magnetic field...
August 16, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28812527/cytokine-concentrations-measured-by-multiplex-assays-in-canine-peripheral-blood-samples
#4
Kristen R Richter, Amirah N Nasr, Angela M Mexas
Cytokines are known to play important roles in a wide range of pathologic conditions spanning all organ systems in every species studied. As our knowledge of the physiology of individual cytokines expands and our ability to measure multiple cytokines in smaller biological samples increases, we gain more insight into the significance and function of each cytokine and the importance of cytokine networks. Previous studies that reported measurements of cytokine concentrations from serum or plasma in dogs with infectious, autoimmune, metabolic, endocrine, and neoplastic diseases yield an appreciation for the complexity of cytokine control and potential applications for cytokine measurements in the diagnosis, prognosis, and therapy of a variety of disease conditions...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/28812131/dna-degrades-during-storage-in-formalin-fixed-and-paraffin-embedded-tissue-blocks
#5
Alice Guyard, Alice Boyez, Anaïs Pujals, Cyrielle Robe, Jeanne Tran Van Nhieu, Yves Allory, Julien Moroch, Odette Georges, Jean-Christophe Fournet, Elie-Serge Zafrani, Karen Leroy
Formalin-fixed paraffin-embedded (FFPE) tissue blocks are widely used to identify clinically actionable molecular alterations or perform retrospective molecular studies. Our goal was to quantify degradation of DNA occurring during mid to long-term storage of samples in usual conditions. We selected 46 FFPE samples of surgically resected carcinomas of lung, colon, and urothelial tract, of which DNA had been previously extracted. We performed a second DNA extraction on the same blocks under identical conditions after a median period of storage of 5...
August 15, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28811337/first-person-dougall-norris
#6
(no author information available yet)
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Dougall Norris is co-first author on 'An improved Akt reporter reveals intra- and intercellular heterogeneity and oscillations in signal transduction', published in Journal of Cell Science. Dougall is a PhD student in the Metabolic Systems Biology Group at The University of Sydney Charles Perkins Centre in Australia, where his project focuses on live-cell imaging, multiplexing fluorescent constructs and imaging modalities, coupled with powerful computational analysis...
August 15, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28810879/quantification-of-mutant-spop-proteins-in-prostate-cancer-using-mass-spectrometry-based-targeted-proteomics
#7
Hui Wang, Christopher E Barbieri, Jintang He, Yuqian Gao, Tujin Shi, Chaochao Wu, Athena A Schepmoes, Thomas L Fillmore, Sung-Suk Chae, Dennis Huang, Juan Miguel Mosquera, Wei-Jun Qian, Richard D Smith, Sudhir Srivastava, Jacob Kagan, David G Camp, Karin D Rodland, Mark A Rubin, Tao Liu
BACKGROUND: Speckle-type POZ protein (SPOP) is an E3 ubiquitin ligase adaptor protein that functions as a potential tumor suppressor, and SPOP mutations have been identified in ~10% of human prostate cancers. However, it remains unclear if mutant SPOP proteins can be utilized as biomarkers for early detection, diagnosis, prognosis or targeted therapy of prostate cancer. Moreover, the SPOP mutation sites are distributed in a relatively short region with multiple lysine residues, posing significant challenges for bottom-up proteomics analysis of the SPOP mutations...
August 15, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28809910/enhanced-depth-of-field-of-an-integral-imaging-microscope-using-a-bifocal-holographic-optical-element-micro-lens-array
#8
Ki-Chul Kwon, Young-Tae Lim, Chang-Won Shin, Munkh-Uchral Erdenebat, Jae-Moon Hwang, Nam Kim
We propose and implement an integral imaging microscope with extended depth-of-field (DoF) using a bifocal holographic micro lens array (MLA). The properties of the two MLAs are switched via peristrophic multiplexing, where different properties of the MLA are recorded onto the single holographic optical element (HOE). The recorded MLA properties are perpendicular to each other: after the first mode is recorded, the HOE is rotated by 90° clockwise, and the second mode is recorded. The experimental results confirm that the DoF of the integral imaging microscopy system is extended successfully by using the bifocal MLA...
August 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28809898/analog-receiver-for-coherent-optical-analog-radio-over-fiber-transmission
#9
Bernhard Schrenk, Markus Hofer, Thomas Zemen
A receiver for low-cost coherent optical applications is presented. Conceptual simplicity is guaranteed through the use of a monolithic integrated externally modulated laser. Local oscillators and fast photodetectors are provided by the distributed feedback section and electro-absorption modulator of the monolithic laser. The injection-locking feature, which is obtained by virtue of the inline configuration of the receiver, guarantees exact frequency translation during coherent reception and obviates the need for digital signal processing typically employed for the purpose of signal recovery...
August 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28809890/tunable-photonic-radiofrequency-filter-with-complementary-bandpass-and-bandstop-responses
#10
Peixuan Li, Wei Pan, Xihua Zou, Lianshan Yan, Yan Pan
A photonic radiofrequency (RF) filter with two complementary bandpass and bandstop responses that is capable of simultaneously providing a single transmission channel at one port and a notch rejection channel at the other port is proposed. An integrated polarization division-multiplexing Mach-Zehnder modulator and the in-fiber stimulated Brillouin scattering effect are used to control the amplitudes and phases of the RF modulation sidebands along two orthogonal states of polarization to generate two complementary bandpass and bandstop responses at two output ports, respectively...
August 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28809889/two-stage-cross-talk-mitigation-in-an-orbital-angular-momentum-based-free-space-optical-communication-system
#11
Zhen Qu, Ivan B Djordjevic
We propose and experimentally demonstrate a two-stage cross-talk mitigation method in an orbital-angular-momentum (OAM)-based free-space optical communication system, which is enabled by combining spatial offset and low-density parity-check (LDPC) coded nonuniform signaling. Different from traditional OAM multiplexing, where the OAM modes are centrally aligned for copropagation, the adjacent OAM modes (OAM states 2 and -6 and OAM states -2 and 6) in our proposed scheme are spatially offset to mitigate the mode cross talk...
August 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28809773/a-macaque-model-for-rectal-lymphogranuloma-venereum-and-non-lymphogranuloma-venereum-chlamydia-trachomatis-impact-on-rectal-simian-human-immunodeficiency-virus-acquisition
#12
Sundaram Ajay Vishwanathan, Rachael D Aubert, Monica R Morris, Chunxia Zhao, Christi Philips, George M Khalil, Frank Deyounks, Kristen Kelley, Jana M Ritter, C Y Chen, Ellen N Kersh, Janet M McNicholl
BACKGROUND: Sustained genital tract inflammation caused by sexually transmitted infections (STIs) is known to increase risk of vaginal human immunodeficiency virus (HIV) infections but, to our knowledge, there are no nonhuman primate studies that have evaluated its link to rectal HIV acquisition. METHODS: Rhesus macaques inoculated with Chlamydia trachomatis (CT) (serovars LGV-L2 and CT-E; n = 7) or saline (n = 7) received up to 20 rectal challenges twice a week of simian/HIV immunodeficiency virus (SHIVSF162p3)...
September 2017: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/28809708/on-multiple-aer-handshaking-channels-over-high-speed-bit-serial-bidirectional-lvds-links-with-flow-control-and-clock-correction-on-commercial-fpgas-for-scalable-neuromorphic-systems
#13
Amirreza Yousefzadeh, Miroslaw Jablonski, Taras Iakymchuk, Alejandro Linares-Barranco, Alfredo Rosado, Luis A Plana, Steve Temple, Teresa Serrano-Gotarredona, Steve B Furber, Bernabe Linares-Barranco
Address event representation (AER) is a widely employed asynchronous technique for interchanging "neural spikes" between different hardware elements in neuromorphic systems. Each neuron or cell in a chip or a system is assigned an address (or ID), which is typically communicated through a high-speed digital bus, thus time-multiplexing a high number of neural connections. Conventional AER links use parallel physical wires together with a pair of handshaking signals (request and acknowledge). In this paper, we present a fully serial implementation using bidirectional SATA connectors with a pair of low-voltage differential signaling (LVDS) wires for each direction...
August 14, 2017: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/28809101/a-microsphere-supported-lipid-bilayer-platform-for-dna-reactions-on-a-fluid-surface
#14
Aurora Fabry-Wood, Madalyn Elise Fetrow, Carl W Brown Iii, Nicholas A Baker, Nadiezda Fernandez Oropeza, Andrew P Shreve, Gabriel A Montano, Darko Stefanovic, Matthew R Lakin, Steven W Graves
We report a versatile microsphere-supported lipid bilayer system that can serve as a general-purpose platform for implementing DNA nanotechnologies on a fluid surface. To demonstrate our platform, we implemented both toehold-mediated strand displacement (TMSD) and DNAzyme reactions, which are typically performed in solution and which are the cornerstone of DNA-based molecular logic and dynamic DNA nanotechnology, on the surface. We functionalized microspheres bearing supported lipid bilayers (µSLBs) with membrane-bound nucleic acid components...
August 15, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28808994/monitoring-dynamic-changes-of-the-cell-surface-glycoproteome-by-quantitative-proteomics
#15
Mathias Kalxdorf, Hans Christian Eberl, Marcus Bantscheff
The analysis of the cell surface accessible proteome provides invaluable information about cellular identity, cellular functions, and interactions. Cell surface labeling in combination with quantitative proteomics enables the unbiased identification and quantification of cell surface proteins. We describe a fast, efficient, and robust protocol for the enrichment of the N-linked plasma membrane glycoproteome and subsequent analysis by mass spectrometry. Precise and multiplexed quantification of relative changes of cell surface protein presentation is enabled by an isobaric labeling strategy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808993/multiplexed-liquid-chromatography-multiple-reaction-monitoring-mass-spectrometry-quantification-of-cancer-signaling-proteins
#16
Yi Chen, Kate J Fisher, Mark Lloyd, Elizabeth R Wood, Domenico Coppola, Erin Siegel, David Shibata, Yian A Chen, John M Koomen
Quantitative evaluation of protein expression across multiple cancer-related signaling pathways (e.g., Wnt/β-catenin, TGF-β, receptor tyrosine kinases (RTK), MAP kinases, NF-κB, and apoptosis) in tumor tissues may enable the development of a molecular profile for each individual tumor that can aid in the selection of appropriate targeted cancer therapies. Here, we describe the development of a broadly applicable protocol to develop and implement quantitative mass spectrometry assays using cell line models and frozen tissue specimens from colon cancer patients...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808128/conjugative-plasmid-transfer-in-xylella-fastidiosa-is-dependent-on-tra-and-trb-operon-functions
#17
Lindsey P Burbank, Christopher R Van Horn
The insect-transmitted plant pathogen Xylella fastidiosa is capable of efficient horizontal gene transfer (HGT) and recombination. Natural transformation occurs at high rates in X. fastidiosa, but there also is evidence that certain strains of X. fastidiosa carry native plasmids equipped with transfer and mobilization genes, suggesting conjugation as an additional mechanism of HGT in some instances. Two operons, tra and trb, putatively encoding a conjugative Type IV secretion system are found in some but not all X...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28808033/multiplex-quantitative-cellular-analysis-in-large-tissue-volumes-with-clearing-enhanced-3d-microscopy-ce3d
#18
Weizhe Li, Ronald N Germain, Michael Y Gerner
Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807549/a-multiplexed-microfluidic-toolbox-for-the-rapid-optimization-of-affinity-driven-partition-in-aqueous-two-phase-systems
#19
Eduardo J S Bras, Ruben R G Soares, Ana M Azevedo, Pedro Fernandes, Miguel Arévalo-Rodríguez, Virginia Chu, João P Conde, M Raquel Aires-Barros
Antibodies and other protein products such as interferons and cytokines are biopharmaceuticals of critical importance which, in order to be safely administered, have to be thoroughly purified in a cost effective and efficient manner. The use of aqueous two-phase extraction (ATPE) is a viable option for this purification, but these systems are difficult to model and optimization procedures require lengthy and expensive screening processes. Here, a methodology for the rapid screening of antibody extraction conditions using a microfluidic channel-based toolbox is presented...
August 5, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28807338/molecular-pathology-diagnosis-of-diffuse-large-b-cell-lymphoma-using-biomed-2-clonal-gene-rearrangements
#20
Saeid Ghorbian
BACKGROUND: Clonality testing for immunoglobulin gene rearrangement analysis could be implemented effectively as a useful technique for conventional diagnosis of lymphoma. The European Biomedicine and Health Concerted Action Project BMH4-CT98-3936 (BIOMED-2) have been suggested a gold standard method to clonality detection. OBJECTIVES: We tested empirically clonality rearrangements of IGH and incomplete IGH D-J, on formalin-fixed, paraffin embedded (FFPE) tissue of patients with diffuse large B cell lymphoma (DLBCL)...
August 2017: Annals of Diagnostic Pathology
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