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Aloma L D'Souza, John R Chevillet, Pejman Ghanouni, Xinrui Yan, Muneesh Tewari, Sanjiv S Gambhir
We have previously shown that low frequency ultrasound can release biomarkers from cells into the murine circulation enabling an amplification and localization of the released biomarker that could be used as a blood-based method to detect cancer earlier and monitor therapy. In this study, we further demonstrate that this technique could be used for characterization of tumors and/or identification of cellular masses of unknown origin due to the release of multiple protein and nucleic acid biomarkers in cells in culture, mice and patients...
2018: PloS One
Elena García-Payá, Marta Fernández, Sergio Padilla, José A García, Catalina Robledano, Victoria Ortiz DE LA Tabla, Félix Gutiérrez, Mar Masiá
OBJECTIVE: The protective effect of ART has not yet been definitively established in men who have sex with men (MSM). We aimed to characterize the factors associated with persistent HIV-1 RNA rectal shedding. METHODS: Prospective study including virologically-suppressed MSM from an HIV cohort. High-resolution anoscopy (HRA) was performed for screening of anal dysplasia, and rectal sampling for HIV-1 RNA quantification and sexually-transmitted infections (STIs) investigation through multiplex PCR...
March 15, 2018: AIDS
Xianhua Wang, Aiguo Ma, Xiuxia Han, Aishan Litifu, Feng Xue
Seven single-nucleotide polymorphism (SNP) sites located in ASAP1 gene have been found associated with tuberculosis (TB) susceptibility by genome-wide association studies in Russia. The case-control study was carried out to test whether these seven SNPs were associated with susceptibility to TB in a Chinese Xinjiang Muslim population. The seven SNPs were genotyped in a case-control design that included 780 Xinjiang Muslim subjects (400 TB patients and 380 controls). Multiplex PCR and direct sequencing were used to detect ASAP1 gene polymorphisms...
April 2018: Experimental and Therapeutic Medicine
Amy M Bittel, Ashley M Davis, Lei Wang, Michel A Nederlof, Jorge O Escobedo, Robert M Strongin, Summer L Gibbs
Multicolor microscopy tools necessary to localize and visualize the complexity of subcellular systems are limited by current fluorophore technology. While commercial fluorophores cover spectral space from the ultraviolet to the near infrared region and are optimized for conventional bandpass based fluorescence microscopy, they are not ideal for highly multiplexed fluorescence microscopy as they tend to have short Stokes shifts, restricting the number of fluorophores that can be detected in a single sample to four to five...
March 15, 2018: Scientific Reports
Alexander B Rosenberg, Charles M Roco, Richard A Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas Gray, David J Peeler, Sumit Mukherjee, Wei Chen, Suzie H Pun, Drew L Sellers, Bosiljka Tasic, Georg Seelig
To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. Over 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation...
March 15, 2018: Science
M-A Dagnelie, A Khammari, B Dréno, S Corvec
BACKGROUND: The Gram-positive, anaerobic-aerotolerant bacterium Cutibacterium acnes is a commensal of human healthy skin, subdivided into six main phylogenetic groups or phylotypes: IA1, IA2, IB, IC, II and III. To decipher how far C. acnes specific subgroups are involved in disease physiopathology, different molecular typing methods have been developed to identify these subgroups (i.e. phylotypes, clonal complexes, SLST-types). However, as there were several molecular typing methods developed over the last decade, comparing the results from one article to another became a difficult task...
March 12, 2018: Clinical Microbiology and Infection
Louise Wogelred, Fredrik Höök, Björn Agnarsson, Peter Sjövall
Accurate detection and quantification of individual molecules is important for the development of improved diagnostic methods as well as biochemical characterization of disease progression and treatments. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a surface analysis technique capable of imaging the distribution of specific molecules on surfaces with a high spatial resolution (<1 μm) and high sensitivity. ToF-SIMS is particularly suitable for detection of molecules up to ∼2 kDa, including lipids, whereas larger molecules, such as peptides and proteins, are fragmented during analysis, which makes them difficult to identify...
March 15, 2018: Biointerphases
Monica Raina, Amber M Bates, Carol L Fischer, Ann Progulske-Fox, Taher Abbasi, Shireen Vali, Kim A Brogden
BACKGROUND: Matrix metalloproteinases (MMPs) are zinc- or calcium-dependent proteinases involved in normal maintenance of extracellular matrix. When elevated, they contribute to the tissue destruction seen in periodontal disease. Recently, we found that human beta defensin 3 (HBD3), a cationic antimicrobial peptide, alters chemokine and proinflammatory cytokine responses in human myeloid dendritic cells exposed to Porphyromonas gingivalis hemagglutinin B (HagB). In this study, the hypotheses that HagB induces MMP production in dendritic cells and that HBD3 mixed with HagB prior to treatment alters HagB-induced MMP profiles were tested...
March 2018: Journal of Periodontology
Marco Pio La Manna, Valentina Orlando, Paolo Li Donni, Guido Sireci, Paola Di Carlo, Antonio Cascio, Francesco Dieli, Nadia Caccamo
We used the Luminex Bead Array Multiplex Immunoassay to measure cytokines, chemokines and growth factors responses to the same antigens used for RD1-based Interferon γ Release Assay (IGRA) test. Seventy-nine individuals, 27 active TB, 32 latent infection subsets, 20 individuals derivative purified protein (PPD) negative (subjects that do not have any indurative cutaneous reaction after 72 hrs of intradermal injection of PPD) and with other pulmonary disease were retrospectively studied. Forty-eight analytes were evaluated by Luminex Assay in plasma obtained from whole blood stimulated cells...
2018: PloS One
Teklab Gebregiworgis, Christopher Boyd Marshall, Tadateru Nishikawa, Nikolina Radulovich, María-José Sandi, Zhenhao Fang, Robert Rottapel, Ming-Sound Tsao, Mitsuhiko Ikura
Small GTPases (sGTPases) are critical switch-like regulators that mediate several important cellular functions and are often mutated in human cancers. They are activated by guanine nucleotide exchange factors (GEFs), which specifically catalyze the exchange of GTP for GDP. GEFs coordinate signaling networks in normal cells, and are frequently deregulated in cancers. sGTPase signaling pathways are complex and interconnected; however, most GEF assays do not reveal such complexity. In this communication, we describe the development of a unique real-time NMR-based multiplexed GEF assay that employs distinct isotopic labeling schemes for each sGTPase protein to enable simultaneous observation of six proteins of interest...
March 15, 2018: Journal of the American Chemical Society
Amado M Velázquez-Benítez, K Yanín Guerra-Santillán, Raúl Caudillo-Viurquez, J Enrique Antonio-López, Rodrigo Amezcua-Correa, Juan Hernández-Cordero
We demonstrate a simple approach based on a photonic lantern spatial-mode multiplexer and a few-mode fiber for optical and manipulation of multiple microspheres. Selective generation of linearly polarized (LP) fiber modes provides light patterns useful for trapping one or multiple microparticles. Furthermore, rotation of the particles can be achieved by switching between degenerate LP modes, as well as through polarization rotation of the input light. Our results show that emerging fiber optic devices such as photonic lanterns can provide a versatile and compact means for developing optical fiber traps...
March 15, 2018: Optics Letters
Thalía Domínguez Bucio, Ali Z Khokhar, Goran Z Mashanovich, Frederic Y Gardes
We report the design and fabrication of a compact angled multimode interferometer (AMMI) on a 600 nm thick N-rich silicon nitride platform (n=1.92) optimized to match the International Telecommunication Union coarse wavelength division (de)multiplexing standard in the O telecommunication band. The demonstrated device exhibited a good spectral response with Δλ=20  nm, BW3 dB ∼11  nm, IL<1.5  dB, and XT∼20  dB. Additionally, it showed a high tolerance to dimensional errors <120  pm/nm and low sensitivity to temperature variations <20  pm/°C, respectively...
March 15, 2018: Optics Letters
Michael Kolano, Benedict Gräf, Stefan Weber, Daniel Molter, Georg von Freymann
We demonstrate a polarization-multiplexed, single-laser system for terahertz (THz) time-domain spectroscopy without an external delay line. The fiber laser emits two pulse trains with independently adjustable repetition rates, utilizing only one laser-active section and one pump diode. With a standard fiber-coupled THz setup and a polarization-multiplexed optical amplifier, we are able to measure transients with a spectral bandwidth of 1.5 THz and a dynamic range of 50 dB in a measurement time of 1 s. Based on the novel laser architecture, we call this new approach single-laser polarization-controlled optical sampling, or SLAPCOPS...
March 15, 2018: Optics Letters
Jacob W P Potuijt, Martijn Baas, Rivka Sukenik-Halevy, Hannie Douben, Picard Nguyen, Deon J Venter, Renée Gallagher, Sigrid M Swagemakers, Steven E R Hovius, Christianne A van Nieuwenhoven, Robert-Jan H Galjaard, Peter J van der Spek, Nadav Ahituv, Annelies de Klein
PurposeThe zone of polarizing activity regulatory sequence (ZRS) is an enhancer that regulates sonic hedgehog during embryonic limb development. Recently, mutations in a noncoding evolutionary conserved sequence 500 bp upstream of the ZRS, termed the pre-ZRS (pZRS), have been associated with polydactyly in dogs and humans. Here, we report the first case of triphalangeal thumb-polysyndactyly syndrome (TPT-PS) to be associated with mutations in this region and show via mouse enhancer assays how this mutation leads to ectopic expression throughout the developing limb bud...
March 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Carina Strell, Markus M Hilscher, Navya Laxman, Jessica Svedlund, Chenglin Wu, Chika Yokota, Mats Nilsson
Single-cell transcriptomics provides us with completely new insights into the molecular diversity of different cell-types and the different states they can adopt. The technique generates inventories of cells that constitute the building blocks of multicellular organisms. However, since the method requires isolation of discrete cells, information about the original location within tissue is lost. Therefore, it is not possible to draw detailed cellular maps of tissue architecture and their positioning in relation to other cells...
March 14, 2018: FEBS Journal
Kotoe Iesato, Tsukasa Hori, Yuko Yoto, Masaki Yamamoto, Natsuko Inazawa, Kenichi Kamo, Hiroshi Ikeda, Satoshi Iyama, Naoki Hatakeyama, Akihiro Iguchi, Junichi Sugita, Ryoji Kobayashi, Nobuhiro Suzuki, Hiroyuki Tsutsumi
BACKGROUND: Patients undergoing hematopoietic stem cell transplantation (HSCT) frequently experience HHV-6 reactivation typically during early phase following HSCT. However, the long-term clinical complications and prognosis among such patients remain unclear. METHODS: Between September 2010 and October 2012, whole blood samples from 105 patients collected weekly from prior to 6 weeks after HSCT underwent multiplex polymerase chain reaction (PCR) to screen for viral DNA, followed by real-time PCR for quantitative estimation...
March 14, 2018: Pediatrics International: Official Journal of the Japan Pediatric Society
Sumire Terasawa, Asuka Kato, Haruki Nishizawa, Takema Kato, Hikari Yoshizawa, Yoshiteru Noda, Jun Miyazaki, Mayuko Ito, Takao Sekiya, Takuma Fujii, Hiroki Kurahashi
Thanatophoric dysplasia (TD) and achondroplasia (ACH) are allelic disorders caused by a constitutively active mutation in the FGFR3 gene. Because TD is a lethal disorder and ACH is non-lethal, they need to be distinguished after ultrasound identification of fetal growth retardation with short limbs. Accordingly, we have developed a noninvasive prenatal test using cell-free fetal DNA in the maternal circulation to distinguish TD and ACH. A multiplex PCR system encompassing five mutation hotspots in the FGFR3 gene allowed us to efficiently identify the responsible mutation in cell-free DNA in all examined pregnancies with a suspected TD or ACH fetus...
March 14, 2018: Congenital Anomalies
Xuan Zhang, Xiaohan Sun
We propose a time division multiplexing passive optical network (TDM-PON) monitoring scheme based on the optical pulse width modulation (OPWM) by using a simple asymmetric loop (AL) located near the optical network unit (ONU). Various pulse widths can be easily obtained by configuring the appropriate length of the patchcord used to generate the path difference between two branches of a 1 × 2 splitter. Different wavelengths can be assigned to the same pulse width, which can further increase the network size...
March 14, 2018: Scientific Reports
Maximilian Bielohuby, Martin Bidlingmaier, Uwe Schwahn
The measurement of circulating hormones by immunoassay remains a cornerstone in preclinical endocrine research. For scientists conducting and interpreting immunoassay measurements of rodent samples, the paramount aim usually is to obtain reliable and meaningful measurement data in order to draw conclusions on biological processes. However, the biological variability between samples is not the only variable affecting the readout of an immunoassay measurement and a considerable amount of unwanted or unintended variability can be quickly introduced during the pre-analytical and analytical phase...
March 14, 2018: Endocrine Connections
Shan Wei, Zachary R Weiss, Zev Williams
Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples' genomic DNA in under three hours, including library preparation and sequencing...
March 14, 2018: G3: Genes—Genomes—Genetics
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