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Статті в журналах з теми "Tag Probe"

Автор: Grafiati

Опубліковано: 10 березня 2023

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1

Lin, Jium Ming, and Po Kuang Chang. "A Novel Remote Health Monitor with Replaceable Non-Fragile Bio-Probes on RFID Tag." Applied Mechanics and Materials 145 (December 2011): 415–19. http://dx.doi.org/10.4028/www.scientific.net/amm.145.415.

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Анотація:

Conventional bio-probes are produced on a silicon substrate, they are not only fragile but unable to dispose according to the profile of human body in a large area manner, and thus the contact resistance between probe and skin may be increased. Besides, the signal processing devices are required to improve both S/N ratio and impedance matching problems. This paper proposes a novel remote human health monitor and an active RFID tag with replaceable non-frangible probes and thin-film-transistor (TFT) amplifiers. The probes are made of bio-degradable polymer (photo resist) and covered with bio-compatible TiN. In addition, we use two pieces of double sides conducting tapes to connect both TFT amplifiers and probe modules. Thus the probe module can be replaced easily by peeling the used probe module away from the double sides conducting tapes to supply a new one. Since the tag is a flexible plastic substrate, e, g. PT, PET and PI, so the probes are easier to deploy and conform to the human body profile. In addition, the signal can be amplified by the TFT amplifier nearby to improve both S/N ratio and impedance matching. Thus the human health conditions can be remotely monitored by measuring various acupuncture impedances via the active RFID tag. The active RFID monitoring range is 15m by using 2.45 GHz ISM band, the probe resistance and parasitic capacitance are as 2735 Ω and 60.7 pf, respectively. Since the typical human acupuncture point resistance is about 40-120KΩ, thus the proposed device and system can be applied.

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2

Xu, Hao, Hairat Sabit, Gordon L. Amidon, and H. D. Hollis Showalter. "An improved synthesis of a fluorophosphonate–polyethylene glycol–biotin probe and its use against competitive substrates." Beilstein Journal of Organic Chemistry 9 (January 15, 2013): 89–96. http://dx.doi.org/10.3762/bjoc.9.12.

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The fluorophosphonate (FP) moiety attached to a biotin tag is a prototype chemical probe used to quantitatively analyze and enrich active serine hydrolases in complex proteomes in an approach called activity-based protein profiling (ABPP). In this study we have designed a novel synthetic route to a known FP probe linked by polyethylene glycol to a biotin tag (FP–PEG–biotin). Our route markedly increases the efficiency of the probe synthesis and overcomes several problems of a prior synthesis. As a proof of principle, FP–PEG–biotin was evaluated against isolated protein mixtures and different rat-tissue homogenates, showing its ability to specifically target serine hydrolases. We also assessed the ability of FP–PEG–biotin to compete with substrates that have high enzyme turnover rates. The reduced protein-band intensities resulting in these competition studies demonstrate a new application of FP-based probes seldom explored before.

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3

Gupta, Vikram, Haoyue Shi, Kevin Gimpel, and Mrinmaya Sachan. "Deep Clustering of Text Representations for Supervision-Free Probing of Syntax." Proceedings of the AAAI Conference on Artificial Intelligence 36, no. 10 (June 28, 2022): 10720–28. http://dx.doi.org/10.1609/aaai.v36i10.21317.

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Анотація:

We explore deep clustering of multilingual text representations for unsupervised model interpretation and induction of syntax. As these representations are high-dimensional, out-of-the-box methods like K-means do not work well. Thus, our approach jointly transforms the representations into a lower-dimensional cluster-friendly space and clusters them. We consider two notions of syntax: Part of Speech Induction (POSI) and Constituency Labelling (CoLab) in this work. Interestingly, we find that Multilingual BERT (mBERT) contains surprising amount of syntactic knowledge of English; possibly even as much as English BERT (E-BERT). Our model can be used as a supervision-free probe which is arguably a less-biased way of probing. We find that unsupervised probes show benefits from higher layers as compared to supervised probes. We further note that our unsupervised probe utilizes E-BERT and mBERT representations differently, especially for POSI. We validate the efficacy of our probe by demonstrating its capabilities as a unsupervised syntax induction technique. Our probe works well for both syntactic formalisms by simply adapting the input representations. We report competitive performance of our probe on 45-tag English POSI, state-of-the-art performance on 12-tag POSI across 10 languages, and competitive results on CoLab. We also perform zero-shot syntax induction on resource impoverished languages and report strong results.

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4

Shen, Jingjing, Guan Liu, Wen Zhang, Wenwen Shi, Yang Zhou, Zejie Yu, Qunbo Mei, Lei Zhang, and Wei Huang. "Design and Detection of Cyanide Raman Tag pH-Responsive SERS Probes." Biosensors 13, no. 1 (December 25, 2022): 21. http://dx.doi.org/10.3390/bios13010021.

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As one of the most important parameters of biochemical analysis and detection, the pH value plays a very important role in cell function, food preservation and production, soil and water sources, and other applications. This makes it increasingly important to explore pH detection methods in depth. In this paper, a pH-responsive SERS probe based on the cyano Raman Tag was designed to realize pH sensing detection through the influence of the pH value of analytes on the displacement of the cyano Raman peak in the SERS probe. This cyano Raman tag exhibited not only excellent sensitivity in the liner range of pH 3.0–9.0 with a limit of detection (LOD) of pH 0.33, but also the anti-interference performance and stability (the relative standard deviation (RSD) was calculated to be 6.68%, n = 5). These results indicated that this pH SERS probe with the Raman cyano tag can provide new research ideas for future biological detection, bioimaging, and environmental detection.

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5

Takei, F., and K. Nakatani. "Fluorescence turn-on hairpin-probe PCR." Chemical Communications 53, no. 8 (2017): 1393–96. http://dx.doi.org/10.1039/c6cc08947j.

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A new fluorescence turn-on type of PCR monitoring system (Hpro-PCR) using a hairpin probe and a primer having a tag sequence at the 5′ end with the fluorescent molecule 2,7-diamino-1,8-naphthyridine derivative (DANP) has been developed.

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6

Qin, Qiu Yan, Yi Ping Qian, Zi Yu Wang, and Xiao Lin Fan. "Design and Synthesis of Fluorescent Betahistine Conjugates with Unique Imaging Property." Advanced Materials Research 557-559 (July 2012): 712–15. http://dx.doi.org/10.4028/www.scientific.net/amr.557-559.712.

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Анотація:

Labeling cardiovascular drugs probes with a fluorescent tag is an alternative method of measuring drugs activities and distributions in vivo, and further using of advanced tools to diagnose or detect cardiovascular diseases. Using this approach, a fluorescent probe (betahistine-Flu, 1) of Betahistine-based was synthesized and characterized by 1H NMR, 13C NMR and LC-MS, and its UV-Vis absorption spectral and fluorescence spectral, and fluorescence imaging in cell model were investigated. It was found that the fluorescent probe display strong green fluorescence, and have good optical effect in cell. This study reveals a good and interesting results of betahistine-directed fluorescent probe, and its may be a possible candidate for cardiovascular disease diagnosis and analysis in vivo.

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7

Faltin, Bernd, Simon Wadle, Günter Roth, Roland Zengerle, and Felix von Stetten. "Mediator Probe PCR: A Novel Approach for Detection of Real-Time PCR Based on Label-Free Primary Probes and Standardized Secondary Universal Fluorogenic Reporters." Clinical Chemistry 58, no. 11 (November 1, 2012): 1546–56. http://dx.doi.org/10.1373/clinchem.2012.186734.

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Анотація:

BACKGROUND The majority of established techniques for monitoring real-time PCR amplification involve individual target-specific fluorogenic probes. For analysis of numerous different targets the synthesis of these probes contributes to the overall cost during assay development. Sequence-dependent universal detection techniques overcome this drawback but are prone to detection of unspecific amplification products. We developed the mediator probe PCR as a solution to these problems. METHODS A set of label-free sequence-specific primary probes (mediator probes), each comprising a target-specific region and a standardized mediator tag, is cleaved upon annealing to its target sequence by the polymerases' 5′ nuclease activity. Release of a mediator triggers signal generation by cleavage of a complementary fluorogenic reporter probe. RESULTS Real-time PCR amplification of human papillomavirus 18 (HPV18), Staphylococcus aureus, Escherichia coli, and Homo sapiens DNA dilution series showed exceptional linearity when detected either by novel mediator probes (r2 = 0.991–0.999) or state-of-the-art hydrolysis probes (TaqMan probes) (r2 = 0.975–0.993). For amplification of HPV18 DNA the limits of detection were 78.3 and 85.1 copies per 10-μL reaction when analyzed with the mediator probe and hydrolysis probe, respectively. Duplex amplification of HPV18 target DNA and internal standard had no effects on back calculation of target copy numbers when quantified with either the mediator probe PCR (r2 = 0.998) or the hydrolysis probe PCR (r2 = 0.988). CONCLUSIONS The mediator probe PCR has equal performance to hydrolysis probe PCR and has reduced costs because of the use of universal fluorogenic reporters.

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8

Burgess, William C. "The bioacoustic probe: A general‐purpose acoustic recording tag." Journal of the Acoustical Society of America 108, no. 5 (November 2000): 2583. http://dx.doi.org/10.1121/1.4743598.

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9

Soejima, Mikiko, and Yoshiro Koda. "Fluorescence Melting Curve Analysis for Concurrent Genotyping of Three Tag SNPs in FUT3." Diagnostics 12, no. 12 (December 4, 2022): 3039. http://dx.doi.org/10.3390/diagnostics12123039.

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The synthesis of Lewis blood group antigens is governed by two fucosyltransferase genes, FUT2 and FUT3. Evidence is accumulating to suggest that functional polymorphisms of FUT2 and FUT3 are associated with a variety of clinical conditions. Fluorescence melting curve analysis (FMCA), using three different dual-labeled probes for concurrent genotyping of three single nucleotide polymorphisms (SNPs) of FUT3, c.59T>G, c.314C>T, and c.484G>A for Lewis-negative allele inference, was developed and validated using Ghanaian and Caucasian subjects. Although two other SNPs, c.55G>A, and c.61C>T, are located in the probe sequence for c.59T>G, it seems feasible to detect these two SNPs along with c.59T>G. The results obtained by probe-based FMCA were in perfect accordance with those obtained by Sanger sequencing for 106 Ghanaians and 100 Caucasians. The present method is useful and reliable for estimating Lewis-negative alleles on a relatively large scale.

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10

Jung, Kwan Ho, Matthew Fares, Leeann S. Grainger, Charles H. Wolstenholme, Anna Hou, Yu Liu, and Xin Zhang. "A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede." Organic & Biomolecular Chemistry 17, no. 7 (2019): 1906–15. http://dx.doi.org/10.1039/c8ob01483c.

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11

Fales, Andrew M., Pietro Strobbia, Tuan Vo-Dinh, Ilko K. Ilev, and T. Joshua Pfefer. "3D-printed phantoms for characterizing SERS nanoparticle detectability in turbid media." Analyst 145, no. 18 (2020): 6045–53. http://dx.doi.org/10.1039/d0an01295e.

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12

Leng, Shuang, Qinglong Qiao, Lu Miao, Wuguo Deng, Jingnan Cui, and Zhaochao Xu. "A wash-free SNAP-tag fluorogenic probe based on the additive effects of quencher release and environmental sensitivity." Chemical Communications 53, no. 48 (2017): 6448–51. http://dx.doi.org/10.1039/c7cc01483j.

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13

Wang, Zhipeng, Xiaozhe Ding, Sijian Li, Jing Shi, and Yiming Li. "Engineered fluorescence tags for in vivo protein labelling." RSC Adv. 4, no. 14 (2014): 7235–45. http://dx.doi.org/10.1039/c3ra46991c.

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14

Ma, Junyan, Yaoyu Xu, Wen Zhao, Beibei Wang, Chunhuan Zhang, and Zhenxing Zhang. "Rapid detection of thioredoxin reductase with a fluorescent probe via a Tag-Sec method." Materials Chemistry Frontiers 5, no. 23 (2021): 8108–17. http://dx.doi.org/10.1039/d1qm01254a.

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15

Zhang, Xiaodong, Zhiwei Ye, Xinfu Zhang, Huizi Man, Zhenlong Huang, Ning Li, and Yi Xiao. "A targetable fluorescent probe for dSTORM super-resolution imaging of live cell nucleus DNA." Chemical Communications 55, no. 13 (2019): 1951–54. http://dx.doi.org/10.1039/c8cc08575g.

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16

Kamikawa, Yuko, Yuichiro Hori, Kazuo Yamashita, Lin Jin, Shinya Hirayama, Daron M. Standley, and Kazuya Kikuchi. "Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins." Chemical Science 7, no. 1 (2016): 308–14. http://dx.doi.org/10.1039/c5sc02351c.

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17

Reja, Shahi Imam, Yuichiro Hori, Takuya Kamikawa, Kohei Yamasaki, Miyako Nishiura, Steven D. Bull, and Kazuya Kikuchi. "An “OFF–ON–OFF” fluorescence protein-labeling probe for real-time visualization of the degradation of short-lived proteins in cellular systems." Chemical Science 13, no. 5 (2022): 1419–27. http://dx.doi.org/10.1039/d1sc06274c.

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18

Zhong, Dongbo. "An ALOHA-Based Algorithm Based on Grouping of Tag Prefixes for Industrial Internet of Things." Security and Communication Networks 2022 (April 13, 2022): 1–8. http://dx.doi.org/10.1155/2022/1812670.

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Анотація:

Nowadays, radio frequency identification (RFID) technology has been widely used in logistics, warehousing, urban transportation, medicine, and other fields due to its advantages of fast identification speed, low cost, and high security. The multitag collision problem causes the reader to fail to complete the identification of the tags in its coverage in time, thus seriously affecting the work efficiency of the entire RFID system. Therefore, the study of an efficient multitag identification algorithm is the basic premise to ensure the industrial application of RFID. Aiming at the problems of the low slot utilization rate of the existing DFSA algorithm in a large-scale tag recognition environment, we proposed a dynamic frame slotting anticollision algorithm based on tags prefix grouping called G-DFSA. G-DFSA uses the tag prefix to recognize the tag set and constructs the probe frame based on the grouping. Then, the slot statistics results of the probe frame are used to process the frames whose frame length does not match the number of tags. As shown in the simulation results, the system efficiency of the proposed algorithm is still close to the theoretical optimal throughput rate of DFSA algorithm 0.368 in the large-scale tag set. Compared with the existing methods, G-DFSA has obvious advantages in system throughput.

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19

Goh, J., A. Fagot, M. Gul, C. Roskas, M. Tytgat, N. Zaganidis, S. Fonseca De Souza, et al. "CMS RPC efficiency measurement using the tag-and-probe method." Journal of Instrumentation 14, no. 10 (October 15, 2019): C10020. http://dx.doi.org/10.1088/1748-0221/14/10/c10020.

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20

Yitzhak, Yonit, Hanmant Gaikwad, Tommy Weiss-Sadan, Emmanuelle Merquiol, Boris Turk, and Galia Blum. "Improved Cathepsin Probes for Sensitive Molecular Imaging." Molecules 27, no. 3 (January 27, 2022): 842. http://dx.doi.org/10.3390/molecules27030842.

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Анотація:

Cysteine cathepsin proteases are found under normal conditions in the lysosomal compartments of cells, where they play pivotal roles in a variety of cellular processes such as protein and lipid metabolism, autophagy, antigen presentation, and cell growth and proliferation. As a consequence, aberrant localization and activity contribute to several pathologic conditions such as a variety of malignancies, cardiovascular diseases, osteoporosis, and other diseases. Hence, there is a resurgence of interest to expand the toolkit to monitor intracellular cathepsin activity and better ascertain their functions under these circumstances. Previous fluorescent activity-based probes (ABPs) that target cathepsins B, L, and S enabled detection of their activity in intact cells as well as non-invasive detection in animal disease models. However, their binding potency is suboptimal compared to the cathepsin inhibitor on which they were based, as the P1 positive charge was capped by a reporter tag. Here, we show the development of an improved cathepsin ABP that has a P1 positive charge by linking the tag on an additional amino acid at the end of the probe. While enhancing potency towards recombinant cathepsins, the new probe had reduced cell permeability due to additional peptide bonds. At a second phase, the probe was trimmed; the fluorophore was linked to an extended carbobenzoxy moiety, leading to enhanced cell permeability and superb detection of cathepsin activity in intact cells. In conclusion, this work introduces a prototype design for the next generation of highly sensitive ABPs that have excellent detection of cellular cathepsin activity.

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21

Lin, Jium-Ming, Po-Kuang Chang, and Zhong-Qing Hou. "INTEGRATING MICROARRAY PROBES AND AMPLIFIER ON AN ACTIVE RFID TAG FOR BIOSENSING AND MONITOR SYSTEM DESIGN." Biomedical Engineering: Applications, Basis and Communications 21, no. 06 (December 2009): 421–25. http://dx.doi.org/10.4015/s1016237209001556.

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Анотація:

This research provides a microarray bio-probe device, integrated with Thin-Film-Transistor (TFT) amplifier formed of top-gate MOS (Metal-Oxide Semiconductor) transistors on an active RFID tag, to improve the signal-to-noise (S/N) ratio and impedance matching problems. The bio-probe device can be disposed to conform to the profile of a living body's portion so as to improve the electrical contact property.

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22

Zhang, Yun, Fang Liu, Jinfang Nie, Fuyang Jiang, Caibin Zhou, Jiani Yang, Jinlong Fan, and Jianping Li. "An electrochemical sensing platform based on local repression of electrolyte diffusion for single-step, reagentless, sensitive detection of a sequence-specific DNA-binding protein." Analyst 139, no. 9 (2014): 2193–98. http://dx.doi.org/10.1039/c4an00096j.

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This paper describes for the first time an electrochemical biosensor, which employs a DNA probe modified with a redox tag close to electrode surface, for picomolar detection of a sequence-specific DNA-binding protein.

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23

Faltin, Bernd, Roland Zengerle, and Felix von Stetten. "Current Methods for Fluorescence-Based Universal Sequence-Dependent Detection of Nucleic Acids in Homogenous Assays and Clinical Applications." Clinical Chemistry 59, no. 11 (November 1, 2013): 1567–82. http://dx.doi.org/10.1373/clinchem.2013.205211.

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Анотація:

BACKGROUND Specific and sensitive nucleic acid (NA) testing in research and clinical diagnostics is usually performed by use of labeled oligonucleotide probes. However, the use of target-specific fluorogenic probes increases the cost of analysis. Therefore, universal sequence-dependent (USD) NA detection methods have been developed to facilitate cost-effective target detection using standardized reagents. CONTENT We provide a comprehensive review of the current methods for fluorescence-based USD NA detection. Initially, we focus on the emergence of these methods as a means to overcome the shortcomings of common NA detection methods, such as hydrolysis probes and molecular beacons. Thereafter, we provide a critical evaluation of the individual detection methods. These methods include (a) target amplification with bipartite primers introducing a universal detection tag to the amplicon (UniPrimer PCR, universal fluorescence energy transfer probe PCR, attached universal duplex probe PCR, and universal strand displacement amplification) or combined with bipartite probes comprising a universal detection region (mediator probe PCR, universal strand displacement amplification, universal quenching probe PCR) and (b) amplification-independent assays employing either a universal variant of the invader assay or universal NA hybridization sensors. We discuss differences between the methods and review clinical applications. SUMMARY The current methods for USD NA testing are cost-effective and flexible and have concordant analytical performance in comparison with common probe-based techniques. They can detect any target sequence by the simple use of a label-free, low-cost primer or probe combined with a universal fluorogenic reporter. The methods differ in the number of target specificities, capability of multiplexing, and incubation requirements (isothermal/thermocycling). Extensive clinical applications comprise detection of single-nucleotide polymorphisms, study of gene expression, in situ PCR, and quantification of pathogen load.

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24

Bell, Jessica L., Andrew J. Haak, Susan M. Wade, Yihan Sun, Richard R. Neubig, and Scott D. Larsen. "Design and synthesis of tag-free photoprobes for the identification of the molecular target for CCG-1423, a novel inhibitor of the Rho/MKL1/SRF signaling pathway." Beilstein Journal of Organic Chemistry 9 (May 21, 2013): 966–73. http://dx.doi.org/10.3762/bjoc.9.111.

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Анотація:

CCG-1423 and related analogues represent a new class of inhibitors of Rho/MKL1/SRF-mediated gene transcription, a pathway that has been implicated in both cancer and fibrosis. The molecular target for these compounds is unknown. To facilitate its identification, a series of tag-free photoaffinity probes was designed and synthesized, each one containing a photoactivatable group and an acetylenic end group for subsequent attachment to a fluorescent tag using click chemistry. All were confirmed to maintain biological activity in a cell-based assay for inhibition of SRE-Luc expression. The functional activity of the most potent probe 24 was further confirmed in an assay for PC-3 cell migration. Photolysis of 24 in intact PC-3 cells followed by cell lysis, click ligation of a fluorescent dye, and gel electrophoresis revealed specific labeling of a single 24 kDa band that could be blocked with an active competitor. Future work will focus on identifying the labeled protein(s).

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25

Canady, Taylor D., Nantao Li, Lucas D. Smith, Yi Lu, Manish Kohli, Andrew M. Smith, and Brian T. Cunningham. "Digital-resolution detection of microRNA with single-base selectivity by photonic resonator absorption microscopy." Proceedings of the National Academy of Sciences 116, no. 39 (September 9, 2019): 19362–67. http://dx.doi.org/10.1073/pnas.1904770116.

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Circulating exosomal microRNA (miR) represents a new class of blood-based biomarkers for cancer liquid biopsy. The detection of miR at a very low concentration and with single-base discrimination without the need for sophisticated equipment, large volumes, or elaborate sample processing is a challenge. To address this, we present an approach that is highly specific for a target miR sequence and has the ability to provide “digital” resolution of individual target molecules with high signal-to-noise ratio. Gold nanoparticle tags are prepared with thermodynamically optimized nucleic acid toehold probes that, when binding to a target miR sequence, displace a probe-protecting oligonucleotide and reveal a capture sequence that is used to selectively pull down the target-probe–nanoparticle complex to a photonic crystal (PC) biosensor surface. By matching the surface plasmon-resonant wavelength of the nanoparticle tag to the resonant wavelength of the PC nanostructure, the reflected light intensity from the PC is dramatically and locally quenched by the presence of each individual nanoparticle, enabling a form of biosensor microscopy that we call Photonic Resonator Absorption Microscopy (PRAM). Dynamic PRAM imaging of nanoparticle tag capture enables direct 100-aM limit of detection and single-base mismatch selectivity in a 2-h kinetic discrimination assay. The PRAM assay demonstrates that ultrasensitivity (<1 pM) and high selectivity can be achieved on a direct readout diagnostic.

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26

Lin, Jiarun, Marcus E. Graziotto, Peter A. Lay, and Elizabeth J. New. "A Bimodal Fluorescence-Raman Probe for Cellular Imaging." Cells 10, no. 7 (July 5, 2021): 1699. http://dx.doi.org/10.3390/cells10071699.

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Анотація:

Biochemical changes in specific organelles underpin cellular function, and studying these changes is crucial to understand health and disease. Fluorescent probes have become important biosensing and imaging tools as they can be targeted to specific organelles and can detect changes in their chemical environment. However, the sensing capacity of fluorescent probes is highly specific and is often limited to a single analyte of interest. A novel approach to imaging organelles is to combine fluorescent sensors with vibrational spectroscopic imaging techniques; the latter provides a comprehensive map of the relative biochemical distributions throughout the cell to gain a more complete picture of the biochemistry of organelles. We have developed NpCN1, a bimodal fluorescence-Raman probe targeted to the lipid droplets, incorporating a nitrile as a Raman tag. NpCN1 was successfully used to image lipid droplets in 3T3-L1 cells in both fluorescence and Raman modalities, reporting on the chemical composition and distribution of the lipid droplets in the cells.

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27

Yano, Yoshiaki, and Katsumi Matsuzaki. "Tag–probe labeling methods for live-cell imaging of membrane proteins." Biochimica et Biophysica Acta (BBA) - Biomembranes 1788, no. 10 (October 2009): 2124–31. http://dx.doi.org/10.1016/j.bbamem.2009.07.017.

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28

Thompson, Andrew, Mark Prescott, Noorhan Chelebi, John Smith, Tom Brown, and Günter Schmidt. "Electrospray ionisation-cleavable tandem nucleic acid mass tag–peptide nucleic acid conjugates: synthesis and applications to quantitative genomic analysis using electrospray ionisation-MS/MS." Nucleic Acids Research 35, no. 4 (December 9, 2006): e28-e28. http://dx.doi.org/10.1093/nar/gkl1123.

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Abstract The synthesis and characterization of isotopomer tandem nucleic acid mass tag–peptide nucleic acid (TNT–PNA) conjugates is described along with their use as electrospray ionisation-cleavable (ESI-Cleavable) hybridization probes for the detection and quantification of target DNA sequences by electrospray ionisation tandem mass spectrometry (ESI-MS/MS). ESI-cleavable peptide TNT isotopomers were introduced into PNA oligonucleotide sequences in a total synthesis approach. These conjugates were evaluated as hybridization probes for the detection and quantification of immobilized synthetic target DNAs using ESI-MS/MS. In these experiments, the PNA portion of the conjugate acts as a hybridization probe, whereas the peptide TNT is released in a collision-based process during the ionization of the probe conjugate in the electrospray ion source. The cleaved TNT acts as a uniquely resolvable marker to identify and quantify a unique target DNA sequence. The method should be applicable to a wide variety of assays requiring highly multiplexed, quantitative DNA/RNA analysis, including gene expression monitoring, genetic profiling and the detection of pathogens.

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29

Schaefer, Kurt M., and Daniel W. Fuller. "Comparative Performance of Current-generation Geolocating Archival Tags." Marine Technology Society Journal 40, no. 1 (March 1, 2006): 15–28. http://dx.doi.org/10.4031/002533206787353673.

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The performances of the current-generation Lotek Wireless LTD2310 and the Wildlife Computers Mk9 geolocating archival tags were compared. The depth, temperature, and light level sensors of 15 LTD 2310 and 15 Mk9 archival tags were evaluated through hydrocasts of these, along with a calibrated Sea-Bird SBE39 temperature and depth probe, to nearly 500 m. Three experiments were conducted; each included five archival tags of each type simultaneously deployed in hydrocasts, along with the SBE39 probe. In all three experiments, the average differences between depth sensors on the Mk9 archival tags and the SBE39 were significantly greater than those between the LTD2310 archival tags and the probe depths for the hydrocast stops at about 500 m, 300 m, and 200 m. The standard errors about the average depth values for those hydrocast stops in Experiments 1 and 2, were greater for the LTD2310 tags, but for Experiment 3 the standard errors were greater for the Mk9 tags. The average differences between the LTD2310 and Mk9 archival tag temperatures measured by their stalk sensors and the SBE39 probe temperatures were similar in all three experiments over a temperature range of from about 9° to 27° C. The standard errors about the average temperature values were similar in all three experiments. The temperatures recorded by the Mk9 archival tag body temperature sensors lagged significantly, while those of the LTD2310 sensors were close to the temperatures recorded by the SBE39 probe during descents and ascents. The standard errors about the average tag body temperature values in all three experiments are greater for the Mk9 tags. Following the stabilization of light sensors at maximum depths (about 500 m) and darkness, during the three hydrocast ascents the 15 LTD2310 and 15 Mk9 archival tag light sensors indicated an average sensitivity to light at 440 m and 380 m, respectively. Two separate experiments conducted with archival tags implanted in the peritoneal cavity of tunas provided estimates of the accuracy and precision of geolocation based on ambient light level data. The computed distances between the average estimated geolocations, from three LTD2310 and three Mk9 archival tags recovered from captive yellowfin tuna Thunnus albacares, to the tank location (7°25'N-80°10'W) were 43.7 nm and 32.1 nm, respectively. The computed distances between the average estimated geolocations, from 13 LTD2310 and 15 Mk9 archival tags from bigeye tuna Thunnus obesus, released and recovered in association with a moored buoy, to the actual buoy location (1°59'S-95°11'W) were 118.5 nm (1.975 dd) and 162.8 nm (2.713 dd), respectively.

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30

Cameron, M. L., P. Levy, T. Nutman, C. R. Vanamala, P. R. Narayanan, and T. V. Rajan. "Use of restriction fragment length polymorphisms (RFLPs) to distinguish between nematodes of pathogenic significance." Parasitology 96, no. 2 (April 1988): 381–90. http://dx.doi.org/10.1017/s0031182000058364.

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SummaryThe availability of restriction fragment length polymorphisms (RFLPs) would be useful for studying the extent of diversity among morphologically indistinguishable populations of filarial parasites. Such polymorphisms may be useful in correlating various physiological and clinical differences with parasite heterogeneity. In order to identify such RFLPs, we isolated DNA from microfilaria of 6 filarial species (Acanthocheilonema viteae, Brugia malayi, Brugia pahangi, Dirofilaria immitis, Litomosoides carinii and Setaria digitatum), digested the DNA with several restriction endonucleases, prepared Southern blots and probed with 32P-labelled DNA probes. The patterns of fragments generated using two restriction endonucleases, Mbo I and Tag I, in combination with two probes, rDNA from the free-living soil nematode Cenorhabditis elegans, and pBM103, an anonymous DNA probe from B. malayi, unequivocally distinguish between all 6 of the species. To ensure that the differences we observed between the species represent true interspecies variation rather than fortuitous individual variations we analysed DNA from several individual B. malayi and B. pahangi worms. The individual B. malayi worms demonstrated restriction profiles that were invariant, as did the individual B. pahangi worms, demonstrating that the differences we observed were true interspecies variations.

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31

Yuce, Meral, Hasan Kurt, and Hikmet Budak. "Characterization of a dual biotin tag for improved single stranded DNA production." Anal. Methods 6, no. 2 (2014): 548–57. http://dx.doi.org/10.1039/c3ay41899e.

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Generation of single-stranded DNA plays a key role in many biotechnology applications including production of aptamers, single strand conformation polymorphism, nuclease S1 mapping, pyrosequencing, genosensors, probe preparation and labelling, subtractive hybridization as well as nucleic acid sensing and microarrays.

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32

Su, Jian, Zhengguo Sheng, Guangjun Wen, and Victor C. M. Leung. "A Time Efficient Tag Identification Algorithm Using Dual Prefix Probe Scheme (DPPS)." IEEE Signal Processing Letters 23, no. 3 (March 2016): 386–89. http://dx.doi.org/10.1109/lsp.2016.2516768.

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33

Uchinomiya, Shohei, Akio Ojida, and Itaru Hamachi. "Peptide Tag/Probe Pairs Based on the Coordination Chemistry for Protein Labeling." Inorganic Chemistry 53, no. 4 (October 16, 2013): 1816–23. http://dx.doi.org/10.1021/ic401612z.

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34

LI, Peijia, Yong HUANG, Min FAN, Haitao LI, Zhenghao ZHANG, and Cheng CHENG. "Compensation for time-tag bias of Doppler measurement from Chang'e-3 probe." SCIENTIA SINICA Informationis 50, no. 12 (October 20, 2020): 1932. http://dx.doi.org/10.1360/ssi-2019-0279.

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35

Mayer, Timo, and Martin E. Maier. "Design and Synthesis of a Tag-Free Chemical Probe for Photoaffinity Labeling." European Journal of Organic Chemistry 2007, no. 28 (October 2007): 4711–20. http://dx.doi.org/10.1002/ejoc.200700188.

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36

Nomura, Wataru, Tomoaki Mino, Tetsuo Narumi, Nami Ohashi, Akemi Masuda, Chie Hashimoto, Hiroshi Tsutsumi, and Hirokazu Tamamura. "Development of crosslink-type tag-probe pairs for fluorescent imaging of proteins." Biopolymers 94, no. 6 (2010): 843–52. http://dx.doi.org/10.1002/bip.21444.

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37

Saaidin, Aimi Suhaily, Yuta Murai, Takuya Ishikawa, and Kenji Monde. "Design and Synthesis of Ligand-Tag Exchangeable Photoaffinity Probe Utilizing Nosyl Chemistry." European Journal of Organic Chemistry 2019, no. 46 (December 3, 2019): 7563–67. http://dx.doi.org/10.1002/ejoc.201901348.

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38

Dong, Hao, Jieqi Kang, James Schafer, and Aura Ganz. "Android-Based Visual Tag Detection for Visually Impaired Users." International Journal of E-Health and Medical Communications 5, no. 1 (January 2014): 63–80. http://dx.doi.org/10.4018/ijehmc.2014010104.

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In this paper the authors introduce PERCEPT-V indoor navigation for the blind system. PERCEPT-V enhances PERCEPT system by enabling visually impaired users to navigate in open indoor spaces that differ in size and lighting conditions. The authors deploy visual tags in the environment at specific landmarks and introduce a visual tag detection algorithm using a sampling probe and cascading approach. The authors provide guidelines for the visual tag size, which is a function of various environmental, and usage scenarios, which differ in lighting, dimensions of the indoor environment and angle of usage. The authors also developed a Smartphone based user interface for the visually impaired users that uses Android accessibility features.

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39

Lubin, Arica A., Brook Vander Stoep Hunt, Ryan J. White, and Kevin W. Plaxco. "Effects of Probe Length, Probe Geometry, and Redox-Tag Placement on the Performance of the Electrochemical E-DNA Sensor." Analytical Chemistry 81, no. 6 (March 15, 2009): 2150–58. http://dx.doi.org/10.1021/ac802317k.

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40

Marcsisin, Sean R., Cary Liptak, Jason Marineau, James E. Bradner, and John R. Engen. "Tag and Capture Flow Hydrogen Exchange Mass Spectrometry with a Fluorous-Immobilized Probe." Analytical Chemistry 87, no. 12 (May 29, 2015): 6349–56. http://dx.doi.org/10.1021/acs.analchem.5b01220.

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41

Nakashima, Sayaka, Zhe Liu, Yuya Yamaguchi, Shunya Saiki, Shintaro Munemasa, Toshiyuki Nakamura, Yoshiyuki Murata, and Yoshimasa Nakamura. "A novel tag-free probe for targeting molecules interacting with a flavonoid catabolite." Biochemistry and Biophysics Reports 7 (September 2016): 240–45. http://dx.doi.org/10.1016/j.bbrep.2016.06.020.

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42

Kato, Akio. "High-density fluorescence in situ hybridization signal detection on barley (Hordeum vulgare L.) chromosomes with improved probe screening and reprobing procedures." Genome 54, no. 2 (February 2011): 151–59. http://dx.doi.org/10.1139/g10-098.

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The barley ( Hordeum vulgare L.) genome was screened to identify sequences that could be used for fluorescence in situ hybridization (FISH). From 2000 transformed bacterium colonies carrying barley clones, 56 colonies were selected on the basis of the patterns that their PCR products produced when subjected to agarose gel electrophoresis. Among them, 42 (75%) exhibited fluorescent signals on barley chromosomes after in situ hybridization using the directly labeled PCR products. Sequencing revealed seven clones, pHv-365, pHv-177, pHv-1112, pHv-689, pHv-1476, pHv-1889, and pHv-1972, to be newly identified FISH-positive sequences. The remainder possess previously described sequences such as 5S, GAA microsatellite, centromere repeats, HVT01, and pHvMWG2315 (324 bp repeat). It is shown here that a combination of five probes, which produce strong signals on barley chromosomes, pHv-38 (5S), pHv-365, pHv-961 (HVT01), GAA, and TAG microsatellites, offer unequivocal recognition of each chromosome. The combination of three probes, i.e., pHv-1123 (barley 324 bp repeat), GAA, and TAG, decorated entire chromosomes with fine dotted signals and was useful for detecting the break points of aberrant chromosomes. The signals’ distributions of pHv-177, pHv-1112, and TAG were highly polymorphic. An improved reprobing procedure and its usefulness are also discussed.

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43

Fujisaki, Kiyotaka. "Performance evaluation of table type RFID reader for library automatic book identification." International Journal of Web Information Systems 16, no. 1 (October 10, 2019): 65–78. http://dx.doi.org/10.1108/ijwis-10-2018-0076.

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Purpose The purpose of this paper is to evaluate the performance of table type radio frequency identification (RFID) reader and verify the effect of the use of a parasitic element on the table type RFID reader to increase the communication performance and improve the automatic identification of books in the library. Design/methodology/approach In this study, the authors observe the magnetic field at each point on the reader by using a small probe antenna and evaluate the reading performance of table type RFID reader at each point on the reader by using a RFID tag. Furthermore, to increase the communication performance, they add a parasitic element on the table type RFID reader and evaluate its usefulness. Findings The power distribution on the table type RFID reader and the communication performance of the table type REID reader were clearly shown. From the experiments of the magnetic field observation, when the coil surface of a tag is put in the parallel with the antenna plane of the reader, the tag can obtain electric power from the reader most effectively. Furthermore, by using a loop coil between the reader and the tag as a parasitic element, the points where communication is enabled with tag increased as the number of turns of coil increased. Originality/value In this research work, the author clearly showed the table type RFID reader’s performance by experiment. Moreover, to increase the communication performance, the author proposed to add a parasitic element to the table type RFID leader.

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44

Luijkx, Yvette M. C. A., Anniek J. Henselijn, Gerlof P. Bosman, Dario A. T. Cramer, Koen C. A. P. Giesbers, Esther M. van ‘t Veld, Geert-Jan Boons та ін. "Detection of Bacterial α-l-Fucosidases with an Ortho-Quinone Methide-Based Probe and Mapping of the Probe-Protein Adducts". Molecules 27, № 5 (28 лютого 2022): 1615. http://dx.doi.org/10.3390/molecules27051615.

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Fucosidases are associated with several pathological conditions and play an important role in the health of the human gut. For example, fucosidases have been shown to be indicators and/or involved in hepatocellular carcinoma, breast cancer, and helicobacter pylori infections. A prerequisite for the detection and profiling of fucosidases is the formation of a specific covalent linkage between the enzyme of interest and the activity-based probe (ABP). The most commonly used fucosidase ABPs are limited to only one of the classes of fucosidases, the retaining fucosidases. New approaches are needed that allow for the detection of the second class of fucosidases, the inverting type. Here, we report an ortho-quinone methide-based probe with an azide mini-tag that selectively labels both retaining and inverting bacterial α-l-fucosidases. Mass spectrometry-based intact protein and sequence analysis of a probe-labeled bacterial fucosidase revealed almost exclusive single labeling at two specific tryptophan residues outside of the active site. Furthermore, the probe could detect and image extracellular fucosidase activity on the surface of live bacteria.

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45

Li, Yuxia, and Zhinan Zhou. "RFID Anti-Collision Detection Algorithm Based on Improved Adaptive N-Tree." International Journal of Online Engineering (iJOE) 14, no. 10 (October 26, 2018): 129. http://dx.doi.org/10.3991/ijoe.v14i10.9310.

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<p style="margin: 1em 0px;"><span style="font-family: Times New Roman; font-size: medium;">This paper proposes a type of improved adaptive N-tree anti-collision algorithm based on the traditional one for RFID system by combination with maximum likelihood estimation and probe pre-detection. This algorithm inherits some features from Alpha- and tree-based anti-collision algorithms and effectively restrain the star-vation of the two algorithms. It has also filled in the gaps of tag collision with higher probability. The study turns out that the improved adaptive N-tree anti-collision algorithm as proposed can feature adaptive choice of the value N of the tree, length breaks of free timeslots, restraints on defects such as more tag classification and higher collision probability just as what the traditional tree-based algorithm has. N-tree built by level-to-level frame identification eliminates the free timeslots, and improves the tag identification precision for the RFID system. The results from simulation experiment reveal that the algorithm proposed in this paper has lower Error Sampling Reckon (ESR) and Throughput Rate Deviation (TRD), and features large throughput rate (87%), low delay of tag recognition and minimum timeslots, and etc. hence to be better applied in large-scale logistics and other fields where fast information recognition is involved.</span></p>

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46

Doh, Julia K., Jonathan D. White, Hannah K. Zane, Young Hwan Chang, Claudia S. López, Caroline A. Enns, and Kimberly E. Beatty. "VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy." Proceedings of the National Academy of Sciences 115, no. 51 (December 5, 2018): 12961–66. http://dx.doi.org/10.1073/pnas.1808626115.

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Many discoveries in cell biology rely on making specific proteins visible within their native cellular environment. There are various genetically encoded tags, such as fluorescent proteins, developed for fluorescence microscopy (FM). However, there are almost no genetically encoded tags that enable cellular proteins to be observed by both FM and electron microscopy (EM). Herein, we describe a technology for labeling proteins with diverse chemical reporters, including bright organic fluorophores for FM and electron-dense nanoparticles for EM. Our technology uses versatile interacting peptide (VIP) tags, a class of genetically encoded tag. We present VIPER, which consists of a coiled-coil heterodimer formed between the genetic tag, CoilE, and a probe-labeled peptide, CoilR. Using confocal FM, we demonstrate that VIPER can be used to highlight subcellular structures or to image receptor-mediated iron uptake. Additionally, we used VIPER to image the iron uptake machinery by correlative light and EM (CLEM). VIPER compared favorably with immunolabeling for imaging proteins by CLEM, and is an enabling technology for protein targets that cannot be immunolabeled. VIPER is a versatile peptide tag that can be used to label and track proteins with diverse chemical reporters observable by both FM and EM instrumentation.

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47

Xiaoyu Liu, J. L. Berger, A. Ogirala, and M. H. Mickle. "A Touch Probe Method of Operating an Implantable RFID Tag for Orthopedic Implant Identification." IEEE Transactions on Biomedical Circuits and Systems 7, no. 3 (June 2013): 236–42. http://dx.doi.org/10.1109/tbcas.2012.2201258.

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48

Yano, Yoshiaki, Akiko Yano, Shinya Oishi, Yukihiko Sugimoto, Gozoh Tsujimoto, Nobutaka Fujii, and Katsumi Matsuzaki. "Coiled-Coil Tag−Probe System for Quick Labeling of Membrane Receptors in Living Cells." ACS Chemical Biology 3, no. 6 (June 2008): 341–45. http://dx.doi.org/10.1021/cb8000556.

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49

Qiao, Qinglong, Wenjuan Liu, Jie Chen, Wei Zhou, Wenting Yin, Lu Miao, Jingnan Cui, and Zhaochao Xu. "A naphthalimide-derived fluorogenic probe for SNAP-tag with a fast record labeling rate." Dyes and Pigments 147 (December 2017): 327–33. http://dx.doi.org/10.1016/j.dyepig.2017.08.032.

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50

Xu, Yang, Roman Holic, Darren Li, Xue Pan, Elzbieta Mietkiewska, Guanqun Chen, Jocelyn Ozga та Randall J. Weselake. "Substrate preferences of long-chain acyl-CoA synthetase and diacylglycerol acyltransferase contribute to enrichment of flax seed oil with α-linolenic acid". Biochemical Journal 475, № 8 (30 квітня 2018): 1473–89. http://dx.doi.org/10.1042/bcj20170910.

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Seed oil from flax (Linum usitatissimum) is enriched in α-linolenic acid (ALA; 18:3Δ9cis,12cis,15cis), but the biochemical processes underlying the enrichment of flax seed oil with this polyunsaturated fatty acid are not fully elucidated. Here, a potential process involving the catalytic actions of long-chain acyl-CoA synthetase (LACS) and diacylglycerol acyltransferase (DGAT) is proposed for ALA enrichment in triacylglycerol (TAG). LACS catalyzes the ATP-dependent activation of free fatty acid to form acyl-CoA, which in turn may serve as an acyl-donor in the DGAT-catalyzed reaction leading to TAG. To test this hypothesis, flax LACS and DGAT cDNAs were functionally expressed in Saccharomyces cerevisiae strains to probe their possible involvement in the enrichment of TAG with ALA. Among the identified flax LACSs, LuLACS8A exhibited significantly enhanced specificity for ALA over oleic acid (18:1Δ9cis) or linoleic acid (18:2Δ9cis,12cis). Enhanced α-linolenoyl-CoA specificity was also observed in the enzymatic assay of flax DGAT2 (LuDGAT2-3), which displayed ∼20 times increased preference toward α-linolenoyl-CoA over oleoyl-CoA. Moreover, when LuLACS8A and LuDGAT2-3 were co-expressed in yeast, both in vitro and in vivo experiments indicated that the ALA-containing TAG enrichment process was operative between LuLACS8A- and LuDGAT2-3-catalyzed reactions. Overall, the results support the hypothesis that the cooperation between the reactions catalyzed by LACS8 and DGAT2 may represent a route to enrich ALA production in the flax seed oil.

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