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Analytical Chemistry

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https://www.readbyqxmd.com/read/29791134/identification-of-yth-domain-containing-proteins-as-the-readers-for-n1-methyladenosine-in-rna
#1
Xiaoxia Dai, Tianlu Wang, Gwendolyn Gonzalez, Yinsheng Wang
N1-methyladenosine (m1 A) is an important post-transcriptional modification in RNA; however, the exact biological role of m1 A remains to be determined. By employing a quantitative proteomics method, we identified multiple putative protein readers of m1 A in RNA, including several YTH domain family proteins. We showed that YTHDF1-3 and YTHDC1, but not YTHDC2, could bind directly to m1 A in RNA. We also found that Trp432 in YTHDF2, a conserved residue in the hydrophobic pocket of the YTH domain that is necessary for its binding to N6 -methyladenosine (m6 A), is required for its recognition of m1 A...
May 25, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792811/tandem-mass-spectrometry-of-peptide-ions-by-microwave-excited-hydrogen-and-water-plasmas
#2
Yuji Shimabukuro, Hidenori Takahashi, Shinichi Iwamoto, Koichi Tanaka, Motoi Wada
A thermal cracking cell that served as the atomic hydrogen source for hydrogen attachment/abstraction dissociation (HAD) analysis has an intrinsic problem to produce a beam of atoms reactive against heated tungsten capillary. A plasma excited by 2.45 GHz microwave power can deliver reactive species to a quadrupole ion trap confining analyte ions without excessive heating of the radical source components. The radical (H•) production performance of the developed source was evaluated by optical emission spectroscopy and H• attachment reaction to fullerene ions...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792807/micelles-protect-intact-metallo-supramolecular-block-copolymer-complexes-from-solution-to-gas-phase-during-electrospray-ionization
#3
Kai Hung Huang, Tsung-Han Tu, Shi-Cheng Wang, Yi-Tsu Chan, Cheng-Chih Hsu
Supramolecular diblock copolymers using metal-ligand coordination can be synthesized under ambient conditions by delicate design of the end groups of the homopolymer chains. However, mass spectrometric analysis of such metallo-supramolecular copolymers is challenging. One of the reasons is the nonpolarity of the polymer chains, making it hard to disperse the complexes in electrospray ionization (ESI)-friendly environments. The other difficulty is the noncovalent nature of such copolymers, which is easily disrupted during the ionization...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792801/developing-a-novel-sulfoxide-containing-ms-cleavable-homobifunctional-cysteine-reactive-cross-linker-for-studying-protein-protein-interactions
#4
Craig B Gutierrez, Sarah A Block, Clinton Yu, Stephanie M Soohoo, Alexander S Huszagh, Scott D Rychnovsky, Lan Huang
Cross-linking mass spectrometry (XL-MS) has become an emerging technology for defining protein-protein interactions (PPIs) and elucidating architectures of large protein complexes. Up to now, the mostly widely used cross-linking reagents are targeting lysines. While such reagents have been successfully applied to map PPIs at the proteome-wide scale, comprehensive PPI profiling would require additional cross-linking chemistries. Cysteine is one of the most reactive amino acids and an attractive target for cross-linking owing to its unique role in protein structures...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792798/structural-analysis-of-phospholipid-using-hydrogen-abstraction-dissociation-and-oxygen-attachment-dissociation-in-tandem-mass-spectrometry
#5
Hidenori Takahashi, Yuji Shimabukuro, Daiki Asakawa, Shosei Yamauchi, Sadanori Sekiya, Shinichi Iwamoto, Motoi Wada, Koichi Tanaka
Gas-phase hydrogen radicals were introduced into a quadrupole ion trap containing singly charged phospholipids to obtain structural fragmentation patterns in tandem mass spectrometry (MS/MS). Saturated and unsaturated phosphatidylcholines were used as a model phospholipid, whose chain-length ranges between 16 and 24. The MS/MS spectrum yielded a continuous series of fragment ions with a mass differencesdifference of 14 Da, representing the saturated fatty acyl chains. The fragment ions corresponding to the double-bond position within a single fatty acyl chain showed thea characteristic mass difference of 12 Da...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792796/nano-lc-nsi-ms-refines-lipidomics-by-enhancing-lipid-coverage-measurement-sensitivity-and-linear-dynamic-range
#6
Niklas Danne-Rasche, Cristina Coman, Robert Ahrends
Nano-liquid chromatography (nLC) - nano-electrospray (NSI) is one of the cornerstones of mass spectrometry based bioanalytics. Nevertheless, the application of nLC is not prevailing lipid analyses so far. In this study, we established a reproducible nLC separation for global lipidomics and describe the merits of using such a miniaturized system for lipid analyses. In order to enable comprehensive lipid analyses that is not restricted to specific lipid classes, we particularly optimized sample preparation conditions and reversed phase separation parameters...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792706/adaptable-detection-strategies-in-membrane-based-immunoassays-calibration-free-quantitation-with-surface-enhanced-raman-scattering-readout
#7
Aleksander Skuratovsky, Robert J Soto, Marc D Porter
This paper presents a method for immunometric biomarker quantitation that uses standard flow-through assay reagents and obviates the need for constructing a calibration curve. The approach relies on a nitrocellulose immunoassay substrate with multiple physical addresses for analyte capture, each modified with different amounts of an analyte-specific capture antibody. As such, each address generates a distinctly different readout signal that is proportional to the analyte concentration in the sample. To establish the feasibility of this concept, equations derived from antibody-antigen binding equilibrium were first applied in modeling experiments...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792685/vertical-ultrafiltration-facilitated-dna-digestion-for-rapid-and-sensitive-uhplc-ms-ms-detection-of-dna-modifications
#8
Weiyi Lai, Cong Lyu, Hailin Wang
LC-MS/MS technologies provide important and powerful analytical tools for chemical structure-dependent identification and quantification of epigenetically crucial DNA modifications. To perform LC-MS/MS analysis, it is better to convert DNA to 2'-deoxynucleosides through enzymatic digestion. Here, we observed that inorganic cations Na+ and K+ and phosphate buffers, which were often found in various DNA solutions, significantly inhibited DNA digestion as catalyzed by typical set of DNase I, snake venom phosphodiesterase, and calf intestine alkaline phosphatase, leading to poor or varying performance on UHPLC-MS/MS analysis...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792684/label-free-optical-marker-for-rbc-phenotyping-of-inherited-anaemias
#9
Martina Mugnano, Pasquale Memmolo, Lisa Miccio, Francesco Merola, Vittorio Bianco, Alessia Bramanti, Antonella Gambale, Roberta Russo, Immacolata Andolfo, Achille Iolascon, Pietro Ferraro
The gold standard methods for anaemia diagnosis are the complete blood count and the peripheral smear observation. However, they do not allow for a complete differential diagnosis, which requires biochemical assays, thus being label-dependent techniques. On the other hand, recent studies focus on label-free quantitative phase imaging (QPI) of blood samples to investigate blood diseases by using video-based morphological methods. However, when sick cells are very similar to healthy ones in terms of morphometric features identification of a blood disease becomes challenging even by morphometric as well as QPI...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792683/top-down-deep-sequencing-of-ubiquitin-using-two-dimensional-mass-spectrometry
#10
Federico Floris, Lionel Chiron, Alice Lynch, Mark P Barrow, Marc-André Delsuc, Peter B O'Connor
Two-dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (2D FT-ICR MS or 2D MS) allows data independent fragmentation of all ions in a sample, and correlation of fragment ions to their precursors without isolation prior to fragmentation. Developments in computer capabilities and implementations in FTMS over of the last decade have allowed the technique to become a useful analytical tool for bottom-up proteomics (BUP), and more recently in top-down protein analysis (TDP). In this work, a new method of TDP is developed using two-dimensional mass spectrometry, called MS/2D FT-ICR MS or MS/2DMS...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792682/calix-4-arene-based-redox-sensitive-molecular-probe-for-sers-guided-recognition-of-labile-iron-pool-in-tumor-cells
#11
Padincharapad Sreedevi, Jyothi B Nair, Preethanuj Preethalayam, Benadicta S Jeeja, Cherumuttathu H Suresh, Kaustabh Kumar Maiti, Ramavarma Luxmi Varma
Targeting the intracellular 'labile' iron pool is turned as a key modulator for cancer progression since the former is responsible for several pathological processes in tumor cells. Herein, we report a non- fluorescent calix[4]arene based triazole appended molecular probe (PTBC) for redox-specific detection of Fe3+ under physiological condition by UV-vis, FT-IR, 1H NMR, HR-MS spectroscopies, ITC and the binding strategy between Calix[4]arene and Fe3+ was modeled by DFT calculations. As a new insight PTBC probe showed significant Raman fingerprint through surface enhanced Raman scattering (SERS) modality revealing the ultrasensitive detection of Fe3+ with a LOD of 2 nM...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792680/quantification-of-cellular-folate-species-by-lc-ms-after-stabilization-by-derivatization
#12
Matthias Schittmayer, Ruth Birner-Gruenberger, Nicola Zamboni
Folate cofactors play a key role in one-carbon metabolism. Analysis of individual folate species is hampered by the low chemical stability and high inter-convertibility of folates which can lead to severe experimental bias. Here we present a complete workflow that employs simultaneous extraction and stabilization of folates by derivatization. We perform reductive methylation employing stable isotope labelled reagents to retain information on position and redox state of one carbon units as well as the redox state of the pteridine ring...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792679/a-nanozyme-and-ambient-light-based-smartphone-platform-for-simultaneous-detection-of-dual-biomarkers-from-exposure-to-organophosphorus-pesticides
#13
Yuting Zhao, Mingming Yang, Qiangqiang Fu, Hui Ouyang, Wei Wen, Yang Song, Chengzhou Zhu, Yuehe Lin, Dan Du
A transparent, lateral-flow test strip coupled with a smartphone-based ambient light sensor was first proposed for detect-ing enzymatic inhibition and phosphorylation. The principle of the platform is based on the simultaneous measurement of the total amount of the enzyme and enzyme activity to biomonitor exposure to organophosphorus (OP) pesticides. In this study, butyrylcholinesterase (BChE) was adopted as the model enzyme and ethyl paraoxon was chosen as an analyte representing OP pesticides. The total amount of BChE was quantified by a sensitive colorimetric signal originating from a sandwich immunochromatographic assay utilizing PtPd nanoparticles as a polyphenol oxidase-mimicking probe, which provided a higher sensitivity than that of a peroxidase-like probe...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792326/common-principles-of-molecular-electronics-and-nanoscale-electrochemistry
#14
Paulo Roberto Bueno
The merging of nanoscale electronics and electrochemistry can potentially modernize the way electronic devices are currently engineered or constructed. It is well known that the greatest challenges will involve not only miniaturizing and improving the performance of mobile devices, but also manufacturing reliable electrical vehicles, and engineering more efficient solar panels and energy storage systems. These are just a few examples of how technological innovation is dependent on both electrochemical and electronic elements...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792323/cellular-beacons-mediated-counting-for-ultrasensitive-detection-of-ebola-virus-on-an-integrated-micromagnetic-platform
#15
Shao-Li Hong, Ya-Nan Zhang, Ya-Hua Liu, Man Tang, Dai-Wen Pang, Gary Wong, Jianjun Chen, Xiangguo Qiu, George F Gao, Wenjun Liu, Yuhai Bi, Zhi-Ling Zhang
Ebola virus (EBOV) disease is a complex zoonosis that is highly virulent in humans, and has caused many deaths. Highly sensitive detection of EBOV is of great importance to early-stage diagnosis for increasing the probability of survival. Herein, we established a cellular beacon-mediated counting strategy for ultrasensitive EBOV assay on a micromagnetic platform. The detection platform that was assisted by on-demand magnetic field manipulation showed high integration, and enhanced complex sample pretreatment ability by magnetophoretic separation and continuous flow washing...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792316/a-chemo-responsive-nanofluidic-pump-that-turns-off-in-the-presence-of-lead-ion
#16
Xiaojian Wu, Juliette Experton, Weihuang Xu, Charles R Martin
There are many applications that require the integration of a pump and a chemical sensor so that the solution being pumped can be analyzed in real time for a specific chemical species and the flow adjusted according to the measured concentration of that species. We describe here an alternative strategy - a chemo-responsive pump where a single device acts as both the sensor and pump simultaneously. We demonstrate this concept with a nanofluidic Pb2+ -responsive pump that uses electroosmotic flow (EOF) as the pumping technology, and a Pb2+ -binding ionophore that allows the device to selectively respond to Pb2+ ...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792032/a-tict-based-turn-on-fluorogenic-nano-probe-for-realtime-detection-of-serum-albumin-in-physiological-condition
#17
Soham Samanta, Senjuti Halder, Gopal Das
Two, cyanine based fluorescent probes L [(E)-2-(4-(diethylamino)-2-hydroxystyryl)-3-ethyl-1,1-dimethyl-1H-benzo[e]indol-3-ium iodide] and L1 [(E)-3-ethyl-1,1-dimethyl-2-(4-nitrostyryl)-1H-benzo[e]indol-3-ium iodide] have been designed and synthesized. Among these two probes; TICT (twisted intramolecular charge transfer) based probe L can preferentially self-assemble to form nanoaggregates. L displayed a selective TURN-ON fluorescence response towards HSA and BSA in ~100% aqueous PBS buffer medium which is noticeable through naked eye whereas L1 failed to sense these albumin proteins...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792027/fast-and-ultrasensitive-detection-of-a-nerve-agent-simulant-using-carbazole-based-nanofibers-with-amplified-ratiometric-fluorescence-responses
#18
Chunyan Sun, Wei Xiong, Wei Dong Ye, Yingxuan Zheng, Ran Duan, Yanke Che, Jincai Zhao
In this work, we report the fast and ultrasensitive detection of a nerve agent simulant in the gas phase, diethyl chloro-phosphate (DCP), by using carbazole-based nanofibers from 1. When exposed to trace DCP, the formed pyridine-phosphorylated product in 1 nanofibers can cause amplified ratiometric fluorescence responses, i.e., amplified fluores-cence quenching via quenching excitons within the diffusion length of 1 nanofibers and simultaneously amplified turn-on fluorescence responses via harvesting excitons within the diffusion length to give the intramolecular charge transfer (ICT) emission at a longer wavelength...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29737162/application-of-dna-machineries-for-the-barcode-patterned-detection-of-genes-or-proteins
#19
Zhixin Zhou, Guofeng Luo, Verena Wulf, Itamar Willner
The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29791795/surface-acoustic-wave-saw-driven-device-for-dynamic-cell-cultures
#20
Gina Greco, Matteo Agostini, Ilaria Tonazzini, Damiano Sallemi, Stefano Barone, Marco Cecchini
In the last decades new types of cell cultures have been introduced to provide better cell survival and development, and micro/nano-environmental physico-chemical conditions aimed to mimic those present in vivo. However, despite the efforts made, the systems available to date are often difficult to replicate and use. Here, an easy-to-use surface acoustic wave (SAW)-based platform is presented for realizing dynamic cell cultures that is compatible with standard optical microscopes, incubators and cell culture dishes...
May 23, 2018: Analytical Chemistry
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