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https://www.readbyqxmd.com/read/28296214/morphological-secondary-metabolite-and-its-rdna-variability-within-usnic-acid-containing-lichen-thalli-of-the-genus-xanthoparmelia-explored-at-the-local-scale-of-rock-outcrop-in-western-italian-alps
#1
Enrica Matteucci, Andrea Occhipinti, Rosanna Piervittori, Massimo E Maffei, Sergio E Favero-Longo
Lichen secondary metabolites (LSMs) are regarded with interest for valuable biological properties, but chemical variability among/within lichen taxa has been only fragmentarily characterized by advanced analytical techniques. Knowledge of variability at a local geographic scale has been particularly neglected, while it should address the collection of chemically homogeneous materials to test and exploit LSMs. Here we evaluated the chemical variability of 48 Xanthoparmelia specimens from two rock outcrops in Western Italian Alps, representative of nine morphotypes and sixteen rDNA ITS haplotypes...
March 11, 2017: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/28290446/live-cell-imaging-of-low-and-non-repetitive-chromosome-loci-using-crispr-cas9
#2
Peiwu Qin, Mahmut Parlak, Cem Kuscu, Jigar Bandaria, Mustafa Mir, Karol Szlachta, Ritambhara Singh, Xavier Darzacq, Ahmet Yildiz, Mazhar Adli
Imaging chromatin dynamics is crucial to understand genome organization and its role in transcriptional regulation. Recently, the RNA-guidable feature of CRISPR-Cas9 has been utilized for imaging of chromatin within live cells. However, these methods are mostly applicable to highly repetitive regions, whereas imaging regions with low or no repeats remains as a challenge. To address this challenge, we design single-guide RNAs (sgRNAs) integrated with up to 16 MS2 binding motifs to enable robust fluorescent signal amplification...
March 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28290315/inactivation-modeling-of-human-enteric-virus-surrogates-ms2-q%C3%AE-and-%C3%AE-x174-in-water-using-uvc-leds-a-novel-disinfecting-system
#3
Do-Kyun Kim, Soo-Ji Kim, Dong-Hyun Kang
In order to assure the microbial safety of drinking water, UVC-LED treatment has emerged as a possible technology to replace the use of conventional low pressure (LP) mercury vapor UV lamps. In this investigation, inactivation of Human Enteric Virus (HuEV) surrogates with UVC-LEDs was investigated in a water disinfection system, and kinetic model equations were applied to depict the surviving infectivities of the viruses. MS2, Qβ, and ΦX 174 bacteriophages were inoculated into sterile distilled water (DW) and irradiated with UVC-LED printed circuit boards (PCBs) (266nm and 279nm) or conventional LP lamps...
January 2017: Food Research International
https://www.readbyqxmd.com/read/28288812/preparation-of-ms2-based-nanoparticles-as-control-and-standard-materials-for-the-molecular-detection-of-dengue-virus-serotypes
#4
Yu Fu, Guojing Wang, Qisheng Wu, Xin Yang, Rui Zhang, Kuo Zhang, Guigao Lin, Yanxi Han, Lihua Bao, Ziyang Li, Jinming Li
To quantify dengue virus (DENV) and evaluate the performance of clinical laboratories using quantitative real-time polymerase chain reaction (qRT-PCR) assays, we constructed high-efficiency expression systems to produce DENV-1 to 4 nanoparticles and assessed their suitability as standard and control materials in 20 laboratories across China. Targeted gene sequences of DENV-1 to 4 were synthesized and inserted into pACYC-Duet 1-MS2 recombinant plasmids to generate corresponding nanoparticle expression systems...
March 10, 2017: Virus Research
https://www.readbyqxmd.com/read/28287711/rapid-identification-of-unknown-organic-iodine-in-small-volume-complex-biological-samples-based-on-nanospray-mass-spectrometry-coupled-with-in-tube-solid-phase-microextraction
#5
Qing Chang, Yue'e Peng, Lifen Yun, Qingxin Zhu, Shenghong Hu, Qin Shuai
A new method for rapid screening of unknown organic iodine (OI) in small-volume complex biological samples was developed using in-tube solid phase microextraction (SPME) nanospray mass spectrometry (MS). The method proposed a new identification scheme for OI based on nanospray high-resolution mass spectrometry (HR-MS). The mass ranges of OI ions were confirmed using the t-MS2 scan mode firstly; then, the possible precursor ions of OI were selected and identified orderly in full MS/ddMS2 and t-MS2 scan mode...
March 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28282563/inactivation-of-ms2-bacteriophage-by-titanium-dioxide-nanoparticles-in-the-presence-of-quartz-sand-with-and-without-ambient-light
#6
Vasiliki I Syngouna, Constantinos V Chrysikopoulos
Virus inactivation by nanoparticles (NPs) is hypothesized to affect virus fate and transport in the subsurface. This study examines the interactions of viruses with titanium dioxide (TiO2) anatase NPs, which is a good disinfectant with unique physiochemical properties. The bacteriophage MS2 was used as a model virus. A series of batch experiments of MS2 inactivation by TiO2 NPs were conducted at room temperature (25°C), in the presence and absence of quartz sand, with and without ambient light. Three sets of experiments were performed in phosphate buffered saline solution (PBS) and one in distilled deionized water (ddH2O)...
February 27, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28259077/assessment-of-the-efficacy-of-membrane-filtration-processes-to-remove-human-enteric-viruses-and-the-suitability-of-bacteriophages-and-a-plant-virus-as-surrogates-for-those-viruses
#7
N Shirasaki, T Matsushita, Y Matsui, K Murai
Here, we evaluated the efficacy of direct microfiltration (MF) and ultrafiltration (UF) to remove three representative human enteric viruses (i.e., adenovirus [AdV] type 40, coxsackievirus [CV] B5, and hepatitis A virus [HAV] IB), and one surrogate of human caliciviruses (i.e., murine norovirus [MNV] type 1). Eight different MF membranes and three different UF membranes were used. We also examined the ability of coagulation pretreatment with high-basicity polyaluminum chloride (PACl) to enhance virus removal by MF...
February 24, 2017: Water Research
https://www.readbyqxmd.com/read/28226246/improvement-of-virus-removal-by-pilot-scale-coagulation-ultrafiltration-process-for-wastewater-reclamation-effect-of-optimization-of-ph-in-secondary-effluent
#8
S Lee, M Ihara, N Yamashita, H Tanaka
Reclaimed water (i.e., reused advanced-treated wastewater) offers an alternative water resource. To reduce the health risks associated with its use, efficient virus removal such as with advanced wastewater treatment processes is important. Virus removal by coagulation followed by ultrafiltration (UF) for the treatment of drinking water has been well examined. But its efficacy in wastewater reclamation purpose using secondary treated effluent (SE) from wastewater treatment plant (WWTP) as feed water is unclear...
February 9, 2017: Water Research
https://www.readbyqxmd.com/read/28225587/compms2miner-an-automatable-metabolite-identification-visualization-and-data-sharing-r-package-for-high-resolution-lc-ms-datasets
#9
William Matthew Bell Edmands, Lauren M Petrick, Dinesh Kumar Barupal, Augustin Scalbert, Mark Wilson, Jeffrey Wickliffe, Stephen M Rappaport
A long-standing challenge of untargeted metabolomic profiling by ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) is efficient transition from unknown mass spectral features to confident metabolite annotations. The compMS2Miner (Comprehensive MS2 Miner) package was developed in the R language to facilitate rapid, comprehensive feature annotation using a peak-picker-output and MS2 data files as inputs. The number of MS2 spectra that can be collected during a metabolomic profiling experiment far outweigh the amount of time required for pain-staking manual interpretation, therefore a degree of software workflow autonomy is required for broad-scale metabolite annotation...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28221984/postharvest-reduction-of-coliphage-ms2-from-romaine-lettuce-during-simulated-commercial-processing-with-and-without-a-chlorine-based-sanitizer
#10
Samantha L Wengert, Tiong Gim Aw, Elliot T Ryser, Joan B Rose
Viral foodborne outbreaks are a serious threat to public health, and fresh produce is becoming increasingly recognized as a transmission vehicle. To limit foodborne disease, ready-to-eat leafy greens are typically washed with a chlorine-based sanitizer during commercial production. This study assessed the efficacy of a chlorine-based sanitizer against coliphage MS2, as a potential surrogate for foodborne viruses, on fresh-cut romaine lettuce during simulated commercial production using a small-scale processing line...
February 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28221934/effect-of-process-temperature-on-virus-inactivation-during-high-hydrostatic-pressure-processing-of-contaminated-fruit-puree-and-juice
#11
Hao Pan, Matthew Buenconsejo, Karl F Reineke, Y Carol Shieh
High pressure processing (HPP) can inactivate pathogens and retain fruit qualities. Elevated HPP pressure or time increases virus inactivation, but the effect of temperature is not consistently observed for norovirus and hepatitis A virus. In the present study, the effectiveness of HPP holding temperatures (<40°C) and pressures were evaluated for inactivating surrogates (murine norovirus [MNV] and MS2 coliphage) in pomegranate and strawberry juices and strawberry puree using a 24-liter HPP system. The holding temperature was established by setting the HPP initial temperature via pretrials...
September 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28219787/a-novel-archaeal-species-belonging-to-methanoculleus-genus-identified-via-de-novo-assembly-and-metagenomic-binning-process-in-biogas-reactors
#12
Panagiotis G Kougias, Stefano Campanaro, Laura Treu, Xinyu Zhu, Irini Angelidaki
Recently, a first comprehensive catalogue of microbial genomes populating biogas reactors treating manure and agro-industrial residues was determined by sequencing samples collected from 22 biogas reactors including laboratory and full scale. Among the archaeal community, one of the most abundant methanogens belongs to Methanoculleus genus and for this reason it was provisionally named Methanoculleus sp. DTU006. Its full length 16S rRNA sequence is 97% similar to Methanoculleus marisnigri JR1 and to Methanoculleus palmolei DSM 4273...
February 17, 2017: Anaerobe
https://www.readbyqxmd.com/read/28213279/tethering-rna-to-chromatin-for-fluorescence-microscopy-based-analysis-of-nuclear-organization
#13
Teresa Pankert, Thibaud Jegou, Maïwen Caudron-Herger, Karsten Rippe
Nuclear RNAs emerge as important factors to orchestrate the dynamic organization of the nucleus into functional subcompartments. By tethering RNAs to distinct genomic loci, the RNA-dependent chromatin changes can be dissected by fluorescence microscopic analysis. Here we describe how this approach is implemented in mammalian cells. It involves two high-affinity protein-nucleic acid interactions that can established with number of different protein domains and DNA and RNA sequences. A prototypic system is described here in detail: It consists of the binding of MS2 bacteriophage coat protein to its RNA recognition sequence and the interaction between the bacterial LacI repressor protein to its target lacO operator DNA sequences...
February 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28207247/ortho-methoxyphenols-as-convenient-oxidative-bioconjugation-reagents-with-application-to-site-selective-heterobifunctional-cross-linkers
#14
Adel M ElSohly, James I MacDonald, Nina B Hentzen, Ioana L Aanei, Kareem M El Muslemany, Matthew B Francis
The synthesis of complex protein-based bioconjugates has been facilitated greatly by recent developments in chemoselective methods for biomolecular modification. The oxidative coupling of o-aminophenols or catechols with aniline functional groups is chemoselective, mild, and rapid; however, the oxidatively sensitive nature of the electron-rich aromatics and the paucity of commercial sources pose some obstacles to the general use of these reactive strategies. Herein, we identify o-methoxyphenols as air-stable, commercially available derivatives that undergo efficient oxidative couplings with anilines in the presence of periodate as oxidant...
March 2, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28194965/extensive-peptide-fractionation-and-y1-ion-based-interference-detection-method-for-enabling-accurate-quantification-by-isobaric-labeling-and-mass-spectrometry
#15
Mingming Niu, Ji-Hoon Cho, Kiran Kodali, Vishwajeeth Pagala, Anthony A High, Hong Wang, Zhiping Wu, Yuxin Li, Wenjian Bi, Hui Zhang, Xusheng Wang, Wei Zou, Junmin Peng
Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from coisolated ions, resulting in ratio compression. Here we report that the ratio compression can be essentially resolved by the combination of pre-MS peptide fractionation, MS2-based interference detection, and post-MS computational interference correction. To recapitulate the complexity of biological samples, we pooled tandem mass tag (TMT)-labeled Escherichia coli peptides at 1:3:10 ratios and added in ∼20-fold more rat peptides as background, followed by the analysis of two-dimensional liquid chromatography (LC)-MS/MS...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28194953/click-chemistry-reagent-for-identification-of-sites-of-covalent-ligand-incorporation-in-integral-membrane-proteins
#16
Melissa M Budelier, Wayland W L Cheng, Lucie Bergdoll, Zi-Wei Chen, Jeff Abramson, Kathiresan Krishnan, Mingxing Qian, Douglas F Covey, James W Janetka, Alex S Evers
Identifying sites of protein-ligand interaction is important for structure-based drug discovery and understanding protein structure-function relationships. Mass spectrometry (MS) has emerged as a useful tool for identifying residues covalently modified by ligands. Current methods use database searches that are dependent on acquiring interpretable fragmentation spectra (MS2) of peptide-ligand adducts. This is problematic for identifying sites of hydrophobic ligand incorporation in integral membrane proteins (IMPs), where poor aqueous solubility and ionization of peptide-ligand adducts and collision-induced adduct loss hinder the acquisition of quality MS2 spectra...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193211/display-of-single-chain-variable-fragments-on-bacteriophage-ms2-virus-like-particles
#17
Christopher A Lino, Jerri C Caldeira, David S Peabody
BACKGROUND: Virus-like particles (VLPs) of the RNA bacteriophage MS2 have many potential applications in biotechnology. MS2 VLPs provide a platform for peptide display and affinity selection (i.e. biopanning). They are also under investigation as vehicles for targeted drug delivery, using display of receptor-specific peptides or nucleic acid aptamers to direct their binding to specific cell-surface receptors. However, there are few molecules more suited to the precise targeting and binding of a cellular receptor than antibodies...
February 13, 2017: Journal of Nanobiotechnology
https://www.readbyqxmd.com/read/28176989/variations-of-thermoelectric-performance-by-electric-fields-in-bilayer-mx2-m-w-mo-x-s-se
#18
Rui-Ning Wang, Guo-Yi Dong, Shu-Fang Wang, Guang-Sheng Fu, Jiang-Long Wang
A gate electrode is usually used to controllably tune the carrier concentrations, further modulating the electrical conductivity and the Seebeck coefficient to obtain the optimum thermoelectric figure of merit (ZT) in two-dimensional materials. On the other hand, it is necessary to investigate how an electric field induced by a gate voltage affects the electronic structures, further determining the thermoelectric properties. Therefore, by using density functional calculations in combination with Boltzmann theory, the thermoelectric properties of bilayer MX2 (M = W, Mo; X = S, Se) with or without a 1 V nm(-1) perpendicular electric field are comparatively investigated...
February 8, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28170237/size-matched-radical-multivalency
#19
Mark C Lipke, Tao Cheng, Yilei Wu, Hasan Arslan, Hai Xiao, Michael R Wasielewski, William A Goddard, J Fraser Stoddart
Persistent π-radicals such as MV(+•) (MV refers to methyl viologen, i.e., N,N'-dimethyl-4,4'-bipyridinum) engage in weak radical-radical interactions. This phenomenon has been utilized recently in supramolecular chemistry with the discovery that MV(+•) and [cyclobis(paraquat-p-phenylene)](2(+•)) (CBPQT(2(+•))) form a strong 1:1 host-guest complex [CBPQT⊂MV](3(+•)). In this full paper, we describe the extension of radical-pairing-based molecular recognition to a larger, square-shaped diradical host, [cyclobis(paraquat-4,4'-biphenylene)](2(+•)) (MS(2(+•)))...
March 8, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28166378/occurrence-and-genetic-characteristics-of-cryptosporidium-hominis-and-cryptosporidium-andersoni-in-horses-from-southwestern-china
#20
Lei Deng, Wei Li, Zhijun Zhong, Chao Gong, Xuefeng Cao, Yuan Song, Wuyou Wang, Xiangming Huang, Xuehan Liu, Yanchun Hu, Hualin Fu, Min He, Ya Wang, Yue Zhang, Kongju Wu, Guangneng Peng
A total of 333 fecal specimens from horses in southwestern China were genotyped based on analysis of the small subunit rRNA (SSU rRNA) gene. Cryptosporidium hominis and Cryptosporidium andersoni were identified in 2 and 4 stool specimens, respectively. The identification of C. hominis was confirmed by sequence analysis of the 70-kDa heat shock protein (HSP70) and oocyst wall protein (COWP) genes. Subtyping analysis of the 60-kDa glycoprotein (GP60) gene sequence of C. hominis revealed a new rare subtype Id, named IdA15; only three Id isolates have been reported in humans to date...
February 6, 2017: Journal of Eukaryotic Microbiology
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