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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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-crosslinkers
#7
Adel M ElSohly, James Irving MacDonald, Nina B Hentzen, Ioana Laura 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...
February 16, 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
#8
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
#9
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 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193211/display-of-single-chain-variable-fragments-on-bacteriophage-ms2-virus-like-particles
#10
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
#11
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
#12
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,Nꞌ-dimethyl-4,4ꞌ-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(+•) (CBPQT2(+•)) 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-4,4ꞌ-biphenylene)]2(+•) (MS2(+•))...
February 7, 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
#13
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
https://www.readbyqxmd.com/read/28165216/comparative-inactivation-of-murine-norovirus-and-ms2-bacteriophage-by-peracetic-acid-and-monochloramine-in-municipal-secondary-wastewater-effluent
#14
Nathan Dunkin, ShihChi Weng, Kellogg J Schwab, James McQuarrie, Kati Bell, Joseph G Jacangelo
Chlorination has long been used for disinfection of municipal wastewater (MWW) effluent while the use peracetic acid (PAA) has been proposed more recently in the United States. Previous work has demonstrated the bactericidal effectiveness of PAA and monochloramine in wastewater, but limited information is available for viruses, especially ones of mammalian origin (e.g., norovirus). Therefore, a comparative assessment was performed of the virucidal efficacy of PAA and monochloramine against murine norovirus (MNV) and MS2 bacteriophage in secondary effluent MWW and phosphate buffer (PB)...
February 24, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28154984/the-impact-of-viral-rna-on-the-association-free-energies-of-capsid-protein-assembly-bacteriophage-ms2-as-a-case-study
#15
Karim M ElSawy
A large number of single-stranded RNA viruses assemble their capsid and their genomic material simultaneously. The RNA viral genome plays multiple roles in this process that are currently only partly understood. In this work, we investigated the thermodynamic basis of the role of viral RNA on the assembly of capsid proteins. The viral capsid of bacteriophage MS2 was considered as a case study. The MS2 virus capsid is composed of 60 AB and 30 CC protein dimers. We investigated the effect of RNA stem loop (the translational repressor TR) binding to the capsid dimers on the dimer-dimer relative association free energies...
February 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28154204/linear-ion-trap-msn-with-high-resolution-mass-spectrometry-reveals-structural-diversity-of-epidermal-1-o-acyl-ceramide-family-in-mouse-epidermis
#16
Meei-Hua Lin, Jeffery Miner, John Turk, Fong-Fu Hsu
1-O-acylceramide is a new class of epidermal ceramide found in humans and mice. Here, we report ESI linear ion-trap (LIT) multiple stage mass spectrometric (MSn) approach with high resolution towards structural characterization of this lipid family isolated from mice. Molecular species desorbed as the [M + H]+ ions was subjected to LIT MS2 to yield predominately the [M + H - H2O]+ ions, followed by MS3 to cleave the 1-O-acyl residue to yield the [M + H - H2O - (1-O-fatty acid)]+ ions. The structures of the N-acyl chain and long-chain base (LCB) of the molecule were determined by MS4 on ([M + H - H2O - (1-O-fatty acid)]+) ions that yielded multiple sets of specific ions...
February 2, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28152075/pathogen-specific-deep-sequence-coupled-biopanning-a-method-for-surveying-human-antibody-responses
#17
Kathryn M Frietze, Juan M Pascale, Brechla Moreno, Bryce Chackerian, David S Peabody
Identifying the targets of antibody responses during infection is important for designing vaccines, developing diagnostic and prognostic tools, and understanding pathogenesis. We developed a novel deep sequence-coupled biopanning approach capable of identifying the protein epitopes of antibodies present in human polyclonal serum. Here, we report the adaptation of this approach for the identification of pathogen-specific epitopes recognized by antibodies elicited during acute infection. As a proof-of-principle, we applied this approach to assessing antibodies to Dengue virus (DENV)...
2017: PloS One
https://www.readbyqxmd.com/read/28130327/insertion-of-inter-domain-linkers-improves-expression-and-bioactivity-of-zygote-arrest-zar-fusion-proteins
#18
Jonathan M Cook, Amanda Charlesworth
Developmentally important proteins that are crucial for fertilization and embryogenesis are synthesized through highly regulated translation of maternal mRNA. The Zygote arrest proteins, Zar1 and Zar2, are crucial for embryogenesis and have been implicated in binding mRNA and repressing mRNA translation. To investigate Zar1 and Zar2, the full-length proteins had been fused to glutathione-S-transferase (GST) or MS2 protein tags with minimal inter-domain linkers derived from multiple cloning sites; however, these fusion proteins expressed poorly and/or lacked robust function...
January 26, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28125778/aerosolization-of-ebola-virus-surrogates-in-wastewater-systems
#19
Kaisen Lin, Linsey C Marr
Recent studies have shown that Ebola virus can persist in wastewater. We evaluated the potential for Ebola virus surrogates to be aerosolized from three types of wastewater systems: toilets, a lab-scale model of an aeration basin, and a lab-scale model of converging sewer pipes. We measured the aerosol size distribution generated by each system, spiked Ebola virus surrogates (MS2 and Phi6) into each system, and determined the emission rate of viruses into the air. The number of aerosols released ranged from 10(5) to 10(7) per flush from the toilets or per minute from the lab-scale models, and the total volume of aerosols generated by these systems was ∼10(-9) to 10(-7) mL per flush or per minute in all cases...
February 10, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28123325/metabolite-profiles-of-ginsenosides-rk1-and-rg5-in-zebrafish-using-ultraperformance-liquid-chromatography-quadrupole-time-of-flight-ms
#20
Wenwen Shen, Yingjie Wei, Daoquan Tang, Xiaobin Jia, Bin Chen
BACKGROUND: In the present study, metabolite profiles of ginsenosides Rk1 and Rg5 from red ginseng or red notoginseng in zebrafish were qualitatively analyzed with ultraperformance liquid chromatography/quadrupole-time-of-flight MS, and the possible metabolic were pathways proposed. METHODS: After exposing to zebrafish for 24 h, we determined the metabolites of ginsenosides Rk1 and Rg5. The chromatography was accomplished on UPLC BEH C18 column using a binary gradient elution of 0...
January 2017: Journal of Ginseng Research
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