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Simon M G Braun, Jacob G Kirkland, Emma J Chory, Dylan Husmann, Joseph P Calarco, Gerald R Crabtree
Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells...
September 15, 2017: Nature Communications
Nathan Dunkin, ShihChi Weng, Caroline G Coulter, Joseph G Jacangelo, Kellogg Schwab
The objective of this study was to characterize human norovirus (hNoV) GI and GII reductions during disinfection by peracetic acid (PAA) and monochloramine in secondary wastewater (WW) and phosphate buffer (PB) as assessed by reverse transcription-qPCR (RT-qPCR). Infectivity and RT-qPCR reductions are also presented for surrogate viruses murine norovirus (MNV) and bacteriophage MS2 under identical experimental conditions to aid in interpretation of hNoV molecular data. In WW, RT-qPCR reductions were less than 0...
September 14, 2017: Environmental Science & Technology
Nathan Dunkin, Shih-Chi Weng, Joseph G Jacangelo, Kellogg J Schwab
Human noroviruses (hNoVs) are a known public health concern associated with the consumption of leafy green vegetables. While a number of studies have investigated pathogen reduction on the surfaces of leafy greens during the postharvest washing process, there remains a paucity of data on the level of treatment needed to inactivate viruses in the wash water, which is critical for preventing cross-contamination. The objective of this study was to quantify the susceptibility of hNoV GI, hNoV GII, murine norovirus (MNV), and bacteriophage MS2 to free chlorine in whole leaf, chopped romaine, and shredded iceberg lettuce industrial leafy green wash waters, each sampled three times over a 4-month period...
September 8, 2017: Applied and Environmental Microbiology
Susanne Fister, Patrick Mester, Julia Sommer, Anna K Witte, Roland Kalb, Martin Wagner, Peter Rossmanith
An increasing number of publications describe the potential of ionic liquids (ILs) as novel antimicrobials, antibacterial coatings and even as active pharmaceutical ingredients. Nevertheless, a major research area, notably their impact on viruses, has so far been neglected. Consequently the aim of this study was to examine the effects of ILs on the infectivity of viruses. A systematic analysis to investigate the effects of defined structural elements of ILs on virus activity was performed using 55 ILs. All structure activity relationships (SARs) were tested on the human norovirus surrogate phage MS2 and phage P100 representing non-enveloped DNA viruses...
2017: Frontiers in Microbiology
Hiva Azizi, Carole Dumas, Barbara Papadopoulou
Leishmania and other trypanosomatid protozoa lack control at the level of transcription initiation and regulate gene expression exclusively posttranscriptionally. We have reported previously that Leishmania harbors a unique class of Short Interspersed DEgenerate Retroposons (SIDERs) that are predominantly located within 3'UTRs and play a major role in posttranscriptional control. We have shown that members of the SIDER2 subfamily initiate mRNA decay through endonucleolytic cleavage within the second conserved 79-nt signature sequence of SIDER2 retroposons...
September 6, 2017: RNA
Khalid Bin Ahsan, Akio Masuda, Mohammad Alinoor Rahman, Jun-Ichi Takeda, Mohammad Nazim, Bisei Ohkawara, Mikako Ito, Kinji Ohno
Dok-7 is a non-catalytic adaptor protein that facilitates agrin-induced clustering of acetylcholine receptors (AChR) at the neuromuscular junction. Alternative selection of 5' splice sites (SSs) of DOK7 intron 4 generates canonical and frame-shifted transcripts. We found that the canonical full-length Dok-7 enhanced AChR clustering, whereas the truncated Dok-7 did not. We identified a splicing cis-element close to the 3' end of exon 4 by block-scanning mutagenesis. RNA affinity purification and mass spectrometry revealed that SRSF1 binds to the cis-element...
September 5, 2017: Scientific Reports
Yi Di, Ying Zhang, Lei Zhang, Tao Tao, Haojie Lu
Data-independent acquisition (DIA) has recently emerged as a powerful quantitative approach for large-scale proteome quantification, providing a sensitive and reproducible alternative to data-dependent acquisition (DDA). However, lack of compatible multiplexed quantification methods is a bottleneck of DIA. To alleviate this challenge, we present a mass defect based four-plex data-independent acquisition strategy, termed "MdFDIA", for parallel analysis of four different protein samples in a DIA experiment without the additional complexity of tandem mass spectrometry (MS(2)) spectra...
September 19, 2017: Analytical Chemistry
Mark Rustad, Allen Eastlund, Ryan Marshall, Paul Jardine, Vincent Noireaux
A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel capabilities to perform basic and applied sciences in test tube reactions. Over the past decade, cell-free TXTL has become a powerful technique for a broad range of novel multidisciplinary research areas related to quantitative and synthetic biology. The new TXTL platforms are particularly useful to construct and interrogate biochemical systems through the execution of synthetic or natural gene circuits...
August 17, 2017: Journal of Visualized Experiments: JoVE
Xianbin Yang, N Dinuka Abeydeera, Feng-Wu Liu, Martin Egli
The well-characterized interaction between the MS2 coat protein and its cognate RNA hairpin was used to evaluate changes in affinity as a result of phosphorodithioate (PS2) replacing phosphate by biolayer interferometry (BLI). A structure-based analysis of the data provides insights into the origins of the enhanced affinity of RNA-protein interactions triggered by the PS2 moiety.
September 4, 2017: Chemical Communications: Chem Comm
Muaaz Gul Awan, Fahad Saeed
Modern high resolution Mass Spectrometry instruments can generate millions of spectra in a single systems biology experiment. Each spectrum consists of thousands of peaks but only a small number of peaks actively contribute to deduction of peptides. Therefore, pre-processing of MS data to detect noisy and non-useful peaks are an active area of research. Most of the sequential noise reducing algorithms are impractical to use as a pre-processing step due to high time-complexity. In this paper, we present a GPU based dimensionality-reduction algorithm, called G-MSR, for MS2 spectra...
August 2017: ACM-BCB: ACM Conference on Bioinformatics, Computational Biology and Biomedicine
S J Park, S H Cha, G A Shin, Y H Ahn
We demonstrate highly sensitive detection of viruses using terahertz split-ring resonators with various capacitive gap widths. Two types of viruses, with sizes ranging from 60 nm (PRD1) to 30 nm (MS2), were detected at low densities on the metamaterial surface. The dielectric constants of the virus layers in the THz frequency range were first measured using thick films, and the large values found identified them as efficient target substances for dielectric sensing. We observed the resonance-frequency shift of the THz metamaterial following deposition of the viruses on the surface at low-density...
August 1, 2017: Biomedical Optics Express
Mario Juhas, James W Ajioka
The majority of the good DNA editing techniques have been developed in Escherichia coli; however, Bacillus subtilis is better host for a plethora of synthetic biology and biotechnology applications. Reliable and efficient systems for the transfer of synthetic DNA between E. coli and B. subtilis are therefore of the highest importance. Using synthetic biology approaches, such as streamlined lambda Red recombineering and Gibson Isothermal Assembly, we integrated genetic circuits pT7L123, Repr-ts-1 and pLT7pol encoding the lysis genes of bacteriophages MS2, ΦX174 and lambda, the thermosensitive repressor and the T7 RNA polymerase into the E...
August 16, 2017: Microbial Biotechnology
Janez Kosel, Ion Gutiérrez-Aguirre, Nejc Rački, Tanja Dreo, Maja Ravnikar, Matevž Dular
The aim of this study was to accurately quantify the impact of hydrodynamic cavitation on the infectivity of bacteriophage MS2, a norovirus surrogate, and to develop a small scale reactor for testing the effect of hydrodynamic cavitation on human enteric viruses, which cannot be easily prepared in large quantities. For this purpose, 3 mL scale and 1 L scale reactors were constructed and tested. Both devices were efficient in generating hydrodynamic cavitation and in reducing the infectivity of MS2 virus. Furthermore, they reached more than 4 logs reductions of viral infectivity, thus confirming the scalability of hydrodynamic cavitation for this particular application...
July 31, 2017: Water Research
Dustin C Frost, Amanda R Buchberger, Lingjun Li
We have developed a novel amine-reactive mass defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), that is compact in size, is suitable for various biological samples, and enables highly multiplexed quantification of peptides at the MS(1) level without increasing mass spectral complexity. The DiPyrO tag structure incorporates heavy isotopes in a variety of configurations to impart as much as 45.3 mDa or as little as 5.8 mDa per tag between labeled peptides. Notably, peptides containing lysine are labeled with two tags, doubling the imparted mass defect to up to 90...
August 28, 2017: Analytical Chemistry
D van Halem, H van der Laan, A I A Soppe, S G J Heijman
Ceramic pot filters are considered safe, robust and appropriate technologies, but there is a general consensus that water revenues are limited due to clogging of the ceramic element. The objective of this study was to investigate the potential of high flow ceramic pot filters to produce more water without sacrificing their microbial removal efficacy. High flow pot filters, produced by increasing the rice husk content, had a higher initial flow rate (6-19 L h(-1)), but initial LRVs for E. coli of high flow filters was slightly lower than for regular ceramic pot filters...
July 20, 2017: Water Research
Xiuye Wang, Yongsheng Shi
Multiple mRNA processing steps, including splicing and 3' processing, take place in macromolecular complexes that contain many proteins and sometimes RNA molecules. A key challenge in the mRNA processing field has been to define the structure-function relationship of these sophisticated molecular machines. A prerequisite for addressing this challenge is to develop tools for purifying mRNA processing complexes in their native and intact forms that are suitable for functional and structural studies. Among many methods that have been developed, RNA affinity-based methods are most widely applied...
2017: Methods in Molecular Biology
Andrew M Armstrong, Mark D Sobsey, Lisa M Casanova
Households that lack piped water supply are often forced to meet water needs by storing in the home, leaving water vulnerable to contamination by viruses. Storage in copper containers can potentially prevent this type of contamination, but the inactivation kinetics of viruses by copper need to be described to make appropriate storage recommendations. This work characterized inactivation kinetics of bacteriophage MS2 as a surrogate for enteric viruses by dissolved ionic copper in water. Reduction of MS2 increased with increasing doses of copper...
July 30, 2017: Applied Microbiology and Biotechnology
Xiuyun Zhang, Zujian Bao, Xiaoshan Ye, Wenxian Xu, Qiang Wang, Yongjun Liu
The energetics and electronic and magnetic properties of G/MS2 hybrid structures embedded with 3d transition metal atoms, TM@(G/MS2) (G = graphene; M = W, Mo; TM = Sc-Ni), have been systematically studied using first-principles calculations. TM atoms were found to be covalently bound to two-sided graphene and MS2 layers with sizable binding energies of 4.35-7.13 eV. Interestingly, a variety of electronic and magnetic properties were identified for these TM@(G/MS2) systems. Except for TM = Ni, all other systems were ferromagnetic, due to exchange splitting of the TM 3d orbitals...
July 28, 2017: Nanoscale
Heba Alhmidi, Amrita John, Thriveen C Mana, Sreelatha Koganti, Jennifer L Cadnum, Melissa B Shelton, Curtis J Donskey
During patient care simulations, cauliflower mosaic virus DNA and bacteriophage MS2 performed similarly as surrogate markers of pathogen dissemination. These markers disseminated to the environment in a manner similar to Clostridium difficile spores but were more frequently detected on skin and clothing of personnel after personal protective equipment removal.
2017: Open Forum Infectious Diseases
Amyrhul Abu-Bakar, Reza Ahmadian, Roger A Falconer
The Loughor Estuary is a macro-tidal coastal basin, located along the Bristol Channel, in the South West of the U.K. The maximum spring tidal range in the estuary is up to 7.5 m, near Burry Port Harbour. This estuarine region can experience severe coastal flooding during high spring tides, including extreme flooding of the intertidal saltmarshes at Llanrhidian, as well as the lower industrial and residential areas at Llanelli and Gowerton. The water quality of this estuarine basin needs to comply with the designated standards for safe recreational bathing and shellfish harvesting industries...
July 3, 2017: Water Research
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