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https://www.readbyqxmd.com/read/28790985/rna-sequencing-reveals-that-endoplasmic-reticulum-stress-and-disruption-of-membrane-integrity-underlie-dimethyl-trisulfide-toxicity-against-fusarium-oxysporum-f-sp-cubense-tropical-race-4
#1
Cunwu Zuo, Weina Zhang, Zhongjian Chen, Baihong Chen, Yonghong Huang
Fusarium wilt of banana, a destructive disease that affects banana production, is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). In a previous study, we confirmed the strong inhibitory effects of Chinese leek (Allium tuberosum) on the incidence of this disease. Sulfur compounds are the primary antifungal constituents of Chinese leek. Among these, dimethyl trisulfide (DT) was the most abundant and exhibited the strongest inhibition of Foc TR4 growth and development. In the present study, the global gene expression profiles of Foc TR4 isolates treated with DT at 4,000-folds dilution (concentration of 1/4,000, v/v) for 1...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28725083/estimation-of-nonlinear-adsorption-isotherms-in-gradient-elution-rp-lc-of-peptides-in-the-presence-of-an-adsorbing-additive
#2
Dennis Åsberg, Marek Leśko, Tomas Leek, Jörgen Samuelsson, Krzysztof Kaczmarski, Torgny Fornstedt
ABSTRACT: In electrostatic repulsive interaction chromatography, using a charged surface hybrid sorbent carrying positive charges can improve the peak shape of peptides in reversed-phase liquid chromatography (RP-LC), especially in overloaded conditions, compared with standard C18 sorbents. However, the positive surface charges can interact with anionic additives commonly used in peptide separations, e.g., trifluoroacetic acid (TFA), complicating adsorption isotherm estimation. We investigated how the competition for available adsorption sites between TFA and two peptides influenced the adsorption isotherm in gradient elution...
2017: Chromatographia
https://www.readbyqxmd.com/read/28634288/qsva-framework-for-rna-quality-correction-in-differential-expression-analysis
#3
Andrew E Jaffe, Ran Tao, Alexis L Norris, Marc Kealhofer, Abhinav Nellore, Joo Heon Shin, Dewey Kim, Yankai Jia, Thomas M Hyde, Joel E Kleinman, Richard E Straub, Jeffrey T Leek, Daniel R Weinberger
RNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on high-quality RNA. We demonstrate here that statistical adjustment using existing quality measures largely fails to remove the effects of RNA degradation when RNA quality associates with the outcome of interest. Using RNA-seq data from molecular degradation experiments of human primary tissues, we introduce a method-quality surrogate variable analysis (qSVA)-as a framework for estimating and removing the confounding effect of RNA quality in differential expression analysis...
July 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28626531/saccharin-aza-bioisosteres-synthesis-and-preclinical-property-comparisons
#4
Yantao Chen, Carl-Johan Aurell, Anna Pettersen, Richard J Lewis, Martin A Hayes, Matti Lepistö, Anna C Jonson, Hanna Leek, Linda Thunberg
Saccharin is a well-known scaffold in drug discovery. Herein, we report the synthesis and preclinical property comparisons of three bioisosteres of saccharin: aza-pseudosaccharins (cluster B), and two new types of aza-saccharins (clusters C and D). We demonstrate a convenient protocol to selectively synthesize products in cluster C or D when primary amines are used. Preclinical characterization of selected matched-pair products is reported. Through comparison of two diastereomers, we highlight how stereochemistry affects the preclinical properties...
June 8, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28536847/an-empirical-investigation-of-the-possibility-of-adaptability-of-arbuscular-mycorrhizal-fungi-to-new-hosts
#5
Akihiro Koyama, Olivia Pietrangelo, Laura Sanderson, Pedro M Antunes
Little is known about the adaptive capacity of arbuscular mycorrhizal (AM) fungi to novel hosts. Here we assessed the possibility of two heterospecific AM fungal isolates to adaptively change, in terms of host biomass response, as a function of host plant identity, over the course of a growing season. First, we produced pure inocula of Rhizophagus clarus and Rhizophagus intraradices, each starting from a single spore. Second, we "trained" each isolate individually in a community with two plants, sudangrass (Sorgum bicolour subsp...
August 2017: Mycorrhiza
https://www.readbyqxmd.com/read/28524772/effects-of-stereoscopic-disparity-on-early-erp-components-during-classification-of-three-dimensional-objects
#6
Alan J Pegna, Alexandre Darque, Mark V Roberts, E Charles Leek
This study investigates the effects of stereo disparity on the perception of three-dimensional (3D) object shape. We tested the hypothesis that stereo input modulates the brain activity related to perceptual analyses of 3D shape configuration during image classification. High-density (256-channel) EEG was used to record the temporal dynamics of visual shape processing under conditions of two-dimensional (2D) and three-dimensional (3D) visual presentation. On each trial, observers made image classification judgements ('Same'/'Different') to two briefly presented, multi-part, novel objects...
May 19, 2017: Quarterly Journal of Experimental Psychology: QJEP
https://www.readbyqxmd.com/read/28499723/a-dual-site-gateway-cloning-system-for-simultaneous-cloning-of-two-genes-for-plant-transformation
#7
Mostafa Aboulela, Yuji Tanaka, Kohji Nishimura, Shoji Mano, Tetsuya Kimura, Tsuyoshi Nakagawa
Analyses of the subcellular localization of proteins and protein-protein interaction networks are essential to uncover the molecular basis of diverse biological processes in plants. To this end, we have created a Gateway cloning-compatible vector system, named dual-site (DS) Gateway cloning system to allow simple cloning of two expression cassettes in a binary vector and to express them simultaneously in plant cells. In the DS Gateway cloning system, (i) a moderate constitutive nopaline synthase promoter (Pnos), which is much suitable for localization analysis, is used to guide each expression cassette, (ii) four series of vectors with different plant resistance markers are established, (iii) N-terminal fusion with 6 fluorescent proteins and 7 epitope tags is available, (iv) both N- and C-terminal fusions with split enhanced yellow fluorescent protein (EYFP) are possible for efficient detection of protein-protein interactions using a bimolecular fluorescence complementation (BiFC) assay...
May 9, 2017: Plasmid
https://www.readbyqxmd.com/read/28464618/syllable-constituent-perception-by-hearing-aid-users-common-factors-in-quiet-and-noise
#8
James D Miller, Charles S Watson, Marjorie R Leek, Judy R Dubno, David J Wark, Pamela E Souza, Sandra Gordon-Salant, Jayne B Ahlstrom
The abilities of 59 adult hearing-aid users to hear phonetic details were assessed by measuring their abilities to identify syllable constituents in quiet and in differing levels of noise (12-talker babble) while wearing their aids. The set of sounds consisted of 109 frequently occurring syllable constituents (45 onsets, 28 nuclei, and 36 codas) spoken in varied phonetic contexts by eight talkers. In nominal quiet, a speech-to-noise ratio (SNR) of 40 dB, scores of individual listeners ranged from about 23% to 85% correct...
April 2017: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/28445154/role-of-delta-like-4-in-jagged1-induced-tumour-angiogenesis-and-tumour-growth
#9
Chern Ein Oon, Esther Bridges, Helen Sheldon, Richard C A Sainson, Adrian Jubb, Helen Turley, Russell Leek, Francesca Buffa, Adrian L Harris, Ji-Liang Li
Delta-like 4 (DLL4) and Jagged1 (JAG1) are two key Notch ligands implicated in tumour angiogenesis. They were shown to have opposite effects on mouse retinal and adult regenerative angiogenesis. In tumours, both ligands are upregulated but their relative effects and interactions in tumour biology, particularly in tumour response to therapeutic intervention are unclear. Here we demonstrate that DLL4 and JAG1 displayed equal potency in stimulating Notch target genes in HMEC-1 endothelial cells but had opposing effects on sprouting angiogenesis in vitro...
June 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28435350/effects-of-arbuscular-mycorrhizal-fungi-and-soil-conditions-on-crop-plant-growth
#10
Sang Joon Kim, Ju-Kyeong Eo, Eun-Hwa Lee, Hyeok Park, Ahn-Heum Eom
We investigated the effects on various crops of inoculation with species of arbuscular mycorrhizal fungi (AMF) in soils from different sources and selected AMF species suitable for domestic environment-friendly farming. Effects on plants varied with the AMF species used. In carrot, Scutellospora heterogama, Acaulospora longula, and Funneliformis mosseae had a positive effect on growth of the host, whereas AMF had only weak effects on the growth of red pepper and leek. AMF inoculation had positive effects on the growth of carrot and sorghum...
March 2017: Mycobiology
https://www.readbyqxmd.com/read/28434710/shifting-the-paradigm-in-gas-chromatography-mass-spectrometry-pesticide-analysis-using-high-resolution-accurate-mass-spectrometry
#11
S Uclés, A Uclés, A Lozano, M J Martínez Bueno, A R Fernández-Alba
In the last 10 years, the majority of the pesticide food control laboratories moved from GC-MS to GC-MS/MS as the preferred analytical technique to address GC amenable compounds. The main reason for this change was the negative impact on the single stage GC-MS analysis caused by the interference from coeluting matrix compounds. The new development of gas chromatography coupled to high resolution accurate mass spectrometry (GC-HRAMS) provides opportunities to overcome such matrix interferences as a result of its much higher selectivity; allowing laboratories to carry out full-scan analysis covering the most exigent analytical performance criteria...
April 14, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28426177/an-efficient-cleanup-method-coupled-with-gas-chromatography-and-mass-spectrometry-for-multi-pesticides-residue-analysis-in-complex-plant-matrices
#12
Xinquan Wang, Peipei Qi, Xiangyun Wang, Qian Zhang, Zhiwei Wang, Xiahong Xu, Hao Xu, Hu Zhang, Qiang Wang
We aimed to develop an efficient cleanup method for multi-pesticides residue analysis in complex plant matrices, shallot, ginger, garlic, onion, leek and celery. Column chromatography was used as the cleanup method and fabricated with florisil and graphitized carbon black as the adsorbents. The amount of the graphitized carbon black adsorbent and the choice of the elution solvent were systematically investigated for exploring the best combination. The target pesticides covered organochlorine, pyrethroid and organophosphorus pesticides, and were 38 in total...
April 20, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28402916/potential-of-chopped-heath-biomass-and-spent-growth-media-to-replace-wood-chips-as-bulking-agent-for-composting-high-n-containing-residues
#13
J Viaene, B Reubens, K Willekens, C Van Waes, S De Neve, B Vandecasteele
We investigated the potential of C-rich byproducts to replace wood chips as bulking agent (BA) during composting. The impact of these alternatives on the composting process and on compost stability and characteristics was assessed. Three BA (chopped heath biomass and spent growth media used in strawberry and tomato cultivation) were used for processing leek residues in windrow composting. All BA resulted in stable composts with an organic matter (OM) content suitable for use as soil amendment. Using chopped heath biomass led to high pile temperatures and OM degradation and a nutrient-poor compost with high C/P ratio appropriate for increasing soil organic carbon content in P-rich soils...
April 9, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28400006/microbiological-quality-of-selected-ready-to-eat-leaf-vegetables-sprouts-and-non-pasteurized-fresh-fruit-vegetable-juices-including-the-presence-of-cronobacter-spp
#14
Anna Berthold-Pluta, Monika Garbowska, Ilona Stefańska, Antoni Pluta
Bacteria of the genus Cronobacter are emerging food-borne pathogens. Foods contaminated with Cronobacter spp. may pose a risk to infants or adults with suppressed immunity. This study was aimed at determining the microbiological quality of ready-to-eat (RTE) plant-origin food products available on the Polish market with special emphasis on the prevalence of Cronobacter genus bacteria. Analyses were carried out on 60 samples of commercial RTE type plant-origin food products, including: leaf vegetables (20 samples), sprouts (20 samples) and non-pasteurized vegetable, fruit and fruit-vegetable juices (20 samples)...
August 2017: Food Microbiology
https://www.readbyqxmd.com/read/28398307/reproducible-rna-seq-analysis-using-recount2
#15
Leonardo Collado-Torres, Abhinav Nellore, Kai Kammers, Shannon E Ellis, Margaret A Taub, Kasper D Hansen, Andrew E Jaffe, Ben Langmead, Jeffrey T Leek
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28368017/risk-assessment-of-candidatus-liberibacter-solanacearum-transmission-by-the-psyllids-bactericera-trigonica-and-b-tremblayi-from-apiaceae-crops-to-potato
#16
C A Antolinez, A Fereres, A Moreno
Candidatus Liberibacter solanacearum (Lso) is bacterium transmitted by psyllids to Solanaceae and Apiaceae plants. So far, Lso is found in Europe affecting Apiaceae. In the Mediterranean region, Bactericera trigonica is the only known vector of Lso, but the leek-onion psyllid Bactericera tremblayi is another widespread psyllid and potential vector of Lso. Commonly, carrot, leek and potato are cultivated in the same zones and it is uncertain if these psyllid species are able to transmit Lso to potato plants...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28366564/systematic-investigations-of-peak-deformations-due-to-co-solvent-adsorption-in-preparative-supercritical-fluid-chromatography
#17
Emelie Glenne, Hanna Leek, Magnus Klarqvist, Jörgen Samuelsson, Torgny Fornstedt
Strangely shaped overloaded bands were recently reported using a standard supercritical fluid chromatographic system comprising a diol column as the stationary phase and carbon dioxide with methanol as the mobile phase. Some of these overloaded elution profiles appeared strongly deformed and even had "anti-Langmuirian" shapes although their solute compounds had "Langmuirian" adsorption. To obtain a more complete understanding of the generality of these effects, the investigation was expanded to cover also other common co-solvents, such as ethanol, 2-propanol, and acetonitrile, as well as various stationary phase materials, such as silica, and 2-ethylpyridine...
May 5, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28363419/the-importance-of-ion-pairing-in-peptide-purification-by-reversed-phase-liquid-chromatography
#18
Dennis Åsberg, Annika Langborg Weinmann, Tomas Leek, Richard J Lewis, Magnus Klarqvist, Marek Leśko, Krzysztof Kaczmarski, Jörgen Samuelsson, Torgny Fornstedt
The adsorption mechanism for three peptides was studied under overloaded conditions through adsorption isotherm measurements in the presence of an ion-pairing reagent, trifluoroacetic acid (TFA), on an end-capped C18-bonded stationary phase. The overall aim of the study was to obtain a better understanding of how the acetonitrile and the TFA fractions in the eluent affected the overloaded elution profiles and the selectivity between peptides using mechanistic modelling and multivariate design of experiments...
May 5, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28324887/association-between-hypoxic-volume-and-underlying-hypoxia-induced-gene-expression-in-oropharyngeal-squamous-cell-carcinoma
#19
Yae-Eun Suh, Katherine Lawler, Rhonda Henley-Smith, Lucy Pike, Russell Leek, Sally Barrington, Edward W Odell, Tony Ng, Francesco Pezzella, Teresa Guerrero-Urbano, Mahvash Tavassoli
BACKGROUND: Hypoxia imaging is a promising tool for targeted therapy but the links between imaging features and underlying molecular characteristics of the tumour have not been investigated. The aim of this study was to compare hypoxia biomarkers and gene expression in oropharyngeal squamous cell carcinoma (OPSCC) diagnostic biopsies with hypoxia imaged with (64)Cu-ATSM PET/CT. METHODS: (64)Cu-ATSM imaging, molecular and clinical data were obtained for 15 patients...
April 11, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28290475/the-development-of-loop-mediated-isothermal-amplification-lamp-assays-for-the-rapid-authentication-of-five-forbidden-vegetables-in-strict-vegetarian-diets
#20
Meng-Shiou Lee, Ting-Ying Su, Yi-Yang Lien, Shyang-Chwen Sheu
Plant-based food ingredients such as garlic, Chinese leek, Chinese onion, green onion and onion are widely used in many cuisines around the world. However, these ingredients known as the "five forbidden vegetables" (FFVs) are not allowed in some vegetarian diets. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed for the detection of FFVs using five respective LAMP primer sets. The specific primers targeted the ITS1-5.8S-ITS2 nuclear ribosomal DNA sequence regions among the five vegetables...
March 14, 2017: Scientific Reports
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