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https://www.readbyqxmd.com/read/28107356/integrity-of-induced-pluripotent-stem-cell-ipsc-derived-megakaryocytes-as-assessed-by-genetic-and-transcriptomic-analysis
#1
Kai Kammers, Margaret A Taub, Ingo Ruczinski, Joshua Martin, Lisa R Yanek, Alyssa Frazee, Yongxing Gao, Dixie Hoyle, Nauder Faraday, Diane M Becker, Linzhao Cheng, Zack Z Wang, Jeff T Leek, Lewis C Becker, Rasika A Mathias
Previously, we have described our feeder-free, xeno-free approach to generate megakaryocytes (MKs) in culture from human induced pluripotent stem cells (iPSCs). Here, we focus specifically on the integrity of these MKs using: (1) genotype discordance between parent cell DNA to iPSC cell DNA and onward to the differentiated MK DNA; (2) genomic structural integrity using copy number variation (CNV); and (3) transcriptomic signatures of the derived MK lines compared to the iPSC lines. We detected a very low rate of genotype discordance; estimates were 0...
2017: PloS One
https://www.readbyqxmd.com/read/28106796/preparative-scale-resolution-of-enantiomers-enables-accelerated-drug-discovery-and-development
#2
Hanna Leek, Shalini Andersson
The provision of pure enantiomers is of increasing importance not only for the pharmaceutical industry but also for agro-chemistry and biotechnology. In drug discovery and development, the enantiomers of a chiral drug depict unique chemical and pharmacological behaviors in a chiral environment, such as the human body, in which the stereochemistry of the chiral drugs determines their pharmacokinetic, pharmacodynamic and toxicological properties. We present a number of challenging case studies of up-to-kilogram separations of racemic or enriched isomer mixtures using preparative liquid chromatography and super critical fluid chromatography to generate individual enantiomers that have enabled the development of new candidate drugs within AstraZeneca...
January 18, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28038678/human-splicing-diversity-and-the-extent-of-unannotated-splice-junctions-across-human-rna-seq-samples-on-the-sequence-read-archive
#3
Abhinav Nellore, Andrew E Jaffe, Jean-Philippe Fortin, José Alquicira-Hernández, Leonardo Collado-Torres, Siruo Wang, Robert A Phillips Iii, Nishika Karbhari, Kasper D Hansen, Ben Langmead, Jeffrey T Leek
BACKGROUND: Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. RESULTS: We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations...
December 30, 2016: Genome Biology
https://www.readbyqxmd.com/read/27999077/analysis-of-dithiocarbamate-fungicides-in-vegetable-matrices-using-hplc-uv-followed-by-atomic-absorption-spectrometry
#4
Josephine Al-Alam, Laura Bom, Asma Chbani, Ziad Fajloun, Maurice Millet
A simple method combining ion-pair methylation, high-performance liquid chromatography (HPLC) analysis with detection at 272 nm and atomic absorption spectrometry was developed in order to determine 10 dithiocarbamate fungicides (Dazomet, Metam-sodium, Ferbam, Ziram, Zineb, Maneb, Mancozeb, Metiram, Nabam and Propineb) and distinguish ethylenbisdithiocarbamates (EBDTCs) Zineb, Maneb and Mancozeb in diverse matrices. This method associates reverse phase analysis by HPLC analysis with detection at 272 nm, with atomic absorption spectrometry in order to distinguish, with the same extraction protocol, Maneb, Mancozeb and Zineb...
December 19, 2016: Journal of Chromatographic Science
https://www.readbyqxmd.com/read/27998093/cucurbit-7-uril-tetramethylrhodamine-conjugate-for-direct-sensing-and-cellular-imaging
#5
Andrew T Bockus, Lauren C Smith, Amy G Grice, Omar A Ali, Carolyn C Young, William Mobley, Ashley Leek, James L Roberts, Brittany Vinciguerra, Lyle Isaacs, Adam R Urbach
This paper describes the design and synthesis of a conjugate (Q7R) comprising the synthetic host cucurbit[7]uril (Q7) linked to the fluorescent dye tetramethylrhodamine (TMR), and the characterization of its optical and guest-binding properties as well as its cellular uptake. Q7R was synthesized in two steps from monofunctionalized azidobutyl-Q7 and NHS-activated TMR. The fluorescence of Q7R is quenched upon guest binding, and this observable was used to determine equilibrium dissociation constant (Kd) values...
December 21, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27979194/a-strategy-for-the-evaluation-of-an-analytical-approach-for-selected-pesticide-residues-in-complex-agricultural-product-matrices-a-case-study-of-leek
#6
Yanyan Xu, Ninghui Song, Qin Zhang, Jining Liu, Guosong Chen, Lili Shi, Jikui Wang
In order to choose a sensitive, selective, simple, rapid, cost-effective and reliable analytical method for a given complex sample, a strategy was proposed for the evaluation of an analytical approach to determining multi-pesticide residue in complex agricultural product matrices, using leek as an example. In this work, the matrix effect of most of pesticides were in the range of -50% to -90%. A simple thin layer chromatography (TLC) was used to evaluate the effect of cleanup. The results agree well with that of matrix effect described above...
April 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/27979090/a-study-on-biomimetic-immunoassay-capillary-electrophoresis-method-based-on-molecularly-imprinted-polymer-for-determination-of-trace-trichlorfon-residue-in-vegetables
#7
Jie Li, Juxiu Lu, Xuguang Qiao, Zhixiang Xu
Pesticide residue in vegetables is a serious problem that has adverse effects on human health. In our study, we designed and synthesized a molecularly imprinted polymer that can selectively recognize trichlorfon. Using the polymer material as biomimetic antibody, we developed a biomimetic immunoassay-capillary electrophoresis method with improved sensitivity for the detection of trichlorfon. We evaluated the competitive reactions between HRP labeled trichlorfon hapten and free trichlorfon with the biomimetic antibody...
April 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/27955886/generation-characterization-and-reuse-of-solid-wastes-from-a-biodiesel-production-plant
#8
Fernando Jorge Santos Oliveira, Daniele Dos Santos Santana, Simone Soraya Brito Costa, Lenise Diniz Oliveira, Vitor Silva Liduino, Eliana Flávia Camporese Servulo
The aim of this study was to identify and characterize industrial solid wastes generated by a biodiesel production plant in Brazil, as well as to present strategies for the management of these materials. This plant produces every year around 100,000tons of biodiesel from vegetable oils and animal fats. The methodology of the study included technical visits, interviews with the operational and environmental management staff as well as analysis of documents, reports and computerized data systems. An approach to reduce the generation of hazardous waste was investigated...
December 7, 2016: Waste Management
https://www.readbyqxmd.com/read/27914370/concurrent-measures-of-contralateral-suppression-of-transient-evoked-otoacoustic-emissions-and-of-auditory-steady-state-responses
#9
Ian B Mertes, Marjorie R Leek
Contralateral suppression of otoacoustic emissions (OAEs) is frequently used to assess the medial olivocochlear (MOC) efferent system, and may have clinical utility. However, OAEs are weak or absent in hearing-impaired ears, so little is known about MOC function in the presence of hearing loss. A potential alternative measure is contralateral suppression of the auditory steady-state response (ASSR) because ASSRs are measurable in many hearing-impaired ears. This study compared contralateral suppression of both transient-evoked otoacoustic emissions (TEOAEs) and ASSRs in a group of ten primarily older adults with either normal hearing or mild sensorineural hearing loss...
September 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27871350/early-description-of-diet-induced-blistering-skin-diseases-in-medieval-persia-avicenna-s-point-of-view
#10
Fatemeh Atarzadeh, Babak Daneshfard, Ladan Dastgheib, Amir-Mohammad Jaladat, Gholamreza Amin
Pemphigus is an autoimmune blistering skin disease that is strongly associated with different environmental factors. Among these, nutritional factors are considered to trigger pemphigus; however, their role may be underestimated. Investigated more recently in conventional medicine, this causative bond between dietary factors and blistering skin diseases was mentioned by Persian scholars such as Avicenna a thousand years ago. Avicenna, a well-known Persian physician and philosopher, who could be considered a pioneer in dermatology, discussed skin diseases in a chapter in The Canon of Medicine...
2016: Skinmed
https://www.readbyqxmd.com/read/27836984/recurrent-innovation-at-genes-required-for-telomere-integrity-in-drosophila
#11
Yuh Chwen G Lee, Courtney Leek, Mia T Levine
Telomeres are nucleoprotein complexes at the ends of linear chromosomes. These specialized structures ensure genome integrity and faithful chromosome inheritance. Recurrent addition of repetitive, telomere-specific DNA elements to chromosome ends combats end-attrition, while specialized telomere-associated proteins protect naked, double-stranded chromosome ends from promiscuous repair into end-to-end fusions. Although telomere length homeostasis and end-protection are ubiquitous across eukaryotes, there is sporadic but building evidence that the molecular machinery supporting these essential processes evolves rapidly...
November 11, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27765204/inorganic-selenium-speciation-analysis-in-allium-and-brassica-vegetables-by-ionic-liquid-assisted-liquid-liquid-microextraction-with-multivariate-optimization
#12
Alexander Castro Grijalba, Estefanía M Martinis, Rodolfo G Wuilloud
A highly sensitive vortex assisted liquid-liquid microextraction (VA-LLME) method was developed for inorganic Se [Se(IV) and Se(VI)] speciation analysis in Allium and Brassica vegetables. Trihexyl(tetradecyl)phosphonium decanoate phosphonium ionic liquid (IL) was applied for the extraction of Se(IV)-ammonium pyrrolidine dithiocarbamate (APDC) complex followed by Se determination with electrothermal atomic absorption spectrometry. A complete optimization of the graphite furnace temperature program was developed for accurate determination of Se in the IL-enriched extracts and multivariate statistical optimization was performed to define the conditions for the highest extraction efficiency...
March 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/27728958/description-of-the-ambulance-services-participating-in-the-aus-roc-australian-and-new-zealand-out-of-hospital-cardiac-arrest-epistry
#13
Ben Beck, Janet E Bray, Karen Smith, Tony Walker, Hugh Grantham, Cindy Hein, Melanie Thorrowgood, Anthony Smith, Madoka Inoue, Tony Smith, Bridget Dicker, Andy Swain, Emma Bosley, Katherine Pemberton, Michael McKay, Malcolm Johnston-Leek, Peter Cameron, Gavin D Perkins, Judith Finn
OBJECTIVE: The present study aimed to describe and examine similarities and differences in the current service provision and resuscitation protocols of the ambulance services participating in the Aus-ROC Australian and New Zealand out-of-hospital cardiac arrest (OHCA) Epistry. Understanding these similarities and differences is important in identifying ambulance service factors that might explain regional variation in survival of OHCA in the Aus-ROC Epistry. METHODS: A structured questionnaire was completed by each of the ambulance services participating in the Aus-ROC Epistry...
December 2016: Emergency Medicine Australasia: EMA
https://www.readbyqxmd.com/read/27721879/associations-between-dietary-allium-vegetables-and-risk-of-breast-cancer-a-hospital-based-matched-case-control-study
#14
Ali Pourzand, Aynaz Tajaddini, Saeed Pirouzpanah, Mohammad Asghari-Jafarabadi, Nasser Samadi, Ali-Reza Ostadrahimi, Zohre Sanaat
PURPOSE: The protective effect of Allium vegetables against carcinogenesis has been reported in experimental studies particularly focusing on the gut. Therefore, we conducted a hospital-based matched case-control study to explore the association between dietary Allium consumption and risk of breast cancer among Iranian women in northwest Iran. METHODS: A validated, quantitative, food frequency questionnaire was completed in 285 women (aged 25-65 years old) newly diagnosed with histopathologically confirmed breast cancer (grade II, III or clinical stage II, III) in Tabriz, northwest Iran, and the completed questionnaires were included in an age- and regional-matched hospital based-control study...
September 2016: Journal of Breast Cancer
https://www.readbyqxmd.com/read/27694310/flexible-expressed-region-analysis-for-rna-seq-with-derfinder
#15
Leonardo Collado-Torres, Abhinav Nellore, Alyssa C Frazee, Christopher Wilks, Michael I Love, Ben Langmead, Rafael A Irizarry, Jeffrey T Leek, Andrew E Jaffe
Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks to identify contiguous regions of the genome showing differential expression signal at single base resolution without relying on existing annotation or potentially inaccurate transcript assembly.We present the derfinder software that improves our annotation-agnostic approach to RNA-seq analysis by: (i) implementing a computationally efficient bump-hunting approach to identify DERs that permits genome-scale analyses in a large number of samples, (ii) introducing a flexible statistical modeling framework, including multi-group and time-course analyses and (iii) introducing a new set of data visualizations for expressed region analysis...
September 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27693710/strategy-for-large-scale-isolation-of-enantiomers-in-drug-discovery
#16
REVIEW
Hanna Leek, Linda Thunberg, Anna C Jonson, Kristina Öhlén, Magnus Klarqvist
A strategy for large-scale chiral resolution is illustrated by the isolation of pure enantiomer from a 5kg batch. Results from supercritical fluid chromatography will be presented and compared with normal phase liquid chromatography. Solubility of the compound in the supercritical mobile phase was shown to be the limiting factor. To circumvent this, extraction injection was used but shown not to be efficient for this compound. Finally, a method for chiral resolution by crystallization was developed and applied to give diastereomeric salt with an enantiomeric excess of 99% at a 91% yield...
September 28, 2016: Drug Discovery Today
https://www.readbyqxmd.com/read/27686466/cytological-and-biophysical-comparative-analysis-of-cell-structures-at-the-microsporogenesis-stage-in-sterile-and-fertile-allium-species
#17
Dorota Tchórzewska, Kamil Deryło, Krystyna Winiarczyk
Using a live-cell-imaging approach and autofluorescence-spectral imaging, we showed quantitative/qualitative fluctuations of chemical compounds within the meiocyte callose wall, providing insight into the molecular basis of male sterility in plants from the genus Allium. Allium sativum (garlic) is one of the plant species exhibiting male sterility, and the molecular background of this phenomenon has never been thoroughly described. This study presents comparative analyses of meiotically dividing cells, which revealed inhibition at the different microsporogenesis stages in male-sterile A...
September 29, 2016: Planta
https://www.readbyqxmd.com/read/27677951/a-global-exploratory-analysis-of-men-participating-in-gender-based-violence-prevention
#18
Richard M Tolman, Erin A Casey, Christopher T Allen, Juliana Carlson, Cliff Leek, Heather L Storer
Organizations addressing gender-based violence (GBV) increasingly include men as partners in prevention efforts. However, little is known about men who get involved in those efforts and what specific actions they take. We present analyses of data from an international sample of men involved in gender-based prevention work that aimed to describe (a) the nature of participants' involvement in prevention efforts, in both formal programming and in their daily lives; (b) characteristics of engaged men, including gender and bystander-related attitudes and beliefs, and social networks; and (c) factors that sustain men's involvement in GBV movements over time...
September 26, 2016: Journal of Interpersonal Violence
https://www.readbyqxmd.com/read/27644025/testing-the-ability-of-plants-to-access-potassium-from-framework-silicate-minerals
#19
David A C Manning, Joana Baptista, Mallely Sanchez Limon, Kirsten Brandt
The availability of K, essential for plant growth, from syenite (a silicate rock in which potassium feldspar is the dominant mineral; >90wt%), and phlogopite mica has been demonstrated using carefully designed plant growth pot experiments in which the only added source of K was the mineral of interest, with no loss of nutrients through drainage. Using pure quartz sand as a soil, both growth (increase in diameter) of leek plants and K-content of the plant material showed a dose-dependent positive response to the application (114-43000mgK/pot) of milled syenite with increases in plant diameter of 0...
September 16, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27641721/peak-deformations-in-preparative-supercritical-fluid-chromatography-due-to-co-solvent-adsorption
#20
Emelie Glenne, Hanna Leek, Magnus Klarqvist, Jörgen Samuelsson, Torgny Fornstedt
In supercritical fluid chromatography (SFC) the mobile phase comprises of carbon dioxide (CO2) as main solvent and smaller amounts of an organic polar solvent (often an alcohol) as co-solvent. The co-solvent is considered to function by changing the overall polarity of the eluent, i.e. by acting as a "modifier". However, recent studies indicate that the co-solvent methanol can also adsorb to some common SFC stationary phases. Hence, the co-solvent should also be able to function as an "adsorbing additive", i...
October 14, 2016: Journal of Chromatography. A
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