Showing papers by "Agilent Technologies published in 2015"
TL;DR: Co-delivering chemically modified sgRNAs with Cas9 mRNA or protein is an efficient RNA- or ribonucleoprotein (RNP)-based delivery method for the CRISPR-Cas system, without the toxicity associated with DNA delivery.
Abstract: CRISPR-Cas-mediated genome editing relies on guide RNAs that direct site-specific DNA cleavage facilitated by the Cas endonuclease. Here we report that chemical alterations to synthesized single guide RNAs (sgRNAs) enhance genome editing efficiency in human primary T cells and CD34+ hematopoietic stem and progenitor cells. Co-delivering chemically modified sgRNAs with Cas9 mRNA or protein is an efficient RNA- or ribonucleoprotein (RNP)-based delivery method for the CRISPR-Cas system, without the toxicity associated with DNA delivery. This approach is a simple and effective way to streamline the development of genome editing with the potential to accelerate a wide array of biotechnological and therapeutic applications of the CRISPR-Cas technology.
886 citations
TL;DR: In this article, the authors use Capture Hi-C (CHi-C) to examine the long-range interactions of almost 22,000 promoters in 2 human blood cell types and identify over 1.6 million shared and cell type-restricted interactions spanning hundreds of kilobases between promoters and distal loci.
Abstract: Transcriptional control in large genomes often requires looping interactions between distal DNA elements, such as enhancers and target promoters. Current chromosome conformation capture techniques do not offer sufficiently high resolution to interrogate these regulatory interactions on a genomic scale. Here we use Capture Hi-C (CHi-C), an adapted genome conformation assay, to examine the long-range interactions of almost 22,000 promoters in 2 human blood cell types. We identify over 1.6 million shared and cell type-restricted interactions spanning hundreds of kilobases between promoters and distal loci. Transcriptionally active genes contact enhancer-like elements, whereas transcriptionally inactive genes interact with previously uncharacterized elements marked by repressive features that may act as long-range silencers. Finally, we show that interacting loci are enriched for disease-associated SNPs, suggesting how distal mutations may disrupt the regulation of relevant genes. This study provides new insights and accessible tools to dissect the regulatory interactions that underlie normal and aberrant gene regulation.
869 citations
TL;DR: The results provide the first genome-wide catalog linking gene promoters to their long-range interacting elements and highlight the complex spatial regulatory circuitry controlling mammalian gene expression.
Abstract: The mammalian genome harbors up to one million regulatory elements often located at great distances from their target genes. Long-range elements control genes through physical contact with promoters and can be recognized by the presence of specific histone modifications and transcription factor binding. Linking regulatory elements to specific promoters genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays. Here we apply a sequence capture approach to enrich Hi-C libraries for >22,000 annotated mouse promoters to identify statistically significant, long-range interactions at restriction fragment resolution, assigning long-range interacting elements to their target genes genome-wide in embryonic stem cells and fetal liver cells. The distal sites contacting active genes are enriched in active histone modifications and transcription factor occupancy, whereas inactive genes contact distal sites with repressive histone marks, demonstrating the regulatory potential of the distal elements identified. Furthermore, we find that coregulated genes cluster nonrandomly in spatial interaction networks correlated with their biological function and expression level. Interestingly, we find the strongest gene clustering in ES cells between transcription factor genes that control key developmental processes in embryogenesis. The results provide the first genome-wide catalog linking gene promoters to their long-range interacting elements and highlight the complex spatial regulatory circuitry controlling mammalian gene expression.
426 citations
TL;DR: PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network and it is proposed that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.
Abstract: The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks. The strongest spatial network is composed of the four Hox gene clusters and early developmental transcription factor genes, the majority of which contact poised enhancers. Removal of Polycomb repression leads to disruption of promoter-promoter contacts in the Hox gene network. In contrast, promoter-enhancer contacts are maintained in the absence of Polycomb repression, with accompanying widespread acquisition of active chromatin signatures at network enhancers and pronounced transcriptional upregulation of network genes. Thus, PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network. We propose that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.
334 citations
TL;DR: A time-of-flight mass spectrometry detector is used to identify fluorinated compounds in natural waters collected from locations with historical perfluorinated compound contamination and detected 12 novel perfluoroalkyl ether carboxylic and sulfonic acids in surface water in North Carolina, USA.
Abstract: Recent scientific scrutiny and concerns over exposure, toxicity, and risk have led to international regulatory efforts resulting in the reduction or elimination of certain perfluorinated compounds from various products and waste streams. Some manufacturers have started producing shorter chain per- and polyfluorinated compounds to try to reduce the potential for bioaccumulation in humans and wildlife. Some of these new compounds contain central ether oxygens or other minor modifications of traditional perfluorinated structures. At present, there has been very limited information published on these “replacement chemistries” in the peer-reviewed literature. In this study we used a time-of-flight mass spectrometry detector (LC-ESI-TOFMS) to identify fluorinated compounds in natural waters collected from locations with historical perfluorinated compound contamination. Our workflow for discovery of chemicals included sequential sampling of surface water for identification of potential sources, nontargeted TOFMS...
262 citations
TL;DR: In this article, the incorporation of in-situ reduced graphene oxide (rGO) into geopolymers was reported for the first time, and the resulting rGO-geopolymeric composites are easy to manufacture and exhibit excellent mechanical properties.
191 citations
TL;DR: This review serves to summarize the available literature on the impacts of fermentation in coffee processing on coffee aroma as well as other unconventional avenues where fermentation is employed for coffee aroma modulation.
178 citations
TL;DR: A novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment and shows that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured differential TF binding.
Abstract: Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the characterization of sequence motifs recognized by TFs, our ability to quantitatively predict TF binding to different regulatory sequences is still limited. Here, we present a novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment. Applying this binding assay to two yeast TFs, we demonstrate that sequences outside the core TF binding site profoundly affect TF binding. We show that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured differential TF binding. We further characterize the dependence of TF binding, accounting for measurements of single and co-occurring binding events, on the number and location of binding sites and on the TF concentration. Finally, by coupling our in vitro TF binding measurements, and another application of our method probing nucleosome formation, to in vivo expression measurements carried out with the same template sequences serving as promoters, we offer insights into mechanisms that may determine the different expression outcomes observed. Our assay thus paves the way to a more comprehensive understanding of TF binding to regulatory sequences and allows the characterization of TF binding determinants within and outside of core binding sites.
155 citations
TL;DR: The autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.
Abstract: An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. As a result of this unique integration, we can analyze large profiling datasets and simultaneously obtain structural identifications. Validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometry data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will u...
152 citations
TL;DR: Results demonstrate that a T2D-associated gene plays an important role in tumour development and that its expression is strictly controlled at the mRNA and protein levels.
Abstract: Cancer stem cells (CSCs) have been identified in various types of cancer; however, the mechanisms by which cells acquire CSC properties such as drug resistance and tumour seeding ability are not fully understood. Here, we identified microRNA-27b (miR-27b) as a key regulator for the generation of a side-population in breast cancer cells that showed CSC properties, and also found that the anti-type II diabetes (T2D) drug metformin reduced this side-population via miR-27b-mediated repression of ectonucleotide pyrophosphatase/phosphodiesterase family member 1 (ENPP1), which is involved in T2D development. ENPP1 induced the generation of the side-population via upregulation of the ABCG2 transporter. ENPP1 was also identified as a substrate of the 26S proteasome, the activity of which is downregulated in CSCs. Overall, these results demonstrate that a T2D-associated gene plays an important role in tumour development and that its expression is strictly controlled at the mRNA and protein levels.
126 citations
TL;DR: A simple and high-throughput multiresidue pesticide analysis method was developed and validated for 219 pesticides in cereals based on QuEChERS procedure combined with gas chromatography-triple quadrupole mass spectrometry (GC-MS/MS).
TL;DR: The capillary electrophoresis-tandem mass spectrometry method was successfully used to determine biogenic amines in commercial samples of beer and wine.
TL;DR: The presence of 5hmC is demonstrated for the first time in human urine, which probably implicates a much higher turnover of5hmC than 5mC in mammalian genomic DNA and underscores the importance of DNA demethylation in daily life.
Abstract: The sixth DNA base 5-hydroxymethylcytosine (5hmC) is the major oxidation product of the epigenetic modification 5-methylcytosine (5mC), mediating DNA demethylation in mammals. Reduced 5hmC levels are found to be linked with various tumors and neurological diseases; therefore, 5hmC is an emerging biomarker for disease diagnosis, treatment, and prognosis. Due to its advantages of being sterile, easily accessible in large volumes, and noninvasive to patients, urine is a favored diagnostic biofluid for 5hmC analysis. Here we developed an accurate, sensitive, and specific assay for quantification of 5mC, 5hmC, and other DNA demethylation intermediates in human urine. The urinary samples were desalted and enriched using off-line solid-phase extraction, followed by stable isotope dilution HPLC-MS/MS analysis for 5hmC and 5mC. By the use of ammonium bicarbonate (NH4HCO3) as an additive to the mobile phase, we improved the online-coupled MS/MS detection of 5mC, 5hmC, and 5-formylcytosine (5fC) by 1.8–14.3 times. T...
TL;DR: Two cases with central nervous system metastases from anaplastic lymphoma kinase (ALK)positive non–small-cell lung cancer (NSCLC) that benefited from the ALK-inhibitor crizotinib are described.
TL;DR: A framework for engineering RNA devices from preexisting aptamers that exhibit ligand-responsive ribozyme tertiary interactions is described, which performed better in terms of gene silencing, activation ratio and ligand sensitivity than optimized RNA devices that rely on secondary-structure changes.
Abstract: Methods for rapidly assessing sequence-structure-function landscapes and developing conditional gene-regulatory devices are critical to our ability to manipulate and interface with biology. We describe a framework for engineering RNA devices from preexisting aptamers that exhibit ligand-responsive ribozyme tertiary interactions. Our methodology utilizes cell sorting, high-throughput sequencing and statistical data analyses to enable parallel measurements of the activities of hundreds of thousands of sequences from RNA device libraries in the absence and presence of ligands. Our tertiary-interaction RNA devices performed better in terms of gene silencing, activation ratio and ligand sensitivity than optimized RNA devices that rely on secondary-structure changes. We applied our method to build biosensors for diverse ligands and determine consensus sequences that enable ligand-responsive tertiary interactions. These methods advance our ability to develop broadly applicable genetic tools and to elucidate the underlying sequence-structure-function relationships that empower rational design of complex biomolecules.
TL;DR: In this article, the authors provide an in-depth understanding of KED in cell-based ICP-MS for analysts to make better use of it. But the intrinsic limitations of this technique are shown to lie in the statistical nature of collision processes, which causes the broadening of ion kinetic energy distribution that hinders efficient KED.
TL;DR: The absolute stereochemistry of compounds with axial and planar chirality is successfully determined by the crystalline sponge method without crystallization or derivatization of the compounds.
Abstract: The absolute stereochemistry of compounds with axial and planar chirality is successfully determined by the crystalline sponge method without crystallization or derivatization of the compounds. This method is applied to absolute structure determination in the asymmetric synthesis of unique compounds with axial and planar chirality.
TL;DR: It is demonstrated that scientific confidence in these pathways can be increased though the use of unconventional information (eg, computational identification of potential initiators) and AOPs at all levels of confidence can contribute to specific uses.
TL;DR: The UHPLC-QToF-MS analysis of pyrrolizidine alkaloids (PAs) from various parts of 37 botanicals and 7 products was performed and the Asteraceae family was found to contain senecionine and lycopsamine type PAs.
TL;DR: A recently developed uniform-field high resolution ion mobility (IM) quadrupole time of flight (Q-TOF) mass spectrometer is used for evaluating the utility of alternate drift gases for complex sample analyses.
Abstract: A recently developed uniform-field high resolution ion mobility (IM) quadrupole time of flight (Q-TOF) mass spectrometer is used for evaluating the utility of alternate drift gases for complex sample analyses. This study provides collision cross section comparison for 275 total pesticides including structural isomers in nitrogen, helium, carbon dioxide, nitrous oxide and sulfur hexafluoride drift gases. Furthermore, a set of small molecules and Agilent tune mix compounds were used to study the trends in experimentally derived collision cross section values in argon and the alternate drift gases. Two isomeric trisaccharides, melezitose and raffinose, were used to evaluate the effect of the drift gasses for mobility separation. The hybrid ion mobility Q-TOF mass analyzer used in this study consists of a low pressure uniform field drift tube apparatus coupled to a high resolution Q-TOF mass spectrometer. Conventionally, low pressure ion mobility instruments are operated using helium drift gas to obtain optimal structural information and collision cross-section (CCS) values that compare to theoretical CCS values. The instrument employed in this study uses nitrogen as the standard drift gas but also allows the utility of alternate drift gases for improved structural analysis and selectivity under certain conditions. The use of alternate drift gases with a wide range of polarizabilities allows the evaluation of mobility separation power in terms of induced dipole interactions between the drift gas and the analyte ions.
TL;DR: In this paper, the impact of pre-set redox conditions on the dynamics of Ba, Cr, Sr, and V in a floodplain soil was assessed using an automatic biogeochemical microcosm system allowing computer controlled regulation of EH by adapting the supply of N2 or O2 to the soil suspension.
Abstract: Floodplain soils are often contaminated with toxic elements such as Ba, Cr, Sr, and V. For an adequate risk assessment of such contaminated sites, the assessment of factors affecting the leaching of those elements from riverine soils into water is fundamental. Since the redox potential (EH) can be important within this context, we aimed to assess the impact of pre-set redox conditions on the dynamics of Ba, Cr, Sr, and V in a floodplain soil. To achieve this aim, we used an automatic biogeochemical microcosm system allowing computer-controlled regulation of EH by adapting the supply of N2 or O2 to the soil suspension. With this system, the effect of EH on the dynamics of Ba, Cr, Sr, and V was studied mechanistically. Chromium and V were negatively correlated with EH possibly due to co-precipitation of these metals with Fe (hydr)oxides at high EH. Vanadium might additionally be oxidized from more soluble V(IV) to less soluble V(V) with rising EH. Barium and Sr were positively correlated with EH, which might be attributed to their association with dissolved organic carbon (DOC). The influence of pH on the dynamics of the studied elements seemed to be of minor importance in our study. A significant negative correlation was observed between the specific UV absorbance at 254 nm (SUVA 254) and EH indicating that oxidizing conditions favored the removal of aromatic DOC molecules from solution via binding to Fe (hydr)oxides. Redox potential is important for metal fate in the current study. Results imply an absorption of Cr and V to Fe (hydr)oxides and an interaction with DOC while particularly Ba and Sr dynamics may be influenced by DOC. In the future, different V species in wetland soils under pre-definite redox conditions should be determined and further studies should elucidate the specific role of DOC and sulfur (S) chemistry on the dynamics of the studied metals.
TL;DR: A quantitation method for 18 aroma compounds reported to contribute to "oxidative" flavor in wines was developed and showed a significant increase in the concentration of some of the monitored compounds in the wine, particularly methional, 2-phenylacetaldehyde, and 3-methylbutanal.
Abstract: A quantitation method for 18 aroma compounds reported to contribute to "oxidative" flavor in wines was developed. The method allows quantitation of the (E)-2-alkenals ((E)-2-hexenal, (E)-2-heptenal, (E)-2-octenal, and (E)-2-nonenal), various Strecker aldehydes (methional, 2-phenylacetaldehyde, 3-methylbutanal, and 2-methylpropanal), aldehydes (furfural, 5-methylfurfural, hexanal, and benzaldehyde), furans (sotolon, furaneol, and homofuraneol), as well as alcohols (methionol, eugenol, and maltol) in the same analysis. The aldehydes were determined after derivatization directly in the wine with O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine hydrochloride; the formed oximes along with the underivatized aroma compounds were isolated by solid-phase extraction and analyzed by means of GC-MS/MS. The method was used to investigate the effect of different closures (synthetic closures, natural corks, and screw cap) on the formation of oxidation-related compounds in 14 year old white wine. Results showed a significant increase in the concentration of some of the monitored compounds in the wine, particularly methional, 2-phenylacetaldehyde, and 3-methylbutanal.
Utrecht University1, Leiden University Medical Center2, Radboud University Nijmegen3, University of Amsterdam4, Maastricht University5, Agilent Technologies6, Erasmus University Rotterdam7, Illumina8, University Medical Center Groningen9, Hoffmann-La Roche10, Life Technologies11, VU University Medical Center12
TL;DR: It is concluded that alternative diagnoses may infer a certain level of ‘greediness’ to come to a positive diagnosis in interpreting sequencing results, and invited clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care.
Abstract: Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patients with cardiomyopathy. We highlight critical implementation choices, including the specific contributions of laboratory and medical specialists, bioinformaticians and researchers to diagnostic genome care, and how these affect interpretation and reporting of variants. Reported pathogenic mutations were consistent for all but one patient. Of the two centers that were inconsistent in their diagnosis, one reported to have found 'no causal variant', thereby underdiagnosing this patient. The other provided an alternative diagnosis, identifying another variant as causal than the other centers. Ethical and legal analysis showed that informed consent procedures in all centers were generally adequate for diagnostic NGS applications that target a limited set of genes, but not for exome- and genome-based diagnosis. We propose changes to further improve and align these procedures, taking into account the blurring boundary between diagnostics and research, and specific counseling options for exome- and genome-based diagnostics. We conclude that alternative diagnoses may infer a certain level of 'greediness' to come to a positive diagnosis in interpreting sequencing results. Moreover, there is an increasing interdependence of clinic, diagnostics and research departments for comprehensive diagnostic genome care. Therefore, we invite clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care.
TL;DR: Findings support that a previously identified decrease in plasma iron levels in AD patients within the AIBL study is attributable to decreased loading of iron into transferrin, and that this subtle but discriminatory change is not observed through routine pathological testing.
Abstract: Plasma iron levels are decreased in Alzheimer's disease (AD) and associated with an idiopathic anemia. We examined iron-binding plasma proteins from AD patients and healthy controls from the Australian Imaging, Biomarkers and Lifestyle (AIBL) Flagship Study of Ageing using size exclusion chromatography-inductively coupled plasma-mass spectrometry. Peak area corresponding to transferrin (Tf) saturation was directly compared to routine pathological testing. We found a significant decrease in transferrin-associated iron in AD that was missed by routine pathological tests of transferrin saturation, and that was able to discriminate between AD and controls. The AD cases showed no significant difference in transferrin concentration, only a decrease in total transferrin-bound iron. These findings support that a previously identified decrease in plasma iron levels in AD patients within the AIBL study is attributable to decreased loading of iron into transferrin, and that this subtle but discriminatory change is not observed through routine pathological testing.
TL;DR: Analysis by collision cell ICP-MS significantly over-estimated As and Se concentration due to REE doubly charged formation; mathematical correction increased the accuracy of analysis but is prone to error when analyte concentration and sensitivity is low and interferent is high.
Abstract: Recent reports of As concentrations in certain food and drinks have garnered public concern and led to a lowering of the US guideline maximum concentration for inorganic As in apple juice and proposed limits for As in rice products. In contrast Se is an essential micro-nutrient that can be limiting when Se-poor soils yield Se-poor food crops. Rare earth element (REE) doubly charged interferences on As and Se can be significant even when initial ICP-MS tuning minimizes doubly charged formation. We analyzed NIST 1547 (peach leaves) and 1515 (apple leaves), which contain high levels of REEs, by quadrupole ICP-MS with (He) collision mode, H2 reaction mode or triple quadrupole ICP-MS (ICP-QQQ) in mass-shift mode (O2 and O2/H2). Analysis by collision cell ICP-MS significantly over-estimated As and Se concentration due to REE doubly charged formation; mathematical correction increased the accuracy of analysis but is prone to error when analyte concentration and sensitivity is low and interferent is high. For Se, H2 reaction mode was effective in suppressing Gd2+ leading to accurate determination of Se in both SRMs without the need for mathematical correction. ICP-QQQ using mass-shift mode for As+ from m/z 75 to AsO+ at m/z 91 and Se+ from m/z 78 to SeO+ at m/z 94 alleviated doubly charged effects and resulted in accurate determination of As and Se in both SRMs without the need for correction equations. Zr and Mo isobars at 91 and 94 were shown to be effectively rejected by the MS/MS capability of the ICP-QQQ.
TL;DR: It is demonstrated that the rigid mineralized bone matrix can alter gene expression and bone destruction in an Iβ3/TGF-β-dependent manner, and suggests that I β3 inhibitors are a potential therapeutic approach for blocking tumor transition to a bone destructive phenotype.
TL;DR: Loop-based multiple heart-cutting two-dimensional liquid chromatography (2D-LC) is presented as a solution to quantify target components in complex matrices, such as additives in polymers, at very high chromatographic resolution.
Abstract: Loop-based multiple heart-cutting (MHC) two-dimensional liquid chromatography (2D-LC) is presented as a solution to quantify target components in complex matrices, such as additives in polymers, at very high chromatographic resolution. The determination of hexabromocyclododecane (HBCD) in polystyrene (PS) is described. One dimensional ((1)D) LC analysis with UV detection did not allow quantitation of the main isomers of HBCD due to peak overlap with polymer components. MHC 2D-LC analysis provided the separation power, accuracy, and repeatability needed for quantitative analysis of the additives of interest. Heart-cuts from peaks of the (1)D-chromatogram or entire regions of interest are sampled into loops, where they remain parked until their sequential reinjection onto the second dimension ((2)D) column. A column set consisting of phenyl ((1)D) and C18 ((2)D) stationary phases gave baseline separation in (2)D between HBCD and PS background. Linearity for spiked polymer samples was achieved over a range of 0.02-1.00 wt % HBCD relative to the amount of polymer. The limit of quantitation was estimated at 0.01 wt % HBCD in PS. A peak area RSD of 0.7% obtained for ten replicates of a real sample demonstrated excellent repeatability of the analysis. MHC 2D-LC is an elegant solution for quantitative analyses of difficult-to-separate samples when conventional (1)D separation fails.
01 Jan 2015-Food Additives and Contaminants Part A-chemistry Analysis Control Exposure & Risk Assessment
TL;DR: In the present study, coumarin and other marker compounds indicative of ‘cinnamon’ were analysed using DART-QToF-MS in various samples of cinnamon and involved the use of [M + H]+ ions in positive mode in addition to principal component analysis (PCA) using Mass Profiler Professional software to visualise several samples for quality.
Abstract: The use of cinnamon as a spice and flavouring agent is widespread throughout the world. Many different species of plants are commonly referred to as ‘cinnamon’. ‘True cinnamon’ refers to the dried inner bark of Cinnamomum verum J. S. Presl (syn. C. zeylanicum) (Lauraceae). Other ‘cinnamon’ species, C. cassia (Nees & T. Nees) J. Presl (syn. C. aromaticum Nees) (Chinese cassia), C. loureiroi Nees (Saigon cassia), and C. burmannii (Nees & T. Nees) Blume (Indonesian cassia), commonly known as cassia, are also marketed as cinnamon. Since there is a prevalence of these various types of ‘cinnamons’ on the market, there is a need to develop a rapid technique that can readily differentiate between true cinnamon (C. verum) and other commonly marketed species. In the present study, coumarin and other marker compounds indicative of ‘cinnamon’ were analysed using DART-QToF-MS in various samples of cinnamon. This method involved the use of [M + H]+ ions in positive mode in addition to principal component analysis (PCA)...
TL;DR: The Human Toxome Project, funded as an NIH Transformative Research grant 2011-2016, is focused on developing the concepts and the means for deducing, validating and sharing molecular pathways of toxicity (PoT) using the test case of estrogenic endocrine disruption.
Abstract: The Human Toxome Project, funded as an NIH Transformative Research grant 2011-2016, is focused on developing the concepts and the means for deducing, validating and sharing molecular pathways of toxicity (PoT). Using the test case of estrogenic endocrine disruption, the responses of MCF-7 human breast cancer cells are being phenotyped by transcriptomics and mass-spectroscopy-based metabolomics. The bioinformatics tools for PoT deduction represent a core deliverable. A number of challenges for quality and standardization of cell systems, omics technologies and bioinformatics are being addressed. In parallel, concepts for annotation, validation and sharing of PoT information, as well as their link to adverse outcomes, are being developed. A reasonably comprehensive public database of PoT, the Human Toxome Knowledge-base, could become a point of reference for toxicological research and regulatory test strategies.
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03 Dec 2015TL;DR: In this paper, modified guide RNAs and their use in clustered, regularly interspaced, short palindromic repeats (CRISPR)/ CRISPR-associated (Cas) systems are described.
Abstract: The present invention relates to modified guide RNAs and their use in clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems.