Single nucleotide extension technology for quantitative site-specific evaluation of (met)C/C in GC-rich regions

The development and use of high throughput technologies for detailed mapping of methylated cytosines ((met)C) is becoming of increasing importance for the expanding field of epigenetics. The single nucleotide primer extension reaction used for genotyping of single nucleotide polymorphisms has been recently adapted to interrogate the bisulfite modification induced ‘quantitative’ C/T polymorphism that corresponds to (met)C/C in the native DNA. In this study, we explored the opportunity to investigate C/T (and G/A) ratios using the Applied Biosystems (ABI) SNaPshot technology. The main effort of this study was dedicated to addressing the complexities in the analysis of DNA methylation in GC-rich regions where interrogation of the target cytosine can be confounded by variable degrees of methylation in other cytosines (resulting in variable C/T or G/A ratios after treatment with bisulfite) in the annealing site of the interrogating primer. In our studies, the mismatches of the SNaPshot primer with the target DNA sequence resulted in a biasing effect of up to 70% while these effects decreased as the location of the polymorphic site moved upstream of the target cytosine. We demonstrated that the biasing effect can be corrected with the SNaPshot primers containing degenerative C/T and G/A nucleotides. A series of experiments using various permutations of quantitative C/T and G/A polymorphisms at various positions of the target DNA sequence demonstrated that SNaPshot is able to accurately report cytosine methylation levels with <5% average SD from the true values. Given the relative simplicity of the method and the possibility to multiplex C/T and G/A interrogations, the SNaPshot approach may become a useful tool for large-scale mapping of (met)C

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 - Meeting Abstracts - Antwerp, Belgium. 15–20 July 2017

This work was produced as part of the activities of FAPESP Research,\ud Disseminations and Innovation Center for Neuromathematics (grant\ud 2013/07699-0, S. Paulo Research Foundation). NLK is supported by a\ud FAPESP postdoctoral fellowship (grant 2016/03855-5). ACR is partially\ud supported by a CNPq fellowship (grant 306251/2014-0)

Extraction and Phytochemical Analysis of Anthemis susiana Nabelek Using Headspace-solid Phase (HS-SPME) and Gas Chromatography-mass Spectrometry (GC-MS)

Chamomile has several variants, such as Anthemis Susiana Nabelek, Matricaria chamomilla L., Chamomilla recutita (L.) Rauschert, Matricaria suaveolens Koch and etc. Medicinal herbs, extracts and essential oils are of particular importance in the pharmaceutical, cosmetic and food industries. The phytoanalysis of these compounds is of particular importance. In April 2019, Anthemis Susiana Nabelek samples were collected from the Thermal Springs area of Dehloran, south of Ilam province, western Iran. The plant was dried and then pulverized. The essential oil was extracted from the plant using HS-SPME and analyzed using GC-MS. GC-MS results showed that Anthemis susiana Nabelek contains 63 chemical compounds. The main chemical compounds included alpha-bisabolol oxide A (19.07), alpha-pinene (15.50), beta-bisabolene (12.56), spathulenol (9.23), beta-farnesen (8.95), alpha-bisabolol (4.72), caryophyllene oxide (4.46), trans-farnesol (3.75), and dl-limonene (3.47)

Method for quantifying arousal and consciousness in healthy states and severe brain injury via EEG-based measures of corticothalamic physiology.

peer reviewed[en] BACKGROUND: Characterization of normal arousal states has been achieved by fitting predictions of corticothalamic neural field theory (NFT) to electroencephalographic (EEG) spectra to yield relevant physiological parameters. NEW METHOD: A prior fitting method is extended to distinguish conscious and unconscious states in healthy and brain injured subjects by identifying additional parameters and clusters in parameter space. RESULTS: Fits of NFT predictions to EEG spectra are used to estimate neurophysiological parameters in healthy and brain injured subjects. Spectra are used from healthy subjects in wake and sleep and from patients with unresponsive wakefulness syndrome, in a minimally conscious state (MCS), and emerged from MCS. Subjects cluster into three groups in parameter space: conscious healthy (wake and REM), sleep, and brain injured. These are distinguished by the difference X-Y between corticocortical (X) and corticothalamic (Y) feedbacks, and by mean neural response rates α and β to incoming spikes. X-Y tracks consciousness in healthy individuals, with smaller values in wake/REM than sleep, but cannot distinguish between brain injuries. Parameters α and β differentiate deep sleep from wake/REM and brain injury. COMPARISON WITH EXISTING METHODS: Other methods typically rely on laborious clinical assessment, manual EEG scoring, or evaluation of measures like Φ from integrated information theory, for which no efficient method exists. In contrast, the present method can be automated on a personal computer. CONCLUSION: The method provides a means to quantify consciousness and arousal in healthy and brain injured subjects, but does not distinguish subtypes of brain injury

Bismuth‐melt trails trapped in cassiterite–quartz veins

Native bismuth in the form of metallic melt has been considered instrumental to the formation of some metallic ore deposits via a mechanism dubbed the ?Liquid Bismuth Collector Model.? Here, we provide petrographical documentation of trail?forming, ?m?sized blebs of native bismuth in cassiterite?quartz veins from the Santa B?rbara greisen Sn deposit in the Rond?nia tin province of northern Brazil. These inclusions suggest the trapping of a Bi melt that took place during vein formation, in a mecha? nism similar to the entrapment of fluid inclusions