Optimized protocol for multigram preparation of emodin anthrone, a precursor in the hypericin synthesis

Haloferaxmediterranei is a haloarchaeon of high interest in biotechnology because it produces and mobilizes intracellular polyhydroxyalkanoate (PHA) granules during growth under stress conditions (limitation of phosphorous in the culture media), among other interesting metabolites (enzymes, carotenoids, etc.). The capability of PHA production by microbes can be monitored with the use of staining-based methods. However, the staining of haloarchaea cells is a challenging task; firstly, due to the high ionic strength of the medium, which is inappropriate for most of dyes, and secondly, due to the low permeability of the haloarchaea S-layer to macromolecules. In this work, Haloferax mediterranei is used as a halophilic archaeon model to describe an optimized protocol for the visualization and analysis of intracellular PHA granules in living cells. The method is based on double-fluorescence staining using Nile red and SYBR Green by confocal fluorescence microscopy. Thanks to this method, the capability of PHA production by new haloarchaea isolates could be easily monitored.

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In Silico Screening of Natural Products Isolated from Mexican Herbal Medicines against COVID-19

Biomolecules ◽

10.3390/biom11020216 ◽

2021 ◽

Vol 11 (2) ◽

pp. 216

Author(s):

Nadia A. Rivero-Segura ◽

Juan C. Gomez-Verjan

Keyword(s):

Natural Products ◽

In Silico ◽

Herbal Medicines ◽

In Silico Screening ◽

Docking Analysis ◽

Physiologically Based Pharmacokinetic ◽

Important Challenge ◽

Emodin Anthrone ◽

Therapeutic Tools ◽

Vaccine Distribution

The COVID-19 pandemic has already taken the lives of more than 2 million people worldwide, causing several political and socio-economic disturbances in our daily life. At the time of publication, there are non-effective pharmacological treatments, and vaccine distribution represents an important challenge for all countries. In this sense, research for novel molecules becomes essential to develop treatments against the SARS-CoV-2 virus. In this context, Mexican natural products have proven to be quite useful for drug development; therefore, in the present study, we perform an in silico screening of 100 compounds isolated from the most commonly used Mexican plants, against the SARS-CoV-2 virus. As results, we identify ten compounds that meet leadlikeness criteria (emodin anthrone, kaempferol, quercetin, aesculin, cichoriin, luteolin, matricin, riolozatrione, monocaffeoyl tartaric acid, aucubin). According to the docking analysis, only three compounds target the key proteins of SARS-CoV-2 (quercetin, riolozatrione and cichoriin), but only one appears to be safe (cichoriin). ADME (absorption, distribution, metabolism and excretion) properties and the physiologically based pharmacokinetic (PBPK) model show that cichoriin reaches higher lung levels (100 mg/Kg, IV); therefore, it may be considered in developing therapeutic tools.

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Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

Nature Communications ◽

10.1038/s41467-021-25411-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Puneet Sharma ◽

Jie Wu ◽

Benedikt S. Nilges ◽

Sebastian A. Leidel

Keyword(s):

Human Cells ◽

Ribosome Profiling ◽

Model Organisms ◽

Treatment Conditions ◽

Genome Wide ◽

Optimized Protocol ◽

Gene Level ◽

Translation Inhibitor ◽

Species Specific ◽

Conformational Restrictions

AbstractRibosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

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HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells

Methods and Protocols ◽

10.3390/mps4030049 ◽

2021 ◽

Vol 4 (3) ◽

pp. 49

Author(s):

Tomas Zelenka ◽

Charalampos Spilianakis

Keyword(s):

T Cells ◽

Long Range ◽

Three Dimensional ◽

Cell Types ◽

Range Interaction ◽

Chromatin Interactions ◽

Optimized Protocol ◽

Long Range Interaction ◽

Chromatin Compactness ◽

Detailed Protocol

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodical protocols have been published so far, yet their reproducibility and efficiency may vary. Most importantly, the high frequency of the dangling ends may dramatically affect the number of usable reads mapped to valid interaction pairs. Additionally, more obstacles arise from the chromatin compactness of certain investigated cell types, such as primary T cells, which due to their small and compact nuclei, impede limitations for their use in various genomic approaches. Here we systematically optimized all the major steps of the HiChIP protocol in T cells. As a result, we reduced the number of dangling ends to nearly zero and increased the proportion of long-range interaction pairs. Moreover, using three different mouse genotypes and multiple biological replicates, we demonstrated the high reproducibility of the optimized protocol. Although our primary goal was to optimize HiChIP, we also successfully applied the optimized steps to Hi-C, given their significant protocol overlap. Overall, we describe the rationale behind every optimization step, followed by a detailed protocol for both HiChIP and Hi-C experiments.

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Optimization of a WGA-Free Molecular Tagging-Based NGS Protocol for CTCs Mutational Profiling

International Journal of Molecular Sciences ◽

10.3390/ijms21124364 ◽

2020 ◽

Vol 21 (12) ◽

pp. 4364

Author(s):

Giuseppa De Luca ◽

Barbara Cardinali ◽

Lucia Del Mastro ◽

Sonia Lastraioli ◽

Franca Carli ◽

...

Keyword(s):

Substantial Reduction ◽

Breast Cancer Patients ◽

Dna Templates ◽

Molecular Tagging ◽

Mutational Profiling ◽

Optimized Protocol ◽

Set Up ◽

Detection Of Mutations ◽

Almost All ◽

Next Generation Sequencing Ngs

Molecular characterization of Circulating Tumor Cells (CTCs) is still challenging, despite attempts to minimize the drawbacks of Whole Genome Amplification (WGA). In this paper, we propose a Next-Generation Sequencing (NGS) optimized protocol based on molecular tagging technology, in order to detect CTCs mutations while skipping the WGA step. MDA-MB-231 and MCF-7 cell lines, as well as leukocytes, were sorted into pools (2–5 cells) using a DEPArray™ system and were employed to set up the overall NGS procedure. A substantial reduction of reagent volume for the preparation of libraries was performed, in order to fit the limited DNA templates directly derived from cell lysates. Known variants in TP53, KRAS, and PIK3CA genes were detected in almost all the cell line pools (35/37 pools, 94.6%). No additional alterations, other than those which were expected, were found in all tested pools and no mutations were detected in leukocytes. The translational value of the optimized NGS workflow is confirmed by sequencing CTCs pools isolated from eight breast cancer patients and through the successful detection of variants. In conclusion, this study shows that the proposed NGS molecular tagging approach is technically feasible and, compared to traditional NGS approaches, has the advantage of filtering out the artifacts generated during library amplification, allowing for the reliable detection of mutations and, thus, making it highly promising for clinical use.

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