A DNA assembly toolkit to unlock the CRISPR/Cas9 potential for metabolic engineering

CRISPR/Cas9-based technologies are revolutionising the way we engineer microbial cells. One of the key advantages of CRISPR in strain design is that it enables chromosomal integration of marker-free DNA, eliminating laborious and often inefficient marker recovery procedures. Despite the benefits, assembling CRISPR/Cas9 editing systems is still not a straightforward process, which may prevent its use and applications. In this work, we have identified some of the main limitations of current Cas9 toolkits and designed improvements with the goal of making CRISPR technologies easier to access and implement. These include 1) A system to quickly switch between marker-free and marker-based integration constructs using both a Cre-expressing and standard Escherichia coli strains, 2) the ability to redirect multigene integration cassettes into alternative genomic loci via Golden Gate-based exchange of homology arms, 3) a rapid, simple in-vivo method to assembly guide RNA sequences via recombineering between Cas9-helper plasmids and single oligonucleotides. We combine these methodologies with well-established technologies into a comprehensive toolkit for efficient metabolic engineering using CRISPR/Cas9. As a proof of concept, we developed the YaliCraft toolkit for Yarrowia lipolytica, which is composed of a basic set of 147 plasmids and 7 modules with different purposes. We used the toolkit to generate and characterize a library of 137 promoters and to build a de novo strain synthetizing 373.8 mg/L homogentisic acid

A study on L-threonine and L-serine uptake in Escherichia coli K-12

In the current study, we report the identification and characterization of the yifK gene product as a novel amino acid carrier in E. coli K-12 cells. Both phenotypic and biochemical analyses showed that YifK acts as a permease specific to L-threonine and, to a lesser extent, L-serine. An assay of the effect of uncouplers and composition of the reaction medium on the transport activity indicates that YifK utilizes a proton motive force to energize substrate uptake. To identify the remaining threonine carriers, we screened a genomic library prepared from the yifK-mutant strain and found that brnQ acts as a multicopy suppressor of the threonine transport defect caused by yifK disruption. Our results indicate that BrnQ is directly involved in threonine uptake as a low-affinity but high-flux transporter, which forms the main entry point when the threonine concentration in the external environment reaches a toxic level. By abolishing YifK and BrnQ activity, we unmasked and quantified the threonine transport activity of the LIV-I branched chain amino acid transport system and demonstrated that LIV-I contributes significantly to total threonine uptake. However, this contribution is likely smaller than that of YifK. We also observed the serine transport activity of LIV-I, which was much lower compared with that of the dedicated SdaC carrier, indicating that LIV-I plays a minor role in the serine uptake. Overall, these findings allow us to propose a comprehensive model of the threonine/serine uptakesubsystem in E. coli cells

ДИНАМИЧЕСКИЙ СКРИНИНГ ПРЕДРАКОВЫХ СОСТОЯНИЙ ПИЩЕВОДА С ПОМОЩЬЮ МОЛЕКУЛЯРНО-ГЕНЕТИЧЕСКОГО АНАЛИЗА

Introduction. Esophageal adenocarcinoma develops from areas of intestinal metaplasia in Barrett’s esophagus, similar to how intestinal metaplasia transforms into gastric adenocarcinomas in the stomach. Atypia with intraepithelial neoplasia is difficult to distinguish from reactive and regenerative changes, especially in erosive mucosa of the esophagus. Observation of patients with Barrett’s esophagus allows the identification of adenocarcinoma in the earlier, more curable stages in many patients.The aim of our study was to study the prospects of using a classifier based on miRNA profiling in histological samples of Barrett’s esophagus to determine the risk of malignancy and treatment tactics.Material and Methods. In this study, 119 samples of archival histological material in the form of paraffin blocks were used: 89 samples of gastric mucosa with dysplasia and 30 samples of Barrett’s esophagus. The expression level of miRNA-145-5p, -150-5p, -20a-5p, -21-5p,-31-5p,-34a-5p,-375 was determined using real-time RT-PC R. Samples were stratified into different groups using the C-RT decision tree algorithm.Results. 26.7 % of Barrett’s esophagus samples were classified by expression of the proposed miRNAs as cancer, which may indicate a potential development of a malignant tumor in the mucosa of the esophagus when morphological changes have not yet been found.Введение. Специализированный кишечный эпителий с признаками атипической гиперплазии при пищеводе Барретта наиболее часто подвергается малигнизации и является предшественником аденокарциномы пищевода, аналогично тому, как в  желудке кишечная метаплазия трансформируется в аденокарциному. Атипия при внутриэпителиальной неоплазии в пищеводе Барретта трудно отличима от реактивных и регенераторных изменений, особенно при эрозированной слизистой пищевода. Анализ молекулярных маркеров является перспективным подходом в качестве дополнения к морфологическому исследованию при эндоскопическом скрининге пищевода Барретта. Цель исследования – изучение перспективности применения классификатора, основанного на профилировании миРНК в гистологических образцах пищевода Барретта, для определения риска злокачественности и тактики лечения.Материал и методы. В работе было использовано 119 образцов архивного гистологического материала в виде парафиновых блоков: 89 образцов язв желудка с дисплазией и 30 образцов пищевода Барретта. Уровень экспрессии микроРНК-145-5p, -150-5p, -20a-5p, -21-5p, -31-5p, -34a-5p, -375 определялся с помощью ОТ-ПЦР в реальном времени. Стратификацию образцов на разные группы проводили с помощью алгоритма построения дерева принятия решений c-Rt. Результаты. С помощью экспрессии предложенного набора миРНК 26,7 % образцов пищевода Барретта были классифицированы как рак, что может свидетельствовать о потенциальном развитии злокачественной опухоли в слизистой пищевода, когда морфологические изменения еще не найдены.

The ART-XC telescope on board the SRG observatory

ART-XC (Astronomical Roentgen Telescope - X-ray Concentrator) is the hard X-ray instrument with grazing incidence imaging optics on board the Spektr-Roentgen-Gamma (SRG) observatory. The SRG observatory is the flagship astrophysical mission of the Russian Federal Space Program, which was successively launched into orbit around the second Lagrangian point (L2) of the Earth-Sun system with a Proton rocket from the Baikonur cosmodrome on 13 July 2019. The ART-XC telescope will provide the first ever true imaging all-sky survey performed with grazing incidence optics in the 4-30 keV energy band and will obtain the deepest and sharpest map of the sky in the energy range of 4-12 keV. Observations performed during the early calibration and performance verification phase as well as during the on-going all-sky survey that started on 12 Dec. 2019 have demonstrated that the in-flight characteristics of the ART-XC telescope are very close to expectations based on the results of ground calibrations. Upon completion of its 4-year all-sky survey, ART-XC is expected to detect ~5000 sources (~3000 active galactic nuclei, including heavily obscured ones, several hundred clusters of galaxies, ~1000 cataclysmic variables and other Galactic sources), and to provide a high-quality map of the Galactic background emission in the 4-12 keV energy band. ART-XC is also well suited for discovering transient X-ray sources. In this paper, we describe the telescope, results of its ground calibrations, major aspects of the mission, the in-flight performance of ART-XC and first scientific results.Comment: 19 pages, 30 figures, accepted for publication in Astronomy and Astrophysic

Effects of molecular structure on the physical, chemical, and electrical properties of ester‐based transformer insulating liquids

This article presents the experimental studies carried out on the environmental friendly polyol ester insulating liquids to investigate the effect of molecular structure on the physical, chemical, and electrical properties. Six different polyol esters that can be produced from the transesterification of various methyl esters with neopentylglycol/trimethylolpropane alcohols were synthesized and compared with those of refined, bleached, and deodorized palm oil (RBDPO) and mineral transformer oil. The finding suggests that the physical properties like fire point, pour point, and viscosity are very much affected by the molecular weight and molecular composition of the polyol esters. The electrical properties are also highly influenced by the molecular structure‐related characteristics, such as the polarity, dipole polarization, carbon chain length, and degree of branching. The results confirm the findings of previous studies that the polyol esters and RBDPO have more polarity and dipole polarization compared to mineral oil. The experimental evidence showed that the newly synthesized insulating liquids have favorable thermal and electrical properties, thus suggesting that the insulating liquids have the potential to replace conventional insulating liquids to provide a more sustainable power system in the future