Novel strong tissue specific promoter for gene expression in human germ cells

<p>Abstract</p> <p>Background</p> <p>Tissue specific promoters may be utilized for a variety of applications, including programmed gene expression in cell types, tissues and organs of interest, for developing different cell culture models or for use in gene therapy. We report a novel, tissue-specific promoter that was identified and engineered from the native upstream regulatory region of the human gene <it>NDUFV1 </it>containing an endogenous retroviral sequence.</p> <p>Results</p> <p>Among seven established human cell lines and five primary cultures, this modified <it>NDUFV1 </it>upstream sequence (mNUS) was active only in human undifferentiated germ-derived cells (lines Tera-1 and EP2102), where it demonstrated high promoter activity (~twice greater than that of the SV40 early promoter, and comparable to the routinely used cytomegaloviral promoter). To investigate the potential applicability of the mNUS promoter for biotechnological needs, a construct carrying a recombinant cytosine deaminase (RCD) suicide gene under the control of mNUS was tested in cell lines of different tissue origin. High cytotoxic effect of RCD with a cell-death rate ~60% was observed only in germ-derived cells (Tera-1), whereas no effect was seen in a somatic, kidney-derived control cell line (HEK293). In further experiments, we tested mNUS-driven expression of a hyperactive <it>Sleeping Beauty </it>transposase (SB100X). The mNUS-SB100X construct mediated stable transgene insertions exclusively in germ-derived cells, thereby providing further evidence of tissue-specificity of the mNUS promoter.</p> <p>Conclusions</p> <p>We conclude that mNUS may be used as an efficient promoter for tissue-specific gene expression in human germ-derived cells in many applications. Our data also suggest that the 91 bp-long sequence located exactly upstream <it>NDUFV1 </it>transcriptional start site plays a crucial role in the activity of this gene promoter <it>in vitro </it>in the majority of tested cell types (10/12), and an important role - in the rest two cell lines.</p

Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways

Sherpa Romeo blue journal. Open access article. Creative Commons Attribution 3.0 License (CC BY 3.0) applies.We recently proposed a new bioinformatic algorithm called OncoFinder for quantifying the activation of intracellular signaling pathways. It was proved advantageous for minimizing errors of high-throughput gene expression analyses and showed strong potential for identifying new biomarkers. Here, for the first time, we applied OncoFinder for normal and cancerous tissues of the human bladder to identify biomarkers of bladder cancer. Using Illumina HT12v4 microarrays, we profiled gene expression in 17 cancer and seven non-cancerous bladder tissue samples. These experiments were done in two independent laboratories located in Russia and Canada. We calculated pathway activation strength values for the investigated transcriptomes and identified signaling pathways that were regulated differently in bladder cancer (BC) tissues compared with normal controls. We found, for both experimental datasets, 44 signaling pathways that serve as excellent new biomarkers of BC, supported by high area under the curve (AUC) values. We conclude that the OncoFinder approach is highly efficient in finding new biomarkers for cancer. These markers are mathematical functions involving multiple gene products, which distinguishes them from “traditional” expression biomarkers that only assess concentrations of single genes.Ye

Wind waves in the North Atlantic and Arctic from ship navigational radar (SeaVision system) and wave buoy Spotter during three research cruises in 2020 and 2021

The purpose of this dataset is to provide in situ wind waves observations in the open ocean. The dataset consists of significant wave heights, wave periods, wave directions, wave energy frequency spectra, meteorological data and other related parameters. Parameters of the wind waves measured with Spotter wave buoy and SeaVision system on the basis of navigational ship X-band radar. The dataset was collected in almost 50 locations during three research cruises on the research vessels Akademik Sergey Vavilov and Akademik Ioffe in the North Atlantic (August 2020 and June 2021) and Arctic (August 2021). The dataset is the supplement to the manuscript "Wind waves in the North Atlantic from ship navigational radar: SeaVision development and its validation with Spotter wave buoy and WaveWatch III" (Tilinina et al., 2022). Technical details, maps with expedition tracks and detailed methodology of the wind wave parameters calculations from both SeaVision and Spotter raw data are described in the manuscript

Wind waves in the North Atlantic from ship navigational radar: SeaVision development and its validation with the Spotter wave buoy and WaveWatch III

International audienceWind waves play an important role in the climate system, modulating the energy exchange between the ocean and the atmosphere and effecting ocean mixing. However, existing ship-based observational networks of wind waves are still sparse, limiting therefore the possibilities of validating satellite missions and model simulations. In this paper we present data collected on three research cruises in the North Atlantic and Arctic in 2020 and 2021 and the SeaVision system for measuring wind wave characteristics over the open ocean with a standard marine navigation X-band radar. Simultaneously with the SeaVision wind wave characteristic measurements, we also collected data from the Spotter wave buoy at the same locations, and we ran the WaveWatch III model in a very high-resolution configuration over the observational domain. SeaVision measurements were validated against co-located Spotter wave buoy data and intercompared with the output of WaveWatch III simulations. Observations of the wind waves with the navigation X-band radar were found to be in good agreement with buoy data and model simulations with the best match for the wave propagation directions. Supporting datasets consist of significant wave heights, wave directions, wave periods and wave energy frequency spectra derived from both SeaVision and the Spotter buoy. All supporting data are available through the PANGAEA repository - https://doi.org/10.1594/PANGAEA.939620 (Gavrikov et al., 2021). The dataset can be further used for validation of satellite missions and regional wave model experiments. Our study shows the potential of ship navigation X-band radars (when assembled with SeaVision or similar systems) for the development of a new near-global observational network providing a much larger number of wind wave observations compared to e.g. Voluntary Observing Ship (VOS) data and research vessel campaigns