TOPAZ4: an ocean-sea ice data assimilation system for the North Atlantic and Arctic

We present a detailed description of TOPAZ4, the latest version of TOPAZ – a coupled ocean-sea ice data assimilation system for the North Atlantic Ocean and Arctic. It is the only operational, large-scale ocean data assimilation system that uses the ensemble Kalman filter. This means that TOPAZ features a time-evolving, state-dependent estimate of the state error covariance. Based on results from the pilot MyOcean reanalysis for 2003–2008, we demonstrate that TOPAZ4 produces a realistic estimate of the ocean circulation in the North Atlantic and the sea-ice variability in the Arctic. We find that the ensemble spread for temperature and sea-level remains fairly constant throughout the reanalysis demonstrating that the data assimilation system is robust to ensemble collapse. Moreover, the ensemble spread for ice concentration is well correlated with the actual errors. This indicates that the ensemble statistics provide reliable state-dependent error estimates – a feature that is unique to ensemble-based data assimilation systems. We demonstrate that the quality of the reanalysis changes when different sea surface temperature products are assimilated, or when in-situ profiles below the ice in the Arctic Ocean are assimilated. We find that data assimilation improves the match to independent observations compared to a free model. Improvements are particularly noticeable for ice thickness, salinity in the Arctic, and temperature in the Fram Strait, but not for transport estimates or underwater temperature. At the same time, the pilot reanalysis has revealed several flaws in the system that have degraded its performance. Finally, we show that a simple bias estimation scheme can effectively detect the seasonal or constant bias in temperature and sea-level

The Atmospheric Chemistry Suite (ACS) of Three Spectrometers for the ExoMars 2016 Trace Gas Orbiter

The Atmospheric Chemistry Suite (ACS) package is an element of the Russian contribution to the ESA-Roscosmos ExoMars 2016 Trace Gas Orbiter (TGO) mission. ACS consists of three separate infrared spectrometers, sharing common mechanical, electrical, and thermal interfaces. This ensemble of spectrometers has been designed and developed in response to the Trace Gas Orbiter mission objectives that specifically address the requirement of high sensitivity instruments to enable the unambiguous detection of trace gases of potential geophysical or biological interest. For this reason, ACS embarks a set of instruments achieving simultaneously very high accuracy (ppt level), very high resolving power (>10,000) and large spectral coverage (0.7 to 17 μm—the visible to thermal infrared range). The near-infrared (NIR) channel is a versatile spectrometer covering the 0.7–1.6 μm spectral range with a resolving power of ∼20,000. NIR employs the combination of an echelle grating with an AOTF (Acousto-Optical Tunable Filter) as diffraction order selector. This channel will be mainly operated in solar occultation and nadir, and can also perform limb observations. The scientific goals of NIR are the measurements of water vapor, aerosols, and dayside or night side airglows. The mid-infrared (MIR) channel is a cross-dispersion echelle instrument dedicated to solar occultation measurements in the 2.2–4.4 μm range. MIR achieves a resolving power of >50,000. It has been designed to accomplish the most sensitive measurements ever of the trace gases present in the Martian atmosphere. The thermal-infrared channel (TIRVIM) is a 2-inch double pendulum Fourier-transform spectrometer encompassing the spectral range of 1.7–17 μm with apodized resolution varying from 0.2 to 1.3 cm−1. TIRVIM is primarily dedicated to profiling temperature from the surface up to ∼60 km and to monitor aerosol abundance in nadir. TIRVIM also has a limb and solar occultation capability. The technical concept of the instrument, its accommodation on the spacecraft, the optical designs as well as some of the calibrations, and the expected performances for its three channels are described

ОБОСНОВАНИЕ ЕМКОСТНОГО МЕТОДА ОПРЕДЕЛЕНИЯ СПРОСА

This article shortly describes idea of capacity method demand determination and give mathematical argumentation of this method. Advantage of this method against classic methods of reconstructing demand from sails history data is shown. The reason of low accuracy of demand determination is described.В статье кратко излагается идея емкостного метода определения скорости потребления продукции (спроса) и дается математическое обоснование этого метода. Показано преимущество этого метода по сравнению с классическим методом восстановления спроса из данных истории продаж по месяцам. Показывается причина низкой точности определения спроса классическим подходом

Manipulations with early mouse embryos for generation of genetically modified animals

Recently, genome-editing technologies have  become more efficient and accessible. The discovery of nucleases for directional genome editing (CRISPR/Cas9, TALEN, ZFNs) significantly accelerated and simplified the production of mice with targeted gene editing in the genome. Until last time, the CRISPR/Cas9 system noticeably simplified the preparation of knockout or transgenic mice. CRISPR/Cas9 technology was successfully applied for gene knockout and knock-in, generation of large deletions or directed insertions in targeted genome regions in embryonic stem cells (ESCs).When injected into blastocysts, such  modified ESCs are able to generate chimeras producing gametes with an identical genotype with ESC. Thus, it can identify animals with modified genomes. More recently, CRISPR/Cas9 technology was successfully applied to mouse zygotes and the birth of genetic modified mice was observed, i. e., the time required for generating genome-modified animals decreased significantly. The CRISPR/Cas9 system allows making gene knockout, large deletions or directed insertions into the target region of the genome by cytoplasm or pronuclear microinjection into zygotes. In addition, this is faster and simpler than similar work with mouse ESCs. Meanwhile, methods of manipulation with early embryos and their transplantation to surrogate mothers may be somewhat tricky. Therefore, it is important to use modern technologies for directional genome editing and perfect mastery in the embryological technics. In this article, we describe the protocols of microinjection into the pronucleus or cytoplasm of zygotes and injection of embryonic stem cells into the blastocyst cavity. We also describe embryological methods, such as superovulation, preparation of early stage  embryos,  surgical operation, production of foster mice. In addition, we describe the assembly and necessary components for the isoflurane anesthetic apparatus and isoflurane anesthesia

Assimilation of Temperatures and Column Dust Opacities Measured by ExoMars TGO-ACS-TIRVIM During the MY34 Global Dust Storm

Funding Information: ExoMars is a space mission of ESA and Roscosmos. The Atmospheric Chemistry Suite (ACS) experiment is led by IKI, the Space Research Institute in Moscow, Russia, assisted by LATMOS in France. This work, exploiting ACS/TIRVIM data, acknowledges funding by the CNES. The science operations of ACS are funded by Roscosmos and ESA. The ACS/TIRVIM team at IKI acknowledges the subsidy of the Ministry of Science and Higher Education of Russia. The authors acknowledge Sandrine Guerlet and the ACS/TGO team for supplying the data and the data center ESPRI/IPSL for their help in accessing the data. R. M. B. Young acknowledges funding from the UAE University grants G00003322 and G00003407. Supercomputing resources were provided by the UAE University High Performance Computing, with technical support from Anil Thomas and Asma Alneyadi, and at LMD by the IPSL mesocentre. The authors thank Luca Montabone for access to processed versions of Mars Climate Sounder temperature and dust observations, and Thomas Navarro and Claus Gebhardt for useful discussions.Peer reviewe

Genome editing using CRISPR/ Cas9 system: a practical guide

Over the past few years, the CRISPR/Cas techniques have become a revolution in genome editing. Since the original paper on CRIPSR/Cas9 genome editing, researches have proposed numerous modifications of the key components of the CRISPR/Cas9 system to make it extremely efficient. Nowadays, CRISPR/Cas systems can be used not only to modify genomes, but also to control expression levels of defined genes, visualize loci of interest in the space of living cell nuclei, change methylation status of mammalian CpG sites, and to serve many other purposes. Due to an extremely high efficacy and ease of usage, the CRISPR/ Cas system has been employed in a large number of studies in various areas of biology and biotechnology. We have recently published a review describing various CRISPR/Cas systems, mechanisms of their functioning, and applications of the techniques in details. Despite the broad range of potential applications of CRISPR/Cas systems, they are mostly used for genome editing. And, however simple the system may be, there is a number of potential pitfalls on the way towards its use in CRISPR/Cas- naïve laboratory settings. In this article, we describe protocols of CRISPR/Cas9 system generation. We start with a short description of theoretical aspects underlying Cas9-mediated genome editing. Next, we describe a step-by-step protocol of guide RNA vector design and assembly, and several ways of qualitative and quantitative evaluations of the system. Finally, we report protocols of genome editing for modification of embryonic stem cells and zygotes