Gasdynamic electron cyclotron ion sources: Basic physics, applications, and diagnostic techniques.

The gasdynamic electron cyclotron resonance (ECR) ion source is a type of the device in which the ionization efficiency is achieved primarily due to a high plasma density. Because of a high particle collision rate, the confinement is determined by a gasdynamic plasma outflow from a magnetic trap. Due to high efficiency of resonant heating, electrons gain energy significantly higher than that in inductively or capacitively coupled plasmas. As a consequence of such a parameter combination, the gasdynamic ECR plasma can be a unique source of low to medium charged ions, providing a high current and an ultimate quality of an ion beam. One of the most demanded directions of its application today is a development of high-current proton injectors for modern accelerators and neutron sources of different intensities. Special plasma parameters allow for the use of diagnostic techniques, traditional for multiply charged ECR plasmas as well as for other types of discharges with a high plasma density. Among the additional techniques, one can mention the methods of numerical simulation and reconstruction of the plasma density and temperature from the parameters of the extracted ion beams. Another point is that the high plasma density makes it possible to measure it from the Stark broadening of hydrogen lines by spectroscopy of plasma emission in the visible range, which is a fairly convenient non-invasive diagnostic method. The present paper discusses the main physical aspects of the gasdynamic ECR plasma, suitable diagnostic techniques, and possibilities and future prospects for its various applications.

[DNA Damage Response in Nucleoli].

Nucleoli, the largest subnuclear compartments, are formed around arrays of ribosomal gene repeats transcribed by RNA polymerase I. The primary function of nucleoli is ribosome biogenesis. Specific DNA damage response mechanisms exist to maintain the genomic stability of ribosomal repeats. Here, we provide a snapshot of our current understanding of processes involved in nucleolar DNA damage response. We discuss structure and function of ribosomal repeats, techniques developed for studying DNA damage response in nucleoli, as well as molecular mechanisms of DNA damage-induced repression of nucleolar transcription and nucleoli reorganization.

Non-backtracking walks reveal compartments in sparse chromatin interaction networks.

Chromatin communities stabilized by protein machinery play essential role in gene regulation and refine global polymeric folding of the chromatin fiber. However, treatment of these communities in the framework of the classical network theory (stochastic block model, SBM) does not take into account intrinsic linear connectivity of the chromatin loci. Here we propose the polymer block model, paving the way for community detection in polymer networks. On the basis of this new model we modify the non-backtracking flow operator and suggest the first protocol for annotation of compartmental domains in sparse single cell Hi-C matrices. In particular, we prove that our approach corresponds to the maximum entropy principle. The benchmark analyses demonstrates that the spectrum of the polymer non-backtracking operator resolves the true compartmental structure up to the theoretical detectability threshold, while all commonly used operators fail above it. We test various operators on real data and conclude that the sizes of the non-backtracking single cell domains are most close to the sizes of compartments from the population data. Moreover, the found domains clearly segregate in the gene density and correlate with the population compartmental mask, corroborating biological significance of our annotation of the chromatin compartmental domains in single cells Hi-C matrices.

The Role of Liquid-Liquid Phase Separation in the Compartmentalization of Cell Nucleus and Spatial Genome Organization.

Functional compartmentalization of the cell nucleus plays an important role in the regulation of genome activity by providing accumulation of enzymes and auxiliary factors in the reaction centers, such as transcription factories, Cajal bodies, speckles, etc. The mechanisms behind the nucleus functional compartmentalization are still poorly understood. There are reasons to believe that the key role in the nucleus compartmentalization belongs to the process of liquid-liquid phase separation. In this brief review, we analyze results of experimental studies demonstrating that liquid-liquid phase separation not only governs functional compartmentalization of the cell nucleus but also contributes to the formation of the 3D genomic architecture.

A powerful pulsed "point-like" neutron source based on the high-current ECR ion source.

The paper presents recent results of a "pointlike" neutron source development based on a D-D fusion in a D-loaded target caused by its bombardment with a sharply focused deuterium ion beam. These developments are undergoing at the Institute of Applied Physics of Russian Academy of Sciences in order to study a possibility to create an effective and compact device for fast-neutron radiography. The last experiments with a beam produced by a gasdynamic high-current ECR ion source and its focusing with a magnetic lens demonstrated that 60 mA of deuterium ions may be constricted to a transversal size of ∼1 mm at the focal plane. With a purpose to improve this result in terms of the beam current and its size, a combined electrostatic and magnetic focusing system is proposed and analyzed. It is shown that the combined system may enhance the total beam current and reduce its footprint down to 0.13 mm. All numerical analysis was performed using the IBSimu code.

Study of gasdynamic electron cyclotron resonance plasma vacuum ultraviolet emission to optimize negative hydrogen ion production efficiency.

Negative hydrogen ion sources are used as injectors into accelerators and drive the neutral beam heating in ITER. Certain processes in low-temperature hydrogen plasmas are accompanied by the emission of vacuum ultraviolet (VUV) emission. Studying the VUV radiation, therefore, provides volumetric rates of plasma-chemical processes and plasma parameters. In the past, we have used gasdynamic ECR discharge for volumetric negative ion production and investigated the dependencies between the extracted H- current density and various ion source parameters. It was shown that it is possible to reach up to 80 mA/cm2 of negative ion current density with a two electrode extraction. We report experimental studies on negative hydrogen ion production in a high-density gasdynamic ECR discharge plasma consisting of two simple mirror traps together with the results of VUV emission measurements. The VUV-power was measured in three ranges-Lyα, Lyman band, and molecular continuum-varying the source control parameters near their optima for H- production. It was shown that the molecular continuum emission VUV power is the highest in the first chamber while Lyα emission prevails in the second one. Modifications for the experimental scheme for further optimization of negative hydrogen ion production are suggested.

L-Ascorbic Acid in the Epigenetic Regulation of Cancer Development and Stem Cell Reprogramming.

Recent studies have significantly expanded our understanding of the mechanisms of L-ascorbic acid (ASC, vitamin C) action, leading to the emergence of several hypotheses that validate the possibility of using ASC in clinical practice. ASC may be considered an epigenetic drug capable of reducing aberrant DNA and histone hypermethylation, which could be helpful in the treatment of some cancers and neurodegenerative diseases. The clinical potency of ASC is also associated with regenerative medicine; in particular with the production of iPSCs. The effect of ASC on somatic cell reprogramming is most convincingly explained by a combined enhancement of the activity of the enzymes involved in the active demethylation of DNA and histones. This review describes how ASC can affect the epigenetic status of a cell and how it can be used in anticancer therapy and stem cell reprogramming.

Modification of Nuclear Compartments and the 3D Genome in the Course of a Viral Infection.

The review addresses the question of how the structural and functional compartmentalization of the cell nucleus and the 3D organization of the cellular genome are modified during the infection of cells with various viruses. Particular attention is paid to the role of the introduced changes in the implementation of the viral strategy to evade the antiviral defense systems and provide conditions for viral replication. The discussion focuses on viruses replicating in the cell nucleus. Cytoplasmic viruses are mentioned in cases when a significant reorganization of the nuclear compartments or the 3D genome structure occurs during an infection with these viruses.

[3D Genomics].

The development of new research methods significantly changed our views on the role that the 3D organization of the genome plays in its functional activity. It was found that the genome is subdivided into structural-functional units that restrict the area of enhancer action at the level of spatial organization. Spatial reconfiguration of an extended genomic fragment was identified as a potential mechanism that activates or represses various genes. Accordingly, a distorted spatial organization of the genome often causes various diseases, including cancer. All these observations contributed to the emergence of 3D genomics as a new avenue of research. The review summarizes the most important discoveries in the field of 3D genomics and discusses the directions of its further development.

Wide-aperture dense plasma fluxes production based on ECR discharge in a single solenoid magnetic field.

Results of experimental investigation of the ECR discharge in a single coil magnetic field as an alternative to rf and helicon discharges for wide-aperture dense plasma fluxes production are presented. A possibility of obtaining wide-aperture high density hydrogen plasma fluxes with homogeneous transverse distribution was demonstrated in such a system. The prospects of using this system for obtaining high current ion beams are discussed.

Status of the gasdynamic ion source for multipurpose operation (GISMO) development at IAP RAS.

A new experimental facility named GISMO (Gasdynamic Ion Source for Multipurpose Operation) was constructed at the IAP RAS to continue investigations in the field of gasdynamic ion sources. The source utilizes 28 GHz/10 kW gyrotron radiation for heating magnetically confined plasma. Magnetic field configuration provided by a fully permanent magnet system is much like a simple mirror trap. The GISMO source is aimed at the production of bright ion beams with hundreds of milliamperes current. The facility has been tested for continuous-wave (CW) operation with 2 kW of heating power to check durability of a microwave injection system and the plasma chamber. A 2-electrode extraction system with an integrated Einzel lens was designed for a formation of CW high current beam with up to 100 kV accelerating voltage. The first results on ion beam production at GISMO are presented together with the general progress status of the facility.

[Role of the Nucleolus in Rearrangements of the IGH Locus].

The review summarizes the results from a series of studies focusing on the role that the nucleolus plays in maturation of the IGH locus and the choice of its partner genes in leukemia-associated translocations. The role of nuclear compartmentalization and nuclear localization of translocated oncogenes in ectopic activation of their transcription is discussed.

Structural-Functional Organization of the Eukaryotic Cell Nucleus and Transcription Regulation: Introduction to This Special Issue of Biochemistry (Moscow).

This issue of Biochemistry (Moscow) is devoted to the cell nucleus and mechanisms of transcription regulation. Over the years, biochemical processes in the cell nucleus have been studied in isolation, outside the context of their spatial organization. Now it is clear that segregation of functional processes within a compartmentalized cell nucleus is very important for the implementation of basic genetic processes. The functional compartmentalization of the cell nucleus is closely related to the spatial organization of the genome, which in turn plays a key role in the operation of epigenetic mechanisms. In this issue of Biochemistry (Moscow), we present a selection of review articles covering the functional architecture of the eukaryotic cell nucleus, the mechanisms of genome folding, the role of stochastic processes in establishing 3D architecture of the genome, and the impact of genome spatial organization on transcription regulation.

Structural-Functional Domains of the Eukaryotic Genome.

It is well known that DNA folding in the eukaryotic cell nucleus is tightly coupled with the operation of epigenetic mechanisms defining the repertoires of the genes expressed in different types of cells. To understand these mechanisms, it is important to know how DNA is packaged in chromatin. About 30 years ago a hypothesis was formulated, according to which epigenetic mechanisms operate not at the level of individual genes, but rather groups of genes localized in structurally and functionally isolated genomic segments that were called structural and functional domains. The question of what exactly these domains constitute has been re-examined multiple times as our knowledge of principles of chromatin folding has changed. In this review, we discuss structural and functional genomic domains in light of the current model of interphase chromosome organization based on the results of analysis of spatial proximity between remote genomic elements.

Genetic and Epigenetic Mechanisms of ß-Globin Gene Switching.

Vertebrates have multiple forms of hemoglobin that differ in the composition of their polypeptide chains. During ontogenesis, the composition of these subunits changes. Genes encoding different α- and ß-polypeptide chains are located in two multigene clusters on different chromosomes. Each cluster contains several genes that are expressed at different stages of ontogenesis. The phenomenon of stage-specific transcription of globin genes is referred to as globin gene switching. Mechanisms of expression switching, stage-specific activation, and repression of transcription of α- and ß-globin genes are of interest from both theoretical and practical points of view. Alteration of balanced expression of globin genes, which usually occurs due to damage to adult ß-globin genes, leads to development of severe diseases - hemoglobinopathies. In most cases, reactivation of the fetal hemoglobin gene in patients with ß-thalassemia and sickle cell disease can reduce negative consequences of irreversible alterations of expression of the ß-globin genes. This review focuses on the current state of research on genetic and epigenetic mechanisms underlying stage-specific switching of ß-globin genes.

[Intersubunit Mobility of the Ribosome].

Ribosomes are ribonucleoprotein nanoparticles synthesizing all proteins in living cells. The function of the ribosome is to translate the genetic information encoded in a nucleotide sequence of mRNA into the amino acid sequence of a protein. Each translation step (occurring after the codon-dependent binding of the aminoacyl-tRNA with the ribosome and mRNA) includes (i) the transpeptidation reaction and (ii) the translocation that unidirectionally drives the mRNA chain and mRNA-bound tRNA molecules through the ribosomal intersubunit space; the latter process is driven by the free energy of the chemical reaction of transpeptidation. Thus, the translating ribosome can be considered a conveying protein-synthesizing molecular machine. In this review we analyze the role of ribosomal intersubunit mobility in the process of translocation.

HIV Tat induces a prolonged MYC relocalization next to IGH in circulating B-cells.

With combined antiretroviral therapy (cART), the risk for HIV-infected individuals to develop a non-Hodgkin lymphoma is diminished. However, the incidence of Burkitt lymphoma (BL) remains strikingly elevated. Most BL present a t(8;14) chromosomal translocation which must take place at a time of spatial proximity between the translocation partners. The two partner genes, MYC and IGH, were found colocalized only very rarely in the nuclei of normal peripheral blood B-cells examined using 3D-FISH while circulating B-cells from HIV-infected individuals whose exhibited consistently elevated levels of MYC-IGH colocalization. In vitro, incubating normal B-cells from healthy donors with a transcriptionally active form of the HIV-encoded Tat protein rapidly activated transcription of the nuclease-encoding RAG1 gene. This created DNA damage, including in the MYC gene locus which then moved towards the center of the nucleus where it sustainably colocalized with IGH up to 10-fold more frequently than in controls. In vivo, this could be sufficient to account for the elevated risk of BL-specific chromosomal translocations which would occur following DNA double strand breaks triggered by AID in secondary lymph nodes at the final stage of immunoglobulin gene maturation. New therapeutic attitudes can be envisioned to prevent BL in this high risk group.

Study of hydrogen ECR plasma in a simple mirror magnetic trap heated by 75 GHz pulsed gyrotron radiation.

Plasma of electron cyclotron resonance (ECR) discharge sustained by millimeter wave radiation is widely used for production of ion beams of different kind. The main trend in ECR ion sources development nowadays is an increase of frequency and power of microwave heating. The most advanced systems use gyrotrons in 24-60 GHz frequency range. In previous studies at IAP RAS it was demonstrated that ECR source SMIS 37 (Simple Mirror Ion Source) with 37.5 GHz heating operating in quasigasdynamic regime of plasma confinement is able to produce proton and deuteron beams with ion current density about 700 mA/cm2. As the next step of these investigations plasma properties of the discharge sustained by 75 GHz radiation have been studied. Plasma density and electron temperature were determined using spectroscopic and Langmuir probe techniques. It was demonstrated that plasma density could reach values close to 1014 cm-3 and that is of great interest for further development of high current ion sources for various applications.

[Comparative analysis of the synchronization methods of normal and transformed human cells].

Reactions of genetically identical cells to various exogenous and endogenous stimuli can vary significantly. One of the main factors of this non-genetic cellular heterogeneity is the cell cycle. The most convenient way to study the subcellular processes depending on the cell cycle stage is the synchronization of the cells. Toxic inhibitors of DNA replication and/or mitotic spindle assembly are typically used to synchronize cells. It is important to accurately select the synchronization method for a particular experiment. In this study, we performed a comparative analysis of the synchronization methods of normal and transformed human cells, paying special attention to the accuracy of synchronization and toxicity of the methods used.