RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome.

Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system level of studying non-coding RNAs. Here we present the RNA-Chrom manually curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https://rnachrom2.bioinf.fbb.msu.ru/), two approaches to the analysis of the RNA-chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome Browser. Database URL https://genome.ucsc.edu/.

[RNA-Chromatin Interactome: What? Where? When?]

It was noticed in the early 1960s that a large amount of RNAs is associated with chromatin. What kind of RNAs are they? Where are they located on chromatin? When and in what processes do these RNAs perform their physiologically normal or pathogenic functions? The review describes the modern approaches that help, to some extent, to answer these questions. Consideration is given to the experimental methods that make it possible to obtain the complete RNA-chromatin interactome of a cell or the genome-wide interaction maps of individual RNAs with chromatin, as well as the methods to process the experimental data. Focus is placed on the noncoding RNAs that function in close contact with chromatin and chromatin-associated protein complexes. A variety of biological examples described using the methods makes it clear that RNAs interacting with chromatin play an important role in the functions of cell systems by finely tuning the chromatin architecture and thus changing the level of gene expression.

[piRNAs: Biology and Bioinformatics].

The discovery of small noncoding RNAs and their roles in a variety of regulatory mechanisms have led many scientists to look at the principles of functioning of the cells on a completely different side. Small RNA molecules play key roles in important processes such as the co- and posttranscriptional regulation of gene expression, epigenetic modification of DNA and histones and antiviral protection. piRNA is one of the most numerous, although the least-studied class of small noncoding RNAs. piRNA is highly expressed in the germ line of most eukaryotes and its main function is to regulate the activity of mobile elements during embryonic development. Moreover, recent studies reveal moderate activity of piRNA in somatic cells. However, the mechanisms of piRNA biogenesis and function are still poorly understood and are the object of intensive researches. This review presents actual information about the biogenesis and various functions of piRNA, as well as bioinformatical aspects of this field of molecular biology.

[Electroencephalograpic Parameters of Healthy Persons with Different Successfulness of Dual-Task Performance (Postural Control and Calculation)].

Complex electroencephalographic (EEG), stabilographic and psychological study was executed during the number dual tasks performance--postural control and calculation in 25 healthy volunteers (age 25 ± 0.7). Successful performances of dual tasks required a high usage of cognitive resources, such as memory and attention as well as good motor command and low level of anxiety. Two EEG-markers of successful dual tasks performance were revealed. An increase of EEG coherence for long diagonal pairs of leads between frontal and parieto-occipital areas was observed. Additionally a decrease of EEG coherence for short pairs of leads was revealed. The poor performance of dual tasks was accompanied by an increase of EEG coherence between local pairs of leads for different spectral bands.

[EEG markers of spontaneous recovery of vertical posture in patients with consequences of severe traumatic brain injury].

9 patients (mean age 23.6 +/- 3.15 y.o.) with severe traumatic brain injury (TBI) and impairment of vertical posture were included in complex clinical and EEG study during spontaneous recovery of vertical posture (VP). Patients were included in three different groups according to severity of deficit according to MPAI, FIM and MMSE scales. EEG data have been compared to those of 10 healthy volunteers (mean age 22.8 +/- 0.67 yo.). In patients with moderate brain impairment and fast recovery of VP (over 2 weeks) change of posture from sitting to standup has been accompanied by EEG-signs similar to those of healthy people. These included predominant increase of coherence in right hemisphere for majority of frequency bands, although in more complex conditions EEG of these patients showed pathological signs. In patients with more severe deficit spontaneous recovery of VP has been accompanied by "hyper-reactive" change of EEG for all frequency bands without local specificity. This finding didn't depend on side ofbrain impairment and could be considered as marker of positive dynamics of VP restoration. In patients with most severe brain impairment and deficit of functions VP didn't recover after 3 month of observation. EEG-investigation has revealed absence of reactive change of EEG during passive verticalisation. This finding can be used as marker of negative prognosis.

[Features of dual--postural and calculation--task performance in patients with consequences of traumatic brain injury].

Dual tasks with voluntary postural control and calculation have been done by 14 patients (25.7 +/- 4.7 yo.) after traumatic brain injury and 40 healthy volunteers (29.8 +/- 2.5 y.o.). Complex clinical (MMSE, FIM, MPAI-3 and Berg scales) and stabilographic evaluation has been performed. According to clinical evaluation 8 patients were included into group 1 with less severe functional deficit and 6 patients formed group 2 with more severe deficit. Parameters of motor and especially cognitive sub-tasks in patients were lower than in healthy subjects in both separate and dual tasks. In group 2 these parameters were lower than in group 1. Certain types of dual task where the quality of sub-tasks, especially of the motor-one increased in healthy subjects and patients of the first group were revealed. The complex of stabilographic parameters which could be used for estimation of quality of sub-tasks performance has been revealed. Dual tasks could be an additional method of evaluation of patients' adaptive possibilities and certain type of dual task could become a promising approach to recovery at late period of rehabilitation.

[EEG-markers of vertical postural organization in healthy persons].

In 10 healthy persons (22.8 +/- 0.67 years) spectral-coherence parameters of EEG were analyzed in different steps of verticalizations--from gorizontal position to seat and stand one. Maximal changes of all EEG parameters were observed in state with absence of visual control. We observed an increase of power for fast spectral bands of EEG (beta- and gamma-bands) in all conditions and additional increase of these EEG parameters was observed at situation of complication of conditions of vertical pose supporting. Results of EEG coherent analysis in conditions of human verticalization showed specific increase of coherence for the majority of rhythm ranges in the right hemisphere especially in the central-frontal and in occipital-parietal areas and for interhemispheric pairs for these leads. This fact can reflect participation of cortical as well as subcortical structures in these processes. In conditions of complicate conditions of vertical pose supporting the additional increase of EEG coherence in fast bands (beta-rhythm) was observed at the frontal areas. This fact can testify about increasing of executive functions in this conditions.

[Integrating role of voluntary postural control recovery during rehabilitation of patients with traumatic brain injury].

Results of complex clinical, stabilographic and electroencephalographic (EEG) examination of 20 patients (28 +/- 6.9 years) suffered a severe traumatic brain injury (STBI) are presented. The examination was carried out in early terms after the STBI before and after a course of stabilographic training (ST) with a visual feedback as compared to a group of 18 healthy volunteers (26 +/- 5.8 years). The 4- to 6-week course of ST consisted of 8-15 sessions. Before the course, the patients experienced problems in different kinds of activity, maximum in the motor sphere. The EEG study revealed a decrease in the power and coherence of the alpha rhythm and an increase in the power of the slow spectral bands (delta). The ST restored not only the postural control of patients, but also reduced the defects in other spheres. The EEG study showed an increase in the alpha-rhythm power maximum in the occipital-parietal areas and a tendency to normalization of its regional specificity. In all examined patients, the interhemispheric coherence increased for different EEG-rhythms, especially of the alpha-band, in the central and parietal brain areas. The described EEG changes can be a marker of the integrating role of postural control and an important stage in restoration of integrative brain activity in early terms after the STBI accompanied by improvement of damaged functions.

[Peculiarities of changes of EEG reactivity during performance of dual tasks in healthy subjects (voluntary postural control and calculation)].

Complex EEG and stabilography investigation with separate and simultaneous performance of motor (voluntary postural control) and cognitive (calculation) tasks has been performed in 20 healthy subjects (22 +/- 0.7 yo.). Specific spatial and frequency reactive changes have been revealed during motor task performance. These included increase of coherence in alpha-band for long pair of channels in right hemisphere as well as in symmetric parietal-occipital regions in both hemispheres. Cognitive task performance has been accompanied by coherence increase for low bands (delta- and theta-) with higher activation in left hemisphere and frontal regions. In dual tasks where both components were performed worse comparing to control, performance led to reactive spatial and frequency changes of both--motor and cognitive--tasks, though these changes were less than during separate task performance. Decrease of coherence in alphal-band in frontal areas appeared as a zone of "conflict of interest - interferention". In dual tasks with better performance of each component comparing to control EEG coherence increased in each specific area as well as in areas of "conflict of interest".

[The use of stabilo-training with feedback in the rehabilitation of patients with posttraumatic Korsakov's syndrome].

The complex research, including clinical scales (FIM, Mayo-Portland) and data on stabilography and electroencephalography (EEG) studies, was conducted in 10 patients with posttraumatic Korsakov's syndrome (KS) before and after the rehabilitation course using stabilo-training (ST) with feedback (7-12 sessions). A control group consisted of 18 healthy people. In patients with KS, more severe cognitive (memory) disorders were noted before ST that was correlated with the maximal reduction of coherence in all frequency bands in frontal and parietal-occipital areas as well as in the long diagonal pairs between the left frontal and the right parietal-occipital areas which was most distinct for the alpha-band. A trend to the normalization of stabilography parameters and step-by step increasing of EEG coherence parameters, especially the alpha-band, was found after the rehabilitation ST course, which was accompanied with the KS regress. It increased initially in parietal-occipital-central areas of the right hemisphere with the following increase in central-frontal areas and then in frontal areas, mostly in the left hemisphere, that was in compliance with the tendency to the normalization of spatial-temporary EEG organization.

Some peculiarities of time-frequency dynamics of spike-wave discharges in humans and rats.

OBJECTIVE: Time-frequency dynamics of spike-wave discharges (SWDs) were investigated in patients with absence seizures and in WAG/Rij rats, a genetic model of absence epilepsy using a specially developed wavelet transform. METHODS: Two types of SWDs were analyzed in both species: the most frequently occurring discharges (of minimal 3.6-4.0 s or more) and shorter ones recorded from various cortical regions. RESULTS: The more prolonged discharges had two phases: during the initial part (from tenth of seconds to 1 s) of the seizure the frequency decreased quickly from 5 to 3.5 Hz in patients and from about 15 to 10 Hz in rats. A slower frequency decrease with periodical fluctuations was observed in both species during the second part of the discharge: the frequency decreased towards the end of the discharge to 3 Hz in patients and to 6-7 Hz in rats. The frequency of the short discharges decreased fast during the whole discharge: from 5 to 2-2.5 Hz and from about 15 to 5 Hz in patients and rats, respectively. CONCLUSIONS: Comparison of data obtained in patients with typical absence epilepsy and WAG/Rij rats with genetic absence epilepsy revealed that the time-frequency dynamics of SWDs had similar properties but in a different frequency range. SIGNIFICANCE: The study of time-frequency dynamics using this specially developed wavelet transform revealed two different types of SWDs, which most likely represent different dynamics in the cortico-thalamo-cortical loop during shorter and more prolonged discharges.

Brain ethanol levels in rats after voluntary ethanol consumption using a sweetened gelatin vehicle.

A novel procedure for initiation of voluntary ethanol consumption in the rat was evaluated in terms of ease of initiation, consistency, and resulting brain ethanol levels. The "jello shot" consists of 10% ethanol in gelatin along with a caloric source (Polycose). Initiation of "jello shot" consumption in Sprague-Dawley rats required no food or water restriction and resulted in initial daily (8.4+/-0.6 g/kg body weight) and eventual hourly (1.1+/-0.1 g/kg body weight) intake of ethanol comparable to other procedures using either alcohol-preferring or non-genetically selected rats. Rat intake of ethanol via "jello shots" recovered quickly from environmental alterations and surgical implantation of a guide cannula. During 1-h free access sessions, consumption of the "jello shot" occurred during the initial 10 min and resulted in a dose-related increase in ethanol levels in nucleus accumbens measured using microdialysis. These brain ethanol levels were comparable to those achieved using other self-administration methods. However, when 0.5 g/kg ethanol was gavaged either in "jello shot" or saline, there was about a 20% decrease in brain ethanol concentrations after gavage of the "jello shot" compared to saline. Even so, lack of a need for initial food or water deprivation and the rapidity with which stable self-administration can be achieved both suggest utility of the "jello shot" as a completely voluntary ethanol procedure.

A pyridinium-substituted analog of the TRH-like tripeptide pGlu-Glu-Pro-NH2 and its prodrugs as central nervous system agents.

A metabolically stable and centrally acting analog of pGlu-Glu-Pro-NH2 ([Glu2]TRH, a tripeptide structurally related to TRH (thyrotropin-releasing hormone)) was designed by replacing the amino-terminal pyroglutamyl residue with a pyridinium moiety. The analeptic action of the analog was used to optimize the efficacy of this novel CNS agent when administered intravenously in its CNS-permeable prodrug forms obtained via the reduction of the pyridinium moiety to the nonionic dihydropyridine and esterifying the central Glu with various alcohols. The maximum effect in antagonizing pentobarbital-induced narcosis in mice was achieved with the hexyl ester that was used subsequently for a comparative evaluation with a prodrug of the parent neuropeptide in the Porsolt swim test as a paradigm for antidepressant effect. The novel analog maintained its antidepressant potency but showed reduced analeptic action compared to [Glu2]TRH; thus, an increase in the selectivity of CNS-action was obtained by the incorporation of the pyridinium moiety.

[Effect of Ligula intestinalis on lipid metabolism in blood of the host Abramis brama]. / Vliianie Ligula intestinalis na kharakter lipidnogo obmena krovi khoziaina Abramis brama.

The results of analysis in the blood of healthy and ones infected with the plerocercoides Ligula intestinalis Bream Abramis brama L. over index common lipids (CL) and them quality content, peroxidation (POL), peroxide gemoliz erythrocytes (PGE), common antioxidant activity (CAA) are displayed. It is plerocercoids L. intestinalis effects points character lipids exchanges. At ones infected individual comparatively with healthy increase of CL, alteration correlation lipids fraction, intensification POI and PGE as well as a decrease of CAA, that negative effects on vital function of the blood.

Integration of mass spectrometry into early-phase discovery and development of central nervous system agents.

The early-phase discovery and development of useful central nervous system (CNS) agents present ample opportunities to exploit mass spectrometry and provide detailed compound/mixture characterization, or to make the process faster and/or more economic. Neuropeptide FF antagonists and centrally active thyrotropin-releasing hormone analogues were used as specific examples in this work. We evaluated the characterization of focused libraries of peptide derivatives by electrospray ionization, tandem mass spectrometry and liquid chromatography/tandem mass spectrometry on a quadrupole ion trap and nanoelectrospray on a Fourier transform ion cyclotron resonance mass spectrometer. Immobilized artificial-membrane chromatography was employed as a model to predict/rank new agents against lead compounds for their potential to reach the central nervous system in pharmacologically significant amounts. Measuring brain concentrations in rodents after the intravenous administration of test compounds was used as an in vivo approach, and we took advantage of microdialysis sampling that furnished samples without interfering tissue matrix and afforded the estimation of extracellular concentrations in a localized part of the brain. Overall, making atmospheric-pressure ionization mass spectrometry an integral part of the process has played a major role in increasing throughput, selectivity, specificity and detection sensitivity and thereby providing useful information about the extent or mechanism of transport and metabolic activation/inactivation in early-phase discovery and development of CNS agents.

Combinatorial lead optimization of a neuropeptide FF antagonist.

The tripeptide Pro-Gln-Arg-NH2, derivatized at the secondary amino group of the proline residue with 5-(dimethylamino)-1-naphthalenesulfonyl (dansyl-PQR-NH2), antagonizes the central anti-opioid action of neuropeptide FF in animals after systemic administration and, therefore, is a therapeutic lead to treat opiate withdrawal. For a combinatorial optimization to improve potency, libraries focused on the possible replacement of the proline and glutamine residues of this lead compound were obtained by a solid-phase split-and-mix method using coded amino acids (excluding cysteine) as building blocks. After screening for competitive binding against a radioiodinated neuropeptide FF analogue, 5-(dimethylamino)-1-naphthalenesulfonyl-Gly-Ser-Arg-NH2 (dansyl-GSR-NH2) has emerged as one of the compounds in the library with high affinity to the NPFF receptor and even with a moderate increase compared to dansyl-PQR-NH2 in its predicted ability to penetrate the central nervous system.

Exploratory pharmacokinetics and brain distribution study of a neuropeptide FF antagonist by liquid chromatography/atmospheric pressure ionization tandem mass spectrometry.

Dansyl-Pro-Gln-Arg-NH(2), an N-terminally modified tripeptide amide and a putative neuropeptide FF antagonist, was amenable to both positive-ion ESI and APCI. The protonated molecule yielded several fragment ions upon collision-induced dissociation in a quadrupole ion trap instrument for the development of LC/MS/MS assay methods. ESI clearly outperformed APCI in limits of detection, and was the method of choice for coupling with narrow-bore reversed-phase liquid chromatography to assess the pharmacokinetic profile and brain concentration of the neuropeptide FF antagonist in experimental animals. While plasma could be analyzed after rapid sample preparation, brain tissue required cleanup (solid phase extraction) and preconcentration before injection, and the assay was prone to matrix interference. This study indicated a rapid disappearance of dansyl-Pro-Gln-Arg-NH(2) from the plasma and the brain, and modest CNS bioavailability after intravenous administration to rats.

Metabolism-based brain-targeting system for a thyrotropin-releasing hormone analogue.

Gln-Leu-Pro-Gly, a progenitor sequence for the thyrotropin-releasing hormone (TRH) analogue [Leu(2)]TRH (pGlu-Leu-Pro-NH(2)), was covalently and bioreversibly modified on its N- and C-termini (by a 1,4-dihydrotrigonellyl and a cholesteryl group, respectively) to create lipoidal brain-targeting systems for the TRH analogue. The mechanism of targeting and the recovery of the parent peptide at the target site involve several enzymatic steps, including the oxidation of the 1,4-dihydropyridine moiety. Due to the lipid insolublity of the peptide pyridinium conjugate obtained after this reaction, one of the rudimentary steps of brain targeting (i.e., trapping in the central nervous system) can be accomplished. Our design also included spacer amino acid(s) inserted between the N-terminal residue of the progenitor sequence and the dihydrotrigonellyl group to facilitate the posttargeting removal of the attached modification. The release of the TRH analogue in the brain is orchestrated by a sequential metabolism utilizing esterase/lipase, peptidyl glycine alpha-amidating monooxygenase (PAM), peptidase cleavage, and glutaminyl cyclase. In addition to in vitro experiments to prove the designed mechanism of action, the efficacy of brain targeting for [Leu(2)]TRH administered in the form of chemical-targeting systems containing the embedded progenitor sequence was monitored by the antagonistic effect of the peptide on the barbiturate-induced anesthesia (measure of the activational effect on cholinergic neurons) in mice, and considerable improvement was achieved over the efficacy of the parent peptide upon using this paradigm.

In vitro and in vivo study of water-soluble prodrugs of dexanabinol.

Trialkylammonium acetoxymethyl esters of dexanabinol were synthesized and evaluated as water-soluble prodrugs. Syntheses were performed by conventional methods; solubility in water and stability in buffers and human plasma were determined by HPLC, and in vivo tissue distribution studies were performed in a rat model. Most of the new derivatives were soluble in water (approximately 50 mg/mL). They were relatively stable in water, while rapidly hydrolyzed in human plasma. Distribution studies indicated that peak concentrations of drug both in blood (30 microg/mL) and brain (2 microg/mL) were rapidly (5 min) achieved after iv administration of a selected prodrug to rats. The blood concentration decreased faster than brain levels which were detectable even after 24 h. Some of the examined esters could be further developed as water soluble prodrugs of dexanabinol.