Classification and monomer-by-monomer annotation dataset of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly.

In the latest hg38 human genome assembly, centromeric gaps has been filled in by alpha satellite (AS) reference models (RMs) which are statistical representations of homogeneous higher-order repeat (HOR) arrays that make up the bulk of the centromeric regions. We analyzed these models to compose an atlas of human AS HORs where each monomer of a HOR was represented by a number of its polymorphic sequence variants. We combined these data and HMMER sequence analysis platform to annotate AS HORs in the assembly. This led to discovery of a new type of low copy number highly divergent HORs which were not represented by RMs. These were included in the dataset. The annotation can be viewed as UCSC Genome Browser custom track (the HOR-track) and used together with our previous annotation of AS suprachromosomal families (SFs) in the same assembly, where each AS monomer can be viewed in its genomic context together with its classification into one of the 5 major SFs (the SF-track). To catalog the diversity of AS HORs in the human genome we introduced a new naming system. Each HOR received a name which showed its SF, chromosomal location and index number. Here we present the first installment of the HOR-track covering only the 17 HORs that belong to SF1 which forms live functional centromeres in chromosomes 1, 3, 5, 6, 7, 10, 12, 16 and 19 and also a large number of minor dead HOR domains, both homogeneous and divergent. Monomer-by-monomer HOR annotation used for this dataset as opposed to annotation of whole HOR repeats provides for mapping and quantification of various structural variants of AS HORs which can be used to collect data on inter-individual polymorphism of AS.

Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly.

Centromeric alpha satellite (AS) is composed of highly identical higher-order DNA repetitive sequences, which make the standard assembly process impossible. Because of this the AS repeats were severely underrepresented in previous versions of the human genome assembly showing large centromeric gaps. The latest hg38 assembly (GCA_000001405.15) employed a novel method of approximate representation of these sequences using AS reference models to fill the gaps. Therefore, a lot more of assembled AS became available for genomic analysis. We used the PERCON program previously described by us to annotate various suprachromosomal families (SFs) of AS in the hg38 assembly and presented the results of our primary analysis as an easy-to-read track for the UCSC Genome Browser. The monomeric classes, characteristic of the five known SFs, were color-coded, which allowed quick visual assessment of AS composition in whole multi-megabase centromeres down to each individual AS monomer. Such comprehensive annotation of AS in the human genome assembly was performed for the first time. It showed the expected prevalence of the known major types of AS organization characteristic of the five established SFs. Also, some less common types of AS arrays were identified, such as pure R2 domains in SF5, apparent J/R and D/R mixes in SF1 and SF2, and several different SF4 higher-order repeats among reference models and in regular contigs. No new SFs or large unclassed AS domains were discovered. The dataset reveals the architecture of human centromeres and allows classification of AS sequence reads by alignment to the annotated hg38 assembly. The data were deposited here: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgt.customText=https://dl.dropboxusercontent.com/u/22994534/AS-tracks/human-GRC-hg38-M1SFs.bed.bz2.

Multidimensional dot-matrices.

A generalization of the dot-matrix of similarity for n sequences is proposed. For the visualization of the n-dimensional dot-matrix, the n projections onto the plane passing through the main diagonal and each of the n axes of Euclidean space En are displayed. The projection is compressed so that the points at the coordinates (xi, sigma j not equal to ixj/(n - 1)) are depicted on the plane. The common regions of similarity are revealed as segments of straight lines parallel to the main diagonal. An algorithm for the n-dimensional dot-matrix calculation of time of the order of O[n*L2 + n*(L2p)2] is suggested where L is the mean length of sequence and p is the stringency parameter of the order of 10(-6). The method is illustrated for the family of plant phenylalanine ammonia-lyase genes.

[Characteristics of the context shift in the frequency of synonymic codons in Escherichia coli]. / Zakonomernosti kontekstnogo smeshcheniia chastot sinonimicheskikh kodonov v Escherichia coli.

We have demonstrated, that coding regions of E. coli DNA exhibit the non-random shifts of codon usage frequency depending both on the type of the 3' nucleotide adjacent to the codon and the degree of gene expression. Analysis of primary data--statistics of tetranucleotide occurrences--was performed by the techniques of contingency tables. The results of the investigation allowed us to suggest that the phenomenon observed is connected with the influence of the 3'-adjacent nucleotide on the level of missens-errors and another types of inaccuracy during translation. The specific advantages of such mutations in the third position of the codon are based on the adaptation of the codon to the 3' context in order to increase the efficiency of translation.

[Changes in the structure of group behavior in callosotomized rhesus monkeys]. / Izmenenie struktury gruppovogo povedeniia u kallozotomirovannykh makak rezusov.

The studies were performed on 4 intact and 3 callosotomized adult male rhesus monkeys that comprised one social group. Group behaviour of all the monkeys was investigated by the frequency method of social contacts registration. Both aggressive and friendly contacts were registered. The results obtained have shown a considerable decrease in social contacts of callosotomized rhesus monkeys, as compared to normal animals. The aggressive contacts prevailed in the behaviour of the operated monkeys. The data suggest that callosotomy does not only significantly decrease the frequency, but also alters the structure of social contacts in the rhesus monkeys.

[Functional organization of the kinesthetic projections of the 1st somatosensory region of the cat cortex]. / Funktsional'naia organizatsiia kinesteticheskikh proektsii pervoi somatosensornoi oblasti kory koshek.

Electrophysiological studies were performed on adult cats under ethaminal anesthesia. Kinesthetic potentials were evoked by passive extension of the ulnar joint and recorded in contralateral primary somatosensory cortical area. Natural (nonelectrical) stimulation of peripheral kinesthetic receptors was performed according to the author's original method. The results obtained show significantly shorter latent period of contralateral kinesthetic potentials in comparison with somatosensory potentials in response to electrical stimulation of the skin. These data demonstrate the possibility of super-rapid conduction of modal-specific volleys to the cortical projection centres in the kinesthetic system of cats.

[Role of the commissural channels of the somatosensory system in the conduction of feedback signals during the control of voluntary movements]. / Rol' komissural'nykh kanalov somatosensornoi sistemy v peredache signalov obratnoi sviazi pri upravlenii proizvol'nymi dvizheniiami.

The time-course of formation of the conditioned defence reflex and electromyograms of the working forelimb were studied on cats with classical and commissural somatosensory pathways transections. It was established that exclusion of the classical somatosensory projections only reduces the rate of the skill formation that is related to the possibility of conducting feedback signals via the remaining commissural pathways. However, the commissural channel in question is not effective enough, since its isolated functioning is accompanied by an increase in the duration of instrumental movement. The combined transection of the classical and commissural somatosensory pathways excludes the possibility of formation of the conditioned reflex on the "deafferented" limb. The lack of direct visual control over the moving forelimb does not essentially affect the behavioral and electromyographic data.

[Geniculate relay of interhemispherical transmission of visual information]. / Genikuliarnoe rele mezhpolusharnoi peredachi zritel'noi informatsii.

Electrophysiological experiments were made on conscious cats with different degree of dissection of the classical and commissural optic tracts to the lateral geniculate body. The data obtained indicated that dissection of the direct retinal tracts to the lateral geniculate body (unilateral dissection of the optic tract) leads merely to the reduction in the amplitude of evoked potentials in response to light flashes. However, the latent period of the first component of the response in this structure appeared the same as in intact animals. Comparison of these data with those obtained in analogous experiments made on the visual cortex allows the conclusion that the geniculate body is the main subcortical relay of the visual commissural effects which are transmitted from the retina to the cortical regions of the brain.

[Role of the neocortical and subcortical commissures in the interhemispheric transfer of visual information to the hippocampus]. / Rol' neokortikal'nykh i podkortikal'nykh komissur v mezhpolusharnoi peredache zritel'noi informatsii v gippokamp.

The light flash evoked potentials were recorded in the hippocamp of cats with transected left optic tract and cerebral commissures. The data obtained show a significant reduction in the response amplitude (by 1.5-2 times) in both hemispheres after unilateral transection of the optic tract. The minimal response amplitude (10-15 times less than normal) was recorded in the left hippocamp of cats with additional transection of the commissures of the endbrain, mesencephalon and diencephalon. In contrast, the latent period of the first and second components of the evoked potential was similar to that in the control group animals. It is suggested that the neocortical commissural visual inputs play the most important role in interhemispheric transmission of visual information to the hippocamp.

[Extracallosal channels of interhemispheric transmission of visual information]. / Ekstrakallozal'nye kanaly mezhpolusharnoi peredachi zritel'noi informatsii.

Evoked potentials (EP) in response to light flashes were recorded in cats with different degree of optical tract disconnection. In intact and operated on animals, the latent period of the first component of these EP was the same as in the visual cortex. The different degree of disconnection of the classic and commissural optical tract brought about an increase in the amplitude of commissural potentials. The data obtained point to the existence of the effective callosal and extracallosal volleys of interhemispheric transmission of visual information, which are also likely to pay an essential part in compensatory processes of the optical system.

[Centro-peripheral organization of the kinesthetic system studied by natural stimulation of peripheral receptors]. / Izuchenie tsentral'no-perifericheskoi organizatsii kinesteticheskoi sistemy metodom estestvennoi stimuliatsii perifericheskikh retseptorov.

A method is suggested for investigation of the central peripheral organization of the kinesthetic system by nonartefact natural stimulation of the receptors in animals with the aid of a kinesthetic stimulator. The data obtained show the evoked potentials in response to natural stimulation in the contralateral somatosensory cortex of cats to have a significantly shorter latent periods as compared with electric stimulation. It is concluded that the rate of kinesthetic afferent volleys conduction in the somatosensory pathway is higher than that of mixed information during electric stimulation. The method suggested can be used both under experimental and clinical conditions.

[Compensation of anisocoria in cats following transection of the optic tract: the role of subcortical commissures]. / Kompensatsiia anizokorii u koshek posle pererezki opticheskogo trakta: rol' podkorkovykh komissur.

Experiments were carried out on cats with unilateral optic tract transection and cerebral commissures. The data obtained indicate that destruction of the afferent part of the pupillary reflex by optic transection led to reversible anisocoria. In cats with combined transection of the optic tract and teleencephalic, diencephalic and mesencephalic commissures, such a rehabilitation did not occur. In contrast, section of telencephalic commissures alone was immaterial for the processes of compensation of papillary system function. The data obtained attest to an important role of subcortical commissures in compensation of anisocoria after destruction of the afferent arc of the papillary reflex to light.

Interaction of the HMG1 protein with nucleic acids.

Binding constants have been measured for the interaction of the protein HMG1 with native DNA, denatured DNA and a number of polynucleotides at near-physiological ionic strengths, using gel filtration and thermal denaturation. The interaction of HMG1 with DNA is shown to be noncooperative and reversible. Nucleic acids form the following series in order of increasing binding constants: poly(U) integral of poly(A) less than poly(dA) less than dsDNA integral of poly(dA) X poly(dT) integral of poly(dG) X poly(dC) much less than poly[d(A-T]) integral of ssDNA.

[Commissural mechanisms of restoring visual functions]. / Komissural'nye mekhanizmy vosstanovleniia zritel'nykh funktsii.

The perimetric studies were carried out in adult cats with reduced classical and commissural visual pathways. The data obtained indicate substantial recovery of the temporal visual fields in cats with unilateral optic tract transection during one year after operation. The animals with combined optic tract and cerebral commissural transection did not demonstrate any remarkable restitution of visual fields. These findings allow the conclusion about the primary role of cerebral commissures in the compensatory mechanisms of visual functions after visual tract injury.

[Interhemispheric transmission of visual information to the cat somatosensory cortex: role of subcortical commissures]. / Mezhpolusharnaia peredacha zritel'noi informatsii v somatosensornuiu koru koshek: rol' podkorkovykh komissur.

Experiments were made on adult cats with combined transection of the visual tract and brain commissures. One to 1.5 month after operation microelectrodes were implanted into the primary somatosensory cortex. Transection of the classical and commissural (with the exception of subventricular and mesencephalon reticular interhemispheric tracts) visual inputs to the somatosensory cortex resulted in a decrease of the number of neurons that responded to visual stimulation. Activation of such neurons was provoked by visual information conduction via two subcortical commissural communications: the third ventricular fundus and midbrain reticular formation.

[Commissural channels of visual information transmission]. / Komissural'nye kanaly peredachi zritel'noi informatsii.

Experiments were made in adult cats with different transections of the classical and commissural visual tracts to study evoked potentials and unit neuronal activity in response to visual stimulation. The commissural channels of the telencephalon, diencephalon and mesencephalon were demonstrated to be highly effective in visual information conduction to the visual cortex. Complete transection of the classical and commissural tracts with the exception of the commissural tract of the third ventricle fundus and midbrain reticular formation resulted in the disappearance of evoked potentials in the visual cortex in response to light flashes, despite the fact that 8 of the 15 recorded neurons responded to photostimulation. Activation of such neurons was caused by visual information conduction via two possible commissural channels: midbrain reticular formation and subventricular interhemispheric commissures of the diencephalon.

[Choice of the optimal regimens for preserving the heart with weak aldehyde solutions using mathematical methods of experimental design]. / Vybor optimal'nykh rezhimov konservirovaniia serdtsa slabymi rastvorami al'degidov s ispol'zovaniem matematicheskikh metodov planirovaniia éksperimenta.

An optimal variant of myocardial conservation was found by means of the methods of experimental design with the use of a small number of experiments. This variant consists of different regimens and conditions affecting the results of transplantation with the use of weak aldehyde concentrations. The conservation regimens in question allow more complete protection of the test organ against long-term ischemic injuries preserving myocardial contractility during the post-transplantation period.