[Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data]

The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation and are important for cancer research. The technique of chromatin immunoprecipitation and subsequent sequencing (ChIP-seq) make possible to determine binding sites of transcription factors that regulate expression of eukaryotic genes; genome transcription factors binding maps have been. The ChIA-PET technology allows exploring not only target protein binding sites, but also pairs of such sites on proximally located and interacting with each other chromosomes co-located in three-dimensional space of the cell nucleus. Here we discuss the principles of the construction of genomic maps and matrices of chromosome contacts according to ChIA-PET and Hi-C data that capture the chromosome conformation and overview existing software for 3D genome analysis including in house programs of gene location analysis in topological domains.

Distribution patterns, population status and conservation of Melanosuchus niger and Caiman yacare (Crocodylia, Alligatoridae) in oxbow lakes of the Ichilo river floodplain, Bolivia

Caiman yacare (lagarto) and Melanosuchus niger (black caiman), sympatric species in the Bolivian Amazon basin, have been severely overexploited in the past. We present the results of a standardized survey of C. yacare and M. niger populations in order to evaluate their actual population status in twelve oxbow lakes of the Ichilo River floodplain. Additionally we explored the effect of environmental and anthropogenic variables on caiman distribution patterns. The average density of C yacare and M niger in the shoreline of floodplain lakes was of 6 and 1 ind/km, respectively. For both species, the population was composed mainly of juvenile individuals. We used regression tree analysis (RTA) to assess patterns of M. niger and C. yacare densities with eight environmental and two anthropogenic variables. The RTA analysis showed that the variation in the densities of both C. yacare (52.4%) and M. niger (36.8 %) was related to water conductivity. For C yacare, higher densities occurred at higher values of water conductivity, while M. niger densities followed an opposite trend, resulting in relatively well spatially segregated populations of the two species. After excluding conductivity, Lake-River Distance (LRD) was shown to be the main splitting variable in the RTA analysis. The observed distribution patterns may be the result of the historical post-hunting situation, in combination with differences in habitat selection by the two species, and competitive exclusion processes between the two species. M. niger, a species reported to be recovering slowly from previous low population levels, appears relatively well protected in the Ichilo river floodplain.