The problems of genetic support of dividing the black kite (Milvus migrans) into subspecies

The black kite Milvus migrans is a common bird of prey demonstrating remarkable ecological plasticity. It inhabits a variety of habitats and is an increasingly synanthropic species. The black kite is widespread in Eurasia, Africa, Australia and adjacent islands. Palearctic kites migrate to Africa, India and China in winter, but kites of Africa and Australia are partly sedentary and partly seasonal migrants. The wide range and high mobility are the reasons of a complex population structure of the black kite. Commonly five to seven M. migrans subspecies are distinguished, each of which is widespread over extensive areas and has more or less an apparent phenotype. Recently, studies of genetic differences between black kite populations started to emerge. On the grounds of earlier studies of mitochondrial and nuclear genes of this species, we check whether there is a genetic support for separation of the black kite subspecies. Recent studies of some mitochondrial loci substantiate the recognition of at least the European (M. m. migrans), Asian (M. m. lineatus and M. m. govinda), African (M. m. aegyptius and M. m. parasitus), and Australian (M. m. affinis) black kite subspecies. Furthermore, the mitochondrial haplotype difference suggests that the African yellow-billed kite, including M. m. aegyptius and M. m. parasitus, should be a separate species as already proposed, or even two separate species

Overexpression of the SuUR gene induces reversible modifications at pericentric, telomeric and intercalary heterochromatin of Drosophila melanogaster polytene chromosomes

The SuUR (suppressor of underreplication) gene controls late replication and underreplication of DNA in Drosophila melanogaster polytene chromosomes: its mutation suppresses DNA underreplication whereas additional doses of the normal allele strongly enhances underreplication. The SuUR protein is localized in late replicating and underreplicating regions. The N-terminal part of the SuUR protein shares modest similarity with the ATPase/helicase domain of SWI2/SNF2 chromatin remodeling factors, suggesting a role in modification of chromatin structure. Here we describe novel structural modifications of polytene chromosomes (swellings) and show that SuUR controls chromatin organization in polytene chromosomes. The swellings develop as the result of SuUR ectopic expression in the transgene system Sgs3-GAL4; UAS-SuUR(+). They are reminiscent of chromosome puffs and appear in similar to190 regions of intercalary, pericentric and telomeric heterochromatin; some of them attain tremendous size. The swellings are temperature sensitive: they are maximal at 29C and are barely visible at 18degreesC. Shifting from 29degreesC to 18degreesC results in the complete recovery of the normal structure of chromosomes. The swellings are transcriptionally inactive, since they do not incorporate [H-3]uridine. The SuUR protein is not visualized in regions of maximally developed swellings. Regular ecdysone-inducible puffs are not induced in cells where these swellings are apparent

Late Replication Domains in Polytene and Non-Polytene Cells of Drosophila melanogaster

In D. melanogaster polytene chromosomes, intercalary heterochromatin (IH) appears as large dense bands scattered in euchromatin and comprises clusters of repressed genes. IH displays distinctly low gene density, indicative of their particular regulation. Genes embedded in IH replicate late in the S phase and become underreplicated. We asked whether localization and organization of these late-replicating domains is conserved in a distinct cell type. Using published comprehensive genome-wide chromatin annotation datasets (modENCODE and others), we compared IH organization in salivary gland cells and in a Kc cell line. We first established the borders of 60 IH regions on a molecular map, these regions containing underreplicated material and encompassing ∼12% of Drosophila genome. We showed that in Kc cells repressed chromatin constituted 97% of the sequences that corresponded to IH bands. This chromatin is depleted for ORC-2 binding and largely replicates late. Differences in replication timing between the cell types analyzed are local and affect only sub-regions but never whole IH bands. As a rule such differentially replicating sub-regions display open chromatin organization, which apparently results from cell-type specific gene expression of underlying genes. We conclude that repressed chromatin organization of IH is generally conserved in polytene and non-polytene cells. Yet, IH domains do not function as transcription- and replication-regulatory units, because differences in transcription and replication between cell types are not domain-wide, rather they are restricted to small “islands” embedded in these domains. IH regions can thus be defined as a special class of domains with low gene density, which have narrow temporal expression patterns, and so displaying relatively conserved organization

ГЛУБИННОЕ СТРОЕНИЕ САЛАИРСКОГО СКЛАДЧАТО-ПОКРОВНОГО СООРУЖЕНИЯ (СЕВЕРО-ЗАПАД ЦЕНТРАЛЬНО-АЗИАТСКОГО СКЛАДЧАТОГО ПОЯСА) ПО ДАННЫМ МАГНИТОТЕЛЛУРИЧЕСКОГО ЗОНДИРОВАНИЯ

The Salair fold-nappe terrane (a.k.a. Salair orogen, Salair) is the northwestern part of the Altai-Sayan folded area of the Central Asian Orogenic Belt. It is composed of Cambrian – Early Ordovician volcanic rocks and island-arc sedimentary deposits. In plan, Salair is a horseshoe-shaped structure with the northeast-facing convex side, which is formed by the outcrops of the Early Paleozoic folded basement. Its inner part is the Khmelev basin composed of Upper Devonian – Lower Carboniferous sandstones and siltstones. The Early Paleozoic volcanic rocks and sediments of Salair are overthrusted onto the Devonian-Permian sediments of the Kuznetsk basin. The Paleozoic thrusts, that were reactivated at the neotectonic stage, are observed in the modern relief as tectonic steps. Our study of the Salair deep structure was based on the data from two profiles of magnetotelluric sounding. These 175-km and 125-km long profiles go across the strike of the Salair structure and the western part of the Kuznetsk basin. Profile 1 detects a subhorizontal zone of increased conductivity (100–500 Ohm·m) at the depths of 8–15 km. At the eastern part of Profile 1, this zone gently continues upward, towards a shallow conducting zone that corresponds to the sediments of the Kuznetsk basin. Two high-resistance bodies (1000–7000 Ohm⋅m) are detected at the depths of 0–6 km in the middle of the section. They are separated by a subvertical conducting zone corresponding to the Kinterep thrust. The main features are the subhorizontal positions and the flattened forms of crustal conductivity anomalies. At the central part of Profile 2, there is a high-resistance block (above 150000 Ohm⋅m) over the entire depth range of the section, from the surface to the depths of about 20 km. In the eastern part of Profile 2, a shallow zone of increased conductivity corresponds to the sediments of the Kuznetsk basin. The subhorizontal mid-crust layer of increased conductivity, which is detected in the Salair crust, is typical of intracontinental orogens. The distribution pattern of electrical conductivity anomalies confirms the Salair thrust onto the Kuznetsk basin. The northern part of the Khmelev basin is characterized by high resistivity, which can be explained by abundant covered Late Permian granite massifs in that part of the Khmelev basin. The Kinterep thrust located in the northeastern part of the Khmelev basin is manifested in the deep geoelectric crust structure as a conducting zone, which can be considered as an evidence of the activity of this fault.Салаирское покровно-складчатое сооружение (Салаирский ороген, Салаир) расположено на северо-западе Алтае-Саянской складчатой области Центрально-Азиатского складчатого пояса и сложено кембрийско-раннеордовикскими вулканогенными и осадочными отложениями островодужного происхождения. В плане Салаир имеет форму подковы, обращенной выпуклой стороной на северо-восток. Во внутренней части этой дугообразной структуры, образованной выходами раннепалеозойского складчатого фундамента, находится Хмелевский прогиб, выполненный терригенными отложениями верхнего девона – нижнего карбона. По системе чешуйчатых надвигов раннепалеозойские отложения Салаира надвинуты на девонско-пермское осадочное выполнение Кузнецкого прогиба. Палеозойские надвиги местами реактивированы на неотектоническом этапе и выражены в современном рельефе тектоногенными уступами. С целью изучения глубинного строения Салаира было пройдено два профиля магнитотеллурического зондирования. Профили имеют длину 175 и 125 км. Они ориентированы вкрест простирания основных структур и пересекают Салаир и западную часть Кузнецкого прогиба. На первом профиле выделяется субгоризонтально залегающая зона повышенной проводимости с удельным электрическим сопротивлением (УЭС) 100–500 Ом⋅м, в диапазоне глубин 8–15 км. В восточной части профиля она полого воздымается в направлении малоглубинной проводящей зоны, соответствующей осадочному выполнению Кузнецкого прогиба. Два высокоомных тела со значениями УЭС 1000–7000 Ом⋅м залегают на глубинах 0–6 км в средней части разреза и разделены субвертикальной проводящей зоной, соответствующей Кинтерепскому надвигу. Главной чертой разреза является субгоризонтальное залегание и уплощенная форма коровых неоднородностей электропроводности. Центральную часть второго профиля занимает высокоомный блок (УЭС более 150000 Ом⋅м), распространяющийся на всю глубину разреза – от поверхности до глубин около 20 км. Восточную часть разреза занимает малоглубинная зона повышенной проводимости, соответствующая осадочному выполнению Кузнецкого прогиба. Земная кора Салаира содержит субгоризонтально залегающую зону повышенной проводимости, типичную для внутриконтинентальных орогенов. Картина распределения аномалий электропроводности подтверждает наличие надвига Салаира на Кузнецкий прогиб. Северная часть Хмелевского прогиба характеризуется высокими значениями УЭС, что может быть объяснено широким развитием невскрытых позднепермских гранитоидных массивов в этой части прогиба. Расположенный в северо-восточной части Хмелевского прогиба Кинтерепский надвиг проявлен в глубинной геоэлектрической структуре земной коры в виде проводящей зоны, что может рассматриваться как свидетельство активности данного разлома

Polytene chromosomes reflect functional organization of the Drosophila genome

Polytene chromosomes of Drosophila melanogaster are a convenient model for studying interphase chromosomes of eukaryotes. They are giant in size in comparison with diploid cell chromosomes and have a pattern of cross stripes resulting from the ordered chromatid arrangement. Each region of polytene chromosomes has a unique banding pattern. Using the model of four chromatin types that reveals domains of varying compaction degrees, we were able to correlate the physical and cytological maps of some polytene chromosome regions and to show the main properties of genetic and molecular organization of bands and interbands, that we describe in this review. On the molecular map of the genome, the interbands correspond to decompacted aquamarine chromatin and 5’ ends of ubiquitously active genes. Gray bands contain lazurite and malachite chromatin, intermediate in the level of compaction, and, mainly, coding parts of genes. Dense black transcriptionally inactive bands are enriched in ruby chromatin. Localization of several dozens of interbands on the genome molecular map allowed us to study in detail their architecture according to the data of whole genome projects. The distribution of proteins and regulatory elements of the genome in the promoter regions of genes localized in the interbands shows that these parts of interbands are probably responsible for the formation of open chromatin that is visualized in polytene chromosomes as interbands. Thus, the permanent genetic activity of interbands and gray bands and the inactivity of genes in black bands are the basis of the universal banding pattern in the chromosomes of all Drosophila tissues. The smallest fourth chromosome of Drosophila with an atypical protein composition of chromatin is a special case.  Using the model of four chromatin states and fluorescent in situ hybridization, its cytological map was refined and the genomic coordinates of all bands and interbands were determined. It was shown that, in spite of the peculiarities of this chromosome, its band organization in general corresponds to the rest of the genome. Extremely long genes of different Drosophila chromosomes do not fit the common scheme, since they can occupy a series of alternating bands and interbands (up to nine chromosomal structures) formed by parts of these genes

Genomic Organization of H2Av Containing Nucleosomes in Drosophila Heterochromatin

H2Av is a versatile histone variant that plays both positive and negative roles in transcription, DNA repair, and chromatin structure in Drosophila. H2Av, and its broader homolog H2A.Z, tend to be enriched toward 5′ ends of genes, and exist in both euchromatin and heterochromatin. Its organization around euchromatin genes and other features have been described in many eukaryotic model organisms. However, less is known about H2Av nucleosome organization in heterochromatin. Here we report the properties and organization of individual H2Av nucleosomes around genes and transposable elements located in Drosophila heterochromatic regions. We compare the similarity and differences with that found in euchromatic regions. Our analyses suggest that nucleosomes are intrinsically positioned on inverted repeats of DNA transposable elements such as those related to the “1360” element, but are not intrinsically positioned on retrotransposon-related elements

ЭКСПРЕССИОННЫЙ ПРОФИЛЬ МИКРОРНК ПРИ ПЛОСКОКЛЕТОЧНОМ РАКЕ ГОЛОВЫ И ШЕИ

Head and neck squamous cell carcinoma (HNSCC) is a highly aggressive disease with long asymptomatic course. New molecular prognostic markers are urgently needed to identify patients at high risk for developing lymph node metastasis. MicroRNAs (miRNAs) are a recently discovered class of small non-coding RNAs. Based on literature and our data, we have chosen 12 miRNAs (miRNA-21, -221, -222, -155, -205, -20a, -125b, -146b, -181b, -200a, -126, -451), involved in HNSCC carcinogenesis. Using real-time quantitative polymerase chain reaction analysis, we have shown a change in the expression miRNA in tumor tissue compared to unmodified tissue. Significant upregulation of five miRNAs: miRNA-21, -155, -181b, -126, -451 (p<0.05) has been shown in tumors. MiRNA-126 has been found to be highly expressed in metastasis tissue (p<0.05), and can be an important factor in understanding the processes of metastasis and development of a new prognostic marker.Плоскоклеточные карциномы головы и шеи (ПКГШ) отличаются высокой агрессивностью и длительным бессимптомным течением. Диагностика заболевания на ранних стадиях и оценка риска метастазирования, а также прогноза течения опухолевого процесса являются приоритетной задачей современной клинической онкологии, что требует поиска и разработки новых прогностических маркеров заболевания. Такими маркерами могут служить микроРНК (миРНК) – относительно недавно открытый класс малых некодирующих РНК. На основании литературных данных и собственных исследований мы выбрали 12 миРНК (миРНК-21, -221, -222, -155, -205, -20a, -125b, -146b, -181b, -200a, -126, -451), участвующих в процессе канцерогенеза ПКГШ. Методом ПЦР в реальном времени определены изменения уровня экспрессии выбранной группы миРНК в опухоли по сравнению с неизмененной тканью. Установлено увеличение уровня экспрессии 5 миРНК: миРНК-21, -155, -181b, -126, -451 (p<0,05) – непосредственно в опухоли по сравнению с окружающей неизмененной тканью. Также в результате исследования получены данные, указывающие на различия в содержании миРНК-126 между опухолями с наличием и без метастазов в регионарные лимфоузлы (p<0,05), что может быть важным аспектом в понимании процессов метастазирования и разработки нового прогностического маркера

Повышение точности и информативности тонкоигольной аспирационной пункционной биопсии опухолей молочной железы путем анализа микроРНК в материале цитологического мазка

Relevance. Breast cancer is the most commonly diagnosed cancer in women. Tumor biopsy, a key diagnostic approach, is required to evaluate the nature of tumor and to determine the therapeutic strategy. In clinical practice methods are being applied: trepan-biopsy and fine needle aspiration biopsy (FNAB). The latter is less traumatic however is used less often because it provides with less information. Moreover, dependence from quality of biopsy and qualification of morphologist are attributes of both techniques. A possibility to use biopsy material for farther analysis of tumor-markers would open a perspective to obtain more information and to improve objectivity of traditional diagnostic approaches, including FNAB. MicroRNAs (miRNAs), regulatory molecules involved in control of virtually all physiologic and pathologic process, emerged as promising tumor markers. Malignant transformation of mammary gland epithelia is associated with specific alterations of cellular miRNAs profile. Analysis of these alterations is of great diagnostic potency.Objective. Development of method for miRNAs analysis in cytological smears material and evaluation of its practical applicability.Material and methods. Archived cytological material (smears on the glass slides) from patients with benign tumor and breast cancer was used. Analysis of miRNAs expression was performed by reverse transcription followed by quantitative PCR. Results of reverse transcription polymerase chain reaction were analyzed with use of relevant cytological and morphological data.Results. Method of miRNAs analysis in material of cytological smears was developed. Expression of 9 miRNAs in 80 samples was evaluated. Statistically significant expression difference between benign and malignant tumor samples was found for 5 miRNAs: miR-21, miR-205, miR-125b, miR-200a, miR-221. MiR-125b exhibited most prominent expression dysregulation: malignant transformation of mammary epithelium is associated with 500 fold decrease of miR-125b expression level. Expression alterations of several miRNAs were revealed to correlate with clinically relevant characteristics of tumors.Conclusions. Results of our study indicated the possibility of miRNAs expression analysis in the FNAB material and the applicability of this method as additive approach to the convention cytological examination. Application of this method will allow to specify diagnosis and to optimize choice of the therapeutic strategy.Актуальность. Рак молочной железы – самое распространенное злокачественное новообразование у женщин. Биопсия ткани опухоли молочной железы является ключевым этапом диагностики, позволяющим оценить природу новообразования и определить тактику лечения. В клинической практике применяются методы трепан-биопсии и тонкоигольной аспирационной пункционной биопсии (ТАПБ). Последний вариант менее травматичен, но используется реже по причине меньшей информативности. Кроме того, при любом из двух методов существует риск забора малоинформативного образца, а точность диагноза определяется квалификацией гистолога/цитолога. Возможность использовать биопсийный материал для анализа онкомаркеров в дополнение к стандартному исследованию открывает перспективы существенного повышения информативности и объективности традиционных подходов, включая метод ТАПБ. Среди потенциальных онкомаркеров особое место занимают микроРНК (миРНК) – класс регуляторных молекул, играющих важную роль в различных физиологических и патологических процессах. Неопластическая трансформация протокового эпителия молочных желез сопровождается специфическими изменениями профиля экспрессии миРНК. Оценка этих изменений имеет большой диагностический потенциал.Цель исследования – разработка и оценка перспективы внедрения в клиническую практику метода анализа миРНК в материале цитологических препаратов.Материалы и методы. В исследовании использованы архивные цитологические препараты, по которым ранее был установлен диагноз доброкачественной или злокачественной опухоли молочной железы. Оценка экспрессии миРНК проводили методом обратной транскрипции и последующей количественной полимеразной цепной реакции. При анализе результатов были использованы соответствующие данные ранее проведенных цитологических и гистологических исследований.Результаты. Разработан метод выделения РНК из препаратов, приготовленных для традиционного цитологического исследования. Проведен анализ экспрессии 9 миРНК. Сравнение результатов анализа материала доброкачественных и злокачественных образований показало статистически значимую разницу экспрессии 5 миРНК: миРНК-21, -205, -125b, -200a и -221. Наиболее значимую разницу наблюдали для миРНК-125b: в ходе неопластической трансформации уровень экспрессии этой молекулы снижается в 500 раз. Установлена корреляция экспрессии некоторых миРНК с рядом клинически значимых характеристик опухолевой ткани.Заключение. Результаты работы показали возможность оценки экспрессии миРНК в материале ТАПБ образований молочной железы и целесообразность ее использования в дополнение к традиционному цитологическому исследованию в целях уточнения диагноза и оптимизации выбора терапии

The N-Terminal Domain of the Drosophila Retinoblastoma Protein Rbf1 Interacts with ORC and Associates with Chromatin in an E2F Independent Manner

The retinoblastoma (Rb) tumor suppressor protein can function as a DNA replication inhibitor as well as a transcription factor. Regulation of DNA replication may occur through interaction of Rb with the origin recognition complex (ORC).We characterized the interaction of Drosophila Rb, Rbf1, with ORC. Using expression of proteins in Drosophila S2 cells, we found that an N-terminal Rbf1 fragment (amino acids 1-345) is sufficient for Rbf1 association with ORC but does not bind to dE2F1. We also found that the C-terminal half of Rbf1 (amino acids 345-845) interacts with ORC. We observed that the amino-terminal domain of Rbf1 localizes to chromatin in vivo and associates with chromosomal regions implicated in replication initiation, including colocalization with Orc2 and acetylated histone H4.Our results suggest that Rbf1 can associate with ORC and chromatin through domains independent of the E2F binding site. We infer that Rbf1 may play a role in regulating replication directly through its association with ORC and/or chromatin factors other than E2F. Our data suggest an important role for retinoblastoma family proteins in cell proliferation and tumor suppression through interaction with the replication initiation machinery