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Logacheva M.D.,Russian Academy of Sciences | Schelkunov M.I.,RAS Engelhardt Institute of Molecular Biology | Penin A.A.,Russian Academy of Sciences
Genome Biology and Evolution | Year: 2011

Plastids are the semiautonomous organelles that possess their own genome inherited from the cyanobacterial ancestor. The primary function of plastids is photosynthesis so the structure and evolution of plastid genomes are extensively studied in photosynthetic plants. In contrast, little is known about the plastomes of nonphotosynthetic species. In higher plants, plastid genome sequences are available for only three strictly nonphotosynthetic species, the liverwort Aneura mirabilis and two flowering plants, Epifagus virginiana and Rhizanthella gardneri. We report here the complete sequence of a plastid genome of nonphotosynthetic mycoheterotrophic orchid Neottia nidus-avis, determined using 454 pyrosequencing technology. It was found to be reduced in both genome size and gene content; this reduction is however not as drastic as in the other nonphotosynthetic orchid, R. gardneri. Neottia plastome lacks all genes encoding photosynthetic proteins, RNA polymerase subunits but retains most genes of translational apparatus. Those genes that are retained have an increased rate of both synonymous and nonsynonymous substitutions but do not exhibit relaxation of purifying selection either in Neottia or in Rhizanthella. © The Author(s) 2010.

Grechko V.V.,RAS Engelhardt Institute of Molecular Biology
Molecular Biology | Year: 2013

The review considers the current problems of molecular phylogenetics based on mitochondrial and chromosomal DNA sequences. The emphasis is placed on mtDNA markers, which are widely employed in reconstructing molecular evolution, but often without a critical analysis of the physiological and biochemical features of mitochondria that affect the adequacy and reliability of the results. In addition to the factors that make mtDNA-based phylogenies difficult to interpret (unrecognized hybridization and introgression events, ancestral polymorphism, and nuclear paralogs of mtDNA sequences), attention is paid to the nonneutrality and unequal mutation rates of mtDNA genes and their fragments, violations of uniparental inheritance of mitochondria, recombination events, natural heteroplasmy, and mtDNA haplotypic diversity. These factors may influence the congruence of phylogenetic inferences and trees constructed for the same organisms with different mtDNA markers or with mitochondrial and nuclear markers. The review supports the viewpoint that mitochondrial genes and their fragments fail to provide reliable evolutionary markers when considered without a thorough study of the environmental conditions and life of the taxa. The influence of external conditions on the metabolism and physiology of mitochondria cannot be taken into account in full nor modeled well enough for phylogenetic applications. It is assumed that mtDNA is valuable as a phylogenetic marker primarily because its complete sequence may be analyzed to identify the apomorphic and synmorphic properties of a taxon and to search for informative nuclear paralogs of mtDNA for phylogeographical studies and estimations of relative evolution times. © 2013 Pleiades Publishing, Ltd.

Sokolova M.I.,RAS Engelhardt Institute of Molecular Biology
The International journal of developmental biology | Year: 2013

Hybrid dysgenesis (HD) syndrome in Drosophila virilis presumably results from the mobilization of several unrelated mobile genetic elements in dysgenic hybrids. Morphogenetic events during oogenesis and spermatogenesis were investigated in detail in the progeny of D. virilis dysgenic crosses. Using germ-cell specific anti-Vasa staining, we monitored the fate of germline cells at different ontogenetic stages in strains of D. virilis and their hybrids. Anti-Vasa staining indicated that the major loss of pole cells occurs in dysgenic embryos at stage 11-14 after primordial germ cells (PGC) pass the midgut wall. At later ontogenetic stages, including larvae, pupae and imagoes, we often observed an abnormal development of gonads in dysgenic individuals with a frequent occurrence of unilateral and bilateral gonadal atrophy. Dysgenic females were characterized by the presence of various sterile ovarian phenotypes that predominantly include agametic ovarioles, while other atypical forms such as tumor-like ovarioles and dorsalized ovariolar follicles may also be present. Testis abnormalities were also frequently observed in dysgenic males. The sterility manifestations depended on the strain, the growing temperature and the age of the flies used in crosses. The observed gonadal sterility and other HD manifestations correlated with the absence of maternal piRNAs homologous to Penelope and other transposons in the early dysgenic embryos. We speculate that gonadal abnormalities mimicking several known sterility mutations probably result from the disturbance of developmental gene expression machinery due to the activation of unrelated families of transposons in early dysgenic embryos.

Deutsches Rheuma Forschungszentrum Berlin and RAS Engelhardt Institute of Molecular Biology | Date: 2013-10-28

The invention relates to isolated bispecific affinity reagents, such as antibodies or antibody fragments that bind TNF and a marker molecule for macrophages and/or neutrophils. The affinity reagents of the invention enable pathogenic sub-populations of TNF to be neutralised, whilst protective sub-populations of TNF are not affected.

Vassetzky N.S.,RAS Engelhardt Institute of Molecular Biology | Kramerov D.A.,RAS Engelhardt Institute of Molecular Biology
Nucleic Acids Research | Year: 2013

SINEBase (http://sines.eimb.ru) integrates the revisited body of knowledge about short interspersed elements (SINEs). A set of formal definitions concerning SINEs was introduced. All available sequence data were screened through these definitions and the genetic elements misidentified as SINEs were discarded. As a result, 175 SINE families have been recognized in animals, flowering plants and green algae. These families were classified by the modular structure of their nucleotide sequences and the frequencies of different patterns were evaluated. These data formed the basis for the database of SINEs. The SINEBase website can be used in two ways: first, to explore the database of SINE families, and second, to analyse candidate SINE sequences using specifically developed tools. This article presents an overview of the database and the process of SINE identification and analysis. © The Author(s) 2012.

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