Арагонитовые и кальцитовые жеоды из пещеры Ботовская

В статье описываются необычные вторичные минеральные образования, обнаруженные в Ботовской пещере в Восточной Сибири, которые представляют собой жеоды, выполненные арагонитом, а в отдельных случаях – кальцитом. Приведены два предположения о формирование жеод: за счет стекающих растворов, размывающих рыхлые пещерные отложения и заполняющих образовавшиеся пустоты, в которых затем происходила кристаллизация минералов, и за счет растворения центрального тела сформированных ранее конкреций и последующего отложения арагонита и кальцита в получившейся полости. Впоследствии жеоды были вскрыты при выносе из пещеры большого объема осадков водными потоками. Вследствие особенностей своей морфологии и генезиса данные образования могут рассматриваться как новый тип спелеотем.У статті описуються незвичайні вторинні мінеральні утворення, виявлені у Ботовской печері у Східному Сибіру, якими є жеоди, виповнені арагонітом, а в окремих випадках - кальцитом. Наведені два припущення про формування жеод: за рахунок стікаючих розчинів, що розмивають пухкі печерні відклади і заповнюють порожнини, що утворилися, в яких потім відбувалася кристалізація мінералів, і за рахунок розчинення центрального тіла сформованих раніше конкрецій і подальшого відкладення арагоніту і кальциту у порожнини, що утворилися. Згодом жеоди були розкриті при винесенні з печери великого об'єму відкладень водними потоками. Внаслідок особливостей своєї морфології і генезису ці утворення можуть розглядатися як новий тип спелеотем.The article describes unusual secondary mineral formation found in Botovskaya Cave in Eastern Siberia, which are geodes, lined byaragonite and, in some cases, by calcite. Two assumptions of the geode formation are put forward: 1) at the expense of draining solutions that erode loose sediments and fill formed cavities, where then mineral crystallization occurs; 2) at the expense of dissolution of the central body of concretions formed earlier, followed by precipitation of aragonite and calcite in the cavity formed. Later on, the geodes were uncovered during erosion of large volumes of sediments by water flows. Due to peculiar features of their morphology and genesis, these formations can be regarded as a new type of speleothems

OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes

OGtree is a web-based tool for constructing genome trees of prokaryotic species based on a measure of combining overlapping-gene content and overlapping-gene order in their whole genomes. The overlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, OGs are ubiquitous in microbial genomes and more conserved between species than non-OGs. Based on these properties, it has been suggested that OGs can serve as better phylogenetic characters than non-OGs for reconstructing the evolutionary relationships among microbial genomes. OGtree takes the accession numbers of prokaryotic genomes as its input. It then downloads their complete genomes from the National Centre for Biotechnology Information and identifies OGs in each genome and their orthologous OGs in other genomes. Next, OGtree computes an overlapping-gene distance between each pair of input genomes based on a combination of their OG content and orthologous OG order. Finally, it utilizes distance-based methods of building tree to reconstruct the genome trees of input prokaryotic genomes according to their pairwise OG distance. OGtree is available online at http://bioalgorithm.life.nctu.edu.tw/OGtree/

Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis

Background: Following gene duplication, retained paralogs undergo functional divergence, which is reflected in changes in DNA sequence and expression patterns. The extent of divergence is influenced by several factors, including protein function. We examine whether an epigenetic modification, trimethylation of histone H3 at lysine 27 (H3K27me3), could be a factor in the evolution of expression patterns after gene duplication. Whereas in animals this repressive mark for transcription is deposited on long regions of DNA, in plants its localization is gene-specific. Because of this and a well-annotated recent whole-genome duplication, Arabidopsis thaliana is uniquely suited for studying the potential association of H3K27me3 with the evolutionary fate of genes. Results: Paralogous pairs with H3K27me3 show the highest coding sequence divergence, which can be explained by their low expression levels. Interestingly, they also show the highest similarity in expression patterns and upstream regulatory regions, while paralogous pairs where only one gene is an H3K27me3 target show the highest divergence in expression patterns and upstream regulatory sequence. These trends in divergence of expression and upstream regions are especially pronounced for transcription factors. Conclusions: After duplication, a histone modification can be associated with a particular fate of paralogs: H3K27me3 is linked to lower expression divergence yet higher coding sequence divergence. Our results show that H3K27me3 constrains expression divergence after duplication. Moreover, its association with higher conservation of upstream regions provides a potential mechanism for the conserved H3K27me3 targeting of the paralogs

Transmembrane Protein Oxygen Content and Compartmentalization of Cells

Recently, there was a report that explored the oxygen content of transmembrane proteins over macroevolutionary time scales where the authors observed a correlation between the geological time of appearance of compartmentalized cells with atmospheric oxygen concentration. The authors predicted, characterized and correlated the differences in the structure and composition of transmembrane proteins from the three kingdoms of life with atmospheric oxygen concentrations in geological timescale. They hypothesized that transmembrane proteins in ancient taxa were selectively excluding oxygen and as this constraint relaxed over time with increase in the levels of atmospheric oxygen the size and number of communication-related transmembrane proteins increased. In summary, they concluded that compartmentalized and non-compartmentalized cells can be distinguished by how oxygen is partitioned at the proteome level. They derived this conclusion from an analysis of 19 taxa. We extended their analysis on a larger sample of taxa comprising 309 eubacterial, 34 archaeal, and 30 eukaryotic complete proteomes and observed that one can not absolutely separate the two groups of cells based on partition of oxygen in their membrane proteins. In addition, the origin of compartmentalized cells is likely to have been driven by an innovation than happened 2700 million years ago in the membrane composition of cells that led to the evolution of endocytosis and exocytosis rather than due to the rise in concentration of atmospheric oxygen

The Molecular Basis of Monopolin Recruitment to the Kinetochore

The monopolin complex is a multifunctional molecular crosslinker, which in S. pombe binds and organises mitotic kinetochores to prevent aberrant kinetochore-microtubule interactions. In the budding yeast S. cerevisiae, whose kinetochores bind a single microtubule, the monopolin complex crosslinks and mono-orients sister kinetochores in meiosis I, enabling the biorientation and segregation of homologs. Here, we show that both the monopolin complex subunit Csm1 and its binding site on the kinetochore protein Dsn1 are broadly distributed throughout eukaryotes, suggesting a conserved role in kinetochore organisation and function. We find that budding yeast Csm1 binds two conserved motifs in Dsn1, one (termed Box 1) representing the ancestral, widely conserved monopolin binding motif and a second (termed Box 2-3) with a likely role in enforcing specificity of sister kinetochore crosslinking. We find that Box 1 and Box 2-3 bind the same conserved hydrophobic cavity on Csm1, suggesting competition or handoff between these motifs. Using structure-based mutants, we also find that both Box 1 and Box 2-3 are critical for monopolin function in meiosis. We identify two conserved serine residues in Box 2-3 that are phosphorylated in meiosis and whose mutation to aspartate stabilises Csm1-Dsn1 binding, suggesting that regulated phosphorylation of these residues may play a role in sister kinetochore crosslinking specificity. Overall, our results reveal the monopolin complex as a broadly conserved kinetochore organiser in eukaryotes, which budding yeast have co-opted to mediate sister kinetochore crosslinking through the addition of a second, regulatable monopolin binding interface

Enrichment of homologs in insignificant BLAST hits by co-complex network alignment

<p>Abstract</p> <p>Background</p> <p>Homology is a crucial concept in comparative genomics. The algorithm probably most widely used for homology detection in comparative genomics, is BLAST. Usually a stringent score cutoff is applied to distinguish putative homologs from possible false positive hits. As a consequence, some BLAST hits are discarded that are in fact homologous.</p> <p>Results</p> <p>Analogous to the use of the genomics context in genome alignments, we test whether conserved functional context can be used to select candidate homologs from insignificant BLAST hits. We make a co-complex network alignment between complex subunits in yeast and human and find that proteins with an insignificant BLAST hit that are part of homologous complexes, are likely to be homologous themselves. Further analysis of the distant homologs we recovered using the co-complex network alignment, shows that a large majority of these distant homologs are in fact ancient paralogs.</p> <p>Conclusions</p> <p>Our results show that, even though evolution takes place at the sequence and genome level, co-complex networks can be used as circumstantial evidence to improve confidence in the homology of distantly related sequences.</p