Фіналь -ич у гідроніміконі Дністра

Статтю присвячено структурно-семантичному аналізу гідронімів басейну Дністра з формантом -ич. Основну увагу зосереджено на функціональній ролі суфікса -ич у назвах Бiлич, Вoнич, Гнилич, Крaсич, Нiчич, Прaвич, Сaвич, Смoтрич, Фрoлич. Зроблено висновок про те, що суф. -ич не у всіх назвах можна вважати патронімним. У низці гідронімів він виконує структурну функцію.Предлагаемая статья посвящена структурно-семантическому анализу гидронимов бассейна Днестра с формантом -ич. Особое внимание обращается на функционирование суффикса -ич в названиях Бiлич, Вoнич, Гнилич, Дядич, Крaсич, Нiчич, Сaвич, Смoтрич, Фрoлич. Предполагается, что суффикс -ич не во всех гидронимах можно считать патронимическим. В некоторых водных названиях он употребляется в структурной функции.The article is devoted to the structural-semantic analysis of the Dniester-bassin hydronyms with -ych formant. The main attention of this article is focused on functional role of -ych-suffix in Бiлич, Вoнич, Гнилич, Крaсич, Нiчич, Прaвич, Сaвич, Смoтрич, Фрoлич names. The conclusion on non-patronymic status of -ych-suffix (at least in part of hydronyms) was drown. In some names this one to do structural functio

Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties

<p>Abstract</p> <p>Background</p> <p>Homology is a key concept in both evolutionary biology and genomics. Detection of homology is crucial in fields like the functional annotation of protein sequences and the identification of taxon specific genes. Basic homology searches are still frequently performed by pairwise search methods such as BLAST. Vast improvements have been made in the identification of homologous proteins by using more advanced methods that use sequence profiles. However additional improvement could be made by exploiting sources of genomic information other than the primary sequence or tertiary structure.</p> <p>Results</p> <p>We test the hypothesis that extrinsic gene properties gene length and gene order can be of help in differentiating spurious sequence similarity from homology in the gray zone. Sharing gene order and similarity in size dramatically increase the chance of a query-hit pair being homologous: gray zone query-hit pairs of similar size and with conserved gene order are homologous in 99% of all cases, while for query-hit pairs without gene order conservation and with different sizes this is only 55%.</p> <p>Conclusion</p> <p>We have shown that using gene length and gene order drastically improves the detection of homologs within the BLAST gray zone. Our findings suggest that the use of such extrinsic gene properties can also improve the performance of homology detection by more advanced methods, and our study thereby underscores the importance of true data integration for fully exploiting genomic information.</p

Comparative Genome Analysis and Genome Evolution

This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies. Using conserved gene order we can predict protein interactions and we study the resulting network of interactions

Complex fate of paralogs

<p>Abstract</p> <p>Background</p> <p>Thanks to recent high coverage mass-spectrometry studies and reconstructed protein complexes, we are now in an unprecedented position to study the evolution of biological systems. Gene duplications, known to be a major source of innovation in evolution, can now be readily examined in the context of protein complexes.</p> <p>Results</p> <p>We observe that paralogs operating in the same complex fulfill different roles: mRNA dosage increase for more than a hundred cytosolic ribosomal proteins, mutually exclusive participation of at least 54 paralogs resulting in alternative forms of complexes, and 24 proteins contributing to <it>bona fide </it>structural growth. Inspection of paralogous proteins participating in two independent complexes shows that an ancient, pre-duplication protein functioned in both multi-protein assemblies and a gene duplication event allowed the respective copies to specialize and split their roles.</p> <p>Conclusion</p> <p>Variants with conditionally assembled, paralogous subunits likely have played a role in yeast's adaptation to anaerobic conditions. In a number of cases the gene duplication has given rise to one duplicate that is no longer part of a protein complex and shows an accelerated rate of evolution. Such genes could provide the raw material for the evolution of new functions.</p

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation

BACKGROUND: The massive scale of microarray derived gene expression data allows for a global view of cellular function. Thus far, comparative studies of gene expression between species have been based on the level of expression of the gene across corresponding tissues, or on the co-expression of the gene with another gene. RESULTS: To compare gene expression between distant species on a global scale, we introduce the "expression context". The expression context of a gene is based on the co-expression with all other genes that have unambiguous counterparts in both genomes. Employing this new measure, we show 1) that the expression context is largely conserved between orthologs, and 2) that sequence identity shows little correlation with expression context conservation after gene duplication and speciation. CONCLUSION: This means that the degree of sequence identity has a limited predictive quality for differential expression context conservation between orthologs, and thus presumably also for other facets of gene function

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

Evidence for the Concerted Evolution between Short Linear Protein Motifs and Their Flanking Regions

BACKGROUND: Linear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein-protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur inside flexible regions that are accessible for interaction. Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids. RESULTS: The evolution of regions flanking 116 functional linear motif instances was studied. The conservation of the amino acid sequence and order/disorder tendency of those regions was related to presence/absence of the instance. For the majority of the analysed instances, the pairs of sequences conserving the linear motif were also observed to maintain a similar local structural tendency and/or to have higher local sequence conservation when compared to pairs of sequences where one is missing the linear motif. Furthermore, those instances have a higher chance to co-evolve with the neighbouring residues in comparison to the distant ones. Those findings are supported by examples where the regulation of the linear motif-mediated interaction has been shown to depend on the modifications (e.g. phosphorylation) at neighbouring positions or is thought to benefit from the binding versatility of disordered regions. CONCLUSION: The results suggest that flanking regions are relevant for linear motif-mediated interactions, both at the structural and sequence level. More interestingly, they indicate that the prediction of linear motif instances can be enriched with contextual information by performing a sequence analysis similar to the one presented here. This can facilitate the understanding of the role of these predicted instances in determining the protein function inside the broader context of the cellular network where they arise

Pengaruh Kerjasama Pasiad Indonesia dengan Indonesia Dibidang Pendidikan Menengah

This study describes the effect of PASIAD Indonesia cooperation with Indonesia in the field of secondary education. PASIAD Indonesia is a non-governmental organization (NGO) engaged in educational, social, economic and cultural PASIAD Indonesia began working in secondary education in Indonesia since 1995. Until now PASIAD Indonesia has collaborated with 7 private foundations and 3 local governments to hold 10 high school.Perspective that used in this research is Pluralisme perspective. The theory used in this research is International Coorporation dan Transnational Advocacy Network ( TAN). This research used a qualitative method that is an explanatory. by using the techniques of data collection through literature and documentation, ie by collecting data from books, journals, magazines, newspapers, and other sources (document analysis).As a result, the effect of Indonesian PASIAD cooperation with Indonesia in the field of secondary education a positive impact on improving the quality of secondary education in Indonesia. Where PASIAD Indonesia Conducting scientific competition in national and international scale that encourage student creativity thinking and promote the spirit of competition to the students. besides school work partners PASIAD also always present medals to Indonesian state education can improve the image of Indonesia in the international arenaKey words : PASIAD Indonesia, non govermental organization, Transnationa Advocacy Network, secondary education

Монастырь Сурб-Хач – очаг национальной армянской культуры

Сегодня современное общество и наука все чаще обращает свои взоры на великую культуру ушедших эпох. Армянский монастырь Сурб-Хач - один из немногих памятников древней архитектуры Крыма, дошедших до наших дней. Поднять из забытья этот уникальный комплекс - одна из задач, которую ставит перед собой авторСьогодні сучасне суспільство і наука все частіше обертає свої погляди на велику культуру епох, що пішли. Вірменський монастир Сурб-Хач - один з небагатьох пам'ятників стародавньої архітектури Криму, що дійшли до наших днів. Підняти із забуття цей унікальний комплекс - одна із задач, яку ставить перед собою авто

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes

A comparison of phosphoproteomics datasets of six eukaryotes shows significant overlap between phosphoproteomes