Mosaicism in old trees and its patterns Zahradníková, Eva; Ficek, Andrej; Brejová, Bronislava ...
Trees (Berlin, West),
04/2020, Letnik:
34, Številka:
2
Journal Article
Recenzirano
Key Message
Mosaicism has been confirmed in several studied old trees from both gymnosperms and angiosperms, in a pattern not always following the actual branching of the tree.
Eight individuals from ...two gymnosperm and three angiosperm species of trees were studied for age-related mosaicism. We compare the level of intra-organismal genetic variability found within an individual old and an individual young tree of the same species to prove its relation to age. In five cases, we found statistically significant differences in intra-organismal genetic variability between young and old trees. In three cases of mosaicism, the constructed dendrogram corresponded with the actual branching of the tree, but it differed in the remaining two. We offer an explanation of the cases when the dendrogram does not correspond with the branching structure of the tree through the patterns of sectorial and mericlinal chimerism. In the studied gymnosperms, we found that the growth rate possibly influenced the level of intra-organismal variability, while in angiosperms the dependence was rather on age. The differences between angiosperm and gymnosperm molecular evolution and meristem stratification may play a role in this, but further research is needed in this area.
The yeast
Magnusiomyces capitatus
is an opportunistic human pathogen causing rare yet severe infections, especially in patients with hematological malignancies. Here, we report the 20.2 megabase ...genome sequence of an environmental strain of this species as well as the genome sequences of eight additional isolates from human and animal sources providing an insight into intraspecies variation. The distribution of single-nucleotide variants is indicative of genetic recombination events, supporting evidence for sexual reproduction in this heterothallic yeast. Using RNAseq-aided annotation, we identified genes for 6518 proteins including several expanded families such as kexin proteases and Hsp70 molecular chaperones. Several of these families are potentially associated with the ability of
M. capitatus
to infect and colonize humans. For the purpose of comparative analysis, we also determined the genome sequence of a closely related yeast,
Magnusiomyces ingens
. The genome sequences of
M. capitatus
and
M. ingens
exhibit many distinct features and represent a basis for further comparative and functional studies.
Abstract
One powerful strategy of how to increase the complexity of cellular proteomes is through posttranslational modifications (PTMs) of proteins. Currently, there are ∼400 types of PTMs, the ...different combinations of which yield a large variety of protein isoforms with distinct biochemical properties. Although mitochondrial proteins undergoing PTMs were identified nearly 6 decades ago, studies on the roles and extent of PTMs on mitochondrial functions lagged behind the other cellular compartments. The application of mass spectrometry for the characterization of the mitochondrial proteome as well as for the detection of various PTMs resulted in the identification of thousands of amino acid positions that can be modified by different chemical groups. However, the data on mitochondrial PTMs are scattered in several data sets, and the available databases do not contain a complete list of modified residues. To integrate information on PTMs of the mitochondrial proteome of the yeast Saccharomyces cerevisiae, we built the yeast mitochondrial posttranslational modification (y-mtPTM) database (http://compbio.fmph.uniba.sk/y-mtptm/). It lists nearly 20,000 positions on mitochondrial proteins affected by ∼20 various PTMs, with phosphorylated, succinylated, acetylated, and ubiquitylated sites being the most abundant. A simple search of a protein of interest reveals the modified amino acid residues, their position within the primary sequence as well as on its 3D structure, and links to the source reference(s). The database will serve yeast mitochondrial researchers as a comprehensive platform to investigate the functional significance of the PTMs of mitochondrial proteins.
Routing in Carrier-Based Mobile Networks Brejová, Bronislava; Dobrev, Stefan; Královič, Rastislav ...
Structural Information and Communication Complexity
Book Chapter
Recenzirano
The past years have seen an intense research effort directed at study of delay/disruption tolerant networks and related concepts (intermittently connected networks, opportunistic mobility networks). ...As a fundamental primitive, routing in such networks has been one of the research foci. While multiple network models have been proposed and routing in them investigated, most of the published results are of heuristic nature with experimental validation; analytical results are scarce and apply mostly to networks whose structure follows deterministic schedule.
In this paper, we propose a simple model of opportunistic mobility network based on oblivious carriers, and investigate the routing problem in such networks. We present an optimal online routing algorithm and compare it with a simple shortest-path inspired routing and the optimal offline routing. In doing so, we identify the key parameters (the minimum non-zero probability of meeting among the carrier pairs, and the number of carriers a given carrier comes into contact) driving the separation among these algorithms.
The emergence of new SARS-CoV-2 variants of concern B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta) that harbor mutations in the viral S protein raised concern about activity of ...current vaccines and therapeutic antibodies. Independent studies have shown that mutant variants are partially or completely resistant against some of the therapeutic antibodies authorized for emergency use.
We employed hybridoma technology, ELISA-based and cell-based S-ACE2 interaction assays combined with authentic virus neutralization assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize the new variants of SARS-CoV-2.
AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). In addition, AX677 is able to bind Omicron Spike protein just like the wild type Spike. The combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. Prophylactic administration of AX290 and AX677, either individually or in combination, effectively reduced viral burden and inflammation in the lungs, and prevented disease in a mouse model of SARS-CoV-2 infection.
The virus-neutralizing properties were fully reproduced in chimeric mouse-human versions of the antibodies, which may represent a promising tool for COVID-19 therapy.
The study was funded by AXON Neuroscience SE and AXON COVIDAX a.s.
Analyzing variants of Shellsort BREJOVA, Bronislava
Information processing letters,
09/2001, Letnik:
79, Številka:
5
Journal Article
Recenzirano
We consider two variants of Shellsort — Dobosiewicz sort and Shaker sort. Not much is known about the running time of these algorithms. We prove that the worst-case time of Shaker sort is
O(n
3/2
log
...3n)
for certain sequences of increments and the average-case time for both variants is
Ω(n
2/c
p)
where
p is the number of increments and
c=2 for Dobosiewicz sort and
c=4 for Shaker sort. In our proofs we adapt techniques and results from analysis of Shellsort.
This thesis introduces new techniques for finding genes in genomic sequences. Genes are regions of a genome encoding proteins of an organism. Identification of genes in a genome is an important step ...in the annotation process after a new genome is sequenced. The prediction accuracy of gene finding can be greatly improved by using experimental evidence. This evidence includes homologies between the genome and databases of known proteins, or evolutionary conservation of genomic sequence in different species. We propose a flexible framework to incorporate several different sources of such evidence into a gene finder based on a hidden Markov model. Various sources of evidence are expressed as partial probabilistic statements about the annotation of positions in the sequence, and these are combined with the hidden Markov model to obtain the final gene prediction. The opportunity to use partial statements allows us to handle missing information transparently and to cope with the heterogeneous character of individual sources of evidence. On the other hand, this feature makes the combination step more difficult. We present a new method for combining partial probabilistic statements and prove that it is an extension of existing methods for combining complete probability statements. We evaluate the performance of our system and its individual components on data from the human and fruit fly genomes. The use of sequence evolutionary conservation as a source of evidence in gene finding requires efficient and sensitive tools for finding similar regions in very long sequences. We present a method for improving the sensitivity of existing tools for this task by careful modeling of sequence properties. In particular, we build a hidden Markov model representing a typical homology between two protein coding regions and then use this model to optimize a component of a heuristic algorithm called a spaced seed. The seeds that we discover significantly improve the accuracy and running time of similarity search in protein coding regions; and are directly applicable to our gene finder.
This thesis introduces new techniques for finding genes in genomic sequences. Genes are regions of a genome encoding proteins of an organism. Identification of genes in a genome is an important step ...in the annotation process after a new genome is sequenced. The prediction accuracy of gene finding can be greatly improved by using experimental evidence. This evidence includes homologies between the genome and databases of known proteins, or evolutionary conservation of genomic sequence in different species.
We propose a flexible framework to incorporate several different sources of such evidence into a gene finder based on a hidden Markov model. Various sources of evidence are expressed as partial probabilistic statements about the annotation of positions in the sequence, and these are combined with the hidden Markov model to obtain the final gene prediction. The opportunity to use partial statements allows us to handle missing information transparently and to cope with the heterogeneous character of individual sources of evidence. On the other hand, this feature makes the combination step more difficult. We present a new method for combining partial probabilistic statements and prove that it is an extension of existing methods for combining complete probability statements. We evaluate the performance of our system and its individual components on data from the human and fruit fly genomes.
The use of sequence evolutionary conservation as a source of evidence in gene finding requires efficient and sensitive tools for finding similar regions in very long sequences. We present a method for improving the sensitivity of existing tools for this task by careful modeling of sequence properties. In particular, we build a hidden Markov model representing a typical homology between two protein coding regions and then use this model to optimize a component of a heuristic algorithm called a spaced seed. The seeds that we discover significantly improve the accuracy and running time of similarity search in protein coding regions, and are directly applicable to our gene finder.
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