BASIC PROCESSES UNDERLYING AGROBACTERIUM-MEDIATED DNA TRANSFER TO PLANT CELLS

Figure 1: The phase diagram depicted is obtained by systematically changing two conditions (e.g., concentration, salt, pH) and determining the regions in which the system switches from a one-phase sta...

Figure 2: Theoretical possibilities of how disease phenotypes can arise from aberrant phase separation and condensate formation. Diseases can arise because of alterations to the mechanism of assembly,...

Figure 3: Evidence for disturbed phase separation and condensate formation in neurodegeneration, cancer, and infectious diseases. In neurodegenerative diseases, mutations or repeat expansions, abnorma...

Figure 1: Actions of pioneer transcription factors. (a) The pioneer transcription factor (gold sphere) scans laterally across chromatin and targets a nucleosome. (b) The pioneer transcription factor e...

Figure 2: Transcription factor DNA-binding domains (spheres) bind to nucleosomes in diverse methods, such as (a) edge binding, (b) near dyad axis, (c) around the nucleosome, (d) dyad axis, and (e) bin...

Figure 3: DNA-binding domain structures that enable or limit binding to nucleosomes. (a) Two different DNA-binding domain structures are shown interacting with DNA orthogonal to the long axis of the d...

Figure 4: Pioneer transcription factors perturb nucleosome structure in different ways. (a) Pioneer factor binding can facilitate the freeing of its target site from the nucleosome. (b) Binding can ca...

Figure 1: The time dynamics of the usage of the terms “ortholog” and “paralog”. The PubMed database was searched using the Entrez search engine with the following queries: “ortholog or orthologs or or...

Figure 2: A hypothetical phylogenetic tree illustrating orthologous and paralogous relationships between three ancestral genes and their descendants in three species. LCA, last common ancestor (of the...

Figure 3: A hypothetical phylogenetic tree illustrating emergence of pseudoorthologs via lineage-specific gene loss.

Figure 4: Effect of horizontal gene transfer on orthology and paralogy. (a) A hypothetical evolutionary scenario with HGT leading to xenology. (b) A hypothetical evolutionary scenario with HGT leading...

Figure 5: Orthology and genome-specific best hits. (A) An evolutionary scheme illustrating the connection between orthology and symmetrical best hits (SymBets). X and Y represent two paralogous genes....

Figure 6: Coverage of selected genomes with clusters of orthologous groups of proteins (C/KOGs). (a) Prokaryotic genomes. (b) Eukaryotic genomes. The data are from (88). Filled volume, genes in C/KOGs...

Figure 7: Distribution of the number of paralogs in COGs for selected prokaryotic genomes. The data were extracted from the current COG version (88). The plot is shown in the double-logarithmic scale.

Figure 8: Xenologous displacement in situ of the ruvB gene in the mycoplasmas. (A) Organization of the Holliday junction resolvasome operon and surrounding genes in bacteria. COG0632, Holliday junctio...

Figure 9: Horizontal gene transfer leading to pseudoparalogy. The two pseudoparalogous peroxiredoxins from Aquifex aeolicus are shown in red, the three pseudoparalogs from the Thermoplasmas in blue, a...

Figure 10: Rearrangements of gene structure and orthology. (a) Domain architectures of bacterial and archaeal DnaG-like primases. (b) Independent fission of the DNA polymerase I gene in multiple bacte...

Figure 1: Summary of replication mechanisms and transposition intermediates, including proposed transposition intermediates and key replication steps for five TE subclasses. YR retrotransposons and Ma...

Figure 2: Structure and taxonomy of eukaryotic transposable elements. The left panel lists unrooted cladograms showing putative relationships between the major TE superfamilies, based on phylogenies o...

Figure 3: Distribution of TEs across the eukaryote phylogeny. Reference genome size (sea green circles) varies dramatically across eukaryotes and is loosely correlated with TE content. Here, the honey...