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The Ecoresponsive Genome of Daphnia pulex
The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions, and the coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random.
Evolution of protein domain promiscuity in eukaryotes.
It is proposed that promiscuous domains persist within a relatively small pool of evolutionarily stable domain combinations from which numerous rare architectures emerge during evolution, contributing to the diversity and evolvability of eukaryotic proteomes and signaling networks.
Origin and evolution of spliceosomal introns
There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns, and introns were a major factor of evolution throughout the history of eukaryotes.
Three distinct modes of intron dynamics in the evolution of eukaryotes.
A comprehensive probabilistic model to obtain a definitive reconstruction of intron evolution was developed and applied to 391 sets of conserved genes from 19 eukaryotic species, inferring that a relatively high intron density was reached early.
Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like Phosphatase Family*
- E. Kuznetsova, M. Proudfoot, A. Yakunin
- Biology, ChemistryJournal of Biological Chemistry
- 24 November 2006
Using a representative set of 80 phosphorylated substrates, the substrate specificities of 23 soluble HADs encoded in the Escherichia coli genome are characterized and the physiological relevance of the phosphatase activity with the preferred substrate was validated in vivo for one of the HADS, YniC.
Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan
Insight is provided into the epigenetic landscape of the authors' closest evolutionary relatives and a window is opened to explore the epigenomes of extinct species by harnessing the natural degradation processes of methylated and unmethylated cytosines.
Robust linear dimensionality reduction
We present a novel family of data-driven linear transformations, aimed at finding low-dimensional embeddings of multivariate data, in a way that optimally preserves the structure of the data. The…
The Function of Introns
It is shown that introns in contemporary species fulfill a broad spectrum of functions, and are involved in virtually every step of mRNA processing, and it is proposed that this great diversity of intronic functions supports the notion that intrins were indeed selfish elements in early eukaryotes, but then independently gained numerous functions in different eUKaryotic lineages.
XX ovarian dysgenesis is caused by a PSMC3IP/HOP2 mutation that abolishes coactivation of estrogen-driven transcription.
Archaic Adaptive Introgression in TBX15/WARS2
It is reported that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population.