Distribution of the mammalian-wide interspersed repeats (MIRs) in the isochores of the human genome

AbstractThe distribution of MIRs (mammalian-wide interspersed repeats) was investigated in 164 human sequences (≥100 kb), which were assigned, according to their GC level, to isochore families L, H1, H2 and H3. MIR elements, whose total number in the genome was estimated to be about 3.3×105, were found to be unevenly distributed in human isochores. The majority of MIRs (55%) were found in the L isochore family. In contrast, MIR density was highest in H2, closely followed by H1, whereas densities in L and H3 were 2- and 3-fold lower than in H2, respectively. For this reason, the assessment of MIR distribution by inter-repeat PCR led to an overestimation of MIR numbers in H2 isochore and an underestimation in L isochores

The brain-computer analogy "A special issue"

In this review essay, we give a detailed synopsis of the twelve contributions which are collected in a Special Issue in Frontiers Ecology and Evolution, based on the research topic "Current Thoughts on the Brain-Computer Analogy All Metaphors Are Wrong, But Some Are Useful." The synopsis is complemented by a graphical summary, a matrix which links articles to selected concepts. As first identified by Turing, all authors in this Special Issue recognize semantics as a crucial concern in the brain-computer analogy debate, and consequently address a number of such issues. What is missing, we believe, is the distinction between metaphor and analogy, which we reevaluate, describe in some detail, and offer a definition for the latter. To enrich the debate, we also deem necessary to develop on the evolutionary theories of the brain, of which we provide an overview. This article closes with thoughts on creativity in Science, for we concur with the stance that metaphors and analogies, and their esthetic impact, are essential to the creative process, be it in Sciences as well as in Arts

A novel neuron-specific regulator of the V-ATPase in Drosophila

The V-ATPase is a highly conserved enzymatic complex that ensures appropriate levels of organelle acidification in virtually all eukaryotic cells. While the general mechanisms of this proton pump have been well studied, little is known about the specific regulations of neuronal V-ATPase. Here, we studied CG31030, a previously uncharacterized Drosophila protein predicted from its sequence homology to be part of the V-ATPase family. In contrast to its ortholog ATP6AP1/VhaAC45 which is ubiquitous, we observed that CG31030 expression is apparently restricted to all neurons, and using CRISPR/Cas9-mediated gene tagging, that it is mainly addressed to synaptic terminals. In addition, we observed that CG31030 is essential for fly survival and that this protein co-immunoprecipitates with identified V-ATPase subunits, and in particular ATP6AP2. Using a genetically-encoded pH probe (VMAT-pHluorin) and electrophysiological recordings at the larval neuromuscular junction, we show that CG31030 knock-down induces a major defect in synaptic vesicle acidification and a decrease in quantal size, which is the amplitude of the postsynaptic response to the release of a single synaptic vesicle. These defects were associated with severe locomotor impairments. Overall, our data indicate that CG31030, which we renamed VhaAC45-related protein (VhaAC45RP), is a specific regulator of neuronal V-ATPase in Drosophila that is required for proper synaptic vesicle acidification and neurotransmitter release

Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes

mRNA polyadenylation is an essential step for the maturation of almost all eukaryotic mRNAs, and is tightly coupled with termination of transcription in defining the 3′-end of genes. Large numbers of human and mouse genes harbor alternative polyadenylation sites [poly(A) sites] that lead to mRNA variants containing different 3′-untranslated regions (UTRs) and/or encoding distinct protein sequences. Here, we examined the conservation and divergence of different types of alternative poly(A) sites across human, mouse, rat and chicken. We found that the 3′-most poly(A) sites tend to be more conserved than upstream ones, whereas poly(A) sites located upstream of the 3′-most exon, also termed intronic poly(A) sites, tend to be much less conserved. Genes with longer evolutionary history are more likely to have alternative polyadenylation, suggesting gain of poly(A) sites through evolution. We also found that nonconserved poly(A) sites are associated with transposable elements (TEs) to a much greater extent than conserved ones, albeit less frequently utilized. Different classes of TEs have different characteristics in their association with poly(A) sites via exaptation of TE sequences into polyadenylation elements. Our results establish a conservation pattern for alternative poly(A) sites in several vertebrate species, and indicate that the 3′-end of genes can be dynamically modified by TEs through evolution

Additional file 2: Figure S1. of Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes

Full phylogeny of Rh50 proteins. Figure S2. Phylogeny of Proteobacteria bacterium. Figure S3. Full phylogeny of Amt proteins. Figure S4. Tree-topology test. (PDF 1490 kb

The isochore organization and the compositional distribution of homologous coding sequences in the nuclear genome of plants

18 p.-7 fig.-1 tab.The isochore structure of the nuclear genome of angiosperms described by Salinas et al. (1) was confirmed by using a different experimental approach, namely by showing that the levels of coding sequences from both dicots and Gramineae are linearly correlated with GC levels of the corresponding flanking sequences. The compositional distribution of homologous coding sequences from several orders of dicots and from Gramineae were also studied and shown to mimick the compositional distributions previously seen (l)for coding sequences in general, most coding sequences from Gramineae being much higher than those of the dicots explored. Thfese differences were even stronger for third codon positions and led to striking codon usages for many coding sequences especially in the case of Gramineae.Peer reviewe

Editorial: Current Thoughts on the Brain-Computer Analogy -All Metaphors Are Wrong, but Some Are Useful

This project kicked off in the fall of 2020. There are two parts of the title of this Research Topic Special Issue. The first one evokes the issue raised by Turing ("Can machines think?", Turing, 1950), a question that we, the Editors, revisit reflecting our complementary multi-disciplinary backgrounds (Evolutionary Biology, GM; Evo-Devo, PM; and Computer Science, BM) and take it up again with a fresh start; this question made us realize how ripe the Brain-Computer analogy has become for a reassessment. The complexity of the subject needed the involvement of experts from the different fields that have been concerned with many related problems, namely Natural Sciences (here Biology and Physics), Mathematics, Psychology and Philosophy. Indeed, the Topic is certainly timely for, while this Issue was going to press, a number of publications have appeared that tackle these very issues both in Sciences (Reynolds, 2022; Yang and Lu, 2022) and Humanities (Kelty-Stephen et al., 2022)