Expression of the paired box domain Pax7 protein in myogenic cells isolated from the porcine semitendinosus muscle after birth

The paired box domain gene Pax7 plays a pivotal role in satellite cell physiology and may represent one of the candidate genes influencing the dynamic stages of early post-natal growth observed in pig. Quiescent satellite cells express Pax7 and, when activated, they co-express the myogenic bHLH protein MyoD. The aims of this study were to investigate, by immunohistochemistry, the putative differential expression of Pax7 and to ascertain the amount of activated satellite cells (Pax7(+)/MyoD(+)) in myogenic cells isolated at different post-natal time points and in adults. Our results indicate that Pax7(+) cells represent between 10 and 15% of the whole myogenic cell population found at birth indicating that these cells provide a modest contribution to the development of new fibres. The number of activated satellite cells (Pax7(+)/MyoD(+)) was scarce after birth but it was higher respect to adults. An interesting result was that at 1 month after birth the number of Pax7(+) cells had increased within the pool of myogenic cells with respect to myogenic cells extracted at birth. We speculate that Pax7 might be one of the molecules involved in controlling the proliferation/differentiation ratio in the pool of satellite cells present in post-natal porcine skeletal muscles.     

Horizontal gene transfer among microbial genomes: new insights from complete genome analysis

The determination and analysis of complete genome sequences has led to the suggestion that horizontal gene transfer may be much more extensive than previously appreciated. Many of these studies, however, rely on evidence that could be generated by forces other than gene transfer including selection, variable evolutionary rates, and biased sampling.     

Insect iron binding proteins: insights from the genomes

Sequencing of the genomes of Drosophila melanogaster, Anopheles gambiae, Apis mellifera, and Bombyx mori provided an opportunity to examine the diversity and organization of genes encoding insect transferrins (Tsf) and ferritins. Information obtained from the genomes significantly advances our knowledge of these major players in insect iron metabolism and complements the results of molecular studies on their temporal, spatial, and inducible expression pattern and regulatory mechanisms conducted in diverse insect species. Analysis of genes encoding new members of the Tsf family and non-secreted ferritin subunits allows making preliminary hypotheses about their possible functions and opens possibilities to study lesser-known aspects of insect iron homeostasis. Proteomic and gene expression studies that followed the whole genome sequencing quickly contribute to defining or better understanding of the important and diverse biological roles of Tsf and ferritin, particularly their involvement in insect's defenses against oxidative stress and infection.     

Phylogeny of the Tachycineta genus of New World swallows: insights from complete mitochondrial genomes

The Tachycineta genus of swallows is comprised of nine species that range from Alaska to southern Chile. We sequenced the entire mitochondrial genome of each member of Tachycineta and generated a completely resolved phylogenetic hypothesis for the corresponding mitochondrial gene tree. Our analyses confirm the presence of two sub-clades within Tachycineta that are associated with geography: a North American/Caribbean clade and a South/Central American clade. We found considerable variation among regions of the mitochondrial genome in both substitution rates and the level of information that each region supplied for phylogenetic reconstruction. We found no evidence of positive directional selection within mitochondrial coding regions, but we identified numerous sites under purifying selection. This finding suggests that, despite differences in life history traits and distributions, mitochondrial genes in Tachycineta are predominantly under purifying selection for conserved function.     

Gene and domain duplication in the chordate Otx gene family: insights from amphioxus Otx

We report the genomic organization and deduced protein sequence of a cephalochordate member of the Otx homeobox gene family (AmphiOtx) and show its probable single-copy state in the genome. We also present molecular phylogenetic analysis indicating that there was single ancestral Otx gene in the first chordates which was duplicated in the vertebrate lineage after it had split from the lineage leading to the cephalochordates. Duplication of a C-terminal protein domain has occurred specifically in the vertebrate lineage, strengthening the case for a single Otx gene in an ancestral chordate whose gene structure has been retained in an extant cephalochordate. Comparative analysis of protein sequences and published gene expression patterns suggest that the ancestral chordate Otx gene had roles in patterning the anterior mesendoderm and central nervous system. These roles were elaborated following Otx gene duplication in vertebrates, accompanied by regulatory and structural divergence, particularly of Otx1 descendant genes.      

Ancient origin of elicitin gene clusters in Phytophthora genomes

The genus Phytophthora belongs to the oomycetes in the eukaryotic stramenopile lineage and is comprised of over 65 species that are all destructive plant pathogens on a wide range of dicotyledons. Phytophthora produces elicitins (ELIs), a group of extracellular elicitor proteins that cause a hypersensitive response in tobacco. Database mining revealed several new classes of elicitin-like (ELL) sequences with diverse elicitin domains in Phytophthora infestans, Phytophthora sojae, Phytophthora brassicae, and Phytophthora ramorum. ELIs and ELLs were shown to be unique to Phytophthora and Pythium species. They are ubiquitous among Phytophthora species and belong to one of the most highly conserved and complex protein families in the Phytophthora genus. Phylogeny construction with elicitin domains derived from 156 ELIs and ELLs showed that most of the diversified family members existed prior to divergence of Phytophthora species from a common ancestor. Analysis to discriminate diversifying and purifying selection showed that all 17 ELI and ELL clades are under purifying selection. Within highly similar ELI groups there was no evidence for positively selected amino acids suggesting that purifying selection contributes to the continued existence of this diverse protein family. Characteristic cysteine spacing patterns were found for each phylogenetic clade. Except for the canonical clade ELI-1, ELIs and ELLs possess C-terminal domains of variable length, many of which have a high threonine, serine, or proline content suggesting an association with the cell wall. In addition, some ELIs and ELLs have a predicted glycosylphosphatidylinositol site suggesting anchoring of the C-terminal domain to the cell membrane. The eli and ell genes belonging to different clades are clustered in the genomes. Overall, eli and ell genes are expressed at different levels and in different life cycle stages but those sharing the same phylogenetic clade appear to have similar expression patterns.     

Cross-talk between the paired domain and the homeodomain of Pax3: DNA binding by each domain causes a structural change in the other domain, supporting interdependence for DNA Binding

The Pax3 protein has two DNA binding domains, a Paired domain (PD) and a paired-type Homeo domain (HD). Although the PD and HD can bind to cognate DNA sequences when expressed individually, genetic and biochemical data indicate that the two domains are functionally interdependent in intact Pax3. The mechanistic basis of this functional interdependence is unknown and was studied by protease sensitivity. Pax3 was modified by the creation of Factor Xa cleavage sites at discrete locations in the PD, the HD, and in the linker segment joining the PD and the HD (Xa172, Xa189, and Xa216) in individual Pax3 mutants. The effect of Factor Xa insertions on protein stability and on DNA binding by the PD and the HD was measured using specific target site sequences. Independent insertions at position 100 in the linker separating the first from the second helix-turn-helix motif of the PD and at position 216 immediately upstream of the HD were found to be readily accessible to Factor Xa cleavage. The effect of DNA binding by the PD or the HD on accessibility of Factor Xa sites inserted in the same or in the other domain was monitored and quantitated for multiple mutants bearing different numbers of Xa sites at each position. In general, DNA binding reduced accessibility of all sites, suggesting a more compact and less solvent-exposed structure of DNA-bound versus DNA-free Pax3. Results of dose response and time course experiments were consistent and showed that DNA binding by the PD not only caused a local structural change in the PD but also caused a conformational change in the HD (P3OPT binding to Xa216 mutants); similarly, DNA binding by the HD also caused a conformational change in the PD (P2 binding to Xa100 mutants). These results provide a structural basis for the functional interdependence of the two DNA binding domains of Pax3.     

Mitogenomic phylogeny of Trochoidea (Gastropoda: Vetigastropoda): New insights from increased complete genomes

Increased mitochondrial (mt) genomes can provide more sets of genome‐level characteristics for resolving deeper phylogeny. Limited information with respect to the Trochoidea mitochondrial genome organization is available; besides, monophyly and internal relationships of the superfamily still remain a matter of discussion. To resolve the monophyly and internal phylogenetic controversies of Trochoidea and expand our understanding for mt genomic characteristic evolution among Trochoidea, the phylogenetic trees were reconstructed using 13 newly sequenced complete mt genomes and 35 genomes from GenBank, and both the maximum likelihood and Bayesian inference analyses were highly supported. Vetigastropoda phylogenetic analyses recovered the monophyly of Trochoidea. Trochoidea phylogenetic analyses and genetic distances supported the non‐monophyly of Tegulidae and Tegula, indicating that the taxonomic status of several genera (Rochia, Tectus and Cittarium) should be revised and Tegula, Omphalius and Chlorostoma should be placed as a same genus. The close affinity between Tectus virgatus and Rochia was also revealed. Three‐nucleotide insertion in nad1, nine‐nucleotide insertion and six‐nucleotide deletion in nad5 are detected in Tegulidae, Tectus and Rochia, respectively. Gene orders within Trochoidea are stable, with gene rearrangements exclusive to tRNA genes observed. Homoplasious convergences because of trnT rearrangement display translocation in Turbinidae and reversion in Trochidae and Calliostomatida. For trnE and trnG, we identify 11 arrangement types, suggesting that the gene rearrangement history needs to be further evaluated. Our study emphasizes the importance of mt genomes in resolving phylogenetic relationships within Trochoidea. In addition, the mt genomic characters would contribute new insights into the classification of Trochoidea.     

Phylogeny of early land plants: insights from genes and genomes

A large body of evidence from molecular systematic studies has confirmed the charophytic origin of land plants, and clarified monophyly of many lineages in charophytes and land plants. These studies have also identified liverworts as the earliest land plants, and the lycopods as the extant sister group to all other vascular plants. Two traditionally defined groups-bryophytes and pteridophytes-are now recognized as early grades of land plant evolution. However, several problems that complicate the use of sequence data in reconstructing plant phylogeny have become apparent; reconstruction of an accurate land plant phylogeny will require analysis of sequences of multiple genes and genomic structural characters of all three genomes.     

The making of eusociality: insights from two bumblebee genomes

The genomes of two bumblebee species characterized by a lower level of sociality than ants and honeybees provide new insights into the origin and evolution of insect societies.     

New insights into the origin of biological chirality

Life is characterized by a selectivity for asymmetric molecules. A great deal of theoretical and experimental work has yet to explain why living organisms utilize only L-amino acids in proteins and D-sugars in RNA and DNA. Also unknown is how a form of life based on asymmetric molecules evolved from an environment containing a racemic mixture of prebiotic molecules. By what mechanism did this selectivity for asymmetric molecules take place?