Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA

The nucleotide excision repair (NER) pathway corrects DNA damage caused by sunlight, environmental mutagens and certain antitumor agents. This multistep DNA repair reaction operates by the sequential assembly of protein factors at sites of DNA damage. The efficient recognition of DNA damage and its repair are orchestrated by specific protein-protein and protein-DNA interactions within NER complexes. We have investigated an essential protein-protein interaction of the NER pathway, the binding of the XPA protein to the ERCC1 subunit of the repair endonuclease ERCC1-XPF. The structure of ERCC1 in complex with an XPA peptide shows that only a small region of XPA interacts with ERCC1 to form a stable complex exhibiting submicromolar binding affinity. However, this XPA peptide is a potent inhibitor of NER activity in a cell-free assay, blocking the excision of a cisplatin adduct from DNA. The structure of the peptide inhibitor bound to its target site reveals a binding interface that is amenable to the development of small molecule peptidomimetics that could be used to modulate NER repair activities in vivo.     

<Emphasis Type="Italic">Slc11a1</Emphasis> (<Emphasis Type="Italic">Nramp1</Emphasis>) alleles interact with acute inflammation loci to modulate wound-healing traits in mice

Lines of mice were obtained by selective breeding for maximum (AIRmax) or minimum (AIRmin) acute inflammation. They present distinct neutrophil influx and show frequency disequilibrium of the solute carrier family 11a member 1 (Slc11a1) alleles. This gene is involved in ion transport at the endosomes within macrophages and neutrophils, interfering in their activation. Homozygous AIRmax and AIRmin sublines for the Slc11a1 gene were produced to examine the interaction of this gene with the acute inflammatory loci. The present work investigated wound-healing traits in AIRmax and AIRmin mice, in F₁ and F₂ intercrosses, and in Slc11a1 sublines. Two-millimeter ear punches were made in the mice and hole closure was measured during 40 days. AIRmax mice demonstrated significant tissue repair while AIRmin mice did not. Significant differences between the responses of male and female mice were also observed. Wound-healing traits demonstrated a correlation with neutrophil influx in F₂ populations. AIRmax ^SS showed higher ear-wound closure than AIRmax ^RR mice, suggesting that the Slc11a1 S allele favored ear tissue repair. QTL analysis has detected two inflammatory loci modulating ear wound healing on chromosomes 1 and 14. These results suggest the involvement of the acute inflammation modifier QTL in the wound-healing phenotype.     

Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution

To demonstrate that a given change in the environment has contributed to the emergence of a given genotypic and phenotypic shift during the course of evolution, one should ask to what extent such shifts would have occurred without environmental change. Of course, such tests are rarely practical but phenotypic novelties can still be correlated to genomic shifts in response to environmental changes if enough information is available. We surveyed and re-evaluated the published data in order to estimate the role of environmental changes on the course of species and genomic evolution. Only a few published examples clearly demonstrate a causal link between a given environmental change and the fixation of a genomic variant resulting in functional modification (gain, loss or alteration of function). Many others suggested a link between a given phenotypic shift and a given environmental change but failed to identify the underlying genomic determinant(s) and/or the associated functional consequence(s). The proportion of genotypic and phenotypic variation that is fixed concomitantly with environmental changes is often considered adaptive and hence, the result of positive selection, even though alternative causes, such as genetic drift, are rarely investigated. Therefore, the second aim herein is to review evidence for the mechanisms leading to fixation.     

New insights to discriminate between Sympterygia acuta Garman 1877 and Sympterygia bonapartii Müller & Henle, 1841 (Rajidae) of the Southwest Atlantic Ocean: on the use of geometric morphometrics and spinulation patterns

Geometric‐morphometric and spinulation pattern approaches were employed to assess the discrimination of two species of Sympterygia skates in the Southwest Atlantic: Sympterygia acuta Garman 1877 and Sympterygia bonapartii Müller & Henle, 1841. Two types of variables were employed: linear morphometrics measurements (LMMs), and interlandmark distances (IlDs). The Principal Component Analysis (PCA) and the discriminant analysis (DA) do not overlap between the species. Morphometrically, S. bonapartii is characterized by a wider disc, larger pelvic fins, larger eyes, a greater distance between nostrils and between the first pair of gill slits, a greater interorbital distance between spiracles, and a wider mouth. On the other hand, S. acuta has a larger disc due to the snout size. Regarding the allometric coefficient analysis performed on the IlDs, S. bonapartii showed a positive allometry for the variables that comprise the Box‐Truss 3 (Ventral protocol), which can be related to the mouth width and the first gill slits. This growth type is consistent with those observed in the Box‐Truss 3 (Outline protocol), which is related to the disc width. It has been interpreted that both structures could develop together. In opposition, S. acuta showed isometric growth for the above‐mentioned variables; on the other hand, S. acuta showed positive allometry for all variables that defined the snout in the three protocols, indicating that the snout has a distinctive growth relative to the size through ontogeny. S. bonapartii, however, showed an isometric snout growth. The remaining variables that defined the morphogeometrical protocols displayed the same type of growth. Regarding spinulation, the thorns and dermal denticles proved to be useful to discriminate both species. Thorns of the caudal region were large and oval with smooth edges in S. bonapartii, and oval with lobed edges in S. acuta. Dermal denticles in S. acuta also presented two elongated ridges with a third small ridge between them, whereas those of S. bonapartii presented three elongated ridges of the same size.     

Fruits of Heterocoma (Vernonieae‐Lychnophorinae): taxonomic significance and a new pattern of phytomelanin deposition in Asteraceae

Heterocoma is a Brazilian endemic genus resulting from the dismemberment of Sipolisiinae, in which only representatives with fruit containing phytomelanin were included in the genus. As the fruits of Asteraceae are known to be systematically important at various taxonomic levels and Heterocoma fruit has not been described previously, we studied the morphology and anatomy of the cypselas of all species of the genus, comparing them with other fruits in the family containing phytomelanin and evaluating the systematic potential at the specific and tribal levels. The fruits were analysed by scanning electron microscopy (SEM) and light microscopy. The morphological features of the fruit, including the carpopodium, ribs and pappi, varied in the genus and demonstrated potential for species discrimination. The anatomy showed a pattern for the genus with a uniseriate exocarp, the outer mesocarp composed of fibres arranged in several layers, the inner mesocarp composed of several layers of parenchyma, the endocarp, and phytomelanin deposited between the inner and outer mesocarp. This anatomical pattern of phytomelanin deposition differs from that of other Asteraceae with phytomelanin in their fruit. Heterocoma is also the only genus in Vernonieae that has phytomelanin deposition in the cypselas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 255–265.