Genome scans and elusive candidate genes: detecting the variation that matters for speciation

Next‐generation sequencing is providing us with vast amounts of genetic data, yet we are currently struggling in our attempts to make sense of them. In particular, it has proven difficult to link phenotypic divergence and speciation to genome level divergence. In the current issue of Molecular Ecology, Ruegg et al. ( 2014 ) present new empirical results from two closely related bird taxa. They use a promising approach combining genome scan and candidate gene analysis. Their results suggest that we may have been looking in vain for candidate speciation genes by focusing only on genes found within genomic islands of divergence. This is because genes important in divergence and speciation may not be detected by genome scans and because features of the genomic architecture per se may have a large effect on the pattern of genome divergence.     

Neurotoxicity,drugs of abuse,and the CuZn-superoxide dismutase transgenic mice

Administration of methamphetamine (METH) to animals causes loss of DA terminals in the brain. The manner by which METH causes these changes in neurotoxicity is not known. We have tested the effects of this drug in copper/zinc (CuZn)-superoxide dismutase transgenic (SOD Tg) mice, which express the human CuZnSOD gene. In nontransgenic (non-Tg) mice, acute METH administration causes significant decreases in DA and dihydroxyphenylacetic acid (DOPAC) in the striata of non-Tg mice. In contrast, there were no significant decreases in striatal DA in the SOD Tg mice. The effects of METH on DOPAC were also attenuated in SOD Tg mice. Chronic METH administration caused decreases in striatal DA and DOPAC in the non-Tg mice, but not in the SOD-Tg mice. Similar studies were carried out with 1-methyl-1,2,3,6-tetrahydropyridine (MPTP), which also causes striatal DA and DOPAC depletion. As in the case of METH, MPTP causes marked depletion of DA and DOPAC in the non-Tg mice, but not in the SOD Tg mice. These results suggest that the mechanisms of toxicity of both METH and MPTP involve superoxide radical formation.     

Histochimie des colorations dans le bloc à base de métaux,application aux coupes semi-fines

Résumé Les auteurs décrivent une nouvelle méthode de coloration dans le bloc de tissu avec différents sels métalliques (alun de fer, tétroxyde d'osmium, acétate d'uranyl et chromeosmium) et l'hématoxyline. Cette technique est utilisée sur des tissus qui sont ensuite inclus en Araldit et permet d'obtenir des coupes semi-fines déjà colorées. Les auteurs ont cherché à préciser la spécificité de fixation du fer dans le tissu au moyen de méthodes d'extraction et de blocage. D'après leurs observations, le fer se fixerait aux groupes tissulaires chargés négativement. La nature des liaisons semble être de type électrostatique et complexe. Les liaisons complexes semblent prédominer au niveau des structures contenant des acides nucléiques.

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Histochemistry of block staining with metals for semifine sections

Summary The authors describe a new method of block staining for semifine sections with various metal salts (ferriammonium-sulphate, osmium tetroxyde, uranyl acetate, chromeosmium) and hematoxylin. They investigated the specificity of iron-alaun-hematoxylin with several extractions and blocking methods. According to their observations the dissociated iron is bounded to the negatively charged tissular groups. The nature of binding is thought to be electrostatic and coordinativ (complex). The last one is probably predominant in nucleic acids containing structures. This method seems to be encouraging for electron-histochemical investigations.

     

Fallacies and false premises—a critical assessment of the arguments for the recognition of paraphyletic taxa in botany

One of the central controversies in contemporary taxonomy and systematics revolves around whether to accept or to reject paraphyletic taxa. The present review is the result of a survey of the ongoing discussion in botany over the past ca. 15 years, and attempts to systematically and critically assess all individual arguments presented for the formal recognition of paraphyletic groups in the classification of life. Where arguments are found to be without merit, rebuttals are presented in the hope of excluding them from further discussion, which can then concentrate on those that have merit. Where arguments are found to be sound, their implications and possible solutions are discussed. The controversy around paraphyletic taxa can be broken down into three questions: whether their rejection or acceptance would lead to a classification better reflecting patterns of biological diversity and evolutionary history; whether their rejection or acceptance would lead to a more practical, useful and predictive classification; and whether their rejection is compatible with ranked and binary Linnaean taxonomy. All available arguments for paraphyletic taxa relating to the first question are demonstrated to be based on various logical fallacies or false premises, especially misunderstandings of the principles of phylogenetic systematics. The issue of usefulness is harder to resolve, as different classifications serve different needs. It is presumably unavoidable but also preferable that phylogenetic and non‐phylogenetic ways of classifying species continue to coexist, serving different needs. Finally, an insistence on monophyletic taxa is found to be incompatible with binary taxonomy under a set of very specific circumstances and assumptions whose presence and accuracy are not universally accepted. © The Willi Hennig Society 2011.     

An Ex vivo Culture System to Study Thyroid Development

The thyroid is a bilobated endocrine gland localized at the base of the neck, producing the thyroid hormones T3, T4, and calcitonin. T3 and T4 are produced by differentiated thyrocytes, organized in closed spheres called follicles, while calcitonin is synthesized by C-cells, interspersed in between the follicles and a dense network of blood capillaries. Although adult thyroid architecture and functions have been extensively described and studied, the formation of the “angio-follicular” units, the distribution of C-cells in the parenchyma and the paracrine communications between epithelial and endothelial cells is far from being understood.This method describes the sequential steps of mouse embryonic thyroid anlagen dissection and its culture on semiporous filters or on microscopy plastic slides. Within a period of four days, this culture system faithfully recapitulates in vivo thyroid development. Indeed, (i) bilobation of the organ occurs (for e12.5 explants), (ii) thyrocytes precursors organize into follicles and polarize, (iii) thyrocytes and C-cells differentiate, and (iv) endothelial cells present in the microdissected tissue proliferate, migrate into the thyroid lobes, and closely associate with the epithelial cells, as they do in vivo.Thyroid tissues can be obtained from wild type, knockout or fluorescent transgenic embryos. Moreover, explants culture can be manipulated by addition of inhibitors, blocking antibodies, growth factors, or even cells or conditioned medium. Ex vivo development can be analyzed in real-time, or at any time of the culture by immunostaining and RT-qPCR.In conclusion, thyroid explant culture combined with downstream whole-mount or on sections imaging and gene expression profiling provides a powerful system for manipulating and studying morphogenetic and differentiation events of thyroid organogenesis.