Evolution under reversals: parsimony and conservation of common intervals

In comparative genomics, gene order data is often modeled as signed permutations. A classical problem for genome comparison is to detect common intervals in permutations, that is, genes that are colocalized in several species, indicating that they remained grouped during evolution. A second largely studied problem related to gene order is to compute a minimum scenario of reversals that transforms a signed permutation into another. Several studies began to mix the two problems and it was observed that their results are not always compatible: Often, parsimonious scenarios of reversals break common intervals. If a scenario does not break any common interval, it is called perfect. In two recent studies, Berard et al. defined a class of permutations for which building a perfect scenario of reversals sorting a permutation was achieved in polynomial time and stated as an open question whether it is possible to decide, given a permutation, if there exists a minimum scenario of reversals that is perfect. In this paper, we give a solution to this problem and prove that this widens the class of permutations addressed by the aforementioned studies. We implemented and tested this algorithm on gene order data of chromosomes from several mammal species and we compared it to other methods. The algorithm helps to choose among several possible scenarios of reversals and indicates that the minimum scenario of reversals is not always the most plausible     

Isozyme differentiation of aldolase and pyruvate kinase in fetal,regenerating, preneoplastic,and malignant rat hepatocytes during culture

Summary Aldolase and pyruvate kinase isozymes were investigated in cultured hepatocytes from fetal, regenerating, and 2-acetyl-aminofluorene-fed rat liver as well as in some epithelial liver cell lines. Our results show that: (a) cell proliferation and prolonged expression of specific isozymes were found only in cultured hepatocytes from 17-day old fetuses; (b) the fetal type of pyruvate kinase expressed in regenerating and carcinogen-treated liver was temporarily lost only in cultured hepatocytes from regenerating liver; (c) the adult type of aldolase and pyruvate kinase was absent in one epithelial cell line derived from a carcinogen-treated liver and in the hepatoma tissue cell (HTC) line but was found in the Faza clone of the Reuber H₃₅ cell line during the 50 first passages in vitro; and (d) the isozyme pattern of pyruvate kinase was always more strongly shifted than that of aldolase. The observations suggest that: (a) hepatocytes from carcinogen-treated liver exhibit the same lack of ability to proliferate in primary culture as normal adult hepatocytes; (b) adult hepatocytes can produce fetal isozymes without prior cell division; (c) pyruvate kinase is a stronger marker of dedifferentiation (retrodifferentiation) than aldolase; and (d) regulatory processes of isozyme expression are different during ontogenesis, regeneration, and hepatocarcinogenesis. This work was supported by the “Institut National de la Santé et de la Recherche Médicale” and the “Fondation pour la Recherche Medicale Fran?aise”     

Excess of multifocal tumors in nephroblastoma: implications for mechanisms of tumor development and genetic counseling

Referring to the mutational theory of carcinogenesis in embryonal tumors, it is commonly accepted that patients with multifocal tumors are hereditary cases. This is based on the implicit assumption that each tumor results from a single mutational event occurring in a cell that has already inherited a mutation, and that these tumors are independent. We studied the distribution of tumors in 1,868 cases where the focality was known (SIOP 1, 2, 5 and 6). Using all the supposed gene carriers (bilateral and unilateral multifocal cases), and assuming a Poisson distribution of tumors, we estimated the mean number m of tumors in each kidney to be 0.37. Comparing the observed distribution of cases to the expected one, we found a very bad fit to this hypothesis (P<10^-9). This is due to an excess of multifocal tumors, particularly in unilateral cases. These findings have important implications in genetic counseling, since the usual practice of considering multifocal tumor patients as hereditary cases may result in a large overestimate of the recurrence risk in such cases. The implications for the mechanisms of tumor development are also discussed.     

How important are Rho GTPases in neurosecretion?

Rho GTPases are small GTP binding proteins belonging to the Ras superfamily which act as molecular switches that regulate many cellular function including cell morphology, cell to cell interaction, cell migration and adhesion. In neuronal cells, Rho GTPases have been proposed to regulate neuronal development and synaptic plasticity. However, the role of Rho GTPases in neurosecretion is poorly documented. In this review, we discuss data that highlight the importance of Rho GTPases and their regulators into the control of neurotransmitter and hormone release in neurons and neuroendocrine cells, respectively.     

L-carnosine as an enhancer to computerized cognitive behaviour therapy in Japanese workers,an unjustified claim

This letter comments on the conclusion drawn by Shirotsuki et al. (2017) in their article entitled “The effect for Japanese workers of a self-help computerized cognitive behaviour therapy program with a supplement soft drink”, recently published in BioPsychoSocial Medicine. The authors concluded that their drink, containing L-carnosine, enhances the effects of a computerized cognitive-behavioural therapy (CCBT) on the psychological well-being of healthy Japanese workers. Yet, we argue that their conclusion is unfounded given their results and the methodological shortcomings of their study. Briefly, while the authors reported improvement on the tension-anxiety subscale of the Profile of Mood States (POMS) in the CCBT only group, they also observed a lack of improvement on this subscale in the CCBT+L-carnosine group suggesting that the drink washes out this beneficial effect of CCBT. Methodological issues include the uncontrolled levels of L-carnosine metabolized by participants jeopardize the study’s internal validity. Also, the clinical meaningfulness of the findings seems dubious as post-treatment scores remained within the range of the general Japanese population. Consequently, we argue that Shirotsuki et al.’s study should be re-conducted before drawing any valid conclusion.     

Quelques Gymnoascaceae Observées Au Microscope Électronique À Balayage

Several selectedGymnoascaceae of the genusAuxarthon, Toxotrichum, Gymnoascus, Arachniotus, Pseudoarachniotus, Myxotrichum etPetalosporus are examined using a scanning electron microscope for surface structure, which display much or no ornamentation.     

Soil organic matter molecular composition and state of decomposition in three locations of the European Arctic

Increased mineralization of the organic matter (OM) stored in permafrost is expected to constitute the largest additional global warming potential from terrestrial ecosystems exposed to a warmer climate. Chemical composition of permafrost OM is thought to be a key factor controlling the sensitivity of decomposition to warming. Our objective was to characterise OM from permafrost soils of the European Arctic: two mineral soils—Adventdalen, Svalbard, Norway and Vorkuta, northwest Russia—and a “palsa” (ice-cored peat mound patterning in heterogeneous permafrost landscapes) soil in Neiden, northern Norway, in terms of molecular composition and state of decomposition. At all sites, the OM stored in the permafrost was at an advanced stage of decomposition, although somewhat less so in the palsa peat. By comparing permafrost and active layers, we found no consistent effect of depth or permafrost on soil organic matter (SOM) chemistry across sites. The permafrost-affected palsa peat displayed better preservation of plant material in the deeper layer, as indicated by increasing contribution of lignin carbon to total carbon with depth, associated to decreasing acid (Ac) to aldehyde (Al) ratio of the syringyl (S) and vanillyl (V) units, and increasing S/V and contribution of plant-derived sugars. By contrast, in Adventdalen, the Ac/Al ratio of lignin and the Alkyl C to O-alkyl C ratio in the NMR spectra increased with depth, which suggests less oxidized SOM in the active layer compared to the permafrost layer. In Vorkuta, SOM characteristics in the permafrost profile did not change substantially with depth, probably due to mixing of soil layers by cryoturbation. The composition and state of decomposition of SOM appeared to be site-specific, in particular bound to the prevailing organic or mineral nature of soil when attempting to predict the SOM proneness to degradation. The occurrence of processes such as palsa formation in organic soils and cryoturbation should be considered when up-scaling and predicting the responses of OM to climate change in arctic soils.