Probabilistic causation and the explanatory role of natural selection

The explanatory role of natural selection is one of the long-term debates in evolutionary biology. Nevertheless, the consensus has been slippery because conceptual confusions and the absence of a unified, formal causal model that integrates different explanatory scopes of natural selection. In this study we attempt to examine two questions: (i) What can the theory of natural selection explain? and (ii) Is there a causal or explanatory model that integrates all natural selection explananda? For the first question, we argue that five explananda have been assigned to the theory of natural selection and that four of them may be actually considered explananda of natural selection. For the second question, we claim that a probabilistic conception of causality and the statistical relevance concept of explanation are both good models for understanding the explanatory role of natural selection. We review the biological and philosophical disputes about the explanatory role of natural selection and formalize some explananda in probabilistic terms using classical results from population genetics. Most of these explananda have been discussed in philosophical terms but some of them have been mixed up and confused. We analyze and set the limits of these problems.     

A comparative study of the short term cold resistance response in distantly related Drosophila species: the role of regucalcin and frost

The molecular basis of short term cold resistance (indexed as chill-coma recovery time) has been mostly addressed in D. melanogaster, where candidate genes (Dca (also known as smp-30) and Frost (Fst)) have been identified. Nevertheless, in Drosophila, the ability to tolerate short term exposure to low temperatures evolved several times independently. Therefore, it is unclear whether variation in the same candidate genes is also responsible for short term cold resistance in distantly related Drosophila species. It should be noted that Dca is a candidate gene for cold resistance in the Sophophora subgenus only, since there is no orthologous gene copy in the Drosophila subgenus. Here we show that, in D. americana (Drosophila subgenus), there is a north-south gradient for a variant at the 5' non-coding region of regucalcin (a Dca-like gene; in D. melanogaster the proteins encoded by the two genes share 71.9% amino acid identities) but in our D. americana F2 association experiment there is no association between this polymorphism and chill-coma recovery times. Moreover, we found no convincing evidence that this gene is up-regulated after cold shock in both D. americana and D. melanogaster. Size variation in the Fst PEST domain (putatively involved in rapid protein degradation) is observed when comparing distantly related Drosophila species, and is associated with short term cold resistance differences in D. americana. Nevertheless, this effect is likely through body size variation. Moreover, we show that, even at two hours after cold shock, when up-regulation of this gene is maximal in D. melanogaster (about 48 fold expression change), in D. americana this gene is only moderately up-regulated (about 3 fold expression change). Our work thus shows that there are important differences regarding the molecular basis of cold resistance in distantly related Drosophila species.     

Preliminary observations on fecundity of the processid shrimp Nikoides schmitti (Decapoda,Caridea) from Mexican Caribbean

Nikoides schmitti is widely distributed along the Atlantic coast of the Americas, from North Carolina to Bahia, Brazil and Cuba and Guadeloupe; however, the knowledge about their reproductive biology is poorly known. In this study, data such as sex ratio, fecundity, size and volume of the embryos, and brood loss of material collected in July 1997 from Mahahual, Quintana Roo, Mexico is provided. The sample of 728 specimens had a sex ratio of 0.40 males per female. Fecundity (N = 31) of ovigerous females (Stage I) varied from 219 to 817, with an average of 432 ± 177 embryos. The newly extruded embryos of N. schmitti were small (0.41 ± 0.030 mm) and similar in size to those reported for other species of the genus. The mean volume of the embryos changed significantly during development, increasing 60.9% from stages I to III. Embryo loss during incubation was estimated in 32.9%. This study provides baseline information about the reproduction of N. schmitti and contributes to a better knowledge of this species little studied.     

Inhibition of Streptococcus mutans biofilm accumulation and development of dental caries in vivo by 7-epiclusianone and fluoride

7-Epiclusianone (7-epi), a novel naturally occurring compound isolated from Rheedia brasiliensis, effectively inhibits the synthesis of exopolymers and biofilm formation by Streptococcus mutans. In the present study, the ability of 7-epi, alone or in combination with fluoride (F), to disrupt biofilm development and pathogenicity of S. mutans in vivo was examined using a rodent model of dental caries. Treatment (twice-daily, 60s exposure) with 7-epi, alone or in combination with 125 ppm F, resulted in biofilms with less biomass and fewer insoluble glucans than did those treated with vehicle-control, and they also displayed significant cariostatic effects in vivo (p < 0.05). The combination 7-epi + 125 ppm F was as effective as 250 ppm F (positive-control) in reducing the development of both smooth- and sulcal-caries. No histopathological alterations were observed in the animals after the experimental period. The data show that 7-epiclusianone is a novel and effective antibiofilm/anticaries agent, which may enhance the cariostatic properties of fluoride.     

p38γ activation triggers dynamical changes in allosteric docking sites

Mitogen-activated protein kinases (MAPKs) are serine-threonine kinases that participate in signal transduction pathways. p38 MAPKs have four isoforms (p38α, p38β, p38γ, and p38δ) which are involved in multiple cellular functions such as proliferation, differentiation, survival, and migration. MAPK kinases phosphorylate p38s in the dual-phosphorylation motif, Thr-Gly-Tyr, located in their activation loop, which induces a conformational change that increases ATP binding affinity and catalytic activity. Several works have proposed that MAPK dynamics is a key factor in determining their function. However, we still do not understand the dynamical changes that lead to MAPK activation. In this work we have used molecular dynamics techniques to study the dynamical changes associated with p38γ activation, the only fully active MAPK crystallized so far. We performed MD simulations of p38γ in three different states, fully active with ATP, active without ATP, and inactive. We found that the dynamical fluctuations of the docking sites, important for protein-protein interactions, are regulated allosterically by changes in the active site. Interestingly, in the phosphorylated and ATP-bound states the whole protein dynamics lead to concerted motions of whole protein domains in contrast to the inactive state. The binding/unbinding of ATP participates in the reorientation of the two domains and in the regulation of protein plasticity. Our study shows that beyond the conformational changes associated with MAPK activation their correlated dynamics are highly regulated by phosphorylation and ATP binding. This means that MAPK plasticity may have a role in their catalytic activity, specificity, and protein-protein interactions and, therefore, in the outcome of the signaling network.     

Polianthes zapopanensis (Agavaceae), una especie nueva de Jalisco, México

Se describe e ilustra como especie nueva a Polianthes zapopanensis , conocida de la parte centro-sur del estado de Jalisco, México. Por su inflorescencia en forma de racimo, esta especie se ubica en Polianthes subgénero Bravoa. Las hojas de las plantas en floración no se agrupan para formar una roseta. A diferencia de las especies hasta ahora descritas tiene el eje de la inflorescencia generalmente ramificado, con una o dos ramas de 6–24 cm de largo, entre el quinto y el octavo nudos, sus flores son infundibuliformes y crasas. Muestra similitudes morfológicas con Polianthes geminiflora var. geminiflora, P. geminiflora var. clivicola, P. geminiflora var. pueblensis, P. graminifolia y P. oaxacana. Se presenta una clave para la determinación de las especies del estado de Jalisco, México.     

Mapping the observed and modelled intracontinental distribution of non-marine ostracods from South America

Ecological niche modelling (ENM) has been used to quantify the potential occurrence of species, by identifying the main environmental factors that determine the presence of species across geographical space. We provide a large-scale survey of the distribution of ostracod species in South America, by using the domains of 25 river basins. From 221 known ostracod species, we estimate the potential distribution of 61 species, using ENM. Ten clusters of potential distribution patterns were found. Clusters 8 and 9 grouped most of the species, which presented high similarity of niche between them. Heterocypris paningi Brehm, 1934 (group 1) obtained higher niche variability. The minimum temperatures of the coldest month and the mean elevation of the river basin were most important to predict the potential distribution of ostracods of most groups. South America has a complex pattern of elevation, which affects species distributions indirectly through changes in local factors. For instance, the Andes mountains might impose a barrier for ostracod distribution in the southern part of South America because of the low temperatures and precipitation. The ENM indicated that some regions and/or basins of South America might be susceptible to the entry of several ostracod species, presently absent, including non-native species.

     

Synthesis,docking and pharmacological evaluation of novel homo- and hetero-bis 3-piperazinylpropylindole derivatives at SERT and 5-HT1A receptor

A series of 3-(3-(4-(3-(1H-indol-3-yl)propyl)piperazin-1-yl)propyl)-1H-indole derivatives (3a–d and 5a–f) as homo- and hetero-bis-ligands, were synthesized and evaluated for in vitro affinity at the serotonin transporter (SERT) and the 5-HT_1A receptor. Compounds 5b and 5f showed nanomolar affinities for both targets. The experimental data were rationalized according to results obtained from docking experiments. These findings are in agreement with our proposal that bis-indole derivatives can bind both targets, and might serve as leads in the quest of ligands endowed with a dual mechanism of action.