The role of head shape and trophic variation in the diversification of the genus Herichthys in sympatry and allopatry

In the present study we evaluated the putative cases of sympatric speciation in the genus Herichthys by studying the variation in head shape using principal component analysis, phylomorphospace and reconstructions of the ancestral states of feeding preferences. Herichthys includes both allopatric and sympatric sister species, as well as sympatric unrelated species and thus offers great potential for evolutionary studies of putatively sympatric speciation. Herichthys is the northernmost group of cichlids in America and one of the most ecologically disparate genera within Middle American cichlids. Fifteen anatomical points were recorded on the heads of 293 specimens of the 11 species recognized within the genus. The results show that in spite of having wide variation in consumed diets, most species of Herichthys are close in morphospace. However, morphological variation was great among the two pairs of sympatric sister species in agreement with the suggested sympatric model of speciation.     

Tyrosine attack by free radicals derived from catalytic decomposition of carbon tetrachloride

The interaction between free radicals derived from the catalytic decomposition of carbon tetrachloride and tyrosine (the N-acetyl tyrosine ethyl ester, ATEE) under anaerobic and aerobic conditions was studied. The structure of the reaction products formed was desciphered by the GLC/MS analysis of their trimethylsilyl derivatives. Under anaerobic conditions the formation of the following products was found: (1) an unsaturated derivative of the amino acid; (2) the trimethylsilyl derivative of N-acetyl chloro tyrosine ethyl ester; (3) a hydroxyl adduct of ATEE ; (4) an ATEE adduct having a chlorine and a CCl₃ group in the molecule (it is suggested that CCl₃ is attached to the benzyl carbon and the chlorine located in the benzene ring); (5) an ATEE adduct having only a CCl₃ group tentatively assigned to be located on the benzyl carbon; and (6) and (7) were found to be two isomers of an ATEE having one CCl₃ on the aromatic ring. Under aerobic conditions the following reaction products were identified: Two products which were similar to those numbered (1) and (2) and formed anaerobically; (8) and (11) two isomeric dichlorinated adducts of ATEE; (9) and (10) two isomeric dichlorinated monohydroxylated derivatives of ATEE. Concerning the potential relevance of these findings, we consider that if similar interactions to those here reported occurred during CCl₄ poisoning, the activity of enzymes having tyrosine in their active center might result in impairment. Further, enzymes operating on tyrosine moieties in proteins might be perturbed in their action if tyrosine groups were attacked by the free radicals arising from catalytic decomposition of CCl₄ evidenced here.     

Species richness of helminth parasites in Mexican amphibians and reptiles

Abstract. Amphibians and reptiles represent an important group of vertebrates in Mexico; on a global scale 10% of the biodiversity of these groups is found in the country, attaining extraordinarily high levels of endemism (60.7% and 53.7%, respectively). However, fewer than 20% of the known species of amphibians and reptiles in Mexico have been surveyed for helminths, so the inventory is far from complete. We assembled a data base that includes a total of 1246 records (entries) of which 460 correspond to helminths in amphibians and 786 to helminths in reptiles. In total, only 41 species of amphibians (14% of those occurring in Mexico) and only 118 species of reptiles (17% of those occurring in Mexico) have been studied for helminth parasites. From amphibians, 119 species of helminths belonging to 60 genera have been recorded, while 239 species of helminths representing 113 genera have been described from Mexican reptiles. One feature of the distribution of helminths of Mexican amphibians and reptiles is its asymmetry, as seen in representation of helminth groups, host groups and geographical range. However, such statistical asymmetry might be an artefact of sampling effort. Based on our data, we estimate that if all the herpetofauna of Mexico could be studied in the following years, approximately 827 additional species of helminths from amphibians and approximately 1403 from reptiles would be described.     

Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

Critical blind assessment of structure prediction techniques is crucial for the scientific community to establish the state of the art, identify bottlenecks, and guide future developments. In Critical Assessment of Techniques in Structure Prediction (CASP), human experts assess the performance of participating methods in relation to the difficulty of the prediction task in a biennial experiment on approximately 100 targets. Yet, the development of automated computational modeling methods requires more frequent evaluation cycles and larger sets of data. The “Continuous Automated Model EvaluatiOn (CAMEO)” platform complements CASP by conducting fully automated blind prediction evaluations based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the Protein Data Bank (PDB). Each week, CAMEO publishes benchmarking results for predictions corresponding to a set of about 20 targets collected during a 4-day prediction window. CAMEO benchmarking data are generated consistently for all methods at the same point in time, enabling developers to cross-validate their method's performance, and referring to their results in publications. Many successful participants of CASP have used CAMEO—either by directly benchmarking their methods within the system or by comparing their own performance to CAMEO reference data. CAMEO offers a variety of scores reflecting different aspects of structure modeling, for example, binding site accuracy, homo-oligomer interface quality, or accuracy of local model confidence estimates. By introducing the "bestSingleTemplate" method based on structure superpositions as a reference for the accuracy of 3D modeling predictions, CAMEO facilitates objective comparison of techniques and fosters the development of advanced methods.     

Effects of Hydraulic Soil Properties on Vegetation Pattern Formation in Sloping Landscapes

Current models of vegetation pattern formation rely on a system of weakly nonlinear reaction–diffusion equations that are coupled by their source terms. While these equations, which are used to describe a spatiotemporal planar evolution of biomass and soil water, qualitatively capture the emergence of various types of vegetation patterns in arid environments, they are phenomenological and have a limited predictive power. We ameliorate these limitations by deriving the vertically averaged Richards’ equation to describe flow (as opposed to “diffusion”) of water in partially saturated soils. This establishes conditions under which this nonlinear equation reduces to its weakly nonlinear reaction–diffusion counterpart used in the previous models, thus relating their unphysical parameters (e.g., diffusion coefficient) to the measurable soil properties (e.g., hydraulic conductivity) used to parameterize the Richards equation. Our model is valid for both flat and sloping landscapes and can handle arbitrary topography and boundary conditions. The result is a model that relates the environmental conditions (e.g., precipitation rate, runoff and soil properties) to formation of multiple patterns observed in nature (such as stripes, labyrinth and spots).     

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes

Over the past decade, there has been a pronounced shift in the study of host–microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes).     

Biochemical characterization and structural prediction of a novel cytosolic leucyl aminopeptidase of the M17 family from Schizosaccharomyces pombe

A new leucyl aminopeptidase activity has been identified in the fission yeast Schizosaccharomyces pombe. The enzyme, which has been purified and named leucyl aminopeptidase yspII (LAP yspII), had a molecular mass of 320 and 54 kDa by gel filtration and SDS/PAGE, respectively, suggesting a homohexameric structure. The enzyme cleaved synthetic aminoacyl-4-nitroanilides at an optimum of pH 8.5, and preferred leucine and methionine as N-terminal amino acids. A clear dependence on Mn2+ concentration for activity was found, and an apparent association constant of 0.33 mM was calculated for the metal ion. Bestatin behaved as a competitive inhibitor of LAP yspII (K(i) = 0.14 microM), while chelating agents such as chloroquine, EDTA and 1,10-phenanthroline also reduced enzyme activity. A MALDI-MS analysis, followed by sequencing of two of the resulting peptides, showed that LAP yspII undoubtedly corresponds to the putative aminopeptidase C13A11.05 identified in the S. pombe genome project. The protein exhibited nearly 40% sequence identity to fungal and mammalian aminopeptidases belonging to the M17 family of metallopeptidases. Catalytic residues (Lys292 and Arg366), as well as those involved in coordination with the cocatalytic metal ions (Lys280, Asp285, Asp303, Asp362 and Glu364) and those forming the hydrophobic pocket for substrate binding (Met300, Asn360, Ala363, Thr390, Leu391, Ala483 and Met486), were perfectly conserved among all known aminopeptidases. The S. pombe enzyme is predicted to be formed two clearly distinguished domains with a well conserved C-terminal catalytic domain showing a characteristic topology of eight beta-sheets surrounded by alpha-helical segments in the form of a saddle.     

Quantitative effects of common genetic variations in the 3′UTR of the human LDL-receptor gene and their associations with plasma lipid levels in the Atherosclerosis Risk in Communities study

The low-density lipoprotein receptor (LDLR) plays a pivotal role in cholesterol homeostasis. However, the role of genetic variations in the 3′UTR of the LDLR in relation to plasma cholesterol has been largely understudied. Six SNPs, G44243A, G44332A, C44506G, G44695A, C44857T and A44964G, within the 5′ region of the 3′UTR fall into three common haplotypes, GGCGCA, AGCACG, and GGCGTA, occurring at frequencies of 0.45, 0.31 and 0.17, respectively, in Caucasians (n = 29) and 0.13, 0.13 and 0.38, respectively, in African Americans (n = 32), with three other haplotypes occurring at lesser frequencies. In a tissue culture based system, expression of a reporter gene carrying a 3′UTR that includes the 1 kb nucleotide sequences corresponding to the AGCACG or GGCGTA was 70 or 63%, respectively, of the same sequence with GGCGCA. Genotyping of two “haplotype tagging” SNPs, C44857T and A44964G, in the Atherosclerosis Risk in Communities (ARIC) study population showed that in Caucasians, but not in African Americans, the inferred TA haplotype had a significant LDL-cholesterol lowering effect. The adjusted LDL-cholesterol levels in the TA/TA diplotypes were lower by 6.10 mg/dl in men (P < 0.001) and by 4.63 mg/dl in women (P < 0.01) than in individuals with other diplotypes. Caucasian men homozygous for CA, in contrast, showed significantly higher LDL-cholesterol (P < 0.04), lower HDL-cholesterol (P < 0.02) and higher LDL/HDL ratios (P < 0.001). Thus our data shows that 3′UTR sequences that cause higher reporter gene expression in vitro are associated in Caucasians with plasma lipid profiles indicative of higher cardiovascular risk, suggesting that further studies of quantitative variants in the LDLR gene will be valuable. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

The effect of root exudates on root architecture in <Emphasis Type=Italic>Arabidopsis thaliana</Emphasis>

Root architecture is of key importance for plant nutrition and performance. It is known that root architecture is determined by genetics and environmental conditions. The aim of the present study was to evaluate if root exudation within a given plant has a role in the development of root architecture. We conducted a series of experiments using Arabidopsis thaliana Ler and Col grown with and without activated charcoal (AC). The addition of AC lowered the concentration of secondary metabolites in the growth media by more than 90%. Our results consistently showed that the addition of AC significantly decreased the number of lateral roots (38% in Ler and 27% in Col), but this decrease was compensated by an increase in the root length per unit of lateral root (83% in Ler and 96% in Col). This compensation resulted in a non-significant effect of AC on the total length of lateral roots. The effects of AC on root architecture were partially or totally reverted by the differential supplementation of root exudates from other plants of the same ecotype. Our results indicate a direct role of secondary metabolites present in the root exudates in the development of root architecture.     

Nitrogen availability increases in a tundra ecosystem during five years of experimental permafrost thaw

Perennially frozen soil in high latitude ecosystems (permafrost) currently stores 1330–1580 Pg of carbon (C). As these ecosystems warm, the thaw and decomposition of permafrost is expected to release large amounts of C to the atmosphere. Fortunately, losses from the permafrost C pool will be partially offset by increased plant productivity. The degree to which plants are able to sequester C, however, will be determined by changing nitrogen (N) availability in these thawing soil profiles. N availability currently limits plant productivity in tundra ecosystems but plant access to N is expected improve as decomposition increases in speed and extends to deeper soil horizons. To evaluate the relationship between permafrost thaw and N availability, we monitored N cycling during 5 years of experimentally induced permafrost thaw at the Carbon in Permafrost Experimental Heating Research (CiPEHR) project. Inorganic N availability increased significantly in response to deeper thaw and greater soil moisture induced by Soil warming. This treatment also prompted a 23% increase in aboveground biomass and a 49% increase in foliar N pools. The sedge Eriophorum vaginatum responded most strongly to warming: this species explained 91% of the change in aboveground biomass during the 5 year period. Air warming had little impact when applied alone, but when applied in combination with Soil warming, growing season soil inorganic N availability was significantly reduced. These results demonstrate that there is a strong positive relationship between the depth of permafrost thaw and N availability in tundra ecosystems but that this relationship can be diminished by interactions between increased thaw, warmer air temperatures, and higher levels of soil moisture. Within 5 years of permafrost thaw, plants actively incorporate newly available N into biomass but C storage in live vascular plant biomass is unlikely to be greater than losses from deep soil C pools.