The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques

The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ∼10,000 years before present (YBP), with signals of expansions at ∼3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈15%) of the Franco-Cantabrian maternal gene pool with a putative pre-Neolithic origin to ≈35%, further supporting the notion of a predominant Paleolithic genetic substrate in extant European populations.     

The RAINFOR database: monitoring forest biomass and dynamics

Problem: Data from over 100 permanent sample plots which have been studied for 10–20 years need a suitable system for storage which allows simple data manipulation and retrieval for analysis. Methods: A relational database linking tree records, taxonomic nomenclature and corresponding environmental data has been built in MS Access as part of the RAINFOR project. Conclusion: The database allows flexible and long‐term use of a large amount of data: more than 100 tree plots across Amazonia, incorporating over 80 000 records of individual trees and over 300 000 total records of tree diameter measurements from successive censuses. The database is designed to enable linkages to existing soil, floristic or plant‐trait databases. This database will be a useful tool for exploring the impact of environmental factors on forest structure and dynamics at local to continental scales, and long term changes in forest ecology. As an early example of its potential, we explore the impact of different methodological assumptions on estimates of tropical forest biomass and carbon storage.     

Colorectal Cancers Mimic Structural Organization of Normal Colonic Crypts

Colonic crypts are stereotypical structures with distinct stem cell, proliferating, and differentiating compartments. Colorectal cancers derive from colonic crypt epithelia but, in contrast, form morphologically disarrayed glands. In this study, we investigated to which extent colorectal cancers phenocopy colonic crypt architecture and thus preserve structural organization of the normal intestinal epithelium. A subset of colon cancers showed crypt-like compartments with high WNT activity and nuclear β-Catenin at the leading tumor edge, adjacent proliferation, and enhanced Cytokeratin 20 expression in most differentiated tumor epithelia of the tumor center. This architecture strongly depended on growth conditions, and was fully reproducible in mouse xenografts of cultured and primary colon cancer cells. Full crypt-like organization was associated with low tumor grade and was an independent prognostic marker of better survival in a collection of 221 colorectal cancers. Our findings suggest that full activation of preserved intestinal morphogenetic programs in colon cancer requires in vivo growth environments. Furthermore, crypt-like architecture was linked with less aggressive tumor biology, and may be useful to improve current colon cancer grading schemes.     

Carotenoids fromCapsicum annuum fruits: Changes during ripening and storage

Contents of individual carotenoids in the fruits of Ramillete cultivar ofCapsicum annuum L. changed during ripening of recently harvested fruits or fruits stored 15 d in a dark and cool room. β-carotene and β-cryptoxanthin contents rose to a maximum and then declined, while the contents of other earotenoids rose to a rather steady level. Capsanthin was the main carotenoid which together with capsorubin were responsihle for the ripening colour.     

A three-dimensional model of the U1 small nuclear ribonucleoprotein particle

Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5′ exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes.     

The natural history, thermal physiology, and ecological impacts of intertidal mesopredators, Oedoparena spp. (Diptera: Dryomyzidae)

Abstract. The ecological roles of small (1–1000 mg) predators in benthic marine systems are poorly understood. We investigated the natural history and predatory impact of one group of such mesopredators—larvae of dipteran flies in the genus Oedoparena —which prey on intertidal barnacles. We 1) quantified patterns of larval Oedoparena distribution and abundance in the Northwest Straits of Washington State, USA, 2) determined larval physiological tolerance limits in the laboratory, and 3) conducted a manipulative field experiment to assess the role of microhabitat temperature on predation rates in Oedoparena . Members of Oedoparena in Washington are univoltine, with peak larval abundance in late spring and early summer. Infestation frequencies in the barnacles Balanus glandula and Chthamalus dalli were as high as 22% and 35%, respectively. In laboratory studies, larvae of O . glauca were able to tolerate temperatures up to 37°C; however, this temperature is often exceeded in high intertidal habitats. In a field manipulation using experimental shades, we demonstrate that the alleviation of physiological stress greatly increased the abundance of larvae of Oedoparena spp. As a result of increased larval densities under shades, adult B. glandula mortality increased from 5% to nearly 30%, and C. dalli mortality increased from less than 20% to over 60%. Because high intertidal barnacles serve as food and habitat for a diverse array of species, Oedoparena spp. have the potential to play a major role in structuring high intertidal communities, particularly in cooler microhabitats.     

Summer dynamics of the deep chlorophyll maximum in Lake Tahoe

Vertical profiles of chlorophyll and phytoplankton biomass weremeasured in Lake Tahoe from July 1976 through April 1977. Adeep chlorophyll maximum (DCM) persisted during summer and earlyautumn (July—October) near 100 m, well below the mixedlayer and at the upper surface of the nitracline. The DCM coincidedwith the phytoplankton biomass maximum as determined from cellcounts. In addition, the composition of the phytoplankton assemblagewas highly differentiated with respect to depth. Cyclotellastelligera was the predominant species in the mixed layer whilethe major species in the DCM layer included C. ocellata andseveral green ultraplanktonic species. In situ cell growth playsa substantial role in maintaining the DCM, but sinking of cellsfrom shallower depths and zooplankton grazing above the DCMmay contribute to the maintenance of the DCM. Calculations supportthe interpretation that the summer DCM persists at the boundarybetween an upper, nutrient-limited phytoplankton assemblageand a deeper, light-limited assemblage.     

Dantrolene prevents the malignant hyperthermic syndrome by reducing free intracellular calcium concentration in skeletal muscle of susceptible swine

Malignant hyperthermia (MH) is a pharmacogenetic disorder of skeletal muscle triggered when susceptible subjects are exposed to volatile anesthetic agents and/or depolarizing muscle relaxants. We have used Ca2+ selective microelectrodes to measure in vivo the intracellular free [Ca2+] in skeletal muscle of MH susceptible swine before and after the administration of dantrolene. We have investigated the effectiveness of this muscle relaxant in preventing clinical MH and the relationship between the resting intracellular free [Ca2+] and the probability of inducing the MH syndrome. The resting intracellular free [Ca2+] was 0.41 +/- 0.01 microM (M +/- SEM), which agrees with our previous measurements in susceptible swine. The administration of 0.5, 1, 2, 2.5 and 3 mg/Kg Dantrolene, reduced the intracellular free [Ca2+] to 0.31, 0.21, 0.09, 0.08, 0.08 microM respectively. The 0.5 mg/Kg dose induced a moderate decrease of [Ca2+]i and failed to prevent the MH syndrome after exposure to halothane (2%). The 1 mg/Kg dose produced a further reduction in [Ca2+]i and was sufficient to prevent the clinical syndrome in 2 out of 3 animals. The 2.5 mg/Kg dose was uniformly protective in all animals. These results suggest that the mechanism by which dantrolene protects susceptible animals exposed to triggering agents is by reducing the intracellular free [Ca2+] in skeletal muscle.