The Littorina sequence database (LSD)--an online resource for genomic data

We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147,491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26,537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.     

Structural evidence for co-evolution of the regulation of contraction and energy production in skeletal muscle

Skeletal muscle phosphorylase kinase (PhK) is a Ca²⁺-dependent enzyme complex, (αβγδ)₄, with the δ subunit being tightly bound endogenous calmodulin (CaM). The Ca²⁺-dependent activation of glycogen phosphorylase by PhK couples muscle contraction with glycogen breakdown in the “excitation-contraction-energy production triad.” Although the Ca²⁺-dependent protein-protein interactions among the relevant contractile components of muscle are well characterized, such interactions have not been previously examined in the intact PhK complex. Here we show that zero-length cross-linking of the PhK complex produces a covalent dimer of its catalytic γ and CaM subunits. Utilizing mass spectrometry, we determined the residues cross-linked to be in an EF hand of CaM and in a region of the γ subunit sharing high sequence similarity with the Ca²⁺-sensitive molecular switch of troponin I that is known to bind actin and troponin C, a homolog of CaM. Our findings represent an unusual binding of CaM to a target protein and supply an explanation for the low Ca²⁺ stoichiometry of PhK that has been reported. They also provide direct structural evidence supporting co-evolution of the coordinate regulation by Ca²⁺ of contraction and energy production in muscle through the sharing of a common structural motif in troponin I and the catalytic subunit of PhK for their respective interactions with the homologous Ca²⁺-binding proteins troponin C and CaM.     

Population genetic structure of the ascidian Styela rustica at Kongsfjorden, Svalbard, Arctic

The actual Arctic biota shows a strong affinity with that of the Boreal Atlantic and Pacific ones, as a result of an active recolonization process after the Quaternary glaciations. The geographic distribution of sessile species is usually linked to larvae dispersive capabilities which can be directly related with time spent in the plankton. Ascidians larvae are lecitothorphic and short-lived, which suggest that ascidians could be not efficient dispersers. However, the solitary ascidian Styela rustica (Linnaeus, 1767) (Tunicata, Ascidiacea) shows a wide distribution pattern from the North Atlantic to the Arctic that, together with the relatively recent colonization of the Arctic system could indicate that this species efficiently disperses and colonizes new habitats. In this study we used ISSR-PCR markers to study the genetic structure of five populations of the ascidian Styela rustica at Kongsfjorden, west Spitsbergen (Svalbard archipelago). We analyzed whether this species presents a low genetic structure, as can be expected due to the historical process of recent post glaciations colonization, or if there is genetic differentiation at a local scale, caused by short-lived larvae and limited dispersal potential. The genetic diversity in each population assessed using the marker diversity index (M) ranged from 0.288 to 0.324. Population HN, situated close to a fast retreating glacier, showed the lowest diversity. Processes associated with deglatiation (icebergs calving from the glacier that scour the benthos and the increment of inorganic particulate matter on the water column) would drive to reduced population sizes and explain the reduced genetic variability observed in the HN population with respect to the others in the fjord. This suggests a possible linkage with the global warming process. Although the weak genetic structure found among the studied populations could indicate a founder effect, the genetic landscape shape analysis together with a positive relationship between genetic and geographic distances also suggest possible current gene flow among populations in the fjord.     

Mitochondrial nucleotide variability in invasive populations of the root weevil Diaprepes abbreviatus (Coleoptera: Curculionidae) of Florida and preliminary assessment of Diaprepes sp. from Dominica

Diaprepes abbreviatus (L.) (Coleoptera: Curculionidae) is a root weevil introduced into the United States from the Caribbean in 1964. It is associated with >300 plants, including citrus, sugarcane, and potatoes. D. abbreviatus is widespread in Florida, and it has recently been detected in limited areas of California and Texas. The purpose of this research is to evaluate the utility of 16S ribosomal (16S rRNA) and cytochrome oxidase I (COI) mitochondrial markers for the delineation of genetic populations of D. abbreviatus in Florida and for the characterization of patterns of dispersion among these populations. We also assessed these markers as genetic tools for the clarification of taxonomic uncertainties in specimens from Dominica (Lesser Antilles). We analyzed 111 weevils from six Florida populations and six specimens from Dominica. In Florida, we found three haplotypes with only one haplotype in each population. Florida haplotypes differed by one to three nucleotide substitutions, possibly the result of a recent divergence from one source population or three different introductions from closely related populations from the Caribbean. In contrast, specimens from Dominica showed a high genetic variability with three 16S haplotypes and six unique COI haplotypes, delineating two mitochondrial clades. We show that these mitochondrial markers are useful for phylogeographic studies of D. abbreviatus.     

YKL-40 is elevated in patients with chronic obstructive pulmonary disease and activates alveolar macrophages

YKL-40 is a chitin-binding protein that is elevated in patients with various inflammatory conditions associated with ongoing remodeling. We investigated whether the levels of YKL-40 were up-regulated in the circulation and the airways of patients with chronic obstructive pulmonary disease (COPD), and whether it promoted the production of inflammatory mediators from macrophages. Serum, bronchoalveolar lavage (BAL), bronchial biopsies, lung tissue specimens, and alveolar macrophages from never-smokers (n = 15), smokers without COPD (n = 20), and smokers with COPD (n = 30) were assessed for YKL-40 levels and immunolocalization. In addition, YKL-40-induced mediator release from alveolar macrophages was examined. We found that smokers with COPD had elevated levels of YKL-40 in serum (p 相似文献   

Wild mouse lemurs revisit artificial feeding platforms: implications for field experiments on sensory and cognitive abilities in small primates

Dealing effectively with space to find important resources in a natural environment is a fundamental ability necessary for survival. Evidence has already been provided that wild gray mouse lemurs revisit stationary feeding sites regularly. In this study, we explore to what extent two sympatric mouse lemur species, Microcebus murinus and M. ravelobensis, revisited artificial feeding sites during a period of food scarcity. As the tested populations are marked with individual transponders, we built up artificial feeding platforms equipped with a transponder reader at nine different locations where mouse lemurs had been previously caught. We baited them with a liquid reward and recorded the visitors' ID, the time and frequency of their visits, as well as all encounters that occurred on the platforms. Only mouse lemurs visited platforms and a total of sixteen individuals across both species were identified. Mouse lemurs visited a platform with a frequency of 2.02 (+/-0.95, range: 1-3.4) times in a night and they revisited it on several consecutive nights following their first visit (percentage of revisits 90.6%+/-11.7, range: 73.3-100%). First visits on a platform occurred on average 44 min (+/-35; range: 13-131) after sunset. We identified encounters between mouse lemurs on platforms: all of them were agonistic and within a species. Within a dyad, chasers were significantly heavier than chasees (N=7 dyads). Our design of platform experiments offers the advantage of observing wild individually known small primates in their natural environment and of setting up controlled experiments to gain insight into their sensory and cognitive abilities.     

East-West cranial differentiation in pre-Columbian populations from Central and North America

In a recent study we found that crania from South Amerindian populations on each side of the Andes differ significantly in terms of craniofacial shape. Western populations formed one morphological group, distributed continuously over 14,000km from the Fuegian archipelago (southern Chile) to the Zulia region (northwestern Venezuela). Easterners formed another group, distributed from the Atlantic Coast up to the eastern foothills of the Andes. This differentiation is further supported by several genetic studies, and indirectly by ecological and archaeological studies. Some authors suggest that this dual biological pattern is consistent with differential rates of gene flow and genetic drift operating on both sides of the Cordillera due to historical reasons. Here we show that such East-West patterning is also observable in North America. We suggest that the "ecological zones model" proposed by Dixon, explaining the spread of the early Americans along a Pacific dispersal corridor, combined with the evolution of different population dynamics in both regions, is the most parsimonious mechanism to explain the observed patterns of within- and between-group craniofacial variability.     

Non-masticatory uses of anterior teeth of Sima de los Huesos individuals (Sierra de Atapuerca, Spain)

In this study we examine the labial and occlusal surfaces of incisors and canines of hominins recovered from the Sima de los Huesos (SH), middle Pleistocene site, in order to establish the possible extra-masticatory use of anterior teeth. We have compared the microwear of these fossils with microwear from the anterior teeth of Australian Aborigines, a population characterized by ethnographic evidence of the use of their teeth as a third hand. These two samples of teeth were microscopically analyzed using Scanning Electron Microscopy (SEM). Our results support the “cultural” origin of microwear observed on fossil teeth: we conclude that the SH hominins used their anterior teeth as a “third hand” for para- or extra-masticatory activities.