Cracking the nut: geographical adjacency of sister taxa supports vicariance in a polytomic salamander clade in the absence of node support

The urodelan genus Lyciasalamandra, which inhabits a relatively small area along the southern Turkish coast and some Aegean islands, provides an outstanding example of a diverse but phylogenetically unresolved taxon. Molecular trees contain a single basal polytomy that could be either soft or hard. We here use the information of nuclear (allozymes) and mitochondrial (fractions of the 16S rRNA and ATPase genes) datasets in combination with area relationships of lineages to resolve the phylogenetic relationships among Lyciasalamandra species in the absence of sufficient node support. We can show that neither random processes nor introgressive hybridization can be invoked to explain that the majority of pairs of sister taxa form geographically adjacent units and interpret that this pattern has been shaped by vicariant events. Topology discordance between mitochondrial and nuclear trees mainly refers to an affiliation of L. helverseni, a taxon restricted to the Karpathos archipelago, to the western-most and geographically proximate mainland taxon in the nuclear tree, while in the organelle tree it turns out to be the sister lineage to the geographically most distant eastern clade. As this discordance cannot be explained by long-branch attraction in either dataset we suppose that oversea dispersal may have accounted for a second colonization of the Karpathos archipelago. It may have initiated introgression and selection driven manifestation of alien eastern mitochondrial genomes on a western nuclear background. Our approach of testing for area relationships of sister taxa against the null hypothesis of random distribution of these taxa seems to be especially helpful in phylogenetic studies where traditional measures of phylogenetic branch support fail to reject the null hypothesis of a hard polytomy.     

Surface expression of Bcl-2 in chronic lymphocytic leukemia and other B-cell leukemias and lymphomas without a breakpoint t(14;18)

Since its discovery in follicular lymphoma cells at the breakpoint t(14;18), Bcl-2 has been studied extensively in many basic and clinical science settings. Bcl-2 can locate as an integral mitochondrial membrane component, where its primary role is to block apoptosis by maintaining membrane integrity. Here we show that Bcl-2 also can position on the outer cell surface membrane of B cells from patients with chronic lymphocytic leukemia (B-CLL) and certain other leukemias that do not classically possess the chromosomal breakpoint t(14;18). Although low levels of Bcl-2 can be detected on the surface membrane of apparently healthy leukemic and normal B cells, expression of Bcl-2 correlates best with spontaneous or induced apoptosis. Notably, upon induction of apoptosis, B-CLL cells were much more efficient in upregulating surface Bcl-2 than normal B cells. It is not clear if this surface membrane expression is a passive consequence of the apoptotic process or an active attempt by the B cell to abort cell death by stabilizing the plasma membrane.     

Possible Role of Light and Polyamines in the Onset of Somatic Embryogenesis of Coffea canephora

The concentration of free and bound polyamines was studied during the somatic embryogenesis induction process in Coffea canephora explants. In the present study we show that when the induction of somatic embryogenesis in C. canephora is carried out under light conditions and in the presence of the plant growth regulator, benzylaminopurine, a cytokinin, a faster response to induction is obtained. In the darkness, the response is delayed for more than 20 days, and the number of embryos is smaller. In the absence of benzylaminopurine no embryogenic response was observed. The pronounced changes in the levels of putrescine, spermidine, and spermine, both free and bound, found in C. canephora suggest that a close correlation exists between polyamine biosynthesis and somatic embryogenesis in C. canephora during a period of cellular differentiation associated with the induction of somatic embryogenesis. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. We would like to dedicate this paper to Dra. Estela Sánchez, the pioneer of the Plant Biochemistry in Mexico, on occasion of her 75th anniversary.     

Microtubule dynamics and the role of molecular motors in Neurospora crassa.

Live-cell imaging methods were used to study microtubule dynamics in the apical regions of leading hyphae and germ tubes of Neurospora crassa expressing beta-tubulin-GFP. Microtubule polymerization rates in hyphae of N. crassa were much faster than those previously reported in any other eukaryotic organism. In order to address the roles of motor proteins in microtubule dynamic instability in N. crassa, the microtubule-motor mutant strains, Deltankin and ro-1, were examined. Polymerization and depolymerization rates in leading hyphae of these strains were reduced by one half relative to the wild type. Furthermore, microtubules in germ tubes of wild type and microtubule-motor mutants exhibited similar dynamic characteristics as those in hyphae of mutant strains. Small microtubule fragments exhibiting anterograde and retrograde motility were present in leading hyphae of all strains and germ tubes of wild-type strains. Our data suggest that microtubule motors play important roles in regulating microtubule dynamic instability in leading hyphae but not in germ tubes.     

Chlamydia trachomatis detection in a population of asymptomatic and symptomatic women: correlation with the presence of serological markers for this infection

A study of 371 women (261 asymptomatic and 110 symptomatic subjects with clinical PID) was performed to detect the presence of Chlamydia trachomatis (C.t.) and to correlate the serological markers against this microrganism, such as antibody to chlamydial hsp60 (Ab-Chsp60) and different levels of IgG, IgM and IgA, with epidemiology, pathology, sexual habits, age, diagnostic methods in the groups of women with and without pelvic inflammatory disease (PID). We found a statistically significant difference between the asymptomatic and symptomatic women regarding the presence of C.t. (3.4% versus 20%; p<0.0001). This presence was affected by the age of women (more in the group < or =25 years old), by having sex with new partners mainly if they did not undergo an antibiotic treatment. The association of antibody Chsp60 with the presence of clinical PID was quite striking. We also found a strict correlation between the detection of Ab-Chsp60 and previous chlamydial infection as well as between Ab-Chsp60 and elevated serum chlamydial IgG or IgA levels. Due to these findings, we can say that the use of serological markers for C.t. in clinical practice may be an important tool for an early screening and diagnosis of women at high risk of chlamydial infection.     

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays

MOTIVATION: Affymetrix SNP arrays can be used to determine the DNA copy number measurement of 11 000-500 000 SNPs along the genome. Their high density facilitates the precise localization of genomic alterations and makes them a powerful tool for studies of cancers and copy number polymorphism. Like other microarray technologies it is influenced by non-relevant sources of variation, requiring correction. Moreover, the amplitude of variation induced by non-relevant effects is similar or greater than the biologically relevant effect (i.e. true copy number), making it difficult to estimate non-relevant effects accurately without including the biologically relevant effect. RESULTS: We addressed this problem by developing ITALICS, a normalization method that estimates both biological and non-relevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects. We compared our normalization method with other existing and available methods, and found that ITALICS outperformed these methods for several in-house datasets and one public dataset. These results were validated biologically by quantitative PCR. AVAILABILITY: The R package ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) has been submitted to Bioconductor.     

Production of a thermophilic maltooligosyl-trehalose synthase in <Emphasis Type="Italic">Lactococcus lactis</Emphasis>

The thermoacidophilic archaeon Sulfolobus solfataricus MT4 encodes a maltooligosyltrehalose synthase (MTS), that catalyzes an intramolecular transglycosylation process converting the glycosidic linkages at the reducing end of dextrins from alpha-1,4 into alpha-1,1. In this research the gene encoding MTS was cloned and expressed in Lactococcus lactis NZ9000 using the so-called NICE system. Growth conditions of the recombinant strain were optimized in flask experiments in relation to enzyme production. Batch experiments in 2 L-fermenters were performed on the best identified semidefined medium and 256 U L(-1) of recombinant MTS were produced. Purified recombinant MTS shows its optimal activity at 70 degrees C and pH 5.5, prefers maltoheptaose and maltohexaose as substrates, and demonstrates minimal side hydrolytic activity.     

Ecological biogeography of cephalopod molluscs in the Atlantic Ocean: historical and contemporary causes of coastal diversity patterns

Aim One of the most recognized ecological paradigms on earth is the increase in species richness from the poles towards the equator. Here we undertake a comprehensive survey of the latitudinal gradients of species richness (LGSR) of coastal cephalopod fauna in the western (WA) and eastern margins (EA) of the Atlantic Ocean, and test climate and non‐climate theories to explain the variation in diversity. Location The coastal Atlantic Ocean. Methods The diversity and geographical ranges of coastal cephalopods were investigated by means of an exhaustive survey of the primary literature, reports and on‐line data bases. In order to test the productivity, ambient energy and area hypotheses, we investigated the relationship between diversity and net primary production (NPP), sea surface temperature (SST; measure of solar energy input) and continental shelf area, respectively. Results LGSR of cephalopod molluscs are present at both Atlantic coasts, but are quite distinct from each other. Historical processes (rise of the Central American Isthmus, formation of ‘Mare Lago’ and glaciations) explained much of the shape and the zenith of LGSR. Contemporary climate and non‐climate variables also each explained over 83% and 50% of the richness variation in WA and EA, respectively, and the best fitted models accounted for > 92% of the variance. By combining latitude with depth a strong Rapoport effect was observed in WA but not in EA. Main conclusions Besides the evolutionary history, we demonstrate that the contemporary environmental gradients (SST and NPP), shelf area and extent of coral habitat can predict many of the diversity patterns. The longitudinal difference in Rapoport's bathymetric rule is attributed to western fauna specialization to shallow coral reef habitats and greater ecological tolerance of eastern fauna to upwelling ecosystem dynamics. A combined approach of historical biogeography and species–area–energy theories was essential to fully understand broad‐scale variation in cephalopod biodiversity.     

Gypsy endogenous retrovirus maintains potential infectivity in several species of Drosophilids

Background  

Sequences homologous to the gypsy retroelement from Drosophila melanogaster are widely distributed among drosophilids. The structure of gypsy includes an open reading frame resembling the retroviral gene env, which is responsible for the infectious properties of retroviruses.