Analysis of mtDNA variability in closely related Baikal sponge species for new barcoding marker development

Limnology - Morphology-based identification and classification of sponge species is complicated, because their morphological features are highly variable. Therefore, molecular markers are ideal...     

Primary photosynthetic processes: The problem of rapid irreversible redistribution of electronic energy

The general principles of a “device” aimed at the transformation of the energy of absorbed light quanta to the energy of a long-lived system with separated charges are analyzed. A set of conditions which must be fulfilled for efficient functioning of such a construction is formulated. A comparison of these results with the experimental data for the bacterial reaction centre is given. Some possibilities are discussed for the further experimental checking of the theory.     

Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes

Morphologic and phylogenetic analysis of freshwater sponges endemic to lakes in Central Sulawesi, Siberia and South-East Europe is presented. We also analyzed several cosmopolitan sponge species from Eurasia and North America and included sponge sequences from public databases. In agreement with previous reports [Addis, J.S., Peterson, K.J., 2005. Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences. Zool. Scr. 34, 549-557], the metaniid sponge Corvomeyenia sp. was the most deeply branching species within a monophyletic lineage of the suborder Spongillina. Pachydictyum globosum (Malawispongiidae) and Nudospongilla vasta (Spongillidae), two morphologically quite distinct species from Sulawesi were found in a joint clade with Trochospongilla (Spongillidae) rendering Trochospongilla paraphyletic. Furthermore, Ochridaspongia sp., another Malawispongiidae, clustered far away from that clade, together with Ephydatia fluviatilis, making the latter family polyphyletic. The Lubomirskiidae endemic to Lake Baikal, Lubomirskia abietina, Baikalospongia bacillifera, B. intermedia, and Swartschewskia papyracea formed a well-supported clade that was most closely linked to the genus Ephydatia (99.9% identity over a total length of 2169 concatenated nucleotide positions). Our study indicates the frequent and independent origin of sponge species endemic to different freshwater ecosystems from a few cosmopolitan founder species. The highly specific primer sets newly developed here facilitate work on the molecular phylogeny and DNA barcoding of sponges.     

Phylogenetic position of sponges from Chagytaĭ and Tore-Khol' lakes

Morphological and molecular genetic data for freshwater sponges from the lakes of Tuva Depression, Baikalospongia dzhegatajensis (Rezvo, 1936), forms Dzh05 and Dzh06, from Chagatai Lake, as well as forms TKhl and TKh2, from the Lake Tore-Khol, were obtained and examined. In the sponges examined, which on phylogenetic tree clustered together with the Ephydatia fluviatilis (Linneaus, 1758) sponge from the family Spongillidae, the ITS rDNA regions were sequenced. Comparison of highly variable interal spacer regions of the mitochondrial genome was performed using corresponding sequences of three sponges from the family Spongillidae (E. fluviatilis, E. muelleri and Spongilla lacustris), sponges from the Chagatai and Tore-Khol lakes (Dzh06 and TKh2) with an unknown status, and sponges from the Baikalian family Lubomirskiidae. Minimum genetic differences were observed between E. fluviatilis, Dzh06, and TKh2 (from 0.003 to 0.01% of nucleotide substitutions), while maximum differences were found between the species of Lubomirskiidae and Spongillidae (from 0.928 to 2.06%). The data obtained indicated that sponges from Chagatai and Tore-Khol lakes were most close to E. fluviatilis.     

Diversity of Polyketide Synthase (PKS) genes in metagenomic community of freshwater sponge Lubomirskia baicalensis

The screening of metagenomic DNA of the microbial community associated with the Baikalian sponge Lubomirskia baicalensis was performed in order to investigate the presence of polyketide synthase (PKS) genes. PKS enzyme systems take part in the synthesis of a great number of biologically active substances. The cloning and sequencing of amplified products of the ketosynthase domain section of the PKS gene cluster revealed 15 fragments of PKS genes with amino acid sequences differing from each other by 35?C65%. A BLASTX analysis showed that all of these sequences belong to KS domains identified in various groups of microorganisms, i.e., Alpha-, Beta-, and Deltaproteobacteria; Verrucomicrobia; Cyanobacteria; and Chlorophyta. Some sequences were related to genes that participate in the biosynthesis of curacin A (CurI, CurJ), stigmatellin (StiC, StiG), nostophycin (NpnB), and cryptophycin (CrpB). The homology of the found sequences with those of the EMBL database lies in the range of 50?C82%, which indicates that the freshwater sponge community contains genes that encode new, not yet studied polyketide substances of potential biotechnological significance.     

Distinctive features of the microbial diversity and the polyketide synthase genes spectrum in the community of the endemic Baikal sponge <Emphasis Type="Italic">Swartschewskia papyracea</Emphasis>

The diversity of the symbiotic community of the endemic Baikal sponge Swartschewskia papyracea was studied, and an analysis of the polyketide synthases genes spectrum in sponge-associated microorganisms was carried out. Six bacterial phyla were detected in the S. papyracea microbiome: Verrucomicrobia, Cyanobacteria, Actinobacteria, Bacteroidetes, Proteobacteria, and Planctomycetes. Unlike the microbial associations of other freshwater sponges, the community under study was dominated by the phylaVerrucomicrobia (42.1%) and Cyanobacteria (17.5%), while the proportion of the Proteobacteria was unusually low (9.7%). In the S. papyracea community metagenome, there were identified 18 polyketide synthases genes fragments, the closest homologues of which included the polyketide synthases of the microorganisms belonging to the bacterial phyla Cyanobacteria, Proteobacteria (classes Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria), and Acidobacteria as well as the eukaryotic algae of the phylum Heterokonta (class Eustigmatophyceae). Polyketide synthase sequences from S. papyracea formed three groups on the phylogenetic tree: a group of hybrid NRPS/PKS complexes, a group of cyanobacterial polyketide synthases, and a group of homologues of the eukaryotic alga Nannochloropsis gaditana. Notably, the identified polyketide synthase genes fragments showed only a 57–88% similarity to the sequences from the databases, which implies the presence of genes controlling the synthesis of the novel, still unstudied, polyketide compounds in the S. papyracea community. It was proposed that the habitat conditions of S. papyracea affect the taxonomic composition of the microorganisms associated with the sponge, including the diversity of the producers of secondary metabolites.     

Evaluation of coronary bed function by positron emission tomography using 13N-ammonium during cold stimulation

The purpose of the present investigation was to study the time course of changes in myocardial blood flow (MBF) in response to cold stimulation. Thirty-eight patients having risk factors of cardiovascular complications were examined. The time course of MBF changes was estimated by positron emission tomography (PET) using 13N-ammonium at rest and during a cold test (CT). Endothelium-dependent vasodilation of the brachial artery was determined from the results of a reactive hyperemia test, by applying ultrasound duplex scanning. No significant MBF increase in response to the cold test was an indicator of coronary arterial endothelial dysfunction at cardiac 13N-ammonium PET. Agreement of the results of brachial arterial ultrasonography during reactive hyperemia and cardiac 13N-ammonium PET in the presence of the cold test suggests that endothelial dysfunction is generalized. Cardiovascular risk factors, such as left ventricular hypertrophy, smoking, dyslipidemia, and diabetes mellitus, substantially affect coronary arterial function. Left ventricular hypertrophy is an independent factor that influences the amount of the coronary reserve and, in combination with endothelial dysfunction, worsens coronary microcirculation.     

Using Re-Sampling Methods in Mortality Studies

Traditional methods of computing standardized mortality ratios (SMR) in mortality studies rely upon a number of conventional statistical propositions to estimate confidence intervals for obtained values. Those propositions include a common but arbitrary choice of the confidence level and the assumption that observed number of deaths in the test sample is a purely random quantity. The latter assumption may not be fully justified for a series of periodic “overlapping” studies. We propose a new approach to evaluating the SMR, along with its confidence interval, based on a simple re-sampling technique. The proposed method is most straightforward and requires neither the use of above assumptions nor any rigorous technique, employed by modern re-sampling theory, for selection of a sample set. Instead, we include all possible samples that correspond to the specified time window of the study in the re-sampling analysis. As a result, directly obtained confidence intervals for repeated overlapping studies may be tighter than those yielded by conventional methods. The proposed method is illustrated by evaluating mortality due to a hypothetical risk factor in a life insurance cohort. With this method used, the SMR values can be forecast more precisely than when using the traditional approach. As a result, the appropriate risk assessment would have smaller uncertainties.     

Molecular phylogeny of the freshwater sponges in Lake Baikal

The phylogenetic relationship of the freshwater sponges (Porifera) in Lake Baikal is not well understood. A polyphyletic and/or monophyletic origin have been proposed. The (endemic) Baikalian sponges have been subdivided into two families: endemic Lubomirskiidae and cosmopolitan Spongillidae. In the present study, two new approaches have been made to resolve the phylogenetic relationship of Baikalian sponges; analysis of (1) nucleotide sequences from one mitochondrial gene, the cytochrome oxidase subunit I (COI) and of (2) one selected intron from the tubulin gene. Specimens from the following endemic Baikalian sponge species have been studied; Lubomirskia baicalensis , Baikalospongia intermedia, Baikalospongia recta , Baikalospongia bacillifera and Swartschewskia papyracea . They are all grouped to the family of Lubomirskiidae. Sequence comparisons were performed with the ubiquitously distributed freshwater sponge Spongilla lacustris (family Spongillidae) as well as with one marine sponge, Suberites domuncula . A sequence comparison * * The sequences reported here are being deposited in the EMBL data base. of the mitochondrial COI gene revealed a monophyletic grouping of the endemic Baikalian sponges with S. lacustris as the most related species to the common ancestor. The sequences of the COI gene from B. recta , B. intermedia , B. bacillifera and L. baicalensis were found to be identical and separated from those of S. lacustris and S. papyracea . In a second approach, the exon/intron sequences framing the intron‐2 of the sponge tubulin gene were chosen for the phylogenetic analysis. The intron sequences were aligned and used for construction of a phylogenetic tree. This analysis revealed again a monophyletic grouping with S. lacustris as the closest related species to the common ancestor. It is concluded that the Baikalian sponges, which have been studied here, are of monophyletic origin. Furthermore, the data suggest that the endemic species S. papyracea is the phylogenetically oldest, extant, endemic Baikalian sponge species.     

Automated classification of atherosclerotic plaque from magnetic resonance images using predictive models

The information contained within multicontrast magnetic resonance images (MRI) promises to improve tissue classification accuracy, once appropriately analyzed. Predictive models capture relationships empirically, from known outcomes thereby combining pattern classification with experience. In this study, we examine the applicability of predictive modeling for atherosclerotic plaque component classification of multicontrast ex vivo MR images using stained, histopathological sections as ground truth. Ten multicontrast images from seven human coronary artery specimens were obtained on a 9.4 T imaging system using multicontrast-weighted fast spin-echo (T1-, proton density-, and T2-weighted) imaging with 39-mum isotropic voxel size. Following initial data transformations, predictive modeling focused on automating the identification of specimen's plaque, lipid, and media. The outputs of these three models were used to calculate statistics such as total plaque burden and the ratio of hard plaque (fibrous tissue) to lipid. Both logistic regression and an artificial neural network model (Relevant Input Processor Network-RIPNet) were used for predictive modeling. When compared against segmentation resulting from cluster analysis, the RIPNet models performed between 25 and 30% better in absolute terms. This translates to a 50% higher true positive rate over given levels of false positives. This work indicates that it is feasible to build an automated system of plaque detection using MRI and data mining.