Migrating silver eels return from the sea to the river of origin after a false start

The European eel''s singular spawning migration from European waters towards the Sargasso Sea remains elusive, including the early phase of migration at sea. During spawning migration, the movement of freshwater resident eels from river to sea has been thought to be irreversible. We report the first recorded incidents of eels returning to the river of origin after spending up to a year in the marine environment. After migrating to the Baltic Sea, 21% of the silver eels, tagged with acoustic transmitters, returned to the Narva River. Half returned 11–12 months after moving to the sea, with 15 km being the longest upstream movement. The returned eels spent up to 33 days in the river and migrated to the sea again. The fastest specimen migrated to the outlet of the Baltic Sea in 68 days after the second start—roughly 1300 km. The surprising occurrence of returning migrants has implications for sustainable management and protection of this critically endangered species.     

KEGGanim: pathway animations for high-throughput data

MOTIVATION: Gene expression analysis with microarrays has become one of the most widely used high-throughput methods for gathering genome-wide functional data. Emerging -omics fields such as proteomics and interactomics introduce new information sources. With the rise of systems biology, researchers need to concentrate on entire complex pathways that guide individual genes and related processes. Bioinformatics methods are needed to link the existing knowledge about pathways with the growing amounts of experimental data. RESULTS: We present KEGGanim, a novel web-based tool for visualizing experimental data in biological pathways. KEGGanim produces animations and images of KEGG pathways using public or user uploaded high-throughput data. Pathway members are coloured according to experimental measurements, and animated over experimental conditions. KEGGanim visualization highlights dynamic changes over conditions and allows the user to observe important modules and key genes that influence the pathway. The simple user interface of KEGGanim provides options for filtering genes and experimental conditions. KEGGanim may be used with public or private data for 14 organisms with a large collection of public microarray data readily available. Most common gene and protein identifiers and microarray probesets are accepted for visualization input. AVAILABILITY: http://biit.cs.ut.ee/KEGGanim/.     

Relationship between extracellular matrix, contractile apparatus, muscle mass and strength in case of glucocorticoid myopathy

The purpose of this study was to evaluate the effect of dexamethasone on the contractile apparatus and extracellular matrix (ECM) components of slow-twitch (ST) soleus (Sol) and fast-twitch (FT) extensor digitorum longus (EDL) muscle. The specific aim was to assess the development of glucocorticoid-induced myopathy on the level of contractile apparatus and ECM, paying attention to the expression of fibrillar forming collagen types I and III and nonfibrillar type IV collagen expression in extracellular compartment of muscle. Degradation of myofibrillar proteins increased from 2.62+/-0.28 to 5.58+/-0.49% per day during glucocorticoids excess. Both fibril- and network-forming collagen-specific mRNA levels decreased at the same time in both types of skeletal muscle. Specific mRNA level for MMP-2 did not change significantly during dexamethasone administration. Hindlimb grip strength simultaneously decreased. The effect of excessive glucocorticoids on the extracellular compartment did not differ significantly in skeletal muscles with different twitch characteristics.     

The ColR-ColS two-component signal transduction system is involved in regulation of Tn4652 transposition in Pseudomonas putida under starvation conditions

Bacteria use two-component signal transduction pathways to sense both extracellular and intracellular environment and to coordinate cellular events according to changing conditions. Adaptation can be either physiological or genetical. Here, we present evidence that a genome reorganization process such as transposition can be controlled by certain environmental cues sensed by a two-component signal transduction system. We demonstrate that transposition-dependent accumulation of phenol-utilizing mutants is severely decreased in Pseudomonas putida defective in a two-component system colRS. Translocation of Tn4652 is decreased both in colR- and colS-defective strains, indicating that signal transduction from a histidine kinase ColS to a response regulator ColR is necessary for the activation of Tn4652 in bacteria starving on phenol. However, overexpression of ColR in a colS-defective strain restores Tn4652 transposition, suggesting that absence of the signal from ColS can be compensated by an elevated amount of ColR. In vitro analysis of purified ColR and ColS proteins evidenced that they constitute a functional phosphorelay. Site-directed mutagenesis revealed that a conserved H221 can be the phosphoryl-accepting residue in ColS and that aspartate residues D8 and D51 of ColR are necessary for the phosphotransfer from ColS to ColR. To our knowledge, Tn4652 is the first bacterial transposon regulated by a two-component system. This finding indicates that transpositional activity can respond to signals sensed and processed by the host.     

Ciliates are the Dominant Grazers on Pico- and Nanoplankton in a Shallow,Naturally Highly Eutrophic Lake

Abundance and biomass of the microbial loop members [bacteria, heterotrophic nanoflagellates (HNF), and ciliates] were seasonally measured in the naturally eutrophic and shallow (2.8 mean depth) Lake Võrtsjärv, which has a large open surface area (average 270 km²) and highly turbid water (Secchi depth <1 m). Grazing rates (filter feeding rates) on 0.5-, 3-, and 6-μm-diameter particles were measured to estimate pico- and nanoplankton grazing (filter feeding) by micro- and metazooplankton. Among grazers, HNF had a low abundance (<50 cells mL^?1) and, due to their low specific filtering rates, they only grazed a minor fraction of the bacterioplankton (≤4.2% of total grazing). Ciliates were relatively abundant (≤158 cells mL^?1) and, considering their high specific feeding rates, were able to graze more than 100% of the bacterial biomass production in the open part of the lake, whereas the average daily grazing accounted for 9.3% of the bacterial standing stock. Ciliates were potentially important grazers of nanoplanktonic organisms (on average, approximately 20% of the standing stock of 3-μm-size particles was grazed daily). Metazooplankton grazed a minor part of the bacterioplankton, accounting for only 0.1% of standing stock of bacteria. Grazing on nanoplankton (3–6 μm) by metazooplankton was higher (0.4% of standing stock). The hypothesis is proposed that ciliates dominate due to a lack of top–down regulation by predators, and HNF have a low abundance due to strong grazing pressure by ciliates.     

Vertical distribution of planktonic ciliates in strongly stratified temperate lakes

The vertical distribution of planktonic ciliates in eight strongly stratified temperate lakes was studied in summer 1998. Ciliate abundance and biomass were highest (mean 39.9 cells ml^–1 and 181.9 g C l^–1) in the epi-, and lowest (mean 8.2 cells ml^–1 and 97.6 g C l^–1) in the hypolimnion. The community of ciliates was dominated by five orders: Oligotrichida, Haptorida, Prostomatida, Scuticociliatida and Peritrichida. The community composition varied greatly with depth. In the epilimnion, the ciliate numbers were dominated by oligotrichs but small algivorous prostomatids, peritrichs and haptorids were also numerous. In the metalimnion, these groups were replaced by scuticociliates and mixotrophic prostomatids. In the hypolimnion species known as benthic migrants appeared. We found a positive significant correlation (p < 0.05) between ciliate numbers and Chl a and bacterial densities. Only in the hypolimnion, the correlation between ciliates numbers and Chl a was not significant.     

The effect of glucocorticoids on the myosin heavy chain isoforms' turnover in skeletal muscle

The purpose of this study was to find the effect of dexamethasone on the myosin heavy chain (MyHC) isoforms' composition in different skeletal muscles and glycolytic (G) fibres in relation with their synthesis rate and degradation of MyHC isoforms by alkaline proteinases. Eighteen-week-old male rats of the Wistar strain were treated with dexamethasone (100 microg/100 g bwt) during 10 days. The forelimb strength decreased from 9.52 to 6.19 N (P<0.001) and hindlimb strength from 15.54 to 8.55 N (P<0.001). Daily motor activity decreased (total activity from 933 to 559 and ambulatory activity from 482 to 226 movements/h, P<0.001). The degradation rate of muscle contractile proteins increased from 2.0 to 5.9% per day (P<0.001), as well as the myosin heavy chain IIB isoform degradation with alkaline proteinase in fast-twitch (F-T) muscles (12 +/- 0.9%; P<0.05) and glycolytic muscle fibres (15 +/- 1.1%; P<0.001). The synthesis rate of MyHC type II isoforms decreased in Pla muscles (P<0.05) and MyHC IIA (P<0.05) and IIB in EDL muscle and G fibres (P<0.001). The relative content of MyHC IIB isoform decreased in F-T muscles (P<0.001) and in G fibres (P<0.01), and the relative content of IIA and IID isoforms increased simultaneously. Dexamethasone decreased the MyHC IIB isoform synthesis rate and increased the sensibility of MyHC IIB isoform to alkaline proteinase, which in its turn led to the decrease of MyHC IIB isoform relative content in F-T muscles with low oxidative potential and G muscle fibres.     

Haplotype Phasing and Inheritance of Copy Number Variants in Nuclear Families

DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.     

Plumage Bacterial Assemblages in a Breeding Wild Passerine: Relationships with Ecological Factors and Body Condition

Microorganisms have been shown to play an important role in shaping the life histories of animals, and it has recently been suggested that feather-degrading bacteria influence the trade-off between parental effort and self-preening behavior in birds. We studied a wild breeding population of great tits (Parus major) to explore habitat-, seasonal-, and sex-related variation in feather-degrading and free-living bacteria inhabiting the birds' yellow ventral feathers and to investigate associations with body condition. The density and species richness of bacterial assemblages was studied using flow cytometry and ribosomal intergenic spacer analysis. The density of studied bacteria declined between the nest-building period and the first brood. The number of bacterial phylotypes per bird was higher in coniferous habitat, while bacterial densities were higher in deciduous habitat. Free-living bacterial density was positively correlated with female mass; conversely, there was a negative correlation between attached bacterial density and female mass during the period of peak reproductive effort. Bacterial species richness was sex dependent, with more diverse bacterial assemblages present on males than females. Thus, this study revealed that bacterial assemblages on the feathers of breeding birds are affected both by life history and ecological factors and are related to body condition.