The genome sequence of the protostome Daphnia pulex encodes respective orthologues of a neurotrophin, a Trk and a p75NTR: Evolution of neurotrophin signaling components and related proteins in the bilateria

Background

Neurotrophins and their Trk and p75NTR receptors play an important role in the nervous system. To date, neurotrophins, Trk and p75NTR have only been found concomitantly in deuterostomes. In protostomes, homologues to either neurotrophin, Trk or p75NTR are reported but their phylogenetic relationship to deuterostome neurotrophin signaling components is unclear. Drosophila has neurotrophin homologues called Spätzles (Spz), some of which were recently renamed neurotrophins, but direct proof that these are deuterostome neurotrophin orthologues is lacking. Trks belong to the receptor tyrosine kinase (RTK) family and among RTKs, Trks and RORs are closest related. Flies lack Trks but have ROR and ROR-related proteins called NRKs playing a neurotrophic role. Mollusks have so far the most similar proteins to Trks (Lymnaea Trk and Aplysia Trkl) but the exact phylogenetic relationship of mollusk Trks to each other and to vertebrate Trks is unknown. p75NTR belongs to the tumor necrosis factor receptor (TNFR) superfamily. The divergence of the TNFR families in vertebrates has been suggested to parallel the emergence of the adaptive immune system. Only one TNFR representative, the Drosophila Wengen, has been found in protostomes. To clarify the evolution of neurotrophin signaling components in bilateria, this work analyzes the genome of the crustacean Daphnia pulex as well as new genetic data from protostomes.

Results

The Daphnia genome encodes a neurotrophin, p75NTR and Trk orthologue together with Trkl, ROR, and NRK-RTKs. Drosophila Spz1, 2, 3, 5, 6 orthologues as well as two new groups of Spz proteins (Spz7 and 8) are also found in the Daphnia genome. Searching genbank and the genomes of Capitella, Helobdella and Lottia reveals neurotrophin signaling components in other protostomes.

Conclusion

It appears that a neurotrophin, Trk and p75NTR existed at the protostome/deuterostome split. In protostomes, a "neurotrophin superfamily" includes Spzs and neurotrophins which respectively form two paralogous families. Trks and Trkl proteins also form closely related paralogous families within the protostomian RTKs, whereby Trkls are absent in deuterostomes. The finding of p75NTR in several protostomes suggests that death domain TNFR superfamily proteins appeared early in evolution.     

Phenotypic reversion in fas mutants of Arabidopsis thaliana by reintroduction of FAS genes: variable recovery of telomeres with major spatial rearrangements and transcriptional reprogramming of 45S rDNA genes

Arabidopsis thaliana mutants dysfunctional in the evolutionarily conserved protein complex chromatin assembly factor‐1 (CAF‐1), which deposits the canonical histone H3 variant H3.1 during DNA synthesis‐dependent chromatin assembly, display complex phenotypic changes including meristem and growth alterations, sensitivity to DNA‐damaging agents, and reduced fertility. We reported previously that mutants in the FAS1 subunit of CAF‐1 progressively lose telomere and 45S rDNA repeats. Here we show that multiple aspects of the fas phenotype are recovered immediately on expression of a reintroduced FAS1 allele, and are clearly independent of the recovery of rDNA copy‐numbers and telomeres. In reverted lines, 45S rDNA genes are recovered to diverse levels with a strikingly different representation of their variants, and the typical association of nucleolar organizing region 4 with the nucleolus is perturbed. One of 45S rDNA variants (VAR1), which is silenced in wild‐type (WT) plants without mutation history (Col‐0 WT), dominates the expression pattern, whereas VAR2 is dominant in Col‐0 WT plants. We propose an explanation for the variability of telomere and 45S rDNA repeats associated with CAF‐1 function, suggesting that the differences in nuclear partitioning and expression of the rDNA variants in fas mutants and their revertants provide a useful experimental system to study genetic and epigenetic factors in gene dosage compensation.     

Effects of intensity and seasonal timing of disturbances on a rocky intertidal benthic community on the southern coast of Korea

The effects of intensity and timing of disturbances on recovery of marine benthic organisms were investigated on a rocky intertidal shore in Gwangyang Bay, Korea. We hypothesized that the recovery pattern of the benthic community structure would be affected by disturbance intensity and season. Twenty-eight permanent plots were set up, with disturbance intensity (cleared plots and sterile plots) and seasonal disturbance (fall 1999 and spring 2000) incorporated into the experimental design. To monitor natural seasonal variation in benthic community abundances, we established seven permanent unmanipulated plots. Turf-forming algae were observed in the unmanipulated plots throughout the experimental period, whereas green algae and invertebrate presence varied with season. In the disturbance-intensity experiment, turf-forming and green algae were dominant in cleared plots. The highest coverage of sessile organisms was observed in sterile plots, which exhibited the highest species richness because of their relatively low macroalgal coverage. Seasonal effects of disturbance were an important factor in the recovery pattern of benthic organisms under high disturbance intensity. Coverage of green algae was higher in sterile spring plots than in sterile fall plots; this result was attributed to low spatial competition, as the disturbances occurred just before green algal blooms. On the other hand, the abundances of barnacles and bivalves were highest on sterile fall plots, as these organisms were suppressed by green algal blooms in other periods. These results indicate that the effects of disturbance intensity on benthic community recovery patterns can be influenced by season of disturbance.     

Sequence similarities of protein kinase substrates and inhibitors with immunoglobulins and model immunoglobulin homologue: Cell adhesion molecule from the living fossil sponge<Emphasis Type="Italic">Geodia cydonium</Emphasis>. Mapping of coherent database similarities and implications for evolution of CDR1 and hypermutation

Sequences of immunoglobulin (Ig) domains of adhesive molecule GSAMS from the living fossil spongeGeodia cydonium were compared with the important motif of peptide protein kinase substrates and inhibitors (PKSI), detail PKSI sequences, and a common template sequence, derived from structures determined previously. We found the site-restricted sequence similarities to these peptide sequences predominantly in the GSAM Ig1 domain of GSAMS in the domain region related to corresponding Ig similarities detected earlier. Additional sequence block-related analysis revealed the presence of CDR1-like segments within PKSI-related regions and resulted in the detection of increased numbers of hypermutation motifs just in the CDR1-like segment of GSAM Ig1 (GSAM(cdr1.1)). In the following database searches with PKSI-related regions and GSAM(cdr1.1) we looked for: (i) peptide similarities present in the context of Ig domains or related structures in a large range of species fromArchaea toVertebrata, and (ii) some special nucleotide similarities. This study was supported by grant ofInternal Grant Agency of the Ministry of Public Health of the Czech Republic no. 6747-3.     

The expression of neurotrophins and their receptors in the prenatal and adult human testis: evidence for functions in Leydig cells

Previous studies have demonstrated local functions for neurotrophins in the developing and mature testis of rodents. To examine whether these signaling molecules are present and also potentially active in the human testis, we characterized immunohistochemically the expression and cellular localization of the known neurotrophins and their receptors during prenatal testicular development as well as in the adult human testis. Results obtained revealed the presence of nerve growth factor (NGF), brain-derived neurotrophic factor, neurotrophin-3 and 4, as well as neurotrophin receptors p75^NTR, TrkA, TrkB, and TrkC during testis morphogenesis. These proteins were also detectable in the adult human testis, and their local expression could be confirmed largely by immunoblot and RT-PCR analyses. Remarkably, the Leydig cells were found to represent the predominant neurotrophin/receptor expression sites within both fetal and adult human testes. Functional assays performed with a mouse tumor Leydig cell line revealed that NGF exposure increases cellular steroid production, indicating a role in differentiation processes. These findings support previously-recognized neuronal characteristics of Leydig cells, provide additional evidence for potential roles of neurotrophins during testis morphogenesis and in the mature testis, and demonstrate for the first time a neurotrophin-induced functional activity in Leydig cells.     

Biosensor for the monitoring of hydrogen peroxide using poly(vinyl alcohol) membrane system

Summary A biosensor system for continuous on-line monitoring of hydrogen peroxide concentration was developed employing catalase and a poly(vinyl alcohol)/poly(tetra fluoro ethylene) bilayer membrane system, Catalase was entrapped between poly(vinyl alcohol) membrane layer and poly(tetra fluoro ethylene) membrane layer outside of the galvanic type DO probe. Since poly(vinyl alcohol) membrane has non-porous, hydrophilic characteristics, the difference in hydrogen peroxide concentration between inside and outside of the membrane was therefore approximately 100 times. The developed hydrogen peroxide sensor has a wide linear range of hydrogen peroxide sensing more than 140 mM and favourable dynamic response characteristics. The sensor showed also good operational stability, rapid response time, and long life time.     

Combination of honokiol and magnolol inhibits hepatic steatosis through AMPK-SREBP-1?c pathway

Honokiol and magnolol, as pharmacological biphenolic compounds of Magnolia officinalis, have been reported to have antioxidant and anti-inflammatory properties. Sterol regulatory element binding protein-1 c (SREBP-1 c) plays an important role in the development and processing of steatosis in the liver. In the present study, we investigated the effects of a combination of honokiol and magnolol on SREBP-1 c-dependent lipogenesis in hepatocytes as well as in mice with fatty liver due to consumption of high-fat diet (HFD). Liver X receptor α (LXRα) agonists induced activation of SREBP-1 c and expression of lipogenic genes, which were blocked by co-treatment of honokiol and magnolol (HM). Moreover, a combination of HM potently increased mRNA of fatty acid oxidation genes. HM induced AMP-activated protein kinase (AMPK), an inhibitory kinase of the LXRα-SREBP-1 c pathway. The role of AMPK activation induced by HM was confirmed using an inhibitor of AMPK, Compound C, which reversed the ability of HM to both inhibit SREBP-1 c induction as well as induce genes for fatty acid oxidation. In mice, HM administration for four weeks ameliorated HFD-induced hepatic steatosis and liver dysfunction, as indicated by plasma parameters and Oil Red O staining. Taken together, our results demonstrated that a combination of HM has beneficial effects on inhibition of fatty liver and SREBP-1 c-mediated hepatic lipogenesis, and these events may be mediated by AMPK activation.     

Arachidonic acid activates tissue transglutaminase and stress fiber formation via intracellular reactive oxygen species

We have investigated whether arachidonic acid could regulate tissue transglutaminase (tTGase) via intracellular reactive oxygen species (ROS) in NIH3T3 cells. tTGase was identified in NIH3T3 cells by Western blot and confocal microscopy. Arachidonic acid elevated in situ tTGase activity in dose- and time-dependent manners with a maximal level at 1h, and ROS scavengers, N-(2-mercaptopropionyl)glycine and catalase, blocked the tTGase activation by arachidonic acid. The activation of tTGase by arachidonic acid was largely inhibited by transfection of tTGase siRNA. The role of intracellular ROS in the activation of in situ tTGase was supported by the activation of in situ tTGase by exogenous H(2)O(2). Arachidonic acid stimulated the formation of stress fibers in a dose- and time-dependent manner, and the ROS scavengers suppressed the arachidonic acid-induced formation of stress fibers. These results suggested that the activation of in situ tTGase and stress fiber formation by arachidonic acid was mediated by intracellular ROS in NIH3T3 cells.     

Loss of nutrients due to litter raking compared to the effect of acidic deposition in two spruce stands, Czech Republic

We evaluated how litter raking removed basic nutrients from forest soils by simulating this historical silvicultural practice on two spruce stands (Picea abies) in the Czech Republic. Experimental litter raking depleted the soil pool of exchangeable base cation nutrients (Ca²⁺, Mg²⁺ and K⁺) by up to 31% after the first litter raking in 2003. A second litter raking in the following year further reduced the soil pool by up to 16%, and the third litter raking in 2005 reduced the pool by up to 6% more. These losses of base cations were substantially greater than their annual input into the forest soil (estimated as from total atmospheric deposition and mineral weathering) as well as their annual runoff. The concentration of Mg and Ca in spruce needless decreased considerably within 3 years from the beginning of the experiment. In addition, the observed litter chemistry was used to estimate historical nutrient removal from litter raking by applying them to historical records of litter removal rates. According to these calculations, the annual loss of total Ca, Mg and K from spruce stands would be from 40% to 100% of its present annual input into the soil, and from 50% to 190% of annual runoff. On the basis of previous results estimated by geochemical modeling, we found that the loss of base cations due to litter raking was similar to their leaching due to acid deposition. We conclude that long-term removal of litter as widely practiced throughout the 19th century in Central Europe may have been responsible for a loss of base cations equivalent to that caused by acid deposition during the 20th century.     

Reproduction of wild birds via interspecies germ cell transplantation

The present study was conducted to apply an interspecies germ cell transfer technique to wild bird reproduction. Pheasant (Phasianus colchicus) primordial germ cells (PGCs) retrieved from the gonads of 7-day-old embryos were transferred to the bloodstream of 2.5-day-old chicken (Gallus gallus) embryos. Pheasant-to-chicken germline chimeras hatched from the recipient embryos, and 10 pheasants were derived from testcross reproduction of the male chimeras with female pheasants. Gonadal migration of the transferred PGCs, their involvement in spermatogenesis, and production of chimeric semen were confirmed. The phenotype of pheasant progenies derived from the interspecies transfer was identical to that of wild pheasants. The average efficiency of reproduction estimated from the percentage of pheasants to total progenies was 17.5%. In conclusion, interspecies germ cell transfer into a developing embryo can be used for wild bird reproduction, and this reproductive technology may be applicable in conserving endangered bird species.