Studying Annelida Regeneration in a Novel Model Organism: The Freshwater Aeolosoma viride.

Aeolosoma viride, a globally distributed freshwater annelid, has a semitransparent appearance with 10 to 12 segments, about 2 to 3 mm in length. It is easy to raise and handle in laboratory conditions. Due to its robust regenerative capacity and applicability of various molecular tools including EdU labeling, whole-mount in situ hybridization (WISH), and RNA interference (RNAi), it rises as a promising model for studying whole-body regeneration.

Monitoring Telomere Maintenance During Regeneration of Annelids.

Telomere shortening is a hallmark of aging and eventually constrains the proliferative capacity of cells. The protocols discussed here are used for monitoring telomeres comprehensively in Aeolosoma viride, a model system for regeneration studies. We present methods for analyzing the activity of telomerase enzyme in regenerating tissue by telomeric repeat amplification protocol (TRAP) assay, for comparing telomere length between existing tissue and newly regenerated tissue by telomere restriction fragment (TRF) assay, as well as for visualizing telomeres by fluorescence in situ hybridization (FISH).

Caspase dependent apoptosis is required for anterior regeneration in Aeolosoma viride and its related gene expressions are regulated by the Wnt signaling pathway.

Although apoptosis has been widely observed during the regenerative process, the mechanisms by which it is regulated and its roles in regeneration remained unclear. In this study, we introduced Aeolosoma viride, a fresh water annelid with an extraordinary regenerative ability as our model organism to study the functions and regulations of apoptotic caspases. Here we showed that major events of apoptosis were detected near the wounded area and showed spatial correlation with the expression patterns of caspase gene namely Avi-caspase X and two apoptosis regulators namely Avi-Bax and Avi-Bcl-xL. Next, we investigated how Avi-caspase X gene expression and apoptosis influence regeneration following head amputation. RNA interference of Avi-caspase X reduced the amounts of apoptotic cells, as well as the percentage of successful regeneration, suggesting a critical role for apoptosis in anterior regeneration of A. viride. In addition, we also discovered that the expression of apoptotic caspases was regulated by the canonical Wnt signaling pathway. Together, our study showed that caspase dependent apoptosis was critical to the anterior regeneration of A. viride, and could be regulated by the canonical Wnt signaling pathway.

Telomere maintenance during anterior regeneration and aging in the freshwater annelid Aeolosoma viride.

Aging is a complex process involving declines in various cellular and physical functionalities, including regenerative ability. Telomere maintenance is thought to be necessary for regeneration, and telomere attrition is one mechanism that contributes to aging. However, it is unclear if aging affects regeneration owing to deterioration of telomeric maintenance. We introduce Aeolosoma viride-a freshwater annelid with strong regenerative abilities-as a new model for studying the effects of aging on telomere functions and regeneration. We show that the anterior regenerative ability of A. viride declines with age. We characterized the A. viride telomere sequence as being composed of TTAGGG repeats and identifyied the telomerase gene Avi-tert. In adult A. viride, telomerase was constantly active and telomere lengths were similar among different body sections and stably maintained with age. Notably, we found that regeneration did not result in telomere shortening at regenerating sites. Moreover, transient up-regulation of Avi-tert expression and telomerase activity was observed at regenerating sites, which might promote telomere lengthening to counteract telomere erosion resulting from cell proliferation. Our study suggests that although aging affects A. viride regeneration independent of steady-state telomere length, timely regulation of telomerase functions is critical for the regeneration process in A. viride.

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.

BACKGROUND: The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. RESULTS: In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. CONCLUSIONS: Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.

New species of earthworms belonging to the Metaphire formosae species group (Clitellata: Megascolecidae) in Taiwan.

The Metaphire formosae species group is a member of the Pheretima complex of the family Megascolecidae. It is composed of 12 nominal taxa, Metaphire bununa Tsai et al., 2000, Metaphire feijani Chang & Chen, 2004, Metaphire formosae (Michaelsen, 1922), Metaphire glareosa Tsai et al., 2000, Metaphire nanaoensis Chang & Chen, 2005, Metaphire paiwanna paiwanna Tsai et al., 2000, Metaphire paiwanna hengchunensis (James et al., 2005), Metaphire paiwanna liliumfordi Tsai et al., 2000, Metaphire tahanmonta Chang & Chen, 2005, Metaphire taiwanensis Tsai et al., 2004, Metaphire trutina Tsai et al., 2003, and Metaphire yuhsi (Tsai, 1964). In this study, we describe a new species, Metaphire tengjhihensis sp. nov., and two new subspecies, Metaphire nanaoensis truku ssp. nov. and Metaphire taiwanensis tsaii ssp. nov., belonging to this species group. DNA barcodes (partial sequences of the mitochondrial cytochrome c oxidase subunit 1, COI) from type specimens of M. feijani, M. tengjhihensis sp. nov., M. nanaoensis truku ssp. nov., M. tahanmonta and M. taiwanensis tsaii ssp. nov. have been deposited in GenBank in previous studies and are explicitly linked to the type specimens for the first time, enabling unambiguous identification using both morphology and DNA barcodes. Finally, we comment on the systematics of the M. formosae species group and suggest an integrative taxonomic approach that combines morphology and DNA barcodes for future descriptions of new species of Amynthas and Metaphire.

Lysophosphatidic acid induces reactive oxygen species generation by activating protein kinase C in PC-3 human prostate cancer cells.

Prostate cancer is one of the most frequently diagnosed cancers in males, and PC-3 is a cell model popularly used for investigating the behavior of late stage prostate cancer. Lysophosphatidic acid (LPA) is a lysophospholipid that mediates multiple behaviors in cancer cells, such as proliferation, migration and adhesion. We have previously demonstrated that LPA enhances vascular endothelial growth factor (VEGF)-C expression in PC-3 cells by activating the generation of reactive oxygen species (ROS), which is known to be an important mediator in cancer progression. Using flow cytometry, we showed that LPA triggers ROS generation within 10min and that the generated ROS can be suppressed by pretreatment with the NADPH oxidase (Nox) inhibitor diphenylene iodonium. In addition, transfection with LPA1 and LPA3 siRNA efficiently blocked LPA-induced ROS production, suggesting that both receptors are involved in this pathway. Using specific inhibitors and siRNA, phospholipase C (PLC) and protein kinase C (PKC) were also suggested to participate in LPA-induced ROS generation. Overall, we demonstrated that LPA induces ROS generation in PC-3 prostate cancer cells and this is mediated through the PLC/PKC/Nox pathway.

Four new earthworm species of the genus Amynthas (Oligochaeta: Megascolecidae) from Kinmen, Taiwan.

Four new species of terrestrial earthworms belonging to the genus Amynthas were collected on the islands of Kinmen and Lieyu, Taiwan from March to November, 2008. They are Amynthas kinmenensis sp. nov., Amynthas wuhumontis sp. nov., Amynthas wujhouensis sp. nov., and Amynthas taiwumontis sp. nov. Amynthas kinmenensis sp. nov. is quadrithecal and is the most abundant earthworm widely distributed on the main island of Kinmen. It has numerous small genital papillae and is closely related to Amynthas polyglandularis (Tsai, 1964) from northern Taiwan. Amynthas wuhumontis sp. nov. is sexthecal and is distributed only in areas around Mt. Wuhu and Mt. Taiwu in east Kinmen. It has male pores each surrounded by three genital papillae: one anterior, one posterior and one medial. Amynthas wujhouensis sp. nov. and Amynthas taiwumontis sp. nov. are octothecal. The former has a sporadic distribution in Kinmen while the latter was only found in areas around Mt. Taiwu. Amynthas wujhouensis sp. nov. has a pair of large genital papillae closely adjacent to the crescent or semicircular shaped male porophores in XVIII. Amynthas taiwumontis sp. nov. has simple male pore structure and no genital papillae or genital markings. DNA barcodes (the 5' end sequences of the mitochondrial cytochrome c oxidase subunit 1 gene) from type specimens and other materials of the first three species are also reported.

Photooxidation and antioxidant responses in the earthworm Amynthas gracilis exposed to environmental levels of ultraviolet B radiation.

Ultraviolet (UV) radiation leads to photooxidation in various organisms. Our previous study demonstrated that ultraviolet B (UV-B) radiation is lethal for particular species of earthworms, but the mechanisms responsible for the lethality are unclear. In our current study, we investigated that ultraviolet light causes photooxidative damage and reduces antioxidant responses in the earthworm Amynthas gracilis. Intact earthworms and skin/muscle tissue extracts were exposed to UV-B radiation for in vivo and in vitro studies. Both in vitro and in vivo results showed that the products of photooxidative damage, MDA and H(2)O(2), increased after UV-B exposure. Glutathione peroxidase (GPx) and catalase were inhibited immediately after exposure to high doses (3000J/m(2)) of UV-B radiation in vivo. Catalase activity was increased following a low UV-B dose (500J/m(2)) in vivo, but decreased in response to all dosage levels in vitro. These data indicate that a relationship exists between UV-B induced damage and photooxidation and also that catalase and GPx act as important antioxidants to prevent photooxidation. According to these data, A. gracilis exhibits high sensitivity to environmental levels of UV-B. Therefore, A. gracilis represents a sensitive and cost-effective model organism for investigations of UV-radiation damage and environmental UV stress.

Three species of land leeches from Taiwan, Haemadipsa rjukjuana comb. n., a new record for Haemadipsa picta Moore, and an updated description of Tritetrabdella taiwana (Oka).

Three species of land leeches, including a new combination Haemadipsa rjukjuanacomb. n., a new record for Haemadipsa picta Moore, as well as an updated description for Tritetrabdella taiwana (Oka), are reported in this study. Morphological characters and DNA barcode analysis were used to identify these species. In addition, since Haemadipsa rjukjuana had been regarded as a variety of the Japanese land leech Haemadipsa japonica for a century, morphological differences between these two species were also compared.

Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma.

The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days' incubation. We found that about 50% of Cd (5mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

Cloning, expression, and characterization of cadmium-induced metallothionein-2 from the earthworms Metaphire posthuma and Polypheretima elongata.

In this study we report the sequences of MT-2 cDNA from two species of Megascoleidae earthworms, Metaphire posthuma and Polypheretima elongata, by mRNA differential display after exposure of the organisms to cadmium. Complementary (c)DNA was verified as the MT-2 gene by the characteristics of its predicted translation product, namely a high cysteine content, conserved CXC motifs, and a molecular weight of around 8 kDa. Amino acid sequence alignment revealed a conserved TKCCG in the cloned MT-2 of both megascolecid earthworms instead of the corresponding conserved TQCCG found in lumbricid earthworms. The cDNAs corresponding to the two megascolecid MT-2 genes were expressed, and the MT-2 proteins were purified for biochemical characterization. The binding of Cu2+ exhibited monophasic kinetics and those of Zn2+ and Cd2+ biphasic kinetics. The proteins bound more tightly to Cd2+ than to Zn2+ and more tightly still to Cu2+. Zn-MT and apo-MT were the most effective at scavenging free radicals, followed by Cd-MT. In conclusion, MT-2s from M. posthuma and P. elongata showed unique sequence features compared to those of lumbricid earthworms. These earthworms could be used to evaluate heavy-metal pollution in soil due to the inducible MT-2 by cadmium exposure.

Molecular systematics and phylogeography of the gigantic earthworms of the Metaphire formosae species group (Clitellata, Megascolecidae).

The earthworms of the Metaphire formosae species group distributed in Taiwan are members of the Pheretima complex within the Megascolecidae. In this study, the systematics and phylogeography of this species group were investigated using DNA sequences of mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal (r)RNA, and NADH dehydrogenase subunit 1 (ND1). The results indicated that the 13 taxa of the M. formosae species group form a clade, including a cryptic species discovered in this study. In addition, Metaphire hengchunensis (James, S.W., Shih, H.-T., Chang, H.-W., 2005. Seven new species of Amynthas (Clitellata: Megascolecidae) and new earthworm records from Taiwan. J. Nat. Hist. 39, 1007-1028) should be regarded as a subspecies of Metaphire paiwanna Tsai, C.-F., Shen, H.-P., Tsai, S.-C., 2000a. Native and exotic species of terrestrial earthworm (Oligochaeta) in Taiwan with reference to Northeast Asia. Zool. Stud. 39, 285-294, Tsai, C.-F., Tsai, S.-C., Liaw, G.-J., 2000b. Two new species of pontandric pheretimoid earthworms belonging to the genus Metaphire (Megascolecidae: Oligochaeta) from Taiwan. J. Nat. Hist. 34, 1731-1741, and Metaphire bununa glareosa Tsai et al. 2000 should be elevated to specific status. Phylogeographical inferences showed that allopatric speciation occurred in this species group during the rapid uplift of the main island of Taiwan between 5.0 and 2.5 million years ago. Our analysis exposes non-monophyly within each of the genera Amynthas and Metaphire, and more generally within the Pheretima complex. Further revisions of this speciose complex are urgently needed.

Influence of ultraviolet radiation on selected physiological responses of earthworms.

The purpose of this study was to investigate the adverse effects of ultraviolet (UV) radiation on earthworms. Earthworms that crawl out of the soil may die within a few hours after sunrise. This study shows that UV exposure can be lethal. In general, UV-B had a stronger damaging effect than UV-A. Different species of earthworms had different tolerances to UV exposure. In this study, Pontoscolex corethrurus showed the highest tolerance of the three tested species to UV radiation, while Amynthas gracilis was the most sensitive. UV radiation induced both acute and chronic responses. The acute response, which occurred immediately on or after UV exposure, was characterized by the appearance of abnormally strong muscle contractions, including S-shaped movements and jumping behavior, possibly caused by bad coordination between the circular and longitudinal muscles. The chronic response included damage to the skin and muscle cells, which resulted in a high mortality rate. Oxygen consumption by A. gracilis was significantly decreased after exposure to UV-A or UV-B. Since the circulation in earthworms is mediated by muscle contraction and the skin is the main organ of respiration, it is reasonable to expect that abnormal muscle contraction and a damaged epithelium could cause suffocation. Because of their sensitive responses, we propose that some earthworms, such as A. gracilis, could serve as a new model for studying UV-induced photodamage.

Lysophospholipids increase IL-8 and MCP-1 expressions in human umbilical cord vein endothelial cells through an IL-1-dependent mechanism.

Lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P) are both low-molecular-weight lysophospholipid (LPL) ligands which are recognized by the Edg family of G protein-coupled receptors (GPCRs). In endothelial cells, these two ligands activate Edg receptors resulting in cell proliferation and cell migration. Interleukin-8 (IL-8) is a C-X-C chemokine and acts as a chemoattractant of neutrophils, whereas monocyte chemoattractant protein-1 (MCP-1) is a C-C chemokine and functions mainly as a chemoattractant of monocytes/macrophages. Both factors are secreted from endothelial cells and have been implicated in the processes leading to atherosclerosis. We examined the effects of LPLs on the expression of IL-8 and MCP-1, key regulators of leukocyte recruitment in human umbilical cord vein endothelial cells (HUVECs). Work illustrated in this article showed that LPA and S1P enhanced IL-8 and MCP-1 mRNA expressions, and protein secretions in dose- and time-dependent fashions. Maximal mRNA expression appeared at 16 hr post-ligand treatment. Using prior treatments with chemical inhibitors, LPLs enhanced IL-8 and MCP-1 expressions through a Gi-, Rho-, and NFkappaB-dependent mechanism. In a chemotaxis assay system, LPL treatments of endothelial cells enhanced monocyte recruitment through upregulating IL-8 and MCP-1 protein secretions. Pre-incubation with AF12198, an IL-1 receptor antagonist or IL-1 functional blocking antibody both suppressed the enhanced effects elicited by LPLs of IL-8 and MCP-1 mRNA expressions in HUVECs. These results suggest that LPLs released by activated platelets might enhance the IL-8- and MCP-1-dependent chemoattraction of monocytes toward the endothelium through an IL-1-dependent mechanism, which may play an important role in facilitating wound-healing and inflammation processes.

Lysophospholipids enhance matrix metalloproteinase-2 expression in human endothelial cells.

Lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P) are both low-molecular-weight lysophospholipids, which promote cell proliferation, migration, and invasion via interaction with a family of specific G protein-coupled receptors. Matrix metalloproteinases (MMPs) are zinc-dependent proteolytic enzymes, which are involved in degradation of the extracellular matrix and play critical roles in endothelial cell migration and matrix remodeling during angiogenesis. Among these MMPs, MMP-2 is known to trigger cell migration. In our present study, we examined the effects of LPA and S1P on MMP-2 expression in human endothelial cells. We showed that LPA and S1P enhanced MMP-2 expression in mRNA, protein levels, and also enzymatic activity of cells of the EAhy926 human endothelial cell line. The enhancement effects occurred in concentration- and time-dependent manners. Results from real-time PCR, Western blots, and substrate gels indicated that these enhancement effects were mediated through MAPK kinase/ERK-, nuclear factor-kappaB-, and calcium influx-dependent pathways. Furthermore, we show that endothelial cell invasion of the gel was enhanced by lysophospholipids, and the induction could be prevented by an MMP inhibitor, GM6001. These observations suggest that LPA and S1P may play important roles in endothelial cell invasion by regulating the expression of MMP-2.

Diurnal rhythm and effect of temperature on oxygen consumption in earthworms, Amynthas gracilis and Pontoscolex corethrurus.

Different species of earthworms show distinct patterns of oxygen consumption pattern. Amynthas gracilis has a diurnal rhythm of oxygen consumption, consuming more oxygen at night, whether being incubated at 20, 25, or 30 degrees C. The higher oxygen consumption of A. gracilis is directly related to its behavior, as it shows higher activity at night. In contrast, Pontoscolex corethrurus showed no obvious diurnal rhythms of oxygen consumption or behavior. In addition, its oxygen demand is not related to temperature. A. gracilis has higher oxygen consumption than P. corethrurus at 20 and 30 degrees C. The difference in temperature adaptation of oxygen consumption between these two species may be a strategy by which earthworms adapt to different temperatures. This might explain why A. gracilis disperses on the soil surface at night after a rain, in contrast to P. corethrurus for which such behavior was not been observed.