Comparative Transcriptome Analysis for Understanding Predator-Induced Polyphenism in the Water Flea Daphnia pulex.

The crustacean Daphnia pulex is one of the best model organisms for studying inducible defense mechanisms due to their inducible morphology in response to the predator Chaoborus larvae. In this study, multiple developmental stages of D. pulex were exposed to C. flavicans larvae and transcriptome profiles of samples from late embryo to fifth instar were sequenced by the RNA-seq technique to investigate the genetic background underlying inducible defenses. In comparison, differentially expressed genes between defensive and normal morphs were identified, including 908 genes in late embryo, 1383 genes in the first-third (1⁻3) instar, and 1042 genes in fourth-fifth (4⁻5) instar. Gene ontology enrichment analysis showed that structural constituents of the cuticle and structural molecule activity genes were prominent up-regulated genes in late embryos. Down-regulated genes in late embryos and 1⁻3 instar comprised metabolic process, hydrolase activity, and peptidase activity gene classes. Pathway analysis indicated that small molecule neurotransmitter pathways were potentially involved in the development of inducible defenses. The characterization of genes and pathways in multiple developmental stages can improve our understanding of inducible defense responses of D. pulex to predation at the molecular level.

Complete mitochondrial genome sequence of Heliocidaris crassispina (Camarodonta, Echinometridae).

The whole mitochondrial genome sequence of sea urchin Heliocidaris crassispina of the family Echinometridae is determined for the first time in this study. The circular mitogenome (15,702 bp) consists of typical Camarodonta gene order and its components including 2 rRNA, 22 tRNA, 13 protein-coding genes and a control region. Phylogenetic analysis based on the 13 concatenated protein-coding gene sequences shows that H. crassispina is closer to the species of Strongylocentrotidae than Parechinidae, but the separation between H. crassispina and the Strongylocentrotid species occurred early in their evolution. The complete mitochondrial genome presented in this study is useful for inferring the phylogenetic relationship among the families of Echinidea sea urchins.

Complete mitochondrial genome of Chilean sea urchin: Loxechinus albus (Camarodonta, Parechinidae).

The complete mitochondrial genome of Chilean sea urchin Loxechinus albus, the single species of the genus Loxechinus, is determined. The circular mitogenome is 15,709 bp in length containing 2 rRNA, 22 tRNA and 13 protein coding genes as well as the control region. The gene order is identical to those of described Camarodonta species. There are 24 bp gene overlaps at 6 locations and 124 bp intergenic spacers at 17 boundaries. The nucleotide composition of the genome is 31.2% A, 22.3% C, 29.7% T, and 16.8% G. The A+T bias (60.9%) is similar to that of P. lividus (60.3%) but slightly higher than those of strongylocentrotid species (58.8-59.8%). The mitogenome sequence of L. albus will provide valuable information on the phylogeny and evolution of the genus Loxechinus in relation to other Camarodonta sea urchins.

The complete mitochondrial genome of the marine polychaete: Perinereis aibuhitensis (Phyllodocida, Nereididae).

We determined the complete mitochondrial genome sequence of the marine polychaete Perinereis aibuhitensis (Grube, 1878) (Phyllodocida, Nereididae), a dominant species in the mudflat of the West Pacific and Indian Ocean. The complete genome of P. aibuhitensis is 15,852 bp in size including 13 protein coding genes (PCGs), 2 rRNA and 22 tRNA with the same gene order and structure as those of other Nereididae species. The nucleotide composition is 29.5% A, 21.2% C, 14.1% G, 35.2% T, showing a high content of A+T with G being used least in the third codon position (6.7%). All PCGs use ATG as the start codon while for the stop codon COI and ND1 use incomplete codon of T. The mitogenome sequence of P. aibuhitensis is second to that of P. nuntia known in the genus Perinereis, which will provide useful information for understanding evolutionary history of the genus Perinereis within the family Nereididae.

Neural stem cell-based intraocular administration of ciliary neurotrophic factor attenuates the loss of axotomized ganglion cells in adult mice.

PURPOSE: To analyze the neuroprotective effect of intravitreally grafted neural stem (NS) cells genetically modified to secrete ciliary neurotrophic factor (CNTF) on intraorbitally lesioned retinal ganglion cells (RGCs) in adult mice. METHODS: Adherently cultivated NS cells were genetically modified to express a secretable variant of mouse CNTF together with the fluorescent reporter protein Venus. Clonal CNTF-secreting NS cell lines were established using fluorescence activated cell sorting, and intravitreally grafted into adult mice 1 day after an intraorbital crush of the optic nerve. Brn-3a-positive RGCs were counted in flat-mounted retinas at different postlesion intervals to evaluate the neuroprotective effect of the CNTF-secreting NS cells on the axotomized RGCs. Anterograde axonal tracing experiments were performed to analyze the regrowth of the injured RGC axons in CNTF-treated retinas. RESULTS: Intravitreally grafted NS cells preferentially differentiated into astrocytes that survived in the host eyes, stably expressed CNTF, and significantly attenuated the loss of the axotomized RGCs over a period of at least 4 months, the latest postlesion time point analyzed. Depending on the postlesion interval analyzed, the number of RGCs in eyes with grafted CNTF-secreting NS cells was 2.8-fold to 6.4-fold higher than in eyes with grafted control NS cells. The CNTF-secreting NS cells additionally induced long-distance regrowth of the lesioned RGC axons. CONCLUSIONS: Genetically modified clonal NS cell lines may serve as a useful tool for preclinical studies aimed at evaluating the therapeutic potential of a sustained cell-based intravitreal administration of neuroprotective factors in mouse models of glaucoma.

Complete mitochondrial genome of sea urchin: Hemicentrotus pulcherrimus (Camarodonta, Strongylocentrotidae).

The complete mitochondrial genome of sea urchin Hemicentrotus pulcherrimus (A. Agassiz, 1863) is determined. The genome is a circular molecule of 15,705 bp in length and the gene content and order are identical to those of other strongylocentrotid species. Lengths of all protein coding genes (PCGs) are identical to those of M. nudus. S. droebachiensis and S. pallidus but ND6 has a deletion of 3 amino acids at the C-terminal. The nucleotide composition of the genome shows a bias toward A + T (59.8%) and the A + T bias in PCGs (59.4%) is slightly higher than the other strongylocentrotid species. The mitogenome of H. pulcherrimus provides genomic information of the single species genus, Hemicentrotus and helps understand the genetic relationship and the evolution of the genus in relation to the other genera of the family Strongylocentrotidae.

Nonneuronal control of the differential distribution of myelin along retinal ganglion cell axons in the mouse.

PURPOSE: In most mammalian species, retinal ganglion cell (RGC) axons are myelinated in the optic nerve, but remain nonmyelinated in the retinal nerve fiber layer and the most proximal (i.e., retina-near) region of the nerve. Here we analyzed whether RGCs are involved in the control of this characteristic distribution of oligodendrocytes and myelin in the primary visual pathway of mice. METHODS: Neurospheres were enriched in oligodendrocyte progenitor cells (OPCs) by a short-term exposure to platelet-derived growth factor (PDGF) and grafted into the retina of young postnatal mice close to the optic disc. Immunohistochemistry was performed to study the integration and differentiation of the grafted cells, and the formation of donor-derived myelin in the normally nonmyelinated retinal nerve fiber layer and intrabulbar and most proximal retrobulbar region of the optic nerve. RESULTS: Intraretinal transplantations of small-sized PDGF-treated neurospheres into young postnatal mice resulted in extensive integration of the grafted cells into host retinas. A significant fraction of the donor cells differentiated into oligodendrocytes that myelinated the nerve fiber layer. Importantly, RGC axon segments within the normally nonmyelinated intrabulbar and most proximal retrobulbar region of the nerve also became myelinated in a fraction of animals. CONCLUSIONS: This is the first report demonstrating that the normally nonmyelinated intrabulbar and retrobulbar segments of RGC axons are competent to become myelinated. Results support the view that the differential distribution of myelin and oligodendrocytes in the primary visual pathway is controlled by nonneuronal factors rather than by the RGCs themselves.

Genetically modified neural stem cells for a local and sustained delivery of neuroprotective factors to the dystrophic mouse retina.

A continuous intraocular delivery of neurotrophic factors (NFs) is being explored as a strategy to rescue photoreceptor cells and visual functions in degenerative retinal disorders that are currently untreatable. To establish a cell-based intraocular delivery system for a sustained administration of NFs to the dystrophic mouse retina, we used a polycistronic lentiviral vector to genetically modify adherently cultivated murine neural stem (NS) cells. The vector concurrently encoded a gene of interest, a reporter gene, and a resistance gene and thus facilitated the selection, cloning, and in vivo tracking of the modified cells. To evaluate whether modified NS cells permit delivery of functionally relevant quantities of NFs to the dystrophic mouse retina, we expressed a secretable variant of ciliary neurotrophic factor (CNTF) in NS cells and grafted the cells into the vitreous space of Pde6b(rd1) and Pde6b(rd10) mice, two animal models of retinitis pigmentosa. In both mouse lines, grafted cells attached to the retina and lens, where they differentiated into astrocytes and some neurons. Adverse effects of the transplanted cells on the morphology of host retinas were not observed. Importantly, the CNTF-secreting NS cells significantly attenuated photoreceptor degeneration in both mutant mouse lines. The neuroprotective effect was significantly more pronounced when clonally derived NS cell lines selected for high expression levels of CNTF were grafted into Pde6b(rd1) mice. Intravitreal transplantations of modified NS cells may thus represent a useful method for preclinical studies aimed at evaluating the therapeutic potential of a cell-based intraocular delivery of NFs in mouse models of photoreceptor degeneration.

Complete mitochondrial genome of sea urchin: Mesocentrotus nudus (Strongylocentrotidae, Echinoida).

The complete nucleotide of mitochondrial DNA of a sea urchin Mesocentrotus nudus was determined for the first time. It is 15,709 bp in length, containing 2 rRNA, 22 tRNA and 13 protein-coding genes generally found in other echinoderm species. The gene order and structure of the genome are identical to those of other Strongylocentrotidae species. The genome was composed of 29.3% A, 23.4% C, 29.5% T and 17.8% G, showing a slight AT bias (58.8%). The G is the least used base and markedly lower at the third codon position (12.74%). Twelve of the 13 mitochondrial protein-coding genes use ATG as their start codon while the ATP8 gene starts with GTG. The control region is 125 bp in length and contains a G-stretch of 19 nucleotides, a typical DNA structure of the echinoid mitochondrial genomes.