Investigating alternative life history trajectories in two species of Edwardsiid sea anemones using ecological, transcriptomic, and molecular approaches

Life histories unfold within the ecological context of an organism's environment, and thus are intimately linked to organismal fitness. The evolution of alternate life history strategies, either within or between taxa, can profoundly affect ontogeny, ecology, and population dynamics. Many cnidarians (sea anemones, corals, jellyfish, etc.) exhibit complex life histories involving sexual reproduction and multiple modes of asexual reproduction. Sea anemones of the family Edwardsiidae exemplify this complexity, and are therefore an attractive system for studying the developmental and ecological ramifications of life history evolution. I used intra- and interspecific comparisons of two Edwardsiid anemones, Edwardsiella lineata, and Nematostella vectensis to investigate alternative life histories using a multifaceted approach that included field-based ecological surveys, functional genetics, transcriptomics, and phylogenetics. Both anemones are capable of sexual and asexual reproduction. N. vectensis produces a rapidly maturing direct developing larva. By contrast, E. lineata has evolved a new larval stage that parasitizes the ctenophore, Mnemiopsis leidyi. Through fieldwork surveys and laboratory culture, I documented several life history traits, such as a previously un-characterized, pre-parasitic larval stage, and the developmental dynamics of early-stage parasitic infections, that augmented gaps in our knowledge of E. lineata's life history. To better understand how and when E. lineata evolved its novel, parasitic life history, I worked with collaborators in the Finnerty lab to sequence, assemble and annotate the transcriptome. Through a multigene molecular clock approach, enabled by the E. lineata transcriptome assembly, I estimated the divergence date for these two anemones between 215-364 million years ago, thereby establishing an upper bound for the innovation of E. lineata's derived, parasitic life history. Testing a hypothesis that Wnt signaling, which patterns the oral-aboral (OA) axis during embryogenesis, also patterns the OA axis during regeneration, I demonstrated that canonical Wnt signaling is sufficient for oral tissue fate across alternate life histories (embryogenesis and regeneration) of N. vectensis. Taken together, these dissertation research activities constitute an integrative approach to investigating the evolution of life histories, and are a step towards establishing E. lineata and N. vectensis as models for studying the evolutionary developmental mechanisms of parasitism and regeneration

Human Bone Marrow Stromal Cells Display Variable Anatomic Site-Dependent Response and Recovery From Irradiation

Objectives Orofacial bone is commonly affected by osteoradionecrosis (ORN) during head and neck cancer radiotherapy possibly due to interactions of several factors including radiation damage to resident bone marrow stromal cells (BMSCs). Irradiation causes DNA damage, triggers p53-dependent signalling resulting in either cell-cycle arrest or apoptosis. In same individuals, disproportionately higher rapid growth of orofacial BMSCs relative to those of axial/appendicular bones suggests their response to radiation is skeletally site-specific. We hypothesised that survival and osteogenic recovery capacity of irradiated human BMSCs is site-dependent based on anatomic skeletal site of origin. Methods Early passage BMSCs from maxilla, mandible and iliac crest of four normal volunteers were exposed to 2.5 to 10 Gy gamma radiation to evaluate clonogenic survival, effects on cell cycle, DNA damage, p53-related response and in vivo osteogenic regenerative capacity. Results Orofacial bone marrow stromal cells (OF-MSCs) survived higher radiation doses and recovered quicker than iliac crest (IC-MSCs) based on clonogenic survival, proliferation and accumulation in G0G1 phase. Post-irradiation p53 level was relatively unchanged but expression of p21, a downstream effector was moderately increased in OF-MSCs. Re-establishment of in vivo bone regeneration was delayed more in irradiated IC-MSCs relative to OF-MSCs. Conclusions Effect of irradiation on human BMSCs was skeletal site-specific with OF-MSCs displaying higher radio-resistance and quicker recovery than IC-MSCs

Comparative Osteogenesis of Maxilla and Iliac Crest Human Bone Marrow Stromal Cells Attached to Oxidized Titanium - a Pilot Study

Objectives Severe alveolar bone loss affects dental implant placement. Bone augmentation by grafting iliac crest bone rich in osteoprogenitor cells like bone marrow stromal cells (BMSCs) requires a second surgical procedure in non-orofacial bone. Skeletal site-specific osteogenesis indicates maxilla and mandible BMSCs are highly proliferative and exhibit osteogenic properties superior to iliac crest BMSCs. Alveolar bone can be easily obtained during routine dental surgery, but it is unclear if titanium-attached alveolar BMSCs will retain their superior osteogenic properties. This study evaluated and compared in vitro osteogenic properties of titanium-attached maxilla and iliac crest BMSCs in same individuals. Materials and Methods Primary culture of maxilla and iliac crest BMSCs from four normal healthy volunteers were expanded in culture. In 24-well plates, first passage BMSCs were seeded directly (1 × 104 cells/well) on oxidized titanium discs (1.27cm diameter and 2mm thickness) or tissue culture plate. Each cell type was assessed for affinity for titanium, post-attachment survival and osteogenic differentiation based on alkaline phosphatase and osteopontin expressions. Results There was no difference in the affinity of maxilla and iliac crest BMSCs to titanium. However, titanium-attached maxilla BMSCs were apparently more osteogenically responsive than iliac crest cells based on calcium accumulation and gene expression of alkaline phosphatase and osteopontin. But these differences were not statistically significant in this small patient sample. Conclusion Maxilla and iliac crest BMSCs have similar attachment affinity for titanium. This pilot study indicate that titanium-attached maxilla BMSCs were more osteogenically responsive and may be a viable and more readily available donor graft material in implant dentistry

Differentiation and Regenerative Capacities of Human Odontoma-Derived Mesenchymal Cells

Regenerating human tooth ex vivo and biological repair of dental caries are hampered by non-viable odontogenic stem cells that can regenerate different tooth components. Odontoma is a developmental dental anomaly that may contain putative post-natal stem cells with the ability to differentiate and regenerate in vivo new dental structures that may include enamel, dentin, cementum and pulp tissues. We evaluated odontoma tissues from 14 patients and further isolated and characterized human odontoma-derived mesenchymal cells (HODCs) with neural stem cell and hard tissue regenerative properties from a group of complex odontoma from 1 of 14 patients. Complex odontoma was more common (9 of 14) than compound type and females (9 of 14) were more affected than males in our set of patients. HODCs were highly proliferative like dental pulp stem cells (DPSCs) but demonstrated stronger neural immunophenotype than both DPSCs and mandible bone marrow stromal cells (BMSCs) by expressing higher levels of nestin, Sox 2 and βIII-tubulin. When transplanted with hydroxyapatite/tricalcium phosphate into immunocompromised mice, HODCs differentiated and regenerated calcified hard tissues in vivo that were morphologically and quantitatively comparable to those generated by DPSCs and BMSCs. When transplanted with polycaprolactone (biodegradable carrier), HODCs differentiated to form new predentin on the surface of a dentin platform. Newly formed predentin contained numerous distinct dentinal tubules and an apparent dentin-pulp arrangement. HODCs represent unique odontogenic progenitors that readily commit to formation of dental hard tissues

Kepler-16: A Transiting Circumbinary Planet

We report the detection of a planet whose orbit surrounds a pair of low-mass stars. Data from the Kepler spacecraft reveal transits of the planet across both stars, in addition to the mutual eclipses of the stars, giving precise constraints on the absolute dimensions of all three bodies. The planet is comparable to Saturn in mass and size, and is on a nearly circular 229-day orbit around its two parent stars. The eclipsing stars are 20% and 69% as massive as the sun, and have an eccentric 41-day orbit. The motions of all three bodies are confined to within 0.5 degree of a single plane, suggesting that the planet formed within a circumbinary disk.Comment: Science, in press; for supplemental material see http://www.sciencemag.org/content/suppl/2011/09/14/333.6049.1602.DC1/1210923.Doyle.SOM.pd

Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons.

Olfactory sensory neurons choose to express a single odorant receptor (OR) from a large gene repertoire and extend axons to reproducible, OR-specific locations within the olfactory bulb. This developmental process produces a topographically organized map of odorant experience in the brain. The axon guidance mechanisms that generate this pattern of connectivity, as well as those that coordinate OR choice and axonal guidance receptor expression, are incompletely understood. We applied the powerful approach of single-cell RNA-seq on newly born olfactory sensory neurons (OSNs) in young zebrafish larvae to address these issues. Expression profiles were generated for 56 individual Olfactory Marker Protein (OMP) positive sensory neurons by single-cell (SC) RNA-seq. We show that just as in mouse OSNs, mature zebrafish OSNs typically express a single predominant OR transcript. Our previous work suggests that OSN targeting is related to the OR clade from which a sensory neuron chooses to express its odorant receptor. We categorized each of the mature cells based on the clade of their predominantly expressed OR. Transcripts expressed at higher levels in each of three clade-related categories were identified using Penalized Linear Discriminant Analysis (PLDA). A genome-wide approach was used to identify membrane-associated proteins that are most likely to have guidance-related activity. We found that OSNs that choose to express an OR from a particular clade also express specific subsets of potential axon guidance genes and transcription factors. We validated our identification of candidate axon guidance genes for one clade of OSNs using bulk RNA-seq from a subset of transgene-labeled neurons that project to a single protoglomerulus. The differential expression patterns of selected candidate guidance genes were confirmed using fluorescent in situ hybridization. Most importantly, we observed axonal mistargeting in knockouts of three candidate axonal guidance genes identified in this analysis: nrp1a, nrp1b, and robo2. In each case, targeting errors were detected in the subset of axons that normally express these transcripts at high levels, and not in the axons that express them at low levels. Our findings demonstrate that specific, functional, axonal guidance related genes are expressed in subsets of OSNs that that can be categorized by their patterns of OR expression

Confirmation of differential gene expression using dual fluorescent <i>in situ</i> hybridization.

<p>(A) Dual-FISH of <i>nrp1a</i> with an <i>or111</i> sub-family probe cocktail. Two cells have been highlighted to show that <i>nrp1a</i> signal (red) is localized in cells with <i>or111</i> subfamily labelling (green). (B) Summary of dual-FISH expression for four candidate guidance receptors. The percentage of OSNs expressing the indicated OR subfamily that also expressed the indicated candidate guidance transcript are noted. The total number of OR subfamily expressing cells counted are shown in parentheses. Pink shading indicates transcripts that showed higher overlap with the <i>or111</i> sub-family probe-mix and green shading indicates transcripts that showed higher overlap with <i>or133</i> sub-family probe mix. <i>nrp1a</i> shows greater overlap with <i>or111</i> subfamily expression than with <i>or133</i> subfamily expression. <i>nrp1b</i>, <i>pcdh11</i>, and <i>robo2</i> show greater overlap with <i>or133</i> subfamily expression than with <i>or111</i> subfamily expression.</p

OR clade choice is related to the expression of distinct guidance gene transcripts.

<p>(A) PLDA using a ‘membrane-associated’ subset of transcripts selected using TargetP. OSNs can be discriminated into three distinct clusters along the two extracted determinants. (B, C) Distribution of the V1 and V2 loading values for 343 genes shows the top candidate plasma membrane associated or secreted transcripts (red dots) that contribute towards OSN discrimination. Top genes that have not been shaded in red localize to intracellular compartments like the endoplasmic reticulum, Golgi complex or lysosomes and hence are not likely to place a direct role in axon guidance. (D) Heatmap of normalized expression values of top 47 candidate guidance related transcripts. Red, blue, and green boxes indicate higher expression of genes in single OSNs expressing ORs from clade A, B or C, respectively. Genes at the bottom are expressed in more than one clade of OSNs and are not boxed.</p

Isolation of single OSNs and identification of mature cells expressing a single predominant OR.

<p>(A) Method of isolation of single OSNs. Transgenic zebrafish embryos expressing OMP:RFP were raised to 48hpf. Olfactory epithelia were dissected and dissociated to obtain single-cell suspensions. OMP:RFP expressing neurons were enriched using FACS and loaded onto a Fluidigm C1 microfluidics chip to isolate single cells in singe wells. cDNA synthesis and amplification were carried out directly on the chip. Samples with high yields of cDNA and smooth distributions of RNA lengths were processed though Nextera library prep and Illumina sequencing. (B) A heatmap of normalized marker gene values for 47 single OSN transcriptomes. 5 cells were enriched in markers of progenitor and/or early mature stages (shaded in black on top bar). 42 cells showed strong expression of mature OSN marker genes and low expression of progenitor/earlier mature genes. High OR expression levels (second bar:cyan) were detected in 29 of these mature cells (shaded in magenta on top bar). Three color keys are shown at the bottom: the first pertains to cell age inferred in the topmost bar, the second pertains to log10 values of normalized (predominant) OR expression, and the third relates to log10 values of normalized developmental gene expression.</p