Danielle M DeLeoSmithsonian Institution · National Museum of Natural History
Danielle M DeLeo
Doctor of Philosophy
About
25
Publications
31,249
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Introduction
Danielle DeLeo currently works at the Smithsonian's National Museum of Natural History in the the Department of Invertebrate Zoology. Danielle does research in Marine and Deep-sea Biology using next-generation sequencing technology and bioinformatic tools.
Additional affiliations
January 2017 - present
Position
- PhD Student
Description
- Investigating the evolution of deep-sea bioluminescence in crustaceans
August 2012 - August 2014
August 2012 - December 2016
Education
August 2012 - December 2016
August 2006 - August 2011
Publications
Publications (25)
Bioluminescence is a widespread phenomenon that has evolved multiple times across the tree of life, converging among diverse fauna and habitat types. The ubiquity of bioluminescence, particularly in marine environments where it is commonly used for communication and defense, highlights the adaptive value of this trait, though the evolutionary origi...
Many marine species can regulate the intensity of bioluminescence from their ventral photophores in order to counterilluminate, a camouflage technique whereby animals closely match the intensity of the downwelling illumination blocked by their bodies, thereby hiding their silhouettes. Recent studies on autogenic cuticular photophores in deep-sea sh...
Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcr...
Corals are a dominant benthic fauna that occur across a vast range of depths from just below the ocean’s surface to the abyssopelagic zone. However, little is known about the evolutionary mechanisms that enable them to inhabit such a wide range of environments. The mitochondrial (mt) genome, which is involved in energetic pathways, may be subject t...
Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcr...
Deep-sea shrimp of the family Sergestidae Dana, 1852 provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores; non-lensed photophores; or internal organs of Pesta. This morphological diversity across the Serge...
Evolutionary processes that generate diversity in the deep sea remain poorly understood, though it has been hypothesised that environmental factors, including depth, serve as strong
selective pressures driving adaptation and speciation in the deep sea. Octocorals (Anthozoa: Octocorallia) are common residents of deep-sea ecosystems, yet little is kn...
Resource extraction from the ocean comes with ecosystem-wide risks, including threats to its biota such as the habitat forming corals that support elevated biomass and biodiversity. Despite catastrophic incidents like the Deepwater Horizon oil spill (DWHOS) disaster that occurred in 2010, offshore oil and gas drilling continues to occur around the...
Understanding the drivers of diversification and processes that maintain biodiversity remains a central theme of evolutionary biology. However, these efforts are often impeded due to disparities across species and environments and the genetic complexity underlying many traits. The factors driving biodiversity can be more readily understood by focus...
Diel vertical migration (DVM) of marine animals represents one of the largest migrations on our planet. Migrating fauna are subjected to a variety of light fields and environmental conditions that can have notable impacts on sensory mechanisms, including an organism’s visual capabilities. Among deep‐sea migrators are oplophorid shrimp, that vertica...
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Extraocular photoreception, the ability to detect and respond to light outside of the eye, has not been previously described in deep-sea invertebrates. Here, we investigate photosensitivity in the bioluminescent light organs (photophores) of deep-sea shrimp, an autogenic system in which the organism possesses the substrates and enzymes to produce l...
A major goal of evolutionary biology is to understand the role of adaptive processes on
sensory systems. Visual capabilities are strongly influenced by environmental and
ecological conditions, and the evolutionary advantages of vision are manifest by its
complexity and ubiquity throughout Metazoa. Crustaceans occupy a vast array of
habitats and eco...
High-quality RNA is an important precursor for high-throughput RNA sequencing (RNAseq) and subsequent analyses.
However, the primary metric used to assess RNA quality, the RNA Integrity Number (RIN), was developed based on model
bacterial and vertebrate organisms. Though the phenomenon is not widely recognized, invertebrate 28S ribosomal RNA
(rRNA)...
Deep‐sea coral communities are key components of the Gulf of Mexico ecosystem and were adversely affected by the Deepwater Horizon (DWH) oil spill. Coral colonies exposed to oil and dispersant exhibited mortality, damage, and physiological signatures of stress. Understanding how corals respond to oil and dispersant exposure at the molecular level i...
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequence...
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ∼7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequence...
The industrialization of the deep sea is expanding worldwide. Increasing oil and gas exploration activities in the absence of sufficient baseline data in deep-sea ecosystems has made environmental management challenging. Here, we review the types of activities that are associated with global offshore oil and gas development in water depths over 200...
To accurately assess the threat that global climate change poses to marine systems, a detailed baseline of the current carbonate chemistry and other oceanographic conditions is required. Despite the heightened vulnerability of deep-sea communities to ocean acidification, there have been relatively few studies investigating the carbonate chemistry i...
The 2010 Deepwater Horizon (DWH) disaster released an unprecedented amount of oil at depth in the Gulf of Mexico, with known adverse effects on deep-sea coral ecosystems. During the ensuing cleanup efforts, dispersants were also applied at depth for the first time. The ultimate fate of these pollutants is still under investigation, although evidenc...
Cold-water corals serve as important foundation species by building complex habitat within deep-sea benthic communities. Little is known about the stress response of these foundation species yet they are increasingly exposed to anthropogenic disturbance as human industrial presence expands further into the deep sea. A recent prominent example is th...
The Deepwater Horizon incident released an unprecedented amount of oil at depth in the Gulf of Mexico, with known adverse effects on deep-sea ecosystems and cold-water corals (White et al. 2012, Fisher et al. 2014). During the ensuing cleanup efforts, dispersants were also applied at depth for the first time. The response of deep-sea organisms to b...
The 2010 Deepwater Horizon disaster released an unprecedented amount of oil at depth in the Gulf of Mexico, with known adverse effects on deep-sea coral ecosystems. During the ensuing cleanup efforts, dispersants were also applied at depth for the first time. The response of deep-sea organisms to both the oil and dispersant are not fully understood...
The Deepwater Horizon incident released an unprecedented amount of oil at depth in the Gulf of Mexico (GoM), with known adverse effects on deep-sea ecosystems. The response of deep-sea organisms to both oil and the dispersant used in the ensuing cleanup efforts are not fully understood. Quantifying these effects on the surrounding communities is cr...
Questions
Questions (5)
Anyone have CA primers that work well for scleractinian corals? Or can point me in the right direction to a descriptive reference paper? I am working with a deep-sea coral species (Lophelia pertusa) but shallow-water/mesophotic references are also welcome.
I have been developing primers for control genes and GOI in a non-model organism (deep water coral) and finally optimized conditions so that they each have good, comparable efficiencies (~100 @ 60C).
Now that I am running an assay, I am getting amplification in my neg. controls (no-RT; no reverse transcriptase but RNA template is present). Although the melting curve indicates later Cts in the no-RT (negative) controls (~34 vs 30) the product looks similar on the melting curve.
However, for the same samples (run on the same plate), I am getting no amplification in my no-RT neg. controls using primers for my control gene rps7 (vs. ~20 Ct among samples for cDNA).
Does anyone have any suggestions or ideas as to what may be happening here?
Does anyone have a tested protocol or literature reference for RNA precipitation (for means of ethanol washing for purification) and subsequently resuspension?
I have been working on a species of deep sea coral and trying to determine the primer efficiency for two potential control genes or HKG. The samples were amplifying and I was able to narrow down optimal annealing temperatures to get the primer efficiency for both in the range of 95-100%.
When I ran out of cDNA for the two samples I was using, more was made but the samples were not amplifying as they were before, some not even at all. I tried cDNA from those same samples and from different samples of the same species with no luck. I would occasionally get amplification in a 1:10 dilution only, or a 1:1 and 1:100 but not the 1:10 or 1:1000 dilution- which makes no sense to me. [Annealing temp. 59C and 10uM primer concentrations]
I also tried re-running a temperature gradient to include the temperature that was originally thought to be optimal (59C) to 63C and only one sample amplified at 63C with a high Ct value (~38). The other sample did not even amplify at that temperature.
I have tried new primer dilutions (from stock) and also ran one of the primers on a different coral species and the amplification was fairly normal.
I tried troubleshooting the RNA extractions, but the 260/260's are ~2 and 260/230 are >1. The 28S and 18S ribosomal bands also appear clear on the gel and no clear sign of degradation is present.
I then tried troubleshooting the cDNA synthesis (SuperScript III First strand kit) thinking there may be contamination, bought a new kit and got similar results.
Any ideas or suggestions are greatly appreciated!
Hi,
I have been testing a series of primers for candidate HKG's for a non-model organism. I have gotten two of three to work and have optimized the reaction conditions. However, for the third gene candidate (EF2) I am having trouble properly assessing the efficiency using a standard curve plot because I am not getting amplification in my most dilute cDNA sample.
I am doing a 10-fold dilution series and am getting amplification in the 1:1, 1:10 and 1:100 but not in the 1:1000 dilution. I am wondering if there is a way to assess the primer efficiency using so few points or if I need to give up on this primer set.
Any ideas or suggestions are greatly appreciated.
Danielle
