Phylogeny and Evolutionary Genomics of Non-Photosynthetic Diatoms

Diatoms are prolific photosynthesizers responsible for some 20% of global primary production. In real terms, the oxygen in one of every five breaths traces back to photosynthesis by marine diatoms. Among the tens of thousands of diatom species, a small handful of colorless diatom species in the genus Nitzschia have lost photosynthesis altogether and rely exclusively on extracellular organic carbon for growth. I used DNA sequence data to reconstruct the phylogeny of this group, and found that nonphotosynthetic diatoms are monophyletic, indicating that photosynthesis was lost just one time over the course of some 200 million years of diatom evolution. Carbon metabolism in nonphotosynthetic diatoms, including the exact source of carbon used by these species, has not been fully characterized. We sequenced the nuclear genome of one species and used it to develop a comprehensive model of central carbon metabolism. Preliminary analysis of Nitzschia metabolism showed that it generally matches to the pattern of previously reported diatom metabolic networks. As well we found some hints regarding Nitzschia external carbon acquisition which possibly can help to explain its heterotrophic mode of life. Overall, this study has provided novel insights into the evolutionary origin and metabolism of non-photosynthetic diatoms, which are unique among diatoms in their ability to sustain their growth solely from extracellular carbon

Axonal transport and life cycle of mitochondria in Parkinson\u27s disease model

In neurons, normal distribution and selective removal of mitochondria are essential for preserving compartmentalized cellular function. Parkin, an E3 ubiquitin ligase associated with familial Parkinson’s disease, has been implicated in mitochondrial dynamics and removal. However, it is not clear how Parkin plays a role in mitochondrial turnover in vivo, and whether the mature neurons possess a compartmentalized Parkin-dependent mitochondrial life cycle. Using the live Drosophila nervous system, here, I investigate the involvement of Parkin in mitochondrial dynamics; organelle distribution, morphology and removal. Parkin deficient animals displayed less number of axonal mitochondria without disturbing organelle motility behaviors, morphology and metabolic state. Instead, loss of Parkin produced tubular and reticular mitochondria specifically in motor neuronal cell body. In addition, unlike in immortalized cells in vitro, Parkin-dependent mitophagy was rarely found in our mature neurons. Thus, my results indicate that mitochondrial morphology is restrictively modulated in the cell body in Parkin-dependent manner, and this further proposes an idea that the organelle supply from the cell body is important for the mitochondrial quality control in mature neurons

\u3ci\u3eZea mays i\u3c/i\u3eRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species

AKAP7γ Regulation of PKA Substrate Phosphorylation

In the cell, cAMP-protein kinase A (PKA) signaling is compartmentalized. Two different receptor types, both utilizing cAMP and PKA as second messenger and signal effector, are able to convey separate signals that result in phosphorylation of distinct substrates. Signal compartmentation is possible primarily because of A Kinase Anchoring Proteins (AKAPs) that bind both PKA and a target substrate, effectively co-localizing them. AKAPs are also capable of binding to other necessary signaling components like adenylate cyclase and phosphodiesterase, thus enabling AKAPs to coordinate a signaling microdomain containing many of necessary components. In this thesis I present multiple lines of evidence demonstrating how AKAP7g is able to regulate PKA phosphorylation. First, I show that AKAP7g is able to self-associate, forming dimers and possibly higher order oligomers. I predict via computational modeling that this behavior will increase both the speed and magnitude of PKA signaling. Next, I demonstrate that AKAP7g participates in a highly dynamic phosphorylation-state dependent interaction with phospholamban (PLB), and predict via computational modeling that this allows low concentrations of AKAP7g to regulate phosphorylation of much higher concentrations of substrate. Finally I demonstrate via computational modeling that contrary to the widely accepted hypothesis of AKAP signaling, the catalytic subunit of PKA is likely retained within the AKAP-PKA complex during signaling events. I further show that the structure of the complex is an important determinant of substrate phosphorylation. This work offers new insight into the function of AKAPs and offers an update to the AKAP signaling hypothesis

Kinetoplastid Phylogenomics and Evolution

This Special Issue, Kinetoplastid Phylogenomics and Evolution, unites a series of research and review papers related to kinetoplastid parasites. The diverse topics represented in this collection display a variety of scientific questions and methodological approaches currently used to study these fascinating organisms

Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites

Dopamine release in the striatum has been implicated in various forms of reward dependent learning. Dopamine leads to production of cAMP and activation of protein kinase A (PKA), which are involved in striatal synaptic plasticity and learning. PKA and its protein targets are not diffusely located throughout the neuron, but are confined to various subcellular compartments by anchoring molecules such as A-Kinase Anchoring Proteins (AKAPs). Experiments have shown that blocking the interaction of PKA with AKAPs disrupts its subcellular location and prevents LTP in the hippocampus and striatum; however, these experiments have not revealed whether the critical function of anchoring is to locate PKA near the cAMP that activates it or near its targets, such as AMPA receptors located in the post-synaptic density. We have developed a large scale stochastic reaction-diffusion model of signaling pathways in a medium spiny projection neuron dendrite with spines, based on published biochemical measurements, to investigate this question and to evaluate whether dopamine signaling exhibits spatial specificity post-synaptically. The model was stimulated with dopamine pulses mimicking those recorded in response to reward. Simulations show that PKA colocalization with adenylate cyclase, either in the spine head or in the dendrite, leads to greater phosphorylation of DARPP-32 Thr34 and AMPA receptor GluA1 Ser845 than when PKA is anchored away from adenylate cyclase. Simulations further demonstrate that though cAMP exhibits a strong spatial gradient, diffusible DARPP-32 facilitates the spread of PKA activity, suggesting that additional inactivation mechanisms are required to produce spatial specificity of PKA activity