Mechanisms of Vocal Learning in Songbirds: how song syllable structure is learned
Year of Dissertation:
2012
Advisor:
Ofer Tchernichovski
When learning to perform continuous actions one needs to cope with conflicting motor requirements: while some parts of the action may require exploratory variability to find motor states that can efficiently produce a desired outcome, other parts may require consolidation if they are already close to the desired goal. A possible solution to this problem is partitioning the action into segments that could be controlled independently, but it is not known if exploratory variability can be locally regulated during the sensory-motor learning of a continuous action. This dissertation explores song learning in songbirds as a model of learning to perform continuous actions. In the first set of experiments we manipulated song learning in zebra finches (Taeniopygia guttata) to experimentally control different requirements for vocal exploration in different parts of the song. We first trained birds to perform a one-syllable song, and once they mastered it we added a new syllable to the song model. Remarkably, when practicing the modified song, birds rapidly alternated between high and low acoustic variability to confine vocal exploration to the newly added syllable. Analysis of exploratory variability within syllables revealed that acoustic variability changed independently across song elements that were only milliseconds apart. The variability of each song element decreased as it approached the target, correlating with momentary local error and less so with the global error (the mean of local errors across the syllable). We concluded that vocal error is computed locally in sub-syllabic time scales and that song elements can be learned and consolidated independently. However, our evidence for partitions singing behavior into segments that may be learned independently, also indicate that those segments are not developmentally stable. For example, we observed that the appearance of distinct syllable types usually precedes the appearance of distinct sub-syllabic song elements, suggesting that the time scales at which syllables are learned might get shorter over development, perhaps in a hierarchical manner, from the learning of course temporal structure to the learning of fine temporal structure. To test this hypothesis we studied song learning at the articulatory level by measuring the control of respiratory pressure during song learning. We found that during early song learning, respiratory pressure patterns were coarse, and fine temporal structure was later added to that pre-existent coarse structure. This effect was not observed in socially isolated birds that developed their song without learning a tutored model. We therefore propose that the learning of continuous singing action is achieved by first partitioning the song into coarse segments, and then to finer units, where exploratory variability in each unit is dynamically gated until a local match to the song model is achieved.
Phytosociology, History and Diversity in Farmer-Managed Landscapes on the Tonle Sap Floodplain, Cambodia
Year of Dissertation:
2011
Driven by the annual flood pulse of the Tonle Sap Lake, the Tonle Sap floodplain in central Cambodia is a landscape characterized by dynamism, both ecological and social. Annual floods and rainfall vary in timing, duration and intensity from year to year. Patterns of burning, grazing, and agricultural expansion and contraction all leave their imprint on the landscape. While in the social domain, the region is likewise as complex. The genocidal, Maoist regime of Pol Pot darkened the 1970s. However, this was both preceded by, and followed by, years of civil war and social unrest. In recent years, Cambodia has shifted from a centrally-planned economy to a free-market economy, and experienced rapid economic growth followed by a dramatic slowdown. In the wake of such flux, the floodplains remain among the most productive rice-growing regions in the country, and are home to one of the most productive inland fisheries in the world. Even so, the region also remains one of the poorest. This project weaves analytical strands from ecology, geography and anthropology to delve into the ways in which people make a living in such a complex, challenging environment by focusing on the relationships between people, the landscape and plants. Results are presented from an analysis of 47 years of land use/land cover change depicted in aerial photography; an analysis of the structure and composition of floodplain plant communities through the use of descriptive ecological inventory; and an analysis of household-level natural resource-based livelihood activities, detailing how plant communities are utilized by village residents. A case study in floodplain land use is also presented, focusing on the Hillock-Depression Complex, a landscape element newly described herein. This case study illustrates the pitfalls of top-down land use planning in the context of a landscape rich in resources important to local residents but illegible to policy-makers. The results of these diverse analytical streams suggest that people do not live on the floodplain in spite of tremendous dynamism. Rather, the opposite is true. They live on the floodplain because of such dynamism, not as passive subjects but as active agents in generating diversity.
Drosophila Dunc-115 Mediates Axon Projection Through Actin Binding
Author:
Christopher Roblodowski
Year of Dissertation:
2011
Axon pathfinding, the process of how neurons reach their correct targets during early neural development, is a critical area in neuroscience research. Though significant progress has been made in identifying the extracellular guidance cues and their membrane receptors, and possible downstream effectors including the Rho GTPases family, little is known regarding how guidance signals are relayed to the actin filaments that are central to the mobility of the growth cone. Our laboratory has identified and characterized Drosophila gene dunc-115 as a possible downstream target in relaying guidance cues further down to the cytoskeleton. Specifically, we have shown that Dunc-115 regulates neural connections in both the eye and the central nervous system in Drosophila. In this thesis, I have identified that (1) the surface receptor Roundabout (Robo) is an upstream regulator of guidance signals relayed through Dunc-115, (2) Dunc-115 receives signals from the Rho GTPases, and (3) Dunc-115 binds to actin via its VHD (Villin Head Piece) domain, suggesting a mechanism for Dunc115 to relay guidance signals. Finally, I have analyzed the genomic structure of the dunc-115 gene in 12 Drosophila genomes, which has generated further insights into how this gene has evolved.
Phylogeography, Phylogenetics, Historical Demography, and Morphology of Milksnakes (Genus Lampropeltis)
Year of Dissertation:
2013
A primary goal for systematists is the discovery and identification of Earth's biodiversity. To meet these goals, coalescent-based phylogenetic and phylogeographic methods have been developed that help quantify diversity and provide a better understanding of processes generating species. Here, I use these methods to examine milksnakes (genus Lampropeltis ). Milksnakes are among the widest ranging of New World squamates and are frequently used as model organisms in Batesian mimicry studies. Despite this, there has been no research detailing their systematics within a molecular phylogenetic framework. Furthermore, previous molecular studies that include milksnakes have shown they do not form a monophyletic group within the genus and that color pattern, which has been the basis for their previous classification may not be informative with respect to evolutionary history. The study detailed here examines milksnakes across their intercontinental range to determine whether there is unrecognized diversity in this group. To meet this goal, I have developed a multi-locus dataset consisting of 11 nuclear genes and one mitochondrial gene. I use a molecular delimitation method to determine support for putative species, assess migration between species, and, within a species-tree framework, infer a phylogeny for the genus Lampropeltis , including all newly elevated milksnakes and all other recognized taxa within the genus. This dataset also provides the opportunity to examine how the inclusion of cryptic taxa and species tree methods provide a more accurate assessment of timing, rates and process of species diversification. After delimiting species, I use both non-genealogical and coalescent-based models to infer the historical demographic patterns of milksnakes. As the milksnake species identified here have representatives in both the temperate and tropical Americas, I am able compare demographic responses with respect to changes in effective population size between the Nearctic and Neotropical taxa. Specifically, I ask, do closely related milksnake species have similar demographic patterns resulting from Pleistocene glacial cycles despite their origination in the Neotropics or Nearctic. Results indicate that milksnakes do not share similar demographic patterns as a taxonomic group or by area and I conclude that authors should use caution in generalizing historical demographic trends based on geography. In addition to examining milksnakes using molecular data, I determine if there are detectable morphological differences independent of color pattern using geometric morphometrics. By taking photographs of 487 specimens, digitizing landmarks on their heads, and using geometric morphometric analyses, I determine that these types of analyses are useful in snake systematics for detecting distinct morphological shape variation among genetically delimited species, although they may not be powerful enough to use as an a priori species discovery tool.
RHYTHM DEVELOPMENT IN THE ZEBRA FINCH SONG
Year of Dissertation:
2009
Advisor:
Ofer Tchernichovski
When we listen to the zebra finch song, the song sounds very rhythmic and repetitive. Each bird has its own song rhythm. In order to study rhythm development in songbirds we introduced a new concept to bird song research, the quantification of rhythm and periodicity in song structure. By developing a technique that gives us insights into the song rhythm we have studied how song structure changes during different stages of the zebra finch life. We found that birds trained from an early age (day 43) exhibit two types of rhythm transformations: the first type is a smooth down-modulation of rhythm during several days of song development. The second type is an abrupt transition from one rhythm to a different rhythm. Smooth transitions might be caused by a slow shift in the timing of neuronal firing, while abrupt transitions might be caused by reorganization of the rhythm generator. We also examined why is it that zebra finches that are isolated until the end of their sensitive period and then trained do not imitate well. We discovered that their poor imitation correlates with inability to add new syllables to the songs. Zebra finches that sing a long motif before the onset of training were able to imitate better than finches with a short motif, perhaps because they have more raw materials to work with. Our findings suggest that at the end of the sensitive period vocal changes still occur, but imitation is constraint at the level of song rhythm and on the level of fine temporal structure.
RELATIONSHIPS BETWEEN POLLUTANT-INDUCED DIGESTIVE TOXICITY AND THE ASSIMILATION AND SUBCELLULAR PARTITIONING OF ELEMENTS BY GRASS SHRIMP PALAEMONETES PUGIO
Year of Dissertation:
2010
Aquatic invertebrates inhabiting urbanized estuaries are typically exposed to pollutants through multiple pathways, including the diet. Biochemical and physical processes within invertebrate guts can be impacted by ingested pollutants, which may influence the assimilation of essential nutrients as well as pollutants. Pre-assimilatory digestive toxicity may result from pollutants circulating in gut fluid. Post-assimilatory toxicity could be due to incorporation of a pollutant into consumer tissues as a result of chronic exposure. This series of studies investigated the influence of chronic exposure to impacted field conditions or pre-exposure to dietary metal (Cd and Hg) in the laboratory on the assimilation of elements (organic carbon, Cd and Hg), subcellular partitioning of assimilated metal and digestive physiology (gut residence time [GRT], feces elimination rates [FER], gut pH and digestive protease activities) in the grass shrimp Palaemonetes pugio. Carbon and Cd assimilation and endpoints related to digestion were also assessed for naïve shrimp following ingestion of a pulse of Cd-contaminated food. Based on these studies, it appears that grass shrimp may be able to maintain carbon assimilation in the laboratory under different forms of pollutant-induced dietary stress. For field-collected shrimp, this phenomenon may be attributable to digestive plasticity (e.g., increased GRT to compensate for reduced digestive enzyme activities). Increased assimilation of Cd and Hg was observed for shrimp collected along an impact gradient. Enhanced non-essential metal assimilation may have implications for accumulation and toxicity in impacted shrimp. In the case of Cd assimilation, a positive correlation with GRT and negative relationship with protease activities suggests that digestive plasticity may also influence assimilation of non-essential elements in the field. Variability in Cd assimilation by shrimp pre-exposed to dietary metal in the laboratory was not dose-dependent, which may be related to interactions between post-assimilatory impacts on gut physiology. Increased assimilation of Hg by Hg pre-exposed shrimp may have been related to a corresponding increase in gut pH (i.e., decreased concentrations of H+ ions in circulating gut fluid).
LIM Domain Proteins TRIP6 and LPP Associate with Shelterin to Mediate Telomere Protection
Year of Dissertation:
2012
POT1 is the single stranded telomeric overhang binding protein of the shelterin complex, a group of six proteins essential for proper telomere function. The abrogation of POT1 DNA binding activity results in telomere elongation, or activation of the ATR DNA damage response at telomeres. Therefore, overhang binding represents the functionally relevant activity of POT1. Novel protein associations with the POT1 DNA binding domain are of great interest to explore and these possible interacting factors were sought using the yeast two-hybrid system. Bait containing the POT1 DNA binding domain was used leading to the isolation of LIM domain protein TRIP6 as a novel POT1 interacting factor. TRIP6 could co-immunoprecipitate with other shelterin components, arguing for association with the whole complex. Additionally, TRIP6 was detected at telomeres by Chromatin Immunoprecipitation and Immunofluorescence in Hela and HTC75 cells, which suggests association with telomeric DNA. TRIP6 depletion by siRNA led to the induction of telomere dysfunction induced foci, indicating a role in telomere protection. A closely related LIM protein, LPP, was also found at telomeres and was important for repressing the DNA damage response. A related LIM protein Zyxin was found not to associate with telomeres. We propose that TRIP6 and LPP represent a novel class of molecules at human telomeres involved in the repression of inappropriate DNA damage response at chromosome ends. All assays incorporate human cancer cell lines HTC75 and Hela 1.2.11. These results could advance our understanding on the repression of telomere-based senescence, an important tumor suppressor mechanism.
Regulation of Microtubule Stability in Saccharomyces Cerevisiae
Year of Dissertation:
2011
The integrity of chromosome segregation during mitosis is essential for the propagation of genetic information to daughter cells during cell division. In yeast, it is achieved in four microtubule-dependent steps: first is spindle assembly, which involves the migration of duplicated microtubule organizing centers to form a bipolar spindle by prophase; second is orientation of the mitotic spindle at the site of cytokinesis; third- chromosome movement along kinetochore microtubules (anaphase A); and fourth, complete chromosome segregation through spindle elongation through interpolar microtubules (anaphase B). Signaling pathways have been implicated in the regulation of microtubule dynamics and stability, which is required for these processes. This work identifies additional protein regulators of microtubule stability using mutants of key mitotic motor proteins, specifically, Cin8p, Kip1p, and Dyn1p. Loss of Cin8p function in the absence of either Kip1p or Dyn1p is lethal. Haploid cells that carry the cin8-3 temperature sensitive allele in a deletion background of either KIP1 or DYN1 cannot grow above 35◦C. Our studies suggest that suppressors of these mutant genotypes act by stabilizing microtubules. We propose that the mechanism of suppression involves enhancing signal-transduction cascades that regulate microtubule stability and dynamics. We found that FCP1 overexpression supressess the microtubule defect in our background and that this suppression requires the following genes to manifest: SWI6, SWI4, CLB2, ELM1, HSL1 and MRS6. These proteins, with a previously uncharacterized role in microtubule stability, may be candidate microtubule-associated proteins (MAPs) or novel regulators of MAPs (direct or indirect). In addition, a putative pathway to MT stability was drawn based on genetic interactions we established, epistatic experiments that were done and physical data we produced, combined with existing knowledge.
The Systematics and Evolution of the Nightjars and their allies (Aves: Caprimulgiformes)
Year of Dissertation:
2013
Recent studies have shown that the avian order Caprimulgiformes includes eight families: the owlet-nightjars (Aegothelidae), the nightjars (Caprimulgidae), the potoos (Nyctibiidae), the frogmouths (Podargidae), the monotypic oilbird (Steatornithidae) and the three families traditionally placed in the order Apodiformes: the swifts (Apodidae), the tree-swifts (Hemiprocnidae) and the hummingbirds (Trochilidae). In this study, a total-evidence approach was utilized to address the relationships of these families. A phylogenetic analysis of a combined dataset of 134 skeletal morphological characters, 14 nuclear loci (exons and introns) and a presence/absence indel matrix, with a taxon sampling of all eight families as well as 16 outgroup taxa provided a better resolved phylogeny for the group than obtained by previous studies. New relationships include the placement of the frogmouths (Podargidae) as the sistergroup to a clade containing the owlet-nightjars (Aegothelidae) and the three "apodiform" families. Both morphological and molecular data supported the sister-relationship of the nightjars (Caprimulgidae) and the potoos (Nyctibiidae).
Functions of Notch and Neuralized in Drosophila hematopoiesis
Year of Dissertation:
2011
In vertebrates, hematopoiesis is commonly divided into two temporal phases, primitive (embryonic) and definitive (adult). Genetic studies in zebrafish and mice have implicated signaling pathways and molecular networks of transcription factors in the control of primitive and definitive hematopoietic programs. Notch signaling is essential for the proper execution of a wide array of cell fate decisions and developmental processes, including hematopoiesis. Many of these same signaling and transcriptional mechanisms also control hematopoiesis in simpler animals, such as the fruit fly Drosophila melanogaster. Because of its simple organization and genetic accessibility, Drosophila hematopoiesis has recently gained attention.