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Evolutionary Analyses on the Core Genome of Borrelia burgdorferi: Elucidating the Genomics of Virulence
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ABSTRACT: Adaptive Evolution in Borrelia burgdorferi by: James Haven Advisor: Dr. Weigang Qiu The availability of multiple genomes of closely related pathogen strains makes it possible to identify genome-wide variations associated with strain-specific phenotypes such as pathogenicity and virulence. One main challenge of gene-trait associative mapping in bacterial species is finding a way to minimize the effect of linkage among loci due to pervasive clonal population structures. A second concern is to distinguish selective sequence variations from random, selectively neutral differences among strains. Here we identified adaptive, strain-specific nucleotide polymorphisms (SSNPs) on the core genome of Borrelia burgdorferi, the Lyme disease pathogen. We minimized the linkage effect by comparing the genomes of seven isolates representing four genospecies (B. burgdorferi sensu stricto, B. bissettii, B. afzelii, and B. garinii) and four clonal groups of a single species (A, C, E, and K clones of B. burgdorferi sensu stricto). Identification of selective nucleotide polymorphisms was achieved by applying codon-based, tests of positive selection based on rates of synonymous (KS) and nonsynonymous (KA) substitutions. We then tested for the presence of positive selection at 824 gene loci on the main chromosome, 68 loci on the linear plasmid lp54, and 26 loci on the circular plasmid cp26. Consequently, we identified 28 genes under positive selection without regard for lineage, 12 genes associated with genospecies divergence, and 7 genes associated with the adaptive divergence of B31, a highly invasive strain. We checked results by excluding loci with high alignment uncertainties, mapping positively selected sites on protein structure models, and evaluating the possibility of false positives. Cell envelope genes are significantly over-represented among the positively selected genes. Additional categories of interest are DNA metabolism, transcription, cell division, and regulation. Focused analyses on copy number variation of established immune elicitors and a survey of intraspecific recombination support a prominent role for adaptive evolution in the maintenance of the B. burgdorferi pathogen cycle. These findings highlight immune escape as a driver of positive natural selection via surface protein variation and possibly pathogen replication dynamics.
cAMP and Polyamines Overcome Inhibition by MAG by Activating Cdk5 via Increased Expression of p35 Regulated by Activation of eIF5A
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Damaged axons in adult mammalian central nervous system (CNS) are unable to regenerate after injury although axons in the peripheral nervous system (PNS) or embryonic CNS can. The inhibitory molecules associated with myelin are one of the major obstacles to successful axon regeneration in the adult mammalian CNS. To date, three inhibitors of regeneration have been identified in myelin: NogoA, myelin-associated glycoprotein (MAG), and oligodendrocyte-myelin glycoprotein (OMpg) (Filbin, 2003). Interestingly, all these three ligands bind to the same receptor Nogo receptor (NgR) to mediate the inhibitory effect. p75NTR or TROY and Lingo-1( LRR and Ig domain-containing, Nogo Receptor interacting protein) are necessary components of the receptor complex as NgR is glycosyl phosphatidylinositol (GPI)-anchored and lacks a signaling domain (Wang et al., 2002a; Mi et al., 2004; Park et al., 2005; Shao et al., 2005). Activation of the receptor complex by myelin inhibitors activates the small GTPase RhoA resulting in rearrangement of the cytoskeleton and inhibition of axonal outgrowth (Hu and Strittmatter, 2004). It has been shown in our lab that elevating intracellular levels of cyclic AMP (cAMP), either via application of a cAMP analog or by prior exposure to neurotrophins (NTs) can block the inhibition of axonal regeneration by MAG and myelin (Cai et al., 1999; Cai et al., 2001; Qiu et al., 2002). Elevation of cAMP results in up-regulation of arginase I (ArgI) and subsequent synthesis of polyamines. Up-regulation of ArgI or priming with the polyamine putrescine or spermidine blocks the inhibition of axonal growth by MAG/myelin (Cai et al., 2002; Deng et al., 2009). Polyamines are known to have effects in regulating cytoskeleton organization in both the short term and the long term, but their downstream effectors have yet to be identified. Many studies have shown that Cyclin-dependent kinase 5 (Cdk5) is involved in neurite outgrowth and regulates the neuronal cytosekeleton, which prompted us to hypothesize that Cdk5 may play a role in blocking MAG/myelin-mediated inhibition. Cdk5 is a multifunctional serine/threonine kinase and its activator, p35, is expressed only in the nervous system (Tsai et al., 1994). It has been shown that activity of Cdk5 is required for neurite elongation (Nikolic et al., 1996; Paglini et al., 1998; Li et al., 2000; Harada et al., 2001). Cdk5 phosphorylates cytoskeleton proteins and regulates the organization of all three cytoskeleton elements microfilaments, microtubules and intermediate filaments (Dhavan and Tsai, 2001). Here we show that Cdk5 is required for db-cAMP and putrescine to overcome inhibition. The effect of db-cAMP and putrescine in overcoming inhibition by MAG is abolished in the presence of a specific inhibitor of Cdk5, Roscovitine. Neurons infected with dominant negative Cdk5 HSV viruses are not able to overcome inhibition by MAG in the presence of db-cAMP or putrescine. Importantly, neurons infected with HSV viruses overexpressing p35, the neuronal specific activator for Cdk5, overcome MAG's inhibition. Moreover, db-cAMP and putrescine increase the expression of p35. This in turn induces the kinase activity of Cdk5. The up-regulation of p35 by putrescine is also reflected in the increased distribution of p35 in neurites and growth cones. Furthermore, we show that putrescine up-regulates p35 protein by hypusine modification of eukaryotic Initiation Factor 5A (eIF5A), and this hypusination is necessary for putrescine to overcome inhibition by MAG. Our findings reveal a previously unknown mechanism by which polyamines encourage regeneration after CNS injury.
Floral Interactions in Van Cortlandt Park, Bronx, New Yrok
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Van Cortlandt Park is New York City’s third-largest park at 464 hectares. Despite 300 years of land-use history, this heavily impacted ecosystem shows surprising resiliency, and can act as a proxy for understanding global issues based on climate change, fragmentation, and anthropogenic impact. A park-wide inventory conducted over six years returned three times the amount of taxa observed in any prior survey suggesting the park has been historically undersampled. At 1102 species, the richness of the park supports the hypothesis that urban regions harbor greater species-richness than historically presumed. Approximately 70.6% of park listings comprise herbaceous plants. Non-natives make up 50% of the total floristic sightings, most of Eurasian or East Asian provenance. With 30 NY state-listed plants, the park represents a refugia for endangered taxa for New York State despite frequent burns, vandalism, and exotic invasion. A parsimony analysis of presence/absence data returns groupings based on species composition responding to environmental factors such as moisture, sun, and forest fragmentation. Partitioning the data set into separate herbaceous versus woody matrices suggests the two components of the flora track different life histories. Findings concur with similar results from non-metric multidimensional (NMS) ordination and unweighted pair group method with arithmetic mean (UPGMA). Parsimony analysis of ecological data has use as a monitoring tool since the read-out produces a list of what taxa can be found at each site. Quantitative ecological analyses based on woody frequency data from a quadrat survey shows the three most abundant trees in the park are Prunus serotina (black cherry), Acer platanoides (Norway maple), and Quercus rubra (red oak). Importance Value analyses return the same three taxa but place Quercus rubra in first place position based on its greater diameter-at-breast height (DBH). Alpha diversity indices suggest the park is biodiverse from a woody perspective yet not necessarily even; addition of herbaceous data significantly increases diversity even more. Overall the northern end of the park is more diverse than the southern end. Disturbance specialists in the canopy of the southern park depress richness and evenness. Beta diversity analysis comparing a southern species-poor region versus a northern species-rich region shows turn-over in the park with the woody data having a higher turn-over rate than the herbaceous data. The ecology of a city environment is a suitable proxy for understanding problems putatively predicted for global warming, e.g. the influence of increased temperatures (e.g. city ‘urban island’ heat effect) and forest fragmentation on diversity. If so, results from VCP suggest richness may increase following climate warming due to non-native recruitment but long term biodiversity may change if areas are not monitored properly.
Adaptive Plasticity in the Human Saccade System
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The rapid point-to-point movements of the eyes called saccades are some of the most commonly made by humans, yet differ from nearly every other type of motor output in that they are completed too quickly to be adjusted during their execution by visual feedback. Yet, saccadic accuracy remains quite high over a lifetime despite inevitable changes to the physical structures controlling the eyes, indicating that the oculomotor system actively monitors and adjusts motor commands to achieve this consistent behavioral production. Indeed, it seems that beyond the ability to compensate for slow, age-related bodily changes, saccades can be modified following traumatic injury or pathology that affects their production, or in response to more short-term systematic alterations to post-saccadic visual feedback in a lab setting. It is, in fact, thought that all of these forms of plasticity rely on the visual detection of accuracy errors by a unified set of mechanisms that support the process known as saccade adaptation. A great deal has been learned about saccade adaptation, as it has been extensively studied as a phenomenon in its own right, as well as being used to explore the process of motor learning in general. However, many fundamental questions about saccade adaptation remain unanswered, often related to the way that saccade adaptation might operate in the natural environment with substantially more complex visual stimuli than are generally used in the lab. Here, we addressed these questions with (in some cases original) variants and more conventional examples of the frequently used intrasaccadic target step (ISS) paradigm (in which an experimenter causes saccadic error by shifting a target during the movement). By exploring the responses to whole-field-ISSs, we have inferred that saccade adaptation might be supported by a trans-saccadic integration mechanism, and may be sensitive to intrasaccadic motion signals. Challenging the oculomotor system by confronting it with multiple post-saccadic targets has revealed that saccade adaptation can occur in a target-identity specific manner, so that even if post-saccadic error varies from trial-to-trial, adaptation seems to reflect the average behavior of the target. At a more basic level, we systematically varied ISSs to determine the lower limits of the oculomotor system's sensitivity to intrasaccadic displacement during adaptation. Also at a more basic level, we looked at the effects of rendering post-saccadic feedback more intermittent during adaptation, finding it to have little effect on the magnitude or rate of adaptive dynamics, similar to other forms of motor learning but somewhat dissimilar from operant conditioning. These experiments also furnished a useful setting to develop and test a novel model of saccade adaptation which more explicitly relies on post-saccadic sensory prediction than previous models, but that is nonetheless in keeping with the ethos of modern motor learning theory. Finally, we found that the establishment and maintenance of a context for saccadic performance by adaptation could be achieved by consistently pairing a target's visual-identity with a specific ISS, extending what had been previously recognized as constituting a cue for contextual motor learning. In general, our results suggest that saccade adaptation is a highly flexible mechanism that not only supports the maintenance of accuracy, but also makes use of a wide range of brain functions to deftly tailor saccadic behavior contingent on task demands.
Systematics of Lecythidoideae (Lecythidaceae) with emphasis on Bertholletia, Corythophora, Eschweilera, and Lecythis
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Phylogenetic analyses based on morphological and DNA sequence data were generated to test the monophyly of Eschweilera and Lecythis and to investigate the relationships of these two genera and their close relatives (Bertholletia and Corythophora). The final results were applied to questions of taxonomic rearrangements and character evolution in traits related to pollination. A cladistic analysis based on morphology indicates that Bertholletia, Corythophora, Eschweilera, and Lecythis form a clade (the Bertholletia clade), but the resolution within the clade is too poor to elucidate the phylogenetic relationships among the genera. Nonetheless, the data support the monophyly of Corythophora. Eschweilera is divided into two clades: Eschweilera section Tetrapetala and Eschweilera s.s. Whether or not the two clades form a clade remains as unresolved. Lecythis is not resolved as monophyletic, but each of the Sections Corrugata, Pisonis, and Poiteaui is monophyletic. A combined analysis based on morphology and nuclear ITS and plastid ndhF, trnL-F, and trnH-psbA sequence data was conducted to improve the resolution of the phylogenetic tree. The results support the generic circumscriptions of Bertholletia and Corythophora based on morphology, but suggest the revision of Eschweilera and Lecythis. Eschweilera is paraphyletic and divided into three clades: the Eschweilera section Tetrapetala clade, the Eschweilera andina clade, and the core Eschweilera clade. Lecythis is polyphyletic and consists of five clades: the Lecythis s.s. clade, the Pachylecythis clade, the Lecythis chartacea clade, the Holopyxidium clade, and the Section Corrugata clade. Based on the results of these analyses, Section Tetrapetala clade merits recognition as an independent genus and should be segregated from Eschweilera. On the other hand, the five clades of Lecythis are distinct from each other and should be recognized as five separate genera. Androecial evolution inferred from the resulting phylogeny demonstrates that features such as floral zygomorphy, closed androecia, coiled ligules, and the production of nectar are homoplasious. Evolution of these characters most likely is because of the adaptation in response to pollinator shift and does not simply represent a process of morphological transformation from a simpler to a more complicated structure as previously suggested.
The Sustainable Management and Conservation Santalum yasi (Sandalwood) in Fiji and Tonga: A Combined Ecological and Genetic Approach
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Valued internationally for the aromatic oil found within its heartwood, Sandalwood (Santalum, Santalaceae) is one of the most heavily exploited groups of plants across its range. While historically, most oil has been harvested from Santalum album in Southeast Asia and India, the decrease of S. album sources has caused a widening gap between supply and demand, which creates profitable market opportunities and increasing harvest pressure for alternative sandalwood oil sources. Santalum yasi, a quality alternative, has been harvested extensively in Fiji and Tonga, yet is vastly under-studied. The absence of basic data on population dynamics and genetic variation for remnant populations remains a major constraint to the sustainable management of this culturally and economically valued resource. This dissertation focuses on the ecological and genetic data and analyses that can aid in developing sustainable management strategies. Population size-class structure data was collected using transects in the three densest natural populations of Santalum yasi. Population dynamics, current species distribution, and ecological threats were investigated to find that the few remaining wild stands display discontinuous size class structures, are under regenerative stress and that the natural distribution has diminished significantly, even to local extinction in some areas. Using a nuclear microsatellite analysis, genetic variability within and between populations was investigated. Results suggest that there is no significant genetic variation between populations, but that most of the genetic variation lies within populations. This genetic distribution suggests that there is a significant level of gene flow between and among populations, most likely through human induced dispersal, showing a more panmictic trend than previously supposed. This may provide molecular evidence confirming the Western documentation and traditional oral history of extensive interaction between Fiji and Tonga and their trade of plants and culture. Based on these dwindling levels of yasi population size and unstructured genetic variation in Fiji and Tonga, further enumerations and resource surveys are not practical to conduct at this time. Rather, forestry and governmental efforts should be focused on promotion of local involvement in assisted natural regeneration of wild stands and preservation of genetic variation through in situ, community-mediated conservation.
The Ecology Of Winter Flounder From An Otolith Perspective
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THE CITY UNIVERSITY OF NEW YORK ABSTRACT THE ECOLOGY OF WINTER FLOUNDER FROM AN OTOLITH PERSPECTIVE By George W. Jackman Advisors: John Waldman (CUNY Queens College) and Karin E. Limburg (SUNY ESF) In this dissertation, sagittal otoliths were used as a lens to examine latent life history patterns in winter flounder (Pseudopleuronectes americanus) and also as a means of interpreting the species’ relationship to their abiotic and biotic environment. Otoliths provide a unique and powerful perspective into the lives of the telost fishes, because they permanently record the spatial and temporal histories through sequential growth patterns from conception to capture. The patterns of growth and dormancy in the otolith are regulated by endogenous and exogenous rhythms, and as the otolith grows, trace elements are absorbed from the ambient environment and incorporated into the calcium carbonate (CaCO3) matrix. Hence, concentric bands in the otolith reliably indicate age and growth conditions similar to the annuli in trees, whereas the chemical chronology contained within the CaCO3 crystal can function as a geochemical tag, to permit retrospective tracking of a fish’s movements and reconstruction of its environmental history. The first chapter in this study demonstrates that winter flounder sagittae are not morphologically, nor are they chemically identical, which is an essential distinction that sets them apart from those found in bilaterally symmetrical fishes. This finding has important implications when using otolith chemistry to investigate population structure of winter flounder and other flatfishes, because indiscriminate use of either otolith can bias statistical results. Consequently, method standardization is recommended when performing otolith chemistry in flatfishes. Furthermore, the results of this investigation provides evidence that the blind-side otolith in flatfishes may be absorbing chemicals differently from their eyed-side counterparts, though these results warrant further testing. In the second chapter, otolith microchemistry is utilized to examine the fine-scale stock structure of winter flounder that were sampled from the coastal margins of Long Island and surrounding areas. Using otolith microchemistry in this manner, group membership was recognizable an on a scale of tens of kilometers with a statistical accuracy that ranged from 83-87% depending upon spatial dimensions when re-classifying the specimens back to their location of capture. The second part of this chapter examines the feasibility of using otolith microchemistry with specific elemental markers to make qualitative assessments of inshore habitat of winter flounder. Through this investigation, it was revealed that some of the most chemically contaminated bodies of water still make important contributions to winter flounder recruitment, and juvenile growth in these systems can potentially exceed growth patterns in more pristine locations. The last chapter of this dissertation looks at the age and growth structure of winter flounder in the Hudson River Estuary (HRE) and western Long Island Sound (WLIS) and compares those results to several large-scale surveys that were performed last century and collectively form the historical record of winter flounder in New York waters. The ensuing results of this analysis show that winter flounder in the HRE and WLIS have incurred a faster growth rate, and larger, if not older fish comprise a greater percentage of the population than they did during the early and middle decades of the twentieth century. The increasing size-at-age shown by winter flounder in the HRE and WLIS correlates with a release from intra-specific competition and increasing pressure generated by size-selective mortality imposed by a resurgent and newly emerging suite of predators. Finally, the conclusions of this thesis summarize the results of these investigations and discuss potential directions for future research.
MUSICAL REGULARITY AND RHYTHMIC PATTERNS: A QUANTITATIVE ANALYSIS OF BIRDSONG STRUCTURE
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Birdsong is a complex, learned behavior that, like music, has meaningful units at multiple timescales. Birds perform by constructing extended presentations of their phrase repertoire. Each bird’s repertoire is built from small units, such as syllables, or groups of syllables with characteristic pitch, rhythm, and timbre. Like a musician each bird has its unique structure of performance that communicates its individual identity. Also contained within a bird’s performance, is information about its group identity and species identity. Like a musician’s performance, a bird’s singing affects the behavioral state of listeners—birds perform to attract mates and defend territory. Subjectively, many can appreciate birdsong as musical but what evidence is there that birds have music? What parameters can be chosen to test the presence of musicality in birdsong? Are there quantitative ways to demonstrate musicality in birdsong? In this study I test quantitatively for the presence of musical structure in birdsong by homing in on two distinct features: structural balance and groove. Music is known for its characteristic balance between complexity and regularity. Groove, in the context of genres such as jazz offers a unique, visceral parameter that is known to vary in nuanced ways. I test for musical features based on understanding of how these two parameters manifest in music. Like music, birdsong affects the behavioral state of conspecifics, but what is it in the acoustic signal that serves to affect the behavioral state of bird listeners in a desired manner? By investigating extensive song databases of birds’ singing performances, I developed methods that facilitate a deeper understanding of what structures are present within song performances and why they may arise. A key feature of these methods is the capacity for multimodal data processing, as well as analysis at micro and macro levels simultaneously. This facilitates an understanding of the relationship between units and performance level structure. I studied two species to test for the presence of musicality within their vocalizations. In the Australian pied butcherbird I investigated temporal regularity in phrase types and demonstrated a characteristic balance analogous to that found in music. In the thrush nightingale I studied regularity in song rhythms and found that performance nuances used in groove rhythms follow similar principles in the context of music and birdsong alike. Australian pied butcherbird song phrases are built from the rearrangement of shared motifs (syllables or stereotyped groupings of notes). If the function of these motifs is to increase the repertoire of different phrase types, then transition probabilities between phrase types should capture most of the structure of singing performances. Alternatively, phrase types can be seen as varied presentations of shared themes, as often is the case in music. If this is the case, temporal regularity in performing shared motifs should be observed beyond phrase types, as if the transitions between phrases are designed to ‘organize’ those motifs over longer time scales. I tested which of those two views can explain more statistical regularity during entire singing performances of wild Australian pied butcherbirds, including thousands of song syllables recorded without interruption for each bird. I found that all birds produced several highly stereotyped phrase types. Most phrase types produced by each bird had shared motifs. Throughout the performance, the temporal gap between a motif’s reappearance was much more regular than what was expected by chance. In contrast, regularity in the performance of phrase types was much weaker. I developed a statistical estimate of the extent to which transition probabilities between phrase types are ‘optimized’ to maximize regularity in the repetition of shared motifs. I found that the phrase-types syntax is selective in achieving a regular repetition of shared motifs over the entire singing performance of the bird. This effect was stronger in birds with a richer song repertoire, suggesting the intriguing possibility that birds may regulate the temporal diversity of dominant themes in their singing performance in a manner that takes their repertoire size into account. The thrush nightingale is a distant relative of the pied butcherbird so it would be surprising to find similarities in the deep structure of the two species. I test whether or not thrush nightingales distribute motifs throughout a performance uniformly as butcherbirds do. I found that thrush nightingales exhibit more regularity in their distribution of phrase types than what is expected from chance. However, I failed to find a distribution of motif types that was balanced against repertoire size. The thrush nightingale ends many of its song phrases with buzzes (or rattles). Upon closer inspection these buzzes emerge from a diversity of repetitive rhythmic patterns of clicks. These clicks are repeated at a regular pace, or in rhythmic groups of two, three, and four or more and they sound like the complex grooves of a jazz drummer. I tested whether or not these patterns contain timing relationships that coincide with small integer ratios and found a no significant bias for small integer ratios. I tested whether or not the range of rhythmic ratios used could be explained by any systematic trend. I tested whether or not thrush nightingales, like jazz drummers adjust their “swing ratio” according to tempo. Swing ratio is a term that describes the non-isochronous manner in which jazz musicians interpret eighth note rhythms, using a “long-short” pattern instead of equal timing between beats. Jazz drummers tend to use a longer long segment at slow tempos and more even segments at fast tempos. I found that thrush nightingales have a significant tendency to adjust the swing ratio in the same manner.
THE ROLE OF Na+/H+ EXCHANGER-1 (NHE1) IN MAMMARY BRANCHING MORPHOGENESIS AND MAINTENANCE OF TISSUE ARCHITECTURE
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Branching morphogenesis in vivo is a highly ordered process that necessitates spatially and temporally choreographed cues by growth factors and hormones, as well as mechanical and signal feedback from the extracellular matrix. Successful completion of this developmental process results in the architectural, and thereby the functional, basis for the lung, collecting ducts of the kidney, salivary, and mammary glands. The quest to understand the basic biological mechanisms underlying this developmental morphogenesis has lead to many seminal findings in the field of epithelial tube generation, as well as provided valuable insight into the pathogenesis of cancer. The primary focus of this thesis was elucidating the role of the Na+/H+ exchanger type 1 (NHE1) in branching morphogenesis of the mouse mammary gland. To accomplish this goal, we used three-dimensional (3D) primary tissue culture of mammary gland pieces (organoids) in a four day organotypic assay of growth factor induced branching morphogenesis. NHE1 is a ubiquitously expressed master regulator of intracellular pH (pHi). We found that blocking the function of this exchanger in the presence of growth factor stimulation led to altered kinase signaling, inhibition of growth factor induced alkalization, sustained proliferation after four days, ectopic expression of keratin 6 (K6), and a dramatic failure to undergo branching morphogenesis. These findings led us to question the role of NHE1 in the maintenance of branched mammary tissue architecture. We, therefore, inhibited NHE1 function on fully branched structures in our assay and found that NHE1 inhibition led to rapid loss (within 24 hours) of branched architecture by a process of branch fusion, with complete loss of the branched morphology after four days. This was not accompanied by cell death or altered proliferation, however, we did record altered intracellular pH (pHi) in the end buds of branched structures that had NHE1 inhibited. NHE1 localization, F-actin organization, and myoepthelial cell location were altered in structures that had undergone a loss of architecture, indicating a loss of tissue organization. Finally, we found that NHE1 inhibition resulted in a decrease in mammary Ecadherin. Having found that NHE1 function is vital for both branching morphogenesis and the maintenance of branched architecture, we considered the role that NHE1 could be playing in the pathology of breast cancer. Both intracellular and extracellular pH is deregulated in cancer. This could be attributed to over activity of NHE1. Additionally, NHE1 is over expressed in many cancers. We used the ER+ breast cancer cell line MCF7 to investigate the therapeutic potential of chemotherapy augmentation by NHE1 inhibition. We found that Cycylophosphamide, a DNA alkylating chemotherapeutic agent known to be more effective in an acidic environment, was roughly 5 times more effective when used along with NHE1 inhibition. These findings indicate that NHE1 is a critical regulator of branching morphogenesis and tissue stability, as well as suggests a potential therapeutic target for the treatment of breast cancer.
CULTURAL EVOLUTION IN NATURAL POPULATIONS: A QUANTITATIVE BIOACOUSTIC ANALYSIS
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Bird song is a powerful model system in behavioral biology, especially for learning and cultural evolution. Understanding the origins and maintenance of vocal diversity in nature is fundamentally important to acoustic biology. Here, we propose a large-scale, integrative population analysis of nearly 2000 songs of the house finch (Haemorhous mexicanus) (190 individuals) collected in western Long Island of New York during an interval of 37 years (between 1975 and 2012) to explore cultural change of bird songs. Generally, I have three aims in this study. In the chapter 1, to facilitate acoustic analysis for field recordings with ambient noise, of large sample sizes and with continuous variation, I introduce an algorithm (FinchCatcher), which extract signals from the background noise, summarizes songs as a series of spectral shapes and performs dynamic classification that optionally combine the advantages of hierarchical clustering and partitioning. I further test the algorithm on a geographical comparison of 240 songs of the house finch from eight localities, using previously published observations as ground truth for estimating transitions of song (or song element) sharing during the spread of the house finch in North America. In Chapter 2, I quantify spatial variation in the songs of the house finch in western Long Island in 2012. Previous studies have suggested large morphological and behavioural differences between house finches in the east and west coast, which may have profound impact on song evolution of eastern house finch. The result shows great acoustic variation across the sampling range, rather than finding discrete areas within which song and syllable repertoires are highly similar between individuals. Nevertheless, spatial differentiation was neither simply clinal change with geographic distance, nor discrete dialects. To further explore the mechanisms underlying cultural change in this study region, in Chapter 3 I perform a temporal comparative analysis of house finch songs spanning nearly four decades. Substantial cultural change is observed in terms of local song and syllable sharing, song complexity and song type consistency. In addition, not a single song type persists over time and half of syllable types defined in the past data are not present in the recent songs. These results illustrate the potential interplay between multiple drivers of spatial and temporal variation. This body of research has provided a framework for understanding the spatiotemporal variation in house finch song in Western Long Island, incorporating partial migration, population growth, relaxed selection by females on male song, and developmental stress playing interacting roles.