Browsing by Subject "Variation"

Recombination is the process in which genetic material is exchanged between one's homologous chromosome pairs during egg or sperm development (meiosis). Recombination is necessary for proper segregation of chromosomes during meiosis, and also plays a role in purging deleterious mutations, accelerating adaptation, and influencing the distribution of genomic features over evolutionary time. While recombination is clearly an important process, recombination rate is known to vary within and between individuals, populations, and species. Furthermore, what causes this variation remains relatively unknown. Using empirical and sequenced based estimates of recombination rate for the closely related species Drosophila pseudoobscura and Drosophila miranda, I seek to understand where recombination happens across the genome, to what extent recombination changes between species, and what genomic features are responsible for these changes. These data will deepen our understanding of mechanisms determining the recombination landscape, and shed light on generalized patterns and exceptions of recombination rate variation across the tree of life.

In an attempt to gain more insight on functional evolution of cAMP-PKA pathway I have taken a comparative approach and examined functional interactions of cAMP-PKA signaling in well-studied yeast developmental programs and closely related Saccharomyces sensu stricto. species. I have shown that variation in cAMP-PKA signaling contributes significantly to variation in developmental responses in S cerevisiae. Variation in pseudohyphal growth and sporulation, two inversely correlated developmental strategies to nutrient limitation in yeast, proportional to variation in intracellular cAMP levels. S. cerevisiae strains proficient in pseudohyphal growth have higher intracellular cAMP concentrations relative to strains that sporulate efficiently. Phenotypic, genetic and signaling data presented here suggest that the cAMP-PKA signaling underlies a phenotypic trade-off between sporulation and pseudohyphal growth in S. cerevisiae.

Further investigation into the role of cAMP-PKA signaling in closely related S paradoxus and S bayanus revealed an antagonistic function of cAMP-PKA signaling for developmental responses in S. bayanus. Unlike in S. cerevisiae, increased cAMP concentrations surprisingly inhibit pseudohyphal response in S. bayanus. Another unanticipated finding in this work is that in S. bayanus. Flo11, required for pseudohyphal differentiation in S. cerevisiae, is dispensable. Additionally, interactions of cAMP-PKA signaling and the general-stress response mechanism appear reversed in S. bayanus. As shown by deletion mutation, gene expression and pharmacological treatment data, altered interactions and alternative targets downstream of cAMP-PKA could critically contribute to alternative regulation of nutrient-induced development in S. bayanus.

Intracellular cAMP concentrations show decaying oscillations upon glucose replenishment in derepressed yeast cells. The quantitative characteristics of oscillations are distinct within and between Saccharomyces species. Given the tight regulation of cAMP levels and its critical role, the variation in cAMP oscillatory dynamics could be reflective of differential interactions of cAMP-PKA signaling that also underlie induction of developmental programs to changing environments. As such, intracellular cAMP levels and dynamics could potentially be used as molecular phenotypes.

The centromere serves as the foundation for the kinetochore and attachment point for spindle microtubules during metaphase. The proper function of this locus is required to ensure chromosome segregation and genomic stability. In humans, repetitive alpha satellite DNA underlies the human centromere region and is organized into specific chromatin domains that are maintained by a complex combination of factors. Although the centromere region is generally thought to be specified epigenetically, some evidence suggests that the underlying DNA sequence is also involved in centromere function. To better define links between alpha satellite and function within the human centromere region, we investigated two attributes of alpha satellite DNA: its transcription into noncoding alpha satellite RNAs and genomic variation within the alpha satellite array. Noncoding transcripts produced from alpha satellite DNA are associated with normal centromere and pericentromere function and evidence from other organisms suggests RNAs from this region are pivotal in the centromere and kinetochore assembly cascade and in maintaining the chromatin environments of the centromere region. However, alpha satellite RNAs have not yet been fully characterized and data reflecting the chromosome-specific nature of alpha satellite arrays is lacking. Additionally, genomic variation within alpha satellite arrays has been linked to reduced centromere protein recruitment and chromosome instability, yet the molecular basis for this is unknown. These gaps in knowledge have stymied our understanding of the role of genomic and epigenetic attributes of alpha satellite that affect function within the human centromere region. Thus, this work aims to functionally characterize the role of alpha satellite transcripts and to determine how genomic variation impacts chromosome stability. Utilizing cytological and molecular techniques that allow the differentiation of alpha satellite RNAs from individual chromosomes and arrays, we have demonstrated that each chromosome produces unique noncoding RNAs that localize in cis to their site of production. Both centromeric and pericentromeric alpha satellite arrays produce noncoding RNAs, but these transcripts are spatially and functionally distinct. Alpha satellite RNAs from the centromere bind at least two key centromere proteins: CENP-A and CENP-C, while alpha satellite RNAs from the pericentromere colocalize with SUV39H1. Centromeric alpha satellite RNAs are required for complete loading of new CENP-A-containing nucleosomes, as well as maintenance of CENP-C levels. Genomic variation affects the origin of alpha satellite transcripts, such that highly variant arrays produce a different set of transcripts than wild type arrays. Further, the long-range organization of variation across the alpha satellite array in unstable chromosomes suggests certain spatial organizations of variation are poor platforms for building a stable centromere and kinetochore. Collectively, these findings implicate alpha satellite RNA and genomic variation and/or the interplay of these two elements as essential factors in the function of the human centromere region.

Recordings of speech play a central role in the diverse subdisciplines of linguistics. The reliance on speech recordings is especially profound in sociolinguistics, where scholars have developed a range of techniques for eliciting and analyzing natural talk. Despite the focus on naturalistic speech data, sociolinguists have rarely focused explicitly on the management (e.g. organization, storage, accessibility, and preservation) of their data, and this lack of focus has had consequences for the advancement of the field. At the same time, the interviews that sociolinguists labor so hard to obtain are often barely mined for their full potential to further our understanding of language. That is, sociolinguists often focus on a handful of phonological and/or morphosyntactic variables to the exclusion of so many other features of speech. The present work both addresses the management of sociolinguistic data and, through an innovative approach to speech data management and analysis, extends the sociolinguistic lens to include the lesser-examined realm of variation in sequential temporal patterns of talk.

The first part of this dissertation describes the Sociolinguistic Archive and Analysis Project (SLAAP), a web-based digitization and preservation initiative at North Carolina State University. SLAAP, which I principally have designed and developed, is more than an archive; it has actively sought to explicate approaches to spoken language data management and to enrich spoken language data through the development of analytic tools designed specifically for sociolinguistic analysis. This dissertation begins by situating SLAAP within the history of data management practices in the field of sociolinguistics. It then provides an overview of many of SLAAP's features, discussing in particular the transcript model that enables most of its analytic and presentational capabilities.

The second part of this dissertation takes advantage of SLAAP's data model and the extensive language data accumulated within its archive to examine variation in speech rate and silent pause duration by North American English speakers of four ethnicities in North Carolina, Ohio, Texas, Washington, DC, and Newfoundland. This work brings a wide range of previous research from different areas of sociolinguistics, psycholinguistics, and corpus linguistics to bear on an array of quantitative analyses, demonstrating that speech rate and pause exhibit meaningful variation at the social level at the same time as they are also constrained by cognitive and articulatory processes.

Specifically, pause and speech rate are shown to vary by region, ethnicity, and gender - albeit not in mono-directional ways - although other factors arise as significant, including, for speech rate, a strong effect of utterance length as well as a number of interactional or discourse-related factors, such as the gender of the interviewer and the number of participants in the speech event. A number of the examinations undertaken relate sociolinguistic conceptions of style to language production and cognitive processes, including a quantitative analysis of sequential temporal patterns as paralinguistic cues to attention to speech, performativity, and the realization of phonological and morphosyntactic variables. Through this analysis, sociolinguistic data and findings are brought to bear on a tradition of psycholinguistic investigations with the hope to benefit both, often disparate, areas of research.