Patterns of community structure may be examined using phylogenetic and morphological data; these patterns can then be used to infer the processes that gave rise to these patterns. Communities made up of similar species may be structured by habitat filtering, wherein only species with traits necessary to survive in a particular location are found there. Communities made up of dissimilar species may have been structured by competition, which reduces overlap in resource use. I examined the sensitivity of phylogenetic community structure (PCS) metrics to changes in phylogeny and community delimitation method, investigated patterns of PCS and correlation to environmental variables at multiple spatial and taxonomic scales, and assessed whether morphological data gave results similar to phylogenetic data using North American desert bats as a model system. I found that PCS metrics were robust to moderate changes to phylogeny and that these metrics also trend in the same direction regardless of delimitation method. Bat communities tended to be made up of species that were significantly more closely related than expected by chance, or phylogenetically clustered, at large spatial and taxonomic scales; this tendency towards clustering decreases with decreasing scale. Phylogenetically clustered communities also tended to occur in harsher environmental conditions than more overdispersed communities, or those made up of species not closely related. From a morphological perspective, communities were made up of species that were morphologically clustered or not significantly different from random. Morphological community structure was positively correlated with PCS, indicating that these different datasets gave similar results. These results indicate that North American desert bat communities are made up of phylogenetically and morphologically similar species and that environmental variables such as temperature and seasonality may influence community structure. This suggests that habitat filtering is playing a predominant role in structuring these communities.

Circadian clocks are the endogenous timing mechanisms that facilitate organisms to adapt to the daily cycles on the earth. Previous studies have demonstrated that cyanobacterial circadian clock enhances fitness under cyclic environment. In this dissertation, the adaptive value of circadian clocks were further confirmed in cyanobacteria under various culture conditions, and the potential mechanism of the clock-mediated fitness enhancement was explored. By establishing the global metabolic profiles of cyanobacterial strains, I found that the metabolism of cyanobacteria can be affected by the disruption of circadian clocks, which could be the potential mechanism of the clock-mediated fitness enhancement. In addition, a novel timing mechanism driven by kaiCRp, which is a homolog of cyanobacterial central clock gene kaiC, was discovered in a purple non-sulfur bacterium, and this timing mechanism also enhances fitness under light-dark cycles.

The zebrafish epithalamus, which includes the dorsal habenular nuclei and pineal complex, displays robust molecular and anatomical asymmetries. The full elaboration of molecular and anatomical differences between the left and right dorsal habenular nuclei depends on the formation of a left-sided parapineal organ. This work has yielded significant insights into the role of Tbx2b during parapineal development using both the candidate gene approach as well as the non-biased, transcriptome analysis approach. Through the candidate approach, it was determined that Tbx2b acts in a permissive manner during parapineal specification, but it is necessary for proper parapineal migration. Further, the inhibitory roles of Flh and Nr2e3 during formation of parapineal neurons have been characterized. Using RNA-sequencing to perform differential expression analysis between wild-type and tbx2b-deficient pineal complex cells has yielded many targets that are downstream of Tbx2b. Together, these studies also provided a novel insight into a potential genetic interaction system between Tbx2b and Nr2e3 during cone versus rod photoreceptor differentiation.

Transcription by RNA polymerase III (Pol III) requires sequential assembly of Pol III-specific transcription factors. At the tRNA gene, the TFIIIC complex recognizes and specifically binds at intragenic promoter elements A-box and B-box and aids the assembly of TFIIIB to upstream of the transcriptional start site. Upon binding, Pol III is recruited near start sites and transcription of tRNA genes is initiated. Apart from transcription of a gene, these bound Pol III complexes influence transcription, chromatin state and genome organization of neighboring RNA polymerase II (Pol II)-transcribed genes. Such effects are known as extra-transcriptional effects of Pol III complex. Our study provides evidence of a unique extra-transcriptional activity of assembled Pol III transcription complexes at the tRNA gene that blocks progression of intergenic RNA polymerase II transcription. We demonstrated that the Pol III transcription complex bound to the tRNA gene upstream of the Saccharomyces cerevisiae ATG31 gene protects the ATG31 promoter against readthrough transcriptional interference from the upstream non-coding intergenic SUT467. The protection is predominately mediated by binding of the TFIIIB complex. Failure to block this readthrough resulted in compromised ATG31 translation. Given the recent discovery of widespread pervasive transcription in yeast, protection of neighboring genes from intergenic transcriptional interference may be a key extra-transcriptional function of assembled RNA polymerase III complexes. Our data from RNA-seq analysis demonstrated genome-wide effects of DNA bound Pol III complexes on neighboring chromosomal loci, by comparing expression profiles from tfc6 under-expressing mutants and wild-type S. cerevisiae strains. Reduced TFIIIC occupancy in mutant strains altered Pol II derived transcripts and displayed 5 or 3 extension of protein-coding genes, readthrough from non-coding transcripts and increase in the transcription of genes near the potential TFIIIC binding sites, including tRNA genes and putative ETC sites. Interestingly, not all genes in the vicinity of TFIIIC binding sites were transcriptionally mis-regulated, suggesting variable strength of influence on Pol II transcripts by TFIIIC bound sites. Finally, as observed in SUT467-ATG31 readthrough, we anticipated translation defects in 5 or 3 extended transcripts in mutants. Overall these genome-wide results suggest much complex regulatory role of Pol III transcription factors bound sites than previously anticipated.

Many eukaryotes use the ribonucleoprotein telomerase to replenish telomeric sequences lost during conventional DNA replication. In Saccharomyces cerevisiae, telomerase contains the catalytic reverse transcriptase, Est2p, the templating RNA, TLC1, and two accessory proteins, Est1p and Est3p. Little is known about how the components of telomerase assemble away from the telomere. However, studies monitoring the localization of TLC1 RNA have led to the hypothesis that the telomerase complex assembles in the cytoplasm and is imported through a pathway previously shown to transport TLC1. Because Est1p abundance is uniquely cell-cycle regulated, we reasoned that the model for telomerase assembly may involve additional complexity. Here we show that the nuclear localization of Est1p requires three cis-acting nuclear localization sequences (NLSs). Mutation of an NLS within Est1p perturbs telomere maintenance in a manner that is rescued by fusion with an exogenous NLS. Nuclear import of Est1p requires a pathway different from that utilized by TLC1 RNA, indicating that assembly of TLC1 and Est1p in the cytoplasm is unlikely. These investigations reveal that one key step of telomerase biogenesis occurs in the nucleus and have implications for how the cell might regulate other such complexes whose activity is restricted in the cell cycle.

<p>DNA sequencing costs have decreased dramatically over recent decades, resulting in a flood of phylogenetic information available to researchers. While it is often assumed that additional data will lead to more accurate conclusions, it also raises a number of problems for phylogeneticists, including mundane computational issues such as data management and complex statistical problems such as obtaining a single species tree from multiple conflicting gene trees. Developing new methods to make better use of existing data and probe the causes of conflicting signal will be necessary to confidently resolve phylogenies in the genomic era.</p> <p>Here, we examine two current problems in statistical phylogenetics and attempt to address them in a Bayesian framework. The first problem involves inflated tree lengths in Bayesian phylogenies, which can be an order of magnitude longer than maximum likelihood estimates. We developed EmpPrior, a program which queries TreeBASE for datasets similar to the focal data, then estimates parameters from each dataset to inform priors on the focal data. This approach greatly improves the tree length credible intervals in four exemplar datasets and, when combined with other approaches such as the use of a compound Dirichlet prior on tree length, can nearly eliminate the problem of inflated trees.</p> <p>The second problem involves incongruence between morphological and molecular phylogenies in squamates. Here, we use posterior prediction with inferential test statistics to investigate whether systematic error may be biasing inference in the molecular data. While we detected some model violation in most of the 44 genes, the genes with the most model violation were more distant from the molecular phylogeny. This suggests that model violation is not a major source of error in the molecular data. Hence, the source of incongruence between the molecular and morphological squamate topologies remains unknown.</p> <p>In both problems, we found that incorporating tools such as informed priors and posterior prediction from Bayesian statistical literature into phylogenetic analyses can improve results and help uncover why different datasets lead to conflicting topologies. As phylogenetic datasets continue to grow, using methodological best practices will only become more important if we want to have confidence in our conclusions.</p>

Obesity has become a widespread concern to human health largely over the past three decades. It is thought that obesity is associated with the over consumption of calorically dense diets. The rewarding value of food is mediated through the mesolimbic dopamine system, though is less understood how appetitive control circuits relay information to existing reward circuitry. The adiposity signaling hormone, leptin, is a critical mediator of food intake and fat storage. Leptin signaling, via the long form of the leptin receptor (LepRb), is predominantly carried out within the hypothalamus. Leptin action specific to the lateral hypothalamus area (LHA) modulates reward function via direct and indirect inhibition of reward circuitry. Here, I have identified a novel leptin receptor population within the LHA that co-expresses the inhibitory neuropeptide galanin (termed Gal-LepRb neurons). To investigate the physiological function of leptin through Gal-LepRb neurons, we selectively deleted LepRb in galanin neurons (referred to as Gal-LepRbKO mice). In a two-bottle-choice paradigm, I assessed nutrient selection for isocaloric lipid and sucrose solutions. Interestingly, Gal-LepRbKO mice demonstrated a significant preference for the sucrose solution and decreased lipid intake compared to controls. Moreover, Gal-LepRbKO mice displayed stronger motivation to work for a sucrose treat. My data further indicate that Gal-LepRb neurons are inhibitory acting neurons that are stimulated by leptin. Gal-LepRb neurons strongly innervate local orexin neurons and noradrenergic neurons in the locus coeruleus (LC). Intriguingly, orexin neurons also strongly innervate the LC, and activation of orexin neurons correlates with motivational and food-seeking behaviors. My data also show that orexin neurons express the Gi-coupled GPCR galanin 1-receptor (GalR1), validating the cellular ability of orexin neurons to respond to galanin. In summary, we have characterized a novel population of LHA LepRb neurons and propose that leptin-mediated inhibition of orexin neurons, possibly via inhibitory galanin-GalR1 signaling, regulates the reward value of nutrients.

Glacial ice currently occupies roughly 11% of Earths surface and contains approximately 70% of the planets freshwater. Once thought to be inhospitable due to the physiochemical challenges presented by freezing temperatures, the basal zones of glaciers and ice sheets have recently been identified as a potential habitat for psychrophilic microorganisms with the ability to mediate biogeochemical cycles on a global scale. Basal ice is found in the deepest layers of a glacier and has distinct chemical and physical characteristics as a result of its proximity to the glacier bed. Basal ice is generally the warmest ice found in a glacier and often contains entrained debris and sediment from the underlying subglacial substrate which may provide nutrients and redox couples for microorganisms immured in the basal ice matrix. ATP/ADP concentrations and ratios, enrichment culturing, 16S rRNA surveys, and cell counts were combined with nutrient, major ion, and gas chemistry analyses to evaluate the microbial assemblages immured in both sediment-rich and sediment-poor basal ice environments. The primary material for this study was a 4 m profile of basal ice collected from Taylor Glacier (Antarctica) but also included basal ice samples from the Matanuska Glacier (Alaska) and Støre Landgletscher Glacier (Greenland). Microbial community abundance varied significantly between the different basal ice samples and was correlated with the presence of sediment in the ice. Sediment-rich banded basal ice from Taylor Glacier contained elevated concentrations of CO₂ (60,000 to 325,000 ppmv) occurring simultaneously with decreased O₂ concentrations (4 to 18% of total gas volume) suggesting the resident microbial assemblages may be respiring in situ and modifying the gas composition of the basal ice. Molecular surveys of 16S rDNA and rRNA sequences revealed species of the genus Paenisporosarcina to be numerically abundant and active members of the microbial assemblages inhabiting these same basal ice horizons. Members of this genus were readily culturable from the basal ice samples and radiolabeled [³H]-leucine and [³H]-thymidine assays with these isolates revealed their ability to conduct macromolecular synthesis while frozen in basal ice melt-water at -15°C. These results support the hypothesis that basal ice environments are microbial habitats harboring bacteria with the physiological capacity to remain metabolically active and cycle elements within the cryosphere.

No description available.

Data on aspects of the breeding biology of a colony of Kittiwakes in North East England, in which all breeding adults are individually colour-marked, have been collected annually since 1954. The inter-relationships between different factors have been investigated and year-to-year changes in the breeding biology of the colony, related to changes in population structure. Date of return to the colony is shown to be primarily determined by age. Synchrony of return between the members of a breeding pair is associated with the maintenance of the pair bond. Other factors influencing the duration of the pair bond are investigated, including the prior association between the members of the pair, breeding success in the previous year and mortality rates in different years. As birds get older, the main cause of the break-up of the pair bond changes from 'divorce' to bereavement. Time of breeding is related to the location of the nest site (centre or edge of the colony) and the breeding experience of the two members of the pair. There is a tendency for breeding to become more synchronised amongst older age groups, with females laying progressively closer to the mean date of laying for the colony as a whole. The possible interactions between environmental cues, stimulus from the mate and stimulus from the rest of the colony are discussed. Clutch size is shown to be independently influenced by breeding experience, date of laying, location of the nest site and the status of the pair (retention of the same mate as in the previous year, or change). Variations in the size and shape of eggs laid by different females are investigated with respect to many of the above factors.