Dynamics of chromatin remodelling during plant cell differentiation

Cell differentiation is the process by which a pluripotent cell acquires a determined, specialised state. This process relies on the precise spatiotemporal control of gene expression, which is partly regulated at the level of chromatin architecture. Chromatin is a complex of nucleic acids and histone proteins which compresses DNA to fit in the cell nucleus. The structure of chromatin modulates the ability of eukaryotic cells to respond to developmental cues. It does so by regulating the accessibility of DNA to transcription factors and the RNA polymerase transcriptional machinery. Histone post-translational modifications are key contributors to the regulation of chromatin architecture during development. This thesis investigates the key histone modifications associated with plant cell differentiation, and the role of auxin, cytokinin and brassinosteroids in guiding chromatin changes during plant cell differentiation. This entailed conducting numerous experiments on the model plant Arabidopsis thaliana, including observing the effect of loss of function of histone-modifying enzymes on root cell differentiation and cytokinin response. In addition, this thesis examined the effect of disturbing the balance of phytohormones on VASCULAR-RELATED NAC-DOMAIN 7 (VND7)- induced xylem transdifferentiation. Finally, protein-protein interaction assays were conducted to identify molecular interactions between hormone signalling genes and histone-modifying enzymes. These experiments revealed that some loss-of-function mutants had a significantly different root meristem size to the wildtype and an impeded cytokinin response. This highlights the regulatory role of chromatin architecture in cell differentiation and indicates that hormone signals may guide histone-modifying enzymes during cell differentiation. Furthermore, disrupting the phytohormone balance resulted in defective VND7-induced xylem transdifferentiation, suggesting that a specific hormonal framework may be necessary to promote VND7 activity. Finally, the negative regulator of brassinosteroid signalling, BR-INSENSITIVE 2 (BIN2), was found to interact with histone methyltransferases SU(V AR)3–9-RELA TED 5 (SUVR5), SU(VAR)3–9 HOMOLOG 5 (SUVH5) and CURLY LEAF (CLF)

Tackling Rapid Radiations With Targeted Sequencing

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiationsEspaña Ministry of Economy and Competitiveness (project CGL2016- 77401-P

DNA extraction from old herbarium material of Veronica subgen. Pseudolysimachium (Plantaginaceae)

Herbarium specimens have become a major source of information in molecular biodiversity research, framing the term "herbarium genomics". However, obtaining good DNA from old herbarium specimens is still a challenge. Currently, DNA extraction methods from old herbarium material often yield highly degraded and fragmented DNA. A number of studies have discussed such methods, especially how to avoid further DNA fragmentation. This study aims to compare different DNA extraction methods applied to old herbarium material from Veronica subg. Pseudolysimachium. One such method is a CTABbased DNA extraction followed by a clean-up with paramagnetic beads that is used in the Jodrell Laboratory, Royal Botanic Gardens Kew, UK. This method was compared to a modified NucleoSpin Plant II protocol, based on silica columns, as used at the Technical University Munich-Freising, which was already successfully used for extracting DNA from a Linnean type specimen. Further tests were conducted on the influence of incubation time on the CTAB DNA extraction protocol with a subsample of specimens. Our preliminary results suggest that CTAB DNA extraction might have some advantages in specific cases but also that silica column-based methods have fewer problems with contamination by polysaccharides and polyphenolic compounds. Regarding the incubation time, we did not observe a clear pattern, but we developed several ideas on how to proceed with tests to find an optimal DNA extraction protocol to deal with highly fragmented DNA. Taking practical considerations into account, the column-based method proves to be preferable, especially when trying to reduce the amount of leaf tissue used, but further modifications of both methods should be explored

Identifying Needs of Potential Transfer Students of Color to Enhance Equity and Inclusion in the College of Health Professions

State Council of Higher Education of Virginia (SCHEV)1 data indicate disparities in recruitment and retention outcomes for transfer students of color and those of Hispanic ethnicity compared to non-Hispanic White peers. With the goal of enhancing equity and inclusion while diversifying the health professions, this project characterizes the needs of this population to inform the development of a new bachelor’s program within the College of Health Professions. The project provides recommendations based on data collected from both prospective and current VCU transfer students

Tackling rapid radiations with targeted sequencing

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations

Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.

Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing in order to: (1) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae and Cypereae; (2) define the limits of Fuireneae s.s., and (3) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognise as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr.nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub‐Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognised tribes and genera are provided

Solo status and women's spatial test performance: the role of individuation tendencies

The impact of anticipated solo status on women's spatial performance was investigated in an experimental study. The study was designed to test whether the underperformance of women entering testing situations who find themselves to be the only woman present is related to a tendency to individuate the self. Women performed a test of spatial ability under conditions of anticipated solo or non-solo status and responded to a measure of self-construal. In line with previous research, we found a disrupting solo status effect on women's performance on the spatial ability test. Most importantly, the negative effect of solo status on performance was partially mediated by individuation tendencies as reflected in a decreased predominance of the interdependent (as compared to the independent) level of the self under solo status conditions. These findings indicate that individuation tendencies play a crucial role in the process triggered in test takers under threatening performance situations. Copyright © 2007 John Wiley & Sons, Ltd.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/60972/1/490_ftp.pd

Occupation and motor neuron disease: a New Zealand case-control study.

OBJECTIVES: To assess associations between occupation and motor neuron disease (MND). METHODS: We conducted a population-based case-control study with cases (n=321) recruited through the New Zealand Motor Neurone Disease Association and hospital discharge data. Controls (n=605) were recruited from the Electoral Roll. Information on personal and demographic details, lifestyle factors and a full occupational history was collected using questionnaires and interviews. Associations with ever/never employed and employment duration were estimated using logistic regression stratified by sex and adjusted for age, ethnicity, socioeconomic deprivation, education and smoking. RESULTS: Elevated risks were observed for field crop and vegetable growers (OR 2.93, 95% CI 1.10 to 7.77); fruit growers (OR 2.03, 95% CI 1.09 to 3.78); gardeners and nursery growers (OR 1.96, 95% CI 1.01 to 3.82); crop and livestock producers (OR 3.61, 95% CI 1.44 to 9.02); fishery workers, hunters and trappers (OR 5.62, 95% CI 1.27 to 24.97); builders (OR 2.90, 95% CI 1.41 to 5.96); electricians (OR 3.61, 95% CI 1.34 to 9.74); caregivers (OR 2.65, 95% CI 1.04 to 6.79); forecourt attendants (OR 8.31, 95% CI 1.79 to 38.54); plant and machine operators and assemblers (OR 1.42, 95% CI 1.01 to 2.01); telecommunications technicians (OR 4.2, 95% CI 1.20 to 14.64); and draughting technicians (OR 3.02, 95% CI 1.07 to 8.53). Industries with increased risks were agriculture (particularly horticulture and fruit growing), construction, non-residential care services, motor vehicle retailing, and sport and recreation. Positive associations between employment duration and MND were shown for the occupations fruit growers, gardeners and nursery growers, and crop and livestock producers, and for the horticulture and fruit growing industry. CONCLUSIONS: This study suggests associations between MND and occupations in agriculture and several other occupations

Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1, 2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3, 4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade