Identification of Chromatin Regulators Perturbed in Hematopoietic Stem and Progenitor Cell Aging

As lifespan is increasing globally, there is a critical need to identify strategies to extend healthspan and prevent chronic diseases into older age. The long-term goal of my research is to identify novel strategies to ameliorate aging-induced decline in hematopoietic stem cell (HSC) function. HSCs give rise to all mature blood and immune cells. With age, HSCs undergo defects in their differentiation ability which correlates with a decline in immune function. Comprehensive knowledge of gene regulatory and epigenetic mechanisms underlying this defect is a barrier to developing therapies to ameliorate aging-associated decline in HSC function. Therefore, my project focuses on understanding the gene regulatory mechanisms underlying this decline in HSC function. Before delving into the gene regulatory mechanisms that go awry with age, it is important to identify which mechanisms are important for the differentiation of HSCs to mature cells. The majority of screening approaches for the identification of novel genes and gene regulatory elements rely on robust in vitro assays. In my thesis work, I have demonstrated in my thesis work that one such assay widely used in the field to differentiate hematopoietic stem and progenitor cells (HSPCs) to B-lymphoid cells performs in a qualitative rather than a quantitative manner which provides implications for interpretations of results this assay. Also, by mining publicly available gene expression data sets and data from an unpublished shRNA knockdown screen, I have identified that the epigenetic regulator lysine acetyltransferase 6b (Kat6b) is important for HSC function as well as demonstrated that KAT6B levels are significantly decreased in expression in aged long term-hematopoietic stem cells (LT-HSCs) at the transcript and protein levels, using qPCR and immunofluorescence. In addition, I have observed that knockdown of Kat6b leads to enhanced myeloid differentiation from LT-HSCs by using in vitro and in vivo assays which partially replicates aging-associated hematopoietic phenotypes. Transcriptome analysis suggests that Kat6b knockdown in LT-HSCs leads to dysregulation of differentiation signatures and an increase in inflammation. These data support increasing the levels of Kat6b as a novel therapeutic strategy for ameliorating aging-associated hematopoietic decline

Optical properties of split ring resonator metamaterial structures on semiconductor substrates

Metamaterials based on single-layer metallic Split Ring Resonators (SRR) and Wires have been demonstrated to have a resonant response in the near infra-red wavelength range. The use of semiconductor substrates gives the potential for control of the resonant properties of split-ring resonator (SRR) structures by means of active changes in the carrier concentration obtained using either electrical injection or photo-excitation. We examine the influence of extended wires that are either parallel or perpendicular to the gap of the SRRs and report on an equivalent circuit model that provides an accurate method of determining the polarisation dependent resonant response for incident light perpendicular to the surface. Good agreement is obtained for the substantial shift observed in the position of the resonances when the planar metalisation is changed from gold to aluminium

Characterisation at infrared wavelengths of metamaterials formed by thin-film metallic split-ring resonator arrays on silicon

The infrared reflectance spectra at normal incidence for split-ring resonator arrays fabricated in thin films of three different metals on a silicon substrate are reported. The results are compared with a finite difference time domain simulation of the structures and a simple and novel equivalent-circuit method for the calculation of the first and second resonant wavelengths

Increasing optical metamaterials functionality

Gold Split Ring Resonators (SRRs) were fabricated on silicon substrates by electron beam lithography and lift-off, with overall dimensions of approximately 200 nm. Reflectance spectra from the SRRs are similar to those published elsewhere. New devices are proposed based on the additional functionality afforded by the use of a silicon substrate

Synthesis of bifunctional alkenes for nucleophile-controlled selenocyclizations

Synthesis of an olefin containing two functional groups, a hydroxy and an acid functionality has been successfully achieved. A methodology for highly selective cyclizations with phenylselenenyl electrophiles has been developed. The exclusive formation of substituted tetrahydrofurans can be achieved using triflate as the counterion and with the addition of acetic acid, whereas cyclizations can also be directed towards complete formation of lactones using hexafluorophosphate or sulfate as the counterion and methanol as an additive. A series of chiral diselenides were synthesized and employed in cyclization of bifunctional olefins. Highest selectivity was obtained with a chiral methoxy substituted alcohol diselenide. A comparison of endo- versus exo-cyclization was estimated using dihydroxy olefins with selenium and iodine electrophiles. The obtained results showed highest diastereomeric ratios in the endo-cyclization compared to exo-cyclization. Cyclization reactions of olefins can lead to heterocycles, which serve as essential building blocks for the synthesis of useful natural products. The most common building blocks are based on lactone and substituted tetrahydrofuran structures and are commonly obtained from individual substrates. The aim was to synthesize an olefin that contained two functional groups: a hydroxy and an acid functional group. 5-exo-cyclization via the hydroxy group of this olefin with an electrophile resulted in substituted tetrahydrofurans while the cyclization via the acid functionality resulted in the formation of lactones. A series of reactions using different additives and a variety of counterions with selenium electrophiles led to the discovery of selective cyclization conditions of each cyclized product. Using phenylselenenyl triflate in the presence of acetic acid the reaction led exclusively to the formation of substituted tetrahydrofurans while lactones could be obtained using hexafluorophosphate or sulfate as a counterion and methanol as an additive. The selective synthesis of each cyclized product indicated the influence of additives on the course of cyclization. The additives (alcohol and the acid) were than incorporated into the selenium reagents. The expected coordination of the selenium electrophile to internal heteroatoms or to the substrate led to independent cyclization and there was no influence of additives on the course of cyclization. As expected, these modified achiral selenium reagents produced a 1:1 mixture of substituted tetrahydrofurans and lactones. The enantioselectivity of known chiral selenium electrophiles containing the heteroatom in a 1,3-relation to the selenium was studied in the reaction with this olefin and the highest selectivity was found with the methoxy substituted alcohol diselenide. To increase the selectivity the synthesis of new chiral selenium reagents were attempted. The synthesis of modified sulfur selenium reagents was carried out according to the reference of Tiecco et al. but showed a lower selectivity in reaction with this substrate. To investigate the results between 5-endo and 5-exo -cyclization other bifunctional olefins containing a dihydroxy functionality were synthesized. The reaction of these olefins with selenium and iodine electrophiles gave a comparison of endo- versus exo-cyclization. The major isomer from exo-cyclization was the cis isomer while in endo-cyclization it was the trans isomer

Alternative splicing and protein diversity: plants versus animals

Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses

Smooth Growth of Organic Semiconductor Films on Graphene for High-Efficiency Electronics

High-quality thin films of conjugated molecules with smooth interfaces are important to assist the advent of organic electronics. Here, we report on the layer-by-layer growth of the organic semiconductor molecule p-sexiphenyl (6P) on the transparent electrode material graphene. Low energy electron microscopy and micro low energy electron diffraction reveal the morphological and structural evolution of the thin film. The layer-by-layer growth of 6P on graphene proceeds by subsequent adding of {(111)} layers