Putting the Pieces Together: Exons and piRNAs: A Dissertation

Analysis of gene expression has undergone a technological revolution. What was impossible 6 years ago is now routine. High-throughput DNA sequencing machines capable of generating hundreds of millions of reads allow, indeed force, a major revision toward the study of the genome’s functional output—the transcriptome. This thesis examines the history of DNA sequencing, measurement of gene expression by sequencing, isoform complexity driven by alternative splicing and mammalian piRNA precursor biogenesis. Examination of these topics is framed around development of a novel RNA-templated DNA-DNA ligation assay (SeqZip) that allows for efficient analysis of abundant, complex, and functional long RNAs. The discussion focuses on the future of transcriptome analysis, development and applications of SeqZip, and challenges presented to biomedical researchers by extremely large and rich datasets

Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation

Many RNAs, including pre-mRNAs and long non-coding RNAs, can be thousands of nucleotides long and undergo complex post-transcriptional processing. Multiple sites of alternative splicing within a single gene exponentially increase the number of possible spliced isoforms, with most human genes currently estimated to express at least ten. To understand the mechanisms underlying these complex isoform expression patterns, methods are needed that faithfully maintain long-range exon connectivity information in individual RNA molecules. In this study, we describe SeqZip, a methodology that uses RNA-templated DNA-DNA ligation to retain and compress connectivity between distant sequences within single RNA molecules. Using this assay, we test proposed coordination between distant sites of alternative exon utilization in mouse Fn1, and we characterize the extraordinary exon diversity of Drosophila melanogaster Dscam1

Creation of a universal experimental protocol for the investigation of transfer and persistence of trace evidence:Part 1 - From design to implementation for particulate evidence

Understanding the transfer and persistence of different types of trace evidence between different donor and receiving surfaces under specific conditions, circumstances and alleged competing defence and prosecution hypotheses is a significant need. Acquiring such a knowledge base enables hypothesis testing to be undertaken more readily and with greater confidence. A longstanding goal has been to develop a unified approach to transfer and persistence studies which are fit for purpose but also scalable.Here we propose a low cost, universal experimental protocol using a recognised and well researched proxy material for the development and aggregation of ground truth transfer and persistence data at scale. We also propose and provide the tools to enable the creation of an open source and open access data repository of experimental data to act as a resource for practitioners and researchers in addressing transfer and persistence questions

Electrical noise spectroscopy of magnons in a quantum Hall ferromagnet

Collective spin-wave excitations-magnons-in a quantum Hall ferromagnet are promising quasi-particles for next-generation spintronics devices, including platforms for information transfer. Detection of these charge-neutral excitations relies on the conversion of magnons into electrical signals in the form of excess electrons and holes, but if these signals are equal the magnon detection remains elusive. In this work, we overcome this shortcoming by measuring the electrical noise generated by magnons. We use the symmetry-broken quantum Hall ferromagnet of the zeroth Landau level in graphene to launch magnons. Absorption of these magnons creates excess noise above the Zeeman energy and remains finite even when the average electrical signal is zero. Moreover, we formulate a theoretical model in which the noise is generated by equilibration (partial or full, depending on the bias voltage) between edge channels and propagating magnons. Our model, which agrees with experimental observations, also allows us to pinpoint the regime of ballistic magnon transport in our device

Creation of a universal experimental protocol for the investigation of transfer and persistence of trace evidence:Part 2 – Implementation and preliminary data

This is the second paper on the development and implementation of a universal experimental protocol for transfer and persistence of trace evidence. Here, we present the results of five individual researchers who implemented the universal experimental protocol for the first time. Over 2500 images were collected, computationally analysed and statistically compared. The results were shown to be reliable and consistent under all conditions tested and were used to model the rate of loss of transferred particles over a 7-day timescale. The protocol was additionally extended to include a test of camera settings. The protocol was found to be useable and robust in this preliminary trial paving the way for it to be deployed more widely

A Collider Signature of the Supersymmetric Golden Region

Null results of experimental searches for the Higgs boson and the superpartners imply a certain amount of fine-tuning in the electroweak sector of the Minimal Supersymmetric Standard Model (MSSM). The "golden region" in the MSSM parameter space is the region where the experimental constraints are satisfied and the amount of fine-tuning is minimized. In this region, the stop trilinear soft term is large, leading to a significant mass splitting between the two stop mass eigenstates. As a result, the decay of the heavier stop into the lighter stop and a Z boson is kinematically allowed throughout the golden region. We propose that the experiments at the Large Hadron Collider (LHC) can search for this decay through an inclusive signature, Z+2jb+missing Et+X. We evaluate the Standard Model backgrounds for this channel, and identify a set of cuts that would allow detection of the supersymmetric contribution at the LHC for the MSSM parameters typical of the golden region. We also discuss other possible interpretations of a signal for new physics in the Z+2jb+missing Et+X channel, and suggest further measurements that could be used to distinguish among these interpretations.Comment: 23 pages, 5 figures. New in v4: an error fixed in Eq. (13); results unaffecte

Nucleation and Bulk Crystallization in Binary Phase Field Theory

We present a phase field theory for binary crystal nucleation. In the one-component limit, quantitative agreement is achieved with computer simulations (Lennard-Jones system) and experiments (ice-water system) using model parameters evaluated from the free energy and thickness of the interface. The critical undercoolings predicted for Cu-Ni alloys accord with the measurements, and indicate homogeneous nucleation. The Kolmogorov exponents deduced for dendritic solidification and for "soft-impingement" of particles via diffusion fields are consistent with experiment.Comment: 4 pages, 4 figures, accepted to PR