Use of RNA secondary structure for evolutionary relationships : investigating RNase P and RNase MRP : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, New Zealand

Bioinformatics is applied here to examine whether RNA secondary structure data can reflect distant evolutionary relationships. This is important when there is little confidence in sequence data such as when looking at the evolution of RNase MRP (MRP). RNase P (P) and RNase MRP (MRP) are ribonucleoproteins (RNPs) that are involved in RNA processing and due to functional and secondary structure similarities, are thought to be evolutionary related. P activity is found in all cells, and fits the criteria for inclusion in the RNA world (Jeffares et al. 1998). MRP is found only in eukaryotes with essential functions in both the nucleus and mitochondria. The RNA components of P and MRP (pRNA and mrpRNA) cannot be aligned with any certainty, which leads to a lack of confidence in any phylogenetic trees constructed from them. If MRP evolved from P only in eukaryotes then it is an exception to the general process of the transfer of catalytic activity from RNA, to ribonucleoproteins, to proteins (Jeffares et al. 1998). An alternative possibility that MRP evolved with P in the RNA world (and has since been lost from all but the eukaryotes) is raised and examined. Quantitative comparisons of the pRNA and mrpRNA biological secondary structures have found that the third possibility of an organellar origin of MRP is unlikely Results show that biological secondary structure can be used in the evaluation of an evolutionary relatedness between MRP and P and may be extended to other catalytic RNA molecules. Although there are many protein families, this may be the first evidence of the existence of a family of RNA molecules, although it would be a very small family. Secondary structures derived with folding programs from pRNA and mrpRNA sequences are examined for use in the characterisation of catalytic RNA sequences. The high AT content in organellar genomes may hinder the identification of their catalytic RNA sequences. A search strategy is developed here to address this problem and is used to identify putative pRNA sequences in the chloroplast genomes of four green plants. A maize chloroplast pRNA-like sequence is examined in more detail and shows many characteristics seen in known pRNA sequences. Folding programs show some potential for the characterisation of possible catalytic RNA sequences with only a small bias in the results due to sequence length and AT content

Performing an aseptic technique in a community setting : fact or fiction?

Background - Maintaining the principles of asepsis when performing wound care and other invasive procedures is one of the fundamental approaches of preventing healthcare-acquired infection. Such an approach has been advocated for community practitioners. Literature - The performance of an aseptic technique is an under-researched area. The few studies that have been conducted have identified how strict adherence to the technique is difficult and contamination of hands/gloves is common and that community nurses often have a fatalistic view about whether asepsis is possible in a community setting. Aim - The overall aim of this research project was to examine how experienced practitioners have adapted the aseptic technique within a community setting and to what extent the changed procedure still adhered to the principles of asepsis. Methods - This study used a mixture of non-participant observation and individual semi-structured interviews to examine adherence to the principles of the aseptic technique among the district nurses. Data were collected from one Trust in England with a total of 10 district nurses taking part and 30 aseptic procedures been observed. Results - The results show that almost all of the staff understood the principles of asepsis and had adapted the standard procedure for use in a patient’s home. Common challenges included wound cleaning using a single nurse procedure, the contents of the pack and the home environment. The research also identified misconceptions about clean versus aseptic procedures and a lack of training for staff. Conclusions - This study highlights the challenges of maintaining the principles of asepsis in a home environment and the fact that district nurses are often relied upon to find creative solutions to such challenges. The study also highlights issues around the implementation of evidence-based practice and the need for clearer guidance about how evidence should be used alongside existing procedures

Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology

ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases

Interview with Master teacher Tanya Channell

Interview with Master Teacher Tanya Channell -- Masters Project Proposal. In partial fulfillment of Educational Research ACES 803. Presented to Dr. Allan Miller, Fort Hays State University.https://scholars.fhsu.edu/ors/1219/thumbnail.jp

The Lived Experiences of Adult Children of Mid to Later-life Parental Divorce: An Interpretative Phenomenological Analysis

This study examined the lived experiences of adult children of mid-later life parental divorce. It was designed and conducted to address the gap in the current literature regarding this phenomenon. The experiences of 5 Adult Children of Divorce (ACD) ages 25 to 45, who experienced mid-later life parental divorce, were examined using in-depth semi-structured interviews. The researcher employed an interpretive phenomenological analysis (IPA) of which the findings illustrated various outcomes for adults experiencing their parents’ mid-later life divorce. The results of this study showed that parents’ waiting until the children are “grown” does not mitigate potentially detrimental outcomes for these “adult children.” Some of these concerns shared by the ACDs interviewed included: dealing with the shock of the divorce, the acrimonious parental relationships post divorce, feeling the need to choose sides, effects of the divorce on the ACDs\u27 children, among others. Future studies and implications for the field of marriage and family therapy were offered

High burden of pulmonary tuberculosis and missed opportunity to initiate treatment among children in Kampala, Uganda

Background: There is uncertainty about the actual burden of childhood TB in Uganda, but underestimation is acknowledged. We aimed at determining prevalence, factors associated with PTB among children attending PHC facilities in Kampala. Methods: This was a cross-sectional study of 255 children, with presumed TB, attending six health facilities in Kampala, Uganda, in March 2015. Socio-demographic, clinical, and laboratory data were collected using a questionnaire. TB was diagnosed using “Desk Guide” algorithms. Sputum based on ZN/FM and/or Gene-Xpert. Logistic regression was used to assess associations with outcomes. Results: Overall, prevalence of PTB 13.7 % (2.6 – 24.8). Among HIV-positive, the prevalence of PTB was 41.7%, while among malnourished children, 21.7% and contacts, 89.3%. The factors that influenced PTB included: tobacco smoker at home (OR =1.6, 95 % CI: 1.07 – 6.86), stunting (OR = 2.2, 95 % CI: 1.01 – 4.15). Only 5.3% of the smear-negative TB children and 81.3% of the smear-positive children were initiated on treatment within a month of diagnosis. Conclusion: Clinical TB among children is underdiagnosed and undertreated. There is a need for more sensitive and specific diagnostic tests, need ways to disseminate and promote uptake of standardized clinical algorithms. Also, contact TB tracing should be strengthened so that such cases can be actively detected even at community level. Keywords: Pediatric; pulmonary; tuberculosis

Neural network parametrization of the lepton energy spectrum in semileptonic B meson decays

We construct a parametrization of the lepton energy spectrum in inclusive semileptonic decays of B mesons, based on the available experimental information: moments of the spectrum with cuts, their errors and their correlations, together with kinematical constraints. The result is obtained in the form of a Monte Carlo sample of neural networks trained on replicas of the experimental data, which represents the probability density in the space of lepton energy spectra. This parametrization is then used to extract the b quark mass m_b^{1S} in a way that theoretical uncertainties are minimized, for which the value m_b^{1S}=4.84 \pm 0.14^{exp}\pm 0.05^{th} GeV is obtained.Comment: 32 pages, 22 figures, JHEP3 class. v4 version accepted for publication in JHE

The Ultraviolet Imaging Telescope: Instrument and Data Characteristics

The Ultraviolet Imaging Telescope (UIT) was flown as part of the Astro observatory on the Space Shuttle Columbia in December 1990 and again on the Space Shuttle Endeavor in March 1995. Ultraviolet (1200-3300 Angstroms) images of a variety of astronomical objects, with a 40 arcmin field of view and a resolution of about 3 arcsec, were recorded on photographic film. The data recorded during the first flight are available to the astronomical community through the National Space Science Data Center (NSSDC); the data recorded during the second flight will soon be available as well. This paper discusses in detail the design, operation, data reduction, and calibration of UIT, providing the user of the data with information for understanding and using the data. It also provides guidelines for analyzing other astronomical imagery made with image intensifiers and photographic film.Comment: 44 pages, LaTeX, AAS preprint style and EPSF macros, accepted by PAS

Biodiversity in changing environments: An external‐driver internal‐topology framework to guide intervention

Accompanying the climate crisis is the more enigmatic biodiversity crisis. Rapid reorganization of biodiversity due to global environmental change has defied prediction and tested the basic tenets of conservation and restoration. Conceptual and practical innovation is needed to support decision making in the face of these unprecedented shifts. Critical questions include: How can we generalize biodiversity change at the community level? When are systems able to reorganize and maintain integrity, and when does abiotic change result in collapse or restructuring? How does this understanding provide a template to guide when and how to intervene in conservation and restoration? To this end, we frame changes in community organization as the modulation of external abiotic drivers on the internal topology of species interactions, using plant-plant interactions in terrestrial communities as a starting point. We then explore how this framing can help translate available data on species abundance and trait distributions to corresponding decisions in management. Given the expectation that community response and reorganization are highly complex, the external-driver internal-topology (EDIT) framework offers a way to capture general patterns of biodiversity that can help guide resilience and adaptation in changing environments

Understanding the Virginia Literacy Act

This research and policy brief from the Metropolitan Educational Research Consortium (MERC) offers an overview of the Virginia Literacy Act. It is structured to explore the following questions: 1) What are the recent trends in reading achievement in Virginia? 2) What are the policy implications of the VLA for Virginia school divisions? 3) What does the research say about Science of Reading (SoR)? 4) What core instructional programs are approved to meet the VLA? It concludes with a series of key takeaways and recommendations