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

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

Computational Identification of Four Spliceosomal snRNAs from the Deep-Branching Eukaryote Giardia intestinalis

Funding: Marsden Fund New Zealand Allan Wilson Centre The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.RNAs processing other RNAs is very general in eukaryotes, but is not clear to what extent it is ancestral to eukaryotes. Here we focus on pre-mRNA splicing, one of the most important RNA-processing mechanisms in eukaryotes. In most eukaryotes splicing is predominantly catalysed by the major spliceosome complex, which consists of five uridine-rich small nuclear RNAs (U-snRNAs) and over 200 proteins in humans. Three major spliceosomal introns have been found experimentally in Giardia; one Giardia U-snRNA (U5) and a number of spliceosomal proteins have also been identified. However, because of the low sequence similarity between the Giardia ncRNAs and those of other eukaryotes, the other U-snRNAs of Giardia had not been found. Using two computational methods, candidates for Giardia U1, U2, U4 and U6 snRNAs were identified in this study and shown by RT-PCR to be expressed. We found that identifying a U2 candidate helped identify U6 and U4 based on interactions between them. Secondary structural modelling of the Giardia U-snRNA candidates revealed typical features of eukaryotic U-snRNAs. We demonstrate a successful approach to combine computational and experimental methods to identify expected ncRNAs in a highly divergent protist genome. Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes

RNase MRP and the RNA processing cascade in the eukaryotic ancestor

BACKGROUND: Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. RESULTS: We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. CONCLUSION: We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches

Odonata community structure and patterns of land use in the Atewa Range Forest Reserve, Eastern Region (Ghana)

The authors are grateful to Worldwide Dragonfly Association (WDA) for providing fund for this study. Special thanks to Tropical Biology Association (www.tropical-biology.org) for their advice and mentoring. My heartfelt appreciation to Viola Clausnitzer and Klaas-Douwe B. Dijkstra for providing us with the identification hand books and for their immense contribution, mentoring, advice and guidance for the species identifications and towards the successful completion of the study. We are greatly indebted to Robb Fitt for his assistance throughout the data analysis at University of Aberdeen. Finally, to Daniel Acquah-Lamptey, George Ashiagbor, Paul Tehoda, Sulemana Bawa and Emmanuel Amoah, for their role in field data gathering.Peer reviewedPostprin

Odonata assemblages along an anthropogenic disturbance gradient in Ghana’s Eastern Region

The authors are grateful to Rufford Foundation for providing financial support (20322-1) for this study. Special thanks to Tropical Biology Association (www.tropical-biology.org) for their advice and mentoring. My heartfelt appreciation to Viola Clausnitzer and Klaas-Douwe B. Dijkstra for providing us with the identification hand books and for their immense contribution, mentoring, advice and guidance for the species identifications and towards the successful completion of the study. Finally, to David Amaning Kwarteng, Daniel Acquah-Lamptey, Paul Tehoda, Sulemana Bawa and Emmanuel Amoah, for their role in field data gathering.Peer reviewedPublisher PD

Lower protein-to-carbohydrate ratio in maternal diet is associated with higher childhood systolic blood pressure up to age four years

The prenatal environment can influence development of offspring blood pressure (BP), which tracks into adulthood. This prospective longitudinal study investigated whether maternal pregnancy dietary intake is associated with the development of child BP up to age four years. Data are from 129 mother-child dyads enrolled in the Women and Their Children\u27s Health study. Maternal diet was assessed using a validated 74-item food frequency questionnaire at 18 to 24 weeks and 36 to 40 weeks, with a reference period of the previous three months. Child systolic and diastolic BP were measured at 3, 6, 9, 12, 24, 36 and 48 months, using an automated BP monitor. Using mixed-model regression analyses adjusted for childhood growth indices, pregnancy intakes of percentage of energy (E%) polyunsaturated fat (β coefficient 0.73; 95% CI 0.003, 1.45; p = 0.045), E% omega-6 fatty acids (β coefficient 0.89; 95% CI 0.09, 1.69; p = 0.03) and protein-to-carbohydrate (P:C) ratio (β coefficient -14.14; 95% CI -27.68, -0.60; p = 0.04) were associated with child systolic BP trajectory up to 4 years. Child systolic BP was greatest at low proportions of dietary protein (<16% of energy) and high carbohydrate (>40% of energy) intakes. There may be an ideal maternal macronutrient ratio associated with optimal infant BP. Maternal diet, which is potentially modifiable, may play an important role in influencing offspring risk of future hypertension

Transforming Learning: Challenges and Opportunities through School Libraries

Researchers will share papers exploring the SIG theme, Transforming Learning: Challenges and Opportunities through School Libraries. This interactive SIG session includes presentation of each research paper followed by open dialogue and Q&A regarding issues raised by the papers, implications for practice, and future areas for research. The following papers were selected for presentation: Teachers’ Perceptions of Students’ News Literacy (Lesley S. J. Farmer), Lead Like a Librarian (Pamela Harland), Challenges and Opportunities: Transforming Learning through Implementation of the 2018 National School Library Standards for Learners, School Librarians, and School Libraries (Carl A. Harvey II, Jen R. Spisak, Karla B. Collins, and Audrey P. Church), and Discourses of Adolescence/ts and Collection Development (Jenna Spiering and Kate Lechtenberg)

Medical nutrition therapy for gestational diabetes mellitus in Australia : what has changed in 10 years and how does current practice compare with best practice?

Background: The present study aimed to report Australian dietetic practice regarding management of gestational diabetes mellitus (GDM) and to make comparisons with the findings from a 2009 survey of dietitians and with the Academy of Nutrition and Dietetics Evidence-Based Nutrition Practice Guidelines (NPG). Methods: Cross-sectional surveys were conducted in 2019 and 2009 of dietitians providing medical nutrition therapy (MNT) to women with GDM in Australia. The present study compares responses on demographics, dietetic assessment and interventions, and guideline use in 2019 vs. 2009. Results: In total, 149 dietitians (2019) and 220 (2009) met survey inclusion criteria. In both surveys >60% of respondents reported dietary interventions aiming for >45% energy from carbohydrate, 15%–25% energy from protein and 15%–30% energy from fat. Many variations in MNT found in 2009 continued to be evident in 2019, including the percentage of energy from carbohydrate aimed for (30%–65% in 2019 vs. 20%–75% in 2009) and the wide range in the recommended minimum daily carbohydrate intake (40–220 and 60–300 g). Few dietitians reported aiming for the NPG minimum of 175 g of carbohydrate daily in both surveys (32% in 2019 vs. 26% in 2009). There were, however, some significant increases in MNT consistent with NPG recommendations in 2019 vs. 2009, including the minimum frequency of visits provided (49%, n = 61 vs. 33%, n = 69; p < 0.001) and provision of gestational weight gain advice (59%, n = 95 vs. 40%, n = 195; p < 0.05). Conclusions: Although many dietitians continue to provide MNT consistent with existing NPG, there is a need to support greater uptake, especially for recommendations regarding carbohydrate intake

Women\u27s preferences for selective estrogen reuptake modulators: an investigation using the time trade off technique

PurposeSelective Estrogen Receptor Modulators (SERMs) reduce the risk of breast cancer for women at increased risk by 38%. However, uptake is extremely low and the reasons for this are not completely understood. The aims of this study were to utilize time trade-off methods to determine the degree of risk reduction required to make taking SERMs worthwhile to women, and the factors associated with requiring greater risk reduction to take SERMs. MethodsWomen at increased risk of breast cancer (N&thinsp;=&thinsp;107) were recruited from two familial cancer clinics in Australia. Participants completed a questionnaire either online or in pen and paper format. Hierarchical multiple linear regression analysis was used to analyze the data. ResultsOverall, there was considerable heterogeneity in the degree of risk reduction required to make taking SERMs worthwhile. Women with higher perceived breast cancer risk and those with stronger intentions to undergo (or who had undergone) an oophorectomy required a smaller degree of risk reduction to consider taking SERMs worthwhile. ConclusionWomen at increased familial risk appear motivated to consider SERMs for prevention. A tailored approach to communicating about medical prevention is essential. Health professionals could usefully highlight the absolute (rather than relative) probability of side effects and take into account an individual&rsquo;s perceived (rather than objective) risk of breast cancer