The covarion model of molecular evolution : a thesis presented in partial fulfilment of the requirements for the degree of Master of Philosophy in Biology at Massey University

Current methods for constructing evolutionary trees generally do not work well for sequences in which multiple substitutions have occurred. The covarion hypothesis may provide a solution to this problem. This hypothesis states that only a limited number of the codons in a given sequence are free to vary, but that the set of variable codons may change as mutations are fixed in the population. Although this is reasonable from a biological point of view, it is a difficult hypothesis to test scientifically because the apparent large number of parameters involved makes it very hard to analyse statistically. In this study, computer simulations were carried out on up to 51 machines running in parallel, using a simple covarion model based on a hidden Markov model (HMM) approach. This model required two new parameters—the proportion of sites that are variable at any given time, and the rate of exchange between fixed and variable states. These two parameters were both varied in the simulations. Sequence and distance data were simulated on a given tree under this covarion model, and these data were used to test the performance of standard tree-building methods at recovering the original tree The neighbour joining and maximum likelihood methods tested were found to perform better with data generated under the covarion model than with data generated under a simpler model in which all sites vary at the same rate. This suggests that current tree-building methods may perform better with biological data than computer simulation studies suggest

Characteristics of quality teaching for students in New Zealand schools whose first language is not English

The current paper draws on the findings of two recent research reports commissioned by the New Zealand Ministry of Education (Alton-Lee, 2003; Franken & McComish, 2003) in order to generate a synthesised statement of characteristics of quality teaching for students for whom English is not the first language (referred to from here as NESB students1) in New Zealand schools. Alton-Lee (2003, see Ministry of Education website, www.minedu.govt.nz) provides a synthesis of research-based evidence addressing the nature of quality teaching in schooling for the full range of diverse students. In this work, diversity encompasses “many characteristics including ethnicity, socio-economic background, home language, gender, special needs, disability, and giftedness” (Alton-Lee, 2003, p. v). Because her synthesis addresses diversity in the student population, she focusses on what is common to diverse students and thus does not specify particular conditions that pertain to any one sub-group of diverse students. Franken and McComish (2003) on the other hand, is a research report into the English language support for NESB (Non English Speaking Background) students in New Zealand schools. It includes a literature review of evidence-based research into second language teaching and learning, particularly classroom based research. It also reports on observations and analysis of practices in New Zealand schools, and discusses how these documented practices relate to the research findings from the literature

Food Habits of Bigmouth and Smallmouth Buffalo in Lewis and Clark Lake and the Missouri River

Food habits were determined for 386 bigmouth buffalo and 277 smallmouth buffalo collected in 1962 and 1963 from Lewis and Clark Lake and the Missouri River. Young-of-the-year bigmouth buffalo stomachs contained 100 percent zooplankton. Bigmouth buffalo (330 to 530 millimeters) stomachs contained 99 percent zooplankton in 1952 and 95 percent in 1963. Digestive tracts of young-of-the-year smallmouth buffalo contained 99 percent copepods and one percent sand. Smallmouth buffalo (250 to 400 millimeters) contained about 65 percent zooplankton, 30 percent phytoplankton, and the remaining five percent consisted of chironomid larvae, plant detritus, and sand

The influence of acid and direct azo dyes and their intermediates on the degradation of wool keratin. The characterisation by yarn strength measurements of the degradation of wool under conditions relevant to dyeing and of the keratin degradation products, by fractionation, electrophoresis and amino acid analysis.

The degradation of wool keratin under conditions relevant to those of wool dyeing was investigated using the techniques of gel permeation chromatography (GPC), ion exchange gel chromatography, and amino acid analysis. Physical testing of the treated and untreated wool was also carried out to determine the physical changes occurring, parameters used being percentage elongation at the break, and the breaking strain of the fibre. Samples of wool keratin were immersed in various aqueous solutions at 1000C for 24 hours and the filtered, aqueous, oxidised extracts were analysed* The solutions used varied only in the dye, or dye intermediate present in the treatment solution. All treatment baths contained 10% owf 1.02 x 10 -2 MSulphuric VI acid; 10%owf 7.04x 10 -3 MSodium sulphate VI ; A 100 :1 liquor ratio was used in each case. Some of the dye intermediates showed a marked catalytic effect, particularly in their effect on breaking strain, a decrease of 40% in some cases. The GPC profiles of the extracted proteins were examined in detail and compared against previous workers' results. An explanation of the behaviour of the dyes and intermediates was proposed. The amino acid composition data of the extracted and fractionated proteins were compared against various morphological components extracted by other workers, as was the total gelatin obtained from each treatment.Science Research Counci

The relationship of mealtime communication and oral-motor feeding skills to later language skills in premature infants

Both clinical and theoretical assumptions exist across disciplines which suggest that early feeding skills may be precursors to later speech and language skills. An additional question that has remained unclear is whether an altered trajectory of early feeding and oral motor skills development sets an infant on a path for altered or disordered speech and language development. The literature is also unclear in determining if there is a link between early feeding communicative behaviors and later speech and language skills. In order to better understand these relationships the current study examined infant communication during feeding and nonfeeding interactions and oral-motor feeding skills at 6 months adjusted age and later language scores at 2 years of age in 42 premature African American infants. In addition, data for variables that put premature infants "at risk" for developmental delays as documented prior to discharge, as well as maternal responsiveness at 6 months adjusted age were explored for relationships between these "at risk" variables and later infant language scores. The results of the study revealed a significant predictive relationship between mealtime communication "red flags" at 6 months adjusted age and language scores on the Preschool Language Scale-4 (Zimmerman, Steiner, & Pond, 2002) at 2 years of age. Analyses also identified a significant predictive relationship between mothers' global level of responsiveness during feeding and nonfeeding interactions and infant language scores at 2 years of age. Additionally, variables that put premature infants "at risk" for developmental delays as documented prior to hospital discharge were also found to be predictive of later language scores. These findings emphasize the potential importance of observing mealtime communication during interactions between African American premature infants and their caregivers. In addition, these findings document the need for further research on the oral-motor feeding problems that may be unique to formerly premature infants. Further, the current investigation reveals the value in examining premature infants' early communication development within the context of their family systems and interactions with caregivers

Ambiguity Uncertainty and Risk: Reframing the task of suicide risk assessment and prevention in acute in-patient mental health

The work of the National Confidential Inquiry into Suicide by People with Mental Illness has served to draw attention to the issue of suicide amongst users of mental health services including inpatient and provided the basis for a series of recommendations aimed at improving practice (Appleby et al., 2001, NIMHE 2003). Such recommendations include further training on risk assessment for practitioners. However, representing the problem of suicide as one which can be 'managed' by risk assessment particularly quantitative actuarial approaches implicitly misrepresents the phenomena of suicidality as something which can predicted and therefore managed may be inherently unpredictable at the level of the individual over the short term. We need instead to acknowledge that our work with service users who may be contemplating suicide embraces and acknowledges both uncertainty and ambiguity and seeks to assess risk phenomenologically at the level of the individual such that by understanding their reasons for living and dying we can work in partnership with them to find hope