Analysis of a high resolution deep ocean acoustic navigation system

Submitted in partial fulfillment of the requirements for the degree of Ocean Engineer at the Woods Hole Oceanographic Institution and the Massachusetts Institute of Technology and for the degree of Master of Science in Ocean Engineering at the Massachusetts Institute of Technology January, 1975A high resolution acoustic navigation system for ocean use is being developed at the Woods Hole oceanographic Institution. The system can yield navigation fixes with respect to a bottom moored reference net with accuracies (on a fix to fix basis) of a few centimeters. In order to use the system to best advantage a survey is required to determine precisely the relative positions of the net elements. Each element combines a pulse transponder with a continuous wave (CW) beacon. Accumulated phase (Doppler shift of the CW beacon) between survey points is measured as well as acoustic travel times between survey points and transponders. Non-linear regression techniques are employed to develop a maximum likelihood estimator for net element positions based on these phase and travel time measurements. An approximate error covariance matrix is generated and an optimum choice of survey points is indicated., The combined system, using these selected locations for performing the survey, can yield reference mooring coordinates with error of ±1 meter. Improved precision appears to be limited by inaccuracies in the pulse and Doppler measuring system

Feeding beets and potatoes for butter

The farmers of Iowa are growing sugar beets to learn the adaptation of the soils and climates of the state to sugar production. The feeding value of the beet entire without the sugar extracted, is a matter of interest to them. The crop of potatoes in 1891 was large, and where they were unsalable owing to remoteness from markets, or for other causes, it became interesting to ascertain feeding values for dairy products. In conformity with inquiries concerning these subjects, this station fed four cows during three months, beginning December 1st, 1891, and ending February 29, 1892

A molecular and population genetics study of the Bluff Oyster (Ostrea chilensis)

New Zealand has a long history of isolation and has evolved a unique biota. Spanning from a sub-tropical climate in the North to a sub-Antarctic climate in the far south New Zealand provides an interesting opportunity to study the processes that lead to evolution. This thesis attempts to study the evolution of Ostrea chilensis at a population genetics and molecular level. Chapter Two: Microsatellite DNA loci represent an ideal marker for population genetics studies due to high levels of length polymorphism between individuals. Genomic sequencing technologies offer the potential to quickly identify thousands of loci, from which PCR primers can be developed and screened for polymorphisms. I aimed to develop PCR primers to amplify length polymorphic microsatellite loci and to use the genomic data set to elucidate patterns and processes of microsatellite evolution. DNA was extracted from a single Ostrea chilensis individual and used for a 1/8 plate sequencing run on a Roche 454. The subsequent quality checked DNA database was annotated for microsatellite loci. 6,208 dinucleotide, 7,326 trinucleotide repeats, 2,414 tetranucleotide, 33 hexanucleotide and 356 pentanucleotides were annotated on the partial genome. Four microsatellite loci were successfully amplified and genotyped. The loci have a low number of alleles compared to other bivalve studies and two have significant departures from HWE (Fst = 0.126 and -0.348). There were a number of highly significant BLAST hits (< 1xE⁻²⁰) with repetitive Oyster DNA sequences obtained from GenBank. Due to difficulties the microsatellite loci were abandoned as markers for later population genetic analysis. This work, however, provides the ground work for further developments of PCR primers for polymorphic microsatellite DNA and provides some observations of molecular evolution of repetitive DNA, which will lead to a greater understanding of these sequences. Chapter Three: This chapter forms the first population genetic study of Ostrea chilensis using New Zealand and Chilean populations. The life history traits of O. chilensis are thought to reduce the dispersal of the species. Using randomly amplified polymorphic DNA (RAPD) I aimed to test the population genetic structure with the null hypothesis that there is panmixia (i.e. high levels of gene flow and no barriers between populations). I then aimed to see if there was an isolation-by-distance (IBD) profile. Barriers to gene flow at around 420S have been identified in a number of studies around New Zealand. I aimed to see if those barriers were present in this study. Significant spatial genetic differentiation was found among populations (Fst= 0.194, p<0.00001). Over all spatial scales a significant IBD was not found, until ‘outlier’ (those with two standard deviations from the mean Fst) were removed, then a slight IBE was found (rxy=0.324, p=0.030, r2 =0.1052). In an AWclust analysis two main clusters were revealed, but they did not correspond to above and below the 42⁰S. It is possible that the brooding life style of Ostrea chilensis has resulted in reduced gene flow between populations. Much of the genetic structure was not congruent with geographic location; this apparent chaotic patchiness could be influenced by human mediated movements and/or environmental variables. Chapter Four: The genetic structure found in the previous chapter was analysed in the context of near shore environmental and geo-spatial variables. My aim was to elucidate the environmental variables that best explain the apparent genetic structure of O. chilensis. Using genetic data from the previous chapter a Generalised Linear Model (GLM) was used to test the effect of ten environmental variables and two geospatial variables on average genetic distance (Fst and PHIst). A complimentary BEST analysis was used to test the effect of the same variables on the individual alleles for each population. Using the BEST analysis the model that best explained the apparent genetic structure (Rs = 0.263) included the environmental variables Sediment (SED) and mean sea surface temperature (SSTGrad). The GLM showed a more complicated model including most of the variables tested. Previous studies have shown that bivalve dispersal patterns are associated with sediment and spawning times can be influenced by temperature. This line of enquiry is important as it could lead to the identification of candidate genes for selection. Chapter Five: Genomic datasets contain a wealth of data that can be used to further understand genome structure and arrangements. My aim was to discover mitochondrial gene fragments in the genomic data set, use them to assemble the Ostrea chilensis mitogenome, and then analyse the genome in a phylogenetic framework with other oyster mitogenomes. A custom BLAST database was created using the 454 genomic DNA data set; this was then BLASTED against all available oyster mitogenomes on GenBank. The DNA sequences with good statistical support (<1 x E⁻²⁰) where mapped against the mitogenome of Ostrea edulis. The O. edulis mitogenome was then used to annotate the resulting mitogenome. I was able to recover 10, 086 bp of mitochondrial DNA – this represents around 65% of the full genome. The subsequent topology of the Bayesian phylogenetic tree was similar to that found in previous studies. PCR primers have been designed to sequence the gaps in the mitogenome. This will allow full annotation. Full genome annotation will aid further research into genome evolution. Chapter Six: In the mitogenome, evolution is thought to mainly result in synonymous substitutions, due to functional constraints. I aimed to describe the selection pressures acting on each protein coding gene of the oyster mitogenome by comparing rates of non-synonymous (dN) and synonymous (dS) substitutions. I then aimed to discover if there was a codon bias in the oyster mitogenomes. Genetic distance was assessed using p-distance. The ratio of dN/dS was calculated using the method of Nei and Gojobori (1986). The overall ratio of dN/dS was <1 for all protein coding genes, this would suggest that the genes are under purifying selection (non-synonymous mutations are selected against). A consistent codon bias was found across all protein coding genes, this could indicate translational selection. This multidisciplinary approach aimed to explain the patterns and processes of evolution in O. chilensis. This thesis research developed molecular tools, and provided information that will aid fisheries and aquaculture management

Child-mediated health communication: A conceptual framework for increasing stroke literacy in hard to reach populations

Effectively engaging economically-disadvantaged ethnic minority communities for promoting health has proved to be challenging for a variety of reasons, including factors related to healthcare access, literacy, inadequate or ineffective cultural appropriateness of materials, and the relatively low priority for health due to competing demands related to economic hardship. We have developed a framework of Child-Mediated Health Communication (CMHC), which focuses on children as channels for carrying out health promotion interventions to parents and other caregivers. CMHC is an innovative, alternative strategy for engaging this underserved population, where traditional methods of health promotion have not been successful. We discuss the theoretical foundation, development, and effectiveness of a CMHC framework in our stroke preparedness communication intervention, Hip Hop Stroke

Nitric oxide sensing in Campylobacter jejuni by NssR

Pathogenic bacteria encounter the toxic free radical nitric oxide (NO) during infection via the activity of host nitric oxide synthases or via the reduction of nitrite and nitrate in the gut by commensal bacteria. Survival of bacterial pathogens during infection depends on various mechanisms for NO sensing and detoxification. The foodborne pathogen Campylobacter jejuni detoxifies NO to nitrate using a globin protein (Cgb), expression of which is induced strongly and specifically by the transcription factor NssR upon exposure to NO. Previous work indicates that nitric oxide does not directly modulate the interaction of NssR with target DNA, suggesting the existence of an indirect method for NO sensing. Bioinformatics analysis has revealed that NssR is likely to bind cyclic nucleotides, and cyclic-di-GMP (c-di-GMP) has previously been linked to NO sensing in other bacteria via a mechanism involving NO-responsive phosphodiesterase and cyclase enzymes. Structural modelling described herein is consistent with NssR binding to cyclic nucleotides, and tryptophan fluorescence quenching confirms the ability of NssR to bind to c-di-GMP, cAMP and cGMP. Subsequently, electrophoretic mobility shift assay (EMSA) suggests that that binding of c-di-GMP to NssR leads to increase in affinity for the cgb promoter. Finally, an in vivo reporter assay provides direct evidence that c-di-GMP can influence NssR activity. Taken together, these data are consistent with an in vivo mechanism whereby NO elevates c-di-GMP levels in the cell, which in turn activates NssR activity resulting in Cgb expression and NO detoxification. This work provides potential molecular explanation for how NO is sensed and detoxified in C. jejuni

Oil film separation and drag torque in disengaged wet brakes

Multi-disc wet brake packs are commonly used for off-highway applications. Unfortunately when disengaged, these components can create significant levels of unwanted parasitic losses. This paper presents a novel, validated model to predict the parasitic losses in disengaged multi-disc wet brake packs. The model employs pertinent boundary conditions to determine the position of the free boundary created by oil film separation. The experimental and analytical results demonstrate the significance of wet brake disengaged losses at a range of angular velocities, typically found in operation. The improved understanding accrued by the expounded time-efficient methodology presents significant opportunity to develop predictive toolsfor driveline system efficiency calculations and component design optimisation for off-highway vehicles