Isolation of DNA sequences with homology to a degenerate FaRP oligonucleotide from the crayfish Procambarus clarkii

The neuropeptide Th1RFamide with the sequence Phe-Met-Arg-Phe-amide was originally isolated in the clam Macrocallista nimbosa (price and Greenberg, 1977). Since its discovery, a large family ofFl\1RFamide-related peptides termed FaRPs have been found to be present in all major animal phyla with functions ranging from modulation of neuronal activity to alteration of muscular contractions. However, little is known about the genetics encoding these peptides, especially in invertebrates. As FaRP-encoding genes have yet to be investigated in the invertebrate Malacostracean subphylum, the isolation and characterization ofFaRP-encoding DNA and mRNA was pursued in this project. The immediate aims of this thesis were: (1) to amplify mRNA sequences of Procambarus clarkii using a degenerate oligonucleotide primer deduced from the common amino acid sequence ofisolated Procambarus FaRPS, (2) to determine if these amplification products encode FaRP gene sequences, and (3) to create a selective cDNA library of sequences recognized by the degenerate oligonucleotide primer. The polymerase chain reaction - rapid amplification of cDNA ends (PCR-RACE) is a procedure in which a single gene-specific primer is used in conjunction with a generalized 3' or 5' primer to amplify copies ofthe region between a single point in the transcript and the 3' or 5' end of cDNA of interest (Frohman et aI., 1988). PCRRACE reactions were optimized with respect to primers used, buffer composition, cycle number, nature ofgenetic substrate to be amplified, annealing, extension and denaturation temperatures and times, and use of reamplification procedures. Amplification products were cloned into plasmid vectors and recombinant products were isolated, as were the recombinant plaques formed in the selective cDNA library. Labeled amplification products were hybridized to recombinant bacteriophage to determine ligated amplification product presence. When sequenced, the five isolated PCR-RACE amplification products were determined not to possess FaRP-encoding sequences. The 200bp, 450bp, and 1500bp sequences showed homology to the Caenorhabditis elegans cosmid K09A11, which encodes for cytochrome P450; transfer-RNA; transposase; and tRNA-Tyr, while the 500bp and 750bp sequences showed homology with the complete genome of the Vaccinia virus. Under the employed amplification conditions the degenerate oligonucleotide primer was observed to bind to and to amplify sequences with either 9 or 10bp of 17bp identity. The selective cDNA library was obselVed to be of extremely low titre. When library titre was increased, white. plaques were isolated. Amplification analysis of eight isolated Agt11 sequences from these plaques indicated an absence of an insertion sequence. The degenerate 17 base oligonucleotide primer synthesized from the common amino acid sequence ofisolated Procambarus FaRPs was thus determined to be non-specific in its binding under the conditions required for its use, and to be insufficient for the isolation and identification ofFaRP-encoding sequences. A more specific primer oflonger sequence, lower degeneracy, and higher melting temperature (TJ is recommended for further investigation into the FaRP-encoding genes of Procambarlls clarkii.

Factors affecting DNA uptake by mammalian cells

The ability to introduce DNA and express custom DNA sequences in bacteria opened the door for improvements in a large number of fields including agriculture, pharmacology, medicine, nutrition, etc. The ability to introduce foreign DNA sequences into mammalian cells in an efficient manner would have a large impact on therapeutic applications especially gene therapy. The methods in use today suffer from low efficiencies and sometimes toxicity. In this work a number of factors were evaluated for their effect onONA uptake efficiency. The factors studied included exposure to sublethal concentration of hydrogen peroxide which have been show to lead to destabilisation ofthe lysosomes. These exposures have proven to be very toxic to cells when combined with either the calcium phosphate or the lipofectAMINE® transfection methods. Another factor evaluated was exposure to Electro-Magnetic Fields (EMF). This was fuelled by the fact that EMF have been shown to mediate a number of effects on cell structure and/or physiology. EMF exposure by itself was not sufficient to induce the cells to pick up the DNA, therefore its effect on calcium phosphate and lipofectAMINE® was tested. Although some positive results were obtained, the variability of these results exceeded by far any observed enhancements which discouraged any further work on EMF. Also tested was the possible effect the presence of the cytomegalovirus (CMV) sequence might have on DNA uptake (based on previous results in this lab). It was found that the presence ofCMV in the DNA sequence does not enhance uptake or slow down degradation of the internalised DNA. The final factor tested was the effect of basic amino acids on transfection efficiency. It was found that arginine can enhance DNA uptake by about 170% v/ith calcium phosphate and about 200% with LipofectAMINE®. A model was proposed to explain the effect of arginine as well as the lack of effect from other amino acids.

Seasonal variation in hatching pattern and chick survival in the ring-billed gull Larus delawarensis

The general objective of my study was to monitor proximate causes and seasonal patterns of hatching asynchrony and chick survival in the Ring-billed Gull (Larus delawarensis). Two different plots were set up at a Ring-billed Gull colony near Port Colborne, Ontario in the summer of 1992. One group was from 'peak' nesting pairs (clutches initiated between 15 April and 1 May); a second group was from 'late' nesting pairs (clutches initiated between 9 .. 22 May). Despite equal intra-clutch egg laying intervals between the peak and late periods, intra-clutch hatching intervals lengthened as the season progressed (ie. hatching became more asynchronous). Clutches from both periods were monitored for nocturnal attendance and brood patch development of parents was monitored during the egg laying period. Late nesters were characterized by an absence of nocturnal desertion, substantial brood patch defeatheration at clutch initiation and a reduction in the number of chicks fledged per pair. Chick survival to 25 days (taken as fledging) reflected patterns of chick mass at brood completion and five days post-brood completion, in peak clutches. In late clutches, survival was poor for all chicks and, was partially independent of hatching order, due in part to stochastic events such as Herring Gull predation and adverse weather. In both the peak and late periods, last-hatched C-chicks realized the poorest survival to fledging among brood mates. An artificial hatching pattern (manipulated synchrony) and an artificial hatching order were created, in three-chick broods, through a series of egg exchanges. In peak and late clutches manipulated to hatch synchronously (s; 24 h): C-chick survival to fledging did not differ from the survival of A- and B-chicks, in the peak period. In the late period, the survival of C-chicks was significantly lower than that of A-chicks. In peak clutches manipulated such that chicks from last-laid eggs (C-chicks) hatched 24 h - 48 h ahead of the A- and B- chicks, C-chick survival was greater than in controls. Within those broods, C-chicks survived better on average than both A- and B- chicks.

Temporal variation in the coral reefs of the east coast of the inner gulf of Thailand

A series of permanent line transects established on fourteen reefs on the eastern seaboard of the Gulf of Thailand were monitored through a three-year period (1995- 1998) using a video transect method. Hierarchical cluster analysis shows three distinctive reef community types dominated by 1) Porites, 2) Acropora and 3) zoantharians. The reefs are developed under naturally turbid conditions and relatively low salinity due to the proximity of four major river outlets located in the uppermost area of the gulf. The number of Acroporid species on the reefs is positively correlated with distance from the major flver outlets. Eighty-seven species of scleractinian coral were found on the transects. Over the three-year period, the comparison of 1995-97-98 matched stations using Repeated Measures ANOV A reveals no significant time-dependent change in percent area cover of reef components except for an overall significant reduction in the faviid coral component. In the 1997-98 matched station comparison, statistical tests reveal significant increases in both Acropora and Porites components that translated into an overall increase in total living coral cover. These findings indicate that the overall environmental conditions have been favorable for coral growth. Outcompetition of massive corals by faster growing corals on several reefs also indicates conditions favorable for reef expansion. Growth of newlyformed Porites colonies over primary rock substrate and dead coral skeleton was presumably responsible for its rapid increase. Although these reefs are in an area of rapid industrialization and population growth, resultant anthropogenic effects have not yet stopped active coral accretion.

Intraspecific and interspecific social variation in the sweat bee Lasioglossum Malachurum and other members of the subgenus Evylaeus

Sweat bees exhibit a range of social behaviours, from solitary nesting, in which no workers are produced, to strong eusociality, in which workers exhibit a high degree of altruism, behaviour that is measured by the degree of personal reproductive sacrifice. Field studies were carried out for seven weeks during May-June 2000 in southern Greece in order to investigate intraspecific social variation, and test the hypothesis of a north-south cline of decreasing eusociality in the obligately eusocial sweat bee L. (E.) malachurum. A comparative study, using principal components analysis, was performed to determine if patterns of intraspecific social variation in L. malachurum reflect the patterns of social variation within the subgenus, Evylaeus, as a whole. The results of the field study reveal that, in Greece, two worker broods were produced followed by a third brood consisting of gynes, males and some workers, indicating that there was an overlap in worker and gyne production. There was strong caste distinction between queens and workers. Workers actively foraged and participated in nest construction as most workers (58%, n=303) had a high degree of mandibular wear. Workers did not participate in the oviposition of Brood 3 gynes since only 0.7% (n=278) of workers were mated. Furthermore, queen survival until the end of Brood 3 and a substantial size differential of 10.6% between queens and workers suggested that queen domination over worker behaviour during the early to mid-part of the colony cycle was plausible. Male production in Brood 3 by some workers was likely, since the timing of worker ovarian development corresponded with the timing of male production. These findings suggest that workers of the first two broods were primarily altruistic, but some (28%) Brood 1 (9%) and Brood 2 (19%) workers produced males, indicating that the degree of altruistic behaviour declined during the lifetime of the colony. In comparison with other L. malachurum populations in Europe, the Greek population of L. malachurum had a weaker social level as a result of the higher proportion of workers potentially involved in male production, thus 3 supporting the hypothesis of a southerly cline of decreasing eusociality. Furthermore, intraspecific variation in social level across Europe appears to be due to longer breeding seasons in more southerly locations that would promote the production of larger colonies and provide opportunities for workers to evade queen control. The comparative study using principal components analysis on 20 solitary (of the subgenera Evylaeus and Lasioglossum), eusocial and socially polymorphic Evylaeus species and populations reveals that six traits are closely associated with stronger eusociality in Evylaeus. These traits are: (1) a reduction in the proportion of males in the early brood(s); (2) a reduction in the proportion of females that mate; (3) an increase in the mean number of first brood workers; (4) a reduction in the proportion of females with developed ovaries; (5) an increase in size dimorphism between castes, and (6) nest guarding. These are traits that most significantly define principal component one and therefore distinguish social type as indicated by a clear separation of the eusocial and the solitary populations, with a socially polymorphic species falling in between. Furthermore, most of these traits are under foundress control and may suggest that the evolutionary loss or gain of eusociality is based on selection pressures on a founding female. Colony size and female ovarian development are common factors distinguishing social variation in L. malachurum and within the subgenus as a whole. The principal components analysis excluding the solitary species and the socially aberrant L. marginatum populations show the L. malachurum populations separated based on an increasing proportion of workers with developed ovaries as populations are found more south, lending further support to the hypothesis of a north-south cline of decreasing eusociality.

Astringency and other oral sensations : biological sources of individual variation and association with food and beverage behaviour

Orosensory perception strongly influences liking and consumption of foods and beverages. This thesis examines the influence of biological sources of individual variation on the perception of prototypical orosensory stimuli, food liking, self-reported alcohol liking and consumption, and indices of health. Two orosensory indices were examined: propylthiouracil (PROP) responsiveness, a genetically-mediated index of individual variation associated with enhanced responsiveness to orosensory stimuli often expressed as PROP taster status (PTS); and thermal taster status (TTS), a recently reported index of orosensory responsiveness. Taster status in PTS and/or TTS confers greater responsiveness to most orosensory stimuli. Gender, age, ethnicity, and fungiform papillae (FP) density were not associated with orosensory responsiveness to tastants, an astringent, and a flavour. Unlike PROP responsiveness, FP density was not associated with TTS. Both PROP responsiveness and TTS were associated with increased responsiveness to orosensory stimuli, including temperature and astringency. For PROP, this association did not hold when stimuli were presented at cold or warm temperatures, which are ecologically valid since most foods and beverages are not consumed at ambient temperature. Thermal tasters (TTs), who perceive 'phantom' taste sensations with lingual thermal stimulation, were more responsive to stimuli at both temperatures than thermal non-tasters (TnTs). While PTS, TIS, and gender affected self-reported liking and consumption of some alcoholic beverages, gender associated with the greatest number of beverage types and consumption parameters, with males generally liking and consuming alcoholic beverages more than females. Age and gender were the best predictors of alcoholic beverageAiking and consumption. As expected, .. liking of bitter and fatty foods and cream was inversely related to PROP responsiveness. TTS did not associate with body mass index or waist circumference, and contrary to previous studies, neither did PROP responsiveness. Taken together, TnTs' greater liking of cooked fruits and vegetables and high alcohol, and astringent alcoholic beverages than TTs suggests differences between TTS groups may be driven by perceived temperature and texture. Neither an interaction between PTS and TTS nor a TTS effect on PROP responsiveness was observed, suggesting these two indices of individual variation exert their influences on orosensory perception independently.

Annual Variation in Bee Community Structure in the Context of Disturbance (Niagara Region, South-Western Ontario)

This study examined annual variation in phenology, abundance and diversity of a bee community during 2003, 2004, 2006, and 2008 in recovered landscapes at the southern end of St. Catharines, Ontario, Canada. Overall, 8139 individuals were collected from 26 genera and sub-genera and at least 57 species. These individuals belonged to the 5 families found in eastern North America (Andrenidae, Apidae, Colletidae, Halictidae and Megachilidae). The bee community was characterized by three distinct periods of flight activity over the four years studied (early spring, late spring/early summer, and late summer). The number of bees collected in spring was significantly higher than those collected in summer. In 2003 and 2006 abundance was higher, seasons started earlier and lasted longer than in 2004 and 2008, as a result of annual rainfall fluctuations. Differences in abundance for low and high disturbance sites decreased with years. Annual trends of generic richness resembled those detected for species. Likewise, similarity in genus and species composition decreased with time. Abundant and common taxa (13 genera and 18 species) were more persistent than rarer taxa being largely responsible for the annual fluctuations of the overall community. Numerous species were sporadic or newly introduced. The invasive species Anthidium oblongatum was first recorded in Niagara in 2006 and 2008. Previously detected seasonal variation patterns were confirmed. Furthermore, this study contributed to improve our knowledge of temporal dynamics of bee communities. Understanding temporal variation in bee communities is relevant to assessing impacts caused on their habitats by diverse disturbances.

DNA-Directed DNA Polymerases Evolve From Reverse Transcriptase

Scientists have been debating for decades the origin of life on earth. A number of hypotheses were proposed as to what emerged first RNA or DNA; with most scientists are in favour of the "RNA World" hypothesis. Assuming RNA emerged first, it fellow that the RNA polymerases would've appeared before DNA polymerases. Using recombinant DNA technology and bioinformatics we undertook this study to explore the relationship between RNA polymerases, reverse transcriptase and DNA polymerases. The working hypothesis is that DNA polymerases evolved from reverse transcriptase and the latter evolved from RNA polymerases. If this hypothesis is correct then one would expect to find various ancient DNA polymerases with varying level of reverse transcriptase activity. In the first phase of this research project multiple sequence alignments were made on the protein sequence of 32 prokaryotic DNA-directed DNA polymerases originating from 11 prokaryotic families against 3 viral reverse transcriptase. The data from such alignments was not very conclusive. DNA polymerases with higher level of reverse transcriptase activity were non-confined to ancient organisms, as one would've expected. The second phase of this project was focused on conditions that may alter the DNA polymerase activity. Various reaction conditions, such as temperature, using various ions (Ni2+, Mn2+, Mg2+) were tested. Interestingly, it was found that the DNA polymerase from the Thermos aquatics family can be made to copy RNA into DNA (i.e. reverse transcriptase activity). Thus it was shown that under appropriate conditions (ions and reactions temperatures) reverse transcriptase activity can be induced in DNA polymerase. In the third phase of this study recombinant DNA technology was used to generate a chimeric DNA polymerase; in attempts to identify the region(s) of the polymerase responsible for RNA-directed DNA polymerase activity. The two DNA polymerases employed were the Thermus aquatic us and Thermus thermophiles. As in the second phase various reaction conditions were investigated. Data indicated that the newly engineered chimeric DNA polymerase can be induced to copy RNA into DNA. Thus the intrinsic reverse transcriptase activity found in ancient DNA polymerases was localized into a domain and can be induced via appropriate reaction conditions.

Human Endogenous Retrovirus (HERV) Insertional Polymorphisms

Human endogenous retroviruses (HERVs) are the result of ancient germ cell infections of human germ cells by exogenous retroviruses. HERVs belong to the long terminal repeat (LTR) group of retrotransposons that comprise ~8% of the human genome. The majority of the HERVs documented have been truncated and/or incurred lethal mutations and no longer encode functional genes; however a very small number of HERVs seem to maintain functional in making new copies by retrotranspositon as suggested by the identification of a handful of polymorphic HERV insertions in human populations. The objectives of this study were to identify novel insertion of HERVs via analysis of personal genomic data and survey the polymorphism levels of new and known HERV insertions in the human genome. Specifically, this study involves the experimental validation of polymorphic HERV insertion candidates predicted by personal genome-based computation prediction and survey the polymorphism level within the human population based on a set of 30 diverse human DNA samples. Based on computational analysis of a limited number of personal genome sequences, PCR genotyping aided in the identification of 15 dimorphic, 2 trimorphic and 5 fixed full-length HERV-K insertions not previously investigated. These results suggest that the proliferation rate of HERVKs, perhaps also other ERVs, in the human genome may be much higher than we previously appreciated and the recently inserted HERVs exhibit a high level of instability. Throughout this study we have observed the frequent presence of additional forms of genotypes for these HERV insertions, and we propose for the first time the establishment of new genotype reporting nomenclature to reflect all possible combinations of the pre-integration site, solo-LTR and full-length HERV alleles.