Advances in DNA sequencing technologies, particularly the advent of next generation sequencing (NGS) platforms, have revolutionised the field of metagenomics and allowed great progress to be made in the way that microbial communities are analysed. However, the wealth of data now available thanks to these advancements has made the possibilities far more numerous than just the obvious applications, with a wide variety of novel and diverse studies conceivable. The technologies themselves have also created further areas for research as better methods of handling the, often overwhelming in quantity and misleading in content, data are sought. The analysis carried out in this thesis demonstrates the wide range of study possible stemming from two experiments involving the sequencing of meiofauna DNA. The first of these involves community analysis of marine benthic meiofauna with particular emphasis on diversity and distribution. The second experiment involves the sequencing of pooled nematode samples in order to investigate the effects of sample richness and species relatedness on the generation of chimeric reads in sequencing data. It is shown that the data generated from these two experiments can be used to help formulate an algorithm to simulate PCR and therefore assist the generation of realistic noisy NGS data. These data can, in turn, be used to generate a simulated in silico microbial community for analysis, the results of which reveal insights into the accuracy of chimera detection software and the reliability of metagenetic community analyses. Worryingly, these results suggest that findings from similar in vitro studies are not as reliable as originally perceived. The same experimental data may also be used to investigate interactions between meiofauna species based on the incidental presence of prey species highlighted from the sequencing of individual meiofauna organisms. It is shown that these data can be used to accurately predict a nematode’s feeding type without having to examine the organism directly. It is also shown that there is no correlation between this method of inferring interactions between species and other methods which have been used in the past. This suggests that the earlier methods are inadequate when used for the detection of feeding interactions.

This dissertation proposes an exploration of a variety of themes in philosophy of science through the lens of a case study in evolutionary biology. It draws from a careful analysis and comparison of the hypotheses from Bill Martin and Tom Cavalier-Smith. These two scientists produced contrasted and competing accounts for one of the main events in the history of life, the origin of eukaryotic cells. This case study feeds four main philosophical themes around which this dissertation is articulated. (1) Theorizing: What kind of theory are hypotheses about unique events in the past? (2) Representation: How do hypotheses about the past represent their target? (3) Evidential claims: What kind of evidence is employed and how do they constrain these hypotheses? (4) Pluralism: What are the benefits and the risks associated with the coexistence of rival hypotheses? This work both seeks to rearticulate traditional debates in philosophy of science in the light of a lesser-known case of scientific practice and to enrich the catalogue of existing case studies in the philosophy of historical sciences.

Inherited retinal degenerative diseases can affect various components of the retina leading to blindness. Five different mutant strains of chicken have been studied extensively as potential models for inherited retinal degeneration. The Smoky Joe (SJ) chicken is a sixth genetically blind strain of White Leghorns that shows various degrees of blindness at hatch and by 8 weeks post-hatch, have complete blindness for those that are homozygous. The objective of this study was to characterize the retinal degeneration in these birds by histology, both during embryonic and post-hatch development, and to the retinal function using electroretinograms (ERG). For both embryonic and post-hatch development, a significantly lower number of cells were found in the retina of blind birds compared to sighted (both p<0.0001). The significant contributor to cell number decrease was the loss of amacrine cells located in the inner nuclear layer. Photoreceptors were also found to potentially decrease in number, but at a later stage. ERG recordings revealed decreases in amplitudes of b-waves and oscillatory potentials in blind birds, but not in sighted. Both histology and ERG findings support the idea that the inner retinal cells are affected. The results indicate that degeneration in the Smoky Joe retina occurs mostly within the inner nuclear layer affecting amacrine cells. This hampers the functional capacity of the retina, causing blindness.

A previous study in chickens revealed that myosin light chain kinase (MLCK), f actin, and myosin are found on the crystalline lens. Their polygonal arrangement at the posterior surface resembles a muscle tissue, which suggests that these proteins may have a contractile role in accommodation. The ciliary muscle in chickens is skeletal in nature and, therefore, chickens were used to test the hypothesis that contractile microfilaments play a role in accommodation. Ciliary nerve-induced accommodation was measured in the presence of an MLCK inhibitor 1-(5-Iodonaphthalene-1-sulfonyl)-1H-hexahydro-1,4-diazepine hydrochloride (ML-7). Eyes of 6-day old white Leghorn chickens (gallus gallus domesticus) were enucleated in Tyrode’s saline solution while keeping the ciliary nerve intact. One eye was treated with ML-7 and the other eye was treated with vehicle only. Three concentrations of ML-7 were used: 1 µM, 10 µM, and 100 µM. Two experiments were carried out, one including a (3×10 min) wash and one without. Focal lengths of the vehicle- and ML-7-treated eyes were measured before, during and after accommodation. Immunoblots were used to detect the amount of phosphorylated myosin with and without the inhibitor. Focal lengths for accommodation were shorter than those at rest (p<0.001). In the wash experiment, vehicle-treated eyes had higher accommodative amplitudes compared to ML-7-treated eyes for all three dosage groups. In the no-wash experiment, only the 1 µM group demonstrated the same trend as the wash experiment. For the 10 µM and 100 µM groups, ML-7-treated eyes had higher accommodative amplitudes compared to vehicle-treated eyes. Immunoblots revealed varying amounts of inhibition within pairs of eyes as well as between birds for both experiments. Results from this experiment indicate that ML-7 was not effective at determining whether contractile microfilaments found on the lens contribute to accommodation.

A previous study in chickens revealed that myosin light chain kinase (MLCK), f actin, and myosin are found on the crystalline lens. Their polygonal arrangement at the posterior surface resembles a muscle tissue, which suggests that these proteins may have a contractile role in accommodation. The ciliary muscle in chickens is skeletal in nature and, therefore, chickens were used to test the hypothesis that contractile microfilaments play a role in accommodation. Ciliary nerve-induced accommodation was measured in the presence of an MLCK inhibitor 1-(5-Iodonaphthalene-1-sulfonyl)-1H-hexahydro-1,4-diazepine hydrochloride (ML-7). Eyes of 6-day old white Leghorn chickens (gallus gallus domesticus) were enucleated in Tyrode’s saline solution while keeping the ciliary nerve intact. One eye was treated with ML-7 and the other eye was treated with vehicle only. Three concentrations of ML-7 were used: 1 µM, 10 µM, and 100 µM. Two experiments were carried out, one including a (3×10 min) wash and one without. Focal lengths of the vehicle- and ML-7-treated eyes were measured before, during and after accommodation. Immunoblots were used to detect the amount of phosphorylated myosin with and without the inhibitor. Focal lengths for accommodation were shorter than those at rest (p<0.001). In the wash experiment, vehicle-treated eyes had higher accommodative amplitudes compared to ML-7-treated eyes for all three dosage groups. In the no-wash experiment, only the 1 µM group demonstrated the same trend as the wash experiment. For the 10 µM and 100 µM groups, ML-7-treated eyes had higher accommodative amplitudes compared to vehicle-treated eyes. Immunoblots revealed varying amounts of inhibition within pairs of eyes as well as between birds for both experiments. Results from this experiment indicate that ML-7 was not effective at determining whether contractile microfilaments found on the lens contribute to accommodation.

Inherited retinal degenerative diseases can affect various components of the retina leading to blindness. Five different mutant strains of chicken have been studied extensively as potential models for inherited retinal degeneration. The Smoky Joe (SJ) chicken is a sixth genetically blind strain of White Leghorns that shows various degrees of blindness at hatch and by 8 weeks post-hatch, have complete blindness for those that are homozygous. The objective of this study was to characterize the retinal degeneration in these birds by histology, both during embryonic and post-hatch development, and to the retinal function using electroretinograms (ERG). For both embryonic and post-hatch development, a significantly lower number of cells were found in the retina of blind birds compared to sighted (both p<0.0001). The significant contributor to cell number decrease was the loss of amacrine cells located in the inner nuclear layer. Photoreceptors were also found to potentially decrease in number, but at a later stage. ERG recordings revealed decreases in amplitudes of b-waves and oscillatory potentials in blind birds, but not in sighted. Both histology and ERG findings support the idea that the inner retinal cells are affected. The results indicate that degeneration in the Smoky Joe retina occurs mostly within the inner nuclear layer affecting amacrine cells. This hampers the functional capacity of the retina, causing blindness.

Ears are a new biometric with major advantage in that they appear to maintain their structure with increasing age. Current approaches have exploited 2D and 3D images of the ear in human identification. Contending that the ear is mainly a planar shape we use 2D images, which are consistent with deployment in surveillance and other planar-image scenarios. So far ear biometric approaches have mostly used general properties and overall appearance of ear images in recognition, while the structure of the ear has not been discussed. In this thesis, we propose a new model-based approach to ear biometrics. Our model is a part-wise description of the ear structure. By embryological evidence of ear development, we shall show that the ear is indeed a composite structure of individual components. Our model parts are derived by a stochastic clustering method on a set of scale invariant features on a training set. We shall review different accounts of ear formation and consider some research into congenital ear anomalies which discuss apportioning various components to the ear's complex structure. We demonstrate that our model description is in accordance with these accounts. We extend our model description, by proposing a new wavelet-based analysis with a specific aim of capturing information in the ear's outer structures. We shall show that this section of the ear is not sufficiently explored by the model, while given that it exhibits large variations in shape, intuitively, it is significant to the recognition process. In this new analysis, log-Gabor filters exploit the frequency content of the ear's outer structures. In recognition, ears are automatically enrolled via our new enrolment algorithm, which is based on the elliptical shape of ears in head profile images. These samples are then recognized via the parts selected by the model. The incorporation of the wavelet-based analysis of the outer ear structures forms an extended or hybrid method. The performance is evaluated on test sets selected from the XM2VTS database. By results, bothin modelling and recognition, our new model-based approach does indeed appear to be a promising new approach to ear biometrics. In this, the recognition performance has improved notably by the incorporation of our new wavelet-based analysis. The main obstacle hindering the deployment of ear biometrics is the potential occlusion by hair. A model-based approach has a further attraction, since it has an advantage in handling noise and occlusion. Also, by localization, a wavelet can offer performance advantages when handling occluded data. A robust matching technique is also added to restrict the influence of corrupted wavelet projections. Furthermore, our automatic enrolment is tolerant of occlusion in ear samples. We shall present a thorough evaluation of performance in occlusion, using PCA and a robust PCA for comparison purposes. Our hybrid method obtains promising results recognizing occluded ears. Our results have confirmed the validity of this approach both in modelling and recognition. Our new hybrid method does indeed appear to be a promising new approach to ear biometrics, by guiding a model-based analysis via anatomical knowledge.

Monitoring microorganisms in natural water is central to understanding and managing risks to human health and ecosystems. Some phytoplankton can produce toxic blooms which are harmful to aquatic ecosystems and human health. Kariena brevis is responsible for Harmful Algal Blooms and produces brevetoxin which can lead to gastrointestinal and neurological problems in mammals. Traditional methods for Harmful Algal Bloom monitoring require sample collection and preservation for later study in laboratories where they are generally processed using microscopy which can take many hours or days. Laboratory equipment for this application has been adapted for ship-board use. Portable instrument systems that incorporate sample preparation and detection have been also developed for environmental applications. However, very few are suitable for deployment in the environment (either as a hand-held or in situ system) and often require laboratory infrastructure or personnel to facilitate sample collection and processing. Current in situ systems are large, expensive, and require expert users to operate them. Thus these existing systems do not provide marine science with the high spatial resolution data required to enable a better understanding of the diversity, function and community structure of marine microorganisms. Ideal in situ sensors should provide sample analysis over wide areas and at many depths for long periods of time. This remains a significant challenge. One possible solution is to develop numerous cheap sensors which could be incorporated into autonomous underwater vehicles or an argofloats network. Micro systems are excellent candidates as when mature, they could be mass produced to enable them to meet this particular spatial mapping requirement. The use of fully automatic and accurate micro total analysis systems, also known as lab-on-a-chip, can overcome the challenges of highly integrated in situ systems for incorporation into environmental monitoring vehicles and stations. Lab-on-a-chip technology appears well suited for environmental monitoring with its main advantages being the possibility of miniaturization, portability, reduced reagent consumption and automation. Molecular biology tools combined with microfluidic technology have been seen as a potential technical solution for in situ environmental applications. The purpose of this work has been to develop key functions in independent microchips that perform elements of a complete biological assay for ribonucleic acid phytoplankton metrology from the sample preparation to the detection step. Specifically the system is being developed to analyse the large subunit of the ribulose-bisphosphate carboxylase (rbcL) gene of phytoplankton Kariena brevis, a species responsible for Harmful Algal Blooms. This thesis reports the development of three lab-on-a-chip devices which perform microalga cell lysis, nucleic acid purification and real-time ribonucleic acid detection. The aim was to demonstrate proof-of concept for each device separately in order to obviate the need to tackle the complications of system integration (which remains a challenge), while understanding performance needed and comparing that achieved to the most likely scenarios for real-world applications. Future research should integrate these separate chips into an integrated single chip design to achieve fully automated chips with “sample-in” to “answer-out” capability.

Using biological traits, such as fingerprints, iris patterns and voice print, in identification and authentication has gained increasing attention due to the demand for a more secure environment. The potential of human walking as a biometric has only attracted interest in the computer vision community since the last decade. Nevertheless, the potential of human running gait as a biometric remains largely unexplored. Here, we propose an approach for an automated non-invasive/markerless person identification system by not only the walking, but also the running gait to explore the potential of these two biomechanically distinct gaits. Two motion models both invariant to walking and running, have been developed based on the concept of harmonic motion. The first is a bilateral symmetric model made up of an upper and a lower pendulum, representing the thigh and the lower leg, joined at the knee. The upper pendulum is simple harmonic motion whilst the lower pendulum uses an empirical model requiring parameter selection for the different gait mode and lacks analytical attributes. The second model has a forced coupled oscillator to describe the knee rotation as legs are considered to be imperfect pendula with energy loss. The rhythm and pattern of gaits are automatically extracted by a temporal evidence gathering technique with the motion models as the underlying temporal templates. The spatio-temporal characteristics of the gait patterns are described by a Fourier representation, which are in turn used to create unique gait signatures for the purpose of identification. Performance analysis demonstrates the potential of gait as a biometric, with running being more potent. This technique not only performs well in discriminating individuals, but also appears capable of distinguishing the gender and gait mode. Moreover, analysis shows that the knee rotation contributes significantly to discrimination capability. Based on the hypothesis that human walking and running gaits are intimately related by the musculo-skeletal structure and that the walking pattern is the phase-modulated version of running (or vice versa), a unique mapping/transform between individuals’ walking and running gait is developed, making the signature invariant to gait mode. Furthermore, this mapping can be used alone as a compressed signature or to buttress the original signature to further improve the recognition capability. Then, a generic relationship between walking and running has been investigated via a neural network. Due to the current size of the experimental dataset, the structure of the two signature spaces could not be drawn, at least not by this approach. However, results do suggest its possible existence. The effect of different camera views is an important application issue. The gait pattern perceived by machine vision at different viewpoints has been investigated. The frequency description of the gait pattern is linearly dependent on the camera sagittal view angle. The changes of both the magnitude and the phase component are symmetric about the fronto-parallel view. This linearity offers a convenient way to map the angular motion obtained from various camera sagittal views to the true motion, for the convenience of gait analysis. More importantly, this linearity can be exploited to develop view invariant gait signatures. The new and interesting findings of this work not only benefit biometrics research, but may also draw attention from other communities such as biomechanics and graphics applications.

Submitted by IZELMA de Souza Costa (izelma.costa@hotmail.com) on 2016-08-09T15:34:19Z No. of bitstreams: 1 Dissertação -Izelma de Souza Costa.pdf: 1037248 bytes, checksum: 05fc10da605ec0a1212f299e9bc5e637 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-08-12T12:33:28Z (GMT) No. of bitstreams: 1 costa_is_me_arafcl.pdf: 1037248 bytes, checksum: 05fc10da605ec0a1212f299e9bc5e637 (MD5) / Made available in DSpace on 2016-08-12T12:33:29Z (GMT). No. of bitstreams: 1 costa_is_me_arafcl.pdf: 1037248 bytes, checksum: 05fc10da605ec0a1212f299e9bc5e637 (MD5) Previous issue date: 2016-07-15 / Governo do Estado do Amapá / O presente estudo buscou conhecer a formação e a prática em educação sexual e sexualidade dos/as professores/as de Ciências e Biologia de algumas escolas estaduais de Macapá. Para tanto, empregou a pesquisa qualitativa. Assim, para a escuta dos/as participantes, optou-se pelo emprego de entrevistas semiestruturadas. Os resultados obtidos apontam que a maioria dos/as professores/as não recebeu nenhum tipo de formação acerca desta temática durante a formação inicial. Dentre os/as que afirmaram ter obtido alguma instrução acerca da educação sexual, constatou-se que esta foi de natureza estritamente biológica com enfoque nos caracteres anatômicos, fisiológicos e embriológicos. Identificou-se também que, embora a secretaria de educação do estado do Amapá possua um departamento cuja função é auxiliar o/a professor/a com as questões que envolvem a sexualidade, nas escolas da rede estadual até o momento não existe, na prática, nenhum programa ou curso de formação continuada para o/as profissionais que se disponibilizam ou tem interesse em trabalhar com as questões envoltas pelo tema. Assim, devido a falta de conhecimentos básicos em sexualidade, os/as professores/as apenas reproduzem conteúdos que se distanciam das necessidades e envolvimento do/as alunos/as. Por isso, sugere-se o investimento maciço na formação continuada dos/as professore/as de Ciências e ou Biologia da rede estadual de educação da citada cidade no que se refere à sexualidade, sobretudo, direcionada aos profissionais que já se encontram atuando, de maneira a afiançar profissionais aptos a atuar com educação sexual no citado estado. Além disso, urge mais estudos e pesquisas que possam colaborar para a compreensão e viabilidade da educação sexual nas escolas de Macapá e, por conseguinte do Estado do Amapá. / This study was done to analyze the achieved training and work experience in sex education and sexuality of teachers of Science and Biology of some public state schools in Macapá (North of Brazil). Therefore the qualitative research was used. Thus, to interview the participants, the semi-structured interview method was used. The results indicate that most teachers did not receive any training on this subject during their graduation. Among those who claimed to have obtained some education about sexual education, it was found that this tuition was strictly a biological nature with focus on anatomy, physiology and embryology. It was also identified that in the Amapá state, the public education department has a subdivision whose role is to assist teachers with doubts regarding sexuality in schools, despite that, by now it does not exist in practice a program on continuing education course for professionals who are interested in working with the issues that this theme brings. Thus, due to the lack of basic knowledge on sexuality, the professionals only talk about contents that are not correlated to the needs of the students. Hence, many investments in continuing education in sexuality are suggested for teachers of Science and or Biology in the state of the mentioned city, especially directed to professionals who are already working with it as a way to support professionals able to work with sex education in that state. There should also be more studies and research that can contribute to the understanding and viability of sex education in schools of Macapá and consequently the State of Amapá. / GEA: 5987