Ribosomal RNA, ribose methylation, and box C/D snoRNAs during embryonic development of teleosts zebrafish (Danio rerio) and medaka (Oryzias latipes)

Doctoral thesis (PhD) - Nord University, 2022publishedVersio

A brain and a head for a different habitat : Size variation in four morphs of Arctic charr (Salvelinus alpinus(L.)) in a deep oligotrophic lake

Adaptive radiation is the diversification of species to different ecological niches and has repeatedly occurred in different salmonid fish of postglacial lakes. In Lake Tinnsjoen, one of the largest and deepest lakes in Norway, the salmonid fish, Arctic charr (Salvelinus alpinus(L.)), has likely radiated within 9,700 years after deglaciation into ecologically and genetically segregated Piscivore, Planktivore, Dwarf, and Abyssal morphs in the pelagial, littoral, shallow-moderate profundal, and deep-profundal habitats. We compared trait variation in the size of the head, the eye and olfactory organs, as well as the volumes of five brain regions of these four Arctic charr morphs. We hypothesised that specific habitat characteristics have promoted divergent body, head, and brain sizes related to utilized depth differing in environmental constraints (e.g., light, oxygen, pressure, temperature, and food quality). The most important ecomorphological variables differentiating morphs were eye area, habitat, and number of lamellae. The Abyssal morph living in the deepest areas of the lake had the smallest brain region volumes, head, and eye size. Comparing the olfactory bulb with the optic tectum in size, it was larger in the Abyssal morph than in the Piscivore morph. The Piscivore and Planktivore morphs that use more illuminated habitats have the largest optic tectum volume, followed by the Dwarf. The observed differences in body size and sensory capacities in terms of vision and olfaction in shallow and deepwater morphs likely relates to foraging and mating habitats in Lake Tinnsjoen. Further seasonal and experimental studies of brain volume in polymorphic species are needed to test the role of plasticity and adaptive evolution behind the observed differences.Peer reviewe

Pharmaceuticals in the environment : occurrence and exposure effects in non-target fish species

A contaminação por fármacos nas zonas costeiras constitui um problema ambiental emergente, onde os fármacos neuroativos são de particular importância porque bioacumulam em espécies não-alvo, afetando o sistema nervoso central e causando efeitos ao nível das populações. Os resultados demonstram, na literatura existente, os diversos efeitos adversos da exposição de fármacos neuroativos em peixes, apesar de incidir sobre poucos compostos e maioritariamente espécies de água-doce. A bioconcentração é também insuficientemente considerada e raramente estudada em combinação com outras respostas biológicas, dificultando a conjugação entre concentração interna e efeitos observados. A estimativa da bioconcentração dos fármacos neuroativos através da sua lipofilicidade não é direta e depende de múltiplos fatores experimentais, o que dificulta a previsão de risco. Contudo, concentrações ambientais de nove fármacos neuroativos excedem ou estão próximas de concentrações que causam efeitos deletérios em peixes. Dados ambientais, com a deteção de até 28 fármacos neuroativos em águas superficiais e peixes, evidenciam a ubiquidade e diversidade destes compostos em estuários, sendo que o padrão de bioacumulação em sete espécies de peixes foi independente da lipofilicidade dos compostos, do uso do habitat ou do nível-trófico das espécies, com maior frequência e concentrações observadas no cérebro, seguido do fígado e músculo. Experiências de curta e longa exposição a fármacos neuroativos com duas espécies estuarinas/marinhas demonstraram a toxicidade de fármacos com diferentes modos-de-ação, revelando maior acumulação e toxicidade do fármaco neuroativo, fluoxetina, em comparação com outros fármacos frequentemente detetados. As respostas sub-individuais revelaram efeitos em processos essenciais (e.g. mecanismos antioxidantes, biotransformação, metabolismo energético), enquanto efeitos individuais de relevância ecológica (e.g. crescimento, comportamentos alimentares e locomotores) ocorreram após exposição crónica, ou aguda a concentrações mais elevadas. Em suma, novos conhecimentos relativos à presença, acumulação e efeitos da exposição em peixes, demonstram a necessidade de priorizar a investigação e monitorização dos fármacos neuroativos em ecossistemas costeiros.Pharmaceutical contamination in coastal ecosystems is an emerging environmental issue, with neuroactive pharmaceuticals of particular concern as they bioaccumulate in non-target fish, affect the central nervous system and can trigger population-level effects. The presented outcomes disclose recent research efforts, revealing multiple adverse effects of exposure to neuroactive pharmaceuticals in fish, albeit skewed data concerning few neuroactive compounds and largely freshwater species exist. Moreover, bioconcentration is seldom considered and rarely determined in combination with other endpoints, hampering the link between internal dosage and effects. Also, estimating the bioconcentration of neuroactive pharmaceuticals through lipophilicity is not straightforward, depending on multiple experimental factors. Here, nine neuroactive compounds were signalled as potentially threatening in aquatic ecosystems due to environmental concentrations either exceeding or near thresholds known to significantly affect fish behaviour, growth and condition or reproduction. Up to 28 neuroactive pharmaceuticals were detected in estuarine surface waters and seven fish species demonstrating the diversity and pervasiveness of neuroactive compounds in both high and slightly impacted coastal ecosystems. Bioaccumulation among all species revealed no clear pattern linked to compounds lipophilicity, species habitat use or trophic level, with higher frequency and concentrations observed in the brain, followed by liver and muscle tissues. Acute and chronic exposure experiments with two estuarine/marine fish species evidenced the toxicity of three pharmaceuticals with different modes-of-action, highlighting higher uptake and toxicity of the neuroactive com-pound fluoxetine in comparison to other frequently detected compounds tested. Sub-individual measurements revealed effects on critical processes (e.g. antioxidant and biotransformation mechanisms, or energetic metabolism), whereas individual-level effects of higher ecological relevance (e.g. alterations to growth, feeding or activity behaviours) followed chronic exposure or acute exposure at higher concentrations. Overall, critical insights on environmental fate and exposure effects in fish are provided, highlighting the need for priority research and continuous monitoring of neuroactive pharmaceuticals in coastal ecosystems

Oogenesis in Unisexual Whiptail Lizards (genus Aspidoscelis)

Parthenogenesis is a reproductive mode that does not require males. Though theoretically advantageous, its rarity among metazoans suggests otherwise. Paradoxically, some unisexual species within the genus Aspidoscelis appear to be thriving by reproducing through obligate parthenogenesis. Formed via hybridization between different bisexual species, these lizards apparently reap the benefits of both hybrid vigor and higher reproductive potential. Previous studies have demonstrated the high degree of heterozygosity between generations, which contributes to the success of these lineages; a loss of heterozygosity would likely be accompanied by a decrease in fitness. How meiosis is modified in these animals is unknown. The predominant hypothesis suggests that endoreplication takes place prior to meiosis, resulting in a two-fold increase in DNA; however this has not been definitively shown. Further, the downstream modifications that result in a heterozygous gamete have merely been speculated upon. In the following thesis, meiosis within three parthenogenetic species is investigated. Quantification of DNA in germinal vesicles of the diploid parthenogen A. tesselata and the bisexual species A. gularis demonstrated that the parthenogen contains two-fold more DNA, despite equivalent somatic cell ploidy. Chiasmata were present on diplotene-stage chromosomes in both species, indicating that recombination is not bypassed. Additionally, synaptonemal complexes were found during pachytene in each species. Maintenance of heterozygosity is highly dependent on chromosome pairing in the parthenogen. Pairing between homologous chromosomes would result in a decrease; whereas pairing between identical (sister) chromosomes resulting from the additional DNA doubling event would preserve heterozygosity. Using homolog specific FISH probes in the parthenogen A. neomexicana, sister chromosome pairing is revealed. Thus, sister chromosome pairing after an additional DNA doubling allows for maintenance of heterozygosity in Aspidoscelis parthenogens. Secondly, four self-sustaining lineages of a new tetraploid species were generated from the mating between the diploid bisexual species Aspidoscelis inornata and triploid parthenogen A. exsanguis. The identity of these hybrids was confirmed by genotyping analysis. Females retain the ability to reproduce parthenogenetically through the doubling mechanism described in diploid species. These tetraploids have demonstrated how ploidy elevation hypothetically occurs in natural parthenogens. The mechanisms described in this thesis may be utilized in other parthenogens. Recent findings and future directions based on this work are presented

Machine learning-based automated segmentation with a feedback loop for 3D synchrotron micro-CT

Die Entwicklung von Synchrotronlichtquellen der dritten Generation hat die Grundlage für die Untersuchung der 3D-Struktur opaker Proben mit einer Auflösung im Mikrometerbereich und höher geschaffen. Dies führte zur Entwicklung der Röntgen-Synchrotron-Mikro-Computertomographie, welche die Schaffung von Bildgebungseinrichtungen zur Untersuchung von Proben verschiedenster Art förderte, z.B. von Modellorganismen, um die Physiologie komplexer lebender Systeme besser zu verstehen. Die Entwicklung moderner Steuerungssysteme und Robotik ermöglichte die vollständige Automatisierung der Röntgenbildgebungsexperimente und die Kalibrierung der Parameter des Versuchsaufbaus während des Betriebs. Die Weiterentwicklung der digitalen Detektorsysteme führte zu Verbesserungen der Auflösung, des Dynamikbereichs, der Empfindlichkeit und anderer wesentlicher Eigenschaften. Diese Verbesserungen führten zu einer beträchtlichen Steigerung des Durchsatzes des Bildgebungsprozesses, aber auf der anderen Seite begannen die Experimente eine wesentlich größere Datenmenge von bis zu Dutzenden von Terabyte zu generieren, welche anschließend manuell verarbeitet wurden. Somit ebneten diese technischen Fortschritte den Weg für die Durchführung effizienterer Hochdurchsatzexperimente zur Untersuchung einer großen Anzahl von Proben, welche Datensätze von besserer Qualität produzierten. In der wissenschaftlichen Gemeinschaft besteht daher ein hoher Bedarf an einem effizienten, automatisierten Workflow für die Röntgendatenanalyse, welcher eine solche Datenlast bewältigen und wertvolle Erkenntnisse für die Fachexperten liefern kann. Die bestehenden Lösungen für einen solchen Workflow sind nicht direkt auf Hochdurchsatzexperimente anwendbar, da sie für Ad-hoc-Szenarien im Bereich der medizinischen Bildgebung entwickelt wurden. Daher sind sie nicht für Hochdurchsatzdatenströme optimiert und auch nicht in der Lage, die hierarchische Beschaffenheit von Proben zu nutzen. Die wichtigsten Beiträge der vorliegenden Arbeit sind ein neuer automatisierter Analyse-Workflow, der für die effiziente Verarbeitung heterogener Röntgendatensätze hierarchischer Natur geeignet ist. Der entwickelte Workflow basiert auf verbesserten Methoden zur Datenvorverarbeitung, Registrierung, Lokalisierung und Segmentierung. Jede Phase eines Arbeitsablaufs, die eine Trainingsphase beinhaltet, kann automatisch feinabgestimmt werden, um die besten Hyperparameter für den spezifischen Datensatz zu finden. Für die Analyse von Faserstrukturen in Proben wurde eine neue, hochgradig parallelisierbare 3D-Orientierungsanalysemethode entwickelt, die auf einem neuartigen Konzept der emittierenden Strahlen basiert und eine präzisere morphologische Analyse ermöglicht. Alle entwickelten Methoden wurden gründlich an synthetischen Datensätzen validiert, um ihre Anwendbarkeit unter verschiedenen Abbildungsbedingungen quantitativ zu bewerten. Es wurde gezeigt, dass der Workflow in der Lage ist, eine Reihe von Datensätzen ähnlicher Art zu verarbeiten. Darüber hinaus werden die effizienten CPU/GPU-Implementierungen des entwickelten Workflows und der Methoden vorgestellt und der Gemeinschaft als Module für die Sprache Python zur Verfügung gestellt. Der entwickelte automatisierte Analyse-Workflow wurde erfolgreich für Mikro-CT-Datensätze angewandt, die in Hochdurchsatzröntgenexperimenten im Bereich der Entwicklungsbiologie und Materialwissenschaft gewonnen wurden. Insbesondere wurde dieser Arbeitsablauf für die Analyse der Medaka-Fisch-Datensätze angewandt, was eine automatisierte Segmentierung und anschließende morphologische Analyse von Gehirn, Leber, Kopfnephronen und Herz ermöglichte. Darüber hinaus wurde die entwickelte Methode der 3D-Orientierungsanalyse bei der morphologischen Analyse von Polymergerüst-Datensätzen eingesetzt, um einen Herstellungsprozess in Richtung wünschenswerter Eigenschaften zu lenken

Proximate and ultimate insights in the evolution of color vision in tropical freshwater fish

Evolutionary biology aims to understand diversity and the different mechanisms shaping this organismal variation. Furthermore, several animals vary greatly in coloration patterns and the adaptive mechanisms they have to optimally perceive visual signals in their light environment. The visual system of fish, due to their extensive variation in spectral sensitivities and their numerous adaptations to the underwater light environment, offers a unique opportunity to disentangle this phenotypic diversity. Throughout this dissertation, I analyze the visual systems of two major groups of Neotropical teleosts: cichlids and characins. Through transcriptome, genome and physiological experiments, I characterized the extant opsin gene complements of their visual system, which is a product of highly dynamic opsin gene evolution, and their color vision, which is based on the expression of at least three spectrally different visual pigments. The diversity of visual pigments found in these fish is the product of several spectral tuning mechanisms, which they use to fine-tune their spectral sensitivities to specific wavelengths. Our results follow the sensitivity hypothesis because the visual sensitivities of cichlids and characins match the available light in Neotropical ecosystems. Furthermore, through behavioral assays complemented with visual modeling, I show that African cichlids possess true color vision, the capacity of discriminating color regardless of brightness. This is followed by behavioral experiments analyzing the limits of their chromatic discrimination and discussing the adaptive significance of color vision and its relevance in the visual ecology of Lake Malawi. This dissertation enhances our understanding of color vision in freshwater fish using molecular and behavioral methods. This work encompasses experiments analyzing the genetic complement of visual pigments, builds knowledge in the evolution of these molecules and their relationship with aquatic environments, and analyzes the color dimensionality of visual systems through behavioral trials. Overall, this dissertation demonstrates the evolution of fish color vision with several methodologies highlighting the importance of an integrative and comparative approach in vision research

Machine Learning Models for Behavioural Diversity of Asian Elephants Prediction Using Satellite Collar Data

Analysis of animal movement data using statistical applications and machine learning has developed rapidly in line with the development and use of various tracking devices. Location and movement data at temporal and spatial scales are collected using the Global Positioning System (GPS) to estimate the location of animals. In contrast, installing a satellite collar can ensure continuous monitoring, as the received data will be sent directly to the electronic mailbox. Nevertheless, identifying an exact pattern of elephant activity from satellite collar data is still challenging. This study aimed to propose a machine learning model to predict the behavioural diversity of Asian elephants. The study involved four main phases, including two levels of model development, to produce initial and primary classification models. The phases were data collection and preparation, data labelling and initial classification model development, all data classification, and primary classification model development. The elephant behaviour data were collected from the satellite collars attached to five elephants, three males and two females, in forest reserves from 2018 to 2020 by the Department of Wildlife and National Parks, Malaysia. The study’s outcome was a novel classification model that can predict the behaviour of the Asian elephant movement. The findings showed that the XGBoost method could produce the predictive model to classify Asian elephants’ behaviour with 100 percent accuracy. This study revealed the capability of machine learning to identify behaviour classes and decision-making in setting initiatives to preserve this species in the future

Program and Abstracts of the Annual Meeting of the Georgia Academy of Science, 2015

The annual meeting of the Georgia Academy of Science took place March 13-14, 2015, at Georgia College & State University, Milledgeville, Georgia. The keynote speaker was Dr. Chryssa Kouveliotou of UA-Huntsville and the Marshall Space Center. Her presentation was entitled The Transient High-Energy Sky. Additional presentations were provided by members of the Academy who represented the following sections: I. Biological Sciences II Chemistry III. Earth & Atmospheric Sciences IV. Physics, Mathematics, Computer Science, Engineering & Technology V. Biomedical Sciences VI. Philosophy & History of Science VII. Science Education VIII. Anthropolog

Long-term effects of oestrogenic effluent exposure on wild fish populations

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University London.Freshwater streams in the developed world are becoming increasingly dominated by treated wastewater. Continually discharged into most surface waters, these effluents contain a suite of bioactive man-made chemicals, including steroid and non-steroid oestrogens, which have been found to feminise male fish, skew sex ratios, and cause reproductive failure. However, the consequences of reproductive disruption remain poorly explored at the population level. This thesis was initiated to evaluate how oestrogenic contaminants might influence the population ecology of a common cyprinid, the roach (Rutilus rutilus). An investigation encompassing population structure, multigenerational exposure and the role of additional drivers of fish population dynamics was undertaken to contextualise the effects of oestrogenic effluents on wild fish populations. Population genetic analysis of UK roach found they exhibit moderately high levels of genetic diversity and significant intra-river genetic structure. Genetically differentiated local subpopulations indicate little interbreeding and limited gene flow, consistent with a typical metapopulation that has not been homogenised by restocking. Similarly, my thesis demonstrates no significant relationship between effluent exposure and Ne (effective population size) or genetic diversity of roach populations, albeit a 65% reduction in Ne is possible at highly polluted sites. River stretches contaminated with high levels of effluent can support breeding populations, which recruit successfully with minimal immigration from less contaminated sites. Multigenerational effects of effluent exposure on roach were also evaluated experimentally using reproductive success from breeding adults over three generations. Lifelong exposure to 100% treated effluent resulted in feminised phenotypes (ovarian cavities and intersex condition) in males but no observable effect on females. Additionally, despite gonadal disruption in males and effluent exposure of their mothers, I found no detrimental effect on their ability to compete with control fish. Instead, reproductive success was primarily determined by body size. A novel approach considering additional fish population drivers suggests that genetic diversity and species diversity decline in parallel with an increasing presence of disturbed land, when combined with geographical isolation. In conclusion, group assemblage and genetic structure of fish populations appears multi-causal and cannot be disaggregated, such that a single environmental characteristic can be shown to drive patterns of population success.NERC (NE/G019355/1) and DEFRA