510 research outputs found
ACARORUM CATALOGUS IX. Acariformes, Acaridida, Schizoglyphoidea (Schizoglyphidae), Histiostomatoidea (Histiostomatidae, Guanolichidae), Canestrinioidea (Canestriniidae, Chetochelacaridae, Lophonotacaridae, Heterocoptidae), Hemisarcoptoidea (Chaetodactylidae, Hyadesiidae, Algophagidae, Hemisarcoptidae, Carpoglyphidae, Winterschmidtiidae)
The 9th volume of the series Acarorum Catalogus contains lists of mites of 13 families, 225 genera and 1268 species of the superfamilies Schizoglyphoidea, Histiostomatoidea, Canestrinioidea and Hemisarcoptoidea. Most of these mites live on insects or other animals (as parasites, phoretic or commensals), some inhabit rotten plant material, dung or fungi. Mites of the families Chetochelacaridae and Lophonotacaridae are specialised to live with Myriapods (Diplopoda). The peculiar aquatic or intertidal mites of the families Hyadesidae and Algophagidae are also included.Publishe
Computational comparative genomics in cyanobacteria
Cyanobacteria are an ancient clade of photosynthetic prokaryotes, varying in morphology, physiology, biochemistry and habitat. They evolve by typical prokaryotic mechanisms including horizontal gene transfer (HGT). Some species produce toxins (cyanotoxins) that present health hazards to humans and animals, with potential harm to local economies. The biosynthetic pathways and roles of some cyanotoxins are unclear. The rapid increase in high quality publicly available genomes presents opportunities for discovery from comparative genomics in cyanobacteria. The work presented here focuses on three topics in cyanobacteria, using bioinformatics analyses of 130 cyanobacterial genomes. Firstly, I consider hypotheses for the biosynthesis and physiology of the non-encoded neurotoxin 2,4-diaminobutanoic acid (2,4-DAB). Secondly, I consider hypotheses for the biosynthesis and potential roles of its structural analogue, β-N-methylaminoalanine (BMAA). These topics use similar methodology: pairwise and multiple sequence alignment, profile hidden Markov models, substrate specificity and active site identification, and the reconstruction of gene phylogenies. We show that some species have genes involved in known biochemical pathways to 2,4-DAB – genes coding for proteins in the aspartate 4-phosphate pathway (including the diaminobutanoate-2-oxo-glutarate transaminase, the downstream decarboxylase, diaminobutanoate decarboxylase, and ectoine synthase) – and BMAA (homologs of the Staphylococcus aureus genes sbnA and sbnB). We highlight the possible involvement of 2,4-DAB and BMAA in the production of siderophores. We show that the biosynthesis of 2,4-DAB and BMAA is likely to be confined to a limited number of species, or to occur via different, unknown, pathways. Thirdly, I investigate hypotheses concerning the association of HGT events with environmental context. I test existing hypotheses claiming that genetic exchanges are more frequent in extreme habitats (versus mesophilic) and in terrestrial habitats (versus aquatic). My results, based on reconciliation of gene trees with the species tree, do not suggest a link between the prevalence of HGT and extreme or terrestrial environments. I highlight the need for complete descriptions of the isolation source and culture type (axenic, non-axenic monocyanobacterial culture, environmental sample), the need for accurate and robust methods for HGT inference, and for more objective and detailed criteria for environmental classification and of cyanobacterial species. This work contributes to research into cyanobacterial neurotoxins and provides insights into the prevalence and distribution of HGT in cyanobacteria
LIPIcs, Volume 261, ICALP 2023, Complete Volume
LIPIcs, Volume 261, ICALP 2023, Complete Volum
Resurrected ancestral proteins as scaffolds for enzyme engineering and evolution
Enzymes are extraordinary efficient natural molecular machines that catalyze chemical
reactions and transformations that sustain life in all organisms. Decades of intensive
research have led to significant advances in the study of enzymes. Researchers have
developed sophisticated methodologies and approaches to extensively study and gain
an in-depth understanding of the molecular basis of enzyme structure, dynamics,
function, and regulation. As a result, it is now possible to accurately describe the
physiochemical implications of every element involved in almost every enzyme’s active
site during the specific molecular processes that drive the catalytic reactions. Moreover,
the extensive knowledge about enzymatic catalysis has allowed us to understand how
enzymes have evolved during billions of years of natural selection to catalyze chemical
reactions with proficient efficiency, specificity and selectivity towards the chemical
transformations and their substrates. Overall, the study of enzymes has provided a
fascinating window into the molecular machinery of life. But also, it has allowed
researchers to accumulate a solid scientific knowledge base that enables to engineer
and tune the molecular architecture of enzymes towards designing efficient artificial and
modified versions of tailored enzymes for catalyzing chemical reactions of
biotechnological and biomedical interest.
However, despite our deep knowledge and advanced understanding about the
fundamentals and evolution of enzymatic catalysis, one elemental question remains
unanswered – How enzymatic catalysis firstly emerged and evolved at the origin of
proteins and enzymes? Understanding the molecular mechanisms underlying the
evolutionary emergence of new enzymatic catalysis would not only be essential to
understand the birth of enzymes and its implications in the origins of life. But also, it
would be critical to design new biotechnological approaches inspired in these molecular
mechanisms to efficiently design and generate novel enzymes to catalyze artificial
unnatural chemical reactions of interest. Yet, the study of modern enzymes with the aim
to shed some light on this fundamental question has not provided significant advances.
In this thesis, we propose the hypothesis that resurrected ancestral proteins might be
better scaffolds than their modern counterparts to study and understand the
emergence of enzymatic catalysis. Ancestral active sites and their molecular
architectures would be more useful to reveal and study the minimal requirements for
catalysis. But also, ancestral proteins might be better starting points for engineering
novel active sites to catalyze artificial unnatural chemical reactions. Advances in both
directions may help us to reveal the molecular processes that drive the emergence of
new catalysis in nature. Ancestral proteins then show the potential to have a profound
impact in our understanding about enzyme catalysis, with critical implications in our
knowledge about the origins of life and our capacity to develop new artificial enzymes.
In order to validate our hypothesis, we have performed several experiments with
different resurrected ancestral protein systems aiming to evolve a de novo artificial active site, as well as to understand how primordial levels of cofactor-dependent
catalysis are promoted in an unevolved ancestral molecular scaffold.
In the first part of the thesis, we describe the evolution of an artificial de novo active
site, previously engineered in a resurrected ancestral β-lactamase scaffold, by means of
computational and experimental low-throughput screenings. As a result, we have
demonstrated how mutations in residues directly involved in a de novo active site or
how the introduction of new additional residues in the protein sequence may improve
the geometrical preorganization of the active site and generate new interactions that
enhance the stabilization of the reaction transition state and promote low initial levels
of activity to reach an efficient enzymatic catalysis comparable to natural enzymes.
These results have direct implications in protein engineering and de novo enzyme
design. But also, it provides new insights about the evolutionary processes that may led
the early optimization of novel active sites during the emergence of enzymatic catalysis.
In the second part of the thesis, we have resurrected an ancestral glycosidase protein
with a typical TIM-barrel fold that displays unusual biochemical and biophysical features.
Mainly, our ancestral TIM-barrel shows the ability to bind a molecule of the redox
cofactor heme in a highly flexible region of the barrel architecture. Upon heme binding,
the ancestral TIM-barrel displays a general rigidification of its structure, an allosteric
modulation of its natural enzymatic activity and an unnatural novel peroxidase activity
based on the redox catalytic power of heme. As a result, the ancestral heme binding
TIM-barrel protein demonstrates the potential of resurrected proteins as scaffolds to
harbor unusual combinations of properties of evolutionary and biotechnological
interest. Additionally, the study of our redox active TIM-barrel provides new insights
about the role cofactor protection in the emergence of proteins and enzymatic catalysis
during the origin of life.
Overall, the results presented in this thesis support the hypothesis that resurrected
ancestral proteins may serve as superior scaffolds for enzyme engineering and
evolutionary studies, aimed to better understand the emergence of enzymatic catalysis
during the origin of life.Las enzimas son máquinas moleculares naturales extraordinariamente eficientes que
catalizan las reacciones y transformaciones químicas que sustentan la vida de todos los
organismos. Décadas de investigación intensiva han logrado avances significativos en el
estudio de las enzimas. Los investigadores han desarrollado metodologías y
aproximaciones sofisticadas para estudiar de manera extensiva y conseguir un
conocimiento en profundidad sobre sobre las bases moleculares de la estructura,
dinámica, función y regulación de las enzimas. Como resultado, hoy en día es posible
describir de forma precisa las implicaciones fisicoquímicas de cada elemento
involucrado en el sitio activo de prácticamente cualquier enzima durante los procesos
moleculares específicos que permiten las reacciones catalíticas. Además, el
conocimiento extensivo sobre la catálisis enzimática nos ha permitido entender cómo
las enzimas han evolucionado durante miles de millones de años de selección natural
para catalizar reacciones químicas con eficiencia, especificidad y selectividad excelentes
con respecto a las reacciones de transformación y sus sustratos. En general, el estudio
de las enzimas ha abierto una fascinante ventana a la maquinaria molecular de la vida.
Pero, además, ha permitido a los investigadores acumular una sólida base de
conocimiento científico que podemos aplicar en el diseño, modificación y optimización
de la arquitectura molecular de las enzimas con el objetivo de diseñar versiones
artificiales y modificadas de enzimas a medida para catalizar reacciones químicas de
interés biotecnológico y biomédico.
A pesar del extenso y avanzado conocimiento sobre los fundamentos y la evolución de
la catálisis enzimática, sigue habiendo una pregunta elemental sin respuesta con
respecto al estudio de las enzimas: ¿Cómo emergió y evolucionó la catálisis enzimática
por primera vez durante el origen de las proteínas y las enzimas? La capacidad de
entender los mecanismos moleculares que subyacen a la emergencia evolutiva de
nuevas capacidades catalíticas en enzimas no solo es fundamental para entender el
nacimiento de las enzimas y sus implicaciones en el origen de la vida. Además, es crítica
para diseñar nuevas aproximaciones biotecnológicas inspiradas en estos mecanismos
moleculares con el objetivo de diseñar y generar de forma eficiente nuevas enzimas para
catalizar reacciones químicas artificiales no naturales de interés. Sin embargo, el estudio
basado en enzimas modernas, encontradas en los organismos actuales, con el objetivo
de responder a esta pregunta fundamental no logrado avances significativos.
En esta tesis proponemos la hipótesis de que las proteínas ancestrales resucitadas
podrían funcionar como mejores “andamios moleculares”, en comparación con sus
homologas modernas, para estudiar y comprender la emergencia de la catálisis
enzimática. El estudio de sitios activos ancestrales y sus arquitecturas moleculares
podría ser más útil para revelar y estudiar los requerimientos mínimos necesarios para
la catálisis enzimática. Además, las proteínas ancestrales podrían ser mejores puntos de
inicio para el diseño de sitios nuevos sitios activos para catalizar reacciones químicas no
naturales artificiales. En este sentido, lograr avances en ambas direcciones tendría importantes implicaciones para entender y revelar los procesos moleculares que dirigen
la emergencia de nuevas catálisis enzimáticas en la naturaleza. Por lo tanto, las proteínas
ancestrales muestran de potencial de tener un profundo impacto en nuestra
comprensión sobre la catálisis enzimática, con implicaciones críticas en nuestro
conocimiento sobre el origen de la vida y la capacidad de desarrollar nuevas enzimas
artificiales. Para validar nuestra hipótesis, hemos realizado diferentes experimentos con
diferentes sistemas de proteínas ancestrales resucitadas con el objetivo de evolucionar
un sitio activo artificial de novo y de entender cómo niveles primordiales de catálisis
dependiente de un cofactor son mejorados en un andamio molecular ancestral sin
evolucionar.
En la primera parte de la tesis describimos la evolución de un sitio activo artificial de
novo, previamente diseñado en el andamio molecular de una β-lactamasa ancestral
mediante cribados computacionales y experimentales de bajo número. Como resultado,
hemos demostrado cómo mutaciones en residuos directamente involucrados en el sitio
activo artificial o cómo la introducción de nuevos residuos adicionales en la secuencia
de la proteína puede mejorar la preorganización geométrica del sitio activo y generar
nuevas interacciones que aumentan la estabilización del estado de transición y mejoran
los bajos niveles de actividad enzimática para llegar a una catálisis enzimática eficiente
comparable a la de enzimas naturales. Estos resultados tienen implicaciones inmediatas
en ingeniería de proteínas y el diseño de novo de enzimas. Pero, adicionalmente, aporta
nuevo conocimiento sobre los mecanismos evolutivos que pudieron dar lugar a la
optimización temprana de sitios activos nuevos durante la emergencia de la catálisis
enzimática.
En la segunda parte de esta tesis, hemos resucitado una glicosidasa ancestral que
presenta un plegamiento típico en forma de barril TIM y que muestra unas propiedades
bioquímicas y biofísicas inusuales. Principalmente, nuestro barril TIM ancestral muestra
la capacidad de unir una molécula del cofactor redox hemo en una región
excepcionalmente flexible de arquitectura del barril. La unión del hemo da lugar a un
aumento general de la rigidez de la estructura de la proteína, a una modulación
alostérica de la actividad natural de la enzima y a la generación de una actividad
peroxidasa nueva no natural basada en el poder catalítico redox intrínseco del hemo.
Como resultado, nuestra proteína ancestral con estructura de barril TIM y con la
capacidad de unir hemo demuestra el potencial de la resurrección ancestral de proteínas
como andamios que muestran combinaciones inusuales de propiedades con interés
biotecnológico. Adicionalmente, el estudio de nuestro barril TIM con actividad redox
aporta nuevos puntos de vista sobre el papel de la protección de los cofactores durante
la emergencia de las proteínas y la catálisis enzimática durante en origen de la vida.
En general, los resultados presentados en esta tesis apoyan la hipótesis de que las
proteínas ancestrales resucitadas pueden servir como mejores andamiajes moleculares
en la ingeniería y estudios evolutivos de enzimas, dirigidos a lograr un mayor
conocimiento sobre la emergencia de la catálisis enzimática durante el origen de la vida.Tesis Univ. Granada
Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria
Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. M. avium bacteria are efficiently phagocytosed and frequently induce granuloma-like structures in zebrafish larvae. Although macrophages can respond to both mycobacterial infections, their migration speed is faster in infections caused by M. marinum. Tlr2 is conservatively involved in most aspects of the defense against both mycobacterial infections. However, Tlr2 has a function in the migration speed of macrophages and neutrophils to infection sites with M. marinum that is not observed with M. avium. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections. In conclusion, we characterized a new M. avium infection model in zebrafish that can be further used in studying pathological mechanisms for NTM-caused diseases
Ancestral Sequence Reconstructions of Stator Proteins of the Bacterial Flagellar Motor
The bacterial flagellar motor (BFM) is a bidirectional nanomachine that confers motility to several bacteria. The BFM is powered by ion transfer across the cell membrane through its stator. The stator consists of two membrane proteins: MotA and MotB in proton (H+)-powered motors or PomA and PomB in sodium (Na+)-powered motors. Over the years, several parts of the BFM have been resolved using numerous mutagenesis studies and different microscopic techniques. However, the entire structure of the BFM, its ion selection mechanism, the functional roles of each structural residue, and how its complexity evolves and adapts over time are not completely known. In this thesis, we used ancestral sequence reconstruction (ASR) to study the evolutionary history and roles of the key structural residues of the stator complex of the BFM.
First, we reconstructed and synthesised thirteen combined transmembrane (TM) and plug domains of ancestral MotBs (MotB-ASRs) to test previously hypothesised critical motifs for the ion-selectivity of BFM. The results showed that all resurrected MotB-ASRs were functional and restored motility with the contemporary E. coli MotA in a stator-deleted strain. In addition, all MotB-ASRs exhibited Na+-independent motility in different ionic conditions, suggesting that the synthesised MotB-ASRs were more likely to be proton-powered.
Secondly, we reconstructed and synthesised ten complete ancient MotAs (MotA-ASRs) to study the role of the key structural residues of MotA in BFM function. We identified that four of the ten MotA-ASRs were functional and restored motility in combination with contemporary E. coli MotB and several previously synthesised MotB-ASRs. The functional MotA-ASRs also showed Na+-independent motility in different ionic conditions, like our MotB-ASRs. Additionally, the resurrected MotA-ASRs provided evidence of several variable regions of MotA and revealed 30 conserved residues that were essential for flagellar function.
Lastly, we screened two novel motility inhibitors, HM2-16F and BB2-50F, and characterised their anti-motility activity on multiple strains and stator types. We also optimised and developed new high-resolution assays for the phenotypic study of stator function to verify the targets of the motility inhibitors. Our results confirmed that these compounds inhibited bacterial swimming but did not target the stator.
In summary, this thesis shows the use of ASR as a tool to study the stator proteins of the BFM
Modelling the genomic structure, and antiviral susceptibility of Human Cytomegalovirus
Human Cytomegalovirus (HCMV) is found ubiquitously in humans worldwide, and once acquired, the
infection persists within the host throughout their life. Although Immunocompetent people rarely are
affected by HCMV infections, their related diseases pose a major health problem worldwide for those
with compromised or suppressed immune systems such as transplant recipients. Additionally,
congenital transmission of HCMV is the most common infectious cause of birth defects globally and
is associated with a substantial economic burden.
This thesis explores the application of statistical modelling and genomics to unpick three key areas of
interest in HCMV research. First, a comparative genomics analysis of global HCMV strains was
undertaken to delineate the molecular population structure of this highly variable virus. By including
in-house sequenced viruses of African origin and by developing a statistical framework to deconvolute
highly variable regions of the genome, novel and important insights into the co-evolution of HCMV
with its host were uncovered.
Second, a rich database relating mutations to drug sensitivity was curated for all the antiviral treated
herpesviruses. This structured information along with the development of a mutation annotation
pipeline, allowed the further development of statistical models that predict the phenotype of a virus
from its sequence. The predictive power of these models was validated for HSV1 by using external
unseen mutation data provided in collaboration with the UK Health Security Agency.
Finally, a nonlinear mixed effects model, expanded to account for Ganciclovir pharmacokinetics and
pharmacodynamics, was developed by making use of rich temporal HCMV viral load data. This model
allowed the estimation of the impact of immune-clearance versus antiviral inhibition in controlling
HCMV lytic replication in already established infections post-haematopoietic stem cell transplant
Understanding virus and microbial evolution in wildlife through meta-transcriptomics
Wildlife harbors a substantial and largely undocumented diversity of RNA viruses and microbial life forms. RNA viruses and microbes are also arguably the most diverse and dynamic entities on Earth. Despite their evident importance, there are major limitations in our knowledge of the diversity, ecology, and evolution of RNA viruses and microbial communities. These gaps stem from a variety of factors, including biased sampling and the difficulty in accurately identifying highly divergent sequences through sequence similarity-based analyses alone. The implementation of meta-transcriptomic sequencing has greatly contributed to narrowing this gap. In particular, the rapid increase in the number of newly described RNA viruses over the last decade provides a glimpse of the remarkable diversity within the RNA virosphere. The central goal in this thesis was to determine the diversity of RNA viruses associated with wildlife, particularly in an Australian context. To this end I exploited cutting-edge meta-transcriptomic and bioinformatic approaches to reveal the RNA virus diversity within diverse animal taxa, tissues, and environments, with a special focus on the highly divergent "dark matter" of the virome that has largely been refractory to sequence analysis. Similarly, I used these approaches to detect targeted common microbes circulating in vertebrate and invertebrate fauna. Another important goal was to assess the diversity of RNA viruses and microbes as a cornerstone within a new eco-evolutionary framework. By doing so, this thesis encompasses multiple disciplines including virus discovery, viral host-range distributions, microbial-virus and host–parasite interactions, phylogenetic analysis, and pathogen surveillance. In sum, the research presented in this thesis expands the known RNA virosphere as well as the detection and surveillance of targeted microbes in wildlife, providing new insights into the diversity, evolution, and ecology of these agents in nature
Genomic diversity associated with polymorphic inversions in humans and their close relatives
Individuals of one species share the bulk of their genetic material, yet no two genomes are the same. Aside from displaying classical variation such as deletions, insertions, or substitutions of base pairs, two DNA segments can also differ in their orientation relative to the rest of their chromosomes. Such inversions are known for a range of biological implications and contribute critically to genome evolution and disease. However, inversions are notoriously challenging to detect, a fact which still impedes comprehensive analysis of their specific properties. This thesis describes several highly inter-connected projects aimed at identifying and functionally characterizing inversions present in the human population and related great ape species.
First, inversions between human and four great ape species were assessed for their potential to disrupt topologically associating domains (TADs), potentially prompting gene misregulation. TAD boundaries co-located with breakpoints of long inversions, and while disrupted TADs displayed elevated rates of differen- tially expressed genes, this effect could be attributed the vicinity to inversion breakpoints, suggesting overall robustness of gene expression in response to TAD disruption.
The second part of this thesis describes contributions to a collaborative project aimed at characterizing the full spectrum of inversions in 43 humans. In this study, I co-developed a novel inversion genotyping algorithm based on Strand- specific DNA sequencing and contributed to the description of 398 inversion polymorphisms. Inversions exhibited various underlying formation mechanisms, promotion of gene dysregulation, widespread recurrence, and association with genomic disease. These results suggest that long inversions are much more prominent in humans than previously thought, with at least 0.6% of the genome subject to inversion recurrence and, sometimes, the associated risk of subsequent deleterious mutation.
With a focus on the link between inversions and disease-causing copy num- ber variations, the last project describes a novel algorithm to identify loci hit sequentially by several overlapping mutation events. This algorithm enabled the description of detailed mutation sequences in 20 highly dynamic regions in the human genome, and additional complex variants on chromosome Y. Six complex loci associate directly with a genomic disease, thereby highlighting in detail the intrinsic link between inversions and CNVs. In summary, these projects provide novel insights into the landscape of in- versions in humans and primates, which are much more frequent, and often more complex than previously thought. These findings provide a basis for future inversion studies and highlight the crucial contribution of this class of mutation to genome variation
Differential evolution of non-coding DNA across eukaryotes and its close relationship with complex multicellularity on Earth
Here, I elaborate on the hypothesis that complex multicellularity (CM, sensu Knoll) is a major evolutionary transition (sensu Szathmary), which has convergently evolved a few times in Eukarya only: within red and brown algae, plants, animals, and fungi. Paradoxically, CM seems to correlate with the expansion of non-coding DNA (ncDNA) in the genome rather than with genome size or the total number of genes. Thus, I investigated the correlation between genome and organismal complexities across 461 eukaryotes under a phylogenetically controlled framework. To that end, I introduce the first formal definitions and criteria to distinguish ‘unicellularity’, ‘simple’ (SM) and ‘complex’ multicellularity. Rather than using the limited available estimations of unique cell types, the 461 species were classified according to our criteria by reviewing their life cycle and body plan development from literature. Then, I investigated the evolutionary association between genome size and 35 genome-wide features (introns and exons from protein-coding genes, repeats and intergenic regions) describing the coding and ncDNA complexities of the 461 genomes. To that end, I developed ‘GenomeContent’, a program that systematically retrieves massive multidimensional datasets from gene annotations and calculates over 100 genome-wide statistics. R-scripts coupled to parallel computing were created to calculate >260,000 phylogenetic controlled pairwise correlations. As previously reported, both repetitive and non-repetitive DNA are found to be scaling strongly and positively with genome size across most eukaryotic lineages. Contrasting previous studies, I demonstrate that changes in the length and repeat composition of introns are only weakly or moderately associated with changes in genome size at the global phylogenetic scale, while changes in intron abundance (within and across genes) are either not or only very weakly associated with changes in genome size. Our evolutionary correlations are robust to: different phylogenetic regression methods, uncertainties in the tree of eukaryotes, variations in genome size estimates, and randomly reduced datasets. Then, I investigated the correlation between the 35 genome-wide features and the cellular complexity of the 461 eukaryotes with phylogenetic Principal Component Analyses. Our results endorse a genetic distinction between SM and CM in Archaeplastida and Metazoa, but not so clearly in Fungi. Remarkably, complex multicellular organisms and their closest ancestral relatives are characterized by high intron-richness, regardless of genome size. Finally, I argue why and how a vast expansion of non-coding RNA (ncRNA) regulators rather than of novel protein regulators can promote the emergence of CM in Eukarya. As a proof of concept, I co-developed a novel ‘ceRNA-motif pipeline’ for the prediction of “competing endogenous” ncRNAs (ceRNAs) that regulate microRNAs in plants. We identified three candidate ceRNAs motifs: MIM166, MIM171 and MIM159/319, which were found to be conserved across land plants and be potentially involved in diverse developmental processes and stress responses. Collectively, the findings of this dissertation support our hypothesis that CM on Earth is a major evolutionary transition promoted by the expansion of two major ncDNA classes, introns and regulatory ncRNAs, which might have boosted the irreversible commitment of cell types in certain lineages by canalizing the timing and kinetics of the eukaryotic transcriptome.:Cover page
Abstract
Acknowledgements
Index
1. The structure of this thesis
1.1. Structure of this PhD dissertation
1.2. Publications of this PhD dissertation
1.3. Computational infrastructure and resources
1.4. Disclosure of financial support and information use
1.5. Acknowledgements
1.6. Author contributions and use of impersonal and personal pronouns
2. Biological background
2.1. The complexity of the eukaryotic genome
2.2. The problem of counting and defining “genes” in eukaryotes
2.3. The “function” concept for genes and “dark matter”
2.4. Increases of organismal complexity on Earth through multicellularity
2.5. Multicellularity is a “fitness transition” in individuality
2.6. The complexity of cell differentiation in multicellularity
3. Technical background
3.1. The Phylogenetic Comparative Method (PCM)
3.2. RNA secondary structure prediction
3.3. Some standards for genome and gene annotation
4. What is in a eukaryotic genome? GenomeContent provides a good answer
4.1. Background
4.2. Motivation: an interoperable tool for data retrieval of gene annotations
4.3. Methods
4.4. Results
4.5. Discussion
5. The evolutionary correlation between genome size and ncDNA
5.1. Background
5.2. Motivation: estimating the relationship between genome size and ncDNA
5.3. Methods
5.4. Results
5.5. Discussion
6. The relationship between non-coding DNA and Complex Multicellularity
6.1. Background
6.2. Motivation: How to define and measure complex multicellularity across eukaryotes?
6.3. Methods
6.4. Results
6.5. Discussion
7. The ceRNA motif pipeline: regulation of microRNAs by target mimics
7.1. Background
7.2. A revisited protocol for the computational analysis of Target Mimics
7.3. Motivation: a novel pipeline for ceRNA motif discovery
7.4. Methods
7.5. Results
7.6. Discussion
8. Conclusions and outlook
8.1. Contributions and lessons for the bioinformatics of large-scale comparative analyses
8.2. Intron features are evolutionarily decoupled among themselves and from genome size throughout Eukarya
8.3. “Complex multicellularity” is a major evolutionary transition
8.4. Role of RNA throughout the evolution of life and complex multicellularity on Earth
9. Supplementary Data
Bibliography
Curriculum Scientiae
Selbständigkeitserklärung (declaration of authorship
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