Desarrollo de cepas vínicas de Saccharomyces cerevisiae superproductoras de manoproteinas mediante tecnicas de DNA recombinante, y su aplicación en enologia

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química Física Aplicada. Fecha de lectura: 21-11-200

Colour polymorphism in the terrestrial snail Cepaea nemoralis: from genetics and genomics to spectroscopy and deep learning

Colour variation in the animal kingdom has been important in science to determine the principles of biology, especially in genetics and evolution. In the past decades, much effort has been targeted at the evolutionary, ecological and genetic basis of colour variation. Although land snails have been relatively neglected, especially in latter years, a comprehension of genetics and the evolution is important to understand colour variation precisely because snails may be representative of many species. When studying colour polymorphism, one of the remaining challenges is to describe colour. Generally, colour is described manually, relying on the judgment of human perception, classifying them into a discrete types. The main issue, then, is that human perception is subjective and colour is continuous. Fortunately, technology has enabled new techniques to score colour, which may help to investigate colour polymorphism. This thesis aims to contribute to the knowledge of the maintenance of colour polymorphism by firstly, understanding the genetics and genomics and secondly, developing new methods for the scoring of colour. To achieve this, the grove snail Cepaea nemoralis was selected as a model species. Cepaea nemoralis was chosen due to their highly polymorphic shell, its easy collection, is widely distributed in all variety of habitats and the colour and banding morphs showing Mendelian inheritance (Cain & Sheppard, 1950, Cain & Sheppard, 1952, Cain & Sheppard, 1954, Lamotte, 1959, Jones et al., 1977). In the first part, I aimed for a better understanding of the inheritance of colour. Hence, new crosses of C. nemoralis were used, with flanking restriction site–associated DNA sequencing (RAD-seq) markers used to identify putative instances of recombination with the supergene that determines colour and banding. No evidence of the predicted recombinants was found. Instead, a better explanation could involve incomplete penetrance and epistasis (Gonzalez et al., 2019). The findings therefore challenge the previous assumption of the supergene architecture and provides a new resource for the future creation of a fine mapping of the supergene (Gonzalez et al., 2019). In the second part, I aimed to understand the evolutionary history of C. nemoralis, by investigating the relationship of the genomic and supergene variation with the geographic distribution over Europe. High-throughput genome-wide genotyping was achieved via a double digest restriction-site associated DNA sequencing (ddRADseq) method. A broad phylogenomic relationship showed geographic structure. However, no relationship between the geographical distribution and colour variation was found. Furthermore, possible genomic regions under selection, which may be driving the genomic variation, were identified. In addition, the phylogeny described the evolution of C. nemoralis and indicated how the Pyrenean lineages colonised Europe after the Pleistocene. The results suggest new roads of research into the evolutionary and genomic mechanisms that have led the geographical genomic and supergene variation of C. nemoralis. In the third part, colour manual scoring was tested using new quantitative methods to describe colour to better understand colour variation. Therefore, a comparative study with historical and present shell colour patterns of C. nemoralis in the Pyrenees was used. Prior studies manually scored shell ground colour into three discrete colours; yellow, pink or brown. However, colour is continuous and the description of discrete colours may incur potential error and biased results. Thus, a quantitative method to score shell colour and to test manual scoring, comparing patterns of C. nemoralis shell colour polymorphism was used. Similar altitudinal trends irrespective of the method were found, even though quantitative measures of shell colour reduced the possibility of error. Moreover, a remarkable stability in the local shell patterns over five decades were found. This study determined that both methods remains valuable illustrating several advantages and disadvantages. In the future, a combination of both methods may be a possible solution. Finally, and as continuation of the third part, a new visual recognition and classification method for C. nemoralis based on spectrophotometry and deep learning was created. Firstly, colour of the shells were quantified by spectrometry, and secondly, pictures were taken of the measured shells, in different backgrounds. Those pictures were used to train and test a Region-based Fully Convolutional Networks (R-FCN). Furthermore, public domain pictures were collected from iNaturalist database (https://www.inaturalist.org/), to validate the model. The results illustrate that this method can achieve high accuracy of detection and classification of snails into the right morph. This work may facilitate the way of how colour polymorphism was investigated, illustrating new avenues for future research. In conclusion, this thesis evaluates the limitations found in prior studies and generates new data for the genetic and genomic understanding of C. nemoralis colour polymorphism. It also produced viable solutions, using new technologies, to score the diverse colour morphs. I also contributed to the geographic evolutionary genomic diversity knowledge

Colour polymorphism in the terrestrial snail Cepaea nemoralis: from genetics and genomics to spectroscopy and deep learning

Colour variation in the animal kingdom has been important in science to determine the principles of biology, especially in genetics and evolution. In the past decades, much effort has been targeted at the evolutionary, ecological and genetic basis of colour variation. Although land snails have been relatively neglected, especially in latter years, a comprehension of genetics and the evolution is important to understand colour variation precisely because snails may be representative of many species. When studying colour polymorphism, one of the remaining challenges is to describe colour. Generally, colour is described manually, relying on the judgment of human perception, classifying them into a discrete types. The main issue, then, is that human perception is subjective and colour is continuous. Fortunately, technology has enabled new techniques to score colour, which may help to investigate colour polymorphism. This thesis aims to contribute to the knowledge of the maintenance of colour polymorphism by firstly, understanding the genetics and genomics and secondly, developing new methods for the scoring of colour. To achieve this, the grove snail Cepaea nemoralis was selected as a model species. Cepaea nemoralis was chosen due to their highly polymorphic shell, its easy collection, is widely distributed in all variety of habitats and the colour and banding morphs showing Mendelian inheritance (Cain & Sheppard, 1950, Cain & Sheppard, 1952, Cain & Sheppard, 1954, Lamotte, 1959, Jones et al., 1977). In the first part, I aimed for a better understanding of the inheritance of colour. Hence, new crosses of C. nemoralis were used, with flanking restriction site–associated DNA sequencing (RAD-seq) markers used to identify putative instances of recombination with the supergene that determines colour and banding. No evidence of the predicted recombinants was found. Instead, a better explanation could involve incomplete penetrance and epistasis (Gonzalez et al., 2019). The findings therefore challenge the previous assumption of the supergene architecture and provides a new resource for the future creation of a fine mapping of the supergene (Gonzalez et al., 2019). In the second part, I aimed to understand the evolutionary history of C. nemoralis, by investigating the relationship of the genomic and supergene variation with the geographic distribution over Europe. High-throughput genome-wide genotyping was achieved via a double digest restriction-site associated DNA sequencing (ddRADseq) method. A broad phylogenomic relationship showed geographic structure. However, no relationship between the geographical distribution and colour variation was found. Furthermore, possible genomic regions under selection, which may be driving the genomic variation, were identified. In addition, the phylogeny described the evolution of C. nemoralis and indicated how the Pyrenean lineages colonised Europe after the Pleistocene. The results suggest new roads of research into the evolutionary and genomic mechanisms that have led the geographical genomic and supergene variation of C. nemoralis. In the third part, colour manual scoring was tested using new quantitative methods to describe colour to better understand colour variation. Therefore, a comparative study with historical and present shell colour patterns of C. nemoralis in the Pyrenees was used. Prior studies manually scored shell ground colour into three discrete colours; yellow, pink or brown. However, colour is continuous and the description of discrete colours may incur potential error and biased results. Thus, a quantitative method to score shell colour and to test manual scoring, comparing patterns of C. nemoralis shell colour polymorphism was used. Similar altitudinal trends irrespective of the method were found, even though quantitative measures of shell colour reduced the possibility of error. Moreover, a remarkable stability in the local shell patterns over five decades were found. This study determined that both methods remains valuable illustrating several advantages and disadvantages. In the future, a combination of both methods may be a possible solution. Finally, and as continuation of the third part, a new visual recognition and classification method for C. nemoralis based on spectrophotometry and deep learning was created. Firstly, colour of the shells were quantified by spectrometry, and secondly, pictures were taken of the measured shells, in different backgrounds. Those pictures were used to train and test a Region-based Fully Convolutional Networks (R-FCN). Furthermore, public domain pictures were collected from iNaturalist database (https://www.inaturalist.org/), to validate the model. The results illustrate that this method can achieve high accuracy of detection and classification of snails into the right morph. This work may facilitate the way of how colour polymorphism was investigated, illustrating new avenues for future research. In conclusion, this thesis evaluates the limitations found in prior studies and generates new data for the genetic and genomic understanding of C. nemoralis colour polymorphism. It also produced viable solutions, using new technologies, to score the diverse colour morphs. I also contributed to the geographic evolutionary genomic diversity knowledge

Quality-Based Conditional Processing in Multi-Biometrics: Application to Sensor Interoperability

As biometric technology is increasingly deployed, it will be common to replace parts of operational systems with newer designs. The cost and inconvenience of reacquiring enrolled users when a new vendor solution is incorporated makes this approach difficult and many applications will require to deal with information from different sources regularly. These interoperability problems can dramatically affect the performance of biometric systems and thus, they need to be overcome. Here, we describe and evaluate the ATVS-UAM fusion approach submitted to the quality-based evaluation of the 2007 BioSecure Multimodal Evaluation Campaign, whose aim was to compare fusion algorithms when biometric signals were generated using several biometric devices in mismatched conditions. Quality measures from the raw biometric data are available to allow system adjustment to changing quality conditions due to device changes. This system adjustment is referred to as quality-based conditional processing. The proposed fusion approach is based on linear logistic regression, in which fused scores tend to be log-likelihood-ratios. This allows the easy and efficient combination of matching scores from different devices assuming low dependence among modalities. In our system, quality information is used to switch between different system modules depending on the data source (the sensor in our case) and to reject channels with low quality data during the fusion. We compare our fusion approach to a set of rule-based fusion schemes over normalized scores. Results show that the proposed approach outperforms all the rule-based fusion schemes. We also show that with the quality-based channel rejection scheme, an overall improvement of 25% in the equal error rate is obtained.Comment: Published at IEEE Transactions on Systems, Man, and Cybernetics - Part A: Systems and Human

Qualitative and quantitative methods show stability in patterns of Cepaea nemoralis shell polymorphism in the Pyrenees over five decades

Over the past century, the study of animal color has been critical in establishing some of the founding principles of biology, especially in genetics and evolution. In this regard, one of the emerging strengths of working with the land snail genus Cepaea is that historical collections can be compared against modern‐day samples, for instance, to understand the impact of changing climate and habitat upon shell morph frequencies. However, one potential limitation is that prior studies scored shell ground color by eye into three discrete colours yellow, pink, or brown. This incurs both potential error and bias in comparative surveys. In this study, we therefore aimed to use a quantitative method to score shell color and evaluated it by comparing patterns of C. nemoralis shell color polymorphism in the Pyrenees, using both methods on present‐day samples, and against historical data gathered in the 1960s using the traditional method. The main finding was that while quantitative measures of shell color reduced the possibility of error and standardized the procedure, the same altitudinal trends were recovered, irrespective of the method. The results also showed that there was a general stability in the local shell patterns over five decades, including altitudinal clines, with just some exceptions. Therefore, although subject to potential error human scoring of snail color data remains valuable, especially if persons have appropriate training. In comparison, while there are benefits in taking quantitative measures of color in the laboratory, there are also several practical disadvantages, mainly in terms of throughput and accessibility. In the future, we anticipate that genomic methods may be used to understand the potential role of selection in maintaining shell morph clines. In addition, photographs generated by citizen scientists conducting field surveys may be used with deep learning‐based methods to survey color patterns

Conversión de Potencia para un Sistema de Almacenamiento Híbrido Batería-Capacitor

Context: Thanks to the low emissions of CO2 generated by electric systems, those solutions have anincreased attention from industry and academia. However, the electrical storage systems required in alarge amount of applications must to have both high energy and power densities. Method: To meet those requirements, this paper proposes an active hybrid energy storage system(HESS), which is formed by a battery, i.e. the device with high energy density, and a capacitor, i.e. the device with high power capability. The proposed power system also protects the battery by limiting the current derivative. Results: Two sliding-mode controllers (SMC) are designed to regulate both the battery current and the load voltage. The design process guarantees the global stability and safe battery operation. Conclusions: The controller avoids the battery degradation caused by the high-frequency current components since the capacitor assumes those components demanded by the load profile.Contexto: Gracias a las bajas emisiones de CO2 de los sistemas el´ectricos, estos han ganado mucha atenci´on por parte de la industria y la academia. Sin embargo, los sistemas de almacenamiento de energ´ıa requeridos en un sin numero de aplicaciones deben garantizar ser de alta densidad de energ´ıa y potencia. M´etodo: Para satisfacer estos requerimientos, este trabajo propone un sistema de almacenamiento de energ´ıa h´ıbrido (HESS) activo, el cual es formado por una bater´ıa como dispositivo de alta densidad de energ´ıa, y un capacitor como el dispositivo de alta densidad de potencia. Asimismo, la soluci´on propuesta protege la bater´ı a trav´es de la limitaci´on de la derivada de la corriente. Resultados: Se dise˜nan dos controladores por modos deslizantes, uno para la corriente de la bater´ıa y otro para regular el voltaje en la carga. El proceso de dise˜no garantiza la estabilidad global del sistema y una operaci´on segura de la bater´ıa

Power Generation and Transmission Expansion Planning under Uncertainty considering Flexibility in Generation Investments

The process of liberalization of power markets has led to a paradigm shift in the joint expansion planning of the generation and transmission segments. The assessment of this problem is even more complex when considering the uncertainties that usually determine the long-term evolution of the system. Moreover, and from the point of view of regulators and policy makers, an optimal assessment is of great interest because the lack of coordination between the two types of investment can jeopardize competition and efficiency in the whole electricity sector. In this regard, the literature suggests the use of holistic approaches, which necessarily evaluate the risks associated with the coordination of investments in the power system, in order to allow regulators to identify an efficient investment alternative, considering scenarios in which the uncertain variables evolve unfavorably. In this context, this paper test a method to assess the joint expansion planning of the generation and transmission segments, considering the inherent flexibility of generation investments, using the Real Options Valuation approach, calculated with the Least Squares Monte Carlo. In order to validate this method, a case study has been simulated. It is shown that the consideration of investments’ flexibility allows increasing the system-wide social benefit through the coordinated planning of the generation and transmission segments.CONACYT - Consejo Nacional de Ciencias y TecnologíaPROCIENCI

Recombination within the Cepaea nemoralis supergene is confounded by incomplete penetrance and epistasis

Although the land snail Cepaea nemoralis is one of the most thoroughly investigated colour polymorphic species, there have been few recent studies on the inheritance of the shell traits. Previously, it has been shown that the shell polymorphism is controlled by a series of nine or more loci, of which five make a single ‘supergene’ containing tightly linked colour and banding loci and more loosely linked pigmentation, spread band and punctate loci. However, one limitation of earlier work was that putative instances of recombination between loci within the supergene were not easily verified. We therefore generated a new set of C. nemoralis crosses that segregate for colour, banding and pigmentation, and several other unlinked shell phenotype loci. The snails were genotyped using a set of RAD-seq-derived loci that flank the supergene, and instances of recombination tested by comparing inferred supergene genotype against RAD-marker genotype. We found no evidence that suspected ‘recombinant’ individuals are recombinant between loci within the supergene. As point estimates of recombination between both colour/banding, and colour/pigmentation loci are zero, incomplete penetrance and epistasis are a better explanation for the apparent ‘recombinant’ phenotype of some snail shells. Overall, this work, therefore, shows that the architecture of the supergene may not be as previously supposed. It also provides a resource for fine mapping of the supergene and other major shell phenotype loci

Deep structure, long-distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

Although snails of the genus Cepaea have historically been important in studying colour polymorphism, an ongoing issue is that there is a lack of knowledge of the underlying genetics of the polymorphism, as well as an absence of genomic data to put findings in context. We, therefore, used phylogenomic methods to begin to investigate the post-glacial history of Cepaea nemoralis, with a long-term aim to understand the roles that selection and drift have in determining both European-wide and local patterns of colour polymorphism. By combining prior and new mitochondrial DNA data from over 1500 individuals with ddRAD genomic data from representative individuals across Europe, we show that patterns of differentiation are primarily due to multiple deeply diverged populations of snails. Minimally, there is a widespread Central European population and additional diverged groups in Northern Spain, the Pyrenees, as well as likely Italy and South Eastern Europe. The genomic analysis showed that the present-day snails in Ireland and possibly some other locations are likely descendants of admixture between snails from the Pyrenees and the Central European group, an observation that is consistent with prior inferences from mitochondrial DNA alone. The interpretation is that C.nemoralis may have arrived in Ireland via long-distance migration from the Pyrenean region, subsequently admixing with arrivals from elsewhere. This work, therefore, provides a baseline expectation for future studies on the genetics of the colour polymorphism, as well as providing a comparator for similar species