Использование быстрого преобразования Фурье и свёрточных функций для сравнения нуклеотидных последовательностей

В бакалаврской работе А.А. Молявко реализовала на языке C# и протестировала новый метод сравнения символьных последовательностей на основе быстрого преобразования Фурье. Сравнение символьных последовательностей является важной задачей, возникающей во многих приложениях математики. В частности, эта проблема существует в биоинформатике, где ей в настоящее время уделяется большое внимание как ключевому инструменту проведения самых разных исследований. В бакалаврской работе рассмотрен новый предложенный профессором В.В. Шайдуровым алгоритм, позволяющий находить в исследуемых последовательностях точно совпадающие участки, а также участки с теми или иными несоответствиями, такими как замены, вставки и/или выпадения отдельных символов

Biometrics

Biometrics uses methods for unique recognition of humans based upon one or more intrinsic physical or behavioral traits. In computer science, particularly, biometrics is used as a form of identity access management and access control. It is also used to identify individuals in groups that are under surveillance. The book consists of 13 chapters, each focusing on a certain aspect of the problem. The book chapters are divided into three sections: physical biometrics, behavioral biometrics and medical biometrics. The key objective of the book is to provide comprehensive reference and text on human authentication and people identity verification from both physiological, behavioural and other points of view. It aims to publish new insights into current innovations in computer systems and technology for biometrics development and its applications. The book was reviewed by the editor Dr. Jucheng Yang, and many of the guest editors, such as Dr. Girija Chetty, Dr. Norman Poh, Dr. Loris Nanni, Dr. Jianjiang Feng, Dr. Dongsun Park, Dr. Sook Yoon and so on, who also made a significant contribution to the book

RNA-SEQ applied to the peacock blenny Salaria pavo: unveiling the gene networks and signalling pathways behind phenotypic plasticity in a littoral fish

Phenotypic plasticity is the ability of an individual genome to produce different phenotypes depending on environmental cues. These plastic responses rely on diverse genomic mechanisms and allow an organism to maximize its fitness in a variety of social and physical settings. The development of next-generation sequencing (NGS) technologies, especially RNA Sequencing (RNA-Seq), has made it possible to investigate the distinct patterns of gene expression known to be underlying plastic phenotypes in species with ecological interest. In teleost fishes, changes in phenotypes is often observed during the reproductive season, with shifts and adjustments in dominance status that can lead to the co-existence of multiple reproductive morphs within the same population. One such example is the peacock blenny Salaria pavo (Risso, 1810), a species where the intensity of mating competition varies among populations due to nest-site availability, such that two different levels of plasticity arise: 1) intraspecific variation in reproductive behaviour for males that can follow either of two developmental pathways, grow directly into nest-holder males, or behave first as female mimics to sneak fertilizations (sneaker males) and later transition into nest-holder males, and 2) inter-population variation in courting roles of females and nest-holder males. This system provides the ideal basis to apply RNA-Seq methods to study plasticity since differences in reproductive traits within and among populations can reveal which genetic and genomic mechanisms underpin the observed variation in behavioural response to changes in the social environment. However, the genomic information available for this species was scarce, and hence multiple sequencing techniques were used and the methodologies applied optimized throughout the work. In this thesis, we start by first obtaining a de novo transcriptome assembly to develop the first genetic markers for this species (Chapter 2). These microsatellites were used to elucidate the reproductive success (i.e. consisting of mating success and fertilization success) of male ARTs, which can be used as a proxy of Darwinian fitness (Chapter 3). In this study, we detected a fertilization success for nestholder males of 95%, and showed a stronger influence of the social environment rather than morphological variables in the proportion of lost fertilizations by nest-holder males of this species. Taking advantage of the developed transcriptome, we used highthroughput sequencing to obtain expression profiles for male morphs (i.e. intraspecific variation) and females in this species, and focus on the role of differential gene expression in the evolution of sequential alternative reproductive tactics (ARTs) that involve the expression of both male and female traits (Chapter 4). Additionally, we show how the distinct behavioural repertoires are facilitated by distinct neurogenomic states, which discriminate not only sex but also male morphs. Lastly, using two different target tissues, gonads and forebrain, we focus on the genomic regulation of sex roles in courtship behaviour between females and males from two populations under different selective regimes (inter-population variation), the Portuguese coastal population with reversed sex roles and the rocky Italian population with ‘conventional’ sex roles (Chapter 5). Here we demonstrate that variation in gene expression at the brain level segregates individuals by population rather than by sex, indicating that plasticity in behaviour across populations drives variation in neurogenomic expression. On the other hand, at the gonad level, variation in gene expression segregates individuals by sex and then by population, indicating that sexual selection is also acting at the intrasexual level, particularly in nestholder males by paralleling differences in gonadal investment. However, the genomic mechanisms underlying courtship behaviour were not fully elucidated, and more studies are necessary.A plasticidade fenotípica consiste na capacidade de o mesmo genoma produzir diferentes fenótipos comportamentais dependendo das pistas ambientais recebidas. Estas respostas plásticas dependem de diversos mecanismos genómicos e permitem que o indivíduo maximize a sua fitness (aptidão) numa variedade de ambientes ecológicos. O desenvolvimento verificado nas tecnologias de sequenciação de alto desempenho ao longo da última década, globalmente denominadas de “Next Generation Sequencing” (NGS), permitiu o estabelecimento de métodos de análise e ferramentas genómicas que podem ser aplicadas em todos os sistemas ecológicos de interesse em biologia, sem a existência prévia de um genoma curado. Nomeadamente a tecnologia de sequenciação de ARN, conhecida globalmente como RNA-Seq, tornou possível a investigação dos perfis de expressão génica que se sabe serem determinantes na emergência de fenótipos plásticos, e consequentemente permitem determinar fenótipos em estados distintos de expressão genómica. Em peixes teleósteos, é possível observar com frequência modificações no fenótipo comportamental durante o período de reprodução, como por exemplo alterações e ajustes no estatuto de dominância que podem levar à coexistência de indivíduos que apresentam diferentes táticas de reprodução dentro da mesma população. Um desses exemplos é o peixe marachomba-pavão Salaria pavo (Risso, 1810), onde a intensidade na competição intra e intersexual varia entre populações sendo modulada pela disponibilidade de locais de nidificação, de forma a que dois níveis diferentes de plasticidade surgem: 1) variação intraespecífica no comportamento reprodutivo em machos que podem seguir uma de duas vias de desenvolvimento, investirem no seu crescimento e tornarem-se machos nidificantes na sua primeira época de reprodução, ou primeiro seguir uma tática de macho parasita onde investem em fertilizações furtivas, sendo que mais tarde no seu desenvolvimento fazem a transição para macho nidificante, e 2) variação interpopulacional nos papeis de corte de fêmeas e machos nidificantes. Os machos parasitas, conhecidos nesta espécie como “sneakers”, possuem uma particularidade que os tornam singulares, para além de imitarem a morfologia das fêmeas também conseguem imitar o seu comportamento de corte direcionado ao macho nidificante, o que lhes permite aproximarem-se discretamente dos ninhos dos machos e fertilizar parte dos ovos que as fêmeas depositam. Este sistema constitui a base ideal para aplicar métodos de RNA-Seq e estudar esta plasticidade fenotípica, uma vez que diferenças nas características reprodutivas dentro e entre populações podem revelar quais os mecanismos genéticos e genómicos subjacentes à variação observada em resposta a mudanças no ambiente ecológico. No entanto, a informação genómica disponível nesta espécie é reduzida e, por isso diferentes técnicas de sequenciação, assim como diferentes métodos de análise foram usados e otimizados ao longo deste trabalho. A presente tese é constituída por quatro trabalhos, sendo que no primeiro estudo se começa pela sequenciação de uma biblioteca de ARN proveniente de uma mistura de múltiplos indivíduos e de tecidos, de forma a captar a diversidade genética e desenvolver os primeiros marcadores genéticos nesta espécie (Capítulo 2). Com base nestes marcadores, microssatélites polimórficos, foi possível genotipar uma fração dos indivíduos da população existente na Ilha da Culatra (Ria Formosa, Portugal) bem como os ovos retirados de ninhos alvo, de forma a fazer análises de paternidade (Capítulo 3). Neste estudo, foi possível estimar o sucesso de fertilização de ovos de cada uma das táticas alternativas de reprodução, e usá-la como medida representativa de fitness de cada tática alternativa de reprodução nesta espécie. Os resultados indicam um sucesso de fertilização para os machos nidificantes de 95%, e mostramos que existe uma maior influência do ambiente social do que de variáveis morfológicas na proporção de fertilizações não obtidas pelos machos nidificantes, quando comparado com estudos anteriores. Usando o transcriptoma obtido no primeiro trabalho, avançámos com a caraterização genómica de cada um dos fenótipos presentas na população da ilha da Culatra, fêmeas, machos nidificantes, machos sneakers e machos de transição (machos que apenas investem no seu crescimento, não se reproduzindo, e consequente transição de sneaker para macho nidificante) (Capítulo 4). Para tal, foi sequenciado em profundidade o transcriptoma de cérebro de cada um deste fenótipos, e os perfis de expressão obtidos para machos e fêmeas desta espécie, onde o foco do estudo se centrava no papel da expressão génica diferencial na evolução de táticas reprodutivas alternativas sequenciais que envolvem a expressão de ambos os traços masculinos e femininos. Os resultados obtidos, mostram como repertórios comportamentais distintos são facilitados por estados neurogenómicos distintos, que discriminam não apenas o sexo, mas também as táticas alternativas de reprodução. Por fim, utilizando dois tecidos-alvo, gónadas e prosencéfalo, focámo-nos na regulação genómica dos papeis sexuais no comportamento de corte entre fêmeas e machos nidificantes de duas populações sob diferentes regimes seletivos, a população costeira portuguesa com papeis sexuais invertidos e a população rochosa italiana, com papeis sexuais ‘convencionais’ (Capítulo 5). Os resultados obtidos mostram que ao nível do cérebro, a variação na expressão génica segrega os indivíduos por população e não por sexo, indicando que a plasticidade no comportamento entre as populações induz uma maior variação na expressão neurogenómica. Por outro lado, ao nível das gónadas, a variação na expressão génica segrega os indivíduos por sexo e também por população, indicando que a seleção sexual está a atuar ao nível intrasexual, particularmente nos machos nidificantes, indo de encontro a diferenças detetadas entre populações no investimento alocado às gónadas. No entanto, os mecanismos genómicos subjacentes ao comportamento de corte não foram totalmente elucidados, e mais estudos são necessários.The work presented here was developed at Instituto Gulbenkian de Ciência (IGC) in Oeiras, with the support of both ISPA – Instituto Universitário in Lisbon, for the maintenance of live fish, and Centro de Ciências do Mar (CCMAR) at Universidade do Algarve, for logistics and support during fieldwork in Ria Formosa

Behaviour recognition and monitoring of the elderly using wearable wireless sensors. Dynamic behaviour modelling and nonlinear classification methods and implementation.

In partnership with iMonSys - an emerging company in the passive care field - a new system, 'Verity', is being developed to fulfil the role of a passive behaviour monitoring and alert detection device, providing an unobtrusive level of care and assessing an individual's changing behaviour and health status whilst still allowing for independence of its elderly user. In this research, a Hidden Markov Model incorporating Fuzzy Logic-based sensor fusion is created for the behaviour detection within Verity, with a method of Fuzzy-Rule induction designed for the system's adaptation to a user during operation. A dimension reduction and classification scheme utilising Curvilinear Distance Analysis is further developed to deal with the recognition task presented by increasingly nonlinear and high dimension sensor readings, and anomaly detection methods situated within the Hidden Markov Model provide possible solutions to identification of health concerns arising from independent living. Real-time implementation is proposed through development of an Instance Based Learning approach in combination with a Bloom Filter, speeding up the classification operation and reducing the storage requirements for the considerable amount of observation data obtained during operation. Finally, evaluation of all algorithms is completed using a simulation of the Verity system with which the behaviour monitoring task is to be achieved

Teacher roles during amusement park visits – insights from observations, interviews and questionnaires

Amusement parks offer rich possibilities for physics learning, through observations and experiments that illustrate important physical principles and often involve the whole body. Amusement parks are also among the most popular school excursions, but very often the learning possibilities are underused. In this work we have studied different teacher roles and discuss how universities, parks or event managers can encourage and support teachers and schools in their efforts to make amusement park visits true learning experiences for their students

Emerging Genomic Technologies for Agricultural Biotechnology: Current Trends and Future Prospects

Twenty years from now, the earth’s population will need 55% more food than it can currently produce. However, agriculture is facing severe challenges such as global climate change, exhausted resources, reduction of arable lands and various pathogen attacks. Advances in genomic technologies may offer potential solutions to these agricultural problems. Recent years have seen the rapid development of new genomic technologies such as CRISPR, TALENS and ODM (collectively gene editing), as well as doubled haploids, molecular markers and mapping populations. Together with the rapidly expanding availability of genome sequence data, these technologies have the potential to transform plant breeding. Cross breeding is a traditionally used technology to improve the crops with desirable traits such as nutritional quality, higher yields, abiotic and biotic stress tolerances. Nowadays, emerging genomic technologies (EGTs) are being used extensively in agriculture and life sciences by researchers all over the world to incorporate desirable genes in different crops such as cereals, pulses, oilseeds, fruits or vegetables. Application of these technologies in new crops is expected to play an important role towards faster growth in productivity so critical for meeting the sustainable development goals, in particular the goals of zero hunger and sustainable food, nutrition and environmental security in the world. This Research Topic will include papers that describe the application of cutting-edge technologies to improve various crops, vegetables and fruits. We aim to attract papers addressing targets from all over the world but not limited to the following: • CRISPR/Cas, ZFN, TALENs • Development of Molecular Markers • Markers Assisted Breeding • SNP Markers • Computer-Aided Drug Design (CADD) in plants • Genetic Engineering and Development of Transgenic (GMO) crops • Current status of regulatory frameworks controlling GMO crops in the world • Risk assessment of GMO crops • New other emerging genomic technologie

Life Sciences Program Tasks and Bibliography for FY 1997

This document includes information on all peer reviewed projects funded by the Office of Life and Microgravity Sciences and Applications, Life Sciences Division during fiscal year 1997. This document will be published annually and made available to scientists in the space life sciences field both as a hard copy and as an interactive internet web page

Life Sciences Program Tasks and Bibliography for FY 1996

This document includes information on all peer reviewed projects funded by the Office of Life and Microgravity Sciences and Applications, Life Sciences Division during fiscal year 1996. This document will be published annually and made available to scientists in the space life sciences field both as a hard copy and as an interactive Internet web page