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Next Generation Sequencing (NGS) or deep sequencing technology enables parallel reading of multiple individual DNA fragments, thereby enabling the identification of millions of base pairs in several hours. Recent research has clearly shown that machine learning technologies can efficiently analyse large sets of genomic data and help to identify novel gene functions and regulation regions. A deep artificial neural network consists of a group of artificial neurons that mimic the properties of living neurons. These mathematical models, termed Artificial Neural Networks (ANN), can be used to solve artificial intelligence engineering problems in several different technological fields (e.g., biology, genomics, proteomics, and metabolomics). In practical terms, neural networks are non-linear statistical structures that are organized as modelling tools and are used to simulate complex genomic relationships between inputs and outputs. To date, Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNN) have been demonstrated to be the best tools for improving performance in problem solving tasks within the genomic field.
Kevan M.A. Gartland, Munis Dundar, Tommaso Beccari, Mariapia Viola Magni and Jill S. Gartland
Genomics, the study of genes, their functions and related techniques has become a crucial science for developing understanding of life processes and how they evolve. Since the advent of the human genome project, huge strides have been made in developing understanding of DNA and RNA sequence information and how it can be put to good use in the biotechnology sector. Newly derived sequencing and bioinformatics tools have added to the torrent of new insights gained, so that ‘sequence once and query often’ type DNA apps are now becoming reality. Genome editing, using tools such as CRISPR/Cas9 nuclease or Cpf1 nuclease, provide rapid methods for inserting, deleting or modifying DNA sequences in highly precise ways, in virtually any animal, plant or microbial system. Recent international discussions have considered human germline gene editing, amongst other aspects of this technology. Whether or not gene edited plants will be considered as genetically modified remains an important question. This will determine the regulatory processes adopted by different groups of nations and applicability to feeding the world’s ever growing population. Questions surrounding the intellectual property rights associated with gene editing must also be resolved. Mitochondrial replacement therapy leading to ‘3-Parent Babies’ has been successfully carried out in Mexico, by an international team, to correct mother to child mitochondrial disease transmission. The UK has become the first country to legally allow ‘cautious use’ of mitochondrial donation in treatment. Genomics and genome editing will continue to advance what can be achieved technically, whilst society determines whether or not what can be done should be applied.
Approximately 15% of couples in western countries have infertility problems. Identification of genetic alterations responsible for infertility is important for therapy and to avoid transmission of genetic abnormalities that could impair the health of offspring, especially for couples with idiopathic infertility and those undergoing assisted reproductive techniques (ART). The aim of this review is to summarize the main genetic tests to offer to infertile couples during diagnostic work-up and in cases of ART, considering future directions of risk assessment in the field of reproductive medicine. Before offering a genetic test to an infertile couple, it is crucial to characterize their clinical and hormonal profile. Genetic testing should only be carried out when appropriate, that is when clinical and family history suggest a genetic cause of infertility. The genetic tests to offer to infertile couples must be targeted at infertility and should always consider the cost/benefit ratio. No causative genes have been identified for certain conditions, making clinical genetic testing impractical. Next generation sequencing (NGS) is a powerful tool for the identification of pathological mutations and for discovering new disease-associated loci in the field of reproduction. Comprehensive multigene panels for infertile risk assessment could simplify the diagnostic and therapeutic process. The main limitation is interpretation of the enormous amount of NGS data, since the clinical role and biological implications of variants, especially those of unknown significance, are still unclear.
Eduardo Berenguer, María-Teresa Solís, Yolanda Pérez-Pérez and Pilar S. Testillano
Microspore embryogenesis is a model system of plant cell reprogramming, totipotency acquisition, stress response and embryogenesis initiation. This in vitro system constitutes an important biotechnological tool for haploid and doubled-haploid plant production, very useful for crop breeding. In this process, microspores (cells that produce pollen grains in planta) are reprogrammed toward embryogenesis by specific stress treatment, but many microspores die after the stress. The occurrence of cell death is a serious limiting problem that greatly reduces microspore embryogenesis yield. In animals, increasing evidence has revealed caspase proteolytic activities as essential executioners of programmed cell death (PCD) processes, however, less is known in plants. Although plant genomes do not contain caspase homologues, caspase-like proteolytic activities have been detected in many plant PCD processes. In the present study, we have analysed caspase 3-like activity and its involvement in stress-induced cell death during initial stages of microspore embryogenesis of Brassica napus. After stress treatment to induce embryogenesis, isolated microspore cultures showed high levels of cell death and caspase 3-like proteolytic activity was induced. Treatments with specific inhibitor of caspase 3-like activity reduced cell death and increased embryogenesis induction efficiency. Our findings indicate the involvement of proteases with caspase 3-like activity in the initiation and/or execution of cell death at early microspore embryogenesis in B. napus, giving new insights into the pathways of stress-induced cell death in plants and opening a new way to improve in vitro embryogenesis efficiency by using chemical modulators of cell death proteases.
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Mario Novak, Antonija Trontel, Anita Slavica, Predrag Horvat and Božidar Šantek
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