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Long sequencing reads offer unprecedented opportunities in analysis and reconstruction of complex genomic regions. However, the gain in sequence length is often traded for quality. Therefore, recently several approaches have been proposed (e.g. higher sequencing coverage, hybrid assembly or sequence correction) to enhance the quality of long sequencing reads. A simple and cost-effective approach includes use of the high quality 2nd generation sequencing data to improve the quality of long reads. We designed a dedicated testing procedure and selected universal programs for long read correction, which provide as the output sequences that can be used in further genomic and transcriptomic studies. Our results show that HALC is the best choice for correction of long PacBio reads, when both, read size and quality, are the main focus of the analysis. However, the tested tools show some unexpected behaviors, including read trimming and fragmentation.
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Algoritmos , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Sequência de DNA , Animais , Bases de Dados Genéticas , Escherichia coli/genética , Genômica , Humanos , Oryza/genética , Trypanosoma/genética , Leveduras/genéticaRESUMO
Innovation is a key determinant of sustainable growth. Biotechnology (BT) is one such industry that has witnessed a revolution in innovative ideas leading to the founding of many new companies based on providing products, solutions and services, stretching from the food industry to environmental remediation, and new medicines. BT holds much promise for the development of national and local economies, however, this requires a strategic approach involving actors within government, industry, and academia working in concert to maximize this potential. This first article reviews the current "state of play" in the field of BT within the Central Eastern European (CEE) countries. For the purposes of this article, CEE refers to the countries of Czech Republic, Hungary, Poland, and Slovakia (the so-called Visegrad - V4 countries). We examine the components that support the creation and development of a BT sector in CEE and also highlight the barriers to these objectives. Clearly setting priorities for the countries' policy agenda, as well as the alignment of Smart Specialization Strategy will help to focus efforts. Recent investments in R&D infrastructure within CEE have been substantial, but conditions will need to be optimized to harness these largely European investments for effective use towards SME high-tech development.
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Biotecnologia , Desenvolvimento Industrial , Indústria Manufatureira , Projetos de Pesquisa , Biotecnologia/economia , Biotecnologia/educação , Biotecnologia/legislação & jurisprudência , Biotecnologia/organização & administração , República Tcheca , Meio Ambiente , Europa (Continente) , Governo , Humanos , Hungria , Indústria Manufatureira/organização & administração , Polônia , EslováquiaRESUMO
Recently, a number of ribosome-associated non-coding RNAs (rancRNAs) have been discovered in all three domains of life. In our previous studies, we have described several types of rancRNAs in Saccharomyces cerevisiae, derived from many cellular RNAs, including mRNAs, rRNAs, tRNAs and snoRNAs. Here, we present the evidence that the tRNA fragments from simple eukaryotic organism S. cerevisiae directly bind to the ribosomes. Interestingly, rancRNA-tRFs in yeast are derived from both, 5'- and 3'-part of the tRNAs and both types of tRFs associate with the ribosomes in vitro The location of tRFs within the ribosomes is distinct from classical A- and P-tRNA binding sites. Moreover, 3'-tRFs bind to the distinct site than 5'-tRFs. These interactions are stress dependent and as a consequence, provoke regulation of protein biosynthesis. We observe strong correlation between tRF binding to the ribosomes and inhibition of protein biosynthesis in particular environmental conditions. These results implicate the existence of an ancient and conserved mechanism of translation regulation with the involvement of ribosome-associating tRNA-derived fragments.
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Of late, global food security has been under threat by the coronavirus disease 2019 (COVID-19) pandemic and the recent military conflict in Eastern Europe. This article presents the objectives of the Sustainable Development Goals and the European Green Deal related to achieving food security and sustainable development in European Union (EU) agriculture, taking the aforementioned threats into account. In addition, it discusses the future of plant agricultural biotechnology and artificial intelligence (AI) systems, considering their potential for reaching the goal of food security. Paradoxically, the present challenging situation may allow politicians and stakeholders of the EU to realize opportunities and use the potential of the biotechnology sector.
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Inteligência Artificial , COVID-19 , Humanos , Abastecimento de Alimentos , COVID-19/epidemiologia , Biotecnologia , Agricultura , Segurança AlimentarRESUMO
The aim of the article is to show the current state of public opinion of Poles on biotechnology and genetic engineering in the context of European Union countries. The authors refer to the results of their own study based on a survey conducted in 2019 in Poland. To introduce the matter of public opinion on biotechnology and genetic engineering in the European Union a short review of research related to the topic is presented, showing discrepancies in perception of biotechnology and genetic engineering. The results of the survey showed that more than half of Poles noticed that products obtained by genetic engineering techniques are available on the market. Despite the fear of the research in the field of biotechnology and genetic engineering, 39 to 69% (depending on the subject of research) of Poles supported them. Moreover, 62% of Poles were opponents of genetically modified feeds as they believed that they can be harmful to human life and health. The findings regarding the current consumer perception, knowledge, and attitude towards genetically modified foods and feeds will help in building strategic approaches to educating society about genetically modified organisms and genetically modified products.
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Bioeconomy is not an autonomous sector of the economy, but rather a complex mechanism involving agriculture, industry, biotechnology, service sectors and consumers. To measure the size of the bioeconomy in European Union (EU) countries, it is necessary to create appropriate indicators that allow it to be monitored with reference to its current state, growth rate and sector description. In many countries, including Poland, there is no complete information or data collection system to monitor bioeconomy development directly, e.g. in the Polish Central Statistical Office. In response to these needs, several groups of indicators related to the circular economy, sustainable development and Europe 2020 were created by the European Commission (EC) in the Eurostat database. These indicators can help monitoring of bioeconomy development in EU countries. The present study discusses factors for bioeconomy development through an analysis of their social, economic and environmental aspects, as well as showing the value of the selected indicators in the EU and Poland. In addition, a separate section is dedicated to public perception of bioeconomy and to legislation regarding genetically modified organisms (GMOs). To date, many research studies have been reported on the public acceptance of bioeconomy issues in the EU, including renewable resources, biofuels, GMOs, bio-based products, food security and climate change. The awareness and perception of society on the bioeconomy, bio-based products and processes, and the sustainable use of resources can contribute to environmental sustainability, but intensified efforts are required to increase public acceptance.
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Biotecnologia/economia , Desenvolvimento Econômico , União Europeia/economia , PolôniaRESUMO
According to a predominant interpretation of the C-528/16 judgment of the Court of Justice of the European Union, mutants resulting from gene editing, even those featuring only single nucleotide variants, should be subject to the authorization procedures designed for organisms developed through genetic modification (i.e. insertion of large DNA fragments). In this article, we illustrate practical problems with the authorization of products of gene editing in the EU. On the basis of these problems, we analyze the influence of the current interpretation of EU legislation and judgment on the practical ability to authorize and detect such products on the EU market. We show that the predominant interpretation of the judgment leads to legally unacceptable consequences, in particular to the violation of the principle of proportionality with regard to individuals who wish to develop and market products of gene editing. As a result of our considerations, we show that the C-528/16 judgment did not need to be interpreted in the dominant way.
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Biotecnologia/legislação & jurisprudência , Edição de Genes/legislação & jurisprudência , Plantas Geneticamente Modificadas/genética , Produtos Agrícolas/genética , União Europeia , HumanosRESUMO
Continuous, inspiring and interconnected step-by-step changes in thought and understanding, knowhow, actions and behaviour have often been instrumental in transitions from one particular age to the next in human history. This also applies to the present century and its sustainability challenges at the planetary, regional and local levels. Therefore, it is of great importance and relevance to move forward on the journey which has been started globally to address the not insignificant number of challenges. It is however essential to go beyond descriptive work by continuing with novel, inspiring and interconnected steps to find solutions to overcome these challenges. As this huge task also requires multidimensional communication, understanding and actions across different regions, cultures, disciplines and knowledge areas, the development of a common conceptual framework such as the concept of bioeconomy has been accepted globally as very valuable. The momentum which has been created in more than 50 countries around the world by the growing number of activities, initiatives and strategies in bioeconomy is very encouraging. This offers great opportunities to mobilize even more stakeholders in science and industry, as well as society, to join the bioeconomy journey. Strategic high-level concepts such as preserving the value of the natural capital of planet earth, connecting economy and ecology, sustaining the boundary conditions and habitability of our biosphere are highly important. It is also essential on the bioeconomy journey to connect with highly specific and actionable missions, programs and plans towards sustainable economic growth under the boundary conditions of our planet.
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Biotecnologia/economia , Conservação dos Recursos Naturais/economia , Desenvolvimento Econômico , HumanosRESUMO
DNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.
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Metilação de DNA , Resistência a Herbicidas/genética , Herbicidas , Estresse Fisiológico , Zea mays , Elementos de DNA Transponíveis , Regulação da Expressão Gênica de Plantas , Herbicidas/efeitos adversos , Zea mays/efeitos dos fármacos , Zea mays/genéticaRESUMO
Growing global demands for food, bioenergy, and specialty products, along with the threat posed by various environmental changes, present substantial challenges for agricultural production. Agricultural biotechnology offers a promising avenue for meeting these challenges; however, ethical and sociocultural concerns must first be addressed, to ensure widespread public trust and uptake. To be effective, we need to develop solutions that are ethically responsible, socially responsive, relevant to people of different cultural and social backgrounds, and conveyed to the public in a convincing and straightforward manner. Here, we highlight how ethical approaches, principled decision-making strategies, citizen-stakeholder participation, effective science communication, and bioethics education should be used to guide responsible use of agricultural biotechnology.
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Bioética , Biotecnologia , AgriculturaRESUMO
A posttranslational protein modification by homocysteine-thiolactone (N-homocysteinylation) is linked to human vascular and neurodegenerative diseases. Although chemical and immunological methods are available to detect and quantify the extent of protein N-homocysteinylation, the determination of site-specific N-homocysteinylation in vivo remains challenging. Here we describe a liquid chromatography/mass spectrometry method that monitors the extent of N-homocysteinylation at albumin lysine-525 in vivo directly in human serum. Using this method, we found that the extent of lysine-525 N-homocysteinylation was significantly increased in patients with cystathionine beta-synthase deficiency.
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Cromatografia Líquida/métodos , Lisina/metabolismo , Espectrometria de Massas/métodos , Albumina Sérica/metabolismo , Sequência de Aminoácidos , Cistationina beta-Sintase/deficiência , Cistationina beta-Sintase/genética , Cistationina beta-Sintase/metabolismo , Homocisteína/sangue , Humanos , Processamento de Proteína Pós-TraducionalRESUMO
To study genetic variations between genomes of plants that are naturally tolerant and sensitive to glyphosate, we used two Zea mays L. lines traditionally bred in Poland. To overcome the complexity of the maize genome, two sequencing technologies were employed: Illumina and Single Molecule Real-Time (SMRT) PacBio. Eleven thousand structural variants, 4 million SNPs and approximately 800 thousand indels differentiating the two genomes were identified. Detailed analyses allowed to identify 20 variations within the EPSPS gene, but all of them were predicted to have moderate or unknown effects on gene expression. Other genes of the shikimate pathway encoding bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase and chorismate synthase were altered by variants predicted to have a high impact on gene expression. Additionally, high-impact variants located within the genes involved in the active transport of glyphosate through the cell membrane encoding phosphate transporters as well as multidrug and toxic compound extrusion have been identified.
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Lr46/Yr29/Pm39 (Lr46) is a gene for slow rusting resistance in wheat. The aim of the study was to analyze the miRNA expression in selected common wheat cultivars carrying resistance genes, Lr46 among others (HN Rod, Pavon'S', Myna'S', Frontana'S', and Sparrow'S') in response to leaf rust infection caused by Puccinia triticina Erikss. In the Pavon 'S', Myna 'S', Frontana'S', and Sparow'S' varieties a product with a length of 242 bp has been identified, which is specific to the Xwmc44 marker linked to the brown rust resistance gene Lr46. In the next step, the differences in the expression of microRNA (miR5085 and miR164) associated with the Lr46 gene, which is responsible for different resistance of selected wheat cultivars to leaf rust, were examined using emulsion PCR (ddPCR). In the experiment, biotic stress was induced in mature plants by infecting them with fungal spores under controlled conditions in a growth chamber. For analysis the plant material was collected before inoculation and 6, 12, 24, and 48 h after inoculation. The experiments also showed that plant infection with Puccinia triticina resulted in an increase in miR164 expression in cultivars carrying the Lr46 gene. The expression of miR164 remained stable in a control cultivar (HN ROD) lacking this gene. This has proved that miR164 can be involved in leaf rust resistance mechanisms.
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Resistência à Doença/genética , MicroRNAs/genética , Proteínas de Plantas/genética , Triticum/genética , Basidiomycota/patogenicidade , Mapeamento Cromossômico , Regulação da Expressão Gênica de Plantas/genética , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Locos de Características Quantitativas/genética , Triticum/crescimento & desenvolvimento , Triticum/microbiologiaRESUMO
Resolution of old problems with new tools seems to be a new way of challenging and finding the keys to innovation. A holistic view of different branches of science and industry, including services for society, is critically important for the development of modern science. The International Congress Eurobiotech 2017 was a special opportunity for such a universal view. In this paper, we discuss the application of different small RNAs, stem cells, epigenetics and sequencing, as well as art and bioeconomy. Our most significant message is not a new one but is very universal: biotechnology is vital for society.
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Biotecnologia , Invenções , Qualidade de Vida , Biotecnologia/economia , Humanos , Genética Reversa , Pesquisa com Células-TroncoRESUMO
Bioeconomy is an emerging paradigm under which the creation, development, and revitalization of economic systems based on a sustainable use of renewable biological resources in a balanced way is rapidly spreading globally. Bioeconomy is building bridges between biotechnology and economy as well as between science, industry, and society. Biotechnology, from its ancient origins up to the present is at the core of the scientific and innovative foundation of bioeconomy policies developed in numerous countries. The challenges and perspectives of bioeconomies are immense, from resource-efficient large-scale manufacturing of products such as chemicals, materials, food, pharmaceuticals, polymers, flavors, and fragrances to the production of new biomaterials and bioenergy in a sustainable and economic way for a growing world population. Key success factors for different countries working on the bioeconomy vary widely from high-tech bioeconomies, emerging diversified or diversified bioeconomies to advanced and basic primary sector bioeconomies. Despite the large variety of bioeconomies, several common elements are identified, which are simultaneously needed altogether.
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Agricultura/métodos , Biotecnologia , Desenvolvimento Sustentável , Biodiversidade , Biotecnologia/economia , Mudança Climática , Ecossistema , União Europeia , Indústria Alimentícia , PlásticosRESUMO
The comparatively low adoption rate of GMO products in the European Union (EU) market seems to be connected with the strictness of authorization regulations and inefficiency of the authorization process itself. These problems will apply to any product deemed to be a GMO that could potentially be marketable in the EU. Since modern methods of plant breeding involving oligonucleotide-directed mutagenesis (ODMs) or site-directed nucleases (SDNs), including Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are becoming ever more popular, it is crucial to establish whether the products of such new breeding techniques (NBTs), in particular those which involve precise methods of mutagenesis, are exempted from the EU legislation on GMOs or not. Legal uncertainty as to their status may result in reluctance to invest in such methods and develop them further. Here, developments are presented in the legal classification of certain NBTs products in the context of recent decisions and jurisprudence. The socioeconomic aspects of GMO adoption in both global and European contexts are discussed. The legal and practical landscape of GMO regulation in the EU is presented and how it may pose an obstacle to investment and the development of new products. The latest jurisprudence (e.g., Case C-528/16) [1] on the interpretation of the legal concept of GMOs and the scope of the legislation are analyzed, with the conclusion that the strict regulations will probably also apply to products of the NBTs involving precise methods of mutagenesis. This in turn will probably result in the restriction of their application in the development of new plant varieties in the EU.
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Biotecnologia/legislação & jurisprudência , Organismos Geneticamente Modificados/genética , Melhoramento Vegetal/legislação & jurisprudência , União EuropeiaRESUMO
Rapeseed is an essential crop which is used in many different areas as edible oil, biodiesel, lubricant, and feed. It is one of the most popular oil crops in Europe (63% of oilseeds production in 2017). The current study highlights the potential for further rapeseed development in European Union (EU), with special emphasis on Germany (19% of EU production) and Poland (12% of EU production). The study focused on three factors: cultivation area, volume of production and the numbers of Intellectual Property Rights (IPR), particularly patents granted for rapeseed or rapeseed-related inventions and plant variety rights. Possible further obstacles to development, such as current legal framework, were also taken under consideration. The analyzed statistical data shows that both the cultivation area, as well as the volume of production of rapeseed fluctuated in the last decade in both examined countries, while the numbers for European patent publications and Community Plant Variety Rights showed a rising trend, indicating investments in the Research and Development (R&D) of the crop. The data analysis seems to confirm a hypothesis that there is a potential for the development of rapeseed as a versatile, multi-use crop; however, the current EU GMO policies and a legal uncertainty as to the status of products of certain modern gene editing techniques may hamper making optimal use of this potential.
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N-homocysteinylation of epsilon-amino group of protein lysine residues by homocysteine (Hcy) thiolactone has been implicated in vascular disease in humans. We have previously generated polyclonal rabbit anti-N-Hcy-protein IgG antibodies that specifically recognize the Nepsilon-Hcy-Lys epitope on N-homocysteinylated proteins. The present work was undertaken to examine the utility of these antibodies for the immunohistochemical detection of N-homocysteinylated proteins in biological samples. We found that the rabbit antibody specifically detected N-Hcy-protein in a dot-blot assay, that the signal resulting from the reaction of the antibody with N-Hcy-protein depended on the amount of the antigen, and that the sensitivity of the assay was protein-dependent. The rabbit anti-N-Hcy-protein IgG also specifically detected Nepsilon-Hcy-Lys epitopes in human tissues, as shown by positive immunohistochemical staining of myocardium and aorta samples from cardiac surgery patients, and a lack of staining when the antibody was pre-adsorbed with N-Hcy-albumin. We also observed increased immunohistochemical staining for N-Hcy-proteins in aortic lesions from ApoE-/- mice with hyperhomocysteinemia induced by a high methionine diet, relative to ApoE-/- mice fed a control chow diet. In conclusion, polyclonal rabbit anti-N-Hcy-protein antibody can detect and monitor N-homocysteinylated proteins in human and mouse tissues with good sensitivity and specificity.
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Homocisteína/química , Proteínas/química , Idoso , Idoso de 80 Anos ou mais , Animais , Apolipoproteínas E/genética , Linhagem Celular Tumoral , Dieta , Ensaio de Imunoadsorção Enzimática , Feminino , Hemocianinas/química , Homocisteína/metabolismo , Humanos , Imunoglobulina G/imunologia , Imunoglobulina G/metabolismo , Imuno-Histoquímica , Indicadores e Reagentes , Masculino , Metionina/farmacologia , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Pessoa de Meia-Idade , Miocárdio/enzimologia , Miocárdio/metabolismo , Proteínas/metabolismoRESUMO
The way from scientific finding through invention to production line and finally to the consument is long and expensive and patent should be taken into account. This is evident because the investment connected with the new application needs clear definition of intellectual property rights. Independently what we personally think about patenting in nature sciences--this is a common practice around the world. The positive and negative parameters of patenting are focus on biotechnology. The development of biotechnology is a cumulative effect of co-operation of several disciplines: biology, biochemistry, chemistry, engineering, genetics, medicines and pharmacy and many more. Between not cited here is law and consequently the needs of cooperation between researchers and lawyers. There are several barriers in this co-operation, for example: nomenclature as well as the way of thinking. These borders could be pass only with intercommunication and cross-understanding. The dialog and transfer of knowledge is a must for understanding the nomenclature, terminology of nature by lawyers and by researchers in case of law. Polish legislation concerning intellectually rights is regulated by the law "Prawo wlasnosci przemyslowej" (30 June, 2000; Dz. U. 2003, Nr 119, pos. 1117, with later amendments). This legislation is related to European Union directives and Munich Convention. Accordingly patenting of product and process is possible in Poland. However, the procedure is time and money consuming, particularly in the case of patent submission in several countries. Amendment of the Polish law to biotechnology made possible patenting of living organism and their parts. It is worth to stress that patented inventions can be used free of charge for research and teaching.