This textbook presents solid tools for in silico engineering biology, offering students a step-by-step guide to mastering the smart design of metabolic pathways. The first part explains the Design-Build-Test-Learn-cycle engineering approach to biology, discussing the basic tools to model biological and chemistry-based systems. Using these basic tools, the second part focuses on various computational protocols for metabolic pathway design, from enzyme selection to pathway discovery and enumeration. In the context of industrial biotechnology, the final part helps readers understand the challenges of scaling up and optimisation. By working with the free programming language Scientific Python, this book provides easily accessible tools for studying and learning the principles of modern in silico metabolic pathway design. Intended for advanced undergraduates and master’s students in biotechnology, biomedical engineering, bioinformatics and systems biology students, the introductory sections make it also useful for beginners wanting to learn the basics of scientific coding and find real-world, hands-on examples.
One of the key features of biological systems is complexity, where the behavior of high level structures is more than the sum of the direct interactions between single components. Synthetic Biologists aim to use rational design to build new systems that do not already exist in nature and that exhibit useful biological functions with different levels of complexity. One such case is metabolic engineering, where, with the advent of genetic and protein engineering, by supplying cells with chemically synthesized non-natural amino acids and sugars as new building blocks, it is now becoming feasible to introduce novel physical and chemical functions and properties into biological entities. The rules of how complex behaviors arise, however, are not yet well understood. For instance, instead of considering cells as inert chassis in which synthetic devices could be easily operated to impart new functions, the presence of these systems may impact cell physiology with reported effects on transcription, translation, metabolic fitness and optimal resource allocation. The result of these changes in the chassis may be failure of the synthetic device, unexpected or reduced device behavior, or perhaps a more permissive environment in which the synthetic device is allowed to function. While new efforts have already been made to increase standardization and characterization of biological components in order to have well known parts as building blocks for the construction of more complex devices, also new strategies are emerging to better understand the biological dynamics underlying the phenomena we observe. For example, it has been shown that the features of single biological components [i.e. promoter strength, ribosome binding affinity, etc] change depending on the context where the sequences are allocated. Thus, new technical approaches have been adopted to preserve single components activity, as genomic insulation or the utilization of prediction algorithms able to take biological context into account. There have been noteworthy advances for synthetic biology in clinical technologies, biofuel production, and pharmaceuticals production; also, metabolic engineering combined with microbial selection/adaptation and fermentation processes allowed to make remarkable progress towards bio-products formation such as bioethanol, succinate, malate and, more interestingly, heterologous products or even non-natural metabolites. However, despite the many progresses, it is still clear that ad hoc trial and error predominates over purely bottom-up, rational design approaches in the synthetic biology community. In this scenario, modelling approaches are often used as a descriptive tool rather than for the prediction of complex behaviors. The initial confidence on a pure reductionist approach to the biological world has left space to a new and deeper investigation of the complexity of biological processes to gain new insights and broaden the categories of synthetic biology. In this Research Topic we host contributions that explore and address two areas of Synthetic Biology at the intersection between rational design and natural complexity: (1) the impact of synthetic devices on the host cell, or "chassis" and (2) the impact of context on the synthetic devices. Particular attention will be given to the application of these principles to the rewiring of cell metabolism in a bottom-up fashion to produce non-natural metabolites or chemicals that should eventually serve as a substitute for petrol-derived chemicals, and, on a long-term view, to provide economical, ecological and ethical solutions to today’s energetic and societal challenges.
The role of cultural heritage and museums in constructing national identity in postcolonial Cuba During Fidel Castro's rule, Cuban revolutionaries coopted and reinterpreted the previous bourgeois national narrative of Cuba, aligning it with revolutionary ideology through the use of heritage and public symbols. By changing uses of the past in the present, they were able to shift ideologies, power relations, epistemological conceptions, and economic contexts into the Cuba we know today. Cuban Cultural Heritage explores the role that cultural heritage and museums played in the construction of a national identity in postcolonial Cuba. Starting with independence from Spain in 1898 and moving through Cuban-American rapprochement in 2014, Pablo Alonso González illustrates how political and ideological shifts have influenced ideas about heritage and how, in turn, heritage has been used by different social actors to reiterate their status, spread new ideologies, and consolidate political regimes. Unveiling the connections between heritage, power, and ideology, Alonso González delves into the intricacies of Cuban history, covering key issues such as Cuba's cultural and political relationships with Spain, the United States, the Soviet Union, and so-called Third World countries; the complexities of Cuba's status as a postcolonial state; and the potential future paths of the Revolution in the years to come. This volume offers a detailed look at the function and place of cultural heritage under socialist states. A volume in the series Cultural Heritage Studies, edited by Paul A. Shackel Publication of the paperback edition made possible by a Sustaining the Humanities through the American Rescue Plan grant from the National Endowment for the Humanities.
In masterful tales of coming of age and becoming marginalized during the Cuban Revolution and its aftermath, Pablo La Rosa nostalgically looks back at a childhood spent by the seaside and creates a mosaic of poignant experiences seen through the glaring lens of race and exile. Neither the advantages of race or education, however, can exempt the disoriented protagonist from their perceived loss of homeland, integrity, identity. In the masterful ñEl Marielito,î La Rosa captures the bewilderment of a black man, marginalized by his race and circumstances in pre and post revolutionary Cuba and during his exile in the United States. Equally on the margin in spite of the advantages of education and race, a Cuban college student can relate only to a Russian janitor; though they share no common language they wordlessly share a longing for their lost homelands. La Rosa exhibits a penchant for the whimsical and experimental in homage to Latin American masters Jose Donoso, Carlos Fuentes, and Julio Cortàzar. His stylistic journey takes us from the magically real to psychological suspense and adventure. La RosaÍs masterful pen captivates our imagination and projects the reader into the souls of his characters.
Draws together the most beautiful, sexy, innovative, and creative Latin record covers, from all the various genres of Latin music: Mambo, Conga, Rumba, Salsa, Bossa Nova, Cubop, Barrio Nuovo.
Traditionally, the concept of quality of life has been viewed through objective indicators. Beyond Facts looks at quality of life through a new lens, namely, the perceptions of millions of Latin Americans. Using an enhanced version of the recently created Gallup World Poll that incorporates Latin America-specific questions, the Inter-American Development Bank surveyed people from throughout the region and found that perceptions of quality of life are often very different from the reality. These surprising findings have enormous significance for the political economy of the region and provide a wealth of information for policymakers and development practitioners to feast upon.
This book focuses on the experimental and theoretical aspects of the time-dependent breakdown of advanced dielectric films used in gigascale electronics. Coverage includes the most important failure mechanisms for thin low-k films, new and established experimental techniques, recent advances in the area of dielectric failure, and advanced simulations/models to resolve and predict dielectric breakdown, all of which are of considerable importance for engineers and scientists working on developing and integrating present and future chip architectures. The book is specifically designed to aid scientists in assessing the reliability and robustness of electronic systems employing low-k dielectric materials such as nano-porous films. Similarly, the models presented here will help to improve current methodologies for estimating the failure of gigascale electronics at device operating conditions from accelerated lab test conditions. Numerous graphs, tables, and illustrations are included to facilitate understanding of the topics. Readers will be able to understand dielectric breakdown in thin films along with the main failure modes and characterization techniques. In addition, they will gain expertise on conventional as well as new field acceleration test models for predicting long term dielectric degradation.
This open access book is an original contribution to the knowledge on fishing and research associated with one of the most enigmatic fish of our seas: bluefin tuna, Thunnus thynnus (L.). Based on available evidence, it reconstructs the possible methods used to catch large spawners in the Strait of Gibraltar thousands of years ago and describes the much more recent overfishing that led to a great reduction in the catches of the trap fishery on the area and the disappearance of the northern European fisheries. It is the first book to relate the overfishing of juvenile fishes in certain areas to the decline of large spawners in other very distant areas, revealing one of the main underlying causes of this decline, which has remained a mystery to the fishing sector and scientists alike for over 50 years. This finding should serve to prevent similar cases from arising in the future.
This is the first sustained exploration of the relationship between post-colonial science fiction, Indian techno-scientific policies, and the non-aligned movement. It shows the critical role played by the science fiction genre in imagining alternative pathways for scientific and geo-political developments to those that dominate our lives now.
Crossroads of Cuisine offers history of food and cultural exchanges in and around Central Asia. It discusses geographical base, and offers historical and cultural overview. A photo essay binds it all together. The book offers new views of the past.
Hepatic Fibrosis: Mechanisms and Targets is a complete volume of liver extracellular matrix biology, including molecular signaling pathways, cells and factors that modulate fibrogenesis and fibrosis. The book uses an integrated approach toward the molecular and cellular mechanisms involved in the synthesis and degradation of hepatic fibrotic tissue, emphasizing the possible molecular targets to fight fibrosis. This important reference describes, in detail and didactically, the cellular and molecular events that are conducive to fibrosis that leads to cirrhosis, hepatocellular carcinoma and death. The provided information allows readers to understand the molecular mechanisms of hepatic fibrogenesis to accelerate the development of new therapies. - Presents progression from inflammation to fibrosis, with a special focus on the molecular mechanisms involved - Didactically explains the participation of cells, cytokines and factors in profibrogenic pathways - Illuminates the causative participation of free radicals in liver fibrogenesis - Explains the role of gut dysbiosis in chronic liver diseases leading to fibrosis - Provides experimental models to study liver fibrosis and describes available, noninvasive monitoring methods
The spiral plant-parasitic nematode genus Rotylenchus contains a cosmopolitan group of nematodes that is predominantly found in temperate regions of the world. In this genus are included a number of species of significant economic importance in agriculture. They parasitize a wide-range of hosts, including vegetables, ornamentals, and fruit and forest trees. The book comprises seven sections and presents summarised and specialised information on various aspects of the spiral nematodes belonging to the genus Rotylenchus. Sections 1 and 2 describe the importance of Rotylenchus species in agricultural crops, their distribution and numerous aspects of their biology, feeding habits, pathogenicity to vegetables, fruit and forest trees, and ecology. Section 3 presents different management strategies for the most important and pathogenic species of Rotylenchus, including chemical control, crop rotation, and biological control by means of nematophagous fungi, entomopathogenic nematodes, the hyperparasitic bacteria Pasteuria penetrans, and nematicidal plants. Sections 4 and 5 describes the most important morphological characters used in characterising and diagnosing species, as well as a broad discussion on the taxonomy and systematics in Rotylenchus and related genera, including a list of nominal species. These sections also include morphometric and cluster analyses in order to separate groups of species in order to facilitate identification. Section 6 provides a complete description and measurements of all populations characterised for each species, as well as their world distribution. Finally, Section 7 includes comprehensive tabular and dichotomous keys for species identification.
This textbook presents solid tools for in silico engineering biology, offering students a step-by-step guide to mastering the smart design of metabolic pathways. The first part explains the Design-Build-Test-Learn-cycle engineering approach to biology, discussing the basic tools to model biological and chemistry-based systems. Using these basic tools, the second part focuses on various computational protocols for metabolic pathway design, from enzyme selection to pathway discovery and enumeration. In the context of industrial biotechnology, the final part helps readers understand the challenges of scaling up and optimisation. By working with the free programming language Scientific Python, this book provides easily accessible tools for studying and learning the principles of modern in silico metabolic pathway design. Intended for advanced undergraduates and master’s students in biotechnology, biomedical engineering, bioinformatics and systems biology students, the introductory sections make it also useful for beginners wanting to learn the basics of scientific coding and find real-world, hands-on examples.
One of the key features of biological systems is complexity, where the behavior of high level structures is more than the sum of the direct interactions between single components. Synthetic Biologists aim to use rational design to build new systems that do not already exist in nature and that exhibit useful biological functions with different levels of complexity. One such case is metabolic engineering, where, with the advent of genetic and protein engineering, by supplying cells with chemically synthesized non-natural amino acids and sugars as new building blocks, it is now becoming feasible to introduce novel physical and chemical functions and properties into biological entities. The rules of how complex behaviors arise, however, are not yet well understood. For instance, instead of considering cells as inert chassis in which synthetic devices could be easily operated to impart new functions, the presence of these systems may impact cell physiology with reported effects on transcription, translation, metabolic fitness and optimal resource allocation. The result of these changes in the chassis may be failure of the synthetic device, unexpected or reduced device behavior, or perhaps a more permissive environment in which the synthetic device is allowed to function. While new efforts have already been made to increase standardization and characterization of biological components in order to have well known parts as building blocks for the construction of more complex devices, also new strategies are emerging to better understand the biological dynamics underlying the phenomena we observe. For example, it has been shown that the features of single biological components [i.e. promoter strength, ribosome binding affinity, etc] change depending on the context where the sequences are allocated. Thus, new technical approaches have been adopted to preserve single components activity, as genomic insulation or the utilization of prediction algorithms able to take biological context into account. There have been noteworthy advances for synthetic biology in clinical technologies, biofuel production, and pharmaceuticals production; also, metabolic engineering combined with microbial selection/adaptation and fermentation processes allowed to make remarkable progress towards bio-products formation such as bioethanol, succinate, malate and, more interestingly, heterologous products or even non-natural metabolites. However, despite the many progresses, it is still clear that ad hoc trial and error predominates over purely bottom-up, rational design approaches in the synthetic biology community. In this scenario, modelling approaches are often used as a descriptive tool rather than for the prediction of complex behaviors. The initial confidence on a pure reductionist approach to the biological world has left space to a new and deeper investigation of the complexity of biological processes to gain new insights and broaden the categories of synthetic biology. In this Research Topic we host contributions that explore and address two areas of Synthetic Biology at the intersection between rational design and natural complexity: (1) the impact of synthetic devices on the host cell, or "chassis" and (2) the impact of context on the synthetic devices. Particular attention will be given to the application of these principles to the rewiring of cell metabolism in a bottom-up fashion to produce non-natural metabolites or chemicals that should eventually serve as a substitute for petrol-derived chemicals, and, on a long-term view, to provide economical, ecological and ethical solutions to today’s energetic and societal challenges.
Bandits seem ubiquitous in Latin American culture. Even contemporary actors of violence are framed by narratives that harken back to old images of the rural bandit, either to legitimize or delegitimize violence, or to intervene in larger conflicts within or between nation-states. However, the bandit seems to escape a straightforward definition, since the same label can apply to the leader of thousands of soldiers (as in the case of Villa) or to the humble highwayman eking out a meager living by waylaying travelers at machete point. Dabove presents the reader not with a definition of the bandit, but with a series of case studies showing how the bandit trope was used in fictional and non-fictional narratives by writers and political leaders, from the Mexican Revolution to the present. By examining cases from Argentina, Brazil, Mexico, Peru, and Venezuela, from Pancho Villa's autobiography to Hugo Chavez's appropriation of his "outlaw" grandfather, Dabove reveals how bandits function as a symbol to expose the dilemmas or aspirations of cultural and political practices, including literature as a social practice and as an ethical experience.
In 1660, a mysterious sect of Dutch mystics arrived to an island in the New World with the objective to create a new society. Their governing principle revolved around the uninterrupted performance of a single dramatic work in seven tableaux vivants. Invoking alchemical imagery and hermetic thought, their goal was to arrive to a higher state of being by collectively embodying the symbolic representation of all of human and divine knowledge. Their experiment, which would last a century, would test the human boundaries of time, physical endurance, and the collective commitment toward an idea. "Like a 'lamb in wolf's clothing, ' Pablo Helguera uses the exoteric mechanisms of historical erudition to lure us to his magical island of the Ourobourians.But right about the time we lose our footing on the land's slippery shores-when we begin to wonder if the artist has gleaned an esoteric tradition for more than just source material for his island's symbols and nomenclature, when we start to navigate his land with the non-verbal hunches of the alchemists' score, and call into question the artifices we employ to gather the world around us-we realize Helguera has really taken us on a journey to another land altogether, the most forbidden of places: the self." -Lise Patt, founder and director of the Institute of Cultural Inquiry, Los Angeles "Pablo Helguera is a splendid liar, a first-class storyteller, a curious mind constantly in search of stories, a creator of parallel universes and impossible characters living in credible situations, which invariably probe our certainties, intuition and knowledge." - Naief Yehya, writer and critic
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