Synthetic biology

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Ethical issues of synthetic biology: a personalist perspective

Ethical issues of synthetic biology: a personalist perspective

81 and bad consequences that will be derived from this technology, and deontologism, which, instead of looking at the consequences, aims to determine if the technology is good in itself or not. Given that Synthetic Biology seems to have great potential for both good and evil, in this paper, the author opts for the deontological evaluation of this discipline. As he states, his aim is to “examine the ethics of synthetic biology from some broadly mainstream deontological perspectives, evaluating how synbio relates to the integrity of nature, the dignity of life, and the relationship of God and his creation” (Heavey, 2013, p. 442). Having answered these three questions, he concludes that Synthetic Biology is, from a deontological point of view, ethically acceptable. Accordingly, regarding the integrity of nature, the author argues that what Synthetic Biology does “is simply a significant technological advance on techniques which have been used for millennia. [...] With proper care, synthetic biology may yield great benefits without damaging nature’s integrity” (p. 444). In relation to the impact of this discipline on the dignity of life, Heavey (2013) considers that Synthetic Biology “may lead to some negative attitudes; it could also be applied in ways that are injurious to life; but that is not to say that synbio per se challenges the dignity of life” (p. 445). Regarding the third question, the author reviews the available literature and concludes that “for a significant part of mainstream religious thought, synthetic biology does not appear to be, in itself, a usurpation of God’s creative role” (p. 450).

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Synthetic Biology: Opportunities for Chilean Bioindustry and education

Synthetic Biology: Opportunities for Chilean Bioindustry and education

Synthetic Biology emphasizes the use of well characterized building blocks and mathematical modeling for predictable design, and aims to minimize the need for ad hoc approaches, iterative debugging and troubleshooting (Smolke and Silver, 2011). For example, although artifi cial genetic switches had already been developed in the 1980’s (Podhajska et al., 1985), pioneering work by Elowitz et al. (2000) and Gardner et al. (2000) led to the realization of predictable programming of more elaborated dynamical processes in cells (McAdams and Arkin, 2000). The idea that biological systems could be treated as reprogrammable material has led to the exploration of a wide variety of applications. These have ranged from multi-chromatic bacterial photo-fi lms (Levskaya et al., 2005; Tabor et al., 2011) to in vivo cell-type classifi ers that recognize molecular profi les in cancer cells (Xie et al., 2011). Synthetic Biology is catalyzing new approaches in biotechnology (Khalil and Collins, 2010), medicine (Ruder et al., 2011; Weber and Fussenegger 2011) and scientifi c research (Elowitz and Lim, 2010; Mukherji and van Oudenaarden, 2012; Nandagopal and Elowitz, 2011). Projects such as the synthesis of artifi cial genomes (Gibson et al. 2010), genome-wide DNA editing

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Bioinspired Engineering at Nanoscale: Integration of Synthetic Biology and Bionanotechnology

Bioinspired Engineering at Nanoscale: Integration of Synthetic Biology and Bionanotechnology

Ricardo Alvarado is a promising young researcher from the Laboratorio Nacional de Nanotecnologìa (LANOTEC) in Costa Rica. At LANOTEC he is working on several projects including: (a) sonochemical synthesis and antimicrobial activity of nanoparticles, (b) biosyn- thesis of magnetic nanoparticles and (c) DNA folding for nanostructure assembly. With a bachelor in biotechnology engineering, now he is aiming for a M.Sc. in Bioinformatics and Systems Biology. Asides his work at LANOTEC, he is one of the leaders of the first synthetic biology team in Costa Rica for the iGEM competition.

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Engineering principles for synthetic biology : from concept to practice

Engineering principles for synthetic biology : from concept to practice

Now is time to explore the other branch of the field, that is the one that very often draws more (public) attention and resources and, as mentioned before, is the one we put our spotlight on in this review: the engineering one. This branch took off when the engineering community met the molecular- biology wetlab. At that time, around the turn of millennium, the necessary ingredients for the emergence of this branch of SB were ready and the momentum was strong enough. A number of new technologies for manipulating and even editing the DNA at wish were available. There was a deeper knowledge than ever of the cellular processes and a map of the interactions taking place at different levels among the cell’s vast catalogue of molecules. Moreover, lots of different computational tools for gathering and analyzing huge amounts of data, for its predictive treatment and even for the in silico modeling of genetic circuits began to be incorporated into the daily life of scientists within the field. Framed around Systems Biology, all this paved the way for the emergence of Synthetic Biology (33). More importantly, it set the groundwork for this engineering branch of SB that had recently gained publicity and that took off at the start of the century.

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¿Biología sintética, solución para los problemas del futuro? / Synthetic biology, solution for the problems of the future?

¿Biología sintética, solución para los problemas del futuro? / Synthetic biology, solution for the problems of the future?

6 science with high economic interests. One of the advantages of Synthetic Biology over the traditional Genetics Engineering is the possibility of starting from scratch, which increases significantly the level of control over the inserted modifications [4]. Ever since the late twentieth century, with the rise of modern Genetics Engineering, it has been argued the need for the standardization of biological parts. By biological part it is understood each DNA particle with a defined function in the whole synthetic gene circuit, such as promoters, coding sequences, enhancers. This would ease the process of assembly and would allow laboratories from all over the world to share those, facilitating research. It was for this purpose that in 2006 the BioBricks foundation was formerly established [5]. It is an online database where standardized sequences are stored and available for free, seeking to ensure the open access of biological engineering.

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Synthetic biology tools for the study of relevant factors in the control of transgene expression

Synthetic biology tools for the study of relevant factors in the control of transgene expression

Some factors can have a strong impact on the orthogonality of a synthetic construct, and the first is the place where it is located within the cell. Episomal plasmids are convenient for the expression of high amount of protein thanks to the use of high-copy number vectors, but these vectors need constant selection to be maintained and also, comparisons can be difficult since copy number can fluctuate depending on the growing conditions. Chromosomal integration presents the advantage of achieving a more stable and consistent expression of the transgenes; moreover, the expression of external genetic elements in a context closer to the host physiological conditions can help in the subsequent fine-tuning of the synthetic genetic circuits. Stable chromosomal integration of transgenes in yeast can be easily achieved by the use of vectors that allow single-copy integration at specific loci by genomic recombination, and where only an initial step of selection is needed (Blount et al., 2012; Matsuyama & Yoshida, 2012; Mirisola et al., 2007; Siddiqui, Choksi, & Smolke, 2014). The control of the expression of transgenes might be favoured by their chromosomal integration, but in that case, it can be influenced by epigenetic effects due to the integration site where they are inserted. An example of this can be found in a publication by Flagfeldt et al., 2009, were twenty integration sites were tested and showed a range of transgene expression up to eight-fold, independently of the promoter used.

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Synthetic wind data series for the Chilean wind park analysis : study of variability, wind energy generation and capacity factor estimation

Synthetic wind data series for the Chilean wind park analysis : study of variability, wind energy generation and capacity factor estimation

The wind resource natural behavior and properties should be considered when assessing and modeling the resource. These properties correspond to the seasonal wind behavior and the positive correlation of wind speed in short periods of time. To demonstrate the relevance of these elements is implemented a model to generate large amounts of data and modeling synthetic wind parks existing or to be installed in Chile. To achieve an effective modeling, real data for average wind speed for a full year were used (10 minutes resolution). This information was used to obtain the seasonal components of the wind in the coastal area of north and central Chilean territory. Data from mesoscale was also used to provide aggregate statistical information about wind behavior in areas where wind generation projects are located. This information was used to generate synthetic wind series to address the lack of detailed information on the conditions of the wind resource at the point of location of wind projects.

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Biology of Healthy Aging and Longevity

Biology of Healthy Aging and Longevity

As human life expectancy is prolonged, age-related diseases are thriving. Aging is a complex multifactorial process of molecular and cellular decline that affects tissue function over time, rendering organisms frail and susceptible to disease and death. Over the last decades, a growing body of scientific literature across different biological models, ranging from yeast, worms, flies, and mice to primates, humans and other long-lived animals, has contributed greatly towards identifying conserved biological mechanisms that ward off structural and functional deterioration within living systems. Collectively, these data offer powerful insights into healthy aging and longevity. For example, molecular integrity of the genome, telomere length, epigenetic landscape stability, and protein homeostasis are all features linked to “youthful” states. These molecular hallmarks underlie cellular functions associated with aging like mitochondrial fitness, nutrient sensing, efficient intercellular communication, stem cell renewal, and regenerative capacity in tissues. At present, calorie restriction remains the most robust strategy for extending health and lifespan in most biological models tested. Thus, pathways that mediate the beneficial effects of calorie restriction by integrating metabolic signals to aging processes have received major attention, such as insulin/insulin growth factor-1, sirtuins, mammalian target of rapamycin, and 5’ adenosine monophosphate-activated protein kinase. Consequently, small- molecule targets of these pathways have emerged in the impetuous search for calorie restriction mimetics, of which resveratrol, metformin, and rapamycin are the most extensively studied. A comprehensive understanding of the molecular and cellular mechanisms that underlie age-related deterioration and repair, and how these pathways interconnect, remains a major challenge for uncovering interventions to slow human aging while extending molecular and physiological youthfulness, vitality, and health. This review summarizes key molecular mechanisms underlying the biology of healthy aging and longevity. (REV INVES CLIN. 2016;68:7-16)

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Numerical simulation of a synthetic jet with OpenFoam

Numerical simulation of a synthetic jet with OpenFoam

Synthetic jets are commonly generated by the time-periodic ejection and suction of fluid across an orifice, resulting in zero-net mass flux [7]. Since the experimental work of Ing˚ard and Labate [9] in the ’50s, the study of synthetic jets has become one of the most attractive subjects of research in fluid mechanics. The primary rea- son behind is that the synthetic jet can be utilized as a flow control method, with several engineering applications [2], [7]. Originally demonstrated in the laboratory

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Botany An Introduction to Plant Biology

Botany An Introduction to Plant Biology

The topics and chapters are organized in a sequence that I find to be the easiest to follow, beginning with the most familiar—structure—and proceeding to the less familiar— metabolism—then finishing with those topics that are probably least familiar to most beginning students—genetics, evolution (in detail), the diversity of organisms, and ecol- ogy. Three initial chapters—chemistry, cell structure, and cell division—are not familiar but are so basic they must come first. Because this order may not be preferred by all instructors, sections have been written to be self-contained so they can be taken up in various orders. In courses that emphasize metabolism, the sequence could be Chapters 1, 2, 3, 10 to 15. Courses emphasizing plant diversity could follow a sequence of Chapters 1, 2, (16, 17), 18 to 25. Gene action appears in Chapter 15 of the growth and development section, whereas gene replication is located in Chapter 16 in the genetics section. Although both topics are based on the DNA molecule, it does not seem necessary to cover DNA replication and Mendelian genetics prior to teaching about mRNA, protein synthesis, and gene regulation. These topics, along with the techniques of recombinant DNA analysis, are covered in considerable detail. I believe that beginning students are fully capable of under- standing these subjects, which are already becoming central to most fields of biology.

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RNA Interference in Biology and Medicine

RNA Interference in Biology and Medicine

Although RNAi as a mechanism of PTGS was first discovered in plants and may have evolved as a cellular defense mechanism against foreign DNA and RNA, it is very clear that RNAi is widely employed in most if not all eukaryotic cells as a mechanism to regulate the ex- pression of endogenous genes. In 1998, it was discovered that injection of dsRNA was much more effective for silencing of gene expression in C. elegans than was sin- gle-stranded antisense RNA (Fire et al., 1998). This experimentally induced PTGS, the first report of the use of RNAi as a tool in biology, was very potent, and re- markably, the PTGS occurred not only in the worms to which the dsRNA was administered, but also in their progeny. It was then demonstrated that the endogenous mRNA was the target of the injected dsRNA by a post- transcriptional mechanism and involving degradation of the targeted mRNA (Montgomery et al., 1998). Surpris- ingly, it was further shown that the dsRNA is effective at very low concentrations, such that the copy numbers of the targeted mRNA are far greater than the number of dsRNAs present in the cell (Fire et al., 1998; Kenner- dell and Carthew, 1998). In addition, the suppression of the protein encoded by the targeted mRNA was found to persist through many rounds of cell division. The latter two observations strongly suggested that cells possess a mechanism for amplifying the RNAi mechanism. Not only can the RNAi process be maintained within cells of a common lineage, but it can also be transferred between cells, as shown in C. elegans where injection of dsRNA into the intestine results in silencing of the targeted gene in all cells of the F1 progeny of that worm (Fire et al., 1998). Indeed, dsRNA can enter cells and induce PTGS when worms are soaked in a solution containing the dsRNA or when the worms are fed bacteria express- ing dsRNA (Tabara et al., 1998; Timmons and Fire, 1998). Recently, a transmembrane protein called SID-1 was identified as a possible mediator of intercellular transfer of RNAi (Winston et al., 2002).

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Mathematical modeling of cancer metabolism

Mathematical modeling of cancer metabolism

A first global reconstruction of the human metabolic network based on a combination of "bibliomic" and genomic data known as Recon 1 was made available ten years ago (Duarte et al., 2007). Several years later, a systems biology roadmap integrating conventional biochemical, molecular biology and post-genomic analyses along with different types of mathematical models was proposed as an efficient procedure for drug discovery in connection with cancer cell metabolism (Alberghina et al., 2014). More recently, Recon 2 was launched as a community- driven "consensus reconstruction" of human metabolism (Thiele et al., 2013). The main findings and importance of this Recon 2 paper has been reviewed elsewhere (Swainston et al., 2013). Very recently, genome scale metabolic modeling of cancer has been critically reviewed, stressing the requirements for successful flux-balance analysis simulations of cancer metabolism and discussing the similarities of the methods used for the modeling of both cancer and microbial metabolism (Nilsson and Nielsen, 2017).

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Gaussian Multiscale Aggregation Applied to Segmentation in Hand Biometrics

Gaussian Multiscale Aggregation Applied to Segmentation in Hand Biometrics

Figure 3. A comparative study of results provided by segmentation algorithm in comparison to ground-truth. First column gathers examples from first database, together with their seg- mentation on second column, considered as ground truth. Third column presents synthetic images based on first column images, providing on the fourth column the final segmenta- tion result. Last two column present the segmentation result provided by the Lossy Data Compression (LDC) [4] and Normalized Cuts [5], respectively.

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Mulier oeconomica  On biopolitical construction of women’s bodies

Mulier oeconomica On biopolitical construction of women’s bodies

24. For a general view of these new materialisms: cfr. S. Alaimo, S. Hekman (eds.), Material Feminisms, Indiana University Press, Bloomington-Indianapolis, 2008; D. Coole, S. Frost (eds.), New Materialisms. Ontology, Agency, and Politics, Duke University Press, Durham-London, 2010. For a first discussion on new materialism: cfr. S. Amhed, “Open Forum Imagi- nary Prohibitions. Some Preliminary Remarks on the Founding Gestures of the ‘New Materialism’”, in European Journal of Women’s Studies, XV, 1, Sage Publications, Los Angeles, London, New Delhi and Singapore, 2008, pp. 23-39. According to Amhed, these ‘new’ materialism do not present a true story inside the feminist thought because authoresses like Donna Haraway, Lynda Birke and Evelyn Fox Keller have always worked with the aim of conciliate biology and feminism.

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From mechanism to complexity in biology [Spanish]

From mechanism to complexity in biology [Spanish]

Abstract: From the mechanical complexity in biology. Through history, each century has brought new discov- eries and beliefs that have resulted in different perspectives to study life organisms. In this essay, I define three periods: in the first, organisms were studied in the context of their environment, in the second, on the basis of physical and chemical laws, and on the third, systemically. My analysis starts with primitive humans, continues to Aristoteles and Newton, Lamarck and Darwin, the DNA doble helix discovery, and the beginnings of reduc- cionism in science. I propose that life is paradigmatical, that it obeys physical and chemical laws but cannot be explained by them I review the systemic theory, autopoiesis, discipative structures and non- linear dynamics. I propose that the deterministic, lineal and quantitative paradigm of nature are not the only way to study nature and invite the reader to explore the complexity paradigm. Rev. Biol. Trop. 56 (1): 399-407. Epub 2008 March 31. Key words: organisms, history, perspectives, mecanicism, complexity.

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The future of evolutionary biology

The future of evolutionary biology

What about the contributions of genetic processes and molecular data to evolutionary biology, with all the implications for understanding the mechanisms and history of evolutionary change? Has that infusion run its course, or at least been so widely recognized as to have lost its excitement? Is there anything else on the horizon, or that we can even conceive, that could have such a great impact on the way we think about and perform our science as the input of molecular genetics into evolutionary biology? In this article, I will attempt to support two points. First, I claim that the molecular-genetic revolution in evolution has just started, such that we can only now begin to see some of the most exciting ways it will advance our field. I will lay out a couple of directions where I see this research going over the next few years and decades. Second, I suggest that there is another revolution on the horizon, one that may basically influence not only the practice of our science, but might even substantially impact the future of our own species. In particular, I am referring to the emergence of artificial life, which results from the fusion of concepts from evolutionary biology with technological advances in computer science, engineering and robot- ics. If I am correct in even one of these claims, then the future of evolution- ary biology will indeed be an exciting one.

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Flood frequency analysis using synthetic samples

Flood frequency analysis using synthetic samples

This paper proposes a new approach to reduce the uncertainty in the estimation of APF quantiles resulting from small sample sizes, and to dispense with neighboring information. This approach consists of simulating multiple APF samples to achieve a more accurate frequency distribution. To improve the accu- racy, these synthetic samples must be conditionally simulated from a steadier variable. In this paper, APF samples are conditionally simulated using the annual mean flows (AMFs).

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Biology and economics : metaphors that economists usually take from biology

Biology and economics : metaphors that economists usually take from biology

But other links can be established between economics and biology. For example, game theory is not only successful in economics but in biology too, nonetheless it has currently more advantages and applicability in economics (Robson, 2001, 12). Division of labor is inherent to human processes and animals in a process denominated adaptive radiation (Ghiselin, 1978, 234), making more connections that tie both sciences in similar directions. Furthermore, maybe rationality is more present in the social context. Experiments in chimpanzees show that they develop more intelligence than required in their environment because of social interactions (Robson, 2001, 28), maybe this is also the case for human beings.

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Activacin de la fosforilacin oxidativa mitocondrial durante una lesin celular del miocardio inducida por el (+/ ) isoproterenol

Activacin de la fosforilacin oxidativa mitocondrial durante una lesin celular del miocardio inducida por el (+/ ) isoproterenol

(v/v). To estimate the synthetic activity of mitochondrial ATPase, rat heart homogenates were incubated during 2 min with 2.0 mM rotenone and 5 mM succinate, and then the velocities of ATP synthesis, after two consecutive additions, were calculated (Fig. 1): (i) with ADP; (ii) with oli- gomycin. The synthetic activity of mitochondrial ATPase was the velocity of ATP synthesis after ADP addition (the reason for this consideration is given in the results section below). Protein was determined by the biuret method, 17 using bovine

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The autonomy of biology

The autonomy of biology

CAN AN AUTONOMOUS BIOLOGY BE UNIFIED WITH PHYSICS? In the two hundred years after Galileo there was a unified science; it was physics. There was no biology to cause problems. But the comforting belief in a unified science became increasingly more difficult to uphold with the rise of biology. This difficulty was widely appreciated and whole organi- zations were founded to undertake a unification of science. The way to accomplish this was through reduction. This view was based on the convic- tion that all tangible phenomena of this world “are based on material processes that are ultimately reducible ... to be laws of physics” (Wilson 1998, p. 266). But this suggestion was based on a faulty analysis of biology, neglecting its autonomous components. Such a reduction would be pos- sible only if all of the theories of biology could be reduced to the theories of physics and molecular biology, but this is impossible. Wilson thought consilience was a mechanism that would make such reduction possible. Indeed he claimed “consilience is the key to unification” (1998, p. 8) and “consilience is to be achieved by reduction to the laws of physics.” This is a beautiful dream but none of the autonomous features of biology can possibly be unified with any of the laws of physics. The endeavor of a unification of the sciences is a search for a Fata Morgana. As is said in the vernacular, “you cannot unify apples with oranges.”

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