Search results for "Synthetic"
showing 10 items of 723 documents
Gödel and the Blind Watchmaker
2015
While accepting that contingency is key to biological evolution, we wonder how much need there is for it. It is extremely difficult to talk about trends in evolution, but the fact remains that they are found here and there when evolutionary experiments are repeated. But we should ask, for example, whether there is an unavoidable tendency of life towards progressive complexity . This chapter deals with certain theoretical considerations from Logic and Computing on the conditions necessary to formulate a predictive evolutionary theory .
The iGEM Competition
2014
The international Genetically Engineered Machine (iGEM) competition is a well-known example of synthetic biology and a workbench for the development of heterodox, multidisciplinary and frontier work made by undergraduate students. We review the origin, organization and structure of the competition; we describe how an iGEM team can be set in place, and briefly summarize some of the main milestones and challenges of a competition that is only one decade old. We discuss the links of the competition with the Registry of Standard Biological Parts and the flagship role of iGEM as a very trench of the synthetic biology revolution.
Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes.
2019
How to make an organelle in eukaryotes A key step in the evolution of complex organisms like eukaryotes was the organization of specific tasks into organelles. Reinkemeier et al. designed an artificial, membraneless organelle into mammalian cells to perform orthogonal translation. In response to a specific codon in a selected messenger RNA, ribosomes confined to this organelle were able to introduce chemical functionalities site-specifically, expanding the canonical set of amino acids. This approach opens possibilities in synthetic cell engineering and biomedical research. Science , this issue p. eaaw2644
Entropy-Based Classifier Enhancement to Handle Imbalanced Class Problem
2017
The paper presents a possible enhancement of entropy-based classifiers to handle problems, caused by the class imbalance in the original dataset. The proposed method was tested on synthetic data in order to analyse its robustness in the controlled environment with different class proportions. As also the proposed method was tested on the real medical data with imbalanced classes and compared to the original classification algorithm results. The medical field was chosen for testing due to frequent situations with uneven class ratios.
Clinically-Driven Virtual Patient Cohorts Generation: An Application to Aorta
2021
The combination of machine learning methods together with computational modeling and simulation of the cardiovascular system brings the possibility of obtaining very valuable information about new therapies or clinical devices through in-silico experiments. However, the application of machine learning methods demands access to large cohorts of patients. As an alternative to medical data acquisition and processing, which often requires some degree of manual intervention, the generation of virtual cohorts made of synthetic patients can be automated. However, the generation of a synthetic sample can still be computationally demanding to guarantee that it is clinically meaningful and that it re…
The ten grand challenges of synthetic life
2011
The construction of artificial life is one of the main scientific challenges of the Synthetic Biology era. Advances in DNA synthesis and a better understanding of regulatory processes make the goal of constructing the first artificial cell a realistic possibility. This would be both a fundamental scientific milestone and a starting point of a vast range of applications, from biofuel production to drug design. However, several major issues might hamper the objective of achieving an artificial cell. From the bottom-up to the selection-based strategies, this work encompasses the ten grand challenges synthetic biologists will have to be aware of in order to cope with the task of creating life i…
Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows
2020
AbstractMany computer-aided design tools are available for synthetic biology and metabolic engineering. Yet, these tools can be difficult to apprehend, sometimes requiring a level of expertise that limits their use by a wider community. Furthermore, some of the tools, although complementary, rely on different input and output formats and cannot communicate with one another. Scientific workflows address these shortcomings while offering a novel design strategy. Among the workflow systems available, Galaxy is a web-based platform for performing findable and accessible data analyses for all scientists regardless of their informatics expertise, along with interoperable and reproducible computat…
Sectors on sectors (SonS): A new hierarchical clustering visualization tool
2011
Clustering techniques have been widely applied to extract information from high-dimensional data structures in the last few years. Graphs are especially relevant for clustering, but many graphs associated with hierarchical clustering do not give any information about the values of the centroids' attributes and the relationships among them. In this paper, we propose a new visualization approach for hierarchical cluster analysis in which the above-mentioned information is available. The method is based on pie charts. The pie charts are divided into several pie segments or sectors corresponding to each cluster. The radius of each pie segment is proportional to the number of patterns included i…
Somatic embryogenesis in Abies nebrodensis, an endangered Sicilian fir
2022
AbstractSomatic embryogenesis, as a promising biotechnological tool for many conifer trees, has never been applied for the Abies nebrodensis species. Although all the encouraging results previously obtained by the EU LIFE (European LIFE program) funded projects in over ten years, the critically endangered Sicilian fir remains alarmingly close to extinction. In this study, we reported the first protocol of somatic embryogenesis obtained from mature zygotic embryos of the Abies nebrodensis. Seeds from Abies adult trees with specific identification numbers (IN) were collected and full seeds were identified by X-ray. Different experiments were carried out for callus initiation, from both zygoti…
Exciton interactions in self-organised bacteriochlorophyll a - aggregates
2002
Exciton interactions of self-organised bacteriochlorophyll a - aggregates in non-polar solution linked via water and dioxane have been studied. Absorption and CD spectra of the aggregates show large red shifts typical of J-aggregates. Femtosecond excitation of the Qy band of the aggregates is followed by wavelength dependent non-exponential picosecond relaxation and anisotropy decay takes place in subpicosecond time scale. To explain these observations exciton theory and semi-empirical MO/CI calculations, that constitute the basis of the CIEM-approach developed by Linnanto et al. (J. Phys. Chem. B, 1999, 103B, 8739) was used. Structural models of aggregates were created by using the molecul…