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James Alastair McLaughlin, Chris J Myers, Zach Zundel, Goksel Misirli, Michael Zhang, Irina Dana Ofiteru, Angel Goñi Moreno, Anil Wipat
The SynBioHub repository ( is an open-source software project which facilitates the sharing of information about engineered biological systems. SynBioHub provides computational access for software and data integration, and a graphical user interface that enables users to search for and share designs in a Web browser. By connecting to relevant repositories (e.g. the iGEM repository, JBEI ICE, and other instances of SynBioHub), the software allows users to browse, upload, and download data in various standard formats, regardless of their location or representation...
January 9, 2018: ACS Synthetic Biology
A J Petkus, C R Beam, W Johnson, J Kaprio, T Korhonen, M McGue, J M Neiderhiser, N L Pedersen, C A Reynolds, M Gatz
BACKGROUND: Numerous factors influence late-life depressive symptoms in adults, many not thoroughly characterized. We addressed whether genetic and environmental influences on depressive symptoms differed by age, sex, and physical illness. METHOD: The analysis sample included 24 436 twins aged 40-90 years drawn from the Interplay of Genes and Environment across Multiple Studies (IGEMS) Consortium. Biometric analyses tested age, sex, and physical illness moderation of genetic and environmental variance in depressive symptoms...
July 2017: Psychological Medicine
Susan Matheson
The new field of synthetic biology promises to change health care, computer technology, the production of biofuels, and more. Students participating in the International Genetically Engineered Machine (iGEM) competition are on the front lines of this revolution.
January 26, 2017: Cell
S Balachandar, M Sethuram, P Muthuraja, T Shanmugavadivu, M Dhandapani
Biologically active Lewis acid-base compound, pyrazolium 3-nitro phthalate (P3NP) has been synthesized and crystallized by slow evaporation - solution method at 30°C. Spectral and single crystal X-Ray diffraction (XRD) were used to characterize the compound. The stability of the P3NP was confirmed by UV-Visible spectral analysis. P3NP crystallizes in monoclinic P21/C space group with cell parameters, a=13.009 (3) Å, b=12.584 (3) Å, c=7.529 (18) Å and β=93.052 (4)(o) with Z=4. Crystal packing was stabilized by N(+)H⋯O(-), OH⋯O and CH⋯O intermolecular hydrogen bonds...
October 2016: Journal of Photochemistry and Photobiology. B, Biology
Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Kim de Mora, Meagan Lizarazo, Jim Hollenhorst, Randy Rettberg
[This corrects the article DOI: 10.1371/journal.pone.0150182.].
2016: PloS One
Michael Florea, Henrik Hagemann, Gabriella Santosa, James Abbott, Chris N Micklem, Xenia Spencer-Milnes, Laura de Arroyo Garcia, Despoina Paschou, Christopher Lazenbatt, Deze Kong, Haroon Chughtai, Kirsten Jensen, Paul S Freemont, Richard Kitney, Benjamin Reeve, Tom Ellis
Bacterial cellulose is a strong and ultrapure form of cellulose produced naturally by several species of the Acetobacteraceae Its high strength, purity, and biocompatibility make it of great interest to materials science; however, precise control of its biosynthesis has remained a challenge for biotechnology. Here we isolate a strain of Komagataeibacter rhaeticus (K. rhaeticus iGEM) that can produce cellulose at high yields, grow in low-nitrogen conditions, and is highly resistant to toxic chemicals. We achieved external control over its bacterial cellulose production through development of a modular genetic toolkit that enables rational reprogramming of the cell...
June 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
Jennifer Tsui, Anne S Meyer
In the yearly Internationally Genetically Engineered Machines (iGEM) competition, teams of Bachelor's and Master's students design and build an engineered biological system using DNA technologies. Advising an iGEM team poses unique challenges due to the inherent difficulties of mounting and completing a new biological project from scratch over the course of a single academic year; the challenges in obtaining financial and structural resources for a project that will likely not be fully realized; and conflicts between educational and competition-based goals...
July 2016: FEMS Microbiology Letters
Sanjana Sood, Krzysztof J Szkop, Asif Nakhuda, Iain J Gallagher, Carl Murie, Robert J Brogan, Jaakko Kaprio, Heikki Kainulainen, Philip J Atherton, Urho M Kujala, Thomas Gustafsson, Ola Larsson, James A Timmons
DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2...
June 20, 2016: Nucleic Acids Research
Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Kim de Mora, Meagan Lizarazo, Jim Hollenhorst, Randy Rettberg
We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5...
2016: PloS One
Michela Casanova, Lorenzo Pasotti, Susanna Zucca, Nicolò Politi, Ilaria Massaiu, Cinzia Calvio, Maria Gabriella Cusella De Angelis, Paolo Magni
BACKGROUND: Circular plasmid-mediated homologous recombination is commonly used for marker-less allelic replacement, exploiting the endogenous recombination machinery of the host. Common limitations of existing methods include high false positive rates due to mutations in counter-selection genes, and limited applicability to specific strains or growth media. Finally, solutions compatible with physical standards, such as the BioBrick™, are not currently available, although they proved to be successful in the design of other replicative or integrative plasmids...
2016: Biological Procedures Online
Carol E Franz, Deborah Finkel, Matthew S Panizzon, Kelly Spoon, Kaare Christensen, Margaret Gatz, William S Kremen, Robert Krueger, Jenae Neiderhiser, Chandra Reynolds, Nancy L Pedersen
OBJECTIVE: Subjective health is a complex indicator predicting longevity independent of objective health. Few studies examine genetic and environmental mechanisms underlying different facets of subjective health across the life course. METHOD: Three subjective health measures were examined in 12,900 twins ( Mage = 63.38, range = 25-102) from nine studies in the Interplay of Genes and Environment across Multiple Studies Consortium: self-rated health (SRH), health compared with others (COMP), and health interfering with activities (ACT)...
February 2017: Journal of Aging and Health
Chandra A Reynolds, Margaret Gatz, Kaare Christensen, Lene Christiansen, Anna K Dahl Aslan, Jaakko Kaprio, Tellervo Korhonen, William S Kremen, Robert Krueger, Matt McGue, Jenae M Neiderhiser, Nancy L Pedersen
Despite emerging interest in gene-environment interaction (GxE) effects, there is a dearth of studies evaluating its potential relevance apart from specific hypothesized environments and biometrical variance trends. Using a monozygotic within-pair approach, we evaluated evidence of G×E for body mass index (BMI), depressive symptoms, and cognition (verbal, spatial, attention, working memory, perceptual speed) in twin studies from four countries. We also evaluated whether APOE is a 'variability gene' across these measures and whether it partly represents the 'G' in G×E effects...
January 2016: Behavior Genetics
Deborah Finkel, Carol E Franz, Briana Horwitz, Kaare Christensen, Margaret Gatz, Wendy Johnson, Jaako Kaprio, Tellervo Korhonen, Jenae Niederheiser, Inge Petersen, Richard J Rose, Karri Silventoinen
From the IGEMS Consortium, data were available from 26,579 individuals aged 23 to 102 years on 3 subjective health items: self-rated health (SRH), health compared to others (COMP), and impact of health on activities (ACT). Marital status was a marker of environmental resources that may moderate genetic and environmental influences on subjective health. Results differed for the 3 subjective health items, indicating that they do not tap the same construct. Although there was little impact of marital status on variance components for women, marital status was a significant modifier of variance in all 3 subjective health measures for men...
October 14, 2015: Behavior Genetics
Richard Kelwick, Laura Bowater, Kay H Yeoman, Richard P Bowater
Synthetic biology has developed rapidly in the 21st century. It covers a range of scientific disciplines that incorporate principles from engineering to take advantage of and improve biological systems, often applied to specific problems. Methods important in this subject area include the systematic design and testing of biological systems and, here, we describe how synthetic biology projects frequently develop microbiology skills and education. Synthetic biology research has huge potential in biotechnology and medicine, which brings important ethical and moral issues to address, offering learning opportunities about the wider impact of microbiological research...
August 2015: FEMS Microbiology Letters
Benjamin R Jack, Sean P Leonard, Dennis M Mishler, Brian A Renda, Dacia Leon, Gabriel A Suárez, Jeffrey E Barrick
Unwanted evolution can rapidly degrade the performance of genetically engineered circuits and metabolic pathways installed in living organisms. We created the Evolutionary Failure Mode (EFM) Calculator to computationally detect common sources of genetic instability in an input DNA sequence. It predicts two types of mutational hotspots: deletions mediated by homologous recombination and indels caused by replication slippage on simple sequence repeats. We tested the performance of our algorithm on genetic circuits that were previously redesigned for greater evolutionary reliability and analyzed the stability of sequences in the iGEM Registry of Standard Biological Parts...
August 21, 2015: ACS Synthetic Biology
Ming Chen
Self-assembling RNA scaffold is designed to co-localize enzymes in engineered biological pathways through interactions between scaffold's protein docking domains and their affinity protein-enzyme fusions, in vivo. Here we introduced a noncoding RNA structure theophylline aptamer that respond to theophylline ligand in order to modulate RNA scaffold and regulate multistep enzymatic activities. We described the specifically designed RNA scaffold increased the fluorescent intensity in a splitting GFP assay by 2...
2015: Methods in Molecular Biology
Razan N Alnahhas, Ben Slater, Yunle Huang, Catherine Mortensen, Jordan W Monk, Yousef Okasheh, Marco D Howard, Neil R Gottel, Michael J Hammerling, Jeffrey E Barrick
The Registry of Standard Biological Parts only accepts genetic parts compatible with the RFC 10 BioBrick format. This combined assembly and submission standard requires that four unique restriction enzyme sites must not occur in the DNA sequence encoding a part. We present evidence that this requirement places a nontrivial burden on iGEM teams developing large and novel parts. We further argue that the emergence of inexpensive DNA synthesis and versatile assembly methods reduces the utility of coupling submission and assembly standards and propose a submission standard that is compatible with current quality control strategies while nearly eliminating sequence constraints on submitted parts...
2014: Journal of Biological Engineering
Julie McNamara, Shlomiya Bar-Yam Lightfoot, Kelly Drinkwater, Evan Appleton, Kenneth Oye
iGEM has spent the past decade encouraging teams to push their projects to the frontiers of synthetic biology. However, as project complexity increases, so too does the level of assumed risk. In the absence of a coherent international framework for evaluating these risks in synthetic biology, iGEM has recently engaged with the MIT Program on Emerging Technologies to develop a progressive approach for handling questions of safety and security. These two groups have worked together to create a rigorous screening program, acknowledging that a strengthened set of iGEM safety policies ultimately serves to expand, not contract, the universe of acceptable projects...
December 19, 2014: ACS Synthetic Biology
Josephina Hendrix, Timothy Read, Jean-Francois Lalonde, Phillip K Jensen, William Heymann, Elijah Lovelace, Sarah A Zimmermann, Michael Brasino, Joseph Rokicki, Robin D Dowell
We have developed a simple system for tagging and purifying proteins. Recent experiments have demonstrated that RTX (Repeat in Toxin) motifs from the adenylate cyclase toxin gene (CyaA) of B. pertussis undergo a conformational change upon binding calcium, resulting in precipitation of fused proteins and making this method a viable alternative for bioseparation. We have designed an iGEM Biobrick comprised of an RTX tag that can be easily fused to any protein of interest. In this paper, we detail the process of creating an RTX tagged version of the restriction enzyme EcoRI and describe a method for expression and purification of the functional enzyme...
December 19, 2014: ACS Synthetic Biology
John Wilson-Kanamori, Vincent Danos, Ty Thomson, Ricardo Honorato-Zimmer
Rule-based modeling, an alternative to traditional reaction-based modeling, allows us to intuitively specify biological interactions while abstracting from the underlying combinatorial complexity. One such rule-based modeling formalism is Kappa, which we introduce to readers in this chapter. We discuss the application of Kappa to three modeling scenarios in synthetic biology: a unidirectional switch based on nitrosylase induction in Saccharomyces cerevisiae, the repressilator in Escherichia coli formed from BioBrick parts, and a light-mediated extension to said repressilator developed by the University of Edinburgh team during iGEM 2010...
2015: Methods in Molecular Biology
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