scholarly journals Jumping Ahead with Sleeping Beauty: Mechanistic Insights into Cut-and-Paste Transposition

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 76
Author(s):  
Matthias T. Ochmann ◽  
Zoltán Ivics
Keyword(s):  
Genetic Engineering ◽  
Structural Data ◽  
Sleeping Beauty ◽  
Preclinical Studies ◽  
Gene Vector ◽  
Functional Information ◽  
Vector Systems ◽  
Novel Variants ◽  
Insight Into ◽  
Cellular Genome

Sleeping Beauty (SB) is a transposon system that has been widely used as a genetic engineering tool. Central to the development of any transposon as a research tool is the ability to integrate a foreign piece of DNA into the cellular genome. Driven by the need for efficient transposon-based gene vector systems, extensive studies have largely elucidated the molecular actors and actions taking place during SB transposition. Close transposon relatives and other recombination enzymes, including retroviral integrases, have served as useful models to infer functional information relevant to SB. Recently obtained structural data on the SB transposase enable a direct insight into the workings of this enzyme. These efforts cumulatively allowed the development of novel variants of SB that offer advanced possibilities for genetic engineering due to their hyperactivity, integration deficiency, or targeting capacity. However, many aspects of the process of transposition remain poorly understood and require further investigation. We anticipate that continued investigations into the structure–function relationships of SB transposition will enable the development of new generations of transposition-based vector systems, thereby facilitating the use of SB in preclinical studies and clinical trials.

Exploring genomes with a game engine

2014 ◽  
Vol 169 ◽  
pp. 443-453 ◽  
Author(s):  
Jeremiah J. Shepherd ◽  
Lingxi Zhou ◽  
William Arndt ◽  
Yan Zhang ◽  
W. Jim Zheng ◽  
...  
Keyword(s):  
Real Time ◽  
Video Game ◽  
Linear Structure ◽  
Structural Data ◽  
Game Engine ◽  
3D Genome ◽  
Genome Viewer ◽  
A Genome ◽  
Visualization Techniques ◽  
Insight Into

More and more evidence indicates that the 3D conformation of eukaryotic genomes is a critical part of genome function. However, due to the lack of accurate and reliable 3D genome structural data, this information is largely ignored and most of these studies have to use information systems that view the DNA in a linear structure. Visualizing genomes in real time 3D can give researchers more insight, but this is fraught with hardware limitations since each element contains vast amounts of information that cannot be processed on the fly. Using a game engine and sophisticated video game visualization techniques enables us to construct a multi-platform real-time 3D genome viewer. The game engine-based viewer achieves much better rendering speed and can handle much larger amounts of data compared to our previous implementation using OpenGL. Combining this viewer with 3D genome models from experimental data could provide unprecedented opportunities to gain insight into the conformation–function relationships of a genome.

Real Time X-Ray Rheology of Polymers

1994 ◽  
Vol 38 ◽  
pp. 531-537 ◽  
Author(s):  
J. A. Pople ◽  
G. R. Mitchell ◽  
C. K. Chai
Keyword(s):  
Liquid Crystalline ◽  
Structural Data ◽  
Liquid Crystalline Polymers ◽  
Polymer Processing ◽  
X Ray ◽  
Crystalline Polymers ◽  
Mechanical Measurements ◽  
Rigid Rods ◽  
Insight Into ◽  
Technological Interest

The ability to prcbe the structure of a polymer during deformation is of considerable technological interest as it lends an insight into the mechanisms involved in polymer processing. The behaviour of Liquid Crystalline Polymers (LCP's) during shear flow has generated much experimental interest by virtue of their unusual behaviour compared to that of simpler polymeric melts. The theory developed by Doi attempts to explain the observed phenomena in terms of considering interactions of rigid-rods Exact solutions to the Doi theory have been compared to experimental procedures using lyotropic LCP systems. Although much of the available data relates to mechanical measurements, the comparisons with quantitative structural data can provide useful insight.

scholarly journals Conformation-independent structural comparison of macromolecules with ProSMART

2014 ◽  
Vol 70 (a1) ◽  
pp. C494-C494 ◽  
Author(s):  
Robert Nicholls ◽  
Marcus Fischer ◽  
Garib Murshudov
Keyword(s):  
Comparative Analysis ◽  
Structural Alignment ◽  
Structural Data ◽  
Visual Assessment ◽  
Biological Macromolecules ◽  
Rna Structures ◽  
Structural Comparison ◽  
Biological Insight ◽  
High Sequence Homology ◽  
Insight Into

Structural comparison often aids insight into the function and mechanics of biological macromolecules. To make such analyses more accessible, we present the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART), which is designed to allow fast but detailed comparative analysis of macromolecular structures despite potential dissimilarities in global arrangement, such as domain motion and distortion. Whilst obtaining a residue alignment between structures is a prerequisite for comparative analysis, conventional alignment methods may fail in cases where conformational differences are dramatic. However, ProSMART achieves a conformation-independent structural alignment by focusing purely on local dissimilarities, rather than enforcing chain/domain rigidity. This allows the sensible comparison of protein (or DNA/RNA) structures in the presence of conformational change. ProSMART allows analysis of the structural conservation of local backbone and side chains in a wide variety of scenarios - the method is sensitive enough to allow identification of subtle dissimilarities between structures sharing high sequence homology, whilst being versatile enough to allow identification of local similarities between more distantly-related structures. In addition, ProSMART can be used for the identification of conserved rigid substructures, which may or may not represent functional domains. ProSMART is also used for the generation of external restraints for use in crystallographic refinement. Results from ProSMART can be visualised in either CCP4mg or PyMOL. All residue-based scores are illustrated using intuitive colour gradients, allowing easy visual assessment of local backbone and side chain conservation. Complementary structural comparison tools such as ProSMART can help break the complexity of the constantly growing pool of available structural data into a more readily accessible form, and consequently may aid biological insight into macromolecular structures.

scholarly journals A Review of Nervonic Acid Production in Plants: Prospects for the Genetic Engineering of High Nervonic Acid Cultivars Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Fang Liu ◽  
Pandi Wang ◽  
Xiaojuan Xiong ◽  
Xinhua Zeng ◽  
Xiaobo Zhang ◽  
...  
Keyword(s):  
Genetic Engineering ◽  
Genetically Engineered ◽  
Commercial Application ◽  
Nervonic Acid ◽  
Plant Oil ◽  
Plant Seed ◽  
Oil Crops ◽  
Transgenic Technologies ◽  
Production Mechanisms ◽  
Insight Into

Nervonic acid (NA) is a very-long-chain monounsaturated fatty acid that plays crucial roles in brain development and has attracted widespread research interest. The markets encouraged the development of a refined, NA-enriched plant oil as feedstocks for the needed further studies of NA biological functions to the end commercial application. Plant seed oils offer a renewable and environmentally friendly source of NA, but their industrial production is presently hindered by various factors. This review focuses on the NA biosynthesis and assembly, NA resources from plants, and the genetic engineering of NA biosynthesis in oil crops, discusses the factors that affect NA production in genetically engineered oil crops, and provides prospects for the application of NA and prospective trends in the engineering of NA. This review emphasizes the progress made toward various NA-related topics and explores the limitations and trends, thereby providing integrated and comprehensive insight into the nature of NA production mechanisms during genetic engineering. Furthermore, this report supports further work involving the manipulation of NA production through transgenic technologies and molecular breeding for the enhancement of crop nutritional quality or creation of plant biochemical factories to produce NA for use in nutraceutical, pharmaceutical, and chemical industries.

scholarly journals A Pipeline for Making 31P NMR Accessible for Small- and Large-Scale Lipidomics Studies

2021 ◽  
Author(s):  
Samuel Furse ◽  
Huw Williams ◽  
Adam Watkins ◽  
Samuel Virtue ◽  
Antonio Vidal-Puig ◽  
...  
Keyword(s):  
Large Scale ◽  
31P Nmr ◽  
A Priori ◽  
Structural Data ◽  
Mass Spectrometry Data ◽  
Head Group ◽  
Sample Extraction ◽  
Tools And Techniques ◽  
Scientific Questions ◽  
Insight Into

Detailed molecular analysis is of increasing importance in research into the regulation of biochemical pathways, organismal growth and disease. Lipidomics in particular is increasingly sought after as it provides insight into molecular species involved in energy storage, signalling and fundamental cellular structures. This has led to the use of a range of tools and techniques to acquire lipidomics data. 31P NMR for lipidomics offers well-resolved head group/lipid class analysis, structural data that can be used to inform and strengthen interpretation of mass spectrometry data and part of structural determination a priori. In the present study, we codify the use of 31P NMR for lipidomics to make the technique more accessible to new users and more useful for a wider range of studies. We describe the process from sample extraction to data processing and analysis. This pipeline is important because it allows greater thoroughness in lipidomics studies and increases scope for answering scientific questions about lipid systems.

Dynamic aspects of enzyme specificity

1975 ◽  
Vol 272 (915) ◽  
pp. 109-122 ◽  
Keyword(s):  
Kinetic Studies ◽  
Structural Data ◽  
Enzyme Specificity ◽  
X Ray Diffraction ◽  
X Ray ◽  
Enzyme Substrate ◽  
Substrate Analogues ◽  
Competitive Inhibitors ◽  
Lactate Dehydrogenases ◽  
Insight Into

There are two aspects of enzyme specificity: recognition of the substrate by the formation of an enzyme-substrate compound and recognition of the transition state by catalysis of the reaction. Kinetic studies with inactive substrate analogues as potential competitive inhibitors, and structural studies of their compounds with enzymes, give information about the first of these specificity elements. Comparative kinetic studies with alternative substrates give information about both. There is a great deal of information from kinetic studies of dehydrogenases about the coenzyme specificities, substrate specificities and stereospecificities and mechanisms of these enzymes, particularly alcohol dehydrogenases. Recent X-ray diffraction studies of dehydrogenases have given insight into the molecular basis of some of their specificity elements. An attempt is made to correlate the available kinetic and structural data for alcohol and lactate dehydrogenases.

scholarly journals An insight into cotton genetic engineering (Gossypium hirsutum L.): current endeavors and prospects

2015 ◽  
Vol 37 (8) ◽  
Author(s):  
Allah Bakhsh ◽  
Emine Anayol ◽  
Sancar Fatih Özcan ◽  
Tahira Hussain ◽  
Muhammad Aasim ◽  
...  
Keyword(s):  
Genetic Engineering ◽  
Gossypium Hirsutum ◽  
Gossypium Hirsutum L ◽  
Insight Into

scholarly journals Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages

2021 ◽  
Author(s):  
Dror Shitrit ◽  
Thomas Hackl ◽  
Raphael Laurenceau ◽  
Nicolas Raho ◽  
Michael C. G. Carlson ◽  
...  
Keyword(s):  
Genetic Engineering ◽  
Attachment Site ◽  
Marine Cyanobacteria ◽  
Engineering System ◽  
Pcr Screening ◽  
Photosynthetic Organisms ◽  
Infection Dynamics ◽  
Attachment Sites ◽  
Insight Into

AbstractMarine cyanobacteria of the genera Synechococcus and Prochlorococcus are the most abundant photosynthetic organisms on earth, spanning vast regions of the oceans and contributing significantly to global primary production. Their viruses (cyanophages) greatly influence cyanobacterial ecology and evolution. Although many cyanophage genomes have been sequenced, insight into the functional role of cyanophage genes is limited by the lack of a cyanophage genetic engineering system. Here, we describe a simple, generalizable method for genetic engineering of cyanophages from multiple families, that we named REEP for REcombination, Enrichment and PCR screening. This method enables direct investigation of key cyanophage genes, and its simplicity makes it adaptable to other ecologically relevant host-virus systems. T7-like cyanophages often carry integrase genes and attachment sites, yet exhibit lytic infection dynamics. Here, using REEP, we investigated their ability to integrate and maintain a lysogenic life cycle. We found that these cyanophages integrate into the host genome and that the integrase and attachment site are required for integration. However, stable lysogens did not form. The frequency of integration was found to be low in both lab cultures and the oceans. These findings suggest that T7-like cyanophage integration is transient and is not part of a classical lysogenic cycle.

scholarly journals A MYT1L Syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation

2020 ◽  
Author(s):  
Jiayang Chen ◽  
Mary E. Lambo ◽  
Xia Ge ◽  
Joshua T. Dearborn ◽  
Yating Liu ◽  
...  
Keyword(s):  
Mouse Model ◽  
Brain Development ◽  
Human Genetics ◽  
Preclinical Studies ◽  
Loss Of Function ◽  
Gene Target ◽  
Brain Anomalies ◽  
Physiological Properties ◽  
Insight Into ◽  
Target Activation

AbstractHuman genetics have defined a new autism-associated syndrome caused by loss-of-function mutations in MYT1L, a transcription factor known for enabling fibroblast-to-neuron conversions. However, how MYT1L mutation causes autism, ADHD, intellectual disability, obesity, and brain anomalies is unknown. Here, we develop a mouse model of this syndrome. Physically, Myt1l haploinsufficiency causes obesity, white-matter thinning, and microcephaly in the mice, mimicking clinical phenotypes. Studies during brain development reveal disrupted gene expression, mediated in part by loss of Myt1l gene target activation, and highlight precocious neuronal differentiation as the mechanism for microcephaly. In contrast, adult studies reveal that mutation results in failure of transcriptional and chromatin maturation, echoed in disruptions in baseline physiological properties of neurons. This results in behavioral features including hyperactivity, hypotonia, and social alterations, with more severe phenotypes in males. Overall, these studies provide insight into the mechanistic underpinnings of this disorder and enable future preclinical studies.

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