scholarly journals Genetic Engineering and Synthetic Genomics in Yeast to Understand Life and Boost Biotechnology

2020 ◽  
Vol 7 (4) ◽  
pp. 137
Author(s):  
Daniel Schindler
Keyword(s):  
Genetic Engineering ◽  
Large Scale ◽  
Model Organisms ◽  
Yeast Saccharomyces Cerevisiae ◽  
Scale Reading ◽  
Vast Number ◽  
Recent Developments ◽  
Synthetic Genomics ◽  
Basic And Applied Research

The field of genetic engineering was born in 1973 with the “construction of biologically functional bacterial plasmids in vitro”. Since then, a vast number of technologies have been developed allowing large-scale reading and writing of DNA, as well as tools for complex modifications and alterations of the genetic code. Natural genomes can be seen as software version 1.0; synthetic genomics aims to rewrite this software with “build to understand” and “build to apply” philosophies. One of the predominant model organisms is the baker’s yeast Saccharomyces cerevisiae. Its importance ranges from ancient biotechnologies such as baking and brewing, to high-end valuable compound synthesis on industrial scales. This tiny sugar fungus contributed greatly to enabling humankind to reach its current development status. This review discusses recent developments in the field of genetic engineering for budding yeast S. cerevisiae, and its application in biotechnology. The article highlights advances from Sc1.0 to the developments in synthetic genomics paving the way towards Sc2.0. With the synthetic genome of Sc2.0 nearing completion, the article also aims to propose perspectives for potential Sc3.0 and subsequent versions as well as its implications for basic and applied research.

Abstract 2722: Large Scale Mutation Discovery Screen Identifies Functionally Variant UGDH Alleles in Patients with Atrioventricular Valve Defects

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Jeroen Bakkers ◽  
Sonja Chocron ◽  
Victor Gouriev ◽  
Kelly Smith ◽  
Ronald Lekanne dit Deprez ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Congenital Heart Defects ◽  
Congenital Heart ◽  
Large Scale ◽  
Heart Defects ◽  
Glucose Dehydrogenase ◽  
Model Organisms ◽  
Missense Mutations ◽  
Coding Regions

Background: Congenital heart defects are the most common birth defects. Although genetic dispositions are believed to cause CHDs, only few genes have been identified that harbour mutations causing such defects. Studies in model organisms have identified many essential genes for cardiac development. UDP-glucose dehydrogenase (UGDH) enzymatic activity is required for the signal transduction of FGF and Wnt ligands and zebrafish jekyll/ugdh mutations lack AV valves. Methods and Results: From literature candidate genes were selected that are essential for AV canal-, septum-, and valve formation. By large scale sequencing we analysed the coding regions of 36 candidate genes in 192 patients with reported AVSDs. As a result we identified 457 genetic variations of which 207 variants are in flanking non-coding regions, 156 variants are in coding regions but silent and 94 variants are non-synonymous variants that alter the protein sequence. Comparison with the available databases such as HapMap and screening 350 control individuals resulted in the validation of 49 non-synonomous missense mutations in 23 genes only present in the patient group. These included novel GATA4 missense mutations (R285C and M224V) located in the highly conserved DNA binding domains, which by in vitro analysis significantly reduce transcriptional activity of the protein. Three patients with mitral valvar prolapse and mitral regurgitation were identified with novel missense mutations in the UDP-glucose dehydrogenase (UGDH) gene (R141C and E416D). In vitro experiments demonstrated a negative affect on enzyme activity and stability by a change in protein conformation. Furthermore, experiments in zebrafish jekyll/ugdh mutants showed that UGDH R141C and UGDH E416D couldn’t rescue the defects in AV formation demonstrating an inactivating effect of these missense mutations in vivo. Conclusions: A model organism based candidate gene screen in CHD patients resulted in the identification of novel functional missense mutations in the UGDH gene not previously implicated in congenital heart defects.

scholarly journals Cannabis sativa: From Therapeutic Uses to Micropropagation and Beyond

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2078
Author(s):  
Tristan K. Adams ◽  
Nqobile A. Masondo ◽  
Pholoso Malatsi ◽  
Nokwanda P. Makunga
Keyword(s):  
Tissue Culture ◽  
Genetic Engineering ◽  
Large Scale ◽  
Gene Editing ◽  
Cannabis Sativa ◽  
Scale Production ◽  
Indirect Organogenesis ◽  
Large Scale Production ◽  
Pharmaceutical Industries

The development of a protocol for the large-scale production of Cannabis and its variants with little to no somaclonal variation or disease for pharmaceutical and for other industrial use has been an emerging area of research. A limited number of protocols have been developed around the world, obtained through a detailed literature search using web-based database searches, e.g., Scopus, Web of Science (WoS) and Google Scholar. This article reviews the advances made in relation to Cannabis tissue culture and micropropagation, such as explant choice and decontamination of explants, direct and indirect organogenesis, rooting, acclimatisation and a few aspects of genetic engineering. Since Cannabis micropropagation systems are fairly new fields, combinations of plant growth regulator experiments are needed to gain insight into the development of direct and indirect organogenesis protocols that are able to undergo the acclimation stage and maintain healthy plants desirable to the Cannabis industry. A post-culture analysis of Cannabis phytochemistry after the acclimatisation stage is lacking in a majority of the reviewed studies, and for in vitro propagation protocols to be accepted by the pharmaceutical industries, phytochemical and possibly pharmacological research need to be undertaken in order to ascertain the integrity of the generated plant material. It is rather difficult to obtain industrially acceptable micropropagation regimes as recalcitrance to the regeneration of in vitro cultured plants remains a major concern and this impedes progress in the application of genetic modification technologies and gene editing tools to be used routinely for the improvement of Cannabis genotypes that are used in various industries globally. In the future, with more reliable plant tissue culture-based propagation that generates true-to-type plants that have known genetic and metabolomic integrity, the use of genetic engineering systems including “omics” technologies such as next-generation sequencing and fast-evolving gene editing tools could be implemented to speed up the identification of novel genes and mechanisms involved in the biosynthesis of Cannabis phytochemicals for large-scale production.

scholarly journals State of Digitisation and Gap Analysis Surveys

2018 ◽  
Vol 2 ◽  
pp. e25969
Author(s):  
Sarah Phillips ◽  
Elspeth Haston ◽  
Laura Green ◽  
Marie-Helene Weech ◽  
Robert Cubey ◽  
...  
Keyword(s):  
Natural History ◽  
Working Group ◽  
Large Scale ◽  
Gap Analysis ◽  
Vast Number ◽  
Natural Heritage ◽  
Future Programme ◽  
Natural History Collection ◽  
Recent Developments ◽  
Successes And Challenges

Recent developments in digitisation technologies and equipment have enabled advances in the rate of natural history specimen digitisation. However Europe’s Natural History Collection Institutions are home to over one billion specimens and currently only a small fraction of these have been digitally catalogued with fewer imaged. It is clear that institutions still face huge challenges when digitising the vast number of specimens in their collections. I will present the results of two surveys that aimed to discover the main successes and challenges facing institutions in their digitisation programmes. The first survey was undertaken in 2014 within the SYNTHESYS 3 project and gathered information from project partners on their current digitisation facilities, equipment and workflows providing some key recommendations based on these findings. The second survey was completed more recently in 2017, through the Consortium of European Taxonomic Facilities (CETAF) Digitisation Working Group. This survey aimed to discover the successful protocols and implementation of digitisation, and to identify the shortfalls in resources and protocols. Results from both surveys will be fed into the future programme of the CETAF Digitisation Working Group as well as forthcoming and proposed EU projects, including Innovation and Consolidation for large-scale Digitisation of natural heritage (ICEDIG).

scholarly journals Microvascularized tumor organoids-on-chips: advancing preclinical drug screening with pathophysiological relevance

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jungeun Lim ◽  
Hanna Ching ◽  
Jeong-Kee Yoon ◽  
Noo Li Jeon ◽  
YongTae Kim
Keyword(s):  
Large Scale ◽  
Recent Progress ◽  
Personalized Cancer Medicine ◽  
Recent Developments ◽  
Functional Features ◽  
Cancer Medicine ◽  
Potential Strategy ◽  
Personalized Cancer ◽  
Tumor Organoids

AbstractRecent developments of organoids engineering and organ-on-a-chip microfluidic technologies have enabled the recapitulation of the major functions and architectures of microscale human tissue, including tumor pathophysiology. Nevertheless, there remain challenges in recapitulating the complexity and heterogeneity of tumor microenvironment. The integration of these engineering technologies suggests a potential strategy to overcome the limitations in reconstituting the perfusable microvascular system of large-scale tumors conserving their key functional features. Here, we review the recent progress of in vitro tumor-on-a-chip microfluidic technologies, focusing on the reconstruction of microvascularized organoid models to suggest a better platform for personalized cancer medicine.

scholarly journals Redox Coenzyme F420 Biosynthesis in Thermomicrobia Involves Reduction by Stand-Alone Nitroreductase Superfamily Enzymes

2020 ◽  
Vol 86 (12) ◽  
Author(s):  
Daniel Braga ◽  
Mahmudul Hasan ◽  
Tabea Kröber ◽  
Daniel Last ◽  
Gerald Lackner
Keyword(s):  
Large Scale ◽  
Reductase Activity ◽  
Protein A ◽  
Model Organisms ◽  
Gram Negative Bacteria ◽  
Scale Production ◽  
Metabolome Analysis ◽  
Gram Negative ◽  
Content Type

ABSTRACT Coenzyme F420 is a redox cofactor involved in hydride transfer reactions in archaea and bacteria. Since F420-dependent enzymes are attracting increasing interest as tools in biocatalysis, F420 biosynthesis is being revisited. While it was commonly accepted for a long time that the 2-phospho-l-lactate (2-PL) moiety of F420 is formed from free 2-PL, it was recently shown that phosphoenolpyruvate is incorporated in Actinobacteria and that the C-terminal domain of the FbiB protein, a member of the nitroreductase (NTR) superfamily, converts dehydro-F420 into saturated F420. Outside the Actinobacteria, however, the situation is still unclear because FbiB is missing in these organisms and enzymes of the NTR family are highly diversified. Here, we show by heterologous expression and in vitro assays that stand-alone NTR enzymes from Thermomicrobia exhibit dehydro-F420 reductase activity. Metabolome analysis and proteomics studies confirmed the proposed biosynthetic pathway in Thermomicrobium roseum. These results clarify the biosynthetic route of coenzyme F420 in a class of Gram-negative bacteria, redefine functional subgroups of the NTR superfamily, and offer an alternative for large-scale production of F420 in Escherichia coli in the future. IMPORTANCE Coenzyme F420 is a redox cofactor of Archaea and Actinobacteria, as well as some Gram-negative bacteria. Its involvement in processes such as the biosynthesis of antibiotics, the degradation of xenobiotics, and asymmetric enzymatic reductions renders F420 of great relevance for biotechnology. Recently, a new biosynthetic step during the formation of F420 in Actinobacteria was discovered, involving an enzyme domain belonging to the versatile nitroreductase (NTR) superfamily, while this process remained blurred in Gram-negative bacteria. Here, we show that a similar biosynthetic route exists in Thermomicrobia, although key biosynthetic enzymes show different domain architectures and are only distantly related. Our results shed light on the biosynthesis of F420 in Gram-negative bacteria and refine the knowledge about sequence-function relationships within the NTR superfamily of enzymes. Appreciably, these results offer an alternative route to produce F420 in Gram-negative model organisms and unveil yet another biochemical facet of this pathway to be explored by synthetic microbiologists.

scholarly journals Recent progress in translational engineered in vitro models of the central nervous system

Brain ◽  
2020 ◽  
Vol 143 (11) ◽  
pp. 3181-3213 ◽  
Author(s):  
Polyxeni Nikolakopoulou ◽  
Rossana Rauti ◽  
Dimitrios Voulgaris ◽  
Iftach Shlomy ◽  
Ben M Maoz ◽  
...  
Keyword(s):  
Large Scale ◽  
Induced Pluripotent Stem Cell ◽  
In Vitro Models ◽  
Model Systems ◽  
Success Rates ◽  
Recent Developments ◽  
Practical Guidelines ◽  
Organ On A Chip ◽  
Induced Pluripotent

Abstract The complexity of the human brain poses a substantial challenge for the development of models of the CNS. Current animal models lack many essential human characteristics (in addition to raising operational challenges and ethical concerns), and conventional in vitro models, in turn, are limited in their capacity to provide information regarding many functional and systemic responses. Indeed, these challenges may underlie the notoriously low success rates of CNS drug development efforts. During the past 5 years, there has been a leap in the complexity and functionality of in vitro systems of the CNS, which have the potential to overcome many of the limitations of traditional model systems. The availability of human-derived induced pluripotent stem cell technology has further increased the translational potential of these systems. Yet, the adoption of state-of-the-art in vitro platforms within the CNS research community is limited. This may be attributable to the high costs or the immaturity of the systems. Nevertheless, the costs of fabrication have decreased, and there are tremendous ongoing efforts to improve the quality of cell differentiation. Herein, we aim to raise awareness of the capabilities and accessibility of advanced in vitro CNS technologies. We provide an overview of some of the main recent developments (since 2015) in in vitro CNS models. In particular, we focus on engineered in vitro models based on cell culture systems combined with microfluidic platforms (e.g. ‘organ-on-a-chip’ systems). We delve into the fundamental principles underlying these systems and review several applications of these platforms for the study of the CNS in health and disease. Our discussion further addresses the challenges that hinder the implementation of advanced in vitro platforms in personalized medicine or in large-scale industrial settings, and outlines the existing differentiation protocols and industrial cell sources. We conclude by providing practical guidelines for laboratories that are considering adopting organ-on-a-chip technologies.

scholarly journals Low membrane fluidity triggers lipid phase separation and protein segregation in vivo

2019 ◽  
Author(s):  
Marvin Gohrbandt ◽  
André Lipski ◽  
Zunera Baig ◽  
Stefan Walter ◽  
Rainer Kurre ◽  
...  
Keyword(s):  
Phase Separation ◽  
Membrane Fluidity ◽  
Lipid Composition ◽  
Large Scale ◽  
Fluid Phase ◽  
Model Organisms ◽  
Lipid Phase ◽  
Lipid Phase Separation

SummaryImportant physicochemical properties of cell membranes such as fluidity sensitively depend on fluctuating environmental factors including temperature, pH or diet. To counteract these disturbances, living cells universally adapt their lipid composition in return. In contrast to eukaryotic cells, bacteria tolerate surprisingly drastic changes in their lipid composition while retaining viability, thus making them a more tractable model to study this process. Using the model organisms Escherichia coli and Bacillus subtilis, which regulate their membrane fluidity with different fatty acid types, we show here that inadequate membrane fluidity interferes with essential cellular processes such as morphogenesis and maintenance of membrane potential, and triggers large-scale lipid phase separation that drives protein segregation into the fluid phase. These findings illustrate why lipid homeostasis is such a critical cellular process. Finally, our results provide direct in vivo support for current in vitro and in silico models regarding lipid phase separation and associated protein segregation.

scholarly journals Emerging Nano-Formulations and Nanomedicines Applications for Ocular Drug Delivery

Nanomaterials ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Dawin Khiev ◽  
Zeinab A. Mohamed ◽  
Riddhi Vichare ◽  
Ryan Paulson ◽  
Sofia Bhatia ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Inorganic Nanoparticles ◽  
In Vivo Studies ◽  
Ocular Diseases ◽  
Sustained Drug Release ◽  
Blood Retinal Barrier ◽  
Vast Number ◽  
Recent Developments

Ocular diseases can deteriorate vision to the point of blindness and thus can have a major impact on the daily life of an individual. Conventional therapies are unable to provide absolute therapy for all ocular diseases due to the several limitations during drug delivery across the blood-retinal barrier, making it a major clinical challenge. With recent developments, the vast number of publications undergird the need for nanotechnology-based drug delivery systems in treating ocular diseases. The tool of nanotechnology provides several essential advantages, including sustained drug release and specific tissue targeting. Additionally, comprehensive in vitro and in vivo studies have suggested a better uptake of nanoparticles across ocular barriers. Nanoparticles can overcome the blood-retinal barrier and consequently increase ocular penetration and improve the bioavailability of the drug. In this review, we aim to summarize the development of organic and inorganic nanoparticles for ophthalmic applications. We highlight the potential nanoformulations in clinical trials as well as the products that have become a commercial reality.

Purification of the Antihemophilic Factor by Gel Filtration on Agarose

1969 ◽  
Vol 22 (03) ◽  
pp. 577-583 ◽  
Author(s):  
M.M.P Paulssen ◽  
A.C.M.G.B Wouterlood ◽  
H.L.M.A Scheffers
Keyword(s):  
Factor Viii ◽  
Plasma Proteins ◽  
Large Scale ◽  
Gel Filtration ◽  
Large Scale Preparation ◽  
Scale Preparation ◽  
Antihemophilic Factor

SummaryFactor VIII can be isolated from plasma proteins, including fibrinogen by chromatography on agarose. The best results were obtained with Sepharose 6B. Large scale preparation is also possible when cryoprecipitate is separated by chromatography. In most fractions containing factor VIII a turbidity is observed which may be due to the presence of chylomicrons.The purified factor VIII was active in vivo as well as in vitro.

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