CRISPR-Cas9 system for fungi genome engineering toward industrial applications

Author(s):  
Lakkakula Satish ◽  
Sasanala Shamili ◽  
Balasubramanian C. Muthubharathi ◽  
Stanislaus Antony Ceasar ◽  
Ariel Kushmaro ◽  
...  
2020 ◽  
Vol 20 (2) ◽  
Author(s):  
Changpyo Han ◽  
Heeun Kwon ◽  
Gyuyeon Park ◽  
Minjeong Jang ◽  
Hye-Jeong Lee ◽  
...  

ABSTRACT Yarrowia lipolytica is a non-conventional, heterothallic, oleaginous yeast with wide range of industrial applications. Increasing ploidy can improve advantageous traits for industrial applications including genetic stability, stress resistance, and productivity, but the construction of knockout mutant strains from polyploid cells requires significant effort due to the increased copy numbers of target genes. The goal of this study was to evaluate the effectiveness of a mating-type switching strategy by single-step transformation without a genetic manipulation vestige, and to optimize the conventional method for increasing ploidy (mating) in Y. lipolytica. In this study, mating-type genes in haploid Y. lipolytica cells were scarlessly converted into the opposite type genes by site-specific homologous recombination, and the resulting MATB-type cells were mated at low temperature (22°C) with addition of sodium citrate with each MATA-type haploid cell to yield a MATA/MATB-type diploid strain with genetic information from both parental strains. The results of this study can be used to increase ploidy and for whole genome engineering of a yeast strain with unparalleled versatility for industrial application.


2016 ◽  
Vol 60 (4) ◽  
pp. 337-346 ◽  
Author(s):  
Bong Hyun Sung ◽  
Donghui Choe ◽  
Sun Chang Kim ◽  
Byung-Kwan Cho

Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput ‘-omics’ research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300–500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis. Current size-reduced genomes are not perfect minimal genomes, but chemically synthesized genomes have just been constructed. Some minimal genomes provide various desirable functions for bioindustry, such as improved genome stability, increased transformation efficacy and improved production of biomaterials. The minimal genome as a chassis genome for synthetic biology can be used to construct custom-designed genomes for various practical and industrial applications.


2021 ◽  
Author(s):  
Stephanie L Brumwell ◽  
Katherine D Van Belois ◽  
Daniel J Giguere ◽  
David R Edgell ◽  
Bogumil J Karas

D. radiodurans has become an attractive microbial platform for the study of extremophile biology and industrial bioproduction. To improve the genomic manipulation and tractability of this species, the development of tools for whole genome engineering and design is necessary. Here, we report the development of a simple and robust conjugation-based transformation system from E. coli to D. radiodurans allowing for the introduction of stable, replicating plasmids expressing antibiotic resistance markers. Using this method with nonreplicating plasmids, we developed a protocol for creating sequential gene deletions in D. radiodurans by target-ing restriction-modification system genes. Importantly, we demonstrated a conjugation-based method for cloning the large (178 kb), high G+C content MP1 megaplasmid from D. radiodurans in E. coli. The conjugation-based tools described here will facili-tate the development of D. radiodurans strains with synthetic genomes for biological studies and industrial applications.


Author(s):  
C. F. Oster

Although ultra-thin sectioning techniques are widely used in the biological sciences, their applications are somewhat less popular but very useful in industrial applications. This presentation will review several specific applications where ultra-thin sectioning techniques have proven invaluable.The preparation of samples for sectioning usually involves embedding in an epoxy resin. Araldite 6005 Resin and Hardener are mixed so that the hardness of the embedding medium matches that of the sample to reduce any distortion of the sample during the sectioning process. No dehydration series are needed to prepare our usual samples for embedding, but some types require hardening and staining steps. The embedded samples are sectioned with either a prototype of a Porter-Blum Microtome or an LKB Ultrotome III. Both instruments are equipped with diamond knives.In the study of photographic film, the distribution of the developed silver particles through the layer is important to the image tone and/or scattering power. Also, the morphology of the developed silver is an important factor, and cross sections will show this structure.


Author(s):  
W.M. Stobbs

I do not have access to the abstracts of the first meeting of EMSA but at this, the 50th Anniversary meeting of the Electron Microscopy Society of America, I have an excuse to consider the historical origins of the approaches we take to the use of electron microscopy for the characterisation of materials. I have myself been actively involved in the use of TEM for the characterisation of heterogeneities for little more than half of that period. My own view is that it was between the 3rd International Meeting at London, and the 1956 Stockholm meeting, the first of the European series , that the foundations of the approaches we now take to the characterisation of a material using the TEM were laid down. (This was 10 years before I took dynamical theory to be etched in stone.) It was at the 1956 meeting that Menter showed lattice resolution images of sodium faujasite and Hirsch, Home and Whelan showed images of dislocations in the XlVth session on “metallography and other industrial applications”. I have always incidentally been delighted by the way the latter authors misinterpreted astonishingly clear thickness fringes in a beaten (”) foil of Al as being contrast due to “large strains”, an error which they corrected with admirable rapidity as the theory developed. At the London meeting the research described covered a broad range of approaches, including many that are only now being rediscovered as worth further effort: however such is the power of “the image” to persuade that the above two papers set trends which influence, perhaps too strongly, the approaches we take now. Menter was clear that the way the planes in his image tended to be curved was associated with the imaging conditions rather than with lattice strains, and yet it now seems to be common practice to assume that the dots in an “atomic resolution image” can faithfully represent the variations in atomic spacing at a localised defect. Even when the more reasonable approach is taken of matching the image details with a computed simulation for an assumed model, the non-uniqueness of the interpreted fit seems to be rather rarely appreciated. Hirsch et al., on the other hand, made a point of using their images to get numerical data on characteristics of the specimen they examined, such as its dislocation density, which would not be expected to be influenced by uncertainties in the contrast. Nonetheless the trends were set with microscope manufacturers producing higher and higher resolution microscopes, while the blind faith of the users in the image produced as being a near directly interpretable representation of reality seems to have increased rather than been generally questioned. But if we want to test structural models we need numbers and it is the analogue to digital conversion of the information in the image which is required.


Author(s):  
C J R Sheppard

The confocal microscope is now widely used in both biomedical and industrial applications for imaging, in three dimensions, objects with appreciable depth. There are now a range of different microscopes on the market, which have adopted a variety of different designs. The aim of this paper is to explore the effects on imaging performance of design parameters including the method of scanning, the type of detector, and the size and shape of the confocal aperture.It is becoming apparent that there is no such thing as an ideal confocal microscope: all systems have limitations and the best compromise depends on what the microscope is used for and how it is used. The most important compromise at present is between image quality and speed of scanning, which is particularly apparent when imaging with very weak signals. If great speed is not of importance, then the fundamental limitation for fluorescence imaging is the detection of sufficient numbers of photons before the fluorochrome bleaches.


Author(s):  
R. T. Chen ◽  
R.A. Norwood

Sol-gel processing has been used to control the structure of a material on a nanometer scale in preparing advanced ceramics and glasses. Film coating using the sol-gel process was also found to be a viable process technology in applications such as optical, porous, antireflection and hard coatings. In this study, organically modified silicate (Ormosil) coatings are applied to PET films for various industrial applications. Sol-gel materials are known to exhibit nanometer scale structures which havepreviously been characterized by small-angle X-ray scattering (SAXS), neutron scattering and light scattering. Imaging of the ultrafine sol-gel structures has also been performed using an ultrahigh resolution replica/TEM technique. The objective of this study was to evaluate the ultrafine structures inthe sol gel coatings using a direct imaging technique: atomic force microscopy (AFM). In addition, correlation of microstructures with processing parameters, coating density and other physical properties will be discussed.The materials evaluated are organically modified silicate coatings on PET film substrates. Refractive index measurement by the prism coupling method was used to assess density of the sol-gel coating.AFM imaging was performed on a Nanoscope III AFM (by Digital Instruments) using constant force mode. Solgel coating samples coated with a thin layer of Ft (by ion beam sputtering) were also examined by STM in order to confirm the structures observed in the contact type AFM. In addition, to compare the previous results, sol-gel powder samples were also prepared by ultrasonication followed by Pt/Au shadowing and examined using a JEOL 100CX TEM.


Author(s):  
G.A. Botton ◽  
C.J. Humphreys

Transition metal aluminides are of great potential interest for high temperature structural applications. Although these materials exhibit good mechanical properties at high temperature, their use in industrial applications is often limited by their intrinsic room temperature brittleness. Whilst this particular yield behaviour is directly related to the defect structure, the properties of the defects (in particular the mobility of dislocations and the slip system on which these dislocations move) are ultimately determined by the electronic structure and bonding in these materials. The lack of ductility has been attributed, at least in part, to the mixed bonding character (metallic and covalent) as inferred from ab-initio calculations. In this work, we analyse energy loss spectra and discuss the features of the near edge structure in terms of the relevant electronic states in order to compare the predictions on bonding directly with spectroscopic experiments. In this process, we compare spectra of late transition metal (TM) to early TM aluminides (FeAl and TiAl) to assess whether differences in bonding can also be detected. This information is then discussed in terms of bonding changes at grain boundaries in NiAl.


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