scholarly journals Agrobacterium-Mediated Plant Transformation: the Biology behind the “Gene-Jockeying” Tool

2003 ◽  
Vol 67 (1) ◽  
pp. 16-37 ◽  
Author(s):  
Stanton B. Gelvin
Keyword(s):  
Genetic Engineering ◽  
Plant Transformation ◽  
Plant Pathogens ◽  
Genetic Determinants ◽  
Genetic Engineer ◽  
Crop Species ◽  
The Past ◽  
Culture Transformation ◽  
Basic Biology ◽  
Host Genes

SUMMARY Agrobacterium tumefaciens and related Agrobacterium species have been known as plant pathogens since the beginning of the 20th century. However, only in the past two decades has the ability of Agrobacterium to transfer DNA to plant cells been harnessed for the purposes of plant genetic engineering. Since the initial reports in the early 1980s using Agrobacterium to generate transgenic plants, scientists have attempted to improve this “natural genetic engineer” for biotechnology purposes. Some of these modifications have resulted in extending the host range of the bacterium to economically important crop species. However, in most instances, major improvements involved alterations in plant tissue culture transformation and regeneration conditions rather than manipulation of bacterial or host genes. Agrobacterium-mediated plant transformation is a highly complex and evolved process involving genetic determinants of both the bacterium and the host plant cell. In this article, I review some of the basic biology concerned with Agrobacterium-mediated genetic transformation. Knowledge of fundamental biological principles embracing both the host and the pathogen have been and will continue to be key to extending the utility of Agrobacterium for genetic engineering purposes.

scholarly journals Adhesion GPCRs in Glioblastoma

2021 ◽  
Author(s):  
Gabriele Stephan ◽  
Niklas Ravn-Boess ◽  
Dimitris G Placantonakis
Keyword(s):  
G Protein ◽  
G Protein Coupled Receptors ◽  
The Past ◽  
Novel Treatment ◽  
The Family ◽  
Health And Disease ◽  
Basic Biology ◽  
G Protein Coupled ◽  
Potential Use ◽  
Receptor Family

Abstract Members of the adhesion family of G protein-coupled receptors (GPCRs) have received attention for their roles in health and disease, including cancer. Over the past decade, several members of the family have been implicated in the pathogenesis of glioblastoma. Here, we discuss the basic biology of adhesion GPCRs and review in detail specific members of the receptor family with known functions in glioblastoma. Finally, we discuss the potential use of adhesion GPCRs as novel treatment targets in neuro-oncology.

scholarly journals Bioactive Secondary Metabolites of the Genus Diaporthe and Anamorph Phomopsis from Terrestrial and Marine Habitats and Endophytes: 2010–2019

2021 ◽  
Vol 9 (2) ◽  
pp. 217
Author(s):  
Tang-Chang Xu ◽  
Yi-Han Lu ◽  
Jun-Fei Wang ◽  
Zhi-Qiang Song ◽  
Ya-Ge Hou ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Small Molecules ◽  
Host Plants ◽  
Plant Pathogens ◽  
Bioactive Metabolites ◽  
Drug Candidates ◽  
The Past ◽  
Marine Habitats ◽  
Bioactive Secondary Metabolites ◽  
Unidentified Species

The genus Diaporthe and its anamorph Phomopsis are distributed worldwide in many ecosystems. They are regarded as potential sources for producing diverse bioactive metabolites. Most species are attributed to plant pathogens, non-pathogenic endophytes, or saprobes in terrestrial host plants. They colonize in the early parasitic tissue of plants, provide a variety of nutrients in the cycle of parasitism and saprophytism, and participate in the basic metabolic process of plants. In the past ten years, many studies have been focused on the discovery of new species and biological secondary metabolites from this genus. In this review, we summarize a total of 335 bioactive secondary metabolites isolated from 26 known species and various unidentified species of Diaporthe and Phomopsis during 2010–2019. Overall, there are 106 bioactive compounds derived from Diaporthe and 246 from Phomopsis, while 17 compounds are found in both of them. They are classified into polyketides, terpenoids, steroids, macrolides, ten-membered lactones, alkaloids, flavonoids, and fatty acids. Polyketides constitute the main chemical population, accounting for 64%. Meanwhile, their bioactivities mainly involve cytotoxic, antifungal, antibacterial, antiviral, antioxidant, anti-inflammatory, anti-algae, phytotoxic, and enzyme inhibitory activities. Diaporthe and Phomopsis exhibit their potent talents in the discovery of small molecules for drug candidates.

scholarly journals Development of oriC-Based Plasmids for Mesoplasma florum

2017 ◽  
Vol 83 (7) ◽  
Author(s):  
Dominick Matteau ◽  
Marie-Eve Pepin ◽  
Vincent Baby ◽  
Samuel Gauthier ◽  
Mélissa Arango Giraldo ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Genetic Engineering ◽  
Genome Engineering ◽  
Antibiotic Resistance Genes ◽  
Viable Cell ◽  
Pathogenic Potential ◽  
Strong Basis ◽  
Content Type ◽  
Basic Biology

ABSTRACT The near-minimal bacterium Mesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. However, the lack of genetic engineering tools for this microorganism has limited our capacity to understand its basic biology and modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first generation of artificial plasmids able to replicate in this bacterium. Selected regions of the predicted M. florum chromosomal origin of replication (oriC) were used to create different plasmid versions that were tested for their transformation frequency and stability. Using polyethylene glycol-mediated transformation, we observed that plasmids harboring both rpmH-dnaA and dnaA-dnaN intergenic regions, interspaced or not with a copy of the dnaA gene, resulted in a frequency of ∼4.1 × 10−6 transformants per viable cell and were stably maintained throughout multiple generations. In contrast, plasmids containing only one M. florum oriC intergenic region or the heterologous oriC region of Mycoplasma capricolum, Mycoplasma mycoides, or Spiroplasma citri failed to produce any detectable transformants. We also developed alternative transformation procedures based on electroporation and conjugation from Escherichia coli, reaching frequencies up to 7.87 × 10−6 and 8.44 × 10−7 transformants per viable cell, respectively. Finally, we demonstrated the functionality of antibiotic resistance genes active against tetracycline, puromycin, and spectinomycin/streptomycin in M. florum. Taken together, these valuable genetic tools will facilitate efforts toward building an M. florum-based near-minimal cellular chassis for synthetic biology. IMPORTANCE Mesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. M. florum is closely related to the mycoides cluster of mycoplasmas, which has become a model for whole-genome cloning, genome transplantation, and genome minimization. However, M. florum shows higher growth rates than other Mollicutes, has no known pathogenic potential, and possesses a significantly smaller genome that positions this species among some of the simplest free-living organisms. So far, the lack of genetic engineering tools has limited our capacity to understand the basic biology of M. florum in order to modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first artificial plasmids and transformation methods for this bacterium. This represents a strong basis for ongoing genome engineering efforts using this near-minimal microorganism.

scholarly journals Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing

2014 ◽  
Vol 67 (2) ◽  
pp. 7247-7260 ◽  
Author(s):  
Pablo Andrés Gutiérrez Sánchez ◽  
Juan Fernando Alzate ◽  
Mauricio Marín Montoya
Keyword(s):  
Dna Sequences ◽  
454 Pyrosequencing ◽  
Plant Pathogens ◽  
Plasmodiophora Brassicae ◽  
Bioinformatic Analysis ◽  
Spongospora Subterranea ◽  
Sequencing Technologies ◽  
Intron Structure ◽  
Basic Biology

Spongospora subterranea, the causal agent of Potato powdery scab, is an important soil-borne obligate protozoan commonly found in Andean soils. This is a serious problem that causes cosmetic damage on the skin of tubers and induces root gall formation, diminishing the yield and commercial value of the potato. Genetic studies on S. subterranea are difficult due to its obligate parasitism, which explains the lack of available knowledge on its basic biology. S. subterranea is a member of the Plasmodiophorida order, a protist taxa that includes other important plant pathogens such as Plasmodiophora brassicae and Spongospora nasturtii. Little is known about the genomes of Plasmodiophorida; however, with the use of Next-Generation Sequencing technologies combined with appropriate bioinformatic techniques, it is possible to obtain genomic sequences from obligate pathogens such as S. subterranea. To gain a better understanding of the biology of this pathogen and Plasmodiophorida in general, DNA sequences from a cystosori-enriched sample of S. subterranea were obtained using 454 pyrosequencing technology. As a first step in understanding the nutritional requirements of S. subterranea as well as its infective and resistance structures, we present a bioinformatic analysis of 24 contigs related to genes involved in the glycolysis, starch, celullose and chitin metabolism. Intron structure and codon usage is also discussed. The genes analyzed in this study are a good source of information for studies aimed at characterizing these enzymes in vitro, as well as the generation of new methods for the molecular detection of S. subterranea in either soils or infected plants.

scholarly journals An Update on Molecular Tools for Genetic Engineering of Actinomycetes—The Source of Important Antibiotics and Other Valuable Compounds

Antibiotics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 494
Author(s):  
Lena Mitousis ◽  
Yvonne Thoma ◽  
Ewa M. Musiol-Kroll
Keyword(s):  
Genetic Engineering ◽  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Molecular Tools ◽  
Biosynthetic Gene Clusters ◽  
Streptomyces Antibioticus ◽  
The Past ◽  
Bioactive Agents ◽  
Valuable Compounds

The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the “actinomycetes era”, in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015–2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.

scholarly journals Extracting novel hypotheses and findings from RNA-seq data

2020 ◽  
Vol 20 (2) ◽  
Author(s):  
Tyler Doughty ◽  
Eduard Kerkhoven
Keyword(s):  
Gene Expression ◽  
Yeast Species ◽  
Rna Seq ◽  
High Quality ◽  
New Techniques ◽  
The Past ◽  
Basic Biology ◽  
Extract Information

ABSTRACT Over the past decade, improvements in technology and methods have enabled rapid and relatively inexpensive generation of high-quality RNA-seq datasets. These datasets have been used to characterize gene expression for several yeast species and have provided systems-level insights for basic biology, biotechnology and medicine. Herein, we discuss new techniques that have emerged and existing techniques that enable analysts to extract information from multifactorial yeast RNA-seq datasets. Ultimately, this minireview seeks to inspire readers to query datasets, whether previously published or freshly obtained, with creative and diverse methods to discover and support novel hypotheses.

Genetic engineering and social justice: A reflection on Amartya Sen’s capability approach

2020 ◽  
pp. 205789112090768
Author(s):  
Gerry F Arambala
Keyword(s):  
Developing Countries ◽  
Genetic Engineering ◽  
Health Care Services ◽  
Medical Science ◽  
Sub Saharan Africa ◽  
Poor People ◽  
Positive Health ◽  
Social Phenomena ◽  
The Past ◽  
Sub Saharan

Over the past decades, biomedical researchers have made great progress in finding the treatment for many diseases which have been considered in the past as incurable. The struggle for longevity and positive health has been addressed by medical science. People who can afford it are assured by the promise of genetic engineering. But while there has been considerable development in the treatment of diseases, the number of mortalities in poor countries remains high, especially in Sub-Saharan Africa and East Asia. Around 8 million people die each year worldwide due to poverty-related health issues. Despite the advancement in the treatment of diseases, poor people in most of the developing countries worldwide are dying each year. This article will argue that human poverty and the existence of infectious diseases are inseparable social phenomena that affect the fate of the poor in developing countries. Following Amartya Sen, this article will argue that access to advanced health care services should be affordable to all, and should form part of individual freedoms that the national policies of a country must secure.

Genetic engineering of crop plants: from genome to gene

1997 ◽  
Vol 33 (01) ◽  
pp. 15-33 ◽  
Author(s):  
B. P. Forster ◽  
M. A. Lee ◽  
U. Lundqvist ◽  
S. Millam ◽  
K. Vamling ◽  
...  
Keyword(s):  
Genetic Engineering ◽  
Plant Breeding ◽  
Crop Plants ◽  
Trade Routes ◽  
The Past ◽  
Naturally Occurring ◽  
New Ideas ◽  
New Varieties ◽  
Transitional Phase ◽  
Selection Of

Genetic engineering of crop plants has been in progress since the dawn of agriculture, about 10 000 years ago. For millennia the genetic make-up of our crop plants has been changed by mankind's selection of naturally occurring variants. As the trade routes were developed, novel plant types were introduced into new environments and provided more variation from which to choose. At the end of the nineteenth century an understanding of the laws of heredity was gained and plant breeding protocols were devised whereby selection became accompanied by deliberate crossing. As the knowledge of the genetic structure of crop plants improved, new ways of manipulation were invented and exploited. Indeed plant breeding became a testing bed for new ideas in genetics. For the plant breeder the techniques which were most widely employed in the past were those which aided breeding, for example techniques which speeded up the production of new varieties, but still used traditional routes of crossing and selection. This was a transitional phase between plant breeding as an art and plant breeding as a science.

scholarly journals Cell and animal models of mtDNA biology: progress and prospects

2007 ◽  
Vol 292 (2) ◽  
pp. C658-C669 ◽  
Author(s):  
Shaharyar M. Khan ◽  
Rafal M. Smigrodzki ◽  
Russell H. Swerdlow
Keyword(s):  
Gene Therapy ◽  
Animal Models ◽  
Human Disease ◽  
Mitochondrial Genetics ◽  
Mtdna Mutation ◽  
Mtdna Mutations ◽  
The Past ◽  
The Future ◽  
Basic Biology ◽  
Over Time

The past two decades have witnessed an evolving understanding of the mitochondrial genome’s (mtDNA) role in basic biology and disease. From the recognition that mutations in mtDNA can be responsible for human disease to recent efforts showing that mtDNA mutations accumulate over time and may be responsible for some phenotypes of aging, the field of mitochondrial genetics has greatly benefited from the creation of cell and animal models of mtDNA mutation. In this review, we critically discuss the past two decades of efforts and insights gained from cell and animal models of mtDNA mutation. We attempt to reconcile the varied and at times contradictory findings by highlighting the various methodologies employed and using human mtDNA disease as a guide to better understanding of cell and animal mtDNA models. We end with a discussion of scientific and therapeutic challenges and prospects for the future of mtDNA transfection and gene therapy.

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