"central to many contemporary areas of modern biology and medicine. In a conventional molecular cloning experiment, the DNA to be cloned is obtained from an organism of interest, then treated with enzymes in the test tube to generate smaller DNA fragments. Subsequently, these fragments are then combined with vector DNA to generate recombinant DNA molecules. The recombinant DNA is then introduced into a host organism (typically an easy-to-grow, benign, laboratory strain of ""E. coli"" bacteria). This will generate a population of organisms in which recombinant DNA molecules are replicated along with the host DNA. Because they contain foreign DNA fragments,"
"common, gram-negative gut bacterium which can be grown and cultured easily and inexpensively in a laboratory setting. It is the most widely used organism in molecular genetics, and is an important species in the fields of biotechnology and microbiology, where it has served as the host organism for the majority of work with recombinant DNA. Simple model eukaryotes include baker's yeast (""Saccharomyces cerevisiae"") and fission yeast (""Schizosaccharomyces pombe""), both of which share many characters with higher cells, including those of humans. For instance, many cell division genes that are critical for the development of cancer have been discovered in yeast."
"the products to be as ready for human consumption as possible. Yeasts are common hosts for the production of proteins from recombinant DNA. They offer relatively easy genetic manipulation and rapid growth to high cell densities on inexpensive media. As eukaryotes, they are able to perform protein modifications like glycosylation which are common in eukaryotic cells, but relatively rare in bacteria. Due to this, yeast can produce complex proteins that are identical or very similar to native products from plants or mammals. The first yeast expression platform was based on the baker’s yeast ""Saccharomyces cerevisiae"". However since then a variety"
"each of the tested host animals. It is one of the most ubiquitous members of the mammalian gut microbiota. In a related discovery, each host seems to have a host-specific strain of ""L. reuteri"", e.g. a rat strain for rats, a pig strain for pigs, etc. The universality of ""L. reuteri"", in conjunction with this evolved host-specificity, led scientists to make inferences about its importance in promoting the health of the host organism. ""L. reuteri"" is marketed by Swedish company BioGaia AB, which owns patents on several strains as well as other patents regarding commercial usage of ""L. reuteri"". ""L."
"the laboratory, such as restriction digests and the polymerase chain reaction. Modern biology and biochemistry make intensive use of these techniques in recombinant DNA technology. Recombinant DNA is a man-made DNA sequence that has been assembled from other DNA sequences. They can be transformed into organisms in the form of plasmids or in the appropriate format, by using a viral vector. The genetically modified organisms produced can be used to produce products such as recombinant proteins, used in medical research, or be grown in agriculture. Forensic scientists can use DNA in blood, semen, skin, saliva or hair found at a"
"an active promoter becomes located next to a previously silent host cell gene, or when a host cell gene that functions to restrain gene expression undergoes insertional inactivation by recombinant DNA. Recombinant DNA is widely used in biotechnology, medicine and research. Today, recombinant proteins and other products that result from the use of DNA technology are found in essentially every western pharmacy, doctor's or veterinarian's office, medical testing laboratory, and biological research laboratory. In addition, organisms that have been manipulated using recombinant DNA technology, as well as products derived from those organisms, have found their way into many farms, supermarkets,"
"avoid cross-contamination of utensils and work spaces when preparing food. Because of its long history of laboratory culture and ease of manipulation, ""E. coli"" plays an important role in modern biological engineering and industrial microbiology. The work of Stanley Norman Cohen and Herbert Boyer in ""E. coli"", using plasmids and restriction enzymes to create recombinant DNA, became a foundation of biotechnology. ""E. coli"" is a very versatile host for the production of heterologous proteins, and various protein expression systems have been developed which allow the production of recombinant proteins in ""E. coli"". Researchers can introduce genes into the microbes using"
"""A. thaliana"" was the first plant to have its genome sequenced. Among vertebrates, guinea pigs (""Cavia porcellus"") were used by Robert Koch and other early bacteriologists as a host for bacterial infections, becoming a byword for ""laboratory animal,"" but are less commonly used today. The classic model vertebrate is currently the mouse (""Mus musculus""). Many inbred strains exist, as well as lines selected for particular traits, often of medical interest, e.g. body size, obesity, muscularity, and voluntary wheel-running behavior. The rat (""Rattus norvegicus"") is particularly useful as a toxicology model, and as a neurological model and source of primary cell"
"all the prokaryotes in the human gut. In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion. Archaean communities also associate with a range of other organisms, such as on the surface of corals, and in the region of soil that surrounds plant roots (the rhizosphere). Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of enzymes that function under these harsh conditions. These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA"
"these are transgenic or genetically modified microorganisms (GMO). This process takes advantage of the fact that a single bacterial cell can be induced to take up and replicate a single recombinant DNA molecule. This single cell can then be expanded exponentially to generate a large amount of bacteria, each of which contain copies of the original recombinant molecule. Thus, both the resulting bacterial population, and the recombinant DNA molecule, are commonly referred to as ""clones"". Strictly speaking, ""recombinant DNA"" refers to DNA molecules, while ""molecular cloning"" refers to the experimental methods used to assemble them. The idea arose that different"
"great tools for scientists looking to study gene function and evolution. Most DNA manipulation takes place within bacterial plasmids before being transferred to another host. Bacteria are the simplest model organism and most of our early understanding of molecular biology comes from studying ""Escherichia coli"". Scientist can easily manipulate and combine genes within the bacteria to create novel or disrupted proteins and observe the effect this has on various molecular systems. Researchers have combined the genes from bacteria and archaea, leading to insights on how these two diverged in the past. In the field of synthetic biology, they have been"
"genetics and biotechnology labs, where they are commonly used to clone and amplify (make many copies of) or express particular genes. A wide variety of plasmids are commercially available for such uses. The gene to be replicated is normally inserted into a plasmid that typically contains a number of features for their use. These include a gene that confers resistance to particular antibiotics (ampicillin is most frequently used for bacterial strains), an origin of replication to allow the bacterial cells to replicate the plasmid DNA, and a suitable site for cloning (referred to as a multiple cloning site). Plasmids are"
"home medicine cabinets, and even pet shops, such as those that sell GloFish and other genetically modified animals. The most common application of recombinant DNA is in basic research, in which the technology is important to most current work in the biological and biomedical sciences. Recombinant DNA is used to identify, map and sequence genes, and to determine their function. rDNA probes are employed in analyzing gene expression within individual cells, and throughout the tissues of whole organisms. Recombinant proteins are widely used as reagents in laboratory experiments and to generate antibody probes for examining protein synthesis within cells and"
"major research tool in the early development of molecular biology. The genetic code, the function of ribozymes, the first recombinant DNA and early genetic libraries were all arrived at using bacteriophages. Certain genetic elements derived from viruses, such as highly effective promoters, are commonly used in molecular biology research today. Growing animal viruses outside of the living host animal is more difficult. Classically, fertilized chicken eggs have often been used, but cell cultures are increasingly employed for this purpose today. Since some viruses that infect eukaryotes need to transport their genetic material into the host cell's nucleus, they are attractive"
"Cohen and Herbert Boyer in ""E. coli"", using plasmids and restriction enzymes to create recombinant DNA, became a foundation of biotechnology. Considered a very versatile host for the production of heterologous proteins, researchers can introduce genes into the microbes using plasmids, allowing for the mass production of proteins in industrial fermentation processes. Genetic systems have also been developed which allow the production of recombinant proteins using ""E. coli"". One of the first useful applications of recombinant DNA technology was the manipulation of ""E. coli"" to produce human insulin. Modified ""E. coli"" have been used in vaccine development, bioremediation, and production"
"self-replicating microbe, dubbed Mycoplasma laboratorium. Twist Bioscience developed a silicon-based manufacturing process to industrialize the production of synthetic DNA. By synthesizing DNA on silicon instead of on traditional plastic plates, cost-effective, high-quality synthesis of genes, gene fragments, oligo pools and variant libraries (groups of gene sequences) for antibody and protein engineering, as well as consumable products for next-generation sequencing is enabled. Oligonucleotide synthesis is the chemical synthesis of sequences of nucleic acids. The process has been automated since the late 1970s and can be used to form desired genetic sequences as well as for other uses in medicine and molecular"
"Genetically modified bacteria Genetically modified bacteria were the first organisms to be modified in the laboratory, due to their simple genetics. These organisms are now used for several purposes, and are particularly important in producing large amounts of pure human proteins for use in medicine. The first example of this occurred in 1978 when Herbert Boyer, working at a University of California laboratory, took a version of the human insulin gene and inserted into the bacterium ""Escherichia coli"" to produce synthetic ""human"" insulin. Four years later, it was approved by the U.S. Food and Drug Administration. The drug industry has"
"chromosomes. This ease made them important tools for the creation of other GMOs. Genes and other genetic information from a wide range of organisms can be added to a plasmid and inserted into bacteria for storage and modification. Bacteria are cheap, easy to grow, clonal, multiply quickly, are relatively easy to transform, and can be stored at −80 °C almost indefinitely. Once a gene is isolated it can be stored inside the bacteria, providing an unlimited supply for research. The large number of custom plasmids make manipulating DNA excised from bacteria relatively easy. Their ease of use has made them"
"Bacteriophage A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria and archaea. The term was derived from ""bacteria"" and the Greek φαγεῖν (""phagein""), ""to devour"". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have relatively simple or elaborate structures. Their genomes may encode as few as four genes and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous"
"The resulting bacterium, named Mycoplasma laboratorium, could replicate and produce proteins. Four years later this was taken a step further when a bacterium was developed that replicated a plasmid containing a unique base pair, creating the first organism engineered to use an expanded genetic alphabet. In 2012, Jennifer Doudna and Emmanuelle Charpentier collaborated to develop the CRISPR/Cas9 system, a technique which can be used to easily and specifically alter the genome of almost any organism. Creating a GMO is a multi-step process. Genetic engineers must first choose what gene they wish to insert into the organism. This is driven by"
"fusion product to the secretion signal of the α-mating factor from ""Saccharomyces cerevisiae"" (baker's yeast). This causes the protein to be secreted into the growth medium, which greatly facilitates subsequent protein purification. Some commercially available plasmids have these features incorporated (such as the pPICZα vector). ""Pichia pastoris"" was used for the production of over 500 biotherapeutics like interferon gamma. However, one drawback of this protein expression system is the over-glycosylation with high mannose structure which is a potential cause of immunogenicity. In standard molecular biology research, the bacterium ""Escherichia coli"" is the most frequently used organism for production of recombinant"
"Recombineering Recombineering (recombination-mediated genetic engineering) is a genetic and molecular biology technique based on homologous recombination systems, as opposed to the older/more common method of using restriction enzymes and ligases to combine DNA sequences in a specified order. Recombineering is widely used for bacterial genetics, in the generation of target vectors for making a conditional mouse knockout, and for modifying DNA of any source often contained on a bacterial artificial chromosome (BAC), among other applications. Although developed in bacteria, much of the inspiration for recombineering techniques came from methods first developed in Saccharomyces cerevisiae where a linear plasmid was used"
"The yeasts brewer's yeast (""Saccharomyces cerevisiae"") and fission yeast (""Schizosaccharomyces pombe"") are important model organisms in science, since they are simple eukaryotes that can be grown rapidly in large numbers and are easily manipulated. They are particularly valuable in genetics, genomics and proteomics, for example in protein production. The easily cultured gut bacterium ""Escherichia coli"", a prokaryote, is similarly widely used as a model organism. Microbes can form an endosymbiotic relationship with larger organisms. For example, the bacteria that live within the human digestive system contribute to human health through gut immunity, the synthesis of vitamins such as folic acid"
"a net to visualize the rich exchange and cooperative effects of HGT among microbes."" Modern biotechnology is challenging traditional concepts of organism and species. Cloning is the process of creating a new multicellular organism, genetically identical to another, with the potential of creating entirely new species of organisms. Cloning is the subject of much ethical debate. In 2008, the J. Craig Venter Institute assembled a synthetic bacterial genome, ""Mycoplasma genitalium"", by using recombination in yeast of 25 overlapping DNA fragments in a single step. ""The use of yeast recombination greatly simplifies the assembly of large DNA molecules from both synthetic"
"the human microbiome, describing the ability of human-associated microbes to produce thiopeptide antibiotics. The Fischbach lab discovered that the gut commensal Bacteroides fragilis produces the immune modulatory sphingolipid alpha-galactosylceramide, showed that the production of neurotransmitters is common among commensal gut bacteria, and discovered the biosynthetic pathway for a common class of bile acids produced by gut bacteria. Fischbach’s lab developed an algorithm, ClusterFinder, that automates the process of identifying biosynthetic genes for small molecules in bacterial genome sequences. With Marnix Medema, he co-developed a second algorithm for identifying biosynthetic gene clusters, antiSMASH, with which ClusterFinder has been merged. Fischbach is"
"production and act as molecular vehicles to transfer DNA to complex organisms such as plants and animals. Scientists have also exploited their knowledge of microbes to produce biotechnologically important enzymes such as Taq polymerase, reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system. Bacteria can be used for the industrial production of amino acids. ""Corynebacterium glutamicum"" is one of the most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine. Since some bacteria have the ability to synthesize antibiotics,"
"are used, too, to form organic acids in pickles and vinegar. Biotechnology bacteria the use of microorganisms including bacteria and fungi in the manufacturing and services industries. These include chemical manufacturing such as ethanol, acetone, organic acid, enzymes, and perfumes. In the chemical industry, bacteria are most important in the production of pharmaceuticals. ""Escherichia coli"" is used for commercial preparation of riboflavin and vitamin K. Genetic engineering is the manipulation of genes. It is also called recombinant DNA technology. In genetic engineering, pieces of DNA (genes) are introduced into a host by a variety of techniques, one of the earliest"
"be encoded in the host nucleus as these endosymbionts are acquiring an organelle-like status in a similar way to mitochondria and chloroplasts. The team started with the bacterium ""M. genitalium"", an obligate intracellular parasite whose genome consists of 482 genes comprising 582,970 base pairs, arranged on one circular chromosome (the smallest genome of any known natural organism that can be grown in free culture). They then systematically removed genes to find a minimal set of 382 genes that can sustain life. This effort was also known as the Minimal Genome Project. The team intends to synthesize chromosome DNA sequences consisting"
"that live in the digestive tracts of humans and other animals. The gut metagenome is the aggregate of all the genomes of gut microbiota. The gut is one niche that human microbiota inhabit. In humans, the gut microbiota has the largest numbers of bacteria and the greatest number of species compared to other areas of the body. In humans the gut flora is established at one to two years after birth, and by that time the intestinal epithelium and the intestinal mucosal barrier that it secretes have co-developed in a way that is tolerant to, and even supportive of, the"
"reproductive process involving DNA transfer from one bacterium to another through the intervening medium, and the integration of the donor sequence into the recipient genome by homologous recombination. ""S. aureus"" was found to be capable of natural genetic transformation, but only at low frequency under the experimental conditions employed. Further studies suggested that the development of competence for natural genetic transformation may be substantially higher under appropriate conditions, yet to be discovered. In humans, ""S. aureus"" is not part of the normal microbiota present in the upper respiratory tract, rather it is a colonization and on skin and in the"
"validation of genes prediction, structure, expression. Thus, by combining the two approaches it is possible to have a more complete representation of bacterial transcriptome. The gut microbiome has emerged in recent years as an important player in human health. Its prevalent functions are related to the fermentation of indigestible food components, competitions with pathogen, strengthening of the intestinal barrier, stimulation and regulation of the immune system. Although much has been learnt about the microbiome community in the last years, the wide diversity of microorganisms and molecules in the gut requires new tools to enable new discoveries. By focusing on the"
"made via recombinant DNA. Sometimes referred to as rHI, under the trade name Humulin, was developed by Genentech, but licensed to Eli Lilly and Company, who manufactured and marketed it starting in 1982. Major kinds of biopharmaceuticals include: Research and development investment in new medicines by the biopharmaceutical industry stood at $65.2 billion in 2008. A few examples of biologics made with recombinant DNA technology include: Many vaccines are grown in tissue cultures. Viral gene therapy involves artificially manipulating a virus to include a desirable piece of genetic material. With the expiration of numerous patents for blockbuster biologics between 2012"
"Gut flora Gut flora, or gut microbiota, or gastrointestinal microbiota, is the complex community of microorganisms that live in the digestive tracts of humans and other animals, including insects. The gut metagenome is the aggregate of all the genomes of gut microbiota. The gut is one niche that human microbiota inhabit. In humans, the gut microbiota has the largest numbers of bacteria and the greatest number of species compared to other areas of the body. In humans, the gut flora is established at one to two years after birth, by which time the intestinal epithelium and the intestinal mucosal barrier"