DNA - Genes - Genetics

Deoxyribonucleic Acid



DNA is a molecule that carries the genetic instructions for growth, development, functioning and reproduction, and delivers the information in the Correct Time and Sequence. All known living organisms and many viruses have DNA. All 6 billion A, C, G and T letters provides precise instructions for how our bodies are built, and how they work. Every living thing exists because the translational system receives messages from DNA delivered to it by RNA and translates the messages into proteins. The system centers on a cellular machine called the ribosome, which is made of multiple large molecules of RNA and protein and is ubiquitous in life as we know it. DNA and RNA are nucleic acids; alongside proteins, lipids and complex carbohydrates (polysaccharides), they are one of the four major types of macromolecules that are essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix, which refers to the structure formed by double-stranded molecules of nucleic acids such as DNA, which contains the instructions for life, encoded within genes. Within all cells, DNA is organized into very long lengths known as chromosomes. In animal and plant cells these are double-ended, like pieces of string or shoelaces, but in bacteria they are circular. Whether stringy or circular, these long chromosomes must be organized and packaged inside a cell so that the genes can be switched on or off when they are required. Hydrogen Bonds. In every human cell, all of the body's blueprints and instructions are stored in the form of DNA inside the nucleus. Molecules that need to travel in and out of the nucleus -- to turn genes on or off or retrieve information -- do so through passageways called nuclear pore complexes (NPCs). Traffic through these NPCs must be tightly controlled in order to prevent DNA hijacking by viruses or faulty functioning as in cancer. To travel through NPCs, many molecules must be attached to proteins called transport factors (TFs), which act as shuttles that the NPC recognizes. But the NPC faces a challenge: It must accurately recognize and bind to TFs to let them through without admitting unwanted traffic, but it must let them through quickly -- in a matter of milliseconds -- in order for the cell to be able to do its duties. Proteins known to accurately bind to specific molecules, like antibodies, normally stay stuck to their targets for periods of up to months. DNA diversity - Damage - Repair. 

Image of DNA (photo) - Gene Editing (Crispr) - Genetic Modification - Gene Therapy - Replication - Regeneration

G-A-C-T stands for the chemicals Adenine, Thymine, Guanine, and Cytosine. An easy way to remember these 4 letters is to visualize looking at a tag on a shirt. CTAG or See Tag, the Fabric Tag that has the instructions and materials list. Glossary.

Mitochondrial DNA - Epigenetics - Replication - Twins - We are all the Same

The DNA molecule is based on the Golden Ratio. It measures 34 angstroms long by 21 angstroms wide for each full cycle of its double helix spiral. 34 and 21, of course, are numbers in the Fibonacci series and their ratio, 1.6190476 closely approximates phi, 1.6180339. DNA is a Linear Script. Linear a continuous long line involving a single dimension. Non-Coding DNA.

Genetic Code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells. Translation is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The code defines how sequences of nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in human mitochondria) exist. While the "genetic code" determines a protein's amino acid sequence, other genomic regions determine when and where these proteins are produced according to various "gene regulatory codes".

Machine Code - Memory Proteins - DNA animations by wehi.tv for Science-Art exhibition (youtube)

Gene is a sequence of nucleotides in DNA or RNA that encodes the synthesis of a gene product, either RNA or protein. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or the number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life. Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotypical traits. Usage of the term "having a gene" (e.g., "good genes," "hair colour gene") typically refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection / survival of the fittest and genetic drift of the alleles. The concept of gene continues to be refined as new phenomena are discovered. For example, regulatory regions of a gene can be far removed from its coding regions, and coding regions can be split into several exons. Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression. Hox Gene - Transcription.

The Molecular Basis of Life (youtube) - These animations show cellular biology on the molecular scale. The structure of chromatin, the processes of transcription, translation, DNA replication, and cell division are shown. All animations are scientifically accurate and derived from molecular biology and crystallography research.

Genome for a human contains about 3 billion bases and about 20,000 genes on 23 pairs of chromosomes. The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. The order, or sequence, of these bases determines what biological instructions are contained in a strand of DNA. For example, the sequence ATCGTT might instruct for blue eyes, while ATCGCT might instruct for brown. The complete DNA instruction book, or genome, for a human contains about 3 billion bases and about 20,000 genes on 23 pairs of chromosomes. DNA contains the instructions needed for an organism to develop, survive and reproduce. To carry out these functions, DNA sequences must be converted into messages that can be used to produce proteins, which are the complex molecules that do most of the work in our bodies. Each DNA sequence that contains instructions to make a protein is known as a gene. The size of a gene may vary greatly, ranging from about 1,000 bases to 1 million bases in humans. Genes only make up about 1 percent of the DNA sequence. DNA sequences outside this 1 percent are involved in regulating when, how and how much of a protein is made. DNA's instructions are used to make proteins in a two-step process. First, enzymes read the information in a DNA molecule and transcribe it into an intermediary molecule called messenger ribonucleic acid, or mRNA. Next, the information contained in the mRNA molecule is translated into the "language" of amino acids, which are the building blocks of proteins. This language tells the cell's protein-making machinery the precise order in which to link the amino acids to produce a specific protein. This is a major task because there are 20 types of amino acids, which can be placed in many different orders to form a wide variety of proteins.

3 Billion Base Pairs encoding almost 30,000 Genes in every cell nucleus. The human genome of Homo sapiens is stored on 23 chromosome pairs. 22 of these are autosomal chromosome pairs, while the remaining pair is sex-determining. The haploid human genome occupies a total of just over 3 billion DNA base pairs that means 6 billion base pairs per diploid cell. DNA base pairs form the "rungs" of the twisted, ladder-shaped DNA molecules. only about 1.5% of the genome codes for proteins, while the rest consists of non-coding RNA genes, regulatory sequences, introns, and noncoding DNA (once known as "junk DNA").

Base Pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes. Intramolecular base pairs can occur within single-stranded nucleic acids. This is particularly important in RNA molecules (e.g., transfer RNA), where Watson-Crick base pairs (guanine-cytosine and adenine-uracil) permit the formation of short double-stranded helices, and a wide variety of non-Watson-Crick interactions (e.g., G-U or A-A) allow RNAs to fold into a vast range of specific three-dimensional structures. In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code. The size of an individual gene or an organism's entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres). The haploid human genome (23 chromosomes) is estimated to be about 3.2 billion bases long and to contain 20,000–25,000 distinct protein-coding genes. A kilobase (kb) is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 × 1037 and weighs 50 billion tonnes. In comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC (trillion tons of carbon).

Nucleobase are nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides; all which are monomers that are the basic building blocks of nucleic acids. Often simply called bases, as in the field of genetics, the ability of nucleobases to form base-pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). We all have three billion bases, or individual pieces, of DNA in every cell. Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary or canonical. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are identical excepting that T includes a methyl group that U lacks.

Nucleotide are organic molecules that serve as the monomer units for forming the nucleic acid polymers DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), both of which are essential biomolecules in all life-forms on Earth. Nucleotides are the building blocks of nucleic acids; they are composed of three subunit molecules: a nitrogenous base, a five-carbon sugar (ribose or deoxyribose), and at least one phosphate group. They are also known as phosphate nucleotides. A nucleoside is a nitrogenuous base and a 5-carbon sugar. Thus a nucleoside plus a phosphate group yields a nucleotide. Nucleotides also play a central role in life-form metabolism at the fundamental, cellular level. They carry packets of chemical energy—in the form of the nucleoside triphosphates ATP, GTP, CTP and UTP—throughout the cell to the many cellular functions that demand energy, which include synthesizing amino acids, proteins and cell membranes and parts; moving the cell and moving cell parts, both internally and intercellularly; dividing the cell, etc. In addition, nucleotides participate in cell signaling (cGMP and cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+). In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to yield radionucleotides.

Human Genome is the complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization creates a zygote) consist of three billion DNA base pairs, while diploid genomes (found in somatic cells) have twice the DNA content. While there are significant differences among the genomes of human individuals (on the order of 0.1%), these are considerably smaller than the differences between humans and their closest living relatives, the chimpanzees (approximately 4%) and bonobos. The Human Genome Project produced the first complete sequences of individual human genomes, with the first draft sequence and initial analysis being published on February 12, 2001. The human genome was the first of all vertebrates to be completely sequenced. As of 2012, thousands of human genomes have been completely sequenced, and many more have been mapped at lower levels of resolution. The resulting data are used worldwide in biomedical science, anthropology, forensics and other branches of science. There is a widely held expectation that genomic studies will lead to advances in the diagnosis and treatment of diseases, and to new insights in many fields of biology, including human evolution. Although the sequence of the human genome has been (almost) completely determined by DNA sequencing, it is not yet fully understood. Most (though probably not all) genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and RNA products. Recent results suggest that most of the vast quantities of noncoding DNA within the genome have associated biochemical activities, including regulation of gene expression, organization of chromosome architecture, and signals controlling epigenetic inheritance. There are an estimated 19,000-20,000 human protein-coding genes. The estimate of the number of human genes has been repeatedly revised down from initial predictions of 100,000 or more as genome sequence quality and gene finding methods have improved, and could continue to drop further. Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA molecules, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined. In June 2016, scientists formally announced HGP-Write, a plan to synthesize the human genome.

Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism).

Genome in modern molecular biology and genetics, the genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes, (the coding regions), the noncoding DNA and the genomes of the mitochondria and chloroplasts.

Gene is a sequence of nucleotides in DNA or RNA that encodes the synthesis of a gene product, either RNA or protein. Gene Expression (hereditary traits).

Genetics is the study of genes, genetic variation, and heredity in living organisms. Longevity.

Geneticist is a biologist who studies genetics, the science of genes, heredity, and variation of organisms.

Genomicist is a scientist whose specialty is genomics.

Molecular Genetics is the field of biology that studies the structure and function of genes at a molecular level and thus employs methods of both molecular biology and genetics. The study of chromosomes and gene expression of an organism can give insight into heredity, genetic variation, and mutations. This is useful in the study of developmental biology and in understanding and treating genetic diseases.

Tiny Machines - Promotor - Symmetry (math)

Purine is a heterocyclic aromatic organic compound that consists of a pyrimidine ring fused to an imidazole ring. Purine gives its name to the wider class of molecules, purines, which include substituted purines and their tautomers, are the most widely occurring nitrogen-containing heterocycle in nature. Purine is water soluble.

Pyrimidine is an aromatic heterocyclic organic compound similar to pyridine. One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has the nitrogen atoms at positions 1 and 3 in the rings.

Helicase are a class of enzymes vital to all living organisms. Their main function is to unpackage an organism's genes. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands (i.e., DNA, RNA, or RNA-DNA hybrid) using energy derived from ATP hydrolysis. There are many helicases resulting from the great variety of processes in which strand separation must be catalyzed. Approximately 1% of eukaryotic genes code for helicases. The human genome codes for 95 non-redundant helicases: 64 RNA helicases and 31 DNA helicases. Many cellular processes, such as DNA replication, transcription, translation, recombination, DNA repair, and ribosome biogenesis involve the separation of nucleic acid strands that necessitates the use of helicases.

Histone are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA). For example, each human diploid cell (containing 23 pairs of chromosomes) has about 1.8 meters of DNA, but wound on the histones it has about 90 micrometers (0.09 mm) of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes.

Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein, and RNA. The primary functions of chromatin are 1) to package DNA into a more compact, denser shape, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells (cells with defined nuclei). Prokaryotic cells have a different organization of their DNA (the prokaryotic chromosome equivalent is called genophore and is localized within the nucleoid region).

Nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. This structure is often compared to thread wrapped around a spool.

Nuclear DNA is the DNA contained within each cell nucleus of a eukaryotic organism. Nuclear DNA encodes for the majority of the genome in eukaryotes, with mitochondrial DNA and plastid DNA coding for the rest. Nuclear DNA adheres to Mendelian inheritance, with information coming from two parents, one male and one female, rather than matrilineally (through the mother) as in mitochondrial DNA. Nuclear DNA is a nucleic acid, a polymeric biomolecule or biopolymer, found in the nucleus of eukaryotic organisms.

Translation

Ribosome is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules. Ribosomes consist of two major components: the small ribosomal subunits, which read the RNA, and the large subunits, which join amino acids to form a polypeptide chain. Each subunit comprises one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins (r-protein or rProtein). The ribosomes and associated molecules are also known as the translational apparatus. Enzymes (catalysis) - Epigenetics - Transcription.

Translation in genetics is the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm. Determine the amino-acid sequence of a protein during its synthesis by using information on the messenger RNA. Language Translation.

Translation in biology is the process in which ribosomes in the cytoplasm or ER synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression. In translation, messenger RNA (mRNA) is decoded in a ribosome to produce a specific amino acid chain, or polypeptide. The polypeptide later folds into an active protein and performs its functions in the cell. The ribosome facilitates decoding by inducing the binding of complementary tRNA anticodon sequences to mRNA codons. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome. Translation proceeds in three phases: Initiation: The ribosome assembles around the target mRNA. The first tRNA is attached at the start codon. Elongation: The tRNA transfers an amino acid to the tRNA corresponding to the next codon. The ribosome then moves (translocates) to the next mRNA codon to continue the process, creating an amino acid chain. The three phases of translation initiation polymerase binds to the DNA strand and moves along until the small ribosomal subunit binds to the DNA. Elongation is initiated when the large subunit attaches and termination end the process of elongation. Termination: When a stop codon is reached, the ribosome releases the polypeptide.

Chromatid is one copy of a newly copied chromosome which is still joined to the original copy by a single centromere. Before replication, one chromosome is composed of one DNA molecule. Following replication, each chromosome is composed of two DNA molecules; in other words, DNA replication itself increases the amount of DNA but does not increase the number of chromosomes. The two identical copies—each forming one half of the replicated chromosome—are called chromatids. During the later stages of cell division these chromatids separate longitudinally to become individual chromosomes. Chromatid pairs are normally genetically identical, and said to be homozygous; however, if mutation(s) occur, they will present slight differences, in which case they are heterozygous. The pairing of chromatids should not be confused with the ploidy of an organism, which is the number of homologous versions of a chromosome. Chromonema is the fibre-like structure in prophase in the primary stage of DNA condensation. In metaphase, they are called chromatids.

Kinetochore is a protein structure on chromatids where the spindle fibers attach during cell division to pull sister chromatids apart. Their proteins help to hold the sister chromatids together and also play a role in chromosome editing. The kinetochore forms in eukaryotes, assembles on the centromere and links the chromosome to microtubule polymers from the mitotic spindle during mitosis and meiosis.

Polynucleotide molecule is a biopolymer composed of 13 or more nucleotide monomers covalently bonded in a chain. DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are examples of polynucleotides with distinct biological function.

Replication

DNA Replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. This process occurs in all living organisms and is the basis for biological inheritance. The cell possesses the distinctive property of division, which makes replication of DNA essential. How one cell builds an entire organism. Every cell in a developing embryo carries within it a copy of the organism's complete genome. Like construction workers using only the relevant portion of a blueprint when laying a building's foundation, cells must express the necessary genes at the appropriate time for the embryo to develop correctly. DNA is made up of a double helix of two complementary strands. During replication, these strands are separated. Each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication. In a cell, DNA replication begins at specific locations, or origins of replication, in the genome. Unwinding of DNA at the origin and synthesis of new strands, accommodated by an enzyme known as helicase, results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the replication fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each (template) strand. DNA replication occurs during the S-stage of interphase. DNA replication (DNA amplification) can also be performed in vitro (artificially, outside a cell). DNA polymerases isolated from cells and artificial DNA primers can be used to initiate DNA synthesis at known sequences in a template DNA molecule. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and transcription-mediated amplification (TMA) are examples.

Mutations - DNA Repair - Cell Division - Molecular Machines

DNA Polymerase is an enzyme that synthesizes DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential for DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones. Every time a cell divides, DNA polymerases are required to help duplicate the cell's DNA, so that a copy of the original DNA molecule can be passed to each daughter cell. In this way, genetic information is passed down from generation to generation. The main function of DNA polymerase is to synthesize DNA from deoxyribonucleotides, the building blocks of DNA. The DNA copies are created by the pairing of nucleotides to bases present on each strand of the original DNA molecule. This pairing always occurs in specific combinations, with cytosine along with guanine, and thymine along with adenine, forming two separate pairs, respectively. By contrast, RNA polymerases synthesize RNA from ribonucleotides from either RNA or DNA. Before replication can take place, an enzyme called helicase unwinds the DNA molecule from its tightly woven form, in the process breaking the hydrogen bonds between the nucleotide bases. This opens up or "unzips" the double-stranded DNA to give two single strands of DNA that can be used as templates for replication. The function of DNA polymerase is not quite perfect, with the enzyme making about one mistake for every billion base pairs copied. Error correction is a property of some, but not all DNA polymerases. This process corrects mistakes in newly synthesized DNA. When an incorrect base pair is recognized, DNA polymerase moves backwards by one base pair of DNA. The 3'–5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading). Following base excision, the polymerase can re-insert the correct base and replication can continue forwards. This preserves the integrity of the original DNA strand that is passed onto the daughter cells. Fidelity is very important in DNA replication. Mismatches in DNA base pairing can potentially result in dysfunctional proteins and could lead to cancer. Many DNA polymerases contain an exonuclease domain, which acts in detecting base pair mismatches and further performs in the removal of the incorrect nucleotide to be replaced by the correct one. Proofreading by DNA polymerase corrects errors during replication. Some errors are not corrected during replication, but are instead corrected after replication is completed; this type of repair is known as mismatch repair.

Origin and Evolution of DNA and DNA Replication Machineries. The transition from the RNA to the DNA world was a major event in the history of life. The invention of DNA required the appearance of enzymatic activities for both synthesis of DNA precursors, retro-transcription of RNA templates and replication of singleand double-stranded DNA molecules. Recent data from comparative genomics, structural biology and traditional biochemistry have revealed that several of these enzymatic activities have been invented independently more than once, indicating that the transition from RNA to DNA genomes was more complex than previously thought. The distribution of the different protein families corresponding to these activities in the three domains of life (Archaea, Eukarya, and Bacteria) is puzzling. In many cases, Archaea and Eukarya contain the same version of these proteins, whereas Bacteria contain another version. However, in other cases, such as thymidylate synthases or type II DNA topoisomerases, the phylogenetic distributions of these proteins do not follow this simple pattern. Several hypotheses have been proposed to explain these observations, including independent invention of DNA and DNA replication proteins, ancient gene transfer and gene loss, and/or nonorthologous replacement. We review all of them here, with more emphasis on recent proposals suggesting that viruses have played a major role in the origin and evolution of the DNA replication proteins and possibly of DNA itself. All cellular organisms have double-stranded DNA genomes. The origin of DNA and DNA replication mechanisms is thus a critical question for our understanding of early life evolution. For some time, it was believed by some molecular biologist that life originated with the appearance of the first DNA molecule! Watson and Crick even suggested that DNA was possibly replicated without proteins, wondering “whether a special enzyme would be required to carry out the polymerization or whether the existing single helical chain could act effectively as an enzyme”.  Such extreme conception was in line with the idea that DNA was the aperiodic crystal predicted by Schroedinger in his influential book “What's life”. Times have changed, and several decades of experimental work have convinced us that DNA synthesis and replication actually require a plethora of proteins. We are reasonably sure now that DNA and DNA replication mechanisms appeared late in early life history, and that DNA originated from RNA in an RNA/protein world. The origin and evolution of DNA replication mechanisms thus occurred at a critical period of life evolution that encompasses the late RNA world and the emergence of the Last Universal Cellular Ancestor (LUCA) to the present three domains of life (Eukarya, Bacteria and Archaea). It is an exciting time to learn through comparative genomics and molecular biology about the details of modern mechanisms for precursor DNA synthesis and DNA replication, in order to trace their histories. DNA can be considered as a modified form of RNA, since the “normal” ribose sugar in RNA is reduced into deoxyribose in DNA, whereas the “simple” base uracil is methylated into thymidine. In modern cells, the DNA precursors (the four deoxyribonucleoties, dNTPs) are produced by reduction of ribonucleotides di- or triphosphate by ribonucleotide reductases. The synthesis of DNA building blocks from RNA precursors is a major argument in favor of RNA preceding DNA in evolution. The direct prebiotic origin of is theoretically plausible (from acetaldehyde and glyceraldehyde-5-phosphate) but highly unlikely, considering that evolution, as stated by F. Jacob, works like a tinkerer, not an engineer.

How to build Synthetic DNA and send it across the internet: Dan Gibson (video and text)

Gene Editing (Crispr) - Genetic Modification (GMO)

Synthetic Genomics is a nascent field of synthetic biology that uses aspects of genetic modification on pre-existing life forms, or artificial gene synthesis to create new DNA or entire life forms.

RNA

RNA or Ribonucleic Acid, is a polymeric molecule implicated in various biological roles in coding, decoding, regulation, and expression of genes. Uracil is one of the four nucleobases in the nucleic acid of RNA that are represented by the letters A, G, C and U. (GACU).

RNA Interference is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules.

Transfer RNA is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the mRNA and the amino acid sequence of proteins. tRNA does this by carrying an amino acid to the protein synthetic machinery of a cell (ribosome) as directed by a 3-nucleotide sequence (codon) in a messenger RNA (mRNA). As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code.

Messenger RNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. Following transcription of primary transcript mRNA (known as pre-mRNA) by RNA polymerase, processed, mature mRNA is translated into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology. As in DNA, mRNA genetic information is in the sequence of nucleotides, which are arranged into codons consisting of three base pairs each. Each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. This process of translation of codons into amino acids requires two other types of RNA: Transfer RNA (tRNA), that mediates recognition of the codon and provides the corresponding amino acid, and ribosomal RNA (rRNA), that is the central component of the ribosome's protein-manufacturing machinery. The existence of mRNA was first suggested by Jacques Monod and François Jacob, and subsequently discovered by Jacob, Sydney Brenner and Matthew Meselson at the California Institute of Technology in 1961. It should not be confused with mitochondrial DNA.

MicroRNA is a small non-coding RNA molecule containing about 22 nucleotides found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression. While the majority of miRNAs are located within the cell, some miRNAs, commonly known as circulating miRNAs or extracellular miRNAs, have also been found in extracellular environment, including various biological fluids and cell culture media.Encoded by eukaryotic nuclear DNA in plants and animals and by viral DNA in certain viruses whose genome is based on DNA, miRNAs function via base-pairing with complementary sequences within mRNA molecules. As a result, these mRNA molecules are silenced, by one or more of the following processes: Cleavage of the mRNA strand into two pieces, Destabilization of the mRNA through shortening of its poly(A) tail, and Less efficient translation of the mRNA into proteins by ribosomes. miRNAs resemble the small interfering RNAs (siRNAs) of the RNA interference (RNAi) pathway, except miRNAs derive from regions of RNA transcripts that fold back on themselves to form short hairpins, whereas siRNAs derive from longer regions of double-stranded RNA. The human genome may encode over 1000 miRNAs, which are abundant in many mammalian cell types and appear to target about 60% of the genes of humans and other mammals. miRNAs are well conserved in both plants and animals, and are thought to be a vital and evolutionarily ancient component of gene regulation. While core components of the microRNA pathway are conserved between plants and animals, miRNA repertoires in the two kingdoms appear to have emerged independently with different primary modes of action. Plant miRNAs usually have near-perfect pairing with their mRNA targets, which induces gene repression through cleavage of the target transcripts. In contrast, animal miRNAs are able to recognize their target mRNAs by using as little as 6–8 nucleotides (the seed region) at the 5' end of the miRNA, which is not enough pairing to induce cleavage of the target mRNAs.Combinatorial regulation is a feature of miRNA regulation in animals. A given miRNA may have hundreds of different mRNA targets, and a given target might be regulated by multiple miRNAs.

P-site or peptidyl, is the second binding site for tRNA in the ribosome. The other two sites are the A-site (aminoacyl), which is the first binding site in the ribosome, and the E-site (exit), is the third and final binding site in the ribosome. During Protein translation, the P-site holds the tRNA which is linked to the growing polypeptide chain. When a stop codon is reached, the peptidyl-tRNA bond of the tRNA located in the P-site is cleaved releasing the newly synthesized protein. During the translocation step of the elongation phase, the mRNA is advanced by one codon, coupled to movement of the tRNAs from the ribosomal A to P and P to E sites, catalyzed by elongation factor EF-G. The deacylated tRNA remains in the P-site and gets released once the peptidyl-tRNA is transferred to the P-site. Prior to peptide bond formation, an aminoacyl-tRNA is bound in the A-site, a peptidyl-tRNA is bound in the P-site, and a deacylated tRNA (ready to exit from the ribosome) is bound to the E-site.

Intron is any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product. The term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation. Control Logic.

Exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature messenger RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome.

DNA-Binding Protein are proteins composed of DNA-binding domains and thus have a specific or general affinity for either single or double stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. However, there are some known minor groove DNA-binding ligands such as netropsin, distamycin, Hoechst 33258, pentamidine, DAPI and others.

RNA Splicing is the editing of the nascent precursor messenger RNA (pre-mRNA) transcript into a mature messenger RNA (mRNA). After splicing, introns are removed and exons are joined together (ligated). For nuclear-encoded genes, splicing takes place within the nucleus either during or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually required in order to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing is carried out in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs). Self-splicing introns, or ribozymes capable of catalyzing their own excision from their parent RNA molecule, also exist.

Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence. It reveals the alleles an individual has inherited from their parents. Traditionally genotyping is the use of DNA sequences to define biological populations by use of molecular tools. It does not usually involve defining the genes of an individual.

Sequence

DNA Sequencing is the process of determining the precise order of nucleotides within a DNA molecule.

Whole Genome Sequencing is the process of determining the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.

Nucleic Acid are biopolymers, or large biomolecules, essential to all known forms of life. They are composed of monomers, which are nucleotides made of three components: a 5-carbon sugar, a phosphate group, and a nitrogenous base. If the sugar is a simple ribose, the polymer is RNA (ribonucleic acid); if the sugar is derived from ribose as deoxyribose, the polymer is DNA (deoxyribonucleic acid). Nucleic acids are arguably the most important of all biomolecules. They are found in abundance in all living things, where they function to create and encode and then store information in the nucleus of every living cell of every life-form organism on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus—to the interior operations of the cell and ultimately to the next generation of each living organism. The encoded information is contained and conveyed via the nucleic acid sequence, which provides the 'ladder-step' ordering of nucleotides within the molecules of RNA and DNA. Strings of nucleotides are bonded to form helical backbones—typically, one tor RNA, two for DNA—and assembled into chains of base-pairs selected from the five primary, or canonical, nucleobases, which are: adenine, cytosine, granine, thymine, and uracil; note, thymine occurs only in DNA and uracil only in RNA. Using amino acids and the process known as protein synthesis, the specific sequencing in DNA of these nucleobase-pairs enables storing and transmitting coded instructions as genes. In RNA, base-pair sequencing provides for manufacturing new proteins that determine the frames and parts and most chemical processes of all life forms.

Nucleic Acid Sequence is a succession of letters that indicate the order of nucleotides within a DNA (using GACT) or RNA (GACU) molecule. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure.

Genetic Testing - Heredity - Genealogy - Risk

Genetic Marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites).

5' end to the 3' end, Directionality in molecular biology is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide sugar-ring means that there will be a 5'-end, which frequently contains a phosphate group attached to the 5' carbon of the ribose ring, and a 3'-end (usually pronounced "five prime end" and "three prime end"), which typically is unmodified from the ribose -OH substituent. In a DNA double helix, the strands run in opposite directions to permit base pairing between them, which is essential for replication or transcription of the encoded information.

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data.

Metagenomics is the study of genetic material recovered directly from environmental samples.

New form of four-stranded 'knot' DNA structure called the i-motif found inside cells. In the knot structure, C letters on the same strand of DNA bind to each other -- so this is very different from a double helix, where 'letters' on opposite strands recognize each other, and where Cs bind to Gs [guanines]. To detect the i-motifs inside cells, the researchers developed a precise new tool -- a fragment of an antibody molecule -- that could specifically recognize and attach to i-motifs with a very high affinity. Crucially, the antibody fragment didn't detect DNA in helical form, nor did it recognize 'G-quadruplex structures' (a structurally similar four-stranded DNA arrangement). With the new tool, researchers uncovered the location of 'i-motifs' in a range of human cell lines. Using fluorescence techniques to pinpoint where the i-motifs were located, they identified numerous spots of green within the nucleus, which indicate the position of i-motifs. The researchers showed that i-motifs mostly form at a particular point in the cell's 'life cycle' -- the late G1 phase, when DNA is being actively 'read'. They also showed that i-motifs appear in some promoter regions (areas of DNA that control whether genes are switched on or off) and in telomeres, 'end sections' of chromosomes that are important in the aging process.

Human Genome could contain up to 20 percent fewer genes. Up to 20% of genes classified as coding (those that produce the proteins that are the building blocks of all living things) may not be coding after all because they have characteristics that are typical of non-coding or pseudogenes (obsolete coding genes). The consequent reduction in the size of the human genome could have important effects in biomedicine since the number of genes that produce proteins and their identification is of vital importance for the investigation of multiple diseases, including cancer, cardiovascular diseases, etc.. The researchers analyzed the genes cataloged as protein coding in the main reference human proteomes: the detailed comparison of the reference proteomes from GENCODE/Ensembl, RefSeq and UniProtKB found 22,210 coding genes, but only 19,446 of these genes were present in all 3 annotations. When they analyzed the 2,764 genes that were present in only one or two of these reference annotations, they were surprised to discover that experimental evidence and manual annotations suggested that almost all of these genes were more likely to be non-coding genes or pseudogenes. In fact, these genes, together with another 1,470 coding genes that are present in the three reference catalogs, were not evolving like typical protein coding genes. The conclusion of the study is that most of these 4,234 genes probably do not code for proteins.

Pseudogene are segments of DNA that are related to real genes. Pseudogenes have lost at least some functionality, relative to the complete gene, in cellular gene expression or protein-coding ability. Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism, but can also be caused by genomic copy number variation (CNV) where segments of 1+ kb are duplicated or deleted. Although not fully functional, pseudogenes may be functional, similar to other kinds of noncoding DNA, which can perform regulatory functions. The "pseudo" in "pseudogene" implies a variation in sequence relative to the parent coding gene, but does not necessarily indicate pseudo-function. Despite being non-coding, many pseudogenes have important roles in normal physiology and abnormal pathology.

Non-Coding DNA sequences are components of an organism's DNA that do not encode protein sequences. Some noncoding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs). Other functions of noncoding DNA include the transcriptional and translational regulation of protein-coding sequences, scaffold attachment regions, origins of DNA replication, centromeres and telomeres. The amount of noncoding DNA varies greatly among species. Often, only a small percentage of the genome is responsible for coding proteins, but a rising percentage is being shown to have regulatory functions. When there is much non-coding DNA, a large proportion appears to have no biological function, as predicted in the 1960s. Since that time, this non-functional portion has controversially been called "junk DNA".

Coding Strand is the DNA strand whose base sequence corresponds to the base sequence of the RNA transcript produced (although with thymine replaced by uracil). It is this strand which contains codons, while the non-coding strand contains anticodons. During transcription, RNA Pol II binds the non-coding strand, reads the anti-codons, and transcribes their sequence to synthesize an RNA transcript with complementary bases. By convention, the coding strand is the strand used when displaying a DNA sequence. It is presented in the 5' to 3' direction.

Single-Nucleotide Polymorphism is a variation in a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population (e.g. > 1%).

Biological Dark Matter is an informal term for genetic material or microorganisms that are unclassified or poorly understood. Biological dark matter includes non-coding DNA (junk DNA) and non-coding RNA. Much of the genomic dark matter is thought to originate from ancient transposable elements and from other low-complexity repetitive elements. Uncategorized genetic material is found in humans and in several other organisms. Their phylogenetic novelty could indicate the cellular organisms or viruses from which they evolved. Biologists are unable to culture and grow 99% of all living microorganisms, so few functional insights exist about the metabolic potential of these organisms.

Gene Therapy

Gene Therapy is the therapeutic delivery of nucleic acid polymers into a patient's cells as a drug to treat disease. Gene therapy involves the transfer of genetic material into the appropriate cells. Cell therapy is the transfer of cells to a patient. For treatment of most diseases by cell therapy, Stem Cells are chosen because their establishment in the patient leads to continual production of the appropriate specialized cells. The first attempt at modifying human DNA was performed in 1980 by Martin Cline, but the first successful nuclear gene transfer in humans, approved by the National Institutes of Health, was performed in May 1989. The first therapeutic use of gene transfer as well as the first direct insertion of human DNA into the nuclear genome was performed by French Anderson in a trial starting in September 1990. Between 1989 and February 2016, over 2,300 clinical trials had been conducted, more than half of them in phase I. It should be noted that not all medical procedures that introduce alterations to a patient's genetic makeup can be considered gene therapy. Bone marrow transplantation and organ transplants in general have been found to introduce foreign DNA into patients. Gene therapy is defined by the precision of the procedure and the intention of direct therapeutic effects.

Gene Therapy - Gene Therapy (youtube) - Stem Cell Therapy - Microbes

When added to gene therapy, plant-based compound may enable faster, more effective treatments. The gene therapy treatment process currently requires isolating a very small population of hemopoietic stem cells from the blood of patients; these young cells can self-renew and give rise to all other types of blood cells. Therapeutic genes are then delivered to these cells via specially engineered viruses, called "lentiviral vectors," which leverage viruses' natural knack for inserting new genetic information into living cells.However, hemopoietic stem cells are highly resilient to viral attacks. They protect themselves with structures known as interferon-induced transmembrane (IFITM) proteins, which intercept lentiviral vectors.

Luxturna gene therapy to treat patients with a rare form of inherited vision loss.

Androgen Receptor is a type of nuclear receptor that is activated by binding either of the androgenic hormones, testosterone, or dihydrotestosterone in the cytoplasm and then translocating into the nucleus. The androgen receptor is most closely related to the progesterone receptor, and progestins in higher dosages can block the androgen receptor. The main function of the androgen receptor is as a DNA-binding transcription factor that regulates gene expression; however, the androgen receptor has other functions as well. Androgen regulated genes are critical for the development and maintenance of the male sexual phenotype.

A new gene therapy strategy, courtesy of nature. Scientists turn a natural cellular process into a drug-delivery system. Scientists have developed a new gene-therapy technique by transforming human cells into mass producers of tiny nano-sized particles full of genetic material that has the potential to reverse disease processes.

Films about DNA

DNA - PBS Film, 5 Episodes (youtube)
Animations of Biology (video)
Nathan Wolfe (video) - Knome
Jennifer Doudna: Editing DNA (video and text)
Journey of Man (youtube)
Cloning the First Human (video)
GATTACA

DNA Resources

The Genetic Atlas
Responsible Genetics
DNA Learning Center
Genetics 
Genetics Society of America
Genomes Project
Genome.gov
Genomics
Cambrian Genomics
Hap Map

ENCODE is a public research project launched by the US National Human Genome Research Institute (NHGRI) in September 2003. Intended as a follow-up to the Human Genome Project (Genomic Research), the ENCODE project aims to identify all functional elements in the human genome.

DNA Variations - Genetic Diversity

Genetic Diversity is the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary. Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. The population will continue for more generations because of the success of these individuals. The academic field of population genetics includes several hypotheses and theories regarding genetic diversity. The neutral theory of evolution proposes that diversity is the result of the accumulation of neutral substitutions. Diversifying selection is the hypothesis that two subpopulations of a species live in different environments that select for different alleles at a particular locus. This may occur, for instance, if a species has a large range relative to the mobility of individuals within it. Frequency-dependent selection is the hypothesis that as alleles become more common, they become more vulnerable. This occurs in host–pathogen interactions, where a high frequency of a defensive allele among the host means that it is more likely that a pathogen will spread if it is able to overcome that allele. We Are 99% The Same, but not totally similar.

Genetic Variation means that biological systems – individuals and populations – are different over space. Each gene pool includes various alleles of genes. The variation occurs both within and among populations, supported by individual carriers of the variant genes. Genetic variation is brought about, fundamentally, by random mutation, which is a permanent change in the chemical structure of chromosomes. Genetic recombination also produces changes within alleles.

Genetic Variability (vary + liable - to or capable of change) is the ability, i.e. capability of a biological system – individual and population – that is changing over time. The base of the genetic variability is genetic variation of different biological systems in space.

Human Genetic Variation is the genetic differences both within and among populations. There may be multiple variants of any given gene in the human population (genes), leading to polymorphism. Many genes are not polymorphic, meaning that only a single allele is present in the population: the gene is then said to be fixed. On average, in terms of DNA sequence all humans are 99.5% similar to any other humans. No two humans are genetically identical. Even monozygotic twins, who develop from one zygote, have infrequent genetic differences due to mutations occurring during development and gene copy-number variation. Differences between individuals, even closely related individuals, are the key to techniques such as genetic fingerprinting. Alleles occur at different frequencies in different human populations, with populations that are more geographically and ancestrally remote tending to differ more. Causes of differences between individuals include independent assortment, the exchange of genes (crossing over and recombination) during meiosis and various mutational events. There are at least two reasons why genetic variation exists between populations. Natural selection may confer an adaptive advantage to individuals in a specific environment if an allele provides a competitive advantage. Alleles under selection are likely to occur only in those geographic regions where they confer an advantage. The second main cause of genetic variation is due to the high degree of neutrality of most mutations. Most mutations do not appear to have any selective effect one way or the other on the organism. The main cause is genetic drift, this is the effect of random changes in the gene pool. In humans, founder effect and past small population size (increasing the likelihood of genetic drift) may have had an important influence in neutral differences between populations. The theory that humans recently migrated out of Africa supports this. The study of human genetic variation has both evolutionary significance and medical applications. It can help scientists understand ancient human population migrations as well as how different human groups are biologically related to one another. For medicine, study of human genetic variation may be important because some disease-causing alleles occur more often in people from specific geographic regions. New findings show that each human has on average 60 new mutations compared to their parents. Apart from mutations, many genes that may have aided humans in ancient times plague humans today. For example, it is suspected that genes that allow humans to more efficiently process food are those that make people susceptible to obesity and diabetes today.

Twins - DNA Code Printed out on Paper

Astronaut's DNA no longer matches that of his identical twin, NASA finds. Spending a year in space not only changes your outlook, it transforms your genes. Preliminary results from NASA's Twins Study reveal that 7% of astronaut Scott Kelly's genes did not return to normal after his return to Earth two years ago. Mason's team also saw changes in the length of Scott's telomeres, caps at the end of chromosomes that are considered a marker of biological aging. First, there was a significant increase in average length while he was in space, and then there was a decrease in length within about 48 hours of his landing on Earth that stabilized to nearly preflight levels. Scientists believe that these telomere changes, along with the DNA damage and DNA repair measured in Scott's cells, were caused by both radiation and calorie restrictions. Space Genes - Body in Space. Why do Humans have Genes in their DNA that changes the body for space travel? Intelligent design?

Damaged DNA

DNA Damage is an alteration in the chemical structure of DNA, such as a break in a strand of DNA, a base missing from the backbone of DNA, or a chemically changed base as 8-OHdG. Damage to DNA that occurs naturally can result from metabolic or hydrolytic processes. Metabolism releases compounds that damage DNA including reactive oxygen species, reactive nitrogen species, reactive carbonyl species, lipid peroxidation products and alkylating agents, among others, while hydrolysis cleaves chemical bonds in DNA. Naturally occurring oxidative DNA damages arise at least 10,000 times per cell per day in humans and 50,000 times or more per cell per day in rats. DNA damage is distinctly different from mutation, although both are types of error in DNA. DNA damage is an abnormal chemical structure in DNA, while a mutation is a change in the sequence of standard base pairs. DNA damage and Mutation have different biological consequences. While most DNA damages can undergo DNA Repair, such repair is not 100% efficient. Un-repaired DNA damages accumulate in non-replicating cells, such as cells in the brains or muscles of adult mammals and can cause aging. (Also see DNA damage theory of aging.) In replicating cells, such as cells lining the colon, errors occur upon replication of past damages in the template strand of DNA or during repair of DNA damages. These errors can give rise to mutations or epigenetic alterations. Both of these types of alteration can be replicated and passed on to subsequent cell generations. These alterations can change gene function or regulation of gene expression and possibly contribute to progression to cancer. UV Damage (sunburn) - Extremophile.

DNA Double Stranded Break is when both strands in the double helix are severed and become particularly hazardous to the cell because they can lead to genome rearrangements. Single-Strand Damage is when only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. In order to repair damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in the undamaged DNA strand.

DNA Repair (Natural Defenses) - Regeneration (stem cells)

Telomeres

Telomere is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos (τέλος) "end" and merοs (μέρος, root: μερ-) "part". For vertebrates, the sequence of nucleotides in telomeres is TTAGGG, with the complementary DNA strand being AATCCC, with a single-stranded TTAGGG overhang. This sequence of TTAGGG is repeated approximately 2,500 times in humans. In humans, average telomere length declines from about 11 kilobases at birth to less than 4 kilobases in old age, with average rate of decline being greater in men than in women. During chromosome replication, the enzymes that duplicate DNA cannot continue their duplication all the way to the end of a chromosome, so in each duplication the end of the chromosome is shortened (this is because the synthesis of Okazaki fragments requires RNA primers attaching ahead on the lagging strand). The telomeres are disposable buffers at the ends of chromosomes which are truncated during cell division; their presence protects the genes before them on the chromosome from being truncated instead. The telomeres themselves are protected by a complex of shelterin proteins, as well as by the RNA that telomeric DNA encodes (TERRA). Over time, due to each cell division, the telomere ends become shorter. They are replenished by an enzyme, telomerase reverse transcriptase.

Telomerase is a ribonucleoprotein that adds a species-dependent telomere repeat sequence to the 3' end of telomeres. A telomere is a region of repetitive sequences at each end of a eukaryotic chromosomes in most eukaryotes. Telomeres protect the end of the chromosome from DNA damage or from fusion with neighbouring chromosomes. The fruit fly Drosophila melanogaster lacks telomerase, but instead uses retrotransposons to maintain telomeres. Telomerase is a reverse transcriptase enzyme that carries its own RNA molecule (e.g., with the sequence "CCCAAUCCC" in vertebrates) which is used as a template when it elongates telomeres. Telomerase, active in normal stem cells and most cancer cells, is normally absent from, or at very low levels in, most somatic cells.

Longevity - Telomere

Copy-Number Variation is a relatively new field in genomics and it is defined as a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals in the human population. Copy number variation is a type of structural variation, specifically, it is a type of duplication or deletion event that affects a considerable number of base pairs. However, note that although modern genomics research is mostly focused on human genomes, copy number variations also occur in a variety of other organisms including E. coli. Recent research indicates that approximately two thirds of the entire human genome is composed of repeats and 4.8-9.5% of the human genome can be classified as copy number variations. In mammals, copy number variations play an important role in generating necessary variation in the population as well as disease phenotype. Copy number variations can be generally categorized into two main groups: short repeats and long repeats. However, there are no clear boundaries between the two groups and the classification depends on the nature of the loci of interest. Short repeats include mainly bi-nucleotide repeats (two repeating nucleotides e.g. A-C-A-C-A-C...) and tri-nucleotide repeats. Long repeats include repeats of entire genes. This classification based on size of the repeat is the most obvious type of classification as size is an important factor in examining the types of mechanisms that most likely gave rise to the repeats, hence the likely effects of these repeats on phenotype.

Mutations in Evolution - Genetic Disorders

Haploinsufficiency is a mechanism of action to explain a phenotype when a diploid organism has lost one copy of a gene and is left with a single functional copy of that gene. Haploinsufficiency is often caused by a loss-of-function mutation, in which having only one copy of the wild-type allele is not sufficient to produce the wild-type phenotype. It occurs when an organism has a single functional copy of a gene, and that single copy does not produce enough product to display the wild type's phenotypic characteristics. The genotypic state in which one of two copies of a gene is absent is called hemizygosity. Hemizygosity is not the same as haploinsufficiency; hemizygosity describes the genotype, and haploinsufficiency is a mechanism that may have caused the phenotype. The general assumption is that the single remaining functional copy of the gene cannot provide sufficient gene product (typically a protein) to preserve the wild-type phenotype leading to an altered or even diseased state. As such, haploinsuffiency is typically transmitted with dominant inheritance, either autosomally or X-linked in female humans. Dominance describes the circumstance in which both alleles in a diploid organism are present but one allele is responsible for the phenotype. That genotypic state is one of heterozygosity (with two different alleles). Co-Dominance is that situation where the effects of both alleles are apparent in the phenotype.

Atavism is an evolutionary throwback, such as traits reappearing that had disappeared generations before. Atavisms can occur in several ways. One way is when genes for previously existing phenotypical features are preserved in DNA, and these become expressed through a mutation that either knocks out the overriding genes for the new traits or makes the old traits override the new one. A number of traits can vary as a result of shortening of the fetal development of a trait (neoteny) or by prolongation of the same. In such a case, a shift in the time a trait is allowed to develop before it is fixed can bring forth an ancestral phenotype. In the social sciences, atavism can also describe a cultural tendency of reversion—for example, people in the modern era reverting to the ways of thinking and acting of a former time. The word atavism is derived from the Latin atavus. An atavus is a great-great-great-grandfather or, more generally, an ancestor.

Chromosomes

Chromosome is a DNA molecule with part or all of the genetic material or genome of an organism. Prokaryotes usually have one single circular chromosome, whereas most eukaryotes are diploid, like humans. Chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes. A nucleosome is a histone octamer with part of a longer DNA strand attached to and wrapped around it. Chromatin fiber, together with associated proteins is known as chromatin. Chromatin is present in most cells, with a few exceptions, for example, red blood cells. Occurring only in the nucleus of eukaryotic cells, chromatin contains the vast majority of DNA, except for a small amount inherited maternally, which is found in the mitochondria. Chromosomes are normally visible under a light microscope only when the cell is undergoing the metaphase of cell division. Before this happens every chromosome is copied once (S phase), and the copy is joined to the original by a centromere resulting in an X-shaped structure. The original chromosome and the copy are now called sister chromatids. During metaphase, when a chromosome is in its most condensed state, the X-shape structure is called a metaphase chromosome. In this highly condensed form chromosomes are easiest to distinguish and study. In prokaryotic cells, chromatin occurs free-floating in cytoplasm, as these cells lack organelles and a defined nucleus. Bacteria also lack histones. The main information-carrying macromolecule is a single piece of coiled double-helix DNA, containing many genes, regulatory elements and other noncoding DNA. The DNA-bound macromolecules are proteins that serve to package the DNA and control its functions. Chromosomes vary widely between different organisms. Some species such as certain bacteria also contain plasmids or other extrachromosomal DNA. These are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. Compaction of the duplicated chromosomes during cell division (mitosis or meiosis) results either in a four-arm structure if the centromere is located in the middle of the chromosome or a two-arm structure if the centromere is located near one of the ends. Chromosomal recombination during meiosis and subsequent sexual reproduction plays a significant role in genetic diversity. If these structures are manipulated incorrectly, through processes known as chromosomal instability and translocation, the cell may undergo mitotic catastrophe and die, or it may unexpectedly evade apoptosis leading to the progression of cancer. In prokaryotes and viruses, the DNA is often densely packed and organized: in the case of archaea, by homologs to eukaryotic histones, and in the case of bacteria, by histone-like proteins. Small circular genomes called plasmids are often found in bacteria and also in mitochondria and chloroplasts, reflecting their bacterial origins. Some use the term chromosome in a wider sense, to refer to the individualized portions of chromatin in cells, either visible or not under light microscopy. However, others use the concept in a narrower sense, to refer to the individualized portions of chromatin during cell division, visible under light microscopy due to high condensation.

X Chromosome is one of the two sex-determining chromosomes (allosomes) in many organisms, including mammals (the other is the Y chromosome), and is found in both males and females. It is a part of the XY sex-determination system and X0 sex-determination system. The X chromosome was named for its unique properties by early researchers, which resulted in the naming of its counterpart Y chromosome, for the next letter in the alphabet, after it was discovered later.

Y Chromosome is one of two sex chromosomes (allosomes) in mammals, including humans, and many other animals. The other is the X chromosome. Y is the sex-determining chromosome in many species, since it is the presence or absence of Y that determines the male or female sex of offspring produced in sexual reproduction. In mammals, the Y chromosome contains the gene SRY, which triggers testis development. The DNA in the human Y chromosome is composed of about 59 million base pairs. The Y chromosome is passed only from father to son. With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of the human genome. To date, over 200 Y-linked genes have been identified. All Y-linked genes are expressed and (apart from duplicated genes) hemizygous (present on only one chromosome) except in the cases of aneuploidy such as XYY syndrome or XXYY syndrome.

How human cells maintain the correct number of chromosomes. Cell division is an essential process in humans, animals and plants as dying or injured cells are replenished throughout life. Cells divide at least a billion times in the average person, usually without any problem. However, when cell division goes wrong, it can lead to a range of diseases, such as cancer, and problems with fertility and development, including babies born with the wrong number of chromosomes as in Down's syndrome. "During cell division, a mother cell divides into two daughter cells, and during this process the DNA in the mother cell, wrapped up in the form of chromosomes, is divided into two equal sets. To achieve this, rope-like structures called microtubules capture the chromosomes at a special site called the kinetochore, and pull the DNA apart," said Dr Viji Draviam, senior lecturer in structural cell and molecular biology from QMUL's School of Biological and Chemical Sciences. We have identified two proteins -- tiny molecular machines -- that enable the correct attachment between the chromosomes and microtubules. When these proteins don't function properly, the cells can lose or gain a chromosome. This finding gives us a glimpse of an important step in the process of cell division.

Polyploid cells and organisms are those containing more than two paired (homologous) sets of chromosomes. Most species whose cells have nuclei (Eukaryotes) are diploid, meaning they have two sets of chromosomes—one set inherited from each parent. However, polyploidy is found in some organisms and is especially common in plants. In addition, polyploidy occurs in some tissues of animals that are otherwise diploid, such as human muscle tissues. This is known as endopolyploidy. Species whose cells do not have nuclei, that is, Prokaryotes, may be polyploid organisms, as seen in the large bacterium Epulopiscium fishelsoni . Hence ploidy is defined with respect to a cell. Most eukaryotes have diploid somatic cells, but produce haploid gametes (eggs and sperm) by meiosis. A monoploid has only one set of chromosomes, and the term is usually only applied to cells or organisms that are normally diploid. Male bees and other Hymenoptera, for example, are monoploid. Unlike animals, plants and multicellular algae have life cycles with two alternating multicellular generations. The gametophyte generation is haploid, and produces gametes by mitosis, the sporophyte generation is diploid and produces spores by meiosis.

Aneuploidy is the presence of an abnormal number of chromosomes in a cell, for example a human cell having 45 or 47 chromosomes instead of the usual 46. It does not include a difference of one or more complete sets of chromosomes, which is called euploidy. An extra or missing chromosome is a common cause of genetic disorders, including some human birth defects. Some cancer cells also have abnormal numbers of chromosomes. Aneuploidy originates during cell division when the chromosomes do not separate properly between the two cells.

Chromosomal Inversion is a chromosome rearrangement in which a segment of a chromosome is reversed end to end. An inversion occurs when a single chromosome undergoes breakage and rearrangement within itself. Inversions are of two types: paracentric and pericentric. Paracentric inversions do not include the centromere and both breaks occur in one arm of the chromosome. Pericentric inversions include the centromere and there is a break point in each arm. nversions usually do not cause any abnormalities in carriers as long as the rearrangement is balanced with no extra or missing DNA. However, in individuals which are heterozygous for an inversion, there is an increased production of abnormal chromatids (this occurs when crossing-over occurs within the span of the inversion). This leads to lowered fertility due to production of unbalanced gametes. The most common inversion seen in humans is on chromosome 9, at inv(9)(p12q13). This inversion is generally considered to have no harmful effects, but there is some suspicion it could lead to an increased risk for miscarriage or infertility for some affected individuals. An inversion does not involve a loss of genetic information, but simply rearranges the linear gene sequence. Families that may be carriers of inversions may be offered genetic counseling and genetic testing.

Transcription

Transcription in genetics is the first step of gene expression, in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. Transcription proceeds in the following general steps: RNA polymerase, together with one or more general transcription factors, binds to promoter DNA. RNA polymerase creates a transcription bubble, which separates the two strands of the DNA helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides. RNA polymerase adds RNA nucleotides (which are complementary to the nucleotides of one DNA strand). RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand. Hydrogen bonds of the RNA–DNA helix break, freeing the newly synthesized RNA strand. If the cell has a nucleus, the RNA may be further processed. This may include polyadenylation, capping, and splicing. The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear pore complex.
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The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene encodes a protein, the transcription produces messenger RNA (mRNA); the mRNA, in turn, serves as a template for the protein's synthesis through translation. Alternatively, the transcribed gene may encode for either non-coding RNA (such as microRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), or other enzymatic RNA molecules called ribozymes. Overall, RNA helps synthesize, regulate, and process proteins; it therefore plays a fundamental role in performing functions within a cell. In virology, the term may also be used when referring to mRNA synthesis from an RNA molecule (i.e., RNA replication). For instance, the genome of a negative-sense single-stranded RNA (ssRNA -) virus may be template for a positive-sense single-stranded RNA (ssRNA +). This is because the positive-sense strand contains the information needed to translate the viral proteins for viral replication afterwards. This process is catalyzed by a viral RNA replicase.

Promoter in genetics is a region of DNA that initiates transcription of a particular gene. Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5' region of the sense strand). Promoters can be about 100–1000 base pairs long.

Gene Regulatory Networks  is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins. These play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo). The regulator can be DNA, RNA, protein and complexes of these. The interaction can be direct or indirect (through transcribed RNA or translated protein). In general, each mRNA molecule goes on to make a specific protein (or set of proteins). In some cases this protein will be structural, and will accumulate at the cell membrane or within the cell to give it particular structural properties. In other cases the protein will be an enzyme, i.e., a micro-machine that catalyses a certain reaction, such as the breakdown of a food source or toxin. Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. Some transcription factors are inhibitory. In single-celled organisms, regulatory networks respond to the external environment, optimising the cell at a given time for survival in this environment. Thus a yeast cell, finding itself in a sugar solution, will turn on genes to make enzymes that process the sugar to alcohol. This process, which we associate with wine-making, is how the yeast cell makes its living, gaining energy to multiply, which under normal circumstances would enhance its survival prospects. In multicellular animals the same principle has been put in the service of gene cascades that control body-shape. Each time a cell divides, two cells result which, although they contain the same genome in full, can differ in which genes are turned on and making proteins. Sometimes a 'self-sustaining feedback loop' ensures that a cell maintains its identity and passes it on. Less understood is the mechanism of epigenetics by which chromatin modification may provide cellular memory by blocking or allowing transcription. A major feature of multicellular animals is the use of morphogen gradients, which in effect provide a positioning system that tells a cell where in the body it is, and hence what sort of cell to become. A gene that is turned on in one cell may make a product that leaves the cell and diffuses through adjacent cells, entering them and turning on genes only when it is present above a certain threshold level. These cells are thus induced into a new fate, and may even generate other morphogens that signal back to the original cell. Over longer distances morphogens may use the active process of signal transduction. Such signalling controls embryogenesis, the building of a body plan from scratch through a series of sequential steps. They also control and maintain adult bodies through feedback processes, and the loss of such feedback because of a mutation can be responsible for the cell proliferation that is seen in cancer. In parallel with this process of building structure, the gene cascade turns on genes that make structural proteins that give each cell the physical properties it needs.

Long time Storage of Information in DNA (Knowledge Preservation)

Profiling

DNA Profiling is a forensic technique used to identify individuals by characteristics of their DNA. A DNA profile is a small set of DNA variations that is very likely to be different in all unrelated individuals, thereby being as unique to individuals as are fingerprints (hence the alternate name for the technique). DNA profiling should not be confused with full genome sequencing. First developed and used in 1984, DNA profiling is used in, for example, parentage testing and criminal investigation, to identify a person or to place a person at a crime scene, techniques which are now employed globally in forensic science to facilitate police detective work and help clarify paternity and immigration disputes. DNA fingerprinting has also been widely used in the study of animal and floral populations and has revolutionized the fields of zoology, botany, and agriculture. Although 99.9% of human DNA sequences are the same in every person, enough of the DNA is different that it is possible to distinguish one individual from another, unless they are monozygotic ("identical") twins. DNA profiling uses repetitive ("repeat") sequences that are highly variable, called variable number tandem repeats (VNTRs), in particular short tandem repeats (STRs), also known as microsatellites, and minisatellites. VNTR loci are very similar between closely related individuals, but are so variable that unrelated individuals are extremely unlikely to have the same VNTRs. Profiling Dangers.

DNA Phenotyping is the process of predicting an organism’s phenotype using only genetic information collected from genotyping or DNA sequencing. This term, also known as molecular photofitting, is primarily used to refer to the prediction of a person’s physical appearance and/or biogeographic ancestry for forensic purposes. DNA phenotyping uses many of the same scientific methods as those being used for genetically-informed personalized medicine, in which drug responsiveness (pharmacogenomics) and medical outcomes are predicted from a patient’s genetic information. Significant genetic variants associated with a particular trait are discovered using a genome-wide association study (GWAS) approach, in which hundreds of thousands or millions of single-nucleotide polymorphisms (SNPs) are tested for their association with each trait of interest. Predictive modeling is then used to build a mathematical model for making trait predictions about new subjects.

Gene Editing

Restriction Fragment is a DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme (restriction endonucleases), a process called restriction. Each restriction enzyme is highly specific, recognising a particular short DNA sequence, or restriction site, and cutting both DNA strands at specific points within this site. Most restriction sites are palindromic, (the sequence of nucleotides is the same on both strands when read in the 5' to 3' direction), and are four to eight nucleotides long. Many cuts are made by one restriction enzyme because of the chance repetition of these sequences in a long DNA molecule, yielding a set of restriction fragments. A particular DNA molecule will always yield the same set of restriction fragments when exposed to the same restriction enzyme. Restriction fragments can be analyzed using techniques such as gel electrophoresis or used in recombinant DNA technology.

Dysgenics is the study of factors producing the accumulation and perpetuation of defective or disadvantageous genes and traits in offspring of a particular population or species. The adjective "dysgenic" is the antonym of "eugenic". It was first used c. 1915 by David Starr Jordan, describing the supposed dysgenic effects of World War I. Jordan believed that healthy men were as likely to die in modern warfare as anyone else, and that war killed only the physically healthy men of the populace whilst preserving the disabled at home.

Eugenics is a set of beliefs and practices that aims at improving the genetic quality of the human population.

Computational Genomics refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, including both DNA and RNA sequence as well as other "post-genomic" data (i.e., experimental data obtained with technologies that require the genome sequence, such as genomic DNA microarrays). These, in combination with computational and statistical approaches to understanding the function of the genes and statistical association analysis, this field is also often referred to as Computational and Statistical Genetics/genomics. As such, computational genomics may be regarded as a subset of bioinformatics and computational biology, but with a focus on using whole genomes (rather than individual genes) to understand the principles of how the DNA of a species controls its biology at the molecular level and beyond. With the current abundance of massive biological datasets, computational studies have become one of the most important means to biological discovery

Gene Deletion is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is lost during DNA replication. Any number of nucleotides can be deleted, from a single base to an entire piece of chromosome. The smallest single base deletion mutations are believed to occur by a single base flipping in the template DNA, followed by template DNA strand slippage, within the DNA polymerase active site. Deletions can be caused by errors in chromosomal crossover during meiosis, which causes several serious genetic diseases. Deletions that do not occur in multiples of three bases can cause a frameshift by changing the 3-nucleotide protein reading frame of the genetic sequence. The examples given below of types and effects of deletions are representative of eukaryotic organisms, particularly humans, but are not relevant to prokaryotic organisms such as bacteria.

Transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). For transformation to take place, the recipient bacteria must be in a state of competence, which might occur in nature as a time-limited response to environmental conditions such as starvation and cell density, and may also be induced in a laboratory. Transformation is one of three processes for'' horizontal gene transfer'', in which exogenous genetic material passes from bacterium to another, the other two being conjugation (transfer of genetic material between two bacterial cells in direct contact) and transduction (injection of foreign DNA by a bacteriophage virus into the host bacterium). In transformation, the genetic material passes through the intervening medium, and uptake is completely dependent on the recipient bacterium. As of 2014 about 80 species of bacteria were known to be capable of transformation, about evenly divided between Gram-positive and Gram-negative bacteria; the number might be an overestimate since several of the reports are supported by single papers.  "Transformation" may also be used to describe the insertion of new genetic material into nonbacterial cells, including animal and plant cells; however, because "transformation" has a special meaning in relation to animal cells, indicating progression to a cancerous state, the process is usually called "transfection". Mutations.

Reprogramming refers to erasure and remodeling of epigenetic marks, such as DNA methylation, during mammalian development or in cell culture. DNA Methylation patterns are largely erased and then re-established between generations in mammals. Almost all of the methylations from the parents are erased, first during gametogenesis, and again in early embryogenesis, with demethylation and remethylation occurring each time. Demethylation of early embryogenesis occurs in the preimplantation period in two stages – initially in the zygote, then the first few embryonic replication cycles of morula and blastula. A wave of methylation then takes place during the implantation stage of the embryo, with CpG islands protected from methylation. This results in global repression and allows housekeeping genes to be expressed in all cells. In the post-implantation stage, methylation patterns are stage- and tissue-specific with changes that would define each individual cell type lasting stably over a long time. Gene Editing (Crispr) - Genetic Modification.

Transdifferentiation also known as lineage reprogramming, is a process in which one mature somatic cell transforms into another mature somatic cell without undergoing an intermediate pluripotent state or progenitor cell type. It is a type of metaplasia, which includes all cell fate switches, including the interconversion of stem cells. Current uses of transdifferentiation include disease modeling and drug discovery and in the future may include gene therapy and regenerative medicine. The term 'transdifferentiation' was originally coined by Selman and Kafatos in 1974 to describe a change in cell properties as cuticle producing cells became salt-secreting cells in silk moths undergoing metamorphosis.

Transgenesis is the process of introducing an exogenous gene—called a transgene—into a living organism so that the organism will exhibit a new property and transmit that property to its offspring. Transgenesis can be facilitated by liposomes, enzymes, plasmid vectors, viral vectors, pronuclear injection, protoplast fusion, and ballistic DNA injection. Transgenesis can occur in nature. Transgenic organisms are able to express foreign genes because the genetic code is similar for all organisms. This means that a specific DNA sequence will code for the same protein in all organisms. Due to this similarity in protein sequence, scientists can cut DNA at these common protein points and add other genes. An example of this is the "super mice" of the 1980s. These mice were able to produce the human protein tPA to treat blood clots.

Parahuman are humans who have undergone a traumatic experience (known as a "trigger event") and awakened superpowers.

Optogenetics is a biological technique which involves the use of light to control cells in living tissue, typically neurons, that have been genetically modified to express light-sensitive ion channels.

Biology - Science

Size Variations (nano) So how does each tiny cell pack a two-meter length of DNA into its nucleus, which is just one-thousandth of a millimeter across?

Polygenes or multiple factor, multiple gene inheritance, or quantitative gene is a group of non-epistatic genes that together influence a phenotypic trait. Traits with polygenic determinism correspond to the classical quantitative characters, as opposed to the qualitative characters with monogenic or oligogenic determinism. In essence instead of two options, such as freckles or no freckles, there are many variations. Like the color of skin, hair, or even eyes. Diversity.

Polygenic Risk Score is a sum of trait-associated alleles across many genetic loci, typically weighted by effect sizes estimated from a genome-wide association study.

Genome-Wide Association Study in genetic epidemiology, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an examination of many common genetic variants in different individuals to see if any variant is associated with a trait. GWASs typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major diseases.

Genetic Epidemiology is the study of the role of genetic factors in determining health and disease in families and in populations, and the interplay of such genetic factors with environmental factors. Genetic epidemiology seeks to derive a statistical and quantitive analysis of how genetics work in large groups.

Epigenetics

Complex Segregation Analysis is a technique within genetic epidemiology to determine whether there is evidence that a major gene underlies the distribution of a given phenotypic trait, which is an obvious, observable, and measurable trait. CSA also provides evidence to whether the implicated trait is inherited in a Mendelian dominant, recessive, or codominant manner.

Single-Nucleotide Polymorphism often abbreviated to SNP (pronounced snip; plural snips), is a variation in a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population.

DNA Methylation is a process by which methyl groups are added to DNA segments. Methylation changes the activity of a DNA segment without changing the sequence. This is known as an epigenetic modification. When located in a gene promoter, DNA methylation typically acts to repress gene transcription. DNA methylation is essential for normal development and is associated with a number of key processes including genomic imprinting, X-chromosome inactivation, repression of repetitive elements, aging and carcinogenesis. Two of DNA's four bases, cytosine and adenine, can be methylated. Cytosine methylation is widespread in both eukaryotes and prokaryotes, even though the rate of cytosine DNA methylation can differ greatly between species: 14% of cytosines are methylated in Arabidopsis thaliana, 8% in Physarum, 4% in Mus musculus, 2.3% in Escherichia coli, 0.03% in Drosophila, 0.006% in Dictyostelium and virtually none (< 0.0002%) in Caenorhabditis or yeast species such as Saccharomyces cerevisiae and S. pombe (but not N. crassa). Adenine methylation has been observed in bacterial, plant, and recently in mammalian DNA, but has received considerably less attention. Methylation of cytosine to form 5-methylcytosine occurs at the same 5 position on the pyrimidine ring where the DNA base thymine's methyl group is located; the same position distinguishes thymine from the analogous RNA base uracil, which has no methyl group. Spontaneous deamination of 5-methylcytosine converts it to thymine. This results in a T:G mismatch. Repair mechanisms then correct it back to the original C:G pair; alternatively, they may substitute G for A, turning the original C:G pair into an T:A pair, effectively changing a base and introducing a mutation. This misincorporated base will not be corrected during DNA replication as thymine is a DNA base. If the mismatch is not repaired and the cell enters the cell cycle the strand carrying the T will be complemented by an A in one of the daughter cells, such that the mutation becomes permanent. The near-universal replacement of uracil by thymine in DNA, but not RNA, may have evolved as an error-control mechanism, to facilitate the removal of uracils generated by the spontaneous deamination of cytosine. DNA methylation as well as many of its contemporary DNA methyltransferases has been thought to evolve from early world primitive RNA methylation activity and is supported by several lines of evidence. In plants and other organisms, DNA methylation is found in three different sequence contexts: CG (or CpG), CHG or CHH (where H correspond to A, T or C). In mammals however, DNA methylation is almost exclusively found in CpG dinucleotides, with the cytosines on both strands being usually methylated. Non-CpG methylation can however be observed in embryonic stem cells,[10] and has also been indicated in neural development. Furthermore, non-CpG methylation has also been observed in hematopoietic progenitor cells, and it occurred mainly in a CpApC sequence context. Gene Silencing - Silent Mutation.

Twins

Twins Early Development Study (TEDS) is an ongoing longitudinal twin study headed by principal investigator psychologist Robert Plomin and based at King's College London. The main goal of TEDS is to use behavioural genetic methods to find out how nature (genes) and nurture (environments) can explain why people differ with respect to their cognitive abilities, learning abilities and behaviours. Over 15,000 pairs of twins originally signed up for the study and more than 13,000 pairs remain involved to the present day. This demonstrates the continued support of all twins and their families for more than a decade.

In the Womb - Identical Twins (youtube)

Monoamniotic Twins are identical twins that share the same amniotic sac within their mother’s uterus. Monoamniotic twins are always identical, always monochorionic and are usually termed Monoamniotic-Monochorionic ("MoMo" or "Mono Mono") twins. They also share the placenta, but have two separate umbilical cords. Monoamniotic twins develop when an embryo does not split until after formation of the amniotic sac, at about 9-13 days after fertilization. Monoamniotic triplets or other monoamniotic multiples are possible, but extremely rare. Other obscure possibilities include multiples sets where monoamniotic twins are part of a larger gestation such as triplets, quadruplets, or more. Reproduction (Birth).

Twin are two offspring produced by the same pregnancy. Twins can be either monozygotic ("identical"), meaning that they develop from one zygote, which splits and forms two embryos, or dizygotic ("fraternal"), meaning that each twin develops from a separate egg and each egg is fertilized by its own sperm cell. In contrast, a foetus that develops alone in the womb is called a singleton, and the general term for one offspring of a multiple birth is multiple. Non-related look-alikes whose resemblance parallels that of twins are referred to as doppelgangers.

A sister and brother in Australia are the second-ever Semi-Identical Twins to be identified. The pair share identical DNA from their mother, but didn’t get identical DNA from their father. But occasionally a single egg gets fertilised by two sperm. Normally, the resulting embryo dies because it has three sets of chromosomes instead of the usual two. This means on average 75 per cent of semi-identical twins’ DNA will be identical. The technical term for semi-identical twins is sesquizygotic. In the case of the Brisbane twins, the embryo split in two with each half somehow ending up with the correct number of chromosomes. They received exactly the same set of chromosomes from their mother, but one twin got their second set of chromosomes from one sperm and one got it from another. Identical twins come about when a single fertilised egg splits in two, meaning they have exactly the same DNA – they are clones. Fraternal twins form when two separate eggs are fertilised by two separate sperm. Because each egg and sperm has a different mix of parental DNA, only 50 per cent of their DNA is identical on average – just like siblings who aren’t twins. Twins Days.

CRISPR - Gene Editing

CRISPR allows researchers to edit genes very precisely, easily and quickly. It does this by harnessing a mechanism that already existed in bacteria. Basically, there's a protein that acts like a scissors and cuts the DNA, and there's an RNA molecule that directs the scissors to any point on the genome you want. The result is basically a word processor for genes. You can take an entire gene out, put one in, or even edit just a single letter within a gene. And you can do it in nearly any species.

Clustered Regularly Interspaced Short Palindromic Repeats.

Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease associated with the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) type II adaptive immunity system in Streptococcus pyogenes, among other bacteria. S. pyogenes utilizes Cas9 to interrogate and cleave foreign DNA, such as invading bacteriophage DNA or plasmid DNA. Cas9 performs this interrogation by unwinding foreign DNA and checking whether it is complementary to the 20 basepair spacer region of the guide RNA. If the DNA substrate is complementary to the guide RNA, Cas9 cleaves the invading DNA. In this sense, the CRISPR-Cas9 mechanism has a number of parallels with the RNA interference (RNAi) mechanism in eukaryotes. Native Cas9 assists in all three CRISPR steps: it participates in adaptation, participates in crRNA processing and it cleaves the target DNA assisted by crRNA and an additional RNA called tracrRNA. Native Cas9 requires a guide RNA composed of two disparate RNAs that associate to make the guide - the CRISPR RNA (crRNA), and the trans-activating RNA (tracrRNA).

CRISPR-Cas9 technique targeting Epigenetics Reverses Disease in mice. A modified CRISPR-Cas9 technique that alters the activity, rather than the underlying sequence, of disease-associated genes.

CRISPR-based Diagnostic Tool advanced, miniature paper test developed. A strip of paper can now indicate presence of pathogens, tumor DNA, or any genetic signature of interest. 100-fold greater sensitivity, the ability to detect multiple targets at once, and other new features further enhance SHERLOCK's power for detecting genetic signatures.

Genome Editing is a type of genetic engineering in which DNA is inserted, deleted, modified or replaced in the genome of a living organism. In 2018, the common methods for such editing use engineered nucleases, or "molecular scissors". These nucleases create site-specific double-strand breaks (DSBs) at desired locations in the genome. The induced double-strand breaks are repaired through nonhomologous end-joining (NHEJ) or homologous recombination (HR), resulting in targeted mutations ('edits'). As of 2015 four families of engineered nucleases were used: meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector-based nucleases (TALEN), and the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system. Nine genome editors were available as of 2017. Genome editing with engineered nucleases, ie all three major classes of these enzymes—zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and engineered meganucleases—were selected by Nature Methods as the 2011 Method of the Year. The CRISPR-Cas system was selected by Science as 2015 Breakthrough of the Year.

Gene Editing can now change an entire species — forever (video and Interactive text)

RapidHIT™ Human DNA Identification System

Gene Expression (hereditary traits) - Gene Therapy

Genetic Engineering without unwanted side effects helps fight parasites. Modified CRISPR-Cas9 gene editing scissors are enabling researchers to make alterations to the genetic material of single-cell organisms that are indistinguishable from natural mutations. This method is making it possible to develop a (harmless) experimental live vaccine for the widespread parasite Toxoplasma gondii.

RNA-Programmed Genome Editing in Human Cells

Easily 'Re-Programmable Cells' could be key in creation of new life forms

A Cell could be Programmed, for example, with a so-called NOT logic gate. This is one of the simplest logic instructions: Do NOT do something whenever you receive the trigger. Cells are basically tiny computers: They send and receive inputs and output accordingly your blood sugar spikes, and your pancreatic cells get the message. Output: more insulin.

CRISPR or Clustered Regularly Interspaced Short Palindromic Repeats, are segments of prokaryotic DNA containing short, repetitive base sequences. In a palindromic repeat, the sequence of nucleotides is the same in both directions. Each repetition is followed by short segments of spacer DNA from previous exposures to foreign DNA (e.g., a virus or plasmid). Small clusters of cas (CRISPR-associated system) genes are located next to CRISPR sequences. The CRISPR/Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity. RNA harboring the spacer sequence helps Cas proteins recognize and cut exogenous DNA. Other RNA-guided Cas proteins cut foreign RNA. CRISPRs are found in approximately 40% of sequenced bacterial genomes and 90% of sequenced archaea. A simple version of the CRISPR/Cas system, CRISPR/Cas9, has been modified to edit genomes. By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or new ones added. The Cas9-gRNA complex corresponds with the CAS III crRNA complex in the above diagram. CRISPR/Cas genome editing techniques have many potential applications, including medicine and crop seed enhancement. The use of CRISPR/Cas9-gRNA complex for genome editing was the AAAS's choice for breakthrough of the year in 2015. Bioethical concerns have been raised about the prospect of using CRISPR for germline editing.

Scientists unveil CRISPR-based diagnostic platform that targets RNA (rather than DNA) as a rapid, inexpensive, highly sensitive diagnostic tool with the potential for a transformative effect on research and global public health. Detecting the presence of Zika virus in patient blood or urine samples within hours; Distinguishing between the genetic sequences of African and American strains of Zika virus; Discriminating specific types of bacteria, such as E. coli; Detecting antibiotic resistance genes; Identifying cancerous mutations in simulated cell-free DNA fragments; and Rapidly reading human genetic information, such as risk of heart disease, from a saliva sample.

Teaching CRISPR and antibiotic resistance to high school students. BioBits Health brings hands-on, low-cost, high-tech synthetic biology into the classroom.

Genome Damage from CRISPR/Cas9 gene editing higher than thought. Caution required for using CRISPR/Cas9 in potential gene therapies.

CRISPR/Cas9 used to Control Genetic Inheritance in Mice. - Heredity.

PCR Analyzer or Polymerase Chain Reaction is a technique used in medical and biological research labs for a variety of applications including qualitative and quantitative nucleic acid analysis; DNA cloning for sequencing, DNA-based phylogeny, or functional analysis of genes; the diagnosis of hereditary.

Computer program can translate a free-form 2-D drawing into a DNA structure. Researchers at MIT and Arizona State University have designed a computer program that allows users to translate any free-form drawing into a two-dimensional,
nanoscale structure made of DNA.

Gene Drive is a technique that promotes the inheritance of a particular gene to increase its prevalence in a population. Gene drives can arise through a variety of mechanisms. They have been proposed to provide an effective means of genetically modifying specific populations and entire species. The technique can employ adding, deleting, disrupting, or modifying genes. Gene drives affect only sexually reproducing species, excluding viruses or bacteria. Applications include exterminating insects that carry pathogens (notably mosquitoes that transmit malaria, dengue and zika pathogens), controlling invasive species or eliminating herbicide or pesticide resistance. As with any potentially powerful technique, gene drives can be misused in a variety of ways or induce unintended consequences. For example, a gene drive intended to affect only a local population might spread across an entire species. Many non-native species have a high likelihood of returning to their original habitats, through natural migration, environmental disruption (storms, floods, etc.), accidental human transportation, or purposeful relocation. Specimens whose reproduction/survival is compromised that somehow return to their native habitat, could unintentionally drive their species to extinction. Several molecular mechanisms can mediate a gene drive. Naturally occurring mechanisms arise when alleles evolve molecular mechanisms that give them a transmission chance greater than (the normal) 50%. Stem Cells.

Somatic Gene Editing doesn't change reproductive cells so it does not get passed on. Germline gene editing modifies reproductive cells so it gets passed down to future generations.

Somatic Cell is any biological cell forming the body of an organism; that is, in a multicellular organism, any cell other than a gamete, germ cell, gametocyte or undifferentiated stem cell. In contrast, gametes are cells that fuse during sexual reproduction, germ cells are cells that give rise to gametes, and stem cells are cells that can divide through mitosis and differentiate into diverse specialized cell types. For example, in mammals, somatic cells make up all the internal organs, skin, bones, blood and connective tissue, while mammalian germ cells give rise to spermatozoa and ova which fuse during fertilization to produce a cell called a zygote, which divides and differentiates into the cells of an embryo. There are approximately 220 types of somatic cells in the human body. Theoretically, these cells are not germ cells (the source of gametes); they never transmit to their descendants the mutations they have undergone. However, in sponges, non-differentiated somatic cells form the germ line and, in Cnidaria, differentiated somatic cells are the source of the germline. (somatic cells die with you).

Germ Cell is any biological cell that gives rise to the gametes of an organism that reproduces sexually. In many animals, the germ cells originate in the primitive streak and migrate via the gut of an embryo to the developing gonads. There, they undergo meiosis, followed by cellular differentiation into mature gametes, either eggs or sperm. Unlike animals, plants do not have germ cells designated in early development. Instead, germ cells can arise from somatic cells in the adult (such as the floral meristem of flowering plants). T-Cells.

Human genome editing to make edits in somatic cells for purposes of treating genetically inherited diseases. Genome editing changes the DNA sequence so that the cells can make the right proteins again. Advances in genome editing hold promise for enabling the treatment of thousands of genetic diseases. Somatic gene therapy is the transfer of genes into the somatic cells of the patient, such as cells of the bone marrow, and hence the new DNA does not enter the eggs or sperm.

Somatic mutation is a genetic alteration acquired by a cell that can be passed to the progeny of the mutated cell in the course of cell division. Somatic mutations differ from germ line mutations, which are inherited genetic alterations that occur in the germ cells (i.e., sperm and eggs).

Germline in a multicellular organism is the population of its bodily cells that are so differentiated or segregated that in the usual processes of reproduction they may pass on their genetic material to the progeny.  As a rule this passing-on happens via a process of sexual reproduction; typically it is a process that includes systematic changes to the genetic material, changes that arise during recombination, meiosis and fertilization for example. However, there are many exceptions, including processes and concepts such as various forms of apomixis, autogamy, automixis, cloning, or parthenogenesis. The cells of the germline commonly are called  Germ Cells, which is any biological cell that gives rise to the gametes of an organism that reproduces sexually.

Germline Mutation or germinal mutation, is any detectable variation within germ cells (cells that, when fully developed, become sperm and ovum). Mutations in these cells are the only mutations that can be passed on to offspring, when either a mutated sperm or oocyte come together to form a zygote. After this fertilization event occurs, germ cells divide rapidly to produce all of the cells in the body, causing this mutation to be present in every somatic and germline cell in the offspring; this is also known as a constitutional mutation. Germline mutation is distinct from somatic mutation.

Homozygous vs. Heterozygous

Gene Delivery is the process of introducing foreign genetic material, such as DNA or RNA, into host cells. Genetic material must reach the nucleus of the host cell to induce gene expression. Successful gene delivery requires the foreign genetic material to remain stable within the host cell and can either integrate into the genome or replicate independently of it. This requires foreign DNA to be synthesized as part of a vector, which is designed to enter the desired host cell and deliver the transgene to that cell's genome. Vectors utilized as the method for gene delivery can be divided into two categories, recombinant viruses and synthetic vectors (viral and non-viral). In complex multicellular eukaryotes (more specifically Weissmanists), if the transgene is incorporated into the host's germline cells, the resulting host cell can pass the transgene to its progeny. If the transgene is incorporated into somatic cells, the transgene will stay with the somatic cell line, and thus its host organism. Gene delivery is a necessary step in gene therapy for the introduction or silencing of a gene to promote a therapeutic outcome in patients and also has applications in the genetic modification of crops. There are many different methods of gene delivery for various types of cells and tissues.

Viral Vector are tools commonly used by molecular biologists to deliver genetic material into cells. This process can be performed inside a living organism (in vivo) or in cell culture (in vitro). Viruses have evolved specialized molecular mechanisms to efficiently transport their genomes inside the cells they infect. Delivery of genes, or other genetic material, by a vector is termed transduction and the infected cells are described as transduced. Molecular biologists first harnessed this machinery in the 1970s. Paul Berg used a modified SV40 virus containing DNA from the bacteriophage ? to infect monkey kidney cells maintained in culture. In addition to their use in molecular biology research, viral vectors are used for gene therapy and the development of vaccines.

Horizontal Gene Transfer is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring. HGT is an important factor in the evolution of many organisms. Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence. It often involves temperate bacteriophages and plasmids. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms such as F-pilus, subsequently arming the antibiotic resistant genes' recipient against antibiotics, which is becoming medically challenging to deal with. It is also postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code. Most thinking in genetics has focused upon vertical transfer, but the importance of horizontal gene transfer among single-cell organisms is beginning to be acknowledged. Gene delivery can be seen as an artificial horizontal gene transfer, and is a form of genetic engineering.

Palindromic Sequence is a nucleic acid sequence on double-stranded DNA or RNA wherein reading 5' (five-prime) to 3' (three prime) forward on one strand matches the sequence reading 5' to 3' on the complementary strand with which it forms a double helix. This definition of palindrome thus depends on complementary strands being palindromic of each other.

Analog DNA Circuit Does Math in a Test Tube DNA computers could one day be programmed to diagnose and treat disease.

Recording analog memories in human cells. Engineers program human cells to store complex histories in their DNA.

The era of Personal DNA Testing is here: Sebastian Kraves (video and interactive text) - Portable DNA analyzers can help us quickly detect viruses, so that we can stop a pandemics and the spreading of disease. With a portable DNA analyzer we can quickly assess whether our food is safe to eat. A farmer can take fluid samples from livestock and then take a drop of that genetic material and put it into a little analyzer smaller than a shoebox, program it to detect DNA or RNA from the swine flu virus. These machines used in a court law can decide whether someone is innocent or guilty based on DNA evidence. These machines can also help verify the identification of a substance by knowing key factors about its DNA. Personal DNA machines are now aboard the International Space Station, where they can help monitor living conditions and protect the lives of astronauts.

A step towards Biological Warfare with Insects? The programme called 'Insect Allies' intends for insects to be used for dispersing genetically modified viruses to agricultural plants in fields. These viruses would be engineered so they can alter the chromosomes of plants through 'genome editing'. This would allow for genetic modifications to be implemented quickly and at a large scale on crops that are already growing in fields, such as corn.

Genetically Modified Mosquitoes. Male Anopheles gambiae mosquitoes engineered with the mutation can mate with normal female mosquitoes, passing along the changed gene. Anopheles gambiae mosquitoes are the primary vector responsible for spreading malaria in sub-Saharan Africa. The ethics of wiping out a Mosquito Species.

Transduction in genetics is the process by which foreign DNA is introduced into a cell by a virus or viral vector. An example is the viral transfer of DNA from one bacterium to another. Transduction does not require physical contact between the cell donating the DNA and the cell receiving the DNA (which occurs in conjugation), and it is DNase resistant (transformation is susceptible to DNase). Transduction is a common tool used by molecular biologists to stably introduce a foreign gene into a host cell's genome (both bacterial and mammalian cells).When viruses, including bacteriophages (viruses that infect bacteria), infect bacterial cells, their normal mode of reproduction is to harness the replicational, transcriptional, and translation machinery of the host bacterial cell to make numerous virions, or complete viral particles, including the viral DNA or RNA and the protein coat.

Genetically Modified - GMO

Genetic Engineering is the direct manipulation of an organism's genome using Biotechnology. It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. New DNA may be inserted in the host genome by first isolating and copying the genetic material of interest using molecular cloning methods to generate a DNA sequence, or by synthesizing the DNA, and then inserting this construct into the host organism. Genes may be removed, or "knocked out", using a nuclease. Gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations. CRISPR.

Genetically Modified Organism or GMO, is any organism whose genetic material has been altered using genetic engineering techniques. The exact definition of a genetically modified organism and what constitutes genetic engineering varies, with the most common being an organism altered in a way that "does not occur naturally by mating and/or natural recombination". A wide variety of organisms have been genetically modified (GM), from animals to plants and microorganisms. Genes have been transferred within the same species, across species (creating transgenic organisms) and even across kingdoms. New genes can be introduced, or endogenous genes can be enhanced, altered or knocked out. Creating a genetically modified organism is a multi-step process. Genetic engineers must isolate the gene they wish to insert into the host organism and combine it with other genetic elements, including a promoter and terminator region and often a selectable marker. A number of techniques are available for inserting the isolated gene into the host genome. Recent advancements using genome editing techniques, notably CRISPR, have made the production of GMO's much simpler. Life from non-living matter.

Ginkgo Bioworks specializes in using genetic engineering to produce bacteria with industrial applications. Ginkgo Bioworks is an analytics company that designs organisms for customers in a range of industries. It is the self-proclaimed "Organism Company". Ginkgo Bioworks designs microbes in analytical labs it calls synthetic biology foundries, which comprise software and hardware tools that allow for rapid prototyping and high-throughput screening. Several publicly-stated products include chemical intermediates, flavors, and fragrances; as well as microbes that provide health benefits to the human gut microbiome and agricultural crop root microbiomes.

Transgene is a gene or genetic material that has been transferred naturally, or by any of a number of genetic engineering techniques from one organism to another. The introduction of a transgene (called "transgenesis") has the potential to change the phenotype of an organism.

Transgenesis is the process of introducing an exogenous gene—called a transgene—into a living organism so that the organism will exhibit a new property and transmit that property to its offspring. Transgenesis can be facilitated by liposomes, enzymes, plasmid vectors, viral vectors, pronuclear injection, protoplast fusion, and ballistic DNA injection. Transgenesis can occur in nature. Transgenic organisms are able to express foreign genes because the genetic code is similar for all organisms. This means that a specific DNA sequence will code for the same protein in all organisms. Due to this similarity in protein sequence, scientists can cut DNA at these common protein points and add other genes. An example of this is the "super mice" of the 1980s. These mice were able to produce the human protein tPA to treat blood clots. Transduction.

Xenotransplantation is the transplantation of living cells, tissues or organs from one species to another. Such cells, tissues or organs are called xenografts or xenotransplants. It is contrasted with allotransplantation (from other individual of same species), Syngeneic transplantation (Grafts transplanted between two genetically identical individuals of the same species) and Autotransplantation (from one part of the body to another in the same person).

Recombinant DNA molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in the genome.

GMO Plants - Genetically Modified Food

GMO Mosquitos Released In High-Security Lab | Science | NPR (youtube) - The mosquitoes are an entirely new kind of genetically modified organism. The insects, members of the species that transmits malaria, were modified using the powerful gene-editing technique CRISPR to carry a sequence of DNA known as a "gene drive," which is designed to drive the genetic modification rapidly through entire populations of the species. The mutation is designed to sterilize populations of malaria-transmitting mosquitoes in the wild, causing them to crash. And that would, hopefully, help stop the spread of the malaria parasite. But the experiment is controversial because of fears that the genetically modified insects could cause unintended consequences on the environment if they were ever released in the wild. So the mosquitoes are being tested first in a specially designed, high-security lab in Terni, Italy. The lab is designed to mimic the natural environment in sub-Saharan Africa — and to make sure none of the insects escapes. If they do escape, they will not survive Italy's climate.

Epigenetics

Epigenetics are stable heritable traits or Phenotypes that cannot be explained by changes in DNA sequence. Epigenetics often refers to changes in a chromosome that affect gene activity and expression, but can also be used to describe any heritable phenotypic change that does not derive from a modification of the genome, such as prions. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal developmental program. The standard definition of epigenetics requires these alterations to be heritable, either in the progeny of cells or of organisms. Epigenetics studies genetic effects not encoded in the DNA sequence of an organism, Such effects on cellular and physiological phenotypic traits may result from external or environmental factors that switch genes on and off and affect how cells express genes. These alterations may or may not be heritable, although the use of the term epigenetic to describe processes that are heritable is controversial. Epigenetics is the study of heritable changes in gene. Activities that do not involve alterations to the genetic code.

Personalized Food - Personalized Medicine - DNA Repair

Epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring via transgenerational epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome. The epigenome is involved in regulating gene expression, development, tissue differentiation, and suppression of transposable elements. Unlike the underlying genome which is largely static within an individual, the epigenome can be dynamically altered by environmental conditions.

Epigenetic Mechanisms modulated by environmental cues such as diet, disease or our lifestyle take a major role in regulating the DNA by switching genes on and off. - Max-Planck-Gesellschaft, München.

Epigenetic Markers tell your genes to switch on or off. There are two types of marks: chemical (e.g., methylation) or. protein (e.g., histones). Polygene - Methylation.

Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence. Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair. Plant flavones are said to be inhibiting epigenomic marks that cause cancers. Two of the most characterized epigenetic modifications are DNA methylation and histone modification. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.

Rhonda Patrick on Diet-Gene Interactions, Epigenetics, the Vitamin D-Serotonin Link and DNA Damage.(youtube)

Epigenetic enzymes affect 160 genes. Enzymes regulate the behavior of genes. Rpd3.

Transgenerational Epigenetic Inheritance is the transmittance of information from one generation of an organism to the next (e.g., parent–child transmittance) that affects the traits of offspring without alteration of the primary structure of DNA (i.e., the sequence of nucleotides)—in other words, epigenetically. The less precise term "epigenetic inheritance" may be used to describe both cell–cell and organism–organism information transfer. Although these two levels of epigenetic inheritance are equivalent in unicellular organisms, they may have distinct mechanisms and evolutionary distinctions in multicellular organisms. For some epigenetically influenced traits, the epigenetic marks can be induced by the environment and some marks are heritable, leading some to view epigenetics as a relaxation of the rejection of soft inheritance of acquired characteristics.

Methyl Group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms — CH3. In formulas, the group is often abbreviated Me. Such hydrocarbon groups occur in many organic compounds. It is a very stable group in most molecules. While the methyl group is usually part of a larger molecule, it can be found on its own in any of three forms: anion, cation or radical. The anion has eight valence electrons, the radical seven and the cation six. All three forms are highly reactive and rarely observed. Anion (−) is an ion with more electrons than protons, giving it a net negative charge (since electrons are negatively charged and protons are positively charged). Cation (+) is an ion with fewer electrons than protons, giving it a positive charge. Radical is an atom, molecule, or ion that has an unpaired valence electron. With some exceptions, these unpaired electrons make radicals highly chemically reactive. Many radicals spontaneously dimerize. Most organic radicals have short lifetimes.

Animal Pharm: Food For Thought - Real Stories (youtube, 51:17) - Explore how science is changing the food that we eat. From double-muscled bulls to featherless chickens, this is breeding on a whole new level. Stepping into the world of transgenics, we encounter rabbits with a jellyfish gene in their DNA (they glow in the dark), and salmon engineered to grow four times faster than normal.

Animal Pharm: From Mouse To Man - Real Stories (youtube, 51:07) - Explore the spooky prospect of regeneration, with mice that show powers no mammal was previously thought to have; and witness how, with tissue engineering, scientists can now manipulate cartilage and skin cells so they can grow them into any shape.

Tissue Engineering is the use of a combination of cells, engineering and materials methods, and suitable biochemical and physicochemical factors to improve or replace biological tissues. Tissue engineering involves the use of a scaffold for the formation of new viable tissue for a medical purpose. While it was once categorized as a sub-field of biomaterials, having grown in scope and importance it can be considered as a field in its own.

Bioreactor manufactured or engineered device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical process is carried out which involves organisms or biochemically active substances derived from such organisms. This process can either be aerobic or anaerobic. These bioreactors are commonly cylindrical, ranging in size from litres to cubic metres, and are often made of stainless steel. A bioreactor may also refer to a device or system meant to grow cells or tissues in the context of cell culture. These devices are being developed for use in tissue engineering or biochemical engineering. Low Gravity Environment.

Zygosity is the degree of similarity of the alleles for a trait in an organism. Most eukaryotes have two matching sets of chromosomes; that is, they are diploid. Diploid organisms have the same loci on each of their two sets of homologous chromosomes, except that the sequences at these loci may differ between the two chromosomes in a matching pair and that a few chromosomes may be mismatched as part of a chromosomal sex-determination system. If both alleles of a diploid organism are the same, the organism is homozygous at that locus. If they are different, the organism is heterozygous at that locus. If one allele is missing, it is hemizygous, and, if both alleles are missing, it is nullizygous.

Epigenetic drug discovery. Scientists create a machine-learning algorithm that automates high-throughput screens of epigenetic medicines and gleans information from microscope images -- allowing for high-throughput epigenetic drug screens that could unlock new treatments for cancer, heart disease, mental illness and more.

Eugenics - Lobotomies - GMO's (Food and Pesticides) - Mutations

DNA Printed Out on Paper - Visualizing Scale

If you Printed Out DNA codes on paper it would take 175 books with 262,000 pages of information, which is about 10,000 ATCG code sequences on each page that is 8.5×11 with an 8pt font size, minus the size of the margins, header and footer. We know around only two percent of those 175 books. 500 pages, or 5 million ATCG code sequences, gives each person their own unique qualities, like facial and body characteristics. The rest of the other 99.9% of DNA code is absolutely identical in everyone, we all share the same 99.9% of DNA code. Everyone is almost exactly the same or equal, except for a few small variations in 3 billion lines of code. Windows operating system has roughly 50 million lines of code. Even though Humans are 97% to 99% genetically similar to chimpanzee's on average, humans have 39 million base DNA differences from chimps and 3 million base DNA differences between each other. Humans are also 90% genetically similar to cats, 85% genetically similar to mice, 80% genetically similar to cows and 60% genetically similar to bananas. But don't worry, everyone is still unique. Even though we are all very similar, we are all slightly different in our own way. Since humans have 23 pairs of chromosomes, meiosis may result in 8,388,608 possible combinations of chromosomes or genetic recombination's. There is 2²³ or 8,388,608 combinations of chromosomes in every male sperm, and 8,388,608 combinations of chromosomes in every female egg, that makes 70,368,744,177,664 possible variations that can happen when a sperm fertilizes an egg. There are also more combinations in the way that proteins fold then there are atoms in the universe.

Diversity - Twins - Brain Memory Capacity

How to read the genome and build a human being (video and interactive text)

How many possible Alpha Numeric Combinations are there using all letters for 4 characters? With a Latin alphabet of 26 letters and the 10 digits 0...9, and allowing for repeats, you get: 36^4 = 36 × 36 × 36 × 36 = 1,679,616 combinations. If you were to include both lower and upper case characters, the number of possible combinations goes up (due to 26 lower case letters + 26 upper case letters + 10 digits = 62 characters to choose from): 62^4 = 14,776,336.

Some where in the DNA code is information from the creator that explains who we are. And that is what we are starting to do now. Kind of brings a whole new meaning to the phrase, "The answers lie within you". Look deep into your heart, or your DNA.

But not all the information that humans need is in our DNA. The rest of the information that we need, we need to learn from the environment so that we can adapt quickly enough so that we don't go extinct, like 99.9% of all other life forms have done on this planet. You can say that life has solved that problem of extinction by creating humans, but life forgot to inform humans of our abilities and our responsibilities, thus we are actually contributing to our own extinction instead of assuring our survival.

Molecular biologists at UC San Diego have unlocked the code that initiates transcription and regulates the activity of more than half of all human genes, an achievement that should provide scientists with a better understanding of how human genes are turned on and off.

Regeneron Genetics Center (RGC) has built one of the world’s most comprehensive genetics databases, pairing the sequenced exomes and de-identified electronic health records of more than 100,000 people so far.

Million Veteran Program: A mega-biobank to study genetic influences on health and disease.

How Does DNA Know What to Do?

How does DNA know when to Communicate and know when not to Communicate?

DNA is essentially a storage molecule. It contains all of the instructions a cell needs to sustain itself. These instructions are found within genes, which are sections of DNA made up of specific sequences of nucleotides. In order to be implemented, the instructions contained within genes must be expressed, or copied into a form that can be used by cells to produce the proteins needed to support life. The instructions stored within DNA are read and processed by a cell in two steps: Transcription and Translation.  Each of these steps is a separate biochemical process involving multiple molecules. During transcription, a portion of the cell's DNA serves as a template for creation of an RNA molecule. (RNA, or ribonucleic acid, is chemically similar to DNA, except for three main differences described later on in this concept page.) In some cases, the newly created RNA molecule is itself a finished product, and it serves an important function within the cell. In other cases, the RNA molecule carries messages from the DNA to other parts of the cell for processing. Most often, this information is used to manufacture proteins. The specific type of RNA that carries the information stored in DNA to other areas of the cell is called messenger RNA, or mRNA. How does transcription proceed? Transcription begins when an enzyme called RNA polymerase attaches to the DNA template strand and begins assembling a new chain of nucleotides to produce a complementary RNA strand. There are multiple types of types of RNA. In eukaryotes, there are multiple types of RNA polymerase which make the various types of RNA. In prokaryotes, a single RNA polymerase makes all types of RNA. Generally speaking, polymerases are large enzymes that work together with a number of other specialized cell proteins. These cell proteins, called transcription factors, help determine which DNA sequences should be transcribed and precisely when the transcription process should occur. Initiation. A schematic shows two horizontal strands of DNA against a white background, one in the lower half of the image and one arcing in the upper half. A transparent green globular structure, representing the enzyme RNA polymerase, is bound to a several-nucleotide-long region along the lower DNA strand on the right side. The sugar-phosphate backbone is depicted as a segmented grey cylinder half as long and twice as wide as the nitrogenous bases. Nitrogenous bases are represented as blue, orange, red, or green vertical rectangles attached to each segment of the sugar-phosphate backbone. About three dozen individual nucleotides float in the background. Two individual nucleotides are visible inside the transparent enzyme at a higher magnification. Transcription begins when RNA polymerase binds to the DNA template strand. Initiation. The first step in transcription is initiation. During this step, RNA polymerase and its associated transcription factors bind to the DNA strand at a specific area that facilitates transcription (Figure 1). This area, known as a promoter region, often includes a specialized nucleotide sequence, TATAAA, which is also called the TATA box (not shown in Figure 1). Strand Elongation. A schematic shows two horizontal strands of DNA against a white background, one in the lower half of the image and one arcing in the upper half. A transparent green globular structure, representing the enzyme RNA polymerase, is bound to a several-nucleotide-long region along the lower DNA strand about 60% of the way from the left side. The sugar-phosphate backbone of the DNA strand is depicted as a segmented grey cylinder, whereas the sugar-phosphate backbone of the RNA strand is depicted as a segmented white cylinder. DNA nitrogenous bases are represented as blue, orange, red, or green vertical rectangles attached to each segment of the sugar-phosphate backbone; RNA nitrogenous bases are represented by blue, green, orange, and yellow vertical rectangles attached to each segment of the sugar-phosphate backbone. RNA polymerase synthesizes a complementary RNA strand, forming DNA-RNA pairs of orange-blue, red-green, blue-orange, or green-yellow, consistent with a thymine to uracil substitution in the RNA strand. About three dozen individual nucleotides float in the background. One individual nucleotide is visible inside the transparent enzyme at a higher magnification. Figure 2: RNA polymerase (green) synthesizes a strand of RNA that is complementary to the DNA template strand below it. Once RNA polymerase and its related transcription factors are in place, the single-stranded DNA is exposed and ready for transcription. At this point, RNA polymerase begins moving down the DNA template strand in the 3' to 5' direction, and as it does so, it strings together complementary nucleotides. By virtue of complementary base- pairing, this action creates a new strand of mRNA that is organized in the 5' to 3' direction. As the RNA polymerase continues down the strand of DNA, more nucleotides are added to the mRNA, thereby forming a progressively longer chain of nucleotides (Figure 2). This process is called elongation. A schematic compares a single-stranded DNA molecule with a single-stranded RNA molecule with a similar sequence. Both RNA and DNA contain nitrogenous bases, represented by vertical colored rectangles, attached to a sugar-phosphate backbone, represented as a segmented cylinder. There are two major differences between the composition of RNA and DNA strands. The sugar in the DNA strand is deoxyribose, represented by a grey cylinder, whereas the sugar in the RNA strand is ribose, represented by a white cylinder. In addition, the nitrogenous base thymine (red) in the DNA strand is replaced by uracil (yellow) in the RNA strand. Figure 3: DNA (top) includes thymine (red); in RNA (bottom), thymine is replaced with uracil (yellow). Three of the four nitrogenous bases that make up RNA — adenine (A), cytosine (C), and guanine (G) — are also found in DNA. In RNA, however, a base called uracil (U) replaces thymine (T) as the complementary nucleotide to adenine (Figure 3). This means that during elongation, the presence of adenine in the DNA template strand tells RNA polymerase to attach a uracil in the corresponding area of the growing RNA strand (Figure 4). A schematic shows two rows of nucleotides. Each individual nucleotide is represented as an elongated, vertical, colored rectangle (a nitrogenous base) bound at one end to a grey horizontal cylinder (a sugar molecule). The top row of nucleotides is from RNA, with an A-C-U-G base sequence. The bottom row of nucleotides is from DNA, with a T-G-A-C base sequence. Figure 4: A sample section of RNA bases (upper row) paired with DNA bases (lower row). When this base-pairing happens, RNA uses uracil (yellow) instead of thymine to pair with adenine (green) in the DNA template below. Interestingly, this base substitution is not the only difference between DNA and RNA. A second major difference between the two substances is that RNA is made in a single-stranded, nonhelical form. (Remember, DNA is almost always in a double-stranded helical form.) Furthermore, RNA contains ribose sugar molecules, which are slightly different than the deoxyribosemolecules found in DNA. As its name suggests, ribose has more oxygen atoms than deoxyribose. Thus, the elongation period of transcription creates a new mRNA molecule from a single template strand of DNA. As the mRNA elongates, it peels away from the template as it grows (Figure 5). This mRNA molecule carries DNA's message from the nucleus to ribosomes in the cytoplasm, where proteins are assembled. However, before it can do this, the mRNA strand must separate itself from the DNA template and, in some cases, it must also undergo an editing process of sort. Termination and editing. A schematic shows a single-stranded region of RNA on a white surface that has had a loop, or intron, removed. Figure 6: In eukaryotes, noncoding regions called introns are often removed from newly synthesized mRNA. Figure Detail. As previously mentioned, mRNA cannot perform its assigned function within a cell until elongation ends and the new mRNA separates from the DNA template. This process is referred to as termination. In eukaryotes, the process of termination can occur in several different ways, depending on the exact type of polymerase used during transcription. In some cases, termination occurs as soon as the polymerase reaches a specific series of nucleotides along the DNA template, known as the termination sequence. In other cases, the presence of a special protein known as a termination factor is also required for termination to occur. Once termination is complete, the mRNA molecule falls off the DNA template. At this point, at least in eukaryotes, the newly synthesized mRNA undergoes a process in which noncoding nucleotide sequences, called introns, are clipped out of the mRNA strand. This process "tidies up" the molecule and removes nucleotides that are not involved in protein production (Figure 6). Then, a sequence of adenine nucleotides called a poly-A tail is added to the 3' end of the mRNA molecule (Figure 7). This sequence signals to the cell that the mRNA molecule is ready to leave the nucleus and enter the cytoplasm. Once an mRNA molecule is complete, that molecule can go on to play a key role in the process known as translation. During translation, the information that is contained within the mRNA is used to direct the creation of a protein molecule. In order for this to occur, however, the mRNA itself must be read by a special, protein-synthesizing structure within the cell known as a ribosome. Replication.

Over and Out, meaning "transmission is over and has ended at that time". This lets the receiver know that the message has ended and there will be no more communication at this time, so the person is not sitting there waiting for a response. The receiver must understand the language of the transmitter, and know when to send a message in return, and also know the length of time between each transmission. Like Morse code, there has to be pauses or breaks, and the receiver must understand what those pauses mean. How does the DNA know when to implement the code and when to stop it? The human body is the interface to our environment. we have an internal system (mind) interacting with a external system (environment), these two systems are separate yet connected in many different ways. Humans are a living system, and people are the cells of this system. This is where that process of information transfer becomes into being. Information has to be written, and the information must know the receiver. You can say that the process doesn't have to know the reciever, only do what is programed. But where did this information originate from? Is it God? Who is creating your dreams when you're sleeping? Is it God? This is like trying to decipher encrypted messages. You have to analyze the patterns and line them up with possible causes that they may have ben effected by these messages that happened before the event. You have to look at everything that is happening and understand that there was a cause and a reason.

D.N.A. - A Flock of Seagulls (youtube)