query: where can nucleic acids be found in a cell

pos: Nucleic acid 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 for RNA, two for DNA—and assembled into chains of base-pairs

pos: Goblet cell the granules and the nucleus. This gives the basal part of the cell a basophilic staining because of nucleic acids within the nucleus and rough endoplasmic reticulum staining with hematoxylin. Mucin within the granules stains pale in routine histology sections, primarily because these carbohydrate-rich proteins are washed out in the preparation of microscopy samples. However, they stain easily with the PAS staining method, which colours them magenta. In mucicarmine stains, deep red mucin is found within goblet cell bodies. Goblet cells can be seen in the examples below as the larger, more pale cells. The main role of goblet cells

pos: Vectors in gene therapy non-covalently bound to various molecules, thus facilitating these molecules’ entry into cells. Cell entry occurs primarily by endocytosis but other entry mechanisms also exist. Examples of cargo molecules of CPPs include nucleic acids, liposomes, and drugs of low molecular weight. CPP cargo can be directed into specific cell organelles by incorporating localization sequences into CPP sequences. For example, nuclear localization sequences are commonly used to guide CPP cargo into the nucleus. For guidance into mitochondria, a mitochondrial targeting sequence can be used; this method is used in protofection (a technique that allows for foreign mitochondrial DNA to be inserted into

pos: RNA RNA has led to many important biological discoveries and numerous Nobel Prizes. Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the nucleus. It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis was suspected already in 1939. Severo Ochoa won the 1959 Nobel Prize in Medicine (shared with Arthur Kornberg) after he discovered an enzyme that can synthesize RNA in the laboratory. However, the enzyme discovered by Ochoa (polynucleotide phosphorylase) was later shown to be

pos: Nucleic acid and the biotechnology and pharmaceutical industries. The term "nucleic acid" is the overall name for DNA and RNA, members of a family of biopolymers, and is synonymous with "polynucleotide". Nucleic acids were named for their initial discovery within the nucleus, and for the presence of phosphate groups (related to phosphoric acid). Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms including within bacteria, archaea, mitochondria, chloroplasts, viruses, and viroids. (note: there is debate as to whether viruses are living or non-living). All living cells contain both DNA and

neg: Biomedicine known as fats, also serve to store energy, but in the long term. Due to their unique structure, lipids provide more than twice the amount of energy that carbohydrates do. Lipids can be used as insulation, as it is present below the layer of skin in living organisms. Moreover, lipids can be used in hormone production to maintain a healthy hormonal balance and provide structure to your cell walls. Nucleic acids are used to store DNA in every living organism. The two types of nucleic acids are DNA and RNA. DNA is the main genetic information storing substance found oftentimes

neg: Genetic engineering techniques cell. Once open, the DNA must be separated from the other cellular components. A ruptured cell contains proteins and other cell debris. By mixing with phenol and/or chloroform, followed by centrifuging, the nucleic acids can be separated from this debris into an upper aqueous phase. This aqueous phase can be removed and further purified if necessary by repeating the phenol-chloroform steps. The nucleic acids can then be precipitated from the aqueous solution using ethanol or isopropanol. Any RNA can be removed by adding a ribonuclease that will degrade it. Many companies now sell kits that simplify the process. The gene

neg: Metabolome studying E. coli as a model organism. Metabolome The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism (such as amino acids, organic acids, nucleic acids, fatty acids, amines, sugars, vitamins, co-factors, pigments, antibiotics, etc.) as well as exogenous chemicals (such as drugs, environmental contaminants, food additives, toxins and other xenobiotics)

neg: Metabolome Metabolome The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism (such as amino acids, organic acids, nucleic acids, fatty acids, amines, sugars, vitamins, co-factors, pigments, antibiotics, etc.) as well as exogenous chemicals (such as drugs, environmental contaminants, food additives, toxins and other xenobiotics) that are not naturally produced by an

neg: Gel electrophoresis of nucleic acids Gel electrophoresis of nucleic acids Nucleic acid electrophoresis is an analytical technique used to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules which are to be analyzed are set upon a viscous medium, the gel, where an electric field induces the nucleic acids (which are negatively charged due to their sugar-phosphate backbone) to migrate toward the anode (which is positively charged because this is an electrolytic rather than galvanic cell). The separation of these fragments is accomplished by exploiting the mobilities with which different sized molecules are able to pass through the gel. Longer molecules migrate

neg: Xenobiology being used as extensions to template DNA strands, XNA activity has been tested for use as genetic catalysts. Although proteins are the most common components of cellular enzymatic activity, nucleic acids are also used in the cell to catalyze reactions. A 2015 study found several different kinds of XNA, most notably FANA (2'-fluoroarabino nucleic acids), as well as HNA, CeNA and ANA (arabino nucleic acids) could be used to cleave RNA during post-transcriptional RNA processing acting as XNA enzymes, hence the name XNAzymes. FANA XNAzymes also showed the ability to ligate DNA, RNA and XNA substrates. Although XNAzyme studies are

neg: Phenol extraction obtain nucleic acid samples, the cell must be lysed and the nucleic acids separated from all other cell materials. Phenol is a useful compound for breaking down superfluous cell materials that would otherwise contaminate the nucleic acid sample. There are two reasons why phenol makes such an effective purifier for nucleic acid samples. The first is that it is a non-polar compound. Because nucleic acids are highly polar, they do not dissolve in the presence of phenol. The second is that phenol has a density of 1.07 g/cm, which is higher than the density of water (1.00 g/cm). Thus, when

neg: Magnet-assisted transfection Magnet-assisted transfection Magnet-assisted transfection is a transfection method which uses magnetic interactions to deliver DNA into target cells. Nucleic acids are associated with magnetic nanoparticles, and magnetic fields drive the nucleic acid-particle complexes into target cells, where the nucleic acids are released. Nanoparticles used as carriers for nucleic acids are mostly iron oxides. These iron oxides can be generated by precipitation from acidic iron-salt solutions upon addition of appropriate bases. The magnetic nanoparticles have an approximate size of 100 nm and are additionally coated with biological polymers to allow loading of nucleic acids. Particles and nucleic acids form complexes by

neg: Magnet-assisted transfection synergistic effects in transfection efficiency can arise from the possible combination of lipofection and magnet-assisted transfection. In future, this technology might be also an alternative strategy to the currently used viral and non-viral vectors in gene-therapy and gene transfer. Magnet-assisted transfection Magnet-assisted transfection is a transfection method which uses magnetic interactions to deliver DNA into target cells. Nucleic acids are associated with magnetic nanoparticles, and magnetic fields drive the nucleic acid-particle complexes into target cells, where the nucleic acids are released. Nanoparticles used as carriers for nucleic acids are mostly iron oxides. These iron oxides can be generated by precipitation

neg: Single cell sequencing cell, cellular functions can be investigated extensively. Like typical NGS experiments, the protocols of single cell sequencing generally contain the following steps: isolation of a single cell, nucleic acid extraction and amplification, sequencing library preparation, sequencing and bioinformatic data analysis. It is more challenging to perform single cell sequencing in comparison with sequencing from cells in bulk. The minimal amount of starting materials from a single cell make degradation, sample loss and contamination exert pronounced effects on quality of sequencing data. In addition, due to the picogram level of the amount of nucleic acids used, heavy amplification is often needed

neg: Molecular diagnostics biopsy. For example, because cell-free nucleic acids exist in human plasma, a simple blood sample can be enough to sample genetic information from tumours, transplants or an unborn fetus. Many, but not all, molecular diagnostics methods based on nucleic acids detection use polymerase chain reaction (PCR) to vastly increase the number of nucleic acid molecules, thereby amplifying the target sequence(s) in the patient sample. PCR is a method that a template DNA is amplified using synthetic primers, a DNA polymerase, and dNTPs. The mixture is cycled between at least 2 temperatures: a high temperature for denaturing double-stranded DNA into single-stranded

neg: RNA world replaced by RNA only later. On the other hand, the discovery in 2009 that activated pyrimidine ribonucleotides can be synthesized under plausible prebiotic conditions suggests that it is premature to dismiss the RNA-first scenarios. Suggestions for 'simple' "pre-RNA" nucleic acids have included peptide nucleic acid (PNA), threose nucleic acid (TNA) or glycol nucleic acid (GNA). Despite their structural simplicity and possession of properties comparable with RNA, the chemically plausible generation of "simpler" nucleic acids under prebiotic conditions has yet to be demonstrated. RNA enzymes, or ribozymes, are found in today's DNA-based life and could be examples of living fossils. Ribozymes

neg: Virus-like particle the host cell ("in vivo"), though the self-assembly event was found "in vitro" from the very beginning of the study about viral assembly. Study also reveals that "in vitro" assembly of VLPs competes with aggregation and certain mechanisms exist inside the cell to prevent the formation of aggregates while assembly is ongoing. Attaching proteins, nucleic acids, or small molecules to the VLP surface, such as for targeting a specific cell type or for raising an immune response is useful. In some cases a protein of interest can be genetically fused to the viral coat protein. However, this approach sometimes leads

neg: Biological effects of radiation on the epigenome Biological effects of radiation on the epigenome Ionizing radiation can cause biological effects which are passed on to offspring through the epigenome. The effects of radiation on cells has been found to be dependent on the dosage of the radiation, the location of the cell in regards to tissue, and whether the cell is a somatic or germ line cell. Generally, ionizing radiation appears to reduce methylation of DNA in cells. Ionizing radiation has been known to cause damage to cellular components such as proteins, lipids, and nucleic acids. It has also been known to cause DNA double-strand breaks. Accumulation

neg: Hypoxanthine Hypoxanthine Hypoxanthine is a naturally occurring purine derivative. It is occasionally found as a constituent of nucleic acids, where it is present in the anticodon of tRNA in the form of its nucleoside inosine. It has a tautomer known as 6-hydroxypurine. Hypoxanthine is a necessary additive in certain cell, bacteria, and parasite cultures as a substrate and nitrogen source. For example, it is commonly a required reagent in malaria parasite cultures, since "Plasmodium falciparum" requires a source of hypoxanthine for nucleic acid synthesis and energy metabolism. In August 2011, a report, based on NASA studies with meteorites found on Earth,

neg: Biotic stress hornworm ("Manduca sexta)." This example demonstrates the importance of MAP kinases in plant defence regulation. Plants are capable of detecting invaders through the recognition of non-self signals despite the lack of a circulatory or immune system like those found in animals. Often a plant's first line of defense against microbes occurs at the plant cell surface and involves the detection of microorganism-associated molecular patterns (MAMPs). MAMPs include nucleic acids common to viruses and endotoxins on bacterial cell membranes which can be detected by specialized pattern-recognition receptors. Another method of detection involves the use of plant immune receptors to detect effector

neg: Nucleic acid metabolism Nucleic acid metabolism Nucleic acid metabolism is the process by which nucleic acids (DNA and RNA) are synthesized and degraded. Nucleic acids are polymers of nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. Destruction of nucleic acid is a catabolic reaction. Additionally, parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases. Nucleotides can be separated into purines and pyrimidines. They

neg: Hypoxanthine in DNA transcription/replication, as it binds with cytosine. Hypoxanthine Hypoxanthine is a naturally occurring purine derivative. It is occasionally found as a constituent of nucleic acids, where it is present in the anticodon of tRNA in the form of its nucleoside inosine. It has a tautomer known as 6-hydroxypurine. Hypoxanthine is a necessary additive in certain cell, bacteria, and parasite cultures as a substrate and nitrogen source. For example, it is commonly a required reagent in malaria parasite cultures, since "Plasmodium falciparum" requires a source of hypoxanthine for nucleic acid synthesis and energy metabolism. In August 2011, a report, based

neg: Nucleotidase 5'-nucleotidase. A new class of nucleotidases called IMP-specific 5'-nucleotidase has been recently defined. 5'-Nucleotidases are involved in varied functions like cell–cell communication, nucleic acid repair, purine salvage pathway for the synthesis of nucleotides, signal transduction, membrane transport, etc. Nucleotidase A nucleotidase is a hydrolytic enzyme that catalyzes the hydrolysis of a nucleotide into a nucleoside and a phosphate. For example, it converts adenosine monophosphate to adenosine, and guanosine monophosphate to guanosine. Nucleotidases have an important function in digestion in that they break down consumed nucleic acids. They can be divided into two categories, based upon the end that is hydrolyzed:

neg: Genetic engineering developed that aid food security by increasing yield, nutritional value and tolerance to environmental stresses. The DNA can be introduced directly into the host organism or into a cell that is then fused or hybridised with the host. This relies on recombinant nucleic acid techniques to form new combinations of heritable genetic material followed by the incorporation of that material either indirectly through a vector system or directly through micro-injection, macro-injection or micro-encapsulation. Genetic engineering does not normally include traditional breeding, in vitro fertilisation, induction of polyploidy, mutagenesis and cell fusion techniques that do not use recombinant nucleic acids or

neg: Macromolecular docking can be estimated by a protein structure prediction technique. Protein–nucleic acid interactions feature prominently in the living cell. Transcription factors, which regulate gene expression, and polymerases, which catalyse replication, are composed of proteins, and the genetic material they interact with is composed of nucleic acids. Modeling protein–nucleic acid complexes presents some unique challenges, as described below. In the 1970s, complex modelling revolved around manually identifying features on the surfaces of the interactors, and interpreting the consequences for binding, function and activity; any computer programmes were typically used at the end of the modelling process, to discriminate between the relatively few

neg: Microvesicles well as many proteins involved in signal transduction, cell structure and motility, and transcription. Most microvesicles contain the so-called "heat-shock proteins" hsp70 and hsp90, which can facilitate interactions with cells of the immune system. Finally, tetraspanin proteins, including CD9, CD37, CD63 and CD81 are one of the most abundant protein families found in microvesicle membranes. Many of these proteins may be involved in the sorting and selection of specific cargos to be loaded into the lumen of the microvesicle or its membrane. Other than lipids and proteins, microvesicles are enriched with nucleic acids (e.g., messenger RNA (mRNA) and microRNA (miRNA).

neg: Nucleic acid Nucleic acid Nucleic acids are the biopolymers, or small biomolecules, essential to all known forms of life. The term "nucleic acid" is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound 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 the most important of all biomolecules. They are found in abundance in all living things, where they

neg: Nucleic acid structure determination Nucleic acid structure determination Structure probing of nucleic acids is the process by which biochemical techniques are used to determine nucleic acid structure. This analysis can be used to define the patterns which can infer the molecular structure, experimental analysis of molecular structure and function, and further understanding on development of smaller molecules for further biological research. Structure probing analysis can be done through many different methods, which include chemical probing, hydroxyl radical probing, SHAPE, nucleotide analog interference mapping (NAIM), and in-line probing. x-ray crystallography is not common for nucleic acids alone, since neither DNA nor RNA readily form crystals.

neg: Morpholino translational frameshifts. Morpholinos can block RNA editing, poly-A tailing and translocation sequences. Morpholino activities against this variety of targets suggest that Morpholinos can be used as a general-purpose tool for blocking interactions of proteins or nucleic acids with mRNA. Morpholinos have become a standard knockdown tool in animal embryonic systems, which have a broader range of gene expression than adult cells and can be strongly affected by an off-target interaction. Following initial injections into frog or fish embryos at the single-cell or few-cell stages, Morpholino effects can be measured up to five days later, after most of the processes of

neg: Nucleic acid RNA (except some cells such as mature red blood cells), while viruses contain either DNA or RNA, but usually not both. The basic component of biological nucleic acids is the nucleotide, each of which contains a pentose sugar (ribose or deoxyribose), a phosphate group, and a nucleobase. Nucleic acids are also generated within the laboratory, through the use of enzymes (DNA and RNA polymerases) and by solid-phase chemical synthesis. The chemical methods also enable the generation of altered nucleic acids that are not found in nature, for example peptide nucleic acids. Nucleic acids are generally very large molecules. Indeed, DNA

neg: Trehalose clusters to percolate and form large, continuous aggregates. Trehalose directly interacts with nucleic acids, facilitates melting of double stranded DNA and stabilizes single-stranded nucleic acids. Organisms ranging from bacteria, yeast, fungi, insects, invertebrates, and lower and higher plants have enzymes that can make trehalose. In nature, trehalose can be found in plants, and microorganisms. In animals, trehalose is prevalent in shrimp, and also in insects, including grasshoppers, locusts, butterflies, and bees, in which trehalose serves as blood-sugar. Trehalose is then broken down into glucose by the catabolic enzyme trehalase for use. Trehalose is also present in the nutrition exchange liquid

neg: Cell (biology) Cell (biology) The cell (from Latin "cella", meaning "small room") is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life. Cells are often called the "building blocks of life". The study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids. Organisms can be classified as unicellular (consisting of a single cell; including bacteria) or multicellular (including plants and animals). While the number of cells in plants and animals varies from species to species, humans

neg: TP53-inducible glycolysis and apoptosis regulator unknown. TIGAR can promote development or inhibition of several cancers depending on the cellular context. TIGAR can have some effect on three characteristics of cancer; the ability to evade apoptosis, uncontrolled cell division, and altered metabolism. Many cancer cells have altered metabolism where the rate of glycolysis and anaerobic respiration are very high whilst oxidative respiration is low, which is called the Warburg Effect (or aerobic glycolysis). This allows cancer cells to survive under low oxygen conditions, and use molecules from respiratory pathways to synthesise amino acids and nucleic acids to maintain rapid growth. In Glioma, a type of brain

neg: Nucleic acid sequence the many bases created through mutagen presence, both of them through deamination (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced from adenine, xanthine from guanine. Similarly, deamination of cytosine results in uracil. In biological systems, nucleic acids contain information which is used by a living cell to construct specific proteins. The sequence of nucleobases on a nucleic acid strand is translated by cell machinery into a sequence of amino acids making up a protein strand. Each group of three bases, called a codon, corresponds to a single amino acid, and there is a specific genetic code by which

neg: Tata Swach germs and other organisms. The bacteriostatic and bactericidal properties of silver are attributed to its ability to react with the sulphhydryl (-SH) groups in the bacterial cells that produces the structural changes in bacterial cell membranes and interacts with nucleic acids. The nano sized particles help in increasing the surface area so that the bacteria get enough reaction time. The Swach can purify water at the rate of about every hour. The purifier consists of two parts; an upper reservoir where the untreated water enters and a lower middle portion with a bulb to which the cartridge can be attached.

neg: Biochemistry the nucleic acid, while the sequence of nitrogenous bases stores the information. The most common nitrogenous bases are adenine, cytosine, guanine, thymine, and uracil. The nitrogenous bases of each strand of a nucleic acid will form hydrogen bonds with certain other nitrogenous bases in a complementary strand of nucleic acid (similar to a zipper). Adenine binds with thymine and uracil; thymine binds only with adenine; and cytosine and guanine can bind only with one another. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for

neg: Gel electrophoresis of nucleic acids Cytidine or guanosine to the electrophoresis buffer at 1 mM concentration may protect the DNA from damage. Alternatively, a blue light excitation source with a blue-excitable stain such as SYBR Green or GelGreen may be used. Gel electrophoresis research often takes advantage of software-based image analysis tools, such as ImageJ. Gel electrophoresis of nucleic acids Nucleic acid electrophoresis is an analytical technique used to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules which are to be analyzed are set upon a viscous medium, the gel, where an electric field induces the nucleic acids (which are negatively

neg: Granzyme viral proteins to inhibit viral activation and replication. The granzymes bind directly to the nucleic acids DNA and RNA; this enhances their cleavage of nucleic acid binding proteins. More recently, in addition to T lymphocytes, granzymes have been shown to be expressed in other types of immune cells such as dendritic cells, B cells and mast cells. In addition, granzymes may also be expressed in non-immune cells such as keratinocytes, pneumocytes and chondrocytes. As many of these cell types either do not express perforin or do not form immunological synapses, granzyme B is released extracellularly. Extracellular granzyme B can accumulate

neg: Denaturation (biochemistry) promotes denaturation of nucleic acids in order to eliminate the influence of nucleic acid shape on their electrophoretic mobility. The optical activity (absorption and scattering of light) and hydrodynamic properties (translational diffusion, sedimentation coefficients, and rotational correlation times) of formamide denatured nucleic acids are similar to those of heat-denatured nucleic acids. Therefore, depending on the desired effect, chemically denaturing DNA can provide a gentler procedure for denaturing nucleic acids than denaturation induced by heat. Studies comparing different denaturation methods such as heating, beads mill of different bead sizes, probe sonification, and chemical denaturation show that chemical denaturation can provide quicker

neg: Nucleic acid thermodynamics from two single stranded oligonucleotides. Under this assumption one can elegantly describe the thermodynamic parameters for forming double-stranded nucleic acid AB from single-stranded nucleic acids A and B. The equilibrium constant for this reaction is formula_1. According to the Van´t Hoff equation, the relation between free energy, Δ"G", and "K" is Δ"G°" = -"RT"ln "K", where "R" is the ideal gas law constant, and "T" is the kelvin temperature of the reaction. This gives, for the nucleic acid system, formula_2. The melting temperature, "T", occurs when half of the double-stranded nucleic acid has dissociated. If no additional nucleic acids are

neg: Microvesicles The identification of RNA molecules in microvesicles supports the hypothesis that they are a biological vehicle for the transfer of nucleic acids and subsequently modulate the target cell's protein synthesis. Messenger RNA transported from one cell to another through microvesicles can be translated into proteins, conferring new function to the target cell. The discovery that microvesicles may shuttle specific mRNA and miRNA suggests that this may be a new mechanism of genetic exchange between cells. Exosomes produced by cells exposed to oxidative stress can mediate protective signals, reducing oxidative stress in recipient cells, a process which is proposed to depend

neg: Monoclonal antibody phenomenon called membrane fouling in later purification steps. In addition, the concentration of product in the sample may not be sufficient, especially in cases where the desired antibody is produced by a low-secreting cell line. The sample is therefore concentrated by ultrafiltration or dialysis. Most of the charged impurities are usually anions such as nucleic acids and endotoxins. These can be separated by ion exchange chromatography. Either cation exchange chromatography is used at a low enough pH that the desired antibody binds to the column while anions flow through, or anion exchange chromatography is used at a high enough pH

neg: Histology be used to determine if a tumour is malignant when it is found incidentally during surgery on a patient. Biological tissue has little inherent contrast in either the light or electron microscope. Staining is employed to give both contrast to the tissue as well as highlighting particular features of interest. Where the underlying mechanistic chemistry of staining is understood, the term histochemistry is used. Hematoxylin and eosin (H&E stain) is the most commonly used light microscopical stain in histology and histopathology. Hematoxylin, a basic dye, stains nuclei blue due to an affinity to nucleic acids in the cell nucleus; eosin,

neg: Lipidome Lipidome The lipidome refers to the totality of lipids in cells. Lipids are one of the four major molecular components of biological organisms, along with proteins, sugars and nucleic acids. Lipidome is a term coined in the context of omics in modern biology, within the field of lipidomics. It can be studied using mass spectrometry and bioinformatics as well as traditional lab-based methods. The lipidome of a cell can be subdivided into the membrane-lipidome and mediator-lipidome. The first cell lipidome to be published was that of a mouse macrophage in 2010. The lipidome of the yeast "Saccharomyces cerevisiae" has been

neg: RUNX2 that Runx2 may play are still unknown, although it is generally accepted that the varying activity and levels of Runx2 throughout the cell cycle contribute to cell cycle entry and exit, as well as cell cycle progression. These functions are especially important when discussing bone cancer, particularly osteosarcoma development, that can be attributed to aberrant cell proliferation control. This protein is a member of the RUNX family of transcription factors and has a Runt DNA-binding domain. It is essential for osteoblastic differentiation and skeletal morphogenesis. It acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene

neg: Antimetabolite and subsequent incorporation of these biomolecules into nucleic acids, inhibits their normal tumor cell function and triggers apoptosis, or the cell death process. Because of this mode of action, most antimetabolites have high cell cycle specificity and can target arrest of cancer cell DNA replication. Antimetabolites may also be antibiotics, such as sulfanilamide drugs, which inhibit dihydrofolate synthesis in bacteria by competing with para-aminobenzoic acid (PABA). PABA is needed in enzymatic reactions that produce folic acid, which acts as a coenzyme in the synthesis of purines and pyrimidines, the building-blocks of DNA. Mammals do not synthesize their own folic acid

neg: Nucleic acid structure determination band the areas of various strength of protection where areas of stronger protection for hydroxyl radicals can be said to have tighter association with a protein, or if no protein associates with the nucleic acid it can be caused by the tertiary fold. Dimethyl sulfate, known as DMS, is a chemical that can be used to modify nucleic acids in order to determine secondary structure. DMS modifies certain bases through methylation. One set of methylation products that is used for RNA is the methylation of N1 adenosine and N3 of cytosine which prevents the natural hydrogen bonds to form between

neg: Nucleic acid structure determination no band corresponding to that position on the gel. This process can be used to evaluate an entire area, where analogs are placed in site specific locations, differing by a single nucleotide, then when functional RNAs are isolated and run on a gel, all areas where bands are produced indicate non-essential nucleotides, but areas where bands are absent from the functional RNA indicate that inserting a nucleotide analog in that position caused the RNA molecule to become non-functional Nucleic acid structure determination Structure probing of nucleic acids is the process by which biochemical techniques are used to determine nucleic acid

neg: Biogenic amine can be found in all foods containing proteins or free amino acids and are found in a wide range of food products including fish products, meat products, dairy products, wine, beer, vegetables, fruits, nuts and chocolate. In non-fermented foods the presence of biogenic amines is mostly undesired and can be used as indication for microbial spoilage. In fermented foods, one can expect the presence of many kinds of microorganisms, some of them being capable of producing biogenic amines. They play an important role as source of nitrogen and precursor for the synthesis of hormones, alkaloids, nucleic acids, proteins, amines and

neg: Prion virus in 10%, or less, of their scrapie-infected cells in culture. In 2016, Sotirios Botsios and Laura Manuelidis showed evidence that TSE specific nucleic acids may be required for infectious transmission of CJD and Scrapie. Evidence in favor of a viral hypothesis includes: Studies propagating TSE infectivity in cell-free reactions and in purified component chemical reactions is thought to strongly suggest against TSE viral nature. However, some viruses, such as Poliovirus, have the ability to replicate in cell-free reactions. The 'virino hypothesis' postulates that the TSE agent is a foreign, self replicating nucleic acid or nucleic acid fragment bound to

neg: Nucleotide sites on sugar molecules in adjacent nucleotides. In a double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA. Unlike in nucleic acid nucleotides, singular cyclic nucleotides are formed when the phosphate group is bound twice to the same sugar molecule, i.e., at the corners of the sugar hydroxyl groups. These individual nucleotides function in cell metabolism rather than the nucleic acid structures of long-chain molecules. Nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units

neg: Nucleic acid structure is found in prokaryotes, while the solenoidal supercoiling is mostly seen in eukaryotes. The quaternary structure of nucleic acids is similar to that of protein quaternary structure. Although some of the concepts are not exactly the same, the quaternary structure refers to a higher-level of organization of nucleic acids. Moreover, it refers to interactions of the nucleic acids with other molecules. The most commonly seen form of higher-level organization of nucleic acids is seen in the form of chromatin which leads to its interactions with the small proteins histones. Also, the quaternary structure refers to the interactions between separate RNA

neg: Nucleic acid sequence each possible combination of three bases corresponds to a specific amino acid. The central dogma of molecular biology outlines the mechanism by which proteins are constructed using information contained in nucleic acids. DNA is transcribed into mRNA molecules, which travels to the ribosome where the mRNA is used as a template for the construction of the protein strand. Since nucleic acids can bind to molecules with complementary sequences, there is a distinction between "sense" sequences which code for proteins, and the complementary "antisense" sequence which is by itself nonfunctional, but can bind to the sense strand. DNA sequencing is the

neg: Marine bacteriophage the biological pump. The argument is that lysis releases unstable compounds, such as amino acids and nucleic acids, which tend to be recycled near the surface, whereas more indigestible carbon-rich material, such as that found in cell walls, is probably exported to deeper waters. Thus, the material that is exported to deeper waters by the 'viral shunt' is probably more carbon rich than the material from which it was derived. This would increase the efficiency of the biological pump. Marine bacteriophage Marine bacteriophages or marine phages are viruses that live as obligate parasitic agents in marine bacteria such as cyanobacteria.

neg: RNA integrity number field to them. As nucleic acids are negatively charged, they are pushed by an electric field through a matrix, usually an agarose gel, with the smaller molecules being pushed farther, faster. Capillary electrophoresis is a technique whereby small amounts of a nucleic acid sample can be run on a gel in a very thin tube. There is a detector in the machine that can tell when nucleic acid samples pass through a detector, with smaller samples passing through first. This can produce an electropherogram such as the one in Figure 1, where length is related to time at which the

neg: Monoclonal antibody nucleases, nucleic acids and viruses. In both cases, other secretions by the hybridomas such as cytokines may be present. There may also be bacterial contamination and, as a result, endotoxins that are secreted by the bacteria. Depending on the complexity of the media required in cell culture and thus the contaminants, one or the other method ("in vivo" or "in vitro") may be preferable. The sample is first conditioned, or prepared for purification. Cells, cell debris, lipids and clotted material are first removed, typically by centrifugation followed by filtration with a 0.45 µm filter. These large particles can cause a

neg: Raman spectroscopy then be used to generate images showing the location and amount of different components. Taking the cell culture example, a hyperspectral image could show the distribution of cholesterol, as well as proteins, nucleic acids, and fatty acids. Sophisticated signal- and image-processing techniques can be used to ignore the presence of water, culture media, buffers, and other interference. Raman microscopy, and in particular confocal microscopy, has very high spatial resolution. For example, the lateral and depth resolutions were 250 nm and 1.7 µm, respectively, using a confocal Raman microspectrometer with the 632.8 nm line from a helium–neon laser with a pinhole

neg: Cell-penetrating peptide covalent bond between CPP and nucleic acid may alter the biological activity of the latter. Thus, a new non-covalent strategy requiring no chemical modification with short amphipathic CPPs, like MPG and Pep-1 as carriers has been successfully applied for delivery of cargoes. These non-covalent conjugates are formed through either electrostatic or hydrophobic interactions. With this method, cargoes such as nucleic acids and proteins could be efficiently delivered while maintaining full biological activity. Short interfering RNA (siRNA) is a very powerful new tool that can interfere with and silence the expression of specific disease gene. To improve cellular uptake of siRNA,

neg: Decellularization to lyse the cell membrane and expose the contents to further degradation. After SDS lyses the cell membrane, endonucleases and exonucleases degrade the genetic contents, while other components of the cell is solubilized and washed out of the matrix. SDS is commonly used even though it has a tendency to slightly disrupt the ECM structure. Akaline and acid treatments can be effective companions with an SDS treatment due to their ability to degrade nucleic acids and solubilize cytoplasmic inclusions. The most well known non-ionic detergent is Triton X-100, which is popular because of its ability to disrupt the interactions between

neg: Gel electrophoresis of nucleic acids more slowly because they experience more resistance within the gel. Because the size of the molecule affects its mobility, smaller fragments end up nearer to the anode than longer ones in a given period. After some time, the voltage is removed and the fragmentation gradient is analyzed. For larger separations between similar sized fragments, either the voltage or run time can be increased. Extended runs across a low voltage gel yield the most accurate resolution. Voltage is, however, not the sole factor in determining electrophoresis of nucleic acids. The nucleic acid to be separated can be prepared in several ways

neg: Nucleic acid analogue analogue that lacks a 3' hydroxyl and mimics adenosine is called cordycepin. Cordycepin is an anticancer drug that targets RNA replication. Another analogue in sequencing is a nucleobase analogue, 7-deaza-GTP and is used to sequence CG rich regions, instead 7-deaza-ATP is called tubercidin, an antibiotic. RNA may be too complex to be the first nucleic acid, so before the RNA world several simpler nucleic acids that differ in the backbone, such as TNA and GNA and PNA, have been offered as candidates for the first nucleic acids. Naturally occurring bases can be divided into two classes according to their structure:

neg: Ribozyme a firmly established belief in biology that catalysis was reserved for proteins. However, the idea of RNA catalysis is motivated in part by the old question regarding the origin of life: Which comes first, enzymes that do the work of the cell or nucleic acids that carry the information required to produce the enzymes? The concept of "ribonucleic acids as catalysts" circumvents this problem. RNA, in essence, can be both the chicken and the egg. In the 1980s Thomas Cech, at the University of Colorado at Boulder, was studying the excision of introns in a ribosomal RNA gene in "Tetrahymena

neg: Raman microscope and amount of different components. Taking the cell culture example, a hyperspectral image could show the distribution of cholesterol , as well as proteins, nucleic acids, and fatty acids . Sophisticated signal- and image-processing techniques can be used to ignore the presence of water, culture media, buffers, and other interference. Raman microscopy, and in particular "confocal microscopy", has very high spatial resolution . For example, the lateral and depth resolutions were 250 nm and 1.7 µm, respectively, using a confocal Raman microspectrometer with the 632.8 nm line from a helium–neon laser with a pinhole of 100 µm diameter. Since the

neg: Denaturation (biochemistry) for proteins include: Chaotropic agents include: Agents that break disulfide bonds by reduction include: Acidic nucleic acid denaturants include: Basic nucleic acid denaturants include: Other nucleic acid denaturants include: Denaturation (biochemistry) Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure, and secondary structure which is present in their native state, by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), radiation or heat. If proteins in a living cell are denatured, this results in disruption of cell

neg: Phenol extraction phenol is added to a cell sample solution the water and phenol remain separate. Two “phases” form when phenol is added to the solution and centrifuged. There is an aqueous, polar phase at the top of the solution containing nucleic acids and water, and an organic phase containing denatured proteins and other cell components at the bottom of the solution. The aqueous phase is always on top of the organic because, as mentioned above, phenol is denser than water. Nucleic acids are polar, and therefore stay in the aqueous phase, whereas non-polar cellular components move into the organic phase. After

neg: Magnet-assisted transfection time, the nanoparticles are degraded and the iron enters the normal iron metabolism. Influence of cellular functions by iron particles has not been reported yet. In most cases the increased iron concentration in culture media does not lead to cytotoxic effects. Magnet-assisted transfection is a relatively new and time-saving method to introduce nucleic acids into a target cell with increased efficiency. In particular, adherent mammalian cell lines and primary cell cultures show very high transfection rates. Suspension cells and cells from other organisms can also be successfully transfected. A major advantage of the method is the mild treatment of the

neg: Abiogenesis geochemistry and biochemistry, and aim to determine how pre-life chemical reactions gave rise to life. The study of abiogenesis can be geophysical, chemical, or biological, with more recent approaches attempting a synthesis of all three, as life arose under conditions that are strikingly different from those on Earth today. Life functions through the specialized chemistry of carbon and water and builds largely upon four key families of chemicals: lipids (fatty cell walls), carbohydrates (sugars, cellulose), amino acids (protein metabolism), and nucleic acids (self-replicating DNA and RNA). Any successful theory of abiogenesis must explain the origins and interactions of these classes

neg: Actinic keratosis have been implicated as causes of AKs. UV-A radiation (wavelength 320-400nm) reaches more deeply into the skin and can lead to the generation of reactive oxygen species, which in turn can damage cell membranes, signaling proteins, and nucleic acids. UV-B radiation (wavelength 290–320nm) causes thymidine dimer formation in DNA and RNA, leading to significant cellular mutations. In particular, mutations in the p53 tumor suppressor gene have been found in 30–50% of AK lesion skin samples. UV radiation has also been shown to cause elevated inflammatory markers such as arachidonic acid, as well as other molecules associated with inflammation. Eventually, over

neg: Nucleoside composed of a nucleoside "and" one or more phosphate groups. Thus, nucleosides can be phosphorylated by specific kinases in the cell on the sugar's primary alcohol group (-CH-OH) to produce nucleotides. Nucleotides are the molecular building-blocks of DNA and RNA. Nucleosides can be produced by de novo synthesis pathways, in particular in the liver, but they are more abundantly supplied via ingestion and digestion of nucleic acids in the diet, whereby nucleotidases break down "nucleotides" (such as the thymidine monophosphate) into "nucleosides" (such as thymidine) and phosphate. The nucleosides, in turn, are subsequently broken down: In addition, nucleotides can be

neg: Dihydropteroate synthase inhibitor Dihydropteroate synthase inhibitor A dihydropteroate synthase inhibitor is a drug that inhibits the action of dihydropteroate synthase. Most are sulfonamides. In bacteria, antibacterial sulfonamides act as competitive inhibitors of the enzyme dihydropteroate synthase, DHPS. DHPS catalyses the conversion of PABA ("para"-aminobenzoate) to dihydropteroate, a key step in folate synthesis. Folate is necessary for the cell to synthesize nucleic acids (nucleic acids are essential building blocks of DNA and RNA), and in its absence cells will be unable to divide. Hence the sulfonamide antibacterials exhibit a bacteriostatic rather than bactericidal effect. Folate is not synthesized in mammalian cells, but is instead

neg: Lymphocytic choriomeningitis used. For this reason, LCMV may be more common than is realized. Another detection assay is the reverse transcription polymerase chain reaction (RT-PCR) tests which may detect nucleic acids in the blood and cerebrospinal fluid.(CSF) Virus isolation is not used for diagnosis in most cases but it can be isolated from the blood or nasopharyngeal fluid early in the course of the disease, or from CSF in patients with meningitis. LCMV can be grown in a variety of cell lines including BHK21, L and Vero cells, and it may be identified with immuno-fluorescence. A diagnosis can also be made by

neg: Nucleic acid thermodynamics that only eight of the ten groups are independent. The nearest-neighbor model can be extended beyond the Watson-Crick pairs to include parameters for interactions between mismatches and neighboring base pairs. This allows the estimation of the thermodynamic parameters of sequences containing isolated mismatches, like e.g. (arrows indicating mismatch) These parameters have been fitted from melting experiments and an extension of Table 1 which includes mismatches can be found in literature. A more realistic way of modeling the behavior of nucleic acids would seem to be to have parameters that depend on the neighboring groups on both sides of a nucleotide,

neg: Asthma-related microbes extracellular, host-associated bacterium that lacks a cell wall and is unable to survive outside of a host due to osmotic instability in the environment. "M. pneumoniae" can cause infections in humans, animals, plants, and cell cultures. It is a parasitic bacterium that invades the mucosal membranes of the upper and lower respiratory tract, including nasopharynx, throat, trachea, bronchi, bronchioles, and alveoli. In order to survive, "M. pneumoniae" needs essential nutrients and compounds such as amino acids, cholesterol, precursors to nucleic acid synthesis, and fatty acids obtained from the mucosal epithelial cells of the host. Its adhesion proteins attach to tracheal

neg: RiboGreen RiboGreen RiboGreen is a proprietary fluorescent dye that is used in the detection and quantification of nucleic acids, including both RNA and DNA. It is synthesized and marketed by Molecular Probes/Invitrogen (a division of Life Technologies, now part of Thermo Fisher Scientific) of Eugene, Oregon, United States. In its free form, RiboGreen exhibits little fluorescence and possesses a negligible absorbance signature. When bound to nucleic acids, the dye fluoresces with an intensity that, according to the manufacturer, is several orders of magnitude greater than the unbound form. The fluorescence can be detected by a sensor and the nucleic acid can

neg: Hybridization assay oligonucleotides. Hybridization assay A hybridization assay comprises any form of quantifiable hybridization "i.e." the quantitative annealing of two complementary strands of nucleic acids, known as nucleic acid hybridization. In the context of biochemistry and drug development, a hybridization assay is a type of Ligand Binding Assay (LBA) used to quantify nucleic acids in biological matrices. Hybridization assays can be in solution or on a solid support such as 96-well plates or labelled beads. Hybridization assays involve labelled nucleic acid probes to identify related DNA or RNA molecules (i.e. with significantly high degree of sequence similarity) within a complex mixture of

neg: Hybridization assay Hybridization assay A hybridization assay comprises any form of quantifiable hybridization "i.e." the quantitative annealing of two complementary strands of nucleic acids, known as nucleic acid hybridization. In the context of biochemistry and drug development, a hybridization assay is a type of Ligand Binding Assay (LBA) used to quantify nucleic acids in biological matrices. Hybridization assays can be in solution or on a solid support such as 96-well plates or labelled beads. Hybridization assays involve labelled nucleic acid probes to identify related DNA or RNA molecules (i.e. with significantly high degree of sequence similarity) within a complex mixture of unlabelled

neg: Isotopic labeling and mass spectrometry(MS). Some of the most common stable isotopes are H, C, and N, which can further be produced into NMR solvents, amino acids, nucleic acids, lipids, common metabolites and cell growth media. The compounds produced using stable isotopes are either specified by the percentage of labeled isotopes (i.e. 30% uniformly labeled C glucose contains a mixture that is 30% labeled with carbon isotope and 70% naturally labeled carbon) or by the specifically labeled carbon positions on the compound (i.e. 1-C glucose which is labeled at the first carbon position of glucose). A network of reactions adopted from the

neg: DNA nanotechnology as programmable molecular cages. Nucleic acid structures can be made to incorporate molecules other than nucleic acids, sometimes called heteroelements, including proteins, metallic nanoparticles, quantum dots, and fullerenes. This allows the construction of materials and devices with a range of functionalities much greater than is possible with nucleic acids alone. The goal is to use the self-assembly of the nucleic acid structures to template the assembly of the nanoparticles hosted on them, controlling their position and in some cases orientation. Many of these schemes use a covalent attachment scheme, using oligonucleotides with amide or thiol functional groups as a chemical

neg: DMBT1 exploited to modulate the pharmacological properties of nucleic acids and/or for nucleic acid delivery to target cells Recently, DMBT1-derived peptides have been successfully harnessed for siRNA intracellular delivery. DMBT1 has been shown to interact with Surfactant protein D. DMBT1-derived peptides also interacts with nucleic acids. DMBT1 Deleted in malignant brain tumors 1 protein is a protein that in humans is encoded by the "DMBT1" gene. Loss of sequences from human chromosome 10q has been associated with the progression of human cancers. The gene DMBT1 was originally isolated based on its deletion in a medulloblastoma cell line. DMBT1 is expressed with

neg: Targeted drug delivery bearing ligands to P-selectin, endothelial selectin (E-selectin) and ICAM-1 have been found to adhere to inflamed endothelium. Therefore, the use of biodegradable particles can also be used for cardiac tissue. The success of DNA nanotechnology in constructing artificially designed nanostructures out of nucleic acids such as DNA, combined with the demonstration of systems for DNA computing, has led to speculation that artificial nucleic acid nanodevices can be used to target drug delivery based upon directly sensing its environment. These methods make use of DNA solely as a structural material and a chemical, and do not make use of its biological

neg: Nucleic acid purine or pyrimidine nucleobase (sometimes termed "nitrogenous base" or simply "base"), a pentose sugar, and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside. Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2'-deoxyribose while RNA contains ribose (where the only difference is the presence of a hydroxyl group). Also, the nucleobases found in the two nucleic acid types are different: adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids

neg: Spin column-based nucleic acid purification Spin column-based nucleic acid purification Spin column-based nucleic acid purification is a solid phase extraction method to quickly purify nucleic acids. This method relies on the fact that nucleic acid will bind to the solid phase of silica under certain conditions. The stages of the method are lyse, bind, wash and elute, i.e. lysis of cells, binding of nucleic acid to silica gel membrane, washing the nucleic acid bound to the silica gel membrane and elution of the nucleic acid. To lyse, the cells of a sample are broken open with a lysis procedure which free breaks the cell membrane

neg: Gene therapy for osteoarthritis two non-viral gene delivery methods that have so far been utilized for gene delivery to cartilage. FuGene 6 is a non-liposomal lipid formulation, which has proved to be successful in transfecting a variety of cell lines. Liposomes have shown to be an appropriate candidate for gene delivery, where cationic liposomes are made to facilitate the interaction with the cell membranes and nucleic acids. Unlike viral vectors, non-viral ones avoid the risk of acquiring replication competence. They have the capacity to deliver a large amount of therapeutic genes repeatedly, and it is convenient to produce them on a large scale. The

neg: Molecular beacon Molecular beacon Molecular beacons are oligonucleotide hybridization probes that can report the presence of specific nucleic acids in homogenous solutions. The term more often used is molecular beacon probes. Molecular beacons are hairpin shaped molecules with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid sequence. This is a novel non-radioactive method for detecting specific sequences of nucleic acids. They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess of the hybridization probes. A typical molecular beacon probe is 25 nucleotides long.

neg: Gunther Hartmann B cell receptors and antibodies), the innate arm of the immune system applies germline-encoded receptors to detect microbial or damaged molecules including nucleic acid (DNA and RNA). Innate immune sensing of nucleic acids is essential for immune recognition of viruses and has been the scientific focus of the Hartmann group for more than 17 years. His scientific achievements have been awarded with the Gottfried Wilhelm Leibniz Prize (information and video:). Besides immune recognition of viruses, immune sensing of nucleic acids is involved in bacterial infection, in tumor biology and autoimmune disease. Hartmann´s group contributed to the understanding of several innate

neg: Maurice Stroun to explore if other methods could be developed to not only detect the overall abundance of nucleic acids in patients with disease (and specifically cancer) but to also detect the disease-specific components of such circulating nucleic acids themselves. Unlike bacterial transformations in plants and animal cells involving clear transfer of separately identifiable nucleic acids, it was not clear how malignancy in cancer arose, although there were many competing theories. Stroun’s postulate that neoplastic malignancy was associated with the presence of tumor specific nucleic acids, led to extensive research by his group of circulating nucleic acids in cancer patients in the

neg: Immunogenicity Immunogenicity Immunogenicity is the ability of a particular substance, such as an antigen or epitope, to provoke an immune response in the body of a human and other animal. In other words, immunogenicity is the ability to induce a humoral and/or cell-mediated immune responses.<br>Distinction has to be made between wanted and unwanted immunogenicity. Proteins are significantly more immunogenic than polysaccharides. T cell response is required to drive immunogenicity. Since lipids and nucleic acids are non-immunogenic haptens, they require conjugation with an epitope such as a protein or polysaccharide before they can evoke an immunologic response. In the rush to deliver

neg: Denaturation (biochemistry) Denaturation (biochemistry) Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure, and secondary structure which is present in their native state, by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), radiation or heat. If proteins in a living cell are denatured, this results in disruption of cell activity and possibly cell death. Protein denaturation is also a consequence of cell death. Denatured proteins can exhibit a wide range of characteristics, from conformational change and loss of

neg: Slow virus caused by an as-yet unidentified slow virus, although there is little evidence to support this finding Prions are so named because they appear to contain only protein. No evidence of nucleic acid has been found in any prion particle studied. Treatments that destroy protein, like denaturation, destroy prion infectivity, but treatments that destroy nucleic acids, like UV radiation, do not destroy prion infectivity. The prion protein is known as PrP and is a cell surface glycophosphatidylinositol(GPI)-anchored protein. Its normal function in the body is unknown, though presumably it serves, or served, some purpose because it is coded for by a

neg: CHON for cell function, and prevent them from diffusing into areas where they should not be. Phosphate groups are also an essential component of the backbone of nucleic acids and are required to form ATP – the main molecule used as energy powering the cell in all living creatures. Carbonaceous asteroids are rich in CHON elements. These asteroids are the most common type, and frequently collide with Earth as meteorites. Such collisions were especially common early in Earth's history, and these impactors may have been crucial in the formation of the planet's oceans. The simplest compounds to contain all of the

neg: Epididymitis necessary to identify underlying causes. In younger children, a urinary tract anomaly is frequently found. In sexually active men, tests for sexually transmitted diseases may be done. These may include microscopy and culture of a first void urine sample, Gram stain and culture of fluid or a swab from the urethra, nucleic acid amplification tests (to amplify and detect microbial DNA or other nucleic acids) or tests for syphilis and HIV. Epididymitis can be classified as acute, subacute, and chronic, depending on the duration of symptoms. Chronic epididymitis is epididymitis that is present for more than 3 months. Chronic epididymitis

neg: Microvesicles on exosomal RNA transfer. These RNAs are specifically targeted to microvesicles, in some cases containing detectable levels of RNA that is not found in significant amounts in the donor cell. Because the specific proteins, mRNAs, and miRNAs in microvesicles are highly variable, it is likely that these molecules are specifically packaged into vesicles using an active sorting mechanism. At this point, it is unclear exactly which mechanisms are involved in packaging soluble proteins and nucleic acids into microvesicles. Once released from their cell of origin, microvesicles interact specifically with cells they recognize by binding to cell-type specific, membrane-bound receptors. Because

neg: Nucleic acid design that the double helix formed by nucleic acid duplexes has a fixed helicity of about 10.4 base pairs per turn, and is relatively stiff. Because of these constraints, the nucleic acid complexes are sensitive to the relative orientation of the major and minor grooves at junction points. Geometrical modeling can detect strain stemming from misalignments in the structure, which can then be corrected by the designer. Geometric models of nucleic acids for DNA nanotechnology generally use reduced representations of the nucleic acid, because simulating every atom would be very computationally expensive for such large systems. Models with three pseudo-atoms per

neg: Hexavalent chromium Inside the cell, hexavalent chromium (chromium(VI)) is reduced first to pentavalent chromium (chromium(V)) then to trivalent chromium (chromium(III)) without the aid of any enzymes. The reduction occurs via direct electron transfer primarily from ascorbate and some nonprotein thiols. Vitamin C and other reducing agents combine with chromate to give chromium(III) products inside the cell. The resultant chromium(III) forms stable complexes with nucleic acids and proteins. This causes strand breaks and Cr-DNA adducts which are responsible for mutagenic damage. According to Shi et al., the DNA can also be damaged by hydroxyl radicals produced during reoxidation of pentavalent chromium by hydrogen

neg: Reading frame Reading frame In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons. A single strand of a nucleic acid molecule has a phosphoryl end, called the 5′-end, and a hydroxyl or 3′-end. These define the 5'→3' direction. There are three reading frames that can be read in this 5'→3' direction, each beginning from a different nucleotide in a triplet. In a double stranded nucleic

neg: Physical factors affecting microbial life smoke a low pH—about 2.5. Some of these compounds are toxic to people as well, and may have health effects in the quantities found in cooking applications. Microorganisms suffer a reduction in viability on contact with ozone which compromises the integrity of their cell walls. Gram-negative bacteria are more vulnerable to ozone than gram-positive organisms. (see Thermization and Pasteurisation)<br> Extreme temperatures destroy viruses and vegetative cells that are active and metabolising. Organic molecules such as proteins, carbohydrates, lipid and nucleic acids, as well as cell walls and membranes, all of which play important roles in cell metabolism, are damaged by

neg: Protein away from other cellular components. This process usually begins with cell lysis, in which a cell's membrane is disrupted and its internal contents released into a solution known as a crude lysate. The resulting mixture can be purified using ultracentrifugation, which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles, and nucleic acids. Precipitation by a method known as salting out can concentrate the proteins from this lysate. Various types of chromatography are then used to isolate the protein or proteins of interest based on properties such as molecular weight, net charge and

neg: Decellularization treatments are used to break the bonds and interactions between nucleic acids, interacting cells through neighboring proteins, and other cellular components. Lipases, thermolysin, galactosidase, nucleases, and trypsin have all been used in the removal of cells. After a cell is lysed with a detergent, acid, physical pressure, etc., endonucleases and exonucleases can begin the degradation of the genetic material. Endonucleases cleave DNA and RNA in the middle of sequences. Benzoase, an endonuclease, produces multiple small nuclear fragments that can be further degraded and removed from the ECM scaffold. Exonucleases act at the end of DNA sequences to cleave the phosphodiester

neg: Maurice Stroun changes and copy-number alterations. "Circulating Nucleic Acids in Plasma and Serum Congress" The early work of Stroun and Anker spurred intense investigation into the relationship of circulating nucleic acids and human conditions, such as disease, trauma, and pregnancy. For example, Lo demonstrated that fetal-specific nucleic acids could be detected in maternal peripheral blood in the late 1990s. As such, the pair organized the first global symposium dedicated to circulating nucleic acid research in 1999 held in Menthon, France. The conference was named CNAPS (Circulating Nucleic Acids in Plasma and Serum) and is held every other year to this day. In

neg: Tobramycin and its serum concentration monitored. Tobramycin is thus said to be a drug with a narrow therapeutic index. Tobramycin works by binding to a site on the bacterial 30S and 50S ribosome, preventing formation of the 70S complex. As a result, mRNA cannot be translated into protein, and cell death ensues. Tobramycin also binds to RNA-aptamers, artificially created molecules to bind to certain targets. However, there seems to be no indication that Tobramycin binds to natural RNAs or other nucleic acids. The effect of tobramycin can be inhibited by metabolites of the Krebs (TCA) cycle, such as glyoxylate. These metabolites