query: extra-chromosomal dna within a bacterial cell is known as

pos: Extrachromosomal DNA membrane bound nucleus like the eukaryotes, they do contain a nucleoid region in which the main chromosome is found. Extrachromosomal DNA exists in prokaryotes outside the nucleoid region as circular or linear plasmids. Bacterial plasmids are typically short sequences, consisting of 1 kilobase (kb) to a few hundred kb segments, and contain an origin of replication which allows the plasmid to replicate independently of the bacterial chromosome. The total number of a particular plasmid within a cell is referred to as the copy number and can range from as few as two copies per cell to as many as several

pos: ParMRC system about this ParMRC system. ParMRC system ParMRC is known as one of the best systems for bacterial segregation. This system uses actin-like filaments to push plasmids, small DNA molecules within a cell that are physically separated from a chromosomal DNA and can replicate independently, to opposite poles of the cell. There the plasmids are segregated and can replicate without interference from the chromosomal DNA. During cell division many plasmids are plagued with low copy numbers and thus evolved active segregation to avoid plasmid loss during cell division The process of this segregation is carried out by a small number of

pos: ParMRC system ParMRC system ParMRC is known as one of the best systems for bacterial segregation. This system uses actin-like filaments to push plasmids, small DNA molecules within a cell that are physically separated from a chromosomal DNA and can replicate independently, to opposite poles of the cell. There the plasmids are segregated and can replicate without interference from the chromosomal DNA. During cell division many plasmids are plagued with low copy numbers and thus evolved active segregation to avoid plasmid loss during cell division The process of this segregation is carried out by a small number of components, three to be

pos: Bacterial cell structure also contain small independent pieces of DNA called plasmids that often encode for traits that are advantageous but not essential to their bacterial host. Plasmids can be easily gained or lost by a bacterium and can be transferred between bacteria as a form of horizontal gene transfer. So plasmids can be described as an extra chromosomal DNA in a bacterial cell. In most bacteria the most numerous intracellular structure is the ribosome, the site of protein synthesis in all living organisms. All prokaryotes have 70S (where S=Svedberg units) ribosomes while eukaryotes contain larger 80S ribosomes in their cytosol. The 70S

pos: Genomic DNA by RNA Polymerase III. Genomic DNA Genomic deoxyribonucleic acid is chromosomal DNA, in contrast to extra-chromosomal DNAs like plasmids. It is also then abbreviated as gDNA. Most organisms have the same genomic DNA in every cell; however, only certain genes are active in each cell to allow for cell function and differentiation within the body. The genome of an organism (encoded by the genomic DNA) is the (biological) information of heredity which is passed from one generation of organism to the next. That genome is transcribed to produce various RNAs, which are necessary for the function of the organism. Precursor

pos: Genomic DNA Genomic DNA Genomic deoxyribonucleic acid is chromosomal DNA, in contrast to extra-chromosomal DNAs like plasmids. It is also then abbreviated as gDNA. Most organisms have the same genomic DNA in every cell; however, only certain genes are active in each cell to allow for cell function and differentiation within the body. The genome of an organism (encoded by the genomic DNA) is the (biological) information of heredity which is passed from one generation of organism to the next. That genome is transcribed to produce various RNAs, which are necessary for the function of the organism. Precursor mRNA (pre-mRNA) is transcribed

pos: Vector (molecular biology) the non-bacterial host organism, however other vectors termed intragenic vectors have also been developed to avoid the transfer of any genetic material from an alien species. Insertion of a vector into the target cell is usually called transformation for bacterial cells, transfection for eukaryotic cells, although insertion of a viral vector is often called transduction. Plasmids are double-stranded extra chromosomal and generally circular DNA sequences that are capable of replication using the host cell's replication machinery. Plasmid vectors minimalistically consist of an origin of replication that allows for semi-independent replication of the plasmid in the host. Plasmids are found widely

pos: Prokaryote in separate circular DNA structures called plasmids. Like Eukaryotes, prokaryotes may partially duplicate genetic material, and can have a haploid chromosomal composition that is partially replicated, a condition known as merodiploidy. Prokaryotes lack mitochondria and chloroplasts. Instead, processes such as oxidative phosphorylation and photosynthesis take place across the prokaryotic cell membrane. However, prokaryotes do possess some internal structures, such as prokaryotic cytoskeletons. It has been suggested that the bacterial order Planctomycetes have a membrane around their nucleoid and contain other membrane-bound cellular structures. However, further investigation revealed that Planctomycetes cells are not compartmentalized or nucleated and like the other bacterial

pos: Plant transformation vector transferred to the plant cell but remains within the bacterial cell. Plasmids replicate to produce many plasmid molecules in each host bacterial cell. The number of copies of each plasmid in a bacterial cell is determined by the replication origin. This is the position within the plasmids molecule where DNA replication is initiated. Most binary vectors have a higher number of plasmids copies when they replicate in "E. coli", the plasmid copy-number is usually less when the plasmid is resident within "Agrobacterium tumefaciens". Plasmids can also be replicated in the polymerase chain reaction (PCR). T-DNA contains two types of genes:

pos: Plasmid that may be replicated in the nucleus. Viruses are the most common examples of this, such as herpesviruses, adenoviruses, and polyomaviruses, but some are plasmids. Other examples include aberrant chromosomal fragments, such as double minute chromosomes, that can arise during artificial gene amplifications or in pathologic processes (e.g., cancer cell transformation). Episomes in eukaryotes behave similarly to plasmids in prokaryotes in that the DNA is stably maintained and replicated with the host cell. Cytoplasmic viral episomes (as in poxvirus infections) can also occur. Some episomes, such as herpesviruses, replicate in a rolling circle mechanism, similar to bacterial phage viruses. Others

pos: Extrachromosomal DNA membrane bound nucleus like the eukaryotes, they do contain a nucleoid region in which the main chromosome is found. Extrachromosomal DNA exists in prokaryotes outside the nucleoid region as circular or linear plasmids. Bacterial plasmids are typically short sequences, consisting of 1 kilobase (kb) to a few hundred kb segments, and contain an origin of replication which allows the plasmid to replicate independently of the bacterial chromosome. The total number of a particular plasmid within a cell is referred to as the copy number and can range from as few as two copies per cell to as many as several

pos: Chromosome is a distinct structure and occupies a defined region of the bacterial cell. This structure is, however, dynamic and is maintained and remodeled by the actions of a range of histone-like proteins, which associate with the bacterial chromosome. In archaea, the DNA in chromosomes is even more organized, with the DNA packaged within structures similar to eukaryotic nucleosomes. 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. In prokaryotes (see nucleoids) and viruses, the DNA is often densely packed and organized;

pos: Plasmid preparation to lack the resistance gene, and thus only colonies representing successful transformations are expected to grow. Bacteria are grown under favourable conditions. When bacteria are lysed under alkaline conditions (pH 12.0–12.5) both chromosomal DNA and protein are denatured; the plasmid DNA however, remains stable. Some scientists reduce the concentration of NaOH used to 0.1M in order to reduce the occurrence of ssDNA. After the addition of acetate-containing neutralization buffer the large and less supercoiled chromosomal DNA and proteins precipitate, but the small bacterial DNA plasmids stay in solution. Kits are available from varying manufacturers to purify plasmid DNA, which are

pos: Plasmid NCBI database. Using the NCBI database, sequences of specific plasmids can be looked up. Plasmid A plasmid is a small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that may benefit the survival of the organism, for example antibiotic resistance. While the chromosomes are big and contain all the essential genetic information for living under normal conditions, plasmids usually are very small

pos: Plasmid Plasmid A plasmid is a small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that may benefit the survival of the organism, for example antibiotic resistance. While the chromosomes are big and contain all the essential genetic information for living under normal conditions, plasmids usually are very small and contain only additional genes that may be useful to the organism under certain

pos: Cytosol many of the enzymes in cytosol are bound to the cytoskeleton. However, the idea that the majority of the proteins in cells are tightly bound in a network called the microtrabecular lattice is now seen as unlikely. In prokaryotes the cytosol contains the cell's genome, within a structure known as a nucleoid. This is an irregular mass of DNA and associated proteins that control the transcription and replication of the bacterial chromosome and plasmids. In eukaryotes the genome is held within the cell nucleus, which is separated from the cytosol by nuclear pores that block the free diffusion of any

pos: DNA extraction than organic extraction or Chelex extraction. Specific techniques must be chosen for isolation of DNA from some samples. Typical samples with complicated DNA isolation are: Extrachromosomal DNA is generally easy to isolate, especially plasmids may be easily isolated by cell lysis followed by precipitation of proteins, which traps chromosomal DNA in insoluble fraction and after centrifugation, plasmid DNA can be purified from soluble fraction. A Hirt DNA Extraction is an isolation of all extrachromosomal DNA in a mammalian cell. The Hirt extraction process gets rid of the high molecular weight nuclear DNA, leaving only low molecular weight mitochondrial DNA and

neg: Alkaline lysis and denature both chromosomal and plasmid DNA. One thing which should be noted is that, after tearing apart the cell membrane by SDS, the cell content will neutralize the NaOH; this is why the pH of the lysis goes down from 12.8 to 12.3. So if there are not enough bacterial cells, the extra NaOH will function to generate small DNA fragment. But 0.5 M L-arginine, which can supply a stable pH, can be used to replace 0.1 M sodium hydroxide. Finally, potassium acetate is added. This acidifies the solution and allows the renaturing of plasmid DNA, but not chromosomal

neg: Bacterial cell structure DNA is not enclosed inside of a membrane-bound nucleus but instead resides inside the bacterial cytoplasm. This means that the transfer of cellular information through the processes of translation, transcription and DNA replication all occur within the same compartment and can interact with other cytoplasmic structures, most notably ribosomes. The bacterial DNA is not packaged using histones to form chromatin as in eukaryotes but instead exists as a highly compact supercoiled structure, the precise nature of which remains unclear. Most bacterial chromosomes are circular although some examples of linear DNA exist (e.g. "Borrelia burgdorferi"). Along with chromosomal DNA, most bacteria

neg: Bacterial conjugation step of this second nicking event. If the F-plasmid that is transferred has previously been integrated into the donor's genome (producing an Hfr strain ["High Frequency of Recombination"]) some of the donor's chromosomal DNA may also be transferred with the plasmid DNA. The amount of chromosomal DNA that is transferred depends on how long the two conjugating bacteria remain in contact. In common laboratory strains of "E. coli" the transfer of the entire bacterial chromosome takes about 100 minutes. The transferred DNA can then be integrated into the recipient genome via homologous recombination. A cell culture that contains in its

neg: Hfr cell Luca Cavalli-Sforza. William Hayes also isolated another Hfr strain independently. An Hfr cell can transfer a portion of the bacterial genome. Despite being integrated into the chromosomal DNA of the bacteria, the F factor of Hfr cells can still initiate conjugative transfer, without being excised from the bacterial chromosome first. Due to the F factor's inherent tendency to transfer itself during conjugation, the rest of the bacterial genome is dragged along with it. Therefore, unlike a normal F cell, Hfr strains will attempt to transfer their "entire" DNA through the mating bridge, in a fashion similar to the normal conjugation.

neg: H19 (gene) cancer. Cellular DNA integrity is often compromised in cancer. Genome instability can refer to the accumulation of extra copies of DNA/chromosomes, chromosomal translocations, chromosomal inversion, chromosome deletions, single stranded breaks in DNA, double stranded breaks in DNA, the intercalation of foreign substances into the DNA double helix, or any abnormal changes in DNA tertiary structure that can cause either the loss of DNA, or the misexpression of genes. It appears that H19 expression is tightly linked to the ploidy of the cell. Diploid liver cells express high levels of H19, whereas the polyploid cell fraction do not express H19. Also,

neg: Min System this family of proteins is attributed to Adler et al. (1967). First identified as "E. coli" mutants that could not produce a properly localized septum, resulting in the generation of minicells due to mislocalized cell division occurring near the bacterial poles. This caused miniature vesicles to pinch off, void of essential molecular constituents permitting it to exist as a viable bacterial cell. Minicells are achromosomal cells that are products of aberrant cell division, and contain RNA and protein, but little or no chromosomal DNA. This finding led to the identification of three interacting proteins involved in a dynamic system of

neg: Cyanobacteria cell resulting from the direct uptake and incorporation of exogenous DNA from its surroundings. For bacterial transformation to take place, the recipient bacteria must be in a state of competence, which may occur in nature as a response to conditions such as starvation, high cell density or exposure to DNA damaging agents. In chromosomal transformation, homologous transforming DNA can be integrated into the recipient genome by homologous recombination, and this process appears to be an adaptation for repairing DNA damage. Historically, bacteria were first classified as plants constituting the class Schizomycetes, which along with the Schizophyceae (blue-green algae/Cyanobacteria) formed the

neg: Lytic cycle Lytic cycle The lytic cycle ( ) is one of the two cycles of viral reproduction (referring to bacterial viruses or bacteriophages), the other being the lysogenic cycle. The lytic cycle results in the destruction of the infected cell and its membrane. Bacteriophages that only use the lytic cycle are called virulent phages (in contrast to temperate phages). In the lytic cycle, the viral DNA exists as a separate free floating molecule within the bacterial cell, and replicates separately from the host bacterial DNA, whereas in the lysogenic cycle, the viral DNA is located within the host DNA. This is

neg: Escherichia coli classified as a facultative anaerobe. It uses oxygen when it is present and available. It can, however, continue to grow in the absence of oxygen using fermentation or anaerobic respiration. The ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates. The bacterial cell cycle is divided into three stages. The B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA. The D period refers to the stage

neg: Nitrofurantoin while in the urine it reaches 200 µg/ml. The mechanism of action is unique and complex. The drug works by damaging bacterial DNA, since its reduced form is highly reactive. This is made possible by the rapid reduction of nitrofurantoin inside the bacterial cell by flavoproteins (nitrofuran reductase) to multiple reactive intermediates that attack ribosomal proteins, DNA, respiration, pyruvate metabolism and other macromolecules within the cell. Nitrofurantoin exerts greater effects on bacterial cells than mammalian cells because bacterial cells activate the drug more rapidly. It is not known which of the actions of nitrofurantoin is primarily responsible for its bactericidal

neg: Topoisomerase that requires the activity of topoisomerase to be replicated. The classes of topoisomerase found in the mitochondria are I, IIβ, IIIα. Many drugs operate through interference with the topoisomerases The broad-spectrum fluoroquinolone antibiotics act by disrupting the function of bacterial type II topoisomerases. These small molecule inhibitors act as efficient anti-bacterial agents by hijacking the natural ability of topoisomerase to create breaks in chromosomal DNA. Some chemotherapy drugs called topoisomerase inhibitors work by interfering with mammalian-type eukaryotic topoisomerases in cancer cells. This induces breaks in the DNA that ultimately lead to programmed cell death (apoptosis). This DNA-damaging effect, outside of

neg: Feulgen stain as much DNA. This gave rise to the division of the interphase period of the cell cycle to G1, S, and G2 phases based on the synthesis of that extra DNA. Feulgen stain Feulgen stain is a staining technique discovered by Robert Feulgen and used in histology to identify chromosomal material or DNA in cell specimens.It is darkly stained. It depends on acid hydrolysis of DNA, therefore fixating agents using strong acids should be avoided. The specimen is subjected to warm (60 °C) hydrochloric acid, then to Schiff reagent. In the past, a sulfite rinse followed, but this is now

neg: Chlorovirus in mammalian cells. Host transcription rates decrease in this early phase of infection, and host transcription facilitators are reprogrammed to transcribe the new viral DNA. Minutes after infection, host chromosomal DNA degradation begins. This is presumed to occur through PBCV-1 encoded and packaged DNA restriction endonucleases. Degradation of the host chromosomal DNA inhibits host transcription. This results in 33-55% of the polyadenylated mRNAs in the infected cell being of viral origin by 20 minutes after initial infection. Viral DNA replication initiates after 60 to 90 minutes, which is then followed by the transcription of late genes within the host cell.

neg: Antibiotic show that both antibiotics and antibiotic resistance are ancient compounds and mechanisms. Useful antibiotic targets are those for which mutations negatively impact bacterial reproduction or viability. Several molecular mechanisms of antibacterial resistance exist. Intrinsic antibacterial resistance may be part of the genetic makeup of bacterial strains. For example, an antibiotic target may be absent from the bacterial genome. Acquired resistance results from a mutation in the bacterial chromosome or the acquisition of extra-chromosomal DNA. Antibacterial-producing bacteria have evolved resistance mechanisms that have been shown to be similar to, and may have been transferred to, antibacterial-resistant strains. The spread of antibacterial

neg: Zygotic induction Zygotic induction Zygotic induction occurs when a bacterial cell carrying the silenced DNA of a bacterial virus in its chromosome transfers the viral DNA along with its own DNA to another bacterial cell lacking the virus, causing the recipient of the DNA to break open. In the donor cell, a repressor protein encoded by the prophage (viral DNA) keeps the viral genes turned off so that virus is not produced. When DNA is transferred to the recipient cell by conjugation, the viral genes in the transferred DNA are immediately turned on because the recipient cell lacks the repressor. As a

neg: Chromosomal crossover that meiosis evolved from bacterial transformation, with the function of propagating genetic diversity. . Thus, this evidence suggests that it is a question of whether cross over is linked to DNA repair or bacterial transformation, as the two do not appear to be mutually exclusive. It is likely that crossing over may have evolved from bacterial transformation, which in turn developed from DNA repair, thus explaining the links between all three processes. Meiotic recombination may be initiated by double-stranded breaks that are introduced into the DNA by exposure to DNA damaging agents or the Spo11 protein. One or more exonucleases

neg: Chromosomal crossover on chromosomes. In an experiment using radiation hybrid mapping on wheat's ("Triticum aestivum L.") 3B chromosome, crossing over and DNA repair were found to occur predominantly in the same regions. Furthermore, crossing over has been correlated to occur in response to stressful, and likely DNA damaging, conditions The process of bacterial transformation also shares many similarities with chromosomal cross over, particularly in the formation of overhangs on the sides of the broken DNA strand, allowing for the annealing of a new strand. Bacterial transformation itself has been linked to DNA repair many times. The second theory comes from the idea

neg: Circular bacterial chromosome eventually lead to the establishment of two complete replisomes for bidirectional replication. DNA sequence elements within "ori"C that are important for its function include DnaA boxes, a 9-mer repeat with a highly conserved consensus sequence 5' – TTATCCACA – 3', that are recognized by the DnaA protein. DnaA protein plays a crucial role in the initiation of chromosomal DNA replication. Bound to ATP, and with the assistance of bacterial histone-like proteins [HU] DnaA then unwinds an AT-rich region near the left boundary of "oriC", which carries three 13-mer motifs, and opens up the double-stranded DNA for entrance of other replication

neg: Endospore the endospore. The core contains the spore chromosomal DNA which is encased in chromatin-like proteins known as SASPs (small acid-soluble spore proteins), that protect the spore DNA from UV radiation and heat. The core also contains normal cell structures, such as ribosomes and other enzymes, but is not metabolically active. Up to 20% of the dry weight of the endospore consists of calcium dipicolinate within the core, which is thought to stabilize the DNA. Dipicolinic acid could be responsible for the heat resistance of the spore, and calcium may aid in resistance to heat and oxidizing agents. However, mutants resistant

neg: Zygotic induction forming had all of the chromosome from the Hfr cell were to be transferred to the F cell. Zygotic induction Zygotic induction occurs when a bacterial cell carrying the silenced DNA of a bacterial virus in its chromosome transfers the viral DNA along with its own DNA to another bacterial cell lacking the virus, causing the recipient of the DNA to break open. In the donor cell, a repressor protein encoded by the prophage (viral DNA) keeps the viral genes turned off so that virus is not produced. When DNA is transferred to the recipient cell by conjugation, the viral

neg: DNA repair Nuclear DNA (nDNA) exists as chromatin during non-replicative stages of the cell cycle and is condensed into aggregate structures known as chromosomes during cell division. In either state the DNA is highly compacted and wound up around bead-like proteins called histones. Whenever a cell needs to express the genetic information encoded in its nDNA the required chromosomal region is unravelled, genes located therein are expressed, and then the region is condensed back to its resting conformation. Mitochondrial DNA (mtDNA) is located inside mitochondria organelles, exists in multiple copies, and is also tightly associated with a number of proteins to form

neg: Transduction (genetics) the lytic cycle of infection upon entering a bacterium, the virus will take control of the cell's machinery for use in replicating its own viral DNA. If by chance bacterial chromosomal DNA is inserted into the viral capsid which is usually used to encapsulate the viral DNA, the mistake will lead to "generalized transduction". If the virus replicates using 'headful packaging', it attempts to fill the nucleocapsid with genetic material. If the viral genome results in spare capacity, viral packaging mechanisms may incorporate bacterial genetic material into the new virion. The new virus capsule now loaded with part bacterial DNA

neg: Restriction modification system other types, type IV restriction enzymes recognize and cut only modified DNA. "Neisseria meningitides" has multiple type II restriction endonuclease systems that are employed in natural genetic transformation. Natural genetic transformation is a process by which a recipient bacterial cell can take up DNA from a neighboring donor bacterial cell and integrate this DNA into its genome by recombination. Although early work on restriction modification systems focused on the benefit to bacteria of protecting themselves against invading bacteriophage DNA or other foreign DNA, it is now known that these systems can also be used to restrict DNA introduced by natural

neg: Hfr cell chromosome. Hfr cell A high-frequency recombination cell (Hfr cell) (also called an Hfr strain) is a bacterium with a conjugative plasmid (for example, the F-factor) integrated into its chromosomal DNA. The integration of the plasmid into the cell's chromosome is through homologous recombination. A conjugative plasmid capable of chromosome integration is also called an episome (a segment of DNA that can exist as a plasmid or become integrated into the chromosome). When conjugation occurs, Hfr cells are very efficient in delivering chromosomal genes of the cell into recipient F cells, which lack the episome. The Hfr strain was first characterized

neg: Hfr cell Hfr cell A high-frequency recombination cell (Hfr cell) (also called an Hfr strain) is a bacterium with a conjugative plasmid (for example, the F-factor) integrated into its chromosomal DNA. The integration of the plasmid into the cell's chromosome is through homologous recombination. A conjugative plasmid capable of chromosome integration is also called an episome (a segment of DNA that can exist as a plasmid or become integrated into the chromosome). When conjugation occurs, Hfr cells are very efficient in delivering chromosomal genes of the cell into recipient F cells, which lack the episome. The Hfr strain was first characterized by

neg: Antimicrobial resistance offspring, which leads to the microevolution of a fully resistant colony. Chromosomal mutations providing antibiotic resistance benefit the bacteria but also confer a cost of fitness. For example, a ribosomal mutation may protect a bacterial cell by changing the binding site of an antibiotic but will also slow protein synthesis. manifesting, in slower growth rate. In Gram-negative bacteria, plasmid-mediated resistance genes produce proteins that can bind to DNA gyrase, protecting it from the action of quinolones. Finally, mutations at key sites in DNA gyrase or topoisomerase IV can decrease their binding affinity to quinolones, decreasing the drug's effectiveness. Bacteria can

neg: Bacterial outer membrane vesicles their host. This mechanism imparts a variety of benefits like, long-distance delivery of bacterial secretory cargo with minimized hydrolytic degradation and extra-cellular dilution, also supplemented with other supportive molecules (e.g., virulence factors) to accomplish a specific job and yet, keeping a safe-distance from the defense arsenal of the targeted cells. Biochemical signals trafficked by OMVs may vary largely during 'war and peace' situations. In 'complacent' bacterial colonies, OMVs may be used to carry DNA to 'related' microbes for genetic transformations, and also translocate cell signaling molecules for quorum sensing and biofilm formation. During 'challenge' from other cell types around, OMVs

neg: Biomolecular engineering Exo, Beta, and Gam, which are created by the genes exo, bet, and gam respectively. Exo is a double stranded DNA exonuclease with 5’ to 3’ activity. It cuts the double stranded DNA leaving 3’ overhangs. Beta is a protein that binds to single stranded DNA and assists homologous recombination by promoting annealing between the homology regions of the inserted DNA and the chromosomal DNA. Gam functions to protect the DNA insert from being destroyed by native nucleases within the cell. Recombinant DNA can be engineered for a wide variety of purposes. The techniques utilized allow for specific modification of

neg: Chromosome instability are taken into account. Disorders such as chromosome instability can be inherited via genes, or acquired later in life due to environmental exposure. One way that Chromosome Instability can be acquired is by exposure to ionizing radiation. Radiation is known to cause DNA damage, which can cause errors in cell replication, which may result in chromosomal instability. Chromosomal instability can in turn cause cancer. However, chromosomal instability syndromes such as Bloom syndrome, ataxia telangiectasia and Fanconi anaemia are inherited and are considered to be genetic diseases. These disorders are associated with tumor genesis, but often have a phenotype on the

neg: Genome instability damage caused by oxidative stress is deficient. In cancer, genome instability can occur prior to or as a consequence of transformation. Genome instability can refer to the accumulation of extra copies of DNA or chromosomes, chromosomal translocations, chromosomal inversions, chromosome deletions, single-strand breaks in DNA, double-strand breaks in DNA, the intercalation of foreign substances into the DNA double helix, or any abnormal changes in DNA tertiary structure that can cause either the loss of DNA, or the misexpression of genes. Situations of genome instability (as well as aneuploidy) are common in cancer cells, and they are considered a "hallmark" for

neg: Nijmegen breakage syndrome Nijmegen breakage syndrome Nijmegen breakage syndrome (NBS), also known as Berlin breakage syndrome, ataxia telangiectasia variant 1 (AT-V1) and Seemanova syndrome, is a rare autosomal recessive congenital disorder causing chromosomal instability, probably as a result of a defect in the double Holliday junction DNA repair mechanism and/or the synthesis dependent strand annealing mechanism for repairing double strand breaks in DNA (see Homologous recombination). NBS1 codes for a protein (nibrin) that has two major functions: (1) to stop the cell cycle in the S phase, when there are errors in the cell DNA (2) to interact with FANCD2 that can activate

neg: Lucy Shapiro chemoreceptor proteins occupy specific areas within the cell. Shapiro and Christine Jacobs-Wagner as well as Janine Maddock showed that signaling phosphokinase also had specific positions at the cell poles. In 2005, using time-lapse microscopy and fluorescent tags, Shapiro was able to demonstrate that chromosomal regions are duplicated in both an orderly and a location-specific manner, involving "a much higher degree of spatial organization than previously thought". By studying the regulation of the cell cycle, asymmetric cell division, and cellular differentiation, Shapiro's work has led to a much deeper understanding of the genetic and molecular processes that cause identical bacterial cells

neg: Filamentation Filamentation Filamentation is the anomalous growth of certain bacteria, such as "E. coli", in which cells continue to elongate but do not divide (no septa formation). The cells that result from elongation without division have multiple chromosomal copies. Bacterial filamentation is often observed as a result of bacteria responding to various stresses, including DNA damage or inhibition of replication. This may happen, for example, while responding to extensive DNA damage through the SOS response system. Nutritional changes may also cause bacterial filamentation. Some of the key genes involved in filamentation in E.coli include "sulA" and "minCD". The following genes have

neg: Cell envelope Cell envelope The cell envelope comprises the inner cell membrane and the cell wall of a bacterium. In gram-negative bacteria an outer membrane is also included. This envelope is not present in the Mollicutes where the cell wall is absent. Bacterial cell envelopes fall into two major categories: a gram-positive type and a gram-negative type, distinguished by Gram staining. Either type may have an enclosing capsule of polysaccharide for extra protection. As a group these are known as polysaccharide encapsulated bacteria. As in other organisms, the bacterial cell wall provides structural integrity to the cell. In prokaryotes, the primary function

neg: Gene map these digested fragments. The sizes of these fragments help indicate the distance between restriction enzyme sites on the DNA analyzed, and provides researchers with information regarding the structure of DNA analyzed. FISH is a method used to detect the presence (or absence) of a DNA sequence within a cell. DNA probes that are specific for chromosomal regions or genes of interest are labeled with fluorochromes. By attaching fluorochromes to probes, researchers are able to visualize multiple DNA sequences simultaneously. When a probe comes into contact with DNA on a specific chromosome, hybridization will occur. Consequently, information regarding the location of

neg: Phage ecology system). In this system, foreign DNA trying to enter the bacterial host is restricted by endonucleases that recognize specific base pairs within the DNA, while the DNA of the cell is protected from restriction due to methylase. RM systems have evolved to keep up with the ever-changing bacteria and phage. In general, these RM types differ in the nucleotide sequences that they recognize. However, there is an occasional slip where the endonuclease misses the DNA sequence of the phage and the phage DNA is able to enter the cell anyway, becoming methylated and protected against the endonuclease. This accident is

neg: Caretaker gene Inactivation of caretaker genes is environmentally equivalent to exposing the cell to mutagens incessantly. For example, a mutation in a caretaker gene coding for a DNA repair pathway that leads to the inability to properly repair DNA damage could allow uncontrolled cell growth. This is the result of mutations of other genes that accumulate unchecked as a result of faulty gene products encoded by the caretakers. In addition to providing genomic stability, caretakers also provide chromosomal stability. Chromosomal instability resulting from dysfunctional caretaker genes is the most common form of genetic instability that leads to cancer in humans. In fact,

neg: Patau syndrome Patau syndrome Patau syndrome is a syndrome caused by a chromosomal abnormality, in which some or all of the cells of the body contain extra genetic material from chromosome 13. The extra genetic material disrupts normal development, causing multiple and complex organ defects. This can occur either because each cell contains a full extra copy of chromosome 13 (a disorder known as trisomy 13 or trisomy D), or because each cell contains an extra partial copy of the chromosome (i.e., Robertsonian translocation) or because of mosaic Patau syndrome. Full trisomy 13 is caused by nondisjunction of chromosomes during meiosis (the

neg: Transduction (genetics) continues to infect another bacterial cell. This bacterial material may become recombined into another bacterium upon infection. When the new DNA is inserted into this recipient cell it can fall to one of three fates "Specialized transduction" is the process by which a "restricted" set of bacterial genes is transferred to another bacterium. The genes that get transferred (donor genes) depend on where the phage genome is located on the chromosome. Specialized transduction occurs when the prophage excises imprecisely from the chromosome so that bacterial genes lying adjacent to the prophage are included in the excised DNA. The excised DNA

neg: Merozygote recombination occurs, the linear fragment of donor DNA in the recipient cytoplasm will be lost after one cycle. These merozygotes help to study dominance variation and mutation can be known. Merozygote Merozygote is a state when a cell, usually bacterial, is temporarily partial diploid as result of DNA transfer processes like conjugation. One example of how merozygotes can be formed is the transfer of genetic material of an Hfr cell to an F- cell through conjugation. When an Hfr cell mates with an F- cell, the chromosome acts as a rolling circle transferring a part of its genomic chromosome across

neg: Min System Min System The Min System is a mechanism composed of three proteins MinC, MinD, and MinE used by "E. coli" as a means of properly localizing the septum prior to cell division. Each component participates in generating a dynamic oscillation of FtsZ protein inhibition between the two bacterial poles to precisely specify the mid-zone of the cell, allowing the cell to accurately divide in two. This system is known to function in conjunction with a second negative regulatory system, the nucleoid occlusion system (NO), to ensure proper spatial and temporal regulation of chromosomal segregation and division. The initial discovery of

neg: Genotoxicity disturb the mitotic apparatus that changes chromosome number; the factors that could influence the genotoxicity are ADME and DNA repair. It can also detect genotoxic agents missed in "in vitro" tests. The positive result of induced chromosomal damage is an increase in frequency of micronucelated PCEs. A micronucleus is a small structure separate from the nucleus containing nuclear DNA arisen from DNA fragments or whole chromosomes that were not incorporated in the daughter cell during mitosis. Causes for this structure are mitotic loss of acentric chromosomal fragments (clastogenicity), mechanical problems from chromosomal breakage and exchange, mitotic loss of chromosomes (aneugenicity),

neg: Phenanthriplatin ligand introduces steric hindrance within the major groove of the DNA, which impedes RNA polymerase II, a major protein used by the cell to transcribe DNA. Since transcription is essential for DNA synthesis and gene expression, phenanthriplatin inhibits both these processes in cancerous cells, ultimately inducing cellular apoptosis. A study examining the effects of monofunctional adducts on bacterial growth reported a significant decrease in "Escherichia coli" (E. coli) cell growth when inoculated with phenanthriplatin. It also demonstrated that phenanthriplatin, like cisplatin, was able to dissolve lysogens as well as alter the morphology of "E. coli" into longer, filamentous cells. These

neg: Recombinant DNA product, especially if it is over-expressed or expressed within inappropriate cells or tissues. In some cases, recombinant DNA can have deleterious effects even if it is not expressed. One mechanism by which this happens is insertional inactivation, in which the rDNA becomes inserted into a host cell's gene. In some cases, researchers use this phenomenon to "knock out" genes to determine their biological function and importance. Another mechanism by which rDNA insertion into chromosomal DNA can affect gene expression is by inappropriate activation of previously unexpressed host cell genes. This can happen, for example, when a recombinant DNA fragment containing

neg: Bacterial genetics transformed, and not all extracellular DNA is competent to transform. To be competent to transform, the extracellular DNA must be double-stranded and relatively large. To be competent to be transformed, a cell must have the surface protein Competent Factor', which binds to the extracellular DNA in an energy requiring reaction. However bacteria that are not naturally competent can be treated in such a way to make them competent, usually by treatment with calcium chloride, which make them more permeable. Bacterial conjugation is the transfer of genetic material (plasmid) between bacterial cells by direct cell-to-cell contact or by a bridge-like connection

neg: Hfr cell it may be cut in the middle), the recipient F cells do not receive the complete F factor sequence, and do not become F due to its inability to form a sex pilus. In conjugation mediated by Hfr cells, transfer of DNA starts at the origin of transfer ("oriT") located within the F factor and then continues clockwise or counterclockwise depending on the orientation of F factor in the chromosome. Therefore, the length of chromosomal DNA transferred into the F cell is proportional to the time that conjugation is allowed to happen. This results in sequential transfer of genes on

neg: Spindle checkpoint would drive a high incidence of tumorigenesis only when alterations in the levels of specific mitotic checkpoint components (either reduction or overexpression) in tissues is also inducing other defects able to predispose them to tumors. That is, defects such as an increase in DNA damage, chromosomal rearrangements, and/or a decreased incidence of cell death. For some mitotic checkpoint components, it is known that they are implicated in functions outside mitosis: nuclear import (Mad1), transcriptional repression (Bub3), and cell death, DNA damage response, aging, and megakaryopoiesis for BubR1. All this supports the conclusion that increase in tumorigenesis is associated with defects

neg: Postzygotic mutation where they occur. As a result consequences can range from being negligible to incredibly detrimental. When an individual has inherited an abnormality it is usually present in all of their cells. However some mutations like DNA code change, epigenetic alterations and chromosomal abnormalities, can occur later in development. This would result in one progeny cell line to be normal while the other cell line(s) to be abnormal. As a result the individual is considered to be a mosaic of normal and abnormal cells. Mosaicism is the occurrence of two or more cell lines with different genotypes within a single individual.

neg: CpG Oligodeoxynucleotide cells and plasmacytoid dendritic cells (pDCs) in humans and other higher primates. Since 1893, it has been recognized that Coley's toxin, a mixture of bacterial cell lysate, has immunostimulatory properties that could reduce the progression of some carcinomas, but it was not until 1983 that Tokunaga et al. specifically identified bacterial DNA as the underlying component of the lysate that elicited the response. Then, in 1995 Krieg et al. demonstrated that the CpG motif within bacterial DNA was responsible for the immunostimulatory effects and developed synthetic CpG ODN. Since then, synthetic CpG ODN have been the focus of intense research

neg: Cancer in dogs animals, and can be diagnosed and treated by specialized veterinarians called veterinary oncologists. Cancer is a complex, multifactorial disease. Carcinogenesis is linked with DNA mutations, chromosomal translocations, chocolate, dysfunctional proteins, and aberrant cell cycle regulators. Cancer alters the DNA of cells and the mutated genetic material is passed on to daughter cells, resulting in neoplasms. The mutated DNA effects genes involved with the cell cycle, classified as either oncogenes or tumor suppressor genes. Oncogenes are responsible for cell proliferation and differentiation. Oncogenes responsible for cell growth are overexpressed in cancerous cells. Tumor suppressor genes prevent cells with erroneous cell cycles

neg: Mantle cell lymphoma Mantle cell lymphoma Mantle cell lymphoma (MCL) is a type of non-Hodgkin's lymphoma (NHL), comprising about 6% of NHL cases. There are only about 15,000 patients presently in the U.S. MCL is a subtype of B-cell lymphoma, due to CD5 positive antigen-naive pregerminal center B-cell within the mantle zone that surrounds normal germinal center follicles. MCL cells generally over-express cyclin D1 due to a t(11:14) chromosomal translocation in the DNA. Specifically, the translocation is at t(11;14)(q13;q32). At diagnosis, patients typically are in their 60s and present to their physician with advanced disease. About half have B symptoms such as fever,

neg: Homologous recombination in sequence between host and recipient DNA. In bacterial conjugation, where DNA is transferred between bacteria through direct cell-to-cell contact, homologous recombination helps integrate foreign DNA into the host genome via the RecBCD pathway. The RecBCD enzyme promotes recombination after DNA is converted from single-strand DNA–in which form it originally enters the bacterium–to double-strand DNA during replication. The RecBCD pathway is also essential for the final phase of transduction, a type of horizontal gene transfer in which DNA is transferred from one bacterium to another by a virus. Foreign, bacterial DNA is sometimes misincorporated in the capsid head of bacteriophage

neg: Patau syndrome Approximately 4% of Patau syndrome with unknown outcomes are likely to result in a live birth, therefore the total number of live births is estimated to be 18. Patau syndrome Patau syndrome is a syndrome caused by a chromosomal abnormality, in which some or all of the cells of the body contain extra genetic material from chromosome 13. The extra genetic material disrupts normal development, causing multiple and complex organ defects. This can occur either because each cell contains a full extra copy of chromosome 13 (a disorder known as trisomy 13 or trisomy D), or because each cell contains

neg: Bacterioplankton counting methods both DNA and RNA structures in biological samples such as bacteria and viruses. However, DNA staining is primarily used for bacterial cell identification. With modern epifluorescence microscopy, the industry standard for estimating and counting bacterial cell quantities is by the use of a DAPI stain. This technique can be performed for samples from a wide range of environments and locations, such as seawater, various sources of freshwater, as well as soils and sediments. In a standard experiment, prepared bacterial samples are placed onto counting slides and then viewed under an epifluorescence microscope. Magnification is set to a level where the

neg: Hershey–Chase experiment incorporated with DNA in the cell's genetic material. All of the S in the protein coats remained outside the cell, showing it was not incorporated into the cell, and that protein is not the genetic material. Hershey and Chase's experiment concluded that little sulfur-containing material entered the bacterial cell. However no specific conclusions can be made regarding whether material that is sulfur-free enters the bacterial cell after phage adsorption. Further research was necessary to conclude that it was solely bacteriophages' DNA that entered the cell and not a combination of protein and DNA where the protein did not contain any

neg: FANCA which are aplastic anaemia in childhood, multiple congenital abnormalities, susceptibility to leukemia and other cancers, and cellular hypersensitivity to interstrand DNA cross-linking agents. Generally cells from Fanconi anaemia patients show a markedly higher frequency of spontaneous chromosomal breakage and hypersensitivity to the clastogenic effect of DNA cross-linking agents such as diepoxybutane (DEB) and mitomycin-C (MMC) when compared to normal cells. The primary diagnostic test for Fanconi anaemia is based on the increased chromosomal breakage seen in afflicted cells after exposure to these agents – the DEB/MMC stress test. Other features of the Fanconi anaemia cell phenotype also include abnormal cell

neg: Eukaryotic DNA replication Eukaryotic DNA replication Eukaryotic DNA replication is a conserved mechanism that restricts DNA replication to once per cell cycle. Eukaryotic DNA replication of chromosomal DNA is central for the duplication of a cell and is necessary for the maintenance of the eukaryotic genome. DNA replication is the action of DNA polymerases synthesizing a DNA strand complementary to the original template strand. To synthesize DNA, the double-stranded DNA is unwound by DNA helicases ahead of polymerases, forming a replication fork containing two single-stranded templates. Replication processes permit the copying of a single DNA double helix into two DNA helices, which are

neg: Thermoplasma volcanium histone-like DNA-binding protein HU, found on a segment known as "huptvo". Similar genes encoding HU proteins have been discovered in numerous bacterial genomes, as it is a vital component in many bacterial DNA and metabolic functions. Thus, further investigation of this protein offers insight into the evolutionary relatedness seen between protein-DNA interactions in bacteria and archaea. Additionally, the ability of "Thermoplasma volcanium" to function in aerobic and anaerobic environments makes it a prime research subject on the endosymbiotic theory of the eukaryotic nuclei. "Thermoplasma volcanium" exhibits extremophile characteristics through its lack of a cell wall to sustain proper functioning at

neg: Prophage Prophage A prophage is a bacteriophage (often shortened to "phage") genome inserted and integrated into the circular bacterial DNA chromosome or existing as an extrachromosomal plasmid. This is a latent form of a phage, in which the viral genes are present in the bacterium without causing disruption of the bacterial cell. Pro means <nowiki>"before"</nowiki>, so, prophage means the stage of a virus in the form of genome inserted into host DNA before attaining its real form inside host. Upon detection of host cell damage, such as UV light or certain chemicals, the prophage is excised from the bacterial chromosome in

neg: Oncovirus nucleus where one strand of the retroviral genome is put into the chromosomal DNA by the help of the virion intergrase. At this point the retrovirus is referred to as provirus. Once in the chromosomal DNA, the provirus is transcribed by the cellular RNA polymerase II. The transcription leads to the splicing and full-length mRNAs and full-length progeny virion RNA. The virion protein and progeny RNA assemble in the cytoplasm and leave the cell, whereas the other copies send translated viral messages in the cytoplasm. Not all oncoviruses are DNA viruses. Some RNA viruses have also been associated such as

neg: Extrachromosomal DNA DNA is an important part of immune responses. For this virus to persist, the circular genome must be replicated and inherited during cell division. Cells can recognize foreign cytoplasmic DNA. Understanding the recognition pathways has implications towards prevention and treatment of diseases. Cells have sensors that can specifically recognize viral DNA such as the Toll-like receptor (TLR) pathway. The Toll Pathway was recognized, first in insects, as a pathway that allows certain cell types to act as sensors capable of detecting a variety of bacterial or viral genomes and PAMPS (pathogen-associated molecular patterns). PAMPs are known to be potent activators

neg: T-even bacteriophages of the T even bacteriophage tail plays a role in the attachment site. Therefore, there must be specific receptor attachment as the receptor determines the host preference. Penetration This stage involves for the virus to penetrate itself in the host cell. It does so by injecting its DNA into the cell. The process of penetration happens when the bacteriophage's tail secretes the enzyme lysozyme, which breaks down the bacterial cell wall into segments. Therefore, the break down of the cell by the enzyme lysozyme forms a hole on the host cell;so, the bacteriophage inserts the DNA (genetic material) within the

neg: Molecular biology the expression of cloned gene. This plasmid can be inserted into either bacterial or animal cells. Introducing DNA into bacterial cells can be done by transformation via uptake of naked DNA, conjugation via cell-cell contact or by transduction via viral vector. Introducing DNA into eukaryotic cells, such as animal cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection, electroporation, microinjection and liposome transfection. The plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection. DNA coding for

neg: Carcinogenesis DNA methylation. Loss of that methylation can induce the aberrant expression of oncogenes, leading to cancer pathogenesis. Known mechanisms of epigenetic change include DNA methylation, and methylation or acetylation of histone proteins bound to chromosomal DNA at specific locations. Classes of medications, known as HDAC inhibitors and DNA methyltransferase inhibitors, can re-regulate the epigenetic signaling in the cancer cell. Epimutations include methylations or demethylations of the CpG islands of the promoter regions of genes, which result in repression or de-repression, respectively of gene expression. Epimutations can also occur by acetylation, methylation, phosphorylation or other alterations to histones, creating a histone

neg: Viral eukaryogenesis many parasitic red algae. A number of precepts in the theory are possible. For instance, a helical virus with a bilipid envelope bears a distinct resemblance to a highly simplified cellular nucleus (i.e., a DNA chromosome encapsulated within a lipid membrane). In theory, a large DNA virus could take control of a bacterial or archaeal cell. Instead of replicating and destroying the host cell, it would remain within the cell, thus overcoming the tradeoff dilemma typically faced by viruses. With the virus in control of the host cell's molecular machinery, it would effectively become a functional nucleus. Through the processes

neg: Nucleoid Nucleoid The nucleoid (meaning "nucleus-like") is an irregularly shaped region within the cell of a prokaryote that contains all or most of the genetic material, called genophore. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. The genome of prokaryotic organisms generally is a circular, double-stranded piece of DNA, of which multiple copies may exist at any time. The length of a genome widely varies, but generally is at least a few million base pairs. As in all cellular organisms, length of the DNA molecules of bacterial and archaeal chromosomes is very

neg: Neomycin/polymyxin B/bacitracin are known for their ability to bind to RNA and to change the proteins being produced by the bacteria with little to no effect on DNA. Neomycin kills bacteria as a result of irregular protein production in the bacterial cell. When the cell can no longer produce the correct proteins, its membrane will be damaged. Like Neomycin, Polymyxin B is an antibiotic. Polymyxin B alters the bacterial cell wall causing the cellular insides to leak out resulting in cell death. This antibiotic also interferes with the production of tetrahydrofolic acid by altering an enzyme. Without the tetrahydrofolic acid, the bacteria

neg: Phagemid a range of techniques, such as transformation and electroporation. However, infection of a bacterial host containing a phagemid with a 'helper' phage, for example VCSM13 or M13K07, provides the necessary viral components to enable single stranded DNA replication and packaging of the phagemid DNA into phage particles. The 'helper' phage infects the bacterial host by first attaching to the host cell's pilus and then, after attachment, transporting the phage genome into the cytoplasm of the host cell. Inside the cell, the phage genome triggers production of single stranded phagemid DNA in the cytoplasm. This phagemid DNA is then packaged into

neg: Circular bacterial chromosome growing his cultures in a medium containing 3H-thymidine. The nucleoside base was incorporated uniformly into the bacterial chromosome. He then isolated the chromosomes by lysing the cells gently and placed them on an electron micrograph (EM) grid which he exposed to X-ray film for two months. This Experiment clearly demonstrates the theta replication model of circular bacterial chromosomes. As described above, bacterial chromosomal replication occurs in a bidirectional manner. This was first demonstrated by specifically labelling replicating bacterial chromosomes with radioactive isotopes. The regions of DNA undergoing replication during the experiment were then visualized by using autoradiography and examining the

neg: Radiobiology evidence for protons and HZE nuclei DSB, etc.) within a localized region of DNA. Complex damage is uncommon for endogenous damage or low-LET radiation, and has been associated with the increased RBE of densely ionizing radiation. The repair of DSB is known to occur through direct end-joining and homologous recombination processes. Indications are that: or While the high effectiveness in cell killing provides the rationale for heavy ion cancer therapy (hadron therapy), residual damage in surviving cells is of concern for carcinogenesis. Heavy charged particles are very effective at producing chromosomal exchanges with RBE values exceeding 30 in interphase (as visualized using premature chromosome condensation) and

neg: Interleukin 26 STAT3, which enhance IL-10 and IL-8 secretion and as expression of the CD54 molecule on the surface of epithelial cells. Interleukin 26 (IL-26), is a natural human antimicrobial that promotes immune sensing of bacterial and host cell death. IL-26, a human TH17 cell–derived cytokine, is a cationic amphipathic protein that kills extracellular bacteria via membrane-pore formation. Furthermore, TH17 cell–derived IL-26 formed complexes with bacterial DNA and self-DNA released by dying bacteria and host cells. The IL-26–DNA complexes triggered the production of type I interferon by plasmacytoid dendritic cells via activation of Toll-like receptor 9, but independently of the IL-26 receptor.

neg: Pilus produced by flagella. However, some bacteria, for example "Myxococcus xanthus", exhibit gliding motility. Bacterial type IV pili are similar in structure to the component flagellins of archaella (archaeal flagella). Genetic transformation is the process by which a recipient bacterial cell takes up DNA from a neighboring cell and integrates this DNA into its genome by homologous recombination. In "Neisseria meningitidis" (also called meningococcus), DNA transformation requires the presence of short DNA uptake sequences (DUSs) which are 9-10 monomers residing in coding regions of the donor DNA. Specific recognition of DUSs is mediated by a type IV pilin. Menningococcal type IV

neg: Comparative genomic hybridization microarray. Now probes of various origins such as cDNA, genomic PCR products and bacterial artificial chromosomes (BACs) can be used on DNA microarrays which may contain up to 2 million probes. Array CGH is automated, allows greater resolution (down to 100 kb) than traditional CGH as the probes are far smaller than metaphase preparations, requires smaller amounts of DNA, can be targeted to specific chromosomal regions if required and is ordered and therefore faster to analyse, making it far more adaptable to diagnostic uses. The DNA on the slide is a reference sample, and is thus obtained from a karyotypically

neg: DNA repair in tumour-suppressor genes and oncogenes, and chromosomal aberrations. However, it has become apparent that cancer is also driven by epigenetic alterations. Epigenetic alterations refer to functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence. Examples of such modifications are changes in DNA methylation (hypermethylation and hypomethylation) and histone modification, changes in chromosomal architecture (caused by inappropriate expression of proteins such as HMGA2 or HMGA1) and changes caused by microRNAs. Each of these epigenetic alterations serves to regulate gene expression without altering the underlying DNA sequence. These changes usually remain through cell divisions, last

neg: DNA re-replication DNA re-replication DNA re-replication (or simply rereplication) is an undesirable and possibly fatal occurrence in eukaryotic cells in which the genome is replicated more than once per cell cycle. Rereplication is believed to lead to genomic instability and has been implicated in the pathologies of a variety of human cancers. To prevent rereplication, eukaryotic cells have evolved multiple, overlapping mechanisms to inhibit chromosomal DNA from being partially or fully rereplicated in a given cell cycle. These control mechanisms rely on cyclin-dependent kinase (CDK) activity. DNA replication control mechanisms cooperate to prevent the relicensing of replication origins and to activate cell

neg: Cell cycle Cell cycle The cell cycle, or cell-division cycle, is the series of events that take place in a cell leading to its division and duplication of its DNA (DNA replication) to produce two daughter cells. In bacteria, which lack a cell nucleus, the cell cycle is divided into the B, C, and D periods. The B period extends from the end of cell division to the beginning of DNA replication. DNA replication occurs during the C period. The D period refers to the stage between the end of DNA replication and the splitting of the bacterial cell into two daughter

neg: Transformation (genetics) in the process. The translocated single-stranded DNA may then be integrated into the bacterial chromosomes by a RecA-dependent process. In Gram-negative cells, due to the presence of an extra membrane, the DNA requires the presence of a channel formed by secretins on the outer membrane. Pilin may be required for competence, but its role is uncertain. The uptake of DNA is generally non-sequence specific, although in some species the presence of specific DNA uptake sequences may facilitate efficient DNA uptake. Natural transformation is a bacterial adaptation for DNA transfer that depends on the expression of numerous bacterial genes whose products

neg: Circulating tumor DNA HiSeq, PARE is applied to the data to analyze chromosomal rearrangements and translocations. This technique was originally designed to analyze solid tumor DNA but was modified for ctDNA applications. Proper epigenetic marking is essential for normal gene expression and cell function and aberrant alterations in epigenetic patterns is a hallmark of cancer. A normal epigenetic status is maintained in a cell at least in part through DNA methylation. Measuring aberrant methylation patterns in ctDNA is possible due to stable methylation of regions of DNA referred to as “CpG islands”. Methylation of ctDNA can be detected through bisulfite treatment. Bisulfite treatment

neg: Disinfectant of < 1 ppm of available chlorine is sufficient to kill bacteria and viruses, spores and mycobacteria requiring higher concentrations. The biguanide polymer polyaminopropyl biguanide is specifically bactericidal at very low concentrations (10 mg/l). It has a unique method of action: The polymer strands are incorporated into the bacterial cell wall, which disrupts the membrane and reduces its permeability, which has a lethal effect to bacteria. It is also known to bind to bacterial DNA, alter its transcription, and cause lethal DNA damage. It has very low toxicity to higher organisms such as human cells, which have more complex and

neg: DNA condensation packed to be readily accessible inside the micrometer-size nucleus. In unicellular eukaryotes known as dinoflagellates, it is possible to distinguish liquid-crystalline chromosomal ordering, that they do not contain easily detectable histones, until recently it was thought that they were completely absent and that dinoflagellates were mesokaryotic though this is no longer the case and they are now classified as alveolates. In other eukaryotes, DNA is arranged in the cell nucleus with the help of histones. In this case, the basic level of DNA compaction is the nucleosome, where the double helix is wrapped around the histone octamer containing two copies

neg: Lambda phage to lysogenize cells – instead, they grow and enter the lytic cycle after superinfecting an already lysogenized cell. The phage particle consists of a head (also known as a capsid), a tail, and tail fibers (see image of virus below). The head contains the phage's double-strand linear DNA genome. During infection, the phage particle recognizes and binds to its host, "E. coli", causing DNA in the head of the phage to be ejected through the tail into the cytoplasm of the bacterial cell. Usually, a "lytic cycle" ensues, where the lambda DNA is replicated and new phage particles are produced

neg: Mutation breeding These breaks in DNA, otherwise known as DSBs, were found to be the source of much chromosomal damage in eukaryotes, causing mutations in plant varieties. REs induce a result on plant DNA similar to that of ionizing radiation or radiomimetic chemicals. Blunt ended breaks in the DNA, unlike sticky ended breaks, were found to produce more variations in chromosomal damage, making them the more useful type of break for mutation breeding. While the connection of REs to chromosomal aberrations is mostly limited to research on mammalian DNA, success in mammalian studies caused scientists to conduct more studies of RE-induced chromosomal

neg: Antibiotic resistance in gonorrhea over many years. Chromosomal mutations in the "penA", "mtr", and "penB" genes are the major mechanisms for CMRNG. The "penA" gene encodes an alternative penicillin-binding protein, PBP-2. This mechanism falls under the second general mechanism for beta-lactam resistance. PBPs, also known as transpeptidases, are targets for beta-lactams. These enzymes (PBPs) are involved in peptidoglycan synthesis which is a major component of the bacterial cell wall. PBPs cross-link the amino acid strands of peptidoglycan during synthesis. Normally, beta-lactams bind the PBPs and thereby inhibit the cross-linking of peptidoglycan. When this occurs, the cell wall of the bacterium is compromised and often

neg: Viral eukaryogenesis Viral eukaryogenesis Viral eukaryogenesis is the hypothesis that the cell nucleus of eukaryotic life forms evolved from a large DNA virus in a form of endosymbiosis within a methanogenic archaeon. The virus later evolved into the eukaryotic nucleus by acquiring genes from the host genome and eventually usurping its role. The hypothesis was proposed by Philip Bell in 2001 and gained support as large, complex DNA viruses (such as Mimivirus) capable of protein biosynthesis were discovered. Recent supporting evidence includes the discovery that, upon the infection of a bacterial cell, the giant bacteriophage 201Phi2-1 assembles a nucleus-like structure that segregates