지레 겁먹고 도전조차 안 하는 것 보다는 해 보고 후회하자.
1) 영어 공부 (토플, 아이엘츠)
2) 글쓰기
3) 논문 읽고 해석하는 방법
2. 차선으로 국내 대학원 지원 생각
1) 전반적인 개념 review
2) 나의 목표 공고히 하기.
결국 최종적인 목적이 무엇인가 이것이 중요한 듯 하다.
할 수 있다.
우선 조급하게 생각하지 말고 차근차근 준비해보자.
2021년 4월 11일 일요일
2020년 6월 4일 목요일
Work-Principle of microbiology
Diversity of bacteria
[The other bacteria]
Bacterioides: Obligate anaerobic, numberically dominant bacterial genus in human instestinal tract. The genus was naemd so due to the rod-kike shape of cells. Synthesize sphingolipids, which are also found in mammalian tissues.
Cytophaga: Obligate aerobic, long, slender and rod shaped genus that move by gliding. The name refers to the ability to digest polysaccarides such as cellulose or chitin.
Cyto-: cell/
Flavobacterium Aerobic, rod shaped genus primarily inhabiting aquatic environments, and also common in soils. The name came form yellow colored colonies. One of Most abundant bacterial groups in freshwater.
Flexibacter: The genus usually require complex media for good growth and are unable to degrade cellulose. Species are common in soil and freshwaters where they degrade polysaccharides, and none have been idntified as pathogens.
* Flexibacter in sphingobacteriales(=containing sphingosine)
Chlamydia: Obligate parasitic genus with poor metabolic capacities. Possess one of the simplest biochemical capacities of all known bacteria with genome sizes around 1 Mb. The disease caused by this genus is currently one of the leading sexually transmitted diseases. The life (infection) cycle includes formation of elementary bodies and reticulate bodies.
*elelment body: small, dense cell resistant to drying and means of dispersal.
*reticulate body: vegetative form divides by binary fission.
Planktomyces: A gram negative genus producing stalks and primarily inhabiting aquatic environment. The name of the genus reflects the planktonic ( floating) nature of life.
Verruncomicrobium: A warty shaped genus due to the presence of prosthecae on cell surface. Aerobic to facultative aerobic, and inhabits freshwater and marine environments as well as forest and agricultural soils.
Thermotoga: Rod-shaped, hyperthermophilic genus producing cells encapsulated by outer membrane(toga). Anaerobic, fermentative, chemoorganotroph. About 20% of genes were likely originated from Archaea.
Aquifex: obligately chemolithotrophic and hyperthermophilic genus that is most thermophilic of all Bacteria which can grow at 95C. The name means 'water maker'.
*Chemolithotrophy: the nergy metabolism of bacteria that can use the oxidation of inorganic substances as a source of energy for cell biosynthesis and maintenenace in the absence of light.
Deinococcus: A genus with red or pink color because of carotenoids. Resist UV radiation, gamma radiation, and desiccation (polyextremophile), and resistant to most mutagenic agents. The name means dreadful sphere.
*Desiccation: the state of extreme dryness./ Dreadful: scary, shock, suffering.
Thermus: Thermophilic, aerobic and organotrophic genus, including the source of Taq DNA polymerase.
*Organotrophic: obtain metabolic energy from the oxidation of organic compounds.
Acidobacterium: A genus widespread in environment, sometimes dominant in soils. Difficult to cultivate, and thus only a few species are known. Phylogenetically and metabolically diverse. Firstly named so because early discovered species were acidophilic, but now includes many non-acidic members.
Nitrospira: a chemolithotrophic bacterial genus with nitrite oxidizing ability and spiral-shaped cells.
Deferribacter: An chemolithotrophic bacterial genus with nitrite oxidizing ability and spiral-shaped cells. The name of the genus measn ' nitrate sprial'.
*Nitrate(NO3-)
Synergistetes: The phylum are gram-negative nonsporulating rods found in assoication with animals and in anoxic environments in terrestrial and marine systems. Described species are typically obligte anaerobes that degrade proteins and are capable of fermenting amino acids.
*Non-sporulating: There is no nearly dormant forms of bacterial. spores can preserve the genetic material of the bacteria.
Fusobacteria: The phylum are gram-negative nonsporulating rods found in sediments and the gastrointestinal systems and oral cvities of animals. Fusobacteria are obligate anaerobes taht ferment carbohydrates, peptides, and amino acids.
Fribrobacteres: The phylum are gram-negative nonsporulating rods unable to ferment proteins or amino acids, but speicalize instead in the fermentation of carbohydrates, including cellulose in the rume.
2020년 6월 3일 수요일
Work- Principle of microbiology
[Diveristy of archaea.]
Euryarchaeota: An archaeal phylum encompassing methanogens, extreme halophiles, thermoplasmas and hyperhermophilies as well as groups growing at ' ordinary environments'. The name of the phylum means ' a broad group of archaea'.
Crenarchaeota: An archaeal phylum including the most thermophilic groups. Many strains are found in terrestrial or submarine volcanic habitats, and the name of the phylum means ' archaea from hot sprins'. Now includes groups growing at mesophilic or psychrophilic environments.
Bacteriorhodopsin: A membrane protein found in extremely halophilic archaea that functions as light driven proton pump and thus gerating proton gradient across the cell membrane, which is used for ATP synthesis.
Methanogen: Organisms capable of methane production through the outcome of anaerobic respiration. Carbon dioxide is used as the electron acceptor. All of the organisms having this type of metabolism belong to archaea.
Tetraether lipid monolayer: Thermoplasmas lack cell walls, but evolved unique cytoplasmic membrane sstructure to maintain positive osmotic pressure and tolerate high temperature and low pH levels. Their cell membranes contain lipopolysaccaride-like material(lipoglycan) consisting of.
* common traits of all Archaea.
Ether- linked lipids, a lack of peptidoglycan in cell walls./ structurally complex RNA polymerases similar to those of Eukarya.
Methanopyrus: a hyperthermophilic and methanogenic genus containing unique membrane lipids called geranylgeraniol.
Thaumarchaeota: An archaeal phylum primarily consisting of aerobic, ammonia-oxidizing chemolithotrophic groups such as Nitrosopumilus and Nitrosophaera.
Nanoarchaeum: An archaeal genus which is an obligate symbiont of Ignicoccus, another archaeal genus. One of the smallest cellular organisms, and contains very small genomes that lack genes for all but core molecular processes. Depends upon host for most of its cellular needs.
Sulfolobus: An archaeal genus belonging to Crenarchaeota, which is found in sulfur-rich acidic hot springs, and grows by aerobic chemolithotrophic metabolism that oxidizes reduced sulfur or iron. The name of the genus came from the lobe-shaped cells.
Desulforococcus: A strictly anaerobic, sulfur-reducing archaeal genus belonging to Crenarchaeota. The name of the genus means sulfur-reducing coccus.
Thermosome: A major chaperonin protein complex found hyperthermophilic archaea such as Pyrodictium.
Reverse DNA gyrase: The enzyme found in hyperthermophilic archaea., which introduces positive supercoils into DNA, thus stabilizing the DNA.
Euryarchaeota: An archaeal phylum encompassing methanogens, extreme halophiles, thermoplasmas and hyperhermophilies as well as groups growing at ' ordinary environments'. The name of the phylum means ' a broad group of archaea'.
Crenarchaeota: An archaeal phylum including the most thermophilic groups. Many strains are found in terrestrial or submarine volcanic habitats, and the name of the phylum means ' archaea from hot sprins'. Now includes groups growing at mesophilic or psychrophilic environments.
Bacteriorhodopsin: A membrane protein found in extremely halophilic archaea that functions as light driven proton pump and thus gerating proton gradient across the cell membrane, which is used for ATP synthesis.
Methanogen: Organisms capable of methane production through the outcome of anaerobic respiration. Carbon dioxide is used as the electron acceptor. All of the organisms having this type of metabolism belong to archaea.
Tetraether lipid monolayer: Thermoplasmas lack cell walls, but evolved unique cytoplasmic membrane sstructure to maintain positive osmotic pressure and tolerate high temperature and low pH levels. Their cell membranes contain lipopolysaccaride-like material(lipoglycan) consisting of.
* common traits of all Archaea.
Ether- linked lipids, a lack of peptidoglycan in cell walls./ structurally complex RNA polymerases similar to those of Eukarya.
Methanopyrus: a hyperthermophilic and methanogenic genus containing unique membrane lipids called geranylgeraniol.
Thaumarchaeota: An archaeal phylum primarily consisting of aerobic, ammonia-oxidizing chemolithotrophic groups such as Nitrosopumilus and Nitrosophaera.
Nanoarchaeum: An archaeal genus which is an obligate symbiont of Ignicoccus, another archaeal genus. One of the smallest cellular organisms, and contains very small genomes that lack genes for all but core molecular processes. Depends upon host for most of its cellular needs.
Sulfolobus: An archaeal genus belonging to Crenarchaeota, which is found in sulfur-rich acidic hot springs, and grows by aerobic chemolithotrophic metabolism that oxidizes reduced sulfur or iron. The name of the genus came from the lobe-shaped cells.
Desulforococcus: A strictly anaerobic, sulfur-reducing archaeal genus belonging to Crenarchaeota. The name of the genus means sulfur-reducing coccus.
Thermosome: A major chaperonin protein complex found hyperthermophilic archaea such as Pyrodictium.
Reverse DNA gyrase: The enzyme found in hyperthermophilic archaea., which introduces positive supercoils into DNA, thus stabilizing the DNA.
2020년 6월 1일 월요일
Work-Immunology
Immunology-part2
Immunoglobulin: The general name for antibodies and B-cell antigen receptors.
Immunoglobulin superfamily: The name given to all the proteins that contain one or more immunoglobulin or immunoglobulin-like domains.
Immunotoxins: conjugate composed of a specific anitbody chemically coupled to a toxic protein usually derived from a plant or microbe. The anitibody is desinged to bind specifically to target cells, such as cancer caells, and deliver the toxin to kill them.(chp 17 conjugates biological toxins and antibodies)
Intravenous immunoglobulin: preparation of serum gamma globulin containing many different antibodies that is used as a treatment to replace antibodies and increase platelets in immunodeficiency and autoimmune diseases.
Intravenous: directly into a vein(within)
Isotype switching(class switching): The process by which a B cell changes the class of immunoglobulin it makes while preserving the antigenic specificity of the immunoglobulin.
Junctional diversity: Diversity present in immunoglobulin and T-cell receptor polypeptides that is created during the process of gene rearragement by the addition or removal of nucleotides at the junctions between gene segments.
Kinin system: Enzymatic cascade of plasma proteins that is triggered by tissue damage and helps to facilitate wound healing.
Lectin: General name for proteins that recognize carbohydrates.
Linear epitope: Antigenic structure in a protein that consists of a linear sequence of amino acids within the protein's primary structure.
Lymphoid follicle: an aggregation of mainly B cells in secondary lymphoid tissues. Where naive B cells proliferate and undergo somatic hypermutation and isotype switching.
Monoclonal antibody: antibody produced by a single clone of B lymphocytes so that all the anitbody molecules are identical in structure and antigen specificity.
Muscosa-associated lymphoid tissue(MALT): aggregations of lymphoid cells in mucosal epithelia and in the lamina propria (thine layer of connective tissue) )beneath.
Multivalent: Having more than one binding site for the same or different ligands.
N nucleotides: non-templated nucleotides added at the junctions between gene segments of T-cell receptor and immunoglobulin heavy-chain variable-region sequences during somatic recombination. They are not encoded in the gene segments but are inserted at random by the enzme TdT.
http://www2.nau.edu/~fpm/immunology/documents/Ch-05.pdf
NADPH oxidase: Multisubunit enzyme that produces superoxide radicals and contributes to the killing of internalized pathogens in neutrophils.
Naive B cells: Mature B cell that has left the bone marrow but has not yet encountered its specific antigen.
Neutralization:The mechanism by which antibodies binding to sites on pathogens prevent growth of the pathogen and/or its entry into cells.
Neutralizing antibody: high-affinity IgA and IgG antibodies taht bind to pathoens and prevent their growth or entry into cells.
Neutrophil extracellular trap(NET), netosis: The neutrophil nucleus swells and bursts, the chromatin dissolves and becomes extruded from the cell in a network of decondensed DNA.
* The mature neutrophil cannot replenish its granule contents; once they are used up, the neutrophil dies. Some neutrophils die by apoptosis and are then phagocytosed by a macrophage. A second way in which neutorphils die is by a process called netosis that trp and kill pathogens. Proteins present in NETs are bactericidal defensins, several proteases and so on which impairs bacteria and terminates the infection.
NK-cell synapse: A structure formed between an NK cell and its target in which interacting sets of receptors and ligands become concentrated at localized regions on the surfaces of the two cells, where they help hold the cells together and where signals and material are exchanged.
*NK cell: Large granular lymphocytes, are a type of cytotoxic lymphocyte critical to the innate immune system.
NKT cells: subset of alpha:beta T cells expressing receptors that recognize lipid antigens presented by the MHC class 1-like protein CD1d.
One-turn/two-turn joining rule(12/23 rule) The fact that V(D)J recombination can only occur between gene segments with particular lengths of spacer in the recombination signal sequences, which means that a VH region cannot be joined directly to a JH region without the involvement of DH. Two types of spacer are 12 and 23 nuclotides in length.
* Somatic recombination- cut and paste the DNA/ The recombination of V,J, and D gene segments is directed by sequences called recombination signal sequences (RSSs), which flank the 3' side of the V segment, both sides of the of the D segment, and the 5' side of the J segemnt. The requirements of RSS recombination, known as the 12/23 rule, recombination in the heavy chain DNA cannot joint a VH directly to a JH.
Opsonin: General name for antibodies and comoplement proteins that coat pathogens, thereby facilitating their phagocytosis by neutrophils or macrophages carrying receptors for this.
Opsonization: The coating of the surface of a pathogen or other particle with any molecule that makes it more readily ingested by phagocytes.
* Neutralizing antibodies: inactivate a pathogen or a toxin and prevent if from interacting with human cells.
P nucleotides: pallindromic nucleotides added into the junctions between immunoglobulin and T-cell receptor gene segments during the somatic recombinations that generate a rearranged variable-region sequence. They are an inverse repeat of the nucleotide sequence at the end of the adjacent gene segments
* DNA repair enzymes open hair pin after initial cleavage of D to J rearrangement. The nick that opens the hairpin can occur at any of several positions for diversity. It generates a single-stranded end in which bases that were complementary in th etwo DNA strands are now on the same strand. This creates a new nucleotide seq taht would be a palindrome in double-stranded DNA. (in DNA terms a plindrome is a seq of base pairs that is identical when read from either end) The additional nucleotides are thus called P nucleotides.
* TdT: Terminal deoxynucleotidyl transferase: randomly adds nucleotids, generating further diversity.
- added nucleotids, N nucleotides.
Paracrine: It describes a cytokine that is released from one type of cell and acts on another type of cell.
* Proliferation and differentiation of activated naive T cells are driven by the cytokine interleukin-2.
It is synthesized and secreted by the activated T cells themselves and acts back on the cells that make it. This type of action is called autocrine action. The alternative is paracrine action, where the cytokine acts on a different type of cell from the one that made it. For example, IL-12 which is made by myeloid cells(dendritic cells and macrophages) but acts on lymphocytes(NK cells and T cells)
Paroxysmal noctournal hemoglobinuria: a genetic disease in which the complement regulatory proteins CD59 and DAF are defective, so that complement activation leads to episodes of spontanous hemolysis. The defect is the attachment of CD59 and DAF to cell membranes by a glycolipid anchor.
* hemolysis- lysis of red cells
* Alternative name for protectin, a complement control protein(any of a diverse grouop of proteins that inhibit complement activation at various stages and by different mechanisms.)
* protectin: a protein on the surface of human cells that prevents the assembly of the complement membrane-attack complex on the cell surface, thus protecting human cells against complement-mediated lysis.
*DAF(Decay-accelerating factor): which interferes with complement activation at human cell surfaces. It binds to the C3b component of the alternative C3 convertase, causing its dissociation and inactivation.
*CCP modules: complement control protein, Many of the diverse proteins that regulate complement are elongated structures built from varying numbers of structureally similar modules
Macrophages: the mature forms of circulating monocytes that have left the blood and taken up residence in the tissues and it is long lived phgocytic cell participates in both innate and adaptive immunity.
Pentraxin: any member of a family of pentameric proteins that circulate in the blood and lymph and can bind to the surfaces a variety of pathogens and target them for destruction, CRP is in.
Peyer's patch: It is organized GALT present in the wall of the small intestine.
Plasma cell: termially differentiated B lymphocytes that secretes antibody.
Plasmacytoid dendritic cells: a type of dendritic cell that produces copious amounts of interferon in response to the defection of viral infection through its TLRs.
* TLR: recognize a variety of microbial ligands and are expressed by different types of innate immune cell.
* Interferon that interferes with the propagation of infection. It is produced by cytokines which is from induced in situation sensor proteins in the cytoplasm detect viral nucleic acids.(by RIG-I-like receptors(RLRs))
* Dendritic cells: take up pathogens and their produects form the envrionment and can be infected with viruses. These events induce changes in the proteins on dendritic cell surfaces that are monitored by the array of cell surface recepotrs on NK-cell surfaces.
Recombination signal sequence(RSS): short stretch of DNA flnaking each of the gene segments that are rearranged to generate V-region exons. The are the sites at which somatic recombination occurs.
Recombination-activating genes(RAG1/RAG2) Two genes that are essential for the rearrangement of immunoglobulin and T-cell receptor gens in B cells and T cells, respectively.
RAG complex binds to one of the RSSs flanking the seq to be joined then recruits the other RSS to the complex. and then DNA is cleaved.
Respiratory burst: metabolic change accompanied by a transient increase in oxygen consumption that occurs in neutrophils and macrophages afer they have taken up opsonized particels. It leads to the generation of toxic oxygen metabolites and other antibacterial substances taht attck the phgagocytosed material.
Scavenger receptor: any of a group of disparate phagocytic cell-surface receptors on macrophages that binds to an assortment of negatively charged lignads, including sulfated polysaccharides, nucleic acids, and the phosphate-containing lipoeichoic acids in the cell walls of Gram-positive bacteria.
SR-A and SR-B are structually unrelated SR-B recognizes lipopeptides, whereas SR-A recognizes the lipopolysaccharide(LPS) of Gram negative bacteria.
Signal joint: The joint present in the circle of DNA that is formed as a byproduct of V(D)J recombination and discarded.
Somatic hypermutation: Mutation that occurs at high frequency in the rearranged variable-region DNA segments of immunoglobulin genes in activated B cells, resulting in the production of variant antibodies, some of which ahve a higher affinity for the antigen.
Switch sequences: short DNA seq preceding each heavy-chain constant region gene, at which somatic recombination occurs when B cells switch from producing one immunoglobulin isotype to another.
T cell anergy, anergy: It cannot be revived, even if its specific antigen is subsequently presented in the context of co-stimulation by a mature dendritiec cell. It reduces the essential cytokine which is related to self-tolerance that works in the peripheral.
Terminal deoxynucleotidyl transferase(TdT): Enzyme that inserts non-templated nucleotides( N nuclotides) into the junctions between gene segments during the rearrangement of the T-cell receptor and immunoglobulin genes.
Transcytosis: the transport of molecules form one side of an epithelium to the other. This involves endocytosis into vesicles within the epitherial cells at one face of the epithelium and release of the vesicels at the other. chapt 9.
V(D)J recombinase: The set of enzymes needed to recombine V,D, and J segments in the rearrangement of immunoglobulin and T-cell receptor genes. It includes the RAG-1 and RAG-2.
Immunoglobulin: The general name for antibodies and B-cell antigen receptors.
Immunoglobulin superfamily: The name given to all the proteins that contain one or more immunoglobulin or immunoglobulin-like domains.
Immunotoxins: conjugate composed of a specific anitbody chemically coupled to a toxic protein usually derived from a plant or microbe. The anitibody is desinged to bind specifically to target cells, such as cancer caells, and deliver the toxin to kill them.(chp 17 conjugates biological toxins and antibodies)
Intravenous immunoglobulin: preparation of serum gamma globulin containing many different antibodies that is used as a treatment to replace antibodies and increase platelets in immunodeficiency and autoimmune diseases.
Intravenous: directly into a vein(within)
Isotype switching(class switching): The process by which a B cell changes the class of immunoglobulin it makes while preserving the antigenic specificity of the immunoglobulin.
Junctional diversity: Diversity present in immunoglobulin and T-cell receptor polypeptides that is created during the process of gene rearragement by the addition or removal of nucleotides at the junctions between gene segments.
Kinin system: Enzymatic cascade of plasma proteins that is triggered by tissue damage and helps to facilitate wound healing.
Lectin: General name for proteins that recognize carbohydrates.
Linear epitope: Antigenic structure in a protein that consists of a linear sequence of amino acids within the protein's primary structure.
Lymphoid follicle: an aggregation of mainly B cells in secondary lymphoid tissues. Where naive B cells proliferate and undergo somatic hypermutation and isotype switching.
Monoclonal antibody: antibody produced by a single clone of B lymphocytes so that all the anitbody molecules are identical in structure and antigen specificity.
Muscosa-associated lymphoid tissue(MALT): aggregations of lymphoid cells in mucosal epithelia and in the lamina propria (thine layer of connective tissue) )beneath.
Multivalent: Having more than one binding site for the same or different ligands.
N nucleotides: non-templated nucleotides added at the junctions between gene segments of T-cell receptor and immunoglobulin heavy-chain variable-region sequences during somatic recombination. They are not encoded in the gene segments but are inserted at random by the enzme TdT.
http://www2.nau.edu/~fpm/immunology/documents/Ch-05.pdfNADPH oxidase: Multisubunit enzyme that produces superoxide radicals and contributes to the killing of internalized pathogens in neutrophils.
Naive B cells: Mature B cell that has left the bone marrow but has not yet encountered its specific antigen.
Neutralization:The mechanism by which antibodies binding to sites on pathogens prevent growth of the pathogen and/or its entry into cells.
Neutralizing antibody: high-affinity IgA and IgG antibodies taht bind to pathoens and prevent their growth or entry into cells.
Neutrophil extracellular trap(NET), netosis: The neutrophil nucleus swells and bursts, the chromatin dissolves and becomes extruded from the cell in a network of decondensed DNA.
* The mature neutrophil cannot replenish its granule contents; once they are used up, the neutrophil dies. Some neutrophils die by apoptosis and are then phagocytosed by a macrophage. A second way in which neutorphils die is by a process called netosis that trp and kill pathogens. Proteins present in NETs are bactericidal defensins, several proteases and so on which impairs bacteria and terminates the infection.
NK-cell synapse: A structure formed between an NK cell and its target in which interacting sets of receptors and ligands become concentrated at localized regions on the surfaces of the two cells, where they help hold the cells together and where signals and material are exchanged.
*NK cell: Large granular lymphocytes, are a type of cytotoxic lymphocyte critical to the innate immune system.
 |
| researchgate.net/figure/Immunological-synapse-and-NK-cell-mediated-cell-death-Upon-synapsing-with-target-cells_fig2_276123848 |
NKT cells: subset of alpha:beta T cells expressing receptors that recognize lipid antigens presented by the MHC class 1-like protein CD1d.
One-turn/two-turn joining rule(12/23 rule) The fact that V(D)J recombination can only occur between gene segments with particular lengths of spacer in the recombination signal sequences, which means that a VH region cannot be joined directly to a JH region without the involvement of DH. Two types of spacer are 12 and 23 nuclotides in length.
* Somatic recombination- cut and paste the DNA/ The recombination of V,J, and D gene segments is directed by sequences called recombination signal sequences (RSSs), which flank the 3' side of the V segment, both sides of the of the D segment, and the 5' side of the J segemnt. The requirements of RSS recombination, known as the 12/23 rule, recombination in the heavy chain DNA cannot joint a VH directly to a JH.
Opsonin: General name for antibodies and comoplement proteins that coat pathogens, thereby facilitating their phagocytosis by neutrophils or macrophages carrying receptors for this.
Opsonization: The coating of the surface of a pathogen or other particle with any molecule that makes it more readily ingested by phagocytes.
* Neutralizing antibodies: inactivate a pathogen or a toxin and prevent if from interacting with human cells.
P nucleotides: pallindromic nucleotides added into the junctions between immunoglobulin and T-cell receptor gene segments during the somatic recombinations that generate a rearranged variable-region sequence. They are an inverse repeat of the nucleotide sequence at the end of the adjacent gene segments
* DNA repair enzymes open hair pin after initial cleavage of D to J rearrangement. The nick that opens the hairpin can occur at any of several positions for diversity. It generates a single-stranded end in which bases that were complementary in th etwo DNA strands are now on the same strand. This creates a new nucleotide seq taht would be a palindrome in double-stranded DNA. (in DNA terms a plindrome is a seq of base pairs that is identical when read from either end) The additional nucleotides are thus called P nucleotides.
* TdT: Terminal deoxynucleotidyl transferase: randomly adds nucleotids, generating further diversity.
- added nucleotids, N nucleotides.
Paracrine: It describes a cytokine that is released from one type of cell and acts on another type of cell.
* Proliferation and differentiation of activated naive T cells are driven by the cytokine interleukin-2.
It is synthesized and secreted by the activated T cells themselves and acts back on the cells that make it. This type of action is called autocrine action. The alternative is paracrine action, where the cytokine acts on a different type of cell from the one that made it. For example, IL-12 which is made by myeloid cells(dendritic cells and macrophages) but acts on lymphocytes(NK cells and T cells)
Paroxysmal noctournal hemoglobinuria: a genetic disease in which the complement regulatory proteins CD59 and DAF are defective, so that complement activation leads to episodes of spontanous hemolysis. The defect is the attachment of CD59 and DAF to cell membranes by a glycolipid anchor.
* hemolysis- lysis of red cells
* Alternative name for protectin, a complement control protein(any of a diverse grouop of proteins that inhibit complement activation at various stages and by different mechanisms.)
* protectin: a protein on the surface of human cells that prevents the assembly of the complement membrane-attack complex on the cell surface, thus protecting human cells against complement-mediated lysis.
*DAF(Decay-accelerating factor): which interferes with complement activation at human cell surfaces. It binds to the C3b component of the alternative C3 convertase, causing its dissociation and inactivation.
Macrophages: the mature forms of circulating monocytes that have left the blood and taken up residence in the tissues and it is long lived phgocytic cell participates in both innate and adaptive immunity.
Pentraxin: any member of a family of pentameric proteins that circulate in the blood and lymph and can bind to the surfaces a variety of pathogens and target them for destruction, CRP is in.
Peyer's patch: It is organized GALT present in the wall of the small intestine.
Plasma cell: termially differentiated B lymphocytes that secretes antibody.
Plasmacytoid dendritic cells: a type of dendritic cell that produces copious amounts of interferon in response to the defection of viral infection through its TLRs.
* TLR: recognize a variety of microbial ligands and are expressed by different types of innate immune cell.
* Interferon that interferes with the propagation of infection. It is produced by cytokines which is from induced in situation sensor proteins in the cytoplasm detect viral nucleic acids.(by RIG-I-like receptors(RLRs))
Recombination signal sequence(RSS): short stretch of DNA flnaking each of the gene segments that are rearranged to generate V-region exons. The are the sites at which somatic recombination occurs.
Recombination-activating genes(RAG1/RAG2) Two genes that are essential for the rearrangement of immunoglobulin and T-cell receptor gens in B cells and T cells, respectively.
RAG complex binds to one of the RSSs flanking the seq to be joined then recruits the other RSS to the complex. and then DNA is cleaved.
Respiratory burst: metabolic change accompanied by a transient increase in oxygen consumption that occurs in neutrophils and macrophages afer they have taken up opsonized particels. It leads to the generation of toxic oxygen metabolites and other antibacterial substances taht attck the phgagocytosed material.
Scavenger receptor: any of a group of disparate phagocytic cell-surface receptors on macrophages that binds to an assortment of negatively charged lignads, including sulfated polysaccharides, nucleic acids, and the phosphate-containing lipoeichoic acids in the cell walls of Gram-positive bacteria.
SR-A and SR-B are structually unrelated SR-B recognizes lipopeptides, whereas SR-A recognizes the lipopolysaccharide(LPS) of Gram negative bacteria.
Signal joint: The joint present in the circle of DNA that is formed as a byproduct of V(D)J recombination and discarded.
Somatic hypermutation: Mutation that occurs at high frequency in the rearranged variable-region DNA segments of immunoglobulin genes in activated B cells, resulting in the production of variant antibodies, some of which ahve a higher affinity for the antigen.
Switch sequences: short DNA seq preceding each heavy-chain constant region gene, at which somatic recombination occurs when B cells switch from producing one immunoglobulin isotype to another.
T cell anergy, anergy: It cannot be revived, even if its specific antigen is subsequently presented in the context of co-stimulation by a mature dendritiec cell. It reduces the essential cytokine which is related to self-tolerance that works in the peripheral.
Terminal deoxynucleotidyl transferase(TdT): Enzyme that inserts non-templated nucleotides( N nuclotides) into the junctions between gene segments during the rearrangement of the T-cell receptor and immunoglobulin genes.
Transcytosis: the transport of molecules form one side of an epithelium to the other. This involves endocytosis into vesicles within the epitherial cells at one face of the epithelium and release of the vesicels at the other. chapt 9.
V(D)J recombinase: The set of enzymes needed to recombine V,D, and J segments in the rearrangement of immunoglobulin and T-cell receptor genes. It includes the RAG-1 and RAG-2.
2020년 5월 31일 일요일
Work- Immunology
Immunolongy- part 1.
Alpha-macroblobulin: A protease inhibitor in plasma that is a component of innate immunity. It inhibits proteases that are produced or acquired by bacteria to aid their invasion.
Activation-induced cytidine deaminase(AID): Enzyme that deaminates DNA at cytosine resides, converting them to uracil. The activity of this enzyme and the consequent repair of the damaged DNA are the basis of somatic hypermutation and isotype switching in activated B cells.
* Deamination: removal of an amino group from a molecule.
*somatic hypermutation: DNA recombination that occurs between gene segments in the immunoglobulin loci and T-cell receptor loci in developing B cells and T-cell, respectively. It generates a complete exon composed of a V gene segment and a J gene segment that encods the variable region of an immunoglobulin or T-cell receptor polypeptide chain.
* isotype switching: The process by which a B cell changes he class of immunoglobulin it makes while the anitgenic specificity of the immunoglobulin.
Acute-phase protein: Any of a number of diverse plasma proteins that are rapidly made in large amounts by the liver in response to infection.
*Actue pahse proteins induce C-reactive protein and serum amyloid A protein.
*C-reactive protein,CRP: a memeber of the pentraxin family of proteins , contains five identical subunits that form a slab-like pentameric molecule with a hole in the middle. It can deliver pathogens to phagocytes to remove it.
* Serum amyloid A protein: a small protein which can interact with various cell-surface receptors, including Toll-like receptors and scavenger receptor to activate cells to produce inflammatory cytokines.
Affinity: measure of the strength with which one molecule binds to another at a single binding site.
Affinity maturation: The increase in affinity of the antigen-binding sites of antibodies for antigen that occurs during the course of an adaptive immune response. It is the result of somatic hypermutation of the rearranged immunoglobulin V-gene region and the consequent selection of mutated B cells that make antigen receptors of higher affinity for their antigen.
Agammaglobulinemia: An inability to make antibodies, reflected by abnormally low amounts or absence of antibodies in the blood.
Allelic exclusion: In reference to B-cell developement, the fact that each mature B cell expresses only one of the two immunoglobulin heavy chain or light cain alleles. For each locus, half of the cells in the B-cell population express the maternal allele, and the remaining cells express the paternal allele.
Anaphylatoxin: General name for complement fragments C3a and C5a, which are produced during complement activation. They induce inflammation, recruiting fluid and inflammatory cells to sites of antigen deposition.
Antibody repertoire: The total number of different specific antibodies that can be made by an individual, estimated at around 10^9
Antibody-dependent cell-mediated cytotoxicity(ADCC): The killing of anitbody-coated target cells by NK cells having the receptor FcrRIII(CD16), which recognizeds the Fc region of the bound antibody.
* Fab: Frgament antigen binding, they bind antigen and the fragments corresponding to the arms.
* Fc: Fragment crystallizable, the fragment corresponding to the stem, it readily crystallizes the effector functions of the antibody molecule by binding to serum proteins and cell-surface receptors.
* Differences in the heavy-chain C regions : 5 main isotypes. light chain has 2 isotypes: kappa > lamda
Antisera: Fluid component of clotted blood from an immune individual that contains antibodies against a given antigen. An antiserum contains a heterogeneous collection of antibodies that bind the antigen.
Autocrine: Describes a cytokine or other secreted molecule that acts on the same type of cell as the one that secreted it.
Avidity: The overall strength of binding of an antibody with multiple binding sites to an antigen(also with multiple sites), in contrast to the affinity, which is the strength of binding at a single site.
Bronchial-assoicated lymphoid tissue(BALT): The lymphoid cells and organized lymphoid tissues of the respiratory tract.
C3 convertase: any of the proteolytic enzymes that are formed during complement activation and cleave complement component C3 to C3b and C3a, thereby enabling C3b to bond covalently to antigens.
Caspase: Type of protease that is involved in generating some cytokines form their inactive pro-proteins as part of a protein comoplex called an inflammasome.
* Inflammasome: Ion channels are activated to lower the intracellular concentration of potassium ions. This ionic chnage facilitates the assembly of a protein complex through the oligomerization of a NOD-like receptor called NLRP3.
NOD-like receptor: Intracellular sensors of pathogen-associated molecular patterns(PAMPs) that enter the cell via phagocytosis or pores.
Catalytic antibody: Antibody that binds an antigen, chemically changes it, and then release it.
Chedlak-Higashi syndrome: genetic disease in which phagocytes malfunction. Their lysosomes fail to fuse properly with phagosomes, and killing of ingested bacteria is impaired.
Chemokine: Any member of a large roup of small proteins involved in guiding white blood cells to sites where their functions are needed. They have a central role in inflammatory responses.
Chimeric monoclonal antibody: monoclonal antibody that combines mouse variable regions with human constant reigons.
Chronic granulomatous disease(CGD) Immunodeficiency disease in which multiple granulomas form as a result of defective elimination of bacteria by phagocytic cells. It is caused by a defect in the NADPH oxidase system of enzymes, which generates the superoxide radical involved in bacterial killing.
Granulomas: a structure formed during inflammtion that is found in many diseases.
Clonal Selection: The central principle of adaptive immunity. It is the mechanism by which adaptive immune responses derive only from individual antigen-specific lymphocytes, which are stimulated by the antigen to proliferate and differentiate in antigen-specific
Coagulation system: Collection of enzymes and other proteins in blood that function to form blood clots. The coagulation system is activated by damage to blood vessels.
Coding joint: The joint betwee he ends of two rearragned immunoglobulin or T-cell receptor gene segments.(VDJ)
Commensal microoraganism: A microorganism that habitually lives on or in the human body; one that normally cuases no disease or harm and can be beneficial.
Complement: Collection of plasma proteins that act in cascade of reactions to attack extracellular forms of pathogens in extracellular spaces and the blood.
Complement activation: The initiation of a series of reactions involving the complement proteins present in plasma and extracellular fluid and leading to the death and elimination of the pathogen. It can be triggered either directly or indirectly by the presence of a pathogen.
Complement fixation: The covalent attachment of C3b or C4b to pathogen surfaces, which is a central feature of the action of complement because it facilitates phagocytosis of the pathogen.
Complementarity-determining regions(CDRs): Short region of high diversity in amino acid sequence within the variable region of immunoglobulin and T-cell receptor chains. There are three regions in each variable region, which collectively contribute to the antigen-binding site and determine the antigenic specificity.
C-reactive protein(CRP): Soluble acute-phase protein that binds to phosphorylcholine, a surface constituent of various bacteria. It binds to bacteria, opsonizing them for uptake by phagocytes. It can also activate the classical pathway of complement fixation and bind to Fc receptors.
*Opsonization: Phenomenon by which a coating of antibody facilitates phagocytes.
Defensin: Any member of a large family of small antimicrobial peptides 35~40 amino acids that can penetrate microbial membranes and disrupt their integrity. They are present at epithelial surfaces and in neutrophil granules.
* Neutrophil: most abundant of the granulocytes, specialized in the capture, engulfment and killing of microorganisms.
Discontinous epitope: An antigenic structure on a protein that is formed from several separate regions in the primary sequrence of a protein brought together by protein folding.
Edema: Abnormal acculmulation of fluid in connective tissue, leading to selling.
Epitope: The protion of a n antigenic molecule that is bound by an antibody or gives rise to the MHC-binding peptide that is recognized by a T-cell receptor. Also called an antigenic determinatn.
Extravasation: The movement of cells or fluid from within blood vessels to the surrounding tissues.
Flow cytometry: A technique in which individual cells can be counted or identified by their cell-surface molecules after fluorescent labeling.
Genetic polymorphism: Variation in a population owing to the existence of two or more alleles of a given gene.
Germinal center: An area in secondary lymphoid tissue that is a site of intense B-cell proliferation,slection, maturation, and cell death.
Germline form or germline configuration: The unrearranged oranization of the immunoglobulin and T-cell receptor genes in the DNA orf germ cells and in somatic cells other than T cells and B cells.
Granuloma: A site of chronic inflammation usually tirggered by persistent infectious agents such as mycobacteria, or by a non-degradable foeign body.
Gut-associciated lymphoid tissue(GALT): All lymphoid tissue closely assoicated with gastrointestinal tract, including the palatine tonsils, peyer's patches in the intestine and layers of intraepithelial lymphocytes.
Hematopoiesis: The generation of the cellular elements of blood, including the red blood cells, white blood cells, and platelets.
*White blood cells(leukocytes): The cells of the immune system that are involved in protecting the body
*Platelets: thrombocytes, component of blood whose function is to reat to bleeding from blood vessel injury.
Humanize: It refers to the process by which a mouse monoclonal IgG having high affinity and specificity for an antigen of clinical interest is converted into an antibody that resembles a human IgG but retains the specificity and affinity of the mouse antibody.
Hybridoma cell line: It makes monoclonal antibodies of defined specificity. They are formed by fusing a specific antibody-producing B lymphocyte with a myeloma cell that grows in tissue culture and does not make any immunoglobulin chains of its own.
Hyper-IgM syndrome: Genetically determined immunodeficiency disease in which B cells cannot switch their immunoglobulin heavy-chain isotype, and so make unusually high amounts of IgM and no ther isotype. It leads to abnormal susceptibility to infections with pyogenic bacteria.
Alpha-macroblobulin: A protease inhibitor in plasma that is a component of innate immunity. It inhibits proteases that are produced or acquired by bacteria to aid their invasion.
Activation-induced cytidine deaminase(AID): Enzyme that deaminates DNA at cytosine resides, converting them to uracil. The activity of this enzyme and the consequent repair of the damaged DNA are the basis of somatic hypermutation and isotype switching in activated B cells.
* Deamination: removal of an amino group from a molecule.
*somatic hypermutation: DNA recombination that occurs between gene segments in the immunoglobulin loci and T-cell receptor loci in developing B cells and T-cell, respectively. It generates a complete exon composed of a V gene segment and a J gene segment that encods the variable region of an immunoglobulin or T-cell receptor polypeptide chain.
* isotype switching: The process by which a B cell changes he class of immunoglobulin it makes while the anitgenic specificity of the immunoglobulin.
Acute-phase protein: Any of a number of diverse plasma proteins that are rapidly made in large amounts by the liver in response to infection.
*Actue pahse proteins induce C-reactive protein and serum amyloid A protein.
*C-reactive protein,CRP: a memeber of the pentraxin family of proteins , contains five identical subunits that form a slab-like pentameric molecule with a hole in the middle. It can deliver pathogens to phagocytes to remove it.
* Serum amyloid A protein: a small protein which can interact with various cell-surface receptors, including Toll-like receptors and scavenger receptor to activate cells to produce inflammatory cytokines.
Affinity: measure of the strength with which one molecule binds to another at a single binding site.
Affinity maturation: The increase in affinity of the antigen-binding sites of antibodies for antigen that occurs during the course of an adaptive immune response. It is the result of somatic hypermutation of the rearranged immunoglobulin V-gene region and the consequent selection of mutated B cells that make antigen receptors of higher affinity for their antigen.
Agammaglobulinemia: An inability to make antibodies, reflected by abnormally low amounts or absence of antibodies in the blood.
Allelic exclusion: In reference to B-cell developement, the fact that each mature B cell expresses only one of the two immunoglobulin heavy chain or light cain alleles. For each locus, half of the cells in the B-cell population express the maternal allele, and the remaining cells express the paternal allele.
Anaphylatoxin: General name for complement fragments C3a and C5a, which are produced during complement activation. They induce inflammation, recruiting fluid and inflammatory cells to sites of antigen deposition.
Antibody repertoire: The total number of different specific antibodies that can be made by an individual, estimated at around 10^9
Antibody-dependent cell-mediated cytotoxicity(ADCC): The killing of anitbody-coated target cells by NK cells having the receptor FcrRIII(CD16), which recognizeds the Fc region of the bound antibody.
* Fab: Frgament antigen binding, they bind antigen and the fragments corresponding to the arms.
* Fc: Fragment crystallizable, the fragment corresponding to the stem, it readily crystallizes the effector functions of the antibody molecule by binding to serum proteins and cell-surface receptors.
* Differences in the heavy-chain C regions : 5 main isotypes. light chain has 2 isotypes: kappa > lamda
Antisera: Fluid component of clotted blood from an immune individual that contains antibodies against a given antigen. An antiserum contains a heterogeneous collection of antibodies that bind the antigen.
Autocrine: Describes a cytokine or other secreted molecule that acts on the same type of cell as the one that secreted it.
Avidity: The overall strength of binding of an antibody with multiple binding sites to an antigen(also with multiple sites), in contrast to the affinity, which is the strength of binding at a single site.
Bronchial-assoicated lymphoid tissue(BALT): The lymphoid cells and organized lymphoid tissues of the respiratory tract.
C3 convertase: any of the proteolytic enzymes that are formed during complement activation and cleave complement component C3 to C3b and C3a, thereby enabling C3b to bond covalently to antigens.
Caspase: Type of protease that is involved in generating some cytokines form their inactive pro-proteins as part of a protein comoplex called an inflammasome.
* Inflammasome: Ion channels are activated to lower the intracellular concentration of potassium ions. This ionic chnage facilitates the assembly of a protein complex through the oligomerization of a NOD-like receptor called NLRP3.
NOD-like receptor: Intracellular sensors of pathogen-associated molecular patterns(PAMPs) that enter the cell via phagocytosis or pores.
Catalytic antibody: Antibody that binds an antigen, chemically changes it, and then release it.
Chedlak-Higashi syndrome: genetic disease in which phagocytes malfunction. Their lysosomes fail to fuse properly with phagosomes, and killing of ingested bacteria is impaired.
Chemokine: Any member of a large roup of small proteins involved in guiding white blood cells to sites where their functions are needed. They have a central role in inflammatory responses.
Chimeric monoclonal antibody: monoclonal antibody that combines mouse variable regions with human constant reigons.
Chronic granulomatous disease(CGD) Immunodeficiency disease in which multiple granulomas form as a result of defective elimination of bacteria by phagocytic cells. It is caused by a defect in the NADPH oxidase system of enzymes, which generates the superoxide radical involved in bacterial killing.
Granulomas: a structure formed during inflammtion that is found in many diseases.
Clonal Selection: The central principle of adaptive immunity. It is the mechanism by which adaptive immune responses derive only from individual antigen-specific lymphocytes, which are stimulated by the antigen to proliferate and differentiate in antigen-specific
Coagulation system: Collection of enzymes and other proteins in blood that function to form blood clots. The coagulation system is activated by damage to blood vessels.
Coding joint: The joint betwee he ends of two rearragned immunoglobulin or T-cell receptor gene segments.(VDJ)
Commensal microoraganism: A microorganism that habitually lives on or in the human body; one that normally cuases no disease or harm and can be beneficial.
Complement: Collection of plasma proteins that act in cascade of reactions to attack extracellular forms of pathogens in extracellular spaces and the blood.
Complement activation: The initiation of a series of reactions involving the complement proteins present in plasma and extracellular fluid and leading to the death and elimination of the pathogen. It can be triggered either directly or indirectly by the presence of a pathogen.
Complement fixation: The covalent attachment of C3b or C4b to pathogen surfaces, which is a central feature of the action of complement because it facilitates phagocytosis of the pathogen.
Complementarity-determining regions(CDRs): Short region of high diversity in amino acid sequence within the variable region of immunoglobulin and T-cell receptor chains. There are three regions in each variable region, which collectively contribute to the antigen-binding site and determine the antigenic specificity.
C-reactive protein(CRP): Soluble acute-phase protein that binds to phosphorylcholine, a surface constituent of various bacteria. It binds to bacteria, opsonizing them for uptake by phagocytes. It can also activate the classical pathway of complement fixation and bind to Fc receptors.
*Opsonization: Phenomenon by which a coating of antibody facilitates phagocytes.
Defensin: Any member of a large family of small antimicrobial peptides 35~40 amino acids that can penetrate microbial membranes and disrupt their integrity. They are present at epithelial surfaces and in neutrophil granules.
* Neutrophil: most abundant of the granulocytes, specialized in the capture, engulfment and killing of microorganisms.
Discontinous epitope: An antigenic structure on a protein that is formed from several separate regions in the primary sequrence of a protein brought together by protein folding.
Edema: Abnormal acculmulation of fluid in connective tissue, leading to selling.
Epitope: The protion of a n antigenic molecule that is bound by an antibody or gives rise to the MHC-binding peptide that is recognized by a T-cell receptor. Also called an antigenic determinatn.
Extravasation: The movement of cells or fluid from within blood vessels to the surrounding tissues.
Flow cytometry: A technique in which individual cells can be counted or identified by their cell-surface molecules after fluorescent labeling.
Genetic polymorphism: Variation in a population owing to the existence of two or more alleles of a given gene.
Germinal center: An area in secondary lymphoid tissue that is a site of intense B-cell proliferation,slection, maturation, and cell death.
Germline form or germline configuration: The unrearranged oranization of the immunoglobulin and T-cell receptor genes in the DNA orf germ cells and in somatic cells other than T cells and B cells.
Granuloma: A site of chronic inflammation usually tirggered by persistent infectious agents such as mycobacteria, or by a non-degradable foeign body.
Gut-associciated lymphoid tissue(GALT): All lymphoid tissue closely assoicated with gastrointestinal tract, including the palatine tonsils, peyer's patches in the intestine and layers of intraepithelial lymphocytes.
Hematopoiesis: The generation of the cellular elements of blood, including the red blood cells, white blood cells, and platelets.
*White blood cells(leukocytes): The cells of the immune system that are involved in protecting the body
*Platelets: thrombocytes, component of blood whose function is to reat to bleeding from blood vessel injury.
Humanize: It refers to the process by which a mouse monoclonal IgG having high affinity and specificity for an antigen of clinical interest is converted into an antibody that resembles a human IgG but retains the specificity and affinity of the mouse antibody.
Hybridoma cell line: It makes monoclonal antibodies of defined specificity. They are formed by fusing a specific antibody-producing B lymphocyte with a myeloma cell that grows in tissue culture and does not make any immunoglobulin chains of its own.
Hyper-IgM syndrome: Genetically determined immunodeficiency disease in which B cells cannot switch their immunoglobulin heavy-chain isotype, and so make unusually high amounts of IgM and no ther isotype. It leads to abnormal susceptibility to infections with pyogenic bacteria.
Work-Principle of microbiology
Diversity of Bacteria- Gram Positive Bacteria
1. Firmicutes: A phylum of bacteria with Gram positive cell walls and low DNA G+C contents. The name of this group means those with firm envelopes.
2. Actinobacteria: Antoher group of bacteria having Gram positive cell walls but with high DNA G+C contents. The name of this group means bacteria growing as filamentous forms.
Actino-: ray, beam
3. Lactobacillus: Typically rod-shaped and grow in chains, varying from long and slender to short, bent rods, and nost are homofermentative, common in dairy products.
4. Streptoccocus: The genus play important roles in the production of buttermilk, silage, and other fermented products, and certain species paly a major role in the formation of dental caries. There are several other genera of homofermentative.
*Dental cries: tooth dacay
*Silage:preserved pasture.
*Homofermentative: Producing a fermentation resulting wholly or pricipally in a single end product.
* fermentation: Chemical process by which molecules such as glucose are broken down anaerobically.
5. The genus Lactococcus contains of dairy significance, wherease the genus Enterococcus that are primarily of fecal orgin and can be human pathogens.
6. Lactic acid bacteria can be classified into two groups depending on the final products of lactic acid fermentation.: Homofermentative group and Heterofermentative group.
7. Listeria monocytogenes: A species of Gram positive bacteria which is a causative agent of listeriosis. The generic name was named after a surgeon, Joseph Lister.
8. Staphylococcus aureus: A species of Gram positive bacteria which is one of the most common inhabitants of human body, and also a common cause of skin infections. The generic name means a bunch of grapes, and the species name golden color.
* Staphylococcus: faculataive aerobe, catalase-positive, gram-positive coccus.
9. Sarcina: Obligate anaerobic, catalase negative and extremly acid tolerant genus belonging to the clostriudium familay(Clostridiaceae). the name means a package or bundle, and the genus was recently reclassified as members of Clostridium.
*Catalase: a common enzyme found in nearly all living organisms exposed to oxygen. It catalyzes the decomposition of hydrogen peroxide to water and oxygen.
10. Bacillus thruingiensis, Paenibacillus popilliae: known to produce insect larvicide crystals in their endospores.
* larvicide: insecticide that is specifically targeted against the larval life stage of an insect.
11. Stickland reactions: A fermentative metabolism of some members of Clostridium, an obligate anaerobic genus, in which a pair of amino acids are used. One serves as an electron donor, and the other as an electron acceptor.
12. Mycoplasma: A genus of Tenericutes(having soft cell enevelope), lacking cell walls, and growing in pleomorphic forms. One of the smallest organisms capable of autonomous growth, and parasitic to animal and plant hosts.
13. Spiroplasma: The genus consists of helical or spiral-shaped. Although they lack a cell wall and flagella. They have rotary screw motility. The organism has benn isolated from ticks, the hemolymph and gut of insects, vascular plant fluids and insects that feed on these fluids, and the surfaces of flowers and other plant parts.
14. Arthrobacter: The genus consisting primarily of soil organisms. They are remarkably resisant to desiccation and starvation, despite the fact that they do not form spores or other resting cells.
15. Propionibacterium: An actinobacterial genus famous for the association with Swiss type chesses. Performs secondary fermentation, which is the fermentation of substrates produced from another fermentation by other bacteria.
16. Corynebacterium glutamicum: An actinobacterial species known to produce glutamic acid. The genus to which this species belongs is characterized by club-shaped, irregularly shpaed, aor V-shaped cell arranagements of cells.
* Glutamic acid: an alpha-amino acid that is used by almost all living beings in the biosynthesis of proteins.
17. Mycobacterium: An acid-fast actinobacterial genus forming tight, compact, wrinkled colonies due to the presence of mycolic acids. Includes pathogens of tuberculosis and leprosy.
* mycolic acids: long fatty acids found in the cell walls
18. Streptomyces: The largest prokaryotic genus blonging to actinobacteria, forming extensively branching aerial and substrate mycelium. The genus is also famous for the production of secondary metabolites, notably antibiotics by many members.
*mycelium: vegetative part of a fungus or fungus like bacterial colony.
1. Firmicutes: A phylum of bacteria with Gram positive cell walls and low DNA G+C contents. The name of this group means those with firm envelopes.
2. Actinobacteria: Antoher group of bacteria having Gram positive cell walls but with high DNA G+C contents. The name of this group means bacteria growing as filamentous forms.
Actino-: ray, beam
3. Lactobacillus: Typically rod-shaped and grow in chains, varying from long and slender to short, bent rods, and nost are homofermentative, common in dairy products.
4. Streptoccocus: The genus play important roles in the production of buttermilk, silage, and other fermented products, and certain species paly a major role in the formation of dental caries. There are several other genera of homofermentative.
*Dental cries: tooth dacay
*Silage:preserved pasture.
*Homofermentative: Producing a fermentation resulting wholly or pricipally in a single end product.
* fermentation: Chemical process by which molecules such as glucose are broken down anaerobically.
5. The genus Lactococcus contains of dairy significance, wherease the genus Enterococcus that are primarily of fecal orgin and can be human pathogens.
6. Lactic acid bacteria can be classified into two groups depending on the final products of lactic acid fermentation.: Homofermentative group and Heterofermentative group.
7. Listeria monocytogenes: A species of Gram positive bacteria which is a causative agent of listeriosis. The generic name was named after a surgeon, Joseph Lister.
8. Staphylococcus aureus: A species of Gram positive bacteria which is one of the most common inhabitants of human body, and also a common cause of skin infections. The generic name means a bunch of grapes, and the species name golden color.
* Staphylococcus: faculataive aerobe, catalase-positive, gram-positive coccus.
9. Sarcina: Obligate anaerobic, catalase negative and extremly acid tolerant genus belonging to the clostriudium familay(Clostridiaceae). the name means a package or bundle, and the genus was recently reclassified as members of Clostridium.
*Catalase: a common enzyme found in nearly all living organisms exposed to oxygen. It catalyzes the decomposition of hydrogen peroxide to water and oxygen.
10. Bacillus thruingiensis, Paenibacillus popilliae: known to produce insect larvicide crystals in their endospores.
* larvicide: insecticide that is specifically targeted against the larval life stage of an insect.
11. Stickland reactions: A fermentative metabolism of some members of Clostridium, an obligate anaerobic genus, in which a pair of amino acids are used. One serves as an electron donor, and the other as an electron acceptor.
12. Mycoplasma: A genus of Tenericutes(having soft cell enevelope), lacking cell walls, and growing in pleomorphic forms. One of the smallest organisms capable of autonomous growth, and parasitic to animal and plant hosts.
13. Spiroplasma: The genus consists of helical or spiral-shaped. Although they lack a cell wall and flagella. They have rotary screw motility. The organism has benn isolated from ticks, the hemolymph and gut of insects, vascular plant fluids and insects that feed on these fluids, and the surfaces of flowers and other plant parts.
14. Arthrobacter: The genus consisting primarily of soil organisms. They are remarkably resisant to desiccation and starvation, despite the fact that they do not form spores or other resting cells.
15. Propionibacterium: An actinobacterial genus famous for the association with Swiss type chesses. Performs secondary fermentation, which is the fermentation of substrates produced from another fermentation by other bacteria.
16. Corynebacterium glutamicum: An actinobacterial species known to produce glutamic acid. The genus to which this species belongs is characterized by club-shaped, irregularly shpaed, aor V-shaped cell arranagements of cells.
* Glutamic acid: an alpha-amino acid that is used by almost all living beings in the biosynthesis of proteins.
17. Mycobacterium: An acid-fast actinobacterial genus forming tight, compact, wrinkled colonies due to the presence of mycolic acids. Includes pathogens of tuberculosis and leprosy.
* mycolic acids: long fatty acids found in the cell walls
18. Streptomyces: The largest prokaryotic genus blonging to actinobacteria, forming extensively branching aerial and substrate mycelium. The genus is also famous for the production of secondary metabolites, notably antibiotics by many members.
*mycelium: vegetative part of a fungus or fungus like bacterial colony.
2020년 5월 30일 토요일
Work: Principle of microbiology.
Diversity of Bacteria.
[Proteobacteria]
1. Proteobacteria: Protean group of bacteria of diverse properties despite a common ancestry. Incluses many of the most commonly encountered Gram negative bacteria such as Rhizobium, Pseudomans and Escherichia. (largest and most metabolically diverse phylum, divided into six classes.)
Protean: taking on different forms
2. Rhizobium: Plant associated bacterial genus forming root nodules in legume plants. Taxonomically belongs to Alphaproteobacteria(oligotrophic: grow under low nutrient concentration)
Rhizo: root/ Rhizobia: fix nitrogen
Alphaproteobacteria:oligotrophic (grow under low nutrient concentration), six major orders(Rhizobiales, Rickettsiales, Rhodobacterales, Rhodospirillales, Caulobacterales, and Sphingomonadales) * -ales: suffix for order.
3. Rickettsia: Alphaproteobacterial genus, mostly obligate intracellular parasites and causative agents of human diseases such as typhus and Rocky Mountain Fever.
4. Hyphomicroibium: Alphaproteobacterial genus that is chemoorganotrophic, forms single hypha from parent cell, and reproduces by budding.
Hypha: long filamentous branches
Chemoorganotrophic: Organisms that conserve envergy from chemicals are called chemotrophs and those atha use organic chemicals are called chemoorganotrophs.
5. Caulobacter: Alphaproteobacterial genus that is chemoorganotrophic, produces cytoplasm-filled stalk. In aquatic environment, several cells may attach to form 'rosettes'. A model system for cell division and development due to unequal cell division.
Rosettes: a rose-like marking ofr formation found on the fur and skin of some animals.
6. Prosthecae: Various kinds of cytoplasmic extrusions bounded by a cell wall, mainly found among members of Alphaproteobactria.
Cytoplasmic extrusion: Sperm plasma membrane is remodeled.
7. Magnetospirillum: Spiral shaped, chemoorganotrophic alphaproteobacterial genus showing magnetotaxis(directed movement ina magnetic field)
8. Burkholderia: The genus includes diverse species orf chemoorganotrophs with strictly respiratory metabolism. All species can grow aerobiacally, some also grow aneorbically with nitrate as the electron acceptor, and many strains are able to fix N2.
Electron acceptor: a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent that is itself reduced in the process.
9. Rhodocyclus: Like most purple nonsulfur bacteria, this species grow best as a photoheterotrophs but most can also grow as photoautotrohs with H2 as elecctron acceptor. Species can also grow by respiration in darkness, but they are typically found in illuminated anoxic environments where organic matter is present.
Photogrophs: Organismas that carry out photosynthesis/ Autotrophs: Photosynthetic organisms are capable orf growing with CO2 as the sole carbon source.
Photoheterotrophs: Phtotrophs can use organic carbon as their carbon source
10. Zoogloea: It is another important genus of the Rhodocyclales. This species are aerobic chemoorganotrophs that are distinctive for producing a thick gelatinous capusle which binds cells together into a complex matrix with brinching, fingerlike projections. Also it is important in aerobic wastewater treatment., causing flocculation(settling out of solution)
11. Neisseria: Betaproteobacterial genus, frequently isolated form animals. Some species are pathogenic, including gonorrhea.
12. Hydorgenophilus: Obligate aerobe that can grow as a chemolithotroph using H2 as an electron donor for respiration and the Calvin cycle to fix CO2. This species is a facultative chemolithotroph and can also grow as a chemoorganotroph on simple carbon sources.
Chemolithotroph: it is able to use inorganic reduced compunds as electron sources.
Faculative aerobes: not required but growth better with O2.
13. Thiobacillus: Chemolithotrophic species of sulfur bacteria that oxidize reduced sulfur compounds as electron donors and grow by aerobic respiration or denitrification.
Denitrification: Nitrate(NO3-) or Nitrite is reduced and ultimately produces molecular nitrogen(N2).
Sulfur bacteria: Many gram negative bacteria and archaea oxidize reduced sulfur compounds, such as hydrogen sulfide(H2S). The oxidation of sulfide generates electrons for use in energy metabolism(chemolithotrophy) or CO2 fixation(autotrophy).
14. Leptothrix: Filamentous betaproteobacterial genus forming sheath. Nutritionally versatile, being able to use organic compounds. Ferrous iron precipitates on sheath.
15. Enteric bacteria are a group of gammaproteobacterial genera, and can be divided into two groups according to the prodcution of end products from sugar fermentation. Mixed-acid fermenters and 2,3-buatnediol fermenters.
16. Escherichia: Species play a nutritional role in the intestinal tract by synthesizing vitamins, particularly vitamin K. As a facultative aerobe, this organism probably also helps consume O2, thus rendering the large intestine anoxic.
Anoxic: depleted of dissolved oxygen
17. Salmonella: Species are alomost always pathogenic, either to humans or to other worm-blooded animals. In humans the most common disease cuased by almonellas are typhoid fever and gastroenteritis.
18. Shigella: Species are typically pathogenic to humans, causing a rather severe gastroenteritis called bacillary dysentery, transmitted by food and water borne routes. The bacterium, which contains endotoxin, invades intestinal epithelial cells, where it excretes a neurotoxin that causes acute gastrointestinal distress.
19. Proteus: A genus of enteric bacteria that is higly motile and capable of swarming. Frequent cause of urinary tract infections in humbans.
20. Enterobacter: Species are a common species in water and sewage as well as the intestinal ract of warm-blooded animals and is an occasional cause of urinary tract infections.
21. Klebsiella: Most commonly found in soil and water and also fix nitrogen, a property not charcteristic of other enteric bacteria.
22. Serratia: Enteric bacterial genus including prodigiosin producers. some may cause infection.
Prodigiosin: red pigment produced by many strains of the bacterium Serratia marcescens.
23. Pseudomonas: Gammaproteobacterial genus found in a wide variety of environment. Capable of utilizing a wide range of organic compounds. The name of the genus literally means a 'false unit'.
24. Vibrio: Motile, curved rod shaped gammaproteobacterial genus. Includes pathogenic species causing cholra etc, and mostly inhabiting marine environment. Some are capable of light production called bioluminescence.
25. Bdellovibiro: Deltaproteobacterial genus preying on other Gram negative bacteria. Obligate aerobic, and highly motile. Widespread in soil and water.
26. Myxobacteria: Deltaproteobacterial genus forming multicellular structures and also capable of gliding movement. Shows complex develpmental life cycles. Lifestyle includes consumption of dead organic matter or other bacterial cells.
27. Pylori: Epsilonproteobacterial genus inhabiting the lining of upper gastrointestinal(GI) tract and liver. Known to be present in up to 50% of human populations, also most infected people show no obvious symptons.
28. Wolinella: An anaerobic bacterium isolated from the bovine rumen. Unlike other Epsilonproteobacteria, grows best as an anaerobe and can catalyze anaerobic respirations using fumarate or nitrate as electron acceptors with H2 or formate as electron donors.
Michael T. Madian, Kelly S. Bender, Daniel H. Buckley, W. Matthew Sattley, David A. Stahl. Brock Biology of Microorganisms(15th edition).(2017) Pearson.
[Proteobacteria]
1. Proteobacteria: Protean group of bacteria of diverse properties despite a common ancestry. Incluses many of the most commonly encountered Gram negative bacteria such as Rhizobium, Pseudomans and Escherichia. (largest and most metabolically diverse phylum, divided into six classes.)
Protean: taking on different forms
2. Rhizobium: Plant associated bacterial genus forming root nodules in legume plants. Taxonomically belongs to Alphaproteobacteria(oligotrophic: grow under low nutrient concentration)
Rhizo: root/ Rhizobia: fix nitrogen
Alphaproteobacteria:oligotrophic (grow under low nutrient concentration), six major orders(Rhizobiales, Rickettsiales, Rhodobacterales, Rhodospirillales, Caulobacterales, and Sphingomonadales) * -ales: suffix for order.
3. Rickettsia: Alphaproteobacterial genus, mostly obligate intracellular parasites and causative agents of human diseases such as typhus and Rocky Mountain Fever.
4. Hyphomicroibium: Alphaproteobacterial genus that is chemoorganotrophic, forms single hypha from parent cell, and reproduces by budding.
Hypha: long filamentous branches
Chemoorganotrophic: Organisms that conserve envergy from chemicals are called chemotrophs and those atha use organic chemicals are called chemoorganotrophs.
5. Caulobacter: Alphaproteobacterial genus that is chemoorganotrophic, produces cytoplasm-filled stalk. In aquatic environment, several cells may attach to form 'rosettes'. A model system for cell division and development due to unequal cell division.
Rosettes: a rose-like marking ofr formation found on the fur and skin of some animals.
6. Prosthecae: Various kinds of cytoplasmic extrusions bounded by a cell wall, mainly found among members of Alphaproteobactria.
Cytoplasmic extrusion: Sperm plasma membrane is remodeled.
7. Magnetospirillum: Spiral shaped, chemoorganotrophic alphaproteobacterial genus showing magnetotaxis(directed movement ina magnetic field)
8. Burkholderia: The genus includes diverse species orf chemoorganotrophs with strictly respiratory metabolism. All species can grow aerobiacally, some also grow aneorbically with nitrate as the electron acceptor, and many strains are able to fix N2.
Electron acceptor: a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent that is itself reduced in the process.
9. Rhodocyclus: Like most purple nonsulfur bacteria, this species grow best as a photoheterotrophs but most can also grow as photoautotrohs with H2 as elecctron acceptor. Species can also grow by respiration in darkness, but they are typically found in illuminated anoxic environments where organic matter is present.
Photogrophs: Organismas that carry out photosynthesis/ Autotrophs: Photosynthetic organisms are capable orf growing with CO2 as the sole carbon source.
Photoheterotrophs: Phtotrophs can use organic carbon as their carbon source
10. Zoogloea: It is another important genus of the Rhodocyclales. This species are aerobic chemoorganotrophs that are distinctive for producing a thick gelatinous capusle which binds cells together into a complex matrix with brinching, fingerlike projections. Also it is important in aerobic wastewater treatment., causing flocculation(settling out of solution)
11. Neisseria: Betaproteobacterial genus, frequently isolated form animals. Some species are pathogenic, including gonorrhea.
12. Hydorgenophilus: Obligate aerobe that can grow as a chemolithotroph using H2 as an electron donor for respiration and the Calvin cycle to fix CO2. This species is a facultative chemolithotroph and can also grow as a chemoorganotroph on simple carbon sources.
Chemolithotroph: it is able to use inorganic reduced compunds as electron sources.
Faculative aerobes: not required but growth better with O2.
13. Thiobacillus: Chemolithotrophic species of sulfur bacteria that oxidize reduced sulfur compounds as electron donors and grow by aerobic respiration or denitrification.
Denitrification: Nitrate(NO3-) or Nitrite is reduced and ultimately produces molecular nitrogen(N2).
Sulfur bacteria: Many gram negative bacteria and archaea oxidize reduced sulfur compounds, such as hydrogen sulfide(H2S). The oxidation of sulfide generates electrons for use in energy metabolism(chemolithotrophy) or CO2 fixation(autotrophy).
14. Leptothrix: Filamentous betaproteobacterial genus forming sheath. Nutritionally versatile, being able to use organic compounds. Ferrous iron precipitates on sheath.
15. Enteric bacteria are a group of gammaproteobacterial genera, and can be divided into two groups according to the prodcution of end products from sugar fermentation. Mixed-acid fermenters and 2,3-buatnediol fermenters.
16. Escherichia: Species play a nutritional role in the intestinal tract by synthesizing vitamins, particularly vitamin K. As a facultative aerobe, this organism probably also helps consume O2, thus rendering the large intestine anoxic.
Anoxic: depleted of dissolved oxygen
17. Salmonella: Species are alomost always pathogenic, either to humans or to other worm-blooded animals. In humans the most common disease cuased by almonellas are typhoid fever and gastroenteritis.
18. Shigella: Species are typically pathogenic to humans, causing a rather severe gastroenteritis called bacillary dysentery, transmitted by food and water borne routes. The bacterium, which contains endotoxin, invades intestinal epithelial cells, where it excretes a neurotoxin that causes acute gastrointestinal distress.
19. Proteus: A genus of enteric bacteria that is higly motile and capable of swarming. Frequent cause of urinary tract infections in humbans.
20. Enterobacter: Species are a common species in water and sewage as well as the intestinal ract of warm-blooded animals and is an occasional cause of urinary tract infections.
21. Klebsiella: Most commonly found in soil and water and also fix nitrogen, a property not charcteristic of other enteric bacteria.
22. Serratia: Enteric bacterial genus including prodigiosin producers. some may cause infection.
Prodigiosin: red pigment produced by many strains of the bacterium Serratia marcescens.
23. Pseudomonas: Gammaproteobacterial genus found in a wide variety of environment. Capable of utilizing a wide range of organic compounds. The name of the genus literally means a 'false unit'.
24. Vibrio: Motile, curved rod shaped gammaproteobacterial genus. Includes pathogenic species causing cholra etc, and mostly inhabiting marine environment. Some are capable of light production called bioluminescence.
25. Bdellovibiro: Deltaproteobacterial genus preying on other Gram negative bacteria. Obligate aerobic, and highly motile. Widespread in soil and water.
26. Myxobacteria: Deltaproteobacterial genus forming multicellular structures and also capable of gliding movement. Shows complex develpmental life cycles. Lifestyle includes consumption of dead organic matter or other bacterial cells.
27. Pylori: Epsilonproteobacterial genus inhabiting the lining of upper gastrointestinal(GI) tract and liver. Known to be present in up to 50% of human populations, also most infected people show no obvious symptons.
28. Wolinella: An anaerobic bacterium isolated from the bovine rumen. Unlike other Epsilonproteobacteria, grows best as an anaerobe and can catalyze anaerobic respirations using fumarate or nitrate as electron acceptors with H2 or formate as electron donors.
Michael T. Madian, Kelly S. Bender, Daniel H. Buckley, W. Matthew Sattley, David A. Stahl. Brock Biology of Microorganisms(15th edition).(2017) Pearson.
"Consistently"
I've been experienced many things while I had posted nothing.
Now, this blog is only for my space to record my own things.
I am gonna post my life, studying, rest, work ,etc.
I'm not a English but I've been interested in English so that I will keep trying to use English in my post even if it is not perfect.
Thank you for reading if there is someone reads this post:)
Sincerely, Daisy.🙏
Now, this blog is only for my space to record my own things.
I am gonna post my life, studying, rest, work ,etc.
I'm not a English but I've been interested in English so that I will keep trying to use English in my post even if it is not perfect.
Thank you for reading if there is someone reads this post:)
Sincerely, Daisy.🙏
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