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Genetic recombination involves...
chromosomes breaking and rejoining to form new combinations
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Homologous recombination happens mostly in
bacteria
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homologous recombination occurs when chromosomes...
cross over during meiosis.
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Homologous recombination is a essential feature for...
all species
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Homologous recombination occurs between...
DNA segments that are homologous
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Site specific recombination is when..
non-homologous DNA segments, are recombined, at sepcific sites.
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Non-homologous DNA segments, are recombined, at sepcific sites such as...
Lambda
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Site-specific recombination occurs...
- 1)when certain viruses intergrate their genomes into host cell DNA
- 2)within genes that encode antibody polypeptides.
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Illegitamate recombination is when...
non-homologous DNA segments recombine randomly
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Illegitamate recombination usually occurs in....
mammalian cells and humans
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A widespread form of recombination is called...
transposition
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When certain viruses intergrate there genome into host cell DNA and within genes that encode antibody polypeptides it is an example of what kind of recombination?
Site specific
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What happens in transposition?
Small segments of DNA called tansposons, can move themselves to multiple locations within the chromosomal DNA
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The major example of transposition is...
multi-colored Corn.
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When crossing over takes place between sister chromatids, the process is called..
Sister chromatid exchange (SCE)
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Why does SCE (sister chromatid exchange) NOT produce a new combination of alleles?
sister chromatids are genetically identical
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Bacteria are usually haploid and they do not have pairs of homologous chromosomes. Despite this, they can undergo homologous recombination. How is this possible?
bacteria may have more than one copy of a chromosome per cell, though the copies are usually identical. These copies can exchange genetic material via homologous recombination.
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During DNA replication, the replicated regions may also undergo....
homologous recombination.
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Homologous recombination is particularly important in the repair of.....
DNA segments that have been damaged.
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In a Recombination between homologous chromosomes during meiosis, a crossover occurs between...
homologous chromatids
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In a Recombination between homologous chromosomes during meiosis, a ________ occurs between homologous chromatids.
Crossover
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In a Recombination between homologous chromosomes during meiosis, meiosis is completed to yield...
4 haploid cells
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In a Recombination between homologous chromosomes during meiosis, meiosis is completed to yield 4 haploid cells. Two of the cells are with a ______ genotype and two of the cells are with a _______ genotype.
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What are the 6 steps of the Holiday model for homologous recombination?
- 1) homologous chromatids get aligned
- 2) both chromatids are nicked at identical locations
- 3) The DNA strands to the left of the nicks invade the homologous chromosomes and attach to the right of the nicks creating a holiday junction
- 4) The holiday junction migrates from left to right (Branch migration) which creates 2 heteroduplex regions that have a few base mismacthes
- 5) The strands that were originally nicked are broken and the strands are connected to create nonrecombinant chromosomes with a short heteroduplex region
- 6) The strands that were not originally nicked are broken and the strands are connected to create recombinant chromosomes with a short heteroduplex region
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What makes drawn chromomsomes in the holiday model look like true Holiday Junctions?
When the figure is redrawn by bending the ends labeled A and B upwards, and bending the ends labeled a and b downwards.
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What is the "resolution" for the holdiay junction?
The heteroduplex region will be repaired but no new strands are made so it's hard to identify
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old and new strands for mismatch repair.
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The Holiday model can account for...
the general properties of recombinant chromosomes in meiosis
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What two forms of research have supported the Holiday model?
- convincing evidence came from electron micrographs of recombination structures
- Structure has a chi (x) form
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What is the purpose of gene disruption by homologous recombination?
To find out the function of the gene after it's sequence is found.
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A double crossover compared to a "regular" crossover is considered to be more...
stable and irreversible
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gene disruption by homologous recombination due to a single crossover is considered to be...
instable
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In a double crossover, only cell that have the _______, will survive.
genes of interest
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for laboratory experiments involving gene disruption by homologous recombination, ________ and __________ are used for mammalian cells in a petri dish.
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when you have a single crossover in H. recombination, it is perferred to knockout 1 of 2 chromosomes or else...
death may occur
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When is there no longer a functional gene of interest?
When a coding sequence has been disrupted
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When a _______ has been disrupted, there is no longer a functional gene of interest.
coding sequence
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You can only do a single crossover if _______ is NOT linearized
plasmid
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You can only do a _________ crossover if plasmid is NOT linearized
single
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You can only do a single crossover if plasmid is NOT....
linearized
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When there is a circle around the plasmid you can't cut the chromosome or else....
death occurs
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after you loop in in the single crossover, the chromosome loops out via ...
a 2nd crossover
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after you loop in in the single crossover, the chromosome loops out via a 2nd crossover which gives you...
the original setup
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after you loop in in the single crossover, the chromosome loops out via a 2nd crossover which gives you the original setup and at that point the gene of interest is not inserted into...
plasmid DNA.
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after you loop in in the single crossover, the chromosome loops out via a 2nd crossover which
- gives you the original setup and at that point the __________ is not inserted into plasmid DNA.
- gene of interest
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What kind of homologous recombination is te recombination that happens in antibodies?
Site specific recombination
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antibodies are...
proteins produced by B cells of the immune system that recognizes foreign material and target them for destruction.
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why is site-specific recombination so important for the function of antibodies?
it allows each B cell to produce an antibody with a different amino acid sequence that can recognize different antigens.
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What chains do antibodies have?
2 light and 2 heavy chains.
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where is the antigen binding site?
at the arm of the antibody
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Redistribution of immunoglobulin genes occurs for the heavy chain during the development from an _________to an _________ producing B lymphocyte.
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Genes from each group V, D and J are bought together in the final form of a functional gene for the _____________ of the long chain of an antibody molecule
variable part
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V(D)J recombinations happen in _______ chains
Heavy
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(D) is in parenthesis because...
This type of domain is only found in heavy-chain genes.
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VJ recombination happens in _______ chains
light
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What makes up antibodies?
Clusters of multiple genes
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What is an exon?
a segment of RNA that is contained within the RNA after splicing has occurred.
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What is splicing?
the process in which pieces of RNA are removed and the remaining pieces are covalently attached to each other.
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What is exon shuffling?
When different parts of the genes will be recombined to form various B lymphocytes from stem cells.
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What does exon shuffling result in?
30 million possible combinations for specific antigen recognition.
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___________ can occur in many genomic locations.
transposisiton
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Transposons are...
Mobile genetic elements found in bacteria, fungi, plant and animal cells.
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Another term for transposons are...
"jumping genes"
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What is TE stand for?
Transposable element
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---TE------- -> -------TE---- (What kind of transposon mechanism is this?)
"Cut and Paste" mechanism or "Simple mechanism"
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the "cut and paste" "simple" transposon mechanism occurs in what organisms?
Bacteria and eukaryotes
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---TE------ -> ---TE----TE--- (What kind of transposon mechanism is this?)
Replicative transposition
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TEs are found in all...
Organisms
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What is the basic composition of transposable elements?
DNA sequences
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Transposable elements have characteristic...
DNA sequences
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Where are direct repeats usually found?
within host DNA
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What are direct repeats?
Identical nucleotide sequences that are in the same direction and repeated
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Direct repeats are adjacent to...
both ends of the element
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What is transporase gene?
A gene that catalyzes tranposon events
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Where are inverted repeats located?
on the ends of inserted sequences.
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What types of inserted sequences may you find inverted repeats on?
transporase or antibiotic resistance genes
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What is the range of length for inverted repeats?
about 9 - 40 base pairs
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The sequences of inverted repeats are considered to be...
identical / similar
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The seqences of inverted repeats are considered to be identical or similar but they run...
in opposite directions
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In what type or organisms are insertion sequences usually found?
bacteria
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---DR-IR---(Transposon gene)---IR-DR--- (What kind of TE organization is this?)
Insertion sequence
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-DR-IR--(Transposon Gene)--IR--(Antibiotic Resistance Gene)--IR-IR-DR (what kind of TE organization is this?)
Composite transposon
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What commonly contains genes that confer a selective advantage to the organism like providing resistance to antibiotics or toxic heavy metals.
composite transposons
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During ransposition of a composite tansposon, only _________ are involved in the transpositional event.
inverted repeats at the ends of the transposon
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Whenever _____ are at both ends of a gene, they create a composite transposon
insertion sequences
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whenever insertion sequences are at both ends of a gene, they create a....
composite transposition
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insertion sequences move via..
simple transposition (cut and paste)
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composite transposons move via...
simple transpotision (cut and paste)
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transporase catalyzes the...
excision and insertion of TEs to another location.
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The features of transposons have made them an important experimental tool in....
molecular biology
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Introduction of transposons into a cell is a convienient way to...
abolish gene expression
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What is a convenient way to abolish gene expression?
Introduction of transposons into a cell
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Transposons can be used to clone a particular gene in an approach called...
transposon tagging
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What is transposon tagging?
When transposons can be used to clone a particular gene
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The TE is about how many base pairs in length?
a few hundred to several thousand base pairs.
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What are the 4 steps of a simple transpoisition?
- 1) Transposase recognizes the inverted repeats in the DNA and cleaves it at both ends of the TE to release it.
- 2) The transposase carries the TE to a new site and cleaves the target DNA at staggered sites
- 3) The TE is inserted into the target site
- 4) DNA gap repair synthesis takes place (direct repeats formed)
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Transposons will randomly "hop" in genes to make ....
mutations
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The molecular mechanism of SCE is similar to homologous recombination between homologs except..
that the two segments of DNA are sister chromatids instead of homologous chromatids.
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If branch migration occurs during SCE, will a heteroduplex be formed?
Branch migration will not create a heteroduplex during SCE because the sister chromatids are genetically identical.
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Branch migration will not create a heteroduplex during SCE because..
the sister chromatids are genetically identical.
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Can gene conversion occur during sister chromatid exchange?
Gene conversion cannot take place because the sister chromatids carry alleles that are already identical to each other.
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Gene conversion cannot take place in SCE because...
the sister chromatids carry alleles that are already identical to each other.
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What two molecular mechanisms can explain the phenomenon of gene conversion?
mismatch DNA repair and gap repair synthesis.
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What are recombinant chromosomes?
one that has been derived from a crossover and contains a combination of alleles that is different from the parental chromosomes.
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A recombinant chromosome is a _______ of the parental chromosomes.
Hybrid
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How do recombinant chromosomes differ from the original parental chromosomes from which they are derived?
They are a hybrid of the parental chromosomes
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What is gene conversion?
occurs when a pair of different alleles is converted to a pair of identical alleles.
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Using the pair of alleles (Bb), show an example of a gene conversion.
(Bb)---> (bb) or (BB)
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In recombinant chromosomes, where is gene conversion likely to have taken place?
near the breakpoint
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In recombinant chromosomes, why is gene conversion likely to have taken place near the breakpoint?
Because, According to the double-strand break model, a gap may be created by the digestion of one DNA strand in the double helix.
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According to the double-strand break model, a gap may be created by...
the digestion of one DNA strand in the double helix
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What are the three ways gene onversion may be caused?
- 1) gap repair synthesis
- 2) mismatch repair
- 3) heteroduplex repair after DNA strand migration
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What are three ways that antibody diversity is produced?
- 1) gene rearrangement of V, D, and J domains occurs within the light- and heavy-chain genes
- 2) within a given B cell, different combinations of light and heavy chains are possible
- 3) imprecise fusion may occur between the V, D, and J domains
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how many segments of DNA are removed during sites-pecific recombination within the gene that encodes the κ (kappa) light chain for IgG proteins?
One segment
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many segments are spliced out of the pre-mRNA?
One segment
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the region between the ___ domain and ___ domain, is removed during pre-mRNA splicing.
J and D
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If you were examining a sequence of chromosomal DNA, what characteristics would cause you to believe that the DNA contained a transposable element?
- 1) The ends of a short region would be flanked by direct repeats.
- 2) Contains IRs or LTRs
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Why is the presence of a transposase or reverse transcriptase gene not a sure way of identifying a DNA that contained a TE?
because nonautonomous transposable elements typically lack transposase or reverse transcriptase.
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What TEs typically lack transposase or reverse transcriptase?
nonautonomous
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Why does transposition always produce direct repeats in the chromosomalDNA?
because transposase or integrase produces staggered cuts in the two strands of chromosomal DNA
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Are TEs considered to be mutagens?
Yes because they alter (disrupt) the sequences of chromosomes and genes within chromosomes
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How do TEs alter (disrupt) the sequences of chromosomes and genes within chromosomes?
inserting themselves into genes
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What kind of TE would Require reverse transcriptase to transpose?
Viral-like retroelements and nonviral-like retroelements
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What kind of TE Require transposase to transpose?
Insertion sequences, composite transposons, and replicative transposons
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What kind of TE Are flanked by direct repeats?
All five types have direct repeats
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What kind of TE Have inverted repeats?
Insertion sequences, composite transposons, and replicative transposons
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Substances that damage DNA tend to increase the..
level of genetic exchange such as SCE.
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