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chromosome and paste them to a backing sheet in an karyotype before chromosomes are secured in

Metaphase cells are required to prepare a standard orderly manner. Alternatively, a digital image of the place.
karyotype, and virtually any population of dividing cells chromosomes can be cut and pasted using a computer. If
could be used. Blood is easily the most frequently
sampled tissue, but at times, karyotypes are prepared from
standard staining was used, the orderly arrangement is 5. A description of the karyotype should be
limited to grouping like-sized chromosomes together in recorded on the karyotype sheet. First record the
cultured skin fibroblasts or bone marrow cells. None of the pairs, whereas if the chromosomes were banded, they can number of chromosomes, including the sex
leukocytes in blood normally divide, but lymphocytes can be unambiguously paired and numbered. chromosomes, followed by a comma (,). The
readily be induced to proliferate, providing a very
sex chromosome constitution is given next. Any
accessible source of metaphase cells. The image below shows chromosomes as they are seen on
structural rearrangements and additional or
the slide (left panel) and after arrangment (right panel).
There are many protocols for preparing a karyotype missing chromosomes are listed next. Refer to
from peripheral blood lymphocytes, but a rather ISCN 1985, table 3 on page 20, for
standard series of steps is involved: Procedure: nomenclature symbols and additional
information. Other information such as the cell
• A sample of blood is drawn and coagulation 1. Count the number of chromosomes. Solid line number, the date karyotype was prepared,
prevented by addition of heparin. stained chromosomes or chromosomes treated the specimen type, and the technologist also
with a trypsin and giemsa stain can be counted should be recorded on the
• Mononuclear cells are purified from the blood at the microscope with a 100X magnification.
by centrifugation through a dense medium that However, for analysis such as identification of Disacovering the Cut-and-Paste Enzymes
allows red cells and granulocytes to pellet, but marker chromosomes or determination of the
number of copies of individual chomosomes, it Recombinant plas
retards the mononuclear cells (lymphocytes and The first major step forward in the
monocytes). is usually necessary to photograph and print the
chromosome spreads. Refer to procedures in ability to chemically modify genes occurred when
this manual for black and white photography American biologist Martin Gellert and his colleagues from
• The mononuclear cells are cultured for 3-4 days and film development. Two prints should be the National Institutes of Health purified and characterized
in the presence of a mitogen like made of each spread. One will be cut for an enzyme in Escherichia coli responsible for the actual
phytohemagglutinin, which stimulates the karyotyping; the uncut print serves as a joining, or recombining, of separate pieces of DNA
lymphocytes to proliferate madly. reference if questions arise about the (Zimmerman et al., 1967). They called their find "DNA-
interpretation of a certain chromosome. joining enzyme," and this enzyme is now known as DNA
• At the end of the culture period, when there is a ligase. All living cells use some version of DNA ligase to
2. Cut out each individual chromosome and "glue together" short strands of DNA during replication.
large population of dividing cells, the culture is
arrange on a karyotype sheet. Chromosomes are Using E. coli extract, the researchers next showed that only
treated with a drug such as colcemid, which
ordered by their length, the position of the in the presence of ligase was it possible to repair single-
disrupts mitotic spindles and prevents
centromere, the position of the chromosome stranded breaks in λ phage DNA. (Discovered in 1950 by
completion of mitosis. This greatly enriches the
bands, and the relative band sizes and American microbiologist Esther Lederberg, λ phage is a
population of metaphase cells.
distributions. Refer to page 10 of the 1985 ISCN virus particle that infects E. coli.) More specifically, they
for the human karyotype. showed that the enzyme was able to form a 3'-5'-
• The lymphocytes are harvested and treated phosphodiester bond between the 5'-phosphate end of the
briefly with a hypotonic solution. This makes 3. In the construction of the karyotype the last nucleotide on one DNA fragment and the 3'-OH end of
the nuclei swell osmotically and greatly aids in autosomes are numbered 1 to 22, in descending the last nucleotide on an adjacent fragment. The
getting preparations in which the chromosomes order of length. The sex chromosomes are identification of DNA ligase was the first of several key
don't lie on top of one another. referred to as X and Y. The symbols p and q are steps that would eventually empower scientists to attempt
used to designate, respectively, the short and their own recombination experiments—experiments that
• The swollen cells are fixed, dropped onto a long arms of each chromosome. There are 7 involved not just recombining the DNA of a single
microscope slide and dried. groups identified in the karyotype and data individual, but recombining DNA from different
pertaining to each group can be found on page 7 individuals, including different species.
of the 1985 ISCN.
• Slides are stained after treatment to induce a A second major step forward in gene modification was the
banding pattern as described above. 4. Secure chromosomes in place with glue. Pair the discovery of restriction enzymes, which cleave DNA at
chromosomes closely together and align the specific sequences. These enzymes were discovered at
Once stained slides are prepared, they are scanned to
centromeres (for easier band comparison and approximately the same time as the first DNA ligases by
identify "good" chromosome spreads (i.e. the chromosomes
checking for structural chromosome Swiss biologist Werner Arber and his colleagues while they
are not too long or too compact and are not overlapping),
aberrations). If possible, have a second were investigating a phenomenon called host-controlled
which are photographed. The photos then are given to
technologist check the interpretation of the restriction of bacteriophages. Bacteriophages are viruses
kindergarten children, who cut out the images of each
that invade and often destroy their bacterial host cells; host- team next used DNA ligase to rejoin, or recombine, the mammalian cell in this experiment, they provided (proved)
controlled restriction refers to the defense mechanisms that DNA fragments from the two different plasmids (Figure 2). the means to do so.
bacterial cells have evolved to deal with these invading Finally, they introduced the newly recombined plasmid
viruses. Arber's team discovered that one such mechanism DNA into E. coli. The researchers were able to join two To obtain rDNA steps involved are:
is enzymatic activity provided by the host cell. The team DNA fragments from completely different plasmids a) The DNA fragment containing the gene sequence to be
named the responsible enzymes "restriction enzymes" because, as they explained, "the nucleotide sequences cloned (also known as ('insert') is isolated.
because of the way they restrict the growth of cleaved are unique and self-complementary so that DNA
bacteriophages. These scientists were also the first to fragments produced by one of these enzymes can associate b) Insertion of these DNA fragments into a host cell using a
demonstrate that restriction enzymes damage invading by hydrogen-bonding with other fragments produced by the "vector" (carrier DNA molecule).
bacteriophages by cleaving the phage DNA at very specific same enzyme" (Cohen et al., 1973).
nucleotide sequences (now known as restriction sites). The c) The rDNA molecules are generated when the vector self
identification and characterization of restriction enzymes Phage ? is an eff replicates in the host cell.
gave biologists the means to cut specific pieces of DNA The same could be said of any DNA
required (or desired) for subsequent recombination. —not just plasmids—from two different species. This d) Transfer of the rDNA molecules into an appropriate host
universality—the capacity to mix and match DNA from cell.
Inserting Foreign DNA into a New Host Cell different species, because DNA has the same structure and
function in all species and because restriction and ligase e) Selection of the host cells carrying the rDNA molecule
Although Griffith and Avery had had demonstrated the using a marker.
ability to transfer foreign genetic material into cells decades enzymes cut and paste the same ways in different genomes
earlier, this "transformation" was very inefficient, and it —makes recombinant DNA biology possible.
f) Replication of the cells carrying rDNA molecules to get a
involved "natural" rather than manipulated DNA. Only in Today, the E. coli λ bacteriophage is one of the most genetically identical cells population or clone.
the 1970s did scientists begin to use vectors to efficiently widely used vectors used to carry recombinant DNA into
transfer genes into bacterial cells. The first such vectors bacterial cells. This virus makes an excellent vector Enzymes used in Recombinant DNA technology
were plasmids, or small DNA molecules that live naturally because about one-third of its genome is considered
inside bacterial cells and replicate separately from a Restriction Enzymes
nonessential, meaning that it can be removed and replaced
bacterium's chromosomal DNA. by foreign DNA (i.e., the DNA being inserted). As For cloning of DNA, the DNA is cut at specific sites, which
Plasmids' utility as a DNA shuttle, or vector, was illustrated in Figure 3, the nonessential genes are removed are recognized and cleaved by specific enzymes. These
discovered by Stanford University biochemist Stanley by restriction enzymes (the specific restriction enzyme enzymes are known as restriction enzymes. These
Cohen. Scientists had already established that some EcoRI is shown in the figure), the foreign DNA inserted in restriction enzymes recognize short sequences of double
bacteria had what were known as antibiotic resistance their place, and then the final recombinant DNA molecule stranded DNA as targets for cleavage. Different enzymes
factors, or R factor-plasmids that replicated independently is packaged into the virus's protein coat and prepped for recognize different but specific sequences, each ranging
inside the bacterial cell. But scientists knew little about introduction into its host cell. from 4-8 base pairs. The enzymes are named by a three
how the different R factor genes functioned. Cohen thought letter (or four letter) abbreviation that identifies their origin
Vectors Used in Mammalian Cells e.g. AluI is derived from Arthrobacter luteus, EcoRI is
that if there were an experimental system for transforming
host bacterial cells with these R-factor DNA molecules, he A fourth major step forward in the field of recombinant derived from E.Coli, HpaI is derived from Haemophilus
and other researchers might be able to better understand R- DNA technology was the discovery of a vector for parainfluenzae
factor biology and figure out exactly what it was about efficiently introducing genes into mammalian cells. Besides cleavage, modification in the form of methylation
these plasmids that made bacteria antibiotic-resistant. He Specifically, researchers learned that recombinant DNA is also brought about by some enzymes called modification
and his colleagues developed that system by demonstrating could be introduced into the SV40 virus, a pathogen that enzymes sometimes also called “methylases”. Different
that calcium chloride-treated E. coli can be genetically infects both monkeys and humans. Indeed, in 1972, species of bacteria contain their own sets of restriction
transformed into antibiotic-resistant cells by the addition of Stanford University researcher Paul Berg and his enzymes and corresponding methylases. Depending on the
purified plasmid DNA (in this case, purified R-factor colleagues integrated segments of λ phage DNA, as well as different modes of action, the restriction enzymes have
DNA) to the bacteria during transformation (Cohen et al., a segment of E. coli DNA containing the galactose operon, been classified into three main classes- type I, type II, type
1972). into the SV40 genome. (The E. coli galactose operon is a III. Out of these, type II restriction enzymes are used in
cluster of genes that plays a role in galactose sugar recombinant technology as they can be used in vitro to
Recombinant Plasmids in Bacteria metabolism.) The significance of their achievement was its recognize and cleave with in specific DNA sequences
The following year, Stanley Cohen and his colleagues were demonstration that recombinant DNA technologies could usually consisting of 4-8 nucleotides.
also the first to construct a novel plasmid DNA from two be applied to essentially any DNA sequences, no matter
separate plasmid species which, when introduced into E. how distantly related their species of origin. In their words, DNA ligases
coli, possessed all the nucleotide base sequences and these researchers "developed biochemical techniques that These enzymes form phosphodiester bonds between the
functions of both parent plasmids. Cohen's team used are generally applicable for joining covalently any two adjacent molecules and, covalently links two individual
restriction endonuclease enzymes to cleave the double- DNA molecules" (Jackson et al., 1972). While the fragments of double stranded DNA. The most commonly
stranded DNA molecules of the two parent plasmids. The scientists didn't actually introduce foreign DNA into a used enzyme for cloning experiment is T4 DNA ligase.
Alkaline phosphatase including the origin of replication and rep gene. These viruses, cauliflower mosaic virus or CaMV and tobacco
vectors have been widely used to study yeast genome. mosaic virus /TMV) are three group of viruses that have
The enzyme alkaline phosphatase (AP) removes the been used as vectors for cloning of DNA segments. CaMV
phosphate group from the 5’ end of a DNA molecule Shuttle vectors has a double stranded DNA molecule, 8kbp in size which
leaving a free 5’ hydroxyl group hence it is used to prevent The vectors containing two types of origin of replication infects the members of Cruciferae family. Geminiviruses
unwanted self-ligation of vector DNA molecules in cloning which helps them to exist in both eukaryotic cell as well as are a group of single stranded DNA plant viruses infecting
procedures. This enzyme is isolated from bacteria (BAP) or E.coli are known as shuttle vectors. E.g.Yep vector. cassava, maize and other cereals.
calf intestine (CAP).
Retriever vectors Animal virus vectors also deliver the foreign genes into the
Cloning vectors for Recombinant DNA A class of vectors which are used to retrieve specific genes cultured cells which get integrated into the host genome.
from the normal chromosome of an organism like yeast The expression of foreign genes can also be amplified
Vectors are the vehicles used to carry a foreign DNA through recombination. They are very useful in isolation of
sequence into a given host cell. A vector should have a) using the promoters of the virus gene. The cloned genes
genes from yeast for molecular experiments like can be used in gene therapy, for the synthesis of important
origin of replication, b) a selectable marker to select the sequencing.
host cells containing the vector from among those which do proteins etc. A vector based on Simian Virus 40 (SV 40)
not have the vector, c) one unique restriction endonuclease Vectors based on bacteriophages was used in the first cloning experiment involving
recognition site to enable foreign DNA to be inserted into mammalian cells in 1979. Retroviruses like murine and
the vector in order to generate a recombinant DNA Bacteriophages are viruses that infect bacterial cells by avian retroviruses are very useful vectors as they are
molecule and, d) it should be relatively small in size. injecting their DNA into these cells. They are used as capable of infecting a large variety of cell types and can
vectors because they have a linear DNA molecule, which clone large genes. Herpes virus is a non-integrating large
Plasmids as vectors generate two fragments after breakage. These are later sized virus (150 kb) which is another useful vector which
joined with foreign DNA to generate chimeric phage can be used for expression of large intact genes.
Plasmids are defined as autonomous elements, whose particle. The injected DNA is selectively replicated and
genomes exist in the cell as extrachromosomal units. They expressed in the host cell resulting in a number of phages Artificial chromosome (YAC and MAC) vectors
are self replicating, circular duplex DNA molecules present which burst out of the cell (lytic pathway) and further infect
in number of copies in a bacterial cell, yeast cell or in YACs or Yeast Artificial Chromosomes are used as vectors
the neighbouring cells. E.g. M13 , Lambda ( ) to clone DNA fragments of more than 1Mb in size. These
organelles in eukaryotic cells. These naturally occurring
plasmids have been modified to serve as vectors in the Cosmids as vectors long molecules of DNA can be cloned in yeast by ligating
laboratory. them to vector sequences that allow their propagation as
Cosmids are plasmid particles into which specific DNA linear artificial chromosomes. These long DNA molecules
pBR322 vectors sequences like cos sites of phage lambda are inserted and can be generated and allow construction of comprehensive
they are constructed by combining certain feature of libraries in microbial hosts. A lot of work is going on to
One of the most commonly used cloning vector in gene plasmids and the ‘cos’ sites of phage lambda. The
cloning procedures is pBR322 (named after Bolivar and create mammalian artificial chromosomes (MACs)
advantage of the using cosmids for cloning is that its following the isolation of mammalian telomeres and
Rodriguez who constructed this) derived from E. coli efficiency is high to produce a complete genomic library of
plasmid ColE1. It is 4,362 bp DNA with genes for centromere. However YACs have a low cloning efficiency
10(6)-10(7) clones from only 1 microgrm of insert DNA. (1000 clones/microgm) DNA as against 106-107
resistance against two antibiotics- tetracycline and
ampicillin. It was constructed after several alterations and Phagemids as vectors clones/microgm DNA for cosmids) and also it is difficult to
modifications in earlier cloning vectors. recover large amount of pure insert DNA from individual
Phagemids are prepared artificially by combining features clones.
pUC vectors of phages with plasmids. E.g. pBluescript II KS is derived
from pUC19 and is 2961 bp long. Transgenic Animals
The plasmids belonging to pUC series of vectors are 2,700
bp long with ampicillin resistance gene, the origin of BAC Vectors Another use of rDNA technology is to add an outside
replication derived from pBR322 and the lac Z gene gene to the DNA of animals, creating a transgenic animal.
derived from E.coli. When the DNA fragments are cloned BACs or Bacterial Artificial Chromosomes are vectors These genes are added to the animal before it is born.
in this region of pUC, the lac gene is inactivated. based on the natural, extra-chromosomal plasmid of E.coli- Genes can be inserted into the animal to alter its protein
the fertility or F-plasmid, and are being used in genome content--for example, to produce a cow with low-lactose
Yeast plasmid vectors sequencing projects. A BAC vector contains genes for milk. Transgenic pigs might have organs that can be used
replication and maintenance of the F-factor, a selectable for human transplantation. Creating disease-resistant
Special vectors used to introduce DNA segments in yeast marker and cloning sites and can accommodate up to 300-
cells or a eukaryotic cell is being used to develop animals is another possibility with rDNA technology. .
350 kb of foreign DNA.
genetically engineered yeast cells. E.g. YIp or yeast I. DEFINITION OF RECOMBINANT DNA:
integrative plasmids which allows transformation by Plant and animal viruses as vectors
crossing over and have no origin of replication. YEp or 1. DNA molecules contructed outside of living cells by
yeast episomal plasmids carry 2 micron DNA sequence A number of plant and animal viruses can also be used as joining natural or synthetic DNA segments to DNA
vectors for introducing foreign genes into cells and/or for molecules that can replicate in a living cell
gene amplification in host cells. Plant viruses like Gemini
2. DNA molecules resulting from replication of a molecule D. Common vectors include PLASMIDS, VIRAL DNA cloning involves isolated, purified DNA; one works
described in 1. above. GENOMES, and (primarily in yeast) "ARTIFICIAL with only a small portion or fragment of the animal's
CHROMOSOMES". A SHUTTLE VECTOR is one that genome; and that only new bacterial colonies are generated.
II. GOALS OF RECOMBINANT DNA can replicate in 2 or more types of cell (e.g., E. coli and In other words, if someone sent you DNA from a blue
TECHNOLOGY yeast, Fig. 3.34A). whale, you could "clone" blue whale DNA even though
A. To ISOLATE and CHARACTERIZE a gene you've never seen a whale and have no intention ever to see
V. JOINING DNA FRAGMENTS: The most common one in your life.
B. To MAKE DESIRED ALTERATIONS in one or more mechanism of JOINING the TARGET DNA into the
isolated genes vector DNA is with COHESIVE RESTRICTION
ENZYME ENDS ("sticky ends") sealed by DNA TRANSGENIC ANIMALS AND PLANTS,
C. To RETURN ALTERED GENES TO LIVING LIGASE, Fig. 3.19.
CELLS (or to multicellular animals or plants) to A. GERMLINE: TRANSGENE is integrated into the
EXAMINE OR UTILIZE THEIR EXPRESSION VI. TARGET DNA: By "target DNA" we mean the DNA chromosome of a germ line cell and can be passed on to
or gene that one wishes to isolate and use as described offspring as a Mendelian trait.
III. BASIC TOOLS OF RECOMBINANT DNA above. As specified in the definition of recombinant DNA,
TECHNOLOGY: the target DNA must be joined to another DNA that can B. SOMATIC: TRANSGENE is integrated into
replicate (the vector). Target DNA can be of several forms chromosome(s) in some cells or tissues, but cannot be
A. NUCLEIC ACID ENZYMES: DNA polymerases, inherited by offspring (e.g., Gene Therapy) .
reverse transcriptase, DNA ligase, RESTRICTION including:
ENDONUCLEASES, Table 3.2 A. CHROMOSOMAL DNA ("GENOMIC DNA") C. Among the most useful transgenics are TRANSGENIC
isolated directly from cells or a tissue MICE, which can be made by growing EMBRYONIC
B. BACTERIAL GENETICS: PLASMIDS, STEM (ES) CELLS in culture dishes (Fig. 3.38),
BACTERIOPHAGES (bacterial viruses) B. COMPLEMENTARY DNA (cDNA) made in vitro (in transfecting them with DNA by standard procedures and
a. Bacteriophages replicate via the LYTIC PHAGE the test tube) using the enzyme reverse transcriptase and then INJECTING THE ALTERED ES CELLS into a
CYCLE: the phage genome is injected into the cell, phage isolated mRNA as template, blastocyst stage (early) embryo. The product offspring is
genes are expressed and phage proteins and DNA are made, genetically CHIMERIC. If the chimerism extends to the
C. SYNTHETIC DNA (rarely), made by machines that germline, some of the offspring of the chimeric mouse will
progeny phage are packaged, and the cell is lysed, Fig. rely on organic chemistry
5.37. Two genetically different phage that infect the same be GERMLINE TRANSGENICS. Transgenic mice can
host cell may recombine during the lytic cycle, VII. RECOMBINANT DNA CLONING also be made by MICROINJECTING PURE DNA
INTO THE PRONUCLEUS (Fig. 3.37) of a 1 cell
b. Some PHAGE can also replicate via the LYSOGENIC A. "CLONING" is the isolation and growth of a single, embryo and reimplantation of the injected embryo. Some of
CYCLE. The phage genome is integrated into the host genetically uniform cell and its offspring. Recombinant these can survive and produce complete or chimeric
chromosome and becomes copied into chromosomes of all DNA cloning is the isolation of a cell line which contains transgenics. Other transgenic vertebrate species similar
daughter bacteria like any gene. This "PROPHAGE" can (and replicates) a single, unique recombinant DNA from a have been made, but with less routine success to date
be induced to enter the lytic cycle and kill its host by a pool (LIBRARY) of many different recombinant DNA’s,
variety of stresses like UV light. Fig. 5.37 Fig. 3.33. Animal Husbandry

c. Plasmids: Circular DNAs that replicate B. To clone (as with all isolation or purification Neither the use of animal vaccines nor adding bovine
autonomously; (Fig. 3.22) techniques), you need two things: a SEPARATION growth hormones to cows to dramatically increase milk
METHOD and an ASSAY. The most common assay for a production can match the real excitement in animal
C. ANIMAL VIRUSES AND ANIMAL CELL specific DNA is NUCLEIC ACID HYBRIDIZATION, husbandry: transgenic animals and clones.
CULTURE TECHNIQUES Fig. 3.28. SEPARATION METHOD: With recombinant Transgenic animals model advancements in DNA
V. VECTORS: A VECTOR IS A DNA MOLECULE DNA technology one can use bacteria or bacteriophage to technology in their development. The mechanism for
INTO WHICH FOREIGN DNA MAY BE INSERTED readily separate thousands or even millions of unique creating one can be described in three steps:
WHICH CAN THEN REPLICATE IN AN colonies or plaques in a clone bank or library.
APPROPRIATE CELL. 1. Healthy egg cells are removed from a female of
Cloning DNA from an animal or any other organism is the host animal and fertilized in the laboratory.
A. Vectors must have one or more ORIGIN OF taking a piece of the purified DNA from that organism
REPLICATION, and and putting it into a bacterium (usually). One then 2. The desired gene from another species is
isolates a single bacterial colony (or CLONE) which can identified, isolated, and cloned.
B. One or more SITE into which the recombinant DNA be used to make millions and millions of copies of the
can be inserted. single DNA fragment you wish to study. The common 3. The cloned genes are injected directly into the
use of the term "cloning" for recombinant DNA cloning eggs, which are then surgically implanted in the
C. They often have convenient means by which cells with host female, where the embryo undergoes a
vectors can be SELECTED from those without: e.g., like that just described is an unfortunate coincidence of the
way these bacteria were first made. Note that recombinant normal development process.
DRUG RESISTANCE GENES, Fig. 3.22.
Transgenics
Cloning in Animals.
Animals have two different classes of cells: germ line
and somatic.
Only alterations in the germ cells can be transmitted to
future generations. However, some forms of somatic
cell gene therapy can be useful in treating patients. For
example, people with cystic fibrosis can receive the
cloned CFTR gene in a nasal spray, which then infects
the lining of their lungs and improves lung function.
The infected (transformed) epithelial cells eventually
are lost, however, during normal processes of tissue
growth, so the treatment needs to be repeated.
Germ-line cloning. There are two basic ways to clone a
gene in the mammalian germ line.

• Inject a DNA fragment containing your gene


into the nucleus of a fertilized egg (germ-line
gene cloning) or of body tissues in a mature
host (somatic gene cloning). The DNA gets
taken up at random somewhere in one of the
chromosomes.

An example of germ-line cloning is the


injection of angiopoietin cDNA into the
fertilized mouse egg.
(An example of somatic cloning is gene
therapy for cystic fibrosis: inhale a vector
containing the CF gene, which gets
incorporated into the DNA of cells lining the
lungs. Somatic cloned genes are not inherited
by offspring.)

• Put a transgene containing positive and


negative selective markers into an embryonic
stem cell tissue culture. The ES cells take up
the gene by homologous recombination,
replacing the host allele. The ES cells now
are injected into a blastula of an unrelated
host, and some of the next generation
progeny arise from the ES cells. To learn
more about this, read Capecchi's article on
Targeted Transgenes, on reserve.

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