U.S. patent application number 10/363464 was filed with the patent office on 2003-10-09 for method and system for identifying commercially distributed organisms.
Invention is credited to Gressel, Jonathan.
Application Number | 20030190655 10/363464 |
Document ID | / |
Family ID | 24631075 |
Filed Date | 2003-10-09 |
United States Patent
Application |
20030190655 |
Kind Code |
A1 |
Gressel, Jonathan |
October 9, 2003 |
Method and system for identifying commercially distributed
organisms
Abstract
A method of marking individuals of commercially distributed
organism or organisms and offspring thereof is disclosed. The
method is effected by genetically marking a plurality of
individuals of the organism or organisms with a plurality of unique
DNA sequences, each of the unique DNA sequences includes a variable
region, so as to produce artificial, inherited and detectable
genetic variability among the plurality of individuals of the
commercially distributed organism or organisms.
Inventors: |
Gressel, Jonathan; (Rehovot,
IL) |
Correspondence
Address: |
Anthony Castorina
GE Ehrlich (1995) Ltd
Suite 207
2001 Jefferson Davis Highway
Arlington
VA
22201
US
|
Family ID: |
24631075 |
Appl. No.: |
10/363464 |
Filed: |
March 4, 2003 |
PCT Filed: |
August 21, 2001 |
PCT NO: |
PCT/IL01/00783 |
Current U.S.
Class: |
435/6.12 ;
435/6.13 |
Current CPC
Class: |
G16B 50/00 20190201;
G16B 30/00 20190201 |
Class at
Publication: |
435/6 |
International
Class: |
C12Q 001/68 |
Claims
What is claimed is:
1. A method of marking individuals of commercially distributed
organism or organisms and offspring thereof, the method comprising
the step of genetically marking a plurality of individuals of the
organism or organisms with a plurality of unique DNA sequences,
each of said unique DNA sequences includes a variable region
selected so as to produce artificial, inherited and detectable
genetic variability among said plurality of individuals of the
commercially distributed organism or organisms.
2. The method of claim 1, wherein each of said unique DNA sequences
further includes a pair of universal regions one on each side of
said variable region.
3. A method of identifying individuals belonging to a commercially
distributed organism, the method comprising the steps of: (a)
genetically marking a plurality of individuals of the organism with
a plurality of unique DNA sequences, each of said unique DNA
sequences includes at least one variable region; (b) providing a
database server including a lookup table associating each of said
plurality of individuals with one of said plurality of unique DNA
sequences; and (c) identifying whether an examined individual of
said organism being one of said plurality of individuals or
offspring thereof, and if so, which of said plurality of
individuals or offspring thereof, by: (i) determining a presence or
absence, and if present, a nucleotide sequence of a unique DNA
sequence of said plurality of unique DNA sequences by which said
examined individual being genetically marked; and (ii) identifying
said examined individual by associating said nucleotide sequence to
one of said plurality of individuals via said lookup table of said
database server.
4. The method of claim 3, wherein each of said unique DNA sequences
further includes a pair of universal regions, one on each side of
said variable region.
5. The method of claim 3, wherein said nucleotide sequence of said
unique DNA sequence of said plurality of unique DNA sequences by
which said examined individual being genetically marked, is
effected by a nucleic acid microarray hybridization technique.
6. An organism having a genome, said organism being genetically
marked by: (a) at least one unique DNA sequence which is known in
public; and (b) at least one unique DNA sequence that is unknown,
at least not as a genetic mark, in public.
7. A system for Assigning DNA sequences to serve as genetic markers
of commercially distributed organisms, the system comprising a
database server being designed and constructed for managing a
sequences database and serving for: (a) assigning at least one
sequence of said sequences to an assignee upon request; and (b)
book-keeping data pertaining to step (a).
8. The system of claim 7, wherein said request is effected via a
communications network.
9. The system of claim 8, wherein said communications network is
the Internet.
10. The system of claim 7, wherein said data pertaining to step (a)
includes an identity of said assignee.
11. The system of claim 7, wherein said data pertaining to step (a)
includes an identity of an organism.
12. The system of claim 7, wherein said database server further
serves for debiting said assignee.
13. The system of claim 7, wherein each of said sequences includes
a variable region.
14. The system of claim 13, wherein each of said sequences includes
a pair of universal regions, one on each side of said variable
region.
15. The system of claim 7, wherein said database server further
serves for receiving a sequence input from a user.
16. The system of claim 7, wherein said database server further
serves for receiving a sequence input from a user and comparing
said sequence input to said sequences database.
17. The system of claim 7, wherein said database server further
serves for: (i) receiving a sequence input from a user and
comparing said sequence input to sequences of said sequences
database which have already been assigned; and, if no matching
sequence is found (ii) identifying said user as an assignee of said
sequence input.
18. The system of claim 7, further comprising a DNA synthesizer
being in data communication with said database server, said DNA
synthesizer serving for automatically synthesizing assigned
sequences.
19. The system of claim 7, wherein said database server includes an
application selected from the group consisting of: (i) determining
sequence identity; (ii) determining sequence homology and degree
thereof; (iii) generating artificial sequences; (iv) combining
sequences of different origins; (v) generating random sequences;
(vi) evaluating a coding potential of a sequence; and (vii) scoring
a coding potential of a sequence.
20. A method assigning DNA sequences to serve as genetic markers of
commercially distributed organisms, the method is effected by a
data processor operatively communicating with a sequences data base
and comprising the steps of: (a) assigning at least one sequence of
said sequences to an assignee upon request; and (b) book-keeping
data pertaining to step (a).
21. The method of claim 20, wherein said request is effected via a
communications network.
22. The method of claim 21, wherein said communications network is
the Internet.
23. The method of claim 20, wherein said data pertaining to step
(a) includes an identity of said assignee.
24. The method of claim 20, wherein said data pertaining to step
(a) includes an identity of an organism.
25. The method of claim 20, further comprising the step of debiting
said assignee.
26. The method of claim 20, wherein each of said sequences includes
a variable region.
27. The method of claim 26, wherein each of said sequences includes
a pair of universal regions, one on each side of said variable
region.
28. The method of claim 20, further comprising the steps of: (c)
receiving a sequence input from a user and comparing said sequence
input to sequences of said sequences database which have already
been assigned; and, if no matching sequence is found (d)
identifying said user as an assignee of said sequence input.
29. The method of claim 20, further comprising the step of
communicating assigned sequences to a DNA synthesizer.
30. The method of claim 20, wherein said data processor operates an
application selected from the group consisting of: (i) determining
sequence identity; (ii) determining sequence homology and degree
thereof; (iii) generating artificial sequences; (iv) combining
sequences of different origins; (v) generating random sequences;
(vi) evaluating a coding potential of a sequence; and (vii) scoring
a coding potential of a sequence.
31. A kit for marking individuals of commercially distributed
organism or organisms and offspring thereof, the kit comprising a
plurality of containers each containing a DNA molecule having a
unique variable region being flanked by a pair of universal
regions, said unique variable region being selected so as to
produce artificial, inherited and detectable genetic variability
among the individuals of commercially distributed organism or
organisms and offspring thereof.
32. The kit of claim 31, further comprising at least one
amplification primer being hybridizable to said universal regions,
so as to enable amplification of said unique variable region of
said DNA molecule.
33. The kit of claim 31, wherein said DNA molecule forms a part of
a vector.
34. A nucleic acid microarray for determining an identity of an
organism, the nucleic acid microarray comprising a solid support
and a plurality of single stranded polynucleotides, each of a
predetermined base sequence, being attached to said solid support
at a predetermined location, said predetermined base sequence of
said plurality of single stranded polynucleotides being designed
for hybridizing with a plurality of variable sequences of genetic
marks, such that a hybridization pattern with each of said variable
sequences of said genetic marks is indicative of an identity of the
genetic mark.
Description
FIELD AND BACKGROUND OF THE INVENTION
[0001] The present invention relates to a method and system for
identifying commercially distributed organisms and/or offspring
thereof. More particularly, the present invention relates to (i)
genetically marked organisms; and (ii) a database server and a
method for assigning sequences to be used to genetically mark
organisms and for book keeping data pertaining to the genetically
marked organisms and/or their owner, producer or source.
[0002] There are a variety of reasons to have organisms tagged with
an "easy to read" code. Such reasons, include, but are not limited
to, (i) recognition of source; (ii) ownership; (iii) regulation;
and (iii) liability.
[0003] For example, valuable bacterial or fungal strains, crop
varieties, or animal strains need be identifiable for effectively
effecting intellectual property (IP) rights or proof of ownership,
as well as identity preservation.
[0004] Transgenic organisms bacterial or fungal strains, crop
varieties, or animal strains need by identifiable for recognition
of source.
[0005] In addition, regulatory authorities and various consumer
groups are demanding labeling of certain transgenic commodities.
They spend vast sums typically probing for common used promoters
(35S, actin enhancer) or selectable marker genes (kanamycin or
hygromycin resistance) and not for the trait genes, in an effort to
save. Even when transgenics are discovered by such "kits", there is
no information as to source. Thus, regulatory authorities may wish
to consider simple, common recognition sequences for detecting
transgenics.
[0006] Organisms which serve as biocontrol agents should be tagged
for reasons of liability. It will be appreciated in this respect
that the use of live organisms to control weed, bacterial, fungal,
or insect pests is increasing. Many of the agents are closely
related to known pathogens or pests and there have already been
claims that a biocontrol organism changed its host range and
attacked valuable species. In all probability, the related species
was the culprit. There are few easy methods to ascertain causality
with accuracy in some cases. There are also fears that biocontrol
agents will mutate or introgress with other organisms, and there
are needs to know whether the biocontrol agent changed host range
(with consequences of liability) or whether an epidemic was due to
wild strains. These issues with biocontrol agents will become more
acute with transgenically-enhanced biocontrol agents.
[0007] There is thus a great need for, and it would be highly
advantageous to have, a database server and a method for assigning
sequences to be used to genetically mark organisms and for book
keeping data pertaining to the genetically marked organisms their
owner, producer or source.
SUMMARY OF THE INVENTION
[0008] According to one aspect of the present invention there is
provided a method of marking individuals of commercially
distributed organism or organisms and offspring thereof, the method
comprising the step of genetically marking a plurality of
individuals of the organism or organisms with a plurality of unique
DNA sequences, each of the unique DNA sequences includes a variable
region, so as to produce artificial, inherited and detectable
genetic variability among the plurality of individuals of the
commercially distributed organism or organisms.
[0009] According to another aspect of the present invention there
is provided a method of identifying individuals belonging to a
commercially distributed organism, the method comprising the steps
of (a) genetically marking a plurality of individuals of the
organism with a plurality of unique DNA sequences, each of the
unique DNA sequences includes at least one variable region; (b)
providing a database server including a lookup table associating
each of the plurality of individuals with one of the plurality of
unique DNA sequences; and (c) identifying whether an examined
individual of the organism being one of the plurality of
individuals or offspring thereof, and if so, which of the plurality
of individuals or offspring thereof, by (i) determining a presence
or absence, and if present, a nucleotide sequence of a unique DNA
sequence of the plurality of unique DNA sequences by which the
examined individual being genetically marked; and (ii) identifying
the examined individual by associating the nucleotide sequence to
one of the plurality of individuals via the lookup table of the
database server.
[0010] According to yet another aspect of the present invention
there is provided an organism having a genome, the organism being
genetically marked by (a) at least one unique DNA sequence which is
known in public; and (b) at least one unique DNA sequence that is
unknown, at least not as a genetic mark, in public.
[0011] According to still another aspect of the present invention
there is provided a system for assigning DNA sequences to serve as
genetic markers of commercially distributed organisms, the system
comprising a database server being designed and constructed for
managing a sequences database and serving for (a) assigning at
least one sequence of the sequences to an assignee upon request;
and (b) book-keeping data pertaining to step (a).
[0012] According to an additional aspect of the present invention
there is provided a method assigning DNA sequences to serve as
genetic markers of commercially distributed organisms, the method
is effected by a data processor operatively communicating with a
sequences data base and comprising the steps of (a) assigning at
least one sequence of the sequences to an assignee upon request;
and (b) book-keeping data pertaining to step (a).
[0013] According to further features in preferred embodiments of
the invention described below, the request is effected via a
communications network, such as the Internet
[0014] According to still further features in the described
preferred embodiments the data pertaining to step (a) includes an
identity of the assignee and/or an identity of an organism.
[0015] According to still further features in the described
preferred embodiments the database server further serves for
debiting the assignee and the method further comprising the step of
debiting the assignee
[0016] According to still further features in the described
preferred embodiments each of the sequences includes a variable
region. Preferably, each of the sequences includes a pair of
universal regions, one on each side of the variable region.
[0017] According to still further features in the described
preferred embodiments the database server further serves for (i)
receiving a sequence input from a user and comparing the sequence
input to sequences of the sequences database which have already
been assigned; and, if no matching sequence is found (ii)
identifying the user as an assignee of the sequence input. Thus,
the method further comprising the steps of (c) receiving a sequence
input from a user and comparing the sequence input to sequences of
the sequences database which have already been assigned; and, if no
matching sequence is found; (d) identifying the user as an assignee
of the sequence input.
[0018] According to still further features in the described
preferred embodiments the system further comprising a DNA
synthesizer being in data communication with the database server,
the DNA synthesizer serving for automatically synthesizing assigned
sequences. The method, thus, further comprising the step of
communicating assigned sequences to a DNA synthesizer.
[0019] According to still further features in the described
preferred embodiments the database server includes an application
selected from the group consisting of (i) determining sequence
identity; (ii) determining sequence homology and degree thereof;
(iii) generating artificial sequences; (iv) combining sequences of
different origins; (v) generating random sequences; (vi) evaluating
a coding potential of a sequence; and (vii) scoring a coding
potential of a sequence.
[0020] According to another aspect of the present invention there
is provided a kit for marking individuals of commercially
distributed organism or organisms and offspring thereof, the kit
comprising a plurality of containers containing a plurality of DNA
molecules, each of the DNA molecules having a variable region being
flanked by a pair of universal regions. The kit preferably further
comprising, in a separate container, at least one amplification
primer being hybridizable to the universal regions, so as to enable
amplification of the variable region of each of the DNA molecules.
Additional components of the kit may include reagents required for
PCR amplification. Preferably, each of the DNA molecules forms a
part of a vector.
[0021] According to still another aspect of the present invention
there is provided a nucleic acid microarray for determining an
identity of an organism, the nucleic acid microarray comprising a
solid support and a plurality of single stranded polynucleotides,
each of a predetermined base sequence, being attached to the solid
support at a predetermined location, the predetermined base
sequence of the plurality of single stranded polynucleotides being
designed for hybridizing with a plurality of variable sequences of
genetic marks, such that a hybridization pattern with each of the
variable sequences of the genetic marks is indicative of an
identity of the genetic mark.
[0022] The present invention successfully addresses the
shortcomings of the presently known configurations by providing a
database server and a method for assigning sequences to be used to
genetically mark organisms and for book keeping data pertaining to
the genetically marked organisms their owner, producer or
source.
[0023] Implementation of the method and system of the present
invention involves performing or completing selected tasks or steps
manually, automatically, or a combination thereof. Moreover,
according to actual instrumentation and equipment of preferred
embodiments of the method and system of the present invention,
several selected steps could be implemented by hardware or by
software on any operating system of any firmware or a combination
thereof. For example, as hardware, selected steps of the invention
could be implemented as a chip or a circuit. As software, selected
steps of the invention could be implemented as a plurality of
software instructions being executed by a computer using any
suitable operating system. In any case, selected steps of the
method and system of the invention could be described as being
performed by a data processor, such as a computing platform for
executing a plurality of instructions.
BRIEF DESCRIPTION OF THE DRAWINGS
[0024] The invention is herein described, by way of example only,
with reference to the accompanying drawings. With specific
reference now to the drawings in detail, it is stressed that the
particulars shown are by way of example and for purposes of
illustrative discussion of the preferred embodiments of the present
invention only, and are presented in the cause of providing what is
believed to be the most useful and readily understood description
of the principles and conceptual aspects of the invention. In this
regard, no attempt is made to show structural details of the
invention in more detail than is necessary for a fundamental
understanding of the invention, the description taken with the
drawings making apparent to those skilled in the art how the
several forms of the invention may be embodied in practice.
[0025] In the drawings:
[0026] FIG. 1 is a simplified depiction of a system according to
the present invention;
[0027] FIG. 2 is a side view of a kit according to the present
invention; and
[0028] FIG. 3 is a perspective view of a nucleic acid microarray
according to the present invention.
DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0029] The present invention is of a method and system which can be
used for identifying commercially distributed organisms and/or
offspring thereof. Specifically, the present invention provides a
database server and a method for assigning sequences to be used to
genetically mark organisms and for book keeping data pertaining to
the genetically marked organisms and/or their owner, producer or
source
[0030] The principles and operation of a system and method
according to the present invention may be better understood with
reference to the drawings and accompanying descriptions.
[0031] Before explaining at least one embodiment of the invention
in detail, it is to be understood that the invention is not limited
in its application to the details of construction and the
arrangement of the components set forth in the following
description or illustrated in the drawings. The invention is
capable of other embodiments or of being practiced or carried out
in various ways. Also, it is to be understood that the phraseology
and terminology employed herein is for the purpose of description
and should not be regarded as limiting.
[0032] In one aspect the present invention provides a system and
method for assigning DNA sequences to serve as genetic markers of
commercially distributed organisms. As shown in FIG. 1, the system
according to this aspect of the invention includes a database
server 10 which includes a data processor, is designed and
constructed for managing a sequences database and which serves for
(a) assigning at least one sequence of the sequences of the
database to an assignee upon request; and (b) book-keeping data
pertaining to step (a), data such as, but not limited to,
particulars including the identity of the assignee and/or of an
organism to be genetically marked.
[0033] Methods of inserting specific DNA sequences at one or more
locations, at random or in a targeted fashion to genomes of
prokaryotes or eukaryotes, unicellular or multicellular organisms,
including, but not limited to, plants, such as crop plants,
bacteria, fungi, insects and higher animals, including,
domesticated animals and live stock, are well known in the art.
Such methods which are known as, or employ steps of,
transformation, transfection, trangenization, bombardment and the
like, are extensively described in the scientific literature and in
laboratory manuals such as, for example, "Molecular Cloning: A
laboratory Manual" Sambrook et al., (1989); "Current Protocols in
Molecular Biology" Volumes I-III Ausubel, R. M., ed. (1994);
Ausubel et al., "Current Protocols in Molecular Biology", John
Wiley and Sons, Baltimore, Md. (1989); Perbal, "A Practical Guide
to Molecular Cloning", John Wiley & Sons, New York (1988);
Watson et al., "Recombinant DNA", Scientific American Books, New
York; Birren et al. (eds) "Genome Analysis: A Laboratory Manual
Series", Vols. 1-4, Cold Spring Harbor Laboratory Press, New York
(1998); "Cell Biology: A Laboratory Handbook", Volumes I-III
Cellis, J. E., ed. (1994); "Culture of Animal Cells--A Manual of
Basic Technique" by Freshney, Wiley-Liss, N. Y. (1994), Third
Edition; "Oligonucleotide Synthesis" Gait, M. J., ed. (1984);
"Nucleic Acid Hybridization" Hames, B. D., and Higgins S. J., eds.
(1985); "Transcription and Translation" Hames, B. D., and Higgins
S. J., eds. (1984); "Animal Cell Culture" Freshney, R. I., ed.
(1986); "A Practical Guide to Molecular Cloning" Perbal, B.,
(1984); "PCR Protocols: A Guide To Methods And Applications",
Academic Press, San Diego, Calif. (1990); all of which are
incorporated by reference as if fully set forth herein.
[0034] Presently preferred characteristics of DNA sequences which
are used according to the present invention to genetically mark and
thereafter identify the organisms or their offspring are described
in the following paragraphs.
[0035] The term "genetic mark" is used herein distinctively from
the common term "genetic marker". While the latter term refers to
naturally occurring genetic variations among individuals in a
population, the term genetic mark as used herein specifically
refers to artificial (man generated), inherited and detectable
genetic variability.
[0036] In order to serve as genetic marks, DNA segments must have
(i) a sequence which is appropriate (e.g., unique) to the genome of
the organism in which it is present; and (ii) sequence variability,
so as to enable the identification of different individuals of the
organism.
[0037] With the advent of the polymerase chain reaction (PCR)
technology and other amplification methods, it is nowadays
relatively simple to determine the presence, absence and sequence
of selected regions in genomes of organisms, provided that a
sequence to be determined is either known or that regions flanking
it from either side are known. Since sequence variability is
required according to the present invention to produce specific
identity, from a practical point of view, a DNA sequence which is
used according to the present invention to genetically mark an
organism preferably includes the variable region flanked by a pair
of common or universal regions. A genetic mark according to the
present invention can also include an identifier region, located,
for example, alongside the variable region and which provides a
more general type of identification. For example, different
identifier regions can be associated with genetic marks used by
different corporations and serve for fast identification using
simple hybridization techniques to genomic DNA (e.g., dot blot
hybridization). Thus, amplification primers which can hybridize
with the universal regions of the mark can be used with PCR to
amplify the variable region and its sequence can thereafter be
determined. To prevent coamplification of sequences of the genome
of the organism, the variable and in particular, the common regions
of a genetic mark according to the present invention are selected
unique to the genome of the organism of choice, or preferably to a
genus, family, order or kingdom of organisms to which the organism
of choice classifies. In addition, in order to prevent the
possibility that the introduction of a genetic mark according to
the present invention will result in expression of whatever genetic
information encoded thereby, it is advantageous to select the
variable and universal regions of the mark to be "non-sense"
sequences, i.e., sequences that do not include an "open reading
frame". To ensure that this is indeed the case, stop codons are
preferably introduced into the sequences in all reading frames in
predetermined intervals, e.g., every 2 to 20 codons.
[0038] In addition, it may be desired that the nucleotide
repertoire used in a genetic mark of the present invention will be
similar to the nucleotides repertoire characterizing the organism
of choice. Thus, for example, for an organism having an AT rich
genome, a similarly AT rich genetic mark will be employed,
especially in the variable region of the genetic mark, whereas for
an organism having a GC rich genome, a similarly GC rich genetic
mark will be employed.
[0039] Furthermore, the degree of sequence variability among
genetic marks of the present invention should be set such that even
if one or several mutations are introduced thereto along
generations, still mark identity is maintained. This is especially
true for organisms characterized by high reproduction rates, such
as bacteria. Variability of at least 1-5% among marks would
typically suffice for marks of about 1000 bp. Higher percentage
should be used for shorter marks.
[0040] Genetic marks of the present invention may be provided to
users in contained in dedicated kits. As shown in FIG. 2, according
to another aspect of the present invention there is provided a kit
20 for marking individuals of commercially distributed organism or
organisms and offspring thereof. Kit 20 includes a plurality of
containers 22 held in a suitable rack 23. Containers 22 contain a
plurality of DNA molecules, each of the DNA molecules is
characterized by a variable region flanked by a pair of universal
(common) regions. The kit preferably further includes, in at least
one separate container 24, at least one amplification primer which
is hybridizable to the universal regions, so as to enable
amplification of the variable region of each of the DNA molecules.
Additional components of the kit may include reagents required for
PCR amplification, such as, but not limited to, a concentrated
(e.g., 10.times.) PCR buffer, a thermostable DNA polymerase, such
as, but not limited to, thermophilus aquaticus (Taq) DNA polymerase
and the four nucleoside tri phosphates (dNTPs). Preferably, each of
the DNA molecules forms a part of a vector, which can be a plasmid,
a viral vector, a cosmid, a bacmid and the like. Viral packaging
reagents may also be included in the kit. Each of the containers of
the kit is identified for its content In particular, the sequence
of each of the DNA molecules contained in the kit is identified
directly or by a code referring to a list of sequences which is
either provided with the kit or otherwise made available to the
user.
[0041] A genetic mark may be cointegrated into a locus of the
genome of an organism along with additional genetic material which
is used to genetically modify the organism. This can be achieved
either by using a single vector for introducing the mark and the
additional genetic material or by employing cotransformation by two
independent vectors, which, in most cases, results in a shared
integration site.
[0042] As is further shown in FIG. 1, a request by a user 12 for a
sequence is effected, according to a preferred embodiment of the
present invention via a communications network 14, such as, but not
limited to, the Internet.
[0043] For purposes of this specification and the accompanying
claims, the term "user" or "user client" generally refers to a
computer and includes, but is not limited to, personal computers
(PC) having an operating system such as DOS, Windows.TM., OS/2.TM.
or Linux; Macintosh.TM. computers; computers having JAVA.TM.-OS as
the operating system; and graphical workstations such as the
computers of Sun Microsystems.TM. and Silicon Graphics.TM., and
other computers having some version of the UNIX operating system
such as AIX.TM. or SOLARIS.TM. of Sun Microsystems.TM.; or any
other known and available operating system; personal digital
assistants (PDA), cellular telephones having Internet browsing
capabilities and Web TVs.
[0044] For purposes of this specification and the accompanying
claims, the term "Windows.TM." includes, but is not limited to,
Windows2000.TM. Windows95.TM., Windows 3.x.TM. in which "x" is an
integer such as "1", Windows NT.TM., Windows98.TM.,
Windows2000.TM., Windows CE.TM. and any upgraded versions of these
operating systems by Microsoft Corp. (USA).
[0045] For purposes of this specification and the accompanying
claims, the term "database server" refers to any computing device
or a plurality thereof acting in concert, capable of transferring,
or serving, at least one electronic file to at least one other
computing device.
[0046] For purposes of this specification and the accompanying
claims, the term "database server" refers to any computing device
capable of data processing.
[0047] For purposes of this specification and the accompanying
claims, "server" and "user client" are indications of function
rather than specific hardware configurations.
[0048] For purposes of this specification and the accompanying
claims, the term "communications" refers to any means of
information transfer, including, but not limited to, a telephone
connection, a cellular telephone connection, an Internet
connection, an Extranet connection, a satellite connection, cables
connection, a local area network connection or a radio connection,
or any other wired or unwired connection or any combination
thereof.
[0049] In a preferred embodiment of the present invention, database
server 10 also serves for debiting the assignee for services
provided thereto. Such services, include, as is mentioned
hereinabove, the provision of unique sequence or sequences and the
registry thereof as being associated with the assignee, etc.
Debiting capabilities over the net are well known in the art and
can be obtained by our sourcing from any one of a plurality of
debiting service providers, which also provide for the security
required for the execution of debiting.
[0050] In some cases, a user may desire to design his own unique
sequence and deposit that sequence in a depository, so as to
prevent a case where a another party will use the same sequence as
a genetic mark. To this end, database server 10 preferably further
serves for (i) receiving a sequence input from a user and comparing
the sequence input to sequences of the sequences database which
have already been assigned; and, if no matching sequence is found
(ii) identifying the user as an assignee of the sequence input.
[0051] Assignment of sequences according to the present invention
may be of virtual sequences, i.e., their letter presentation, which
can be used by the assignee to synthesize a molecule corresponding
to the virtual sequence. Preferably, assignment of sequences
according to the present invention is accompanied by provision of
an actual DNA molecule to be used by the assignee in the process of
marking an organism. To this end, the system of the present
invention further includes a DNA synthesizer 16 in data
communication with database server 10. DNA synthesizer 16 serves
for automatically synthesizing assigned sequences.
[0052] Synthesized sequences may then be shipped directly to the
assignee or may be further processed using techniques such as
restriction and ligation so as to be included in a vector which is
adapted to introduce an assigned sequence into the genome of an
organism to be genetically marked. Such further processing can also
be executed using automated machinery, such that packaging,
labeling and shipment procedures are all executed without direct
man intervention. It will be appreciated that DNA synthesizer 16
need not be in proximity to database server 10, as the data
communication therebeween can be effected via any suitable
communications network including the Internet, Intranet, Extranet,
local area network, etc.
[0053] As used herein the term "DNA synthesizer" refers to a
complex machinery which stores suitable chemicals and is capable of
solid phase synthesis of oligonucleotides. DNA synthesizers and the
chemistry of oligonucleotide synthesis are well known in the art.
To this end, see, for example, "Oligonucleotide Synthesis" Gait, M.
J., ed. (1984).
[0054] Efficiently managing sequence depository data which will
comply with the requirements imposed by the present invention, that
is to ensure that a given sequence is assigned only once and
further that the identity of an assignee or organism is associated
with the appropriate sequences, calls for certain sequence
management capabilities, such as, but not limited to, (i)
determining sequence identity; (ii) determining sequence homology
and degree thereof; (iii) generating artificial sequences; (iv)
combining sequences of different origins; (v) generating random
sequences; (vi) evaluating a coding potential of a sequence; (vii)
scoring a coding potential of a sequence and the like. Such
computational functions are well known in the art and can be
readily integrated into a comprehensive system acting in concert to
serve registry functions as herein described.
[0055] Thus, according to the present invention there is provided a
method of marking individuals of commercially distributed organism
or organisms and offspring thereof. The method according to the
present invention is effected by genetically marking a plurality of
individuals of the organism or organisms with a plurality of unique
DNA sequences, each of the unique DNA sequences includes a variable
region, so as to produce artificial, inherited and detectable
genetic variability among the plurality of individuals of the
commercially distributed organism or organisms.
[0056] Also according to the present invention there is provided a
method of identifying individuals belonging to a commercially
distributed organism. The method is effected by (a) genetically
marking a plurality of individuals of the organism with a plurality
of unique DNA sequences, each of the unique DNA sequences includes
at least one variable region; (b) providing a database server
including a lookup table associating each of the plurality of
individuals with one of the plurality of unique DNA sequences; and
(c) identifying whether an examined individual of the organism
being one of the plurality of individuals or offspring thereof, and
if so, which of the plurality of individuals or offspring thereof,
by (i) determining a presence or absence, and if present, a
nucleotide sequence of a unique DNA sequence of the plurality of
unique DNA sequences by which the examined individual being
genetically marked; and (ii) identifying the examined individual by
associating the nucleotide sequence to one of the plurality of
individuals via the lookup table of the database server.
[0057] For some, e.g., regulatory, purposes it may be desired to
mark commercially distributed organisms with publicly known marks,
so as to enable regulatory authorities to readily identify the
mark, and, by using the system and method of the invention, to
identify the manufacturer, distributor, owner or user of the marked
organism. For other purposes secrecy may be advantageous. The
latter is true, for example, for preventing an attempt to
genetically modify the genetic mark of a supreme strain protected
by intellectual property laws. Thus, according to a preferred
embodiment of the present invention, database server 10 is
constructed and designed so as to enable unlimited access to some
of the data stored thereby and to restrict access to classified
data stored thereby to authorized users only. Methods of achieving
same are well known in the art.
[0058] An intellectual property protected organism which is also
subject to regulation will therefore be, according to a useful
embodiment of the present invention, genetically marked by (a) at
least one unique DNA sequence which is known in public; and (b) at
least one unique DNA sequence that is unknown, at least not as a
genetic mark, in public.
[0059] The sequence of a variable region of a genetic mark
according to the present invention can be determined by
conventional DNA sequencing of PCR amplified fragments. In a
presently preferred embodiment, however, the sequence of a variable
region of a genetic mark according to the present invention is
determined by hybridization techniques, using a nucleic acid
microarray, e.g., a DNA chip. DNA chips, their construction,
methods of use and analysis of results are well known in the
art.
[0060] Hence, according to another aspect of the present invention,
as shown in FIG. 3, there is provided a nucleic acid microarray 30
which is useful in determining an identity of an organism. Nucleic
acid microarray 30 comprises a solid support 32 having a plurality
of locations 33 and a plurality of single stranded polynucleotides
34, each of a predetermined base-sequence, being attached to solid
support 32 at predetermined locations of plurality of locations 33.
The predetermined base sequence of the plurality of single stranded
polynucleotides 34 are designed for hybridizing with a plurality of
variable sequences of genetic marks, such that a hybridization
pattern with each of the variable sequences of the genetic marks is
indicative of an identity of the genetic mark. Such hybridization
pattern may include a single positive hybridization signal.
[0061] Although the invention has been described in conjunction
with specific embodiments thereof, it is evident that many
alternatives, modifications and variations will be apparent to
those skilled in the art. Accordingly, it is intended to embrace
all such alternatives, modifications and variations that fall
within the spirit and broad scope of the appended claims. All
publications, patents and patent applications mentioned in this
specification are herein incorporated in their entirety by
reference into the specification, to the same extent as if each
individual publication, patent or patent application was
specifically and individually indicated to be incorporated herein
by reference. In addition, citation or identification of any
reference in this application shall not be construed as an
admission that such reference is available as prior art to the
present invention.
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