Download Attachment A - Recombinant DNA and Viral

Attachment A.
Recombinant Nucleic Acids, Synthetic Nucleic Acids and Viral Vectors
PI:
BUA#:
General Project Title:
Definitions:
Recombinant or Synthetic Nucleic Acid Molecules:
(i) molecules that
a) are constructed by joining nucleic acid molecules, and
b) can replicate in a living cell (i.e. recombinant nucleic acids);
(ii) nucleic acid molecules that are chemically or by other means synthesized or amplified, including those that are chemically or otherwise
modified but can base pair with naturally occurring nucleic acid molecules (i.e. synthetic nucleic acids); or
(iii) molecules that result from the replication of those described in (i) or (ii) above.
Viral Vector:
Virus modified to introduce genetic material into a cell
Oncogene:
A gene, generally defective, that can cause a cell to divide in an unregulated manner
YES
N/A
Does your research involve recombinant or synthetic nucleic acid molecules, recombinant
or synthetic nucleic acid-containing organisms or cell cultures?
If “Not Applicable”, skip Attachment A and proceed to the next applicable attachment. If
“YES” go to the next question.
1.
YES NO
Are all the recombinant or synthetic nucleic acid molecules and recombinant procedures
used in your research EXEMPT from the NIH Guidelines as described in III-F Experiments and
Appendix C. of the NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic
Acid Molecules? (Refer to Section vi) If “YES” to all EXEMPT recombinant activities,
complete and submit Attachment A and General BUA Application (Sections I-III and VIII only)
for IBC review and registration. If “NO” complete all of General BUA Application, Attachment
A and all other applicable attachments.
2.
i.
Recombinant or Synthetic Nucleic Acids and Vector Summary (Check all that apply)
This project involves:
Foreign nucleic acids inserted into a vector or organism for the purpose of cloning. The nucleic acid to be cloned will:
be from a Risk Group (RG) 3 agent;
represents more than two-thirds of the genome of a RG1 or 2 agent;
encode a known oncogene;
encode molecules known to be toxic to vertebrates at concentrations less than 1 mg/ml;
encode molecules that impart pharmaceutical resistance;
contain synthetic nucleic acid
Construction and/or use of synthetic DNA/RNA (e.g., probes, DNA or RNA oligonucleotides, base-pair analogs).
Creation of c-DNA/genomic libraries
DNA/RNA sequencing
Recombinants or synthetics are expected to alter virulence or infectivity, change resistance or susceptibility to drug
therapy, or change host range.
Recombinants or synthetics are deliberately created for the biosynthesis of toxin molecules with an LD 50 of less than
100nanogram per kilogram body weight.
The host into which I am introducing foreign DNA is a cell or organism other than E. coli K12 or its derivatives,
Saccharomyces cerevisiae, S. uvarum, Bacillus subtilis or B. licheniformis.
Use of recombinant or synthetic nucleic acids in animals (somatic cells or germ-line transgenics) including insects,
nematodes, and mammals.
Creation of a transgenic organism via introduction of recombinant or synthetic nucleic acid molecules or breeding.
Use of recombinant or synthetic DNA/RNA in plants (somatic cells or germ-line transgenics)
We will be handling or culturing more than or equal to 10 liters at any one time. Complete Attachment H.
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Attachment A of
General BUA Application
Deliberately transferring recombinant DNA, or DNA or RNA derived from recombinant DNA into one or more human
research participants. Complete Attachment I.
Assaying for the production of wild type/helper/replication competent viral particles. Please describe methods and
stage in the experiment at which these assays will be performed.
Potential for infectious agents to be produced/released from recombinant cells, animals, or plants.
Environmental release or field testing of genetically engineered organisms.
Not Applicable
Provide additional information, including the function of all genes inserted or deleted, the method of transfer or
transfection, at what point and how recombinant product or cells will be inactivated or lysed: Briefly summarize the overall
goal, specific objectives and experimental design involving work with these materials ( e.g. using gene therapies for human macular
degeneration)
ii.
Gene Delivery Techniques
If not applicable, check here
.
This project includes research with recombinant or synthetic nucleic acids with the following enhanced gene delivery
techniques:
Liposome complex
Electroporation
Calcium Phosphate precipitation
Nanomaterial (<100 nm in length)
Ballistic (e.g., gene gun)
Viral Delivery
Hydrostatic Pressure
Sonication
Other (specify):
List all gene delivery methods in the table below as they apply to gene transfer experiments and the use of
recombinant cells and microorganisms (engineered in your laboratory or obtained from another source). If additional
spaces are needed, complete and submit as attachment.
Gene Delivery Method
Gene Inserts
& Key
Regulatory
Elements+
In Vitro
In Vivo
Source
(Specify cell type and
activities)
(specify species and
activities)
(i.e. created in lab, purchased from
vendor, MTA)
*If gene insert is a high risk recombinant DNA inserts, (e.g. toxins with LD50<100 g/kg body weight, antibiotic resistance cassettes or regions of
genomes from RG 2, RG3, or RG4 or restricted organisms) complete Attachment D or E if applicable.
+
General categories of cellular genes and functions: (S) structural proteins: actin, myosin, etc.; (E) enzymatic proteins: serum proteases, transferases,
oxidases, phosphatases, etc.; (M) metabolic enzymes: amino acids metabolism, nucleotide synthesis, etc.; (G) cell growth, housekeeping; (CC) cell
cycle, cell division; (DR) DNA replication, chromosome segregation, mitosis, meiosis; (MP) membrane proteins, ion channels, G-coupled protein
receptors, transporters, etc.; (T) tracking genes such as GFP, luciferase, photoreactive genes; (TX) active subunit genes for toxins such as ricin,
botulinum toxin, Shiga toxin, and Shiga-like toxins; (R) regulatory genes, transcription, cell activators such as cytokines, lymphokines, tumor
suppressors; (Ov and Oc) oncogenes identified via transforming potential of viral and cellular analogs, or mutations in tumor suppressor genes,
resulting in a protein that inhibits/moderates the normal cellular wild-type protein
iii.
Vector Description(s) (Please specify vectors, helper viruses, etc.) If not applicable, check here
Vector
Type
Vector Name
(plasmid, viral,
phage, etc)
Risk Group
(e.g. vector lineage)
(Genus, species; if plasmid or
viral)
More Than
2/3 of viral
genome?
Yes
Yes
Yes
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No
No
No
.
Risk Attenuation
(If yes, indicate how attenuated)
Yes
Yes
Yes
No
No
No
Attachment A of
General BUA Application
*Viral vectors containing Adenovirus or Lentivirus require detailed description of risk attenuation and Guidelines for Research with Adenovirus and Guidelines
for Research with Lentivirus will need to be reviewed and integrated into a lab specific Biosafety SOP.
Negative replication competent virus testing has been performed on the above viral vectors.
iv.
Non-commercially Purchased Vector Risk Attenuation If not applicable, check here
.
If vector is not commercially purchased, describe risk attenuation: (Examples: replicative defective)
v.
Vector Packaging
Name of packaging cell
line(s) or Helper
plasmids used in cotransfection to produce
viral particles
If not applicable, check here
Sources of
cells
(i.e. species)
.
Tropism
Source of
envelope
(i.e. what
species of cell
virus infects)
glycoprotein
(if retro- or lentivirus)
Agents previously
passed through
animals or cell
lines?
Yes
Yes
Yes
vi.
Target
animal/plant/c
ell for
constructs
No
No
No
Experiments Covered by the NIH Guidelines
The NIH Guidelines can be found at http://oba.od.nih.gov/oba/rac/Guidelines/NIH_Guidelines.htm.
Note: While certain recombinant/synthetic nucleic acid experiments are considered by the NIH Guidelines to be exempt
(Section III-F and Appendix C), research of this nature is not exempt from review and oversight from the SDSU IBC.
Contact the Biosafety Officer for any assistance in completing this section (Jennifer Ramil, x46965, [email protected])
III-A. Experiments that require IBC Approval, RAC Review, and NIH Director Approval Before Initiation
 The deliberate transfer of a drug resistance trait to microorganisms that are not known to acquire the trait
naturally
III-B. Experiments that require NIH OSP and IBC Approval Before Initiation
 Experiments involving the cloning of toxin molecules with LD50 of less than 100 ng per kg body weight
III-C. Experiments that require IBC, IRB, and RAC review registration before research participant enrollment
 Experiments involving the transfer of recombinant/synthetic nucleic acids human subjects (human gene
transfer)
III-D. Experiments that require IBC approval at a convened meeting before initiation
 The introduction of any recombinant/synthetic nucleic acid molecule into any Risk Group 2, 3, 4, or
restricted agent, including adenoviral and lentiviral vectors
 Experiments in which DNA from Risk Group 2, 3, 4, or restricted agents is cloned into host-vector systems
 Experiments involving the use of DNA or RNA viruses (infectious or defective) in the presence of a helper
virus in tissue culture systems (This includes AAV production with adenovirus or HSV)
 Experiments involving the transfer of rDNA to any whole animals (vertebrate or invertebrate), at any
biosafety level, excluding the generation or purchase of transgenic rodents under BL1 containment. Click
here for examples of animal experiments covered under the NIH Guidelines
 Experiments involving whole plants with exotic infectious agents, cloned genomes of readily transmissible
exotic infectious agents, or microbial pathogens of insects or small animals associated with plants
 Experiments involving more than 10 liters of culture
 Experiments involving influenza viruses
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Attachment A of
General BUA Application
III-E. Experiments that require IBC review at a convened meeting before initiation
 Experiments not classified in III-A, III-B, III-C, III-D, or III-F and involving the formation of recombinant or
synthetic nucleic acid molecules containing no more than two-thirds of the genome of any eukaryotic
virus. It must be demonstrated that the cells lack helper virus for the families of defective viruses being
used
 Experiments not classified in III-A, III-B, III-D, or III-F and involving recombinant/synthetic nucleic acid
molecule associated with whole plants
 Experiments involving the generation of rodents in which the animal’s genome has been altered by a stable
introduction of recombinant/synthetic nucleic acid molecules into the germ-line (transgenic rodents) with
BL1 containment excluding breeding
III-F. Experiments that require IBC administrative review before initiation
 Synthetic nucleic acids that (1) can neither replicate nor generate nucleic acids that can replicate in any
living cell (no origin of replication), and (2) are not designed to integrate into DNA, and (3) do not produce a
toxin
 Experiments not in organisms, cells, or viruses and that have not been modified or manipulated (e.g.,
encapsulated into synthetic or natural vehicles) to render them capable of penetrating cellular membranes
 Experiments that consist solely of the exact recombinant or synthetic nucleic acid sequence from a single
source that exists contemporaneously in nature
 Experiments that consist entirely of nucleic acids from a prokaryotic host, including its indigenous plasmids
or viruses when propagated only in that host (or a closely related strain of the same species), or when
transferred to another host by well-established physiological means
 Experiments that consist entirely of nucleic acids from a eukaryotic host including its chloroplasts,
mitochondria, or plasmids (but excluding viruses) when propagated only in that host (or closely related
strain of the same species)
 Experiments that consist entirely of DNA segments from different species that exchange DNA by known
physiological processes, though one or more of the segments may be a synthetic equivalent (see Appendix
A of the NIH Guidelines for a list of natural exchangers approved by the NIH)
 Genomic DNA molecules that have acquired a transposable element, provided the transposable element
does not contain any recombinant and/or synthetic DNA
 Experiments that do not present a significant risk to health or the environment not described above and as
listed in Appendix C of the NIH Guidelines

rDNA in tissue culture containing less than ½ of any eukaryotic viral genome

Experiments using the following host-vector systems: E. coli K-12, Saccharomyces,
Kluyveromyces, B. subtilis, B. licheniformis

Purchase, transfer, and breeding (with exceptions) of transgenic rodents under BL1 containment
Submission
Submit completed Attachment A with General BUA Application to the IBC at Gateway Center
3519D, MC 1933 and an electronic copy to [email protected].
Acronyms
ABSL – Animal Biosafety Level
BSL – Biosafety Level
NIH – National Institute of Health
NIH Guidelines – NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules
OBA – Office of Biotechnology Activities
PBSL – Plant Biosafety Level
RAC – Recombinant DNA Advisory Committee
RG – Risk Group
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Attachment A of
General BUA Application