an introduction to nesdep · 2018. 12. 20. · biochip. inspect biochip cubed laboratories has...
TRANSCRIPT
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An Introduction To NESDEP® February 2018
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Cubed Laboratories offers NESDEP® as a novel and exclusive solution to
intractable diagnostic needs.
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Overview
Extract Genes NESDEP® uses US Patent 9,670,479 to continue
the sample preparation process by releasing DNA
from the collected bacteria. The process is
highly resistant to traditional inhibitors and
eliminates the need for clean-up kits..
Amplify Genes The final utility of US Patent 9,670,479 by Cubed
Laboratories is to amplify the captured DNA and
de-hybridize those DNA into single-strand DNA for
presentation to the patented NESDEP® disposable
biochip.
Inspect Biochip Cubed Laboratories has exclusive use of US
Patents 7,744,738 and 8,771,938 to present single-
stranded DNA to the functionalized carbon
nanotube array. In the presence of target DNA a
capacitive reaction is triggered.
NESDEP® Overview NESDEP® offers a combination of significant time
savings and better accuracy versus traditional
biological and molecular methods. NESDEP®
requires no special training and offers reliability
that comes from world class manufacturing.
Cell Capture Cubed Laboratories exclusively uses US Patent
9,670,479 to provide a simple, quick, and effective
method by which target bacteria is retrieved from
either environmental swabs or food matrix
samples.
Intellectual Property Cubed Laboratories designed NESDEP® around
US Patents 7,744,738, 8,771,938, and 9,670,479. In
addition, patents pending and sensitive trade
secrets ensure that superior and novel
intellectual property is put into service for
NESDEP® users.
Application Areas Cubed Laboratories offers NESDEP® for food safety
applications. In the near future NESDEP® will be
available for applications that range from medical
diagnostics to environmental science to oil and gas
extraction.
Certifications Cubed Laboratories uti l izes processes in
accordance with ISO 13485:2016 and ISO17025:2017
to design and manufacture NESDEP®. The device
is also compliant with AIHA and AOAC performance
methods.
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NESDEP® permits easy on-site testing and dramatically reduces
pathogen detection time.
No training required NESDEP® is an app-guided device. By focusing
on the power of intuitive software, the user
becomes an expert operator from the very first
use. And with less then five minutes of hands-on
time required, users can focus on important day-
to-day tasks.
Quality is assured Cubed Laboratories exclusively works with a
leading instrument manufacturer to produce
NESDEP® in a Six Sigma environment, ensuring
absolute product quality and reliability. After-sales
service is simplified with a 24-hour no-questions-
asked replacement program.
Significant time savings NESDEP® eliminates the need for a laboratory
and therefore makes on-site testing a reality. By
shortening the time from sample collection to a
dependable test result, the need for warehousing
of perishable food product can be reduced or
eliminated.
Improved accuracy Sensitivity and specificity are enhanced by the
advanced technology found in NESDEP®. In addition, by removing the need to transport
samples and eliminate numerous complex
laboratory steps, repeatability is significantly
improved.
Up to 94% precision
(validated in the
laboratory)
ISO and AOAC
certifications are in
place
Raw sample to assay
in less than 90
minutes
Portable with installed
wheels and low
voltage power
Design renders false
positives virtually
impossibleProtected by 3 US and
international patents and
with 3 patents pending
Tablet user-Interface
and Wi-Fi and
Cloud-enabled
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NESDEP® Cell Capture module optimizes the task of finding and
isolating pathogenic bacteria
Principle of operation Cubed Laboratories exclusively uses US Patent
9,670,479 to provide a proven, simple, quick, and
effective method by which target bacteria is
retrieved from either environmental swabs or food
matrix samples.
Module. The Cell Capture module is shown above.
Sample collection1. Cubed Laboratories
recommends that users continue with their current
standard operating procedure (SOP) for collection
of environmental sample swabs or food matrix
materials. NESDEP® requires a liquid sample.
Liquid Sample Introduction. A 50 mL sample is
introduced into NESDEP® using the designated
materials provided in the disposable test kit2. The
sample is vacuumed by NESDEP® into the Sample
Prep Cartridge (SPC) shown below.
Cell capture. The built-in NESDEP® vacuum works
to collect bacterial cells into the SPC, as well as
other non-liquid debris present in the sample
matrix. Depending upon the bacteria and other
debris, this process may take 1 to 2 minutes.
Disposable test kits NESDEP® disposable test kits are currently
available for E.coli (sp. and O157:H7), Listeria (sp.
and Monocytogenes), Salmonella (sp.), and
Campylobacter (sp.). The disposable test kit
contains all needed materials to complete a single
test on NESDEP®.
NESDEP® Assay Design Guide3 Cubed Laboratories utilizes the proprietary
NESDEP® Assay Design Guide to develop new test
kits. New disposable test kits can be developed
and validated (excluding AOAC performance
method approval) in as little as five days from
approved customer requests.
Liquid Sample Introduction Disposable test kits
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Unlimited sample volume NESDEP® minimum sample volume is 50mL,
however the system is designed to take up to
500mL per sample with the built-in waste bottle. If
needed, an external waste bottle can be used for
sample volumes up to 2 liters. The SPC captures
bacteria cells and other debris and is optimized for
50mL sample volumes. Specialized environmental
samples up to 2 liters may require several minutes
to complete. Please consult Cubed Laboratories
for additional details.
Composite samples The unique design of the Cell Capture module
permits up to 15 individual samples to be loaded
into an SPC as part of an individual disposable test
kit. Cubed Laboratories has developed an SOP4
that permits an entire production line to be tested
with one SPC.
Under certain circumstances it may be useful to
collect a group of samples from a production line
or area after that line has been sanitized. The
Composite Samples SOP will help determine if the
complete sanitization effort has been successful in
less than 90 minutes.
The Composite Samples SOP permits the use of
50% or 25mL of each of the collected samples to
be used without compromising the specificity of
the assay. This is done to permit retesting if a
presumptive positive is returned from the assay.
In the case of a presumptive positive test result,
the remaining samples can be retested with
confidence, with the understanding that collecting
new samples would not reflect an accurate view of
the state of sanitization of the production line or
area in question.
It should be noted that this SOP does not pinpoint
the result from each sample collected from the
production line or area. If the assay returns a
presumptive positive, the SOP requires that the
production line or area be retested, as noted
above.
The Composite Samples SOP should be reviewed
by users to ensure that it complies with their
company quality assurance plans. Cubed
Laboratories offers technical support to help
integrate the SOP into the quality plans of users.
Speciation NESDEP® was developed to identify pathogenic
bacteria in sample volumes. In addition, Cubed
Laboratories has developed disposable test kits to
differentiate species of tissue for quality assurance
purposes5.
The NESDEP® Assay Design Guide is used to
develop disposable test kits that can differentiate
the DNA of tissue types by identifying target
genes in the samples. For tissue types that have
been sequenced, NESDEP® can identify the
presence of designated tissue types.
For users interested in determining if tissue is
exclusively bovine in nature, speciation disposable
test kits can be a useful tool. Disposable test kits
are under development for differentiation of
various fish species and will be released in 2018.
Important benchmarks6 ISO 17025:2017 QOP-84-05 Sensitivity Analysis.
Cubed Laborator ies has developed ISO
documentation demonstrating the ability of
NESDEP® to detect as few as one cellular
equivalent in between 25mL and 50mL of sample
volume.
ISO 17025:2017 QOP-84-07 Composite Samples.
Cubed Laborator ies has developed ISO
documentation demonstrating the efficacy of the
SOP. This SOP should be tested by users as part of
their quality assurance plans.
ISO 17025:2017 QOP-84-15 Speciation. ISO
documentation has been developed that
demonstrates the abil ity of NESDEP® to
differentiate between equine and bovine tissues.
Additional speciation disposable test kits will be
developed in 2018
Cell Capture module
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NESDEP® Extract Genes module speeds and simplifies the process
of capturing DNA
Principle of operation NESDEP® uses US Patent 9,670,479 to continue
the sample preparation process by releasing DNA
from the collected bacteria. The process is highly
resistant to traditional inhibitors and eliminates the
need for clean-up kits.
Module. The Extract Genes module is shown above.
Cellular homogenizing. NESDEP® utilizes
mechanical lysing to disrupt cell membranes. The
SPC is placed in the device and DNA is forced
from the cell and migrates through the SPC
membrane. DNA is then available for retrieval
from the SPC.
Extraction. A simple syringe from the disposable
test kit is connected to the SPC. It is used to
collect the DNA from the SPC. Extensive testing
has proven that the bacterial material (should it be
present) and debris trapped in the SPC is totally
deactivated and harmless.
Lysing efficiency The NESDEP® cellular homogenizer activates the
microscopic glass beads in the SPC to effectively
lyse bacteria trapped inside. This system ensures
that weak and strong cell membranes will be
effectively disrupted and permit the release of
DNA.
Destruction of cellular material The primary goal of the NESDEP® Extract Gene
module is to disrupt cell membranes and permit
the release of DNA for use in the Amplify Gene
module (described below). However, the Extract
Gene module serves an additional safety function.
The secondary goal of the Extract Gene module is
to ensure that all materials trapped in the SPC are
thoroughly disrupted and destroyed, ensuring that
the SPC is non-hazardous and can be disposed of
as normal waste in user processes.
Inhibitors and non-target materials Typical molecular detection systems are
challenged by the presence of inhibitors and non-
target DNA, which are often removed with
specialized clean-up kits in manual or automated
processes. Cubed Laboratories has shown
NESDEP® to be quite different.
NESDEP® utilizes AC Dielectrophoresis and Shear
Force in the Inspect Biochip process, making the
system highly resistant to inhibitors and immune
to the effects of non-target DNA. As result, typical
clean-up kits are completely unnecessary
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Important benchmarks6 ISO 17025:2017 QOP-84-10 Bacterial Control.
Cubed Laborator ies has developed ISO
documentation demonstrating that the NESDEP®
Extract Gene module is completely effective in
disrupting and destroyed bacteria, should they be
present.
Extract Genes module
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NESDEP® Amplify Genes module uniquely prepares target DNA copies for precise detection
Principle of operation The final utility of US Patent 9,670,479 by Cubed
Laboratories is to amplify the captured DNA and
de-hybridize those DNA into single-stranded DNA
for presentation to the patented NESDEP®
disposable biochip.
Module. The Amplify Gene module is shown above.
Sample vial. The NESDEP® disposable test kit
contains a sample vial which includes freeze dried
reagents7. The product removed from the SPC is
placed in the sample vial, which is then placed in
one of the two Amplify Gene module stations.
PCR. NESDEP® uses a modified PCR process to
take as few as one gene copy and amplify it into a
sufficient quantity for use in the Inspect Biochip
module. NESDEP® uses proprietary reagents as
part of the PCR process.
NAP. The final step of the NESDEP® Amplify Gene
module is to de-hybridize the amplified DNA,
thereby taking DNA strands and splitting them into
single-strand DNA.
The Inspect Biochip process uses single-stranded
DNA as part of the detection process.
PCR explained The NESDEP® PCR (Polymerase Chain Reaction) is
a process that replicates a selected sequence of
DNA. All DNA is made of 4 base pairs (A-T and C-
G). NESDEP® PCR uses a patented device to
rapidly alter the temperatures for a specific
duration.
The temperatures used are preprogrammed into
the NESDEP®. The set temperatures are a melting temperature
and an annealing temperature. Depending on the
DNA being replicated, an additional set point
temperature will be used to make the process
more efficient.
The NESDEP® proprietary primers (the target
sequences’ start and end points) are based on
specific regions of the pathogen bacteria of
interest. These sequences may be variant, species,
or family specific, depending on the nature of the
assay.
The NESDEP® proprietary primers will only
replicate the target DNA found between the start
and end points. The replicated region is typically
25 to 120 base pairs in length, as selected during
use of the NESDEP® Assay Design Guide.
Cubed Laboratories has developed a technique,
NAP, to rapidly replicate one side of the base-pair
chain, known as single-strand DNA (ssDNA). If pathogen of interest is present, the DNA
sequence will be replicated and available for use
in the Inspect Biochip module.
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Staging The NESDEP® Amplify Gene module requires
approximately 40 minutes to complete, making
this the longest stage of the NESDEP® process. As
a result, NESDEP® has been designed with two
Amplify Gene modules.
By using two NESDEP® Amplify Gene modules, the
average test time per individual test is reduced to
less than 45 minutes. This means that at least 15
tests can be conducted per 8-hour work shift
(including anticipated breaks).
Important benchmarks6 ISO 17025:2017 NES-002 NESDEP® Description.
Cubed Laborator ies has developed ISO
documentation demonstrating how the NESDEP®
Amplify Gene module amplifies genetic material,
and de-hybridizes genes into single-strand DNA.
Amplify Genes module
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NESDEP® Inspect Biochip module precisely compares captured
DNA with target pathogens
Principle of operation Cubed Laboratories has exclusive use of US
Patents 7,744,738 and 8,771,938 to present single-
stranded DNA to the functionalized carbon
nanotube array. In the presence of target DNA a
capacitive reaction is triggered.
Module. The Inspect Biochip module is shown
above.
Biochip. The NESDEP® biochip is shown below.
Specificity. NESDEP® Inspect Biochip module
utilizes a patented electrochemical system that
includes AC Dielectrophoresis and Shear Force to
ensure that only target DNA is detected if it is
present in the original sample collected by the
user.
Sensitivity. NESDEP® Inspect Biochip module
utilizes a functionalized carbon nanotube (fCNT)
array consisting of millions of nanostructures to
ensure that target ssDNA is detected and non-
target ssDNA is rejected from the assay.
Cleaning. As with all other modules, one-handed
operation is assured. Once a test is complete on
NESDEP®, the device automatically cleans itself
and is fully prepared for the next test with no
possibility of residual contamination.
AC Dielectrophoresis AC Dielectrophoresis (DEP) on NESDEP® occurs
within the Inspect Biochip module. The biochip
included in the disposable test kit is 15mm x 6mm
and includes a nanometer-scale electrode array
on polyester with a flowcell to create a
microfluidic detection channel.
The biochip is encased in a sealed plastic case to
make the fluidic and electrical connections easy to
operate for the user. Each biochip contains
millions of randomly arrayed double-walled
carbon nanotube (CNT) layers, as shown in the
simplified illustration on the next Page.
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Attached to the CNTs are target ssDNA probes.
The electrodes in the array are approximately
25µm apart. When voltage is applied to the
electrode array, the resulting electrical field is
capable of trapping the particulates (i.e., ssDNA)
into the array.
The functionalized Carbon Nanotubes (fCNTs)
correspond to the sequence of ssDNA from the
replicated region of the target pathogen DNA
sequence. The ssDNA is permanently bonded to
the CNT in a process called functionalization.
The assay system works by first transferring buffer
solution through the biochip. An impedance
measurement scan is taken; this scan is called the
Baseline Scan. The sample is then pushed into the
biochip.
The built-in NESDEP® analyzer outputs a voltage
to the electrode array creating a large electrical
field. The charged particles from the sample are
drawn to the electrode array. The ssDNA from the
sample hybridizes to the ssDNA of the fCNTs’
probe.
Hybridization occurs when two ssDNA sequences
come together. If the resulting double stranded
DNA structure does not match, the DNA is cleaved
off through the presence of a high shear force,
thus ensuring specificity and selectivity. An
illustration is shown below:
If the proper sequence of DNA has been replicated
and it does hybridize to the functionalized ssDNA
probe, the sequence will not separate in the
presence of high shear force. An impedance
measurement scan is then taken.
An Impedance Scan is series of impedance
measurements taken at frequencies in the kHz to
MHz range. Each point has a real and imaginary
impedance, where the imaginary impedance is a
measurement of the capacitance of the system.
A baseline impedance scan is taken before the
sample is automatically added by NESDEP®. DEP
draws charged particles, including ssDNA toward
the electrodes. The ssDNA will hybridize to the
CNT’s ssDNA probes.
Shear force In the event that non-target ssDNA is replicated in
the Amplify Gene module, it may hybridize with
the ssDNA probes, however, it will not match so
that it will bulge out or overhang in the electrical
field created in the biochip, as shown below:
The flowrate is such that fluid flow exerts a strong
shear force, separating the non-matching DNA
from the ssDNA probe, yielding a presumptive
negative result. If target ssDNA is present, the flow
rate will not shear it from the ssDNA probe,
yielding a presumptive positive.
Inspect Biochip module
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Important benchmarks FDA Pre-Sub Q130508 NESDEP®. Cubed
Laboratories participated in pre-clinical trials with
the US FDA and South Bend Memorial Hospital for
the detection of MRSA in patients. Third-party
data is shown in the chart below:
Inspect Biochip module
Accuracy Sensitivity SpecificityNegative
Predictive ValuePositive Predictive
Value
93.85% 100.00% 87.50% 93.02% 95.46%
100%
50%
0%
100%
50%
0%
100%
50%
0%
100%
50%
0%
100%
50%
0%Average
Low
NESD
EP
High
Average
Low
NESD
EP
High
Average
Low
NESD
EP
High
Average
Low
NESD
EP
High
Average
Low
NESD
EP
High
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Overview Early in its history, Cubed Laboratories deliberately
designed NESDEP® to meet the strictest medical
devices standards available. More recently, the
company has worked to ensure that they can also
meet the requirements of the food safety industry.
ISO 13485:2016 Cubed Laboratories developed and implemented
a quality management system with regard to
medical diagnostic standards to demonstrate its
ability to consistently provide product that meets
customer and regulatory requirements, and to
address customer satisfaction through the
effective application of the system, including
continual improvement and the prevention of
nonconformity.
The quality system complies with the international
standard ISO 13485:2016. The manual is divided
into eight sections modelled on the sectional
organization of the ISO 13485:2016 standard.
Sections are further divided into several
subsections representing main quality system
processes. Each subsection defines general
policies and basic principles for the pertinent
q u a l i t y s y s t e m p r o c e s s ; s u m m a r i z e s
responsibilities and methods; and references
relevant operational procedures and other
documents.
The purpose of this manual is to define and
describe the quality system, to define authorities
and responsibilities of the management personnel
involved in the operation of the system, and to
provide a general description of all processes
comprising the quality system.
Another purpose of this manual is to present the
quality system to customers, suppliers, regulators
and other external interested parties, and to inform
them what specific controls are implemented at
Cubed Laboratories to assure quality.
Cubed Laboratories expects to conduct its first
independent ISO 13485:2016 audit in the first half
of 2018.
ISO 17025:2017 As with ISO 17025:2017, Cubed Laboratories
d eve l o p e d a n d i m p l e m e n t e d a q u a l i t y
management system to demonstrate its ability to
consistently provide product that meets customer
and regulatory requirements with regard to food
safety applications, and to address customer
satisfaction through the effective application of
the system, including continual improvement and
the prevention of nonconformity.
Cubed Laboratories ISO 17025:2017 includes a
specific quality system for the production of
diagnostic devices and disposable test kits for
food safety purposes. In addition, it includes a
quality system for on-site operation of the
NESDEP® product, as well as a quality system for
the Cubed Laboratories facility in which test
methods are developed and independent
microbiological tests and molecular tests are
Cubed Laboratories designed NESDEP® to meet strict world
class certification requirements
ISO AIHA API AOAC
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conducted as part of the product development
and certification process.
Cubed Laboratories expects to conduct its first
independent ISO 17025:2017 audit in the first half
of 2018.
AIHA In mid-2017 the company elected to complete the
Laboratory Accreditation program of the American
Industrial Hygiene Association (AIHA) with the
guidance of a certified AIHA consultant and
auditor. Specifically, this includes demonstration
of our compliance with Module 2A (General
Management Systems Requirements), Module 2F
(Food Laboratory Accreditation Program), Module
3 ( A c c r e d i t a t i o n , M a i n t e n a n c e , A n d
Reaccreditation), and Module 6 (Proficiency
Testing). In addition, Appendix G (Estimation Of
Uncertainty Measurement) and Appendix H
(Traceability Of Measurement) are included in this
assessment.
API As part of the AIHA effort at Cubed Laboratories,
the company successfully participated in 2017
Food Microbiology 3rd Event. This event included
Campylobacter and a Qualitative Package for Meat
(E. coli 0157:H7, Listeria, and Salmonella). The
company is scheduled to participate in all three
events offered in 2018.
AOAC Cubed Laboratories developed a purposeful and
detailed strategy with AIHA consultant and auditor
to demonstrate compliance with Performance
Methods developed by the American Association
of Analytical Chemists.
The first pillar of this strategy was to document our
processes for the design, development, and
production of NESDEP® in accordance with ISO
13485:2016. The company extended its quality
compliance methods with the completion of ISO
17025:2017. Cubed Laboratories ensures that all of
its material and service suppliers (including
research and development services, component
suppliers, and manufacturing partners are ISO
certified as well). Furthermore, they must also
have Six Sigma and Lean certifications.
The second pillar of our strategy was to seek AIHA
certification for our company laboratory. Our fully
equipped BSL-1 and BSL-2 facilities are designed
to accomplish two missions: First, to utilize our
NESDEP® Assay Design Guidelines to continually
validate existing disposable test kits, as well as
develop new test kits for detection of pathogenic
bacteria, other bacteria of interest, and also
consumable test kits designed for determination
of species. Second, to utilize our certified
laboratories to demonstrate our compliance with
various AOAC Performance Methods as utilized
with NESDEP®. Our ISO documented process
includes an independent review of data associated
with AOAC Performance Methods by our AIHA
consultant and auditor, as well as other AIHA
organizations to ensure that we comply with AIHA
requirements and AOAC test methods.
Furthermore, to ensure that Cubed Laboratories
remains compliant with the spirit and intention of
ISO 13485:2016 and ISO 17025:2017, the company
has become a member of the AOAC OA, which
grants the company access to both important
AOAC documents, but also AOAC subject matter
experts who can assist us as needed with
development of new disposable test kits and
understanding of the most efficient AOAC
Performance Method to use as a reference.
Industry Partners Cubed Laboratories values the insight and input of
a variety of well-established nationally recognized
corporations and well-known subject matter
experts who are under retainer to consistently and
thoroughly review and challenge our approaches
t o d ev i c e d e s i g n , c o n s u m a b l e t e s t k i t
development, certification approvals, and
documentation development and distribution.
Certifications
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NESDEP® intellectual property provides a strong technology
foundation
Overview Cubed Laboratories has licensed and developed
intellectual property underlying the novel
technology used in NESDEP®. Some of this
technology is expressed in the form of awarded
US Patents, other as US Patent applications, and
still others as trade secrets used in our
development and manufacturing processes.
US Patent 7,744,7389 Title: “Method and apparatus for rapid particle
manipulation and characterization”
Abstract: “The present invention provides a
method and apparatus for use in rapid particle
t r a n s p o r t a t i o n , s e p a r a t i o n , f o c u s i n g ,
characterization, and release. Dielectrophoresis
and electro-osmotic driven fluid convection are
used independently or in tandem as the driving
forces for particle manipulation and on occasion
characterization. Although dielectrophoresis has
been acknowledged for decades as a powerful
technique for part icle manipulat ion and
characterization, long processing times and
measurement inaccuracies that emerge from
using disjointed electrodes have limited its
usefulness in diagnostic kits. The present
invention provides for a continuous wire that
enables fluid flow patterns and dielectrophoretic
forces with optimal configurations for rapid and
s e n s i t i v e p a r t i c l e m a n i p u l a t i o n a n d
characterization.”
US Patent 8,771,9389 Title: “Microfluidic platforms for multi-target detection”
Abstract: “Disclosed are example methods and
devices for detecting one or more targets. An
example method includes placing a sample
including a first target within a microfluidic device
and hybridization plurality of copies of the first
target with a plurality of nanostructures. The
example method includes applying an electric
current to the plurality of nanostructures and
using an electric field created by the electric
current to move the plurality of nanostructures. In
addition. the plurality of nanostructures are sorted
and evaluated to determine at least one of a
presence, an absence, or a quantity of the first
target.”
US Patent 7,744,7389
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US Patent 9,670,4799 Title: “Sample preparation device and method of use”
Abstract: “A device for isolating DNA from a
sample containing cells, including a cartridge
having an entrance port and an exit port, a
membrane disposed between the entrance port
and the exit port, and a plurality of channels
between the membrane and the exit port.
Additionally, systems and methods for isolating
DNA from the sample containing cells and also
systems and methods for amplifying and isolating
single-stranded DNA from a sample containing
DNA.”
Patent Applications Cubed Laboratories is currently pursuing US
Patents for a number of novel areas, including
quantitation of particles in our microfluidic
platform. Materials and assembly processes for
our microfluidic biochip. A process for ensuring
that our nanostructure-rich fluids remain stable
during the manufacturing process.
Trade Secrets The company has a variety of valuable trade
secrets that range from our ISO-documented
procedures for design and testing of our
diagnostic instruments to the precise method
used to create single-stranded DNA probes used
in our microfluidic biochips.
The novel and unique nature of the NESDEP®
device is backed up by a decade of thorough
academic research at the University of Notre
Dame10, empirical testing by the University of
Notre Dame and the Cubed Laboratories team,
and clinical and industrial testing by the company
across a wide variety of application areas from
medical diagnostics, environmental science, oil
and gas, and food safety.
Intellectual Property
US Patent 8,771,9389
US Patent 9,670,4799
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NESDEP® was designed to serve multiple application areas across
multiple industries
Overview Cubed Laboratories created NESDEP® as an easy-to-use and powerful molecular diagnostic tool,
bringing speed and accuracy to a variety of difficult customer business problems from food safety to
medical diagnostics. NESDEP® is now ready for service to food processors. In the very near future
Cubed Laboratories will extend the use of NESDEP® to other areas as regulatory approvals from
government bodies and and industry groups are secured.
Food safety The safety and quality of food products is the
absolute priority of food processors worldwide.
NESDEP® by Cubed Laboratories offers a novel
solution that permits real-time collection of test
data without incurring additional organizational
costs.
The ability to process environmental swabs and
food matrices in real-time offers food processors
the opportunity to reduce or el iminate
warehousing associated with the current test-
and-hold methodology currently in practice.
Environmental science Recreational and drinking water is subjected to
thorough testing to ensure the safety of the public.
Cubed Laboratories participates in a Cooperative
Research And Development Agreement (CRADA) to
make this task easier.
NESDEP® offers the possibility of reducing a multi-
day test time to that of less than 90 minutes,
allowing decision makers the opportunity to open
public beaches more quickly and clear water main
breaks more rapidly, ensuring clean water
availability more quickly.
Medical diagnostics Clinicians have often been hamstrung by the
necessary wait time between testing patient
samples for MRSA and C. Diff and the
administration of powerful antibiotic treatments.
Cubed Laboratories has a simple and powerful
bedside tool to offer in NESDEP®.
In the next 18 months clinical trials for NESDEP®
will be completed, potentially permitting
clinicians to test wound product at the patient
bedside in 90 minutes and substantially
improving patient outcomes by speeding
treatments.
Oil and gas extraction Oilfield bacteria are implicated in sub-optimal
productivity and damaging corrosion of critical
infrastructure from wells to pipelines. Chemical
treatments are often used and over-used to fight
such oilfield bacteria.
Cubed Laboratories has successfully tested
NESDEP® to identify oilfield bacteria and thereby
optimize the use of chemical treatments, often
resulting in the decreased use of such chemicals,
reducing production costs and reducing potential
chemical pollution.
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Footnotes
Footnote 1 Sample Collection: Cubed Laboratories highly
recommends that users seek professional advice
with regard to the appropriate methods for
collecting samples in a food processing
environment or other production areas.
Footnote 2 Disposable Test Kit: The NESDEP® disposable test
kit consists of SPC, biochip, and all other needed
reagents and components to complete a single
test. The disposable test kit is individually bar
coded for ease of use by operators.
Footnote 3 NESDEP® Assay Design Guide: The guide is a
proprietary document that is not available to the
public. However, a Cubed Laboratories
representative can provide a comprehensive
overview of the guide and how the process works.
Footnote 4 Composite Samples SOP: The Standard Operating
Procedure can be made avai lable upon
completion of a Non-Disclosure Agreement with
Cubed Laboratories. Please contact your Cubed
Laboratories representative for further details.
Footnote 5 Speciation Disposable Test Kit: The speciation
disposable kit is a useful tool for ensuring product
quality. Cubed Laboratories can develop
customized disposable test kits as needed.
Please contact your Cubed Laboratories
representative for details.
Footnote 6 ISO Documents: Cubed Laboratories ISO
documents are proprietary and not available to the
public. However, a Cubed Laboratories
representative can provide a summary document
for review upon completion of a Non-Disclosure
Agreement.
Footnote 7 NESDEP® Reagents: Reagents are freeze dried
into a bioball that is stable under specified
circumstances. The user is not required to do
premixing or engage in additional steps to activate
reagents, other than add SPC contents to the
sample vial.
Footnote 8 NESDEP® Test Result: NESDEP® reports a test in
terms of presumptive negative (no pathogenic
bacteria present) or presumptive positive (if
pathogenic bacteria is present). A sample of each
report is shown in the illustrations below:
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Footnote 9 US Patents: Cubed Laboratories has licensed US
Patents 7,744,738 and 8,771,938 from the University
of Notre Dame. These licenses are exclusive,
perpetual, and may be used across all application
areas by Cubed Laboratories.
US Patent 9,670,479 was developed by Cubed
Laboratories. All US Patents have also been
applied and granted in the European Union, China,
India, and a variety of other countries for
protection of Cubed Laboratories product and
services.
Footnote 10 Academic Papers: The technology underlying
NESDEP® and embodied in its intellectual
property was academically researched by
collaborators at the University of Notre Dame. In
addition, empirical engineering studies were
completed as well.
Cubed Laboratories does not own the copyrights
to such academic papers and publications, and as
such cannot provide links to the documents.
However, the papers are listed below for
interested users.
Cheng, I-Fang; Senapati, Satyajyoti; Cheng, Xinguang; Basuray, Sagnik; Chang, Hsien-Chang; and Chang, Hsueh-Chia, “A Rapid Field-use Assay for Mismatch Number and Location of Hybridized DNAs,” Lab-on-a-Chip, 2010, 10, 828-31.
Basuray, Sagnik; Senapati, Satyajyoti; Aijian, Andrew; Mahon, Andrew R.; and Chang, Hsueh-Chia, “Shear and AC Field Enhanced Carbon Nanotube Impedance Assay for Rapid, Sensitive, and Mismatch-discriminating DNA Hybridization,” ACS Nano, 2009, 4, 7, 1823-30.
Senapati, Satyajyoti; Mahon, Andrew R.; Gordon, Jason; Nowak, Carsten; Sengupta, Shramik; Powell, Thomas H. Q.; Feder, Jeffrey; Lodge, David M.; and
Chang, Hsueh-Chia, “Rapid On-chip Genetic Detection Microfluidic Platform for Real World Applications,” Biomicrofluidics, 2009, 3, 2, 022407-13.
Gagnon, Zachary; Senapati, Satyajyoti; Gordon, Jason; and Chang, Hsueh-Chia, “Dielectrophoretic Detection and Quantification of Hybridized DNA M o l e c u l e s o n N a n o - g e n e t i c P a r t i c l e s , ” Electrophoresis, 2008, 29, 4808-12.
Gagnon, Z. and Chang, H.-C., “Aligning fast alternating current electroosmotic flow fields and characteristic frequencies with Dielectrophoretic traps to achieve rapid bacteria detection”, Electrophoresis, 26, 3725-3737(2008).
Chang, Hsueh-Chia, “Nanobead Electrokinetics: The
Enabling Microfluidic Platform for Rapid Multi-
target Pathogen Detection,” AIChE Journal, 2007, 53,
10, 2486-92
Cheng, I-F.,Chang, H.-C., Hou, D. and Chang, H.-C., "An Integrated Dielectrophoretic Chip for Continuous Bioparticle Trapping and Detecting", Biomicrofluidics, 1, 021503(2007).
Basuray, S. and Chang, H.-C., “Induced Dipoles and Dielectrophoresis of Nano-Colloids in Electrolytes”, Phys Rev E., 75, 060501-060504(2007).
Zhou, R., Wang, P. and Chang, H.-C., “Bacteria capture, concentration and detection by alternating current Dielectrophoresis and self-assembly of d ispersed s ing le-wa l l carbon nanotubes” , Electrophoresis, 27, 1376-1385 (2006).
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