Attachment_5,_TO_0001_SOO_-_Engineered_Biosensors_for_Assessment_Augmentation_of_Human_Performance.pdf

STATEMENT OF OBJECTIVES

ENGINEERED BIOSENSORS FOR ASSESSMENT AND AUGMENTATION OF HUMAN

PERFORMANCE

TASK ORDER 0001

1.0 BACKGROUND

The warfighter’s physical and emotional endurance are tasked beyond that experienced by the general public in today’s highly dynamic mission theater. The need for augmentation tools to elevate warfighter performance levels is critical for mission success. Biosensors are defined within the scope of this work, as any complex system utilizing only biological components or their combination with non-biological parts, including organic or inorganic nanomaterials, polymers and others. Engineering nanomaterials with biorecognition elements (BREs) including peptides and aptamers have resulted in fast and sensitive sensing platforms with great potential to realize the real time detection of biomarkers. The emerging field of synthetic biology shows promise for human performance augmentation from engineering biosensors to sense and respond to molecular cues indicative of stress-induced changes experienced by warfighter, early detection of work-induced stress and physiological performance assessment through biomarker detection to the ultimate goal of increasing performance. Finally, the combination of both fields could provide unprecedented means to control biological function and novel sensing modalities.

The Department of Defense (DoD) recognizes synthetic biology can be harnessed to engineer biology in a systematic manner. DoD and United States Air Force (USAF) participation in defining this new research space will be pivotal to mission success. Biosensors can sense and respond to a variety of analytes, including biomarkers, explosives, and chem/bio agents;

additionally, this ability can be targeted to detection of human performance biomarkers and their restoration, if imbalanced. Potential application of engineered sensing platforms include cell (or microorganism)-based sensors, cell-free transcription/translation system-based sensors (CFS), colorimetric sensors in aqueous and solid phases, optical tracking of neurochemicals, and point-of-care diagnostics.

Cell-based sensors have appealing characteristics, including that they are self-powered, have enhanced selectivity, and are modular. However, realization of a functional modular cell-based sensor has presented challenges, especially concerning BREs that were optimized in vitro but subsequently incorporated into the cell chassis where their performance may be impacted.

Similarly, these methods assume that the ligand of interest is able to enter the cell at concentrations that enable BRE activation, and that the ligand is not toxic to the cell.

Computational tools designed to optimize BRE function in vitro do not accurately represent the cellular environment, which limits their capacity to improve BRE design and function in cell chassis. CFS mitigate these issues and enable downstream technologies, such as paper-based point of care sensors. Combining cell-based and cell-free systems, whereby BREs such as riboswitches in cell free systems regulate expression of downstream genes and communicate with cell-based systems to allow cellular response to metabolites is appealing. Similarly, engineering cells to enable riboswitch control could overcome current limitations related to cell-based sensor modularity by separating the sensing and reporting platforms, which then could be independently optimized.

Characterizing and modifying the human microbiome represents a new avenue for augmenting human performance. By assessing how the host-microbe symbiosis responds to the stresses experienced by the warfighter during their deployment, and recognizing the link between the gut microbiome and the brain, will lead to performance enhancement. For example, members of the gut microbiota respond to neurotransmitters and may be able to influence cognition, anxiety, and possibly mood and behavior through the secretion of various compounds.

Elucidation of microbiome changes and mechanism of action will enable modification of symbiotic microbes using synthetic biology approaches to detect human molecular signatures present in the gastrointestinal system indicative of cognition, stress and vigilance. Furthermore, other bacteria could be designed to secrete small molecules with a cognitive benefit or stress-relieving effect similar to those produced by the normal gut flora.

2.0 OBJECTIVE

The objective of this task order is to advance the understanding, development, and application of engineered biosensors for assessment and augmentation of human performance as well as the impact of chemical or genetic exposures to human health and performance.

3.0 SCOPE

The overall goals for this task order include: 1) development of novel BREs for human performance sensors; 2) assessment of host microbiome and develop engineered cells (smart probiotics) for human performance enhancement; 3) continued development of genetic and cellular assessment and monitoring technologies for individual assessment; 4) automate imaging and data acquisition platforms; 5) integration of suitable databases and computational and bioinformatics analysis tools.

4.0 TASKS/TECHNICAL REQUIREMENTS

4.1 ASSESSMENT OF BIOMETRICS AND BIOMARKERS FOR SENSOR DESIGN

The focus is to research appropriate biometrics and biomarkers for incorporation into future sensor designs by working in close consultation with the Air Force sponsors and address the attributes to be measured. In addition, to research and identify the appropriate suite of biometrics and biomarkers to be measured, individually and simultaneously, for accurate assessment of the cognitive and/or physiological status of the warfighter. Finally, perform human studies to measure some or all of the potential biometrics and/or biomarkers to assess correlation with measurable events such as stress, fatigue, vigilance and/or recovery status.

4.2 BIORECOGNITION ELEMENT SELECTION, CHARACTERIZATION AND

ENGINEERING

The focus is to (1) develop novel methods to design, select and/or engineer novel recognition elements based on nucleic acids, peptides and other bio-inspired elements providing selective and sensitive means to detect biomarkers of interest; and (2) implement microfluidics systems and automated robotics for the unsupervised identification and characterization of potential BREs and utilize advanced techniques for structural characterization of selected BREs including but not limited to nuclear magnetic resonance, small angle X-Ray diffraction, atomic force microscopy, transmission electron microscopy and others.

4.3 BIOLOGICALLY-INSPIRED SELECTIVE SENSORS

Use synthetic biology approaches to develop engineered biosensors that sense and respond to stress-related biomarkers. Utilize genetic tools to modify bacteria and/or their cell-free transcription/translation systems to sense and respond to AF-related targets of interest.

Develop biomarker-responsive riboswitches and other elements of regulatory control in bacteria to activate different response mechanisms, including but not limited to, the degradation of harmful chemicals and the synthesis of active species, like enzymes, antibodies and peptides. Optimize CFS from different organisms, including extremophiles, to create novel and robust sensing platforms. Develop a two-part sensor composed of a CFS and a cell-based reporting system using riboswitch-controlled cellular function.

4.4 NANOBIOHYBRIDS FOR FAST BIOMARKER DETECTION

The focus is to develop means to interface functional biomolecules and nanomaterials based on experimental and modeling approaches to develop rapid and sensitive biomarker detection platforms. These sensors will be designed in the nanoscale with multiple functionalities and with BREs for selective binding of neurotransmitters and neuropeptides. Sensing platforms will be developed in easy-to-use formats, including paper-based assays, lateral flow assays, microfluidics systems and others to allow the simple and rapid quantification of biomarkers in point-of-use settings. The contractor will develop sensing platforms for the simultaneous quantification of multiple biomarkers from small volumes of biofluids in non-invasive wearable sensors.

4.5 POINT OF USE ASSAYS FOR BIOFLUID BIOMARKER QUANTIFICATION

The focus is to identify appropriate point of use assays for biofluid biomarker quantification and Air Force applications. In addition to test, evaluate, validate and verify device performance in Air Force relevant applications. The Air Force will provide sensor specific guidelines for the application when necessary.

4.6 MICROBIOME ASSESSMENTS, MODIFICATIONS, AND TREATMENTS

The focus is to develop methodologies to: 1) assess effects of host genetics on microbiome composition; 2) utilize multi-omic approaches to assess effects of microbiome composition on human health and performance; 3) develop methods to effect microbiome composition as may be related to protection and/or enhancement of human health and performance; 4) assay development that will accurately identity microbes to the species level using metagenomics and targeted sequencing; 5) assess the effects of RNA transcriptome changes affecting human performance and health as related to gut microbiome populations; 6) assess host interactions biomarkers by developing sequencing methodologies to monitor how the gut microbiome affects human performance either through enhancement or degradation; 7) will develop suitable pipelines to compile large data sets and provide the analytical tools needed assess such data with downstream visualization.

4.7 RUGGEDIZATION OF BIOLOGICAL SENSORS

The focus is to develop matrices composed of organic and inorganic materials to host engineered microorganisms or their CFS and maintain their function under different deployment conditions, including but not limited to, the human gut, soil and other military relevant environments.

4.8 CHEMICAL-BASED ASSESSMENTS AND TREATMENTS

The focus is to assess correlation and combinatorial effects of chemical/pharmaceutical/toxicological effects to the individual at the molecular level. The Contractor will develop new exposure assessment and chemical treatment methods that target an individual’s genetic signature to enhance benefits and reduce adverse effects. The Contractor will use multi-parameter approaches to identify synergistic enhancements and reduce toxic side effects. The Contractor will also develop in silico modeling to include physiologically based pharmacokinetic (PBPK) and quantitative structure activity relationship (QSAR) models to assess cognitive and physiologic exposure impacts. The Contactor will develop novel sampling devices for monitoring of particulate and volatile contaminants. The Contractor will determine the performance characteristics of the devices (sensitivity, specificity, background interferences, dynamic range). The Contractor will perform quantitative and other statistical analyses of the data to verify sensor performance.

4.9 SUPERCOMPUTING DATA STRUCTURES

Advance data acquisition, curation, and storage protocols, and graphical user interfaces for implementation on the Air Force Research Laboratory (AFRL) DoD Supercomputing Resource Center (DSRC) systems as advanced computational requirements for analysis of genetic data increasingly require supercomputers with different software and database requirements.

4.10 BIOINFORMATIC ANALYSIS AND COMPUTATION

Research and develop suitable methods to compile and store large data sets and the analytical tools necessary to properly assess such data. Developed approaches will present data in easy-to-interpret enhanced visualization approaches.

5.0 OTHER REQUIREMENTS

5.1 MANAGEMENT OF EFFORT: The contractor shall manage technical schedule and cost satisfaction of the task order; plan, prepare, conduct and document reviews; track CDRL satisfaction; and interface with the customer to assess performance satisfaction and re-plan the project as needed. Contractor shall comply with all applicable human use and animal use regulations.

5.2 CONTRACT HOLIDAYS: The prices/costs in Section B of the contract include holiday observances; accordingly, the Government shall not be billed for such holidays, except when services are required by the Government and are actually performed on a holiday.

The following days are contract holidays: New Year’s Day, Martin Luther King Jr. Day, Presidents Day, Memorial Day,4th of July, Labor Day, Columbus Day, Veterans Day, Thanksgiving Day, and Christmas Day.

5.3 PROTECTION OF HUMAN SUBJECTS: The Contractor shall perform research using subjects in various laboratory experiments. The Contractor shall provide screening, scheduling, and training of subjects in order to accomplish this task order research, and will provide technical information required by the USAF IRB to approve the study design. The Contractor shall comply with the provisions of the following directives/regulations:

(i) Department of Defense (DoD), Title 32, Code of Federal Regulations, Part 219 (32 CFR 219), ”Protection of Human Subjects,” July 2004;

(ii) Department of Health and Human Services Regulations, 45 CFR 46, “Protection of Human Subjects,” 14 July 2009;

(iii) DoD Directive 3216.2, “Protection of Human Subjects and Adherence to Ethical Standards in DoD Supported Research,” 8 Nov 2011;

(iv) Air Force Instruction (AFI) 40-402, “Protection of Human Subjects and Adherence to Ethical Standards in Air Force Supported Research,” 10 Sep 2014.;” and

(v) AFRL Instruction 40-402 “Protection of Human Subjects in Research,” 9 Jul 2014.

Human testing shall not commence until approval from the Air Force Internal Review Board (IRB) has been obtained. If an exemption to the above is granted by the IRB, the provisions above are no longer applicable.

5.4 WORKING WITH HAZARDOUS MATERIALS: The Contractor shall adhere to all safety requirements regarding working with hazardous materials, including the Chemical Hygiene Plan and/or Material Information Sheets. The Contractor shall execute hazardous materials responsibilities in accordance with all applicable federal and military procurement policies and requirements, to include, but not limited to AFI 32-7086 “Hazardous Materials Management”, AFI 32-7086 WPAFB Supplement, and the Wright-Patterson AFB (WPAFB) Installation HAZMAT Management Program (IHMP) Plan. This documents will be provided by the Program Manager upon award.

5.5 OPERATIONS SECURITY: The Contractor shall provide Operations Security (OPSEC) protection for all sensitive/critical information as defined by AFI 10-701 (Operations Security), the 711 HPW OPSEC Plan, and critical information list. The Contractor shall participate in the 711 HPW sustained OPSEC awareness training or include OPSEC training as part of their ongoing security program. The 711 HPW OPSEC Coordinator shall evaluate the OPSEC posture of Air Force contract activities and operations.

5.6 INFORMATION SECURITY AND FORCE PROTECTION: The Contractor shall provide information security and force protection training as defined by AFI 16-1404 (Air Force Information Security Program) and AFI 10-245 (Antiterrorism (AT)). The Contractor shall participate in the 711 HPW sustained information security and force protection/antiterrorism training or include this training as part of their on-going security program. The 711 HPW Security Managers will evaluate the training posture of Air Force contract activities and operations. This requirement is set forth in AFI 16-1404, AFI 10-245 and applicable Air Force Materiel Command (AFMC) and local supplements.

5.7 USE OF LIVE ANIMALS SUBJECTS: The Contractor shall comply, as appropriate, with the provisions of the following directives/regulations: (i) Air Force Manual 40-401(I), "The Care and Use of Laboratory Animals in DoD Programs", (July 2006); (ii) DoD Directive 3216.1, "Use of Laboratory Animals in DoD Programs" (13 September 2010).

The use of live animals shall not commence until:

a. The Air Force Institutional Animal Care and Use Committee (IACUC) has approved the animal protocol.

b. The appropriate DoD/service veterinarian has reviewed and approved the animal protocol.

c. The appropriate DoD/service veterinarian has conducted, if necessary, a site visit to the Contractor's facilities.

5.8 SECURITY REQUIREMENTS: This effort is unclassified.

5.9 PERIOD OF PERFORMANCE: 39 months total; 36 months of technical effort and 3 months for final reporting.

5.10 DELIVERABLES:

5.10.1 CDRLs:

5.10.2 SOFTWARE: Software deliverables include specialized data software, modeling software, algorithms, and source code.

5.10.3 HARDWARE: Hardware deliverables include prototypes.

CDRL # CDRL NAME FREQUENCY

A001 Scientific and Technical Reports – Final Report ONE/R A002 Funds and Man-Hour Expenditure Report MTHLY A003 Contract Funds Status Report QRTLY A004 Status Report MTHLY A005 Presentation Material ASREQ