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Infrastructure Resilience

Infrastructure systems have been major contributors to the growth of the United States. Hoover Dam helped desert regions in the west to bloom. The Interstate Highway System spanned the states and opened up the country to growth and provided corridors for trade. As the country grew, new technologies developed, and infrastructures developed around them that are integral to our daily lives. These infrastructures can be vulnerable to a variety of disruptions, including human events, earthquakes, extreme weather events and climate change impacts. The creation of the President’s Commission on Critical Infrastructure Protection (PCCIP) in 1996 ^[1] resulted in the development of a national plan to identify the critical infrastructure sectors and how to identify and reduce their vulnerabilities to natural or deliberate threats. Subsequent extreme natural disasters like Hurricanes Katrina and Sandy pointed out additional limitations in the resilience of infrastructure due to the interconnected nature of infrastructure systems. Infrastructure cannot be made totally immune to disruptive events, but it can be made more resilient by considering the dependencies and interdependencies within and between systems and by taking a system-of-systems view of the vulnerabilities and threats to them.

Introduction

Infrastructure systems have always been an important aspect of the United States and signature elements of the country’s growth—examples such as Hoover Dam, Grand Central Station, and the Interstate Highway System. As the country grew and evolved, other infrastructure elements took on important aspects of everyday life, such as Global Positioning System (GPS) and the World Wide Web (WWW). Vulnerabilities in these systems were largely taken for granted until terrorist events such as the | Tokyo sarin gas subway attacks, the 1993 terrorist bombing of the U.S. World Trade Center, and the bombing of the Federal Building in Oklahoma City demonstrated the reality of threats from human elements. The subsequent creation of the President’s Commission on Critical Infrastructure Protection (PCCIP) in 1996[1] resulted in the development of a national plan to identify the critical infrastructure sectors and how to identify and reduce their vulnerabilities to natural or deliberate threats. Subsequent extreme natural disasters like Hurricanes Katrina and Sandy pointed out additional limitations in the resilience of infrastructure due to the interconnected nature of infrastructure systems. In its October 1997 report, the PCCIP^[3] defined an infrastructure as “a network of independent, mostly privately owned, man-made systems and processes that function collaboratively and synergistically to produce and distribute a continuous flow of essential goods and services.” In the original PCCIP assessments considered eight critical infrastructures whose “…incapacity or destruction would have a debilitating impact on our defense and economic security.”^[1]The U.S. Department of Homeland Security has subsequently increased the number of critical infrastructures to the 16 sectors^[4], listed in Table 1, and detailed a plan to strengthen and maintain, secure, functioning, and resilient critical infrastructure^[2].

Table 1. DHS Critical Infrastructure Sectors^[4]
Chemical Sector	Commercial Facilities Sector	Communications Sector	Critical Manufacturing Sector
Dams Sector	Defense Industrial Base Sector	Emergency Services Sector	Energy Sector
Financial Services Sector	Food and Agriculture Sector	Government Facilities Sector	Healthcare and Public Health Sector
Information Technology Sector	Nuclear Reactors, Materials, and Waster Sector	Transportation Systems Sector	Water and Wastewater Systems Sector

Analyzing Infrastructure Vulnerabilities

Early studies on critical infrastructure vulnerabilities focused on physical threats, and the strategies to mitigate those vulnerabilities focused primarily on providing physical protection with “guns, gates, and guards.” As the array of potential threats expanded to include factors such as cyber, chemical, biological, radiological, and nuclear attacks, the vulnerability assessment methodologies evolved and expanded to include the consideration of the dependencies and interdependencies within and between infrastructure assets. The myriad of interdependencies in infrastructure systems can result in a disruption in a component of one infrastructure cascading through a network of dependencies and resulting in the taking down of a larger infrastructure, such as the northeast blackout in August 2003. The cause of the blackout was attributed to a software bug in a control room alarm system in Ohio, which made operators unaware of a need to redistribute the electrical load after transmission lines drooped into foliage. Events like this demonstrate that protecting infrastructure from all hazards is impossible. Instead, one must understand the dependencies and interdependencies in infrastructures, and how they differ, so they can be designed to be resilient to disruptions when they inevitably occur.

System View of Infrastructure Resilience

Numerous definitions can be found for resilience that depends upon the perspective of the problem being addressed, such as material physics, ecosystems, engineering, and psychological well-being, to name just a few. For the study of infrastructure resilience and how it contributes to regional and community resilience, the following definition is used:^[5] “Resilience is the ability of an entity—e.g., asset, organization, community, region—to anticipate, resist, absorb, respond to, adapt to, and recover from a disturbance from either natural or man-made events.” Analyses of the resilience of infrastructure should be taken from an integrated systems perspective^[2]of the infrastructure and the community and region being supported. Figure 1 provides a schematic representation of the systems that support resilience^[6]. The high-level systems shown in Figure 1 can be expanded to finer scale system as needed. The Governing System in Figure 1 is deliberately not called a Government System because the intent is to be able to represent governing systems at multiple levels of population granularity—groups, villages, tribes, communities, countries, etc. These groups have different ways in which they organize themselves, and the organizing details may or may not be formalized and may or may not be codified. Organized criminal networks, for example, have strong governing and enforcement mechanisms that members clearly understand, but these mechanisms are not codified in any written form.

Figure 1. Schematic Representation of the Interconnected Systems that Contribute to Resilience^[6]

.

The Human Landscape System is often the most overlooked system in resilience assessments of communities and infrastructure, yet it is probably the most important. It represents the actors who are the decision makers, the implementers of plans and activities, and the groups in the general population that will be impacted by the plans and the external forces that can disrupt the community ^[7]. The Human Landscape is also the system where the measures of effectiveness of resilience activities are assessed. For example, during the COVID-19 pandemic, the efforts to reduce the spread of the virus depended upon the collective behaviors of people to shelter in place, practice social distancing, and wear facial masks in public. The basic measures of the effectiveness of the efforts to control the spread of the virus were the number of cases of infection hospital strain and lives lost. The Natural Environment system in Figure 1 consists of the terrain, air, ocean, and space environments where the infrastructure and community systems are located and operated. The natural environment can be a driver for where an infrastructure is located and will be the source of the natural forces to which it must respond.

Assessing and Mitigating Climate Impacts on Infrastructure

The DHS Regional Resiliency Assessment Program^[8] (RRAP) has conducted analyses of the vulnerabilities of infrastructure to a variety of disruptions, including earthquakes, climate impacts, and extreme weather events. These assessments utilize a variety of models and tools in the resiliency assessments, depending upon the context of the study. For example, an RRAP study done in the Casco Bay Region of Maine examined the disruptions to infrastructure from projections of coastal flooding triggered by sea level rise and heavy precipitation. In that study, inundation models driven by sea level and precipitation projections generated areas of flooding in the Casco Bay area. Overlays of the existing infrastructure elements were then used to identify the locations of electric power assets that could be disrupted by the projected flooding.

Figure 2. Potential Impacts from Flooding of Electric Assets in the Casco Bay Region of Maine

.

In California, an integrated water system was developed in the second half of the 20th century, the California State Water Project (SWP), to collect and store water from the northern portion of the state and deliver it to communities in the central and southern regions of the state. The SWP was developed based on the climatic conditions of the time and the locations of the dams, reservoirs, canals, and aqueduct were selected based on the historic precipitation patterns of the mid-20th century. The effectiveness of the SWP to continue to collect and deliver water under projected climate conditions has been studied by combining high-resolution climate projections and overlaying the results against the SWP elements. The projections of 21st mid-century and end-of-century climate conditions^[9] indicate changes in the timing of precipitation in California and how it falls (rain or snow). The changes in timing indicate that more of the precipitation may fall earlier in the year and in the form of rain, when the existing SWP is least able to collect and store the water because the reservoirs are required to have lower storage levels for flood control purposes. This could result in a requirement for significant investment in new reservoirs at new locations better able to capture and store the precipitation. The 2021 power crisis in Texas pointed to the importance of the role of the natural environment in energy system planning. Energy grids are a combination of numerous nodes and links and disruptions in any component can potentially cascade through the system. Energy planning in Texas has traditionally considered only historical environmental factors when planning for future energy needs in terms of estimating future energy loads and did not include the consideration of extreme weather events—hot or cold—in planning. The extreme cold weather event resulted in two significant issues for the energy planners. First, many natural gas wells and pipelines were not winterized and failed or shutdown, depriving the electrical generating facilities of the natural gas to power the facilities. Second, it takes far more energy to warm households up from near freezing temperatures than it does to cool them down from a summer heat wave, increasing the demand load on the electric grid. Tools such EPfAST ^[10] and NGFast ^[11] can be used to study integrated electric power and natural gas system interdependencies. In many coastal areas of the country, transportation systems are having to contend with disruptions from storm surges and high-tide flooding ^[12], which occurs when local sea level rises above a given threshold in the absence of storm surge or riverine flooding. This type of flooding is occurring on a regular basis along portions of the U.S. east coast and portions of the south Florida coast and is expected to worsen as sea levels rise. In south Florida, the problem is made worse because much of the area sits on porous limestone which allows the ocean to seep up from the ground – meaning that residents face the climate impacts from storm surges from the sea and rising ground waters from below. The intrusion of ocean water into the aquifers can impact the availability of potable water from aquifers as well as reduce the ability of the ground to absorb runoff, so floodwaters will remain longer^[13]. In developing mitigation strategies for climate change impacts, infrastructure developers look at ways to protect or retrofit existing systems and how to develop new systems that take into account potential climate change impacts. As an example, the predictions of higher summer temperatures from climate change can mean that the operating ranges for heat, ventilation, and air-conditioning systems may change and require new designs for such systems. These changes may also result in changes in building codes in different areas^[14]^[15]^[16]. Hurricane Sandy provided a number of critical lessons for infrastructure developers. One major lesson learned was that basements in building should not be used for any back-up or critical systems – power, computers, or telecommunications. Many of the hospitals in New York City lost power because their reserve generators were in basements which flooded. Another one was that waterproof doors should be installed at entrances to subway stations. One of the major challenges facing developers is what environmental conditions should they build for. The majority of building codes are based on analyses based on historical environmental conditions and are not representative of current conditions. The Federal Emergency Management Agency (FEMA) has the responsibility to update floodplain maps every five years. These maps are used to identify flood prone areas and locations where flood insurance is required. However, it was estimated in early 2020 that only one-third of nation’s 3.5 million miles of streams and 46% of shoreline have had maps generated^[17]. In addition, climate projections are pointing towards more frequent severe precipitation events and in urban areas where developments are changing runoff patterns, the chances for flooding events may increase.

Climate Change and National Security

The CNA Military Advisory Board, a group of retired three- and four-star military officers, stated in 2007^[18] and reaffirmed in 2014^[19] that climate change will impact U.S. national security interests by increasing the chances for conflict around the world and by threatening U.S. military facilities. These assessments were also noted in a report from the National Intelligence Council in 2008^[20]. As an example, a prolonged drought that hit the Mediterranean area near Syria from 2006 to 2011 is now felt to have been the precursor of factors that led to the civil war in Syria. As crops were destroyed, rural residents moved to the cities where tensions over lack of food and jobs ultimately triggered the political tensions that led to the Syrian civil war^[21]. The Department of Defense (DoD) conducted a survey in 2018^[22] to determine which DoD facilities have experienced negative effects from past extreme weather events in order to identify facilities that might be vulnerable to future extreme weather event. The impact of extreme weather events on military operations was demonstrated in October 2018 when Hurricane Michael, a Category 5 hurricane, devastated Tyndall AFB, damaging or destroying 95% of the base’s 1,300 structures and forcing the primary support missions to be relocated to other military installations. Tyndall AFB is home to two F-22 fighter squadrons, and it was estimated that about 10% of the U.S. F-22 inventory was damaged or destroyed by Hurricane Michael^[23]. In addition to the U.S.-based facilities, DoD operates a number of facilities around the world. Some of them involve unique facilities located at strategic locations. One example is Diego Garcia, an island in the British Indian Ocean Territory that is part of Chagos Archipelago. Diego Garcia is home to U.S. naval and air facilities that provide critical force projection activities in the Asia Pacific region. Analyses of the impact of climate change indicate that many Pacific atolls could be rendered uninhabitable by sea level rise and wave-driven flooding^[24]. U.S. based military facilities are already facing climate change impacts. In 2019, the U.S. Government Accountability Office (GAO) released a report to Congress detailing how DoD installation managers need to assess the risks from climate change to their facilities and to incorporate those risks into the master plans for the facilities (GAO, 2019)^[25].

Naval Station Norfolk in Virginia has been on the front line of climate change impacts, having dealt with high tide flooding for a number of years in which low-lying areas are flooded during high tides. This problem is not unique to the Norfolk area but is being felt in a number of areas along the east coast of the United States. The majority of the Norfolk area is under 10 feet (ft) above sea level and the worst-case scenario estimates that sea level rise by the end of the century could be on the order of 6 ft. Under these conditions, portions of the Norfolk area could experience flooding during any high tide. This flooding could result in land loss as the flooded area become part of the tidal zone. The high sea level could also expose previously unexposed areas to storm surge flooding^[26].

References

^ ^1.0 ^1.1 ^1.2 | Executive Order 13010. Critical Infrastructure Protection, 61 Fed. Reg., No. 138, July 17, 1996
^ ^2.0 ^2.1 ^2.2 | Presidential Policy Directive – Critical Infrastructure Security and Resilience. The White House Office of the Press Secretary, February 12, 2013.
^ President’s Commission on Critical Infrastructure Protection, 1997. Critical Foundations: Protecting America’s Infrastructures. Washington, DC Report pdf
^ ^4.0 ^4.1 U.S. Department of Homeland Security, Cybersecurity & Infrastructure Security Agency, | “Critical Infrastructure Sectors”.
^ Hummel, J. R. and Lewis, L.P., 2013. Analytical Support for Societal and Regional Resilience in Support of National Security. Phalanx, 46(3), pp 10-17, | JSTOR.
^ ^6.0 ^6.1 Hummel, J.R., 2016. The Last Word Resilience: Buzz Word or Critical Analytical Issue? Phalanx, 49(3), pp. 60–63, | JSTOR.
^ Hummel, J.R. and Schneider, J.L., 2016. The Human Landscape – The Functional Bridge between the Physical, Economic, and Social Elements of Community Resilience. Center for Infrastructure Protection and Homeland Security Report. Report pdf
^ U.S. Department of Homeland Security, Cybersecurity & Infrastructure Security Agency, | “Regional Resilience Assessment Program”.
^ Reich, K.D., Berg, N., Walton D.B., Schwartz, M., Sun, F., Huang, X., and Hall, A., 2018. “Climate Change in the Sierra Nevada: California’s Water Future. UCLA (University of California at Los Angeles) Center for Climate Science. Report pdf
^ Portante, E.C., Craig B.A., Talaber Malone l., Kavicky, J., Folga S.F., and Cedres S., 2011. EPfast: A model for simulating uncontrolled islanding in large power systems. Proceedings of the 2011 Winter Simulation Conference (WSC), pp. 1758-1769. | doi: 10.1109/WSC.2011.6147891
^ Portante, E. C., Kavicky J.A., Craig B.A., Talaber L.E., and Folga, S.M., 2017. Modeling Electric Power and Natural Gas System Interdependencies. Journal of Infrastructure Systems, 23(4), 04017035 | 10.1061/(ASCE)IS.1943-555X.0000395 Article pdf
^ U.S. Federal Government, 2021. | High-Tide Flooding. U.S. Climate Resilience Toolkit.
^ A 20-Foot Sea Wall? Miami Faces the Hard Choices of Climate Change, New York Times. | Article
^ Ministry of Environment of Denmark/Environmental Protection Agency. | Climate Change Adaptation, Climate Change Impact on Buildings and Constructions
^ Enker, R.A., and Morrison G.M., 2020. The potential contribution of building codes to climate change response policies for the built environment. Energy Efficiency, 13, pp. 789-807. | doi:10.1007/s12053-020-09871-7
^ Myers, A., 2020. Building Codes: A Powerful yet Underused Climate Policy that Could Save Billions. Forbes. | Article
^ Association of State Floodplain Managers. 2020. Flood Mapping for the Nation: A Cost Analysis for Completing and Maintaining the Nation’s NFIP Flood Map Inventory. Madison, WI. Report pdf
^ CNA Military Advisory Board, 2007. National Security and the Threat of Climate Change. CNA Corporation, Arlington, VA. Report pdf
^ CNA Military Advisory Board, 2014. National Security and the Accelerating Risks of Climate Change. CNA Corporation, Arlington, VA. Report pdf
^ National Intelligence Council, 2008. Global Trends 2025: A Transformed World. US Government Printing Office, Washington, DC Report pdf
^ Polk, W. R., 2013. Understanding Syria: From Pre-Civil War to Post-Assad. The Atlantic. | Article
^ Department of Defense, 2018. Climate-Related risk to DoD Infrastructure Initial Vulnerability Assessment Survey (SLVAS) Report. Office of the Undersecretary of Defense for Acquisition, Technology, and Logistics. Report pdf
^ Panda, A., 2018. Nearly 20 Percent of the US F-22 Inventory Was Damaged or Destroyed in Hurricane Michael. The Diplomat. | Article
^ Storlazzi, C.D., Gingerich, S.B., van Dongeren, A., Cheriton, O.M., Swarzenski, P. W., Quataert, E., Voss, C. I., Field, D. W., Annamalai, H., Piniak, G. A., and McCall, R., 2018. Most atolls will be uninhabitable by the mid-21st century because of sea-level rise exacerbating wave-driven flooding. Science Advances, 4(4). doi: 10.1126/sciadv.aap9741 Article pdf
^ United States Government Accountability Office, 2019. Climate Resilience, DOD Needs to Assess Risk and Provide Guidance on Use of Climate projections in Installation Master Plans and Facilities Designs, GAO-19-453. Report pdf
^ Kramer, D., 2016. Norfolk: A case study in sea-level rise. Physics Today, 69(5), pp. 22-25. | doi: 10.1063/PT.3.3163 Article pdf

@@ Line 1: / Line 1: @@
 I have installed SandboxLink extension that provides each user their own sandbox accessible through their personal menu bar (top right)
-Proteomics is the analysis of proteins present in a sample. Proteogenomics is the combined use of proteomics with genomics and transcriptomics to support protein identifications and analyses. As tools, proteomics and proteogenomics allow researchers and practitioners to understand the functional gene products and relevant microbial metabolisms in a system, which in turn can lead to informed decision-making in remediation situations.
+Infrastructure Resilience
+Infrastructure systems have been major contributors to the growth of the United States. [[wikipedia:Hoover Dam | Hoover Dam]] helped desert regions in the west to bloom. The [[wikipedia:Interstate Highway System  | Interstate Highway System]] spanned the states and opened up the country to growth and provided corridors for trade. As the country grew, new technologies developed, and infrastructures developed around them that are integral to our daily lives. These infrastructures can be vulnerable to a variety of disruptions, including human events, earthquakes, extreme weather events and [[Climate Change Primer | climate change]] impacts. The creation of the President’s Commission on Critical Infrastructure Protection (PCCIP) in 1996 <ref name="EO13010">[https://itlaw.fandom.com/wiki/Executive_Order_13010 | Executive Order 13010]. Critical Infrastructure Protection, 61 Fed. Reg., No. 138, July 17, 1996</ref> resulted in the development of a national plan to identify the critical infrastructure sectors and how to identify and reduce their vulnerabilities to natural or deliberate threats. Subsequent extreme natural disasters like Hurricanes [[wikipedia:Hurricane Katrina | Katrina]] and [[wikipedia:Hurricane Sandy | Sandy]] pointed out additional limitations in the resilience of infrastructure due to the interconnected nature of infrastructure systems. Infrastructure cannot be made totally immune to disruptive events, but it can be made more resilient by considering the dependencies and interdependencies within and between systems and by taking a system-of-systems view of the vulnerabilities and threats to them.
 <div style="float:right;margin:0 0 2em 2em;">__TOC__</div>
 '''Related Article(s):'''
-*[[Molecular Biological Tools - MBTs]]
+*Climate Change Impacts on Water Resources (Coming soon)
-*[[Metagenomics]]
+*[[Climate Change Primer]]
+*[[Downscaled High Resolution Datasets for Climate Change Projections]]
-'''Contributor(s):''' Dr. Kate H. Kucharzyk, Dr. Morgan V. Evans, Dr. Robert W. Murdoch, and Dr. Fadime Kara Murdoch
+'''Contributor(s):''' Dr. John Hummel and Dr. Frederic Petit
 '''Key Resources(s):'''
-*[[Media: Arsene-Ploetze2015.pdf | Proteomic tools to decipher microbial community structure and functioning]]<ref name="Arsène-Ploetze2015">Arsène-Ploetze, F., Bertin, P.N., and Carapito, C., 2015.  Proteomic tools to decipher microbial community structure and functioning. Environmental Science and Pollution Research, 22, pp. 13599-13612. [https://doi.org/10.1007/s11356-014-3898-0 DOI: 10.1007/s11356-014-3898-0] [[Media: Arsene-Ploetze2015.pdf | Article pdf]]</ref>.
+*[https://itlaw.fandom.com/wiki/Executive_Order_13010 | President’s Commission on Critical Infrastructure Protection (Executive Order 13010, Critical Infrastructure Protection, 61 Fed. Reg., No. 138, July 17, 1996).]<ref name="EO13010"/>
+*[https://obamawhitehouse.archives.gov/the-press-office/2013/02/12/presidential-policy-directive-critical-infrastructure-security-and-resil | Presidential Policy Directive (PPD-21) – Critical Infrastructure Security and Resilience]<ref name="PPD2013">[https://obamawhitehouse.archives.gov/the-press-office/2013/02/12/presidential-policy-directive-critical-infrastructure-security-and-resil | Presidential Policy Directive – Critical Infrastructure Security and Resilience]. The White House Office of the Press Secretary, February 12, 2013.</ref>
 ==Introduction==
-'''Proteomics''' is the comprehensive analysis of the proteins produced by single organisms or by microbial community (e.g., “meta”-proteomics). In this regard, proteomics represents the identification of functional gene products, providing information and insight into structural proteins and the molecular machinery produced and utilized by organisms to sustain the metabolic processes. While proteomics data can be analyzed in a de novo manner by comparing to global protein sequence databases, from a systems biology perspective, the ideal starting point for all considerations and the key enabling information is the (meta)genome of the sample under study.
+Infrastructure systems have always been an important aspect of the United States and signature elements of the country’s growth—examples such as [[wikipedia:Hoover Dam | Hoover Dam]], [[wikipedia:Grand Central Terminal | Grand Central Station]], and the [[wikipedia:Interstate Highway System  | Interstate Highway System]]. As the country grew and evolved, other infrastructure elements took on important aspects of everyday life, such as [[wikipedia: Global Positioning System | Global Positioning System (GPS)]] and the [[wikipedia:World Wide Web | World Wide Web (WWW)]]. Vulnerabilities in these systems were largely taken for granted until terrorist events such as the [https://www.britannica.com/event/Tokyo-subway-attack-of-1995 | Tokyo sarin gas subway attacks], the [[wikipedia: 1993 World Trade Center bombing  | 1993 terrorist bombing of the U.S. World Trade Center]], and [[Wikipedia: Oklahoma City bombing | the bombing of the Federal Building in Oklahoma City]] demonstrated the reality of threats from human elements. The subsequent creation of the President’s Commission on Critical Infrastructure Protection (PCCIP) in 1996[1] resulted in the development of a national plan to identify the critical infrastructure sectors and how to identify and reduce their vulnerabilities to natural or deliberate threats. Subsequent extreme natural disasters like Hurricanes [[wikipedia:Hurricane Katrina | Katrina]]  and [[wikipedia:Hurricane Sandy | Sandy]]  pointed out additional limitations in the resilience of infrastructure due to the interconnected nature of infrastructure systems.
+In its October 1997 report, the PCCIP<ref name="PCCIP1997">President’s Commission on Critical Infrastructure Protection, 1997. Critical Foundations: Protecting America’s Infrastructures. Washington, DC [[Media: PCCIP1997.pdf  | Report pdf]]</ref> defined an infrastructure as “a network of independent, mostly privately owned, man-made systems and processes that function collaboratively and synergistically to produce and distribute a continuous flow of essential goods and services.”
-'''Proteogenomics''' combines proteomics with (meta)genomics and/or transcriptomics to better analyze and identify proteins<ref name="Helbling2012">Helbling, D.E., Ackermann, M., Fenner, K., Kohler, H.P., and Johnson, D.R., 2012.  The activity level of a microbial community function can be predicted from its metatranscriptome. The ISME Journal, 6(4), pp. 902-904. [https://doi.org/10.1038/ismej.2011.158 doi: 10.1038/ismej.2011.158] [[Media: Helbling2012.pdf | Article pdf]]</ref>. For environmental applications, proteomics can be applied to soil, groundwater, sediment, or other environmental samples. Proteomics allows for functional characterization of a sample, enabling investigators to infer what relevant metabolisms may be active in a system (e.g., hydrocarbon degradation, reductive dechlorination). The large-scale characterization of any given proteome is accomplished by comparing measured peptide spectra with predicted protein or peptide data derived from (meta)genomic information. Thus, it is vital to have complete (meta)genome sequence information for the system being studied <ref name="Ansong2008">Ansong C., Purvine, S.O., Adkins, J.N., Lipton, M.S., and Smith, R.D., 2008.  Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Briefings in Functional Genomics, 7(1), pp. 50-62. [https://doi.org/10.1093/bfgp/eln010 doi: 10.1093/bfgp/eln010] [[Media: Ansong2008.pdf | Article pdf]]</ref>.This has led to the term proteogenomics to describe the strong linkage between genomics and proteomics. As implied, the quality of the proteomic measurements is inextricably linked to the quality of the genomic or metagenomic sequence data. Proteogenomics is an inherently more uncertain technique when compared to nucleic acid sequencing or qPCR technologies, yet it provides unparalleled global insights into biological structure and function.
+In the original PCCIP assessments considered eight critical infrastructures whose “…incapacity or destruction would have a debilitating impact on our defense and economic security.”<ref name="EO13010"/>The [[wikipedia:United States Department of Homeland Security | U.S. Department of Homeland Security]] has subsequently increased the number of critical infrastructures to the 16 sectors<ref name="CISAcis">U.S. Department of Homeland Security, Cybersecurity & Infrastructure Security Agency, [https://www.cisa.gov/critical-infrastructure-sectors  | “Critical Infrastructure Sectors”.]</ref>, listed in Table 1, and detailed a plan to strengthen and maintain, secure, functioning, and resilient critical infrastructure<ref name="PPD2013"/>.
+{| class="wikitable" style="float:left; text-align: center; margin-right: 20px;"
-DNA-based methods such as shotgun metagenomics and 16S rRNA amplicon sequencing provide important information and guidance for potential function of microbial communities. Like shotgun proteomics, both methods also provide <u>relative abundances of many features</u>. On the other hand, quantitative real time PCR (qPCR) provides <u>absolute quantities of few features</u> with greater sensitivity (at least 1 order of magnitude) than metagenomics approaches<ref name="Clark2018">Clark K., Taggart, D.M., Baldwin, B.R., Ritalahti, K.M., Murdoch, R.W., Hatt, J.K., and Löffler, F.E., 2018.  Normalized Quantitative PCR Measurements as Predictors for Ethene Formation at Sites Impacted with Chlorinated Ethenes. Environmental Science & Technology, 52(22), pp. 13410-13420. [https://doi.org/10.1021/acs.est.8b04373 doi: 10.1021/acs.est.8b04373]</ref>.As with all nucleic-acid-based (eg. DNA or RNA) methods, qPCR only informs potential activity, not actual activity. By detecting gene expression rather than simply genes, RNA-based methods such as metatranscriptomics provide insight into which genes are active<ref name="Czaplicki2016">Czaplicki, L.M. and Gunsch, C.K., 2016.  Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. Journal of Environmental Engineering, 142(10), pp. 1-13. [https://doi.org/10.1061/(ASCE)EE.1943-7870.0001141 doi: 10.1061/(ASCE)EE.1943-7870.0001141]</ref>, but at the cost of additional challenges posed by increased difficulty with RNA isolation and instability. Proteomics provides the actual catalytic activity by detection and quantification of proteins of interest.
+|+ Table 1. DHS Critical Infrastructure Sectors<ref name= "CISAcis"/>
+|-
-==Advantages==
+| Chemical Sector || Commercial Facilities Sector || Communications Sector || Critical Manufacturing Sector
+|-
-The two main advantages of the application of metaproteomics are:
+| Dams Sector || Defense Industrial Base Sector || Emergency Services Sector || Energy Sector
-#the ability to directly measure microbial enzymes (not just potential for enzyme synthesis), and
+|-
-#the ability to generate detailed information on hundreds of microorganisms and proteins in one assay.
+| Financial Services Sector || Food and Agriculture Sector || Government Facilities Sector
+|| Healthcare and Public Health Sector
-The process of obtaining the information does not require culturing of microorganisms or performance of any molecular assays. To measure features that are directly correlated to microbial activity, metaproteomics can be used to identify and relatively quantify proteins<ref name="Hettich2013">Hettich, R.L., Pan, C., Chourey, K., and Giannone, R.J., 2013.  Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities. Analytical Chemistry, 85(9), pp. 4203-4214. [https://doi.org/10.1021/ac303053e doi: 10.1021/ac303053e] [[Media: Hettich2013.pdf | Article pdf]]</ref><ref name="Keller2009">Keller, M. and Hettich, R.L., 2009.  Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level. Microbiology and Molecular Biology Reviews, 73(1), pp. 62-70. [https://doi.org/10.1128/MMBR.00028-08 doi: 10.1128/MMBR.00028-08] [[Media: Keller2009.pdf | Article pdf]]</ref><ref name="Schneider2010">Schneider, T. and Riedel, K., 2010.  Environmental proteomics: Analysis of structure and function of microbial communities. Proteomics, 10(4), pp. 785-98. [https://doi.org/10.1002/pmic.200900450 doi: 10.1002/pmic.200900450]</ref>. These proteins provide important information about community activities, such as which microbial organisms are most active and what proteins are present (including proteins catalyzing reactions involved in bioremediation)<ref name="Arsène-Ploetze2015"/><ref name="Johnson2015">Johnson, D.R., Helbling, D.E., Men, Y., and Fenner, K., 2015.  Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products? Environmental Science: Water Research & Technology, 1, pp. 272-278. [https://doi.org/10.1039/C5EW00016E doi: 10.1039/C5EW00016E] [[Media: Johnson2015.pdf | Article pdf]]</ref>.
+|-
+| Information Technology Sector || Nuclear Reactors, Materials, and Waster Sector || Transportation Systems Sector || Water and Wastewater Systems Sector
-==Limitations==
+|}
-Limitations associated with this technology are related to composition of the proteome to be analyzed, mainly concerning protein expression levels and limitations of the analytical equipment. Limitations are summarized as follows:
-*'''''Sample preparation''''' - the vast diversity of protein molecular sizes, charge states, conformational states, post-translational modifications etc., make it unfeasible to use a single sample preparation protocol that captures the entire proteome for a given microbial community. Thus, use of a protocol that allows isolation of protein content from a biological sample and eliminates non-specific contaminants (e.g., keratins, fatty acids, plastic polymers, nucleic acids and salt clusters) should be developed and tested prior to sample analysis<ref name="Chourey2010">Chourey, K., Jansson, J., VerBerkmoes, N., Shah, M., Chavarria, K.L., Tom, L.M., Brodie, E.L., and Hettich, R.L., 2010. Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics. Journal of Proteome Research, 9(12), pp. 6615-6622. [https://doi.org/10.1021/pr100787q doi: 10.1021/pr100787q]</ref><ref name="Qian2017">Qian, C. and Hettich, R.L., 2017. Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements. Journal of Proteome Research, 16(7), pp. 2537-2546. [https://doi.org/10.1021/acs.jproteome.7b00103 doi: 10.1021/acs.jproteome.7b00103]</ref>
-*'''''Proteins are not expressed in equal amounts''''' and there may be large differences in protein levels in proteomes in samples collected from the same site. A proteomic analysis must employ proper technologies for the detection of all proteins or proteins of interest. In a small sample volume that is usually used in a proteomic analysis, a large percentage of the expressed proteins occur at low abundance levels and cannot be readily detected in the analysis due to high-abundance proteins effectively monopolizing the “sampling effort”. These rare proteins may be of particular interest in environmental samples because proteins associated with contaminant degradation are often a very small fraction of the total expressed proteins. The practical protein detection limit for Liquid Chromatography-Tandem Mass Spectrometry-Time-of-Flight (LC-MS/MS-TOF) analysis lies in the femtomol (10-15 [fmol]) range. However, due to losses during protein extraction and sample clean up and dilution, the sufficient protein concentration for detection is more realistically in the low picomol (10-12 [pmol]) to high fmol range. This limitation can be addressed by collecting a greater volume of groundwater for analysis; however, this may not be possible at all sampling locations.
-*'''''Detection of proteins at low concentrations''''' (low abundance) may be limited by other proteins present in high concentrations (high abundance). The successful search for low-abundance proteins may be mitigated by use of chromatography for separation of high-abundance proteins and precipitation for elution of proteins of interest prior to analytical detection. However, complete removal of high-abundance proteins may not be recommended because they may trap the low-abundance proteins along with their associated fragments and peptides, which will be lost and not detected. An alternative approach relies on 2-dimensional chromatography coupled with tandem mass spectrometry.
-*'''''Success in the identification of proteins may vary with the sensitivity of the mass spectrometer.''''' Proper analytic equipment can be costly. Of the most sensitive mass spectrometers, electrospray ionization and laser desorption ionization-based instruments can detect peptides with low detection limits.
-*'''''Not all biological variation can be accounted for.''''' Despite great improvements in the costs of genomic sequencing and gene prediction, there remain some aspects of biology that cannot be accurately or consistently predicted.  For example, the presence and variety of post-translational modifications remains problematic and, if present and not accounted for during analysis, such modified proteins will not be efficiently detected.
-*'''''Selection of the appropriate analytical method determines the success of the study.''''' Depending on the study goals and context, some methodological adjustments should be considered, including pre-enrichment of key low-abundance proteins, adjustment of protein extraction methods or tuning of the analytical equipment.  A single methodological approach is not suitable for all purposes.
-==Assessing Changes in Microbial Community Composition and Dynamics – Common Applications==
-Environmental metaproteomics is used in applied in research areas such as:
-#'''Bioenergy''' – characterization of feedstock conversion into energy e.g., cellulose or lignin degradation to biofuels<ref name="Ndimba2013"> Ndimba, B.K., Ndimba, R.J., Johnson, T.S., Waditee-Sirisattha, R., Baba, M., Sirisattha, S., Shiraiwa, Y., Agrawal, G.K., and Rakwal, R, 2013. Biofuels as a sustainable energy source: an update of the applications of proteomics in bioenergy crops and algae Journal of Proteomics, 20(93), pp. 234-244. [https://doi.org/10.1016/j.jprot.2013.05.041 doi: 10.1016/j.jprot.2013.05.041]</ref>
-#'''Human health''' – characterization of microbial involvement in impact/control of disease vs health in human bodies<ref name="Brooks2015">Brooks, B., Mueller, R.S., Young, J.C., Morowitz, M.J., Hettich, R.L., and Banfield, J.F., 2015. Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Frontiers in Microbiology, 1(6) pp. 654. [https://doi.org/10.3389/fmicb.2015.00654 doi: 10.3389/fmicb.2015.00654] [[Media: Brooks2015.pdf | Article pdf]]</ref><ref name="Carr2014">Carr, S.A., Abbatiello, S.E., Ackermann, B.L., Borchers, C., Domon, B., Deutsch, E.W.,, Grant, R.P., Hoofnagle, A.N., Hüttenhain, R., Koomen, J.M., Liebler, D.C., Liu, T., MacLean, B., Mani, D.R., Mansfield, E., Neubert, H., Paulovich, A.G., Reiter, L., Vitek, O., Aebersold, R., Anderson, L., Bethem, R., Blonder, J., Boja, E., Botelho, J., Boyne, M., Bradshaw, R.A., Burlingame, A.L., Chan, D., Keshishian, H., Kuhn, E., Kinsinger, C., Lee, J.S., Lee, S.W., Moritz, R., Oses-Prieto, J., Rifai, N., Ritchie, J., Rodriguez, H., Srinivas, P.R., Townsend, R.R., Van Eyk, J., Whiteley, G., Wiita, A., and Weintraub, S., 2014.  Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Molecular and Cellular Proteomics, 13(3), pp. 907-917. [https://doi.org/10.1074/mcp.M113.036095 doi: 10.1074/mcp.M113.036095] [[Media: Carr2014.pdf | Article pdf]]</ref>
-#'''Bioremediation''' – characterization of degradation of contaminants in sediments, soils, and groundwater by microorganisms<ref name="Bansal2009">Bansal, R., Deobald, L.A., Crawford, R.L., Paszczynski, A.J., 2009. Proteomic detection of proteins involved in perchlorate and chlorate metabolism. Biodegradation, 20(5), pp.603-620. [https://doi.org/10.1007/s10532-009-9248-0 doi: 10.1007/s10532-009-9248-0]</ref><ref name="Fuller2020">Fuller, M. E., van Groos, P. G. K., Jarrett, M., Kucharzyk, K. H., Minard-Smith, A., Heraty, L. J., and Sturchio, N. C., 2020. Application of a multiple lines of evidence approach to document natural attenuation of hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX) in groundwater. Chemosphere. 250, pp. 126210. [https://doi.org/10.1016/j.chemosphere.2020.126210 doi: 10.1016/j.chemosphere.2020.126210]</ref><ref name="Kucharzyk2020">Kucharzyk, K. H., Meisel, J. E., Kara-Murdoch, F., Murdoch, R. W., Higgins, S. A., Vainberg, S., and Löffler, F. E., 2020. Metagenome-guided proteomic quantification of reductive dehalogenases in the Dehalococcoides mccartyi-containing consortium SDC-9. Journal of Proteome Research, 9(4), pp. 1812-1823. [https://doi.org/10.1021/acs.jproteome.0c00072 doi: 10.1021/acs.jproteome.0c00072]</ref><ref name="Kucharzyk2018">Kucharzyk, K.H., Rectanus, H.V., Bartling, C., Chang, P., Rosansky. S., Neil, K., and Chaudhry, T., 2018. Assessment of post remediation performance of a biobarrier oxygen injection system at a methyl tert-butyl ether (MTBE)-contaminated site, Marine Corps Base Camp Pendleton San Diego, California. Environmental Security Technology Certification Program, Alexandria, VA. [https://www.serdp-estcp.org/Program-Areas/Environmental-Restoration/Contaminated-Groundwater/Emerging-Issues/ER-201588 ER-201588]. [[Media: Kucharzyk2018.pdf | Report pdf]]</ref><ref name="Michalsen2020a"> Michalsen, M. M., Kucharzyk, K. H., Bartling, C., Meisel, J. E., Hatzinger, P., Wilson, J., Istok, J., and Loffler, F, 2020. Validation of advanced molecular biological tools to monitor chlorinated solvent bioremediation and estimate cVOC degradation rates. Environmental Security Technology Certification Program, Alexandria, VA. [https://www.serdp-estcp.org/Program-Areas/Environmental-Restoration/Contaminated-Groundwater/Monitoring/ER-201726 ER-201726]. [[Media: Michalsen2020a.pdf | Report pdf]]</ref><ref name="Michalsen2020b">Michalsen, M. M., King, A. S., Istok, J. D., Crocker, F. H., Fuller, M. E., Kucharzyk, K. H., and Gander, M. J., 2020. Spatially distinct redox conditions and degradation rates following field-scale bioaugmentation for RDX-contaminated groundwater remediation. Journal of Hazardous Materials, 387, 121529. [https://doi.org/10.1016/j.jhazmat.2019.121529 doi: 10.1016/j.jhazmat.2019.121529]</ref>
-#'''Carbon cycling''' – characterization of a role of microorganisms in carbon flow in an ecosystem.
-#'''Agricultural metabolism''' – characterization of microbial interactions with plants<ref name="Tan2017">Tan, B.C, Lim, Y.S., and Lau, S.E., 2017. Proteomics in commercial crops: An overview. Journal of Proteomics, 169, pp. 176-188. [https://doi.org/10.1016/j.jprot.2017.05.018 doi:10.1016/j.jprot.2017.05.018]</ref>
-==Targeted vs Shotgun Proteomics==
-Proteomics techniques can be broadly classified into two categories:
-#'''Untargeted or shotgun proteomics,''' aimed at comprehensively identifying and characterizing relative abundances of the totality of proteins in a sample.
-#'''Targeted proteomics,''' focused on identifying and absolutely quantifying one protein.
-''Shotgun proteomics'' refers to digestion of the total proteome and subjecting all resulting peptides to separation, mass-spectroscopy, and identification based on a reference protein database (ideally derived from in silico translation of the (meta)genome).
-Notably, shotgun proteomics generates only an approximated ''relative abundance'' for identified proteins. On the other hand, ''targeted proteomics'' allows for ''absolute quantification'' of a single protein within a complex sample, which in turn allows for analysis of any potential correlation to a degradation rate. Prediction of degradation rates based on enzyme concentration is a crucial step towards better understanding of the molecular events underlying metabolic processes. By measuring key biomarkers, proteomic studies present an opportunity to gain profound into ecosystem health, degradation of recalcitrant compounds, and bioremediation. Quantitative proteomics can also guide regulatory agencies to make better site management decisions, thereby minimizing radiation costs and chemically induced adverse effects.
-''Targeted Proteomics'' targets peptides of a specific protein in a complex mixture of other peptides and determines their presence (if they are above the detection limit) and quantity in one sample or across multiple samples (Figure 1)<ref name="Zhang2013"/>. This analysis usually utilizes a triple quadrupole mass spectrometer (QqQ-MS), an instrument which has traditionally been used to quantify small molecules. Only recently has it been utilized for peptides. Parallel Reaction Monitoring (PRM) and data independent analysis are alternative options that can be far cheaper than developing a method for a QqQ-MS.
-Each targeted proteomics assay must be carefully developed.  The assay specifically “targets” peptides enzymatically digested from the target protein, necessitating careful selection of peptides and method. Development of a new assay also requires preliminary analyses to ensure the method is robust. Once a method is developed and verified, it can be applied to an unlimited number of samples.
-[[File: ProteomicsFig1.png|thumb|650px|left | Figure 1. Targeted proteomic workflow<ref name="Zhang2013">Zhang, Y., Fonslow, B.R, Shan, B., Baek, M.C., and Yates, J.R. III., 2013. Protein analysis by shotgun/bottom-up proteomics. Chemical Reviews, 113(4), pp 2343-94. [https://doi.org/10.1021/cr3003533 doi:10.1021/cr3003533]</ref>]]
-'''Bottom-Up Proteomics'''
-''Bottom-up proteomics'' (Figure 2) begins by analyzing of mass spectrum fragmentation patterns of peptides, which are generated after proteolytic digestion of proteins<ref name="Zhang2013"/>. Spectra are identified by comparison to a database of reference proteins which are digested ''in silico''.  The creation or selection of this database is one of the most crucial steps in the analysis; ideally, the database consists of proteins encoded by the genome or metagenome of the organisms present in the sample under study.  While the rapidly decreasing cost of DNA sequencing and emergence of standard assembly and annotation pipelines make obtaining (meta)genomes increasingly cost-effective, it remains an option to use global reference protein databases, such as UniProt (see [https://unipept.ugent.be/ unipept.ugent.be]). However, making peptide-spectrum matches (a.k.a. PSMs) is a statistically uncertain process, as the alignment of mass fragmentation pattern of the peptide to the database is seldom perfect. Several algorithms have been developed to tackle this problem (Comet, X! Tandem, MyriMatch, OMSSA, Tide, etc.). PSM matching must carefully consider factors such as what enzyme was used to digest the proteome and how specific and complete digestion was.  Additionally, peptide modifications, chemical modification of amino acids which lead to differences in mass and fragmentation pattern, are a wide-spread complication that must be accounted for. Some are intentional, for example carbiodomethylation of cysteine residues, which is applied to protect sulfur residues from becoming oxidized. Other modifications occur unintentionally during sample preparation, such as oxidation of methionine residues.
-PSMs are inherently statistically uncertain. A given shotgun proteome may involve hundreds of thousands of PSMs, which leads to the danger of false discovery. Traditionally, a formal false discovery rate (FDR) is applied; this is an adjustment of the threshold for statistical significance based on the number of tests performed, i.e. the more PSMs, the more stringent the testing must be.  The risk is greatly exacerbated by using reference protein databases that do not reflect the sample. Use of the (meta)genome correlating to the sample under study makes this danger of false identification much less risky when compared to traditional approaches.  It is generally acknowledged that rigid adherence to FDR thresholds is a serious impediment to thorough PSM assignment<ref name="Heyer2017"> Heyer, R., Schallert, K., Zoun, R., Becher, B., Saake, G., and Benndorf, D., 2017. Challenges and perspectives of metaproteomic data analysis. Journal of Biotechnology, 261, pp. 24–36. [https://doi.org/10.1016/j.jbiotec.2017.06.1201 doi: 10.1016/j.jbiotec.2017.06.1201] [[Media: Heyer2017.pdf | Article pdf]]</ref> but is generally advisable when analyzing a proteome without any pre-existing knowledge on sample composition.
-Following PSM assignment, whether by use of a global reference protein database with application of FDR or by comparison to a sample-specific reference (meta)genome, peptides are matched to proteins. This step acts as a second statistical filtering step and can employ several criteria such as whether the peptide identified is unique in the database, how many peptides match a given protein, and what score was assigned to the PSMs by the PSM algorithm. A metaproteome protein identification might, for example, require three or six matching PSMs.
-Software for making PSMs and protein identifications can be obtained as individual packages, but several convenient open-source packages are available, some of which include several PSM algorithms (SearchGUI) and even pipelines for making further sample comparisons (PatternLab for Proteomics) or functional interpretations (MetaProteomeAnalyzer). Many of these features are also available in commercial software packages, such as Progenesis QI (Waters) and ProteinPilot (SCIEX).  Global bottom-up shotgun proteomics data analysis remains an actively evolving discipline.
-[[File: ProteomicsFig2.png|thumb|650px|Figure 2. Bottom- up shotgun proteomics]]
-==Selecting Sample Locations==
+==Analyzing Infrastructure Vulnerabilities==
-Below are a few guidelines for selecting sampling locations to aid in drawing conclusions from metaproteomics data.
+Early studies on critical infrastructure vulnerabilities focused on physical threats, and the strategies to mitigate those vulnerabilities focused primarily on providing physical protection with “guns, gates, and guards.” As the array of potential threats expanded to include factors such as cyber, chemical, biological, radiological, and nuclear attacks, the vulnerability assessment methodologies evolved and expanded to include the consideration of the dependencies and interdependencies within and between infrastructure assets. The myriad of interdependencies in infrastructure systems can result in a disruption in a component of one infrastructure cascading through a network of dependencies and resulting in the taking down of a larger infrastructure, such as [[wikipedia: Northeast blackout of 2003 | the northeast blackout in August 2003]]. The cause of the blackout was attributed to a software bug in a control room alarm system in Ohio, which made operators unaware of a need to redistribute the electrical load after transmission lines drooped into foliage. Events like this demonstrate that protecting infrastructure from all hazards is impossible. Instead, one must understand the dependencies and interdependencies in infrastructures, and how they differ, so they can be designed to be resilient to disruptions when they inevitably occur.
+==System View of Infrastructure Resilience==
+Numerous definitions can be found for resilience that depends upon the perspective of the problem being addressed, such as material physics, ecosystems, engineering, and psychological well-being, to name just a few. For the study of infrastructure resilience and how it contributes to regional and community resilience, the following definition is used:<ref name="Hummel2013"> Hummel, J. R. and Lewis, L.P., 2013. Analytical Support for Societal and Regional Resilience in Support of National Security. Phalanx, 46(3), pp 10-17, [https://www.jstor.org/stable/24911162 | JSTOR]. </ref>
+''“Resilience is the ability of an entity—e.g., asset, organization, community, region—to anticipate, resist, absorb, respond to, adapt to, and recover from a disturbance from either natural or man-made events.” ''
+Analyses of the resilience of infrastructure should be taken from an integrated systems perspective<ref name="PPD2013"/>of the infrastructure and the community and region being supported. Figure 1 provides a schematic representation of the systems that support resilience<ref name="Hummel2016">Hummel, J.R., 2016.  The Last Word Resilience: Buzz Word or Critical Analytical Issue? Phalanx, 49(3), pp. 60–63, [https://www.jstor.org/stable/24910216 | JSTOR]. </ref>. The high-level systems shown in Figure 1 can be expanded to finer scale system as needed. The Governing System in Figure 1 is deliberately '''not''' called a Government System because the intent is to be able to represent governing systems at multiple levels of population granularity—groups, villages, tribes, communities, countries, etc. These groups have different ways in which they organize themselves, and the organizing details may or may not be formalized and may or may not be codified. Organized criminal networks, for example, have strong governing and enforcement mechanisms that members clearly understand, but these mechanisms are not codified in any written form.
+[[File: InfrastrFig1.png | thumb | 650px | Figure 1. Schematic Representation of the Interconnected Systems that Contribute to Resilience<ref name="Hummel2016"/>]].
+The Human Landscape System is often the most overlooked system in resilience assessments of communities and infrastructure, yet it is probably the most important. It represents the actors who are the decision makers, the implementers of plans and activities, and the groups in the general population that will be impacted by the plans and the external forces that can disrupt the community <ref name="CIP2016"> Hummel, J.R. and Schneider, J.L., 2016. The Human Landscape – The Functional Bridge between the Physical, Economic, and Social Elements of Community Resilience. Center for Infrastructure Protection and Homeland Security Report. [[Media:Hummel2016.pdf  | Report pdf]]</ref>. The Human Landscape is also the system where the measures of effectiveness of resilience activities are assessed. For example, during the COVID-19 pandemic, the efforts to reduce the spread of the virus depended upon the collective behaviors of people to shelter in place, practice social distancing, and wear facial masks in public. The basic measures of the effectiveness of the efforts to control the spread of the virus were the number of cases of infection hospital strain and lives lost.
+The Natural Environment system in Figure 1 consists of the terrain, air, ocean, and space environments where the infrastructure and community systems are located and operated. The natural environment can be a driver for where an infrastructure is located and will be the source of the natural forces to which it must respond.
+==Assessing and Mitigating Climate Impacts on Infrastructure==
+The DHS Regional Resiliency Assessment Program<ref name="CISArrap">U.S. Department of Homeland Security, Cybersecurity & Infrastructure Security Agency, [https://www.cisa.gov/regional-resiliency-assessment-program | “Regional Resilience Assessment Program”.]</ref> (RRAP) has conducted analyses of the vulnerabilities of infrastructure to a variety of disruptions, including earthquakes, climate impacts, and extreme weather events. These assessments utilize a variety of models and tools in the resiliency assessments, depending upon the context of the study.
+For example, an RRAP study done in the Casco Bay Region of Maine examined the disruptions to infrastructure from projections of coastal flooding triggered by sea level rise and heavy precipitation. In that study, inundation models driven by sea level and precipitation projections generated areas of flooding in the Casco Bay area.  Overlays of the existing infrastructure elements were then used to identify the locations of electric power assets that could be disrupted by the projected flooding.
+[[File: InfrastrFig2.png | thumb | 650px | Figure 2. Potential Impacts from Flooding of Electric Assets in the Casco Bay Region of Maine]].
-*'''Background:'''Samples from non-impacted background area can be compared with results from impacted areas to examine the impact of contamination on composition of microbial proteomes that reflect the ongoing metabolical processes.
+In California, an integrated water system was developed in the second half of the 20th century, the [[wikipedia:California State Water Project | California State Water Project (SWP)]], to collect and store water from the northern  portion of the state and deliver it to communities in the central and southern regions of the state. The SWP was developed based on the climatic conditions of the time and the locations of the dams, reservoirs, canals, and aqueduct were selected based on the historic precipitation patterns of the mid-20th century. The effectiveness of the SWP to continue to collect and deliver water under projected climate conditions has been studied by combining high-resolution climate projections and overlaying the results against the SWP elements. The projections of 21st mid-century and end-of-century climate conditions<ref name="Reich2018"> Reich, K.D., Berg, N., Walton D.B., Schwartz, M., Sun, F., Huang, X., and Hall, A., 2018. “Climate Change in the Sierra Nevada: California’s Water Future. UCLA (University of California at Los Angeles) Center for Climate Science. [[Media: Reich2018.pdf | Report pdf]]</ref> indicate changes in the timing of precipitation in California and how it falls (rain or snow). The changes in timing indicate that more of the precipitation may fall earlier in the year and in the form of rain, when the existing SWP is least able to collect and store the water because the reservoirs are required to have lower storage levels for flood control purposes. This could result in a requirement for significant investment in new reservoirs at new locations better able to capture and store the precipitation.
-*'''Baseline:'''These samples are collected and analyzed prior to treatment as a baseline for evaluating changes in the microbial metabolism in response to the remediation.
+The [[wikipedia: 2021 Texas power crisis | 2021 power crisis in Texas]] pointed to the importance of the role of the natural environment in energy system planning. Energy grids are a combination of numerous nodes and links and disruptions in any component can potentially cascade through the system. Energy planning in Texas has traditionally considered only historical environmental factors when planning for future energy needs in terms of estimating future energy loads and did not include the consideration of extreme weather events—hot or cold—in planning. The extreme cold weather event resulted in two significant issues for the energy planners. First, many natural gas wells and pipelines were not winterized and failed or shutdown, depriving the electrical generating facilities of the natural gas to power the facilities. Second, it takes far more energy to warm households up from near freezing temperatures than it does to cool them down from a summer heat wave, increasing the demand load on the electric grid. Tools such EPfAST <ref name="Portante2011"> Portante, E.C., Craig B.A., Talaber Malone l., Kavicky, J., Folga S.F., and Cedres S., 2011. EPfast: A model for simulating uncontrolled islanding in large power systems. Proceedings of the 2011 Winter Simulation Conference (WSC), pp. 1758-1769.  [https://ieeexplore.ieee.org/document/6147891 | doi: 10.1109/WSC.2011.6147891]</ref> and NGFast <ref name="Portante2017"> Portante, E. C., Kavicky J.A., Craig B.A., Talaber L.E., and Folga, S.M., 2017. Modeling Electric Power and Natural Gas System Interdependencies. Journal of Infrastructure Systems, 23(4), 04017035 [https://ascelibrary.org/doi/full/10.1061/%28ASCE%29IS.1943-555X.0000395 | 10.1061/(ASCE)IS.1943-555X.0000395] [[Media:Portante2017.pdf | Article pdf]] </ref> can be used to study integrated electric power and natural gas system interdependencies.
-*'''Plume:'''These samples are collected from distinct zones within the source area or contaminant plume to reflect variations in contaminant concentrations, geochemical conditions, and other site-specific criteria.
+In many coastal areas of the country, transportation systems are having to contend with disruptions from storm surges and high-tide flooding <ref name="Toolkit2021"> U.S. Federal Government, 2021. [https://toolkit.climate.gov/topics/coastal-flood-risk/shallow-coastal-flooding-nuisance-flooding | High-Tide Flooding. U.S. Climate Resilience Toolkit.]</ref>, which occurs when local sea level rises above a given threshold in the absence of storm surge or riverine flooding. This type of flooding is occurring on a regular basis along portions of the U.S. east coast and portions of the south Florida coast and is expected to worsen as sea levels rise.  In south Florida, the problem is made worse because much of the area sits on porous limestone which allows the ocean to seep up from the ground – meaning that residents face the climate impacts from storm surges from the sea and rising ground waters from below.  The intrusion of ocean water into the aquifers can impact the availability of potable water from aquifers as well as reduce the ability of the ground to absorb runoff, so floodwaters will remain longer<ref name="Mazzei2021"> A 20-Foot Sea Wall? Miami Faces the Hard Choices of Climate Change, New York Times. [https://www.nytimes.com/2021/06/02/us/miami-fl-seawall-hurricanes.html | Article]</ref>.
+In developing mitigation strategies for [[Climate Change Primer | climate change]] impacts, infrastructure developers look at ways to protect or retrofit existing systems and how to develop new systems that take into account potential [[Climate Change Primer | climate change]] impacts.  As an example, the predictions of higher summer temperatures from [[Climate Change Primer | climate change]] can mean that the operating ranges for heat, ventilation, and air-conditioning systems may change and require new designs for such systems. These changes may also result in changes in building codes in different areas<ref name="CCA">Ministry of Environment of Denmark/Environmental Protection Agency. [https://en.klimatilpasning.dk/sectors/buildings/climate-change-impact-on-buildings/ | Climate Change Adaptation, Climate Change Impact on Buildings and Constructions]</ref><ref name="Enker2020">Enker, R.A., and Morrison G.M., 2020. The potential contribution of building codes to climate change response policies for the built environment. Energy Efficiency, 13, pp. 789-807. [https://doi.org/10.1007/s12053-020-09871-7 | doi:10.1007/s12053-020-09871-7]</ref><ref name="Myers2020"> Myers, A., 2020.  Building Codes: A Powerful yet Underused Climate Policy that Could Save Billions. Forbes. [https://www.forbes.com/sites/energyinnovation/2020/12/02/a-powerful-yet-underused-climate-tool-building-codes/?sh=363a2c1d978c | Article]</ref>.
+[[wikipedia:Hurricane Sandy | Hurricane Sandy]]  provided a number of critical lessons for infrastructure developers. One major lesson learned was that basements in building should not be used for any back-up or critical systems – power, computers, or telecommunications. Many of the hospitals in New York City lost power because their reserve generators were in basements which flooded. Another one was that waterproof doors should be installed at entrances to subway stations.
+One of the major challenges facing developers is what environmental conditions should they build for. The majority of building codes are based on analyses based on historical environmental conditions and are not representative of current conditions.
+The Federal Emergency Management Agency (FEMA) has the responsibility to update floodplain maps every five years. These maps are used to identify flood prone areas and locations where flood insurance is required. However, it was estimated in early 2020 that only one-third of nation’s 3.5 million miles of streams and 46% of shoreline have had maps generated<ref name="ASFPM2020"> Association of State Floodplain Managers. 2020. Flood Mapping for the Nation: A Cost Analysis for Completing and Maintaining the Nation’s NFIP Flood Map Inventory. Madison, WI. [[Media:ASFPM2020.pdf | Report pdf]]</ref>. In addition, climate projections are pointing towards more frequent severe precipitation events and in urban areas where developments are changing runoff patterns, the chances for flooding events may increase.
+==Climate Change and National Security==
+The CNA Military Advisory Board, a group of retired three- and four-star military officers, stated in 2007<ref name="CNA2007"> CNA Military Advisory Board, 2007. National Security and the Threat of Climate Change. CNA Corporation, Arlington, VA. [[Media:CNA2007.pdf | Report pdf]] </ref> and reaffirmed in 2014<ref name="CNA2014">CNA Military Advisory Board, 2014. National Security and the Accelerating Risks of Climate Change. CNA Corporation, Arlington, VA. [[Media:CNA2014.pdf | Report pdf]]</ref> that [[Climate Change Primer | climate change]] will impact U.S. national security interests by increasing the chances for conflict around the world and by threatening U.S. military facilities. These assessments were also noted in a report from the National Intelligence Council in 2008<ref name="NIC2008"> National Intelligence Council, 2008.  Global Trends 2025: A Transformed World. US Government Printing Office, Washington, DC [[Media: GlobalTrends2008.pdf | Report pdf]]</ref>.  As an example, a prolonged drought that hit the Mediterranean area near Syria from 2006 to 2011 is now felt to have been the precursor of factors that led to the civil war in Syria. As crops were destroyed, rural residents moved to the cities where tensions over lack of food and jobs ultimately triggered the political tensions that led to the Syrian civil war<ref name="Polk2013"> Polk, W. R., 2013.  Understanding Syria: From Pre-Civil War to Post-Assad. The Atlantic.  [https://www.theatlantic.com/international/archive/2013/12/understanding-syria-from-pre-civil-war-to-post-assad/281989/ | Article]</ref>.
+The Department of Defense (DoD) conducted a survey in 2018<ref name="SLVAS2018"> Department of Defense, 2018. Climate-Related risk to DoD Infrastructure Initial Vulnerability Assessment Survey (SLVAS) Report. Office of the Undersecretary of Defense for Acquisition, Technology, and Logistics. [[Media: SLVAS2018.pdf | Report pdf]]</ref> to determine which DoD facilities have experienced negative effects from past extreme weather events in order to identify facilities that might be vulnerable to future extreme weather event. The impact of extreme weather events on military operations was demonstrated in October 2018 when Hurricane Michael, a Category 5 hurricane, devastated Tyndall AFB, damaging or destroying 95% of the base’s 1,300 structures and forcing the primary support missions to be relocated to other military installations. Tyndall AFB is home to two F-22 fighter squadrons, and it was estimated that about 10% of the U.S. F-22 inventory was damaged or destroyed by Hurricane Michael<ref name="Panda2018"> Panda, A., 2018. Nearly 20 Percent of the US F-22 Inventory Was Damaged or Destroyed in Hurricane Michael. The Diplomat. [https://thediplomat.com/2018/10/nearly-10-percent-of-the-us-f-22-inventory-was-damaged-or-destroyed-in-hurricane-michael/ | Article]</ref>. In addition to the U.S.-based facilities, DoD operates a number of facilities around the world. Some of them involve unique facilities located at strategic locations. One example is [[Wikipedia:Diego Garcia | Diego Garcia]], an island in the British Indian Ocean Territory that is part of Chagos Archipelago. Diego Garcia is home to U.S. naval and air facilities that provide critical force projection activities in the Asia Pacific region.  Analyses of the impact of [[Climate Change Primer | climate change]] indicate that many Pacific atolls could be rendered uninhabitable by sea level rise and wave-driven flooding<ref name="Storlazzi2018"> Storlazzi, C.D., Gingerich, S.B., van Dongeren, A., Cheriton, O.M., Swarzenski, P. W., Quataert, E., Voss, C. I., Field, D. W., Annamalai, H., Piniak, G. A., and McCall, R., 2018. Most atolls will be uninhabitable by the mid-21st century because of sea-level rise exacerbating wave-driven flooding. Science Advances, 4(4). [https://www.science.org/doi/10.1126/sciadv.aap9741| doi: 10.1126/sciadv.aap9741] [[Media: Storlazzi2018.pdf | Article pdf]]</ref>.
+U.S. based military facilities are already facing [[Climate Change Primer | climate change]] impacts. In 2019, the U.S. Government Accountability Office (GAO) released a report to Congress detailing how DoD installation managers need to assess the risks from climate change to their facilities and to incorporate those risks into the master plans for the facilities (GAO, 2019)<ref name="gao2019"> United States Government Accountability Office, 2019. Climate Resilience, DOD Needs to Assess Risk and Provide Guidance on Use of Climate projections in Installation Master Plans and Facilities Designs, GAO-19-453. [[Media: gao2019.pdf | Report pdf]]</ref>.
-==Sample Collection, Preservation, and Shipping==
+Naval Station Norfolk in Virginia has been on the front line of [[Climate Change Primer | climate change]] impacts, having dealt with high tide flooding for a number of years in which low-lying areas are flooded during high tides. This problem is not unique to the Norfolk area but is being felt in a number of areas along the east coast of the United States. The majority of the Norfolk area is under 10 feet (ft) above sea level and the worst-case scenario estimates that sea level rise by the end of the century could be on the order of 6 ft. Under these conditions, portions of the Norfolk area could experience flooding during any high tide. This flooding could result in land loss as the flooded area become part of the tidal zone. The high sea level could also expose previously unexposed areas to storm surge flooding<ref name="kramer2016"> Kramer, D., 2016. Norfolk: A case study in sea-level rise. Physics Today, 69(5), pp. 22-25. [https://doi.org/10.1063/PT.3.3163 | doi: 10.1063/PT.3.3163] [[Media:kramer2016.pdf | Article pdf]]</ref>.
-Sampling procedures for proteomics analyses are straightforward and readily integrated into existing monitoring programs. Almost any type of sample matrix (soil, sediment, groundwater), filters (on-site filtration) can be analyzed. All samples should be shipped to the laboratory on ice or dry ice (-20 °C) using an overnight carrier to minimize the potential for changes in the microbial community between collection and analysis and keep integrity of proteins.
-Groundwater samples (typically 1 L) can be shipped directly to the laboratory or filtered in the field. For on-site filtration, groundwater is pumped through a Sterivex<sup>&reg;</sup> or Bio-Flo<sup>&reg;</sup> filter using standard low flow sampling techniques. The groundwater may then be discarded appropriately. As with other sample types, filters should be shipped on ice (4 °C) using an overnight carrier.
 ==References==
 <references />
 ==See Also==
-*[[Media: Cantarel2011.pdf | Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments]]
+*U.S. Department of Defense, 2019. [[Media:DoD2019.pdf  | Report on Effects of a Changing Climate to the Department of Defense]]
-*[https://www.nature.com/articles/nbt.1661  Options and considerations when selecting a quantitative proteomics strategy]
+* Naval Facilities Engineering Command, 2017. [[Media: NAVFACHandbook2017.pdf | Climate Change Planning Handbook Installation Adaptation and Resilience]]
-*[[Media: Ge2013.pdf | Environmental OMICS: Current Status and Future Directions]]
+*[https://www.serdp-estcp.org/Program-Areas/Resource-Conservation-and-Resiliency/Infrastructure-Resiliency/(language)/eng-US | Strategic Environmental Research and Development Program (SERDP) and Environmental Security Technology Certification Program (ESTCP) – Infrastructure Resiliency]
-*[https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00239  An Alignment-Free “Metapeptide” Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing]
+*U.S. Department of Homeland Security, 2012. [[Media: Climate Change Adaptation Plan | Climate Change Adaptation Roadmap]]
-*[https://www.sciencedirect.com/science/article/abs/pii/S0038071713003799  Environmental proteomics: A long march in the pedosphere]
-*[https://www.sciencedirect.com/science/article/abs/pii/S0038071713003799  Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor]
-*[https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00716  Unipept 4.0: Functional Analysis of Metaproteome Data]
-*[https://www.nature.com/articles/nbt0808-860  Guidelines for reporting the use of mass spectrometry in proteomics]
-*[https://www.nature.com/articles/nbt1329  The minimum information about a proteomics experiment (MIAPE)]
-*[https://pubs.acs.org/doi/10.1021/es501673s  Next-Generation Proteomics: Toward Customized Biomarkers for Environmental Biomonitoring]
-*[[Media: Wilmes2015.pdf | A decade of metaproteomics: Where we stand and what the future holds]]

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Analyzing Infrastructure Vulnerabilities

System View of Infrastructure Resilience

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