Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “SPORES”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29

High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain

Abstract Ensifer meliloti Mlalz-1 (INSDC = ATZD00000000 ) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata . This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of E. meliloti Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to Ensifer meliloti IAM 12611 T , Ensifer medicae A 321 T and Ensifer numidicus ORS 1407 T , based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as E. meliloti . Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata -nodulating Ensifer strains, but ≤93% with nodC of Ensifer strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced E. meliloti strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In E. medicae strain WSM419 , lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of E. medicae strains, which suggests genetic recombination between strain Mlalz-1 and E. medicae and the horizontal gene transfer of lpiA-acvB .

59 BASIC BIOLOGICAL SCIENCES↗

Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes

Abstract Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 ( CMPUJU 515 ), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0–3.0 μm × 0.5–1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis strain CT14–3 T . The draft genome of P. extremaustralis strain USBA-GBX-515 consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665 genes were predicted and of those, 5544 were protein coding genes and 121 were RNA genes. The distribution of genes into COG functional categories showed that most genes were classified in the category of amino acid transport and metabolism (10.5%) followed by transcription (8.4%) and signal transduction mechanisms (7.3%). We performed experimental analyses of the lipolytic activity and results showed activity mainly on short chain fatty acids. The genome analysis demonstrated the existence of two genes, lip515A and est515A, related to a triacylglycerol lipase and carboxylesterase, respectively. Ammonification genes were also observed, mainly nitrate reductase genes. Genes related with synthesis of poly-hydroxyalkanoates (PHAs), especially poly-hydroxybutyrates (PHBs), were detected. The phaABC and phbABC operons also appeared complete in the genome. P. extremaustralis strain USBA-GBX-515 conserves the same gene organization of the type strain CT14–3 T . We also thoroughly analyzed the potential for production of secondary metabolites finding close to 400 genes in 32 biosynthetic gene clusters involved in their production.

16S rRNA↗

Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes

The unambiguous application of fungal names is important to communicate scientific findings. Names are critical for (clinical) diagnostics, legal compliance, and regulatory controls, such as biosafety, food security, quarantine regulations, and industrial applications. Consequently, the stability of the taxonomic system and the traceability of nomenclatural changes is crucial for a broad range of users and taxonomists. The unambiguous application of names is assured by the preservation of nomenclatural history and the physical organisms representing a name. Fungi are extremely diverse in terms of ecology, lifestyle, and methods of study. Predominantly unicellular fungi known as yeasts are usually investigated as living cultures. Methods to characterize yeasts include physiological (growth) tests and experiments to induce a sexual morph; both methods require viable cultures. Thus, the preservation and availability of viable reference cultures are important, and cultures representing reference material are cited in species descriptions. Historical surveys revealed drawbacks and inconsistencies between past practices and modern requirements as stated in the International Code of Nomenclature for Algae, Fungi, and Plants (ICNafp). Improper typification of yeasts is a common problem, resulting in a large number invalid yeast species names. With this opinion letter, we address the problem that culturable microorganisms, notably some fungi and algae, require specific provisions under the ICNafp. We use yeasts as a prominent example of fungi known from cultures. But viable type material is important not only for yeasts, but also for other cultivable Fungi that are characterized by particular morphological structures (a specific type of spores), growth properties, and secondary metabolites. We summarize potential proposals which, in our opinion, will improve the stability of fungal names, in particular by protecting those names for which the reference material can be traced back to the original isolate.

59 BASIC BIOLOGICAL SCIENCES↗

Interactions between Bacillus anthracis and Plants May Promote Anthrax Transmission

Environmental reservoirs are essential in the maintenance and transmission of anthrax but are poorly characterized. The anthrax agent, Bacillus anthracis was long considered an obligate pathogen that is dormant and passively transmitted in the environment. However, a growing number of laboratory studies indicate that, like some of its close relatives, B. anthracis has some activity outside of its vertebrate hosts. Here we show in the field that B. anthracis has significant interactions with a grass that could promote anthrax spore transmission to grazing hosts. Using a local, virulent strain of B. anthracis, we performed a field experiment in an enclosure within a grassland savanna. We found that B. anthracis increased the rate of establishment of a native grass (Enneapogon desvauxii) by 50% and that grass seeds exposed to blood reached heights that were 45% taller than controls. Further we detected significant effects of E. desvauxii, B. anthracis, and their interaction on soil bacterial taxa richness and community composition. We did not find any evidence for multiplication or increased longevity of B. anthracis in bulk soil associated with grass compared to controls. Instead interactions between B. anthracis and plants may result in increased host grazing and subsequently increased transmission to hosts.

54 ENVIRONMENTAL SCIENCES↗

Arrangement of the Clostridium baratii F7 Toxin Gene Cluster with Identification of a σ Factor That Recognizes the Botulinum Toxin Gene Cluster Promoters

Botulinum neurotoxin (BoNT) is the most poisonous substances known and its eight toxin types (A to H) are distinguished by the inability of polyclonal antibodies that neutralize one toxin type to neutralize any of the other seven toxin types. Infant botulism, an intestinal toxemia orphan disease, is the most common form of human botulism in the United States. It results from swallowed spores of Clostridium botulinum (or rarely, neurotoxigenic Clostridium butyricum or Clostridium baratii) that germinate and temporarily colonize the lumen of the large intestine, where, as vegetative cells, they produce botulinum toxin. Botulinum neurotoxin is encoded by the bont gene that is part of a toxin gene cluster that includes several accessory genes. In this paper, we sequenced for the first time the complete botulinum neurotoxin gene cluster of nonproteolytic C. baratii type F7. Like the type E and the nonproteolytic type F6 botulinum toxin gene clusters, the C. baratii type F7 had an orfX toxin gene cluster that lacked the regulatory botR gene which is found in proteolytic C. botulinum strains and codes for an alternative σ factor. In the absence of botR, we identified a putative alternative regulatory gene located upstream of the C. baratii type F7 toxin gene cluster. This putative regulatory gene codes for a predicted σ factor that contains DNA-binding-domain homologues to the DNA-binding domains both of BotR and of other members of the TcdR-related group 5 of the σ 70 family that are involved in the regulation of toxin gene expression in clostridia. We showed that this TcdR-related protein in association with RNA polymerase core enzyme specifically binds to the C. baratii type F7 botulinum toxin gene cluster promoters. Finally, this TcdR-related protein may therefore be involved in regulating the expression of the genes of the botulinum toxin gene cluster in neurotoxigenic C. baratii.

59 BASIC BIOLOGICAL SCIENCES↗

Bacterial community structure transformed after thermophilically composting human waste in Haiti

Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles

Fusarium fujikuroi causes bakanae (“foolish seedling”) disease of rice which is characterized by hyper-elongation of seedlings resulting from production of gibberellic acids (GAs) by the fungus. This plant pathogen is also known for production of harmful mycotoxins, such as fusarins, fusaric acid, apicidin F and beauvericin. Recently, we generated the first de novo genome sequence of F. fujikuroi strain IMI 58289 combined with extensive transcriptional, epigenetic, proteomic and chemical product analyses. GA production was shown to provide a selective advantage during infection of the preferred host plant rice. Here, we provide genome sequences of eight additional F. fujikuroi isolates from distant geographic regions. The isolates differ in the size of chromosomes, most likely due to variability of subtelomeric regions, the type of asexual spores (microconidia and/or macroconidia), and the number and expression of secondary metabolite gene clusters. Whilst most of the isolates caused the typical bakanae symptoms, one isolate, B14, caused stunting and early withering of infected seedlings. In contrast to the other isolates, B14 produced no GAs but high amounts of fumonisins during infection on rice. Furthermore, it differed from the other isolates by the presence of three additional polyketide synthase (PKS) genes (PKS40, PKS43, PKS51) and the absence of the F. fujikuroi-specific apicidin F (NRPS31) gene cluster. Analysis of additional field isolates confirmed the strong correlation between the pathotype (bakanae or stunting/withering), and the ability to produce either GAs or fumonisins. Deletion of the fumonisin and fusaric acid-specific PKS genes in B14 reduced the stunting/withering symptoms, whereas deletion of the PKS51 gene resulted in elevated symptom development. Phylogenetic analyses revealed two subclades of F. fujikuroi strains according to their pathotype and secondary metabolite profiles.

59 BASIC BIOLOGICAL SCIENCES↗

Coccidioides undetected in soils from agricultural land and uncorrelated with time or the greater soil fungal community on undeveloped land

Coccidioidomycosis is a typically respiratory fungal disease that, in the United States, occurs primarily in Arizona and California. In California, most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily agricultural region where the disease poses a risk for outdoor workers. We collected 710 soil samples and 265 settled dust samples from nine sites in the San Joaquin Valley and examined how Coccidioides detection varied by month, site, and the presence and abundance of other fungal species. We detected Coccidioides in 89 of 238 (37.4%) rodent burrow soil samples at five undeveloped sites and were unable to detect Coccidioides in any of 472 surface and subsurface soil samples at four agricultural sites. In what is the largest sampling effort undertaken on agricultural land, our results provide no evidence that agricultural soils in the San Joaquin Valley harbor Coccidioides . We found no clear association between Coccidioides and the greater soil fungal community, but we identified 19 fungal indicator species that were significantly associated with Coccidioides detection in burrows. We also did not find a seasonal pattern in Coccidioides detection in the rodent burrow soils we sampled. These findings suggest both the presence of a spore bank and that coccidioidomycosis incidence may be more strongly associated with Coccidioides dispersal than Coccidioides growth. Finally, we were able to detect Coccidioides in only five of our 265 near-surface settled dust samples, one from agricultural land, where Coccidioides was undetected in soils, and four from undeveloped land, where Coccidioides was common in the rodent burrow soils we sampled. Our ability to detect Coccidioides in few settled dust samples indicates that improved methods are likely needed moving forward, though raises questions regarding aerial dispersal in Coccidioides , whose key transmission event likely occurs over short distances in rodent burrows from soil to naïve rodent lungs.

59 BASIC BIOLOGICAL SCIENCES↗

Characteristics and sources of fluorescent aerosols in the central Arctic Ocean

The Arctic is sensitive to cloud radiative forcing. Due to the limited number of aerosols present throughout much of the year, cloud formation is susceptible to the presence of cloud condensation nuclei and ice nucleating particles (INPs). Primary biological aerosol particles (PBAP) contribute to INPs and can impact cloud phase, lifetime, and radiative properties. We present yearlong observations of hyperfluorescent aerosols (HFA), tracers for PBAP, conducted with a Wideband Integrated Bioaerosol Sensor, New Electronics Option during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition (October 2019–September 2020) in the central Arctic. We investigate the influence of potential anthropogenic and natural sources on the characteristics of the HFA and relate our measurements to INP observations during MOSAiC. Anthropogenic sources influenced HFA during the Arctic haze period. But surprisingly, we also found sporadic “bursts” of HFA with the characteristics of PBAP during this time, albeit with unclear origin. The characteristics of HFA between May and August 2020 and in October 2019 indicate a strong contribution of PBAP to HFA. Notably from May to August, PBAP coincided with the presence of INPs nucleating at elevated temperatures, that is, >–9°C, suggesting that HFA contributed to the “warm INP” concentration. The air mass residence time and area between May and August and in October were dominated by the open ocean and sea ice, pointing toward PBAP sources from within the Arctic Ocean. As the central Arctic changes drastically due to climate warming with expected implications on aerosol–cloud interactions, we recommend targeted observations of PBAP that reveal their nature (e.g., bacteria, diatoms, fungal spores) in the atmosphere and in relevant surface sources, such as the sea ice, snow on sea ice, melt ponds, leads, and open water, to gain further insights into the relevant source processes and how they might change in the future.

54 ENVIRONMENTAL SCIENCES↗

Exploring the Genome and Proteome of Desulfitobacterium hafniense DCB2 for its Protein Complexes Involved in Metal Reduction and Dechlorination

Desulfitobacteria are of interest to DOE mission because of their ability to reduce many electron acceptors including Fe(III), U(VI), Cr(VI), As(V), Mn(IV), Se(VI), NO 3 - and well as CO 2 , sulfite, fumarate and humates, their ability to colonize more stressful environments because they form spores, fix nitrogen and they have the more protective Gram positive cell walls. Furthermore at least some of them reductively dechlorinate aromatic and aliphatic pollutants. Importantly, most of the metals and the organochlorine reductions are coupled to ATP production and support growth providing for the organism's natural selection at DOE's contaminant sites. This work was undertaken to gain insight into the genetic and metabolic pathways involved in dissimilatory metal reduction and reductive dechlorination, (ii) to discern the commonalities among these electron-accepting processes, (iii) to identify multi-protein complexes catalyzing these functions and (iv) to elucidate the coordination in expression of these pathways and processes.

59 BASIC BIOLOGICAL SCIENCES↗

Remediation Guidance for Major Airports after a Bioterrorist Attack

This document provides general guidelines for airport managers, local officials, and other stakeholders for developing a response and recovery plan for a major airport following the release of a biological warfare agent, with specific guidance for remediation. San Francisco International Airport was selected as the example airport during development of the guidance to illustrate specific details. The spore-forming bacterium Bacillus anthracis was selected as the biological agent of primary concern because it is the most difficult of known bioterrorism agents to inactivate and is considered to be one of the agents most likely to be used as a biological weapon. The focus of the guidance is on cleanup and disposal activities associated with the Characterization, Decontamination, and Clearance Phases that are defined herein. Activities associated with the Notification and First-Response Phases are brieÀy discussed in Appendixes A and B, respectively. In addition to the main text of this Remediation Guidance document and associated appendixes, a data supplement was developed specifically for San Francisco International Airport. Requests for the data supplement must be made directly to the Emergency Planning Operations Division of San Francisco International Airport. This document does not describe public health responses to release of a biological warfare agent. If laboratory analytical results confirm the presence of a biological agent, the responsible public health agency involved in the response will commence appropriate public health actions, such as treatment (CDC 2004) and decontamination of potentially contaminated individuals, distribution of prophylaxis, and medical examinations. See the Centers for Disease Control and Prevention web site for more information on emergency public health responses (http://www.bt.cdc.gov/). Effective communication with the media and the public is an essential component of airport remediation and recovery. Whereas such communication is beyond the scope of this document, many helpful resources are available. (See Section 1.1 for more information.) The concept of operations described in this document for cleanup of a Bacillus anthracis release at a major airport conforms to the National Response Framework (NRF) (DHS 2008) and implementation of the National Incident Management System (NIMS 2004). In most cases, a Unified Command would be formed to direct the cleanup process jointly and to take ultimate responsibility for all cleanup decisions. The Unified Command would likely include the Airport Manager or Airport Emergency Operations Manager, representatives from state and local public health and emergency management agencies, and Federal agencies, such as the U.S. Environmental Protection Agency. The Unified Command and Incident Command Staff would ideally be co-located in an Incident Command Post in an uncontaminated area of the airport. If a release is large or complex, co-location of all key players may not be possible. If a major incident is declared, a Principal Federal Official may be appointed by the Department of Homeland Security to facilitate Federal support to the Unified Command. In some facilities and jurisdictions, additional response plans or procedures (such as BioWatch or other emergency response plans, procedures, or protocols) may govern notification and first response. Facility personnel, responders, and emergency management coordinators should be aware of all applicable plans and procedures and how to implement them. Cleanups following the anthrax attacks of 2001 in the U.S. pre-dated the NRF and NIMS and did not make use of a NIMS Incident Command System as we know it today. Most Incident Commanders for the larger of those cleanups chose to convene a Technical Working Group (TWG) of multi-agency, multi-disciplinary, outside experts to advise in developing sampling and decontamination plans. Most of the Incident Commanders also convened a separate Environmental Clearance Committee (ECC) to independently review pre- and post decontamination sampling data as well as data on decontamination parameters, to evaluate whether the decontamination was effective, and to add credibility regarding a decision that decontaminated areas may be reoccupied. Use of such specialized technical expertise is strongly recommended, although it would now operate within the construct of the NIMS Incident Command System. The TWG, if convened, would act in an advisory capacity to the Environmental Unit within the Planning Section. Likewise, the ECC, if convened, would provide independent peer review of products and recommendations by the Environmental Unit. For maximum impartiality, the ECC could also provide recommendations directly to the Unified Command. Cleanup activities commence with site characterization. The principal goal of characterization is to define the extent of contamination and to gather information needed to design the decontamination approach. Initial sampling data collected by first responders are assessed to approximate the location(s) of contamination. Confirmation of the agent type and viability is obtained from a Laboratory Response Network laboratory. Additional characterization data are collected to determine the extent of contamination and where decontamination actions are needed. Areas suspected of being contaminated are contained and isolated to the degree possible to prevent further movement of an agent to uncontaminated areas or the environment, and to reduce the potential for future exposure from the agent or fumigant, if fumigation is needed. Agent air monitoring in areas adjacent to the contained contamination zones is done to ensure the protection of remediation personnel and to monitor any release from the contained zones. Various sampling approaches are considered. For example, wipe samples can be used to sample hard, nonporous surfaces. Swab samples can be used to sample nooks, crannies, joints, and seams. Appendix I is a template for preparing an incident-specific, operational characterization plan. Upon completion of the characterization plan, an internal review is initiated. Upon approval of the plan by the Unified Command, characterization commences. The Site Safety Officer develops a Health and Safety Plan to ensure that coordinated health and safety measures are in place for all responding personnel. This plan describes physical, chemical, and biological hazards at the site, personal protective equipment, personal decontamination procedures, and emergency procedures to be used by sampling and remediation personnel. An incident-specific Remediation Action Plan is developed, which describes the decontamination methods to be used and other details, including waste disposal. Under NIMS, this overall plan, as well as other plans described below, are implemented through a series of standardized, shorter-term Incident Action Plans, which describe specific activities that will take place during a shift or a day. The template in Appendix J is designed to facilitate preparation of the Remediation Action Plan. If fumigation will be done, a Sampling and Analysis Plan will be needed, as well as an Ambient Air Monitoring Plan, which can be a component of the Remediation Action Plan. These three plans are needed to obtain a crisis exemption from the U.S. Environmental Protection Agency for authorized use of an unregistered sterilant or pesticide during cleanup. If pesticide products become registered for inactivation of B. anthracis in the future, the three plans will likely be required by the product’s labeling, but the plans would no longer be submitted to the U.S. Environmental Protection Agency for approval; rather, the Incident Commander would approve them. If fumigation is used, an Emergency Response Plan is also recommended, although such a plan is not required for a crisis exemption. For some nonpersistent biological warfare agents, natural attenuation may be an adequate decontamination option. In cases where contamination is not extensive or an agent is not persistent, application of surface decontaminants or other methods of medical infection control may be effective. For extensive contamination by persistent agents, such as Bacillus anthracis, fumigation may be necessary. In those cases, the Decontamination Phase commences with source reduction, such as pre-cleaning surfaces to reduce the contaminant load. To expedite cleanup and prevent costs from escalating unnecessarily, a cost–benefit analysis should be incorporated in the decision process related to retention versus disposal of facility items and materials. Certain materials and structural components can be decontaminated for reuse, but it may not be feasible or cost-effective to decontaminate other items. Those items must be pre-treated, packaged (with the package decontaminated externally), and removed for disposal as waste. Site preparation includes sealing openings to prevent leaks and setting up equipment. Decontamination reagents and delivery systems are selected, and pre-testing all systems is done before carrying out chemical treatment(s). The important choice of decontamination technologies depends on characteristics of the agent, the nature and extent of contamination, and other site parameters identified during characterization. Decontamination-related decisions can have a major impact on waste-disposal costs, and it is necessary to develop a disposal plan that identifies a means of disposal, necessary approvals, transportation, and other details. A clearance strategy is developed to ensure that after decontamination, the risk of exposure to residual contamination is negligible. A clearance sampling plan is developed, which sets clearance criteria, specifies how to determine whether the criteria have been met, and describes how and where to collect clearance samples after decontamination. In most cases, clearance sampling includes both surface and aggressive air samples. Appendix K is a clearance plan template that identifies the types of required information. To determine whether the decontaminated area may be reoccupied, the Environmental Unit (and the ECC separately, if one is convened) evaluates the results of clearance samples. For the anthrax incidents to date, and given methods that have been used, cleanup was considered successful only when there was no growth of B. anthracis cultured from any environmental samples taken after decontamination. Other factors that will be considered include the decontamination process parameters (e.g., temperature, relative humidity, decontaminant concentration, and contact time) and the results from post-decontamination culture of biological indicators that may have been used during fumigation or sterilization processes. From such an evaluation the Environmental Unit or ECC, or both, recommend whether the area may be reoccupied, or whether further decontamination is necessary. The UC makes the final decision that a facility is appropriately decontaminated for reoccupancy. The facility owner or responsible public health agency makes the final decision to reopen a decontaminated facility. A theme that is emphasized throughout this document is that many activities can greatly reduce the time required to restore airport operations if those activities are conducted prior to an actual release of biological warfare agent. A summary of specific resources (such as Federal, state, and local agency contacts; contractors; prospective team members; subject-matter experts; laboratory facilities; and other entities) that should be identified in advance by airport officials is provided in each pertinent section of this document, and summary contact lists of such resources are provided in Appendix L. A summary of overall pre-planning actions that should be completed by airport officials is presented at the end of this document.

59 BASIC BIOLOGICAL SCIENCES↗

Summary of the Seattle Urban Area Consequence Management Guidance for a Wide-Area Biological Attack

A terrorist attack involving a release of biological warfare agent in the Seattle urban area would require decision-makers to make a host of important, and sometimes untested, choices concerning how best to respond and recover. This technical supplement supports the Puget Sound Regional Biological Attack Recovery Plan Annex to the Regional Catastrophic Plan, which structures the region’s response and recovery approach, by providing technical details on how to conduct a biological remediation. More specifically, the technical supplement identifies the principal issues that must be addressed following a wide-area release of aerosolized Bacillus anthracis (B. anthracis) spores; explains the resources that are available to address the release; sets forth strategies to reduce the time required for consequence management; and focuses on remediation options, procedures, and tools that can be implemented today should such an incident occur. The content is intended to be used with the Interim Consequence Management Guidance for a Wide-Area Biological Attack (LLNL 2009). A second and related purpose of this technical supplement is to serve as a detailed guide for other geographical regions interested in formulating their own consequence management plans. This technical supplement is funded by, and was developed as part of, the Interagency Biological Restoration Demonstration (IBRD) program—a collaborative effort among Department of Homeland Security, Department of Defense, and numerous other Federal, state, and local agencies—to improve the nation’s ability to respond to and recover from a wide-area biological incident. Content of the technical supplement follows the six-phase diagram for responding to and recovering from a biological contamination incident (see Figure 1 on the next page), which represents a consensus scheme developed after multi-agency review and approval. Whereas the focus of the document is on remediation/cleanup activities, the topics of response and recovery structure (Section 2), notification (Section 3), and initial response (also known as first response, Section 4) are discussed relatively briefly because some early decisions related to those three topics can affect subsequent decisions pertaining to remediation and potentially affect timelines and overall effectiveness.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Interim Consequence Management Guidance for a Wide-Area Biological Attack

The Interagency Biological Restoration Demonstration (IBRD) program is a collaborative, interagency effort co-chaired by the Department of Homeland Security and Department of Defense aimed at improving the nation‘s ability to respond to and recover from a large-scale, wide-area, domestic attack involving the release of an environmentally persistent biological warfare agent. The program is focused on understanding interactions between the civilian and military sectors, and in building mutual support to carry out such remediations. This Interim Consequence Management Guidance document provides guidance for decisionmakers in executing activities required to respond to and recover from a biological incident affecting a wide urban area insofar as information is currently available. The spore-forming bacterium Bacillus anthracis is discussed as the biological agent of primary concern because it is the most difficult of known bioterrorism agents to inactivate and is considered to be one of the key threat agents. Most other biological threat agents are much easier to remediate, and in many cases, inactivation would occur naturally within days as a result of environmental exposure; however, the framework and operational questions that need to be addressed are expected to remain the same. The guidance in this document is applicable to (1) enclosed facilities, such as commercial, residential, and continental U.S. military facilities; (2) semi-enclosed facilities, such as subways and public transit facilities; (3) outdoor areas (both localized and wide area), such as building exteriors, streets, parks, and other open spaces; (4) drinking water facilities; and (5) drinking water sources. This document follows an interagency framework [Planning Guidance for Recovery Following Biological Incidents (DHS and EPA 2009)]—which considered Raber et al. (2002) in its development—but takes the framework to a more operational level and provides guidance at key action and decision points.

59 BASIC BIOLOGICAL SCIENCES↗

Experimental Design for a Macrofoam Swab Study Relating the Recovery Efficiency and False Negative Rate to Low Concentrations of Two Bacillus anthracis Surrogates on Four Surface Materials

This report describes the experimental design for a laboratory study to quantify the recovery efficiencies and false negative rates of a validated, macrofoam swab sampling method for low concentrations of Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus (BG) spores on four surface materials (stainless steel, glass, vinyl tile, plastic light cover panel). Two analytical methods (plating/counting and polymerase chain reaction) will be used. Only one previous study has investigated false negative as a function of affecting test factors. The surrogates BAS and BG have not been tested together in the same study previously. Hence, this study will provide for completing gaps in the available information on the performance of macrofoam swab sampling at low concentrations.

Bacillus Anthracis↗

Experimental Design for a Macrofoam-Swab Study Relating the Recovery Efficiency and False Negative Rate to Low Concentrations of Two Bacillus anthracis Surrogates on Four Surface Materials

This report describes the experimental design for a laboratory study to quantify the recovery efficiencies and false negative rates of a validated, macrofoam-swab sampling method for low concentrations of Bacillus anthracis Sterne (BAS) and Bacillus atrophaeus (BG) spores on four surface materials (stainless steel, glass, vinyl tile, plastic light cover panel). Two analytical methods (culture and polymerase chain reaction) will be used. Only one previous study has investigated how the false negative rate depends on test factors. The surrogates BAS and BG have not been tested together in the same study previously. Hence, this study will provide for completing gaps in the available information on the performance of macrofoam-swab sampling at low concentrations.

36 MATERIALS SCIENCE↗

GoAmazon 2014/15 Thermal Desorption Chemical Ionization Mass Spectrometer (TDCIMS) Field Campaign Report

The Thermal Desorption Chemical Ionization Mass Spectrometer (TDCIMS) deployment to the U.S. Department of Energy (DOE)’s Atmospheric Radiation Measurement (ARM) Climate Research Facility T3 site in Manacapuru, Brazil, was motivated by two main scientific objectives of the Green Ocean Amazon (GoAmazon) 2014/15 field campaign. 1) Study the interactions between anthropogenic and biogenic emissions by determining important molecular species in ambient nanoparticles. To address this, TDCIMS data will be combined with coincident measurements such as gas-phase sulfuric acid to determine the contribution of sulfuric acid condensation to nucleation and growth. We can then compare that result to TDCIMS-derived nanoparticle composition to determine the fraction of growth that can be attributed to the uptake of organic compounds. The molecular composition of sampled particles will also be used to attribute specific chemical species and mechanisms to growth, such as the condensation of low-volatility species or the oligomerization of α-dicarbonyl compounds. 2) Determine the source of new ambient nanoparticles in the Amazon. The hypothesis prior to measurements was that potassium salts formed from the evaporation of primary particles emitted by fungal spores can provide a unique and important pathway for new particle production in the Amazon basin. To explore this hypothesis, the TDCIMS recorded the mass spectra of sampled ambient particles using a protonated water cluster Chemical Ionization Mass Spectrometer (CIMS). Laboratory tests performed using potassium salts show that the TDCIMS can detect potassium with high sensitivity with this technique.

54 ENVIRONMENTAL SCIENCES↗

Solar Living House Final Technical Report

The Solar Living House is a high-performance solar-powered dwelling designed by a team of faculty and students from the University of Florida, in collaboration with Santa Fe College, the National University of Singapore, and Alachua Habitat for Humanity. The project was designed in accordance with the Solar Decathlon 2015, a research, design, education, and outreach program developed by the U.S. Department of Energy (DOE). The Solar Living House is fundamentally a house for living, centered on people and the activities of daily life while quietly introducing advanced design, construction, and engineering technologies. The 993 square-foot two-bedroom one-bath home was designed to embrace and frame an exterior courtyard space. This courtyard acts as an extension of the interior living spaces, maximizing the spatial potentials of a modest building footprint and introducing natural light into the primary living spaces of the house. Research Outcomes: The Solar Living House advances work on high-performance buildings through three principal technological innovations: wet/dry modular construction, a building automation system, and solar dehumidification systems. Wet / Dry Modular Construction: The house is designed as a series of five modules, including one that is designated as the “wet core.” The wet core consolidates the mechanical systems and bathroom into a single module to reduce plumbing runs, efficiency losses, and on-site construction time. The other four modules are designed to eliminate interior load bearing walls to allow for maximum flexibility in the reconfiguring of the space over time. The modules are designed to meet the structural challenges of both Florida’s hurricanes and California’s earthquakes. Building Automation System: The house is equipped with an integrated building automation system, allowing the houses environmental systems, lights, security systems, and smoke detectors to be programmed, monitored, and controlled through any mobile or computing device. These systems allow for more precise calibrations of temperature/humidity/lighting to correspond with user needs and preferences, minimizing energy losses with economical night- or day-time setbacks. Solar Dehumidification System: The most significant technological innovation in the Solar Living House is the solar thermal dehumidification system. This system generates hot water through two rooftop-mounted evacuated tube solar thermal collectors. The hot water is used to continually dry a regenerative solid desiccant material, typically white silica gel. The solid desiccant is used to adsorb moisture and humidity from the air without additional mechanical cooling. This strategy allows humidity to be modulated independently of air temperature, providing greater thermal comfort and reducing the opportunity for the growth of mold spores within the house while also reducing the overall energy consumption of the HVAC system. Economic Feasibility: The team set aggressive goals for affordability, targeting a construction cost of $138,710. An independent professional cost estimator determined the overall project costs, as designed, would be $333,799, or $336.15 per square foot of finished floor area. This is more than 2.4 times the target construction cost. By comparison, the average construction cost for a home in the United States in 2015 was $289,415, or $103.29 per square foot of finished floor area. Following work on the Solar Living House, team leaders incorporated many of its objectives into a net-zero energy home on a site in Gainesville, Florida. This site-built home avoided many of the constraints and complications of modular construction necessitated by the Solar Decathlon, allowing it to be built for a much more modest budget. This two-bedroom two bath 1,800 square foot home was constructed for $135.39 per square foot, including active photovoltaic solar systems, careful attention to continuous air barriers, increased insulation levels, and permanent site constructions. This project suggest that high-performance buildings can be realized for more modest budgets. Public Benefits: Work on the Solar Living House and Solar Decathlon 2015 offered our student team unparalleled learning opportunities. Because of the duration of the project, a number of students participated at different points in their education, from first year undergraduates all the way through to advanced graduate students. The opportunity for collaboration with students and faculty from the National University of Singapore was also extraordinary, allowing for a sharing of technical knowledge and cultural exchange. The wider public has benefited from this work as its findings have been shared through public presentations and publications. It serves as a useful stepping stone along the path towards affordable, high-performance buildings.

14 SOLAR ENERGY↗

Brazil-USA Collaborative Research: Modifications by Anthropogenic Pollution of the Natural Atmospheric Chemistry and Particle Microphysics of the Tropical Rain Forest During the GoAmazon Intensive Operating Periods (IOPs)

Manaus, a city of nearly two million people, represents an isolated urban area having a distinct urban pollution plume within the otherwise pristine Amazon Basin. The plume has high concentrations of oxides of nitrogen and sulfur, carbon monoxide, particle concentrations, and soot, among other pollutants. Critically, the distinct plume in the setting of the surrounding tropical rain forest serves as a natural laboratory to allow direct comparisons between periods of pollution influence to those of pristine conditions. The funded activity of this report is related to the Brazil-USA collaborative project during the two Intensive Operating Periods (wet season, 1 Feb - 31 Mar 2014; dry season, 15 Aug - 15 Oct 2014) of GoAmazon2014/5. The project addresses key science questions regarding the modification of the natural atmospheric chemistry and particle microphysics of the forest by present and future anthropogenic pollution. The first objective of the project was to understand and quantify the interactions of biogenic and anthropogenic emissions with respect to the production of secondary organic material. In clean conditions in the Amazon basin, secondary organic material dominates the diameter distribution of the submicron particles. How and why is the diameter distribution shifted by pollution? The second objective followed from the first in that, although the diameter distribution is dominated by secondary organic material, the actual source of new particle production remains uncertain (i.e., the number concentration). The second objective was to test the hypothesis that new particles under natural conditions are produced as a result of evaporation of primary particles emitted by fungal spores as well as to investigate any shifts in this mechanism under pollution conditions, e.g., in consequence to the high concentrations of SO 2 in the pollution plume. Combined, the number-diameter distribution is the key connection to upscaling to the effects of aerosol particles on clouds and climate. Understanding this upscaling under clean and pollution conditions, including differences, was the third objective.

54 ENVIRONMENTAL SCIENCES↗