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Article ; Online: Techno-Economic Assessment of Electromicrobial Production of

Adams, Jeremy David / Clark, Douglas S

Environmental science & technology

2024 Volume 58, Issue 17, Page(s) 7302–7313

Abstract: Electromicrobial production (EMP), where electrochemically generated substrates (e.g., ... ...

Abstract	Electromicrobial production (EMP), where electrochemically generated substrates (e.g., H
MeSH term(s)	Carbon Dioxide ; 1-Butanol
Chemical Substances	Carbon Dioxide (142M471B3J) ; 1-Butanol (8PJ61P6TS3)
Language	English
Publishing date	2024-04-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.3c08748
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Article ; Online: Phase-separated biomolecular condensates for biocatalysis.

Lim, Samuel / Clark, Douglas S

Trends in biotechnology

2023 Volume 42, Issue 4, Page(s) 496–509

Abstract: Nature often uses dynamically assembling multienzymatic complexes called metabolons to achieve spatiotemporal control of complex metabolic reactions. Researchers are aiming to mimic this strategy of organizing enzymes to enhance the performance of ... ...

Abstract	Nature often uses dynamically assembling multienzymatic complexes called metabolons to achieve spatiotemporal control of complex metabolic reactions. Researchers are aiming to mimic this strategy of organizing enzymes to enhance the performance of artificial biocatalytic systems. Biomolecular condensates formed through liquid-liquid phase separation (LLPS) can serve as a powerful tool to drive controlled assembly of enzymes. Diverse enzymatic pathways have been reconstituted within catalytic condensates in vitro as well as synthetic membraneless organelles in living cells. Furthermore, in vivo condensates have been engineered to regulate metabolic pathways by selectively sequestering enzymes. Thus, harnessing LLPS for controlled organization of enzymes provides an opportunity to dynamically regulate biocatalytic processes.
MeSH term(s)	Biocatalysis ; Biomolecular Condensates ; Catalysis ; Artificial Cells ; Phase Separation
Language	English
Publishing date	2023-11-02
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	47474-5
ISSN	1879-3096 ; 0167-7799
ISSN (online)	1879-3096
ISSN	0167-7799
DOI	10.1016/j.tibtech.2023.10.003
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Zs.A 2750: Show issues

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Article: Ammonia Retention in Biowaste via Low-Temperature-Plasma-Synthesized Nitrogen Oxyacids: Toward Sustainable Upcycling of Animal Waste.

Miller, Victor V / Clark, Douglas S / Mesbah, Ali

ACS sustainable chemistry & engineering

2024 Volume 12, Issue 7, Page(s) 2621–2631

Abstract: Sustainable fertilizer production is a pressing challenge due to a growing human population. The manufacture of synthetic nitrogen fertilizer involves intensive emissions of greenhouse gases. The synthetic nitrogen that ends up in biowaste such as animal ...

Abstract	Sustainable fertilizer production is a pressing challenge due to a growing human population. The manufacture of synthetic nitrogen fertilizer involves intensive emissions of greenhouse gases. The synthetic nitrogen that ends up in biowaste such as animal waste perturbs the nitrogen cycle through significant nitrogen losses in the form of ammonia volatilization, a major human health and environmental hazard. Low-temperature air-plasma treatment of animal waste holds promise for sustainable fertilizer production on farmlands by enabling nitrogen fixation via ionization, forming nitrogen oxyacids. Although the formation of nitrogen oxyacids in plasma treatment of water is well-established, the extent of nitrogen oxyanion enrichment in animal waste and its downstream effects on acidifying the waste remain elusive because many compounds found in complex biowaste media may interfere with absorbed NO
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ISSN	2168-0485
ISSN	2168-0485
DOI	10.1021/acssuschemeng.3c06423
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Article ; Online: Detection of Traumatic Ankle Arthrotomies: Computed Tomography Scan Versus Saline Load Test.

Kallevang, Jonathan K / Berault, Thomas J / Olsen, Aaron A / Zuppke, Julia N / Clark, James K / Douglas, Thomas J / Smith, Christopher S

Journal of orthopaedic trauma

2024 Volume 38, Issue 4, Page(s) 200

Abstract: Objective: Periarticular wounds present a common diagnostic dilemma for emergency providers and orthopedic surgeons because traumatic arthrotomies (TA) often necessitate different management from superficial soft tissue wounds. Historically, TA have ... ...

Abstract	Objective: Periarticular wounds present a common diagnostic dilemma for emergency providers and orthopedic surgeons because traumatic arthrotomies (TA) often necessitate different management from superficial soft tissue wounds. Historically, TA have been diagnosed with the saline load test (SLT). Computed tomography (CT) scan has been studied as an alternative to SLT in diagnosing TA in several joints, but there are limited data specifically pertaining to the ankle. This study aimed to compare the ability of a CT scan to identify an ankle TA versus a traditional SLT. The hypothesis was that there would be no significant difference between a CT scan and SLT in diagnosing ankle TA in a cadaveric model. Methods: This cadaveric study used 10 thawed fresh-frozen cadaveric ankles. A baseline CT scan was performed to ensure no intra-articular air existed before simulated TA. After the baseline CT, a 1 cm TA was created in the anterolateral arthroscopy portal site location. The ankles then underwent a postarthrotomy CT scan to evaluate for the presence of intra-articular air. After the CT scan, a 30 mL SLT was performed using the anteromedial portal site location. Results: After arthrotomy, intra-articular air was visualized in 7 of 10 cadavers in the postarthrotomy CT scan. All the ankles had fluid extravasation during the SLT with <10 mL of saline. The sensitivity of the SLT for TA was 100% versus 70% for the CT scan. Conclusions: The SLT was more sensitive in diagnosing 1-cm ankle TA than a CT scan in a cadaveric model.
MeSH term(s)	Humans ; Ankle ; Ankle Joint/diagnostic imaging ; Ankle Joint/surgery ; Arthroscopy/methods ; Tomography, X-Ray Computed ; Cadaver
Language	English
Publishing date	2024-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	639099-7
ISSN	1531-2291 ; 0890-5339
ISSN (online)	1531-2291
ISSN	0890-5339
DOI	10.1097/BOT.0000000000002768
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Zs.A 2234: Show issues

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Article ; Online: A Comprehensive Modeling Analysis of Formate-Mediated Microbial Electrosynthesis*.

Abel, Anthony J / Clark, Douglas S

ChemSusChem

2020 Volume 14, Issue 1, Page(s) 344–355

Abstract: Mediated microbial electrosynthesis (MES) represents a promising strategy for the capture and conversion of ... ...

Abstract	Mediated microbial electrosynthesis (MES) represents a promising strategy for the capture and conversion of CO
Language	English
Publishing date	2020-10-20
Publishing country	Germany
Document type	Journal Article
ISSN	1864-564X
ISSN (online)	1864-564X
DOI	10.1002/cssc.202002079
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Article ; Online: The Impact of Choice Architecture on Sepsis Fluid Resuscitation Decisions: An Exploratory Survey-Based Study.

Mansoori, Jason N / Clark, Brendan J / Havranek, Edward P / Douglas, Ivor S

MDM policy & practice

2022 Volume 7, Issue 1, Page(s) 23814683221099454

Abstract: ... randomized to distinct answer sets: control (6 fluid options), time constraint (6 fluid options with a 10-s ... was reduced in time constraint (9.5 s, interquartile range [IQR] 7.3 s to 10.0 s, : Conclusions ...

Abstract	Background: Discordance with well-known sepsis resuscitation guidelines is often attributed to rational assessments of patients at the point of care. Conversely, we sought to explore the impact of choice architecture (i.e., the environment, manner, and behavioral psychology within which options are presented and decisions are made) on decisions to prescribe guideline-discordant fluid volumes. Design: We conducted an electronic, survey-based study using a septic shock clinical vignette. Physicians from multiple specialties and training levels at an academic tertiary-care hospital and academic safety-net hospital were randomized to distinct answer sets: control (6 fluid options), time constraint (6 fluid options with a 10-s limit to answer), or choice overload (25 fluid options). The primary outcome was discordance with Surviving Sepsis Campaign fluid resuscitation guidelines. We also measured response times and examined the relationship between each choice architecture intervention group, response time, and guideline discordance. Results: A total of 189 of 624 (30.3%) physicians completed the survey. Time spent answering the vignette was reduced in time constraint (9.5 s, interquartile range [IQR] 7.3 s to 10.0 s, Conclusions: Choice architecture may affect fluid resuscitation decisions in sepsis regardless of patient conditions, warranting further investigation in real-world contexts. These effects should be considered when implementing practice guidelines. Highlights: Time constrained clinical decision making was associated with increased proportion of guideline-discordant responses and relative risk of failure to prescribe guideline-recommended intravenous fluids using a sepsis clinical vignette.Choice overload increased response times and was associated with decreased proportion of guideline-discordant responses and relative risk of guideline discordance.Physician odds of choosing to prescribe guideline-discordant fluid volumes were reduced with increased deliberation as measured by response times.Clinicians, researchers, policy makers, and administrators should consider the effect of choice architecture on clinical decision making and guideline discordance when implementing guidelines for sepsis and other acute care conditions.
Language	English
Publishing date	2022-05-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2861432-X
ISSN	2381-4683 ; 2381-4683
ISSN (online)	2381-4683
ISSN	2381-4683
DOI	10.1177/23814683221099454
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Article ; Online: Progress, Challenges, and Opportunities with Artificial Metalloenzymes in Biosynthesis.

Bloomer, Brandon J / Clark, Douglas S / Hartwig, John F

Biochemistry

2022 Volume 62, Issue 2, Page(s) 221–228

Abstract: In this Perspective, we present progress, outstanding challenges, and opportunities for the incorporation of artificial metalloenzymes (ArMs) into biosynthetic pathways. We first explain discoveries within the field of ArMs that led to the potential ... ...

Abstract	In this Perspective, we present progress, outstanding challenges, and opportunities for the incorporation of artificial metalloenzymes (ArMs) into biosynthetic pathways. We first explain discoveries within the field of ArMs that led to the potential inclusion of these enzymes in biosynthesis. We then describe the specific barriers that our laboratory, in collaboration with the laboratories of Keasling and Mukhopadhyay, addressed to establish a biosynthetic pathway containing an ArM. This biosynthesis produced an unnatural cyclopropyl terpenoid by combining heterologous production of the terpene with modification of its terminal alkene by an ArM built from a cytochrome P450. Finally, we describe the remaining challenges and opportunities related to the application of ArMs in synthetic biology.
MeSH term(s)	Metalloproteins/metabolism ; Terpenes/metabolism ; Cytochrome P-450 Enzyme System/metabolism ; Biosynthetic Pathways
Chemical Substances	Metalloproteins ; Terpenes ; Cytochrome P-450 Enzyme System (9035-51-2)
Language	English
Publishing date	2022-02-23
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.1c00829
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Zs.A 217: Show issues

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Article ; Online: Fluorescence in situ hybridisation in Carnoy's fixed tonsil tissue.

Clark, S T / Waldvogel-Thurlow, S / Wagner Mackenzie, B / Douglas, R G / Biswas, K

Scientific reports

2022 Volume 12, Issue 1, Page(s) 12395

Abstract: Fluorescence in situ hybridisation (FISH) is a powerful molecular technique that enables direct visualisation of specific bacterial species. Few studies have established FISH protocols for tonsil tissue in Carnoy's fixative, accordingly limiting its ... ...

Abstract	Fluorescence in situ hybridisation (FISH) is a powerful molecular technique that enables direct visualisation of specific bacterial species. Few studies have established FISH protocols for tonsil tissue in Carnoy's fixative, accordingly limiting its application to investigate the pathogenesis of tonsillar hyperplasia. Tonsil tissue from 24 children undergoing tonsillectomy for either recurrent tonsillitis or sleep-disordered breathing were obtained during a previous study. The specificity of each of the five FISH probes (Fusobacterium spp., Bacteroides spp., Streptococcus spp., Haemophilus influenzae and Pseudomonas spp.) were successfully optimised using pure and mixed bacterial isolates, and in Carnoy's fixed tonsil tissue. Bacteroides spp. were present in 100% of patients with microcolonies. In comparison, the prevalence of Fusobacterium spp. was 93.8%, Streptococcus spp. 85.7%, H. influenzae 82.35% and Pseudomonas spp. 76.5%. Notable differences in the organisation of bacterial taxa within a single microcolony were also observed. This is the first study to establish a robust FISH protocol identifying multiple aerobic and anaerobic bacteria in Carnoy's fixed tonsil tissue. This protocol provides a strong foundation for combining histological and microbiological analyses of Carnoy's fixed tonsil samples. It may also have important implications on the analysis of microorganisms in other human tissues prepared using the same techniques.
MeSH term(s)	Bacteria/genetics ; Child ; Fixatives ; Haemophilus influenzae ; Humans ; In Situ Hybridization, Fluorescence ; Palatine Tonsil/pathology ; Streptococcus ; Tonsillectomy ; Tonsillitis/pathology
Chemical Substances	Fixatives
Language	English
Publishing date	2022-07-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-16309-w
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Article ; Online: Systems-informed genome mining for electroautotrophic microbial production.

Abel, Anthony J / Hilzinger, Jacob M / Arkin, Adam P / Clark, Douglas S

Bioelectrochemistry (Amsterdam, Netherlands)

2022 Volume 145, Page(s) 108054

Abstract: Electromicrobial production (EMP) systems can store renewable energy and ... ...

Abstract	Electromicrobial production (EMP) systems can store renewable energy and CO
MeSH term(s)	Carbon Dioxide/metabolism ; Electrons ; Phylogeny
Chemical Substances	Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2022-01-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2010650-6
ISSN	1878-562X ; 0302-4598 ; 1567-5394
ISSN (online)	1878-562X
ISSN	0302-4598 ; 1567-5394
DOI	10.1016/j.bioelechem.2022.108054
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Zs.A 1178: Show issues

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Article ; Online: Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products.

Adams, Jeremy David / Sander, Kyle B / Criddle, Craig S / Arkin, Adam P / Clark, Douglas S

Microbial cell factories

2023 Volume 22, Issue 1, Page(s) 69

Abstract: Background: Intracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of ...

Abstract	Background: Intracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of the bacterial cell wall to effect release of cytoplasmic contents. Cell lysis is typically achieved either through mechanical disruption or reagent-based methods, which introduce issues of energy demand, material needs, high costs, and scaling problems. Osmolysis, a cell lysis method that relies on hypoosmotic downshock upon resuspension of cells in distilled water, has been applied for bioseparation of intracellular products from extreme halophiles and mammalian cells. However, most industrial bacterial strains are non-halotolerant and relatively resistant to hypoosmotic cell lysis. Results: To overcome this limitation, we developed two strategies to increase the susceptibility of non-halotolerant hosts to osmolysis using Cupriavidus necator, a strain often used in electromicrobial production, as a prototypical strain. In one strategy, C. necator was evolved to increase its halotolerance from 1.5% to 3.25% (w/v) NaCl through adaptive laboratory evolution, and genes potentially responsible for this phenotypic change were identified by whole genome sequencing. The evolved halotolerant strain experienced an osmolytic efficiency of 47% in distilled water following growth in 3% (w/v) NaCl. In a second strategy, the cells were made susceptible to osmolysis by knocking out the large-conductance mechanosensitive channel (mscL) gene in C. necator. When these strategies were combined by knocking out the mscL gene from the evolved halotolerant strain, greater than 90% osmolytic efficiency was observed upon osmotic downshock. A modified version of this strategy was applied to E. coli BL21 by deleting the mscL and mscS (small-conductance mechanosensitive channel) genes. When grown in medium with 4% NaCl and subsequently resuspended in distilled water, this engineered strain experienced 75% cell lysis, although decreases in cell growth rate due to higher salt concentrations were observed. Conclusions: Our strategy is shown to be a simple and effective way to lyse cells for the purification of intracellular biomacromolecules and may be applicable in many bacteria used for bioproduction.
MeSH term(s)	Animals ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Ion Channels/genetics ; Cupriavidus necator/metabolism ; Sodium Chloride/pharmacology ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Bacteria/metabolism ; Water ; Mammals/metabolism
Chemical Substances	Ion Channels ; Sodium Chloride (451W47IQ8X) ; Escherichia coli Proteins ; Water (059QF0KO0R) ; MscL protein, E coli
Language	English
Publishing date	2023-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2091377-1
ISSN	1475-2859 ; 1475-2859
ISSN (online)	1475-2859
ISSN	1475-2859
DOI	10.1186/s12934-023-02064-8
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