Engineering Papers⌕ Search

Engineering topics

Laible, Philip D.

Publications and source records attributed to Laible, Philip D..

10 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Feedstock variability impacts the bioconversion of sugar and lignin streams derived from corn stover by Clostridium tyrobutyricum and engineered Pseudomonas putida

Abstract Feedstock variability represents a challenge in lignocellulosic biorefineries, as it can influence both lignocellulose deconstruction and microbial conversion processes for biofuels and biochemicals production. The impact of feedstock variability on microbial performance remains underexplored, and predictive tools for microbial behaviour are needed to mitigate risks in biorefinery scale‐up. Here, twelve batches of corn stover were deconstructed via deacetylation, mechanical refining, and enzymatic hydrolysis to generate lignin‐rich and sugar streams. These batches and their derived streams were characterised to identify their chemical components, and the streams were used as substrates for producing muconate and butyrate by engineered Pseudomonas putida and wildtype Clostridium tyrobutyricum , respectively. Bacterial performance (growth, product titers, yields, and productivities) differed among the batches, but no strong correlations were identified between feedstock composition and performance. To provide metabolic insights into the origin of these differences, we evaluated the effect of twenty‐three isolated chemical components on these microbes, including three components in relevant bioprocess settings in bioreactors, and we found that growth‐inhibitory concentrations were outside the ranges observed in the streams. Overall, this study generates a foundational dataset on P. putida and C. tyrobutyricum performance to enable future predictive models and underscores their resilience in effectively converting fluctuating lignocellulose‐derived streams into bioproducts.

09 BIOMASS FUELS↗
DOE OSTI2024

Two pathways to understanding electron transfer in reaction centers from photosynthetic bacteria: A comparison of Rhodobacter sphaeroides and Rhodobacter capsulatus mutants

The rates, yields, mechanisms and directionality of electron transfer (ET) are explored in twelve pairs of Rhodobacter (R.) sphaeroides and R. capsulatus mutant RCs designed to defeat ET from the excited primary donor (P*) to the A-side cofactors and re-direct ET to the normally inactive mirror-image B-side cofactors. In general, the R. sphaeroides variants have larger P + H B - yields (up to similar to ~90%) than their R. capsulatus analogs (up to similar to ~60%), where H B is the B-side bacteriopheophytin. Substitution of Tyr for Phe at L-polypeptide position L181 near B B primarily increases the contribution of fast P* → P + B B - → P + H B - two-step ET, where B-B is the "bridging" B-side bacteriochlorophyll. The second step (similar to ~6-8 ps) is slower than the first (similar to ~3-4 ps), unlike A-side two-step ET (P* → P + B A - → P + H A - ) where the second step (similar to ~1 ps) is faster than the first (similar to ~3-4 ps) in the native RC. Substitutions near H B , at L185 (Leu, Trp or Arg) and at M-polypeptide site M133/131 (Thr, Val or Glu), strongly affect the contribution of slower (20-50 ps) P* → P + H B - one-step superexchange ET. Here, both ET mechanisms are effective in directing electrons "the wrong way" to H B and both compete with internal conversion of P* to the ground state (similar to ~200 ps) and ET to the A-side cofactors. Collectively, the work demonstrates cooperative amino-acid control of rates, yields and mechanisms of ET in bacterial RCs and how A- vs. B-side charge separation can be tuned in both species.

Charge Separation↗
DOE OSTI2023

Tunable nanotextured materials

A material with nanopillar structures extending from a substrate. The nanopillars are engageable by organisms to cause an interaction, such as cellular destruction.

Laible, Philip D.↗
DOE OSTI2022

High Yield of B-Side Electron Transfer at 77 K in the Photosynthetic Reaction Center Protein from Rhodobacter sphaeroides

In this work, the primary electron transfer (ET) processes at 295 K and 77 K are compared for the Rhodobacter sphaeroides reaction center (RC) pigment-protein complex from thirteen mutants including a wild-type control. The engineered RCs bear mutations in the L and M polypeptides that largely inhibit ET from the excited state P* of the primary electron donor (P, a bacteriochlorophyll dimer) to the normally photoactive A-side cofactors and enhance ET to the C 2 -symmetry related, and normally photoinactive, B-side cofactors. P* decay is multi-exponential at both temperatures and modeled as arising from subpopulations that differ in contributions of two-step ET (e.g., P* → P + B B – → P + H B – ), one-step superexchange ET (e.g., P* → P + H B – ) and P* → ground state. [H B and B B are monomeric bacteriopheophytin and bacteriochlorophyll, respectively.] The relative abundances of the subpopulations and the inherent rate constants of the P* decay routes vary with temperature. Regardless, ET to produce P + H B – is generally faster at 77 K than at 295 K by about a factor of two. A key finding is that the yield of P + H B – , which ranges from ~5% to ~90% among the mutant RCs, is essentially the same at 77 K as at 295 K in each case. Overall, the results show that ET from P* to the B-side cofactors in these mutants does not require thermal activation and involves combinations of ET mechanisms analogous to those operative on the A side in the native RC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida KT2440 and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

09 BIOMASS FUELS↗
DOE OSTI2022

Localized functionalization of nanotextured surfaces

A material with a nanotexture comprising structures extending from a substrate. The structures are modified by coating the nanotexture with a protective coating and partially removing the coating, exposing a portion of the structure for functionalization.

Michalska, Martyna↗
DOE OSTI2022

Hidden vibronic and excitonic structure and vibronic coherence transfer in the bacterial reaction center

We report two-dimensional electronic spectroscopy (2DES) experiments on the bacterial reaction center (BRC) from purple bacteria, revealing hidden vibronic and excitonic structure. Through analysis of the coherent dynamics of the BRC, we identify multiple quasi-resonances between pigment vibrations and excitonic energy gaps, and vibronic coherence transfer processes that are typically neglected in standard models of photosynthetic energy transfer and charge separation. We support our assignment with control experiments on bacteriochlorophyll and simulations of the coherent dynamics using a reduced excitonic model of the BRC. We find that specific vibronic coherence processes can readily reveal weak exciton transitions. While the functional relevance of such processes is unclear, they provide a spectroscopic tool that uses vibrations as a window for observing excited state structure and dynamics elsewhere in the BRC via vibronic coupling. Vibronic coherence transfer reveals the upper exciton of the “special pair” that was weakly visible in previous 2DES experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Antimicrobial properties of nanostructured surfaces – demonstrating the need for a standard testing methodology

Bioinspired nanostructured materials that exhibit antimicrobial properties are being synthesized and tested at increasing rates for use in healthcare, manufacturing processes, and diagnostics. Although progress has been made in improving and understanding their bactericidal activity, arguably, the biggest problem currently in the field is the lack of a standard testing methodology that allows for optimal characterization and better comparison of emerging nanostructures. In this work, we examine two forms of nanostructured silicon that vary in their ability to kill certain bacterial species due to different physical mechanisms and derive guidelines for the comparative testing. We perform a comprehensive evaluation of methodologies used extensively in the field (e.g., colony counting and live dead analysis) and the novel application of high-throughput flow cytometry. The data reveal how the techniques are complementary but not always directly equivalent or correlative. Therefore, comparison of results obtained using different methodologies on different materials can be grossly misleading. We report significant variations in bactericidal efficiencies depending on experimental environments (medium type, etc.) and methodologies employed. In addition, we demonstrate how cytometry is yet another powerful complementary tool that can aid the mechanistic understanding of antimicrobial activities of rough surfaces. Besides standardization for comparison, ultimately, evaluation methods need to consider anticipated applications. Then and only then can the true potential (or limitation) of a novel material be determined for its suitability for advancement in a particular field of use.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

In Situ, Protein-Mediated Generation of a Photochemically Active Chlorophyll Analogue in a Mutant Bacterial Photosynthetic Reaction Center

All possible natural amino acids have been substituted for the native LeuL185 positioned near the B-side bacteriopheophytin (H B ) in the bacterial reaction center (RC) from Rhodobacter sphaeroides. Additional mutations are present that enhance electron transfer to the normally inactive B-side cofactors. About half the isolated RCs with Glu at L185 contain a magnesium chlorin (C B ) in place of H B . The chlorin is not the common BChl a oxidation product 3-desvinyl-3-acetyl chlorophyll a with a C-C bond in ring D and a C=C bond in ring B, but has properties consistent with reversal of these bond orders, giving 17,18-didehydro BChl a. In such RCs, charge-separated state P + C B – forms with ~5% yield. The other half of the GluL185-containing RCs have a bacteriochlorophyll a (BChl a) denoted β B in place of H B . Residues His, Asp, Asn and Gln at L185 yield RCs with ≥85% β B in the H B site, while most other amino acids result in RCs that retain H B (≥95%). To our knowledge, neither bacterial RCs that harbor five BChl a and one chlorophyll analog nor ones with six BChl a have been reported previously. The finding that altering the local environment within a cofactor binding site of a transmembrane complex leads to in situ generation of a photoactive chlorin with an unusual ring oxidation pattern suggests new strategies for amino-acid control over pigment type at specific sites in photosynthetic proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗