scholarly journals Dynamic control systems that mimic natural regulation of catabolic pathways enable rapid production of lignocellulose-derived bioproducts

2022 ◽  
Author(s):  
Joshua R Elmore ◽  
George L Peabody ◽  
Ramesh K Jha ◽  
Gara N Dexter ◽  
Taraka Dale ◽  
...  
Keyword(s):  
Growth Rate ◽  
Caulobacter Crescentus ◽  
Dynamic Control ◽  
Xylose Isomerase ◽  
Growth Defect ◽  
Catabolic Pathway ◽  
Muconic Acid ◽  
Catabolic Pathways ◽  
Pathway Expression ◽  
Wide Range

Expanding the catabolic repertoire of engineered microbial bioproduction hosts enables more efficient use of complex feedstocks such as lignocellulosic hydrolysates, but the deleterious effects of existing expression systems limit the maximum carry capacity for heterologous catabolic pathways. Here we demonstrate use of a conditionally beneficial oxidative xylose catabolic pathway to improve performance of a Pseudomonas putida strain that has been engineered for growth-coupled bioconversion of glucose into the valuable bioproduct cis,cis-muconic acid. In the presence of xylose, the pathway enhances growth rate, and therefor productivity, by >60%, but the metabolic burden of constitutive pathway expression reduces the its growth rate by >20% in the absence of xylose. To mitigate this growth defect, we develop a xylose biosensor based on the XylR transcription factor from Caulobacter crescentus NA1000 to autonomously regulate pathway expression. We generate a library of engineered xylose-sensitive promoters that cover a three order-of-magnitude range of expression levels to tune pathway expression. Using structural modeling to guide mutations, we engineer XylR with two and three orders-of-magnitude reduced sensitivity to xylose and L-arabinose, respectively. A previously developed heterologous xylose isomerase pathway is placed under control of the biosensor, which improves the growth rate with xylose as a carbon source by 10% over the original constitutively expressed pathway. Finally, the oxidative xylose catabolic pathway is placed under control of the biosensor, enabling the bioproduction strain to maintain the increased growth rate in the presence of xylose, without the growth defect incurred from constitutive pathway expression in the absence of xylose. Utilizing biosensors to autonomously regulate conditionally beneficial catabolic pathways is generalizable, and will be critical for engineering bioproduction hosts bacteria with the wide range of catabolic pathways required for bioconversion of complex feedstocks.

scholarly journals Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds

2004 ◽  
Vol 68 (3) ◽  
pp. 474-500 ◽  
Author(s):  
David Tropel ◽  
Jan Roelof van der Meer
Keyword(s):  
Aromatic Compounds ◽  
Transcriptional Control ◽  
Structural Information ◽  
Environmental Pollutants ◽  
Control Mechanisms ◽  
Catabolic Pathway ◽  
Transcription Control ◽  
Catabolic Pathways ◽  
Regulatory Systems ◽  
Pathway Expression

SUMMARY Human activities have resulted in the release and introduction into the environment of a plethora of aromatic chemicals. The interest in discovering how bacteria are dealing with hazardous environmental pollutants has driven a large research community and has resulted in important biochemical, genetic, and physiological knowledge about the degradation capacities of microorganisms and their application in bioremediation, green chemistry, or production of pharmacy synthons. In addition, regulation of catabolic pathway expression has attracted the interest of numerous different groups, and several catabolic pathway regulators have been exemplary for understanding transcription control mechanisms. More recently, information about regulatory systems has been used to construct whole-cell living bioreporters that are used to measure the quality of the aqueous, soil, and air environment. The topic of biodegradation is relatively coherent, and this review presents a coherent overview of the regulatory systems involved in the transcriptional control of catabolic pathways. This review summarizes the different regulatory systems involved in biodegradation pathways of aromatic compounds linking them to other known protein families. Specific attention has been paid to describing the genetic organization of the regulatory genes, promoters, and target operon(s) and to discussing present knowledge about signaling molecules, DNA binding properties, and operator characteristics, and evidence from regulatory mutants. For each regulator family, this information is combined with recently obtained protein structural information to arrive at a possible mechanism of transcription activation. This demonstrates the diversity of control mechanisms existing in catabolic pathways.

scholarly journals Wide range continuously tunable and fast thermal switching based on compressible graphene composite foams

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tingting Du ◽  
Zixin Xiong ◽  
Luis Delgado ◽  
Weizhi Liao ◽  
Joseph Peoples ◽  
...  
Keyword(s):  
Thermal Management ◽  
Dynamic Control ◽  
Operating Conditions ◽  
Dynamic Thermal Management ◽  
Graphene Composite ◽  
Continuous Tuning ◽  
Composite Foams ◽  
Wide Range ◽  
Thermal Switches ◽  
Thermal Switching

AbstractThermal switches have gained intense interest recently for enabling dynamic thermal management of electronic devices and batteries that need to function at dramatically varied ambient or operating conditions. However, current approaches have limitations such as the lack of continuous tunability, low switching ratio, low speed, and not being scalable. Here, a continuously tunable, wide-range, and fast thermal switching approach is proposed and demonstrated using compressible graphene composite foams. Large (~8x) continuous tuning of the thermal resistance is achieved from the uncompressed to the fully compressed state. Environmental chamber experiments show that our variable thermal resistor can precisely stabilize the operating temperature of a heat generating device while the ambient temperature varies continuously by ~10 °C or the heat generation rate varies by a factor of 2.7. This thermal device is promising for dynamic control of operating temperatures in battery thermal management, space conditioning, vehicle thermal comfort, and thermal energy storage.

Dependence of Microstructures and Mechanical Properties on the Growth Rate and Composition in Directionally Solidified Mg-Gd Alloys

2022 ◽  
Vol 327 ◽  
pp. 82-97
Author(s):  
He Qin ◽  
Guang Yu Yang ◽  
Shi Feng Luo ◽  
Tong Bai ◽  
Wan Qi Jie
Keyword(s):  
Mechanical Properties ◽  
Growth Rate ◽  
Tensile Strength ◽  
Ultimate Tensile Strength ◽  
Dendritic Structure ◽  
Directionally Solidified ◽  
Dendrite Morphology ◽  
Microstructural Parameters ◽  
Wide Range ◽  
Microstructures And Mechanical Properties

Microstructures and mechanical properties of directionally solidified Mg-xGd (5.21, 7.96 and 9.58 wt.%) alloys were investigated at a wide range of growth rates (V = 10-200 μm/s) under the constant temperature gradient (G = 30 K/mm). The results showed that when the growth rate was 10 μm/s, different interface morphologies were observed in three tested alloys: cellular morphology for Mg-5.21Gd alloy, a mixed morphology of cellular structure and dendritic structure for Mg-7.96Gd alloy and dendrite morphology for Mg-9.58Gd alloy, respectively. Upon further increasing the growth rate, only dendrite morphology was exhibited in all experimental alloys. The microstructural parameters (λ1, λ2) decreased with increasing the growth rate for all the experimental alloy, and the measured λ1 and λ2 values were in good agreement with Trivedi model and Kattamis-Flemings model, respectively. Vickers hardness and the ultimate tensile strength increased with the increase of the growth rate and Gd content, while the elongation decreased gradually. Furthermore, the relationships between the hardness, ultimate tensile strength, the growth rate and the microstructural parameters were discussed and compared with the previous experimental results.

Study of the low cycle fatigue of 12Cr18Ni10Ti steel based on fractal analysis and artificial intelligence approaches

2021 ◽  
Vol 87 (9) ◽  
pp. 59-67
Author(s):  
A. A. Khlybov ◽  
Yu. G. Kabaldin ◽  
M. S. Anosov ◽  
D. A. Ryabov ◽  
D. A. Shatagin
Keyword(s):  
Neural Network ◽  
Growth Rate ◽  
Fractal Dimension ◽  
Low Temperatures ◽  
Main Crack ◽  
Fatigue Loading ◽  
Wide Range ◽  
Lower Temperature ◽  
Number Of Cycles ◽  
Dimension Index

The evolution of the structure and assessment of the age limit of steel 12Cr18Ni10Ti upon fatigue loading is considered using neural network modeling and approaches of fractal analysis of the microstructure. An algorithm for processing images of the microstructures has been developed to improve their quality. An indicator of the fractal dimension of the image is used as a quantitative indicator for assessing the evolution of the microstructure of the surface metal layer. A quantitative assessment of the structures at different stress amplitudes is carried out in a wide range of low temperatures using the fractal dimension index. Correlation of the fractal dimension index with the run of the sample material is shown. The appearance of the main crack was observed in the range of 0.7 - 0.8 from the number of cycles to failure, after which the crack growth rate increased. At a lower temperature, the main crack is formed later, but further loading results in a higher crack growth rate. Formation of the secondary phases in austenitic steel at a lower temperature occurred at earlier stages than that at a temperature of t = +20°C, which led to hardening of the material. An artificial neural network (ANN) has been developed and trained for assessing structural changes in metal proceeding from the fractal dimensionality of the microstructure images at different stages of fatigue loading. The developed neural network made it possible to estimate with a sufficiently high accuracy the number of cycles before damage of the sample and the residual life of the material. Thus, the developed ANN can be used to assess the current state of the material in a wide range of low temperatures.

scholarly journals Genome-Wide fitness analysis of group B Streptococcus in human amniotic fluid reveals a transcription factor that controls multiple virulence traits

2021 ◽  
Vol 17 (3) ◽  
pp. e1009116
Author(s):  
Allison N. Dammann ◽  
Anna B. Chamby ◽  
Andrew J. Catomeris ◽  
Kyle M. Davidson ◽  
Hervé Tettelin ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Amniotic Fluid ◽  
Deletion Strain ◽  
Growth Defect ◽  
Wild Type ◽  
Human Amniotic Fluid ◽  
Wide Range ◽  
Pregnant Mice ◽  
Group B

Streptococcus agalactiae (group B Streptococcus; GBS) remains a dominant cause of serious neonatal infections. One aspect of GBS that renders it particularly virulent during the perinatal period is its ability to invade the chorioamniotic membranes and persist in amniotic fluid, which is nutritionally deplete and rich in fetal immunologic factors such as antimicrobial peptides. We used next-generation sequencing of transposon-genome junctions (Tn-seq) to identify five GBS genes that promote survival in the presence of human amniotic fluid. We confirmed our Tn-seq findings using a novel CRISPR inhibition (CRISPRi) gene expression knockdown system. This analysis showed that one gene, which encodes a GntR-class transcription factor that we named MrvR, conferred a significant fitness benefit to GBS in amniotic fluid. We generated an isogenic targeted deletion of the mrvR gene, which had a growth defect in amniotic fluid relative to the wild type parent strain. The mrvR deletion strain also showed a significant biofilm defect in vitro. Subsequent in vivo studies showed that while the mutant was able to cause persistent murine vaginal colonization, pregnant mice colonized with the mrvR deletion strain did not develop preterm labor despite consistent GBS invasion of the uterus and the fetoplacental units. In contrast, pregnant mice colonized with wild type GBS consistently deliver prematurely. In a sepsis model the mrvR deletion strain showed significantly decreased lethality. In order to better understand the mechanism by which this newly identified transcription factor controls GBS virulence, we performed RNA-seq on wild type and mrvR deletion GBS strains, which revealed that the transcription factor affects expression of a wide range of genes across the GBS chromosome. Nucleotide biosynthesis and salvage pathways were highly represented among the set of differentially expressed genes, suggesting that MrvR may be involved in regulating nucleotide availability.

scholarly journals Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR

2015 ◽  
Vol 1 (11) ◽  
pp. e1501087 ◽  
Author(s):  
Chaowei Shi ◽  
Pascal Fricke ◽  
Lin Lin ◽  
Veniamin Chevelkov ◽  
Melanie Wegstroth ◽  
...  
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Caulobacter Crescentus ◽  
Heavy Atom ◽  
Cytoskeletal Proteins ◽  
Atomic Resolution ◽  
Hydrophobic Core ◽  
X Ray Crystallography ◽  
Wide Range ◽  
Resolution Structure

Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the speciesCaulobacter crescentusis not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR–derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

Latitude and Relative Growth in the Razor Clam, Siliqua Patula

1931 ◽  
Vol 8 (3) ◽  
pp. 228-249
Author(s):  
F. W. WEYMOUTH ◽  
H. C. McMILLIN ◽  
WILLIS H. RICH
Keyword(s):  
Growth Rate ◽  
Life Span ◽  
Relative Growth Rate ◽  
Growth Data ◽  
Natural Conditions ◽  
Relative Growth ◽  
Absolute Growth Rate ◽  
Mathematical Expressions ◽  
Wide Range ◽  
Absolute Growth

1. The present paper is a study of the growth of a clam (Siliqua patula) under natural conditions and over a wide range of latitude. 2. Various constants derived from the growth data are compared for the different localities. For this species, over the range considered, growth in the southern localities as compared with the northern is initially more rapid but less sustained, leads to a smaller total length and is associated with a shorter life span. 3. Reasons are presented for considering the relative growth-rate as a particularly significant constant leading to more sound biological conclusions than the use of the absolute growth-rate. 4. On the basis of the relative growth-rate, current mathematical expressions for the course of growth are discussed and a formula used which emphasises Minot's conception of a growth-rate constantly declining with age. This expression L = Be-ce-ce-kt, in which L = length at time t, e = base of natural logarithms, and B, c and k are constants, is found to graduate the extensive data in clam growth with significant accuracy.

Microbial community composition is linked to Sphagnum acclimation to warming

2021 ◽  
Author(s):  
Tatjana Živković ◽  
Alyssa A Carell ◽  
Gustaf Granath ◽  
Mats B Nilsson ◽  
Manuel Helbig ◽  
...  
Keyword(s):  
Growth Rate ◽  
Host Plant ◽  
Climate Warming ◽  
Elevated Temperatures ◽  
Critical Role ◽  
Temperature Acclimation ◽  
Microbial Interactions ◽  
Germ Free ◽  
Wide Range ◽  
Thermal Origin

<p>Peatlands store about third of the terrestrial carbon (C) and exert long-term climate cooling. Dominant plant genera in acidic peatlands, <em>Sphagnum</em> mosses, are main contributors to net primary productivity. Through associative relationships with diverse microbial organisms (microbiome), <em>Sphagnum</em> mosses control major biogeochemical processes, namely uptake, storage and potential release of carbon and nitrogen. Climate warming is expected to negatively impact C accumulation in peatlands and alter nutrient cycling, however <em>Sphagnum</em>-dominated peatland resilience to climate warming may depend on <em>Sphagnum</em>-microbiome associations. The ability of the microbiome to rapidly acclimatize to warming may aid <em>Sphagnum</em> exposed to elevated temperatures through host-microbiome acquired thermotolerance. We investigated the role of the microbiome on <em>Sphagnum</em>’s ability to acclimate to elevated temperatures using a microbiome-transfer approach to test: a) whether the thermal origin of the microbiome influences acclimation of <em>Sphagnum</em> growth and b) if microbial benefits to <em>Sphagnum</em> growth depend on donor <em>Sphagnum</em> species.</p><p>            Using a full-factorial design, microbiomes were separated from <em>Sphagnum</em> “donor” species from four different peatlands across a wide range of thermal environments (11.4-27°C). The microbiomes were transferred onto germ-free “recipient” <em>Sphagnum</em> species in the laboratory and exposed to a range of experimental temperatures (8.5 – 26.5°C) for growth analysis over 4 weeks.</p><p>            Normalized growth rates were maximized for plants that received a microbiome from a matched “donor” and with a similar origin temperature (ΔT<sub>treatment-origin</sub>: 0.3±0.9°C [±standard error], p = 0.73). For non-matched “donor-recipient” <em>Sphagnum</em> pairs, ΔT<sub>treatment-origin</sub> was slightly negative with -4.1±2.1°C (p = 0.06). The largest growth rate of the “recipient” was measured when grown with a microbiome from a matching “donor” <em>Sphagnum</em> species and was 252% and 48% larger than the maximum growth rate of the germ-free <em>Sphagnum</em> and the non-matched “donor-recipient” <em>Sphagnum</em> pairs, respectively.</p><p>            Our results suggest that the composition of the <em>Sphagnum</em> microbiome plays a critical role in host plant temperature acclimation. We found that microbially-provided benefits to the host plant were most pronounced when: 1) the thermal origin of the microbiome is similar to experimental temperatures, and 2) when donor and recipient <em>Sphagnum</em> species are the same. Together, these results suggest that <em>Sphagnum</em> temperature acclimation can be modulated, in part, by microbial interactions and may potentially play a role in peatland resilience to climate warming.</p>

Functional Contacts With a Range of Splicing Proteins Suggest a Central Role for Brr2p in the Dynamic Control of the Order of Events in Spliceosomes ofSaccharomyces cerevisiae

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1451-1467 ◽  
Author(s):  
Rob W van Nues ◽  
Jean D Beggs
Keyword(s):  
Protein Interactions ◽  
Dynamic Control ◽  
Splicing Factors ◽  
Functional Protein ◽  
U6 Snrna ◽  
Wide Range ◽  
Snrnp Protein ◽  
Associated Proteins ◽  
Step Factor ◽  
Hybrid Screening

AbstractMapping of functional protein interactions will help in understanding conformational rearrangements that occur within large complexes like spliceosomes. Because the U5 snRNP plays a central role in pre-mRNA splicing, we undertook exhaustive two-hybrid screening with Brr2p, Prp8p, and other U5 snRNP-associated proteins. DExH-box protein Brr2p interacted specifically with five splicing factors: Prp8p, DEAH-box protein Prp16p, U1 snRNP protein Snp1p, second-step factor Slu7p, and U4/U6.U5 tri-snRNP protein Snu66p, which is required for splicing at low temperatures. Co-immunoprecipitation experiments confirmed direct or indirect interactions of Prp16p, Prp8p, Snu66p, and Snp1p with Brr2p and led us to propose that Brr2p mediates the recruitment of Prp16p to the spliceosome. We provide evidence that the prp8-1 allele disrupts an interaction with Brr2p, and we propose that Prp8p modulates U4/U6 snRNA duplex unwinding through another interaction with Brr2p. The interactions of Brr2p with a wide range of proteins suggest a particular function for the C-terminal half, bringing forward the hypothesis that, apart from U4/U6 duplex unwinding, Brr2p promotes other RNA rearrangements, acting synergistically with other spliceosomal proteins, including the structurally related Prp2p and Prp16p. Overall, these protein interaction studies shed light on how splicing factors regulate the order of events in the large spliceosome complex.

scholarly journals Magnetic Rayleigh–Taylor instability at a contact discontinuity with an oblique magnetic field

2020 ◽  
Vol 634 ◽  
pp. A96
Author(s):  
E. Vickers ◽  
I. Ballai ◽  
R. Erdélyi
Keyword(s):  
Magnetic Field ◽  
Growth Rate ◽  
Dispersion Relation ◽  
Contact Discontinuity ◽  
Homogeneous Magnetic Field ◽  
Taylor Instability ◽  
Wide Range ◽  
Rayleigh Taylor Instability ◽  
The Magnetic Field ◽  
Theoretical Results

Aims. We investigate the nature of the magnetic Rayleigh–Taylor instability at a density interface that is permeated by an oblique homogeneous magnetic field in an incompressible limit. Methods. Using the system of linearised ideal incompressible magnetohydrodynamics equations, we derive the dispersion relation for perturbations of the contact discontinuity by imposing the necessary continuity conditions at the interface. The imaginary part of the frequency describes the growth rate of waves due to instability. The growth rate of waves is studied by numerically solving the dispersion relation. Results. The critical wavenumber at which waves become unstable, which is present for a parallel magnetic field, disappears because the magnetic field is inclined. Instead, waves are shown to be unstable for all wavenumbers. Theoretical results are applied to diagnose the structure of the magnetic field in prominence threads. When we apply our theoretical results to observed waves in prominence plumes, we obtain a wide range of field inclination angles, from 0.5° up to 30°. These results highlight the diagnostic possibilities that our study offers.

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