A
bstract
We study the dynamics of a black hole in an asymptotically
AdS
d
×
S
d
space-time in the limit of a large number of dimensions,
d
→ ∞. Such a black hole is known to become dynamically ...unstable below a critical radius. We derive the dispersion relation for the quasinormal mode that governs this instability in an expansion in 1
/d
. We also provide a full nonlinear analysis of the instability at leading order in 1
/d
. We find solutions that resemble the lumpy black spots and black belts previously constructed numerically for small
d
, breaking the SO(
d
+ 1) rotational symmetry of the sphere down to SO(
d
). We are also able to follow the time evolution of the instability. Due possibly to limitations in our analysis, our time dependent simulations do not settle down to stationary solutions. This work has relevance for strongly interacting gauge theories; through the AdS/CFT correspondence, the special case
d
= 5 corresponds to maximally supersymmetric Yang-Mills theory on a spatial
S
3
in the microcanonical ensemble and in a strong coupling and large number of colors limit.
Carbon source-dependent control of bacterial growth is fundamental to bacterial physiology and survival. However, pinpointing the metabolic steps important for cell growth is challenging due to the ...complexity of cellular networks. Here, the elastic net model and multilayer perception model that integrated genome-wide gene-deletion data and simulated flux distributions were constructed to identify metabolic reactions beneficial or detrimental to
Escherichia coli
grown on 30 different carbon sources. Both models outperformed traditional in silico methods by identifying not just essential reactions but also nonessential ones that promote growth. They successfully predicted metabolic reactions beneficial to cell growth, with high convergence between the models. The models revealed that biosynthetic pathways generally promote growth across various carbon sources, whereas the impact of energy-generating pathways varies with the carbon source. Intriguing predictions were experimentally validated for findings beyond experimental training data and the impact of various carbon sources on the glyoxylate shunt, pyruvate dehydrogenase reaction, and redundant purine biosynthesis reactions. These highlight the practical significance and predictive power of the models for understanding and engineering microbial metabolism.
Synopsis
Explainable machine learning models were developed to understand the effects of 30 different carbon sources on
E. coli
growth and their mechanisms down to the individual metabolic steps.
A regression model of elastic net (EN) and a deep learning model of multilayer perception (MLP) were trained to learn patterns and relationships between the simulated flux distributions and gene-deletion dataset.
The lack of interpretability of the traditional MLP model was overcome with the SHAP interpretation method.
This approach outperformed the previous reaction deletion simulation by identifying non-essential growth-promoting reactions in addition to the essential reactions.
The models’ practical application was demonstrated by experimentally validating the predicted reactions responsible for increased or decreased cell growth under different carbon conditions.
Explainable machine learning models were developed to understand the effects of 30 different carbon sources on
E. coli
growth and their mechanisms down to the individual metabolic steps.
Pseudomonas putida S12 is a gram-negative bacterium renowned for its high tolerance to organic solvents and metabolic versatility, making it attractive for various applications, including ...bioremediation and the production of aromatic compounds, bioplastics, biofuels, and value-added compounds. However, a metabolic model of S12 has yet to be developed.
In this study, we present a comprehensive and highly curated genome-scale metabolic network model of S12 (iSH1474), containing 1,474 genes, 1,436 unique metabolites, and 2,938 metabolic reactions. The model was constructed by leveraging existing metabolic models and conducting comparative analyses of genomes and phenomes. Approximately 2,000 different phenotypes were measured for S12 and its closely related KT2440 strain under various nutritional and environmental conditions. These phenotypic data, combined with the reported experimental data, were used to refine and validate the reconstruction. Model predictions quantitatively agreed well with in vivo flux measurements and the batch cultivation of S12, which demonstrated that iSH1474 accurately represents the metabolic capabilities of S12. Furthermore, the model was simulated to investigate the maximum theoretical metabolic capacity of S12 growing on toxic organic solvents.
iSH1474 represents a significant advancement in our understanding of the cellular metabolism of P. putida S12. The combined results of metabolic simulation and comparative genome and phenome analyses identified the genetic and metabolic determinants of the characteristic phenotypes of S12. This study could accelerate the development of this versatile organism as an efficient cell factory for various biotechnological applications.
Nissle 1917 (EcN) is an intestinal probiotic that is effective for the treatment of intestinal disorders, such as inflammatory bowel disease and ulcerative colitis. EcN is a representative ...Gram-negative probiotic in biomedical research and is an intensively studied probiotic. However, to date, its genome-wide metabolic network model has not been developed. Here, we developed a comprehensive and highly curated EcN metabolic model, referred to as iDK1463, based on genome comparison and phenome analysis. The model was improved and validated by comparing the simulation results with experimental results from phenotype microarray tests. iDK1463 comprises 1463 genes, 1313 unique metabolites, and 2984 metabolic reactions. Phenome data of EcN were compared with those of
intestinal commensal K-12 MG1655. iDK1463 was simulated to identify the genetic determinants responsible for the observed phenotypic differences between EcN and K-12. Further, the model was simulated for gene essentiality analysis and utilization of nutrient sources under anaerobic growth conditions. These analyses provided insights into the metabolic mechanisms by which EcN colonizes and persists in the gut. iDK1463 will contribute to the system-level understanding of the functional capacity of gut microbes and their interactions with microbiota and human hosts, as well as the development of live microbial therapeutics.
This study investigates the effect of annealing on the mechanical properties of fused deposition modeling (FDM) 3D-printed recycled carbon fiber (rCF)-reinforced composites. In this study, filaments ...for FDM 3D printers are self-fabricated from pure acrylonitrile butadiene styrene (ABS) and ABS reinforced with fiber content of 10 wt% and 20 wt% rCF. This study explores the tensile and flexural properties as a function of the annealing temperature and time for the three different fiber content values. In addition, dimensional measurements of the shape changes are performed to determine the suitability of applying annealing in practical manufacturing processes. The results show that annealing improves the mechanical properties by narrowing the voids between the beads, which occur during the FDM process, and by reducing the gaps between the fibers and polymer. Following annealing, the largest tensile and flexural strength improvements are 12.64% and 42.33%, respectively, for the 20 wt% rCF content samples. Moreover, compared with the pure ABS samples, the annealing effect improves the mechanical properties of the rCF-reinforced samples more effectively, and they have higher dimensional stability, indicating their suitability for annealing. These results are expected to expand the application fields of rCF and greatly increase the potential use of FDM-printed parts.
This study investigates the surface properties and adhesive strength of polypropylene (PP) in order to enhance the bond between PP injection-molded specimens and polyvinyl chloride (PVC) synthetic ...artificial leather. Plasma, primer, and flame treatments were applied to the surface of each specimen prepared using the two types of injection molds. The surface morphology, surface roughness, and contact angle were analyzed, and peel-strength analyses and a morphological inspections of the peeled specimens were performed. The peeling strength of the PP injection molding was measured, followed by a morphological examination of the peeled specimens. The plasma and flame treatments improved the peel strength, and the plasma and flame treatments changed the rough exterior to a hydrophilic surface, improving the peel strength. In addition, the primer treatment exhibited a lower peel strength than did the other treatments. This confirmed the low adhesion of the primer to the hydrophobic PP surface. The outcomes of this study can be employed across a multitude of industries that require improved adhesion for PP injection molded products.
Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a ...chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportunity to investigate the full range of cellular responses to thermal stress, ranging from temporary adjustment to phenotypic adaptation at multi-omics levels. Heat-responsive and time-resolved changes in the transcriptome and metabolome of a widely used E. coli strain BL21(DE3) were explored in which the temperature was upshifted from 37 to 42 °C. Omics profiles were categorized into early (2 and 10 min), middle (0.5, 1, and 2 h), and late (4, 8, and 40 h) stages of heat stress, each of which reflected the initiation, adaptation, and phenotypic plasticity steps of the stress response. The continued heat stress modulated global gene expression by controlling the expression levels of sigma factors in different time frames, including unexpected downregulation of the second heatshock sigma factor gene (rpoE) upon the heat stress. Trehalose, cadaverine, and enterobactin showed increased production to deal with the heat-induced oxidative stress. Genes highly expressed at the late stage were experimentally validated to provide thermotolerance. Intriguingly, a cryptic capsular gene cluster showed considerably high expression level only at the late stage, and its expression was essential for cell growth at high temperature. Granule-forming and elongated cells were observed at the late stage, which was morphological plasticity occurred as a result of acclimation to the continued heat stress. Whole process of thermal adaptation along with the genetic and metabolic changes at fine temporal resolution will contribute to far-reaching comprehension of the heat shock response. Further, the identified thermotolerant genes will be useful to rationally engineer thermotolerant microorganisms.
On the stability of U.S. politics Congleton, Roger D.; Kim, Youngshin; Marsella, Alexander
Public choice,
04/2020, Volume:
183, Issue:
1/2
Journal Article
Peer reviewed
An important issue associated with empirical research is the extent to which statistical results continue to hold in the post-sample period. Although many tests of robustness within the period of a ...given study are routinely reported, relatively little attention is paid to model performance in the post-sample period. This paper examines the post-sample performance of the Congleton and Shughart (Econ Inq 28(1): 109–132, 1990) estimates of three public choice models of Social Security benefit levels. The Social Security program is the single largest line item in the federal budget; so, examining the post-sample performance of the Congleton–Shughart estimates also sheds light on the long-run stability of political processes in the United States. In general, we find that the three public choice models perform well in the post-sample period, although there are several caveats to that conclusion. The results of our post-sample study also suggest that the political processes of the United States with respect to major fiscal policies are more stable and robust than news reports suggest.
Maintaining a vacuum between the two glasses to maximize the heat insulating performance, it is indispensable to array the pillar for the vacuum glazing to maintain the vacuum gap. In this paper, to ...investigate the effect of the spacing of the pillars arranged using the screen printing method on the strength of the glass, a bending strength test was carried out by design and fabricating a ROR bending strength test jig based on the Euro standard. In the strength test results, the experimental results were analyzed using the Weibull distribution, which is a statistical analysis method mainly used for evaluating the breaking strength of brittle material. Based on the analysis results, the placement spacing of the pillars proved validity for maintaining the vacuum glass gaps.
D-Tagatose is a promising low-calorie sugar-substituting sweetener in the food industry. Most ingested D-tagatose is fermented by intestinal microorganisms. Until now, Escherichia coli has been ...considered incapable of growing on D-tagatose. Here, we discovered a gene cluster involved in D-tagatose utilization in E. coli. The chromosome of the intestinal probiotic E. coli Nissle 1917 contains a six-gene cluster encoding the ABC transporter, D-tagatose kinase, D-tagatose-bisphosphate aldolase, and putative aldose 1-epimerase. The functionality of the gene cluster was experimentally validated. Based on single-gene deletions, D-tagatose dissimilation occurs via D-tagatose 6-phosphate to D-tagatose 1,6-bisphosphate to D-glyceraldehyde 3-phosphate plus dihydroxyacetone phosphate. Remarkably, this gene cluster was located in 93% of the completely sequenced genomes of the E. coli B2 phylogroup, which contains the majority of extraintestinal pathogenic and adherent-invasive E. coli strains prevalent in patients with inflammatory bowel disease. This highlights the importance of understanding the clinical significance of D-tagatose in microbiota alterations.
Display omitted
•A gene cluster for D-tagatose utilization was found in Escherichia coli•D-Tagatose catabolic pathway was experimentally identified•Expression of the gene cluster changed the phenotype from Tag− to Tag+•The gene cluster is prevalent in virulence-associated E. coli B2 phylogroup
Genetics; Bacteriology.
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