Distribution of particles which produces a "smart" material

If $A_q(\beta, \alpha, k)$ is the scattering amplitude, corresponding to a potential $q\in L^2(D)$, where $D\subset\R^3$ is a bounded domain, and $e^{ik\alpha \cdot x}$ is the incident plane wave, then we call the radiation pattern the function $A(\beta):=A_q(\beta, \alpha, k)$, where the unit vector $\alpha$, the incident direction, is fixed, and $k>0$, the wavenumber, is fixed. It is shown that any function $f(\beta)\in L^2(S^2)$, where $S^2$ is the unit sphere in $\R^3$, can be approximated with any desired accuracy by a radiation pattern: $||f(\beta)-A(\beta)||_{L^2(S^2)}<\epsilon$, where $\epsilon>0$ is an arbitrary small fixed number. The potential $q$, corresponding to $A(\beta)$, depends on $f$ and $\epsilon$, and can be calculated analytically. There is a one-to-one correspondence between the above potential and the density of the number of small acoustically soft particles $D_m\subset D$, $1\leq m\leq M$, distributed in an a priori given bounded domain $D\subset\R^3$. The geometrical shape of a small particle $D_m$ is arbitrary, the boundary $S_m$ of $D_m$ is Lipschitz uniformly with respect to $m$. The wave number $k$ and the direction $\alpha$ of the incident upon $D$ plane wave are fixed.It is shown that a suitable distribution of the above particles in $D$ can produce the scattering amplitude $A(\alpha',\alpha)$, $\alpha',\alpha\in S^2$, at a fixed $k>0$, arbitrarily close in the norm of $L^2(S^2\times S^2)$ to an arbitrary given scattering amplitude $f(\alpha',\alpha)$, corresponding to a real-valued potential $q\in L^2(D)$.Comment: corrected typo

Comparative analysis reveals the modular functional build-up of megaplasmid pTTS12 of Pseudomonas putida S12: a paradigm for transferable traits, plasmid stability and inheritance?

Microbial Biotechnolog

Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: Genetic and physiological basis for improved production

The unknown genetic basis for improved phenol production by a recombinant Pseudomonas putida S12 derivative bearing the tpl (tyrosine-phenol lyase) gene was investigated via comparative transcriptomics, nucleotide sequence analysis, and targeted gene disruption. We show upregulation of tyrosine biosynthetic genes and possibly decreased biosynthesis of tryptophan caused by a mutation in the trpE gene as the genetic basis for the enhanced phenol production. In addition, several genes in degradation routes connected to the tyrosine biosynthetic pathway were upregulated. This either may be a side effect that negatively affects phenol production or may point to intracellular accumulation of tyrosine or its intermediates. A number of genes identified by the transcriptome analysis were selected for targeted disruption in P. putida S12TPL3. Physiological and biochemical examination of P. putida S12TPL3 and these mutants led to the conclusion that the metabolic flux toward tyrosine in P. putida S12TPL3 was improved to such an extent that the heterologous tyrosine-phenol lyase enzyme had become the rate-limiting step in phenol biosynthesis. Copyright © 2008, American Society for Microbiology. All Rights Reserved

Physiological and genome-wide transcriptional responses of Saccharomyees cerevisiae to high carbon dioxide concentrations

Microbial Biotechnolog

Novel toxin-antitoxin module slvT-slvA regulates megaplasmid stability and incites solvent tolerance in Pseudomonas putida S12

Pseudomonas putida S12 is highly tolerant of organic solvents in saturating concentrations, rendering this microorganism suitable for the industrial production of various aromatic compounds. Previous studies revealed that P. putida S12 contains the single-copy 583-kbp megaplasmid pTTS12. pTTS12 carries several important operons and gene clusters facilitating P. putida S12 survival and growth in the presence of toxic compounds or other environmental stresses. We wished to revisit and further scrutinize the role of pTTS12 in conferring solvent tolerance. To this end, we cured the megaplasmid from P. putida S12 and conclusively confirmed that the SrpABC efflux pump is the major determinant of solvent tolerance on the megaplasmid pTTS12. In addition, we identified a novel toxin-antitoxin module (proposed gene names slvT and slvA, respectively) encoded on pTTS12 which contributes to the solvent tolerance phenotype and is important for conferring stability to the megaplasmid. Chromosomal introduction of the srp operon in combination with the slvAT gene pair created a solvent tolerance phenotype in non-solvent-tolerant strains, such as P. putida KT2440, Escherichia coli TG1, and E. coli BL21(DE3).Microbial Biotechnolog

The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur

FWN – Publicaties zonder aanstelling Universiteit Leide

Toward microbial recycling and upcycling of plastics: prospects and challenges

Annually, 400 Mt of plastics are produced of which roughly 40% is discarded within a year. Current plastic waste management approaches focus on applying physical, thermal, and chemical treatments of plastic polymers. However, these methods have severe limitations leading to the loss of valuable materials and resources. Another major drawback is the rapid accumulation of plastics into the environment causing one of the biggest environmental threats of the twenty-first century. Therefore, to complement current plastic management approaches novel routes toward plastic degradation and upcycling need to be developed. Enzymatic degradation and conversion of plastics present a promising approach toward sustainable recycling of plastics and plastics building blocks. However, the quest for novel enzymes that efficiently operate in cost-effective, large-scale plastics degradation poses many challenges. To date, a wide range of experimental set-ups has been reported, in many cases lacking a detailed investigation of microbial species exhibiting plastics degrading properties as well as of their corresponding plastics degrading enzymes. The apparent lack of consistent approaches compromises the necessary discovery of a wide range of novel enzymes. In this review, we discuss prospects and possibilities for efficient enzymatic degradation, recycling, and upcycling of plastics, in correlation with their wide diversity and broad utilization. Current methods for the identification and optimization of plastics degrading enzymes are compared and discussed. We present a framework for a standardized workflow, allowing transparent discovery and optimization of novel enzymes for efficient and sustainable plastics degradation in the future.Microbial Biotechnolog

Regulation of solvent tolerance in Pseudomonas putida S12 mediated by mobile elements

Organic solvent-tolerant bacteria are outstanding and versatile hosts for the bio-based production of a broad range of generally toxic aromatic compounds. The energetically costly solvent tolerance mechanisms are subject to multiple levels of regulation, involving among other mobile genetic elements. The genome of the solvent-tolerant Pseudomonas putida S12 contains many such mobile elements that play a major role in the regulation and adaptation to various stress conditions, including the regulation of expression of the solvent efflux pump SrpABC. We recently sequenced the genome of P. putida S12. Detailed annotation identified a threefold higher copy number of the mobile element ISS12 in contrast to earlier observations. In this study, we describe the mobile genetic elements and elaborate on the role of ISS12 in the establishment and maintenance of solvent tolerance in P. putida. We identified three different variants of ISS12 of which a single variant exhibits a high translocation rate. One copy of this variant caused a loss of solvent tolerance in the sequenced strain by disruption of srpA. Solvent tolerance could be restored by applying selective pressure, leading to a clean excision of the mobile element.Microbial Biotechnolog

Cell-to-cell heterogeneity of phosphate gene expression in yeast is controlled by alternative transcription, 14-3-3 and Spl2

Dependent on phosphate availability the yeast Saccharomyces cerevisiae expresses either low or high affinity phosphate transporters. In the presence of phosphate yeast cells still express low levels of the high affinity phosphate transporter Pho84. The regulator Spl2 is expressed in approximately 90% of the cells, and is not expressed in the remaining cells. Here we report that deletion of RRP6, encoding an exonuclease degrading non-coding RNA, or BMH1, encoding the major 14-3-3 isoform, resulted in less cells expressing SPL2 and in increased levels of RNA transcribed from sequences upstream of the SPL2 coding region. SPL2 stimulates its own expression and that of PHO84 ensuing a positive feedback. Upon deletion of the region responsible for upstream SPL2 transcription almost all cells express SPL2. These results indicate that the cell-to-cell variation in PHO84 and SPL2 expression is dependent on a specific part of the SPL2 promoter and is controlled by Bmh1 and Spl2.Microbial Biotechnolog

Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae - A chemostat culture study

FWN – Publicaties zonder aanstelling Universiteit Leide