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https://www.readbyqxmd.com/read/28639170/bistability-and-asynchrony-in-a-boolean-model-of-the-l-arabinose-operon-in-escherichia-coli
#1
Andy Jenkins, Matthew Macauley
The lactose operon in Escherichia coli was the first known gene regulatory network, and it is frequently used as a prototype for new modeling paradigms. Historically, many of these modeling frameworks use differential equations. More recently, Stigler and Veliz-Cuba proposed a Boolean model that captures the bistability of the system and all of the biological steady states. In this paper, we model the well-known arabinose operon in E. coli with a Boolean network. This has several complex features not found in the lac operon, such as a protein that is both an activator and repressor, a DNA looping mechanism for gene repression, and the lack of inducer exclusion by glucose...
June 21, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28494968/bistability-and-nonmonotonic-induction-of-the-lac-operon-in-the-natural-lactose-uptake-system
#2
Dominique Zander, Daniel Samaga, Ronny Straube, Katja Bettenbrock
The Escherichia coli lac operon is regulated by a positive feedback loop whose potential to generate an all-or-none response in single cells has been a paradigm for bistable gene expression. However, so far bistable lac induction has only been observed using gratuitous inducers, raising the question about the biological relevance of bistable lac induction in the natural setting with lactose as the inducer. In fact, the existing experimental evidence points to a graded rather than an all-or-none response in the natural lactose uptake system...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28463205/aggregation-for-computing-multi-modal-stationary-distributions-in-1-d-gene-regulatory-networks
#3
Neslihan Avcu, Nihal Pekergin, Ferhan Pekergin, Cuneyt Guzelis
This paper proposes aggregation-based, three-stage algorithms to overcome the numerical problems encountered in computing stationary distributions and mean first passage times for multi-modal birth-death processes of large state space sizes. The considered birth-death processes which are defined by Chemical Master Equations are used in modeling stochastic behavior of gene regulatory networks. Computing stationary probabilities for a multi-modal distribution from Chemical Master Equations is subject to have numerical problems due to the probability values running out of the representation range of the standard programming languages with the increasing size of the state space...
April 27, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28463103/a-conserved-hexanucleotide-motif-is-important-in-uv-inducible-promoters-in-sulfolobus-acidocaldarius
#4
Thuong Ngoc Le, Alexander Wagner, Sonja-Verena Albers
Upon DNA damage, Sulfolobales exhibit a global gene regulatory response resulting in the expression of DNA transfer and repair proteins and the repression of the cell division machinery. Because the archaeal DNA damage response is still poorly understood, we investigated the promoters of the highly induced ups operon. Ups pili are involved in cellular aggregation and DNA exchange between cells. With LacS reporter gene assays we identified a conserved, non-palindromic hexanucleotide motif upstream of the ups core promoter elements to be essential for promoter activity...
May 3, 2017: Microbiology
https://www.readbyqxmd.com/read/28387245/design-and-application-of-a-lactulose-biosensor
#5
Jieyuan Wu, Peixia Jiang, Wei Chen, Dandan Xiong, Linglan Huang, Junying Jia, Yuanyuan Chen, Jian-Ming Jin, Shuang-Yan Tang
In this study the repressor of Escherichia coli lac operon, LacI, has been engineered for altered effector specificity. A LacI saturation mutagenesis library was subjected to Fluorescence Activated Cell Sorting (FACS) dual screening. Mutant LacI-L5 was selected and it is specifically induced by lactulose but not by other disaccharides tested (lactose, epilactose, maltose, sucrose, cellobiose and melibiose). LacI-L5 has been successfully used to construct a whole-cell lactulose biosensor which was then applied in directed evolution of cellobiose 2-epimerase (C2E) for elevated lactulose production...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28382022/occlusion-of-the-ribosome-binding-site-connects-the-translational-initiation-frequency-mrna-stability-and-premature-transcription-termination
#6
Mette Eriksen, Kim Sneppen, Steen Pedersen, Namiko Mitarai
Protein production is controlled by ribosome binding to the messenger RNA (mRNA), quantified in part by the binding affinity between the ribosome and the ribosome binding sequence on the mRNA. Using the E. coli lac operon as model, Ringquist et al. (1992) found a more than 1,000-fold difference in protein yield when varying the Shine-Dalgarno sequence and its distance to the translation start site. Their proposed model accounted for this large variation by only a variation in the binding affinity and the subsequent initiation rate...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28193904/effector-overlap-between-the-lac-and-mel-operons-of-escherichia-coli-induction-of-the-mel-operon-with-%C3%AE-galactosides
#7
Atul Narang, Stefan Oehler
The lac (lactose) operon (which processes β-galactosides) and the mel (melibiose) operon (which processes α-galactosides) of Escherichia coli have a close historical connection. A number of shared substrates and effectors of the permeases and regulatory proteins have been reported over the years. Until now, β-thiogalactosides like TMG (methyl-β-d-thiogalactopyranoside) and IPTG (isopropyl-β-d-thiogalactopyranoside) have not generally been considered to be inducers of the mel operon. The same is true for β-galactosides such as lactose [β-d-galactopyranosyl-(1→4)-d-glucose], which is a substrate but is not itself an inducer of the lac operon...
May 1, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28113910/robust-reachability-of-boolean-control-networks
#8
Fangfei Li, Yang Tang
Boolean networks serve a powerful tool in analysis of genetic regulatory networks since it emphasizes the fundamental principles and establishes a nature framework for capturing the dynamics of regulation of cellular states. In this paper, the robust reachability of Boolean control networks is investigated by means of semi-tensor product. Necessary and sufficient conditions for the robust reachability of Boolean control networks are provided, in which control inputs relying on disturbances or not are considered, respectively...
April 20, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27785540/construction-properties-and-application-of-the-pcb5-plasmid-a-novel-conjugative-shuttle-vector-with-a-cupriavidus-basilensis-origin-of-replication
#9
Sheng Wang, Mei-Nan Zhang, Na-Ling Bai, Hai-Tao Ding, Xu-Fen Zhu, Yu-Hua Zhao
Cupriavidus basilensis is a species with diverse metabolic capabilities, including degradation of xenobiotics and heavy metal resistance. Although the genomes of several strains of this species have been sequenced, no plasmid has yet been constructed for genetic engineering in this species. In this study, we identified a novel plasmid, designated pWS, from C. basilensis WS with a copy number of 1-3 per cell and a length of 2150 bp. pWS contained three protein-coding genes, among which only rep was required for plasmid replication...
February 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27783696/supercoiling-effects-on-short-range-dna-looping-in-e-coli
#10
Lauren S Mogil, Nicole A Becker, L James Maher
DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades. Here we adapt this model to test the hypothesis that negative superhelical strain facilitates the formation of short-range (6-8 DNA turns) repression loops in E. coli. The natural negative superhelicity of E. coli DNA is regulated by the interplay of gyrase and topoisomerase enzymes, adding or removing negative supercoils, respectively. Here, we measured quantitatively DNA looping in three different E...
2016: PloS One
https://www.readbyqxmd.com/read/27747296/the-spl-serine-proteases-modulate-staphylococcus-aureus-protein-production-and-virulence-in-a-rabbit-model-of-pneumonia
#11
Alexandra E Paharik, Wilmara Salgado-Pabon, David K Meyerholz, Mark J White, Patrick M Schlievert, Alexander R Horswill
The Spl proteases are a group of six serine proteases that are encoded on the νSaβ pathogenicity island and are unique to Staphylococcus aureus. Despite their interesting biochemistry, their biological substrates and functions in virulence have been difficult to elucidate. We found that an spl operon mutant of the community-associated methicillin-resistant S. aureus USA300 strain LAC induced localized lung damage in a rabbit model of pneumonia, characterized by bronchopneumonia observed histologically. Disease in the mutant-infected rabbits was restricted in distribution compared to that in wild-type USA300-infected rabbits...
September 2016: MSphere
https://www.readbyqxmd.com/read/27672157/rna-polymerase-supply-and-flux-through-the-lac-operon-in-escherichia-coli
#12
Bandar Sendy, David J Lee, Stephen J W Busby, Jack A Bryant
Chromatin immunoprecipitation, followed by quantification of immunoprecipitated DNA, can be used to measure RNA polymerase binding to any DNA segment in Escherichia coli By calibrating measurements against the signal from a single RNA polymerase bound at a single promoter, we can calculate both promoter occupancy levels and the flux of transcribing RNA polymerase through transcription units. Here, we have applied the methodology to the E. coli lactose operon promoter. We confirm that promoter occupancy is limited by recruitment and that the supply of RNA polymerase to the lactose operon promoter depends on its location in the E...
November 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27354444/impact-of-sara-and-phenol-soluble-modulins-on-the-pathogenesis-of-osteomyelitis-in-diverse-clinical-isolates-of-staphylococcus-aureus
#13
Allister J Loughran, Dana Gaddy, Karen E Beenken, Daniel G Meeker, Roy Morello, Haibo Zhao, Stephanie D Byrum, Alan J Tackett, James E Cassat, Mark S Smeltzer
We used a murine model of acute, posttraumatic osteomyelitis to evaluate the virulence of two divergent Staphylococcus aureus clinical isolates (the USA300 strain LAC and the USA200 strain UAMS-1) and their isogenic sarA mutants. The results confirmed that both strains caused comparable degrees of osteolysis and reactive new bone formation in the acute phase of osteomyelitis. Conditioned medium (CM) from stationary-phase cultures of both strains was cytotoxic to cells of established cell lines (MC3TC-E1 and RAW 264...
September 2016: Infection and Immunity
https://www.readbyqxmd.com/read/27252300/development-of-a-lac-operon-concept-inventory-loci
#14
Katherine M Stefanski, Grant E Gardner, Rebecca L Seipelt-Thiemann
Concept inventories (CIs) are valuable tools for educators that assess student achievement and identify misconceptions held by students. Results of student responses can be used to adjust or develop new instructional methods for a given topic. The regulation of gene expression in both prokaryotes and eukaryotes is an important concept in genetics and one that is particularly challenging for undergraduate students. As part of a larger study examining instructional methods related to gene regulation, the authors developed a 12-item CI assessing student knowledge of the lac operon...
2016: CBE Life Sciences Education
https://www.readbyqxmd.com/read/27197249/jacob-monod-the-lac-operon-and-the-pajama-experiment-gene-expression-circuitry-changing-the-face-of-cancer-research
#15
Stephen B Baylin
No abstract text is available yet for this article.
April 15, 2016: Cancer Research
https://www.readbyqxmd.com/read/27191726/the-mechanistic-holistic-divide-revisited-the-case-of-the-lac-operon
#16
Valérie Racine
In this paper, I revisit the development of the repression model of genetic regulation in the lac operon to challenge a common application of a conceptual framework in the history of biology. I take Allen's (1978) account of the changes in the life sciences during the early and mid-twentieth century as an example of a common application of a framework based on the dichotomy between a mechanistic, or reductionist, approach to science and a holistic one. From this conceptual framework, Allen infers two general claims about the process of science and its goals: (1) that "mechanistic materialism" has often presented a more practical way to begin the study of complex phenomena in the life sciences, and (2) that the approach described as "holistic materialism" provides a more complete or accurate description of the natural world...
October 2016: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/27148753/an-orthogonal-permease-inducer-repressor-feedback-loop-shows-bistability
#17
Robert Gnügge, Lekshmi Dharmarajan, Moritz Lang, Jörg Stelling
Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S...
October 21, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/26966093/evaluation-of-novel-inducible-promoter-repressor-systems-for-recombinant-protein-expression-in-lactobacillus-plantarum
#18
Silvia Heiss, Angelika Hörmann, Christopher Tauer, Margot Sonnleitner, Esther Egger, Reingard Grabherr, Stefan Heinl
BACKGROUND: Engineering lactic acid bacteria (LAB) is of growing importance for food and feed industry as well as for in vivo vaccination or the production of recombinant proteins in food grade organisms. Often, expression of a transgene is only desired at a certain time point or period, e.g. to minimize the metabolic burden for the host cell or to control the expression time span. For this purpose, inducible expression systems are preferred, though cost and availability of the inducing agent must be feasible...
2016: Microbial Cell Factories
https://www.readbyqxmd.com/read/26763930/dna-supercoiling-a-critical-signal-regulating-the-basal-expression-of-the-lac-operon-in-escherichia-coli
#19
Geraldine Fulcrand, Samantha Dages, Xiaoduo Zhi, Prem Chapagain, Bernard S Gerstman, David Dunlap, Fenfei Leng
Escherichia coli lac repressor (LacI) is a paradigmatic transcriptional factor that controls the expression of lacZYA in the lac operon. This tetrameric protein specifically binds to the O1, O2 and O3 operators of the lac operon and forms a DNA loop to repress transcription from the adjacent lac promoter. In this article, we demonstrate that upon binding to the O1 and O2 operators at their native positions LacI constrains three (-) supercoils within the 401-bp DNA loop of the lac promoter and forms a topological barrier...
January 14, 2016: Scientific Reports
https://www.readbyqxmd.com/read/26539432/construction-of-a-modular-arsenic-resistance-operon-in-e-coli-and-the-production-of-arsenic-nanoparticles
#20
Matthew Charles Edmundson, Louise Horsfall
Arsenic is a widespread contaminant of both land and water around the world. Current methods of decontamination such as phytoremediation and chemical adsorbents can be resource and time intensive, and may not be suitable for some areas such as remote communities where cost and transportation are major issues. Bacterial decontamination, with strict controls preventing environmental release, may offer a cost-effective alternative or provide a financial incentive when used in combination with other remediation techniques...
2015: Frontiers in Bioengineering and Biotechnology
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