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lac operon review

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https://www.readbyqxmd.com/read/27252300/development-of-a-lac-operon-concept-inventory-loci
#1
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/26771674/the-unmasking-of-junk-rna-reveals-novel-srnas-from-processed-rna-fragments-to-marooned-riboswitches
#2
REVIEW
Nicholas R De Lay, Danielle A Garsin
While the notion that RNAs can function as regulators dates back to early molecular studies of gene regulation of the lac operon, it is only over the last decade that the ubiquity and diversity of regulatory RNAs are being realized. Advancements in high throughput sequencing and the adoption of these approaches to rapidly sequence genomes and transcriptomes and to examine gene expression and RNA binding protein specificity have revealed an ever-expanding RNA world. In this review, we focus on recent studies revealing that RNA fragments cleaved from larger coding or noncoding RNAs can have regulatory functions...
April 2016: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/23790365/systems-biophysics-of-gene-expression
#3
REVIEW
Jose M G Vilar, Leonor Saiz
Gene expression is a process central to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular and extracellular changes. This diversity in scales poses fundamental challenges to the use of traditional approaches to fully understand even the simplest gene expression systems. Recent advances in computational systems biophysics have provided promising avenues to reliably integrate the molecular detail of biophysical process into the system behavior...
June 18, 2013: Biophysical Journal
https://www.readbyqxmd.com/read/23292776/dna-looping-in-prokaryotes-experimental-and-theoretical-approaches
#4
REVIEW
Axel Cournac, Jacqueline Plumbridge
Transcriptional regulation is at the heart of biological functions such as adaptation to a changing environment or to new carbon sources. One of the mechanisms which has been found to modulate transcription, either positively (activation) or negatively (repression), involves the formation of DNA loops. A DNA loop occurs when a protein or a complex of proteins simultaneously binds to two different sites on DNA with looping out of the intervening DNA. This simple mechanism is central to the regulation of several operons in the genome of the bacterium Escherichia coli, like the lac operon, one of the paradigms of genetic regulation...
March 2013: Journal of Bacteriology
https://www.readbyqxmd.com/read/23011886/lacz-%C3%AE-galactosidase-structure-and-function-of-an-enzyme-of-historical-and-molecular-biological-importance
#5
REVIEW
Douglas H Juers, Brian W Matthews, Reuben E Huber
This review provides an overview of the structure, function, and catalytic mechanism of lacZ β-galactosidase. The protein played a central role in Jacob and Monod's development of the operon model for the regulation of gene expression. Determination of the crystal structure made it possible to understand why deletion of certain residues toward the amino-terminus not only caused the full enzyme tetramer to dissociate into dimers but also abolished activity. It was also possible to rationalize α-complementation, in which addition to the inactive dimers of peptides containing the "missing" N-terminal residues restored catalytic activity...
December 2012: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/22983621/chip-seq-and-the-complexity-of-bacterial-transcriptional-regulation
#6
James Galagan, Anna Lyubetskaya, Antonio Gomes
Transcription factors (TFs) play a central role in regulating gene expression in all bacteria. Yet, until recently, studies of TF binding were limited to a small number of factors at a few genomic locations. Chromatin immunoprecipitation followed by sequencing enables mapping of binding sites for TFs in a global and high-throughput fashion. The NIAID funded TB systems biology project http://www.broadinstitute.org/annotation/tbsysbio/home.html aims to map the binding sites for every transcription factor in the genome of Mycobacterium tuberculosis (MTB), the causative agent of human TB...
2013: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/22936444/tracking-stem-cell-migration-and-survival-in-brain-injury-current-approaches-and-future-prospects
#7
REVIEW
Ali Darkazalli, Cathy W Levenson
In recent years, stem cell-mediated therapies have gained considerable ground as potential treatments for a wide variety of brain pathologies including traumatic brain injury, stroke and neurodegenerative diseases. Despite extensive preclinical studies, many of these therapies have not been fully translated into viable clinical approaches. This is partly due to our inability to reliably track and monitor transplanted stem cells longitudinally over long periods of time in vivo. In this review, we discuss the predominant histological cell tracing methodologies, such as immunohistochemistry, and fluorescent cellular dyes and proteins, and compare them to emerging cellular imaging technologies...
October 2012: Histology and Histopathology
https://www.readbyqxmd.com/read/22516977/the-physics-of-protein-dna-interaction-networks-in-the-control-of-gene-expression
#8
REVIEW
Leonor Saiz
Protein-DNA interaction networks play a central role in many fundamental cellular processes. In gene regulation, physical interactions and reactions among the molecular components together with the physical properties of DNA control how genes are turned on and off. A key player in all these processes is the inherent flexibility of DNA, which provides an avenue for long-range interactions between distal DNA elements through DNA looping. Such versatility enables multiple interactions and results in additional complexity that is remarkably difficult to address with traditional approaches...
May 16, 2012: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/21414326/design-of-the-lac-gene-circuit-revisited
#9
REVIEW
Michael A Savageau
The lactose (lac) operon of Escherichia coli serves as the paradigm for gene regulation, not only for bacteria, but also for all biological systems from simple phage to humans. The details of the systems may differ, but the key conceptual framework remains, and the original system continues to reveal deeper insights with continued experimental and theoretical study. Nearly as long lasting in impact as the pivotal work of Jacob and Monod is the classic experiment of Novick and Weiner in which they demonstrated all-or-none gene expression in response to an artificial inducer...
May 2011: Mathematical Biosciences
https://www.readbyqxmd.com/read/21272588/operating-on-chromatin-a-colorful-language-where-context-matters
#10
Kathryn E Gardner, C David Allis, Brian D Strahl
Histones, the fundamental packaging elements of eukaryotic DNA, are highly decorated with a diverse set of post-translational modifications (PTMs) that are recognized to govern the structure and function of chromatin. Ten years ago, we put forward the histone code hypothesis, which provided a model to explain how single and/or combinatorial PTMs on histones regulate the diverse activities associated with chromatin (e.g., gene transcription). At that time, there was a limited understanding of both the number of PTMs that occur on histones and the proteins that place, remove, and interpret them...
May 27, 2011: Journal of Molecular Biology
https://www.readbyqxmd.com/read/21195233/quantitative-methods-for-measuring-dna-flexibility-in-vitro-and-in-vivo
#11
Justin P Peters, Nicole A Becker, Emily M Rueter, Zeljko Bajzer, Jason D Kahn, L James Maher
The double-helical DNA biopolymer is particularly resistant to bending and twisting deformations. This property has important implications for DNA folding in vitro and for the packaging and function of DNA in living cells. Among the outstanding questions in the field of DNA biophysics are the underlying origin of DNA stiffness and the mechanisms by which DNA stiffness is overcome within cells. Exploring these questions requires experimental methods to quantitatively measure DNA bending and twisting stiffness both in vitro and in vivo...
2011: Methods in Enzymology
https://www.readbyqxmd.com/read/20643748/the-genetic-basis-of-evolutionary-change-in-gene-expression-levels
#12
J J Emerson, Wen-Hsiung Li
The regulation of gene expression is an important determinant of organismal phenotype and evolution. However, the widespread recognition of this fact occurred long after the synthesis of evolution and genetics. Here, we give a brief sketch of thoughts regarding gene regulation in the history of evolution and genetics. We then review the development of genome-wide studies of gene regulatory variation in the context of the location and mode of action of the causative genetic changes. In particular, we review mapping of the genetic basis of expression variation through expression quantitative trait locus studies and measuring the cis/trans component of expression variation in allele-specific expression studies...
August 27, 2010: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/20438443/computational-prediction-of-dna-protein-interactions-a-review
#13
REVIEW
Xue-Mei Ding, Xiao-Yong Pan, Chen Xu, Hong-Bin Shen
The interaction between DNA and proteins comprises a pivotal role in almost every cellular process, including gene regulation and DNA replication. Given a novel protein, it is very important to know whether it is a DNA-binding protein or not and where the binding sites are. Over the last three decades, since the discovery that lac operon was regulated by a protein, knowledge of the DNA-protein interactions has soared. However, it is very difficult to use experimental techniques to identify the DNA-binding proteins because these experiments can be prohibitively laborintensive in studying all the possible mutations of the residues on the molecular surface...
September 2010: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/20008486/selections-that-optimize-rna-display-in-the-yeast-three-hybrid-system
#14
REVIEW
Susan E Wurster, L James Maher
The yeast three-hybrid system (Y3H) is a powerful tool to select or confirm RNA-protein interactions. Target protein recognition of an RNA insert within a test transcript depends on at least three factors: intrinsic protein affinity for the properly folded insert, retention of RNA insert tertiary structure within a longer RNA transcript, and accessibility of the RNA insert to the target protein. Y3H reporter gene readout reflects the combination of these factors. Here, we discuss RNA insert tertiary structure and accessibility in the Y3H as "RNA display...
February 2010: RNA
https://www.readbyqxmd.com/read/18652543/individuality-in-bacteria
#15
REVIEW
Carla J Davidson, Michael G Surette
While traditionally microbiologists have examined bacterial behavior averaged over large populations, increasingly we are becoming aware that bacterial populations can be composed of phenotypically diverse individuals generated by a variety of mechanisms. Though the results of different mechanisms, the phenomena of bistability, persistence, variation in chemotactic response, and phase and antigenic variation are all strategies to develop population-level diversity. The understanding of individuality in bacteria requires an appreciation of their environmental and ecological context, and thus evolutionary theory regarding adaptations to time-variable environments is becoming more applicable to these problems...
2008: Annual Review of Genetics
https://www.readbyqxmd.com/read/18426771/quantitative-approaches-to-the-study-of-bistability-in-the-lac-operon-of-escherichia-coli
#16
REVIEW
Moisés Santillán, Michael C Mackey
In this paper, the history and importance of the lac operon in the development of molecular and systems biology are briefly reviewed. We start by presenting a description of the regulatory mechanisms in this operon, taking into account the most recent discoveries. Then we offer a survey of the history of the lac operon, including the discovery of its main elements and the subsequent influence on the development of molecular and systems biology. Next the bistable behaviour of the operon is discussed, both with respect to its discovery and its molecular origin...
August 6, 2008: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/18338329/syn-anti-and-finally-both-conformations-of-cyclic-amp-are-involved-in-the-crp-dependent-transcription-initiation-mechanism-in-e-coli-lac-operon
#17
REVIEW
Yusuf Tutar
The cyclic AMP receptor protein (CRP) of Escherichia coli regulates the activity of more than 150 genes. Allosteric changes in CRP structure accompanied by cAMP binding, initiate transcription through protein binding to specific DNA sequences. Initially, researchers proposed a two-site cAMP-binding model for CRP-dependent transcription activation since biophysical methods showed two transitions during titration experiments. Three conformational states were considered; apo-CRP, CRP:(cAMP)(1) and CRP:(cAMP)(2), and CRP:(cAMP)(1) was proposed as the active form in this initial model...
June 2008: Cell Biochemistry and Function
https://www.readbyqxmd.com/read/17990127/cell-tracing-techniques-in-stem-cell-transplantation
#18
REVIEW
Li Yan, Ying Han, Yuanlong He, Huahong Xie, Jingmei Liu, Lina Zhao, Jingbo Wang, Liuchun Gao, Daiming Fan
Pluripotent stem cells have shown great therapeutic promise because of their natural capacity to regenerate damaged tissue. Likewise, autologous stem cells or genetically modified stem cells have already been successfully applied in animal or clinical experimental studies including cardiopathy, diabetic disease, system lupus erythema, pancreatic disease, and liver disease. In these studies regarding stem cell transplants in different diseases, identifying the location of implanted cells and distinguishing them from endogenous cells is the first and most important step...
December 2007: Stem Cell Reviews
https://www.readbyqxmd.com/read/17451901/genetically-controlled-mri-contrast-mechanisms-and-their-prospects-in-systems-neuroscience-research
#19
REVIEW
Gil G Westmeyer, Alan Jasanoff
Application of MRI contrast agents to neural systems research is complicated by the need to deliver agents past the blood-brain barrier or into cells, and the difficulty of targeting agents to specific brain structures or cell types. In the future, these barriers may be wholly or partially overcome using genetic methods for producing and directing MRI contrast. Here we review MRI contrast mechanisms that have used gene expression to manipulate MRI signal in cultured cells or in living animals. We discuss both fully genetic systems involving endogenous biosynthesis of contrast agents, and semi-genetic systems in which expressed proteins influence the localization or activity of exogenous contrast agents...
July 2007: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/16959249/molecular-events-in-early-development-of-the-ciliary-body-a-question-of-folding
#20
REVIEW
H R L Napier, S H Kidson
Ciliary body morphogenesis is a complicated, multi-step process requiring coordinated changes in cell shape, flexure of epithelial sheets and dynamic shifts in mitotic rates. Very little is known of how these cellular events are triggered or regulated. This review summarises current models of ciliary body morphogenesis. The role of intraocular pressure as a driver of morphogenesis is re-evaluated in the light of new information. An update on the role of the lens in ciliary body morphogenesis is presented. In the second part of the review current gene expression data is related to ciliary body morphogenesis...
April 2007: Experimental Eye Research
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