Works (21)
Updated: July 5th, 2023 15:18
2022 article
Experimental and Analytical Framework for "Mix-and-Read" Assays Based on Split Luciferase
McArthur, N., Cruz-Teran, C., Thatavarty, A., Reeves, G. T., & Rao, B. M. (2022, July 1). ACS OMEGA.
www.ncbi.nlm.nih.gov (repository)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 26, 2022
2022 journal article
Experimental and Analytical Framework for "Mix-and-Read" Assays Based on Split Luciferase
ACS OMEGA, 7(28), 24551–24560.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 8, 2022
2020 journal article
Discovery of Membrane-Permeating Cyclic Peptides via mRNA Display
BIOCONJUGATE CHEMISTRY, 31(10), 2325–2338.
MeSH headings : Animals; Cell Line; Cell-Penetrating Peptides / chemistry; Cell-Penetrating Peptides / genetics; Cell-Penetrating Peptides / pharmacokinetics; Drosophila melanogaster / embryology; Gene Library; Humans; Mice; Models, Molecular; NIH 3T3 Cells; Peptides, Cyclic / chemistry; Peptides, Cyclic / genetics; Peptides, Cyclic / pharmacokinetics; Permeability; RNA, Messenger / genetics
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 21, 2020
2020 article
Formation, interpretation, and regulation of the Drosophila Dorsal/NF-kappa B gradient
GRADIENTS AND TISSUE PATTERNING, Vol. 137, pp. 143–191.
MeSH headings : Animals; Body Patterning; Computational Biology / methods; Drosophila Proteins / genetics; Drosophila Proteins / metabolism; Drosophila melanogaster / embryology; Drosophila melanogaster / physiology; Embryo, Nonmammalian / cytology; Embryo, Nonmammalian / physiology; Gene Expression Regulation, Developmental; NF-kappa B / genetics; NF-kappa B / metabolism; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Phosphoproteins / genetics; Phosphoproteins / metabolism; Signal Transduction; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
The mechanisms behind the initiation of the Dorsal gradient and its regulation of target genes are described, and a discussion of quantitative and computational studies ofThe Dl gradient system, including regulation of theDl gradient is discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: May 26, 2020
2020 journal article
Robustness of the Dorsal morphogen gradient with respect to morphogen dosage
PLOS COMPUTATIONAL BIOLOGY, 16(4).
MeSH headings : Animals; Body Patterning / genetics; Cell Nucleus / metabolism; Cytoplasm / metabolism; DNA-Binding Proteins / metabolism; Drosophila / embryology; Drosophila / genetics; Drosophila Proteins / genetics; Drosophila Proteins / metabolism; Embryo, Nonmammalian / metabolism; Gene Expression Regulation, Developmental / genetics; Morphogenesis / genetics; NF-kappa B / metabolism; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Phosphoproteins / genetics; Phosphoproteins / metabolism; Signal Transduction; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
The robustness of the Dorsal/NF-κB signaling module with respect to perturbations to the dosage of maternally-expressed dorsal mRNA is investigated and the need for quantitative understanding of biophysical mechanisms of morphogen gradients in order to understand emergent phenotypes, such as robustness is highlighted.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: May 26, 2020
2020 journal article
Spatiotemporal control of gene expression boundaries using a feedforward loop
DEVELOPMENTAL DYNAMICS, 249(3), 369–382.
author keywords: dorsal morphogen; Drosophila embryo; feedforward loop; gene expression model; spatiotemporal dynamics; transcription factor; Twist; Zelda
MeSH headings : Animals; Body Patterning / genetics; Body Patterning / physiology; Drosophila Proteins / genetics; Drosophila Proteins / metabolism; Drosophila melanogaster; Embryo, Nonmammalian / metabolism; Gene Expression Regulation, Developmental / genetics; Gene Expression Regulation, Developmental / physiology; NF-kappa B / metabolism; Signal Transduction / genetics; Signal Transduction / physiology
TL;DR:
This work studied the spatiotemporal behavior of a coherent FFL in two contexts: a generic, oscillating morphogen gradient and the dorsal-ventral patterning of the early Drosophila embryo by a gradient of the NF-κB homolog Dorsal with its early target Twist.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: February 3, 2020
2020 article
Spatiotemporal control of gene expression boundaries using a feedforward loop
Reeves, G., Bandodkar, P., & Al Asafen, H. (2020, April). FASEB JOURNAL, Vol. 34.
TL;DR:
This work studied the spatiotemporal behavior of a coherent FFL in two contexts: a generic, oscillating morphogen gradient and the dorsal‐ventral patterning of the early Drosophila embryo by a gradient of the NF‐κB homolog Dorsal with its early target Twist.
(via Semantic Scholar)
Source: Web Of Science
Added: October 12, 2020
2020 journal article
Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems
PLOS ONE, 15(4).
MeSH headings : Animals; Drosophila / genetics; Eukaryota / genetics; Eukaryota / metabolism; Eukaryotic Cells / metabolism; Gene Expression / genetics; Gene Expression / physiology; Gene Expression Regulation / genetics; Gene Expression Regulation / physiology; Genetic Engineering / methods; Nucleic Acid Conformation; Proof of Concept Study; RNA, Catalytic / genetics; RNA, Catalytic / physiology; RNA, Messenger / metabolism; Synthetic Biology / methods
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: June 22, 2020
2019 journal article
The engineering principles of combining a transcriptional incoherent feedforward loop with negative feedback
JOURNAL OF BIOLOGICAL ENGINEERING, 13.
author keywords: Incoherent feedforward loop; Negative feedback; Gene regulation; Network motif; Engineering principles
TL;DR:
It is shown that an incoherent feedforward loop Type 1 (I1-FFL), from within a gene regulatory circuit, can be finely-tuned for perfect adaptation after a stimulus, and that the robustness of this behavior is increased by the presence of moderate negative feedback.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 5, 2019
2013 journal article
Image analysis and empirical modeling of gene and protein expression
Methods, 62(1), 68–78.
author keywords: Quantitative measurements; Gene expression; Protein gradient; Drosophila melanogaster; Dorsal-ventral patterning; Empirical modeling
MeSH headings : Animals; Body Patterning / genetics; Drosophila Proteins / genetics; Drosophila Proteins / metabolism; Drosophila melanogaster / embryology; Drosophila melanogaster / genetics; Drosophila melanogaster / metabolism; Embryo, Nonmammalian / cytology; Embryo, Nonmammalian / metabolism; Embryo, Nonmammalian / ultrastructure; Gene Expression Regulation, Developmental; Homeodomain Proteins / genetics; Homeodomain Proteins / metabolism; Image Processing, Computer-Assisted / statistics & numerical data; In Situ Hybridization; Microscopy, Confocal; Models, Genetic; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Phosphoproteins / genetics; Phosphoproteins / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
Computational methods to quantitatively measure the positions of gene expression domains and the gradients of protein expression along the dorsal-ventral axis in the Drosophila embryo are discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: June 6, 2020
2013 journal article
Size-dependent regulation of dorsal–ventral patterning in the early Drosophila embryo
Developmental Biology, 381(1), 286–299.
author keywords: Developmental patterning; Dorsal gradient; Gene expression; Morphogen; Scaling; Drosophila melanogaster
MeSH headings : Animals; Body Patterning; Body Size; Cell Nucleus / metabolism; Drosophila Proteins / metabolism; Drosophila melanogaster / embryology; Gene Expression Profiling; Gene Expression Regulation, Developmental; Mutation; Snail Family Transcription Factors; Transcription Factors / metabolism
TL;DR:
The results argue against the idea that the Dorsal gradient works as a global system of relative coordinates along the DV axis and suggest that individual targets respond to changes in embryo size in a gene-specific manner.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: June 6, 2020
2012 journal article
Dorsal-Ventral Gene Expression in the Drosophila Embryo Reflects the Dynamics and Precision of the Dorsal Nuclear Gradient
Developmental Cell, 22(3), 544–557.
MeSH headings : Animals; Body Patterning / genetics; Computer Simulation; Drosophila Proteins / genetics; Drosophila melanogaster / cytology; Drosophila melanogaster / embryology; Drosophila melanogaster / genetics; Embryo, Nonmammalian / metabolism; Female; Gene Expression Regulation, Developmental; Microscopy / methods; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
It is proposed that mRNA levels remain plastic during transient signaling events, allowing tissues to refine patterns in the face of genetic or environmental variation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: June 6, 2020
2011 journal article
Size-dependent regulation of dorsal-ventral patterning in the early Drosophila embryo
Developmental Biology, 356(1), 119.
Source: Crossref
Added: June 6, 2020
2009 journal article
Quantitative imaging of the Dorsal nuclear gradient reveals limitations to threshold-dependent patterning in Drosophila
Proceedings of the National Academy of Sciences, 106(52), 22317–22322.
author keywords: development; gene expression
MeSH headings : Animals; Body Patterning / genetics; Body Patterning / physiology; Cell Nucleus / metabolism; Drosophila Proteins / genetics; Drosophila Proteins / metabolism; Drosophila melanogaster / embryology; Drosophila melanogaster / genetics; Drosophila melanogaster / metabolism; Female; Gene Expression Regulation, Developmental; Genes, Insect; In Situ Hybridization, Fluorescence; Male; Models, Biological; Mutation; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Phosphoproteins / genetics; Phosphoproteins / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
It is proposed that the Dorsal gradient supplies positional information throughout nuclear cycles 10-14, providing additional evidence for the idea that compensatory combinatorial interactions between DorsAl and other factors effect differential gene expression along the DV axis.
(via Semantic Scholar)
Source: Crossref
Added: November 14, 2020
2006 journal article
Quantifying the Gurken Morphogen Gradient in Drosophila Oogenesis
Developmental Cell, 11(2), 263–272.
MeSH headings : Animals; Drosophila / physiology; Drosophila Proteins / genetics; Drosophila Proteins / physiology; Ligands; Models, Biological; Oogenesis / physiology; Protein Transport / physiology; Signal Transduction / physiology; Transforming Growth Factor alpha / genetics; Transforming Growth Factor alpha / physiology
TL;DR:
A parameter estimation approach for quantifying the spatial distribution of Gurken, a TGFalpha-like EGFR ligand that acts as a morphogen in Drosophila oogenesis, shows that the shape of the Gurken gradient is controlled by a single dimensionless parameter, the Thiele modulus.
(via Semantic Scholar)
Source: Crossref
Added: November 14, 2020
2006 journal article
Quantitative Models of Developmental Pattern Formation
Developmental Cell, 11(3), 289–300.
MeSH headings : Animals; Body Patterning; Cell Polarity; Developmental Biology; Drosophila / embryology; Models, Biological; Morphogenesis; Wings, Animal / embryology
TL;DR:
Using a number of problems in fruit fly development, this work discusses how models can be used to test the feasibility of proposed patterning mechanisms and characterize their systems-level properties.
(via Semantic Scholar)
Source: Crossref
Added: November 14, 2020
2005 journal article
Computational analysis of EGFR inhibition by Argos
Developmental Biology, 284(2), 523–535.
author keywords: EGFR inhibition; Argos; Spitz
MeSH headings : Animals; Basic Helix-Loop-Helix Transcription Factors; Body Patterning / genetics; Computational Biology; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Drosophila / embryology; Drosophila / metabolism; Drosophila Proteins / biosynthesis; Drosophila Proteins / genetics; Drosophila Proteins / metabolism; Ectoderm / cytology; Ectoderm / metabolism; Enzyme Induction; Epidermal Growth Factor / metabolism; ErbB Receptors / antagonists & inhibitors; ErbB Receptors / metabolism; Eye Proteins / genetics; Eye Proteins / metabolism; Feedback, Physiological; Gene Dosage; Genes, Insect; In Situ Hybridization; Insect Proteins / genetics; Insect Proteins / metabolism; Kinetics; Membrane Proteins / biosynthesis; Membrane Proteins / metabolism; Models, Biological; Mutation; Nerve Tissue Proteins / genetics; Nerve Tissue Proteins / metabolism; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; RNA, Messenger / metabolism
TL;DR:
Computational modeling shows that Argos need not be long-ranged to account for genetic data, and can actually have very short range, and the spatial range of Argos does not have to be tightly regulated or may act at different ranges in distinct developmental contexts.
(via Semantic Scholar)
Source: Crossref
Added: November 14, 2020
2004 journal article
Argos inhibits epidermal growth factor receptor signalling by ligand sequestration
Nature, 430(7003), 1040–1044.
MeSH headings : Animals; Binding Sites; Down-Regulation; Drosophila Proteins / antagonists & inhibitors; Drosophila Proteins / metabolism; Drosophila melanogaster / metabolism; Electron Spin Resonance Spectroscopy; Epidermal Growth Factor / antagonists & inhibitors; Epidermal Growth Factor / metabolism; ErbB Receptors / antagonists & inhibitors; ErbB Receptors / metabolism; Eye Proteins / metabolism; Ligands; Membrane Proteins / antagonists & inhibitors; Membrane Proteins / metabolism; Nerve Tissue Proteins / metabolism; Protein Binding; Protein Kinase Inhibitors; Protein Kinases / metabolism; Receptors, Invertebrate Peptide / antagonists & inhibitors; Receptors, Invertebrate Peptide / metabolism; Signal Transduction
TL;DR:
It is shown that Argos inhibits DER signalling without interacting directly with the receptor, but instead by sequestering the DER-activating ligand Spitz, which provides an insight into the mechanism of Argos function, and suggests new strategies for EGFR inhibitor design.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: Crossref
Added: November 14, 2020
2004 journal article
Growth of mixed cultures on mixtures of substitutable substrates: the operating diagram for a structured model
Journal of Theoretical Biology, 226(2), 143–157.
author keywords: microbial growth; mathematical model; mixed cultures; mixed substrate; substitutable substrates; coexistence
MeSH headings : Bacteria; Coculture Techniques / methods; Culture Media; Models, Biological
TL;DR:
The model is analysed to determine the conditions for existence and stability of the various steady states of growth of two species on two substitutable substrates and it is shown that if the interaction between the two species is purely competitive, then at any given flow rate, coexistence is possible only if the ratio of the two feed concentrations lies within a certain interval.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: Crossref
Added: November 14, 2020
2004 journal article
Predicting stability of mixed microbial cultures from single species experiments: 1. Phenomenological model
Mathematical Biosciences, 192(2), 85–109.
author keywords: microbial growth; phenomenological model; mixed cultures; substitutable substrates; mutual uptake inhibition; coexistence; growth isocline; consumption curve
MeSH headings : Culture Media; Escherichia coli / growth & development; Escherichia coli / metabolism; Mathematics; Microbiology / statistics & numerical data; Models, Biological; Pichia / growth & development; Pichia / metabolism
TL;DR:
This work formulate and analyze a general mathematical model of mixed microbial growth on mixtures of substitutable substrates and provides geometric criteria for stability of various types of equilibria corresponding to non-competitive exclusion, competitive exclusion, and coexistence of two competing species in terms of growth isoclines and consumption curves.
(via Semantic Scholar)
Source: Crossref
Added: November 14, 2020
2004 journal article
Predicting stability of mixed microbial cultures from single species experiments: 2. Physiological model
Mathematical Biosciences, 192(2), 111–136.
author keywords: microbial growth; physiological model; mixed cultures; substitutable substrates; peripheral enzyme; stable coexistence; growth isocline; consumption curve
MeSH headings : Culture Media; Enzymes / metabolism; Escherichia coli / growth & development; Escherichia coli / metabolism; Kinetics; Mathematics; Microbiology / statistics & numerical data; Models, Biological; Pichia / growth & development; Pichia / metabolism
TL;DR:
The influence of the peripheral enzymes that catabolize the substrate uptake on the stability of the mixed culture is investigated and the stability criteria in terms of intracellular properties are presented, establishing a link between ecology and molecular biology.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: Crossref
Added: November 14, 2020
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