scholarly journals Quantitative Measurement of Histone Tail Acetylation Reveals Stage-Specific Regulation and Response to Environmental Changes during Drosophila Development

Biochemistry ◽  
2016 ◽  
Vol 55 (11) ◽  
pp. 1663-1672 ◽  
Author(s):  
Ryan A. Henry ◽  
Tanu Singh ◽  
Yin-Ming Kuo ◽  
Alison Biester ◽  
Abigail O’Keefe ◽  
...  
Keyword(s):  
Quantitative Measurement ◽  
Environmental Changes ◽  
Histone Tail ◽  
Drosophila Development ◽  
Specific Regulation

scholarly journals Bioluminescence dynamics in single germinating bacterial spores reveal metabolic heterogeneity

2020 ◽  
Vol 17 (170) ◽  
pp. 20200350
Author(s):  
Zak Frentz ◽  
Jonathan Dworkin
Keyword(s):  
Cell Fate ◽  
Quantitative Measurement ◽  
Environmental Changes ◽  
Reducing Power ◽  
Extreme Case ◽  
Bacterial Bioluminescence ◽  
Highly Sensitive ◽  
Germination Timing ◽  
Metabolic Heterogeneity ◽  
Spore Forming Bacteria

Spore-forming bacteria modulate their metabolic rate by over five orders of magnitude as they transition between dormant spores and vegetative cells and thus represent an extreme case of phenotypic variation. During environmental changes in nutrient availability, clonal populations of spore-forming bacteria exhibit individual differences in cell fate, the timing of phenotypic transitions and gene expression. One potential source of this variability is metabolic heterogeneity, but this has not yet been measured, as existing single-cell methods are not easily applicable to spores due to their small size and strong autofluorescence. Here, we use the bacterial bioluminescence system and a highly sensitive microscope to measure metabolic dynamics in thousands of B. subtilis spores as they germinate. We observe and quantitate large variations in the bioluminescence dynamics across individual spores that can be decomposed into contributions from variability in germination timing, the amount of endogenously produced luminescence substrate and the intracellular reducing power. This work shows that quantitative measurement of spore metabolism is possible and thus it opens avenues for future study of the thermodynamic nature of dormant states.

scholarly journals Responses of neurogenesis and neuroplasticity related genes to elevated CO 2 levels in the brain of three teleost species

2017 ◽  
Vol 13 (8) ◽  
pp. 20170240 ◽  
Author(s):  
Floriana Lai ◽  
Cathrine E. Fagernes ◽  
Nicholas J. Bernier ◽  
Gabrielle M. Miller ◽  
Philip L. Munday ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Gasterosteus Aculeatus ◽  
Environmental Changes ◽  
Nuclear Antigen ◽  
Mrna Levels ◽  
Continuous Increase ◽  
Expression Levels ◽  
Specific Regulation ◽  
The Brain ◽  
Mrna Expression Levels

The continuous increase of anthropogenic CO 2 in the atmosphere resulting in ocean acidification has been reported to affect brain function in some fishes. During adulthood, cell proliferation is fundamental for fish brain growth and for it to adapt in response to external stimuli, such as environmental changes. Here we report the first expression study of genes regulating neurogenesis and neuroplasticity in brains of three-spined stickleback ( Gasterosteus aculeatus ), cinnamon anemonefish ( Amphiprion melanopus ) and spiny damselfish ( Acanthochromis polyacanthus ) exposed to elevated CO 2 . The mRNA expression levels of the neurogenic differentiation factor (NeuroD) and doublecortin (DCX) were upregulated in three-spined stickleback exposed to high-CO 2 compared with controls, while no changes were detected in the other species. The mRNA expression levels of the proliferating cell nuclear antigen (PCNA) and the brain-derived neurotrophic factor (BDNF) remained unaffected in the high-CO 2 exposed groups compared to the control in all three species. These results indicate a species-specific regulation of genes involved in neurogenesis in response to elevated ambient CO 2 levels. The higher expression of NeuroD and DCX mRNA transcripts in the brain of high-CO 2 –exposed three-spined stickleback, together with the lack of effects on mRNA levels in cinnamon anemonefish and spiny damselfish, indicate differences in coping mechanisms among fish in response to the predicted-future CO 2 level.

scholarly journals Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling

2019 ◽  
Author(s):  
Bilal El Houdaigui ◽  
Raphaël Forquet ◽  
Thomas Hindré ◽  
Dominique Schneider ◽  
William Nasser ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Bacterial Genome ◽  
Transcriptional Regulator ◽  
Dna Supercoiling ◽  
Mechanistic Modeling ◽  
Mechanical Constraints ◽  
A Genome ◽  
Specific Regulation

AbstractDNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcription-supercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcription assays, and highlights the role of genes’ local orientation in their supercoiling sensitivity. Consistently with predictions, we show that chromosomal relaxation artificially induced by gyrase inhibitors selectively activates convergent genes in several enterobacteria, while conversely, an increase in DNA supercoiling naturally selected in a long-term evolution experiment with Escherichia coli favours divergent genes. Simulations show that these global expression responses to changes in DNA supercoiling result from fundamental mechanical constraints imposed by transcription, independently from more specific regulation of each promoter. These constraints underpin a significant and predictable contribution to the complex rules by which bacteria use DNA supercoiling as a global but fine-tuned transcriptional regulator.

scholarly journals Bioluminescence dynamics in single germinating bacterial spores reveal metabolic heterogeneity

2020 ◽  
Author(s):  
Zak Frentz ◽  
Jonathan Dworkin
Keyword(s):  
Cell Fate ◽  
Quantitative Measurement ◽  
Environmental Changes ◽  
Reducing Power ◽  
Extreme Case ◽  
Bacterial Bioluminescence ◽  
Highly Sensitive ◽  
Germination Timing ◽  
Metabolic Heterogeneity ◽  
Spore Forming Bacteria

AbstractSpore-forming bacteria modulate their metabolic rate by over 5 orders of magnitude as they transition between dormant spores and vegetative cells, and thus represent an extreme case of phenotypic variation. During environmental changes in nutrient availability, clonal populations of spore-forming bacteria exhibit individual differences in cell fate, timing of phenotypic transitions, and gene expression. One potential source of this variability is metabolic heterogeneity, but this has not yet been measured, as existing single-cell methods are not easily applicable to spores due to their small size and strong autofluorescence. Here, we use the bacterial bioluminescence system and a highly sensitive microscope to measure metabolic dynamics in thousands of B. subtilis spores as they germinate. We observe and quantitate large variations in the bioluminescence dynamics across individual spores that can be decomposed into contributions from variability in germination timing, the amount of endogenously produced luminescence substrate, and the intracellular reducing power. This work shows that quantitative measurement of spore metabolism is possible and thus it opens venues for future study of the thermodynamic nature of dormant states.

scholarly journals Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling

2019 ◽  
Vol 47 (11) ◽  
pp. 5648-5657 ◽  
Author(s):  
Bilal El Houdaigui ◽  
Raphaël Forquet ◽  
Thomas Hindré ◽  
Dominique Schneider ◽  
William Nasser ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Bacterial Genome ◽  
Transcriptional Regulator ◽  
Dna Supercoiling ◽  
Mechanistic Modeling ◽  
Mechanical Constraints ◽  
A Genome ◽  
Specific Regulation

Abstract DNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcription-supercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcription assays, and highlights the role of genes’ local orientation in their supercoiling sensitivity. Consistently with predictions, we show that chromosomal relaxation artificially induced by gyrase inhibitors selectively activates convergent genes in several enterobacteria, while conversely, an increase in DNA supercoiling naturally selected in a long-term evolution experiment with Escherichia coli favours divergent genes. Simulations show that these global expression responses to changes in DNA supercoiling result from fundamental mechanical constraints imposed by transcription, independently from more specific regulation of each promoter. These constraints underpin a significant and predictable contribution to the complex rules by which bacteria use DNA supercoiling as a global but fine-tuned transcriptional regulator.

Isoform-Specific Regulation of the Na+-K+ Pump in Heart

Physiology ◽  
2000 ◽  
Vol 15 (4) ◽  
pp. 176-180 ◽  
Author(s):  
R. T. Mathias ◽  
I. S. Cohen ◽  
J. Gao ◽  
Y. Wang
Keyword(s):  
Signal Transduction ◽  
Guinea Pig ◽  
Physical Environment ◽  
Environmental Changes ◽  
Ventricular Myocytes ◽  
Cell Type ◽  
Specific Regulation

Guinea pig ventricular myocytes coexpress two isoforms of the Na+-K+ pump. These two isoforms respond differently to the physical environment and are coupled to autonomic input through different signal transduction cascades. The expression of different isoforms provides each cell type with a mechanism of programming specific responses to environmental changes.

scholarly journals An integrated computational and experimental study to elucidate Staphylococcus aureus metabolism

2019 ◽  
Author(s):  
Mohammad Mazharul Islam ◽  
Vinai C. Thomas ◽  
Matthew Van Beek ◽  
Jong-Sam Ahn ◽  
Abdulelah A. Alqarzaee ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Environmental Changes ◽  
Model Performance ◽  
Metabolic Model ◽  
Exchange Reactions ◽  
Chemical Balance ◽  
Manual Curation ◽  
Specific Regulation ◽  
Reaction Stoichiometry

AbstractStaphylococcus aureus is a metabolically versatile pathogen that colonizes nearly all organs of the human body. A detailed and comprehensive knowledge of staphylococcal metabolism is essential to understanding its pathogenesis. To this end, we have reconstructed and experimentally validated an updated and enhanced genome-scale metabolic model of S. aureus USA300_FPR3757. The model combined genome annotation data, reaction stoichiometry, and regulation information from biochemical databases and previous strain-specific models. Reactions in the model were checked and fixed to ensure chemical balance and thermodynamic consistency. To further refine the model, growth assessment of 1920 non-essential mutants from the Nebraska Transposon Mutant Library was performed and metabolite excretion profiles of important mutants in carbon and nitrogen metabolism were determined. The growth and no-growth inconsistencies between the model predictions and in vivo essentiality data were resolved using extensive manual curation based on optimization-based reconciliation algorithms. Upon intensive curation and refinements, the model contains 840 metabolic genes, 1442 metabolites, and 1566 reactions including transport and exchange reactions. To improve the accuracy and predictability of the model to environmental changes, condition-specific regulation information curated from the existing knowledgebase was incorporated. These critical additions improved the model performance significantly in capturing gene essentiality, substrate utilization, and metabolite production capabilities and increased the ability to generate model-based discoveries of therapeutic significance. Use of this highly curated model will enhance the functional utility of omics data and, therefore, serve as a resource to support future investigations of S. aureus and to augment staphylococcal research worldwide.

A quantitative image analysis method for the determination of cocontinuity in polymer blends

1993 ◽  
Vol 51 ◽  
pp. 894-895
Author(s):  
William A. Heeschen
Keyword(s):  
Image Analysis ◽  
Polymer Blends ◽  
Quantitative Measurement ◽  
Morphological Evolution ◽  
Phase Ratio ◽  
Irregular Shapes ◽  
Quantitative Image ◽  
Discrete Domains ◽  
A Domains

Two new morphological measurements based on digital image analysis, CoContinuity and CoContinuity Balance, have been developed and implemented for quantitative measurement of morphology in polymer blends. The morphology of polymer blends varies with phase ratio, composition and processing. A typical morphological evolution for increasing phase ratio of polymer A to polymer B starts with discrete domains of A in a matrix of B (A/B < 1), moves through a cocontinuous distribution of A and B (A/B ≈ 1) and finishes with discrete domains of B in a matrix of A (A/B > 1). For low phase ratios, A is often seen as solid convex particles embedded in the continuous B phase. As the ratio increases, A domains begin to evolve into irregular shapes, though still recognizable as separate domains. Further increase in the phase ratio leads to A domains which extend into and surround the B phase while the B phase simultaneously extends into and surrounds the A phase.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

Seeking to uncover biology's chemical roots

2019 ◽  
Vol 3 (5) ◽  
pp. 435-443 ◽  
Author(s):  
Addy Pross
Keyword(s):  
Environmental Changes ◽  
Biological Systems ◽  
Significant Development ◽  
The Road ◽  
Physical Chemical ◽  
Systems Chemistry ◽  
Biological World ◽  
Inanimate Matter ◽  
The Origin Of Life ◽  
Opening Up

Despite the considerable advances in molecular biology over the past several decades, the nature of the physical–chemical process by which inanimate matter become transformed into simplest life remains elusive. In this review, we describe recent advances in a relatively new area of chemistry, systems chemistry, which attempts to uncover the physical–chemical principles underlying that remarkable transformation. A significant development has been the discovery that within the space of chemical potentiality there exists a largely unexplored kinetic domain which could be termed dynamic kinetic chemistry. Our analysis suggests that all biological systems and associated sub-systems belong to this distinct domain, thereby facilitating the placement of biological systems within a coherent physical/chemical framework. That discovery offers new insights into the origin of life process, as well as opening the door toward the preparation of active materials able to self-heal, adapt to environmental changes, even communicate, mimicking what transpires routinely in the biological world. The road to simplest proto-life appears to be opening up.

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