The integrative biology of pigment organelles, a quantum chemical approach

2021 ◽  
Author(s):  
Florent Figon ◽  
Jérôme Casas
Keyword(s):  
Quantum Chemistry ◽  
Main Property ◽  
Computational Method ◽  
Phenotypic Trait ◽  
Visual Effects ◽  
Cellular Environment ◽  
Integrative Studies ◽  
Quantum Chemical Approach ◽  
Cellular Components ◽  
Physical And Chemical

Abstract Coloration is a complex phenotypic trait involving both physical and chemical processes at a multiscale level, from molecules to tissues. Pigments, whose main property is to absorb specific wavelengths of visible light, are usually deposited in specialized organelles or complex matrices comprising proteins, metals, ions and redox compounds, among others. By modulating electronic properties and stability, interactions between pigments and these molecular actors can lead to color tuning. Furthermore, pigments are not only important for visual effects but also provide other critical functions, such as detoxification and antiradical activity. Hence, integrative studies of pigment organelles are required to understand how pigments interact with their cellular environment. In this review, we show how quantum chemistry, a computational method that models the molecular and optical properties of pigments, has provided key insights into the mechanisms by which pigment properties, from color to reactivity, are modulated by their organellar environment. These results allow to rationalize and to predict the way pigments behave in supramolecular complexes, up to the complete modelling of pigment organelles. We also discuss the main limitations of quantum chemistry, emphasizing the need for carrying experimental work with identical vigor. We finally suggest that taking into account the ecology of pigments (i.e. how they interact with these various other cellular components and at higher organizational levels) will lead to a greater understanding of how and why animals are vividly and variably colored, two fundamental questions in organismal biology.

Review: The skeletal muscle extracellular matrix: Possible roles in the regulation of muscle development and growth

2012 ◽  
Vol 92 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Sandra G. Velleman ◽  
Jonghyun Shin ◽  
Xuehui Li ◽  
Yan Song
Keyword(s):  
Skeletal Muscle ◽  
Extracellular Matrix ◽  
Growth Factors ◽  
Muscle Cell ◽  
Muscle Development ◽  
Muscle Growth ◽  
Architecture Framework ◽  
Cellular Environment ◽  
Structural Architecture ◽  
Cellular Components

Velleman, S. G., Shin, J., Li, X. and Song, Y. 2012. Review: The skeletal muscle extracellular matrix: Possible roles in the regulation of muscle development and growth. Can. J. Anim. Sci. 92: 1–10. Skeletal muscle fibers are surrounded by an extrinsic extracellular matrix environment. The extracellular matrix is composed of collagens, proteoglycans, glycoproteins, growth factors, and cytokines. How the extracellular matrix influences skeletal muscle development and growth is an area that is not completely understood at this time. Studies on myogenesis have largely been directed toward the cellular components and overlooked that muscle cells secrete a complex extracellular matrix network. The extracellular matrix modulates muscle development by acting as a substrate for muscle cell migration, growth factor regulation, signal transduction of information from the extracellular matrix to the intrinsic cellular environment, and provides a cellular structural architecture framework necessary for tissue function. This paper reviews extracellular matrix regulation of muscle growth with a focus on secreted proteoglycans, cell surface proteoglycans, growth factors and cytokines, and the dynamic nature of the skeletal muscle extracellular matrix, because of its impact on the regulation of muscle cell proliferation and differentiation during myogenesis.

scholarly journals Comparison of Mechanical Tests on the Dye-3, Greenland Ice Core and Artificial Laboratory Ice

1985 ◽  
Vol 6 ◽  
pp. 305 ◽  
Author(s):  
H. Shoji ◽  
C. C. Langway
Keyword(s):  
Ice Core ◽  
Ice Sheet ◽  
Main Property ◽  
Mechanical Tests ◽  
Horizontal Velocity ◽  
Axis Orientation ◽  
Horizontal Velocity Component ◽  
Temperature Levels ◽  
Property Changes ◽  
Physical And Chemical

The horizontal velocity of a thick ice sheet is maximum at the surface and decreases with increasing depth. The horizontal velocity profile at a given location differs from another location depending upon thein situstress and temperature conditions and the changing but distinctive physical and chemical character of the ice profile. The main property changes that influence the behavior of horizontal ice flow include chemical impurity concentration levels (both solid and dissolved components) and c-axis orientation. Shoji and Langway (1984) calculated the velocity profiles for both the Camp Century and Dye-3 Greeland location by taking into consideration possible enhancement factor variations over the profiles. This analysis was compared with the theoretical and experimental strain rate data obtained for laboratory ice at the same stress and temperature levels. This study indicated that the largest horizontal velocity component is the result of a highly enhanced shear deformation zone, a few hundred meters thick existing at the base of the ice sheet.

scholarly journals Proteasomes tether to two distinct sites at the nuclear pore complex

2017 ◽  
Vol 114 (52) ◽  
pp. 13726-13731 ◽  
Author(s):  
Sahradha Albert ◽  
Miroslava Schaffer ◽  
Florian Beck ◽  
Shyamal Mosalaganti ◽  
Shoh Asano ◽  
...  
Keyword(s):  
Nuclear Pore Complex ◽  
Binding Sites ◽  
Electron Tomography ◽  
Nuclear Pore ◽  
Cellular Environment ◽  
Subtomogram Averaging ◽  
Substrate Processing ◽  
Cellular Components ◽  
Transport Of Macromolecules

The partitioning of cellular components between the nucleus and cytoplasm is the defining feature of eukaryotic life. The nuclear pore complex (NPC) selectively gates the transport of macromolecules between these compartments, but it is unknown whether surveillance mechanisms exist to reinforce this function. By leveraging in situ cryo-electron tomography to image the native cellular environment of Chlamydomonas reinhardtii, we observed that nuclear 26S proteasomes crowd around NPCs. Through a combination of subtomogram averaging and nanometer-precision localization, we identified two classes of proteasomes tethered via their Rpn9 subunits to two specific NPC locations: binding sites on the NPC basket that reflect its eightfold symmetry and more abundant binding sites at the inner nuclear membrane that encircle the NPC. These basket-tethered and membrane-tethered proteasomes, which have similar substrate-processing state frequencies as proteasomes elsewhere in the cell, are ideally positioned to regulate transcription and perform quality control of both soluble and membrane proteins transiting the NPC.

scholarly journals Labelling of DNA and RNA in the cellular environment by means of bioorthogonal cycloaddition chemistry

2020 ◽  
Vol 1 (3) ◽  
pp. 86-97 ◽  
Author(s):  
Dorothée Ganz ◽  
Dennis Harijan ◽  
Hans-Achim Wagenknecht
Keyword(s):  
Nucleic Acids ◽  
Biological Processes ◽  
Dna And Rna ◽  
Cellular Environment ◽  
Cellular Components

Labelling of nucleic acids as biologically important cellular components is a crucial prerequisite for the visualization and understanding of biological processes.

scholarly journals miReg: a resource for microRNA regulation

2010 ◽  
Vol 7 (1) ◽  
Author(s):  
Debmalya Barh ◽  
Dattatraya Bhat ◽  
Cedric Viero
Keyword(s):  
Complete Picture ◽  
Regulate Gene Expression ◽  
Microrna Regulation ◽  
Downstream Targets ◽  
Web Resource ◽  
User Friendly ◽  
Cellular Components ◽  
Physical And Chemical ◽  
Posttranscriptional Level ◽  
Upstream Regulators

SummaryMicroRNAs (miRNAs/miRs) are important cellular components that regulate gene expression at posttranscriptional level. Various upstream components regulate miR expression and any deregulation causes disease conditions. Therefore, understanding of miR regulatory network both at upstream and downstream level is crucial and a resource on this aspect will be helpful. Currently available miR databases are mostly related to downstream targets, sequences, or diseases. But as of now, no database is available that provides a complete picture of miR regulation in a specific condition.Our miR regulation web resource (miReg) is a manually curated one that represents validated upstream regulators (transcription factor, drug, physical, and chemical) along with downstream targets, associated biological process, experimental condition or disease state, up or down regulation of the miR in that condition, and corresponding PubMed references in a graphical and user friendly manner, browseable through 5 browsing options. We have presented exact facts that have been described in the corresponding literature in relation to a given miR, whether it’s a feed-back/feed-forward loop or inhibition/activation. Moreover we have given various links to integrate data and to get a complete picture on any miR listed. Current version (Version 1.0) of miReg contains 47 important human miRs with 295 relations using 190 absolute references. We have also provided an example on usefulness of miReg to establish signalling pathways involved in cardiomyopathy. We believe that miReg will be an essential miRNA knowledge base to research community, with its continuous upgrade and data enrichment.This HTML based miReg can be accessed from: www.iioab-mireg.webs.com or www.iioab.webs.com/mireg.htm.

scholarly journals Paraconsistent Annotated Logic Algorithms Applied in Management and Control of Communication Network Routes

Sensors ◽  
2021 ◽  
Vol 21 (12) ◽  
pp. 4219
Author(s):  
João Inácio Da Silva Filho ◽  
Jair Minoro Abe ◽  
Alessandro de Lima Marreiro ◽  
Angel Antonio Gonzalez Martinez ◽  
Cláudio Rodrigo Torres ◽  
...  
Keyword(s):  
Communication Network ◽  
Communication Networks ◽  
Classical Logic ◽  
Paraconsistent Logic ◽  
Logic Gates ◽  
Main Property ◽  
Computational Method ◽  
Stream Control ◽  
Routing Management ◽  
And Control

This paper presents a computational method based on non-classical logic dedicated to routing management and information stream control in communication networks. Paraconsistent logic (PL) was used to create an algorithmic structure whose main property is to accept contradiction. Moreover, a computational structure, the denominated paraconsistent data analyzer (PDAPAL2v), was constructed to perform routing management in communication networks. Direct comparisons of PDAPAL2v with a classical logic system that simulates routing conditions were made in the laboratory. In the conventional system, the paraconsistent algorithms were considered as binary logic gates, and in the tests, the same adjustment limits of PDAPAL2v were applied. Using a database with controlled insertion of noise, we obtained an efficacy of 97% in the detection of deteriorated packets with PDAPAL2v and 72% with the conventional simulation system. Functional tests were carried out, showing that PDAPAL2v is able to assess the conditions and degradation of links and perform the analysis and correlation of various inputs and variables, even if the signals have contradictory values. From practical tests in the laboratory, the proposed method represents a new way of managing and controlling communication network routes with good performance.

scholarly journals A quantum chemical approach for the mechanisms of redox-active metalloenzymes

RSC Advances ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 3495-3508
Author(s):  
Per E. M. Siegbahn
Keyword(s):  
Quantum Chemistry ◽  
Quantum Chemical ◽  
Significant Part ◽  
The Past ◽  
Chemical Approach ◽  
Redox Active ◽  
Quantum Chemical Approach

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes.

scholarly journals In Vivo Rate of Formaldehyde Condensation with Tetrahydrofolate

Metabolites ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 65 ◽  
Author(s):  
Hai He ◽  
Elad Noor ◽  
Perla A. Ramos-Parra ◽  
Liliana E. García-Valencia ◽  
Jenelle A. Patterson ◽  
...  
Keyword(s):  
Condensation Reaction ◽  
Carbon Sources ◽  
Flux Balance ◽  
Spontaneous Condensation ◽  
Cellular Environment ◽  
Balance Analysis ◽  
Reactive Compound ◽  
Cellular Components ◽  
Spontaneous Reaction

Formaldehyde is a highly reactive compound that participates in multiple spontaneous reactions, but these are mostly deleterious and damage cellular components. In contrast, the spontaneous condensation of formaldehyde with tetrahydrofolate (THF) has been proposed to contribute to the assimilation of this intermediate during growth on C1 carbon sources such as methanol. However, the in vivo rate of this condensation reaction is unknown and its possible contribution to growth remains elusive. Here, we used microbial platforms to assess the rate of this condensation in the cellular environment. We constructed Escherichia coli strains lacking the enzymes that naturally produce 5,10-methylene-THF. These strains were able to grow on minimal medium only when equipped with a sarcosine (N-methyl-glycine) oxidation pathway that sustained a high cellular concentration of formaldehyde, which spontaneously reacts with THF to produce 5,10-methylene-THF. We used flux balance analysis to derive the rate of the spontaneous condensation from the observed growth rate. According to this, we calculated that a microorganism obtaining its entire biomass via the spontaneous condensation of formaldehyde with THF would have a doubling time of more than three weeks. Hence, this spontaneous reaction is unlikely to serve as an effective route for formaldehyde assimilation.

scholarly journals Effect of Physical and Chemical Treatments on Viability, Sub-Lethal Injury, and Release of Cellular Components from Bacillus clausii and Bacillus coagulans Spores and Cells

Foods ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1814
Author(s):  
Antonio Bevilacqua ◽  
Leonardo Petruzzi ◽  
Milena Sinigaglia ◽  
Barbara Speranza ◽  
Daniela Campaniello ◽  
...  
Keyword(s):  
Essential Oils ◽  
Dipicolinic Acid ◽  
Bacillus Coagulans ◽  
Antimicrobial Effect ◽  
Microbial Stability ◽  
Citrus Extract ◽  
Physical Treatments ◽  
Cellular Components ◽  
Physical And Chemical

Bacterial spores are of concern to the food industry due to their ability to survive processing and their potential to subsequently germinate and grow in food. In this paper, two strains belonging to the genus Bacillus (B. clausii DSM 8716 and B. coagulans DSM 1) were studied under in vitro conditions after the application of essential oils, and physical treatments; cells and spores’ susceptibility, the extent of sub-lethal injury and the release of cellular components as a function of treatment and targets (cells, spores, old or activated spores) were studied. The highest antimicrobial effect was found for cells treated through citrus extract, while both essential oils and physical treatments could cause a sub-lethal injury on the surviving cells and spores; in addition, the spores of B. coagulans released dipicolinic acid (DPA) and proteins. Sub-lethal injury should be considered when designing a food processing treatment, because injured microorganisms could either repair the damage or be inactivated with a different effect on microbial stability of foods.

X-RAY STUDIES OF BIOLOGICAL MATTER IN MICROFLUIDIC ENVIRONMENTS

2012 ◽  
Vol 26 (26) ◽  
pp. 1230018 ◽  
Author(s):  
SARAH KÖSTER ◽  
THOMAS PFOHL
Keyword(s):  
Imaging Techniques ◽  
Chemical Properties ◽  
X Rays ◽  
Concentration Gradients ◽  
Length Scales ◽  
X Ray ◽  
Biological Matter ◽  
And Behavior ◽  
Cellular Components ◽  
Physical And Chemical

Biological systems such as cells and cellular components are governed by processes, which take place on nanometer to micrometer length scales. X-ray scattering, diffraction and imaging techniques are extremely well suited to study these processes as the spatial resolution extends well into the relevant length scales. At the same time, the investigation of physical and chemical properties and behavior of such systems requires well-defined and controllable sample environments. One successful way to establish such environments, including specified flow fields, concentration gradients and confinement regimes is by employing microfluidic technology tailored to the particular scientific question. This brief review focuses on microfluidic techniques that have been used to investigate biological matter by X-rays. In particular, we show how the characteristics of flow on the micron scale enable new scientific approaches as compared to macroscale experiments.

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