scholarly journals Fluctuating Diffusivity of RNA-Protein Particles: Analogy with Thermodynamics

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 333
Author(s):  
Yuichi Itto
Keyword(s):  
Internal Energy ◽  
Messenger Rna ◽  
Living Cells ◽  
Statistical Fluctuation ◽  
Rna Molecules ◽  
Average Value ◽  
Thermodynamic Entropy ◽  
Laws Of Thermodynamics ◽  
Protein Particles ◽  
Quantity Of Heat

A formal analogy of fluctuating diffusivity to thermodynamics is discussed for messenger RNA molecules fluorescently fused to a protein in living cells. Regarding the average value of the fluctuating diffusivity of such RNA-protein particles as the analog of the internal energy, the analogs of the quantity of heat and work are identified. The Clausius-like inequality is shown to hold for the entropy associated with diffusivity fluctuations, which plays a role analogous to the thermodynamic entropy, and the analog of the quantity of heat. The change of the statistical fluctuation distribution is also examined from a geometric perspective. The present discussions may contribute to a deeper understanding of the fluctuating diffusivity in view of the laws of thermodynamics.

First and second laws of thermodynamics: relationship, “inconsistency”, hidden effects

2020 ◽  
pp. 63-73
Author(s):  
A. M. Savchenko ◽  
Yu. V. Konovalov ◽  
A. V. Laushkin
Keyword(s):  
Free Energy ◽  
Internal Energy ◽  
Second Law Of Thermodynamics ◽  
Second Law ◽  
Entropy Of Mixing ◽  
Ideal Mixing ◽  
Laws Of Thermodynamics ◽  
Relationship Of ◽  
The Relationship

The relationship of the first and second laws of thermodynamics based on their energy nature is considered. It is noted that the processes described by the second law of thermodynamics often take place hidden within the system, which makes it difficult to detect them. Nevertheless, even with ideal mixing, an increase in the internal energy of the system occurs, numerically equal to an increase in free energy. The largest contribution to the change in the value of free energy is made by the entropy of mixing, which has energy significance. The entropy of mixing can do the job, which is confirmed in particular by osmotic processes.

Self-Assembled Growing DNA Tree Mediated by Exosomes for Amplified Imaging of Messenger RNA in Living Cells

2021 ◽  
Author(s):  
Cheng Fang ◽  
Yuming Li ◽  
Song Hu ◽  
Hao Wang ◽  
Xiaoxia Chen ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Living Cells ◽  
Self Assembled

Use of Frog Eggs and Oocytes for the Study of Messenger RNA and its Translation in Living Cells

Nature ◽  
1971 ◽  
Vol 233 (5316) ◽  
pp. 177-182 ◽  
Author(s):  
J. B. GURDON ◽  
C. D. LANE ◽  
H. R. WOODLAND ◽  
G. MARBAIX
Keyword(s):  
Messenger Rna ◽  
Living Cells

scholarly journals Ultrastructural visualization of cytoskeletal mRNAs and their associated proteins using double-label in situ hybridization.

1989 ◽  
Vol 108 (6) ◽  
pp. 2343-2353 ◽  
Author(s):  
R H Singer ◽  
G L Langevin ◽  
J B Lawrence
Keyword(s):  
In Situ Hybridization ◽  
High Resolution ◽  
Colloidal Gold ◽  
Messenger Rna ◽  
Signal To Noise Ratio ◽  
Simultaneous Detection ◽  
Gold Particles ◽  
Rna Molecules ◽  
Nucleic Acid Molecule

We have been able to visualize cytoskeletal messenger RNA molecules at high resolution using nonisotopic in situ hybridization followed by whole-mount electron microscopy. Biotinated cDNA probes for actin, tubulin, or vimentin mRNAs were hybridized to Triton-extracted chicken embryo fibroblasts and myoblasts. The cells were then exposed to antibodies against biotin followed by colloidal gold-conjugated antibodies and then critical-point dried. Identification of mRNA was possible using a probe fragmented to small sizes such that hybridization of several probe fragments along the mRNA was detected as a string of colloidal gold particles qualitatively and quantitatively distinguishable from nonspecific background. Extensive analysis showed that when eight gold particles were seen in this iterated array, the signal to noise ratio was greater than 30:1. Furthermore, these gold particles were colinear, often spiral, or circular suggesting detection of a single nucleic acid molecule. Antibodies against actin, vimentin, or tubulin proteins were used after in situ hybridization, allowing simultaneous detection of the protein and its cognate message on the same sample. This revealed that cytoskeletal mRNAs are likely to be extremely close to actin protein (5 nm or less) and unlikely to be within 20 nm of vimentin or tubulin filaments. Actin mRNA was found to be more predominant in lamellipodia of motile cells, confirming previous results. These results indicate that this high resolution in situ hybridization approach is a powerful tool by which to investigate the association of mRNA with the cytoskeleton.

Light-Induced Gene Expression Using Messenger RNA Molecules

2010 ◽  
Vol 20 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Sigurd Bøe ◽  
Stein Sæbøe-Larssen ◽  
Eivind Hovig
Keyword(s):  
Gene Expression ◽  
Messenger Rna ◽  
Rna Molecules

In SituHybridization in Living Cells: Detection of RNA Molecules

1997 ◽  
Vol 231 (1) ◽  
pp. 226-233 ◽  
Author(s):  
S. Paillasson ◽  
M. Van De Corput ◽  
R.W. Dirks ◽  
H.J. Tanke ◽  
M. Robert-Nicoud ◽  
...  
Keyword(s):  
Living Cells ◽  
Rna Molecules ◽  
In Situhybridization

scholarly journals Effects on protein synthesis of injecting synthetic polyribonucleotides into living cells

1974 ◽  
Vol 144 (1) ◽  
pp. 11-19 ◽  
Author(s):  
Hugh Woodland ◽  
Sarah E. Ayers
Keyword(s):  
Protein Synthesis ◽  
Xenopus Laevis ◽  
Potent Inhibitor ◽  
Living Cells ◽  
Initiation Factor ◽  
Rna Molecules ◽  
Endogenous Protein ◽  
Limited Supply ◽  
Inhibitor Of Protein Synthesis ◽  
Haemoglobin Synthesis

Micro-injection into the oocytes and eggs of Xenopus laevis was used to ascertain the effects of synthetic polyribonucleotides on protein synthesis in living cells. Poly(U) and poly(A) were not translated detectably, nor did they change the rate of endogenous protein synthesis. The same was true of poly(G,U), poly(A,G,U), poly(A,C,G,U), G-U-G-(U)n, A-(U)n and AUG. In contrast, A-U-G-(U)n was a potent inhibitor of protein synthesis in the cell. This might be because it is initiated normally but lacks a termination codon, or because it inhibits the translation of other molecules in some way not dependent on its normal initiation. Poly(G,U), poly(A,G,U) and poly(A,C,G,U) inhibited haemoglobin synthesis when they were injected into the oocyte with haemoglobin mRNA. The synthetic polyribonucleotides did not inhibit the translation of the natural mRNA when the two sorts of molecules were injected at different times. It is suggested that the synthetic RNA molecules compete with the natural mRNA for a pre-initiation factor in limited supply.

scholarly journals The Impact of Dietary Compounds in Functional Foods on MicroRNAs Expression

2021 ◽  
Author(s):  
Wittaya Chaiwangyen
Keyword(s):  
Messenger Rna ◽  
Positive Impact ◽  
Biologically Active ◽  
Transcriptional Gene Silencing ◽  
Cellular Mirnas ◽  
Rna Molecules ◽  
Post Transcriptional Gene Silencing ◽  
Molecular Machinery ◽  
Different Origins ◽  
The Impact

MicroRNAs (miRNAs) are a class of non-coding endogenous RNA molecules that are involved in post-transcriptional gene silencing via binding to their target messenger RNA, leading to mRNA degradation or translational repression. MicroRNAs can be modulated by several factors including hormones, transcription factors, and dietary compounds. These biologically active compounds have positive impact on the progression of human pathology including non-communicable diseases, which indicating that administration of diet may have potential as therapeutic agents in modulating the risk of chronic diseases. Interestingly, evidence emerging in recent years suggests that dietary miRNAs can be absorbed in human circulation, modulated human gene expression and biological functions. The exploitation of the miRNA functioning within different origins, cellular miRNAs and dietary miRNAs will help us to understand the molecular machinery as well as the regulatory mechanisms involved in fundamentally important biological processes. Therefore, this knowledge may be applied of natural bioactive compounds in preventive or therapeutic approaches.

"Cap" sequences is poly(A)-rich RNA from dry wheat embryos

1981 ◽  
Vol 59 (10) ◽  
pp. 868-870 ◽  
Author(s):  
Byron G. Lane
Keyword(s):  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
Messenger Rna ◽  
High Performance ◽  
Higher Plants ◽  
Rna Molecules ◽  
Wheat Embryos ◽  
The Subject ◽  
Widespread Interest

Although template-active RNA in dry seeds and embryos has attracted widespread interest, there have been no published reports about 5′-terminai "capping" sequences in such RNA. Boro[3H]hydride labeling of periodate-oxidized termini and high performance liquid chromatography of cap oligonucleotides have been used to compare terminal sequences in poly(A)-rich RNA from dry and germinating embryos. As is the case in germinating embryos, poly(A)-rich RNA from dry embryos contains only "type 0" cap sequences, i.e., m7G(5′)ppp(5′)N, in which m7G is the 7-methylguanosine cap and N is any of the classical ribonucleosides: adenosine (A), guanosine (G), cytidine (C), and uridine (U). Striking differences between the cell-free translational capacities of bulk messenger RNA (mRNA) populations from dry and germinating embryos are not reflected in signal differences in their proportions of "type 0" cap structures: in general, there is approximately 40% m7G(5′)ppp(5′)A, with roughly equivalent amounts of m7G(5′)ppp(5′)G and m7G(5′)ppp(5′)C accounting for most of the remaining sequences. The findings with mRNA from dry plant embryos serve to emphasize interesting differences between patterns of methylation in the capped and uncapped RNA molecules in higher plants and animals; these differences have not been previously noted in the literature and are the subject of brief comment in this paper.

Origin and spatial distribution of maternal messenger RNA during oogenesis of an insect, Oncopeltus fasciatus

1979 ◽  
Vol 39 (1) ◽  
pp. 63-76
Author(s):  
D.G. Capco ◽  
W.R. Jeffery
Keyword(s):  
Spatial Distribution ◽  
Messenger Rna ◽  
Germinal Vesicle ◽  
Oncopeltus Fasciatus ◽  
Follicle Cells ◽  
Rna Molecules ◽  
Maternal Mrna ◽  
Chorion Formation ◽  
Oocyte Cytoplasm ◽  
Rna Accumulation

In order to investigate the origin and spatial distribution of maternal mRNA during oogenesis, in situ hybridization with [3H]-poly(U) was utilized for the detection of poly(A)-containing RNA [poly(A)+RNA] in histological sections of Oncopeltus fasciatus ovaries. In the germarium poly(A)+RNA was found to accumulate in the trophocyte cytoplasm concomitant with the maturation of these cells. Poly(A)+RNA was also detected in the trophic cores and nutritive tubes suggesting that these channels participate in the transport of trophocyte-derived mRNA to the oocytes. Although large amounts of poly(A)+RNA were also detected in the cytoplasm of the follicle cells, particularly during late vitellogenesis when pseudopod-like processes projected into the ooplasm, no evidence was obtained for the transport of poly(A)+RNA from these processes to the oocytes. The content of poly(A)+RNA in the oocyte cytoplasm continually increased during oogenesis. In stage 2–4 oocytes poly(A)+RNA accumulation occurred in the apparent absence of transcriptional activity in the germinal vesicle nuclei suggesting that most maternal mRNA molecules synthesized during early oogenesis are of trophocyte origin. Poly(A)+RNA also continued to accumulate after chorion formation, when the nutritive tubes are longer active in RNA transport. This implies that other sources of maternal mRNA may exist during late oogenesis. The distribution of poly(A)+RNA molecules in the oocyte cytoplasm appeared to be uniform throughout oogenesis with one exception. During late vitellogenesis poly(A)+RNA activity was significantly enhanced in the anterior and posterior periplasmic cytoplasms relative to the lateral periplasm and the endoplasm. After chorion formation these variations disappeared. The results suggest that maternal mRNA molecules arise from at least 2 sources during oogenesis. During late vitellogenesis these molecules appear to be subject to differential localization in the polar perimeters of the oocyte cytoplasm.

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