Ordinary randomness

2021 ◽  
pp. 15-34
Author(s):  
Arlin Stoltzfus
Keyword(s):  
Cell Cycle ◽  
Electromagnetic Radiation ◽  
Biological Process ◽  
Radioactive Decay ◽  
External Effects ◽  
Genomic Position ◽  
Replication Errors ◽  
Foreign Dna ◽  
Quantum Indeterminacy

Chapter 2 addresses how well the biological process of mutation is described by some of the ordinary meanings of “chance“ or “randomness“ in science: lack of purpose or foresight, uniformity (homogeneity), stochasticity, indeterminacy, unpredictability, spontaneity, and independence (chance). Ordinary mutations exhibit various kinds of heterogeneity (nonuniformity), e.g., by genomic position, or by cell-cycle state. The occurrence of mutations is affected by various conditions inside the cell, e.g., the spectrum of replication errors is shaped by the composition of DNA precursor pools. Many of the processes that lead to mutation are spontaneous in the sense of emerging internally, but some processes reflect external effects such as radiation or uptake of foreign DNA. Though most of the processes that lead to mutations are “macroscopic,” some processes (e.g., damage caused by radioactive decay or electromagnetic radiation) implicate quantum indeterminacy.

scholarly journals Intricate Regulatory Mechanisms of the Anaphase-Promoting Complex/Cyclosome and Its Role in Chromatin Regulation

2021 ◽  
Vol 9 ◽  
Author(s):  
Tatyana Bodrug ◽  
Kaeli A. Welsh ◽  
Megan Hinkle ◽  
Michael J. Emanuele ◽  
Nicholas G. Brown
Keyword(s):  
Cell Cycle ◽  
Signaling Pathways ◽  
Biological Process ◽  
Conformational Dynamics ◽  
Intimate Relationship ◽  
Regulatory Mechanisms ◽  
Cell Cycle Regulators ◽  
Chromatin Regulation ◽  
Anaphase Promoting Complex

The ubiquitin (Ub)-proteasome system is vital to nearly every biological process in eukaryotes. Specifically, the conjugation of Ub to target proteins by Ub ligases, such as the Anaphase-Promoting Complex/Cyclosome (APC/C), is paramount for cell cycle transitions as it leads to the irreversible destruction of cell cycle regulators by the proteasome. Through this activity, the RING Ub ligase APC/C governs mitosis, G1, and numerous aspects of neurobiology. Pioneering cryo-EM, biochemical reconstitution, and cell-based studies have illuminated many aspects of the conformational dynamics of this large, multi-subunit complex and the sophisticated regulation of APC/C function. More recent studies have revealed new mechanisms that selectively dictate APC/C activity and explore additional pathways that are controlled by APC/C-mediated ubiquitination, including an intimate relationship with chromatin regulation. These tasks go beyond the traditional cell cycle role historically ascribed to the APC/C. Here, we review these novel findings, examine the mechanistic implications of APC/C regulation, and discuss the role of the APC/C in previously unappreciated signaling pathways.

Experience of application of neutron shooting in the complex with geoelectrochemical methods on reference tybes of the Zimmeberezhny diamondiferous area

2020 ◽  
pp. 3-8
Author(s):  
N. F. Skopenko ◽  
S. I. Krasotkin ◽  
A. S. Galkin ◽  
V. N. Shirobokov ◽  
V. A. Krivitsky ◽  
...  
Keyword(s):  
Electromagnetic Radiation ◽  
Radioactive Decay ◽  
Low Energy ◽  
Deep Center ◽  
Geological Model ◽  
Search Technique ◽  
First Time

The method of registration of free neutrons applied in a complex with geoelectrochemical methods is for the first time tested in the Arkhangelsk diamondiferous province. The basis on its application is the concept developed now about formation of diamonds in the deep center, screened dense breeds. As a result density of energy of the excited environment increases that leads to course of nuclear dissociation of nuclear kernels, cluster radioactive decay and a low-energy transmutation of elements. At formation of a kimberlite tube in the course of cluster radioactive decay and a low-energy transmutation of nuclear kernels there is an electromagnetic radiation with energy of quantum about tens and hundreds kiloelectronvolt. By results of the carried-out skilled and methodical works on the reference blocked tubes Pioneer and Verkhnetovsky confirmation of this concept is received and the search technique leaning on this geological model is offered.

Genes

2019 ◽  
pp. 145-161
Keyword(s):  
Complex System ◽  
Cell Cycle ◽  
Cell Death ◽  
Mitochondrial Dna ◽  
Cell Division ◽  
Genetic Information ◽  
Replication Errors ◽  
Dna Molecule ◽  
Dna And Rna ◽  
Dna Replication Errors

Two types of nucleic acids, DNA and RNA, carry genetic information of organisms across generations. Many researchers are credited with the early work that laid the foundation of the discovery of the structure of DNA. During cell division, the cell replicates its DNA and organelles during the synthesis (S) phase of the cell cycle. Four main steps are involved in the processes of replication. DNA replication errors and cells have evolved a complex system of fixing most (but not all) of those replication errors proofreading and mismatch repair. With repeated cell division, the DNA molecule shortens with the loss of critical genes, leading to cell death. In gonads, a special enzyme called telomerase lengthens telomeres from its own RNA sequence which serves as a template to synthesize new telomeres. Although most DNA is packaged within the nucleus, mitochondria have a small amount of their own DNA called mitochondrial DNA. This chapter explores this aspect of genes.

scholarly journals Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae

2020 ◽  
Vol 10 (7) ◽  
pp. 2345-2351
Author(s):  
Rosa M. Bermudez ◽  
Peter I-Fan Wu ◽  
Deanna Callerame ◽  
Staci Hammer ◽  
James C. Hu ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Biological Process ◽  
Loss Of Function ◽  
Gain Of Function ◽  
Cycle Progression ◽  
Computational Approaches ◽  
Cell Cycle Genes ◽  
Functional Screens

A long-standing effort in biology is to precisely define and group phenotypes that characterize a biological process, and the genes that underpin them. In Saccharomyces cerevisiae and other organisms, functional screens have generated rich lists of phenotypes associated with individual genes. However, it is often challenging to identify sets of phenotypes and genes that are most closely associated with a given biological process. Here, we focused on the 166 phenotypes arising from loss-of-function and the 86 phenotypes from gain-of-function mutations in 571 genes currently assigned to cell cycle-related ontologies in S. cerevisiae. To reduce this complexity, we applied unbiased, computational approaches of correspondence analysis to identify a minimum set of phenotypic variables that accounts for as much of the variability in the data as possible. Loss-of-function phenotypes can be reduced to 20 dimensions, while gain-of-function ones to 14 dimensions. We also pinpoint the contributions of phenotypes and genes in each set. The approach we describe not only simplifies the categorization of phenotypes associated with cell cycle progression but might also potentially serve as a discovery tool for gene function.

scholarly journals Cellular Senescence: Mechanisms and Therapeutic Potential

Biomedicines ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1769
Author(s):  
Zehuan Liao ◽  
Han Lin Yeo ◽  
Siaw Wen Wong ◽  
Yan Zhao
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Arrest ◽  
Cellular Senescence ◽  
Biological Process ◽  
Therapeutic Potential ◽  
Biological Processes ◽  
Limb Patterning ◽  
Cycle Arrest ◽  
Major Interest ◽  
Secretory Phenotype

Cellular senescence is a complex and multistep biological process which cells can undergo in response to different stresses. Referring to a highly stable cell cycle arrest, cellular senescence can influence a multitude of biological processes—both physiologically and pathologically. While phenotypically diverse, characteristics of senescence include the expression of the senescence-associated secretory phenotype, cell cycle arrest factors, senescence-associated β-galactosidase, morphogenesis, and chromatin remodelling. Persistent senescence is associated with pathologies such as aging, while transient senescence is associated with beneficial programmes, such as limb patterning. With these implications, senescence-based translational studies, namely senotherapy and pro-senescence therapy, are well underway to find the cure to complicated diseases such as cancer and atherosclerosis. Being a subject of major interest only in the recent decades, much remains to be studied, such as regarding the identification of unique biomarkers of senescent cells. This review attempts to provide a comprehensive understanding of the diverse literature on senescence, and discuss the knowledge we have on senescence thus far.

Significance of cell-cycle delay, multiple initiation pathways, misrepair and replication errors in a model of radiobiological effects

2001 ◽  
Vol 77 (4) ◽  
pp. 519-527 ◽  
Author(s):  
H. Schöllnberger ◽  
M. R. Mebust ◽  
D. J. Crawford-Brown ◽  
P. M. Eckl ◽  
W. Hofmann
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Delay ◽  
Replication Errors ◽  
Radiobiological Effects

scholarly journals Human Amniotic Epithelial Cells as a Tool to Investigate the Effects of Cyanidin 3-O-Glucoside on Cell Differentiation

2021 ◽  
Vol 22 (7) ◽  
pp. 3768
Author(s):  
Shinya Takahashi ◽  
Farhana Ferdousi ◽  
Yun-Wen Zheng ◽  
Tatsuya Oda ◽  
Hiroko Isoda
Keyword(s):  
Cell Cycle ◽  
Gene Ontology ◽  
Cell Differentiation ◽  
Epithelial Cells ◽  
Cellular Therapy ◽  
Biological Process ◽  
Fold Change ◽  
P Value ◽  
Amniotic Epithelial Cells ◽  
Human Amniotic Epithelial Cells

Cyanidin, a kind of anthocyanin, has been reported to have chemotherapeutic activities in humans. Human amniotic epithelial cells (hAECs) are considered a potential source of pluripotent stem cells. hAECs have been used as a novel tool in regenerative cellular therapy and cell differentiation studies. In this study, to explore the effects of cyanidin-3-O-glucoside (Cy3G) on hAECs and their mechanisms, we investigated the transcriptomic changes in the Cy3G-treated cells using microarray analysis. Among the differentially expressed genes (Fold change > 1.1; p-value < 0.05), 109 genes were upregulated and 232 were downregulated. Ratios of upregulated and downregulated genes were 0.22% and 0.47% of the total expressed genes, respectively. Next, we explored the enriched gene ontology, i.e., the biological process, molecular function, and cellular component of the 37 upregulated (>1.3-fold change) and 124 downregulated (<1.3-fold change) genes. Significantly enriched biological processes by the upregulated genes included “response to muscle activity,” and the genes involved in this gene ontology (GO) were Metrnl and SRD5A1, which function in the adipocyte. On the other hand, the cell cycle biological process was significantly enriched by the downregulated genes, including some from the SMC gene family. An adipogenesis-associated gene DDX6 was also included in the cell cycle biological process. Thus, our findings suggest the prospects of Cy3G in modulating adipocyte differentiation in hAECs.

scholarly journals Influence of intense coherent electromagnetic radiation on several types of radioactive decay

2017 ◽  
Vol 149 ◽  
pp. 02017
Author(s):  
S.N. Andreev ◽  
E.V. Barmina ◽  
A.K. Kaminsky ◽  
S.N. Sedykh ◽  
G.A. Shafeev ◽  
...  
Keyword(s):  
Electromagnetic Radiation ◽  
Radioactive Decay

scholarly journals Phenotypic associations among cell cycle genes in Saccharomyces cerevisiae

2020 ◽  
Author(s):  
María Bermudez-Cruz ◽  
Peter I. Wu ◽  
Deanna Callerame ◽  
Staci Hammer ◽  
James C. Hu ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Biological Process ◽  
Loss Of Function ◽  
Gain Of Function ◽  
Cycle Progression ◽  
Computational Approaches ◽  
Cell Cycle Genes ◽  
Functional Screens

ABSTRACTA long-standing effort in biology is to precisely define and group phenotypes that characterize a biological process, and the genes that underpin them. In Saccharomyces cerevisiae and other organisms, functional screens have generated rich lists of phenotypes associated with individual genes. However, it is often challenging to identify sets of phenotypes and genes that are most closely associated with a given biological process. Here, we focused on the 166 phenotypes arising from loss-of-function and the 86 phenotypes from gain-of-function mutations in 571 genes currently assigned to cell cycle-related ontologies in S. cerevisiae. To reduce this complexity, we applied unbiased, computational approaches of correspondence analysis to identify a minimum set of phenotypic variables that accounts for as much of the variability in the data as possible. Loss-of-function phenotypes can be reduced to 20 dimensions, while gain-of-function ones to 14 dimensions. We also pinpoint the contributions of phenotypes and genes in each set. The approach we describe not only simplifies the categorization of phenotypes associated with cell cycle progression but can also serve as a discovery tool for gene function.

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