Encrypted Genes and Their Assembly in Ciliates

2004 ◽  
Author(s):  
David M. Prescott ◽  
Grzegorz Rozenberg
Keyword(s):  
Life Cycle ◽  
Normal Cell ◽  
Cell Function ◽  
Gene Evolution ◽  
Gene Density ◽  
Somatic Nucleus ◽  
New Genes ◽  
Species Survival ◽  
The Stability ◽  
Spacer Dna

Maintenance of normal cell function and structure requires some level of stability of the cell’s DNA—at least the DNA that makes up the genes of the cell. In most eukaryotes most of the DNA in the genome does not encode genes and has no known function beyond forming long spacers between successive genes. For example, the gene density in the germline (micronuclear) genome of stichotrich ciliates (formerly referred to as hypotrich ciliates) is very low; only a few percent of the DNA encodes the approximately 27,000 different genes, and more than 95% is spacer DNA. Powerful DNA repair systems guard the stability both of nongene and gene DNA in contemporary cells, protecting it against mutagenesis. Although species survival depends on DNA stability, cell evolution requires changes in DNA. Presumably, there is a balance between instability of DNA that allows evolution and a stability that protects species from mutational extinction. Could cells evolve strategies that change the balance, allowing a greater rate of DNA change (gene evolution) without jeopardizing species survival? The stichotrichs may, in fact, have evolved such a mechanism, dramatically modifying their germline DNA during evolution to facilitate creation of new genes without reducing the level of cell survival. The modifications of germline DNA in ciliates, in turn, require dramatic DNA processing to convert germline DNA into somatic DNA during the life cycle of the organisms. The ciliate strategy rests on the evolution of nuclear dimorphism: the inclusion both of a germline nucleus (micronucleus) and a somatic nucleus (macronucleus) in the same cell (Figure 9.1; for a general review, see Prescott [6, 7]). Like the example in Figure 9.1, most stichotrich species contain two or more micronuclei and two or more macronuclei per cell. The multiple micronuclei are genetically identical to each other, and the multiple macronuclei are genetically identical; these multiplicities of nuclei have no bearing on the issues addressed in this chapter. The micronucleus is used only in cell mating, and its genes are silent. Hence, micronuclear genes do not support the maintenance, growth, or division of the cell.

scholarly journals Telomeric G-Quadruplexes: From Human to Tetrahymena Repeats

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Erika Demkovičová ◽  
Ľuboš Bauer ◽  
Petra Krafčíková ◽  
Katarína Tlučková ◽  
Petra Tóthova ◽  
...  
Keyword(s):  
Life Cycle ◽  
Base Substitution ◽  
Telomeric Dna ◽  
Purine Base ◽  
Telomeric Sequences ◽  
G Quadruplex ◽  
The Stability ◽  
Scientific Value ◽  
The Relationship ◽  
Adenine Base

The human telomeric and protozoal telomeric sequences differ only in one purine base in their repeats; TTAGGG in telomeric sequences; and TTGGGG in protozoal sequences. In this study, the relationship between G-quadruplexes formed from these repeats and their derivatives is analyzed and compared. The human telomeric DNA sequence G3(T2AG3)3 and related sequences in which each adenine base has been systematically replaced by a guanine were investigated; the result is Tetrahymena repeats. The substitution does not affect the formation of G-quadruplexes but may cause differences in topology. The results also show that the stability of the substituted derivatives increased in sequences with greater number of substitutions. In addition, most of the sequences containing imperfections in repeats which were analyzed in this study also occur in human and Tetrahymena genomes. Generally, the presence of G-quadruplex structures in any organism is a source of limitations during the life cycle. Therefore, a fuller understanding of the influence of base substitution on the structural variability of G-quadruplexes would be of considerable scientific value.

scholarly journals Personality Traits Across the Life Cycle: Disentangling Age, Period, and Cohort Effects

2021 ◽  
Author(s):  
Bernd Fitzenberger ◽  
Gary Mena ◽  
Jan Nimczik ◽  
Uwe Sunde
Keyword(s):  
Life Cycle ◽  
Personality Traits ◽  
Economic Outcomes ◽  
Cohort Effects ◽  
Specification Tests ◽  
Age Patterns ◽  
Age Profile ◽  
Time Periods ◽  
The Stability

Abstract Economists increasingly recognise the importance of personality traits for socio-economic outcomes, but little is known about the stability of these traits over the life cycle. Existing empirical contributions typically focus on age patterns and disregard cohort and period influences. This paper contributes novel evidence for the separability of age, period, and cohort effects for a broad range of personality traits based on systematic specification tests for disentangling age, period and cohort influences. Our estimates document that for different cohorts, the evolution of personality traits across the life cycle follows a stable, though non-constant, age profile, while there are sizeable differences across time periods.

scholarly journals Characterization of Recombinant Flaviviridae Viruses Possessing a Small Reporter Tag

2017 ◽  
Vol 92 (2) ◽  
Author(s):  
Tomokazu Tamura ◽  
Takasuke Fukuhara ◽  
Takuro Uchida ◽  
Chikako Ono ◽  
Hiroyuki Mori ◽  
...  
Keyword(s):  
Life Cycle ◽  
Amino Acid ◽  
Viral Life Cycle ◽  
Luciferase Gene ◽  
Content Type ◽  
Recombinant Viruses ◽  
Nanoluc Luciferase ◽  
The Stability ◽  
Split Luciferase

ABSTRACTThe familyFlaviviridaeconsists of four genera,Flavivirus,Pestivirus,Pegivirus, andHepacivirus, and comprises important pathogens of human and animals. Although the construction of recombinant viruses carrying reporter genes encoding fluorescent and bioluminescent proteins has been reported, the stable insertion of foreign genes into viral genomes retaining infectivity remains difficult. Here, we applied the 11-amino-acid subunit derived from NanoLuc luciferase to the engineering of theFlaviviridaeviruses and then examined the biological characteristics of the viruses. We successfully generated recombinant viruses carrying the split-luciferase gene, including dengue virus, Japanese encephalitis virus, hepatitis C virus (HCV), and bovine viral diarrhea virus. The stability of the viruses was confirmed by five rounds of serial passages in the respective susceptible cell lines. The propagation of the recombinant luciferase viruses in each cell line was comparable to that of the parental viruses. By using a purified counterpart luciferase protein, this split-luciferase assay can be applicable in various cell lines, even when it is difficult to transduce the counterpart gene. The efficacy of antiviral reagents against the recombinant viruses could be monitored by the reduction of luciferase expression, which was correlated with that of viral RNA, and the recombinant HCV was also useful to examine viral dynamicsin vivo. Taken together, our findings indicate that the recombinantFlaviviridaeviruses possessing the split NanoLuc luciferase gene generated here provide powerful tools to understand viral life cycle and pathogenesis and a robust platform to develop novel antivirals againstFlaviviridaeviruses.IMPORTANCEThe construction of reporter viruses possessing a stable transgene capable of expressing specific signals is crucial to investigations of viral life cycle and pathogenesis and the development of antivirals. However, it is difficult to maintain the stability of a large foreign gene, such as those for fluorescence and bioluminescence, after insertion into a viral genome. Here, we successfully generated recombinantFlaviviridaeviruses carrying the 11-amino-acid subunit derived from NanoLuc luciferase and demonstrated that these viruses are applicable toin vitroandin vivoexperiments, suggesting that these recombinantFlaviviridaeviruses are powerful tools for increasing our understanding of viral life cycle and pathogenesis and that these recombinant viruses will provide a robust platform to develop antivirals againstFlaviviridaeviruses.

scholarly journals Unraveling the Impact of Cysteine-to-Serine Mutations on the Structural and Functional Properties of Cu(I)-Binding Proteins

2019 ◽  
Vol 20 (14) ◽  
pp. 3462 ◽  
Author(s):  
Pavlin ◽  
Qasem ◽  
Sameach ◽  
Gevorkyan-Airapetov ◽  
Ritacco ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Cell Function ◽  
Working Mechanism ◽  
Essential Requirement ◽  
Aggregation Propensity ◽  
Structural And Functional Properties ◽  
Stability Structure ◽  
The Stability ◽  
The Impact ◽  
Partner Proteins

Appropriate maintenance of Cu(I) homeostasis is an essential requirement for proper cell function because its misregulation induces the onset of major human diseases and mortality. For this reason, several research efforts have been devoted to dissecting the inner working mechanism of Cu(I)-binding proteins and transporters. A commonly adopted strategy relies on mutations of cysteine residues, for which Cu(I) has an exquisite complementarity, to serines. Nevertheless, in spite of the similarity between these two amino acids, the structural and functional impact of serine mutations on Cu(I)-binding biomolecules remains unclear. Here, we applied various biochemical and biophysical methods, together with all-atom simulations, to investigate the effect of these mutations on the stability, structure, and aggregation propensity of Cu(I)-binding proteins, as well as their interaction with specific partner proteins. Among Cu(I)-binding biomolecules, we focused on the eukaryotic Atox1-ATP7B system, and the prokaryotic CueR metalloregulator. Our results reveal that proteins containing cysteine-to-serine mutations can still bind Cu(I) ions; however, this alters their stability and aggregation propensity. These results contribute to deciphering the critical biological principles underlying the regulatory mechanism of the in-cell Cu(I) concentration, and provide a basis for interpreting future studies that will take advantage of cysteine-to-serine mutations in Cu(I)-binding systems.

scholarly journals Activity of Plasmodium vivax promoter elements in Plasmodium knowlesi, and a centromere-containing plasmid that expresses NanoLuc throughout the parasite life cycle

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Roberto R. Moraes Barros ◽  
Kittisak Thawnashom ◽  
Tyler J. Gibson ◽  
Jennifer S. Armistead ◽  
Ramoncito L. Caleon ◽  
...  
Keyword(s):  
Life Cycle ◽  
Plasmodium Vivax ◽  
Rhesus Macaque ◽  
Plasmodium Knowlesi ◽  
Luciferase Expression ◽  
Parasite Life Cycle ◽  
Anopheles Dirus ◽  
Exogenous Dna ◽  
The Stability

Abstract Background Plasmodium knowlesi is now the major cause of human malaria in Malaysia, complicating malaria control efforts that must attend to the elimination of multiple Plasmodium species. Recent advances in the cultivation of P. knowlesi erythrocytic-stage parasites in vitro, transformation with exogenous DNA, and infection of mosquitoes with gametocytes from culture have opened up studies of this pathogen without the need for resource-intensive and costly non-human primate (NHP) models. For further understanding and development of methods for parasite transformation in malaria research, this study examined the activity of various trans-species transcriptional control sequences and the influence of Plasmodium vivax centromeric (pvcen) repeats in plasmid-transfected P. knowlesi parasites. Methods In vitro cultivated P. knowlesi parasites were transfected with plasmid constructs that incorporated Plasmodium vivax or Plasmodium falciparum 5′ UTRs driving the expression of bioluminescence markers (firefly luciferase or Nanoluc). Promoter activities were assessed by bioluminescence, and parasites transformed with human resistant allele dihydrofolate reductase-expressing plasmids were selected using antifolates. The stability of transformants carrying pvcen-stabilized episomes was assessed by bioluminescence over a complete parasite life cycle through a rhesus macaque monkey, mosquitoes, and a second rhesus monkey. Results Luciferase expression assessments show that certain P. vivax promoter regions, not functional in the more evolutionarily-distant P. falciparum, can drive transgene expression in P. knowlesi. Further, pvcen repeats may improve the stability of episomal plasmids in P. knowlesi and support detection of NanoLuc-expressing elements over the full parasite life cycle from rhesus macaque monkeys to Anopheles dirus mosquitoes and back again to monkeys. In assays of drug responses to chloroquine, G418 and WR9910, anti-malarial half-inhibitory concentration (IC50) values of blood stages measured by NanoLuc activity proved comparable to IC50 values measured by the standard SYBR Green method. Conclusion All three P. vivax promoters tested in this study functioned in P. knowlesi, whereas two of the three were inactive in P. falciparum. NanoLuc-expressing, centromere-stabilized plasmids may support high-throughput screenings of P. knowlesi for new anti-malarial agents, including compounds that can block the development of mosquito- and/or liver-stage parasites.

scholarly journals Lymphotoxin: stimulation and regulation of colony-stimulating factors in fibroblasts

Blood ◽  
1989 ◽  
Vol 74 (7) ◽  
pp. 2383-2390
Author(s):  
M Akashi ◽  
M Saito ◽  
HP Koeffler
Keyword(s):  
Cell Function ◽  
Mrna Levels ◽  
Necrosis Factor Alpha ◽  
Activated Lymphocytes ◽  
Colony Stimulating Factors ◽  
Gm Csf ◽  
Csf Proteins ◽  
Consensus Region ◽  
The Stability ◽  
And Function

Colony-stimulating factors (CSFs) are pivotal for proliferation and function of hematopoietic cells. We found that lymphotoxin, a product of activated lymphocytes, stimulates accumulation of granulocyte- macrophage (GM)-CSF and macrophage (M)-CSF proteins and mRNAs in fibroblasts. An increase in GM- and M-CSF mRNA levels occurred within 2 hours after addition of 1,000 U/mL lymphotoxin and levels plateaued over the next 24 hours. Tumor necrosis factor alpha (TNF alpha) was about five times more potent than lymphotoxin at low concentrations, and was nearly 1.5 to to 2 times more potent at maximally stimulating concentrations of the cytokines. Stimulation by lymphotoxin did not require either new protein synthesis or protein kinase-C stimulation. Stability studies of GM- and M-CSF transcripts in fibroblasts showed that M-CSF mRNA was five times more stable (half-life [t 1/2], 100 minutes) than GM-CSF mRNA (t 1/2, 20 minutes). Stability of these mRNAs was unchanged after stimulation of the cells with lymphotoxin. In addition, exposure of cells to 12-O-tetradecanoylphorbol 13-acetate did not alter stability of M-CSF mRNA but markedly prolonged the stability of GM-CSF mRNA. This is consistent with data showing that the AT-rich consensus region in the 3′ untranslated region of many transiently expressed cytokines including GM-CSF but not M-CSF, play a major role in their mRNA stability. Our results suggest that activated lymphocytes can affect hematopoietic cell function and growth by stimulating production of CSFs by mesenchymal cells.

scholarly journals Involvement of Mitochondrial Dynamics and Mitophagy in Sevoflurane-Induced Cell Toxicity

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Ming Li ◽  
Jiguang Guo ◽  
Hongjie Wang ◽  
Yuzhen Li
Keyword(s):  
Pediatric Surgery ◽  
Cell Function ◽  
Mitochondrial Dynamics ◽  
Mitochondrial Pathway ◽  
Cell Toxicity ◽  
Mitochondrial Homeostasis ◽  
Unpleasant Odor ◽  
Inhalational Anesthetic ◽  
Indispensable Tool ◽  
The Stability

General anesthesia is a powerful and indispensable tool to ensure the accomplishment of surgical procedures or clinical examinations. Sevoflurane as an inhalational anesthetic without unpleasant odor is commonly used in clinical practice, especially for pediatric surgery. However, the toxicity caused by sevoflurane has gained growing attention. Mitochondria play a key role in maintaining cellular metabolism and survival. To maintain the stability of mitochondrial homeostasis, they are constantly going through fusion and fission. Also, damaged mitochondria need to be degraded by autophagy, termed as mitophagy. Accumulating evidence proves that sevoflurane exposure in young age could lead to cell toxicity by triggering the mitochondrial pathway of apoptosis, inducing the abnormalities of mitochondrial dynamics and mitophagy. In the present review, we focus on the current understanding of mitochondrial apoptosis, dynamics and mitophagy in cell function, the implications for cell toxicity in response to sevoflurane, and their underlying potential mechanisms.

scholarly journals Destabilization of chromosome structure by histone H3 lysine 27 methylation

2018 ◽  
Author(s):  
Mareike Möller ◽  
Klaas Schotanus ◽  
Jessica Soyer ◽  
Janine Haueisen ◽  
Kathrin Happ ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Normal Cell ◽  
Genome Stability ◽  
Large Scale ◽  
Chromosome Structure ◽  
Cell Function ◽  
Pathogenic Fungus ◽  
The Impact ◽  
Accessory Chromosomes

AbstractChromosome and genome stability are important for normal cell function as instability often correlates with disease and dysfunction of DNA repair mechanisms. Many organisms maintain supernumerary or accessory chromosomes that deviate from standard chromosomes. The pathogenic fungus Zymoseptoria tritici has as many as eight accessory chromosomes, which are highly unstable during meiosis and mitosis, transcriptionally repressed, show enrichment of repetitive elements, and enrichment with heterochromatic histone methylation marks, e.g., trimethylation of H3 lysine 9 or lysine 27 (H3K9me3, H3K27me3). To elucidate the role of heterochromatin on genome stability in Z. tritici, we deleted the genes encoding the methyltransferases responsible for H3K9me3 and H3K27me3, kmt1 and kmt6, respectively, and generated a double mutant. We combined experimental evolution and genomic analyses to determine the impact of these deletions on chromosome and genome stability, both in vitro and in planta. We used whole genome sequencing, ChIP-seq, and RNA-seq to compare changes in genome and chromatin structure, and differences in gene expression between mutant and wildtype strains. Analyses of genome and ChIP-seq data in H3K9me3-deficient strains revealed dramatic chromatin reorganization, where H3K27me3 is mostly relocalized into regions that are enriched with H3K9me3 in wild type. Many genome rearrangements and formation of new chromosomes were found in the absence of H3K9me3, accompanied by activation of transposable elements. In stark contrast, loss of H3K27me3 actually increased the stability of accessory chromosomes under normal growth conditions in vitro, even without large scale changes in gene activity. We conclude that H3K9me3 is important for the maintenance of genome stability because it disallows H3K27me3 in these regions. In this system, H3K27me3 reduces the overall stability of accessory chromosomes, generating a “metastable” state for these quasi-essential regions of the genome.Author SummaryGenome and chromosome stability are essential to maintain normal cell function and viability. However, differences in genome and chromosome structure are frequently found in organisms that undergo rapid adaptation to changing environmental conditions, and in humans are often found in cancer cells. We study genome instability in a fungal pathogen that exhibits a high degree of genetic diversity. Regions that show extraordinary diversity in this pathogen are the transposon-rich accessory chromosomes, which contain few genes that are of unknown benefit to the organism but maintained in the population and thus considered “quasi essential”. Accessory chromosomes in all fungi studied so far are enriched with markers for heterochromatin, namely trimethylation of H3 lysine 9 and 27 (H3K9me3, H3K27me3). We show that loss of these heterochromatin marks has strong but opposing effects on genome stability. While loss of the transposon-associated mark H3K9me3 destabilizes the entire genome, presence of H3K27me3 favors instability of accessory chromosomes. Our study provides insight into the relationship between chromatin and genome stability and why some regions are more susceptible to genetic diversity than others.

scholarly journals Academia as a league system

2022 ◽  
Author(s):  
Aloys Prinz ◽  
Thomas Ehrmann
Keyword(s):  
Life Cycle ◽  
Research Universities ◽  
Financial Resources ◽  
Recent Attempt ◽  
Competitive Advantages ◽  
University System ◽  
Societal Costs ◽  
Mature Phase ◽  
The Stability ◽  
Super League

AbstractIn this paper, we explain the stability of top university ranks and discuss attempts to create top national universities. Firstly, it is shown theoretically that in a world with differently-gifted poor and rich students, a three-tier university system may become very stable, with a super league of the best research universities that attract the best students, whether rich or poor. Secondly, it is empirically demonstrated that half of the highest ranked universities enjoy very stable competitive advantages. Thirdly, we examine attempts of China, France and Germany to overcome these disadvantages and to get into this super league. The recent attempt of China to create such super league universities shows the financial and societal costs of these attempts. France demonstrates how the concentration of financial resources on two newly built universities that complement the forces of existing ones—either real or only by labelling—may succeed. Despite the complexly designed and competitive German Excellence Initiative, ongoing since 2004, no German university was among the top 50 in the Shanghai ranking in 2021 (compared to one university in 2004). The mixed results of all these worldwide attempts may reflect the problem that late market entry into the super league may be too costly, given that the classical university business model is in the mature phase of its life cycle.

scholarly journals Lymphotoxin: stimulation and regulation of colony-stimulating factors in fibroblasts

Blood ◽  
1989 ◽  
Vol 74 (7) ◽  
pp. 2383-2390 ◽  
Author(s):  
M Akashi ◽  
M Saito ◽  
HP Koeffler
Keyword(s):  
Cell Function ◽  
Mrna Levels ◽  
Necrosis Factor Alpha ◽  
Activated Lymphocytes ◽  
Colony Stimulating Factors ◽  
Gm Csf ◽  
Csf Proteins ◽  
Consensus Region ◽  
The Stability ◽  
And Function

Abstract Colony-stimulating factors (CSFs) are pivotal for proliferation and function of hematopoietic cells. We found that lymphotoxin, a product of activated lymphocytes, stimulates accumulation of granulocyte- macrophage (GM)-CSF and macrophage (M)-CSF proteins and mRNAs in fibroblasts. An increase in GM- and M-CSF mRNA levels occurred within 2 hours after addition of 1,000 U/mL lymphotoxin and levels plateaued over the next 24 hours. Tumor necrosis factor alpha (TNF alpha) was about five times more potent than lymphotoxin at low concentrations, and was nearly 1.5 to to 2 times more potent at maximally stimulating concentrations of the cytokines. Stimulation by lymphotoxin did not require either new protein synthesis or protein kinase-C stimulation. Stability studies of GM- and M-CSF transcripts in fibroblasts showed that M-CSF mRNA was five times more stable (half-life [t 1/2], 100 minutes) than GM-CSF mRNA (t 1/2, 20 minutes). Stability of these mRNAs was unchanged after stimulation of the cells with lymphotoxin. In addition, exposure of cells to 12-O-tetradecanoylphorbol 13-acetate did not alter stability of M-CSF mRNA but markedly prolonged the stability of GM-CSF mRNA. This is consistent with data showing that the AT-rich consensus region in the 3′ untranslated region of many transiently expressed cytokines including GM-CSF but not M-CSF, play a major role in their mRNA stability. Our results suggest that activated lymphocytes can affect hematopoietic cell function and growth by stimulating production of CSFs by mesenchymal cells.

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