scholarly journals Codon stabilization coefficient as an index for prediction of codon bias and its potential applications

2018 ◽  
Author(s):  
Rodolofo L. Carneiro ◽  
Rodrigo D. Requião ◽  
Silvana Rossetto ◽  
Tatiana Domitrovic ◽  
Fernando L. Palhano
Keyword(s):  
Half Life ◽  
Codon Bias ◽  
Accurate Method ◽  
Optimal Codons ◽  
Genome Wide ◽  
Life Measurement ◽  
Stabilization Coefficient ◽  
Potential Applications ◽  
Positive Correlations ◽  
Mrna Half Life

SummaryDifferent methods of mRNA half-life measurements are available, but genome-wide measurements of mRNA half-life in yeast showed a weak correlation between the methods. Moreover, when we compared mRNA half-life determined by these methods with other cellular measurements such as mRNA and protein abundance low correlation was found. To clarify this matter, we analyzed mRNA half-life datasets from nine different groups to determine the most accurate method of measurement. Since codon optimality is one of the significant determinants of mRNA stability, we used the codon stabilization coefficient (CSC) as a reference for mRNA half-life measurement accuracy. After CSC calculation for each dataset, we find strong positive correlations between the CSC from some datasets with other parameters that reflect codon optimality such as tRNA abundance and ribosome residence time. By the use of CSC parameter, we observed that most genes contain non-optimal codons and that codon bias exists toward optimized and non-optimized genes. We also observed that stretches of non-optimal are not randomly distributed since it causes impacts on translation.

scholarly journals High precision half-life measurement of 125Cs and 125Xe with γ-spectroscopy

2019 ◽  
Vol 986 ◽  
pp. 213-222 ◽  
Author(s):  
T.N. Szegedi ◽  
G.G. Kiss ◽  
I. Öksüz ◽  
T. Szücs ◽  
Gy. Gyürky ◽  
...  
Keyword(s):  
High Precision ◽  
Half Life ◽  
Life Measurement

Statistical considerations in half-life measurement, I

1970 ◽  
Vol 81 (1) ◽  
pp. 155-163 ◽  
Author(s):  
A.H. Jaffey
Keyword(s):  
Half Life ◽  
Life Measurement

CHARACTERISTIC OF AGGREGATHOSCOPY METHOD FOR REGISTERING OF ERYTHROCYTES MICRORHEOLOGY

2017 ◽  
Author(s):  
А. Муравьев ◽  
И. Тихомирова ◽  
А. Замышляев ◽  
П. Михайлов ◽  
Е. Петроченко ◽  
...  
Keyword(s):  
Image Processing ◽  
Prostaglandin F2α ◽  
Accurate Method ◽  
Erythrocyte Aggregation ◽  
Suspension Stability ◽  
Ionophore A23187 ◽  
Test Results ◽  
Rate Test ◽  
Positive Correlations ◽  
Special Computer Program

Введение. Две микрореологические характеристики определяют кровоток в системе сосудов микроциркуляции — агрегация и деформируемость эритроцитов. В подавляющем большинстве приборов для регистрации агрегации эритроцитов (АЭ) отсутствует визуализация процесса, и интерпретация данных основывается на его косвенных характеристиках. Материалы и методы. Проведено исследование АЭ на созданной установке — агрегатоскопе, получены данные регистрации картины АЭ с последующей обработкой изображения с помощью специальной программы для ЭВМ. Информативность полученных данных была проверена в сравнительных исследованиях с использованием агрегометра эритроцитов Myrenne M1 и теста СОЭ. Результаты. Получены значительные положительные корреляции (r=0,90 и r=0,86, соответственно). Показано, что агрегатоскоп дает четкую картину изменения АЭ (ее снижение) при инкубации эритроцитов с хелатором Са2+ (ЭДТА, верапамил, изобутилметилксантин, монафрам). В ответ на инкубацию с препаратами другой группы, известными как стимуляторы АЭ (CaCl2, ионофор А23187, фенилэфрин, простагландин F2α), был получен достоверный прирост агрегации. Заключение. Метод агрегатоскопии в сочетании с программной обработкой изображений является удобным и надежным инструментом оценки суспензионной стабильности крови и точным методом измерения важной микрореологической характеристики эритроцитов — их агрегации. Introduction. Aggregation and deformability of erythrocytes are two microrheological characteristics that determine the blood fl ow in microcirculation vessels. In large majority of devices for registration of erythrocyte aggregation (EA) there is no visualization of the process, and the interpretation of the data is based on its indirect characteristics. Materials and methods. EA investigation was carried out on the created unit — aggregatoscop. Data were obtained for registration of EA followed by image processing using a special computer program. Data informativeness was verified in comparative studies using erythrocyte aggregometer Myrenne M1 and erythrocyte sedimentation rate test. Results. Significant positive correlations were obtained (r=0,90 and r=0,86, respectively). It was shown that aggregatoscop gave a clear picture of EA changes (its reduction) during erythrocytes incubation with Са2+ chelator (EDTA, verapamil, isobutylmethylxanthine, monaphram). Reliable increasing of aggregation was obtained in response to incubation with other agents — EA stimulants (CaCl2, ionophore A23187, phenylephrine, prostaglandin F2α). Conclusion. Aggregoscopy method in combination with software image processing is a convenient and reliable tool for assessing of blood suspension stability and an accurate method for measuring of important microrheological characteristics of erythrocytes — their aggregation.

scholarly journals Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Joseph R. Peterson ◽  
ShengShee Thor ◽  
Lars Kohler ◽  
Petra R.A. Kohler ◽  
William W. Metcalf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Half Life ◽  
Methanosarcina Acetivorans ◽  
Genome Wide ◽  
Metabolic Behavior ◽  
Genome Wide Gene Expression

The KH-type splicing regulatory protein (KSRP) regulates type III interferon expression post-transcriptionally

2019 ◽  
Vol 476 (2) ◽  
pp. 333-352 ◽  
Author(s):  
Lisa Schmidtke ◽  
Katharina Schrick ◽  
Sabrina Saurin ◽  
Rudolf Käfer ◽  
Fabian Gather ◽  
...  
Keyword(s):  
Half Life ◽  
Rna Binding ◽  
Binding Protein ◽  
Regulatory Protein ◽  
Rna Binding Protein ◽  
Luciferase Reporter ◽  
Regulatory Function ◽  
Type Iii ◽  
Type Iii Ifn ◽  
Mrna Half Life

Abstract Type III interferons (IFNs) are the latest members of the IFN family. They play an important role in immune defense mechanisms, especially in antiviral responses at mucosal sites. Moreover, they control inflammatory reactions by modulating neutrophil and dendritic cell functions. Therefore, it is important to identify cellular mechanisms involved in the control of type III IFN expression. All IFN family members contain AU-rich elements (AREs) in the 3′-untranslated regions (3′-UTR) of their mRNAs that determine mRNA half-life and consequently the expressional level of these cytokines. mRNA stability is controlled by different proteins binding to these AREs leading to either stabilization or destabilization of the respective target mRNA. The KH-type splicing regulatory protein KSRP (also named KHSRP) is an important negative regulator of ARE-containing mRNAs. Here, we identify the interferon lambda 3 (IFNL3) mRNA as a new KSRP target by pull-down and immunoprecipitation experiments, as well as luciferase reporter gene assays. We characterize the KSRP-binding site in the IFNL3 3′-UTR and demonstrate that KSRP regulates the mRNA half-life of the IFNL3 transcript. In addition, we detect enhanced expression of IFNL3 mRNA in KSRP−/− mice, establishing a negative regulatory function of KSRP in type III IFN expression also in vivo. Besides KSRP the RNA-binding protein AUF1 (AU-rich element RNA-binding protein 1) also seems to be involved in the regulation of type III IFN mRNA expression.

scholarly journals Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1786
Author(s):  
Soumeya Rida ◽  
Oula Maafi ◽  
Ana López-Malvar ◽  
Pedro Revilla ◽  
Meriem Riache ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Breeding Programs ◽  
Seedling Traits ◽  
Genome Wide ◽  
A Genome ◽  
Positive Correlations ◽  
Genomic Regions ◽  
Magic Population

Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.

Depression of nuclear transcription and extension of mRNA half-life under anoxia in Artemia franciscana embryos

2000 ◽  
Vol 203 (7) ◽  
pp. 1123-1130 ◽  
Author(s):  
F. van Breukelen ◽  
R. Maier ◽  
S.C. Hand
Keyword(s):  
Half Life ◽  
Mammalian Cells ◽  
Transcriptional Activity ◽  
Artemia Franciscana ◽  
Mrna Levels ◽  
Compensatory Mechanisms ◽  
Depressed State ◽  
Initiation Of Transcription ◽  
Mrna Half Life

Transcriptional activity, as assessed by nuclear run-on assays, was constant during 10 h of normoxic development for embryos of the brine shrimp Artemia franciscana. Exposure of embryos to only 4 h of anoxia resulted in a 79.3+/−1 % decrease in levels of in-vivo-initiated transcripts, and transcription was depressed by 88. 2+/−0.7 % compared with normoxic controls after 24 h of anoxia (means +/− s.e.m., N=3). Initiation of transcription was fully restored after 1 h of normoxic recovery. Artificially lowering the intracellular pH of aerobic embryos to the value reflective of anoxia (pH 6.7) showed that acidification alone explained over half the transcriptional arrest. Initiation of transcription was not rescued by application of 80 % carbon monoxide under anoxia, which suggests that heme-based oxygen sensing is not involved in this global arrest. When these transcriptional data are combined with the finding that mRNA levels are unchanged for at least 6 h of anoxia, it is clear that the half-life of mRNA is extended at least 8.5-fold compared with that in aerobic embryos. In contrast to the activation of compensatory mechanisms to cope with anoxia that occurs in mammalian cells, A. franciscana embryos enter a metabolically depressed state in which gene expression and mRNA turnover are cellular costs apparently not compatible with survival and in which extended tolerance supercedes the requirement for continued metabolic function.

Half-life measurement of excited states in neutron-rich nuclei

2009 ◽  
pp. 463-464
Author(s):  
J. K. Hwang ◽  
A. V. Ramayya ◽  
J. H. Hamilton ◽  
D. Fong ◽  
C. J. Beyer ◽  
...  
Keyword(s):  
Excited States ◽  
Half Life ◽  
Life Measurement

scholarly journals New precise half-life measurement for the superallowed β+ emitter Ar34

2020 ◽  
Vol 101 (1) ◽  
Author(s):  
V. E. Iacob ◽  
J. C. Hardy ◽  
H. I. Park ◽  
M. Bencomo ◽  
L. Chen ◽  
...  
Keyword(s):  
Half Life ◽  
Life Measurement

Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation

Science ◽  
2018 ◽  
Vol 361 (6403) ◽  
pp. 701-704 ◽  
Author(s):  
Jaechul Lim ◽  
Dongwan Kim ◽  
Young-suk Lee ◽  
Minju Ha ◽  
Mihye Lee ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Half Life ◽  
Messenger Rna ◽  
Mrna Translation ◽  
Posttranscriptional Gene Regulation ◽  
And Function ◽  
Mrna Half Life ◽  
In Cells

RNA tails play integral roles in the regulation of messenger RNA (mRNA) translation and decay. Guanylation of the poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TENT4A (PAPD7) and TENT4B (PAPD5) as the enzymes responsible for mRNA guanylation. Purified TENT4 proteins generate a mixed poly(A) tail with intermittent non-adenosine residues, the most common of which is guanosine. A single guanosine residue is sufficient to impede the deadenylase CCR4-NOT complex, which trims the tail and exposes guanosine at the 3′ end. Consistently, depletion of TENT4A and TENT4B leads to a decrease in mRNA half-life and abundance in cells. Thus, TENT4A and TENT4B produce a mixed tail that shields mRNA from rapid deadenylation. Our study unveils the role of mixed tailing and expands the complexity of posttranscriptional gene regulation.

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