scholarly journals The translation inhibitor cycloheximide affects ribosome profiling data in a species-specific manner

2019 ◽  
Author(s):  
Puneet Sharma ◽  
Benedikt S. Nilges ◽  
Jie Wu ◽  
Sebastian A. Leidel
Keyword(s):  
Positional Information ◽  
Human Cells ◽  
Ribosome Profiling ◽  
Model Organisms ◽  
Specific Effects ◽  
Treatment Conditions ◽  
Yeast Data ◽  
Translation Inhibitor ◽  
Pre Treatment ◽  
Species Specific

AbstractRibosome profiling provides genome-wide snapshots of translation dynamics by determining ribosomal positions at sub-codon resolution. To maintain this positional information, the translation inhibitor cycloheximide (CHX) has been widely used to arrest translating ribosomes prior to library preparation. Several studies have reported CHX-induced biases in yeast data casting uncertainty about its continued use and questioning the accuracy of many ribosome profiling studies. However, the presence of these biases has not been investigated comprehensively in organisms other than Saccharomyces cerevisiae. Here, we use a highly standardized and optimized protocol to compare different CHX-treatment conditions in yeast and human cells. Our data suggest that unlike in S. cerevisiae, translating ribosomes in human cells are not susceptible to conformational restrictions by CHX. Furthermore, CHX-induced codon-specific effects on ribosome occupancy are not detectable in human cells nor in other model organisms including Schizosaccharomyces pombe and Candida albicans. In fact, we find that even in S. cerevisiae most biases can be avoided by omitting CHX pre-treatment, indicating that other parameters of library generation contribute to differences between ribosome profiling experiments. Together our findings provide a framework for researchers who plan their own ribosome profiling experiments or who analyze published datasets to draw judicious conclusions.

scholarly journals Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Puneet Sharma ◽  
Jie Wu ◽  
Benedikt S. Nilges ◽  
Sebastian A. Leidel
Keyword(s):  
Human Cells ◽  
Ribosome Profiling ◽  
Model Organisms ◽  
Treatment Conditions ◽  
Genome Wide ◽  
Optimized Protocol ◽  
Gene Level ◽  
Translation Inhibitor ◽  
Species Specific ◽  
Conformational Restrictions

AbstractRibosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

Tissue and species-specific effects of small molecular weight nuclear RNA's on transcription in isolated mammalian nuclei

1981 ◽  
Vol 59 (5) ◽  
pp. 343-352 ◽  
Author(s):  
Wing-Cheong Liu ◽  
Roseline Godbout ◽  
Ernest Jay ◽  
Kenneth K.-Y. Yu ◽  
Margarida O. Krause
Keyword(s):  
Molecular Weight ◽  
Human Cells ◽  
Kidney Cells ◽  
Small Molecular Weight ◽  
Isolated Nuclei ◽  
Specific Effects ◽  
Specific Manner ◽  
Normal Human ◽  
Species Specific ◽  
Slab Gels

Small molecular weight nuclear RNA's (SnRNA's) purified from the 0.35 M NaCl extract of chromatin from human and monkey tissues have been found to stimulate transcription of chromatin in isolated nuclei in a tissue- and species-specific manner. While SnRNA from normal human cells (WI38 fibroblasts and placenta) stimulates homologous transcription to some extent, it has a greater activity on transcription of heterologous tissue of the same species and no activity on heterologous tissue of a different species (monkey kidney cells). Likewise SnRNA from monkey cells stimulates transcription of homologous chromatin but has no effect on human cells. Fractionation of the RNA's in polyacrylamide gradient slab gels revealed that in all cases the active RNA was 160–175 nucleotides in length. Our results are compatible with the hypothesis that the active RNA's are involved in the determination and maintenance of tissue differentiation by recognizing promoter or regulator sequences in the DNA and act at the level of the nucleosome to induce tissue-specific genes.

scholarly journals RiboDiPA: A Novel tool for differential pattern analysis in Ribo-seq data

2020 ◽  
Author(s):  
Keren Li ◽  
Matthew Hope ◽  
Xiaozhong A. Wang ◽  
Ji-Ping Wang
Keyword(s):  
Pattern Analysis ◽  
Positional Information ◽  
R Package ◽  
Ribosome Profiling ◽  
Model Organisms ◽  
Translational Efficiency ◽  
Data Sets ◽  
Novel Approach ◽  
Occupancy Patterns ◽  
Differential Pattern

AbstractRibosome profiling (also known as Ribo-seq) has become an important technique to investigate changes in translation across a wide variety of contexts. Ribo-seq data not only provides the abundance of ribosomes bound to transcripts, but also positional information across transcripts that could be indicative of differences in translation dynamics between conditions. While many computational tools exist for the analysis of Ribo-seq data, including those that assess differences in translational efficiency between conditions, no tool currently exists for rigorous test of the pattern differences in ribosome footprint. In this paper we propose a novel approach together with an R package, RiboDiPA, for Differential PPattern Analysis of Ribo-seq data. RiboDiPA allows for quick identification of genes with statistically significant differences in ribosome occupancy patterns for model organisms ranging from yeast to mammals. We show that differential pattern analysis reveals information that is distinct and complimentary to the existing methods that focus on translational efficiency analysis. Using both simulated Ribo-seq footprint data and two benchmark data sets, we illustrate that RiboDiPA can not only uncover meaningful global translational differences between conditions, but also the detailed differential ribosome binding patterns to a single codon resolution.

scholarly journals RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data

2020 ◽  
Vol 48 (21) ◽  
pp. 12016-12029
Author(s):  
Keren Li ◽  
C Matthew Hope ◽  
Xiaozhong A Wang ◽  
Ji-Ping Wang
Keyword(s):  
Pattern Analysis ◽  
Positional Information ◽  
R Package ◽  
Global Scale ◽  
Ribosome Profiling ◽  
Model Organisms ◽  
Translational Efficiency ◽  
Translation Efficiency ◽  
Occupancy Patterns ◽  
Differential Pattern

Abstract Ribosome profiling, also known as Ribo-seq, has become a popular approach to investigate regulatory mechanisms of translation in a wide variety of biological contexts. Ribo-seq not only provides a measurement of translation efficiency based on the relative abundance of ribosomes bound to transcripts, but also has the capacity to reveal dynamic and local regulation at different stages of translation based on positional information of footprints across individual transcripts. While many computational tools exist for the analysis of Ribo-seq data, no method is currently available for rigorous testing of the pattern differences in ribosome footprints. In this work, we develop a novel approach together with an R package, RiboDiPA, for Differential Pattern Analysis of Ribo-seq data. RiboDiPA allows for quick identification of genes with statistically significant differences in ribosome occupancy patterns for model organisms ranging from yeast to mammals. We show that differential pattern analysis reveals information that is distinct and complimentary to existing methods that focus on translational efficiency analysis. Using both simulated Ribo-seq footprint data and three benchmark data sets, we illustrate that RiboDiPA can uncover meaningful pattern differences across multiple biological conditions on a global scale, and pinpoint characteristic ribosome occupancy patterns at single codon resolution.

Density-dependent and species-specific effects on self-organization modulate the resistance of mussel bed ecosystems to hydrodynamic stress

2021 ◽  
Author(s):  
Gerardo I. Zardi ◽  
Katy Rebecca Nicastro ◽  
Christopher D. McQuaid ◽  
Monique de Jager ◽  
Johan van de Koppel ◽  
...  
Keyword(s):  
Self Organization ◽  
Mussel Bed ◽  
Hydrodynamic Stress ◽  
Density Dependent ◽  
Specific Effects ◽  
Species Specific

scholarly journals In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2226
Author(s):  
Sazia Kunvar ◽  
Sylwia Czarnomska ◽  
Cino Pertoldi ◽  
Małgorzata Tokarska
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Bos Taurus ◽  
Model Organism ◽  
Genotyping By Sequencing ◽  
Model Organisms ◽  
European Bison ◽  
Model Animal ◽  
Pcr Duplicates ◽  
Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

scholarly journals Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anastasiya Börsch ◽  
Daniel J. Ham ◽  
Nitish Mittal ◽  
Lionel A. Tintignac ◽  
Eugenia Migliavacca ◽  
...  
Keyword(s):  
Muscle Mass ◽  
Inflammatory Responses ◽  
Molecular Data ◽  
Model Organisms ◽  
Sequencing Data ◽  
Phenotypic Analysis ◽  
Age Related ◽  
Analogous Data ◽  
Species Specific ◽  
And Function

AbstractSarcopenia, the age-related loss of skeletal muscle mass and function, affects 5–13% of individuals aged over 60 years. While rodents are widely-used model organisms, which aspects of sarcopenia are recapitulated in different animal models is unknown. Here we generated a time series of phenotypic measurements and RNA sequencing data in mouse gastrocnemius muscle and analyzed them alongside analogous data from rats and humans. We found that rodents recapitulate mitochondrial changes observed in human sarcopenia, while inflammatory responses are conserved at pathway but not gene level. Perturbations in the extracellular matrix are shared by rats, while mice recapitulate changes in RNA processing and autophagy. We inferred transcription regulators of early and late transcriptome changes, which could be targeted therapeutically. Our study demonstrates that phenotypic measurements, such as muscle mass, are better indicators of muscle health than chronological age and should be considered when analyzing aging-related molecular data.

scholarly journals Exogenous 5-azaCitidine accelerates flowering and external GA3 increases ornamental value in Iranian Anemone accessions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Vahideh Yari ◽  
Zeynab Roein ◽  
Atefeh Sabouri
Keyword(s):  
Morphological Characteristics ◽  
Flower Longevity ◽  
Cut Flowers ◽  
Stem Height ◽  
Flowering Stage ◽  
Potted Plants ◽  
Dormancy Period ◽  
Treatment Conditions ◽  
Number Of Leaves ◽  
Pre Treatment

AbstractThe Anemone genus is a tuberous geophyte which undergoes a dormancy period during unfavorable environmental conditions for growth. Five species of the Anemone genus naturally grow in several regions of Iran. The diverse uses of Anemone in gardens for landscaping, cut flowers, and potted plants indicate its high ornamental potential. Its dormancy and flowering are influenced by various factors. The present paper was conducted to explore the flowering behavior of Anemone accessions in response to different pre-treatments. For this purpose, tubers of 18 Anemone accessions (A. coronaria and A. biflora) were collected from natural regions of six provinces in Iran. These tubers were subjected to different conditions of non-chilling (20 °C, 90 days), chilling (4 °C, 90 days), GA3 (150 mgL-1; 24 h), and 5-azaCitidine (5-azaC; 40 µM; 24 h) prior to the cultivation. Most of the accessions were able to enter the flowering stage without chilling. The shortest period for the sprouting of tubers (16.89 ± 7.83 days) belonged to 5-azaC pre-treatment. In addition, this treatment accelerated the flowering time (about 30 days earlier) and diameter of the stem, bud, and flower. Morphological characteristics, such as stem height, number of leaves, bud, and petal and the longevity of flowers on the plant were significantly affected by GA3 pre-treatment. Our results indicated a positive correlation between flower length, stem height, and stem diameter with flower longevity under different pre-treatment conditions. The present study demonstrated that accessions Anm3, Anm12, and Anm18 had ornamental values higher than the population mean across four conditions.

Variation in vegetation cover and seedling performance of tree species in a forest-savanna ecotone

2019 ◽  
Vol 35 (2) ◽  
pp. 74-82 ◽  
Author(s):  
Hamza Issifu ◽  
George K. D. Ametsitsi ◽  
Lana J. de Vries ◽  
Gloria Djaney Djagbletey ◽  
Stephen Adu-Bredu ◽  
...  
Keyword(s):  
Vegetation Cover ◽  
Seedling Recruitment ◽  
Seedling Survival ◽  
Tree Cover ◽  
First Year ◽  
Transplant Experiment ◽  
Tree Seedling ◽  
Savanna Woodland ◽  
Specific Effects ◽  
Species Specific

AbstractDifferential tree seedling recruitment across forest-savanna ecotones is poorly understood, but hypothesized to be influenced by vegetation cover and associated factors. In a 3-y-long field transplant experiment in the forest-savanna ecotone of Ghana, we assessed performance and root allocation of 864 seedlings for two forest (Khaya ivorensis and Terminalia superba) and two savanna (Khaya senegalensis and Terminalia macroptera) species in savanna woodland, closed-woodland and forest. Herbaceous vegetation biomass was significantly higher in savanna woodland (1.0 ± 0.4 kg m−2 vs 0.2 ± 0.1 kg m−2 in forest) and hence expected fire intensities, while some soil properties were improved in forest. Regardless, seedling survival declined significantly in the first-year dry-season for all species with huge declines for the forest species (50% vs 6% for Khaya and 16% vs 2% for Terminalia) by year 2. After 3 y, only savanna species survived in savanna woodland. However, best performance for savanna Khaya was in forest, but in savanna woodland for savanna Terminalia which also had the highest biomass fraction (0.8 ± 0.1 g g−1 vs 0.6 ± 0.1 g g−1 and 0.4 ± 0.1 g g−1) and starch concentration (27% ± 10% vs 15% ± 7% and 10% ± 4%) in roots relative to savanna and forest Khaya respectively. Our results demonstrate that tree cover variation has species-specific effects on tree seedling recruitment which is related to root storage functions.

Bifidobacteria exert species-specific effects on constipation in BALB/c mice

2017 ◽  
Vol 8 (10) ◽  
pp. 3587-3600 ◽  
Author(s):  
Linlin Wang ◽  
Lujun Hu ◽  
Qi Xu ◽  
Tian Jiang ◽  
Shuguang Fang ◽  
...  
Keyword(s):  
Specific Effects ◽  
Species Specific

Edible bifidobacteria exerted species-specific effects in relieving constipation.

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