scholarly journals Dynamics of transposable element invasions with piRNA clusters

2018 ◽  
Author(s):  
Robert Kofler
Keyword(s):  
Drosophila Melanogaster ◽  
Equilibrium State ◽  
Transposable Element ◽  
Negative Selection ◽  
Large Scale ◽  
Real Data ◽  
Copy Numbers ◽  
Pirna Cluster ◽  
The Impact ◽  
Random Insertion

AbstractIn mammals and in invertebrates the proliferation of a newly invading transposable element (TE) is thought to be stopped by a random insertion of one member of the invading TE family into a piRNA cluster. This view is known as the trap model. Here we explore the dynamics of TE invasions under the trap model using large-scale computer simulations. We found that piRNA clusters confer a substantial benefit, effectively preventing extinction of host populations from an uncontrollable proliferation of deleterious TEs. We show that TE invasions under the trap model consists of three distinct phases: first the TE rapidly amplifies within the population, next TE proliferation is stopped by segregating cluster insertions and finally the TE is permanently inactivated by fixation of a cluster insertion. Suppression by segregating cluster insertions is unstable and bursts of TE activity may yet occur. The transpositon rate and the population size mostly influence the length of the phases but not the amount of TEs accumulating during an invasion. Solely the size of piRNA clusters was identified as a major factor influencing TE abundance. Investigating the impact of different cluster architectures we found that a single non-recombining cluster (e.g. the somatic cluster flamenco in Drosophila) is more efficient in stopping invasions than clusters distributed over several chromosomes (e.g germline cluster in Drosophila). With the somatic architecture fewer TEs accumulate during an invasion and fewer cluster insertions are required to stop the TE. The inefficiency of the germline architecture stems from recombination among cluster sites which makes it necessary that each diploid carries, on the average, four cluster insertions, such that most individuals will end up with at least one cluster insertion. Surprisingly we found that negative selection in a model with piRNA clusters can lead to a novel equilibrium state, where TE copy numbers remain stable despite only some individuals in a population carrying a cluster insertion. Finally when applying our approach to real data from Drosophila melanogaster we found that the trap model reasonably well accounts for the abundance of germline TEs but not of somatic TEs. The abundance of somatic TEs, such as gypsy, is much lower than expected.

scholarly journals An Exploration of the Sequence of a 2.9-Mb Region of the Genome of Drosophila melanogaster: The Adh Region

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 179-219 ◽  
Author(s):  
M Ashburner ◽  
S Misra ◽  
J Roote ◽  
S E Lewis ◽  
R Blazej ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Large Scale ◽  
Chromosome Region ◽  
Complete Sequence ◽  
Test Methods ◽  
P Element ◽  
Cdna Libraries ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized “Adh region.” A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species.

scholarly journals Quantile regression for challenging cases of eQTL mapping

2019 ◽  
Vol 21 (5) ◽  
pp. 1756-1765
Author(s):  
Bo Sun ◽  
Liang Chen
Keyword(s):  
Quantile Regression ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Linear Models ◽  
Real Data ◽  
Type I ◽  
Eqtl Mapping ◽  
Size Estimation ◽  
Rna Seq ◽  
The Impact

Abstract Mapping of expression quantitative trait loci (eQTLs) facilitates interpretation of the regulatory path from genetic variants to their associated disease or traits. High-throughput sequencing of RNA (RNA-seq) has expedited the exploration of these regulatory variants. However, eQTL mapping is usually confronted with the analysis challenges caused by overdispersion and excessive dropouts in RNA-seq. The heavy-tailed distribution of gene expression violates the assumption of Gaussian distributed errors in linear regression for eQTL detection, which results in increased Type I or Type II errors. Applying rank-based inverse normal transformation (INT) can make the expression values more normally distributed. However, INT causes information loss and leads to uninterpretable effect size estimation. After comprehensive examination of the impact from overdispersion and excessive dropouts, we propose to apply a robust model, quantile regression, to map eQTLs for genes with high degree of overdispersion or large number of dropouts. Simulation studies show that quantile regression has the desired robustness to outliers and dropouts, and it significantly improves eQTL mapping. From a real data analysis, the most significant eQTL discoveries differ between quantile regression and the conventional linear model. Such discrepancy becomes more prominent when the dropout effect or the overdispersion effect is large. All the results suggest that quantile regression provides more reliable and accurate eQTL mapping than conventional linear models. It deserves more attention for the large-scale eQTL mapping.

Comparison Between Dichotomous and Polytomous Scoring of Innovative Items in a Large-Scale Computerized Adaptive Test

2011 ◽  
Vol 72 (3) ◽  
pp. 493-509 ◽  
Author(s):  
Hong Jiao ◽  
Junhui Liu ◽  
Kathleen Haynie ◽  
Ada Woo ◽  
Jerry Gorham
Keyword(s):  
Large Scale ◽  
Credit Scoring ◽  
Real Data ◽  
Simulation Studies ◽  
Partial Credit ◽  
Ability Estimates ◽  
Operational Test ◽  
Dichotomous Scoring ◽  
Scoring Algorithms ◽  
The Impact

This study explored the impact of partial credit scoring of one type of innovative items (multiple-response items) in a computerized adaptive version of a large-scale licensure pretest and operational test settings. The impacts of partial credit scoring on the estimation of the ability parameters and classification decisions in operational test settings were explored in one real data analysis and two simulation studies when two different polytomous scoring algorithms, automated polytomous scoring and rater-generated polytomous scoring, were applied. For the real data analyses, the ability estimates from dichotomous and polytomous scoring were highly correlated; the classification consistency between different scoring algorithms was nearly perfect. Information distribution changed slightly in the operational item bank. In the two simulation studies comparing each polytomous scoring with dichotomous scoring, the ability estimates resulting from polytomous scoring had slightly higher measurement precision than those resulting from dichotomous scoring. The practical impact related to classification decision was minor because of the extremely small number of items that could be scored polytomously in this current study.

scholarly journals Language structure is influenced by the number of speakers but seemingly not by the proportion of non-native speakers

2019 ◽  
Vol 6 (2) ◽  
pp. 181274 ◽  
Author(s):  
Alexander Koplenig
Keyword(s):  
Adult Learners ◽  
Negative Selection ◽  
Large Scale ◽  
Native Speakers ◽  
Relative Proportion ◽  
Statistical Structure ◽  
Information Theoretic ◽  
Language Structure ◽  
Large Numbers ◽  
The Impact

Large-scale empirical evidence indicates a fascinating statistical relationship between the estimated number of language users and its linguistic and statistical structure. In this context, the linguistic niche hypothesis argues that this relationship reflects a negative selection against morphological paradigms that are hard to learn for adults, because languages with a large number of speakers are assumed to be typically spoken and learned by greater proportions of adults. In this paper, this conjecture is tested empirically for more than 2000 languages. The results question the idea of the impact of non-native speakers on the grammatical and statistical structure of languages, as it is demonstrated that the relative proportion of non-native speakers does not significantly correlate with either morphological or information-theoretic complexity. While it thus seems that large numbers of adult learners/speakers do not affect the (grammatical or statistical) structure of a language, the results suggest that there is indeed a relationship between the number of speakers and (especially) information-theoretic complexity, i.e. entropy rates. A potential explanation for the observed relationship is discussed.

scholarly journals Is hobo permissivity related to I reactivity and sensitive to chromatin compaction in Drosophila melanogaster?

2004 ◽  
Vol 84 (2) ◽  
pp. 71-79
Author(s):  
CLAUDE BAZIN ◽  
BÉATRICE DEJONGHE ◽  
DOMINIQUE HIGUET
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Position Effect ◽  
Hybrid Dysgenesis ◽  
Chromatin State ◽  
Position Effect Variegation ◽  
Chromatin Compaction ◽  
Effect Variegation ◽  
The Impact ◽  
Strain Variability

In Drosophila melanogaster, the hobo transposable element is responsible for a hybrid dysgenesis syndrome. It appears in the germline of progenies from crosses between females devoid of hobo elements (E) and males bearing active hobo elements (H). In the HE system, permissivity is the ability of females to permit hobo activity in their progeny when they have been crossed with H males. Permissivity displays both intra- and inter-strain variability and decreases with the age of the females. Such characteristics are reminiscent of those for the reactivity in the IR system. The reactivity is the ability of R females (devoid of I factors) to permit activity of the I LINE retrotransposon in the F1 females resulting from crosses with I males (bearing I factors). Here we investigated permissivity properties in the HE system related to reactivity in the IR system. Previously it had been shown that reactivity increases with the number of Su(var)3-9 genes, which increases chromatin compaction near heterochromatin. Using the same lines, we show that permissivity increases with the number of Su(var)3-9 genes. To investigate the impact of chromatin compaction on permissivity we have tested the polymorphism of position-effect variegation (PEV) on the whitemottled4 locus in RE strains. Our results suggest a model of regulation in which permissivity could depend on the chromatin state and on the hobo vestigial sequences.

scholarly journals When tension is just a fluctuation

2021 ◽  
Vol 647 ◽  
pp. L5
Author(s):  
B. Joachimi ◽  
F. Köhlinger ◽  
W. Handley ◽  
P. Lemos
Keyword(s):  
Large Scale ◽  
Model Comparison ◽  
Bayes Factor ◽  
Computational Cost ◽  
Real Data ◽  
Microwave Background ◽  
Order Unity ◽  
Physical Experiments ◽  
Bayesian Evidence ◽  
The Impact

Summary statistics of likelihood, such as Bayesian evidence, offer a principled way of comparing models and assessing tension between, or within, the results of physical experiments. Noisy realisations of the data induce scatter in these model comparison statistics. For a realistic case of cosmological inference from large-scale structure, we show that the logarithm of the Bayes factor attains scatter of order unity, increasing significantly with stronger tension between the models under comparison. We develop an approximate procedure that quantifies the sampling distribution of the evidence at a small additional computational cost and apply it to real data to demonstrate the impact of the scatter, which acts to reduce the significance of any model discrepancies. Data compression is highlighted as a potential avenue to suppressing noise in the evidence to negligible levels, with a proof of concept demonstrated using Planck cosmic microwave background data.

Impact of Delayed Flowback on Well Performance: Case Study

2022 ◽  
Author(s):  
Ruqia Al Shidhani ◽  
Ahmed Al Shueili ◽  
Hussain Al Salmi ◽  
Musallam Jaboob
Keyword(s):  
Hydraulic Fracturing ◽  
Large Scale ◽  
Gas Permeability ◽  
Real Data ◽  
Formation Damage ◽  
Single Fracture ◽  
Well Performance ◽  
Fracture Conductivity ◽  
Wellhead Pressure ◽  
The Impact

Abstract Due to a resource optimization and efficiency improvements, wells that are hydraulically fractured in the tight gas Barik Formation of the Khazzan Field in the Sultanate of Oman are often temporarily left shut-in directly following a large scale massive hydraulic fracturing stimulation treatment. Extensive industry literature has often suggested (and reported), that this may result in a significant direct loss of productivity due to the delayed flowback and the resulting fracture conductivity and formation damage. This paper will review the available data from the Khazzan Field address these concerns; indicating where the concerns should and should not necessarily apply. The Barik Formation in the Khazzan Field is an over-pressured gas-condensate reservoir at 4,500 m with gas permeability ranging from 0.1 to 20 mD. The average well after hydraulic fracturing produces 25 MMscfd and 500 bcpd against a wellhead pressure of 4,000 psi. A typical hydraulic fracturing stimulation treatment consists of 14,000 bbl of a borate-crosslinked guar fluid, placing upwards of 1MM Lbs of high conductivity bauxite proppant within a single fracture. In order to assess the potential production loss due to delayed flowback operations, BP Oman performed a suite of formation damage tests including core samples from the Barik reservoir, fracture conductivity considerations and dynamic behaviors. Additionally, normalized production was compared between offset wells that were cleaned-up and put onto production at different times after the hydraulic fracturing operations. Core tests showed a range of fracture conductivities over time with delayed flowback after using the breaker concentrations from actual treatments. As expected, enhanced conductivity was achieved with additional breaker. The magnitude of the conductivity being created in these massive treatments was also demonstrated to be dominant with respect to damage effects. Finally, a normalized comparison of an extensive suite of wells clearly showed no discernible loss of production resulted from any delay in the flowback operations. This paper describes in details the workflow and resulting analysis of the impact of extensive shut-in versus immediate flowback post massive hydraulic fracturing. It indicates that the impact of such events will be limited if the appropriate steps have been taken to minimize the opportunity for damage to occur. Whereas the existing fracturing literature takes the safe stance of indicating that damage will always result from such shut-ins, this paper will demonstrate the limitations of such assumptions and the flexibility that can be demonstrated with real data.

scholarly journals Dynamics of the hobo transposable element in transgenic lines of Drosophila melanogaster

2001 ◽  
Vol 77 (2) ◽  
pp. 135-142 ◽  
Author(s):  
V. LADEVEZE ◽  
S. AULARD ◽  
N. CHAMINADE ◽  
C. BIEMONT ◽  
G. PERIQUET ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
High Frequency ◽  
Chromosomal Distribution ◽  
Extensive Survey ◽  
Transgenic Lines ◽  
Insertion Sites ◽  
Selection For ◽  
Genomic Regions ◽  
The Impact

The impact of the hobo transposable element in global reorganization of the Drosophila melanogaster genome has been investigated in transgenic lines generated by injection of hobo elements into the Hikone strain, which lacked them. In the present extensive survey, the chromosomal distribution of hobo insertion sites in the line 28 was found to be homogeneous and similar for all chromosomal arms, except 3L, when compared with other transgenic lines. However, some original features were observed in this line at the genetic and chromosomal levels. Several hotspots of insertion sites were observed on the X, second and third chromosomes. Five sites with a high frequency of hobo insertions were present on the 3L arm in most individuals tested, suggesting the action of selection for hobo element in some sites. The presence of doublets or triplet was also observed, implying that hobo inserts can show local jumps or insertions in preferred regions. This local transposition occurred independently in 11 specific genomic regions in many individuals and generations. The dynamics of this phenomenon were analysed across generations. These results support the use of the hobo system as an important tool in fundamental and applied Drosophila genetics.

Impact of COVID-19 on Nuclear Medicine in Germany, Austria and Switzerland: An International Survey in April 2020

2020 ◽  
Vol 59 (04) ◽  
pp. 294-299 ◽  
Author(s):  
Lutz S. Freudenberg ◽  
Ulf Dittmer ◽  
Ken Herrmann
Keyword(s):  
Nuclear Medicine ◽  
Health Systems ◽  
Personal Protective Equipment ◽  
Large Scale ◽  
Diagnostic Procedures ◽  
Protective Equipment ◽  
Current Crisis ◽  
Web Based ◽  
Public Versus Private ◽  
The Impact

Abstract Introduction Preparations of health systems to accommodate large number of severely ill COVID-19 patients in March/April 2020 has a significant impact on nuclear medicine departments. Materials and Methods A web-based questionnaire was designed to differentiate the impact of the pandemic on inpatient and outpatient nuclear medicine operations and on public versus private health systems, respectively. Questions were addressing the following issues: impact on nuclear medicine diagnostics and therapy, use of recommendations, personal protective equipment, and organizational adaptations. The survey was available for 6 days and closed on April 20, 2020. Results 113 complete responses were recorded. Nearly all participants (97 %) report a decline of nuclear medicine diagnostic procedures. The mean reduction in the last three weeks for PET/CT, scintigraphies of bone, myocardium, lung thyroid, sentinel lymph-node are –14.4 %, –47.2 %, –47.5 %, –40.7 %, –58.4 %, and –25.2 % respectively. Furthermore, 76 % of the participants report a reduction in therapies especially for benign thyroid disease (-41.8 %) and radiosynoviorthesis (–53.8 %) while tumor therapies remained mainly stable. 48 % of the participants report a shortage of personal protective equipment. Conclusions Nuclear medicine services are notably reduced 3 weeks after the SARS-CoV-2 pandemic reached Germany, Austria and Switzerland on a large scale. We must be aware that the current crisis will also have a significant economic impact on the healthcare system. As the survey cannot adapt to daily dynamic changes in priorities, it serves as a first snapshot requiring follow-up studies and comparisons with other countries and regions.

Sign in / Sign up

Export Citation Format

Share Document