scholarly journals The transposition rate has little influence on equilibrium copy numbers of the P-element

2021 ◽  
Author(s):  
Robert Kofler ◽  
Viola Nolte ◽  
Christian Schloetterer
Keyword(s):  
Copy Number ◽  
Specific Activity ◽  
Culture Conditions ◽  
P Element ◽  
Element Abundance ◽  
Transposition Rate ◽  
Copy Numbers ◽  
Pirna Cluster ◽  
Order Of Magnitude ◽  
A Minor

The invasion of transposable elements (TEs) in mammals and invertebrates, is likely stopped by piRNAs that emerge after insertion of the TE into a piRNA cluster (the trap model). It remains, however, still unclear which factors influence the dynamics of TE invasions. The activity of the TE (i.e. transposition rate) is one of the frequently discussed key factors. Here we take advantage of the temperature-dependent activity of the P-element, a widely studied eukaryotic TE, to test how TE activity affects the dynamics of a TE invasion. Taking advantage of the temperature-specific activity of the P-element, we monitored its invasion dynamics in experimental Drosophila simulans populations at hot and cold culture conditions. Despite marked differences in transposition rates, the P-element reached very similar copy numbers at both temperatures. The reduction of the insertion rate upon approaching the copy number plateau was accompanied by the emergence of similar amounts of piRNAs against the P-element at both temperatures. Interestingly, the ping-pong cycle, which degrades TE transcripts, becomes only active after the copy number has reached the plateau. We show that the P-element abundance is an order of magnitude lower and fewer P-element insertions in piRNA clusters were observed than expected under the trap model. We conclude that the transposition rate has at the most only a minor influence on TE abundance, but other factors, such as paramutations or selection against TE insertions are shaping the TE composition of organism.

scholarly journals The relationship between the rate of transposition and transposable element copy number for copia and Doc retrotransposons of Drosophila melanogaster

1998 ◽  
Vol 72 (1) ◽  
pp. 1-11 ◽  
Author(s):  
ELENA G. PASYUKOVA ◽  
SERGEY V. NUZHDIN ◽  
DMITRY A. FILATOV
Keyword(s):  
Drosophila Melanogaster ◽  
Copy Number ◽  
Self Regulation ◽  
Natural Populations ◽  
Strong Positive Correlation ◽  
Positive Correlation ◽  
Transposition Rate ◽  
Copy Numbers ◽  
Starting Point ◽  
The Relationship

We present data on the relationship between the rate of transposition and copy number in the genome for the copia and Doc retrotransposons of Drosophila melanogaster. copia and Doc transposition rates were directly measured in sublines of the isogenic 2b line using individual males or females, respectively, with a range of copia copy numbers from 49 to 103 and Doc copy numbers from 112 to 235 per genome. Transposition rates varied from 3×10−4 to 2×10−2 for copia and from 2×10−4 to 2×10−3 for Doc. A positive relationship between transposition rate and copy number was found both for copia and for Doc when the data were analysed across all the 2b individuals; no significant correlation was found when the data were analysed across the subline means for both retrotransposons tested. Overall, correlation between copia and Doc transposition rate and their copy number in the genome, if any, was not negative, which would be expected if transposable elements (TEs) self-regulate their copy number. Thus, for copia and Doc no evidence for self-regulation was provided, and at least for these two TEs this hypothesis is not favoured for explaining the maintenance of the stable copy number that is characteristic for natural populations. The transposition rate of copia was measured twice, and a strong positive correlation between copy number and transposition rate both across individuals and subline means was found in 1994, while in 1995 no correlation was found. This fact is in agreement with the hypothesis that a positive correlation between the rate of transposition and TE copy number may be a default starting point for future host–TE coevolution.

scholarly journals Novel Modification of a Confirmatory SMA Sequencing Assay that Can Be Used to Determine SMN2 Copy Number

2021 ◽  
Vol 7 (3) ◽  
pp. 47
Author(s):  
Binod Kumar ◽  
Samantha Barton ◽  
Jolanta Kordowska ◽  
Roger B. Eaton ◽  
Anne M. Counihan ◽  
...  
Keyword(s):  
Newborn Screening ◽  
New England ◽  
Copy Number ◽  
Screening Program ◽  
Muscular Atrophy ◽  
Base Substitution ◽  
Copy Numbers ◽  
Copy Number Assay ◽  
Second Tier ◽  
A Minor

Promising treatments for spinal muscular atrophy (SMA), the leading genetic cause of infant mortality, prompted calls for inclusion in newborn screening (NBS). In January 2018, the New England Newborn Screening Program (NENSP) began statewide screening for SMA using a tiered algorithm looking for the absence of SMN1 Exon 7. When results from the first and second tier needed reconciliation, we developed and validated a third tier DNA sequencing assay to ensure the presence or absence of SMN1 Exon 7. All nine infants referred to specialty centers through NBS showed single base substitution of c.840C>T, and were confirmed to have SMA. Further, a minor sequencing protocol modification allowed the estimation of SMN2 copy number in SMA affected patients; we developed and validated a copy-number assay yielding 100% match with seven previously characterized specimens of SMA patients. All nine SMA-affected infants found through NBS were also assayed for SMN2 copy number. Results were comparable but not 100% matched with those that were reported by independent diagnostic laboratories. In conclusion, a sequencing protocol confirms NBS findings from real-time qPCR, and its modified application allows NBS programs that have sequencing capabilities to provide SMN2 copy numbers without the need for additional instrumentation.

scholarly journals Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xinping Fan ◽  
Guanghao Luo ◽  
Yu S. Huang
Keyword(s):  
Copy Number ◽  
Bayesian Learning ◽  
Kernel Smoothing ◽  
Gaussian Mixture ◽  
Copy Number Alterations ◽  
Sequencing Data ◽  
Copy Numbers ◽  
Allele Specific ◽  
Tumor Sequencing ◽  
Low Coverage

Abstract Background Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. Results We introduce Accucopy, a method to infer total copy numbers (TCNs) and allele-specific copy numbers (ASCNs) from challenging low-purity and low-coverage tumor samples. Accucopy adopts many robust statistical techniques such as kernel smoothing of coverage differentiation information to discern signals from noise and combines ideas from time-series analysis and the signal-processing field to derive a range of estimates for the period in a histogram of coverage differentiation information. Statistical learning models such as the tiered Gaussian mixture model, the expectation–maximization algorithm, and sparse Bayesian learning were customized and built into the model. Accucopy is implemented in C++ /Rust, packaged in a docker image, and supports non-human samples, more at http://www.yfish.org/software/. Conclusions We describe Accucopy, a method that can predict both TCNs and ASCNs from low-coverage low-purity tumor sequencing data. Through comparative analyses in both simulated and real-sequencing samples, we demonstrate that Accucopy is more accurate than Sclust, ABSOLUTE, and Sequenza.

scholarly journals Discharge of debris from ice at the margin of the Greenland ice sheet

2002 ◽  
Vol 48 (161) ◽  
pp. 192-198 ◽  
Author(s):  
Peter G. Knight ◽  
Richard I. Waller ◽  
Carrie J. Patterson ◽  
Alison P. Jones ◽  
Zoe P. Robinson
Keyword(s):  
Ice Sheet ◽  
Greenland Ice Sheet ◽  
High Rate ◽  
Outlet Glacier ◽  
Tidewater Glaciers ◽  
Sediment Production ◽  
Basal Ice ◽  
Order Of Magnitude ◽  
Sediment Transfer ◽  
A Minor

AbstractSediment production at a terrestrial section of the ice-sheet margin in West Greenland is dominated by debris released through the basal ice layer. The debris flux through the basal ice at the margin is estimated to be 12–45 m3 m−1 a−1. This is three orders of magnitude higher than that previously reported for East Antarctica, an order of magnitude higher than sites reported from in Norway, Iceland and Switzerland, but an order of magnitude lower than values previously reported from tidewater glaciers in Alaska and other high-rate environments such as surging glaciers. At our site, only negligible amounts of debris are released through englacial, supraglacial or subglacial sediment transfer. Glaciofluvial sediment production is highly localized, and long sections of the ice-sheet margin receive no sediment from glaciofluvial sources. These findings differ from those of studies at more temperate glacial settings where glaciofluvial routes are dominant and basal ice contributes only a minor percentage of the debris released at the margin. These data on debris flux through the terrestrial margin of an outlet glacier contribute to our limited knowledge of debris production from the Greenland ice sheet.

The stress generated in a non-dilute suspension of elongated particles by pure straining motion

1971 ◽  
Vol 46 (4) ◽  
pp. 813-829 ◽  
Author(s):  
G. K. Batchelor
Keyword(s):  
Theoretical Formula ◽  
Rigid Sphere ◽  
Cross Sectional ◽  
Outer Flow ◽  
Rigid Particles ◽  
Bulk Stress ◽  
Order Of Magnitude ◽  
Sectional Plane ◽  
Dilute Suspension ◽  
A Minor

In a pure straining motion, elongated rigid particles in suspension are aligned parallel to the direction of the greatest principal rate of extension, provided the effect of Brownian motion is weak. If the suspension is dilute, in the sense that the particles are hydrodynamically independent, each particle of length 2l makes a contribution to the bulk deviatoric stress which is of roughly the same order of magnitude as that due to a rigid sphere of radius l. The fractional increase in the bulk stress due to the presence of the particles is thus equal to the concentration by volume multiplied by a factor of order l2/b2, where 2b is a measure of the linear dimensions of the particle cross-section. This suggests that the stress due to the particles might be relatively large, for volume fractions which are still small, with interesting implications for the behaviour of polymer solutions. However, dilute-suspension theory is not applicable in these circumstances, and so an investigation is made of the effect of interactions between particles. It is assumed that, when the average lateral spacing of particles (h) satisfies the conditions b [Lt ] h [Lt ] l, the disturbance velocity vector is parallel to the particles and varies only in the cross-sectional plane. The velocity near a particle is found to have the same functional form as for an isolated particle, and the modification to the outer flow field for one particle is determined by replacing the randomly placed neighbouring particles by an equivalent cylindrical boundary. The resulting expression for the contribution to the bulk stress due to the particles differs from that for a dilute suspension only in a minor way, viz. by the replacement of log 2l/b by log h/b, and the above suggestion is confirmed. The relative error in the expression for the stress is expected to be of order (log h/b)−1. Some recent observations by Weinberger of the stress in a suspension of glass-fibre particles for which 2l/h = 7·4 and h/2b = 7·8 do show a particle stress which is much larger than the ambient-fluid stress, although the theoretical formula is not accurate under these conditions.

scholarly journals Re-evaluation of the interaction of malonyl-CoA with the rat liver mitochondrial carnitine palmitoyltransferase system by using purified outer membranes

1990 ◽  
Vol 267 (1) ◽  
pp. 85-90 ◽  
Author(s):  
M P Kolodziej ◽  
V A Zammit
Keyword(s):  
Rat Liver ◽  
Specific Activity ◽  
Liver Mitochondria ◽  
Subsequent Treatment ◽  
Carnitine Palmitoyltransferase ◽  
Rat Liver Mitochondria ◽  
Outer Membranes ◽  
High Affinity ◽  
Malonyl Coa ◽  
Order Of Magnitude

1. The interaction of malonyl-CoA with the outer carnitine palmitoyltransferase (CPT) system of rat liver mitochondria was re-evaluated by using preparations of highly purified outer membranes, in the light of observations that other subcellular structures that normally contaminate crude mitochondrial preparations also contain malonyl-CoA-sensitive CPT activity. 2. In outer-membrane preparations, which were purified about 200-fold with respect to the inner-membrane-matrix fraction, malonyl-CoA binding was largely accounted for by a single high-affinity component (KD = 0.03 microM), in contrast with the dual site (low- and high-affinity) previously found with intact mitochondria. 3. There was no evidence that the decreased sensitivity of CPT to malonyl-CoA inhibition observed in outer membranes obtained from 48 h-starved rats (compared with those from fed animals) was due to a decreased ratio of malonyl-CoA binding to CPT catalytic moieties. Thus CPT specific activity and maximal high-affinity [14C]malonyl-CoA binding (expressed per mg of protein) were increased 2.2- and 2.0-fold respectively in outer membranes from 48 h-starved rats. 4. Palmitoyl-CoA at a concentration that was saturating for CPT activity (5 microM) decreased the affinity of malonyl-CoA binding by an order of magnitude, but did not alter the maximal binding of [14C]malonyl-CoA. 5. Preincubation of membranes with either tetradecylglycidyl-CoA or 2-bromopalmitoyl-CoA plus carnitine resulted in marked (greater than 80%) inhibition of high-affinity binding, concurrently with greater than 95% inhibition of CPT activity. These treatments also unmasked an effect of subsequent treatment with palmitoyl-CoA to increase low-affinity [14C]malonyl-CoA binding. 6. These data are discussed in relation to the possible mechanism of interaction between the malonyl-CoA-binding site and the active site of the enzyme.

RyR1 exhibits lower gain of CICR activity than RyR3 in the SR: evidence for selective stabilization of RyR1 channel

2004 ◽  
Vol 287 (1) ◽  
pp. C36-C45 ◽  
Author(s):  
Takashi Murayama ◽  
Yasuo Ogawa
Keyword(s):  
Binding Sites ◽  
Skeletal Muscles ◽  
Specific Activity ◽  
Adenine Nucleotides ◽  
Minor Effect ◽  
Mammalian Skeletal Muscle ◽  
Selective Stabilization ◽  
Underlying Mechanisms ◽  
A Minor

We showed that frog α-ryanodine receptor (α-RyR) had a lower gain of Ca2+-induced Ca2+ release (CICR) activity than β-RyR in sarcoplasmic reticulum (SR) vesicles, indicating selective “stabilization” of the former isoform (Murayama T and Ogawa Y. J Biol Chem 276: 2953–2960, 2001). To know whether this is also the case with mammalian RyR1, we determined [3H]ryanodine binding of RyR1 and RyR3 in bovine diaphragm SR vesicles. The value of [3H]ryanodine binding (B) was normalized by the number of maximal binding sites (Bmax), whereby the specific activity of each isoform was expressed. This B/Bmax expression demonstrated that ryanodine binding of individual channels for RyR1 was <15% that for RyR3. Responses to Ca2+, Mg2+, adenine nucleotides, and caffeine were not substantially different between in situ and purified isoforms. These results suggest that the gain of CICR activity of RyR1 is markedly lower than that of RyR3 in mammalian skeletal muscle, indicating selective stabilization of RyR1 as is true of frog α-RyR. The stabilization was partly eliminated by FK506 and partly by solubilization of the vesicles with CHAPS, each of which was additive to the other. In contrast, high salt, which greatly enhances [3H]ryanodine binding, caused only a minor effect on the stabilization of RyR1. None of the T-tubule components, coexisting RyR3, or calmodulin was the cause. The CHAPS-sensitive intra- and intermolecular interactions that are common between mammalian and frog skeletal muscles and the isoform-specific inhibition by FKBP12, which is characteristic of mammals, are likely to be the underlying mechanisms.

Role of glucose in corneal metabolism

1985 ◽  
Vol 249 (5) ◽  
pp. C409-C416 ◽  
Author(s):  
R. S. Thies ◽  
L. J. Mandel
Keyword(s):  
Oxygen Consumption ◽  
Steady State ◽  
Specific Activity ◽  
Krebs Cycle ◽  
Lactate Production ◽  
Minor Component ◽  
Acid Oxidation ◽  
Endogenous Fatty Acid ◽  
Nonsteady State ◽  
A Minor

Glucose catabolism by glycolysis and the Krebs cycle was examined in the isolated rabbit cornea incubated with [6-14C]glucose. The production of [14C]lactate and 14CO2 from this substrate provided minimal values for the fluxes through these pathways since the tissue was in metabolic steady state but not isotopic steady state during the 40-min incubation. The specific activity of lactate under these conditions was one-third of that for [6-14C]glucose, and label dilution by exchange with unlabeled alanine was minimal, suggesting that glycogen degradation was primarily responsible for this dilution of label in the Embden-Meyerhof pathway. In addition, considerable label accumulation was found in glutamate and aspartate. Calculations revealed that these endogenous amino acid pools were not isotopically equilibrated after the incubation period, suggesting that they were responsible for the isotopic nonsteady state by exchange dilution through transaminase reactions with labeled intermediates. An estimate of glucose oxidation by the Krebs cycle, which was corrected for label dilution by exchange, indicated that glucose could account for most of the measured corneal oxygen consumption that was coupled to oxidative phosphorylation. A minor component of this respiration could not be accounted for by glucose or glycogen oxidation. Additional experiments suggested that endogenous fatty acid oxidation was probably also active under these conditions. Finally, reciprocal changes in plasma membrane Na+-K+-ATPase activity induced by ouabain and nystatin were found to concomitantly alter oxygen consumption rates and [14C]lactate production from [6-14C]glucose. These results demonstrated the capacity for regulating glycolysis and the Krebs cycle in response to changing energy demands in the cornea.

scholarly journals Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number

2021 ◽  
Author(s):  
Matheus Fernandes Gyorfy ◽  
Emma R Miller ◽  
Justin L Conover ◽  
Corrinne E Grover ◽  
Jonathan F Wendel ◽  
...  
Keyword(s):  
Copy Number ◽  
Nuclear Genome ◽  
Plant Genome ◽  
Whole Genome ◽  
Genome Copy ◽  
Relative Copy Number ◽  
Organellar Genome ◽  
Plastid Genomes ◽  
Copy Numbers ◽  
Genome Copy Number

The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication events (WGDs) in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follow WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR (ddPCR) to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.

scholarly journals Studies on the production of glucose isomerase by Bacillus licheniformis

2015 ◽  
Vol 17 (3) ◽  
pp. 84-88 ◽  
Author(s):  
Ogbonnaya Nwokoro
Keyword(s):  
Enzyme Activity ◽  
Bacillus Licheniformis ◽  
Organic Nitrogen ◽  
Specific Activity ◽  
Inorganic Nitrogen ◽  
Glucose Isomerase ◽  
Culture Conditions ◽  
Enzyme Productivity ◽  
Carbon Substrates ◽  
Optimum Ph

Abstract This work reports the effects of some culture conditions on the production of glucose isomerase by Bacillus licheniformis. The bacterium was selected based on the release of 3.62 mg/mL fructose from the fermentation of glucose. Enzyme was produced using a variety of carbon substrates but the highest enzyme activity was detected in a medium containing 0.5% xylose and 1% glycerol (specific activity = 6.88 U/mg protein). Media containing only xylose or glucose gave lower enzyme productivies (specific activities= 4.60 and 2.35 U/mg protein respectively). The effects of nitrogen substrates on glucose isomerase production showed that yeast extract supported maximum enzyme activity (specific activity = 5.24 U/mg protein). Lowest enzyme activity was observed with sodium trioxonitrate (specific activity = 2.44 U/mg protein). In general, organic nitrogen substrates supported higher enzyme productivity than inorganic nitrogen substrates. Best enzyme activity was observed in the presence of Mg2+ (specific activity = 6.85 U/mg protein) while Hg2+ was inhibitory (specific activity = 1.02 U/mg protein). The optimum pH for best enzyme activity was 6.0 while optimum temperature for enzyme production was 50ºC.

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