Time-course and degradation rate of membrane scaffold protein (MSP1D1) during recombinant production

Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles because of differences in transcription time, degradation rate, and RNA-processing kinetics. Recent studies have shown that a splicing-associated RNA production delay can be significant. To investigate this issue more generally, it is useful to develop methods applicable to genome-wide datasets. We introduce a joint model of transcriptional activation and mRNA accumulation that can be used for inference of transcription rate, RNA production delay, and degradation rate given data from high-throughput sequencing time course experiments. We combine a mechanistic differential equation model with a nonparametric statistical modeling approach allowing us to capture a broad range of activation kinetics, and we use Bayesian parameter estimation to quantify the uncertainty in estimates of the kinetic parameters. We apply the model to data from estrogen receptor α activation in the MCF-7 breast cancer cell line. We use RNA polymerase II ChIP-Seq time course data to characterize transcriptional activation and mRNA-Seq time course data to quantify mature transcripts. We find that 11% of genes with a good signal in the data display a delay of more than 20 min between completing transcription and mature mRNA production. The genes displaying these long delays are significantly more likely to be short. We also find a statistical association between high delay and late intron retention in pre-mRNA data, indicating significant splicing-associated production delays in many genes.

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Genotypic variation in in sacco dry matter degradation kinetics in perennial ryegrass (Lolium perenne L.)

Animal Production Science ◽

10.1071/an11290 ◽

2012 ◽

Vol 52 (7) ◽

pp. 566 ◽

Cited By ~ 2

Author(s):

X. Z. Sun ◽

G. C. Waghorn ◽

J.-H. B. Hatier ◽

H. S. Easton

Keyword(s):

Lolium Perenne ◽

Perennial Ryegrass ◽

Dry Matter ◽

Time Course ◽

Degradation Rate ◽

Degradation Kinetics ◽

Vegetative State ◽

Genotypic Variation ◽

Lolium Perenne L ◽

In Sacco

Fast degrading perennial ryegrass (Lolium perenne L.) is a desirable characteristic to select for because it can result in increased feed intake by grazing ruminants. Sufficient range in genotypic variation of dry matter (DM) degradation kinetics is a prerequisite for selection. To investigate the genotypic variation, 77 perennial ryegrass accessions sourced internationally, grown in autumn in the same conditions and harvested in the vegetative state, were examined using an in sacco technique. From the time course of DM disappearance, soluble fraction ‘A’, potentially degradable fraction ‘B’, indigestible fraction ‘C’ and the degradation rate k of fraction ‘B’ were estimated. The results indicated that a large range in genotypic variation was present in all degradation parameters. Fraction ‘A’ ranged from 0.48 to 0.60, with the highest five accessions being 21% higher than the lowest five. Degradation rate k of fraction ‘B’ ranged from 0.069 to 0.199/h, with the fastest five being 125% higher than the slowest five. There were no strong correlations between degradation parameters and chemical composition. In conclusion, there was considerable genotypic variation in DM degradation kinetics among perennial ryegrass accessions and this presents plant breeders with ample opportunity to select for fast degrading perennial ryegrasses.

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Rates of synthesis and degradation of Na+-K+-ATPase during chronic ouabain treatment

AJP Cell Physiology ◽

10.1152/ajpcell.1989.256.1.c75 ◽

1989 ◽

Vol 256 (1) ◽

pp. C75-C80 ◽

Cited By ~ 23

Author(s):

B. M. Rayson

Keyword(s):

Steady State ◽

Time Course ◽

Degradation Rate ◽

Cellular Mechanism ◽

Transient Increase ◽

Maximal Velocity ◽

Full Time ◽

Kidney Tubules ◽

Degradation Rate Constant ◽

Synthesis And Degradation

Chronic inhibition of Na+-K+-ATPase activity in outer medullary kidney tubules has previously been demonstrated to elicit a 60% increase in activity, measured under maximal velocity (Vmax) conditions (J. Biol. Chem. 260: 12740-12743, 1985). To investigate the cellular mechanism of this response, we measured the rates of Na+-K+-ATPase synthesis and degradation over its full time course. A transient increase in the rate of synthesis occurred after 12 h of ouabain treatment. After 24-h treatment, the rate of synthesis returned to a level not different from control levels. The relative degradation rate after 24-h treatment, however, was markedly lower in ouabain-treated cells than in control cells. Thus the augmentation of the number of Na+-K+-ATPase sites, elicited by the transient increase in synthesis described, was maintained under steady-state conditions by a reduction in apparent degradation rate constant.

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Protein metabolism and beta-myosin heavy-chain mRNA in unweighted soleus muscle

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.1989.257.2.r300 ◽

1989 ◽

Vol 257 (2) ◽

pp. R300-R305 ◽

Cited By ~ 64

Author(s):

D. B. Thomason ◽

R. B. Biggs ◽

F. W. Booth

Keyword(s):

Protein Synthesis ◽

Soleus Muscle ◽

Time Course ◽

Degradation Rate ◽

Synthesis Rate ◽

Protein Synthesis Rate ◽

Hindlimb Unweighting ◽

First Order ◽

Degradation Rate Constant ◽

Myofibril Protein

To investigate the relative influence of protein synthetic and degradative control mechanisms in vivo during skeletal muscle atrophy, we measured myofibril and total mixed protein synthesis rates in muscles of rats prevented from hindlimb weight-bearing for 5 h and 7 days. Protein synthesis rates were determined by infusing the animals with [3H]Leu for 5 h and measuring the specific activity of [3H]Leu in the aminoacyl-tRNA precursor and protein product fractions of the muscles. In the soleus muscle, myofibril protein synthesis rates decreased from a control value of 5.9 to 4.6%/day during 5 h of hindlimb unweighting and to 2.4%/day after 7 days of hindlimb unweighting. The relatively more phasic muscles (plantaris, medial gastrocnemius, quadriceps) showed a tendency for increased myofibril protein synthesis rates (117-127% of control) during the first 5 h followed by a decrease (46-62% of control) at 7 days of hindlimb unweighting. A predicted time course of soleus muscle myofibril protein degradation rate was obtained from a numerical model of the decrease in soleus myofibril protein synthesis rate as a first-order process [half-time (t1/2) = 0.3 day by least-squares fit] and the time course of soleus muscle myofibril protein previously observed with hindlimb unweighting (Thomason et al., J. Appl. Physiol. 63: 130-137, 1987). The degradation rate model makes specific, testable predictions for the mechanism of myofibril protein degradation during soleus muscle atrophy: 1) the first-order degradation rate constant does not obtain a fixed value over a 24-day period but is continuously changing throughout atrophy, and 2) the first-order degradation rate constant changes on a time scale slower than protein synthesis rate.(ABSTRACT TRUNCATED AT 250 WORDS)

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The time course of recombinant production inStreptomyces coelicolor

Genetics Research ◽

10.1017/s0016672300012532 ◽

1971 ◽

Vol 18 (2) ◽

pp. 133-145 ◽

Cited By ~ 4

Author(s):

G. Sermonti ◽

A. Maria Puglia ◽

Giuseppina Ficarra

Keyword(s):

Time Course ◽

Streptomyces Coelicolor ◽

Complete Medium ◽

Zygote Formation ◽

Gene Recombination ◽

Filamentous Bacteria ◽

Time Intervals ◽

Recombinant Production ◽

Donor Chromosome ◽

Transfer Origin

SUMMARYThe process leading to gene recombination can be interrupted in the filamentous bacteriaStreptomyces coelicolorby growing mixed cultures on cellophane disks lying on complete medium. The mycelium is harvested, broken, diluted and the broken hyphae plated at different time intervals. By this means some markers can be excluded from heteroclones or from recombinant progeny in early samples. The recombinant pattern clearly changes with time, with an increase of markers contributed to the recombinant progeny. In crosses between male (NF) and female (UF) strains, the maleness is the first donor trait to appear in the cells of the recipient parent. The fertility factor does not produce a transfer origin on the donor chromosomes; the donor contribution may extend on either side or on both sides of the factor which appears to be compulsory for zygote formation. The longer the time of contact between parental cells, the longer the segment of the donor chromosome contributing to the recombinant progeny. When spores are formed they contain almost exclusively recombinant nuclei derived from segregation processes.

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Ultrastructural Changes of the Symbiotic Chlorella-Like Alga Isolated from Hydra Viridis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100054212 ◽

1982 ◽

Vol 40 ◽

pp. 320-321

Author(s):

K.W. Lee ◽

R.H. Meints ◽

D. Kuczmarski ◽

J.L. Van Etten

Keyword(s):

Time Course ◽

Reciprocal Cross ◽

Ultrastructural Level ◽

Ultrastructural Changes ◽

Symbiotic Relationship ◽

Cell Recognition ◽

Green Hydra ◽

Different Strains ◽

Hydra Viridis

The physiological, biochemical, and ultrastructural aspects of the symbiotic relationship between the Chlorella-like algae and the hydra have been intensively investigated. Reciprocal cross-transfer of the Chlorellalike algae between different strains of green hydra provide a system for the study of cell recognition. However, our attempts to culture the algae free of the host hydra of the Florida strain, Hydra viridis, have been consistently unsuccessful. We were, therefore, prompted to examine the isolated algae at the ultrastructural level on a time course.

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