scholarly journals Protein-mediated error correction for de novo DNA synthesis

2004 ◽  
Vol 32 (20) ◽  
pp. e162-e162 ◽  
Author(s):  
P. A. Carr
Keyword(s):  
Dna Synthesis ◽  
Error Correction ◽  
De Novo

Abstract 396: Regulation of Cardiomyocyte Proliferation by the Hippo Pathway and Dystrophin Complex

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Yuka Morikawa ◽  
John Leach ◽  
Todd Heallen ◽  
Ge Tao ◽  
James F Martin
Keyword(s):  
Cell Cycle ◽  
Muscular Dystrophy ◽  
Dna Synthesis ◽  
De Novo ◽  
Hippo Pathway ◽  
Myocardial Damage ◽  
Heart Regeneration ◽  
Cardiomyocyte Proliferation ◽  
Heart Repair ◽  
The Hippo Pathway

Regeneration in mammalian hearts is limited due to the extremely low renewal rate of cardiomyocytes and their inability to reenter the cell cycle. In rodent hearts, endogenous regenerative capacity exists during development but is rapidly repressed after birth, at which time growth is by hypertrophy. During the developmental and neonatal periods, heart regeneration occurs through proliferation of pre-existing cardiomyocytes. Our approach of activating heart regeneration is to uncover the mechanisms responsible for repression of cardiomyocyte proliferation. The Hippo pathway controls heart size by repressing cardiomyocyte proliferation during development. By deleting Salv , a modulator of the Hippo pathway, we found that myocardial damage in postnatal and adult hearts was repaired both anatomically and functionally. This heart repair occurred primary through proliferation of preexisting cardiomyocytes. During repair, cardiomyocytes reenter the cell cycle; de novo DNA synthesis, karyokinesis, and cytokinesis all take place. The dystrophin glycoprotein complex (DGC) is essential for muscle maintenance by anchoring the cytoskeleton and extracellular matrix. Disruption of the DGC results in muscular dystrophies, including Duchenne muscular dystrophy, resulting in both skeletal and cardiac myopathies. Recently the DGC was shown to regulate cardiomyocyte proliferation and we found that the DGC and the Hippo pathway components directly interact. To address if the DGC and the Hippo pathway coordinately regulate cardiomyocyte proliferation, we conditionally deleted Salv in the mouse model of muscular dystrophy, the mdx line. We found that simultaneous disruption of both the DGC and Hippo pathway leads an increased de novo DNA synthesis and cytokinesis in cardiomyocytes after heart damage. Our findings provide new insights into the mechanisms leading to heart repair through proliferation of endogenous cardiomyocytes.

Dexamethasone modulates ErbB tyrosine kinase expression and signaling through multiple and redundant mechanisms in cultured rat hepatocytes

2007 ◽  
Vol 293 (3) ◽  
pp. G552-G559 ◽  
Author(s):  
Lawrence A. Scheving ◽  
Renee Buchanan ◽  
Michael A. Krause ◽  
Xiuqi Zhang ◽  
Mary C. Stevenson ◽  
...  
Keyword(s):  
Growth Factor ◽  
Dna Synthesis ◽  
Transforming Growth Factor ◽  
De Novo ◽  
Rat Hepatocytes ◽  
Immunological Methods ◽  
High Dose ◽  
Transforming Growth Factor Α ◽  
High Dose Dexamethasone ◽  
Cultured Rat Hepatocytes

Glucocorticoids paradoxically exert both stimulatory and inhibitory effects on the proliferation of cultured rat hepatocytes. We studied the effects of dexamethasone, a synthetic glucocorticoid, on the proliferation of cultured rat hepatocytes. The timing of growth factor addition modified the action of high-dose dexamethasone (10−6 M) on DNA synthesis. When we added transforming growth factor-α at the time of plating, 10−6 M dexamethasone weakly stimulated DNA synthesis by 26% relative to cells cultured in dexamethasone-free media. When we delayed growth factor addition until 24–48 h after plating, 10−6 M dexamethasone inhibited DNA synthesis by 50%. Using immunological methods, we analyzed the expression and signaling patterns of the ErbB kinases in dexamethasone-treated cells. High-dose dexamethasone stabilized the expression of epidermal growth factor receptor (EGFr) and ErbB3, and it suppressed the de novo expression of ErbB2 that occurs during the third and fourth day of culture in 10−8 M dexamethasone. High-dose dexamethasone by 72 h suppressed basal and EGF-associated phosphorylation of ERK and Akt. The reduction in ERK1/2 phosphorylation correlated with suppression of a culture-dependent increase in Son-of sevenless 1 (Sos1) and ERK1/2 expression. High-dose dexamethasone in hepatocytes stabilized or upregulated several inhibitory effectors of EGFr/ErbB2 and ERK, including receptor-associated late transducer (RALT) and MKP-1, respectively. Thus 10−6 M dexamethasone exerts a time-dependent and redundant inhibitory effect on EGFr-mediated proliferative signaling in hepatocytes, targeting not only the ErbB proteins but also their various positive and negative effectors.

Error Correction in Nanopore Reads for de novo Genomic Assembly

2020 ◽  
pp. 754-762
Author(s):  
Jacqueline Aldridge-Águila ◽  
Diego Álvarez-Saravia ◽  
Marcelo Navarrete ◽  
Roberto Uribe-Paredes
Keyword(s):  
Error Correction ◽  
De Novo

scholarly journals Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

2015 ◽  
Author(s):  
Sara Goodwin ◽  
James Gurtowski ◽  
Scott Ethe-Sayers ◽  
Panchajanya Deshpande ◽  
Michael Schatz ◽  
...  
Keyword(s):  
Error Correction ◽  
De Novo Assembly ◽  
De Novo ◽  
Correction Algorithm ◽  
Membrane Pore ◽  
Complete Representation ◽  
Oxford Nanopore ◽  
Long Read ◽  
Error Correction Algorithm ◽  
Sequencing Instrument

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

De Novo DNA Synthesis Using Single-Molecule PCR

2012 ◽  
pp. 35-47 ◽  
Author(s):  
Tuval Ben Yehezkel ◽  
Gregory Linshiz ◽  
Ehud Shapiro
Keyword(s):  
Dna Synthesis ◽  
Single Molecule ◽  
De Novo

Stretch-mediated visceral smooth muscle growth in vitro

1992 ◽  
Vol 262 (5) ◽  
pp. R895-R900
Author(s):  
O. M. Karim ◽  
K. Pienta ◽  
N. Seki ◽  
J. L. Mostwin
Keyword(s):  
Smooth Muscle ◽  
Dna Synthesis ◽  
De Novo ◽  
Specific Activity ◽  
Muscle Growth ◽  
Mechanical Stimulus ◽  
Trophic Factors ◽  
Taenia Coli ◽  
Visceral Smooth Muscle

An in vitro model of smooth muscle stretch was developed to study mechanical stimulus as a possible mediator of visceral smooth muscle growth and differences in the growth response of smooth muscle from young and old animals. De novo DNA synthesis as measured by the aphidicolin-sensitive specific activity of DNA was used as an index of cell growth. Compared with old tissue, the rate of aphidicolin-sensitive DNA synthesis in smooth muscle from young animals was 3-5 and 1.5-2 times greater in bladder and taenia coli, respectively. Stretch of bladder muscle and taenia coli strips from young animals for 6 h increased the aphidicolin-sensitive specific activity of DNA 3-fold (P less than 0.01) and 1.5-fold (P less than 0.01), respectively. Tissue from old animals, however, under the same conditions increased the rate of aphidicolin-resistant DNA synthesis, possibly implying DNA repair. Autoradiography showed only labeled myocyte nuclei. These results indicate that homeostatic mechanisms modulating myocyte growth in visceral smooth muscle can respond to mechanical stimulus in the absence of other trophic factors.

Apoptosis in megaloblastic anemia occurs during DNA synthesis by a p53-independent, nucleoside-reversible mechanism

Blood ◽  
2000 ◽  
Vol 96 (9) ◽  
pp. 3249-3255 ◽  
Author(s):  
Mark J. Koury ◽  
James O. Price ◽  
Geoffrey G. Hicks
Keyword(s):  
Dna Synthesis ◽  
De Novo ◽  
Megaloblastic Anemia ◽  
Experimental Studies ◽  
Hematopoietic Cells ◽  
S Phase ◽  
De Novo Synthesis ◽  
Complete Reversal ◽  
Phase Accumulation

Abstract Deficiency of folate or vitamin B12 (cobalamin) causes megaloblastic anemia, a disease characterized by pancytopenia due to the excessive apoptosis of hematopoietic progenitor cells. Clinical and experimental studies of megaloblastic anemia have demonstrated an impairment of DNA synthesis and repair in hematopoietic cells that is manifested by an increased percentage of cells in the DNA synthesis phase (S phase) of the cell cycle, compared with normal hematopoietic cells. Both folate and cobalamin are required for normal de novo synthesis of thymidylate and purines. However, previous studies of impaired DNA synthesis and repair in megaloblastic anemia have concerned mainly the decreased intracellular levels of thymidylate and its effects on nucleotide pools and misincorporation of uracil into DNA. An in vitro model of folate-deficient erythropoiesis was used to study the relationship between the S-phase accumulation and apoptosis in megaloblastic anemia. The results indicate that folate-deficient erythroblasts accumulate in and undergo apoptosis in the S phase when compared with control erythroblasts. Both the S-phase accumulation and the apoptosis were induced by folate deficiency in erythroblasts fromp53 null mice. The complete reversal of the S-phase accumulation and apoptosis in folate-deficient erythroblasts required the exogenous provision of specific purines or purine nucleosides as well as thymidine. These results indicate that decreased de novo synthesis of purines plays as important a role as decreased de novo synthesis of thymidylate in the pathogenesis of megaloblastic anemia.

scholarly journals Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using Language Models

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mustafa Abdallah ◽  
Ashraf Mahgoub ◽  
Hany Ahmed ◽  
Somali Chaterji
Keyword(s):  
Error Correction ◽  
Language Processing ◽  
De Novo ◽  
Geometric Mean ◽  
Language Modeling ◽  
Error Rates ◽  
Language Models ◽  
Hill Climbing ◽  
Strong Negative Correlation ◽  
Best Value

Abstract The performance of most error-correction (EC) algorithms that operate on genomics reads is dependent on the proper choice of its configuration parameters, such as the value of k in k-mer based techniques. In this work, we target the problem of finding the best values of these configuration parameters to optimize error correction and consequently improve genome assembly. We perform this in an adaptive manner, adapted to different datasets and to EC tools, due to the observation that different configuration parameters are optimal for different datasets, i.e., from different platforms and species, and vary with the EC algorithm being applied. We use language modeling techniques from the Natural Language Processing (NLP) domain in our algorithmic suite, Athena, to automatically tune the performance-sensitive configuration parameters. Through the use of N-Gram and Recurrent Neural Network (RNN) language modeling, we validate the intuition that the EC performance can be computed quantitatively and efficiently using the “perplexity” metric, repurposed from NLP. After training the language model, we show that the perplexity metric calculated from a sample of the test (or production) data has a strong negative correlation with the quality of error correction of erroneous NGS reads. Therefore, we use the perplexity metric to guide a hill climbing-based search, converging toward the best configuration parameter value. Our approach is suitable for both de novo and comparative sequencing (resequencing), eliminating the need for a reference genome to serve as the ground truth. We find that Athena can automatically find the optimal value of k with a very high accuracy for 7 real datasets and using 3 different k-mer based EC algorithms, Lighter, Blue, and Racer. The inverse relation between the perplexity metric and alignment rate exists under all our tested conditions—for real and synthetic datasets, for all kinds of sequencing errors (insertion, deletion, and substitution), and for high and low error rates. The absolute value of that correlation is at least 73%. In our experiments, the best value of k found by Athena achieves an alignment rate within 0.53% of the oracle best value of k found through brute force searching (i.e., scanning through the entire range of k values). Athena’s selected value of k lies within the top-3 best k values using N-Gram models and the top-5 best k values using RNN models With best parameter selection by Athena, the assembly quality (NG50) is improved by a Geometric Mean of 4.72X across the 7 real datasets.

scholarly journals MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors

2020 ◽  
Vol 36 (11) ◽  
pp. 3322-3326
Author(s):  
Michael Schwarz ◽  
Marius Welzel ◽  
Tolganay Kabdullayeva ◽  
Anke Becker ◽  
Bernd Freisleben ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Web Application ◽  
De Novo ◽  
Supplementary Information ◽  
Dna Fragments ◽  
Synthetic Dna ◽  
Custom Made ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Error Probabilities

Abstract Summary The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes. Availability and implementation MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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