scholarly journals A semiparametric Bayesian model for comparing DNA copy numbers

2016 ◽  
Vol 30 (3) ◽  
pp. 345-365
Author(s):  
Luis Nieto-Barajas ◽  
Yuan Ji ◽  
Veerabhadran Baladandayuthapani
Keyword(s):  
Bayesian Model ◽  
Copy Numbers ◽  
Dna Copy Numbers

scholarly journals Spontaneous germ line virus infection and retroviral insertional mutagenesis in eighteen transgenic Srev lines of mice.

1989 ◽  
Vol 9 (1) ◽  
pp. 177-184 ◽  
Author(s):  
S E Spence ◽  
D J Gilbert ◽  
D A Swing ◽  
N G Copeland ◽  
N A Jenkins
Keyword(s):  
Dna Replication ◽  
High Frequency ◽  
Insertional Mutagenesis ◽  
Germ Line ◽  
Integration Site ◽  
Viral Integration ◽  
Mammalian Development ◽  
Copy Numbers ◽  
Cell Embryo ◽  
Dna Copy Numbers

SWR/J-RF/J hybrid mice spontaneously acquire new germ line ecotropic proviruses at high frequency. In the studies described here, we used these hybrids to produce 18 transgenic mouse lines, each carrying a single newly acquired Srev locus (SWR/J-RF/J ecotropic proviral locus). All of the newly acquired proviruses identified in mosaic founder SWR/J-RF/J mice that could be transmitted through the germ line were also present in somatic tissues, demonstrating that viral integration occurred before the germ line was set aside from the somatic lineages. Quantitative analysis of proviral DNA copy numbers in somatic and germinal tissues of mosaic founder parents combined with structural analysis of Srev loci indicated that these proviruses are acquired after multiple rounds of somatic viral reinfection and that most of these viral integration events occurred after DNA replication in the zygote and before DNA replication in the four-cell embryo. The frequency of provirus acquisition in Srev lines that expressed the infectious ecotropic virus was similar to that in SWR.RF mice carrying Emv-16 and Emv-17, suggesting that the chromosomal integration site of the parental locus is not an important determinant for high-frequency provirus acquisition. The frequency of recessive lethal mutations induced by spontaneous viral integration was 5%, which was similar to that induced by preimplantation embryo infection. This approach represents a simple and viable strategy for inducing and studying mutations that affect mammalian development.

scholarly journals Sperm mitochondrial DNA copy numbers in normal and abnormal semen analysis: a systematic review and meta-analysis.

2021 ◽  
Author(s):  
Daria Popova ◽  
Priya Bhide ◽  
Francesco DAntonio ◽  
Purusotam Basnet ◽  
Ganesh Acharya
Keyword(s):  
Mitochondrial Dna ◽  
Sperm Motility ◽  
Semen Quality ◽  
Semen Analysis ◽  
Meta Analysis ◽  
Semen Parameters ◽  
Spermatozoa Motility ◽  
Standard Methodology ◽  
Copy Numbers ◽  
Dna Copy Numbers

Background: Normal mature sperm have a considerably reduced number of mitochondria which provide the energy required for progressive sperm motility. Literature suggests that disorders of sperm motility may be linked to abnormal sperm mitochondrial number and function. Objectives: To summarise the evidence from literature regarding the association of mitochondrial DNA copy numbers and semen quality with a particular emphasis on the spermatozoa motility. Search strategy: Standard methodology recommended by Cochrane. Selection criteria: All published primary research reporting on differences in mitochondrial DNA copy numbers between the sperm of males with a normal and abnormal semen analysis. Data collection and analysis: Using standard methodology recommended by Cochrane we pooled results using a random effects model and the findings were reported as a standardised mean difference. Main results: We included 10 trials. The primary outcome was sperm mitochondrial DNA copy numbers. A meta-analysis including five studies showed significantly higher mitochondrial DNA copy numbers in abnormal semen analysis as compared to normal semen analysis(SMD 1.08, 95% CI 0.74-1.43). Three other studies not included in the meta-analysis showed a significant negative correlation between mitochondrial DNA copy numbers and semen parameters. The quality of evidence was assessed as good to very good in 60% of studies. Conclusions: Our review demonstrates significantly higher mitochondrial DNA in human sperm cells of men with abnormal semen analysis in comparison to men with normal semen analysis. PROSPERO registration: CRD42019118841 Funding None received

scholarly journals Detection of Cytomegalovirus DNA in Human Specimens by LightCycler PCR

2000 ◽  
Vol 38 (11) ◽  
pp. 4006-4009 ◽  
Author(s):  
Lars Schaade ◽  
Peter Kockelkorn ◽  
Klaus Ritter ◽  
Michael Kleines
Keyword(s):  
Viral Load ◽  
Human Origin ◽  
Pcr Assay ◽  
Clinical Specimens ◽  
Copy Numbers ◽  
Dna Copy Numbers ◽  
Lightcycler Technology ◽  
High Level ◽  
Sensitivity Specificity ◽  
Cmv Disease

Detection of human cytomegalovirus (CMV) DNA in clinical specimens is considered a cornerstone in the diagnosis of CMV disease. The aim of this study was to evaluate a newly designed LightCycler-based quantitative CMV PCR. Specimens of human origin (n = 200) were tested using the LightCycler PCR, the quantitative COBAS AMPLICOR CMV MONITOR (CACM) assay, and a qualitative in-house PCR assay for the presence of CMV DNA. Samples that were reactive in at least two of the three assays were considered CMV DNA positive (n = 95 [47.5%]), while samples that were nonreactive in two of the three assays were considered CMV DNA negative (n = 105 [52.5%]). Using the LightCycler assay, CMV DNA was detected in 91 of the 95 CMV DNA-positive human specimens (sensitivity, 95.8%; 95% confidence interval [CI], 89.6 to 98.8) and in 1 of the CMV DNA-negative specimens (specificity, 99%; 95% CI, 94.8 to 99.8). Results of CMV load determination as assessed by both quantitative test systems were correlated (r = 0.73;P < 0.0001; 95% CI, 0.61 to 0.81). Results for undiluted samples containing a high CMV load were more accurate with the LightCycler test than were results obtained with the CACM test, which underestimated the viral load of samples containing high DNA copy numbers. The high level of sensitivity, specificity, accuracy, and rapidity provided by the LightCycler technology are favorable for the use of this system in the detection of CMV DNA in clinical specimens.

scholarly journals Effect of bariatric surgery on circulating and urinary mitochondrial DNA copy numbers in obesity with or without diabetes

2020 ◽  
Vol 8 (1) ◽  
pp. e001372
Author(s):  
Mihae Seo ◽  
Hyoungnae Kim ◽  
Hyunjin Noh ◽  
Jin Seok Jeon ◽  
Dong Won Byun ◽  
...  
Keyword(s):  
Bariatric Surgery ◽  
Mitochondrial Dna ◽  
Mitochondrial Dysfunction ◽  
Control Group ◽  
Copy Numbers ◽  
Patient Groups ◽  
Dna Copy Numbers ◽  
Nicotinamide Adenine Dinucleotide Dehydrogenase ◽  
Design And Methods ◽  
Obesity Patient

IntroductionRecent studies have suggested that extracellular circulating and urinary mitochondrial DNA (mtDNA) are associated with mitochondrial dysfunction in obesity and type 2 diabetes mellitus (T2DM). However, the changes to cell-free serum and urinary mtDNA after bariatric surgery in patients with obesity with T2DM have not been investigated to date.Research design and methodsWe prospectively recruited patients with obesity (n=18), and with obesity and T2DM (n=14) who underwent bariatric surgery, along with healthy volunteers (HV) as a control group (n=22). Serum and urinary mitochondrial nicotinamide adenine dinucleotide dehydrogenase subunit-1 (mtND-1) and cytochrome-c oxidase 3 (mtCOX-3) copy numbers were measured using quantitative PCR (qPCR). The mtDNA copy numbers of patients with obesity (with and without T2DM) were followed up 6 months after surgery.ResultsThe copy numbers of urinary mtND-1 and mtCOX-3 in patients with obesity, with or without T2DM, were higher than those in the HVs. Moreover, urinary mtCOX-3 copy number increased in patients with obesity with T2DM compared with patients with obesity without T2DM (p=0.018). Meanwhile, serum mtCOX-3 copy numbers in HV were higher in both obesity patient groups (p=0.040). Bariatric surgery reduced urinary mtND-1 and mtCOX-3 copy numbers, as well as serum mtCOX-3 copy numbers only in patients with obesity with T2DM.ConclusionThese results suggest that T2DM induces greater kidney mitochondrial dysfunction in patients with obesity, which can be effectively restored with bariatric surgery.

Spontaneous germ line virus infection and retroviral insertional mutagenesis in eighteen transgenic Srev lines of mice

1989 ◽  
Vol 9 (1) ◽  
pp. 177-184
Author(s):  
S E Spence ◽  
D J Gilbert ◽  
D A Swing ◽  
N G Copeland ◽  
N A Jenkins
Keyword(s):  
Dna Replication ◽  
High Frequency ◽  
Insertional Mutagenesis ◽  
Germ Line ◽  
Integration Site ◽  
Viral Integration ◽  
Mammalian Development ◽  
Copy Numbers ◽  
Cell Embryo ◽  
Dna Copy Numbers

SWR/J-RF/J hybrid mice spontaneously acquire new germ line ecotropic proviruses at high frequency. In the studies described here, we used these hybrids to produce 18 transgenic mouse lines, each carrying a single newly acquired Srev locus (SWR/J-RF/J ecotropic proviral locus). All of the newly acquired proviruses identified in mosaic founder SWR/J-RF/J mice that could be transmitted through the germ line were also present in somatic tissues, demonstrating that viral integration occurred before the germ line was set aside from the somatic lineages. Quantitative analysis of proviral DNA copy numbers in somatic and germinal tissues of mosaic founder parents combined with structural analysis of Srev loci indicated that these proviruses are acquired after multiple rounds of somatic viral reinfection and that most of these viral integration events occurred after DNA replication in the zygote and before DNA replication in the four-cell embryo. The frequency of provirus acquisition in Srev lines that expressed the infectious ecotropic virus was similar to that in SWR.RF mice carrying Emv-16 and Emv-17, suggesting that the chromosomal integration site of the parental locus is not an important determinant for high-frequency provirus acquisition. The frequency of recessive lethal mutations induced by spontaneous viral integration was 5%, which was similar to that induced by preimplantation embryo infection. This approach represents a simple and viable strategy for inducing and studying mutations that affect mammalian development.

scholarly journals Mitochondria in human oogenesis and preimplantation embryogenesis: engines of metabolism, ionic regulation and developmental competence

Reproduction ◽  
2004 ◽  
Vol 128 (3) ◽  
pp. 269-280 ◽  
Author(s):  
Jonathan Van Blerkom
Keyword(s):  
Early Embryo ◽  
Developmental Competence ◽  
Atp Production ◽  
Mammalian Oocyte ◽  
Copy Numbers ◽  
Preimplantation Stage ◽  
Functional Implications ◽  
Intracellular Ca ◽  
Dna Copy Numbers ◽  
Human Oogenesis

Mitochondria are the most abundant organelles in the mammalian oocyte and early embryo. While their role in ATP production has long been known, only recently has their contribution to oocyte and embryo competence been investigated in the human. This review considers whether such factors as mitochondrial complement size, mitochondrial DNA copy numbers and defects, levels of respiration, and stage-specific spatial distribution, influence the developmental normality and viability of human oocytes and preimplantation-stage embryos. The finding that mitochondrial polarity can differ within and between oocytes and embryos and that these organelles may participate in the regulation of intracellular Ca2+homeostasis are discussed in the context of how focal domains of differential respiration and intracellular-free Ca2+regulation may arise in early development and what functional implications this may have for preimplantation embryogenesis and developmental competence after implantation.

Variations in Mitochondrial DNA Copy Numbers in MS Brains

2008 ◽  
Vol 35 (3) ◽  
pp. 283-287 ◽  
Author(s):  
Andrei Blokhin ◽  
Tamara Vyshkina ◽  
Samuel Komoly ◽  
Bernadette Kalman
Keyword(s):  
Mitochondrial Dna ◽  
Copy Numbers ◽  
Dna Copy Numbers
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