scholarly journals Variations in ribosomal DNA copy numbers in a genome of Trichophyton interdigitale

Mycoses ◽  
2020 ◽  
Vol 63 (10) ◽  
pp. 1133-1140
Author(s):  
Tomoyuki Iwanaga ◽  
Kazushi Anzawa ◽  
Takashi Mochizuki
Keyword(s):  
Ribosomal Dna ◽  
Trichophyton Interdigitale ◽  
Copy Numbers ◽  
A Genome ◽  
Dna Copy Numbers

scholarly journals Strain-Dependent Variation in 18S Ribosomal DNA Copy Numbers in Aspergillus fumigatus

2009 ◽  
Vol 47 (5) ◽  
pp. 1325-1332 ◽  
Author(s):  
M. L. Herrera ◽  
A. C. Vallor ◽  
J. A. Gelfond ◽  
T. F. Patterson ◽  
B. L. Wickes
Keyword(s):  
Aspergillus Fumigatus ◽  
Ribosomal Dna ◽  
Copy Numbers ◽  
Dna Copy Numbers ◽  
Strain Dependent

scholarly journals PCR amplification and sequence analyses of reverse transcriptase-like genes in Crinipellis perniciosa isolates

2007 ◽  
Vol 32 (5) ◽  
pp. 373-380 ◽  
Author(s):  
Jorge F. Pereira ◽  
Mariana D.C. Ignacchiti ◽  
Elza F. Araújo ◽  
Sérgio H. Brommonschenkel ◽  
Júlio C.M. Cascardo ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Pathogenic Fungus ◽  
Pcr Amplification ◽  
Restriction Enzymes ◽  
Sequence Comparisons ◽  
Copy Numbers ◽  
A Genome ◽  
Close Relationship ◽  
Pcr Products ◽  
Broom Disease

Reverse transcriptase (RT) sequence analysis is an important technique used to detect the presence of transposable elements in a genome. Putative RT sequences were analyzed in the genome of the pathogenic fungus C. perniciosa, the causal agent of witches' broom disease of cocoa. A 394 bp fragment was amplified from genomic DNA of different isolates of C. perniciosa belonging to C-, L-, and S-biotypes and collected from various geographical areas. The cleavage of PCR products with restriction enzymes and the sequencing of various RT fragments indicated the presence of several sequences showing transition events (G:C to A:T). Southern blot analysis revealed high copy numbers of RT signals, forming different patterns among C-, S-, and L-biotype isolates. Sequence comparisons of the predicted RT peptide indicate a close relationship with the RT protein from thegypsy family of LTR-retrotransposons. The possible role of these retrotransposons in generating genetic variability in the homothallic C. perniciosa is discussed.

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

Chromosomal localization and characterization of rDNA loci in the Brassica A and C genomes

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 582-587 ◽  
Author(s):  
R. J. Snowdon ◽  
W. Köhler ◽  
A. Köhler
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Ribosomal Dna ◽  
Diploid Species ◽  
Rdna Locus ◽  
Chromosome Morphology ◽  
Rdna Site ◽  
A Genome ◽  
Rdna Loci

Using fluorescence in situ hybridization, we located ribosomal DNA loci on prometaphase chromosomes of the diploid species Brassica rapa and Brassica oleracea and their amphidiploid Brassica napus. Based on comparisons of chromosome morphology and hybridization patterns, we characterized the individual B. napus rDNA loci according to their presumed origins in the Brassica A and C genomes. As reported in other studies, the sum of rDNA loci observed on B. rapa (AA genome) and B. oleracea (CC genome) chromosomes was one greater than the total number of loci seen in their amphidiploid B. napus (AACC). Evidence is presented that this reduction in B. napus rDNA locus number results from the loss of the smallest A genome rDNA site in the amphidiploid.Key words: Brassica, fluorescence in situ hybridization, ribosomal DNA, rDNA.

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 Bacteria differently regulate mRNA abundance to specifically respond to various stresses

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150069 ◽  
Author(s):  
Alexander Bartholomäus ◽  
Ivan Fedyunin ◽  
Peter Feist ◽  
Celine Sin ◽  
Gong Zhang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Global Analysis ◽  
Start Codon ◽  
Specific Response ◽  
Copy Numbers ◽  
Genome Wide ◽  
A Genome ◽  
Temperature Upshift ◽  
Global Reduction

Environmental stress is detrimental to cell viability and requires an adequate reprogramming of cellular activities to maximize cell survival. We present a global analysis of the response of Escherichia coli to acute heat and osmotic stress. We combine deep sequencing of total mRNA and ribosome-protected fragments to provide a genome-wide map of the stress response at transcriptional and translational levels. For each type of stress, we observe a unique subset of genes that shape the stress-specific response. Upon temperature upshift, mRNAs with reduced folding stability up- and downstream of the start codon, and thus with more accessible initiation regions, are translationally favoured. Conversely, osmotic upshift causes a global reduction of highly translated transcripts with high copy numbers, allowing reallocation of translation resources to not degraded and newly synthesized mRNAs.

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 Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level

2021 ◽  
Vol 12 ◽  
Author(s):  
Xuhao Song ◽  
Tingbang Yang ◽  
Xinyi Zhang ◽  
Ying Yuan ◽  
Xianghui Yan ◽  
...  
Keyword(s):  
Genome Size ◽  
Gc Content ◽  
Distribution Patterns ◽  
Functional Roles ◽  
Tree Shrews ◽  
Copy Numbers ◽  
Genome Wide ◽  
A Genome ◽  
Dinucleotide Motif ◽  
Evolution Of Mammals

Microsatellite or simple sequence repeat (SSR) instability within genes can induce genetic variation. The SSR signatures remain largely unknown in different clades within Euarchontoglires, one of the most successful mammalian radiations. Here, we conducted a genome-wide characterization of microsatellite distribution patterns at different taxonomic levels in 153 Euarchontoglires genomes. Our results showed that the abundance and density of the SSRs were significantly positively correlated with primate genome size, but no significant relationship with the genome size of rodents was found. Furthermore, a higher level of complexity for perfect SSR (P-SSR) attributes was observed in rodents than in primates. The most frequent type of P-SSR was the mononucleotide P-SSR in the genomes of primates, tree shrews, and colugos, while mononucleotide or dinucleotide motif types were dominant in the genomes of rodents and lagomorphs. Furthermore, (A)n was the most abundant motif in primate genomes, but (A)n, (AC)n, or (AG)n was the most abundant motif in rodent genomes which even varied within the same genus. The GC content and the repeat copy numbers of P-SSRs varied in different species when compared at different taxonomic levels, reflecting underlying differences in SSR mutation processes. Notably, the CDSs containing P-SSRs were categorized by functions and pathways using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes annotations, highlighting their roles in transcription regulation. Generally, this work will aid future studies of the functional roles of the taxonomic features of microsatellites during the evolution of mammals in Euarchontoglires.

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