Repetitive Deoxyribonucleic Acid Research Articles

Biodiversity of Tricholoma matsutake (syn. T. nauseosum) and its related species based on repetitive DNA and genomics

Tricholoma matsutake and its related species are ectomycorrhizal Agaricomycetes that produce prized mushrooms collectively called “ matsutake”. These mushrooms are mainly distributed in the Northern Hemisphere. In this review, we describe both the pioneering work and recent advances in our understanding of the distribution and evolution of matsutake, with a special focus on genomic studies. Deoxyribonucleic acid (DNA) sequence analyses revealed that Tricholoma caligatum was the earliest species within this group, followed by Tricholoma fulvocastaneum, the cluster with Tricholoma ilkkae, Tricholoma dulciolens, and Tricholoma bakamatsutake, and finally the cluster with Tricholoma murrillianum, Tricholoma mesoamericanum, Tricholoma anatolicum, and Tricholoma matsutake. Although analyses based on mobile DNAs and whole-genome sequences revealed a similar clustering pattern, there are distinct differences in the distribution of mobile DNAs and genomic structure of Tricholoma bakamatsutake and Tricholoma matsutake. Furthermore, repetitive DNA can be used as markers to distinguish among strains and populations of Tricholoma matsutake from different geographical regions, including identifying dispersals of basidiospores. “Telomere-to-telomere genome sequencing” analyses unearthed that both Tricholoma matsutake and Tricholoma bakamatsutake underwent explosive multiplications of retrotransposons within their genomes but with different mobile DNA elements expanded between them. Contrastingly, the structure of the mating loci between Tricholoma matsutake and Tricholoma bakamatsutake is highly conserved.

Human Consciousness: A Theoretical Prospective on Repetitive DNA Base Pairs Relation to Psychological Behavior

In this paper an attempt has been made to bridge the gap between the repetitive Deoxyribonucleic acid (DNA) base pair sequences and psychological human behavior. Assuming the brain as a perfect fluid, the DNA coefficient between the biological and non-biological forms of the brain is calculated. These calculations are based on the Friedman density equations that describe the expansion or contraction of the universe in homogeneous and isotropic way in physical cosmology (only time independent equation is considered). We have tested this DNA coefficient with a sample size of eighty persons with belief constructs on consciousness behavior. The Pearson’s coefficient thus obtained is then compared with DNA coefficient. A logical justification is made for the comparison of these two values. The coefficient values are found to tally but with an error margin of thirteen percent. The major result of this research study is in finding a relation between the experimental DNA values with that of psychology of consciousness behavior in terms of coefficient values. NeuroQuantology | December 2013 | Volume 11 | Issue4 |Page 618-626

Clustering heterochromatin: Sir3 promotes telomere clustering independently of silencing in yeast

A general feature of the nucleus is the organization of repetitive deoxyribonucleic acid sequences in clusters concentrating silencing factors. In budding yeast, we investigated how telomeres cluster in perinuclear foci associated with the silencing complex Sir2-Sir3-Sir4 and found that Sir3 is limiting for telomere clustering. Sir3 overexpression triggers the grouping of telomeric foci into larger foci that relocalize to the nuclear interior and correlate with more stable silencing in subtelomeric regions. Furthermore, we show that Sir3's ability to mediate telomere clustering can be separated from its role in silencing. Indeed, nonacetylable Sir3, which is unable to spread into subtelomeric regions, can mediate telomere clustering independently of Sir2-Sir4 as long as it is targeted to telomeres by the Rap1 protein. Thus, arrays of Sir3 binding sites at telomeres appeared as the sole requirement to promote trans-interactions between telomeres. We propose that similar mechanisms involving proteins able to oligomerize account for long-range interactions that impact genomic functions in many organisms.

Transgene methylation in mice reflects copy number but not expression level.

In mammals, CpG methylation is one of the mechanisms of epigenetic control over the linear sequence of bases of deoxyribonucleic acid (DNA); about 70% of CpG dinucleotides are methylated. The actual signal that triggers DNA methylation is not known, although repetitive DNA has been shown to be an attractive template for DNA methylases. To address methylation events associated with transgenic copy number, we have analyzed transgenes that are actively transcribed in a tissue-specific manner. We have compared gross transgene methylation by restriction-enzyme digestion in expressing and nonexpressing tissues. The observed pattern suggests that the DNA methylation machinery can recognize repeated genomic sequences independently of their transcriptional activity.

Epidemiology and diagnosis of African trypanosomiasis using DNA probes

The accurate identification of trypanosome species has been a challenging problem in the epidemiology of African trypanosomiasis, both human and animal. The last 10 years have seen great progress through the application of deoxyribonucleic acid (DNA) probe technology, although this has also revealed greater complexity than supposed. While a single repetitive DNA probe can identify all members of the subgenus Trypanosoma (Trypanozoon), including the human pathogens T. brucei gambiense and T. b. rhodesiense as well as the non-tsetse-transmitted trypanosomes T. evansi and T. equiperdum, at least 6 probes are needed to distinguish members of the subgenus Nannomonas, in which only 2 species, T. congolense and T. simiae, were previously recognized. Similarly, the subgenus Duttonella appears to consist of more than one species. Use of this battery of DNA probes to identify the trypanosomes carried by tsetse flies in the field has yielded some surprises about the accuracy (or inaccuracy) of previous identification methods. An unexpectedly high prevalence of mixed infections has been found in all the field studies carried out so far. The large number of infections that remain unidentified by the available probes suggests the existence of other, as yet unknown, trypanosome species. Limited use of the polymerase chain reaction has been made for diagnosis of human and animal trypanosomiasis, due to its high cost.

The Insertion of Foreign DNA Into Mammalian Genomes and Its Consequences: A Concept in Oncogenesis

Publisher Summary This chapter examines the consequences of foreign deoxyribonucleic acid (DNA) insertion into established mammalian genomes. In mammalian cells, the ever-present repetitive DNA sequences possibly constitute a reservoir of insertion targets whose disturbance may have less immediate functional consequences. Among the consequences of the insertion of foreign DNA into the established genomes and of the transformed cell phenotype are the de novo methylation of the foreign DNA and alterations in the existing patterns of DNA methylation in the preexisting cellular genome. Diet-ingested foreign DNA could play an important role in eliciting mutagenic and oncogenic events in mammals. In light of these findings, the postulated cellular defense mechanism by methylation of integrated foreign DNA becomes plausible. The results of studies on the model of adenovirus DNA integration in mammalian cells suggested that the insertion of foreign DNA had to be rather pliable. There is a possibility that the insertion of foreign DNA into an established mammalian genome can lead to far-reaching alterations in the patterns of cellular DNA methylation and gene expression. The classical concept of insertional mutagenesis relates to damage caused to cellular functions or genes that are encoded at the sites of foreign (adenoviral) DNA insertion into the host genome.

Polymerase chain reaction detection of Plasmodium falciparum in mosquitoes

The polymerase chain reaction (PCR) procedure using a primer set derived from a repetitive deoxyribonucleic acid (DNA) sequence specific to Plasmodium falciparum was used to detect parasite DNA in mosquitoes. In laboratory-infected mosquitoes, PCR could detect as few as 10 sporozoites in a dissected salivary gland and a single oocyst in a dissected midgut. The ability to detect P. falciparum DNA in wild-caught mosquitoes indicated an advantage of the PCR over enzyme-linked immunosorbent assay for the detection of Plasmodium sporozoites in mosquitoes with low-grade parasite infections.

Early replication of repetitive DNA associated with inactive centromeres

Four types of stable dicentric and one octacentric chromosomes from mouse brain tumor cells and L-929 cells were analyzed for the timing of replication of repetitive deoxyribonucleic acid (DNA) located in the centric and pericentric regions associated with active versus inactive centromeres. The repetitive DNA present in the heterochromatin blocks of inactive centromeres replicates much earlier than similar DNA associated with the active centromeres. The former appears to replicate during early to mid S when several euchromatic segments are still replicating. There seems to be little or no overlap in the timing of replication of the repetitive DNA present in the vicinity of prematurely separating centromeres (which are accessory and nonfunctional) and those that separate at meta-anaphase junction (which are the functional centromeres). In the absence of any information about the mechanism(s) controlling initiation and completion of DNA synthesis in the two types of heterochromatic blocks, the differential timing of replication of the DNA with similar base composition remains an enigma.

Effect of the menstrual cycle on detection and typing of human papillomavirus in uterine cervical cells

We observe fluctuations in human papillomavirus detection and variation in genotyping between sequential cervical cell specimens analyzed by filter in situ hybridization. Furthermore, specimen adequacy for analysis varies. To determine whether these phenomena are correlated with menstrual cycle stage at the time of sampling, we analyzed cervical cell specimens from women with cervical intraepithelial neoplasia. Specimens were categorized on the basis of a 28-day menstrual cycle and were analyzed by hybridization to combined probes for virus types 6 and 11 or types 16 and 18. Specimen adequacy was determined by hybridization to a human Alu I repetitive deoxyribonucleic acid probe. Analysis of data with chi 2 revealed that fluctuations in virus detection and type variation are unrelated to menstrual cycle stage. Specimen adequacy is stage-dependent for women who take oral contraceptives. Whereas specimens can be collected at any time other than the first week of the menstrual cycle, accurate determination of infection status requires multiple assessments.

Repetitive Deoxyribonucleic Acid (DNA) and Human Genome Variation—A Concise Review Relevant to Forensic Biology

The various classes of human repetitive deoxyribonucleic acid (DNA) are described, with particular emphasis being given to their variation in the human genome. The significance of this information to forensic science is discussed.

A repetitive deoxyribonucleic acid sequence distinguishesTrypanosoma simiaefromT. congolense

The dominant repetitive deoxyribonucleic acid (DNA) sequence in the genome of a clone of Trypanosoma (Nannomonas) simiae has been identified and cloned as a recombinant plasmid. The recombinant plasmid was used in hybridization analyses of DNA samples obtained from various trypanosome species and subspecies. The results indicated that the T. simiae repetitive DNA sequence hybridized with DNA derived only from T. simiae; it did not hybridize with DNA derived from clones or stocks of T. congolense, or from any other trypanosome species examined. A preliminary characterization of the cloned DNA sequence and its use in the identification of T. simiae of similar genotypes are presented.

Use of single (4B-2) and repetitive copy (pS4) deoxyribonucleic acid (DNA) probes to characterize translocated Y DNA in a pedigree with recurrent abortion

Probes for unique and repetitive copy deoxyribonucleic acid (DNA) are available to detect and characterize Y DNA. The probe pS4 detects repetitive copy DNA mapped to Yq12. The upper limits of the pS4 sequences are defined by the upper limits of C-banding. The probe 4B-2 is a recombinant phage construct developed from a Y library and contains a unique copy 3.3 kb Eco RI fragment mapped to Yq11. A family was ascertained through a pregnant female who had a history of four consecutive abortions and two normal daughters. Cytogenetic analysis revealed the mother and one of her daughters to have a 46,XX,15p+ karyotype. Amniocytes were karyotyped as 46,XY,15p+. Genomic DNA from controls, mother, daughters, and amniocytes was digested with Mbo I and hybridized to 32P-labeled pS4 probe. DNAs from both 46,XX,15p+ females and 46,XY,15p+ amniocytes demonstrated a clear male-specific 2.3 kb band. Digestion of the same genomic DNAs with Eco RI and blot hybridization to 32P-labeled 4B-2 probe revealed the 3.3 kb male-specific band only in the 46,XY,15p+ amniocyte DNA. The additional sequences located on 15p segregating in the female members of this family correspond to Yq12. The effect of this additional DNA on gametogenesis is unknown.

Strain-specific 1.7 kilobase repetitive deoxyribonucleic acid sequence family in Trichinella spiralis

Eco RI digestion of bulk DNA from Trichinella spiralis P 1, an isolate from domestic pig, reveals the presence of families of repetitive sequences. One of the most prominent of these has a monomer size of 1.7 kb, which exists in minimally dispersed direct tandem arrays, with a copy number of about 2800, and represents 2% of the genome. Although there is evidence that the Eco RI site is missing in some of the family members and that a 1.9 kb variant of the sequence also occurs, the family is highly homogeneous. When bulk DNA from other pig isolates (P 2, PB 1) and two black bear isolates from Pennsylvania (UPB 6, UPB 8) is probed with a typical member of the 1.7 kb sequence family cloned into pUC9, hybridization is identical in pattern and intensity with self-hybridization, indicating that the 1.7 kb family exists equally in the repetitive fraction of all of these isolates. When blots of bulk DNA from wild carnivore isolates (MSIL, PF 1, AF 1, AF 2, AF 3, AF 4, SL, TC) are probed with pPRA, no hybridization can be detected. Faint hybridization of the probe to DNA from T. spiralis var. pseudospiralis occurs at 1.7 kb on an Eco RI profile and indicates that the 1.7 kb sequence has been conserved in the course of strain evolution.

A putative tRNATrp gene cloned from Dictyostelium discoideum: its nucleotide sequence and association with repetitive deoxyribonucleic acid.

Using a total tRNA population labeled with 32P, we have cloned a number of tRNA genes from Dictyostelium discoideum. A partial sequence of a cloned 1250-base-pair DNA insert, pDT-513, revealed the occurrence of a putative tRNATrp gene. In addition to the cloverleaf secondary structure, the tRNATrp gene contained all of the invariant and semiinvariant residues found in most tRNA sequences and has a 13-base-pair intron which is located one base removed from the 3' residue of the anticodon. The genomic distribution of the tRNA gene and its flanking sequences was examined via Southern annealing experiments. The structural gene is represented on at least six EcoRI fragments in the D. discoideum genome. Sequences flanking the 5' terminus of the cloned gene are repeated many times in the genome while the sequence flanking the 3' terminus of the pDT-513 DNA insert structural tRNA gene is present only once in the genome.

Repeated deoxyribonucleic acid clusters in the chicken genome contain homologous sequence elements in scrambled order.

Part of the repeated deoxyribonucleic acid (DNA) in the chicken genome had a clustered organization. The following description of clustered repeated sequences is derived both from analysis of DNA segments cloned in lambda and from hybridization of individual cloned sequences to Southern blots of restricted total DNA. A cluster usually exceeds 20 kbp in length and consists principally, if not entirely, or repetitive DNA. Each cluster contains one cope of several different repeated sequences. The individual sequences occur several hundred times in the genome, but only once per cluster. Many of the clusters contain the same assortment of sequences but in scrambled order. In the genome, those repeated sequences that are elements of clusters occur mainly within the clustered context and are seldom, if ever, found as isolated elements flanked by nonrepeated DNA. These aspects of cluster organization suggest that the clustered sequences undergo limited rearrangement, maintaining the associations within clusters but allowing variability of sequence arrangement from cluster to cluster. The clusters that occupy the cloned DNA segments together represent at least 10% of the repetitive DNA of the chicken.

Electron microscopy of Achlya deoxyribonucleic acid sequence organization.

Electron microscopic analysis of reassociated deoxyribonucleic acid (DNA) from the aquatic fungus Achlya bisexualis revealed details of the sequence arrangement of the inverted repeats and both the highly and moderately repetitive sequence clusters. We used the gene 32 protein-ethidium bromide technique for visualizing the DNA molecules, a procedure which provides excellent contrast between single- and double-stranded DNA regions. Long (greater than 6-kilobase) DNA fragments were isolated after reannealing to two different repetitive C0t values, and the renatured structures were then visualized in an electron microscope. Our results showed that the inverted repeat sequences were short (0.5 kilobase, number-average) and separated by nonhomologous DNA of various lengths. These pairs of sequences were not clustered within the genome. Both highly repetitive and moderately repetitive DNA sequences were organized as tandem arrays of precisely paired, regularly repeating units. No permuted clusters of repeating sequences were observed, nor was there evidence of interspersion of repetitive with single-copy DNA sequences in the Achlya genome.

Electron microscopy of Achlya deoxyribonucleic acid sequence organization.

Electron microscopic analysis of reassociated deoxyribonucleic acid (DNA) from the aquatic fungus Achlya bisexualis revealed details of the sequence arrangement of the inverted repeats and both the highly and moderately repetitive sequence clusters. We used the gene 32 protein-ethidium bromide technique for visualizing the DNA molecules, a procedure which provides excellent contrast between single- and double-stranded DNA regions. Long (greater than 6-kilobase) DNA fragments were isolated after reannealing to two different repetitive C0t values, and the renatured structures were then visualized in an electron microscope. Our results showed that the inverted repeat sequences were short (0.5 kilobase, number-average) and separated by nonhomologous DNA of various lengths. These pairs of sequences were not clustered within the genome. Both highly repetitive and moderately repetitive DNA sequences were organized as tandem arrays of precisely paired, regularly repeating units. No permuted clusters of repeating sequences were observed, nor was there evidence of interspersion of repetitive with single-copy DNA sequences in the Achlya genome.