Breaking up the chromosomes of Baetica ustulata by in situ treatments with restriction endonucleases

Genome ◽  
1989 ◽  
Vol 32 (2) ◽  
pp. 208-215 ◽  
Author(s):  
C. Sentís ◽  
J. Santos ◽  
J. Fernández-Piqueras
Keyword(s):  
Chromosome Complement ◽  
Restriction Enzymes ◽  
Rates Of Convergence ◽  
Restriction Endonucleases ◽  
Dna Base Composition ◽  
Dna Base ◽  
Different Response ◽  
High Level ◽  
Differential Digestion

Fixed chromosomes of Baetica ustulata were treated with restriction endonucleases and subsequently stained with either Giemsa or the DNA-specific dye propidium iodide. Each enzyme produces a specific banding pattern with both dyes, which demonstrates the value of restriction endonucleases for chromosome banding in this species. The results obtained agree with the hypothesis that the action of restriction enzymes is based on cutting and extraction of DNA and is essentially determined by DNA base composition rather than by chromatin structure. However, strictly centric bands could be an exception. At least nine chromatin types can be distinguished in B. ustulata according to their different response to enzyme digestion and to the fluorescence banding patterns. Differential digestion of specific heterochromatic areas in band 4.4 and in the supernumerary segment of M5 by the HpaII – MspI enzyme pair suggests a high level of DNA methylation at these regions. The distribution of the different classes of DNA repeated sequences in the chromosome complement of B. ustulata indicates that some bands seem to follow the general principles of heterochromatin equilocality, while conceited evolution of heterochromatic DNA in other regions might have different rates of convergence in this species.Key words: restriction endonucleases, chromatin heterogeneity, methylated bands, equilocality, concerted evolution.

DNA methylation pattern during the encystment of Physarum flavicomum

1990 ◽  
Vol 68 (6) ◽  
pp. 944-948 ◽  
Author(s):  
Chengming Zhu ◽  
Henry R. Henney Jr.
Keyword(s):  
Dna Methylation ◽  
High Performance ◽  
Restriction Enzymes ◽  
Methylation Pattern ◽  
Dna Base Composition ◽  
Metabolic Role ◽  
Growing Cell ◽  
Dna Base ◽  
Intracellular Content ◽  
Methylation Patterns

In Physarum flavicomum Berk., haploid myxamoebae convert to dormant microcysts under conditions of nutrient imbalance. Exogenous adenine increases the intracellular content of S-adenosylmethionine (SAM) and inhibits this process. However, treatments that reduce the intracellular SAM levels relieve the inhibition of encystment induced by adenine. SAM plays a major metabolic role in cellular transmethylation reactions. In this study, we compared the DNA methylation patterns of growing cells, encysting cells, adenine-inhibited cells, and cysts using three different approaches: incubation of the cells with [14C]methylmethionine and detection of the labeled methyl group in purified DNA samples; analyses of DNA base composition by high performance liquid chromatography; and restriction endonuclease analyses of DNA. We found that DNA from the adenine-treated cells was labelled 1.3 times more with [14C]methylmethionine than was the DNA of untreated encysting cells. The DNA G + C content of this species was about 41%. The DNA of growing cells had the highest 5-methylcytosine (5MC) content, while DNA from the cysts had the lowest (about 27% that of growing cells). Adenine-inhibited cells had about 1.2 times more DNA-5MC than did encysting cells. Using the restriction enzymes SmaI, PvuI, and XhoI (which are inhibited by C residue methylation), we found that cyst DNA had more cutting sites than did amoebal DNA. By using the restriction enzyme DpnI which cuts DNA at GmATC sites, we found that cyst DNA, but not growing cell DNA, contained N6-methyladenine.Key words: amoebae, cysts, methylation, 5-methylcytosine, N6-methyladenine, DNA, encystment, Physarum flavicomum, development, inhibition.

Heterochromatin heterogeneity in the holocentric X chromatin of Megoura viciae (Homoptera, Aphididae)

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 465-470 ◽  
Author(s):  
G. C. Manicardi ◽  
D. Bizzaro ◽  
E. Galli ◽  
U. Bianchi
Keyword(s):  
X Chromosome ◽  
Holocentric Chromosomes ◽  
Dna Base Composition ◽  
Banding Patterns ◽  
Dna Base ◽  
Embryo Cells ◽  
Chromatin Compactness ◽  
Megoura Viciae ◽  
Endonuclease Digestion

Holocentric chromosomes, prepared by spreading embryo cells obtained from Megoura viciae parthenogenetic females, have been C-banded, enzymatically digested in situ using the specific endonucleases DdeI (C↓TNAG), DraI (TTT↓AAA), Tru9I (TT↓AA), and CfoI (GCG↓C), and subsequently stained with Giemsa, DAPI, CMA3, and AgNO3. We observed that the X chromosome had the best defined banding patterns. In the M. viciae X chromosome there is a certain amount of heterogeneity in heterochromatic DNA composition. In fact, the GC-rich NOR-associated heterochromatin differs from other heterochromatic bands that are characterized by AT-rich DNAs. Our data also indicate that, in M. viciae holocentric chromosomes, all heterochromatic blocks are accessible to in situ enzyme attack, the only limit to the digestion being the presence or absence of recognition targets. This is an interesting point, since, in monocentric chromosomes, it is well known that in situ endonuclease digestion is heavily affected not only by DNA base composition but also by chromatin compactness that may limit enzyme accessibility to their specific targets. Key words : heterochromatin, holocentric chromosomes, aphids.

Mutants with altered DNA base composition inBacterium paracoli — the evidence from a marker

1971 ◽  
Vol 11 (2) ◽  
pp. 91-95 ◽  
Author(s):  
G. F. Gause ◽  
A. V. Laiko ◽  
M. V. Bibikova ◽  
L. I. Kusovkova ◽  
T. I. Selesneva ◽  
...  
Keyword(s):  
Base Composition ◽  
Dna Base Composition ◽  
Dna Base

scholarly journals Wheat, Rye, and Barley Genomes Can Associate during Meiosis in Newly Synthesized Trigeneric Hybrids

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 113
Author(s):  
María-Dolores Rey ◽  
Carmen Ramírez ◽  
Azahara C. Martín
Keyword(s):  
Chromosome Segregation ◽  
Genome Duplication ◽  
Triticum Turgidum ◽  
Aegilops Tauschii ◽  
Genomic In Situ Hybridization ◽  
Hordeum Chilense ◽  
Genomic Constitution ◽  
Chromosome Associations ◽  
High Level

Polyploidization, or whole genome duplication (WGD), has an important role in evolution and speciation. One of the biggest challenges faced by a new polyploid is meiosis, in particular, discriminating between multiple related chromosomes so that only homologs recombine to ensure regular chromosome segregation and fertility. Here, we report the production of two new hybrids formed by the genomes of species from three different genera: a hybrid between Aegilops tauschii (DD), Hordeum chilense (HchHch), and Secale cereale (RR) with the haploid genomic constitution HchDR (n = 7× = 21); and a hybrid between Triticum turgidum spp. durum (AABB), H. chilense, and S. cereale with the constitution ABHchR (n = 7× = 28). We used genomic in situ hybridization and immunolocalization of key meiotic proteins to establish the chromosome composition of the new hybrids and to study their meiotic behavior. Interestingly, there were multiple chromosome associations at metaphase I in both hybrids. A high level of crossover (CO) formation was observed in HchDR, which shows the possibility of meiotic recombination between the different genomes. We succeeded in the duplication of the ABHchR genome, and several amphiploids, AABBHchHchRR, were obtained and characterized. These results indicate that recombination between the genera of three economically important crops is possible.

scholarly journals A cookbook for DNase Hi-C

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Maria Gridina ◽  
Evgeniy Mozheiko ◽  
Emil Valeev ◽  
Ludmila P. Nazarenko ◽  
Maria E. Lopatkina ◽  
...  
Keyword(s):  
Rational Design ◽  
Restriction Enzymes ◽  
Nucleotide Exchange ◽  
Computational Tools ◽  
3 Dimensional ◽  
Cultured Human Cells ◽  
Dna Ends ◽  
By Products ◽  
Robust Protocol

Abstract Background The Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation. Results In this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming. Conclusions We propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality.

Some observations on rock weathering, Cumberland Peninsula, Baffin Island

1979 ◽  
Vol 16 (5) ◽  
pp. 977-983 ◽  
Author(s):  
Stephen H. Waits
Keyword(s):  
Salt Crystallization ◽  
Rock Weathering ◽  
Baffin Island ◽  
Significant Modification ◽  
Bedrock Weathering ◽  
Arctic Conditions ◽  
Selective Preservation ◽  
Mechanical Weathering ◽  
High Level

A variety of bedrock weathering features—both modern and remnant—including surface grus, polygonal cracks, siliceous glaze, tors, weathering pits, and tafoni typify upland outcrops on the Cumberland Peninsula. Tor ridges are particularly prevalent and at lower elevations they show significant modification and streamlining by flowing ice. On summit areas at elevations above 750 m, however, remnant corestones are preserved in situ, suggesting selective preservation of upland surfaces. Bedrock structure and composition, topographic position, and intensity of process strongly influence tor development. Weathering pits are common on high level, open summit surfaces where weathering occurs in response to both climate and continued removal of derived debris. Pit enlargement through lateral undercutting has been favoured by accumulation of protective bottom residua, mechanical weathering, and the presence of exfoliation crusts. It is postulated that salt crystallization plays a role in outcrop microweathering under present upland arctic conditions.

scholarly journals Intrastrand parity rules of DNA base composition and usage biases of synonymous codons

1996 ◽  
Vol 42 (2) ◽  
pp. 323-323 ◽  
Author(s):  
Noboru Sueoka
Keyword(s):  
Base Composition ◽  
Dna Base Composition ◽  
Synonymous Codons ◽  
Dna Base

DNA base composition heterogeneity in some agarophytes (Gracilariales, Rhodophyta) from Mexico and the Philippines

1996 ◽  
Vol 8 (3) ◽  
pp. 229-237 ◽  
Author(s):  
Donald F. Kapraun ◽  
Juan Lopez-Bautista ◽  
Kimon T. Bird
Keyword(s):  
Base Composition ◽  
The Philippines ◽  
Dna Base Composition ◽  
Dna Base

Comparative Karyotype Investigations in the European Crayfish Astacus astacus and A. leptodactylus (Decapoda, Astacidae)

Crustaceana ◽  
2011 ◽  
Vol 84 (12-13) ◽  
pp. 1497-1510 ◽  
Author(s):  
M. Pavlica ◽  
M. Mcžić ◽  
G. Klobučar ◽  
M. Šrut ◽  
I. Maguire ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Complement ◽  
Size Difference ◽  
45S Rdna ◽  
Astacus Astacus ◽  
Fluorochrome Staining ◽  
Rdna Sites ◽  
Freshwater Habitats ◽  
Acrocentric Chromosomes

AbstractThis study reports on the chromosome number and karyological characteristics of the endangered species of European crayfish, Astacus astacus and A. leptodactylus (Decapoda, Astacidae), both native to Croatian freshwater habitats. The karyotype of A. astacus and A. leptodactylus consists of 2n = 176 and 2n = 180 chromosomes, respectively. The haploid chromosome complement of A. astacus consists of 52 metacentric, 35 metacentric-submetacentric, and 1 acrocentric chromosomes. Fluorochrome staining with 4,6-diamino-2-phenylindole (DAPI) has revealed that the karyotypes of A. astacus and A. leptodactylus are characterized by large heterochromatic blocks located at centromeric and intercalary positions on the chromosomes. Interstitial heterochromatic blocks were more frequent in A. astacus than in A. leptodactylus. In both species pairing of chromosomes in meiosis was regular with the majority of bivalents in a ring- and a dumbbell-form. Fluorescence in situ hybridization (FISH) has revealed that two 45S rDNA loci were present in the investigated species. In A. astacus one of the two 45S rDNA-bearing chromosome pairs was highly heteromorphic, exhibiting a three-fold size difference between 45S rDNA sites on homologous chromosomes. Such a size difference was significantly less pronounced in A. leptodactylus. The karyotype differences between A. astacus and A. leptodactylus suggest changes in chromosome number as well as position of repetitive DNAs have played a role in the karyotype evolution of the species of Astacus.

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