Cleavage Chart

[Alethia Tiell]

Oneof the characteristics of crystals is that they have cleavage. Cleavage is the tendency of a crystal to break cleanly along distinct planes. Since most gemstones are crystals, cleavage is an issue that gem buyers as well as jewelers and gem cutters need to take into account.

Minerals can possess anywhere from one to five cleavage planes, and each plane is assigned a grade or rating that denotes the level of ease with which the crystal can be cleaved. Cleavage is categorized as perfect, good, indistinct, or "none" (in instances where a gemstone lacks any cleavage).

The following chart lists the cleavage ratings for many well known gemstones. You'll note that different members of the same species or family, such as quartz or beryl, have the same cleavage. That's because members of the same species have the same crystal structure.See our feature article on gemstone cleavage for more information.

Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction endonucleases. We have proposed a method of restriction analysis of Alu repeats sequences in silico.

Simple software to analyze Alu repeats database has been suggested and Alu repeats digestion patterns for several restriction enzymes' recognition sites have been constructed. Restriction maps of Alu repeats cleavage for corresponding restriction enzymes have been calculated and plotted. Theoretical data have been compared with experimental results on DNA hydrolysis with restriction enzymes, which we obtained earlier.

Alu repeats digestions provide the main contribution to the patterns of human chromosomal DNA cleavage. This corresponds to the experimental data on total human DNA hydrolysis with restriction enzymes.

The human genome includes a substantial amount of interspersed repetitive DNA (about 45%) which is divided into several groups (LINEs, SINEs, LTR retroposons, DNA transposons and others) [1]. The Alu family of DNA repeats, which belongs to SINE group, is one of the most abundant and well characterized repetitive elements. The total number of annotated Alu sequences in the database of human genome is more than 1 million copies and their fraction in genome is about 10% [1].

Alu repetitive elements were first described about 30 years ago and were named after conserved AluI restriction site (AGCT), which is present in the most of studied members of the family [2, 3]. The Alu repeat sequence is about 300 bp in length and probably originated from the 7SL RNA [4]. The details of Alu repeats retroposition in human genome are still unclear and it is difficult to explain Alu repeats abundance in genomic sequence [5].

A goal of this work is to 1) develop a software for analysis of a big number of Alu repeats, 2) compare the calculation data on cleavage of the whole human genome and a set of Alu repeats, 3) carry out a comparative analysis of experimental results of DNA hydrolysis and theoretical data on various Alu repeats families' digestion and 4) present a physical map of Alu repeats cleavage with 9 restriction enzymes.

As indicated in "Methods" each nucleotide sequence from more than 1,190,000 annotated Alu repeats sequences has been searched for a presence of recognition sequence of restriction enzymes, a number and positions of these sites in Alu repeat sequences have been determined. Then, Alu repeats digestion diagram, a diagram of the obtained DNA fragments number versus the length of these fragments has been plotted for each recognition sequence.

Earlier we have observed a similarity between distribution diagrams of whole genome and Alu repeats digestion in the case of AluI and Bst2UI recognition sequences [13]. Fig. 1 shows a comparison of distribution diagrams of a whole genome and Alu repeats digestion for recognition sites of 9 restriction enzymes. As it is clearly seen from the figure all peaks of 300 bp and less are present both in diagrams of the whole human genome digestion and in diagrams of the annotated Alu repeats cleavage in silico. Thus, indeed, the corresponding fragments of genomic DNA are formed due to a cleavage of Alu repeats. A cleavage of remaining DNA forms a background curve of a whole genomic DNA digestion. A structure of this background fragments curve depends mainly on GC-content of genomic DNA, enzymes recognition site and has been discussed earlier [12]. On Fig. 1 there are some smaller peaks in whole genome cleavage diagrams. Our analysis has shown that these peaks are formed mainly due to a cleavage of human LINE1 repeat (data not shown).

Comparison of distribution diagrams. Distribution diagrams obtained for complete human genomic sequence are shown at top, whereas those for the complete set of annotated Alu repeats are shown at bottom. The highest peak values are indicated.

Preliminary analysis has shown that Alu repeat sequences differ in length. On Fig. 2 we have presented a diagram of Alu repeats number versus a length of Alu repeats sequences, which are presented in data base. Fig. 2 shows that a big number of Alu repeats shorter than 250 bp are listed in data base. We have made some additions to 5'-truncated short Alu repeats sequences to unify them for a subsequent analysis. As indicated in "Methods" we have aligned all DNA sequences, which originally were 5'-truncated, by adding extra nucleotides at 5'-end of Alu repeats. A total number of all obtained human Alu repeat sequences, which has been considered in a further analysis, is 1,193,407. These aligned Alu repeats are presented at SibEnzyme data base [14].

On Fig. 4 we provide a physical map of Alu repeats cleavage by various restriction endonucleases. This map has been constructed based on the data given in Table 2. Experimental data on chromosomal DNA cleavage [13] are given on a left side of Fig. 4. There is a good correspondence of the experimental results and the theoretical data, which is discussed in details below.

A method of theoretical analysis of Alu repeats sequences from the database has been proposed in this work. It includes a) a search for restriction enzymes recognition sites in all Au repeats sequences, b) additional alignment of annotated Alu repeats sequences with formation a new set of Alu repeats sequences, c) determination of location of the restriction enzymes recognition sites in a new set of Alu repeats and calculation of a number of these sites in each positions, d) calculation of a number of DNA fragments, which are produced in the course of Alu repeats cleavage at these sites. We also have compared data on sites' distribution among main Alu repeats subfamilies. There is a definite preference in distribution of some restriction enzymes recognition sequences among different families of Alu repeats, for example, AluI site at position 216 is characteristic for "young" AluY sequences. Thus, such preference may be used to characterize Alu subfamilies by restriction enzymes analysis. Finally, we have constructed a physical map of Alu repeats cleavage by restriction endonucleases and have shown a good correspondence of theoretical and experimental data.

The suggested method of Alu repeats analysis allows to simplify a study of human DNA digestion with restriction endonucleases considering set of Alu repeats sequences instead of the whole human genomes. Thus, time and efforts, which are necessary for such calculations, may be significantly reduced.

The DNA fragments distribution diagrams for a whole human genome digestion at the recognition sites of restriction endonucleases have been obtained in our previous publication [13]. The distribution diagrams for Alu repeats digestion at the recognition sites of restriction endonucleases AluI and Bst2UI have been presented earlier [13]. The DNA fragments distribution diagrams of Alu repeats digestion at the recognition sites of restriction endonucleases AsuHPI, BstSCI, Bpu10I, BssECI, BstDEI, BstMAI and HinfI were constructed according to the previously described technique [11] with some modifications as described below.

For each restriction endonuclease the data on recognition site positions in the set of Alu repeats have been extracted from Table 1. The data on valuable number of each DNA fragment have been obtained from the Table 2.

MAA carried out the data analysis and drafted the manuscript. VNT developed software and participated in computer analysis. VAC carried out a comparison of the obtained results with experimental data on DNA hydrolysis. SKD coordinated the project and prepared the final manuscript. All authors have read and approved the final manuscript.

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Because ions are very reactive and short-lived, their formation and manipulation must be conducted in a vacuum. Atmospheric pressure is around 760 torr (mm of mercury). The pressure under which ions may be handled is roughly 10-5 to 10-8 torr (less than a billionth of an atmosphere). Each of the three tasks listed above may be accomplished in different ways. In one common procedure, ionization is effected by a high energy beam of electrons, and ion separation is achieved by accelerating and focusing the ions in a beam, which is then bent by an external magnetic field. The ions are then detected electronically and the resulting information is stored and analyzed in a computer. A mass spectrometer operating in this fashion is outlined in the following diagram. The heart of the spectrometer is the ion source. Here molecules of the sample (black dots) are bombarded by electrons (light blue lines) issuing from a heated filament. This is called an EI (electron-impact) source. Gases and volatile liquid samples are allowed to leak into the ion source from a reservoir (as shown). Non-volatile solids and liquids may be introduced directly. Cations formed by the electron bombardment (red dots) are pushed away by a charged repeller plate (anions are attracted to it), and accelerated toward other electrodes, having slits through which the ions pass as a beam. Some of these ions fragment into smaller cations and neutral fragments. A perpendicular magnetic field deflects the ion beam in an arc whose radius is proportional to the mass of each ion. Lighter ions are deflected more than heavier ions. By varying the strength of the magnetic field, ions of different mass can be focused progressively on a detector fixed at the end of a curved tube (also under a high vacuum).

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