Qur’an & Genetics

Qur’an & Genetics

On Giant Chromosomes in the Qur`an

Ahmad Shammazadeh

Topics:

1.     Which Chromosomes are called Giant Chromosomes?

2.     What interested me toconduct a research on Giant Chromosomes?

3.     Why and how the Almighty God has guided us to study the Giant

Chromosomes?

4.     The situation and importance of Giant Chromosomes in modern Genetics.

5.     Is it possible that Giant Chromosomes have brought life to Earth?

*****

Which chromosomes are called Giant Chromosomes?

The 23rd pair of human chromosomes is the sexual Chromosome and the 22 remaining pairs are called Autosomal Chromosomes. Eight pairs(from no. 1 to no. 8) of them, are Giant Chromosomes. These 8 pairs of chromosomes are very important for human life, because every giant chromosome is made up of about 181 million letters that make up the human genetic code.

ENDOMITOSIS AND ENDOREDUPLICATION

Nagl et al. (1985) described polytene chromosomes as giant chromosomes produced by changes in the mitotic cycle during the interphase stage. In such a modified nuclear cycle, the chromatin duplicates its DNA content during the G1 and S stages, but, instead of passing to the G2 stage, the nucleus initiates a new G1 phase, thus starting a new cycle of chromatin duplication. This type of cycle was first described in 1939 by Geitler, as occurring in the somatic cells of the insect Gerrislateralis (Painter and Reindorp, 1939; D''''''''''''Amato, 1964), and was named the endomitotic cycle because it develops within the nuclear envelop without either achromatic spindle formation or nuclear or cellular division (Nagl, 1970a; Brodsky and Uryvaeva, 1985). The term endomitosis is, however, generally used to describe the formation of both polyploid and polytene nuclei (q.v. Nagl, 1974). Nagl (1978, 1981, 1987) has suggested the term endocycle rather than endomitosis, and D''''''''''''Amato (1984) has adopted the term endomitotic and endoreduplication to distinguish between those that produce polyploid and polytene nuclei, respectively.

The endomitotic cycle (endomitosis) starts with a normal prophase (endoprophase), after which the chromosome contracts further (endometaphase), their sister chromatids separate from each other (endoanaphase) and decondense to assume the interphase nuclear structure, resulting in polyploid cells, with double the chromosome number (endopolyploidy) at the end of each cycle. The essential difference between endomitosis and the normal cell cycle is the absence of nuclear membrane dissolution in endomitosis, with the whole cycle occurring inside the nucleus. Such cycles have been observed in the anther tapetum of some angiosperm species, as in some Passiflora species and in Papaverrhoeas( Figure 1a).

The endoreduplication cycle differs from endomitosis because it results in polytene cells (cells with many identical paired chromatids). In the endoreduplication cycle, the chromatid number is duplicated, but they do not segregate, and after various endoreduplication cycles, larger and thicker chromosomes are produced, called polytenics. In the endoreduplication cycle, the condensation and decondensation stages are not evident (DAmato 1984, 1989), except in some cells where it is possible to see the chromocenter dispersion phase, known as the Z-phase (Nagl, 1970b, 1972; Cavallini et al., 1981). (Plant polytene chromosome, Gianna Maria Griz Carvalheira). *

*The full paper can be found in the final page.

*****

What interested me to conduct a research on Giant Chromosomes?

When reading the Qur`an during my teens, I encountered the sixth verse of surah Zumar and the eleventh verse of surah Shura. In these verses The Almighty God explains the human embryonic stages, and the word “An’aam” is used in this verse, which means cattle such as camel, sheep, cow etc. The use of the word “An’aam”  made me think that possibly almighty God did not mean the normal cattle, but possibly another type of creatures.

I went through many translations and interpretations of these Qur’anic verses, but they all considered “An’aam” to be normal cattle .None used another meaning, and because cattle does not fit to these verses, interpreters and translators have made up a translation to adjust the text!

When I was forty, a schematic shape of a pair of chromosomes in the Encyclopedia Britannica caught my eyes.The shape showed that it has two short arms as hands, two long arms as legs, and a central part(centromere) as original body, exactly as cattle(An’aam!). On that day I felt very happy because I finally found the original meaning of “An’aam” in those verses, after such a long time!

Why and how The Almighty God Has guided us to know the Giant Chromosomes?

By this discovery, only fifty percent of the problem or understanding of the verses was solved, because in the 6^th verse of surah Zomar, it mentions eight pairs of An’aam, meanwhile human chromosomes are 23 pairs. This, of course is an important point! Because if The Almighty God had told us that the 23 pairs of An’aam, everybody in today`s time, would immediately realize, that “An’aam” is chromosomes, without any use for human life!

But the Almighty God by mentioning eight pairs of An’aam, invited us to know what these 8 pairs of An’aam are, and encouraged us to think about them, to conduct research on them, to find about their characteristics, and use the results in our lives.

When The Almighty God describes Himself proudly as the highest at the top and the in end of the verses would not like to tell us about such insignificant matters which is written in the interpretations and translations of Qur’an!

Therefore, while He describes Himself in the verse as “flourisher of the universe” on the top of the verse, and “there is nothing like Him; and He is the All-Hearer and the All-Seer”, in the end of the verse, of course, He would like to announce us certainly a very important matter!

„خَلَقَكُم مِّن نَّفْسٍ وَاحِدَةٍ ثُمَّ جَعَلَ مِنْهَا زَوْجَهَا وَأَنزَلَ لَكُم مِّنَ الْأَنْعَامِ ثَمَانِيَةَ أَزْوَاجٍ ۚ يَخْلُقُكُمْ فِي بُطُونِ أُمَّهَاتِكُمْ خَلْقًا مِّن بَعْدِ خَلْقٍ فِي ظُلُمَاتٍ ثَلَاثٍ ۚ ذَٰلِكُمُ اللَّهُ رَبُّكُمْ لَهُ الْمُلْكُ ۖ لَا إِلَٰهَ إِلَّا هُوَ ۖ فَأَنَّىٰ تُصْرَفُونَ(Zumar :6) „

„فَاطِرُ السَّمَاوَاتِ وَالْأَرْضِ ۚ جَعَلَ لَكُم مِّنْ أَنفُسِكُمْ أَزْوَاجًا وَمِنَ الْأَنْعَامِ أَزْوَاجًا ۖ يَذْرَؤُكُمْ فِيهِ ۚ لَيْسَ كَمِثْلِهِ شَيْءٌ ۖ وَهُوَ السَّمِيعُ الْبَصِيرُ(Shura :11)”

Below, are the various translations of the above verses:

Traditional and old-fashioned translation (from King Fahad complex for the printing of the Holy Qur’an),

·        “He created you(all) from a single person(Adam) then made from him his wife [havva(Eve)]. And He has sent down for you of cattle eight pairs(of the sheep, two, male and female, of the goats, two, male and female, of the oxen, two, male and female, and of the camel, two, male and female). He creates you in the wombs of your mothers: creation after creation in three veils of darkness “  (Zumar verse 6)

·        “The creator of the heavens and the earth. He has made for you mates from yourselves, and for the cattle(also) mates. By this means He creates you(in the wombs)” (Shura verse 11)  

Modern translation (by Ali QuliQarai- Printed by Islamic college for advanced studies- London)

·        “ He created you from a single soul, then made from it its mate, and He has sent down for you eight mates of the cattle. He creates you in the wombs of your mothers, creation after creation, in a threefold darkness” (Zumar verse 6)

·        “The originator of the heavens and the earth, He made for you mates from your own selves, and mates of the cattle, by which means He multiplies you” (Shura verse 11) 

My translation

·        He created you from unique soul. Then organized of it its mate, and He sent down for you eight pairs of An’aam. He creates you in the wombs of your mothers, a creation after another creation in three stages of darkness.(Zumar verse 6)

·        “The flourisher of the universe, organized for you of yourselves mates and of An’aam pairs, He reduplicates you in it(An’aam) there is nothing like Him; and He is the All-Hearer and the All-Seer” (Shura verse 11)

Notes:

-         In the 11^th verse of surah Shura The Almighty God is clearly explaining the merging process of sexual chromosomes of man(X&Y) and of woman(X&X), and reduplication human embryo by this combined pair  chromosome, and the perfected and completed creation and prolongation of mankind, which He is proud of it.

-         Not only these two translations but all translations of Qur’an in every language has omitted the statement “He reduplicates you in it”, because translators can not understand the meaning of An’aam, then, they add the phrase “by this means” to complete the translation.

-         In the Qur`anic vocabulary, the heavens and the earth means the universe

-         “He sent down for you eight pairs of An’aam”. This statement is translated correctly in all translations, but none ask how God has sent us eight pairs of cattle from the heaven and why?

On the other hand, it is against scientific achievements!

-         In the traditional translations, translators would like to explain the eight pairs of cattle, but all of them explain only four pairs of cattle! As you can see in the first translation.

The situation and importance of Giant Chromosomes in modern Genetics.

From the  “Plant Polytene Chromosome”, which is a brief history of Giant Chromosomes with 80 reference articles, I understood the researches which have been conducted on Giant Chromosomes, considered them as Polytene Chromosomes. In this way, I knew why the title of Giant chromosomes could rarely be found on the net.

I also found the following information on the net. It shows Giant Chromosomes play an important role in therapy of many diseases. I underline the most important achievements below:

 

Scientists Analyze Chromosomes 2 and 4

NHGRI-Supported Researchers Discover Largest "Gene Deserts"; Find New Clues to Ancestral Chromosome Fusion Event

BETHESDA, Md., Wed., April 6, 2005 - A detailed analysis of chromosomes 2 and 4 has detected the largest "gene deserts" known in the human genome and uncovered more evidence that human chromosome 2 arose from the fusion of two ancestral ape chromosomes, researchers supported by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported today.

In a study published in the April 7 issue of the journal Nature, a multi-institution team, led by Washington University School of Medicine in St Louis, described its analysis of the high quality, reference sequence of chromosomes 2 and 4. The sequencing work on the chromosomes was carried out as part of the Human Genome Project at Washington University; Broad Institute of MIT, Cambridge, Mass.; Stanford DNA Sequencing and Technology Development Center, Stanford, Calif.; Welcome Trust Sanger Institute, Hinxton, England; National Yang-Ming University, Taipei, Taiwan; Genoscope, Evry, France; Baylor College of Medicine, Houston; University of Washington Multi mega base Sequencing Center, Seattle; U.S. Department of Energy (DOE) Joint Genome Institute, Walnut Creek, Calif.; and Roswell Park Cancer Institute, Buffalo, N.Y.

"This analysis is an impressive achievement that will deepen our understanding of the human genome and speed the discovery of genes related to human health and disease. In addition, these findings provide exciting new insights into the structure and evolution of mammalian genomes," said Francis S. Collins, M.D., Ph.D., director of NHGRI, which led the U.S. component of the Human Genome Project along with the DOE.

Chromosome 4 has long been of interest to the medical community because it holds the gene for Huntington's disease, polycystic kidney disease, a form of muscular dystrophy and a variety of other inherited disorders. Chromosome 2 is noteworthy for being the second largest human chromosome, trailing only chromosome 1 in size. It is also home to the gene with the longest known, protein-coding sequence - a 280,000 base pair gene that codes for a muscle protein, called titin, which is 33,000 amino acids long.

One of the central goals of the effort to analyze the human genome is the identification of all genes, which are generally defined as stretches of DNA that code for particular proteins. The new analysis confirmed the existence of 1,346 protein-coding genes on chromosome 2 and 796 protein-coding genes on chromosome 4.

As part of their examination of chromosome 4, the researchers found what are believed to be the largest "gene deserts" yet discovered in the human genome sequence. These regions of the genome are called gene deserts because they are devoid of any protein-coding genes. However, researchers suspect such regions are important to human biology because they have been conserved throughout the evolution of mammals and birds, and work is now underway to figure out their exact functions.

Humans have 23 pairs of chromosomes - one less pair than chimpanzees, gorillas, orangutans and other great apes. For more than two decades, researchers have thought human chromosome 2 was produced as the result of the fusion of two mid-sized ape chromosomes and a Seattle group located the fusion site in 2002.

In the latest analysis, researchers searched the chromosome's DNA sequence for the relics of the center (centromere) of the ape chromosome that was inactivated upon fusion with the other ape chromosome. They subsequently identified a 36,000 base pair stretch of DNA sequence that likely marks the precise location of the inactivate centromere. That tract is characterized by a type of DNA duplication, known as alpha satellite repeats, that is a hallmark of centromeres. In addition, the tract is flanked by an unusual abundance of another type of DNA duplication, called a segmental duplication.

"These data raise the possibility of a new tool for studying genome evolution. We may be able to find other chromosomes that have disappeared over the course of time by searching other mammals' DNA for similar patterns of duplication," said Richard K. Wilson, Ph.D., director of the Washington University School of Medicine's Genome Sequencing Center and senior author of the study.

In another intriguing finding, the researchers identified a messenger RNA (mRNA) transcript from a gene on chromosome 2 that possibly may produce a protein unique to humans and chimps. Scientists have tentative evidence that the gene may be used to make a protein in the brain and the testes. The team also identified "hypervariable" regions in which genes contain variations that may lead to the production of altered proteins unique to humans. The functions of the altered proteins are not known, and researchers emphasized that their findings still require "cautious evaluation."

In October 2004, the International Human Genome Sequencing Consortium published its scientific description of the finished human genome sequence in Nature. Detailed annotations and analyses have already been published for chromosomes 5, 6, 7, 9, 10, 13, 14, 16, 19, 20, 21, 22, X and Y. Publications describing the remaining chromosomes are forthcoming.

The sequence of chromosomes 2 and 4, as well as the rest of the human genome sequence, can be accessed through the following public databases:

GenBank (www.ncbi.nih.gov/Genbank) at NIH's National Center for Biotechnology Information (NCBI); the UCSC Genome Browser (www.genome.ucsc.edu) at the University of California at Santa Cruz; the Ensembl Genome Browser (www.ensembl.org) at the Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute; the DNA Data Bank of Japan (www.ddbj.nig.ac.jp);

and EMBL-Bank (www.ebi.ac.uk/embl/index.html) at EMBL's Nucleotide Sequence Database.

NHGRI is one of the 27 institutes and centers at NIH, an agency of the Department of Health and Human Services. The NHGRI Division of Extramural Research supports grants for research and for training and career development at sites nationwide. Additional information about NHGRI can be found at www.genome.gov.

For more information, contact:Geoff Spencer, NHGRI

(301) 402-0911- spencerg@mail.nih.gov

******

Human genome hits halfway mark

Human chromosomes: Cracking the human code has been a bit like painting a picture.Four years after publishing a draft of the human genetic sequence, researchers have hit the halfway mark in producing the "gold standard" version.

They have just published a detailed run-down of a 12th chromosome - known as chromosome five - which means there are just 12 left to complete.

Chromosome five is the largest so far, with 923 recorded genes, of which 66 are involved in human disease.

The chromosome, which was sequenced by US scientists, is detailed in Nature.

It is the second of three chromosomes that the Department of Energy Joint Genome Institute (JGI) has finalised in collaboration with colleagues at the Stanford Human Genome Center (SHGC)

Code breakers

Cracking the human code has been a bit like painting a picture. First comes a rough sketch followed by a slightly fuller version before, finally, the minute detail is added.

When the draft version of the human genome was unveiled in June 2000, 97% of the "book of life" had been read. Then, last year, scientists announced the decoding was almost 100% complete.

Now, several institutions around the world have divided up the 24 humanchromosomes - the cellular structures into which DNA is wound - and are going through them with a fine-tooth comb for a final time, to fill gaps and correct errors.

This extremely accurate sequence will be a powerful tool for scientists trying to understand human disease.

Spencer Abraham, Secretary of Energy

They are, as it were, dotting the I's and crossing the T's and giving the whole sequence a thorough spell-check.

"It is about getting everything in the right order," commented Dr Tim Hubbard, of the Human Genetics group at the Sanger Institute in Cambridge, UK.

"In the draft version there were 100,000 gaps in the whole genome. It was a small percentage of the sequence, but it meant you were uncertain about the order of the pieces.

"It is important for doing experiments to have the complete sequence - to have no gaps at all."

********

Giant chromosome

According to researchers at the JGI and SHGC, the landmark chromosome five is a genetic behemoth, containing key disease genes and a wealth of information about how humans evolved.

"This extremely accurate sequence will be a powerful tool for scientists trying to understand human disease," said US Secretary of Energy, Spencer Abraham.

DNA IN HUMAN CELLS

The double-stranded DNA molecule is held together by chemical components called basesAdenine (A) bonds with thymine (T); cytosine(C) bonds with guanine (G)

These letters form the "code of life". There are estimated to be about 2.9 billion base-pairs in the human genome wound into 24 distinct bundles, or chromosomes

Written in the DNA are about 30,000 genes, which human cells use as starting templates to make proteins. These sophisticated molecules build and maintain our bodies.

The giant chromosome is made up of 180.9 million letters - A's, T's, G's and C's that make up the genetic code.

Of the 923 genes that sit on chromosome five, 66 are known to be link to disease when they go wrong. Another 14 diseases seem to be connected to chromosome five genes, but they have not been linked to specific genes yet.

Having a detailed picture of chromosome five will be an immense help to researchers investigating these illnesses.

"It is very useful to have a base sequence which you can then compare individuals to," Dr Hubbard told BBC News Online.

"Then you can look for key differences between people that do have the disease and people that don't have the disease."

Another feature of chromosome five will pique the interest of scientists studying the difference between humans and chimpanzees.

Despite great similarities between the genomes of the two species, there are some key structural variations.

In particular, one large section of chromosome five is flipped backwards in humans compared with chimps.

Such an inversion makes it impossible for the two chromosomes to pair up during reproduction, which could have driven a wedge between the evolving ancestral populations.

'Junk' DNA

It is not just the genes in chromosome five that the scientists are interested in. Volumes of genetic materiallie in between the genes, which for a long time were dismissed as "junk" by researchers.

But on closer inspection, it seems this judgement was premature. The fact that sequences of junk were conserved for hundreds of generations suggests they have a function worth holding on to.

"Important genetic motifs gleaned from vast stretches of non-coding sequence have been found on chromosome five," said Eddy Rubin, JGI's director.

"Comparative studies conducted by our scientists of the vast gene desert... have shown these regions, conserved across many mammals, actually have a powerful regulatory influence."

Over the next few months, the remaining 12 human chromosomes should be completed to a final gold standard of accuracy.

Dr. Hubbard concluded: "Severalgroups are working on the remaining chromosomes - tidying them up - and they should all be complete by the end of the year."

Is it possible that Giant Chromosomes have brought life to Earth?

As I have stated , the sixth verse of surah Ana`m states that “God sent down for you eight pairs of An`am ”, as God is using the word “sent down”, He is possibly telling us that the primary source of life have arrived from interstellar space to Earth in eight pairs of chromosomes ,this also confirms modern scientific theories which state that the primary elements of life have been brought to Earth by comets.

It had been previously expected that the “Rosetta” research satellite in 2014 will have scientific achievements for us, but it seems that researchers have not still achieved a desired result. Because so far I have been unable to find the results of the mission.

Finally, we can also ask the question, are Giant Chromosomes responsible for turning the primitive man to the modern man? and if the answer is yes, then will this make Darwin`s evolutionary school in the context of anthropology crumble.

Note:

The complete Persian/Farsi text of this article(13 pages), since 2006 has been published in some of the famous Iranian Qur’anic websites under the title of: چهارپایان ویژه قرآنی

March 2015- Ahmad Shammazadeh- hmdshmzdeh@gmail.com

Attached paper:

                                     Plant Polytene Chromosome

Gianna Maria GrizCarvalheira

Laboratَrio de Citogenética Vegetal, ءrea de Genética, Departamento de Biologia, UFRPE, 52171-030 Recife, PE, Brasil. E-mail: carva@elogica.com.br

INTRODUCTION

Polytene chromosomes are structures found in highly specialized tissues in some animal and plant species, which are amplified through successive cycles of endoreduplication, finally producing several copies of each chromosome. For this reason, they have been very important in elucidating chromosome fine structure and physiology, especially in diptera.

In plants, polytene chromosomes have been observed in only a few species, and seemed to be restricted to ovary and immature seed tissues, e.g., in Phaseoluscoccineus and P. vulgaris (Nagl, 1981), until relatively recently, when they were observed in the cells of the anther tapetum of Vignaunguiculata (Guerra and Carvalheira, 1994) and of some Phaseolus species (Carvalheira and Guerra, 1994). With the discovery of the polytenics in tapetum tissue, it was observed that in many other species of various angiosperm families the tapetal cells also display polytene, polyploid or both types of nuclei. In some species of Phaseolus and Vigna the polytenics are more clearly defined and, therefore, better suited to the study of this type of chromatin organization. It is, however, important to differentiate between the nuclear cycles that result in polyploid nuclei and those that produce polytene nuclei, because these two terms of the nuclear types are often used indiscriminately in the literature. In this paper some aspects of the occurrence of plant polytenes will be summarized along with the structure and function of these chromosomes.

ENDOMITOSIS AND ENDOREDUPLICATION

Nagl et al. (1985) described polytene chromosomes as giant chromosomes produced by changes in the mitotic cycle during the interphase stage. In such a modified nuclear cycle, the chromatin duplicates its DNA content during the G1 and S stages, but, instead of passing to the G2 stage, the nucleus initiates a new G1 phase, thus starting a new cycle of chromatin duplication. This type of cycle was first described in 1939 by Geitler, as occurring in the somatic cells of the insect Gerrislateralis (Painter and Reindorp, 1939; D''''''''''''Amato, 1964), and was named the endomitotic cycle because it develops within the nuclear envelop without either achromatic spindle formation or nuclear or cellular division (Nagl, 1970a; Brodsky and Uryvaeva, 1985). The term endomitosis is, however, generally used to describe the formation of both polyploid and polytene nuclei (q.v. Nagl, 1974). Nagl (1978, 1981, 1987) has suggested the term endocycle rather than endomitosis, and D''''''''''''Amato (1984) has adopted the term endomitotic and endoreduplication to distinguish between those that produce polyploid and polytene nuclei, respectively.

The endomitotic cycle (endomitosis) starts with a normal prophase (endoprophase), after which the chromosome contracts further (endometaphase), their sister chromatids separate from each other (endoanaphase) and decondense to assume the interphase nuclear structure, resulting in polyploid cells, with double the chromosome number (endopolyploidy) at the end of each cycle. The essential difference between endomitosis and the normal cell cycle is the absence of nuclear membrane dissolution in endomitosis, with the whole cycle occurring inside the nucleus. Such cycles have been observed in the anther tapetum of some angiosperm species, as in some Passiflora species and in Papaverrhoeas( Figure 1a ).

The endoreduplication cycle differs from endomitosis because it results in polytene cells (cells with many identical paired chromatids). In the endoreduplication cycle, the chromatid number is duplicated, but they do not segregate, and after various endoreduplication cycles, larger and thicker chromosomes are produced, called polytenics. In the endoreduplication cycle, the condensation and decondensation stages are not evident (DAmato 1984, 1989), except in some cells where it is possible to see the chromocenter dispersion phase, known as the Z-phase (Nagl, 1970b, 1972; Cavallini et al., 1981).

Depending on the behavior of the sister chromatids, polytene nuclei can be divided into two structural types. The first, and most well studied, are the chromosomes of the larval cells of Drosophila, Chironomidae and other diptera (Ashburner, 1970; Brodsky and Uryvaeva, 1985). These polytenics are characterized by numerous transverse bands along their linear axis, produced by the exact pairing of sister chromatids and the intimate association of their chromomeres (Ashburner, 1970). The somatic pairing of homologous chromosomes gives the false impression that there has been a decrease in chromosome number, because each nucleus appears to contain the haploid number of giant chromosomes.

The other structural type of polytene nuclei also has the grouping of sister chromatid bundles resulting from several endoreduplication cycles, but in this case is characterized by the lack of any intimate pairing of the chromatids ( Figure 1b ). This nucleus type is observed more frequently, typical examples being found in the gianttrophoblast cells of mammals (Nagl, 1985), the trophocit cells of many insects (Painter and Reindorp, 1939), some ovary tissues during the development of many angiosperms (Corsi et al., 1973; Nagl, 1976) and in the anther tapetum of some plant species (D''''''''''''Amato, 1984; Guerra and Carvalheira, 1994; Carvalheira and Guerra, 1994, 1998). In these nuclei, which can be recognized both by the large size of their chromocenters and by the diploid number of polytene chromosomes, the chromosome number does not appear to be reduced as in polytene-type nuclei. Another peculiar giant chromosome type, which likewise does not present somatic pairing, has been found in some ciliates (e.g., Stylonychiamytilus) that have a macronucleus with polytene chromosomes and a diploid micronucleus (Ammermann, 1971; Ammermann et al., 1974). The polytenics of these ciliates display band and interband patterns (also seen in Drosophila), but the macronucleus disintegrates after its development while the micronucleus remains active.

It is interesting to note that the endocycles are not processes of cell multiplication but are associated with cell differentiation and seem to be genetically controlled, with both endopolyploidy and polyteny leading to cell specialization in certain tissues. These nuclei have generally been observed in ephemeral tissues made up of only a few cells with intense metabolic activity, the main function of which is to provide nutritional support to vital organs during certain periods of development (e.g., the larval salivary glands of insects, the mammalian trophoblasts and the embryo suspensor cells of angiosperms). In such tissues, the cytoplasmatic volume and nuclei DNA content of the cells are increased by endomitosis or endoreduplication cycles (Nagl, 1974, 1985; Nagl et al., 1985).

OCCURRENCEOF POLYTENE CHROMOSOMES

Polytene nuclei were first observed in the larval salivary glands of Chironomidae, by Balbiani in 1881, but only at the beginning of the 1930s did Heitz and Bauer & Painter, independently and simultaneously, rediscover these enormous nuclei in the Malpighian tubules of Bibiohortulanus and in the larval salivary glands of Drosophila melanogaster, respectively (Ashburner, 1970). A few years later, Koltzoff, in 1934, and Bauer, in 1935, proposed the term polytenics for the giant chromosomes observed in these nuclei (Ashburner, 1970); polytene cells have since been described in many species (Nagl, 1978; Brodsky and Uryvaeva, 1985; Carvalheira and Guerra, 1998).

In plants, the first giant nuclei were observed by Osterwalder in 1898, in the enormous antipodal cells (antipodes) of the embryo sac of Aconitum (Nagl, 1981). However, as with the discovery of the giant cells of Chironomidae, the antipodal nuclei were largely forgotten for about 60 years. Only in 1956 did Tschermack-Woess and collaborators, during a reappraisal of the genus Aconitum genus and other plant species, recognize that the chromosomes observed in the antipodes were polytenics (Nagl, 1981). Unlike Drosophila polytene chromosomes, which present numerous bands and interbands, plant polytenics have a granular and fibril structure with no distinct bands (see Figure 1 ). This structure probably occurs because of the absence of intimate synapsis between the sister chromatids. It is also believed that the chromocenter dispersion phase (Z phase) has some influence on the morphology of plant polytenics, as it results in a slight separation of these chromatids (Nagl, 1970a). However, Nagl (1969a) has reported that in Phaseolus vulgaris the structure of polytene chromosomes of embryo suspensor cells seems to be altered when these cells are submitted to low temperatures, becoming partly compacted and forming bands similar to those seen in Drosophila. Such results have not been observed again, remaining the only report of plant polytenics with bands and interbands.

Since the discovery of the polytene nuclei in antipodes, many other tissues composed of polytene cells have also been described ( Table I ). It is interesting to note that, until very recently, the cells with polytene chromosomes seemed to be limited to ovary tissues (antipodal cells, synergids, endosperm and embryo suspensor cells); however, polytenics have now been observed in anther hair, glandular hair and anther tapetal cells ( Table I ).

Polyteny can also be induced in vitro and it has been found that the meristematic tissues of root tips and the cotyledon cells of some plant species are able to form polytene chromosomes when submitted to specific treatments, including high temperatures (Shang and Wang, 1991) or an appropriate amount of certain growth regulators (mainly auxin and cytocinin) in the medium (Marks and Davies, 1979; Therman and Murashige, 1984).

POLYTENE CHROMOSOMES OF EMBRYO SUSPENSOR

The most widely studied plant tissues with polytene cells is the Phaseolus embryo suspensor tissue. This tissue is found in the developing ovary of several angiosperm species (Esau, 1974). In P. coccineus and P. vulgaris, the suspensor is composed of about 200 cells, distributed between the basal and junction regions. The basal region is formed of about 20 giantmononucleate cells with a high level of polytenization, and with the DNA content of some cells being up to 8.192 C (Brady, 1973a,b). The junction region is composed of about 180 cells linking the basal region to the embryo proper. This last region possesses polyploid cells and/or cells with low polyteny level (Brady and Clutter, 1974).

The embryo suspensor provides nutritional support for the immature embryo, supplying proteins or synthesizing the substances necessary for embryo development (Schulz and Jensen, 1969). The underdevelopment of the cell wall of suspensor cells and their other structural characteristics indicate their secretory function in transporting nutrients through their membranes to the embryo (Nagl, 1974; Cionini, 1987). Analyses of the growth regulator level and transcription activity indicate that the suspensor tissue may play an important role during embryo ontogenesis, and seems to have a function in the synthesis of phytohormones needed for embryo development (Walbot et al., 1972; Clutter et al., 1974; Alpi et al., 1975; Cionini et al., 1976; Lorenzi et al., 1978).

The basal cells of the embryo suspensor tissue of P. coccineus display 22 polytene chromosomes that are up to 30 times larger than the mitotic ones (Nagl, 1974), the 11 chromosome pairs having been identified earlier by their heteropycnosis pattern (Nagl, 1967). All mitotic chromosomes present heterochromatic centromeric bands and some weak interstitial and terminal ones (Schweizer and Ambros, 1979). Staining with the fluorochromes CMA and DAPI has revealed that most of these bands are CMA+, although unlike mitotic bands they contain a small amount of DAPI+ heterochromatin (Schweizer, 1976). The difference observed in the fluorescent pattern has been attributed to the better structural resolution of the giant chromosomes.

In situ hybridization experiments, with isotopic (q.v. Schumann et al., 1990) and non-isotopic markers (q.v. Nenno et al., 1994), have contributed considerably to the characterization of polytenics. These techniques have permitted both the location of many of their DNA sequences and the study of their replication cycle (Brady and Clutter, 1974). For example, the cytolocalization of the ribosomal genes in P. coccineus has been demonstrated by the use of RNAr-H3, revealing RNA puff activity both in satellite pairs and in the heterochromatin of chromosome pairs, without satellites (Avanzi et al., 1971, 1972; Durante et al., 1977). Isotopic techniques have also made it possible to observe the extra nucleoli associated with the telomeres of the polytenics without satellites, suggesting the existence of amplification in this region (Nagl, 1973). Actually, the extra DNA synthesis in the polytenics of the Phaseolus suspensor occurs at the beginning of embryogenesis and not simultaneously with the endoreduplication cycles (Avanzi et al., 1970). Such gene amplification can occur both in the ribosomal cistrons and other regions of the genome and involves some polytene chromosome chromatids (Cremonini and Cionini, 1977). Some of these amplified regions are released from the polytenics to form micronucleoli. According to Avanzi et al. (1971), the micronucleoli are composed of a spherical mass of ribonucleoprotein covered by a layer of DNA. These micronucleoli seem to be associated with the intense metabolism of the suspensor basal cells (Nagl, 1973).

With advances in the fluorescence in situ hybridization technique (FISH), several other sequences have been located in plant polytene chromosomes. The first genic sequence hybridized in polytenics was that of the phaseolin group (Schumann et al., 1990; Nenno et al., 1993, 1994). This gene encodes the main seed storage protein of Phaseolus species. In these papers, it was demonstrated that the phaseolin gene seems to be located in chromosome 7 of P. coccineus. Another gene that has been located in the polytenics of P. vulgaris is the PGIP gene which encodes for polygalacturonase-inhibiting protein, a cell wall protein that specifically inhibits fungal endopolygalacturonases that are important during the early stages of plant pathogenesis. The PGIP gene has been located in a single region of the pericentromeric heterochromatin of the chromosome pair X, next to the euchromatin (Frediani et al., 1993).

The FISH technique as applied in polytene chromosomes has also been a useful tool to study gene evolution. Nagl (1991) hybridized telomeric DNA and the aromatase gene sequence (both from human genome) in P. coccineus and P. vulgaris polytenics. The results showed that these sequences also hybridize with plant chromosomes, supporting the hypothesis of the evolutionary conservation of important coding or non-encoding sequences throughout living organisms.

POLYTENE CHROMOSOMES OF ANTHER TAPETUM

Polytene chromosomes are also observed in other plant tissues, of which the anther tapetum tissue has made valuable contributions to the understanding of polytenics in angiosperms. This tissue is widely conserved, being found in groups ranging from bryophytes to angiosperms (Pacini and Franchi, 1993).

The tapetum is the innermost layer of the anther wall in close contact with the pollen grains ( Figure 1c ). It is generally composed of a simple layer of cells, characterized by the presence of dense cytoplasm and quite a well-developed nucleus (Echlin, 1971). During the differentiation of the tapetum, the cells increase both their cytoplasmatic and nuclear volume and then undergo autolysis and degenerate (Mascarenhas, 1990). The tapetum''''''''''''s function seems to be related to the maturation of pollen grain, with biochemical and cytological studies demonstrating the intense metabolic activity in its cells at the end of the tetrad stage and during exine formation (Rowley, 1993).

Until recently, most of the information on the nuclear development of the tapetal cells has come from studies of anther ontogenesis, based on histological analyses by optical or electronic microscopy. Cytological analyses in tapetum were done mainly by Cooper (1933), Brown (1949), Oksala and Therman (1977), Franceschi and Horner (1979), and D''''''''''''Amato (1984, 1989). However, cytogenetical analysis of the tapetal cells of Vigna species has revealed that this tissue can present very peculiar characteristics (Guerra and Carvalheira, 1994). Anther tapetum cells are characterized by the presence of endomitotic or endoreduplication cycles (Cooper, 1933; D''''''''''''Amato, 1984, 1989; Malallah et al, 1996). In species where the tapetum layer is composed of mononucleate cells, the increase in DNA content is generally a consequence of several endoreduplication cycles, while in species with bi- or multinucleate cells in the tapetum it is the endomitotic cycle which is responsible. In spite of the endoreduplication cycle producing mononucleate cells, tapetalbinucleate cells with polytene nuclei have sometimes been observed (Carvalheira and Guerra, 1994).

In general, at the beginning of meiosis, the tapetal cells are mononucleate and diploid. During the tapetal differentiation, three cellular types can be observed, i.e. multinucleate cells, with more than one diploid nucleus (Malallah et al., 1996), mononucleate cells, with a single polyploid nuclei (Carvalheira, G.M.G. and Guerra, M., unpublished data), and mono- or binucleate cells, with one or two polytene nuclei (Carvalheira and Guerra, 1994). In each of these cases, the DNA content per cell is often increased, suggesting that this tissue needs several copies of most genes to supply specific substances for exine development and consequent pollen grain maturation.

The increase in the ploidy level is probably caused either by suppression of anaphase movement (producing a dumbbell-shaped polyploid interphase nucleus) or by the occurrence of endomitotic cycles (DAmato, 1989), while the increase in the number of nuclei per cell is due to the occurrence of one or more mitosis cycles without cytokinesis, resulting in multinucleate cells. Polytene nuclei, on the other hand, are formed through the endoreduplication cycles, and could remain in the interphase stage until the S phase, or progress to the prophase stage and return to a new G1 phase (Guerra and Carvalheira, 1994).

Analysis of both ploidy level and nuclear structures in tapetal cells in genera of several subfamilies has revealed that their chromatin structure may be constant at the genus level. In the family Scrophulariaceae, for example, some species of the genera Pedicularis and Melampyrum have tapetal cells with tetraploid nuclei, in the post-meiotic period. On the other hand, in this same family, the genera Odontetis, Euphrasia and Bellardia have nuclei with enormous chromocenters, but with the same ploidy level (Greilhuber, 1974).

Like the other plant tissue with polytene chromosomes, anther tapetum cells can display polytenics that vary in structure and morphology from species to species (q.v. Nagl, 1974, 1981; Carvalheira and Guerra, 1994, 1998). For example, polytene nuclei in the antipodes of Papaverrhoeas were classified by Nagl (1981) into four different types, i.e., nuclei with chromocenters associated with radial chromatin bundles; decondensed nuclei with isolated chromatin fibers; nuclei with condensed chromatin, and nuclei with polytenics proper. Similar variation was found in suspensor cells of Phaseolus embryos, where the polytenics sometimes had granular or fibril form, depending on the degree of contraction in the interchromomeres (Nagl, 1978).

According to Carvalheira and Guerra (1998), the chromatin structure of the polytene nuclei in tapetal cells may basically be divided into three different types:

1. Individualized polytene chromosomes whose chromatin bundles are heteropycnotic in the proximal region and dispersed in the distal region ( Figure 1d ), characteristic of Phaseoluscoccineus, P. vulgaris (Carvalheira and Guerra, 1994), Vignaunguiculata (Guerra and Carvalheira, 1994; Carvalheira and Guerra; 1998), V. umbellata, V. radiata (Carvalheira and Guerra, 1998), Lathyrus and Sesbaniamarginata.

2. Polytene nuclei with chromocenters associated with the chromatin bundles ( Figure 1e ), found in most of the species analyzed, including Arachishypogeae, Caesalpineaechinata, Clitoriacajanifolia, Crotalaria retusa, in three Habenaria species, Luffacylindrica, Macroptiliumpeduncularis, two Phaseolus species (Carvalheira and Guerra, 1994), Pithecellobiumdulce, Pisumsativum, Sophoratomentosa, Tropaeolummajus and Zomicarpariedeliana.

3. Polytene nuclei with chromocenters unassociated with chromatin bundles ( Figure 1f ), a less frequent type, characteristic of Genipaamericana, Indigoferahirsuta, Lupinuspolyphyllus, Vignavexillata (Carvalheira and Guerra, 1998) and Vicia sp.

Of these three types of chromatin organization, only the first is ideal for karyological analyses. The polytenics of this group is generally individualized and condensed. This type of chromatin organization has allowed good chromosome spreads to be obtained, facilitating the chromosome counting. In most Phaseolus and Vigna species analyzed that had this type of organization, it was possible to observe all 22 chromosomes of the karyotype (q.v. Guerra and Carvalheira, 1994; Carvalheira and Guerra, 1994).

Although this type of chromatin organization seems to be ideal for karyological analyses, these polytene chromosomes are somewhat smaller than those observed in the embryo suspensor of Phaseolus or those of some other genera (compare Figure 1b and d ). The largest polytenics of the anther tapetal cells (observed in Vignaunguiculata) are about 3.5 times bigger than the mitotic ones (Guerra and Carvalheira, 1994). The difference in size observed between polytenics of the embryo suspensor and anther tapetum is probably related to the number of endoreduplicated cells present in each of these tissues. As was mentioned previously, only a few basal cells undergo many endoreduplication cycles in the embryo suspensor tissue (Nagl, 1981), while in the anther tapetum hundreds of cells undergo this process. The low level of chromatin endoreduplication associated with a large number of cells seems to satisfy the metabolic necessities of both the anther tapetum and microspores. On the other hand, in the giant cell of the embryo suspensor, many endoreduplication cycles seem to be necessary to maintain the perfect functional and nutritional stage of the embryo, most of whose nutrients are supplied by the suspensor cell.

Although the polytenics of the anther tapetum are reduced in size, they have helped in the cytolocalization of DNA sequences. The first in situ hybridization in tapetalpolytenics has revealed interesting data different from that which was observed in the polytene chromosomes of the embryo suspensor (Guerra and Kenton, 1996). As stated earlier, after in situ hybridization with the human telomere DNA probe, Nagl (1991) observed that the embryo suspensor polytenics of Phaseolus show a group of dots or compact bands at the telomeres. However, when synthetic telomere oligomers were hybridized with tapetumpolytenics in an amphidiploid hybrid of Phaseolus, the oligo was preferentially located at, or close to, the chromocenters. These fluorescent areas were distributed randomly in the nuclear area, although association with the nuclear boundary was never observed (Guerra and Kenton, 1996). This may suggest that, at least in some aspects, the basic molecular organization of diploid nuclei in the anther tapetum is not completely conserved after the endoreduplication cycles. In fact, the loss of telomere association with the nuclear membrane has been documented in some special chromosome types, such as pigeon lampbrush chromosomes (Solovei and Macgregor, 1995) and Dipterapolytenic chromosomes (Agar and Sedat, 1983). In plant polytene nuclei, however, this loss of telomeric association with the nuclear envelope was reported for the first time in anther tapetumpolytenics (Guerra and Kenton, 1996).

These chromosomes have also helped in the identification of the 45S ribosomal sites in Phaseoluscoccineus and Vignaunguiculata (Guerra et al., 1996), and 5S sites, in V. radiata and V. unguiculata (Carvalheira et al., 1998). In P. coccineus, six ribosomal sites were observed in tapetal cells, as has been reported previously (see Avanzi et al., 1972; Durante et al., 1977). Surprisingly, however, ten ribosomal sites were observed in V. unguiculatatapetumpolytenics (Guerra et al., 1996), instead of one or two pairs as earlier reported (Frahm-Leliveld, 1965; Barone and Saccardo, 1990; Galasso et al., 1992). The large number of ribosomal sites observed in V. unguiculata when compared with Phaseolus has suggested that this increase in ribosomal sites may have been initiated by genetic mechanisms, such as gene conversion. According to Guerra et al. (1996), the variation in the number of rDNA sites observed between species of related taxa could be due to the differential amplification and fixation of rDNA sequences at different chromosomal sites. On the other hand, four 5S ribosomal sites were observed in V. radiata and V. unguiculata (Carvalheira et al., 1998), confirming the previous reports for V. unguiculata (Galasso et al., 1995), although these reports were first published for V. radiata.

In conclusion, although the polytenics of the anther tapetum are smaller than those in suspensor cells, both the large number of polytene cells in this tissue and their structural polytene morphology make these chromosomes more convenient for the study of plant polyteny and chromosome organization. Guerra and Carvalheira (1994) and Carvalheira and Guerra (1994, 1998) have suggested that such chromosomes present cycles of diffuse and condensed stages. The change from diffuse to condensed stage seems to depend on the endoreduplication level, genetic background and environmental factors. All these observations suggest that bundled polytene chromosomes of plants, at least in tapetal cells, are most probably the consequence of advanced endoreduplication cycles resulting in prophase or prophase-like chromosomes that may still be able to perform some DNA and RNA synthesis (Brady and Clutter, 1974; Cionini et al, 1982).