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Is DNA a single molecule or 46 separate pieces (out of 23 chromosome pairs)?

Is DNA a single molecule or 46 separate pieces (out of 23 chromosome pairs)?


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It seems that biology books refer to DNA as 'a' molecule (implying that it is a single continuous uninterrupted double strand)… but in those same books chromosomes are depicted as 23 separate objects (chromosome pairs) containing DNA. Are these illustrations misleading ? Are chromosomes somehow connected end-to-end or are they disjoint ? Is it a single noodle or is it 46 pieces ?


Unbroken strands of DNA are single molecules. So Yes, DNA is a molecule. However, the sequence of nucleotides allow for a near infinite variety. So unlike other molecules, like collagen, or water, they cannot be characterized with a unique descriptive name, other than by their sequence. I think this is the cause for confusion, because in this sense, DNA is a class of molecules, and we don't generally give them names. Each chromosome has two unique DNA molecules in diploid organisms (except in rare cases of highly inbred individuals where the two molecules might be identical). So if you have 23 chromosomes, you have 46 DNA molecules in each cell nucleus.


When a book talks about "the DNA of a cell" it is talking about all the DNA molecules which are contained in the cell.

The DNA in a cell exists as separate objects called chromosomes, each of which is usually described as a single long molecule of DNA. (The long molecule has two strands, and coils up around many copies of special protein molecules.)

The chromosomes of a cell are separate, and do not have DNA running between them.


Detection of Circulating Tumor DNA with a Single-Molecule Sequencing Analysis Validated for Targeted and Immunotherapy Selection

Comprehensive genetic cancer profiling using circulating tumor DNA has enabled the detection of National Comprehensive Cancer Network (NCCN) guideline-recommended somatic alterations from a single, non-invasive blood draw. However, reliably detecting somatic variants at low variant allele fractions (VAFs) remains a challenge for next-generation sequencing (NGS)-based tests. We have developed the single-molecule sequencing (SMSEQ) platform to address these challenges.

Methods

The OncoLBx assay utilizes the SMSEQ platform to optimize cell-free DNA extraction and library preparation with variant type-specific calling algorithms to improve sensitivity and specificity. OncoLBx is a pan-cancer panel for solid tumors targeting 75 genes and five microsatellite sites analyzing five classes of NCCN-recommended somatic variants: single-nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), fusions and microsatellite instability (MSI). Circulating DNA was extracted from plasma, followed by library preparation using SMSEQ. Analytical validation was performed according to recently published American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines and established the limit of detection (LOD), sensitivity, specificity, accuracy and reproducibility using 126 gold-standard reference samples, healthy donor samples verified by whole-exome sequencing by an external College of American Pathologists (CAP) reference lab and cell lines with known variants. Results were analyzed using a locus-specific modeling algorithm.

Results

We have demonstrated that OncoLBx detects VAFs of ≥ 0.1% for SNVs and indels, ≥ 0.5% for fusions, ≥ 4.5 copies for CNVs and ≥ 2% for MSI, with all variant types having specificity ≥ 99.999%. Diagnostic performance of paired samples displays 80% sensitivity and > 99.999% clinical specificity. Clinical utility and performance were assessed in 416 solid tumor samples. Variants were detected in 79% of samples, for which 87.34% of positive samples had available targeted therapy.

This article outlines the creation and rigorous validation of a novel single-molecule sequencing (SMSEQ) platform and a custom gene panel covering 75 genes and five microsatellite site markers for diagnosis of cancer and therapy selection.
We assay National Comprehensive Cancer Network (NCCN) guideline-recommended somatic genomic alterations for solid tumors using a single, non-invasive blood draw.
The platform analyzes, and we report the validation of, five classes of somatic variants: single-nucleotide variants, insertions and deletions, copy number variants, fusions, and microsatellite instability.

Abstract

The double stranded DNA molecule undergoes drastic structural changes during biological processes such as transcription during which it opens locally under the action of RNA polymerases. Local spontaneous denaturation could contribute to this mechanism by promoting it. Supporting this idea, different biophysical studies have found an unexpected increase in the flexibility of DNA molecules with various sequences as a function of the temperature, which would be consistent with the formation of a growing number of locally denatured sequences. Here, we take advantage of our capacity to detect subtle changes occurring on DNA by using high throughput tethered particle motion to question the existence of bubbles in double stranded DNA under physiological salt conditions through their conformational impact on DNA molecules ranging from several hundreds to thousands of base pairs. Our results strikingly differ from previously published ones, as we do not detect any unexpected change in DNA flexibility below melting temperature. Instead, we measure a bending modulus that remains stable with temperature as expected for intact double stranded DNA.


DNA is transcribed into RNA, which is translated to form proteins

Francis Crick coined the phase “the Central Dogma” to describe the flow of information from nucleic acid to protein. Information encoded in DNA is transcribed to a similar alphabet called RNA (still four letters only, but not quite the same four letters as DNA). RNA is translated to a linear sequence of amino acids in protein. This video gives a concise overview of the central dogma of molecular biology:

We will go into more detail about gene expression later in the course.

Your chromosomes provide the instructions for how your body will develop before you’re born, and how it will function as you grow. Typically, humans are born with 23 pairs of chromosomes (46 chromosomes in total). Human chromosomes 1 through 22 are called autosomes, and the final or 23rd chromosome is a pair of sex chromosomes, so-called because they determine the biological sex of the human.

Recall that half of your chromosomes come from your mother and half come from your father. Through a process called meiosis each of your parents creates a sex cell (either a sperm or an egg) that contains half of their chromosomes. When the sperm cell and the egg cell combine, they create a zygote that contains 46 chromosomes.


Cell division: mitosis and meiosis

Cell division cycle, figure from Wikipedia. Cells that stop dividing exit the G1 phase of the cell cycle into a so-called G0 state.

Cells reproduce genetically identical copies of themselves by cycles of cell growth and division. The cell cycle diagram on the left shows that a cell division cycle consists of 4 stages:

  • G1 is the period after cell division, and before the start of DNA replication. Cells grow and monitor their environment to determine whether they should initiate another round of cell division.
  • S is the period of DNA synthesis, where cells replicate their chromosomes.
  • G2 is the period between the end of DNA replication and the start of cell division. Cells check to make sure DNA replication has successfully completed, and make any necessary repairs.
  • M is the actual period of cell division, consisting of prophase, metaphase, anaphase, telophase, and cytokinesis.

Chromosomes

Chromosomes were first named by cytologists viewing dividing cells through a microscope. The modern definition of a chromosome now includes the function of heredity and the chemical composition. A chromosome is a DNA molecule that carries all or part of the hereditary information of an organism. In eukaryotic cells, the DNA is packaged with proteins in the nucleus, and varies in structure and appearance at different parts of the cell cycle.
Chromosomes condense and become visible by light microscopy as eukaryotic cells enter mitosis or meiosis. During interphase (G1 + S + G2), chromosomes are fully or partially decondensed, in the form of chromatin, which consists of DNA wound around histone proteins (nucleosomes).

In G1, each chromosome is a single chromatid. In G2, after DNA replication in S phase, as cell enter mitotic prophase, each chromosome consists of a pair of identical sister chromatids, where each chromatid contains a linear DNA molecule that is identical to the joined sister. The sister chromatids are joined at their centromeres, as shown in the image below. A pair of sister chromatids is a single replicated chromosome, a single package of hereditary information.

Human karyotype “painted” using fluorescent DNA probes. These mitotic chromosomes each consist of a pair of sister chromatids joined at their centromeres. The images of the homologous chromosome pairs (e.g., 2 copies of chromosome 1) have been lined up next to each other. Image from Bolzer et al., (2005) Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes. PLoS Biol 3(5): e157 DOI: 10.1371/journal.pbio.0030157

Ploidy
Humans are diploid, meaning we have two copies of each chromosome. We inherited one copy of each chromosome from other mother, and one copy of each from our father. Gametes (sperm cells or egg cells) are haploid, meaning that they have just one complete set of chromosomes.
Chromosomes that do not differ between males and females are called autosomes, and the chromosomes that differ between males and females are the sex chromosomes, X and Y for most mammals. Humans most commonly have 22 pairs of autosomes and 1 pair of sex chromosomes (XX or XY), for a total of 46 chromosomes. We say that humans have 2N = 46 chromosomes, where N = 23, or the haploid number of chromosomes.
Cells with complete sets of chromosomes are called euploid cells with missing or extra chromosomes are called aneuploid. The most common aneuploid condition in people is variation in the number of sex chromosomes: XO (having just one copy of the X), XXX, or XYY. Having no X chromosome results in early embryonic death.
The two copies of a particular chromosome, such as chromosome 1, are called homologous. The karyotype image above shows the homologous pairs for all the autosomes. Homologous chromosomes are not identical to each other, unlike sister chromatids. They frequently have different variants of the same hereditary information – such as blue eye color vs brown eye color, or blood type A versus blood type B.
Mitosis
Mitosis produces two daughter cells that are genetically identical to each other, and to the parental cell. A diploid cell starts with 2N chromosomes and 2X DNA content. After DNA replication, the cells is still genetically diploid (2N chromosome number), but has 4X DNA content because each chromosome has replicated its DNA. Each chromosome now consists of a joined pair of identical sister chromatids. During mitosis the sister chromatids separate and go to opposite ends of the dividing cell. Mitosis ends with 2 identical cells, each with 2N chromosomes and 2X DNA content. All eukaryotic cells replicate via mitosis, except germline cells that undergo meiosis (see below) to produce gametes (eggs and sperm).

  • prophase – chromosomes condense each chromosome consists of a pair of identical sister chromatids joined at the centromere.
  • metaphase – chromosomes line up at the middle of the cell, along the plane of cell division, pushed and pulled by microtubules of the spindle apparatus
  • anaphase – sister chromatids separate and migrate towards opposite ends of the cell
  • telophase – chromatids cluster at opposite ends of the cell and begin to decondense
  • cytokinesis – the membrane pinches in to divide the two daughter cells

Here is a simplified diagram illustrating the overall process and products of mitosis:

Source: Wikimedia Commons (https://commons.wikimedia.org/wiki/File:MajorEventsInMeiosis_variant_int.svg)

Questions or points to ponder or note about the figure above (answers at bottom of page):

  1. are the two daughter cells the same or different from each other, and from the parent cell at the start?
  2. why does the cartoon illustration of the chromosomes change (from a single rod to joined double rods) after DNA replication, and again (back to single rods) during mitosis?
  3. does the figure show 2 different chromosomes or a single pair of homologous chromosomes?
  4. can haploid cells undergo mitosis? what about triploid cells (cells that have 3N chromosomes)?

This animation below shows the packaging of DNA and condensation of chromosomes as a cell undergoes mitosis.

The video narration has a major error at time 1:22: chromosomes exist throughout the entire cell cycle (at all times in a cell’s life) they are visible in their condensed form only during mitosis and meiosis.

Meiosis

This is a special sequence of 2 cell divisions that produces haploid gametes from diploid germline cells. It starts with a diploid cell that has undergone chromosomal DNA replication: 2N chromosomes, 4X DNA content. Two successive divisions, with no additional DNA replication, results in 4 haploid gametes: 1N chromosomes, 1X DNA content.
NOVA has a good interactive side-by-side comparison of mitosis and meiosis on this page: How cells divide
Meiosis sets the stage for Mendelian genetics. Students need to know that most of the genetics action occurs in the first meiotic division:

  • homologous chromosomes pair up and align end-to-end (synapsis) in prophase I
  • crossing over occurs between homologous chromosomes in prophase I, before chromosomes line up at the metaphase plate
  • homologous chromosomes separate to daughter cells (sister chromatids do not separate) in the first division, creating haploid (1N) cells
  • the separation of each pair of homologous chromosomes occurs independently, so all possible combinations of maternal and paternal chromosomes are possible in the two daughter cells – this is the basis of Mendel’s Law of Independent Assortment
  • the first division is when daughter cells become functionally or genetically haploid

The last point appears to be the most difficult for students to grasp. Consider the X and Y chromosomes. They pair in prophase I, and then separate in the first division. The daughter cells of the first meiotic division have either an X or a Y they don’t have both. Each cell now has only one sex chromosome, like a haploid cell.
One way of thinking about ploidy is the number of possible alleles for each gene a cell can have. Right after meiosis I, the homologous chromosomes have separated into different cells. Each homolog carries one copy of the gene, and each gene could be a different allele, but these two homologs are now in two different cells. Though it looks like there are two of each chromosome in each cell, these are duplicated chromosomes ie, it is one chromosome which has been copied, so there is only one possible allele in the cell (just two copies of it).
The second meiotic division is where sister (duplicated) chromatids separate. It resembles mitosis of a haploid cell. At the start of the second division, each cell contains 1N chromosomes, each consisting of a pair of sister chromatids joined at the centromere.
Here is a simplified diagram illustrating the overall process and products of meiosis:

Meiosis Overview from Wikipedia by Rdbickel

And here is a video that walks through the steps of meiosis:

It is very important that you recognize how and why cells become haploid after meiosis I.
To confirm for yourself that you understand meiosis, work through one or more of these interactive tutorials:

  • The U. Arizona Cell Biology Project’s Meiosis tutorial has a click-through animation of meiosis, with 10 thought-provoking problem questions.
  • Jung Choi’s interactive flash tutorial, programmed by Pearson, uses human chromosome 7, with wild type and cystic fibrosis alleles for CFTR, to track segregation through meiosis, with and without crossing over: Meiotic Segregation tutorial

Chromosomes, chromatids, what is the difference and how many chromosomes are there at different times of the cell cycle and after mitosis and meiosis?

Chromosomes by definition contain the DNA that makes up the fundamental genome of the cell. In a prokaryote, the genome is usually packaged into one circular chromosome consisting of a circular DNA molecule of a few million base pairs (Mbp). In eukaryotes, the genome is packaged into multiple linear chromosomes, each consisting of a linear DNA molecule of tens or hundreds of Mbp. Chromosomes exist at all different phases of the cell cycle. They condense and become visible to light microscopy in prophase of mitosis or meiosis, and they decondense during interphase, in the form of chromatin (DNA wrapped around nucleosomes, like “beads on a string”).
The chromosome number, N, in eukaryotes, refers to the number of chromosomes in a haploid cell, or gamete (sperm or egg cell). Diploid cells (all the cells in our body except our gametes) have 2N chromosomes, because a diploid organism is created by union of 2 gametes each containing 1N chromosomes. In terms of chromosome number (ploidy), it’s useful to think of chromosomes as packages of genetic information. A pair of sister chromatids is one chromosome because it has genetic information (alleles) inherited from only one parent. A pair of homologous chromosomes, each consisting of a single chromatid in a daughter cell at the end of mitosis, has alleles from the father and from the mother, and counts as 2 chromosomes.
This chromosome number stays the same after chromosome replication during S phase: each chromosome entering cell division now consists of a pair of sister chromatids joined together at the centromere. Then in mitosis, the sister chromatids of each chromosome separate, so each daughter cell receives one chromatid from each chromosome. The result of mitosis is two identical daughter cells, genetically identical to the original cell, all having 2N chromosomes. So during a mitotic cell cycle, the DNA content per chromosome doubles during S phase (each chromosome starts as one chromatid, then becomes a pair of identical sister chromatids during S phase), but the chromosome number stays the same.
A chromatid, then, is a single chromosomal DNA molecule. The number of chromatids changes from 2X in G1 to 4X in G2 and back to 2X, but the number of chromosomes stays the same.
The chromosome number is reduced from 2N to 1N in the first meiotic division, and stays at 1N in the second meiotic division. Because homologous chromosomes separate in the first division, the daughter cells no longer have copies of each chromosome from both parents, so they have haploid genetic information, and a 1N chromosome number. The second meiotic division, where sister chromatids separate, is like mitosis. Chromosome number stays the same when sister chromatids separate.
Using the information above, compare these two simplified diagrams of mitosis and meiosis to visualize why cells are haploid after meiosis I. Specifically, compare the chromosomes in cells at the end of mitosis vs the end of meiosis I, recognizing that the diagram of mitosis tracks just a single pair of homologous chromosomes, whereas the diagram of meiosis tracks two pairs of homologous chromosomes (one long chromosome and short chromosome):

Meiosis Overview from Wikipedia by Rdbickel

The video below is geared toward a high school audience, but it does present a helpful way for recognizing how many chromosomes are present in a cell (and thus the ploidy level of that cell). While watching, see if you can recognize why the products of meiosis 1 are haploid cells:


A gene is a distinct portion of your cell’s DNA. Genes are coded instructions for making everything your body needs, especially proteins. You have about 25,000 genes. Researchers have yet to determine what that majority of our genes do, however, some of our genes can be associated with disorders such as cystic fibrosis or Huntington’s disease.

Proteins are chains of chemical building blocks called amino acids. A protein could contain just a few amino acids in its chain or it could have several thousand. Proteins form the basis for most of what your body does such as digestion, making energy, and growing.


How ar e DNA profiles stored?

  • The UK was the first country to set up a national database of DNA profiles in 1995.
  • The UK National DNA Database holds the DNA profiles from a select number of UK individuals, most of which are linked to serious crimes.
  • The Protection of Freedom Act 2013 ensured that 1,766,000 DNA profiles taken from innocent adults and children were deleted from the UK National DNA Database.
  • Most countries now have a national DNA database.

CLEP Biology Practice Test Questions

1. How many chromosomes does a human cell have after meiosis I?
A) 92
B) 46
C) 23
D) 22
E) 12
2. In plants and animals, genetic variation is introduced during
A) Crossing over in mitosis
B) Chromosome segregation in mitosis
C) Cytokinesis of meiosis
D) Anaphase I of meiosis
E) Anaphase II of meiosis
3. DNA replication occurs during which of the following phases?
A) Prophase I
B) Prophase II
C) Interphase I
D) Interphase II
E) Telophase I
4. The synaptonemal complex is present in which of the following phases of the cell cycle?
A) Metaphase of mitosis
B) Metaphase of meiosis I
C) Telophase of meiosis I
D) Metaphase of meiosis II
E) Telophase of meiosis II
5. A length of DNA coding for a particular protein is called a(n)
A) Allele
B) Genome
C) Gene
D) Transcript
E) Codon
6. In DNA replication, which of the following enzymes is required for separating the DNA molecule into two strands?
A) DNA polymerase
B) Single strand binding protein
C) DNA gyrase
D) Helicase
E) Primase
7. Which of the following chemical moieties forms the backbone of DNA?
A) Nitrogenous bases
B) Glycerol
C) Amino groups
D) Pentose and phosphate
E) Glucose and phosphate
For questions 8 and 9, refer to the list below.
A) Okazaki fragments
B) RNA primer
C) Single-strand binding protein
D) Leading strand
E) Replication fork
8. Required for the activity of DNA polymerase
9. Substrate for DNA ligase
10. Which of the following is true of the enzyme telomerase?
A) It is active on the leading strand during DNA synthesis
B) It requires a chromosomal DNA template
C) It acts in the 3→5 direction
D) It adds a repetitive DNA sequence to the end of chromosomes
E) It takes the place of primase at the ends of chromosomes


The structure of DNA

DNA is an example of a macromolecule, i.e. a large molecule with a special shape, which is built up from many smaller parts called sub- units .
If you could magnify part of a nucleus, you would see the DNA molecule looking like a twisted rope ladder - a double helix .
The two strands forming the sides of the ladder give it a strong yet flexible structure, which does not vary along its length.
Stretched between these are the "rungs" of the ladder, the parts of the DNA molecule which vary, and so the differences carry genetic information. These parts are made up of sections called bases , which fit together in pairs. The 4 bases (so called because on their own they react with acids) are also usually known by their initials, as shown alongside:
A (adenine), paired with T (thymine)
and C (cytosine) paired with G (guanine).

Since T pairs with A, and G with C, there are actually 4 different possibilities at any position on a strand. The sequence or order of these bases in DNA is used to store and pass on the genetic information, in a similar way to computer data on a disc or tape.

If one strand of DNA has the base sequence C A T G A G C G C G A T , what will be the sequence on the other strand? > GTA CTC GCG CTA


This explanation using stylised graphic representations was developed to assist in the understanding of DNA action.


Is DNA a single molecule or 46 separate pieces (out of 23 chromosome pairs)? - Biology

M13   A single-stranded DNA bacteriophage used as a vector for DNA sequencing.

M13 strand   The single-stranded DNA molecule that is present in the infective form of bacteriophage M13.

mAB    See monoclonal antibody.

macerate   To disintegrate tissues to obtain a cell dissociation. Cutting, soaking or enzymatic actions are commonly used.

macromolecule   Molecule of large molecular weight, such as proteins, nucleic acids and polysaccharides.

macronutrient (Gr. makros , large + L. nutrire , to nourish) For growth media: an essential element normally required in concentrations >0.5 millimole/l.

macrophages   Large, white blood cells that ingest foreign substances and display on their surfaces antigens produced from the foreign substances, to be recognized by other cells of the immune system.

macropropagation   Production of plant clones from growing parts.

major histocompatibility antigen   A cell-surface macromolecule that allows the immune system to distinguish foreign or "non-self" from "self". A better term is histoglobulin ( See histocompatibility antigen). These are the antigens that must be matched between donors and recipients during organ and tissue transplants to prevent rejection.

major histocompatibility complex   The large cluster of genes that encode the major histocompatibility antigens in mammals.

malignant   Having the properties of cancerous growth.

malt extract   A mixture of organic compounds from malt, used as a culture medium adjunct. See organic complex undefined.

malting   A process of generating starch-degrading enzymes in grain by allowing it to germinate in a humid atmosphere. See brewing.

mammary glands   The milk-producing organs of female mammals, which provide food for the young.

mammary tumours   Tumours of the milk glands.

management of farm animal genetic resources   In AnGR: The sum total of technical, policy and logistical operations involved in understanding (characterization), using and developing (utilization), maintaining (conservation), accessing, and sharing the benefits of animal genetic resources. (Source: FAO, 1999)

mannitol (C 6 H 14 O 6 f.w.𧆶.17)  A sugar alcohol widely distributed in plants. Mannitol is commonly used as a nutrient and osmoticum (q.v.) in suspension medium for plant protoplasts.

mannose (C 6 H 12 O 6 f.w.𧆴.16)  A hexose component of many polysaccharides and mannitol. Mannose is occasionally used as a carbohydrate source in plant tissue culture media.

map  ف. Verb: To determine the relative positions of loci on a DNA molecule. Linkage mapping is done by estimating the recombination fraction between loci, from the genotypes of offspring of particular matings. The further apart two loci are on a chromosome, the greater will be the frequency of recombination between them up to a maximum of 50%, the situation observed when they are sufficiently far apart on a chromosome that recombinant gametes are as frequent as non-recombinant gametes, or when they are on different chromosomes. Physical mapping is usually performed by the use of in situ hybridisation of cloned DNA fragments to metaphase chromosomes.

2. Noun: A diagram showing the relative positions of, and distances between, loci.

map distance   The standard measure of distance between loci, expressed in centiMorgans (cM). Estimated from recombination fraction via a mapping function (q.v.). For small recombination fractions, map distance equals the percentage of recombination (recombination frequency) betwen two genes. 1% recombination = 1 cM. Sometimes called a map unit.

mapping   Determining the location of a locus (gene or genetic marker) on a chromosome. See continuous map linkage map physical map.

mapping function A mathematical expression relating observed recombination fraction (q.v.) to map distance expressed in centiMorgans. Two common mapping functions are those developed by Haldane (1919 J. Genet., 8 : 299-309) and Kosambi (1944 Ann. Eugen ., 12 : 172-175). In both functions, the relationship between recombination fraction and map distance is approximately linear for recombination fractions less than 10% as recombination fraction increases above 10% (up to its maximum of 50%), map distance is increasingly greater than recombination fraction.

map unit   See map distance crossing-over unit.

marker   An identifiable DNA sequence that facilitates the study of inheritance of a trait or a gene. Such markers are used in mapping the order of genes along chromosomes and in following the inheritance of particular genes: genes closely linked to the marker will generally be inherited with it. Markers must be readily identifiable in the phenotype, for instance by controlling an easily observable feature (such as eye colour) or by being readily detectable by molecular means, e.g., microsatellite markers (q.v.). S ee gene tracking.

marker-assisted introgression   The use of DNA markers to increase the speed and efficiency of introgression (q.v.) of a new gene or genes into a population. The markers will be closely linked to the gene(s) in question.

marker-assisted selection (MAS)  The use of DNA markers to increase the response to selection in a population. The markers will be closely linked to one or more quantitative trait loci (q.v.).

marker gene   A gene of known function and known location on the chromosome. cf genetic marker.

marker peptide   A portion of fusion protein that facilitates its identification or purification.

MAS    See marker-assisted selection.

mass selection   As practised in plant and animal breeding, the choosing of individuals for reproduction from the entire population on the basis of individual phenotypes.

maternal effect   An effect attributable to some aspect of performance of the mother of the individual being evaluated.

maternal inheritance   Inheritance controlled by extrachromosomal (cytoplasmic) factors that are transmitted through the egg.

matric potential   A water potential component, always of negative value, resulting from capillary, imbibitional and adsorptive forces. See pressure potential.

maturation   The formation of gametes or spores.

MDA   Multiple drop array.    See microdroplet array.

mean   In statistics, the arithmetic average the sum of all measurements or values in a sample divided by the sample size.

media    See culture medium medium.

median   In a set of measurements, the central value above and below which there are an equal number of measurements.

medium (pl: media) ف. In plant tissue culture, a term for the liquid or solidified formulation upon which plant cells, tissues or organs develop. See culture medium.

2. In general terms, it could also means a substrate for plant growth, such as nutrient solution, soil, sand, etc., e.g., potting medium.

medium formulation   In tissue culture, the particular formula for the culture medium. It commonly contains macro-elements and micro-elements (high and low salt), some vitamins (B vitamins, inositol), plant growth regulators (auxin, cytokinin and sometimes gibberellin), a carbohydrate source (usually sucrose or glucose) and often other substances, such as amino acids or complex growth factors. Media may be liquid or solidified with agar the pH is adjusted (ca. 5-6) and the solution is sterilized (usually by filtration or autoclaving). Some formulations are very specific in the kind of explant or plant species that can be maintained some are very general.

megabase (abbr: Mb)  A length of DNA consisting of 10 6 base pairs (if double-stranded) or 10 6 bases (if single-stranded). 1 Mb = 10 3  kb = 10 6  bp.

megabase cloning   The cloning of very large DNA fragments. See  cloning.

megadalton  (MDa)  One megadalton is equal to 10 6  daltons. See  dalton.

megaspore macrospore   A haploid (n) spore developing into a female gametophyte in heterosporous plants.

meiosis (Gr. meioun , to make smaller)  The special cell division process by which the chromosome number of a reproductive cell becomes reduced to half (n) the diploid (2n) or somatic number. Two consecutive divisions occur. In the first division, homologous chromosomes became paired and may exchange genetic material (via crossing over) before moving away from each other into separate daughter nuclei (reduction division). These new nuclei divide by mitosis to produce four haploid nuclei. Meiosis results in the formation of gametes in animals or of spores in plants. It is an important source of variability through recombination.

meiotic analysis   A technique used to analyse chromosome-pairing relationships.

meiotic drive   Any mechanism that causes alleles to be recovered unequally in the gametes of a heterozygote.

meiotic product(s)    See gametes.

melanin   Pigment, as typically produced by specialised epidermal cells called melanocytes.

melting temperature (abbr: T m )  The temperature at which a double-stranded DNA or RNA molecule denatures into separate single strands. The T m is characteristic of each DNA species and gives an indication of its base composition. DNAs rich in G:C base pairs are more resistant to thermal denaturation than A:T rich DNA since three hydrogen bonds are formed between G and C, but only two between A and T.

membrane bioreactors   Bioreactors where cells grow on or behind a permeable membrane, which lets the nutrients for the cell through but retains the cells themselves. A variations on this theme is the hollow-fibre reactor.

memory cells   Long-lived B and T cells that mediate rapid secondary immune responses to a previously encountered antigen.

Mendelian population   A natural, interbreeding unit of sexually reproducing plants or animals sharing a common gene pool.

Mendelism   The theory of heredity that forms the basis of classical genetics, proposed by Gregor Mendel in 1866 and formulated in two laws ( see Mendel's Laws).

Mendel's Laws   Two laws summarizing Gregor Mendel's theory of inheritance. The Law of Segregation states that each hereditary characteristic is controlled by two `factors' (now called alleles), which segregate and pass into separate germ cells. The Law of Independent Assortment states that pairs of `factors' segregate independently of each other when germ cells are formed. See  independent assortment linkage.

mericlinal   Refers to a chimera with tissue of one genotype partly surrounded by that of another genotype.

mericloning   A propagation method using shoot tips in culture to proliferate multiple buds, which can then be separated, rooted and planted out.

meristele   The vascular cylinder tissue in the stem. See stele.

meristem   (Gr. meristos , divisible)  Undifferentiated but determined tissue, the cells of which are capable of active cell division and differentiation into specialized and permanent tissue such as shoots and roots.

meristem culture   A tissue culture containing meristematic dome tissue without adjacent leaf primordia or stem tissue. The term may also imply the culture of meristemoidal regions of plants, or meristematic growth in culture.

meristem tip   An explant comprising the meristem (meristematic dome) and usually one pair of leaf primordia. Also refers to explants originating from apical meristem tip or lateral or axillary meristem tip. Do not confuse the meristem tip with the term "shoot tip," which is much larger and usually has more immature leaves and stem tissue.

meristem tip culture   Cultures derived from meristem tip explants. The use of meristem tip culture is for virus elimination or axillary shoot proliferation purposes, but less commonly for callus production.

meristemoid   A localized group of cells in callus tissue, characterized by an accumulation of starch, RNA and protein, and giving rise to adventitious shoots or roots.

merozygote   Partial zygote produced by a process of partial genetic exchange, such as transformation in bacteria.

mesh bioreactor   See filter bioreactor.

mesoderm   The middle germ layer that forms in the early animal embryo and gives rise to parts such as bone and connective tissue.

mesophile   A micro-organism able to grow in the temperature range 20 to 50°C optimal growth often occurs at about 37°C.

mesophyll  (Gr. mesos , middle + phyllon , leaf)  Leaf parenchyma tissue occurring between epidermal layers.

metabolic cell   A cell that is not dividing.

metabolism  (M.L. from the Gr. metobolos , to change)  In an organism or a single cell, the biochemical process by which nutritive material is built up into living matter, or aids in building living matter, or by which complex substances and food are broken down into simple substances.

metabolite  ف. A low-molecular-weight biological compound that is usually synthesized by an enzyme.

2. A compound that is essential for a metabolic process. A substance synthesized by the organism, or taken in from the environment. Autotrophic organisms take in inorganic metabolites, such as water, CO 2 , nitrates and some trace elements.

metacentric chromosome   A chromosome with the centromere near the middle and, consequently, two arms of about equal length.

metallothionein   A protective protein that binds heavy metals such as cadmium and lead.

metaphase (Gr. meta , after + phasis , appearance)  Stage of mitosis during which the chromosomes, or at least the kinetochores, lie in the central plane of the spindle. It is the stage following prophase and preceding anaphase.

metastasis   The spread of cancer cells to previously unaffected organs.

methionine   A sulphur-containing amino acid.

methylation   The addition of a methyl group (-CH 3 ) to a macromolecule, such as the addition of a methyl group to specific cytosine and, occasionally, adenine residues in DNA.

Michaelis constant    See K m .

microalgal culture   Culture in bioreactors of microalgae microalgae include seaweeds.

micro-array, DNA   See DNA micro-array.

microbe   A general term for a micro-organism.

microbial mats   Layered groups or communities of microbial populations.

microbody (Gr. mikros , small + body)  A cellular organelle always bound by a single membrane, frequently spherical, from 20 to 60 nm in diameter, containing a variety of enzymes.

micro-carriers   Small particles used as a support material for cells, and particularly mammalian cells, which are too fragile to be pumped and stirred as bacterial cells are in a large-scale culture.

microdroplet array multiple drop array (MDA) hanging droplet technique . Introduced by Kao and Konstabel (1970), this technique is used to evaluate large numbers of media modifications, employing small quantities of medium into which are placed small numbers of cells. Droplets of liquid are arranged on the lid of a Petri dish, inverted over the bottom half of the dish containing a solution with a lower osmotic pressure, and the dish is sealed. The cells or protoplasts form a monolayer at the droplet meniscus and can easily be examined.

micro-element   An element required in very small quantities.

micro-encapsulation   A process of enclosing a substance in very small sealed capsules from which material is released by heat, solution or other means.

micro-environment (Gr. mikros , small + O.F. environ , about)  The environment close enough to the surface of a living or non-living object to be influenced by it.

microfibrils (Gr. mikros , small + fibrils , diminutive of fibre)  Microfibrils are exceedingly small fibres visible only at the high magnification of the electron microscope.

microgametophytes    See anther.

micrograft   See shoot-tip graft.

micro-injection   The introduction of small amounts of material (DNA, RNA, enzymes, cytotoxic agents) into a single eukaryotic cell with a fine, microscopic needle, penetrating the cell membrane.

micro-isolating system   Mechanical separation of single cells or protoplasts thus allowing them to proliferate individually.

micron micrometre (Gr. mikros , small)  A unit of distance: 10 -6  m 0.001 mm. Symbol: m m.

2-micron plasmid   See 2 m m plasmid.

micronutrient (Gr. mikros , small + L. nutrire , to nourish)  For growth media: An essential element normally required in concentrations < 0.5 millimole/litre.

micro-organism   Organism visible only under magnification.

microplasts   Vesicles produced by subdivision and fragmentation of protoplasts or thin-walled cells.

micropyle  ف. A small opening in the surface of a plant ovule through which the pollen tube passes prior to fertilization.

2. A small pore in some animal cells or tissues.

microprojectile bombardment   A procedure for modifying cells by shooting DNA-coated metal (tungsten or gold) particles into them. See  biolistics.

micropropagation   Miniaturized in vitro multiplication and/or regeneration of plant material under aseptic and controlled environmental conditions on specially prepared media that contain substances necessary for growth used for three general types of tissue: excised embryos (= embryo culture) shoot-tips (= meristem culture or mericloning) and pieces of tissue that range from bits of stems to roots. Four stages of plant tissue culture have been defined by Murashige:
Stage I. Establishment of an aseptic culture.
Stage II. The multiplication of propagules.
Stage III. Preparation of propagules for successful transfer to soil (rooting and hardening).
Stage IV. Establishment in soil.

microsatellite   A form of VNTR (q.v.). Specifically, a segment of DNA characterized by the occurrence of a variable number of copies (from a few up to 30 or so) of a sequence of around 5 or fewer bases (called a repeat unit, q.v.). A typical microsatellite is the repeat unit AC, which occurs at approximately 100𧄀 different sites in a typical mammalian genome. At any one site (locus), there are usually several different "alleles," each identifiable according to the number of repeat units. These alleles can be detected by PCR (q.v.), using primers designed from the unique sequence that is located on either side of the microsatellite. When the PCR product is run on an electrophoretic gel, alleles are seen to differ in length in units equal to the size of the repeat unit, e.g., if the primers correspond to the unique sequence immediately on either side of the microsatellite and are each 20 bases long, and an individual is heterozygous for an AC microsatellite with one allele comprising 5 repeats and the other comprising 6 repeats, the heterozygote will exhibit two bands on the gel, one band being 20 + (2 ×م) + 20 = 50 bases long, and the other allele being 20 + (2 ×ن) + 20 = 52 bases long. Microsatellites have been the standard DNA marker: they are easily detectable by PCR, and they tend to be evenly located throughout the genome. Thousands have been mapped in many different species.

microspore   The smaller of the two kinds of meiospores produced by heterosporous plants in the course of microsporogenesis in seed plants, microspores give rise to the pollen grain, the male gametophyte.

microtuber   Cultured tissue capable of growing into tuberous plant.

microtubules   A minute filament in living cells that is composed of the protein tubulin and occurs singly, in pairs, triplets or bundles. Microtubules help cells to maintain their shape they also occur in cilia, flagella and the centrioles, and form the spindle during nuclear division.

middle lamella (L. lamella , a thin plate or scale). Original thin membrane separating two adjacent protoplasts and remaining as a distinct cementing layer between adjacent cell walls.

mid-parent value   In quantitative genetics, the average of the phenotypes of two mates.

minimum effective cell density   The inoculum density below which the culture fails to give reproducible cell growth. The minimum density is a function of the tissue (species, explant, cell line) and the culture phase of the inoculum suspension. Minimum density decreases inversely to the aggregate size and division rate of the stock culture.

minimum inoculum size   The critical volume of inoculum (q.v.) required to initiate culture growth, due to the diffusive loss of cell materials into the medium. The subsequent culture growth cycle is dependent on the inoculum size, which is determined by the volume of medium and size of the culture vessel.

mini-prep   A small-scale (mini-) preparation of plasmid or phage DNA. Used to analyse DNA in a cloning vector after a cloning experiment.

minisatellite   A form of VNTR (q.v.) in which the repeat units (q.v.) typically range from 10 to 100 bases. They are usually detected by Southern hybridization (q.v.), using a probe comprising a clone of the repeat unit. The first DNA fingerprints (q.v.) were minisatellites detected in this way. Minisatellites tend to be located at the ends of chromosomes and in regions with a high frequency of recombination.

minitubers   Small tubers (5-15 mm in diameter) formed on shoot cultures or cuttings of tuber-forming crops, such as potato.

mismatch   The lack of a complementary pair of bases in a double helix of DNA, e.g., A:C, G:T.

mismatch repair   DNA repair processes that correct mismatched base pairs.

missense mutation   A mutation that changes a codon for one amino acid into a codon specifying another amino acid.

mist propagation   Application of fine droplets of water to leafy cuttings in the rooting stage to reduce transpiration. cf  fog.

mites   Free-living and parasitic animals belonging to the order Acarina, class Arachnida (with spiders). Mites may infest plant crops, reducing their harvest. They may also infest plant tissue culture work areas and incubation facilities in search of sugars, and so contaminate culture vessels and spread bacteria and fungi.

mitochondrial DNA (mtDNA)  A circular ring of DNA found in mitochondria. In mammals, mtDNA makes up less than 1% of the total cellular DNA, but in plants the amount is variable. It codes for ribosomal RNA and transfer RNA, but only some mitochondrial proteins (up to 30 proteins in animals), the nuclear DNA being required for encoding most of these.

mitochondrion  (Gr. mitos , thread + chondrion , a grain pl: mitochondria)  A small cytoplasmic organelle that carries out aerobic respiration. Oxidative phosphorylation takes place to produce ATP.

mitosis (Gr. mitos , a thread adj: mitotic pl: mitoses)  Disjunction of replicated chromosomes and division of the cytoplasm to produce two genetically identical daughter cells. The division involves the appearance of chromosomes, their longitudinal duplication, and equal distribution of newly formed parts to daughter nuclei. It is separated into five stages: interphase, prophase, metaphase, anaphase and telophase.

mixed bud   A bud containing both rudimentary leaves and flowers.

mixoploid   Cells with variable (euploid, aneuploid) chromosome numbers. Mosaics or chimeras differ in chromosome number as a result of a variety of mitotic irregularities.

mobilization  ف. The transfer between bacteria of a non-conjugative plasmid by a conjugative plasmid.

2. The transfer between bacteria of chromosomal genes by a conjugative plasmid.

mobilizing functions   The genes on a plasmid that give it the ability to facilitate the transfer of either a non-conjugative or a conjugative plasmid from one bacterium to another.

modal class mode   In a frequency distribution, the class having the greatest frequency.

model   A mathematical description of a biological phenomenon.

modification  ف. Enzymatic methylation of a restriction enzyme DNA recognition site.

2. Specific nucleotide changes in DNA or RNA molecules.

modifier modifying gene   A gene that affects the expression of some other gene.

MOET    See multiple ovulation and embryo transfer.

molality   The number of moles of solute per litre of solvent.

molarity   The number of moles of a substance contained in a kilogram of solution. See mole.

mole (symbol: M). Amount of substance that has a weight in grams numerically equal to the molecular weight of the substance. Also called gram molecular weight. A mole contains 6.023 ×㺊 23 molecules or atoms of a substance.

molecular biology   The area of knowledge concerned with the molecular aspects of organisms and their cells.

molecular cloning   The biological amplification of a specific DNA sequence through mitotic division of a host cell into which it has been transformed or transfected. See cloning.

molecular genetics   The area of knowledge concerned with the genetic aspects of molecular biology, especially with DNA, RNA and protein molecules.

molecule (L. diminutive of moles, a little mass)  A unit of matter, the smallest portion of an element or a compound that retains chemical identity with the substance in mass. The molecule usually consist of a union of two or more atoms some organic molecules containing a very large number of atoms.

monoclonal antibody  (mAB) A single type of antibody that is directed against a specific epitope (antigen, antigenic determinant) and is produced by a single clone of B cells or a single hybridoma cell line, which is formed by the fusion of a lymphocyte cell with a myeloma cell. Some myeloma cells synthesize single antibodies naturally.

monocot   See monocotyledon.

monocotyledon   (Gr. monos , solitary + kotyledon , a cup-shaped hollow) A plant whose embryo has one seed leaf (cotyledon). Examples are cereal grains (corn, wheat, rice), asparagus, and lily. Colloquially called a monocot. cf  dicotyledon.

monoculture   The agricultural practice of cultivating a single crop on a whole farm or area.

monoecious   Denoting plant species that have separate male and female flowers on the same plant (e.g ., maize).

monogastric animals   Animals with simple stomachs that do not ruminate. cf  ruminant animals.

monophyletic   Describing any group of organisms that are assumed to have originated from the same ancestor.

monogenic   Controlled by a single gene, as opposed to multigenic.

monohybrid   (Gr. monos , solitary + L. hybrida , a mongrel)  The offspring of two homozygous parents that differ from one another by the alleles present at only one locus.

monohybrid cross   A cross between parents differing in only one trait or in which only one trait is being considered.

monolayer   A single layer of cells growing on a surface.

monomer   A single molecular entity that may combine with others to form more complex structures.

monosaccharide   A single sugar. cf  polysaccharide.

monosomic (n: monosomy)  describing a diploid organism lacking one chromosome (2n -1) of its proper (disomic) complement a form of aneuploidy. See also disomy.

mono-unsaturates   Oils containing mono-unsaturated fatty acids.

monozygotic twins   One-egg or identical twins twins derived from the splitting of a single fertilized ovum.

morphogen   A substance that stimulates the development of form or structure in an organism.

morphogenesis   The development, through growth and differentiation, of form and structure in an organism.

morphogenic response   The effect on the developmental history of a plant or its parts exposed to a given set of growth conditions or to a change in the environment.

morphology (Gr. morphe , form + logos , discourse) ف.The science of studying form and its development.

2. General: Shape, form, external structure or arrangement.

mosaic   An organism or part of an organism that is composed of cells with different origin.

mother plant   See donor plant.

movable genetic element    See transposon.

mRNA messenger RNA   The RNA transcript of a protein-encoding gene. The information encoded in the mRNA molecule is translated into a polypeptide of specific amino acid sequence by the ribosomes. In eukaryotes, mRNAs transfer genetic information from the DNA to ribosomes, where it is translated into protein.

MRUs   Minimum recognition units. See dabs.

mtDNA   See mitochondrial DNA.

multi-copy   Describing plasmids which replicate to produce many plasmid molecules per host genome, e.g., pBR322 is a multi-copy plasmid, there are usually 50 pBR322 molecules (or copies) per E. coli genome.

multigene family   A group of genes that are similar in nucleotide sequence or that produce polypeptides with similar amino acid sequences.

multigenic   Controlled by several genes, as opposed to monogenic.

multi-locus probe   A probe that hybridizes to a number of different sites in the genome of an organism. See probe.

multimer multimeric   A protein made up of more than one peptide chain.

multiple alleles   The existence of more than two alleles at a locus in a population.

multiple cloning site    See polylinker.

multiple drop array (MDA)   See microdroplet array.

multiple ovulation and embryo transfer   (MOET)  A technology by which a single female that usually produces only one or two offspring can produce a litter of offspring. Involves stimulation of a female to shed large numbers of ova natural mating or artificial insemination collection of fertilized ova (either surgically, or non-surgically through the cervix) and transfer (usually non-surgical, through the cervix) of these fertilized ova to recipient females.

multivalent vaccine   A single vaccine that is designed to elicit an immune response either to more than one infectious agent or to several different epitopes of a molecule.

mutable genes   Genes with an unusually high mutation rate.

mutagen   An agent or process which is capable of inducing a mutation, such as UV light. cf mutation.

mutagenesis   Change(s) in the genetic constitution of a cell through alterations to its DNA.

mutant   An organism or an allele that differs from the wild type because it carries one or more genetic changes in its DNA. A mutant organism may carry mutated gene(s) (= gene mutation) mutated chromosome(s) (= chromosome mutation) or mutated genome(s) (= genome mutation). a.k.a. a variant.

mutation   (L. mutare , to change)  A sudden, heritable change appearing in an individual as the result of a change in the structure of a gene (= gene mutation) changes in the structure of chromosomes (= chromosome mutation) or in the number of chromosomes (= genome mutation). cf genetic diversity genetic drift.

mutation pressure   A constant mutation rate that adds mutant genes to a population repeated occurrences of mutations in a population.

mycelium (pl: mycelia)  Threadlike filament making up the vegetative portion of thallus fungi.

mycoprotein   Fungal protein.

mycotoxin   Toxic substance of fungal origin, such as aflatoxin.

mycorrhiza   (Gr. mykos , fungus + riza , root)  Fungi that form an association with or have a symbiotic relationship with roots of more developed plants.