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I want to name a new diatom species in the honor of Prof. Vodyanitskiy. What will be the species epithet: "vodyanitskiya", or other? Are there any rules that regulates how the end of such epithets is changed?
The correct form of the specific epithet depends on the generic name (masculine, feminine, and neuter generic names will each require the corresponding, grammatically correct, form of the specific epithet), and on the type of the specific epithet itself:
Thalassiosira bradburyi is named after J.P. Bradbury. Thalassiosira hendeyi is named after N. I. Hendey. The letter "i" is added to the person's last name in both cases. Hence, Thalassiosira species named after V. A. Vodyanitskiy should be, in my opinion, Thalassiosira vodyanitskiyi.
You should check the article 60 of ICN: http://www.iapt-taxon.org/nomen/main.php?page=art60
See in particular Recommendation 60C about specific epithet, and in the specific case, the rule 60C.1 (specific epithet derived from a person name).
You can use the genitive case (as Plant of Vodyanitskiy) as in rule (a), which is independent of generic name, so if the professor is male: X. vodyanitskiyi, and she is female: X. vodyanitskiyae.
or as adjective (so inflected according the genera), in rule (c): X. vodyanitskiyana, X. vodyanitskiyanus, X. vodyanitskiyanum
Note: there are other rules to have a valid published name, and it is recommended to explain why you choose such name. In additional to the ICN code, there is the companion book: The code decoded. A user's guide to the International Code of Nomenclature for algae, fungi, and plants(Regnum Vegetabile 155), by Nicolas Turland
Genus, Species, and Cultivars, Oh My?
I've talked with many gardeners, green and seasoned, who have a hard time remembering what is what within a botanical name as well as how to use it. This is a quick reference, reminder, or education for anyone who has a tough time (and most of us do at one time or another) with botanical Latin.
Each plant is categorized under a long list of classifications such as Kingdom, Division, Subdivision, Class, Genus, etc. Lucky for us, we only have to know a couple of the classifications in order to obtain information. Can you imagine trying to look up information on a Hellebore and having to remember Plantae Tracheobionta Spermatophyta Magnoliophyta Magnoliopsida Magnoliidae Ranunculales Ranunculaceae Helleborus orientalis? For the record, that is the Kingdom, Subkingdom, Superdivision, Division, Class, Subclass, Order, Family, Genus and Species of a common Lenten Rose.
It is interesting but superfluous to note that a plant as different from the Lenten Rose as say, a Penstemon, will have the exact same classification through Magnoliopsida, which just implies that it is in the class of dicotyledons. Beyond this classification, the Penstemon and the Hellebore diverge.
So if I lost you with all that botanical jargon, come back to me. All you really need is the genus, species and sometimes cultivar name to search about a plant.
The Big Three: Genus, Species, and Cultivar
The last three classifiers of botanical taxonomy are genus, species and cultivar. These are the most important and arguably all you need in any plant search, classification, or reference. Even if each individual generic (genus) or specific epithet (species name) is confusing and hard to pronounce, their function is not.
Most often, people that have knowledge of botanical Latin do not know the background or historical context of the nomenclature they have simply memorized Latin names in order to be more precise in referencing. Seven out of ten times, a person that uses botanical Latin is not trying to show off, that is just how they refer to plants by rule. If you are completely out of the loop on this method, truly it just takes a little understanding and you'll be on the same page in no time. DG's own Jill M. Nicholaus wrote a great article on why it is important to use botanical Latin if you need some convincing. (And if you are one of the remaining 30% who are curious about plant names, Botanary contains thousands of botanical terms, their meanings and pronunciation.)
How can you tell the difference?
This is easy once you know how to read botanical Latin. The only problem is that plant names are written in many different permutations, much like a woman could be referred to as Jane Doe, Mrs. Doe, Mrs. John Doe, Ms. Jane Doe, etc. However, because you know how to identify a first name from a surname and a woman's name from a man's, you can classify any of those permutations in your head logically. Her first name is Jane and her last name is Doe. Botanical Latin is the exact same way once you know how to logically categorize what you see, it is as easy as that.
Some good rules of thumb:
It is always, always, always the case that:
- If there are three names given, one capitalized, the second lower case, and the third is in single quotations you have respectively the genus, species and cultivar names.
Echinacea purpurea &lsquoMagnus'
You will not see them in any other order, unless the author is mistaken. You will never see purpurea Echinacea &lsquoMagnus.' You should also never see the cultivar name in any other form than in single quotations.
- If there are two names given, the first (which should be capitalized) is the genus name and the second is the species name, or more properly, specific epithet. For example, Sorbus scopulina: even though I've never heard of this plant (western mountain-ash) I know that Sorbus is the genus and scopulina is the specific epithet. Combined, they create a binomial name referred to as the species: Sorbus scopulina.
- If there is only one name given and it does not sound like the English I know, it is the genus and no other classification. For example, Euonymus, whether or not it is italicized, when seen alone I know that it is the genus name. In this case, it also happens to be the common name. See how this can be confusing?
- If you see 2 names, one capitalized and one in single quotations, you have the genus name and cultivar name. For example, Dahlia 'Silentia,' is a cultivar of dahlia named &lsquoSilentia,' but the species is not given for one reason or another, usually because it is a hybrid or cultivated specimen.
- Another common way to write botanical Latin names, is by abbreviating the genus name by its first initial and spelling out the specific epithet. An example of this is E. purpurea. You would mainly see this practice in a larger discussion about the genus or about a commonly talked about plant. For instance, on the peony forum it might be appropriate to write P. lactiflora, shorthand for Paeonia lactiflora, but only because people are aware that you are talking about a peony, otherwise the "P." might be too confusing. In many cases, as with E. purpurea (purple coneflower), which could be easily confused with I. purpurea (morning glory), it is generally best to spell out the entire species name (genus and specific epithet).
- You will never see a specific epithet alone, because without a genus name, the epithet means nothing. Specific epithets generally refer to a plant's color or habit, native habitat, the person who discovered or named them, or another feature of the plant. Epithets often repeat throughout different genera. For example, Agave parryi, Penstemon parryi, and Townsendia parryi, all named for 19 th century botanist, C.C. Parry, would not function by just the epithet parryi  .
- Likewise, you will rarely see a cultivar name stand alone. If you do see what looks like a proper noun (first letter of every word capitalized) in single quotation marks, it is likely a cultivar name. Example: Gaillardia pulchella 'Razzledazzle'.
It is important to differentiate between a genus name and a common name before you search for a plant, much like tissue versus Kleenex. Obvious? What about these plants:
Brugmansia. If you search the PlantFiles by putting &lsquoBrugmansia' in the Common Name field, you will only fetch 4 results. We all know there are more brugs than that out there! However, if you type Brugmansia into the Genus field, you will net 388 results, because in fact Angel's Trumpet is the common name and Brugmansia, which is commonly used, is actually its genus classification. The same goes for often-referred-to-by-their-genus-names Artemisia, Buddleja, Viburnum, and Penstemon.
Hibiscus. On the other hand, some plants such as hibiscus are searchable both ways. Hibiscus is both the common name and the genus name and searching either fetches over 7,500 results. This is also true for c annas, irises and narcissus.
Carex. Some plants, like carex (sedge), are known equally well by their genus name and by their common name. However, if you run a search for the common name carex, nothing will result. You would either have to search sedge as the common name or Carex as the genus. This is the same case for Echinacea, the genus name for purple coneflower. You will not find any results if you search echinacea in the common name field, even though many people use that name to commonly refer to the plant.
Crepe Myrtle. Plants that are less confusing, like the crepe myrtle or Japanese maple, are easily differentiated between common name and genus name. Rarely will you hear someone say, "I saw the most beautiful Lagerstroemia while in Texas." For these plants you just have to be aware of which search box you are typing in.
How to use this information in a search
People often get needlessly frustrated when using the PlantFiles search feature. If you understand the basics of how to identify each part of a plant's name, you will be able to search successfully. Now that you know the difference between a genus, species and cultivar, you'll know which word to put in which search category. In all honesty, even people that have a vast understanding of botanical nomenclature can still mess up while searching for information.
Make sure that when you are searching you put the genus name in the search box separate from the species name. If you type "Rosa rugosa" into the genus or species field of a search, you will find nothing. Separating "Rosa" from "rugosa" into the proper fields of genus and species, you will net 24 matches.
Similarly, if you put the genus name into the common name search box and your search comes back with nothing or not what you were looking for, try another search with it in the genus box to see what you find.
On a sidenote, when using correct botanical Latin names such as genus and species, the correct way to format it is by using italics as seen in this article. If you are referring to a common name it neither needs to be capitalized nor italicized even if the word can also be used as the genus name (i.e. brugmansia vs. Brugmansia). Do note though that in the search feature you don't not have to bother with italics or capitalizing, but your spelling is crucial.
If your searches are not fruitful in any variation, try using the more generalized search.
Pop Quiz for Understanding:
Label the classifications: genus, species, and cultivar
&bull1 1. Arisarum proboscideum
&bull2 2. Hakonechloa macra 'Aureola'
&bull5 5. Impatiens niamniamensis 'Queen Congo'
How did you do? Answers will be posted below. If you are becoming more familiar with the classifications, how they look, and how to use them, then you likely did very well on the quiz and you will likely be much more successful in your future searches. Please use the PlantFiles search features often because the more we know about our plants, the better care we can take of them.
Science is a process of gaining knowledge and understanding of the world around us. It is a never-ending process, and what we think are true facts today might change tomorrow. In science we are aiming for having the best understanding possible today based on what we and our predecessors have learned until now.
This means that what is botanically accurate from a scientific viewpoint might (and will) change. Other experts in the field of botany know a lot more about their particular research plants than I do. New scientific findings and conclusions are being published every day. This is just normal and part of the scientific process we improve on our knowledge all the time.
The important thing is our willingness to continuously aim for botanical accuracy and the highest scientific standards in our use of names and facts. When things are wrong, let's correct them. Let us not perpetuate wrong botanical knowledge by accepting its incorrect use on commercial products, in everyday language, or in other parts of our contemporary cultures. Through scientific education and specific corrections we will improve botany and science for everybody, in supermarkets, restaurants, and garden centers.
It is the perpetuation of incorrect facts that are the problem, not the need for correction. Everybody makes mistakes, and everybody learns, throughout their lives. We need words to be able to communicate and talk about things, so let's use the right words and the right species names.
How to Write Scientific Names of Animals
In ZO 150, points are deducted from lab practical answers, discussion question answers, and genus reports if names are not printed or written and used correctly. Refer to this short guide every time you come across a scientific name in lecture notes or the text, and see how the rules are applied in those examples until you learn to use them properly yourself. Correct your notes, labels of drawings, etc. as necessary when you do them, rather than allowing bad habits to develop.
- A taxon is a group of organisms defined by particular reproductive, anatomical, or genetically determined similarities.
- Each taxon is named. Names are almost always unique, but sometimes the same name will be used inadvertently for both plant and animal orders, or for two, very distantly related animal families.
The basic taxonomic levels are domain, kingdom, phylum, class, order, family and species binomial (genus + specific epithet).
- Examples: subkingdom, subphylum, infraclass, superfamily.
- Some hierarchies include a level between sub- or infra-family and genus, called "tribe."
- Example: the scientific order name of lemurs, monkeys, apes and humans, Primates
- Examples: tiger shark, timber wolf, daisy, puffball fungus
- Examples: Chordata becomes chordates, Hominidae becomes hominids, Eukarya becomes eukaryotes
- Examples: Kirtland's warbler, Carolina wren
- Example: hydra, Hydra
- Example: animals with a hydra-like body form may be in any of these genera Hydra, Chlorohydra or Pelmatohydra. When the particular genus is not identified, the name should be written lower case and not italicized -- hydra.
- More exactly, there should be at least a small probability that the genes of any two individuals belonging to the same species can eventually, over many generations, be mingled in the genome of a single, common descendant, and that this will happen without human intervention or disturbance of normal environments or habitats. In other words, there should be no geographical, anatomical or other absolute physical barriers that completely isolate any group of individuals from all other such groups of the same species.
- Further, the offspring of any two individuals in a species (assuming they are of opposite sexes, or hermaphroditic), must be fertile and capable of interbreeding with other members of that species.
- Special problems in defining species arise for animals which reproduce exclusively by parthenogenesis or simpler, asexual means, so that their ability to interbreed cannot be tested.
- There are no absolute standards for the amount of genetic or morphological difference that must exist between two individuals to put them in separate species. Nevertheless, nearly all animal species are defined by their morphology. Interbreeding limits have been fully tested in only a tiny percentage of named species.
- The article in which the name is assigned must include a sufficient description of the organism to which it applies, and be published in one of a short list of accepted languages.
- Example: Our specific epithet "sapiens" should never be written by itself, but always as Homo sapiens or H. sapiens.
The genus name must be unique, that is, never applied to any other type of organism.
- Examples: Anolis carolinensis , Gastrophryne carolinensis, Terrapene carolina, Lissodendoryx carolinensis, Polymesoda caroliniana.
- Notice in the examples that the ending of the epithet is changed to agree with the gender of the genus name.
- Example: correct - Homo. INCORRECT - homo or Homo
- Examples: epithets based on "Carolina" above.
- Example: Hyla andersoni, named after a Mr. or Ms. Anderson
- Example: After using Homo sapiens in a document, one may refer to it throughout the rest of the document as H. sapiens.
- Example If Hirudo medicinalis is mentioned together with Homo sapiens, neither Homo nor Hirudo should be abbreviated when they occur again in the same document.
- The describing author(s) is (are) the scientist (or scientists) who assigns a name for the first time, and meets the other requirements for establishing the official name for that kind of animal.
The earliest version of rules for establishing species names was proposed by Karl Linne', a Swedish naturalist in the 18th century, who then proceeded to publish official descriptions of hundreds, perhaps even thousands, of species.
Linne' latinized his name to Carolus Linnaeus. Linnaeus, sometimes abbreviated L., is given as describing author with many of the most common species of plants and animals, including ours, Homo sapiens Linnaeus.
Notice that the describing author's name is capitalized but not italicized.
Where do I find my inspiration?
Great species names tell you something about the creature itself, so get creative.
You can draw on any feature of the species, such as its appearance, behaviour, habitat or geographic location.
Taxonomists draw on all kinds of inspiration when naming new species, for example:
- Five species of fungus beetle — a beastie that is small and round — were named Gelae baen (sounding like "jelly bean"), Gelae balae ("jelly belly"), Gelae donut ("jelly doughnut"), Gelae fish ("jelly fish"), and Gelae rol ("jelly roll").
- The spider Aphonopelma johnnycashi was named after Johnny Cash because the the 'species can be found near the area of Folsom Prison in California, and like Cash's distinctive style of dress . mature males of this species are generally black in colour.'
- A new genus of sea snail was called Ittibittium, because it is smaller than sea snails from the genus T. Bittium.
- A giant fossil turtle was named Ninjemys oweni, Owen's Ninja Turtle, with the authors explaining that the name was from "ninja, in allusion to that totally rad, fearsome foursome epitomising shelled success" and "emys" from the Latin for turtle.
AVH Help Assitance with using Australia's Virtual Herbarium
At the simplest level of scientific classification, each plant has a name made up of two parts, a generic (or genus) name and a specific name or epithet. Together, these two names are referred to as a binomial.
A generic name is a &lsquocollective name&rsquo for a group of plants. It indicates a grouping of organisms that all share a suite of similar characters. Ideally these should all have evolved from one common ancestor. The specific name, allows us to distinguish between different organisms within a genus.
Binomial names are always written with the generic name first, starting with a capital letter, e.g.: Grevillea
The specific epithet always follows the generic name, starting with a lower-case letter, e.g.: victoriae
The full species name or binomial being Grevillea victoriae .
Generic and specific names are generally in Latin or are Latinised words from other languages, particularly Greek. Other derivations are also sometimes used, such as Aboriginal names or even acronyms. Specific epithets also need to conform to certain grammatical rules depending on the form of the generic name.
There are hierarchical levels of classification (ranks) above and below the genus and species, the most commonly referred to is the grouping of several genera (plural of genus) into a family. As with plants within the same genus, plants in the same family have many characteristics in common. Grevillea victoriae is in the family Proteaceae , along with Banksia, Hakea, Macadamia and many other genera. Family names start with a capital letter and generally end in &ldquo&hellipceae&rdquo.
There are a number of levels of classification below that of species, with the most commonly used being subspecies and variety, abbreviated to 'subsp.', (or less usefully 'ssp.') and 'var.' respectively. This allows further subdivision of plant groups to reflect the variation in form and distribution we see in nature. These subdivisions, along with species, genera, families and other groupings or ranks within plant classification, are referred to as taxa (plural) or a taxon (singular).
For example, three subspecies are recognised within Grevillea victoriae:
Grevillea victoriae subsp. victoriae the one closest to the original description of the species.
Grevillea victoriae subsp. nivalis differing slightly from the original description of the species.
Grevillea victoriae subsp. brindabella a subspecies described in 2010 from the Southern Tablelands of NSW-ACT.
Grevillea victoriae subsp. victoriae
Grevillea victoriae subsp. nivalis
Whenever a subspecies, variety or other subdivision below the rank of species is published, an additional name, called an autonym, is automatically generated. In the case of Grevillea victoriae above, the publication of Grevillea victoriae subsp. nivalis in 2000 created the autonym Grevillea victoriae subsp. victoriae .
In other words, in 2000 the author chose to recognise a subdivision within the species which differs from what are considered to be &ldquotypical&rdquo Grevillea victoriae, and named it Grevillea victoriae subsp. nivalis. Plants regarded to represent typical Grevillea victoriae assume the name Grevillea victoriae subsp. victoriae.
When referring to a plant in a genus when we do not know which species it is, we use the generic name followed by 'sp.' ie: Grevillea sp.
When referring collectively to some or all of the species in a genus we use the generic name followed by 'spp.' ie: Grevillea spp.
As noted in the examples above, plant names are usually written in italics within a sentence of plain type, or at least in a different type-face, or underlined, to distinguish them from other words. Family names are not italicised, nor are abbreviations like 'subsp.' or 'sp.'.
Naming the plant
The name of a plant is based on an original description, the earliest use of the name generally being the most relevant, dating back as far as 1753 for flowering plants, when Linnaeus published his concept of the binomial naming system.
Each plant name is associated with an original description, including a brief description in Latin (before 2012), which is called a protologue and a nominated 'type specimen' which is an herbarium specimen lodged with a recognised herbarium somewhere in the world.
This original description (the protologue) must be published in a journal or other recognised printed medium. (Since 2012 certain PDF publications on the web, in English, are permitted).
The person/s making this original description in a published journal or book is called the 'author' for that plant name, and their name follows the genus and species in a full citation, for example:
Grevillea victoriae F.Muell.
In this case Ferdinand von Mueller (F.Muell. is a standard abbreviation) published the original description for this species in the Transactions of the Philosophical Society of Victoria, Vol. 1, page 107 in 1855. The author name is not written in italics.
Since our knowledge-base and opinions change with time as more becomes known about the plant group in question, the author citation can become quite complicated as it reflects the published opinion of botanists over time. Thus we can have, for example:
Grevillea pyramidalis subsp. leucadendron (A.Cunn. ex R.Br.) Makinson
(A.Cunn. ex R.Br.) Makinson
The suppliment to Robert Brown's Prodromus in 1830 containing the original description.
The Flora of Australia volume containing Makinson's treatment of Grevillea in 2000.
This name reflects the view of Alan Cunningham in a book published by Robert Brown in 1830, and its status in the opinion of Bob Makinson in 2000 published in the Flora of Australia, Vol. 17A, page 505.
Rules for naming plants
The science of naming plants, or &lsquonomenclature&rsquo is governed by a series of internationally accepted rules and regulations, contained in the International Code of Botanical Nomenclature (or 'Code' for short). The Code was first formulated 1905, and has since been revised at about six-year intervals, based on a consensus of views of taxonomic botanists from around the world. The current International Code of Botanical Nomenclature is known as the Vienna Code, adopted by the Seventeenth International Botanical Congress in Vienna, Austria, in July 2005. If a plant name is published according to the rules of the Code, we say it is a 'valid publication' or it has been 'validly published'.
The most recent (18th) International Botanical Congress held in Melbourne in August 2011 will result in a new edition of the International Code of Botanical Nomenclature.
Type specimens (or &lsquotypes&rsquo) are an integral part of plant nomenclature. Types are generally preserved plant specimens, lodged in a herbarium, but in certain cases types may also be represented by illustrations. Types serve as the designated &lsquostandard&rsquo for a particular author's concept of a published plant name, and they help us determine how names should be applied.
Determining exactly how a particular type specimen affects the application of a particular plant name can be quite complex, and various factors need to be considered. Because of this complexity, the International Code of Botanical Nomenclature recognises many different kinds of types. These are indicated by a prefix before the word '-type', for example: holotype, lectotype, neotype, etc.
Names for cultivars (= cultivated varieties) is more complicated and dictated by another set of rules known as the International Code of Nomenclature for Cultivated Plants, the latest edition published in 2004.
The cultivar name is always added after a valid scientific name at the genus or species level, is not Latinised, is put in single quotes, and is not italicised. ie:
Grevillea 'Robyn Gordon' a cultivar which is a man-made hybrid between two species [photo]
Grevillea rosmarinifolia 'Rosy Posy' a cultivar which is a selected form of a valid species [photo]
Grevillea 'Rosy Posy' is an alternative way of naming this plant, acceptable, but less informative [photo].
For more information on cultivar names, see the web site of the Australian Cultivar Registration Authority.
There is no international convention governing the way common names can be written or used. In fact, in their truest form common names arise from common use by people in contact with the plants &ndash often people who are not aware of the scientific naming of plants.
These true 'common names' are therefore in a range of different languages, different scripts and not codified in any way. The same species of plant can have very different common names in different places, and could have different common names in the same place according to different groups of people. Thus Aboriginal and European people living in the same area might each have very different common names for the same plant.
Sometimes names used by one group of people are adopted by another, sometimes the pronunciation gets corrupted in the process. The aquatic fern Marsilea drummondii is now known by the common name 'Nardoo' , an attempt at converting the spoken Aboriginal name for this plant in one part of Australia into English [another photo].
Using Common (vernacular) Names
There is no universally accepted way of writing common names. However, the following is generally recommended:
- For a name used in a general sense covering a group or genus (e.g. bottlebrush, conifer, oak) start with a lower case letter this also applies to botanical names used in a general sense e.g. banksias, camellias and acacias.
Lumley, Peter & Spencer, Roger (1991) 'Plant Names: A Guide to Botanical Nomenclature', Royal Botanic Gardens, Melbourne.
1 Red Flowering Gum = Corymbia ficifolia
but there are many different species of red flowering gums, ie eucalypts with red flowers.
Initial observations Edit
During the third global pandemic of cholera (1852–1859), there were several scientific research to understand the etiology of the disease.  The miasma theory, which posited that infections spread through contaminated air, was no longer a satisfactory explanation. An English physician John Snow was the first to give convincing evidence in London in 1854 that cholera was spread from drinking water – a contagion, not miasma. Yet he could not identify the pathogens, which made most people still believe in the miasma origin. 
V. cholerae was first observed and recognized under microscope by a French zoologist Félix-Archimède Pouchet. In 1849, Pouchet examined the stool samples of four people having cholera.  His presentation before the French Academy of Sciences on 23 April was recorded as: "[Pouchet] could verify that there existed in these [cholera patients] dejecta an immense quantity of microscopic infusoria." But he made a mistake in believing that the organisms were infusoria, a name then used for microscopic protists, thereby attributing them as Vibrio rigula, a species of protozoan described by Danish naturalist Otto Friedrich Müller in 1786. 
Identification of the bacterium Edit
An Italian physician, Filippo Pacini, while investigating cholera outbreak in Florence in the late 1854, identified the causative pathogen as a new type of bacterium. He performed autopsies of corpses and made meticulous microscopic examinations of the tissues and body fluids. From feces and intestinal mucosa, he identified many comma-shaped bacilli.   Reporting his discovery before the Società Medico-Fisica Fiorentina (Medico-Physician Society of Florence) on 10 December, and published in the 12 December issue of the Gazzetta Medica Italiana (Medical Gazette of Italy), Pacini stated:
Le poche materia del vomito che ho potuto esaminare seconde e terzo caso di cholera. e di plù trovai degli ammassi granulosi appianati, simili a quelli che si formano all superficie delle acque corrotte, quando sono per svilupparsi dei vibrioni dei quali de fatto ne trovai alcuni del genere Bacterium. Mentre la massima parte, per la loro estrema piccoleza, erano stati eliminati con la decantazione del fluido. [From samples of vomit that I have been able to examined in the second and third cases of cholera. I found smoothed granular masses, similar to those which form on the surface of dirty waters, when vibrioni are about to develop in fact I found a genus of Bacterium.  ]
Pacini thus introduced the name vibrioni (Latin vībro means "to move rapidly to and fro, to shake, to agitate"). A Catalan physician Joaquim Balcells i Pascual also reported such bacterium around the same time.   The discovery of the new bacterium was not regarded as medically important as the bacterium was not directly attributed to cholera. Pacini also stated that there was no reason to say that the bacterium caused the disease since he failed to make pure culture and perform experiment, which was necessary ‘to attribute the quality of contagion to cholera’.  The miasma theory was still not ruled out. 
The medical importance and relationship of the bacterium and cholera was discovered by a German physician Robert Koch. In August 1883, Koch, with a team of German physicians, went to Alexandria, Egypt, to investigate cholera epidemic there.  Koch found that the intestinal mucosa of people who died of cholera always had the bacterium, yet could not confirm if it was the causative agent. He moved to Calcutta (now Kolkata) India, where the epidemic was more severe. It was from here that he isolated the bacterium in pure culture on 7 January 1884. He subsequently confirmed that the bacterium was a new species, and described as "a little bent, like a comma."  He reported his discovery to the German Secretary of State for the Interior on 2 February, and published in the Deutsche Medizinische Wochenschrift (German Medical Weekly). 
Although Koch was convinced that the bacterium was the cholera pathogen, he could not entirely establish a critical evidence the bacterium produced the symptoms in healthy subjects (an important element in what was later known Koch's postulates). His experiment on animals using his pure bacteria culture did not cause the disease, and correctly explained that animals are immune to human pathogen. The bacterium was by then known as "the comma bacillus."  It was only in 1959 when an Indian physician Sambhu Nath De in Calcutta isolated the cholera toxin and showed that it caused cholera in healthy subjects that the bacterium-cholera relationship was fully proven.  
Pacini had used the name "vibrio cholera", without proper binomial rendering, for the name of the bacterium.  Following Koch's description, a scientific name Bacillus comma was popularised. But an Italian bacteriologist Vittore Trevisan published in 1884 that Koch's bacterium was the same as that of Pacini's and introduced the name Bacillus cholerae.  A German physician Richard Friedrich Johannes Pfeiffer renamed it as Vibrio cholerae in 1896.  The named was adopted by the Committee of the Society of American Bacteriologists on Characterization and Classification of Bacterial Types in 1920.  In 1964, Rudolph Hugh of the George Washington University School of Medicine proposed to use the genus Vibrio with the type species V. cholerae (Pacini 1854) as a permanent name of the bacterium, regardless of the same name for protozoa.  It was accepted by the Judicial Commission of the International Committee on Bacteriological Nomenclature in 1965,  and the International Association of Microbiological Societies in 1966. 
V. cholerae is a highly motile, comma shaped, gram-negative rod. The active movement of V. cholerae inspired the genus name because "vibrio" in Latin means "to quiver".  Except for v.cholerae and v.mimicus, all other vibrio species are halophilic. Initial isolates are slightly curved, whereas they can appear as straight rods upon laboratory culturing. The bacterium has a flagellum at one cell pole as well as pili. It tolerates alkaline media that kill most intestinal commensals, but they are sensitive to acid. It is a facultative anaerobe, and can undergo respiratory and fermentative metabolism.  It measures 0.3 μm in diameter and 1.3 μm in length  with average swimming velocity of around 75.4 μm/sec. 
V. cholerae pathogenicity genes code for proteins directly or indirectly involved in the virulence of the bacteria. To adapt the host intestinal environment and to avoid being attacked by bile acids and antimicrobial peptides, V. cholera uses its outer membrane vesicles (OMVs). Upon entry, the bacteria sheds its OMVs, containing all the membrane modifications that make it vulnerable for the host attack. 
During infection, V. cholerae secretes cholera toxin (CT), a protein that causes profuse, watery diarrhea (known as "rice-water stool").   This cholera toxin contains 5 B subunits that plays a role in attaching to the intestinal epithelial cells and 1 A subunit that plays a role in toxin activity. Colonization of the small intestine also requires the toxin coregulated pilus (TCP), a thin, flexible, filamentous appendage on the surface of bacterial cells. Expression of both CT and TCP is mediated by two component systems (TCS), which typically consist of a membrane-bound histidine kinase and an intracellular response element.  TCS enable bacteria to respond to changing environments.  In V. cholerae several TCS have been identified to be important in colonization, biofilm production and virulence.  Small RNAs (sRNA) have been identified as targets of V. cholerae TCS.    Here, sRNA molecules bind to mRNA to block translation or induce degradation of inhibitors of expression of virulence or colonization genes.   In V. cholerae the TCS EnvZ/OmpR alters gene expression via the sRNA coaR in response to changes in osmolarity and pH. An important target of coaR is tcpI, which negatively regulates expression of the major subunit of the TCP encoding gene (tcpA). When tcpI is bound by coaR it is no longer able to repress expression tcpA, leading to an increased colonization ability.  Expression of coaR is upregulated by EnvZ/OmpR at a pH of 6,5, which is the normal pH of the intestinal lumen, but is low at higher pH values.  V. cholerae in the intestinal lumen utilizes the TCP to attach to the intestinal mucosa, not invading the mucosa.  After doing so it secretes cholerae toxin causing its symptoms. This then increases cyclic AMP or cAMP by binding (cholerae toxin) to adenylyl cyclase activating the GS pathway which leads to efflux of water and sodium into the intestinal lumen causing watery stools or rice watery stools.
V. cholerae can cause syndromes ranging from asymptomatic to cholera gravis.  In endemic areas, 75% of cases are asymptomatic, 20% are mild to moderate, and 2-5% are severe forms such as cholera gravis.  Symptoms include abrupt onset of watery diarrhea (a grey and cloudy liquid), occasional vomiting, and abdominal cramps.   Dehydration ensues, with symptoms and signs such as thirst, dry mucous membranes, decreased skin turgor, sunken eyes, hypotension, weak or absent radial pulse, tachycardia, tachypnea, hoarse voice, oliguria, cramps, kidney failure, seizures, somnolence, coma, and death.  Death due to dehydration can occur in a few hours to days in untreated children. The disease is also particularly dangerous for pregnant women and their fetuses during late pregnancy, as it may cause premature labor and fetal death.    A study done by the Centers for Disease Control (CDC) in Haiti found that in pregnant women who contracted the disease, 16% of 900 women had fetal death. Risk factors for these deaths include: third trimester, younger maternal age, severe dehydration, and vomiting  Dehydration poses the biggest health risk to pregnant women in countries that there are high rates of cholera. In cases of cholera gravis involving severe dehydration, up to 60% of patients can die however, less than 1% of cases treated with rehydration therapy are fatal. The disease typically lasts 4–6 days.   Worldwide, diarrhoeal disease, caused by cholera and many other pathogens, is the second-leading cause of death for children under the age of 5 and at least 120,000 deaths are estimated to be caused by cholera each year.   In 2002, the WHO deemed that the case fatality ratio for cholera was about 3.95%. 
V. cholerae infects the intestine and causes diarrhea, the hallmark symptom of cholera. Infection can be spread by eating contaminated food or drinking contaminated water.  It also can spread through skin contact with contaminated human feces. Not all infection indicate symptoms, only about 1 in 10 people develop diarrhea. The major symptoms include: watery diarrhea, vomiting, rapid heart rate, loss of skin elasticity, low blood pressure, thirst, and muscle cramps.  This illness can get serious as it can progress to kidney failure and possible coma. If diagnosed, it can be treated using medications. 
V. cholerae has an endemic or epidemic occurrence. In countries where the disease has been for the past three years and the cases confirmed are local (within the confines of the country) transmission is considered to be "endemic."  Alternatively, an outbreak is declared when the occurrence of disease exceeds the normal occurrence for any given time or location.  Epidemics can last several days or over a span of years. Additionally, countries that have an occurrence of an epidemic can also be endemic.  The longest standing V. chloerae epidemic was recorded in Yemen. Yemen had two outbreaks, the first occurred between September 2016 and April 2017, and the second began later in April 2017 and recently was considered to be resolved in 2019.  The epidemic in Yemen took over 2,500 lives and impacted over 1 million people of Yemen  More outbreaks have occurred in Africa, the Americas, and Haiti.
When visiting areas with epidemic cholera, the following precautions should be observed: drink and use bottled water frequently wash hands with soap and safe water use chemical toilets or bury feces if no restroom is available do not defecate in any body of water and cook food thoroughly. Supplying proper, safe water is important.  A precaution to take is to properly sanitize.  Hand hygiene is an essential in areas where soap and water is not available. When there is no sanitation available for hand washing, scrub hands with ash or sand and rinse with clean water.  A single dose vaccine is available for those traveling to an area where cholera is common.
There is a V. cholerae vaccine available to prevent disease spread. The vaccine is known as the, "oral cholera vaccine" (OCV). There are three types of OCV available for prevention: Dukoral®, Shanchol™, and Euvichol-Plus®. All three OCVs require two doses to be fully effective. Countries who are endemic or have an epidemic status are eligible to receive the vaccine based on several criteria: Risk of cholera, Severity of cholera, WASH conditions and capacity to improve, Healthcare conditions and capacity to improve, Capacity to implement OCV campaigns, Capacity to conduct M&E activities, Commitment at national and local level  Since May the start of the OCV program to May 2018 over 25 million vaccines have been distributed to countries who meet the above criteria. 
The basic, overall treatment for Cholera is re-hydration, to replace the fluids that have been lost. Those with mild dehydration can be treated orally with an oral re hydration solution also known as, (ORS).  When patients are severely dehydrated and unable to take in the proper amount of ORS, IV fluid treatment is generally pursued. Antibiotics are used in some cases, typically fluoroquinolones and tetracyclines. 
V. cholerae has two circular chromosomes, together totalling 4 million base pairs of DNA sequence and 3,885 predicted genes.  The genes for cholera toxin are carried by CTXphi (CTXφ), a temperate bacteriophage inserted into the V. cholerae genome. CTXφ can transmit cholera toxin genes from one V. cholerae strain to another, one form of horizontal gene transfer. The genes for toxin coregulated pilus are coded by the Vibrio pathogenicity island (VPI). The entire genome of the virulent strain V. cholerae El Tor N16961 has been sequenced,  and contains two circular chromosomes.  Chromosome 1 has 2,961,149 base pairs with 2,770 open reading frames (ORF's) and chromosome 2 has 1,072,315 base pairs, 1,115 ORF's. The larger first chromosome contains the crucial genes for toxicity, regulation of toxicity, and important cellular functions, such as transcription and translation. 
The second chromosome is determined to be different from a plasmid or megaplasmid due to the inclusion of housekeeping and other essential genes in the genome, including essential genes for metabolism, heat-shock proteins, and 16S rRNA genes, which are ribosomal subunit genes used to track evolutionary relationships between bacteria. Also relevant in determining if the replicon is a chromosome is whether it represents a significant percentage of the genome, and chromosome 2 is 40% by size of the entire genome. And, unlike plasmids, chromosomes are not self-transmissible.  However, the second chromosome may have once been a megaplasmid because it contains some genes usually found on plasmids. 
V. cholerae contains a genomic island of pathogenicity and is lysogenized with phage DNA. That means that the genes of a virus were integrated into the bacterial genome and made the bacteria pathogenic. The molecular pathway involved in expression of virulence is discussed in the pathology and current research sections below.
Bacteriophage CTXφ Edit
CTXφ (also called CTXphi) is a filamentous phage that contains the genes for cholera toxin. Infectious CTXφ particles are produced when V. cholerae infects humans. Phage particles are secreted from bacterial cells without lysis. When CTXφ infects V. cholerae cells, it integrates into specific sites on either chromosome. These sites often contain tandem arrays of integrated CTXφ prophage. In addition to the ctxA and ctxB genes encoding cholera toxin, CTXφ contains eight genes involved in phage reproduction, packaging, secretion, integration, and regulation. The CTXφ genome is 6.9 kb long. 
The main reservoirs of V. cholerae are aquatic sources such as rivers, brackish waters, and estuaries, often in association with copepods or other zooplankton, shellfish, and aquatic plants. 
Cholera infections are most commonly acquired from drinking water in which V. cholerae is found naturally or into which it has been introduced from the feces of an infected person. Cholera is most likely to be found and spread in places with inadequate water treatment, poor sanitation, and inadequate hygiene. Other common vehicles include raw or undercooked fish and shellfish. Transmission from person to person is very unlikely, and casual contact with an infected person is not a risk for becoming ill.  V. cholerae thrives in an aquatic environment, particularly in surface water. The primary connection between humans and pathogenic strains is through water, particularly in economically reduced areas that do not have good water purification systems. 
Nonpathogenic strains are also present in water ecologies. The wide variety of pathogenic and nonpathogenic strains that co-exist in aquatic environments are thought to allow for so many genetic varieties. Gene transfer is fairly common amongst bacteria, and recombination of different V. cholerae genes can lead to new virulent strains. 
A symbiotic relationship between V. cholerae and Ruminococcus obeum has been determined. R. obeum autoinducer represses the expression of several V. cholerae virulence factors. This inhibitory mechanism is likely to be present in other gut microbiota species which opens the way to mine the gut microbiota of members in specific communities which may utilize autoinducers or other mechanisms in order to restrict colonization by V. cholerae or other enteropathogens.
Outbreaks of Cholera cause an estimated 120,000 deaths annually worldwide. There has been roughly seven pandemics since 1817, the first. These pandemics first arose in the Indian subcontinent and spread. 
Two serogroups of V. cholerae, O1 and O139, cause outbreaks of cholera. O1 causes the majority of outbreaks, while O139 – first identified in Bangladesh in 1992 – is confined to Southeast Asia. Many other serogroups of V. cholerae, with or without the cholera toxin gene (including the nontoxigenic strains of the O1 and O139 serogroups), can cause a cholera-like illness. Only toxigenic strains of serogroups O1 and O139 have caused widespread epidemics.
V. cholerae O1 has two biotypes, classical and El Tor, and each biotype has two distinct serotypes, Inaba and Ogawa. The symptoms of infection are indistinguishable, although more people infected with the El Tor biotype remain asymptomatic or have only a mild illness. In recent years, infections with the classical biotype of V. cholerae O1 have become rare and are limited to parts of Bangladesh and India.  Recently, new variant strains have been detected in several parts of Asia and Africa. Observations suggest these strains cause more severe cholera with higher case fatality rates.
An erection occurs when two tubular structures, called the corpora cavernosa, that run the length of the penis, become engorged with venous blood. This may result from any of various physiological stimuli, also known as sexual stimulation and sexual arousal. The corpus spongiosum is a single tubular structure located just below the corpora cavernosa, which contains the urethra, through which urine and semen pass during urination and ejaculation respectively. This may also become slightly engorged with blood, but less so than the corpora cavernosa.
The scrotum may, but not always, become tightened during erection. Generally, in uncircumcised males, the foreskin automatically and gradually retracts, exposing the glans, though some men may have to manually retract their foreskin.
In the presence of mechanical stimulation, erection is initiated by the parasympathetic division of the autonomic nervous system with minimal input from the central nervous system. Parasympathetic branches extend from the sacral plexus into the arteries supplying the erectile tissue upon stimulation, these nerve branches release acetylcholine, which in turn causes release of nitric oxide from endothelial cells in the trabecular arteries.  Nitric oxide diffuses to the smooth muscle of the arteries (called trabecular smooth muscle  ), acting as a vasodilating agent.  The arteries dilate, filling the corpus spongiosum and corpora cavernosa with blood. The ischiocavernosus and bulbospongiosus muscles also compress the veins of the corpora cavernosa, limiting the venous drainage of blood.  Erection subsides when parasympathetic stimulation is discontinued baseline stimulation from the sympathetic division of the autonomic nervous system causes constriction of the penile arteries and cavernosal sinosoids, forcing blood out of the erectile tissue via erection-related veins which include one deep dorsal vein, a pair of cavernosal veins, and two pairs of para-arterial veins between Buck's fascia and the tunica albuginea.   Erection rigidity is mechanically controlled by reduction blood flow via theses veins, and thereby building up the pressure of the corpus cavernosum and corpus spongiosum, an integral instructure, the distal ligament, buttresses the glans penis. 
After ejaculation or cessation of stimulation, erection usually subsides, but the time taken may vary depending on the length and thickness of the penis. 
Voluntary and involuntary control
The cerebral cortex can initiate erection in the absence of direct mechanical stimulation (in response to visual, auditory, olfactory, imagined, or tactile stimuli) acting through erectile centers in the lumbar and sacral regions of the spinal cord. [ citation needed ] The cortex may suppress erection, even in the presence of mechanical stimulation, as may other psychological, emotional, and environmental factors. [ citation needed ]
The penis may become erect during sleep or be erect on waking up. Such an erection is medically known as nocturnal penile tumescence (informally: morning wood or morning glory).    
An erection is a common indicator of sexual arousal and is required for a male to effect vaginal penetration or sexual intercourse. An erection is necessary for natural insemination as well as for the harvesting of sperm for artificial insemination.
Erections are common for children and infants, and even occur before birth.  After reaching puberty, erections occur much more frequently.  The penile plethysmograph, which measures erections, has been used by some governments and courts of law to measure sexual orientation. An unusual aversion to the erect penis is sometimes referred to as phallophobia. 
Spontaneous or random erections
Spontaneous erections, also known as involuntary, random or unwanted erections, are commonplace and a normal part of male physiology. Socially, such erections can be embarrassing if they happen in public or when undesired.  Such erections can occur at any time of day, and if clothed may cause a bulge which (if required) can be disguised or hidden by wearing close-fitting underwear, a long shirt, or baggier clothes. 
The length of the flaccid penis is not necessarily indicative of the length of the penis when it becomes erect, with some smaller flaccid penises growing much longer, while some larger flaccid penises growing comparatively less.  Generally, the size of an erect penis is fixed throughout post-pubescent life. Its size may be increased by surgery,  although penile enlargement is controversial, and a majority of men were "not satisfied" with the results, according to one study. 
Though the size of a penis varies considerably between males, the average length of an erect human penis is 13.12 cm (5.17 inches), while the average circumference of an erect human penis is 11.66 cm (4.59 inches). 
Although many erect penises point upwards, it is common and normal for the erect penis to point nearly vertically upwards or nearly vertically downwards or even horizontally straight forward, all depending on the tension of the suspensory ligament that holds it in position. An erect penis can also take on a number of different shapes, ranging from a straight tube to a tube with a curvature up or down or to the left or right. An increase in penile curvature can be caused by Peyronie's disease. This may cause physical and psychological effects for the affected individual, which could include erectile dysfunction or pain during an erection. Treatments include oral medication (such as colchicine) or surgery, which is most often performed only as a last resort.
The following table shows how common various erection angles are for a standing male. In the table, zero degrees (0°) is pointing straight up against the abdomen, 90° is horizontal and pointing straight forward, and 180° is pointing straight down to the feet. An upward pointing angle is most common.
|Angle (°)||Percent of population|
Erectile dysfunction (also known as ED or "(male) impotence") is a sexual dysfunction characterized by the inability to develop and/or maintain an erection.   The study of erectile dysfunction within medicine is known as andrology, a sub-field within urology. 
Erectile dysfunction occurs for a variety of reasons. Ultimately, the cause for erectile dysfunction is that not enough nitric oxide (NO) is released by the vascular endothelium of the branches of the perineal artery, a branch of the internal pudendal artery.
Erectile dysfunction may occur due to physiological or psychological reasons, most of which are amenable to treatment. Common physiological reasons include diabetes, kidney disease, chronic alcoholism, multiple sclerosis, atherosclerosis, vascular disease, including arterial insufficiency and venogenic erectile dysfunction,  and neurologic disease which collectively account for about 70% of ED cases.  Some drugs used to treat other conditions, such as lithium and paroxetine, may cause erectile dysfunction.  
Erectile dysfunction, tied closely as it is to cultural notions of potency, success and masculinity, can have devastating psychological consequences including feelings of shame, loss or inadequacy.  There is a strong culture of silence and inability to discuss the matter. Around one in ten men experience recurring impotence problems at some point in their lives. 
Priapism is a painful condition in which the penis does not return to its flaccid state, despite the absence of both physical and psychological stimulation. Priapism lasting over four hours is a medical emergency.
At the time of penetration, the canine penis is not erect, and only able to penetrate the female because it includes a narrow bone called the baculum, a feature of most placental mammals. After the male achieves penetration, he will often hold the female tighter and thrust faster, and it is during this time that the male's penis expands. Unlike human sexual intercourse, where the male penis commonly becomes erect before entering the female, canine copulation involves the male first penetrating the female, after which swelling of the penis to erection occurs. 
An elephant's penis is S-shaped when fully erect and has a Y-shaped orifice. 
Given the small amount of erectile tissue in a bull's penis, there is little enlargement after erection. The penis is quite rigid when non-erect, and becomes even more rigid during erection. Protrusion is not affected much by erection, but more by relaxation of the retractor penis muscle and straightening of the sigmoid flexure.  
A male fossa's penis reaches to between his forelegs when erect. 
When not erect, a horse's penis is housed within the prepuce, 50 centimetres (20 in) long and 2.5 to 6 centimetres (0.98 to 2.36 in) in diameter with the distal end 15 to 20 centimetres (5.9 to 7.9 in). The retractor muscle contracts to retract the penis into the sheath and relaxes to allow the penis to extend from the sheath.  When erect, the penis doubles in length  and thickness and the glans increases by 3 to 4 times .  Erection and protrusion take place gradually, by the increasing tumescence of the erectile vascular tissue in the corpus cavernosum penis.   Most stallions achieve erection within 2 minutes of contact with an estrus mare, and mount the estrus mare 5–10 seconds afterward. 
A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood.  The penis of the lake duck can reach about the same length as the animal himself when fully erect, but more commonly is about half the bird's length.  
Clinically, erection is often known as "penile erection", and the state of being erect, and process of erection, are described as "tumescence" or "penile tumescence". The term for the subsiding or cessation of an erection is "detumescence".
Colloquially and in slang, erection is known by many informal terms. Commonly encountered English terms include 'stiffy', 'hard-on', 'boner' and 'woody'.  There are several slang words, euphemisms and synonyms for an erection in English and in other languages. (See also The WikiSaurus entry.)
Serratia Marcescens as a Cancer Therapy?
Prodigiosin taken from strains of S. marcescens has been shown to be toxic to cancerous cells but much less so to non-cancerous ones. Because of this, prodigiosin is currently being studied as a natural medicine for cancer therapy. Cell toxicity – even to healthy cells – has always been a problem in the development of anticancer drugs. Microorganism metabolites such as prodigiosin – the pigment that produces the red coloration in S. marcescens colonies – inhibit certain cancer cell signaling pathways causing early cancer cell death however, the exact action is not yet understood. Current studies have shown anticancerous activity of prodigiosin in breast cancer, prostate cancer, and choriocarcinoma although all of these studies took place in the laboratory. This area of study is known as bacteria-mediated cancer therapy or BMCT and is becoming increasingly popular as a pharmaceutical industry research topic.
1. Which of these numbers represents a 5-log reduction?
C. 9999 log
2. SSR refers to:
A. Starvation-stress cross-reference response
B. Starvation-survival response
C. Starvation-induced cross-resistance response
D. Starvation-stress response
3. What is BMTC?
A. A type of bacterial resistance to antimicrobial drugs
B. A pigment found in S. marcescens bacteria
C. Therapy for cancer using products produced by some single-celled microorganisms
D. A temperature-linked mechanism that increases bacterial survival in higher temperatures
Class 12 Biology Chapter 6 DNA Fingerprinting
DNA fingerprinting is a technique used to identify the individual by sample of their respective DNA profiles.
DNA fingerprinting was invented in 1984 by British geneticist Sir Alec Jeffreys.
The basis of identification by DNA Profiling is polymorphism. These highly variable sequences of DNA are known as VNTRs (Variable Number of Tandem Repeats) and STRs (Short Tandem Repeats) often referred to as Minisatellites and Microsatellites. These are numerous small non-coding but inheritable sequences of bases which are repeated many times.
Each individual has a unique pattern of minisatellite and microsatellite DNA, except identical twins or monozygotic twins. Identical twins have the same genotype as they develop from the same zygote.
DNA fingerprinting is also known as DNA probe, DNA profiling, DNA typing, genetic fingerprinting, restriction fragment length polymorphism.
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Steps Of DNA Fingerprinting:
- Isolation of DNA
- Digestion of DNA by restriction endonucleases
- Separation of DNA fragments by electrophoresis,
- Transferring (blotting) of separated DNA fragments to synthetic membranes, such as nitrocellulose or nylon,
- Hybridisation using labelled VNTR probe, and
- Detection of hybridised DNA fragments by autoradiography.
Extracting DNA from Cells
Collecting a sample containing genetic material must be treated with different chemicals. Common sample types used today include blood and cheek swabs.
These samples must be treated with a series of chemicals to break open cell membranes, expose the DNA sample, and remove unwanted components – such as lipids and proteins – until relatively pure DNA emerges.
If the amount of DNA in a sample is small, scientists may wish to perform PCR – Polymerase Chain Reaction – amplification of the sample.
Treatment with Restriction Enzymes
The best markers for use in quick and easy DNA profiling are those which can be reliably identified using common restriction enzymes, but which vary greatly between individuals.
For this purpose, scientists use repeat sequences – portions of DNA that have the same sequence so they can be identified by the same restriction enzymes, but which repeat a different number of times in different people. Types of repeats used in DNA profiling include Variable Number Tandem Repeats (VNTRs), especially short tandem repeats (STRs), which are also referred to by scientists as “microsatellites” or “minisatellites.”
Once sufficient DNA has been isolated and amplified, if necessary, it must be cut with restriction enzymes to isolate the VNTRs. Restriction enzymes are enzymes that attach to specific DNA sequences and create breaks in the DNA strands.
In genetic engineering, DNA is cut up with restriction enzymes and then “sewn” back together by ligases to create new, recombinant DNA sequences. In DNA profiling, however, only the cutting part is needed. Once the DNA has been cut to isolate the VNTRs, it’s time to run the resulting DNA fragments on a gel to see how long they are.
Gel electrophoresis is a brilliant technology that separates molecules by size. The “gel” in question is a material that molecules can pass through, but only at a slow speed.
Just as air resistance slows a big truck more than it does a motorcycle, the resistance offered by the electrophoresis gel slows large molecules down more than small ones. The effect of the gel is so precise that scientists can tell exactly how big a molecule is by seeing how far it moves within a given gel in a set amount of time.
In this case, measuring the size of the DNA fragments from the sample that has been treated with a restriction enzyme will tell scientists how many copies of each VTNR repeat the sample DNA contains.
It’s called 𠇎lectrophoresis” because, to make the molecules move through the gel, an electrical current is applied. Because the sugar-phosphate backbone of the DNA has a negative electrical charge, the electrical current tugs the DNA along with it through the gel.
By looking at how many DNA fragments the restriction enzymes produced and the sizes of these fragments, the scientists can 𠇏ingerprint” the DNA donor.
Performing Southern Blot
Now that the DNA fragments have been separated by size, they must be transferred to a medium where scientists can “read” and record the results of the electrophoresis.
To do this, scientists treat the gel with a weak acid, which breaks up the DNA fragments into individual nucleic acids that will more easily rub off onto paper. They then 𠇋lot” the DNA fragments onto nitrocellulose paper, which fixes them in place.
Treatment with Radioactive Probe
Now that the DNA is fixed onto the blotting paper, it is treated with a special probe chemical that sticks to the desired DNA fragments. This chemical is radioactive, which means that it will create a visible record when exposed to X-ray paper.
This method of blotting DNA fragments onto nitrocellulose paper and then treating it with a radioactive probe was discovered by a scientist named Ed Southern – hence the name “Southern blot.”
Amusingly, the fact that the Southern blot is named after a scientist and not the direction “south” did not stop scientists from naming similar methods “northern” and “western” blots in honor of the Southern blot.
X-Ray Film Exposure
The last step of the process is to turn the information from the DNA fragments into a visible record. This is done by exposing the blotting paper, with its radioactive DNA bands, to X-ray film.
X-ray film is veloped” by radiation, just like camera film is developed by visible light, resulting in a visual record of the pattern produced by the person’s DNA 𠇏ingerprint.”
To ensure a clear imprint, scientists often leave the X-ray film exposed to the weakly radioactive Southern blot paper for a day or more.
Once the image has been developed and fixed to prevent further light exposure from changing the image, this 𠇏ingerprint” can be used to determine if two DNA samples are the same or similar.
APPLICATIONS OF FINGERPRINTING DNA:
This process is frequently used in following cases:
Criminal investigations to determine whether blood or tissue samples found at crime scenes could belong to a given suspect.
- Match tissues of organ donors with those of people who need transplants.
- Identify diseases that are passed down through your family.
- Help find cures for those diseases, called hereditary conditions.
In science, DNA fingerprinting is used in the story of plant and animal populations to determine how closely related species and populations are to other species and populations. Further, it can track their spread over time. This ability to look directly at an organism’s gene markers has revolutionized our understanding of zoology, botany, agriculture, and even human history.