Sudoku, the Imitation Game, pizza, a robot sorter and transposons - the real ways of science are more amazing than all imaginable and unimaginable inventions. Following these paths, biologists create genetic maps and legends for them, understanding what each gene is responsible for.
Researchers at Princeton and Harvard have figured out how to create a tool to figure out gene function faster and cheaper. A report on the work appeared in the scientific journal Nature Communications.
Why are genes knocked out?
“We have no idea what quite large groups of genes do,” admits Baz Barstow, co-author of the paper and a Burroughs-Wellcome Research Fellow in the chemistry department at Princeton University. Even if the genome of an organism has been deciphered and read, this does not mean that there are no mysteries left in it. You can find out where a gene is located, imagine what protein it encodes, but it is almost impossible to understand what this protein does in the body using only calculations.
How do they do this? To answer this question, imagine a situation: in one room you see endless rows of switches, and in another room there are a huge number of light bulbs on. The wires are hidden in the wall. The best way to figure out which light bulb the switch is connected to is to turn it off and see which one goes out. The same thing is done with genes. The light bulbs are the phenotypic traits we observe in an organism, and the light switches are the genome. To understand what a gene is responsible for, the easiest way is to “turn off” it and look at the result. In English, this deliberate blocking of a gene is called “knocking-out,” that is, “knockout.”
But to find out the functions of a large number of genes requires a huge investment of time and money - years and millions of dollars. Because of this, genetic maps with fully deciphered functions of each gene exist only for a small number of well-studied model organisms, such as baker's yeast or bacteria. Escherichia coli(Escherichia coli), although the enormous information content and usefulness of such knockout collections is beyond doubt. Since their publication, thousands of research groups have accessed them.
Even pizza didn't help
Scientists from Princeton and Harvard universities have found a way to establish the functions of each gene quickly and easily. Now it will only take a few thousand dollars, and the whole process will take less than a month. The new technology is called “knockout Sudoku” in honor of the puzzle of the same name.
This technique is based on random gene knockout and a powerful algorithm that helps “fill in the missing cells” in the genomic puzzle. None of the research groups that have previously tried the same approach have come close to the cost and speed that Knockout Sudoku will bring to the scientific community. “We hope that genetics will finally move beyond the study of model organisms,” says Michael Baum, co-author of the paper from Harvard Medical School.
Knockout Sudoku scheme
The research began with a huge pile of pizza receipts and transposon mutagenesis. This method allows you to insert one DNA sequence into a random gene, blocking its operation. However, this requires many mutant copies to be sure that each gene is turned off in at least one of them. Scientists started with a colony of 40,000 bacteria Shewanella oneidensis, which has about 3600 genes. To manually sort the mutants and resettle them into different holes, Barstow hired students, whose labor he promised to pay with pizza. After a whole day of work, the results were disappointing: only a few thousand bacteria were sorted.
As a result, it was decided to rent a sorting robot. In just two days, he distributed all the mutants into 417 individual wells on 96-well plates. But the real test was to read the genomes of all the mutant variants so that they could be listed, identifying the function of each knocked-out gene. To do this, the DNA of each mutant variant is usually amplified (“multiplied”) and then sequenced (its sequence read). Genetics proposed to simplify this complex and time-consuming part of the work by grouping various mutants in a special way, as a result of which it was necessary to read not 417 genomes, but 61, which is almost 7 times less.
“Multicellular” puzzles were tested on single-celled genomes
But even the results of this entire long process are received by scientists in the form of a huge pile of data that needs to be processed in order to understand from which mutants the sequences (read genomic sequences) were obtained. To cope with this problem, the researchers created an algorithm that, like a person solving Sudoku, could identify the tablet, column and row of the hole where the mutant variant came from. There was one more problem. Since the mutations were caused by a transposon spontaneously inserting into the genome, they could be repeated randomly. To find a solution, Barstow even watched The Imitation Game, a film about Alan Turing cracking the code of the German Enigma cipher machine. In his opinion, the work was truly akin to cracking a code. “For example, in English the letter “a” is used with a frequency of 8.2%. Therefore, if you encounter an unknown letter that appears with a frequency of 8.2%, you can assume that the letter you are looking for is "a." This simple statistical inference, also called Bayesian (in honor of the 18th-century English mathematician and priest Thomas Bayes), became the key to solving “knockout Sudoku.”
The authors of the work emphasize that the mathematical methods underlying the technology make it possible to obtain much more results from fewer experiments. This method helped them understand the work of bacterial genes. Shewanella oneidensis, which are known for their ability to transfer electrons, are potential sources of electricity that does not harm nature and can be used in artificial photosynthesis (which you can read more about in the review site: and) and to neutralize nuclear waste. Using old methods, this would have required about 15 years of research.
The accuracy of the results was quite low at first. Having rechecked the mathematical calculations and found no errors there, the scientists turned to the plates and wells. It turned out that the problem was that one of the assistants had placed one wrong sample there. The researchers breathed a sigh of relief: the most unreliable part of their technology turned out to be humans.
“Genetically modified products” - “Yes” - 26 people “No” - 24 people “Difficult to answer” - 1 person. Hypotheses. 130 RESPONDENTS/students of 1st, 2nd, 3rd, and 4th courses took part in the survey. “Yes” - 44 people “No” - 5 people “Sometimes” - 2 people. B-12 Dyakova Nadezhda. The work was carried out by student gr. Methods: Do you use GMO products?
“Gene interaction” - Phenotype splitting in F2 3:1. Dictionary. Inheritance under incomplete dominance. R. Complete dominance. Cooperation. Prepared: Art. 18 groups of 1st year of medical faculty. Gene. H. J.B. Epistasis. G. III group. Gene interaction.
"Transgenic organisms" - What do we eat? Tomatoes with the flounder gene. Whose products contain transgenic components. Genetic engineering. A breed of pigs with a “growth” gene. How are GMOs made? Genetics have learned to make chimeras. Transgenic animals. TO EAT OR NOT TO EAT? - that is the question. Gmo: for or against? GMP is a large and promising business. Transgenic goats produce a unique milk that replaces human breast milk.
"Translation" - Model of hybrid states. Initiation factors associated with the small ribosomal subunit (prokaryotes). Translation regulation: export of mRNA from the nucleus to the cytoplasm. Degradation of mRNA by endonucleases. Programmed reading frame shift. Trans broadcast. Translation regulation: ribo switches. Secondary structure of rRNA (1).
“GMO” - And in nature there are organisms that are unsuitable for human food (poisonous and mutagenic). Presentation on the topic Genetically modified organism (GMO). How to distinguish GM products? Safety of GMOs. Work on the creation of GMOs must continue. Creators of GMOs. Use of GMOs. Content. Greenpeace's position.
“Discoveries in genetics” - 1935 -N. Present genetics Transgenic organisms. O. Avery. Discovery of the laws of heredity. Development of chromosome theory. The past of genetics. A. Hershey. Cloning. John Gurdon is an English microbiologist who pioneered cloning. Decoding the structure of the DNA molecule. In 1953, the English biophysicist and geneticist F. Crick and the American biochemist J.
There are 16 presentations in total
Alchemy-Genetics - game on Android, with which you will cross different animals and eventually get new species. Select animals and fix them on the screen to quickly view various combinations. And there can be a lot of them, up to 450 new species, from obvious to incredible. Russian language: yes Supports installation on an external SD card: no. Download Alchemy Alchemy for Android for free. Peculiarities games: Animated figures of magical creatures Hints for beginners Detailed training course Several modes games Clear interface Ability to change camera angle System requirements: OS: Windows XP Processor: Intel Pentium® III 800 MHz RAM: 128 MB Free space on HDD: 100 MB Year of manufacture: 2008 Language: Russian Medicine: not required Size: 49.79 MB. GameXworld.net - Download games free » game alchemy genetics tips.
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Android games» Puzzles » Alchemy~Genetics. Game language: English. Release date: December 13, 2013 Interesting selections - Games, entertainment and programs - Game - alchemy game genetics answers. Area 51 ( English. Area 51) - American military airfield, deleted by crisis 2 - game year. Crysis 2 (pronounced [?kr??s?s tu?]) - computer game, Poker card game.
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Alchemy Genetics Alchemy~genetics. Game from the series Alchemy, where you need to connect different Alchemy-Genetics- a fun logic puzzle that asks the player to cross a variety of animals. Adviсe And tips.. A powerful healing elixir, available at skill level 7 alchemy, .. Unlike other plants, the Forbidden Fruit can only be created through a genetic experiment in a scientific facility. Answers Alchemy-Genetics games. Meaning games such is Chicken + Elephant[GIANT] = Ostrich(Giant chicken). That's all, if you are too lazy to rummage through the notes, you can ask in the discussion. Answers Alchemy-Genetics games. seagull + tyrannosaurus = sea gull. Russian language. Description games Alchemy Genetics (Alchemy Genetics): You are crazy geneticist and at your disposal is a whole laboratory, equipped with everything possible to conduct various experiments. Your task will be to cross different types of animals, birds and fish in order to breed new species. English language for children and adults. A month of training for free!
Alchemy, as we know, has long been no good as a science. But as a fun activity that allows you to practice logic and just have a great time, alchemy is both loved and respected. Otherwise, where would so many popular games with this title come from on Google Play? But if usually games of this type offer you to conjure with inanimate objects, Alchemy-Genetics offers to try on the robe of a mad scientist, who, out of the kindness of his heart, crosses a variety of creatures, getting... However, what you get - you will see for yourself.
The developer immediately warns: the game is exclusively for those who have a good sense of humor. Like the recipes for historical alchemy, the proposed actions are completely unscientific and not educational. As in any Alchemy game, crossing creatures is done by simply dragging them on top of each other. No matter how counterintuitive many combinations may seem, there is always a little common sense in these combinations. Every creature, be it a real animal or a mythical creature, has your trait, your “gene”, which ensures the desired transformation in the end.
The developer illustrates his idea like this:
- An ant (insect) in combination with a rat (the “tailed” gene) gives the result Scorpio- tailed (rat) arthropod (ant)
- Anchovy (fish) in combination with chicken (the “domestic” gene) gives goldfish- domestic (chicken) fish (anchovy)
So you don’t always need to think about what can come out of a marriage between two different animals - rather, you need to take only one of their characteristics, resulting in something unexpected with some logical constructions and completely natural with others. It is difficult to imagine the descendant of a chicken and a fish, but it is not at all difficult to imagine what a domestic fish looks like.
For the most meticulous players, I offer a selection of 113 recipes to the game Alchemy-Genetics from different players. I organized the combinations that seemed the most difficult to them into a list and saved everything in PDF format. You can download the game itself and recipes for it using the links below this article. I leave half of the recipes I collected under the spoiler. It is more convenient to use this list in the full file - there you can search for the creature you want to get (or the combinations of which you are interested in), and immediately find the recipe or make sure it is missing. This is exactly how I recommend using it.
- Ant+pike=fire ant
- Butterfly + elephant = common tongue
- Blue frog + man=NAVI
- Eagle+man=Ra
- Dwarf+squirrel=Hobbit
- Chicken+golden carp=pigeon
- Piranha+snake=shark
- Jackal+guinea pig=dog
- Android + human = wallie
- Human + alien = sea mermaid
- Coyote + man = anubis
- Dog + fire ant = wolf
- Dog + wolf = dingo dog
- Raccoon + tiger = ring-tailed lemur
- Octopus + scorpion = blue-ringed octopus
- Wolf + kangaroo = thylacine
- Ghost + piranha = dementor.
- Ant + rat = scorpio
- Anchovy + chicken = goldfish
- Seal+chicken=penguin
- Monitor lizard + Hippopotamus = crocodile
- Iguana + fly = monitor lizard
- Ant + snake = spider
- Cat+chameleon=Cheshire cat
- Eagle + ostrich = falcon
- Crab+griffin=headcrab
- Crab+hornbird=headcrab
- Eagle+hornbird=griffin
- Horse+hornbird=Moose
- Monitor lizard + dolphin = crocodile
- Deer + camel = giraffe
- Hamster+rat=Hamster rat
- Pigeon + chipmunk = Do-do
- Piranha + do-do = shark.
- Crab + snake = sea cucumber
- Snake+horned bird=Horned snake
- Rat+snake+pasyuk
- Snake+emperor scorpion=Boa
- Snake+duck=eel
- Snake+shrimp=moray eel
- Snake+bee=coral snake
- Snake+hare=Lizard
- Snake+lion=tatzelwurm
- Snake+Guppy=Brahman blind bird
- Worm + goliath tarantula = snake
- Monkey + ant = man
- Ring-tailed lemur + flying squirrel = monkey
- Squirrel + Flying Fish = Flying Squirrel
- Raven+dove=parrot
- Dove+parrot=pied dove
- Duck+dove=swan
- Pigeon+pig=Do-Do
- Pigeon+raccoon=Jacobins
- Dove+Griffin=angel
- Cat+hippo=lynx
- Cat+mangrove ant=garfield
- Cat+seal=manul
- Seal+cat=dolphin
