159-566: Variants: CRISPR ( / ˈ k r ɪ s p ər / ) (an acronym for c lustered r egularly i nterspaced s hort p alindromic r epeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea . Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play
318-428: A numeronym . For example, "i18n" abbreviates " internationalization ", a computer-science term for adapting software for worldwide use; the "18" represents the 18 letters that come between the first and the last in "internationalization". Similarly, "localization" can be abbreviated "l10n"; " multilingualization " "m17n"; and " accessibility " "a11y". In addition to the use of a specific number replacing that many letters,
477-645: A single word ("television" or "transvestite", for instance), and is in general spelled without punctuation (except in the plural). Although "PS" stands for the single English word " postscript " or the Latin postscriptum , it is often spelled with periods ("P.S.") as if parsed as Latin post scriptum instead. The slash ('/', or solidus ) is sometimes used to separate the letters in an acronym, as in "N/A" ("not applicable, not available") and "c/o" ("care of"). Inconveniently long words used frequently in related contexts can be represented according to their letter count as
636-600: A 'staggered' cut in double stranded DNA as opposed to the 'blunt' cut produced by Cas9, relying on a 'T rich' PAM (providing alternative targeting sites to Cas9), and requiring only a CRISPR RNA (crRNA) for successful targeting. By contrast, Cas9 requires both crRNA and a trans-activating crRNA (tracrRNA). These differences may give Cas12a some advantages over Cas9. For example, Cas12a's small crRNAs are ideal for multiplexed genome editing, as more of them can be packaged in one vector than can Cas9's sgRNAs. The sticky 5′ overhangs left by Cas12a can also be used for DNA assembly that
795-507: A 1940 translation of a novel by the German writer Lion Feuchtwanger . It is an unsettled question in English lexicography and style guides whether it is legitimate to use the word acronym to describe forms that use initials but are not pronounced as a word. While there is plenty of evidence that acronym is used widely in this way, some sources do not acknowledge this usage, reserving
954-417: A 2015 paper by Chinese scientists P. Liang and Y. Xu. The system made a successful cleavage of mutant Beta-Hemoglobin ( HBB ) in 28 out of 54 embryos. Four out of the 28 embryos were successfully recombined using a donor template. The scientists showed that during DNA recombination of the cleaved strand, the homologous endogenous sequence HBD competes with the exogenous donor template. DNA repair in human embryos
1113-597: A European encounter with yogurt occurs in French clinical history: Francis I suffered from a severe diarrhea which no French doctor could cure. His ally Suleiman the Magnificent sent a doctor, who allegedly cured the patient with yogurt. The grateful king told many of the food that had cured him. Until the 1900s, yogurt was a staple in diets of people in the Russian Empire (and especially Central Asia and
1272-524: A PAM sequence, with the other end of the spacer cut using a ruler mechanism, thus maintaining the regularity of the spacer size in the CRISPR array. The conservation of the PAM sequence differs between CRISPR-Cas systems and appears to be evolutionarily linked to Cas1 and the leader sequence . New spacers are added to a CRISPR array in a directional manner, occurring preferentially, but not exclusively, adjacent to
1431-586: A cluster of interrupted direct repeats (DR) in that bacterium. They recognized the diversity of the sequences that intervened in the direct repeats among different strains of M. tuberculosis and used this property to design a typing method called spoligotyping , still in use today. Francisco Mojica at the University of Alicante in Spain studied the function of repeats in the archaeal species Haloferax and Haloarcula . Mojica's supervisor surmised that
1590-836: A cold soup. Ashe-Mâst is a warm yogurt soup with fresh herbs, spinach and lentils. Even the leftover water extracted when straining yogurt is cooked to make a sour cream sauce called kashk , which is usually used as a topping on soups and stews. Matsoni is a Georgian yogurt in the Caucasus and Russia. Tarator and cacık are cold soups made from yogurt during summertime in eastern Europe. They are made with ayran , cucumbers , dill , salt, olive oil, and optionally garlic and ground walnuts . Tzatziki in Greece and milk salad in Bulgaria are thick yogurt-based salads similar to tarator. Khyar w Laban (cucumber and yogurt salad)
1749-530: A complex of Cas proteins called Cascade, that in E. coli cut the CRISPR RNA precursor within the repeats into mature spacer-containing RNA molecules called CRISPR RNA (crRNA), which remained bound to the protein complex. Moreover, it was found that Cascade, crRNA and a helicase/nuclease ( Cas3 ) were required to provide a bacterial host with immunity against infection by a DNA virus . By designing an anti-virus CRISPR, they demonstrated that two orientations of
SECTION 10
#17327648894191908-568: A dessert in India, is made from strained yogurt, saffron , cardamom , nutmeg and sugar and sometimes fruits such as mango or pineapple . In North America, strained yogurt is commonly called "Greek yogurt". Powdered milk is sometimes added in lieu of straining to achieve thickness. In Britain as "Greek-style yogurt". In Britain the name "Greek" may only be applied to yogurt made in Greece. Ayran, doogh ("dawghe" in Neo-Aramaic ) or dhallë
2067-417: A different Cas protein in the complex, Cas10. The DNA cleavage was shown to be transcription dependent. The mechanism for distinguishing self from foreign DNA during interference is built into the crRNAs and is therefore likely common to all three systems. Throughout the distinctive maturation process of each major type, all crRNAs contain a spacer sequence and some portion of the repeat at one or both ends. It
2226-625: A different meaning. Medical literature has been struggling to control the proliferation of acronyms, including efforts by the American Academy of Dermatology. Acronyms are often taught as mnemonic devices: for example the colors of the rainbow are ROY G. BIV (red, orange, yellow, green, blue, indigo, violet). They are also used as mental checklists: in aviation GUMPS stands for gas-undercarriage-mixture-propeller-seat belts. Other mnemonic acronyms include CAN SLIM in finance, PAVPANIC in English grammar, and PEMDAS in mathematics. It
2385-464: A few more weeks. It is sometimes used with onions, meat, and nuts as a stuffing for a variety of pies or kibbeh balls. Some types of strained yogurts are boiled in open vats first, so that the liquid content is reduced. The East Indian dessert, a variation of traditional dahi called mishti dahi , offers a thicker, more custard-like consistency, and is usually sweeter than western yogurts. In western Indian (Marathi and Gujarati) cuisine, strained yogurt
2544-712: A filter, traditionally made of muslin and more recently of paper or non-muslin cloth. This removes the whey , giving a much thicker consistency. Strained yogurt is made at home, especially if using skimmed milk which results in a thinner consistency. Yogurt that has been strained to filter or remove the whey is known as Labneh in Middle Eastern countries. It has a consistency between that of yogurt and cheese. It may be used for sandwiches in Middle Eastern countries. Olive oil, cucumber slices, olives, and various green herbs may be added. It can be thickened further and rolled into balls, preserved in olive oil, and fermented for
2703-686: A horse-drawn wagon inscribed with the Armenian word " madzoon " which was later changed to "yogurt", the Turkish language name of the product, as Turkish was the lingua franca between immigrants of the various Near Eastern ethnicities who were the main consumers at that time. Yogurt's popularity in the United States was enhanced in the 1950s and 1960s, when it was presented as a health food by scientists like Hungarian-born bacteriologist Stephen A. Gaymont . Plain yogurt still proved too sour for
2862-410: A key role in the antiviral (i.e. anti- phage ) defense system of prokaryotes and provide a form of heritable, acquired immunity . CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea. Cas9 (or "CRISPR-associated protein 9") is an enzyme that uses CRISPR sequences as a guide to recognize and open up specific strands of DNA that are complementary to
3021-928: A lower risk of developing type 2 diabetes and a lower incidence of hip fracture in post-menopausal women. A 2021 review found a cause-and-effect relationship between yogurt consumption and improved lactose tolerance and digestion, and that potential associations exist between yogurt consumption and improving bone health, as well as lowering the risk of some diseases, including cancers and metabolic syndrome . Yogurt made with raw milk can be contaminated with bacteria that can cause significant illness and even result in death, including Listeria , Cryptosporidium , Campylobacter , Brucella , Escherichia coli and Salmonella . Yogurts can also be contaminated with aflatoxin -producing Aspergillus flavus , Aspergillus parasiticus and Aspergillus nomius . Contamination occurs in traditionally prepared yogurts more often than industrially processed ones, but may affect
3180-781: A medial decimal point . Particularly in British and Commonwealth English , all such punctuation marking acronyms and other capitalized abbreviations is now uncommon and considered either unnecessary or incorrect. The presence of all-capital letters is now thought sufficient to indicate the nature of the UK , the EU , and the UN . Forms such as the U.S.A. for "the United States of America " are now considered to indicate American or North American English . Even within those dialects, such punctuation
3339-462: A minority variant of the French yaourt , although yogurt and yoghurt are also used. Analysis of the L. delbrueckii subsp. bulgaricus genome indicates that the bacterium may have originated on the surface of a plant. Milk may have become spontaneously and unintentionally exposed to it through contact with plants, or bacteria may have been transferred from the udder of domestic milk-producing animals. The origins of yogurt are unknown but it
SECTION 20
#17327648894193498-407: A period when the letters are pronounced individually, as in " K.G.B. ", but not when pronounced as a word, as in " NATO ". The logic of this style is that the pronunciation is reflected graphically by the punctuation scheme. When a multiple-letter abbreviation is formed from a single word, periods are in general not used, although they may be common in informal usage. "TV", for example, may stand for
3657-514: A phage infection, the sequence of the CRISPR spacer must correspond perfectly to the sequence of the target phage gene. Phages can continue to infect their hosts' given point mutations in the spacer. Similar stringency is required in PAM or the bacterial strain remains phage sensitive. A study of 124 S. thermophilus strains showed that 26% of all spacers were unique and that different CRISPR loci showed different rates of spacer acquisition. Some CRISPR loci evolve more rapidly than others, which allowed
3816-522: A proportion of the Daily Value (DV), a serving of yogurt is a rich source of vitamin B 12 (31% DV) and riboflavin (23% DV), with moderate content of protein, phosphorus , and selenium (14 to 19% DV; table). Tilde (~) represents missing or incomplete data. The above shows little difference exists between whole milk and yogurt made from whole milk with respect to the listed nutritional constituents. Because it may contain live cultures, yogurt
3975-549: A role for the RNA transcript of spacers on target recognition in a mechanism that could be analogous to the RNA interference system used by eukaryotic cells. Koonin and colleagues extended this RNA interference hypothesis by proposing mechanisms of action for the different CRISPR-Cas subtypes according to the predicted function of their proteins. Experimental work by several groups revealed the basic mechanisms of CRISPR-Cas immunity. In 2007,
4134-420: A role in the dynamic structure of the CRISPR loci. In this publication, the acronym CRISPR was used as the universal name of this pattern, but its function remained enigmatic. In 2005, three independent research groups showed that some CRISPR spacers are derived from phage DNA and extrachromosomal DNA such as plasmids . In effect, the spacers are fragments of DNA gathered from viruses that previously attacked
4293-432: A safe product. Acidity alone has been questioned by recent outbreaks of food poisoning by E. coli O157:H7 that is acid-tolerant. E. coli O157:H7 is easily destroyed by pasteurization (heating); the initial heating of the milk kills pathogens as well as denaturing proteins. The microorganisms that turn milk into yogurt can tolerate higher temperatures than most pathogens, so that a suitable temperature not only encourages
4452-476: A sequence-independent manner. Representative Cas2 proteins have been characterised and possess either (single strand) ssRNA- or (double strand) dsDNA- specific endoribonuclease activity. In the I-E system of E. coli Cas1 and Cas2 form a complex where a Cas2 dimer bridges two Cas1 dimers. In this complex Cas2 performs a non-enzymatic scaffolding role, binding double-stranded fragments of invading DNA, while Cas1 binds
4611-408: A single long transcript encompassing much of the CRISPR array. This transcript is then cleaved by Cas proteins to form crRNAs. The mechanism to produce crRNAs differs among CRISPR-Cas systems. In type I-E and type I-F systems, the proteins Cas6e and Cas6f respectively, recognise stem-loops created by the pairing of identical repeats that flank the crRNA. These Cas proteins cleave the longer transcript at
4770-561: A single phage. During the same interval, the phage developed single-nucleotide polymorphisms that became fixed in the population, suggesting that targeting had prevented phage replication absent these mutations. Another S. thermophilus experiment showed that phages can infect and replicate in hosts that have only one targeting spacer. Yet another showed that sensitive hosts can exist in environments with high-phage titres. The chemostat and observational studies suggest many nuances to CRISPR and phage (co)evolution. Acronym An acronym
4929-436: A single word, such as NATO (as distinct from B-B-C )" but adds later "In everyday use, acronym is often applied to abbreviations that are technically initialisms, since they are pronounced as separate letters." The Chicago Manual of Style acknowledges the complexity ("Furthermore, an acronym and initialism are occasionally combined (JPEG), and the line between initialism and acronym is not always clear") but still defines
CRISPR - Misplaced Pages Continue
5088-665: A small yogurt business in Barcelona , Spain, naming the business Danone ("little Daniel") after his son. The brand later expanded to the United States under an Americanized version of the name, Dannon . Yogurt with added fruit jam was patented in 1933 by the Radlická Mlékárna dairy in Prague . Yogurt was introduced to the United States in the first decade of the twentieth century, influenced by Élie Metchnikoff 's The Prolongation of Life; Optimistic Studies (1908); it
5247-515: A twentieth-century phenomenon. Linguist David Wilton in Word Myths: Debunking Linguistic Urban Legends claims that "forming words from acronyms is a distinctly twentieth- (and now twenty-first-) century phenomenon. There is only one known pre-twentieth-century [English] word with an acronymic origin and it was in vogue for only a short time in 1886. The word is colinderies or colinda , an acronym for
5406-709: A wide range of organisms, including baker's yeast ( Saccharomyces cerevisiae ), the opportunistic pathogen Candida albicans , zebrafish ( Danio rerio ), fruit flies ( Drosophila melanogaster ), ants ( Harpegnathos saltator and Ooceraea biroi ), mosquitoes ( Aedes aegypti ), nematodes ( Caenorhabditis elegans ), plants, mice ( Mus musculus domesticus ) , monkeys and human embryos. CRISPR has been modified to make programmable transcription factors that allows activation or silencing of targeted genes. The CRISPR-Cas9 system has been shown to make effective gene edits in Human tripronuclear zygotes , as first described in
5565-502: A word rather than as a sequence of letters. In this sense, NASA / ˈ n æ s ə / is an acronym but USA / j uː ɛ s ˈ eɪ / is not. The broader sense of acronym , ignoring pronunciation, is its original meaning and in common use. Dictionary and style-guide editors dispute whether the term acronym can be legitimately applied to abbreviations which are not pronounced as words, and they do not agree on acronym spacing , casing , and punctuation . The phrase that
5724-471: A word, an abbreviation is not an acronym." In contrast, some style guides do support it, whether explicitly or implicitly. The 1994 edition of Merriam-Webster's Dictionary of English Usage defends the usage on the basis of a claim that dictionaries do not make a distinction. The BuzzFeed style guide describes CBS and PBS as "acronyms ending in S". Acronymy, like retronymy , is a linguistic process that has existed throughout history but for which there
5883-677: A word. American English dictionaries such as Merriam-Webster , Dictionary.com's Random House Webster's Unabridged Dictionary and the American Heritage Dictionary as well as the British Oxford English Dictionary and the Australian Macquarie Dictionary all include a sense in their entries for acronym equating it with initialism , although The American Heritage Dictionary criticizes it with
6042-549: Is a dish in Lebanon and Syria. Also, a wide variety of local Lebanese and Syrian dishes are cooked with yogurt like "Kibbi bi Laban" Rahmjoghurt , a creamy yogurt with much higher fat content (10%) than many yogurts offered in English-speaking countries. Dovga , a yogurt soup cooked with a variety of herbs and rice, is served warm in winter or refreshingly cold in summer. Jameed , yogurt salted and dried to preserve it,
6201-488: Is a question about how to pluralize acronyms. Often a writer will add an 's' following an apostrophe, as in "PC's". However, Kate L. Turabian 's A Manual for Writers of Research Papers, Theses, and Dissertations , writing about style in academic writings, allows for an apostrophe to form plural acronyms "only when an abbreviation contains internal periods or both capital and lowercase letters". Turabian would therefore prefer "DVDs" and "URLs" but "Ph.D.'s". The style guides of
6360-425: Is a type of abbreviation consisting of a phrase whose only pronounced elements are the initial letters or initial sounds of words inside that phrase. Acronyms are often spelled with the initial letter of each word in all caps with no punctuation . For some, an initialism or alphabetism , connotes this general meaning, and an acronym is a subset with a narrower definition: an initialism pronounced as
6519-485: Is a yogurt-based beverage that is usually slightly salty or sweet, and may be commercially flavored with rosewater , mango or other fruit juice. Salty lassi is usually flavored with ground, roasted cumin and red chilies , and may be made with buttermilk . An unsweetened and unsalted yogurt drink usually called simply jogurt is consumed with burek and other baked goods in the Balkans . Sweetened yogurt drinks are
CRISPR - Misplaced Pages Continue
6678-461: Is a yogurt-based, salty drink. It is made by mixing yogurt with water and (sometimes) salt. Borhani (or burhani) is a spicy yogurt drink from Bangladesh . It is usually served with kacchi biryani at weddings and special feasts. Key ingredients are yogurt blended with mint leaves ( mentha ), mustard seeds and black rock salt ( Kala Namak ). Ground roasted cumin , ground white pepper , green chili pepper paste and sugar are often added. Lassi
6837-469: Is at least 1 million CFU per milliliter. The bacterial culture is mixed in, and a warm temperature of 30–45 °C (86–113 °F) is maintained for 4 to 12 hours to allow fermentation to occur, with the higher temperatures working faster but risking a lumpy texture or whey separation. The word for yogurt is derived from the Ottoman Turkish : یوغورت , romanized : yoğurt , and
6996-721: Is becoming increasingly uncommon. Some style guides , such as that of the BBC , no longer require punctuation to show ellipsis ; some even proscribe it. Larry Trask , American author of The Penguin Guide to Punctuation , states categorically that, in British English , "this tiresome and unnecessary practice is now obsolete." Nevertheless, some influential style guides , many of them American , still require periods in certain instances. For example, The New York Times Manual of Style and Usage recommends following each segment with
7155-411: Is common for grammatical contractions (e.g. don't , y'all , and ain't ) and for contractions marking unusual pronunciations (e.g. a'ight , cap'n , and fo'c'sle for "all right", "captain", and "forecastle"). By the early twentieth century, it was standard to use a full stop/period/point , especially in the cases of initialisms and acronyms. Previously, especially for Latin abbreviations , this
7314-517: Is common in Nepal , where it is served as both an appetizer and dessert. Locally called dahi , it is a part of the Nepali culture, used in local festivals, marriage ceremonies, parties, religious occasions, family gatherings, and so on. One Nepalese yogurt is called juju dhau , originating from the city of Bhaktapur . In Tibet , yak milk (technically dri milk, as the word yak refers to the male animal)
7473-544: Is complementary to the repeat sequence, known as a trans-activating crRNA (tracrRNA). Transcription of the tracrRNA and the primary CRISPR transcript results in base pairing and the formation of dsRNA at the repeat sequence, which is subsequently targeted by RNaseIII to produce crRNAs. Unlike the other two systems, the crRNA does not contain the full spacer, which is instead truncated at one end. CrRNAs associate with Cas proteins to form ribonucleotide complexes that recognize foreign nucleic acids. CrRNAs show no preference between
7632-588: Is consumed in Jordan . Zabadi is the type of yogurt made in Egypt, usually from the milk of the Egyptian water buffalo . It is particularly associated with Ramadan fasting, as it is thought to prevent thirst during all-day fasting. To offset its natural sourness , yogurt is also sold sweetened, sweetened and flavored or in containers with fruit or fruit jam on the bottom. The two styles of yogurt commonly found in
7791-590: Is divided into types II, V, and VI. The 6 system types are divided into 33 subtypes. Each type and most subtypes are characterized by a "signature gene" found almost exclusively in the category. Classification is also based on the complement of cas genes that are present. Most CRISPR-Cas systems have a Cas1 protein. The phylogeny of Cas1 proteins generally agrees with the classification system, but exceptions exist due to module shuffling. Many organisms contain multiple CRISPR-Cas systems suggesting that they are compatible and may share components. The sporadic distribution of
7950-631: Is especially important for paper media, where no search utility is available to find the first use.) It also gives students a convenient review list to memorize the important acronyms introduced in a textbook chapter. Expansion at first use and abbreviation keys originated in the print era, but they are equally useful for electronic text . While acronyms provide convenience and succinctness for specialists, they often degenerate into confusing jargon . This may be intentional, to exclude readers without domain-specific knowledge. New acronyms may also confuse when they coincide with an already existing acronym having
8109-464: Is generally said as two letters, but IPsec for Internet Protocol Security is usually pronounced as / ˌ aɪ ˈ p iː s ɛ k / or / ˈ ɪ p s ɛ k / , along with variant capitalization like "IPSEC" and "Ipsec". Pronunciation may even vary within a single speaker's vocabulary, depending on narrow contexts. As an example, the database programming language SQL is usually said as three letters, but in reference to Microsoft's implementation
SECTION 50
#17327648894198268-445: Is hard to trace. The non-random evolution of these spacer regions has been found to be highly dependent on the environment and the particular foreign mobile genetic elements it contains. CRISPR-Cas can immunize bacteria against certain phages and thus halt transmission. For this reason, Koonin described CRISPR-Cas as a Lamarckian inheritance mechanism. However, this was disputed by a critic who noted, "We should remember [Lamarck] for
8427-424: Is macerated with sugar and spices such as saffron, cardamom and nutmeg to make the dessert "shrikhand". Strained yogurt is also enjoyed in Greece and is the main component of tzatziki (from Turkish " cacık "), a well-known accompaniment to gyros and souvlaki pita sandwiches: it is a yogurt sauce or dip made with the addition of grated cucumber , olive oil , salt and, optionally, mashed garlic. Srikhand ,
8586-574: Is made into yogurt (and butter and cheese) and consumed. In Northern Iran , Mâst Chekide is a variety of kefir yogurt with a distinct sour taste. It is usually mixed with a pesto -like water and fresh herb purée called delal . Common appetizers are spinach or eggplant borani , Mâst-o-Khiâr with cucumber, spring onions and herbs, and Mâst-Musir with wild shallots . In the summertime, yogurt and ice cubes are mixed together with cucumbers, raisins , salt, pepper and onions and topped with some croutons made of Persian traditional bread and served as
8745-451: Is made up of an AT-rich leader sequence followed by short repeats that are separated by unique spacers. CRISPR repeats typically range in size from 28 to 37 base pairs (bps), though there can be as few as 23 bp and as many as 55 bp. Some show dyad symmetry , implying the formation of a secondary structure such as a stem-loop ('hairpin') in the RNA, while others are designed to be unstructured. The size of spacers in different CRISPR arrays
8904-577: Is much more complicated and particular than in derived stem cells. In 2015, the nuclease Cas12a (formerly called Cpf1 ) was characterized in the CRISPR-Cpf1 system of the bacterium Francisella novicida . Its original name, from a TIGRFAMs protein family definition built in 2012, reflects the prevalence of its CRISPR-Cas subtype in the Prevotella and Francisella lineages. Cas12a showed several key differences from Cas9 including: causing
9063-462: Is much more target-specific than traditional restriction enzyme cloning. Finally, Cas12a cleaves DNA 18–23 base pairs downstream from the PAM site. This means there is no disruption to the recognition sequence after repair, and so Cas12a enables multiple rounds of DNA cleavage. By contrast, since Cas9 cuts only 3 base pairs upstream of the PAM site, the NHEJ pathway results in indel mutations that destroy
9222-459: Is not uncommon for acronyms to be cited in a kind of false etymology , called a folk etymology , for a word. Such etymologies persist in popular culture but have no factual basis in historical linguistics , and are examples of language-related urban legends . For example, " cop " is commonly cited as being derived, it is presumed, from "constable on patrol", and " posh " from " port outward, starboard home ". With some of these specious expansions,
9381-413: Is often associated with probiotics , which have been postulated as having positive effects on immune , cardiovascular or metabolic health. As of the early 21st century, high-quality clinical evidence was insufficient to conclude that consuming yogurt lowers the risk of diseases or otherwise improves health. Meta-analyses found that consuming 80 grams per day of low-fat yogurt was associated with
9540-456: Is produced using a culture of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus bacteria. Other lactobacilli and bifidobacteria are sometimes added during or after culturing yogurt. Some countries require yogurt to contain a specific amount of colony-forming units (CFU) of bacteria; for example, in China the requirement for the number of lactobacillus bacteria
9699-490: Is recorded in the books Dīwān Lughāt al-Turk by Mahmud Kashgari and Kutadgu Bilig by Yusuf Has Hajib written in the 11th century. Both texts mention the word "yogurt" in different sections and describe its use by nomadic Turks. The earliest yogurts were probably spontaneously fermented by wild bacteria in goat skin bags. Some accounts suggest that Mughal Indian emperor Akbar 's cooks would flavor yogurt with mustard seeds and cinnamon. Another early account of
SECTION 60
#17327648894199858-511: Is the partial repeat sequence that prevents the CRISPR-Cas system from targeting the chromosome as base pairing beyond the spacer sequence signals self and prevents DNA cleavage. RNA-guided CRISPR enzymes are classified as type V restriction enzymes . The cas genes in the adaptor and effector modules of the CRISPR-Cas system are believed to have evolved from two different ancestral modules. A transposon -like element called casposon encoding
10017-415: Is traditionally pronounced like the word sequel . In writing for a broad audience, the words of an acronym are typically written out in full at its first occurrence within a given text. Expansion At First Use (EAFU) benefits readers unfamiliar with the acronym. Another text aid is an abbreviation key which lists and expands all acronyms used, a reference for readers who skipped past the first use. (This
10176-422: Is typically 32 to 38 bp (range 21 to 72 bp). New spacers can appear rapidly as part of the immune response to phage infection. There are usually fewer than 50 units of the repeat-spacer sequence in a CRISPR array. Small clusters of cas genes are often located next to CRISPR repeat-spacer arrays. Collectively the 93 cas genes are grouped into 35 families based on sequence similarity of the encoded proteins. 11 of
10335-533: Is usually related to the verb yoğurmak , "to knead", or "to be curdled or coagulated; to thicken". It may be related to yoğun , meaning thick or dense. The sounds historically represented by the Arabic letter ghayn in the Turkish language ranging from a voiced velar fricative to a voiced velar plosive were traditionally romanized as "gh" prior to the introduction of a new Latin-based Turkish alphabet and
10494-694: The Caucasus ), Western Asia, South Eastern Europe / Balkans , Central Europe, and the Indian subcontinent . Stamen Grigorov (1878–1945), a Bulgarian student of medicine in Geneva , first examined the microflora of the Bulgarian yogurt. In 1905, he described it as consisting of a spherical and a rod-like lactic acid-producing bacteria. In 1907, the rod-like bacterium was called Bacillus bulgaricus (now Lactobacillus delbrueckii subsp. bulgaricus ). The Russian biologist and Nobel laureate Ilya Mechnikov , from
10653-516: The Colonial and Indian Exposition held in London in that year." However, although acronymic words seem not to have been employed in general vocabulary before the twentieth century (as Wilton points out), the concept of their formation is treated as effortlessly understood (and evidently not novel) in an Edgar Allan Poe story of the 1830s, " How to Write a Blackwood Article ", which includes
10812-539: The Institut Pasteur in Paris, was influenced by Grigorov's work and hypothesized that regular consumption of yogurt was responsible for the unusually long lifespans of Bulgarian peasants. Believing Lactobacillus to be essential for good health, Mechnikov worked to popularize yogurt as a foodstuff throughout Europe. Industrialization of yogurt production is credited to Isaac Carasso , who, in 1919, started
10971-623: The Modern Language Association and American Psychological Association prohibit apostrophes from being used to pluralize acronyms regardless of periods (so "compact discs" would be "CDs" or "C.D.s"), whereas The New York Times Manual of Style and Usage requires an apostrophe when pluralizing all abbreviations regardless of periods (preferring "PC's, TV's and VCR's"). Possessive plurals that also include apostrophes for mere pluralization and periods appear especially complex: for example, "the C.D.'s' labels" (the labels of
11130-517: The Nobel Prize in Chemistry in 2020 awarded to Emmanuelle Charpentier and Jennifer Doudna . The discovery of clustered DNA repeats took place independently in three parts of the world. The first description of what would later be called CRISPR is from Osaka University researcher Yoshizumi Ishino and his colleagues in 1987. They accidentally cloned part of a CRISPR sequence together with
11289-539: The Restoration witticism arranging the names of some members of Charles II 's Committee for Foreign Affairs to produce the "CABAL" ministry . OK , a term of disputed origin, dates back at least to the early nineteenth century and is now used around the world. Acronyms are used most often to abbreviate names of organizations and long or frequently referenced terms. The armed forces and government agencies frequently employ acronyms; some well-known examples from
11448-410: The S. thermophilus CRISPR system can also be reprogrammed to target a site of their choosing by changing the sequence of its crRNA. These advances fueled efforts to edit genomes with the modified CRISPR-Cas9 system. Groups led by Feng Zhang and George Church simultaneously published descriptions of genome editing in human cell cultures using CRISPR-Cas9 for the first time. It has since been used in
11607-498: The " iap" gene (isozyme conversion of alkaline phosphatase) from their target genome, that of Escherichia coli . The organization of the repeats was unusual. Repeated sequences are typically arranged consecutively, without interspersing different sequences. They did not know the function of the interrupted clustered repeats. In 1993, researchers of Mycobacterium tuberculosis in the Netherlands published two articles about
11766-480: The "belief" that the etymology is acronymic has clearly been tongue-in-cheek among many citers, as with "gentlemen only, ladies forbidden" for " golf ", although many other (more credulous ) people have uncritically taken it for fact. Taboo words in particular commonly have such false etymologies: " shit " from "ship/store high in transit" or "special high-intensity training" and " fuck " from "for unlawful carnal knowledge", or "fornication under consent/command of
11925-601: The "delicate and smooth structure" of "conventional yogurts". Since plant-based milks do not contain lactose (the food of Streptococcus thermophilus and Lactobacillus bulgaricus ), plant-based products usually contain different bacterial strains than yogurt, such as Lactobacillus casei , Lactobacillus rhamnosus , and Bifidobacterium bifidum . Plant-based products also vary considerably in their nutrition and ingredients and may contain gums, stabilizers, high-intensity sweeteners, and artificial colors. In Europe, companies may not market their plant-based products using
12084-463: The 160-character SMS limit, and to save time, acronyms such as "GF" ("girlfriend"), "LOL" ("laughing out loud"), and "DL" ("download" or "down low") have become popular. Some prescriptivists disdain texting acronyms and abbreviations as decreasing clarity, or as failure to use "pure" or "proper" English. Others point out that languages have always continually changed , and argue that acronyms should be embraced as inevitable, or as innovation that adapts
12243-461: The 18 letters between the initial "i" and the final "n"). Authors of expository writing will sometimes capitalize or otherwise distinctively format the initials of the expansion for pedagogical emphasis (for example, writing: "the onset of Congestive Heart Failure (CHF)" or "the onset of c ongestive h eart f ailure (CHF)"). Capitalization like this, however, conflicts with the convention of English orthography, which generally reserves capitals in
12402-509: The 2000s, using soy milk , rice milk , and nut milks such as almond milk and coconut milk fermented with cultures. These products may be suitable for people with lactose intolerance or those who prefer plant-based foods such as vegetarians or vegans . Plant-based milks have different structures and components than dairy milk . Though they can be used to make many products similar to those made from dairy, there are differences in taste and texture, and some consumers may feel that they lack
12561-426: The 35 families form the cas core, which includes the protein families Cas1 through Cas9. A complete CRISPR-Cas locus has at least one gene belonging to the cas core. CRISPR-Cas systems fall into two classes. Class 1 systems use a complex of multiple Cas proteins to degrade foreign nucleic acids. Class 2 systems use a single large Cas protein for the same purpose. Class 1 is divided into types I, III, and IV; class 2
12720-597: The American palate and in 1966 Colombo Yogurt sweetened the yogurt and added fruit preserves, creating "fruit on the bottom" style yogurt. This was successful and company sales soon exceeded $ 1 million per year. By the late 20th century, yogurt had become a common American food item and Colombo Yogurt was sold in 1993 to General Mills , which discontinued the brand in 2010. In 2017, the average American ate 13.7 pounds (6.2 kg) of yogurt. The average consumption of yogurt has been declining since 2014. Sale of yogurt
12879-466: The British press may render it "Nato"), but uses lower case in " Unicef " (from "United Nations International Children's Emergency Fund") because it is more than four letters, and to style it in caps might look ungainly (flirting with the appearance of "shouting capitals"). While abbreviations typically exclude the initials of short function words (such as "and", "or", "of", or "to"), this is not always
13038-476: The CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within living organisms. This editing process has a wide variety of applications including basic biological research, development of biotechnological products, and treatment of diseases. The development of the CRISPR-Cas9 genome editing technique was recognized by
13197-413: The CRISPR-Cas subtypes suggests that the CRISPR-Cas system is subject to horizontal gene transfer during microbial evolution . CRISPR-Cas immunity is a natural process of bacteria and archaea. CRISPR-Cas prevents bacteriophage infection, conjugation and natural transformation by degrading foreign nucleic acids that enter the cell. When a microbe is invaded by a bacteriophage , the first stage of
13356-506: The Cas1-like integrase and potentially other components of the adaptation module was inserted next to the ancestral effector module, which likely functioned as an independent innate immune system. The highly conserved cas1 and cas2 genes of the adaptor module evolved from the ancestral module while a variety of class 1 effector cas genes evolved from the ancestral effector module. The evolution of these various class 1 effector module cas genes
13515-452: The DNA target specified by the guide RNA. This contribution was so significant that it was recognized by the Nobel Prize in Chemistry in 2020. By manipulating the nucleotide sequence of the guide RNA, the artificial Cas9 system could be programmed to target any DNA sequence for separation. Another collaboration comprising Virginijus Šikšnys , Gasiūnas, Barrangou, and Horvath showed that Cas9 from
13674-572: The Danish food company Danisco, then developed phage-resistant S. thermophilus strains for yogurt production. Danisco was later bought by DuPont , which owns about 50 percent of the global dairy culture market, and the technology spread widely. A major advance in understanding CRISPR came with Jansen's observation that the prokaryote repeat cluster was accompanied by four homologous genes that make up CRISPR-associated systems, cas 1–4. The Cas proteins showed helicase and nuclease motifs , suggesting
13833-467: The PAM is recognized on the same strand as the crRNA (the opposite strand to type I systems). Type III systems, like type I require six or seven Cas proteins binding to crRNAs. The type III systems analysed from S. solfataricus and P. furiosus both target the mRNA of phages rather than phage DNA genome, which may make these systems uniquely capable of targeting RNA-based phage genomes. Type III systems were also found to target DNA in addition to RNA using
13992-564: The U.S. Navy, is "COMCRUDESPAC", which stands for "commander, cruisers destroyers Pacific"; it is also seen as "ComCruDesPac". Inventors are encouraged to anticipate the formation of acronyms by making new terms "YABA-compatible" ("yet another bloody acronym"), meaning the term's acronym can be pronounced and is not an offensive word: "When choosing a new name, be sure it is 'YABA-compatible'." Acronym use has been further popularized by text messaging on mobile phones with short message service (SMS), and instant messenger (IM). To fit messages into
14151-497: The United States are among the " alphabet agencies " (jokingly referred to as " alphabet soup ") created under the New Deal by Franklin D. Roosevelt (himself known as "FDR"). Business and industry also coin acronyms prolifically. The rapid advance of science and technology also drives the usage, as new inventions and concepts with multiword names create a demand for shorter, more pronounceable names. One representative example, from
14310-610: The United States are not heat treated after culturing, and contain live cultures. Yogurt with live cultures is more beneficial than pasteurized yogurt for people with lactose malabsorption. Lactose intolerance is a condition in which people have symptoms due to the decreased ability to digest lactose, a sugar found in dairy products. In 2010, the European Food Safety Authority (EFSA) determined that lactose intolerance can be alleviated by ingesting live yogurt cultures (lactobacilli) that are able to digest
14469-411: The acronym may use normal case rules, e.g. it would appear generally in lower case, but with an initial capital when starting a sentence or when in a title. Once knowledge of the words underlying such an acronym has faded from common recall, the acronym may be termed an anacronym . Examples of anacronyms are the words " scuba ", " radar ", and " laser ". The word "an acro nym" should not be confused with
14628-545: The acronym stands for is called its expansion . The meaning of an acronym includes both its expansion and the meaning of its expansion. The word acronym is formed from the Greek roots akro- , meaning 'height, summit, or tip', and -nym , 'name'. This neoclassical compound appears to have originated in German , with attestations for the German form Akronym appearing as early as 1921. Citations in English date to
14787-590: The adoption of acronyms was modern warfare, with its many highly technical terms. While there is no recorded use of military acronyms dating from the American Civil War (acronyms such as "ANV" for " Army of Northern Virginia " post-date the war itself), they became somewhat common in World War I , and by World War II they were widespread even in the slang of soldiers, who referred to themselves as G.I.s . The widespread, frequent use of acronyms across
14946-506: The apostrophe should be reserved for the possessive ("the TV's antenna"). In some languages, the convention of doubling the letters in the acronym is used to indicate plural words: for example, the Spanish EE.UU. , for Estados Unidos ('United States'). This old convention is still sometimes followed for a limited number of English abbreviations, such as SS. for Saints , pp. for
15105-1163: The case. Sometimes function words are included to make a pronounceable acronym, such as CORE ( Congress of Racial Equality ). Sometimes the letters representing these words are written in lower case, such as in the cases of "TfL" (" Transport for London ") and LotR ( The Lord of the Rings ); this usually occurs when the acronym represents a multi-word proper noun. Numbers (both cardinal and ordinal ) in names are often represented by digits rather than initial letters, as in "4GL" (" fourth generation language ") or "G77" (" Group of 77 "). Large numbers may use metric prefixes , as with " Y2K " for "Year 2000". Exceptions using initials for numbers include " TLA " ("three-letter acronym/abbreviation") and "GoF" (" Gang of Four "). Abbreviations using numbers for other purposes include repetitions, such as " A2DP " ("Advanced Audio Distribution Profile"), " W3C " ("World Wide Web Consortium"), and T3 ( Trends, Tips & Tools for Everyday Living ); pronunciation, such as " B2B " ("business to business"); and numeronyms , such as "i18n" ("internationalization"; "18" represents
15264-462: The cell. The source of the spacers was a sign that the CRISPR- cas system could have a role in adaptive immunity in bacteria . All three studies proposing this idea were initially rejected by high-profile journals, but eventually appeared in other journals. The first publication proposing a role of CRISPR-Cas in microbial immunity, by Mojica and collaborators at the University of Alicante , predicted
15423-559: The clustered repeats had a role in correctly segregating replicated DNA into daughter cells during cell division, because plasmids and chromosomes with identical repeat arrays could not coexist in Haloferax volcanii . Transcription of the interrupted repeats was also noted for the first time; this was the first full characterization of CRISPR. By 2000, Mojica and his students, after an automated search of published genomes, identified interrupted repeats in 20 species of microbes as belonging to
15582-407: The coding and non-coding strands, which is indicative of an RNA-guided DNA-targeting system. The type I-E complex (commonly referred to as Cascade) requires five Cas proteins bound to a single crRNA. During the interference stage in type I systems, the PAM sequence is recognized on the crRNA-complementary strand and is required along with crRNA annealing. In type I systems correct base pairing between
15741-413: The compact discs). In some instances, however, an apostrophe may increase clarity: for example, if the final letter of an abbreviation is "S", as in "SOS's" (although abbreviations ending with S can also take "-es", e.g. "SOSes"), or when pluralizing an abbreviation that has periods. A particularly rich source of options arises when the plural of an acronym would normally be indicated in a word other than
15900-564: The contrived acronym "P.R.E.T.T.Y.B.L.U.E.B.A.T.C.H." The use of Latin and Neo-Latin terms in vernaculars has been pan-European and pre-dates modern English. Some examples of acronyms in this class are: The earliest example of a word derived from an acronym listed by the OED is "abjud" (now " abjad "), formed from the original first four letters of the Arabic alphabet in the late eighteenth century. Some acrostics pre-date this, however, such as
16059-668: The crRNA (sense/antisense) provided immunity, indicating that the crRNA guides were targeting dsDNA . That year Marraffini and Sontheimer confirmed that a CRISPR sequence of S. epidermidis targeted DNA and not RNA to prevent conjugation . This finding was at odds with the proposed RNA-interference-like mechanism of CRISPR-Cas immunity, although a CRISPR-Cas system that targets foreign RNA was later found in Pyrococcus furiosus . A 2010 study showed that CRISPR-Cas cuts strands of both phage and plasmid DNA in S. thermophilus . A simpler CRISPR system from Streptococcus pyogenes relies on
16218-489: The crRNA and the protospacer signals a conformational change in Cascade that recruits Cas3 for DNA degradation. Type II systems rely on a single multifunctional protein, Cas9 , for the interference step. Cas9 requires both the crRNA and the tracrRNA to function and cleave DNA using its dual HNH and RuvC/RNaseH-like endonuclease domains. Basepairing between the PAM and the phage genome is required in type II systems. However,
16377-468: The development of various diagnostic technologies. In 2016, the nuclease Cas13a (formerly known as C2c2 ) from the bacterium Leptotrichia shahii was characterized. Cas13 is an RNA-guided RNA endonuclease, which means that it does not cleave DNA, but only single-stranded RNA. Cas13 is guided by its crRNA to a ssRNA target and binds and cleaves the target. Similar to Cas12a, the Cas13 remains bound to
16536-438: The dictionary entries and style guide recommendations regarding the term acronym through the twentieth century did not explicitly acknowledge or support the expansive sense. The Merriam–Webster's Dictionary of English Usage from 1994 is one of the earliest publications to advocate for the expansive sense, and all the major dictionary editions that include a sense of acronym equating it with initialism were first published in
16695-415: The early 21st century, yogurt flavors inspired by desserts, such as chocolate or cheesecake, became common. There is concern about the health effects of sweetened yogurt due to its high sugar content, although research indicates that use of sugar in yogurt manufacturing has decreased since 2016 in response to WHO and government initiatives to combat obesity . Strained yogurt has been strained through
16854-512: The edge of the paired region, leaving a single crRNA along with a small remnant of the paired repeat region. Type III systems also use Cas6, however, their repeats do not produce stem-loops. Cleavage instead occurs by the longer transcript wrapping around the Cas6 to allow cleavage just upstream of the repeat sequence. Type II systems lack the Cas6 gene and instead utilize RNaseIII for cleavage. Functional type II systems encode an extra small RNA that
17013-664: The exclusive sense for acronym and its earliest citation was from 1943. In early December 2010, Duke University researcher Stephen Goranson published a citation for acronym to the American Dialect Society e-mail discussion list which refers to PGN being pronounced "pee-gee-enn", antedating English language usage of the word to 1940. Linguist Ben Zimmer then mentioned this citation in his December 16, 2010 " On Language " column about acronyms in The New York Times Magazine . By 2011,
17172-405: The final position. It is likely that in those systems, a blunt end is generated at the very end of the direct repeat and the protospacer during acquisition. Analysis of Sulfolobus solfataricus CRISPRs revealed further complexities to the canonical model of spacer insertion, as one of its six CRISPR loci inserted new spacers randomly throughout its CRISPR array, as opposed to inserting closest to
17331-763: The final word if spelled out in full. A classic example is "Member of Parliament", which in plural is "Members of Parliament". It is possible then to abbreviate this as "M's P", which was fairly common in mid-twentieth-century Australian news writing (or similar ), and used by former Australian Prime Minister Ben Chifley . This usage is less common than forms with "s" at the end, such as "MPs", and may appear dated or pedantic. In common usage, therefore, "weapons of mass destruction" becomes "WMDs", "prisoners of war" becomes "POWs", and "runs batted in" becomes "RBIs". Abbreviations that come from single, rather than multiple, words – such as "TV" ("television") – are usually pluralized without apostrophes ("two TVs"); most writers feel that
17490-487: The first experimental evidence that CRISPR was an adaptive immune system was published. A CRISPR region in Streptococcus thermophilus acquired spacers from the DNA of an infecting bacteriophage . The researchers manipulated the resistance of S. thermophilus to different types of phages by adding and deleting spacers whose sequence matched those found in the tested phages. In 2008, Brouns and Van der Oost identified
17649-464: The first letter of acronyms, reserving all-caps styling for initialisms, writing the pronounced acronyms "Nato" and "Aids" in mixed case, but the initialisms "USA" and "FBI" in all caps. For example, this is the style used in The Guardian , and BBC News typically edits to this style (though its official style guide, dating from 2003, still recommends all-caps ). The logic of this style is that
17808-411: The first nt of the protospacer. This nt becomes the final base in the first direct repeat. This suggests that the spacer acquisition machinery generates single-stranded overhangs in the second-to-last position of the direct repeat and in the PAM during spacer insertion. However, not all CRISPR-Cas systems appear to share this mechanism as PAMs in other organisms do not show the same level of conservation in
17967-535: The five elixirs, or panchamrita , often used in Hindu ritual. Sweetened dahi ( mishti doi or meethi dahi ) is common in eastern parts of India, made by fermenting sweetened milk. While cow's milk is currently the primary ingredient for yogurt, goat and buffalo milk were widely used in the past, and valued for the fat content (see buffalo curd ). Dadiah or dadih is a traditional West Sumatran yogurt made from water buffalo milk, fermented in bamboo tubes. Yogurt
18126-532: The formation of yogurt, but inhibits pathogenic microorganisms. Once the yogurt has formed it can, if desired, be strained to reduce the whey content and thicken it. Two types of yogurt are supported by the Codex Alimentarius for import and export. Under US Food and Drug Administration regulations, milk must be pasteurized before it is cultured, and may optionally be heat treated after culturing to increase shelf life. Most commercial yogurts in
18285-460: The genome of Archaeoglobus fulgidus were transcribed into long RNA molecules subsequently processed into unit-length small RNAs, plus some longer forms of 2, 3, or more spacer-repeat units. In 2005, yogurt researcher Rodolphe Barrangou discovered that Streptococcus thermophilus , after iterative phage infection challenges, develops increased phage resistance due to the incorporation of additional CRISPR spacer sequences. Barrangou's employer,
18444-466: The good he contributed to science, not for things that resemble his theory only superficially. Indeed, thinking of CRISPR and other phenomena as Lamarckian only obscures the simple and elegant way evolution really works". But as more recent studies have been conducted, it has become apparent that the acquired spacer regions of CRISPR-Cas systems are indeed a form of Lamarckian evolution because they are genetic mutations that are acquired and then passed on. On
18603-903: The grocery store are set-style yogurt and Swiss-style yogurt. Set-style yogurt is poured into individual containers to set, while Swiss-style yogurt is stirred prior to packaging. Either may have fruit added to increase sweetness. Lassi is a common Indian beverage made from stirred liquified yogurt that is either salted or sweetened with sugar commonly, less commonly honey and combined with fruit pulp to create flavored lassi. Consistency can vary widely, with urban and commercial lassis having uniform texture through being processed, whereas rural and rustic lassi has discernible curds or fruit pulp. Large amounts of sugar – or other sweeteners for low-energy yogurts – are often used in commercial yogurt. Some yogurts contain added modified starch , pectin (found naturally in fruit) or gelatin to create thickness and creaminess. This type of yogurt may be marketed under
18762-658: The immune response is to capture phage DNA and insert it into a CRISPR locus in the form of a spacer. Cas1 and Cas2 are found in both types of CRISPR-Cas immune systems, which indicates that they are involved in spacer acquisition. Mutation studies confirmed this hypothesis, showing that removal of Cas1 or Cas2 stopped spacer acquisition, without affecting CRISPR immune response. Multiple Cas1 proteins have been characterised and their structures resolved. Cas1 proteins have diverse amino acid sequences. However, their crystal structures are similar and all purified Cas1 proteins are metal-dependent nucleases/ integrases that bind to DNA in
18921-435: The king". In English, abbreviations have previously been marked by a wide variety of punctuation . Obsolete forms include using an overbar or colon to show the ellipsis of letters following the initial part. The forward slash is still common in many dialects for some fixed expressions—such as in w/ for "with" or A/C for " air conditioning "—while only infrequently being used to abbreviate new terms. The apostrophe
19080-500: The label "usage problem". However, many English language dictionaries, such as the Collins COBUILD Advanced Dictionary , Cambridge Advanced Learner's Dictionary , Macmillan Dictionary , Longman Dictionary of Contemporary English , New Oxford American Dictionary , Webster's New World Dictionary , and Lexico from Oxford University Press do not acknowledge such a sense. Most of
19239-535: The lactose in other dairy products. The scientific review by EFSA enabled yogurt manufacturers to use a health claim on product labels, provided that the "yogurt should contain at least 10 CFU live starter microorganisms ( Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus ) per gram. The target population is individuals with lactose maldigestion". A 2021 review found that yogurt consumption could improve lactose tolerance and digestion. A variety of plant-based yogurt alternatives appeared in
19398-836: The language to changing circumstances. In this view, the modern practice is just the "proper" English of the current generation of speakers, much like the earlier abbreviation of corporation names on ticker tape or newspapers. Exact pronunciation of "word acronyms" (those pronounced as words rather than sounded out as individual letters) often vary by speaker population. These may be regional, occupational, or generational differences, or simply personal preference. For instance, there have been decades of online debate about how to pronounce GIF ( / ɡ ɪ f / or / dʒ ɪ f / ) and BIOS ( / ˈ b aɪ oʊ s / , / ˈ b aɪ oʊ z / , or / ˈ b aɪ ɒ s / ). Similarly, some letter-by-letter initialisms may become word acronyms over time, especially in combining forms: IP for Internet Protocol
19557-484: The latter as well if manufacturing and packaging practices are suboptimal. When mold forms on yogurt it can not be scraped away. The consistency of yogurt allows the mold to penetrate deeply under the surface where it spreads. Dahi is a yogurt from the Indian subcontinent , known for its characteristic taste and consistency. The word dahi seems to be derived from the Sanskrit word dadhi ("sour milk"), one of
19716-515: The leader sequence. Multiple CRISPRs contain many spacers to the same phage. The mechanism that causes this phenomenon was discovered in the type I-E system of E. coli . A significant enhancement in spacer acquisition was detected where spacers already target the phage, even mismatches to the protospacer. This 'priming' requires the Cas proteins involved in both acquisition and interference to interact with each other. Newly acquired spacers that result from
19875-403: The leader sequence. Analysis of the type I-E system from E. coli demonstrated that the first direct repeat adjacent to the leader sequence is copied, with the newly acquired spacer inserted between the first and second direct repeats. The PAM sequence appears to be important during spacer insertion in type I-E systems. That sequence contains a strongly conserved final nucleotide (nt) adjacent to
20034-480: The letter "ğ" in 1929, thus "yoghurt" spelled with a "gh" is first attested in sources from 1615 to 1625. In English, spelling variations include yogurt , yoghurt , and to a lesser extent yoghourt or yogourt . In the United Kingdom, Australia, New Zealand and South Africa the word is usually spelled yoghurt , while in the United States the spelling is yogurt . Canada has its own spelling, yogourt ,
20193-649: The metagenomes produced for the Human Microbiome Project . Although most were body-site specific, some within a body site are widely shared among individuals. One of these loci originated from streptococcal species and contained ≈15,000 spacers, 50% of which were unique. Similar to the targeted studies of the oral cavity, some showed little evolution over time. CRISPR evolution was studied in chemostats using S. thermophilus to directly examine spacer acquisition rates. In one week, S. thermophilus strains acquired up to three spacers when challenged with
20352-530: The middle of sentences for proper nouns; when following the AMA Manual of Style , this would instead be rendered as "the onset of congestive heart failure (CHF)". Yogurt Yogurt ( UK : / ˈ j ɒ ɡ ə t / ; US : / ˈ j oʊ ɡ ər t / , from Ottoman Turkish : یوغورت , romanized : yoğurt ; also spelled yoghurt , yogourt or yoghourt ) is a food produced by bacterial fermentation of milk. Fermentation of sugars in
20511-438: The milk by these bacteria produces lactic acid , which acts on milk protein to give yogurt its texture and characteristic tart flavor. Cow's milk is most commonly used to make yogurt. Milk from water buffalo , goats, ewes , mares , camels, and yaks is also used to produce yogurt. The milk used may be homogenized or not. It may be pasteurized or raw . Each type of milk produces substantially different results. Yogurt
20670-532: The milk into yogurt, inoculating certain bacteria ( starter culture ), usually Streptococcus thermophilus and Lactobacillus bulgaricus , into the milk, and finally keeping it warm for several hours (4–12 hours). Milk with a higher concentration of solids than normal milk may be used; the higher solids content produces a firmer yogurt. Solids can be increased by adding dried milk. The yogurt-making process provides two significant barriers to pathogen growth, heat and acidity (low pH). Both are necessary to ensure
20829-466: The more general "x" can be used to replace an unspecified number of letters. Examples include "Crxn" for "crystallization" and the series familiar to physicians for history , diagnosis , and treatment ("hx", "dx", "tx"). Terms relating to a command structure may also sometimes use this formatting, for example gold, silver, and bronze levels of command in UK policing being referred to as Gx, Sx, and Bx. There
20988-399: The name Swiss-style, although it is unrelated to conventional Swiss yogurt. Some yogurts, often called "cream line", are made with whole milk which has not been homogenized so the cream rises to the top. In many countries, sweetened, flavored yogurt is common, typically sold in single-serving plastic cups . Common flavors may include vanilla , honey , and toffee , and various fruits. In
21147-635: The other biofilm, suggesting a higher phage activity/prevalence in one community than the other. In the oral cavity, a temporal study determined that 7–22% of spacers were shared over 17 months within an individual while less than 2% were shared across individuals. From the same environment, a single strain was tracked using PCR primers specific to its CRISPR system. Broad-level results of spacer presence/absence showed significant diversity. However, this CRISPR added three spacers over 17 months, suggesting that even in an environment with significant CRISPR diversity some loci evolve slowly. CRISPRs were analysed from
21306-425: The other hand, the evolution of the Cas gene machinery that facilitates the system evolves through classic Darwinian evolution. Analysis of CRISPR sequences revealed coevolution of host and viral genomes. The basic model of CRISPR evolution is newly incorporated spacers driving phages to mutate their genomes to avoid the bacterial immune response, creating diversity in both the phage and host populations. To resist
21465-729: The plural of 'pages', or mss. for manuscripts . The most common capitalization scheme seen with acronyms is all-uppercase ( all caps ). Small caps are sometimes used to make the run of capital letters seem less jarring to the reader. For example, the style of some American publications, including the Atlantic Monthly and USA Today , is to use small caps for acronyms longer than three letters; thus "U.S." and " FDR " in normal caps, but " nato " in small caps. The acronyms " AD " and " BC " are often smallcapped as well, as in: "From 4004 bc to ad 525 ". Where an acronym has linguistically taken on an identity as regular word,
21624-412: The priming mechanism are always found on the same strand as the priming spacer. This observation led to the hypothesis that the acquisition machinery slides along the foreign DNA after priming to find a new protospacer. CRISPR-RNA (crRNA), which later guides the Cas nuclease to the target during the interference step, must be generated from the CRISPR sequence. The crRNA is initially transcribed as part of
21783-483: The pronunciation is reflected graphically by the capitalization scheme. However, it conflicts with conventional English usage of first-letter upper-casing as a marker of proper names in many cases; e.g. AIDS stands for acquired immuno-deficiency syndrome which is not a proper name, while Aids is in the style of one. Some style manuals also base the letters' case on their number. The New York Times , for example, keeps "NATO" in all capitals (while several guides in
21942-502: The protein Cas9 . The Cas9 endonuclease is a four-component system that includes two small molecules: crRNA and trans-activating CRISPR RNA (tracrRNA). In 2012, Jennifer Doudna and Emmanuelle Charpentier re-engineered the Cas9 endonuclease into a more manageable two-component system by fusing the two RNA molecules into a " single-guide RNA " that, when combined with Cas9, could find and cut
22101-685: The publication of the 3rd edition of the Oxford English Dictionary added the expansive sense to its entry for acronym and included the 1940 citation. As the Oxford English Dictionary structures the senses in order of chronological development, it now gives the "initialism" sense first. English language usage and style guides which have entries for acronym generally criticize the usage that refers to forms that are not pronounceable words. Fowler's Dictionary of Modern English Usage says that acronym "denotes abbreviations formed from initial letters of other words and pronounced as
22260-478: The recognition sequence, thereby preventing further rounds of cutting. In theory, repeated rounds of DNA cleavage should cause an increased opportunity for the desired genomic editing to occur. A distinctive feature of Cas12a, as compared to Cas9, is that after cutting its target, Cas12a remains bound to the target and then cleaves other ssDNA molecules non-discriminately. This property is called "collateral cleavage" or "trans-cleavage" activity and has been exploited for
22419-455: The same family. Because those sequences were interspaced, Mojica initially called these sequences "short regularly spaced repeats" (SRSR). In 2001, Mojica and Ruud Jansen , who were searching for an additional interrupted repeats, proposed the acronym CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) to unify the numerous acronyms used to describe these sequences. In 2002, Tang, et al. showed evidence that CRISPR repeat regions from
22578-470: The sides of railroad cars (e.g., "Richmond, Fredericksburg and Potomac Railroad" → "RF&P"); on the sides of barrels and crates; and on ticker tape and newspaper stock listings (e.g. American Telephone and Telegraph Company → AT&T). Some well-known commercial examples dating from the 1890s through 1920s include " Nabisco " ("National Biscuit Company"), " Esso " (from "S.O.", from " Standard Oil "), and " Sunoco " ("Sun Oil Company"). Another field for
22737-442: The single-stranded flanks of the DNA and catalyses their integration into CRISPR arrays. New spacers are usually added at the beginning of the CRISPR next to the leader sequence creating a chronological record of viral infections. In E. coli a histone like protein called integration host factor ( IHF ), which binds to the leader sequence, is responsible for the accuracy of this integration. IHF also enhances integration efficiency in
22896-437: The strains' phylogenetic relationships to be determined. A comparative genomic analysis showed that E. coli and S. enterica evolve much more slowly than S. thermophilus . The latter's strains that diverged 250,000 years ago still contained the same spacer complement. Metagenomic analysis of two acid-mine-drainage biofilms showed that one of the analyzed CRISPRs contained extensive deletions and spacer additions versus
23055-604: The target and then cleaves other ssRNA molecules non-discriminately. This collateral cleavage property has been exploited for the development of various diagnostic technologies. In 2021, Dr. Hui Yang characterized novel miniature Cas13 protein (mCas13) variants, Cas13X and Cas13Y. Using a small portion of N gene sequence from SARS-CoV-2 as a target in characterization of mCas13, revealed the sensitivity and specificity of mCas13 coupled with RT-LAMP for detection of SARS-CoV-2 in both synthetic and clinical samples over other available standard tests like RT-qPCR (1 copy/μL). The CRISPR array
23214-409: The term acronym only for forms pronounced as a word, and using initialism or abbreviation for those that are not. Some sources acknowledge the usage, but vary in whether they criticize or forbid it, allow it without comment, or explicitly advocate it. Some mainstream English dictionaries from across the English-speaking world affirm a sense of acronym which does not require being pronounced as
23373-502: The terms as mutually exclusive. Other guides outright deny any legitimacy to the usage: Bryson's Dictionary of Troublesome Words says "Abbreviations that are not pronounced as words (IBM, ABC, NFL) are not acronyms; they are just abbreviations." Garner's Modern American Usage says "An acronym is made from the first letters or parts of a compound term. It's read or spoken as a single word, not letter by letter." The New York Times Manual of Style and Usage says "Unless pronounced as
23532-570: The twenty-first century. The trend among dictionary editors appears to be towards including a sense defining acronym as initialism : the Merriam-Webster's Collegiate Dictionary added such a sense in its 11th edition in 2003, and both the Oxford English Dictionary and The American Heritage Dictionary added such senses in their 2011 editions. The 1989 edition of the Oxford English Dictionary only included
23691-583: The type I-F system of Pectobacterium atrosepticum . but in other systems, different host factors may be required Bioinformatic analysis of regions of phage genomes that were excised as spacers (termed protospacers) revealed that they were not randomly selected but instead were found adjacent to short (3–5 bp) DNA sequences termed protospacer adjacent motifs (PAM). Analysis of CRISPR-Cas systems showed PAMs to be important for type I and type II, but not type III systems during acquisition. In type I and type II systems, protospacers are excised at positions adjacent to
23850-557: The usual form in Europe (including the UK) and the US, containing fruit and added sweeteners. These are typically called "drinkable yogurt". Also available are "yogurt smoothies", which contain a higher proportion of fruit and are more like smoothies . Yogurt production involves preparing warm milk to a temperature (30–45 °C (86–113 °F)) that will not kill the live microorganisms that turn
24009-536: The whole range of linguistic registers is relatively new in most languages, becoming increasingly evident since the mid-twentieth century. As literacy spread and technology produced a constant stream of new and complex terms, abbreviations became increasingly convenient. The Oxford English Dictionary ( OED ) records the first printed use of the word initialism as occurring in 1899, but it did not come into general use until 1965, well after acronym had become common. In English, acronyms pronounced as words may be
24168-425: The word " an achro nym ", which is a type of misnomer. Words derived from an acronym by affixing are typically expressed in mixed case, so the root acronym is clear. For example, "pre-WWII politics", "post-NATO world", " DNase ". In some cases a derived acronym may also be expressed in mixed case. For example, " messenger RNA " and " transfer RNA " become "mRNA" and "tRNA". Some publications choose to capitalize only
24327-459: Was a form of yogurt. Galen (AD 129 – c. 200/c. 216) mentioned that oxygala was consumed with honey , similar to the way thickened Greek yogurt is eaten today. The oldest writings mentioning yogurt are attributed to Pliny the Elder , who remarked that certain "barbarous nations" knew how "to thicken the milk into a substance with an agreeable acidity". The use of yogurt by medieval Turks
24486-553: Was available in tablet form for those with digestive intolerance and for home culturing. It was popularized by John Harvey Kellogg at the Battle Creek Sanitarium , where it was used both orally and in enemas , and later by Armenian immigrants Sarkis and Rose Colombosian, who started "Colombo and Sons Creamery" in Andover, Massachusetts , in 1929. Colombo Yogurt was originally delivered around New England in
24645-511: Was done with a full space between every full word (e.g. A. D. , i. e. , and e. g. for " Anno Domini ", " id est ", and " exempli gratia "). This even included punctuation after both Roman and Arabic numerals to indicate their use in place of the full names of each number (e.g. LII. or 52. in place of "fifty-two" and "1/4." or "1./4." to indicate "one-fourth"). Both conventions have fallen out of common use in all dialects of English, except in places where an Arabic decimal includes
24804-510: Was down 3.4 percent over the 12 months ending in February 2019. The decline of Greek-style yogurt has allowed Icelandic skyr to gain a foothold in the United States with sales of the latter increasing 24 percent in 2018 to $ 173 million. Yogurt (plain yogurt from whole milk) is 81% water, 9% protein , 5% fat, and 4% carbohydrates , including 4% sugars (table). A 100-gram amount provides 406 kilojoules (97 kcal) of dietary energy. As
24963-534: Was guided by various mechanisms, such as duplication events. On the other hand, each type of class 2 effector module arose from subsequent independent insertions of mobile genetic elements. These mobile genetic elements took the place of the multiple gene effector modules to create single gene effector modules that produce large proteins which perform all the necessary tasks of the effector module. The spacer regions of CRISPR-Cas systems are taken directly from foreign mobile genetic elements and thus their long-term evolution
25122-449: Was little to no naming , conscious attention, or systematic analysis until relatively recent times. Like retronymy, it became much more common in the twentieth century than it had formerly been. Ancient examples of acronymy (before the term "acronym" was invented) include the following: During the mid- to late nineteenth century, acronyms became a trend among American and European businessmen: abbreviating corporation names, such as on
25281-498: Was probably discovered first by Neolithic people in Central Asia and Mesopotamia around 5000 BC, when the first milk-producing animals were domesticated. They most likely found out how to ferment milk by chance and in all likelihood, yogurt was discovered independently in this way in many different places at different times. The cuisine of ancient Greece included a dairy product known as oxygala ( οξύγαλα ) which
#418581