Etymology
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de- 

active word-forming element in English and in many verbs inherited from French and Latin, from Latin de "down, down from, from, off; concerning" (see de), also used as a prefix in Latin, usually meaning "down, off, away, from among, down from," but also "down to the bottom, totally" hence "completely" (intensive or completive), which is its sense in many English words.

As a Latin prefix it also had the function of undoing or reversing a verb's action, and hence it came to be used as a pure privative — "not, do the opposite of, undo" — which is its primary function as a living prefix in English, as in defrost (1895), defuse (1943), de-escalate (1964), etc. In some cases, a reduced form of dis-.

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entero- 
before vowels enter-, word-forming element meaning "intestine," from Greek enteron "an intestine, piece of gut" (see enteric).
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litho- 
before vowels, lith-, word-forming element meaning "stone, rock;" from Greek lithos "stone, a precious stone, marble; a piece on a game board," a word of unknown origin.
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deoxy- 

also desoxy-, word-forming element used to make chemical names for compounds which contain fewer oxygen atoms than other compounds, from de- + first two syllables of oxygen.

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desmo- 

before vowels desm-, word-forming element used in scientific compounds and meaning "band, bond, ligament," from Greek desmos "bond, fastening, chain," related to dein "to bind," from PIE root *dē- "to bind."  

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di- (2)

word-forming element of Latin origin meaning "apart, asunder," the form of dis- before certain voiced consonants. As des- was a form of dis- in Old French, some Middle English words have forms in both de- and di-; compare devise, which really belongs to di- and is related to divide.

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xylo- 
before vowels xyl-, word forming element meaning "wood," from Greek xylon "wood cut and ready for use, firewood, timber; piece of wood; stocks, a plank, beam, or bench," in New Testament, "the Cross," a word of uncertain origin. It seems to correspond with Lithuanian šulas "post, pole, stave," Russian šulo "garden-pole," Serbo-Croatian šulj "block," Old High German sul "style, pole," Gothic sauls "pillar," but the exact relationship is unclear, and Beekes asks, "Was the word taken from a non-IE substrate language?"
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gluco- 

before vowels, gluc-, word-forming element used since c. 1880s, a later form of glyco-, from Greek glykys "sweet," figuratively "delightful; dear; simple, silly," from *glku-, a dissimilation in Greek from PIE root *dlk-u- "sweet" (source also of Latin dulcis). De Vaan writes that "It is likely that we are dealing with a common borrowing from an unknown source." Now usually with reference to glucose.

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nano- 

introduced 1947 (at 14th conference of the Union Internationale de Chimie) as a prefix for units of one thousand-millionth part (now "one-billionth"), from Greek nanos "a dwarf." According to Watkins, this is originally "little old man," from nannos "uncle," masc. of nanna "aunt" (see nana), but Beekes calls it "An onomatopoeic word of unknown origin." Earlier nano- was used as a prefix to mean "dwarf, dwarfish," and still it is used in a non-scientific sense of "very small."

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dis- 
Origin and meaning of dis-

word-forming element of Latin origin meaning 1. "lack of, not" (as in dishonest); 2. "opposite of, do the opposite of" (as in disallow); 3. "apart, away" (as in discard), from Old French des- or directly from Latin dis- "apart, asunder, in a different direction, between," figuratively "not, un-," also "exceedingly, utterly." Assimilated as dif- before -f- and to di- before most voiced consonants.

The Latin prefix is from PIE *dis- "apart, asunder" (source also of Old English te-, Old Saxon ti-, Old High German ze-, German zer-). The PIE root is a secondary form of *dwis- and thus is related to Latin bis "twice" (originally *dvis) and to duo, on notion of "two ways, in twain" (hence "apart, asunder").

In classical Latin, dis- paralleled de- and had much the same meaning, but in Late Latin dis- came to be the favored form and this passed into Old French as des-, the form used for compound words formed in Old French, where it increasingly had a privative sense ("not"). In English, many of these words eventually were altered back to dis-, while in French many have been altered back to de-. The usual confusion prevails.

As a living prefix in English, it reverses or negatives what it is affixed to. Sometimes, as in Italian, it is reduced to s- (as in spend, splay, sport, sdain for disdain, and the surnames Spencer and Spence).

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