Etymology
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inter- 
word-forming element used freely in English, "between, among, during," from Latin inter (prep., adv.) "among, between, betwixt, in the midst of" (also used extensively as a prefix), from PIE *enter "between, among" (source also of Sanskrit antar, Old Persian antar "among, between," Greek entera (plural) "intestines," Old Irish eter, Old Welsh ithr "among, between," Gothic undar, Old English under "under"), a comparative of root *en "in."

A living prefix in English from 15c. and used with Germanic as well as Latinate words. Spelled entre- in French; most words borrowed into English in that form were re-spelled 16c. to conform with Latin except entertain, enterprise. In Latin, spelling shifted to intel- before -l-, hence intelligence, etc.
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mis- (2)

word-forming element of Latin origin (in mischief, miscreant, misadventure, misnomer, etc.), from Old French mes- "bad, badly, wrong, wrongly," from Vulgar Latin *minus-, from Latin minus "less" (from suffixed form of PIE root *mei- (2) "small"), which was not used as a prefix in Latin but in the Romanic languages was affixed to words as a depreciative or negative element. The form in French perhaps was influenced in Old French by *miss-, the Frankish (Germanic) form of mis- (1).

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to- 
particle expressing separation, putting asunder, from West Germanic *ti- (source also of Old Frisian ti-, Old High German zi-, German zer-), from Proto-Germanic *tiz-, cognate with Latin-derived dis-. According to OED, some 125 compound verbs with this element are recorded in Old English; their number declined rapidly in Middle English and disappeared by c. 1500 except as conscious archaisms (such as to-shiver "break to pieces;" all to-brast).
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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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over- 

word-forming element meaning variously "above; highest; across; higher in power or authority; too much; above normal; outer; beyond in time, too long," from Old English ofer (from PIE root *uper "over"). Over and its Germanic relations were widely used as prefixes, and sometimes could be used with negative force. This is rare in Modern English, but compare Gothic ufarmunnon "to forget," ufar-swaran "to swear falsely;" Old English ofercræft "fraud."

In some of its uses, moreover, over is a movable element, which can be prefixed at will to almost any verb or adjective of suitable sense, as freely as an adjective can be placed before a substantive or an adverb before an adjective. [OED]

Among the old words not now existing are Old English oferlufu (Middle English oferlufe), literally "over-love," hence "excessive or immoderate love." Over- in Middle English also could carry a sense of "too little, below normal," as in over-lyght "of too little weight" (c. 1400), overlitel "too small" (mid-14c.), overshort, etc.

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loxo- 
word-forming element meaning "oblique," before vowels lox-, from Greek loxos "bent to the side, slanting, oblique," figuratively "ambiguous," a word of uncertain origin. As in loxodromics "art of oblique sailing" (1670s).
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cerato- 

word-forming element meaning "horn, horn-like part," from Latinized form of Greek keras (genitive keratos) "horn of an animal; horn as a substance," from PIE root *ker- (1) "horn, head."

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phago- 

word-forming element meaning "eating," from Greek phago- "eating, devouring," from PIE root *bhag- "to share out, apportion; to get a share." As in Phagiphany, the name of the Church festival celebrating the miracle of the fishes and loaves.

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theo- 
word-forming element meaning "god, gods, God," from Greek theos "god," from PIE root *dhes-, forming words for religious concepts, such as Latin feriae "holidays," festus "festive," fanum "temple."
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steno- 
before vowels sten-, word-forming element meaning "narrow," from Greek stenos "narrow, strait," as a noun "straits of the sea, narrow strip of land," also metaphorically, "close, confined; scanty, petty," from PIE *sten- "narrow."
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