Etymology
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Words related to *en

and (conj.)
Old English and, ond, originally meaning "thereupon, next," from Proto-Germanic *unda (source also of Old Saxon endi, Old Frisian anda, Middle Dutch ende, Old High German enti, German und, Old Norse enn), from PIE root *en "in."

Introductory use (implying connection to something previous) was in Old English. To represent vulgar or colloquial pronunciation often written an', 'n'. Phrase and how as an exclamation of emphatic agreement dates from early 1900s.
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atoll (n.)
"island consisting of a strip or ring of coral around a central lagoon," 1620s, atollon, from Malayalam (Dravidian) atolu "reef," which is said to be from adal "closing, uniting." Watkins writes, "Perhaps ultimately from Sanskrit antara-, interior" (from PIE root *en "in"). The original use was in reference to the Maldives. Popularized in present form by Darwin's writings.
dysentery (n.)

diseased characterized by inflammation of the mucous membrane of the large intestine, late 14c., dissenterie, from Old French disentere (13c.) and directly from Medieval Latin dysenteria, from Greek dysenteria, coined by Hippocrates, from dys- "bad, abnormal, difficult" (see dys-) + entera "intestines, bowels," from PIE *enter "between, among," comparative of root *en "in." Related: Dysenteric.

embargo (n.)
"order forbidding ships from certain other nations from entering or leaving a nation's ports," 1590s, from Spanish embargo "seizure, arrest; embargo," noun of action from embargar "restrain, impede, arrest, embargo," from Vulgar Latin *imbarricare, from assimilated form of in- "into, upon" (from PIE root *en "in") + *barra (see bar (n.1)). As a verb, from 1640s. Related: Embargoed.
embarrass (v.)

1670s, "perplex, throw into doubt," from French embarrasser (16c.), literally "to block," from Italian imbarrazzo, from imbarrare "to bar," from assimilated form of in- "into, upon" (from PIE root *en "in") + Vulgar Latin *barra "bar" (see bar (n.1)).

Meaning "to hamper, hinder" is from 1680s. Meaning "make (someone) feel awkward" is attested by 1809. The original sense is preserved in embarras de richesse "the condition of having more wealth than one knows what to do with" (1751), from French (1726). Related: Embarrassed; embarrassing; embarrassingly.

embryo (n.)
"fetus in utero at an early stage of development," mid-14c., from Medieval Latin embryo, properly embryon, from Greek embryon "a young one," in Homer, "young animal," later, "fruit of the womb," literally "that which grows," from assimilated form of en "in" (from PIE root *en "in") + bryein "to swell, be full."
empire (n.)

mid-14c., "territory subject to an emperor's rule;" in general "realm, dominion;" late 14c. as "authority of an emperor, supreme power in governing; imperial power," in Middle English generally of the Roman Empire.

From Old French empire "rule, authority, kingdom, imperial rule" (11c.), from Latin imperium "a rule, a command; authority, control, power; supreme power, sole dominion; military authority; a dominion, realm," from imperare "to command," from assimilated form of in- "in" (from PIE root *en "in") + parare "to order, prepare" (from PIE root *pere- (1) "to produce, procure").

Not etymologically restricted to "territory ruled by an emperor," but used that way. The Empire, meaning "the British Empire," first recorded 1772 (it officially devolved into "The Commonwealth" in 1931); before that it meant the Holy Roman Empire (1670s).

[P]roperly an empire is an aggregate of conquered, colonized, or confederated states, each with its own government subordinate or tributary to that of the empire as a whole. [Century Dictionary] 

Empire as the name of a style (especially in reference to a style of dresses with high waistlines) is by 1860, in reference to the affected classicism prevailing in France during the reign of Napoleon I (1804-15). Second Empire is in reference to the rule of Napoleon III of France (1852-70). New York has been called the Empire State since 1834.

employ (v.)
early 15c., "apply or devote (something to some purpose); expend or spend," from Old French emploiier (12c.) "make use of, apply; increase; entangle; devote," from Latin implicare "enfold, involve, be connected with, unite, associate," from assimilated form of in- (from PIE root *en "in") + plicare "to fold" (from PIE root *plek- "to plait").

Imply, which is the same word, retains more of the original sense. Sense of "hire, engage" first recorded in English 1580s, from meaning "involve in a particular purpose," which arose in Late Latin. Related: Employed; employing; employable.
en- (1)
word-forming element meaning "in; into," from French and Old French en-, from Latin in- "in, into" (from PIE root *en "in"). Typically assimilated before -p-, -b-, -m-, -l-, and -r-. Latin in- became en- in French, Spanish, Portuguese, but remained in- in Italian.

Also used with native and imported elements to form verbs from nouns and adjectives, with a sense "put in or on" (encircle), also "cause to be, make into" (endear), and used as an intensive (enclose). Spelling variants in French that were brought over into Middle English account for parallels such as ensure/insure, and most en- words in English had at one time or another a variant in in-, and vice versa.
en- (2)
word-forming element meaning "near, at, in, on, within," from Greek en "in," cognate with Latin in (from PIE root *en "in"), and thus with en- (1). Typically assimilated to em- before -p-, -b-, -m-, -l-, and -r-.