Etymology
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para- (2)

word-forming element of Latin origin meaning "defense, protection against; that which protects from," from Italian para, imperative of parare "to ward off," from Latin parare "make ready" (from PIE root *pere- (1) "to produce, procure"). It figures in parachute, parasol, parapet, etc.

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phylo- 

before vowels phyl-, modern word-forming element, mostly in the sciences, often meaning "phylum," from Greek phylon, phylē "a tribe," also a political subdivision in ancient Athens, from base of phyein "to bring forth, produce, make to grow," whence also physis "nature" (from PIE root *bheue- "to be, exist, grow").

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histo- 
medical word-forming element, from Greek histos "warp, web," literally "anything set upright," from histasthai "to stand," from PIE root *sta- "to stand, make or be firm." Taken by 19c. medical writers as the best Greek root from which to form terminology for "tissue, structural element of the animal body."
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bene- 
sometimes beni-, word-forming element meaning "well," from Latin bene (adv.) "well, in the right way, honorably, properly," from PIE *dwenelo-, suffixed (adverbial) form of root *deu- (2) "to do, perform; show favor, revere." Opposed to mal-. From the same source come Latin bonus "good," bellus "handsome, fine, pretty," and possibly beatus "blessed," beare "to make blessed."
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be- 

word-forming element of verbs and nouns from verbs, with a wide range of meaning: "about, around; thoroughly, completely; to make, cause, seem; to provide with; at, on, to, for;" from Old English be- "about, around, on all sides" (the unstressed form of bi "by;" see by (prep.)). The form has remained by- in stressed positions and in some more modern formations (bylaw, bygones, bystander).

The Old English prefix also was used to make transitive verbs and as a privative prefix (as in behead). The sense "on all sides, all about" naturally grew to include intensive uses (as in bespatter "spatter about," therefore "spatter very much," besprinkle, etc.). Be- also can be causative, or have just about any sense required. The prefix was productive 16c.-17c. in forming useful words, many of which have not survived, such as bethwack "to thrash soundly" (1550s) and betongue "to assail in speech, to scold" (1630s).

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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.
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