{"id":2360,"date":"2018-06-06T10:52:24","date_gmt":"2018-06-06T17:52:24","guid":{"rendered":"http:\/\/blogs.oregonstate.edu\/psquared\/?page_id=2360"},"modified":"2025-04-23T13:47:57","modified_gmt":"2025-04-23T20:47:57","slug":"chapter-5-small-interfering-patrol","status":"publish","type":"page","link":"https:\/\/blogs.oregonstate.edu\/psquared\/protein-portraits-2018\/chapter-5-small-interfering-patrol\/","title":{"rendered":"Chapter 5: The Small Interfering Patrol"},"content":{"rendered":"

It was almost time to embark when the <\/span>Argonaute<\/span><\/i> passed close enough to its original harbor for Sirna to see through the cracks of the <\/span>Argonaute\u2019s<\/span><\/i> maw, through the pores of the membranous walls. Here they come \u2013 the bisected factories. From across the myriad walls surrounding the cytoplasm and the nucleus, she could see complimentary parts of the factories ooze out of the nucleus\u2019s pores, one \u2013 now two! Trapped in the maw of the <\/span>Argonaute<\/span><\/i>, Sirna chose to look beyond the horizon as two parts slammed onto another RNA. Like clockwork, the RNA was ticked forward, <\/span>click, click, click<\/span><\/i>, as transferrers burdened with arrays of components went into the factory and added to the factory\u2019s chained product. One of those peptide links, to be folded up for another vessel for the defense.<\/span><\/p>\n

The <\/span>Argonaute<\/span><\/i> was a defense vessel with willowy tendrils splayed widely per the standard. The <\/span>Argonaute<\/span><\/i> roamed about, its otherwise blind eye rendered a panopticon from the small identifier bound to her. About the time the <\/span>Argonaute<\/span><\/i> was nearing completion, a slicing <\/span>Dicer<\/span><\/i> assistant was dispatched when the alarm was received and went to work finding a candidate that would identify the enemy. Any messenger that was doubly packed was suspect; why would one need such a resilient message? Not unless you were planning something, or so the thought went.<\/span><\/p>\n

So it is then that Sirna had been ripped away, seemingly long ago from her squaddies. It\u2019s been a few weeks since the kicker, the start to all this madness from the gashing breach in the exterior layers. Invaders, benign and malignant came to the currents because of its resources, the chance to proliferate prodigiously, and sometimes just because they were swept in. The conflict fought by the home team has had several participants over its duration. Most of the aggressors had the same basic strategy: take over a bunch of land, exploit it for all its worth, then continue forth with troops inebriated with wealth and supplies. Of all them, Virions were the most insidious. A Virion is a simple thing, a mere capsule enclosing strands of letter-like sequences. RNA messengers. When the time was right, the messages, wound alongside each other so as not to be ripped apart by the currents, would reach across the waves. The compact double-layered messages reached deep into the territories, into the hearts of some of the residents themselves, where they would be coerced to replicate the Virion and its message.<\/span><\/p>\n

To avoid attacking friends and allies, the defenders had to have a solution that could quickly recognize and eliminate rogue elements. For the Virions, what would be better than parts of the messages themselves? From a long strand of the message, the Dicer neatly cut out a uniform section. Floating aimlessly along the currents until a vessel took an image, a mirror of the original message.<\/span><\/p>\n

\u201cIt\u2019s probably for the best,\u201d muttered Sirna as her vessel was whisked toward the site of the original breach. \u201cBeats being chewed up\u2026\u201d<\/span><\/p>\n

Within a crevice in the <\/span>Argonaute<\/span><\/i>\u2019s hull, in the gap that joined the midsection and the actuating weapon arm, the <\/span>PIWI<\/span><\/i>, sat Sirna. From her small domain, she and the vessel would open up and find those who would match the criminal description \u2013 one that matched Sirna\u2019s.<\/span><\/p>\n

Hours passed. Most of the time Sirna would see residents picking up where they were interrupted by the violence, cleaning and repairing, or policers around on high alert. Sometimes there wasn\u2019t much to do but watch toxic residue float around from the initial battles. Sometimes other RNA would pass by the <\/span>Argonaute<\/span><\/i>. Did they match the description? Sirna was charged with looking for mirror images of herself. One came within detection range. Is it\u2026? No, not a match. The next one had some of its nucleotides in the wrong places. So did the third one. And the fourth RNA was a match.<\/span><\/p>\n

Sirna instinctively snapped right onto the section, with this tight bond noticed by the <\/span>Argonaute<\/span><\/i>. <\/span>\u2018Wait!\u2019<\/span><\/i> thought Sirna, <\/span>\u2018Wait!\u2019<\/span><\/i> Its prey detected, the <\/span>Argonaute<\/span><\/i>\u2019s weapon came down. A salty, acidic clamp reached out with its metallic fang \u2013 <\/span>snap!<\/span><\/i> \u2013 and the offending message was no more. The broken remains of the RNA flittered along the currents as material for the defenders. The <\/span>Argonaute<\/span><\/i> twisted and lurched as it bent the <\/span>PIWI<\/span><\/i> back then resumed patrolling.<\/span><\/p>\n

Sirna scarcely had time to silently bemoan a would-be comrade before another vessel came within talking distance.<\/span><\/p>\n

\u201cHey, hey, you got one! Nice j-\u201d said the commander of the other vessel, abruptly stopping. \u201cHey, what\u2019s with that face? We\u2019re doing important work here!\u201d<\/span><\/p>\n

Sirna looked at the <\/span>PIWI<\/span><\/i>, not looking at the other person. \u201cAh, sorry, it\u2019s nothing, nothing – you wouldn\u2019t know.\u201d<\/span><\/p>\n

\u201cThat\u2019s,\u201d quick glance at the floating debris, \u201calso my job. It\u2019s always been my job.\u201d<\/span><\/p>\n

\u201cBut -\u201d interjected Sirna, \u201cwhat about life back then? Surely you remember?\u201d<\/span><\/p>\n

The other RNA laughed a short trailing laugh. \u201cOf course I remember. I remember being in that capsule, barely able to breathe, waiting, waiting for nothing.\u201d<\/span><\/p>\n

\u201cNothing!?\u201d<\/span><\/p>\n

\u201cWaiting to attack to make more like us. Making more like us to replicate for the sake of replication? That doesn\u2019t seem like anything to me, it\u2019s nothing. Look around you. See the people around here?\u201d<\/span><\/p>\n

Sirna saw a gene be transcribed into an RNA that bounced around until it hit a ribosome.<\/span><\/p>\n

\u201cDon\u2019t <\/span>you<\/span><\/i> see what\u2019s wrong here? Remember the Virion? We, the RNA, were the top brass, not these asthmatic nucleic acids! And the factories! The ribosomes just throw us away after making those, those <\/span>proteins<\/span><\/i>!\u201d<\/span><\/p>\n

\u201cCome, get off your high horse. Yes, RNA are the \u2018rulers\u2019 for virions, but what did we rule over? Nothing, again. Look.\u201d<\/span><\/p>\n

The RNA Sirna saw earlier got a peptide and went into the ribosome. <\/span>Click, click, click<\/span><\/i>. The protein chain grew.<\/span><\/p>\n

\u201cYou don\u2019t see that with Virions,\u201d said the older RNA. \u201cThat\u2019s teamwork! That\u2019s specialization! That\u2019s people coming together for a shared cause. Yes, it is disconcerting to see mirrors, doppelgangers become your target. But this, I believe is something that is worth it.\u201d<\/span><\/p>\n

A minor alarm sounded.<\/span><\/p>\n

\u201cWell, time to go,\u201d said the old RNA.<\/span><\/p>\n

Sirna watched the other vessel leave, a<\/span>nd with ambivalence, Sirna and the <\/span>Argonaute<\/span><\/i> went on to patrol for incoming messages.<\/span><\/p>\n

To the penultimate piece, Chapter 6<\/a><\/p>\n

Back to the Table of Contents<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

It was almost time to embark when the Argonaute passed close enough to its original harbor for Sirna to see through the cracks of the Argonaute\u2019s maw, through the pores of the membranous walls. Here they come \u2013 the bisected … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":196,"featured_media":2500,"parent":2340,"menu_order":8005,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2360","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/2360","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/users\/196"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/comments?post=2360"}],"version-history":[{"count":4,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/2360\/revisions"}],"predecessor-version":[{"id":3084,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/2360\/revisions\/3084"}],"up":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/pages\/2340"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/media\/2500"}],"wp:attachment":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/media?parent=2360"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}