{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:18:40Z","timestamp":1785403120506,"version":"3.56.0"},"posted":{"date-parts":[[2026,7,27]]},"group-title":"Bioengineering","reference-count":0,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T00:00:00Z","timestamp":1785110400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"award":["GM122567"],"award-info":[{"award-number":["GM122567"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NS142167"],"award-info":[{"award-number":["NS142167"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NS123719"],"award-info":[{"award-number":["NS123719"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["EB028143"],"award-info":[{"award-number":["EB028143"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NS111039"],"award-info":[{"award-number":["NS111039"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["HL166522"],"award-info":[{"award-number":["HL166522"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,27]]},"abstract":"<jats:p>\n                  Compact near-infrared (NIR) fluorescent proteins (FPs) with red-shifted emission are needed for deep-tissue short-wavelength infrared (SWIR) imaging. We engineered a GAF domain from the JSC1 cyanobacteriochrome of thermophilic\n                  <jats:italic>Leptolyngbya sp.<\/jats:italic>\n                  into three monomeric, biliverdin-binding NIR FPs of 19.1 kDa: miRFP729nano, miRFP732nano and miRFP735nano, with excitation\/emission maxima of 714\/729, 716\/732 and 719\/735 nm, respectively. Their off-peak fluorescence beyond 1000 nm was several-fold higher than that of miRFP718nano previously used for SWIR imaging. miRFP732nano functioned as a fusion tag, a component of target-stabilized nanobodies, and a reporter of NF-kappaB and AP-1 transcriptional activities. It enabled single-laser, dual-color three-photon imaging with EGFP to depths of ~950 micrometers in cortex and ~300 micrometers in spinal cord. In mice, miRFP732nano supported SWIR imaging of skeletal muscle, inflammatory signaling and intracellular targets. Combining SWIR detection with biocompatible 4-aminoantipyrine-based in vivo tissue clearing enhanced signal and image sharpness. These red-shifted NIR FPs expand the genetically encoded toolkit for deep-tissue imaging.\n                <\/jats:p>","DOI":"10.64898\/2026.07.25.740731","type":"posted-content","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T20:50:18Z","timestamp":1785185418000},"source":"Crossref","is-referenced-by-count":0,"title":["Compact red-shifted near-infrared fluorescent proteins enable deep-tissue SWIR imaging with in vivo optical clearing."],"prefix":"10.64898","author":[{"given":"Kyrylo Yu.","family":"Manoilov","sequence":"first","affiliation":[{"name":"Albert Einstein College of Medicine;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yirui","family":"Xu","sequence":"additional","affiliation":[{"name":"Duke University;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinhuan","family":"Luo","sequence":"additional","affiliation":[{"name":"Duke University;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olena S.","family":"Oliinyk","sequence":"additional","affiliation":[{"name":"University of Helsinki;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin","family":"Carey","sequence":"additional","affiliation":[{"name":"Salk Institute for Biological Studies;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kateryna O.","family":"Tokarchuk","sequence":"additional","affiliation":[{"name":"University of Helsinki;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinghang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Albert Einstein College of Medicine;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guosong","family":"Hong","sequence":"additional","affiliation":[{"name":"Stanford University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0875-7855","authenticated-orcid":false,"given":"Axel","family":"Nimmerjahn","sequence":"additional","affiliation":[{"name":"Salk Institute for Biological Studies;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junjie","family":"Yao","sequence":"additional","affiliation":[{"name":"Duke University;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladislav V.","family":"Verkhusha","sequence":"additional","affiliation":[{"name":"Albert Einstein College of Medicine;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.07.25.740731","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T20:50:18Z","timestamp":1785185418000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.07.25.740731"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,27]]},"references-count":0,"URL":"https:\/\/doi.org\/10.64898\/2026.07.25.740731","relation":{},"subject":[],"published":{"date-parts":[[2026,7,27]]},"subtype":"preprint"}}