Marine Ecology: Current and Future Developments

Volume: 2

Single-Cell Imaging and Sequencing-Based Detection of Microorganisms Using Highly Sensitive Fluorescence in situ Hybridization (FISH)

Author(s): Tsuyoshi Yamaguchi and Shuji Kawakami * .

Pp: 161-176 (16)

DOI: 10.2174/9789811437250120020017

* (Excluding Mailing and Handling)

Abstract

Fluorescence in situ hybridization (FISH) has become a standard technique in the visual detection and phylogenetic identification of environmental microorganisms in marine microbiology. Thirty years have passed since the appearance of FISH, and now FISH can detect not only ribosomal RNA but also mRNA and functional genes with high sensitivity. This chapter describes the principles, drawbacks, and applications of FISH and highly sensitive FISH. In particular, we introduce two high-sensitivity FISH methods developed by the authors. The first is in situ DNA hybridization chain reaction (HCR), a highly sensitive and highly penetrating detection technique for ribosomal-RNA–targeting FISH, and the second is two-pass tyramide signal amplification (TSA)-FISH that can detect single-copy genes. Finally, we discuss how the FISH technique has contributed to the field of marine microbiology.


Keywords: CARD-FISH, Environmental microbiology, FISH, Functional genes, GeneFISH, HCR-FISH, Highly sensitive FISH, in situ DNA-HCR, ISH, Marine bacteria, Microscopic observation, Oligonucleotide probe, Phylogenetic identification, Polynucleotide probe, Probe permeabilization, Single cell imaging, Two-pass TSA-FISH, Visual detection.

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      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Trial Access" as access_base_text, CASE j.type WHEN 111 THEN true ELSE false END as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_trail` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 309679543 and j.to_ip >=309679543 )) and ((j.from_date <= 1739834427 and j.to_date >= 1739834427 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 13406) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Subscribed" as access_base_text, false as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_corporate` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 309679543 and j.to_ip >=309679543 )) and ((j.from_date <= 1739834427 and j.to_date >= 1739834427 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 13406) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Token Based Access" as access_base_text, false as terms_popup, "R" as content_download_type, j.uc_id as restricted_user_access_key, "v" as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_token` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 309679543 and j.to_ip >=309679543 )) and ((j.from_date <= 1739834427 and j.to_date >= 1739834427 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 13406)
      770μsalphaeurekaselec_live_10_06_2022UserAccess.php#1266
      Backtrace
      • 13. app/Models/UserAccess/UserAccess.php:1266
      • 14. app/Http/Controllers/ChapterController.php:1549
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • select b.banner_link, b.banner_name, b.banner_script, b.banner_remarks, b.banner_file_name, b.banner_placement, bd.content_type, bd.content_id from `tbl_banner` as `b` inner join `tbl_banner_detail` as `bd` on `bd`.`banner_id` = `b`.`banner_id` inner join `users` as `u` on `u`.`id` = `b`.`updated_by` where `b`.`banner_ebook` = 1 and `bd`.`content_type` = 'B' and `bd`.`content_id` = 2806 and `b`.`banner_from_date` <= 1739834427 and `b`.`banner_to_date` >= 1739834427 and `b`.`banner_status` = 'A' order by `b`.`banner_id` desc
      1.09msalphaeurekaselec_live_10_06_2022Banner.php#95
      Bindings
      • 0: 1
      • 1: B
      • 2: 2806
      • 3: 1739834427
      • 4: 1739834427
      • 5: A
      Backtrace
      • 13. app/Models/Banner.php:95
      • 14. app/Http/helpers.php:404
      • 17. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 18. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    • select count(*) as aggregate from `uc_cart_products` where cart_id='eefdd9c4a606d718b5efb59fcb9442ad'
      240μsalphaeurekaselec_live_10_06_2022Cart.php#271
      Backtrace
      • 15. app/Models/Cart.php:271
      • 16. view::layouts._header:260
      • 18. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 20. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    App\Models\Keywords
    18Keywords.php#?
    App\Models\Chapter
    1Chapter.php#?
    App\Models\Ebook
    1Ebook.php#?
        _token
        jFUrqw4A1i0UJJWSaN49ixrUCxQWXeM5r5e9YbgA
        uc_cart_id
        eefdd9c4a606d718b5efb59fcb9442ad
        _previous
        array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/13406" ]
        _flash
        array:2 [ "old" => [] "new" => [] ]
        PHPDEBUGBAR_STACK_DATA
        []
        path_info
        /chapter/13406
        status_code
        200
        
        status_text
        OK
        format
        html
        content_type
        text/html; charset=UTF-8
        request_query
        []
        
        request_request
        []
        
        request_headers
        0 of 0
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        request_cookies
        0 of 0
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        response_headers
        0 of 0
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        session_attributes
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        array:5 [ "_token" => "jFUrqw4A1i0UJJWSaN49ixrUCxQWXeM5r5e9YbgA" "uc_cart_id" => "eefdd9c4a606d718b5efb59fcb9442ad" "_previous" => array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/13406" ] "_flash" => array:2 [ "old" => [] "new" => [] ] "PHPDEBUGBAR_STACK_DATA" => [] ]
        ClearShow all
        Date ↕MethodURLData
        #12025-02-17 23:20:27GET/chapter/134061121920