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antibiotics","due_date":null,"description":null,"x":0,"y":50,"my_module_group_id":1185,"created_at":"2018-11-09T10:47:34.880Z","updated_at":"2018-12-19T13:28:00.803Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":1,"experiment_id":430,"state":"uncompleted","completed_on":null},"outputs":[{"id":6012,"input_id":2132,"output_id":2127}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3453,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2127,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T10:47:34.945Z","updated_at":"2018-12-24T09:08:20.547Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4369,"name":"Dilute antibiotic stock","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eDilute the 10 mg/mL antibiotic stock solution 1:10 in sterile broth or water to achieve a 1 mg/mL solution.\u003cbr\u003e Dilute the 1 mg/mL solution 1:10 in sterile broth or water to achieve a 0.1 mg/mL solution\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T12:10:09.672Z","updated_at":"2018-12-20T13:06:27.384Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4370,"name":"Prepare agar plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003ePrepare agar plates following guidelines bellow.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T12:22:03.852Z","updated_at":"2018-12-24T09:08:20.489Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[{"checklist":{"id":966,"name":"Guidelines:","step_id":4370,"created_at":"2018-12-21T11:52:37.302Z","updated_at":"2018-12-21T11:52:37.302Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3975,"text":"Dispense appropriate amounts of antibiotic solution into the respective containers. Follow table steps.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.304Z","updated_at":"2018-12-21T11:52:37.304Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3976,"text":"For each agar plate, add 25 mL agar (now at a temperature of 50°C) into the container, mix well (avoid bubbles) and pour 25 ml into a petri dish labelled with the respective antibiotic concentration.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.311Z","updated_at":"2018-12-21T11:52:37.311Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3977,"text":"Pour a control agar plate without any antibiotic. Adjust the number if necessary.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.317Z","updated_at":"2018-12-21T11:52:37.317Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3978,"text":"Allow agar to set.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.324Z","updated_at":"2018-12-21T11:52:37.324Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3979,"text":"Dry the surface of the agar plates either in an incubator or in a laminar airflow hood for 30 min. Leave the lid ajar.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.330Z","updated_at":"2018-12-21T11:52:37.330Z","created_by_id":null,"last_modified_by_id":null,"position":4},{"id":3980,"text":"Mark the bottom of the agar plates to define an orientation.","checked":false,"checklist_id":966,"created_at":"2018-12-21T11:52:37.336Z","updated_at":"2018-12-21T11:52:37.336Z","created_by_id":null,"last_modified_by_id":null,"position":5}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":545,"step_id":4370,"table_id":682}],"tables":[{"id":682,"created_at":"2018-12-20T13:07:47.021Z","updated_at":"2018-12-24T09:08:20.452Z","created_by_id":202,"last_modified_by_id":202,"name":"","team_id":1,"contents":"eyJkYXRhIjpbWyJBbnRpbWljcm9iaWFsIGNvbmNlbnRyYXRpb24gKG1nL0wp\nIiwiVm9sdW1lIG9mIGFudGliaW90aWMgc3RvY2sgc29sdXRpb24gKM68TCki\nLCJGaW5hbCBjb25jZW50cmF0aW9uIHdoZW4gYWRkaW5nIDI1bUwgb2YgYWdh\nciJdLFsiMTAiLCIzMjAiLCIxMjgiXSxbIjEwIiwiMTYwIiwiNjQiXSxbIjEw\nIiwiODAiLCIzMiJdLFsiMTAiLCI0MCIsIjE2Il0sWyIxIiwiMjAwIiwiOCJd\nLFsiMSIsIjEwMCIsIjQiXSxbIjEiLCI1MCIsIjIiXSxbIjAuMSIsIjI1MCIs\nIjEiXSxbIjAuMSIsIjEyNSIsIjAuNSJdLFsiMC4xIiwiNjIuNSIsIjAuMjUi\nXSxbIjAuMSIsIjMxLjI1IiwiMS4xMjUiXV19\n","data_vector":"JzAuMSc6MzksNDIsNDUsNDggJzAuMjUnOjQ3ICcwLjUnOjQ0ICcxJzozMCwz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\nZW4nOjEz\n"}]},{"step":{"id":4367,"name":"Calculate the amount of antibiotic solutions","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp style=\"text-align: justify;\"\u003eAs the medium cools down, calculate the amount of antibiotic solutions (10, 1 and 0.1 mg/L) needed. 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Autoclaving at 121.1°C for 15 minutes at 1 bar. Cool medium to 50°C after that. Around 25 mL is necessary to pour one 15 100 mm petri dish to produce the required depth of 3–4 mm. \u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\u003c/div\u003e\n\u003cdiv class=\"row\"\u003e \u003c/div\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:00:24.509Z","updated_at":"2018-12-20T12:56:25.184Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2126,"name":"Growth method","due_date":null,"description":null,"x":0,"y":17,"my_module_group_id":1185,"created_at":"2018-11-09T10:25:56.551Z","updated_at":"2018-12-19T13:28:00.808Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":2,"experiment_id":430,"state":"uncompleted","completed_on":null},"outputs":[{"id":6011,"input_id":2132,"output_id":2126}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3452,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2126,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T10:25:56.621Z","updated_at":"2018-12-24T09:01:33.704Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5201,"name":"Take samples for cell count","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eTake samples for cell count and follow protocol in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#cou\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":5,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:33:52.646Z","updated_at":"2018-12-17T14:33:52.646Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4361,"name":"Assessment of turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cstrong\u003eTurbidity can be assessed visually by comparing the test and the McFarland Standard.\u003c/strong\u003e \u003cbr\u003e\u003cbr\u003eMix the McFarland 0.5 BaSO\u003csub\u003e4\u003c/sub\u003e standard vigorously using a vortex mixer. The turbidity is verified measuring the absorbance of the suspension spectrophotometrically. The absorbance should be in the same range as that of the McFarland standard 0.5 (OD625 nm should be at 0.08–0.13).\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.657Z","updated_at":"2018-12-21T11:15:08.233Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4360,"name":"Adjustment of suspension turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAdjust the suspension’s turbidity to that of a McFarland Standard 0.5 by adding sterile distilled water, saline or broth, if the turbidity is too high, or by adding more bacterial material if is too low.\u003cbr\u003e\u003cbr\u003eGo back to step 4.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.635Z","updated_at":"2018-12-21T11:15:35.763Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4362,"name":"Isolate preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow steps bellow for isolate preparation.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.680Z","updated_at":"2018-12-24T09:01:33.668Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[{"checklist":{"id":964,"name":"Guidelines:","step_id":4362,"created_at":"2018-12-21T11:14:19.776Z","updated_at":"2018-12-21T11:14:19.776Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3965,"text":"For each isolate, select three to five morphologically similar colonies from the fresh agar plate from task .","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.778Z","updated_at":"2018-12-21T11:14:19.778Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3966,"text":"Plate 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mixer.","checked":false,"checklist_id":964,"created_at":"2018-12-21T11:14:19.805Z","updated_at":"2018-12-21T11:14:19.805Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4363,"name":"Pure cultures of bacterial isolates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollowing guidelines below will get you to obtain bacterial isolates.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:25:56.700Z","updated_at":"2018-12-24T09:00:48.862Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[{"checklist":{"id":963,"name":"Guidelines:","step_id":4363,"created_at":"2018-12-21T11:12:20.820Z","updated_at":"2018-12-21T11:12:20.820Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3962,"text":"Prepare media (store at 4°C).","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.822Z","updated_at":"2018-12-21T11:12:20.822Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3963,"text":"Prepare antibiotic stock solutions.","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.831Z","updated_at":"2018-12-21T11:12:20.831Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3964,"text":"Streak the bacterial isolates to be tested onto nutrient-rich agar plates without inhibitor to obtain single colonies","checked":false,"checklist_id":963,"created_at":"2018-12-21T11:12:20.838Z","updated_at":"2018-12-21T11:12:20.838Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[{"id":2788,"step_id":4363,"asset_id":3410}],"assets":[{"id":3410,"created_at":"2018-12-21T11:12:20.990Z","updated_at":"2018-12-24T09:00:48.810Z","file_file_name":"Streak_plate.PNG","file_content_type":"image/png","file_file_size":160488,"file_updated_at":"2018-12-21T15:31:42.468Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":176536,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":4364,"name":"Incubate the broth","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eIncubation conditions:\u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e35–37°C\u003c/li\u003e\n\u003cli\u003eShaker set at 225 r.p.m. until it reaches turbidity that is equal to or greater than the turbidity of a McFarland Standard 0.5.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003eCulture growth will require 2–6 h depending on the growth rate of the bacteria to be tested. This pause period can be used to prepare the antibiotic or peptide dilutions.\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:35:37.405Z","updated_at":"2018-12-21T11:35:00.293Z","last_modified_by_id":202,"protocol_id":3452},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2125,"name":"Colony suspension","due_date":null,"description":null,"x":0,"y":0,"my_module_group_id":1185,"created_at":"2018-11-09T09:15:09.287Z","updated_at":"2018-12-19T13:28:00.805Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":3,"experiment_id":430,"state":"uncompleted","completed_on":null},"outputs":[{"id":6009,"input_id":2132,"output_id":2125}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3450,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2125,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T09:15:09.296Z","updated_at":"2018-12-24T08:59:10.733Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5202,"name":"Take samples for cell count","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the protocol in \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:34:48.930Z","updated_at":"2018-12-17T14:34:48.930Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4357,"name":"Isolate preparation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eFollow the guidelines below to prepare an isolate.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T09:26:34.638Z","updated_at":"2018-12-24T08:59:10.687Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[{"checklist":{"id":962,"name":"Guidelines","step_id":4357,"created_at":"2018-12-21T11:09:29.266Z","updated_at":"2018-12-21T11:09:29.266Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3957,"text":"For each isolate, select three to five morphologically similar colonies from the fresh agar plate from task","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.268Z","updated_at":"2018-12-21T11:09:29.268Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3958,"text":"Plate preparation","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.276Z","updated_at":"2018-12-21T11:09:29.276Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3959,"text":"Touch the top of each selected colony using a sterile loop or cotton swab.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.287Z","updated_at":"2018-12-21T11:09:29.287Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3960,"text":"Transfer the growth into a sterile capped glass tube containing sterile broth or saline solution.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.300Z","updated_at":"2018-12-21T11:09:29.300Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3961,"text":"Mix using a vortex mixer.","checked":false,"checklist_id":962,"created_at":"2018-12-21T11:09:29.307Z","updated_at":"2018-12-21T11:09:29.307Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5195,"name":"Pure cultures of bacterial isolates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003eGrowth conditions:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e18-24h\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T13:07:04.214Z","updated_at":"2018-12-24T08:55:09.983Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[{"checklist":{"id":961,"name":"Guidelines:","step_id":5195,"created_at":"2018-12-21T10:50:36.576Z","updated_at":"2018-12-21T10:50:36.576Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3954,"text":"Prepare media (store at 4°C)","checked":false,"checklist_id":961,"created_at":"2018-12-21T10:50:36.577Z","updated_at":"2018-12-21T10:50:36.577Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3955,"text":"Prepare antibiotic stock solutions","checked":false,"checklist_id":961,"created_at":"2018-12-21T10:50:36.584Z","updated_at":"2018-12-21T10:50:36.584Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3956,"text":"Streak the bacterial isolates to be tested onto nutrient-rich agar plates without inhibitor to obtain single colonies","checked":false,"checklist_id":961,"created_at":"2018-12-21T10:50:36.592Z","updated_at":"2018-12-21T10:50:36.592Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[{"id":2742,"step_id":5195,"asset_id":3358}],"assets":[{"id":3358,"created_at":"2018-12-17T13:09:17.744Z","updated_at":"2018-12-21T15:31:33.117Z","file_file_name":"Streaking_bacteria_method.png","file_content_type":"image/png","file_file_size":100610,"file_updated_at":"2018-12-21T15:31:32.844Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":110671,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]},{"step":{"id":4359,"name":"Adjustment of suspension turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eAdjust the suspension’s turbidity to that of a McFarland Standard 0.5 by adding sterile distilled water, saline or broth, if the turbidity is too high, or by adding more bacterial material if is too low.\u003cbr\u003e\u003cbr\u003eGo back to step 3.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:13:32.396Z","updated_at":"2018-12-17T13:09:32.630Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4358,"name":"Assessment of turbidity","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003e\u003cstrong\u003eTurbidity can be assessed visually by comparing the test and the McFarland Standard.\u003c/strong\u003e \u003cbr\u003e\u003cbr\u003eMix the McFarland 0.5 BaSO\u003csub\u003e4\u003c/sub\u003e standard vigorously using a vortex mixer. The turbidity is verified measuring the absorbance of the suspension spectrophotometrically. The absorbance should be in the same range as that of the McFarland standard 0.5 (OD625 nm should be at 0.08–0.13).\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T10:11:24.463Z","updated_at":"2018-12-21T11:10:10.216Z","last_modified_by_id":202,"protocol_id":3450},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2132,"name":"Antimicrobial susceptibility testing","due_date":null,"description":null,"x":34,"y":26,"my_module_group_id":1185,"created_at":"2018-11-09T14:20:10.098Z","updated_at":"2018-12-19T13:28:00.798Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":4,"experiment_id":430,"state":"uncompleted","completed_on":null},"outputs":[{"id":6010,"input_id":2134,"output_id":2132}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3458,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2132,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T14:20:10.107Z","updated_at":"2018-12-24T09:38:55.415Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":5198,"name":"Broth macrodilutions","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp\u003e\u003cstrong\u003eBroth dilutions preparation:\u003c/strong\u003e Add 1 mL of each antibiotic dilution into one test tube for each isolate to be tested. Fill the control tubes with 1 mL sterile broth without an antimicrobial agent. Mix the bacterial suspension well. The suspension should be adjusted to 1x10\u003csup\u003e8\u003c/sup\u003e CFU mL/L from \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#grow\"\u003e[#Growth method~tsk~YI]\u003c/span\u003e  and \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#colo\"\u003e[#Colony suspension~tsk~YH]\u003c/span\u003e  by vortexing, and dilute it by a factor of 1:100 by adding 200 µL bacterial suspension to 19.8 mL sterile MHB in a sterile 50 mL Erlenmeyer flask to prepare a 20 mL inoculum. Adjust volumes if necessary. \u003cbr\u003e\u003cstrong\u003eInoculation:\u003c/strong\u003e Inoculate each test tube containing the antibiotic solution and one control test tube (growth control) with 1 mL of the bacterial suspension. This results in the final desired inoculum of 5x10\u003csup\u003e5\u003c/sup\u003e CFU mL/L.\u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eIncubation:\u003c/strong\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e16-20h\u003c/li\u003e\n\u003cli\u003eShaking at 225 r.p.m.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cstrong\u003eCount colonies\u003c/strong\u003e the next day( \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e ).\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:06:59.583Z","updated_at":"2018-12-24T09:38:55.366Z","last_modified_by_id":202,"protocol_id":3458},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5200,"name":"Agar plates","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\n\u003cp style=\"text-align: justify;\"\u003e\u003cstrong\u003eBacterial suspension preparation:\u003c/strong\u003e Mix the bacterial suspension, adjusted to 1x10\u003csup\u003e8\u003c/sup\u003e CFU/mL from \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#grow\"\u003e[#Growth method~tsk~YI]\u003c/span\u003e  or  \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#colo\"\u003e[#Colony suspension~tsk~YH]\u003c/span\u003e  by vortexing and dilute it 1:10 into a cavity of a sterile 96-well microtiter plate by pipetting 10 mL into a well containing 90 ml of sterile broth or saline. Repeat for each bacterial isolate to be tested. Be sure to make a note of the content of each well and to inoculate the microtiter plate in a way that the inocula can be transferred to the agar plates using a 48-pin replicator. For up to 48 tests, inoculate only within rows A–H, columns 1–6 of the microtiter plate. As an alternative to the replicator, a multichannel micropipette set at 1µL can be used to deliver the spots. Make sure that the required number of bacterial cells is going to be transferred. A 48-pin replicator with 1.5 mm pins delivers 1 µL. The final inoculum for a spot with a size of 5–8 mm should deliver the desired cell density of around 10\u003csup\u003e4\u003c/sup\u003e CFU per spot. \u003cbr\u003e\u003cbr\u003e\u003cstrong\u003eInoculation:\u003c/strong\u003e Sterilize the 48-pin replicator by soaking the pins in 95% ethanol and passing them through a Bunsen burner flame. Hold the pins in an upright position until the flame extinguishes. Let the pins cool in an inverted position to maintain sterility. Place the sterilized replicator into the microtiter plate to soak the pins and transfer it onto the agar plate. Start by inoculating a growth control plate without antibiotic. Make sure that each agar plate has the same orientation while inoculating and to make a note of the orientation so that spots on the agar plate can be assigned to the respective isolate tested. Inoculate the antibiotic-containing agar plates starting with the lowest concentration. Let the inoculum spots dry at room temperature before inverting the plates. Plate 100 µL of the last two 1:10 dilutions (10\u003csup\u003e–4\u003c/sup\u003e to 10\u003csup\u003e–5\u003c/sup\u003e) evenly onto antibiotic-free nutrient-rich agar plates using a sterile cell spreader.\u003c/p\u003e\n\u003cstrong\u003eIncubation:\u003cbr\u003e\u003c/strong\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e16-20h\u003c/li\u003e\n\u003c/ul\u003e\nCount colonies the next day ( \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#coun\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e )\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-12-17T14:27:56.093Z","updated_at":"2018-12-21T12:02:30.778Z","last_modified_by_id":202,"protocol_id":3458},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2134,"name":"MIC agar dilutions","due_date":null,"description":null,"x":70,"y":26,"my_module_group_id":1185,"created_at":"2018-11-09T14:35:06.102Z","updated_at":"2018-12-19T13:28:00.795Z","archived":false,"archived_on":null,"created_by_id":202,"last_modified_by_id":202,"archived_by_id":null,"restored_by_id":null,"restored_on":null,"nr_of_assigned_samples":0,"workflow_order":5,"experiment_id":430,"state":"uncompleted","completed_on":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3460,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2134,"team_id":1,"protocol_type":"unlinked","parent_id":null,"parent_updated_at":null,"archived_by_id":null,"archived_on":null,"restored_by_id":null,"restored_on":null,"created_at":"2018-11-09T14:35:06.105Z","updated_at":"2018-12-21T12:03:19.161Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4387,"name":"Interpretation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e\n\u003chtml\u003e\u003cbody\u003e\u003cp\u003eIn order for the test to be valid, the agar plates for the cell count have to be checked to verify that the right number of CFU were used. The presence of around 100–200 colonies on the lower of the two dilutions (10\u003csup\u003e-5\u003c/sup\u003e) of the initial bacterial suspension is expected when using the correct bacterial suspension density of 1–2x10\u003csup\u003e8\u003c/sup\u003e CFU/mL. If the cell numbers are within the desired range, the test can be analyzed to determine the MIC. Also check the antibiotic-free growth control plate. Visible growth needs to occur for the test to be valid.\u003cbr\u003e\u003cbr\u003e\u003cem\u003e\u003cstrong\u003eThe MIC is defined as the lowest concentration of the antimicrobial substance that inhibits visible growth of the tested isolate.\u003c/strong\u003e\u003c/em\u003e The growth of a single colony or faint film caused by the inoculum should be disregarded. When growth of the tested organism occurs on all agar plates with antimicrobial agent, the MIC is recorded as greater than the highest concentration tested. The MIC is recorded as less than or equal to the lowest concentration when no growth occurs on any of the agar plates but the growth control.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T14:42:15.692Z","updated_at":"2018-12-21T15:30:31.074Z","last_modified_by_id":202,"protocol_id":3460},"checklists":[],"step_comments":[],"step_assets":[{"id":2314,"step_id":4387,"asset_id":2839}],"assets":[{"id":2839,"created_at":"2018-11-09T14:42:15.835Z","updated_at":"2018-12-21T15:30:31.064Z","file_file_name":"Example.png","file_content_type":"image/png","file_file_size":159276,"file_updated_at":"2018-12-21T15:30:30.611Z","created_by_id":202,"last_modified_by_id":202,"estimated_size":175203,"file_present":true,"lock":null,"lock_ttl":null,"version":1,"file_processing":false,"team_id":1}],"step_tables":[],"tables":[]}]}],"results":[]}],"my_module_groups":[{"id":1185,"created_at":"2018-12-19T13:28:00.792Z","updated_at":"2018-12-19T13:28:00.792Z","created_by_id":3,"experiment_id":430}]}