scinote-web/app/assets/templates/experiment_430/experiment.json

{"experiment":{"id":430,"name":"Determination of (MIC) by agar and broth dilution","description":"Minimum inhibitory concentrations (MICs) are defined as the lowest concentration of an antimicrobial that will inhibit the visible growth of a microorganism after overnight incubation.  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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. \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T13:14:16.763Z","updated_at":"2018-11-09T13:15:33.885Z","last_modified_by_id":202,"protocol_id":3454},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4373,"name":"Replicator 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\u003eSterilize the 48-pin replicator by soaking the pins in 95% ethanol and passing them through a Bunsen burner flame. Hold the pins in upright position until the flame extinguishes. Let the pins cool in an inverted position to maintain sterility.\u003cbr\u003ePlace 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.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T13:16:33.964Z","updated_at":"2018-11-09T13:24:33.582Z","last_modified_by_id":202,"protocol_id":3454},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4374,"name":"Inoculation","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\u003eInoculate the antibiotic-containing agar plates starting with the lowest concentration.\u003cbr\u003eLet the inoculum spots dry at room temperature before inverting the plates.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T13:25:54.701Z","updated_at":"2018-11-09T13:25:54.701Z","last_modified_by_id":202,"protocol_id":3454},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4380,"name":"Incubation","description":"\u003c!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\"\u003e","position":5,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T14:04:23.798Z","updated_at":"2018-11-09T14:04:23.798Z","last_modified_by_id":202,"protocol_id":3454},"checklists":[{"checklist":{"id":785,"name":"Parameters","step_id":4380,"created_at":"2018-11-09T14:04:23.802Z","updated_at":"2018-11-09T14:04:23.802Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3302,"text":"37°C","checked":false,"checklist_id":785,"created_at":"2018-11-09T14:04:23.804Z","updated_at":"2018-11-09T14:04:23.804Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3303,"text":"16-20h","checked":false,"checklist_id":785,"created_at":"2018-11-09T14:04:23.814Z","updated_at":"2018-11-09T14:04:23.814Z","created_by_id":null,"last_modified_by_id":null,"position":1}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4381,"name":"Colonies 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 task \u003cspan class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#cel\"\u003e[#Cell count~tsk~YL]\u003c/span\u003e \u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":6,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T14:05:49.670Z","updated_at":"2018-11-09T14:05:49.670Z","last_modified_by_id":202,"protocol_id":3454},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4379,"name":"Plating","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\u003ePlate 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\u003c/body\u003e\u003c/html\u003e","position":4,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T14:03:38.121Z","updated_at":"2018-11-09T14:03:38.121Z","last_modified_by_id":202,"protocol_id":3454},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":5199,"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\u003cul\u003e\n\u003cli style=\"text-align: justify;\"\u003eMix 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.\u003c/li\u003e\n\u003cli style=\"text-align: justify;\"\u003eRepeat for each bacterial isolate to be tested. 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count","due_date":null,"description":null,"x":41,"y":0,"my_module_group_id":null,"created_at":"2018-11-09T13:28:22.716Z","updated_at":"2018-12-19T13:28:00.727Z","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,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3455,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2129,"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":"2018-11-09T13:28:22.724Z","updated_at":"2018-12-24T09:11:23.453Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4375,"name":"Sampling","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\u003eTo confirm that the size of the bacterial inoculum was appropriate, determine the viable count of the bacterial suspension used for preparing the initial inoculum. \u003cbr\u003e\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T13:29:23.180Z","updated_at":"2018-12-21T12:05:41.321Z","last_modified_by_id":202,"protocol_id":3455},"checklists":[{"checklist":{"id":967,"name":"Guidelines:","step_id":4375,"created_at":"2018-12-21T12:05:41.323Z","updated_at":"2018-12-21T12:05:41.323Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3981,"text":"Dilute this suspension 1:100 by pipetting 10 µL into sterile capped Eppendorf tubes containing 990 µL nutrient-rich broth or sterile saline solution (10-2)","checked":false,"checklist_id":967,"created_at":"2018-12-21T12:05:41.325Z","updated_at":"2018-12-21T12:05:41.325Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3982,"text":"Dilute this solution sequentially 1:10 three times until you reach a dilution of 10–5.","checked":false,"checklist_id":967,"created_at":"2018-12-21T12:05:41.338Z","updated_at":"2018-12-21T12:05:41.338Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3983,"text":"Plate 100 mL of the last two 1:10 dilutions (10–4 to 10–5) evenly onto antibiotic-free nutrient-rich agar plates using a sterile cell spreader.","checked":false,"checklist_id":967,"created_at":"2018-12-21T12:05:41.345Z","updated_at":"2018-12-21T12:05:41.345Z","created_by_id":null,"last_modified_by_id":null,"position":2}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4377,"name":"Colonies 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\u003eCount colonies on plates (taking into account only plates with up to 500 colonies).\u003cbr\u003eIt is best to determine the relationship between OD600 and the microbial number basing the calculation on plates displaying a number of colonies between 100 and 400. \u003cstrong\u003eHigher numbers do not accurately represent the original suspension as errors created by coincidence of colonies and nutrient limitation lead to numbers that are lower than expected.\u003c/strong\u003e Relying on fewer than 100 colonies might, on the other hand, lead to incorrect conclusions due to the addition of statistical and methodological errors while performing the dilutions.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":2,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T13:44:18.697Z","updated_at":"2018-12-21T12:07:52.643Z","last_modified_by_id":202,"protocol_id":3455},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4376,"name":"Incubation","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 parameters:\u003cbr\u003e\n\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e37°C\u003c/li\u003e\n\u003cli\u003e16-20h\u003c/li\u003e\n\u003c/ul\u003e\n\u003cbr\u003e\u003cbr\u003e\n\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T13:41:55.993Z","updated_at":"2018-12-21T12:06:50.983Z","last_modified_by_id":202,"protocol_id":3455},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]},{"step":{"id":4378,"name":"Calculation of CFU","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\u003eCalculate the CFU per mL that were in the overnight culture according to the following formula, where N=(Cx10)/10\u003csup\u003e-D\u003c/sup\u003e (CFU/mL); C= number of colonies per plate; D= number of 1:10 dilution.\u003cbr\u003e\u003cbr\u003eAverage the results from three tests performed with the microbial isolate and correlate this number with the OD600 value obtained from the overnight culture. This relationship holds true for subsequent cultures of the same bacterium grown in the same way.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":3,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T13:46:56.839Z","updated_at":"2018-12-24T09:11:23.400Z","last_modified_by_id":202,"protocol_id":3455},"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,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":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":{"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,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":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":2131,"name":"Macrodilutions of antibiotics","due_date":null,"description":null,"x":0,"y":35,"my_module_group_id":1185,"created_at":"2018-11-09T14:09:52.226Z","updated_at":"2018-12-19T13:28:00.800Z","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":0,"experiment_id":430,"state":"uncompleted","completed_on":null,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":null},"outputs":[{"id":6013,"input_id":2132,"output_id":2131}],"my_module_tags":[],"task_comments":[],"my_module_repository_rows":[],"user_my_modules":[],"protocols":[{"protocol":{"id":3457,"name":null,"authors":null,"description":null,"added_by_id":null,"my_module_id":2131,"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":"2018-11-09T14:09:52.235Z","updated_at":"2019-01-02T22:17:16.558Z","published_on":null,"nr_of_linked_children":0},"protocol_protocol_keywords":[],"steps":[{"step":{"id":4382,"name":"Prepare antibiotic dilutions","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 antibiotic dilutions following steps bellow.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":0,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T14:16:11.568Z","updated_at":"2018-12-24T09:07:19.921Z","last_modified_by_id":202,"protocol_id":3457},"checklists":[{"checklist":{"id":965,"name":"Guideline:","step_id":4382,"created_at":"2018-12-21T11:38:45.338Z","updated_at":"2018-12-21T11:38:45.338Z","created_by_id":null,"last_modified_by_id":null},"checklist_items":[{"id":3970,"text":"Prepare antibiotic dilutions in sterile MHB in sterile test tubes according to table.","checked":false,"checklist_id":965,"created_at":"2018-12-21T11:38:45.340Z","updated_at":"2018-12-21T11:38:45.340Z","created_by_id":null,"last_modified_by_id":null,"position":0},{"id":3971,"text":"As the antibiotic solution is later inoculated with an equal amount of bacteria in broth, the dilutions are prepared at a concentration twice the desired final concentration.","checked":false,"checklist_id":965,"created_at":"2018-12-21T11:38:45.347Z","updated_at":"2018-12-21T11:38:45.347Z","created_by_id":null,"last_modified_by_id":null,"position":1},{"id":3972,"text":"Start by dispensing sterile broth into twelve sterile 13x100 mm tubes closed with metal caps. A single 10 mL pipette can be used to pipette the 9 mL and 3 mL volumes of broth into the respective tubes. Use a single 1 mL pipette for pipetting the 1 mL of broth in stages 2, 5, 8 and 11.","checked":false,"checklist_id":965,"created_at":"2018-12-21T11:38:45.354Z","updated_at":"2018-12-21T11:38:45.354Z","created_by_id":null,"last_modified_by_id":null,"position":2},{"id":3973,"text":"It is possible to use the same pipette for pipetting 1 mL of the antibiotic stock solution into the first test tube. Mix thoroughly using a vortex mixer.","checked":false,"checklist_id":965,"created_at":"2018-12-21T11:38:45.361Z","updated_at":"2018-12-21T11:38:45.361Z","created_by_id":null,"last_modified_by_id":null,"position":3},{"id":3974,"text":"Use separate pipettes/pipette tips when preparing each of the other antibiotic solutions. Mix thoroughly using a vortex mixer.","checked":false,"checklist_id":965,"created_at":"2018-12-21T11:38:45.371Z","updated_at":"2018-12-21T11:38:45.371Z","created_by_id":null,"last_modified_by_id":null,"position":4}]}],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":546,"step_id":4382,"table_id":683}],"tables":[{"id":683,"created_at":"2018-12-21T11:38:45.382Z","updated_at":"2018-12-21T11:48:45.258Z","created_by_id":202,"last_modified_by_id":202,"name":"","team_id":1,"contents":"eyJkYXRhIjpbWyJTdGFnZSIsIkFudGltaWNyb2JpYWwgY29uY2VudHJhdGlv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\nLCJTdGFnZSAxMCIsIjEiLCIzIiwiMC4wNiIsIjAuMDMiXV19\n","data_vector":"JzAuMDMnOjExOSAnMC4wNic6MTExLDExOCAnMC4xMjUnOjEwMywxMTAgJzAu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\nMjMgJ3ZvbHVtZSc6NiwxMg==\n"}]},{"step":{"id":4383,"name":"Labeling of test tubes","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\u003eFor every bacterial isolate, label twelve sterile 13x100 mm test tubes closed with cotton buds or metal caps with the respective antibiotic concentration to be tested. \u003cbr\u003eLabel control tubes for bacterial growth and a single tube for sterility control for the entire measurement.\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T14:17:30.554Z","updated_at":"2019-01-02T22:17:16.507Z","last_modified_by_id":16,"protocol_id":3457},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[],"tables":[]}]}],"results":[]},{"my_module":{"id":2127,"name":"Agar plate with 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,"electronic_signature_status":"unlocked","electronic_signature_status_locked_at":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. The table is an example of the volumes needed for a concentration range between 0.125 and 128 mg/L for one 25 mL agar plate per concentration. Adjust if a different concentration range is needed. The volumes of antibiotic and agar can also be varied depending on the number of plates to be poured. As each agar plate can be used for up to 48 tests, more than one plate might be necessary if a larger amount of isolates is going to be tested.\u003cbr\u003e\u003cbr\u003eLabel sterile containers appropriately (glass Erlenmeyer flasks closed with metal caps, tinfoil caps or cotton buds) with the final antibiotic concentration.\u003cbr\u003e\u003cbr\u003e\u003c/p\u003e\u003c/body\u003e\u003c/html\u003e","position":1,"completed":false,"completed_on":null,"user_id":202,"created_at":"2018-11-09T11:07:28.842Z","updated_at":"2018-12-21T11:50:54.557Z","last_modified_by_id":202,"protocol_id":3453},"checklists":[],"step_comments":[],"step_assets":[],"assets":[],"step_tables":[{"id":544,"step_id":4367,"table_id":681}],"tables":[{"id":681,"created_at":"2018-12-20T13:03:47.611Z","updated_at":"2018-12-21T11:50:54.563Z","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":5197,"name":"Preparation and autoclaving of media","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\u003cdiv class=\"row\"\u003e\n\u003cdiv class=\"col-xs-12\"\u003e\n\u003cdiv class=\"ql-editor\"\u003e\n\u003cp\u003ePrepare MHA medium following manufacturer’s instructions. Autoclaving at 121.1°C for 15 minutes at 1 bar. Cool medium to 50°C after that. 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