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Megabase DNA Extraction from Animal Blood Resource Report Resource Website |
Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin | DOI:10.17504/protocols.io.gagbsbw | GigaScience Press, High molecular weight DNA extraction from all kingdoms | This protocol provides an efficient and reliable technique for obtaining HMW DNA(>1Mb) from animal blood. It accompanies:Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin (2016): Supporting data for 'Comparative optical genome analysis of two Pangolin species Manis pentadactyla and Manis javanica'. GigaScience Database. | GigaScience, GigaScience, GigaScience, GigaScience, GigaScience, GigaScience, GigaScience, GigaScience, GigaScience | https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giw001/2756882/Comparative-optical-genome-analysis-of-two | 1 | 2016 | Huang Zhihai, Xu Jiang, Xiao Shuiming, Liao Baosheng, Gao Yuan, Zhai Chaochao, Qiu Xiaohui, Xu Wen, Chen Shilin 2016. Megabase DNA Extraction from Animal Blood. protocols.io https://dx.doi.org/10.17504/protocols.io.gagbsbw | 2021-04-15 09:14:33 | ||
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Prepare NGM plates for nematode, with peptone, without fungizone Resource Report Resource Website |
Cancer Research UK / Wellcome Gurdon Institute media kitchen | DOI:10.17504/protocols.io.3ntgmen | Prepare NGM plates for nematodes, with peptone, without fungizone | Cancer Research UK / Wellcome Gurdon Institute | 1 | 2019 | Cancer Research UK / Wellcome Gurdon Institute media kitchen 2019. Prepare NGM plates for nematode, with peptone, without fungizone. protocols.io https://dx.doi.org/10.17504/protocols.io.3ntgmen | 2021-04-15 09:14:26 | ||||
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Protocol to UCSC Genome Browser & BLAST Resource Report Resource Website |
UCSC BME 22L | UCSC | 1 | 2020 | 2020. Protocol to UCSC Genome Browser & BLAST . protocols.io https:// | 2021-04-15 09:14:27 | ||||||
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The impact of patient-ventilator asynchrony in adult mechanically ventilated patients on outcomes：A systematic review and meta-analysis Resource Report Resource Website |
Michihito Kyo, Tatsutoshi Shimatani, Koji Hosokawa, Shunsuke Taito, Yuki Kataoka, Shinichiro Ohshimo, Nobuaki Shime | DOI:10.17504/protocols.io.bsqtndwn | 1.BackgroundPatients-ventilator asynchrony (PVA) is defined as a mismatch between the patient breathing efforts with a ventilator’s breath delivery. (1) PVA is a common problem in mechanically ventilated patients, (2, 3) which could potentially induce the exhaustion of diaphragm and respiratory muscles and deliver high tidal volume to the lung leading to ventilator-induced lung injury (VILI). (4, 5)The impact of PVA including an acute phase of mechanical ventilation on clinical outcomes was not similar across studies. Thille AW et al. reported that higher incidence of PVA was associated with longer duration of mechanical ventilation, while this was not associated with mortality. (2) Conversely, Blanch L et al. showed that ICU mortality of the patients with higher incidence of PVA was significantly higher than that with lower incidence of PVA. (6) Furthermore, to date, there is no systematic review regarding PVA in the acute phase of mechanical ventilation.Furthermore, although adjustment of sedatives or ventilator settings were thought to be effective for improving PVA, there is no definitive intervention for improving PVA without closed-loop-ventilation such as Neurally Adjusted Ventilatory Assist (NAVA) and Proportional Assist Ventilation (PAV) in the weaning phase of mechanical ventilation. (7, 8, 9) Therefore, we will conduct this systematic review and meta-analysis to clarify the impact of PVA on specific clinical outcomes and the effect of interventions in order to improve PVA for mechanically ventilated patients in the acute phase of mechanical ventilation.2.Review questionPart A. The impact of PVA on clinical outcomesTo clarify the impact of patient-ventilator asynchrony in adult mechanically ventilated patients in acute phase of mechanical ventilation on outcomes.Part B. The impact of interventions for mechanically ventilated patients on PVATo clarify the impact of interventions for adult mechanically ventilated patients in acute phase of mechanical ventilation on PVA.3.Method3.1.1 Types of study to be includedPart A. The impact of PVA on clinical outcomesWe will include published and unpublished observational studies and secondary analysis of randomized controlled trials (RCTs) including crossover trials, cluster-randomized trials, quasi-randomized trials.We will include studies presented only in abstract or letter form, in any language, from any country and with any length of follow-up.Part B. The impact of interventions for mechanically ventilated patients on PVAWe will include published and unpublished observational studies and randomized controlled trials (RCTs) including crossover trials, cluster-randomized trials, quasi-randomized trials.We will include studies presented only in abstract or letter form, in any language, from any country and with any length of follow-up.3.1.2 ParticipantsInclusion criteriaAdults aged 18 years and olderWe define “acute phase” as within 72 hrs of initiation of mechanical ventilation, as soon as patients were not able to trigger all ventilator breaths or using assist-control ventilation mode.Patients who have received mechanical ventilation including acute phase of mechanical ventilation.Exclusion criteriaWe will exclude the studies which assess the effects of interventions of NAVA and PAV. We will also exclude patients with weaning phase of mechanical ventilation, post-operation, do-not-resuscitate orders, suspected bronchopleural fistula or air leaks, those admitted for organ donation, less than 18 years old, pregnant patients.3.1.3 Exposure(s)/Intervention(s)Part A. The impact of PVA on clinical outcomesWe will include studies that have evaluated whether the incidence of PVA defined as asynchrony index (AI) > 10% or ineffective trigger index (ITI) > 10% or higher index defined by the trialists is associated with clinical outcomes in the acute phase of mechanical ventilation.AI is defined as the number of asynchronous breaths, according to each study, divided by the total number of breaths (both requested and delivered) multiplied by 100. (2)ITI is defined as the number of ineffective triggered breaths divided by the total number of triggered and ineffectively triggered breaths multiplied by 100. (3)Part B. The impact of interventions for mechanically ventilated patients on PVAWe will include studies that have evaluated the impact of interventions that possibly affect PVA including acute phase of mechanical ventilation.3.1.4 Control(s)Part A. The impact of PVA on clinical outcomesasynchrony index (AI) Part B. The impact of interventions for mechanically ventilated patients on PVAPatients who have been defined as a control by the study authors3.2 OutcomesPart A. The impact of PVA on clinical outcomes3.2.1 Primary outcomesWe will assess the association between PVA as AI, ITI or index defined by the study authors, respectively, with the following outcomes. 1. Duration of mechanical ventilation2. ICU mortality3. Hospital mortality3.2.2 Secondary outcomes 4. Rate of reintubation5. Rate of tracheostomy6. All adverse events (as defined by the study authors).3.2.3 summary of PVA defined by the study authorsWe will summarize the results as the same type of PVA such as breathe stacking, auto-triggering or double triggering, etc.Part B. Interventions for improving PVA3.2.1 Primary outcomes1. Incidence of PVA2. Duration of mechanical ventilation3.2.2 Secondary outcomes3. ICU mortality4. Hospital mortality5. Rate of reintubation6. Rate of tracheostomy7. All adverse events (as defined by the study authors).3.3 Searches3.3.1 Electronic searches 1.the Cochrane Central Register of Controlled Trials(CENTRAL) ;2.MEDLINE via Ovid;3.EMBASE;See Appendix 1, 2, and 3 for the search strategies.No restriction in languages.3.3.2 Other resources 1.the World Health Organization International Clinical Trials Platform Search Portal ( ICTRP)See Appendix 4 for the search strategies.2.ClinicalTrials.govSee Appendix 5 for the search strategies.We will also inspect the references of extracted studies and the international guideline “mechanical ventilation in adult patients with acute respiratory distress syndrome” from American Thoracic Society, European Society of Intensive Care Medicine, and Society of Critical Care Medicine. (10)3.4 Strategy for data synthesis3.4.1 Search strategyThe search strategy described above will be used to obtain the titles and abstracts of studies that may be of relevance to the review. These titles and abstracts will be screened independently by two authors who will discard any studies which are not applicable, although any studies and reviews which might include relevant data or information on trials will be retained initially. We will contact the authors of these studies in order to assist in the screening of these studies if necessary. Two authors will then independently assess the remaining abstracts and, if necessary, their full texts, to determine whether they satisfy the inclusion criteria or not. The two authors will then compare their lists, and any differences in opinion between them will be resolved by discussion and, if this fails, through arbitration by a third author.3.4.2 Data extractionData extraction will then be carried out independently on the studies selected for inclusion by two authors using standard data extraction forms. Again, we will contact authors of these studies if necessary during this process, and any differences in opinion regarding data collection between the authors will be resolved by discussion, or through arbitration by a third author if required. If more than one publication of a given study exists, the reports will be grouped together and the publication with the most complete data used in the analyses. If relevant outcomes have only been published in earlier versions of studies, these data will be used, and any discrepancies between the published versions will be highlighted.3.5 Risk of bias assessmentPart A. The impact of PVA on clinical outcomesTwo researchers independently will assess the risk of bias for each study using QUIPS tool (Hyden 2013) (11). We will assess the following domains:1. Study Participation2. Study Attrition3. Prognostic Factor Measurement4. Outcome Measurement5. Study Confounding (Age, Severity score, Duration of mechanical ventilation)6. Statistical Analysis and ReportingAgreement between the two review researchers with regard to the primary outcomes. Disagreement will be resolved by discussion and if necessary a third review researcher.Part B. Interventions for improving PVATwo researchers independently will assess the risk of bias for each randomized control study using risk of bias 2 tool (12).Two researchers independently will assess the risk of bias for each observational study using ROBINS-I tool (13).3.6 Assessment of effects of prognostic factor and interventionsFor the dichotomous variables of mortality and prevalence of reintubation and tracheostomy, pooled odds ratios (ORs) with 95% CIs are provided.For the continuous outcomes including duration of mechanical ventilation (expressed in days) and incidence of PVA (expressed in percentage), the standardised mean differences or the mean differences with 95% CIs were calculated, as recommended by the Cochrane Handbook. (14)Adverse events were narratively summarised because their definition often varies across studies.3.8Missing values3.8.1 Discrete variablesFor discrete variables, we will analyze all the data following the concept of intention-to-treat (ITT). For continuous variables, we will not perform imputation of missing values, in accordance with the recommendations set out in the Cochrane handbook (14). We will perform meta-analyses using original data.3.8.2Missing valuesWe will contact the study authors about missing values.3.8.3Statistical measurement for missing valuesIf only standard errors or p-values are reported, the Altman method(15) is used to calculate the standard deviation. If the author is not known, the standard deviation is calculated from the confidence intervals and t-values using the method described in the Cochrane handbook(16) or supplemented by a validated method(17). Alternatively, the standard deviations are complemented by the validated method(17). The validity of these methods will be verified by a sensitivity analysis.3.9 Assessment of heterogeneityWe will calculate I2 as a measure of variation across studies that is due to heterogeneity rather than chance, and interpreted the values as follows: 0%–40%, negligible heterogeneity; 30%–60%, mild-to-moderate heterogeneity; 50%–90%, moderate-to-substantial heterogeneity; 75%–100%, considerable heterogeneity. If heterogeneity is identified for an outcome (I2 >50%), we will investigate the underlying reasons and conduct the χ2 test, with a p value of 3.10 Assessment of publication biasWe will search trial registers (the World Health Organization International Clinical Trials Platform Search Portal, ClinicalTrials.gov) to identify completed but unpublished trials. If more than 10 studies are included in this review, we will perform a funnel plot analysis and will use Egger's test (a p value of 3.11 Meta-analysis We will conduct all analyses using the STATA version 16 (StataCorp, College Station, Texas, USA).We will use the random-effects models for all analyses.3.12 Subgroup analysisWe will also carry out prespecified subgroup analyses according to the following variables.1. Causes of admission to ICU: Internal diseases vs. Traumatic diseases2. Coexisting ARDS: ARDS vs. not ARDS3. Ventilator mode: Assist control or pressure support ventilation vs. other ventilator mode4. Timing: Acute phase (within 72 hrs of initiation of mechanical ventilation or as soon as patients were not able to trigger all ventilator breaths) vs Whole period of mechanical ventilation5. Ways of evaluating PVA: Human vs Software3.13 Sensitivity analysis We plan the following prespecified sensitivity analyses for the primary outcomes: exclusion of studies (i) using imputed statistics, (ii) including timing when assessing the PVA is not only acute phase but without acute phase, (iii) including post-operative patients and (iv) with high or moderate risk of bias. Statistical significance was also set at p4. Summary of findingsWe will create a summary-of-findings table that included an overall grading of the certainty of evidence for each of the main outcomes, which was evaluated using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. (18)Part A. The impact of PVA on clinical outcomes1. Duration of mechanical ventilation2. ICU mortality3. Hospital mortality4. Reintubation5. Tracheostomy6. All adverse events (as defined by the study authors)Part B. Interventions for improving PVA1. Incidence of PVA2. Duration of mechanical ventilation3. ICU mortality4. Hospital mortality5. Reintubation6. Tracheostomy7. All adverse events (as defined by the study authors)5. Conflict of InterestWe have no conflict of interest.6. References1. Gilstrap D, MacIntyreN. Patient-ventilator interactions. Implications for clinical management. Am J Respir Crit Care Med 2013;188:1058–1068.2. Thille AW, Rodriguez P, CabelloB, et al. Patient-ventilator asynchrony during assisted mechanical ventilation. Intensive Care Med 2006;32:1515–22.3. de Wit M, Miller KB, GreenDA, et al. Ineffective triggering predicts increased duration of mechanical ventilation. Crit Care Med 2009;37:2740–5.4. Beitler JR, Sands SA, Loring SH, et al. Quantifying unintended exposure to high tidal volumes from breath stacking dyssynchrony in ARDS: the BREATHE criteria. Intensive Care Med 2016;42:1427–1436.5. Pohlman MC, McCallister KE, SchweickertWD, et al. Excessive tidal volume from breath stacking during lung-protective ventilation for acute lung injury. Crit Care Med 2008;36:3019 –3023.6. Blanch L, Villagra A, SalesB, et al. Asynchronies during mechanical ventilation are associated with mortality. Intensive Care Med 2015;41:633–641.7. Chanques G, Kress JP, Pohlman A, et al. Impact of ventilator adjustment and sedation-analgesia practices on severe asynchrony in patients ventilated in assist-control mode. Crit Care Med. 2013;41:2177–2187.8. Pettenuzzo T, Aoyama H, Englesakis M, et al. Effect of Neurally Adjusted Ventilatory Assist on Patient-Ventilator Interaction in Mechanically Ventilated Adults: A Systematic Review and Meta-Analysis. Crit Care Med 2019;47:e602–609.9. Kataoka J, Kuriyama A, Norisue Y, et al. Proportional modes versus pressure support ventilation: a systematic review and meta-analysis. Ann Intensive Care 2018;8:123.10.FanE, Del SorboL, GoligherEC, et al; American Thoracic Society, European Society of Intensive Care Medicine, and Society of Critical Care Medicine.An official American Thoracic Society/European Society of Intensive Care Medicine/Society of Critical Care Medicine clinical practice guideline: mechanical ventilation in adult patients with acute respiratory distress syndrome. Am J Respir Crit Care Med. 2017;195:1253-1263.11. Hayden JA, van der Windt DA, Cartwright JL, et al. Assessing Bias in Studies of Prognostic Factors. Ann Intern Med. 2013;158:280.12. Sterne JAC, SavovićJ, Pageet MJ, et al. RoB 2: a revised tool for assessing risk of bias in randomised trials. BMJ 2019;366:l4898.13. Sterne JAC, Hernán MA, Reeveset BC, et al. ROBINS-I: a tool for assessing risk of bias in non-randomised studies of interventions. BMJ 2016;355:i4919.14. Higgins JPT, Green S E. Cochrane Handbook for Systematic Reviews of Interventions Version 6. updated Ma. The Cochrane Collaboration; 2019. Available at: www.cochrane-handbook.org.15.Altman DG, Bland JM. Statistics Notes Detecting skewness from summary information Lesson of the Week. 1996;313(November):1996.16. Higgins JPT, Green S E. Cochrane Handbook for Systematic Reviews of Interventions Version 5.1.0. updated Ma. The Cochrane Collaboration; 2011. Available at: www.cochrane-handbook.org.17. Furukawa TA, Barbui C, Cipriani A, et al. Imputing missing standard deviations in meta-analyses can provide accurate results. J Clin Epidemiol. 2006;59:7–10.18. Foroutan F, Guyatt G, Zuk V, et al. GRADE Guidelines 28: Use of GRADE for the assessment of evidence about prognostic factors: rating certainty in identification of groups of patients with different absolute risks.J Clin Epidemiol. 2020;121:62-70. | Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551 Japan, Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551 Japan, Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551 Japan, Division of Rehabilitation, Department of Clinical Practice and Support, Hiroshima University Hospital, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551 Japan, Hospital Care Research Unit, Hyogo Prefectural Amagasaki General Medical Center, Higashinaniwa-cho 2-17-77, Amagasaki 660-8550 JAPAN, Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551 Japan, Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima, 734-8551 Japan | 2 | 2021 | Michihito Kyo, Tatsutoshi Shimatani, Koji Hosokawa, Shunsuke Taito, Yuki Kataoka, Shinichiro Ohshimo, Nobuaki Shime 2021. The impact of patient-ventilator asynchrony in adult mechanically ventilated patients on outcomes：A systematic review and meta-analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.bsqtndwn | 2021-04-15 09:14:27 | ||||
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PCR Master Mix Aliquoting Resource Report Resource Website |
Rodolfo Salido Benitez | DOI:10.17504/protocols.io.ua8eshw | The protocol outlines how to aliquot PCR Master Mix for 5µL miniaturized amplification of 16S gene in 384-well format using the epMotion. | Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R, High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. mSystems 3(6). doi: 10.1128/mSystems.00166-18 | Knight Lab @ UC San Diego Health | https://doi.org/10.1128/mSystems.00166-18 | 1 | 2018 | Rodolfo Salido Benitez 2018. PCR Master Mix Aliquoting . protocols.io https://dx.doi.org/10.17504/protocols.io.ua8eshw | 2021-04-15 09:14:38 | ||
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U Mass - Alkaline Phosphatase Resource Report Resource Website |
Jason Kim | DOI:10.17504/protocols.io.xptfmnn | Mouse Metabolic Phenotyping Centers | This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Serum levels of alkaline phosphatase reflect liver function. | University of Massachusetts | https://mmpc.org/shared/document.aspx?id=177&docType=Protocol | 1 | 2019 | Jason Kim 2019. U Mass - Alkaline Phosphatase. protocols.io https://dx.doi.org/10.17504/protocols.io.xptfmnn | 2021-04-15 09:14:29 | ||
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T-maze (light vs dark) Resource Report Resource Website |
Björn Brembs | DOI:10.17504/protocols.io.c8azsd | Brembs Lab | This is the protocol we are using to assess the Light/Dark preference in flies. | Gorostiza EA, Colomb J, Brembs B, A decision underlies phototaxis in an insect. Open Biology 6(12). doi: 10.1098/rsob.160229 | Björn Brembs lab, Universität Regensburg | https://doi.org/10.1098/rsob.160229 | 1 | 2015 | Björn Brembs 2015. T-maze (light vs dark). protocols.io https://dx.doi.org/10.17504/protocols.io.c8azsd | 2021-04-15 09:14:38 | |
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Preparation of M9 Media Resource Report Resource Website |
Nus Igem | DOI:10.17504/protocols.io.7pghmjw | National University of Singapore | 1 | 2019 | Nus Igem 2019. Preparation of M9 Media. protocols.io https://dx.doi.org/10.17504/protocols.io.7pghmjw | 2021-04-15 09:14:38 | |||||
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CTAB extraction of DNA and RNA of respiratory samples for microbial work Resource Report Resource Website |
Leah Cuthbertson, Michael Cox, Phillip James , Colin Churchward, Bill Cookson, Miriam Moffatt | DOI:10.17504/protocols.io.bf28jqhw | This extraction method is modified from Griffiths et al 2000 Applied Environmental Microbiology 66(12): 5488–5491 and DeAngelis et al 2009 ISME Journal 3 pp 168-178.In comparison with DNA extraction kits, nucleic acid yields tend to be higher, though it is more laborious for larger numbers of samples.The extraction uses CTAB and Phenol:Chloroform:Isoamyl alcohol for lysis and the precipitation of nucleic acid is PEG based. An alternative to bead-beating is described, which should only be used for extracting DNA from cultured isolates. Bead-beating is avoided in this case in order to minimise shearing of DNA prior to genomic DNA sequencing.For all other samples use bead-beating is recommended.This Protocol will cover the extraction of the following sample types;Bacterial isolatesUpper respiratory tract swabs (nasal and throat swabs)Upper respiratory tract lavage and aspirates (nasopharyngeal aspirate, endotracheal aspirate, nasal lavage, Mouth wash)SalivaSputum (expectorated spontaneously produced, and induced sputum)Upper and lower respiratory tract synthetic absorptive matrix (SAM) stripsLower respiratory tract samples obtained via bronchoscopy - lung brushes, bronchoalveolar lavage and pleural fluidLung tissue – human or mouseLung biopsiesCerebral spinal fluid (CSF)This is a double extraction protocol, you are adding a second volume of Phenol:Chloroform:Isoamyl alcohol to each sample, precipitating two aqueous phases per sample and then recombining the resulting DNA pellets.This approach significantly increases the yield of DNA from samples and strains. | National Heart and Lung Institute, Imperial College, London, UK, SW3 6LY, National Heart and Lung Institute, Imperial College, London, UK, SW3 6LY, National Heart and Lung Institute, Imperial College, London, UK, SW3 6LY, National Heart and Lung Institute, Imperial College, London, UK, SW3 6LY, National Heart and Lung Institute, Imperial College, London, UK, SW3 6LY, National Heart and Lung Institute, Imperial College, London, UK, SW3 6LY | 1 | 2020 | Leah Cuthbertson, Michael Cox, Phillip James , Colin Churchward, Bill Cookson, Miriam Moffatt 2020. CTAB extraction of DNA and RNA of respiratory samples for microbial work. protocols.io https://dx.doi.org/10.17504/protocols.io.bf28jqhw | 2021-04-15 09:14:29 | ||||
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Picking colonies Resource Report Resource Website |
Sarah Hessen-Schmidt | DOI:10.17504/protocols.io.e7gbhjw | Picking colonies from TCBS Agar plates to 96 well plates for growth | University of Southern California | 1 | 2016 | Sarah Hessen-Schmidt 2016. Picking colonies. protocols.io https://dx.doi.org/10.17504/protocols.io.e7gbhjw | 2021-04-15 09:14:38 | ||||
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Copy of Protocol for the production of crude alcoholic extracts from native plants Resource Report Resource Website |
Marissol Leite, Hadda Tercya Lima Silva, Zanderluce Gomes Luis, Aline Coutinho Cavalcante, Caio Maximino, Diogenes Silva | DOI:10.17504/protocols.io.9vch62w | Medicinal Plants Southeastern Pará Research Group | This protocol describes the method to obtaining crude alcoholic extracts from plant organs, such leaves and inflorescences. The used plants were the popularly called “João Brandinho” Piper Callosum and “Jambu” Spilanthes acmella. The crude extracts were used in our laboratory to anesthetize the native silver tetra fish Ctenobrycon sp. and Zebrafish Danio rerio, by immersion method. | Universidade federal do sul e sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará | 1 | 2019 | Marissol Leite, Hadda Tercya Lima Silva, Zanderluce Gomes Luis, Aline Coutinho Cavalcante, Caio Maximino, Diogenes Silva 2019. Copy of Protocol for the production of crude alcoholic extracts from native plants. protocols.io https://dx.doi.org/10.17504/protocols.io.9vch62w | 2021-04-15 09:14:29 | |||
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Drug Behaviour Imaging on Phenix Resource Report Resource Website |
Ida Barlow, Adam Mcdermott-Rouse | DOI:10.17504/protocols.io.bfgvjjw6 | Behavioural Genomics | For imaging drug-treated young adult C. elegans in liquids using the Multiworm tracker. Worms are synchronised by picking L4s, and then the young adults are exposed to drugs for 4 hours prior to imaging for 15 mins in a liquid droplet on a coverslip mounted on a 3.5cm plate. | Imperial College London, Imperial College London | 1 | 2020 | Ida Barlow, Adam Mcdermott-Rouse 2020. Drug Behaviour Imaging on Phenix. protocols.io https://dx.doi.org/10.17504/protocols.io.bfgvjjw6 | 2021-04-15 09:14:38 | |||
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SNPs calling of Apostichopus japonicus color-variants genome Resource Report Resource Website |
Jihoon Jo, Jooseong Oh, Hyun Gwan Lee, Hyun Hee Hong, Sung Gwon Lee, Seongmin Cheon, Elizabeth MA Kern, Soyeong Jin, Sung Jin Cho, Joong Ki Park, Chungoo Park | DOI:10.17504/protocols.io.gmbbu2n | GigaScience Press | SNPs calling protocol for analysis the genetic polymorphism among natural color variants. This protocol accompanies the following GigaScience publication:Jihoon Jo, et al. (2016): Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants. GigaScience... | School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University, School of Biological Sciences and Technology, Chonnam National University | https://doi.org/10.1093/gigascience/giw006 | 1 | 2016 | Jihoon Jo, Jooseong Oh, Hyun Gwan Lee, Hyun Hee Hong, Sung Gwon Lee, Seongmin Cheon, Elizabeth MA Kern, Soyeong Jin, Sung Jin Cho, Joong Ki Park, Chungoo Park 2016. SNPs calling of Apostichopus japonicus color-variants genome. protocols.io https://dx.doi.org/10.17504/protocols.io.gmbbu2n | 2021-04-15 09:14:29 | ||
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Bacterial Plating Quantification Resource Report Resource Website |
Kenneth Schackart, Kattika Kaarj | DOI:10.17504/protocols.io.3irgkd6 | Yoon Lab | This protocol describes how to serially dilute and plate cultured bacteria in suspension for quantification. | University of Arizona, University of Arizona | 1 | 2019 | Kenneth Schackart, Kattika Kaarj 2019. Bacterial Plating Quantification. protocols.io https://dx.doi.org/10.17504/protocols.io.3irgkd6 | 2021-04-15 09:14:38 | |||
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Immunohistochemistry - Drosophila Embryo Resource Report Resource Website |
Sonia Hall | DOI:10.17504/protocols.io.cutwwm | Hall S, Ward RE, Septate Junction Proteins Play Essential Roles in Morphogenesis Throughout Embryonic Development in . G3: Genes|Genomes|Genetics 6(8). doi: 10.1534/g3.116.031427 | https://doi.org/10.1534/g3.116.031427 | 1 | 2015 | Sonia Hall 2015. Immunohistochemistry - Drosophila Embryo. protocols.io https://dx.doi.org/10.17504/protocols.io.cutwwm | 2021-04-15 09:14:30 | ||||
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16S Bacteria 338F-516P-805R BSA Resource Report Resource Website |
Roey Angel, Eva Petrova, Ana Lara | DOI:10.17504/protocols.io.m7qc9mw | Universal 16S rRNA BActeria 338F-516P-805RBAC338F ACT CCT ACG GGA GGC AG , target E.coli : 338-354, Yu et al. (2005), B&BBAC516P* TGC CAG CAG CCG CGG TAA TA, target E.coli : 516-536, 'BAC805R GAC TAC CAG GGT ATC TAA TC , target E.coli : 785-805, '* Probe must be dual-labelled either with 5’-6-FAM, 3’-BHQ1 or any other valid combination. | Soil and Water Research Infrastructure, Soil and Water Research Infrastructure, Soil and Water Research Infrastructure | 1 | 2020 | Roey Angel, Eva Petrova, Ana Lara 2020. 16S Bacteria 338F-516P-805R BSA. protocols.io https://dx.doi.org/10.17504/protocols.io.m7qc9mw | 2021-04-15 09:14:38 | ||||
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SYSB 3036 W06: Annotating a Complete Genome with HMMs Resource Report Resource Website |
Frank Aylward | DOI:10.17504/protocols.io.ytcfwiw | Virginia Tech | 1 | 2019 | Frank Aylward 2019. SYSB 3036 W06: Annotating a Complete Genome with HMMs. protocols.io https://dx.doi.org/10.17504/protocols.io.ytcfwiw | 2021-04-15 09:14:29 | |||||
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Complete Yeast Protein Extraction Resource Report Resource Website |
Tobias von der Haar | DOI:10.17504/protocols.io.g8wbzxe | This protocol is suitable for rapidly generating extracts of fungal cells for gel electrophoresis or western blots. It was optimised for complete extraction of difficult-to-solubilise proteins. This protocol was originally described in von der Haar 2007. | Kent Fungal Group, School of Bioscienes, University of Kent, Canterbury, CT2 7NJ, UK | http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001078 | 1 | 2017 | Tobias von der Haar 2017. Complete Yeast Protein Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.g8wbzxe | 2021-04-15 09:14:40 | |||
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Fungal Plate Photography Resource Report Resource Website |
Craig Bateman | DOI:10.17504/protocols.io.bnu6meze | Protocols Bark Beetle Mycobiome | This protocol describes how to photograph fungal plates.This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coordination Network. For more information on the BBM international network: Hulcr J, Barnes I, De Beer ZW, Duong TA, Gazis R, Johnson AJ, Jusino MA, Kasson MT, Li Y, Lynch S, Mayers C, Musvuugwa T, Roets F, Seltmann KC, Six D, Vanderpool D, & Villari C. 2020. Bark beetle mycobiome: collaboratively defined research priorities on a widespread insect-fungus symbiosis. Symbiosis 81: 101–113 https://doi.org/10.1007/s13199-020-00686-9. | University of Florida | 1 | 2020 | Craig Bateman 2020. Fungal Plate Photography. protocols.io https://dx.doi.org/10.17504/protocols.io.bnu6meze | 2021-04-15 09:14:30 | |||
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DNA quantitative assay using Fluorometry Resource Report Resource Website |
Xueying Zhong | DOI:10.17504/protocols.io.ef5bbq6 | Thomas Crouzier Lab | The protocol follow the instruction manual from BIO-RAD of Catalog number 170-2480 | 1 | 2016 | Xueying Zhong 2016. DNA quantitative assay using Fluorometry. protocols.io https://dx.doi.org/10.17504/protocols.io.ef5bbq6 | 2021-04-15 09:14:40 |
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