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Authors: Ralph-Sydney Mboumba Bouassa, Zita Aleyo Nodjikouambaye, Damtheou Sadjoli, Chatté Adawaye, Hélène Péré, David Veyer, Mathieu Matta, Leman Robin, Serge Tonen-Wolyec, Ali Mahamat Moussa, Donato Koyalta and Laurent Belec., Laurent Bélec
Summary: Adult Chadian women from 5 of the 10 districts of N’Djamena, the capital city of Chad, were randomly selected for inclusion. Peer educators contacted adult women in community-churches or women association networks to participate to the survey and come to the clinic for women’s sexual health “La Renaissance Plus”, N'Djamena. Medical, socio-demographical and behavioral informations were collected. HPV DNA was detected and genotyped in endocervical swab using Anyplex™ II HPV28 genotyping test (Seegene, Seoul, South Korea).
Proper citation: Ralph-Sydney Mboumba Bouassa, Zita Aleyo Nodjikouambaye, Damtheou Sadjoli, Chatté Adawaye, Hélène Péré, David Veyer, Mathieu Matta, Leman Robin, Serge Tonen-Wolyec, Ali Mahamat Moussa, Donato Koyalta and Laurent Belec., Laurent Bélec 2018. Laboratory protocols for the detection and genotyping of Cervical high-risk human papillomavirus (HR-HPV) among adult women living in N'Djamena the capital city of Chad.. protocols.io dx.doi.org/10.17504/protocols.io.wgefbte Copy
Authors: Oriol Pavón Arocas, Tiago Branco
Summary: Here we describe two different approaches to prepare acute midbrain slices from young adult mice for slice electrophysiology experiments. We also provide general advice for troubleshooting common issues leading to suboptimal slice quality, as well as some suggestions to ensure good maintenance of a patch-clamp rig.
Proper citation: Oriol Pavón Arocas, Tiago Branco 2021. Preparation of acute midbrain slices for patch-clamp recordings. protocols.io dx.doi.org/10.17504/protocols.io.bhfzj3p6 Copy
Authors: Christopher M.. Bartley
Proper citation: Christopher M.. Bartley 2015. 10x TBST (Tris-Buffered Saline and Tween 20). protocols.io dx.doi.org/10.17504/protocols.io.cvjw4m Copy
Authors: G-Biosciences
Group: G-Biosciences
Summary: SpinOUT™ protocol for buffer exchange of peptide and protein samples.(Cat. # 786-170 to 786-173, 786-703 to 786-708, 786-865 to 786-869)
Proper citation: G-Biosciences 2016. SpinOUT™: Buffer Exchange. protocols.io dx.doi.org/10.17504/protocols.io.e5hbg36 Copy
Authors: G Jason Smith
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Environmental Biotechnology Lab
Summary: This is a modification of the origianl Chelex 100 extraction described by Walsh, Metzger and Higuchi (1991 BioTechniques 10(4):506). Adding PVPP facilitates working with environmental samples as well as pure cultures hi in phenolics or other contaminants.
Proper citation: G Jason Smith 2017. Simple DNA Extraction for Phytoplankton Using Chelex 100. protocols.io dx.doi.org/10.17504/protocols.io.hinb4de Copy
Authors: Jeff Hodgin
Group: Mouse Metabolic Phenotyping Centers
Summary: This is the protocol for measuring Glomerular Filtration Rate (GFR) with minipump FITC-inulin clearance in mice. In brief, Alzet micro-osmotic pumps (minipumps, Model 1007D) are filled with 3% FITC-inulin solution. These pumps release FITC-inulin at a rate of 0.5 μl/hr at least seven days. Mouse is temporarily anesthetized and then two mini-pumps are implanted in mouse peritoneal cavity through a tiny midline incision. After surgery, 24-hour urine is collected with metabolic cage and 100 μl of blood from saphenous vein is obtained at the same time. The concentrations of FITC-inulin in urine and blood samples are measured by flurometer and GFR is calculated by the concentration of FITC-inulin in 24-hour-urine and the concentration of FITC-inulin in plasma.
Proper citation: Jeff Hodgin 2019. U Michigan - Glomerular Filtration Rate Determination with Minipump Inulin Clearance. protocols.io dx.doi.org/10.17504/protocols.io.x63frgn Copy
Authors: Addgene The Nonprofit Plasmid Repository
Summary: This protocol is for Lentivirus production. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data
Proper citation: Addgene The Nonprofit Plasmid Repository 2019. Lentivirus Production. protocols.io dx.doi.org/10.17504/protocols.io.4xwgxpe Copy
Authors: Stefano Orlando, Isotta triulzi, Fausto Ciccacci, Ilaria Palla, Leonardo Palombi, Maria Cristina Marazzi, Marina Giuliano, Marco Floridia, Sandro Mancinelli, Elsa Mutemba, Giuseppe Turchetti
Summary: BACKGROUNDTuberculosis (TB) represents the ninth leading cause of death worldwide. In 2016, are estimated 1.3 million TB deaths among HIV negative people and an additional 374,000 deaths among HIV positive people.In2016, are estimated 1.4 million new cases of TB in people living with HIV (PLWH), 74% of whom were living in Africa. In light of these data, the reduction of mortality caused by TB in PLWH is strongly required specially in low-income countries as Mozambique. According to international guidelines, the initial TB screening in HIV+ patients should be done with the four symptoms screening (4SS: fever, current cough, night sweats and weight loss). The diagnostic test more used in resource-limited countries is smear microscopy (SMEAR). World Health Organization (WHO) recommended Lateral Flow urine LipoArabinoMannan assay (LF-LAM) in immunocompromised patients; in 2010 WHO endorsed the use of Mycobacterium Tuberculosis/Rifampicin (MTB/RIF) test for rapid TB diagnosis but the assay is not used as screening test in all HIV+ patients irrespectively of symptoms due to cost and logistical barriers.The paper aims to evaluate the cost-effectiveness of three screening protocols: standard (4SS and SMEAR in positive patients to 4SS);MTB/RIF; LF-LAM / MTB/RIF.METHODSWe developed a model to assess the cost-effectiveness of the MTB/RIFprotocol versus the common standard and LF-LAM / MTB/RIF protocol. The model considered a sample of 1,000 HIV+ antiretroviral treatment naïve patients in Mozambique. We evaluated disability-adjusted life year (DALY) averted for each protocol, cost per DALY, and incremental cost-effectiveness ratio (ICER), over 1-year, assuming a national healthcare system perspective.The model considered the delayed diagnosis and treatment as the time elapsed between the a false negative test and the diagnosis of TB. On top of that there is a possible health system delay defined as the time interval between positive test and treatment initiation due to the a delay in the delivery of results due to weaknesses in the organization of services. We conducted a sensitivity analysis on more relevant variables.RESULTSThe MTB/RIF protocol was cost-effective as compared to the standard protocol with an ICER of $56.54 per DALY saved. In a cohort of 1,000 patients MTB/RIF and LF-LAM / MTB/RIF protocol generated 1,281 and 1,254 DALY’s saved respectively, with a difference of 174 and 147 DALY respect to the standard protocol.The total cost of MTB/RIF protocol was lower ($92,263) than the standard ($147,226) and the LF-LAM / MTB/RIF protocol ($113,196).Therefore, the cost per DALY saved including new infections due to delayed diagnosis and treatment with the standard protocol was $79.06, about 5 fold higher than MTB/RIFand LF-LAM / MTB/RIF protocols.The cost of new and additional TB infections due to delays in diagnosis plus health system delay seemed the more relevant costs in our analysis.The low sensibility and sensitivity of the standard protocol led to a high number of false negatives, thus delayed TB diagnoses and treatment lead to the development of newly transmitted TB infections. CONCLUSIONSOur study shows that the MTB/RIF adoption could lead an increasing of TB case-finding and a reduction in costs compared with standard and LF-LAM / MTB/RIFprotocols
Proper citation: Stefano Orlando, Isotta triulzi, Fausto Ciccacci, Ilaria Palla, Leonardo Palombi, Maria Cristina Marazzi, Marina Giuliano, Marco Floridia, Sandro Mancinelli, Elsa Mutemba, Giuseppe Turchetti 2018. Delayed diagnosis and treatment of tuberculosis in HIV+ patients in Mozambique: a cost-effectiveness analysis of screening protocols based on four symptom screening, smear microscopy, urine LAM test and Xpert MTB/RIF. protocols.io dx.doi.org/10.17504/protocols.io.qnndvde Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This electroporation protocol is for use with the NEB Turbo Electrocompetent E. coli cells (C2986). These cells are suitable for high efficiency electroporation and rapid colony growth; they are ideal for DNA library constructions and all cloning purposes.
Proper citation: New England Biolabs 2015. Electroporation Protocol (C2986). protocols.io dx.doi.org/10.17504/protocols.io.crgv3v Copy
Authors: Collin Closek, Anni Djurhuus, Katie Pitz, Ryan Kelly, Reiko Michisaki, Kristine Walz, Hilary Starks, Francisco Chavez, Alexandria Boehm, Mya Breitbart
Group: MBON eDNA
Summary: This protocol is aimed at amplifying the 18S rRNA hypervariable region 9 (18S V9) in eukaryotes with a focus on microbial eukaryotes. Amplicons generated using this protocol can then be sequenced using the Illumina platform. The primers (1391F, EukBr) utilized in this protocol are based on the primer utilized in Amaral-Zettler et al 2009 and the Earth Microbiome Project (EMP).Citations
Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM (2009) A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes. PLoS ONE 4(7): e6372. doi:10.1371/journal.pone.0006372
Earth Microbiome Project - http://www.earthmicrobiome.org/emp-standard-protocols/18s/
Proper citation: Collin Closek, Anni Djurhuus, Katie Pitz, Ryan Kelly, Reiko Michisaki, Kristine Walz, Hilary Starks, Francisco Chavez, Alexandria Boehm, Mya Breitbart 2018. Environmental DNA (eDNA) 18S metabarcoding Illumina MiSeq NGS PCR Protocol. protocols.io dx.doi.org/10.17504/protocols.io.mv2c68e Copy
Authors: Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko
Summary: Protocol for extraction of nuclei from frozen tissue in preparation for single-nuclei sequencing (droplet-based/10X). This protocol is based strongly on a similar extraction protocol from the McCarroll lab.
Proper citation: Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko 2020. Frozen Tissue Nuclei Extraction (for 10xV3 snSEQ). protocols.io dx.doi.org/10.17504/protocols.io.bi62khge Copy
Authors: Eric Carpenter
Group: GigaScience Press
Summary: Implemented by: Henrietta Myburg and Marc JohnsonThis protocol is a modification of protocol 8. It was developed after protocol 8 and several commercially available plant RNA isolation kits failed to produce a sufficient yield and quality of RNA from Oenothera spp. (Onagraceae) for next-generation sequencing. Oenothera are rich in polysaccharides, oils, flavonoids and complex ellagitannins that likely interfere with isolation.We suspect that this protocol will be most useful for species and tissues with complex secondarychemistry and rich in oils (e.g. some Rosaceae and Pinaceae). The most important modifications to this protocol versus Protocol 8 is the use of less plant tissue, more extraction buffer, and repeating solvent extractions until the interphase is clean of debris. The protocol is regrettably longer and more involved than Protocol 8. We attempted to remove or reduce the replication of the solvent extractions steps without success (i.e. yield and quality are always decreased in Oenothera when any steps are removed).This protocol is part of a collection of eighteen protocols used to isolate total RNA from plant tissue. (RNA Isolation from Plant Tissue Collection: https://www.protocols.io/view/rna-isolation-from-plant-tissue-439gyr6)
Proper citation: Eric Carpenter 2019. RNA Isolation from Plant Tissue Protocol 9: CTAB/Acid Phenol/Silica Membrane Method. protocols.io dx.doi.org/10.17504/protocols.io.4yegxte Copy
Authors: Fatma Gomaa, Roberto Docampo, Zhuhong Li, Peter Girguis, Virginia Edgcomb
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Stable transfection of B. saltans has been achieved using plasmid for EF 1 alpha C terminal tagging.
Proper citation: Fatma Gomaa, Roberto Docampo, Zhuhong Li, Peter Girguis, Virginia Edgcomb 2019. Bodo saltans transfection with plasmid for tagging EF1alpha gene__IG BsTub. protocols.io dx.doi.org/10.17504/protocols.io.7fchjiw Copy
Authors: Joshua Welsh, Jennifer Jones
Group: Translational Nanobiology Section
Summary: This protocol outlines the steps required to catalogue light scatter reference materials using the FCMPASS software. This is one of a number of protocols in the pipeline for performing small particle calibration using the fcmpass software package.
Proper citation: Joshua Welsh, Jennifer Jones 2020. FCMPASS - Cataloguing light scatter reference materials. protocols.io dx.doi.org/10.17504/protocols.io.bhvuj66w Copy
Authors: Yves Sauve
Summary: To obtain anatomical images that allow for measurement of structural changes in physiology, using Vevo 770,or Vevo 2100 Visual Sonics Integrated Rail System, which includes rat/mouse handling platform.
Proper citation: Yves Sauve 2018. Ultrasound for Small Animal Imaging. protocols.io dx.doi.org/10.17504/protocols.io.u83ezyn Copy
Authors: Qi Wang, Hee Jin Jeon
Summary: Biases perpetuate when people think that they are innocent whereas others are guilty of biases. We examined whether people would detect biased thinking and behavior in others but not themselves as influenced by preexisting beliefs (myside bias) and social stigmas (social biases). The results of three large studies showed that, across demographic groups, participants attributed more biases to others than to themselves, and that this self-other asymmetry was particularly salient among those who hold strong beliefs about the existence of biases (Study 1 and Study 2). The self-other asymmetry in bias recognition dissipated when participants made simultaneous predictions about others’ and their own thoughts and behaviors (Study 3). People thus exhibit bias in bias recognition, and this metacognitive bias may be remedied when it is highlighted to people that we are all susceptible to biasing influences.
Proper citation: Qi Wang, Hee Jin Jeon 2020. Bias in Bias Recognition - Research Materials. protocols.io dx.doi.org/10.17504/protocols.io.bjiikkce Copy
Authors: Malte Kühnemund, Ivan Hernandez, Mohd Istiaq Sharif, Matteo Cornaglia, Martin A.M. Gijs, Mats Nilsson
Group: Molecular Diagnostics - Mats Nilsson Group
Summary: Here is described the protocol used to detect bacteria and antibiotic resistance markers using padlock probes and Rolling circle amplification. This method allows for single-molecule/digital quantification in a semi-quantitative way.
Proper citation: Malte Kühnemund, Ivan Hernandez, Mohd Istiaq Sharif, Matteo Cornaglia, Martin A.M. Gijs, Mats Nilsson 2019. Detection of bacterial pathogens and drug resistance markers using Rolling circle amplification. protocols.io dx.doi.org/10.17504/protocols.io.zp8f5rw Copy
Authors: Maximilian Dietsch, Miriam D
Group: Axmann Lab, CyanoWorld, iGEM Duesseldorf 2018
Summary: In this protocol, the extraction of template DNA out of Synechocystis sp. PCC 6803 samples, the PCR of the template and the application on a agarosegel are described. The protocol was handed over by Maximilian Dietsch MSc.
Proper citation: Maximilian Dietsch, Miriam D 2018. Colony PCR (DreamTaq) with Synechocystis sp. PCC 6803 and gel electrophoresis. protocols.io dx.doi.org/10.17504/protocols.io.mk5c4y6 Copy
Authors: Jonathan King
Group: VERVE Net, Sullivan Lab
Summary: This mixture is used in the CsCl Step Gradient to Purify Phage Protocol
Proper citation: Jonathan King 2016. CsCl Step Gradient Buffer. protocols.io dx.doi.org/10.17504/protocols.io.dmj44m Copy
Authors: Andrew M. Scheidler, Dominique Kinnett-Hopkins, Yvonne C. Learmonth, Robert Motl, Citlali Lopez-Ortiz
Summary: Experimental procedural checklist. Detailed description of sample exercises with images. Example class outline for the TBP that includes chair, barre, and across the floor exercises.
Proper citation: Andrew M. Scheidler, Dominique Kinnett-Hopkins, Yvonne C. Learmonth, Robert Motl, Citlali Lopez-Ortiz 2018. Targeted ballet program mitigates ataxia and improves balance in females with mild-to-moderate multiple sclerosis. protocols.io dx.doi.org/10.17504/protocols.io.mezc3f6 Copy
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