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Authors: Alex Rajewski, Cecilia McGregor
Summary: This is a quick (and very cheap) genomic DNA extraction protocol for fresh leaf or seed tissue in many plant species. It should be use preferably for extractions that do not require exceptional lengths of DNA, and is suitable for routine PCR, sanger sequencing, and restriction digests. The protocol is modified from Edwards et al. Nucleic Acids Research 19(6): 1349, and has been adapted since then by Zach King, Jonathan Serrano, and Cecilia McGregor. Typical yeilds of DNA are ~200ng/µL.

Proper citation: Alex Rajewski, Cecilia McGregor 2019. Leaf Punch DNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.yxufxnw Copy   

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Authors: Yasna K Palmeiro-Silva, Pelusa Orellana, Pia Venegas, Aneta Dobierzewska, Lara Monteiro, Manuel Varas-Godoy, Errol Norwitz, Greg Rice, Eduardo Osorio, Sebastián E Illanes
Summary: Background: Natural disasters increase the level population stress, including pregnant women, who can experience prenatal maternal stress, affecting to the fetus and trigger perinatal complications, such as low birth weight, smaller head circumference, etc. However, little is known about effects of earthquake on perinatal outcomes.  Objective: To evaluate the effect of earthquake occurred on February 27, 2010 and perinatal outcomes of Chilean pregnant women, and to examine these effects by timing of exposure during pregnancy and newborn gender.Methods: A register-based study was performed using data collected from women who had a vaginal delivery in a large private health center in Santiago, Chile, during 2009 and 2010. The study population was categorized according to exposure to earthquake and timing during gestation. Primary perinatal outcomes were gestational age at birth, birth weight, length and head circumference. Analyses adjusted for gender, gestational age at exposure, parity, maternal age and income.Results: A total of 1,966 eligible vaginal deliveries occurred during 2009 and 2,110 in 2010. Birth weight was not affected by the trimester of exposure; however, length, head circumference and gestational age at birth were significantly different according to trimester of exposure and gender of newborn. In multivariable analysis, newborns were shorter by 2 mm, 5 mm and 4.5 mm, if they were exposed during their first, second and third trimester, respectively. Furthermore, newborns had a smaller head circumference by 1.2 mm and 1.5 mm if they were exposed during first and second trimester of gestation.Conclusion: In this cohort, exposure to the February 2010 earthquake resulted in earlier delivery and reduced length and head circumference in the offspring. This association varied according to trimester of exposure and fetal gender. Health workers should include exposed to high levels of stress associated with natural disasters when assessing pregnancy risk factors.

Proper citation: Yasna K Palmeiro-Silva, Pelusa Orellana, Pia Venegas, Aneta Dobierzewska, Lara Monteiro, Manuel Varas-Godoy, Errol Norwitz, Greg Rice, Eduardo Osorio, Sebastián E Illanes 2017. Effects of earthquake on perinatal outcomes: A Chilean register-based study. protocols.io https://dx.doi.org/10.17504/protocols.io.j55cq86 Copy   

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Authors: tclark , Ahmad Hashem, Jun Yong Ha, Charlie Mize
Group: XPRIZE Rapid Covid Testing

Proper citation: tclark , Ahmad Hashem, Jun Yong Ha, Charlie Mize 2020. Boston Biopharma CareStart™ Rapid Diagnostic Antigen Test. protocols.io https://dx.doi.org/10.17504/protocols.io.bkzxkx7n Copy   

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Authors: yang1832 , Julia Laskin
Group: NanoDESI MSI Julia Laskin group Purdue
Summary: Scope:Acquire imaging mass spectrometry (IMS) datasets of proteins on human kidney tissue with ~12μm spatial resolution.Expected Outcome:Visualize the proteins distribution localizing to physiological regions within the human kidney by generating ion images of multiply charged protein peaks.

Proper citation: yang1832 , Julia Laskin 2020. High resolution Nano-DESI mass spectrometry imaging of proteomics of tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bm2nk8de Copy   

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Authors: Matus Valach
Summary: The identity of a nucleotide or the presence of a bulky modification or strand break in an RNA can be determined by several approaches. When the 3′ region of the analyzed RNA is known, extending a (radio)labeled primer by reverse transcription and analyzing the reaction products using denaturing polyacrylamide gel electrophoresis and subsequent (radio)imaging allows mapping of cDNA chain-termination sites. (Based on the design of the experiment, these can be, for example, a strand break, 5′ end, pause-inducing site, or site of dideoxynucleotide incorporation.) This procedure is adapted from the previously published protocol by Walker and Lorsch (DOI: 10.1016/B978-0-12-420037-1.00020-8).

Proper citation: Matus Valach 2016. Primer extension assay and sequencing by dideoxynucleotide incorporation on RNA templates. protocols.io https://dx.doi.org/10.17504/protocols.io.ejtbcnn Copy   

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Authors: Dale Abel
Group: Diabetic Complications Consortium
Summary: This protocol describes the procedure used by the DiaComp for inducing pressure overload hypertrophy in mice.Diabetic Complication:

Proper citation: Dale Abel 2019. Aortic Banding in Mice. protocols.io https://dx.doi.org/10.17504/protocols.io.7rvhm66 Copy   

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Authors: Gage Moreno, David O'connor
Summary: This protocol outlines the methods to perform unbiased direct metagenomic sequencing of nucleic acid extracts from cell-free fluids. This protocol can be adapted to be run on Illumina and Nanopore sequencing platforms. The protocol is based off of the work from Kafetzopoulou et al. (PMID: 30563591). Liana has provided the lab with detailed protocols, and has worked with us extensively on optimizing and getting protocols running efficiently. Please note that this protocol has been updated to use SuperScript IV with it’s optimal temperature which has been reflected in Lewandowski et al. (DOI: https://doi.org/10.1128/JCM.00963-19)Notes:* This protocol has been used to sequence influenza direction from respiratory clinical samples (DOI: https://doi.org/10.1128/JCM.00963-19).* A team from China published last week on a 2019-nCoV familial cluster using the SISPA protocol as for coronavirus whole genome sequencing (DOI: https://doi.org/10.1016/S0140-6736(20)30154-9)SISPA-Primer A - 5'-GTT TCC CAC TGG AGG ATA-(N9)-3'SISPA-Primer B - 5′-GTT TCC CAC TGG AGG ATA-3′

Proper citation: Gage Moreno, David O'connor 2020. Sequence-Independent, Single-Primer Amplification of RNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.bb3miqk6 Copy   

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Authors: Manuela De Las Casas
Group: AEGIS - Madrid iGEM 2019
Summary: The aim of this protocol is to check the efficiency of the detection system that will be present in the strips. The result expected is a good binding between the streptavidin and the aptamers, great hybridization between both aptamers and a clear visible result when yielding with peroxidase.

Proper citation: Manuela De Las Casas 2019. Streptavidin dot blot with aptamers. protocols.io https://dx.doi.org/10.17504/protocols.io.6gyhbxw Copy   

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Authors: Angel Justiz-Vaillant1, Arvind Kurhade1, Chandrashekhar Unakal1, Patrick E. Akpaka1, Sade Aisha Folashade John1
Group: University of the West Indies, [email protected]

Proper citation: Angel Justiz-Vaillant1, Arvind Kurhade1, Chandrashekhar Unakal1, Patrick E. Akpaka1, Sade Aisha Folashade John1 2020. Isolation of Escherichia coli pathogens from oysters. protocols.io https://dx.doi.org/10.17504/protocols.io.bj6ikrce Copy   

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Authors: Mohammad Abdus Salam
Group: Prebiotic research protocol
Summary: The dietary chitosan promotes growth, biochemical composition, hematological parameter and morphology of internal organs by improving gut microbiota status of juvenile Barbonymus gonionotus.

Proper citation: Mohammad Abdus Salam 2021. Prebiotic research protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bt2knqcw Copy   

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Authors: Jose Mendoza-Sanchez
Summary: Multicriteria desicion analysis (MCDA) is a tool used to perform quantitative benefit-risks assessment (BRA) anlysis in drugs, procedures and devices in health. It allows comparisons in the same indication, that allows quantitative BRA balances, is useful to shows results in a transparency and consistency manner and also to communicate easily to the stakeholders.MCDA has emerged as a promising tool in the decision context for drugs, although its use has been relegated to assess drugs in the context of medicine reimbursment and a few for benefits, risks and others assessments in medicines for a particular indication. One of the major advantages of MCDA is the inclusion of criterian weights that is "preferences". this roadmap to formulate a MCDA compile the recomendations of IMI-PROTECT and ISPOR task force to easy, explicit and transparent election of criteria included in a MCDA.

Proper citation: Jose Mendoza-Sanchez 2018. Roadmap to formulate a Multicriteria Decision Analysis (MCDA). protocols.io https://dx.doi.org/10.17504/protocols.io.mwbc7an Copy   

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Authors: Girija Goyal
Summary: This protocol describes the steps conventionally used to differentiate dendritic cells from human monocytes isolated from fresh whole blood or leukopaks. While these DC mimic many of the functions of the dendritic cell lineage, they are not considered classical DC which are a different lineage and very rare. By day 4 CD1c+ cells are emerging with a reduction in CD14 positivity

Proper citation: Girija Goyal 2019. Differentiation of dendritic cells from human monocytes. protocols.io https://dx.doi.org/10.17504/protocols.io.xjrfkm6 Copy   

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Authors: Steven Wilhelm, Gary Lecleir, Ashley Humphrey
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: BIOLOGICAL SPILL RESPONSE method to be used in the event of a biosafety incident.

Proper citation: Steven Wilhelm, Gary Lecleir, Ashley Humphrey 2019. Cleaning up a biohazardous spill outside of a biosafety cabinet. protocols.io https://dx.doi.org/10.17504/protocols.io.wgjfbun Copy   

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Authors: Isabelle Vea, Stevie Bain
Group: Mealybug Team

Proper citation: Isabelle Vea, Stevie Bain 2021. Karyotype on fixed mealybug tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.mnec5be Copy   

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Authors: Luciano Martelotto
Group: Human Cell Atlas Method Development Community, Single Cell Core, Harvard Medical School
Summary: This protocol is the result of the combination of various nuclei isolation protocols for single cell RNA-seq experiments using droplet-based methods, and is an extension of the Frankenstein (D.O.F means Daughter Of Frankenstein). Developed to prepare nuclei isolates from fresh and frozen material of small-to-large sizes. The good thing is that it does not uses FACS but OptiPrep® continuous gradient to remove debris. It is the alternative protocol when FACS is not available. This protocol works better with smaller samples. After centrifugation the nuclei will form a pellet and contaminating membranes will float at the top. This continuous gradient can be applied for as many times as needed to the same prep to continue cleaning up your nuclei suspensions.

Proper citation: Luciano Martelotto 2021. Daughter of Frankenstein protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® continuous gradient. protocols.io https://dx.doi.org/10.17504/protocols.io.bstznep6 Copy   

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Authors: Laura Mcwhirter, Craig Ritchie, Alan Carson, Jon Stone
Summary: Functional cognitive disorders are likely to account for a significant proportion of adults presenting with cognitive (memory and thinking) symptoms which are not caused by neurodegenerative disease or structural brain lesions, incorporating those with isolated functional cognitive symptoms, those with primary psychiatric disorders, and those with health anxiety or who attend excessively to normal cognitive lapses. There is a need for improved diagnostic methods to identify those with functional cognitive symptoms so that they might be offered appropriate treatment, protected from iatrogenic harms, and also in order to improve the specificity of prodromal neurodegenerative disease phenotypes.This study aims to identify elements of clinical, neurological, cognitive examination which can, in combination as part of a diagnostic scoring tool, accurately discriminate functional cognitive symptoms from those more likely to be due to neurodegenerative disease. The study will recruit 120 participants with mild or subjective memory symptoms (but not dementia) from memory, neurology, and neuropsychiatry clinics. Each subject will attend for a structured research assessment examining interactional, linguistic, metacognitive features, as well as psychiatric, physical, and sleep disorder comorbidity. Multiple outcomes will be compared with panel consensus diagnosis using discriminant factor analysis. The intention is to follow up medical record / general practice diagnosis at 1-2 years, and ultimately it is hoped that further studies beyond this will re-examine the cohort in the future.

Proper citation: Laura Mcwhirter, Craig Ritchie, Alan Carson, Jon Stone 2019. Improving Diagnosis in Cognitive Disorders. protocols.io https://dx.doi.org/10.17504/protocols.io.z97f99n Copy   

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Authors: Moshe Sade-Feldman, Miguel Reyes, Alexandra-Chloe Villani
Group: Human Cell Atlas Method Development Community, Coronavirus Method Development Community
Summary: This protocol outlines the steps and methods for blood processing for PBMC to assist the MGH COVID-19 effort.

Proper citation: Moshe Sade-Feldman, Miguel Reyes, Alexandra-Chloe Villani 2020. MGH COVID-19 Effort Blood Processing Protocol for PBMC, Neutrophils and Plasma Isolation. protocols.io https://dx.doi.org/10.17504/protocols.io.bjhnkj5e Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: This is a technique for isolating phage from agar plates. When working with lytic phage, well-isolated, cleared areas in a lawn of bacteria (called plaques) are removed from the agar (by coring with a sterile pipette) and used to infect fresh bacteria in liquid medium. The lysed culture can be used for a new plaque assay after 0.2 um filtering to remove residual bacteria. New phage are "plaque-purified" a minimum of three times before they are considered to be free of other phage.

Proper citation: Matthew Sullivan Lab 2015. Coring Technique. protocols.io https://dx.doi.org/10.17504/protocols.io.c3zyp5 Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. One-step growth curves for Cellulophaga phages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddh235 Copy   

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Authors: Shiwei Liu, Xin Li, Yaru Wu, Ruixue Duan, Jiaxin Zhang, Fang Du, Qi Zhang, Yuanbin Li, and Naishi Li

Proper citation: Shiwei Liu, Xin Li, Yaru Wu, Ruixue Duan, Jiaxin Zhang, Fang Du, Qi Zhang, Yuanbin Li, and Naishi Li 2017. Effects of Vaspin on Pancreatic ? Cell Secretion via PI3K/Akt and NF-?B Signaling Pathways. protocols.io https://dx.doi.org/10.17504/protocols.io.kjicuke Copy   

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