Volume 9(1); 2024

Methods Article

tANCHOR cell-based ELISA approach as a surrogate for antigen-coated plates to monitor specific IgG directed to the SARS-CoV-2 receptor-binding domain

Hubert Bernauer, Josef Maier, Norbert Bannert, Daniel Ivanusic

Biol Methods Protoc. 2024; 9(1): bpae001. Published online 2024 Jan 19. doi: 10.1093/biomethods/bpae001

PMCID:: PMC10850845

Article PDF–1.9M

Identification and quantitation of multiple variants in RNA virus genomes

Johnny Sena, Lovkesh Karwal, Callum Bell, Nicholas Devitt, Faye Schilkey, Claire Huang, Jill Livengood, Subash Das, Hansi J Dean

Biol Methods Protoc. 2024; 9(1): bpae004. Published online 2024 Feb 3. doi: 10.1093/biomethods/bpae004

PMCID:: PMC10898329

Article PDF–979K

Establishment of new transurethral catheterization methods for male mice

Xi Duan, Zhibin Chen, Zhean Zhan, Langhui Li, Xianying Lei, Yang Long, Xiang Xie, Huan Chen

Biol Methods Protoc. 2024; 9(1): bpae005. Published online 2024 Feb 5. doi: 10.1093/biomethods/bpae005

PMCID:: PMC10898326

Article PDF–2.4M

Protocol for preliminary, multicenteric validation of “PoCOsteo device”: A point of care tool for proteomic and genomic study of osteoporosis

Farideh Razi, Afshin Ostovar, Noushin Fahimfar, Mahsa M. Amoli, Saeed Ebrahimi Fana, Hans Peter Dimai, Barbara Obermayer-Pietsch, Barbara Luegger, Fernando Rivadeneira, Iraj Nabipour, Bagher Larijani, Patricia Khashayar

Biol Methods Protoc. 2024; 9(1): bpae006. Published online 2024 Mar 22. doi: 10.1093/biomethods/bpae006

PMCID:: PMC10978377

Article PDF–622K

An amplicon-based protocol for whole-genome sequencing of human respiratory syncytial virus subgroup A

Joel Armando Vazquez-Pérez, Eber Martínez-Alvarado, Alberto Antony Venancio-Landeros, Carlos Santiago-Olivares, Fidencio Mejía-Nepomuceno, Enrique Mendoza-Ramírez, Evelyn Rivera-Toledo

Biol Methods Protoc. 2024; 9(1): bpae007. Published online 2024 Feb 6. doi: 10.1093/biomethods/bpae007

PMCID:: PMC10873904

Article PDF–1.0M

A methodological primer of extracellular vesicles isolation and characterization via different techniques

Farhang Aliakbari, Noah B Stocek, Maxximuss Cole-André, Janice Gomes, Giovanni Fanchini, Stephen H Pasternak, Gunna Christiansen, Dina Morshedi, Kathryn Volkening, Michael J Strong

Biol Methods Protoc. 2024; 9(1): bpae009. Published online 2024 Feb 13. doi: 10.1093/biomethods/bpae009

PMCID:: PMC10902684

Article PDF–3.1M

Development of a highly sensitive TaqMan method based on multi-probe strategy: its application in ASFV detection

Shuxiang Ding, Tianren Shen, Zixuan Feng, Sujing Diao, Yan Yan, Zhenkun Du, Yulan Jin, Jinyan Gu, Jiyong Zhou, Min Liao, Weiren Dong

Biol Methods Protoc. 2024; 9(1): bpae011. Published online 2024 Feb 19. doi: 10.1093/biomethods/bpae011

PMCID:: PMC10939455

Article PDF–1.4M

Rapid IDH1-R132 genotyping panel utilizing locked nucleic acid loop-mediated isothermal amplification

Kristian A Choate, Edward J Raack, Paul B Mann, Evan A Jones, Robert J Winn, Matthew J Jennings

Biol Methods Protoc. 2024; 9(1): bpae012. Published online 2024 Feb 21. doi: 10.1093/biomethods/bpae012

PMCID:: PMC10984729

Article PDF–1.7M

A rapid and accurate method for evaluating the degradation of pan-Akt in cells by PROTACs using NanoLuc luciferase

Xiaojun Ji, Lei Miao, Yebin Wu, Tingli Zhao, Yaxuan Si, Xiaoyun Tan, Qiuhua Zhou, Rui Zuo, Junjie Pei, Jian Wu, Changyou Ma, Zhongjun Ma, Dan Xu

Biol Methods Protoc. 2024; 9(1): bpae014. Published online 2024 Mar 5. doi: 10.1093/biomethods/bpae014

PMCID:: PMC10965420

Article PDF–2.7M

An improved method for measuring catalase activity in biological samples

Mahmoud Hussein Hadwan, Marwah Jaber Hussein, Rawa M Mohammed, Asad M Hadwan, Hawraa Saad Al-Kawaz, Saba S M Al-Obaidy, Zainab Abbas Al Talebi

Biol Methods Protoc. 2024; 9(1): bpae015. Published online 2024 Mar 5. doi: 10.1093/biomethods/bpae015

PMCID:: PMC10957919

Article PDF–1.6M

TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research

Lucas Sá Barreto Jordão, Marli Pires Morim, José Fernando A Baumgratz, Marcelo Fragomeni Simon, André L C Eppinghaus, Vicente A Calfo

Biol Methods Protoc. 2024; 9(1): bpae017. Published online 2024 Mar 14. doi: 10.1093/biomethods/bpae017

PMCID:: PMC10984730

Article PDF–2.9M

A semi-automated spectral approach to analyzing cyclical growth patterns using fish scales

Julien A Chaput, Gérald Chaput

Biol Methods Protoc. 2024; 9(1): bpae018. Published online 2024 Mar 18. doi: 10.1093/biomethods/bpae018

PMCID:: PMC10990686

Article PDF–3.4M

Intra-arterial delivery of neurospheres into isolated perfused porcine colons: a proof of concept

Richard D Martel, Nicolas A Hoyos, María Ángeles Tapia-Laliena, Irmgard Herrmann, Martin Herrmann, Rasul Khasanov, Karl-Herbert Schäfer

Biol Methods Protoc. 2024; 9(1): bpae022. Published online 2024 Apr 2. doi: 10.1093/biomethods/bpae022

PMCID:: PMC11018533

Article PDF–1.0M

Serum metallomics reveals insights into the associations of elements with the progression of preleukemic diseases toward acute leukemia

Amna Jabbar Siddiqui, Noman Khan, Kauser Fatima, Sabiha Farooq, Muhammad Ramzan, Hesham R El-Seedi, Jalal Uddin, Abdullatif Bin Muhsinah, Syed Ghulam Musharraf

Biol Methods Protoc. 2024; 9(1): bpad027. Published online 2023 Nov 1. doi: 10.1093/biomethods/bpad027

PMCID:: PMC10790676

Article PDF–1.5M

Long amplicon nanopore sequencing of Botrytis cinerea and other fungal species present in infected grapevine leaf samples

Vladimer Baramidze, Luca Sella, Tamar Japaridze, Nino Abashidze, Daviti Lamazoshvili, Nino Dzotsenidze, Giorgi Tomashvili

Biol Methods Protoc. 2024; 9(1): bpad042. Published online 2024 Jan 5. doi: 10.1093/biomethods/bpad042

Correction in:: Biol Methods Protoc. 2024; 9(1): bpae010.

PMCID:: PMC10789308

Article PDF–635K

Reviews

Baricitinib statistically significantly reduced COVID-19-related mortality: a systematic review and meta-analysis of five phase III randomized, blinded and placebo-controlled clinical trials

Sivananthan Manoharan, Lee Ying Ying

Biol Methods Protoc. 2024; 9(1): bpae002. Published online 2024 Jan 23. doi: 10.1093/biomethods/bpae002

PMCID:: PMC10873572

Article PDF–753K

Pyrimethamine reduced tumour growth in pre-clinical cancer models: a systematic review to identify potential pre-clinical studies for subsequent human clinical trials

Sivananthan Manoharan, Lee Ying Ying

Biol Methods Protoc. 2024; 9(1): bpae021. Published online 2024 Mar 29. doi: 10.1093/biomethods/bpae021

PMCID:: PMC11014785

Article PDF–1.1M

Protocols

Optimized protocol for shotgun label-free proteomic analysis of pancreatic islets

Juliana SanchesTrevizol, Aline Dionizio, Aislan Quintiliano Delgado, Talita Mendes Oliveira Ventura, Caroline Fernanda da Silva Ribeiro, Nathalia Rabelo Buzalaf, José Roberto Bosqueiro, Marília Afonso Rabelo Buzalaf

Biol Methods Protoc. 2024; 9(1): bpae003. Published online 2024 Jan 25. doi: 10.1093/biomethods/bpae003

PMCID:: PMC10893585

Article PDF–1.0M

Efficient regeneration of protoplasts from Solanum lycopersicum cultivar Micro-Tom

Yeong Yeop Jeong, Yoo-Sun Noh, Suk Weon Kim, Pil Joon Seo

Biol Methods Protoc. 2024; 9(1): bpae008. Published online 2024 Feb 6. doi: 10.1093/biomethods/bpae008

PMCID:: PMC10898868

Article PDF–3.0M

Special Collection - Teaching and Outreach in Molecular Biology and Evolution

Teaching New Methods

Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom

Melinda A Yang, Kylie Korsnack

Biol Methods Protoc. 2024; 9(1): bpae013. Published online 2024 Feb 28. doi: 10.1093/biomethods/bpae013

PMCID:: PMC10924719

Article PDF–1.6M

Pre-Registered Study Protocols

Alternative community-led intervention to improve uptake of cataract surgery services in rural Tanzania—The Dodoma Community Cataract Acceptance Trial (DoCCAT): a protocol for intervention co-designing and implementation in a cluster-randomized controlled trial

Frank Sandi, Gareth Mercer, Robert Geneau, Kenneth Bassett, Deogratius Bintabara, Albino Kalolo

Biol Methods Protoc. 2024; 9(1): bpae016. Published online 2024 Mar 8. doi: 10.1093/biomethods/bpae016

PMCID:: PMC10987207

Article PDF–1.0M

Protocols Article

An optimized protocol for generating appendage-bearing skin organoids from human-induced pluripotent stem cells

Imaan Ahmed, Jane Sun, Jason Brown, Kiarash Khosrotehrani, Abbas Shafiee

Biol Methods Protoc. 2024; 9(1): bpae019. Published online 2024 Mar 22. doi: 10.1093/biomethods/bpae019

PMCID:: PMC11009018

Article PDF–1.8M

Special Collection- Teaching and Outreach in Molecular Biology and Evolution

Teaching New Methods

Teaching at the intersection of science and society: An activity on healthcare disparities

Paula E Adams, Enya Granados, Abby E Beatty, Cissy J Ballen

Biol Methods Protoc. 2024; 9(1): bpad041. Published online 2024 Jan 5. doi: 10.1093/biomethods/bpad041

PMCID:: PMC10833140

Article PDF–1.7M

Correction

Correction to: Long amplicon nanopore sequencing of Botrytis cinerea and other fungal species present in infected grapevine leaf samples

Biol Methods Protoc. 2024; 9(1): bpae010. Published online 2024 Feb 23. doi: 10.1093/biomethods/bpae010

Corrects:: Biol Methods Protoc. 2024; 9(1): bpad042.

PMCID:: PMC10888514

Correction PDF–217K

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