Article
Chemistry, Applied
Sanchez Mirna Lorena, Penaloza Coronas Cynthia, Avila Rodriguez Maria Isabela, Viana Mendieta Pamela, Rivera Hernandez Gabriela, Benavides Jorge, Grasselli Mariano
Summary: This review summarizes the evolution of silica-based nucleic acid purification strategies, highlights the current challenges that can be addressed by new purification methods, and surveys the quality and quantity of purified DNA/RNA for subsequent techniques. This information is crucial for the success of molecular diagnostics and provides guidance for scientists and engineers in choosing suitable DNA/RNA purification techniques for research or bioprocessing applications.
SEPARATION AND PURIFICATION REVIEWS
(2023)
Article
Chemistry, Analytical
Shruti Soni, Bhushan J. Toley
Summary: This article provides a comprehensive review of the development of paper-based nucleic acid sample preparation techniques for complex samples. The authors categorize the nucleic acid amplification tests (NAATs) into three unit operations and propose a new way to classify the workflows of paper-assisted NA sample preparation. The article also discusses the progress in the field and identifies important gaps for future research.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biochemical Research Methods
Xiaoli Zhao, Yong Li, Yake Duan, Amr Amin, Yingqiu Xie, Chao Shi, Cuiping Ma
Summary: Researchers have developed a rapid and cost-effective method for isolating RNA from bacteria, which can be completed within 15 minutes and yields RNA with comparable purity to that of commercial kits. The extracted RNA has been successfully used in downstream enzymatic reactions, showing promise for gene expression analyses in bacterial organisms.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Eunbin Cho, Jayoung Namgung, Jong Sam Lee, Jinmin Jang, Bong-Hyun Jun, Dong-Eun Kim
Summary: Researchers have developed a simple method using mesoporous silica particles as RNA adsorbents to remove double-stranded RNA (dsRNA) impurities from synthesized RNA. Among various polyamines tested, spermidine showed superior capability of RNA binding to the silica matrix. By adjusting the EDTA concentration, at least 80% of the dsRNA can be removed from the mesoporous silica-adsorbed RNA. Compared to cellulose-based methods, using mesoporous silica particles with spermidine and EDTA for binding and elution, respectively, demonstrated more effective removal of dsRNA contaminants from synthesized RNA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Jing Xu, Pawan K. Pandoh, Richard D. Corbett, Duane Smailus, Reanne Bowlby, Denise Brooks, Helen McDonald, Simon Haile, Sundeep Chahal, Steve Bilobram, Karen L. Mungall, Andrew J. Mungall, Robin Coope, Richard A. Moore, Yongjun Zhao, Steven J. M. Jones, Marco A. Marra
Summary: This article presents a high-throughput TNA purification protocol based on SPRI beads, which can be used for both genomic and transcriptomic applications. It also introduces modifications to enhance small RNA recovery, addressing the issue of weak binding of small RNA to SPRI beads. The benchmarking results show that the GRAB-ALL protocol efficiently purifies TNA, including small RNA, in a plate-based format suitable for automated high-throughput sample preparation for next-generation sequencing applications.
Article
Chemistry, Multidisciplinary
Yujin Chu, Jiaoyan Qiu, Yihe Wang, Min Wang, Yu Zhang, Lin Han
Summary: A new strategy for the rapid and ultrasensitive detection of SARS-CoV-2 RNA without the need of RNA extraction and amplification was developed using a microfluidic biochip. This strategy has an ultralow limit of detection and a large linear detection range, and can simultaneously process multiple samples in a short period of time.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Review
Cell Biology
Mahtab Razlansari, Somayeh Jafarinejad, Abbas Rahdar, Milad Shirvaliloo, Rabia Arshad, Sonia Fathi-Karkan, Shekoufeh Mirinejad, Saman Sargazi, Roghayeh Sheervalilou, Narges Ajalli, Sadanand Pandey
Summary: RNA aptamers have great potential as theranostic tools against a variety of disorders, including cancer. They can bind to diverse structures and limit their activities with negligible side effects. Clinical investigations have shown their efficacy in imaging modalities. This review provides new insights into the development, classification, and modification of RNA aptamers, as well as their applications in cancer theranostics.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Chemistry, Analytical
Shanglin Li, Bingqian Han, Donggen Zhou, Yin Gu, Bao Li, Jianxin Ma, Rongxin Fu, Xiao Qi, Peng Liu
Summary: The surveillance of SARS-CoV-2 in aquatic environments is important for human health and ecology, especially in countries with poor sanitation standards. We developed an ultrasensitive method using a polyacrylamide derivative-modified filter disc (PAD-FD) that can efficiently concentrate and amplify highly diluted RNA. Our method showed a higher detection rate (62.5%) compared to a commercial kit (18.8%) when testing suspected SARS-CoV-2 samples. The PAD-FD method provides an accurate testing tool for monitoring viral RNA in aquatic environments.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Kamfai Chan, Arunkumar Arumugam, Cole Markham, Ryan Jenson, Hao-Wei Wu, Season Wong
Summary: Biological testing on the International Space Station (ISS) through a compact microgravity-compatible, automated versatile sample preparation platform (VSPP) is important for monitoring microbial burden and identifying risks to crew health. The VSPP, created with modified 3D printers, has the potential to rapidly identify microorganisms and process samples from various matrices, yielding high-quality nucleic acids. Tests in ground-level laboratories showed successful extraction of viral RNA from urine and human DNA from blood, with consistent results. Microgravity testing and future research are planned to further improve the VSPP's effectiveness in space environments.
Article
Chemistry, Multidisciplinary
Rajat Chauhan, Theodore S. Kalbfleisch, Chinmay S. Potnis, Meenakshi Bansal, Mark W. Linder, Robert S. Keynton, Gautam Gupta
Summary: The study demonstrates a water-soluble silica sol-gel matrix for optimized storage of biospecimens, maintaining the stability of DNA and proteins and long-term preservation of miRNA. This technique is effective in preserving biospecimens at room temperature, unlike refrigeration and freezing methods.
Article
Biochemistry & Molecular Biology
Jitendra K. Biswal, Rajeev Ranjan, Shyam Singh Dahiya, Smrutirekha Mallick, Jajati K. Mohapatra
Summary: In this study, a warm alkaline solution containing Triton X-100 was used to completely remove residual SARS-CoV2 RNA from used RNA-binding silica columns. The regenerated columns showed viral RNA purification capability comparable to fresh silica columns, and can be reused for at least five cycles. This method may benefit SARS-CoV2 diagnostic laboratories by reducing the need for commercial RNA-purification columns.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Chemistry, Analytical
Aaron M. Jankelow, Hankeun Lee, Weijing Wang, Trung-Hieu Hoang, Amanda Bacon, Fu Sun, Seol Chae, Victoria Kindratenko, Katherine Koprowski, Robert A. Stavins, Dylann D. Ceriani, Zachary W. Engelder, William P. King, Minh N. Do, Rashid Bashir, Enrique Valera, Brian T. Cunningham
Summary: In this study, we report an integrated system for rapid detection of viral pathogens. The system can perform sample processing and nucleic acid amplification in 20 minutes and can analyze the results using a smartphone. The system offers the advantages of low cost, high accuracy, and simplicity in operation while achieving rapid detection.
Article
Microbiology
Nina M. Pollak, Daniel J. Rawle, Kexin Yan, Cameron Buckley, Thuy T. Le, Claire Y. T. Wang, Nicole G. Ertl, Karla van Huyssteen, Nicole Crkvencic, Misha Hashmi, Russell E. Lyons, David M. Whiley, Andreas Suhrbier, Joanne Macdonald
Summary: This study presents a method using TNA-Cifer Reagent E to inactivate SARS-CoV-2 and prepare samples for RT-qPCR. Compared to traditional column-based RNA extraction, TNA-Cifer Reagent E shows high specificity and sensitivity, and provides cost and time savings.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Analytical
Edyta Biskup, Lone Schejbel, Douglas Nogueira Perez de Oliveira, Estrid Hogdall
Summary: This article presents a successful attempt to enhance the quantity of RNA isolated from clinical specimens. By comparing different purification methods, it was found that the addition of proteinase K can significantly increase RNA and DNA yield. The AllPrep DNA/RNA/miRNA Universal Kit can be used to extract comparable amounts of RNA as the phenol-chloroform extraction method, and it is also capable of simultaneous extraction of DNA and total RNA, regardless of the tissue of origin.
Article
Infectious Diseases
Annie Cheng, Stefan Riedel, Ramy Arnaout, James E. Kirby
Summary: The multiplex PCR assay Abbott Alinity m Resp-4Plex is accurate, precise, and sensitive for detecting SARS-CoV2, influenza A, influenza B, and RSV infections. With its near random access automation on the Alinity m platform, this assay is believed to be significantly useful in addressing the current COVID-19 pandemic and future needs during anticipated endemic circulation of SARS-CoV-2 with other respiratory viruses.
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
(2022)
Article
Immunology
Brendan Flannery, Jessie R. Chung, Arnold S. Monto, Emily T. Martin, Edward A. Belongia, Huong Q. McLean, Manjusha Gaglani, Kempapura Murthy, Richard K. Zimmerman, Mary Patricia Nowalk, Michael L. Jackson, Lisa A. Jackson, Melissa A. Rolfes, Sarah Spencer, Alicia M. Fry, Joshua G. Petrie, Ryan E. Malosh, E. J. McSpadden, Hannah E. Segaloff, Caroline K. Cheng, Rachel Truscon, Emileigh Johnson, Lois E. Lamerato, Lynn C. Ivacic, Jennifer P. King, Jennifer K. Meece, Madalyn M. Palmquist, Sherri A. Guzinski, Anne Robertson, Ashley Kossie, Michael Smith, Vanessa Hoelscher, Lydia Clipper, Kimberley Walker, Marcus Volz, Arundhati Rao, Robert Fader, Yolanda Munoz-Maldonado, Michael Reis, John V. Williams, Goundappa K. Balasubramani, Evelyn C. Reis, Heather Eng, Samantha Ford, Todd M. Bear, Edmund M. Ricci, Robert W. Hickey, Krissy K. Moehling, Jonathan M. Raviotta, Theresa M. Sax, Michael Susick, Monika Johnson, Rose Azrak, LaShondra Berman, Angie Foust, Wendy Sessions, Juliana DaSilva, Thomas Stark, John Barnes
CLINICAL INFECTIOUS DISEASES
(2019)
Article
Virology
Piet Maes, Gaya K. Amarasinghe, Maria A. Ayllon, Christopher F. Basler, Sina Bavari, Kim R. Blasdell, Thomas Briese, Paul A. Brown, Alexander Bukreyev, Anne Balkema-Buschmann, Ursula J. Buchholz, Kartik Chandran, Ian Crozier, Rik L. de Swart, Ralf G. Dietzgen, Olga Dolnik, Leslie L. Domier, Jan F. Drexler, Ralf Duerrwald, William G. Dundon, W. Paul Duprex, John M. Dye, Andrew J. Easton, Anthony R. Fooks, Pierre B. H. Formenty, Ron A. M. Fouchier, Juliana Freitas-Astua, Elodie Ghedin, Anthony Griffiths, Roger Hewson, Masayuki Horie, Julia L. Hurwitz, Timothy H. Hyndman, Daohong Jiang, Gary P. Kobinger, Hideki Kondo, Gael Kurath, Ivan V. Kuzmin, Robert A. Lamb, Benhur Lee, Eric M. Leroy, Jianrong Li, Shin-Yi L. Marzano, Elke Muhlberger, Sergey V. Netesov, Norbert Nowotny, Gustavo Palacios, Bernadett Palyi, Janusz T. Paweska, Susan L. Payne, Bertus K. Rima, Paul Rota, Dennis Rubbenstroth, Peter Simmonds, Sophie J. Smither, Qisheng Song, Timothy Song, Kirsten Spann, Mark D. Stenglein, David M. Stone, Ayato Takada, Robert B. Tesh, Keizo Tomonaga, Noel Tordo, Jonathan S. Towner, Bernadette van den Hoogen, Nikos Vasilakis, Victoria Wahl, Peter J. Walker, David Wang, Lin-Fa Wang, Anna E. Whitfield, John V. Williams, Gongyin Ye, F. Murilo Zerbini, Yong-Zhen Zhang, Jens H. Kuhn
ARCHIVES OF VIROLOGY
(2019)
Article
Emergency Medicine
Natan Cramer, Neil Munjal, Danielle Ware, Sriram Ramgopal, Dennis Simon, Megan C. Freeman, Marian G. Michaels, Christopher Stem, Kavita Thakkar, John V. Williams, Ashok Panigrahy, Desiree N. W. Neville, Sylvia Owusu-Ansah
ANNALS OF EMERGENCY MEDICINE
(2019)
Article
Immunology
Melissa A. Rolfes, Brendan Flannery, Jessie R. Chung, Alissa O'Halloran, Shikha Garg, Edward A. Belongia, Manjusha Gaglani, Richard K. Zimmerman, Michael L. Jackson, Arnold S. Monto, Nisha B. Alden, Evan Anderson, Nancy M. Bennett, Laurie Billing, Seth Eckel, Pam Daily Kirley, Ruth Lynfield, Maya L. Monroe, Melanie Spencer, Nancy Spina, H. Keipp Talbot, Ann Thomas, Salina M. Torres, Kimberly Yousey-Hindes, James A. Singleton, Manish Patel, Carrie Reed, Alicia M. Fry, Huong Q. McLean, Jennifer P. King, Mary Patricia Nowalk, G. K. Balasubramani, Todd M. Bear, Robert Hickey, John V. Williams, Evelyn C. Reis, Krissy K. Moehling, Heather Eng, Lisa A. Jackson, Michael Smith, Chandni Raiyani, Lydia Clipper, Kempapura Murthy, Wencong Chen, Michael Reis, Joshua G. Petrie, Ryan E. Malosh, E. J. McSpadden, Hannah E. Segaloff, Caroline K. Cheng, Rachel Truscon, Emileigh Johnson, Lois E. Lamerato
CLINICAL INFECTIOUS DISEASES
(2019)
Article
Virology
J. Tyler Kinder, Edita M. Klimyte, Andres Chang, John Williams, Rebecca Ellis Dutch
Article
Pediatrics
Alicia M. Alcamo, Michael S. Wolf, Lauren J. Alessi, Hey J. Chong, Michael Green, John V. Williams, Dennis W. Simon
Review
Virology
Bethany K. Sederdahl, John Williams
Article
Multidisciplinary Sciences
Thomas Klink, Danielle A. Rankin, Bhinnata Piya, Andrew J. Spieker, Samir Faouri, Asem Shehabi, John V. Williams, Najwa Khuri-Bulos, Natasha B. Halasa
Article
Pediatrics
Brian Rha, Aaron T. Curns, Joana Y. Lively, Angela P. Campbell, Janet A. Englund, Julie A. Boom, Parvin H. Azimi, Geoffrey A. Weinberg, Mary A. Staat, Rangaraj Selvarangan, Natasha B. Halasa, Monica M. McNeal, Eileen J. Klein, Christopher J. Harrison, John V. Williams, Peter G. Szilagyi, Monica N. Singer, Leila C. Sahni, Daniella Figueroa-Downing, Darius McDaniel, Mila M. Prill, Brett L. Whitaker, Laura S. Stewart, Jennifer E. Schuster, Barbara A. Pahud, Gina Weddle, Vasanthi Avadhanula, Flor M. Munoz, Pedro A. Piedra, Daniel C. Payne, Gayle Langley, Susan I. Gerber
Article
Virology
Meredith C. Rogers, Margot Miranda-Katz, Yu Zhang, Tim D. Oury, Melissa B. Uccellini, Adolfo Garcia-Sastre, John Williams
Article
Virology
Jens H. Kuhn, Scott Adkins, Daniela Alioto, Sergey V. Alkhovsky, Gaya K. Amarasinghe, Simon J. Anthony, Tatjana Avsic-Zupanc, Maria A. Ayllon, Justin Bahl, Anne Balkema-Buschmann, Matthew J. Ballinger, Tomas Bartonicka, Christopher Basler, Sina Bavari, Martin Beer, Dennis A. Bente, Eric Bergeron, Brian H. Bird, Carol Blair, Kim R. Blasdell, Steven B. Bradfute, Rachel Breyta, Thomas Briese, Paul A. Brown, Ursula J. Buchholz, Michael J. Buchmeier, Alexander Bukreyev, Felicity Burt, Nihal Buzkan, Charles H. Calisher, Mengji Cao, Inmaculada Casas, John Chamberlain, Kartik Chandran, Remi N. Charrel, Biao Chen, Michela Chiumenti, Il-Ryong Choi, J. Christopher S. Clegg, Ian Crozier, John V. da Graca, Elena Dal Bo, Alberto M. R. Davila, Juan Carlos de la Torre, Xavier de Lamballerie, Rik L. de Swart, Patrick L. Di Bello, Nicholas Di Paola, Francesco Di Serio, Ralf G. Dietzgen, Michele Digiaro, Valerian V. Dolja, Olga Dolnik, Michael A. Drebot, Jan Felix Drexler, Ralf Duerrwald, Lucie Dufkova, William G. Dundon, W. Paul Duprex, John M. Dye, Andrew J. Easton, Hideki Ebihara, Toufic Elbeaino, Koray Ergunay, Jorlan Fernandes, Anthony R. Fooks, Pierre B. H. Formenty, Leonie F. Forth, Ron A. M. Fouchier, Juliana Freitas-Astua, Selma Gago-Zachert, George Fu Gao, Maria Laura Garcia, Adolfo Garcia-Sastre, Aura R. Garrison, Aiah Gbakima, Tracey Goldstein, Jean-Paul J. Gonzalez, Anthony Griffiths, Martin H. Groschup, Stephan Guenther, Alexandro Guterres, Roy A. Hall, John Hammond, Mohamed Hassan, Jussi Hepojoki, Satu Hepojoki, Udo Hetzel, Roger Hewson, Bernd Hoffmann, Seiji Hongo, Dirk Hoeper, Masayuki Horie, Holly R. Hughes, Timothy H. Hyndman, Amara Jambai, Rodrigo Jardim, Daohong Jiang, Qi Jin, Gilda B. Jonson, Sandra Junglen, Serpil Karadag, Karen E. Keller, Boris Klempa, Jonas Klingstrom, Gary Kobinger, Hideki Kondo, Eugene V. Koonin, Mart Krupovic, Gael Kurath, Ivan V. Kuzmin, Lies Laenen, Robert A. Lamb, Amy J. Lambert, Stanley L. Langevin, Benhur Lee, Elba R. S. Lemos, Eric M. Leroy, Dexin Li, Jianrong Li, Mifang Liang, Wenwen Liu, Yan Liu, Igor S. Lukashevich, Piet Maes, William Marciel de Souza, Marco Marklewitz, Sergio H. Marshall, Giovanni P. Martelli, Robert R. Martin, Shin-Yi L. Marzano, Sebastien Massart, John W. McCauley, Nicole Mielke-Ehret, Angelantonio Minafra, Maria Minutolo, Ali Mirazimi, Hans-Peter Muehlbach, Elke Muhlberger, Rayapati Naidu, Tomohide Natsuaki, Beatriz Navarro, Jose A. Navarro, Sergey V. Netesov, Gabriele Neumann, Norbert Nowotny, Marcio R. T. Nunes, Are Nylund, Arnfinn L. Okland, Renata C. Oliveira, Gustavo Palacios, Vicente Pallas, Bernadett Palyi, Anna Papa, Colin R. Parrish, Alex Pauvolid-Correa, Janusz T. Paweska, Susan Payne, Daniel R. Perez, Florian Pfaff, Sheli R. Radoshitzky, Aziz-ul Rahman, Pedro L. Ramos-Gonzalez, Renato O. Resende, Carina A. Reyes, Bertus K. Rima, Victor Romanowski, Gabriel Robles Luna, Paul Rota, Dennis Rubbenstroth, Jonathan A. Runstadler, Daniel Ruzek, Sead Sabanadzovic, Jiri Salat, Amadou Alpha Sall, Maria S. Salvato, Kamil Sarpkaya, Takahide Sasaya, Martin Schwemmle, Muhammad Z. Shabbir, Xiaohong Shi, Zhengli Shi, Yukio Shirako, Peter Simmonds, Jana Sirmarova, Manuela Sironi, Sophie Smither, Teemu Smura, Jin-Won Song, Kirsten M. Spann, Jessica R. Spengler, Mark D. Stenglein, David M. Stone, Petra Strakova, Ayato Takada, Robert B. Tesh, Natalie J. Thornburg, Keizo Tomonaga, Noel Tordo, Jonathan S. Towner, Massimo Turina, Ioannis Tzanetakis, Rainer G. Ulrich, Anna Maria Vaira, Bernadette van den Hoogen, Arvind Varsani, Nikos Vasilakis, Martin Verbeek, Victoria Wahl, Peter J. Walker, Hui Wang, Jianwei Wang, Xifeng Wang, Lin-Fa Wang, Taiyun Wei, Heather Wells, Anna E. Whitfield, John V. Williams, Yuri I. Wolf, Zhiqiang Wu, Xin Yang, Xinglou Yang, Xuejie Yu, Natalya Yutin, F. Murilo Zerbini, Tong Zhang, Yong-Zhen Zhang, Guohui Zhou, Xueping Zhou
ARCHIVES OF VIROLOGY
(2020)
Article
Microbiology
Krista G. Freeman, Katherine S. Wetzel, Yu Zhang, Kira M. Zack, Deborah Jacobs-Sera, Sara M. Walters, Dominique J. Barbeau, Anita K. McElroy, John V. Williams, Graham F. Hatfull
Summary: Researchers explored the potential of using mycobacteriophages as a vaccine platform, citing advantages such as a large variety of characterized phages and the ability to display multiple antigen copies on a single particle. They found that mycobacteriophage Bxb1 and its recombinants displaying SARS-CoV-2 antigens exhibit strong immunogenicity.
Review
Infectious Diseases
Samuel Brayer, Alexandra Linn, Stephanie Holt, Kate Ellery, Stephanie Mitchell, John Williams
JOURNAL OF THE PEDIATRIC INFECTIOUS DISEASES SOCIETY
(2019)
Meeting Abstract
Immunology
Yu Zhang, Jiuyang Xu, Margot Miranda-Katz, Helen E. Rich, Michelle L. Manni, Sharon Tollefson, Saumendra N. Sarkar, John F. Alcorn, John Williams
JOURNAL OF IMMUNOLOGY
(2019)
Meeting Abstract
Immunology
Kristina D. Lamens, Meredith C. Rogers, Justin T. Tometich, Timothy W. Hand, John V. Williams
JOURNAL OF IMMUNOLOGY
(2019)