Article
Chemistry, Analytical
Nornazliya Mohamad, Amalia Mohd Hashim, Nur Fadhilah Khairil Mokhtar, Mohd Hafis Yuswan, Shuhaimi Mustafa
Summary: This study screened, characterized, and validated aptamers bound to pork proteins. The results showed that the selected aptamers could bind to multiple proteins in negative samples, suggesting a need for further research to develop aptamers with higher specificity towards porcine protein.
MICROCHEMICAL JOURNAL
(2024)
Article
Biochemistry & Molecular Biology
Shaymaviswanathan Karnaneedi, Roger Huerlimann, Elecia B. Johnston, Roni Nugraha, Thimo Ruethers, Aya C. Taki, Sandip D. Kamath, Nicholas M. Wade, Dean R. Jerry, Andreas L. Lopata
Summary: This study successfully identified seven known crustacean allergens and up to 39 unreported allergens in different shrimp species through mining complete transcriptomes. Multiple sequence alignment revealed high homology of these shrimp allergens with allergens from other invertebrates such as mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Shuwen Qian, Dingran Chang, Sisi He, Yingfu Li
Summary: This review analyzes SELEX experiments to compare synthetic and natural aptamers, and proposes ideas for improving aptamer performance to address real-world challenges.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biochemical Research Methods
Linghui Guo, Ying Song, Yanwen Yuan, Jinlei Chen, Haifeng Liang, Fei Guo, Zhi Yu, Pei Liang, Yapei Wang, Pu Wang
Summary: Nucleic acid aptamers were identified through 9 rounds of screening from a length-mixed single-stranded DNA library using SELEX technology, showing improved affinity after the 3rd and 7th rounds, with aptamers from the 7th to 9th rounds demonstrating stronger affinity. Among the 15 selected candidate LDH aptamer sequences, LDH7-1, LDH7-9, LDH8-2, and LDH9-1 exhibited high affinity and specificity for binding to LDH protein.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Review
Biotechnology & Applied Microbiology
Ricardo Oliveira, Eva Pinho, Ana Luisa Sousa, Jeffrey J. DeStefano, Nuno Filipe Azevedo, Carina Almeida
Summary: This article discusses the advantages and limitations of using nucleic acid mimics to enhance the versatility of aptamers, including the applicability of existing engineered polymerases to replicate nucleic acid mimics and methodologies to improve aptamers. It also explores the limitations of existing methods for sequencing nucleic acid mimic sequences and bioinformatic tools for predicting aptamer structures.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Ju Qiu, Rui Guo, Yidan Li, Yuyao Zhang, Kangsheng Jia, Yinghu Lei, Linsen Zan, Anning Li
Summary: The golden takin, an endemic ruminant species, has been listed as endangered and vulnerable. This study used RNA sequencing and microsatellite prediction to assess the transcriptome of its muscles, providing valuable genetic information for conservation efforts and further studies on takins.
Review
Pharmacology & Pharmacy
Mei-Yue Wang, Rong Zhao, Yu-Lan Wang, De-Ping Wang, Ji-Min Cao
Summary: This review provides an overview of the biology of flaviviruses and the current advances in RNA-based therapeutics for them. The authors also discuss the challenges and possible solutions in this area. They emphasize the importance of maintaining the current momentum in the development of safe and effective anti-flavivirus drugs through joint efforts of academia, government, and industry.
EXPERT OPINION ON DRUG DISCOVERY
(2023)
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
Biochemistry & Molecular Biology
Francesco Morena, Chiara Argentati, Ilaria Tortorella, Carla Emiliani, Sabata Martino
Summary: This study utilized molecular dynamic simulation and binding free energy calculation to identify an aptamer with the strongest interaction, which could serve as a potential candidate for inhibiting SARS-CoV-2 M-pro as a therapeutic drug for COVID-19.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Zheng Li, Ming Wang, Zhenhui Zhong, Javier Gallego-Bartolome, Suhua Feng, Yasaman Jami-Alahmadi, Xinyi Wang, James Wohlschlegel, Sylvain Bischof, Jeff A. Long, Steven E. Jacobsen
Summary: The study reveals that MOM1 plays a crucial role in RNA-directed DNA methylation, and is involved in maintaining DNA methylation and closed chromatin state at specific sites. Additionally, MOM1 is able to colocalize with genes near active chromatin through MORC6, demonstrating its multifaceted role in genome regulation.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Takayuki Miki, Taichi Nakai, Masahiro Hashimoto, Keigo Kajiwara, Hiroshi Tsutsumi, Hisakazu Mihara
Summary: De novo designed self-assembling peptides (SAPs) are promising building blocks for supramolecular biomaterials. In this study, a self-assembling peptide Y15 was designed to induce intracellular clustering of target proteins and modulate their signaling functions. This innovative approach highlights the potential of genetically encoded SAPs in cell biology research.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Physics, Applied
Yucheng Zhang, Jinzhe Zhang, Kuniko Suzuki, Masato Sumita, Kei Terayama, Jiawen Li, Zetian Mao, Koji Tsuda, Yuji Suzuki
Summary: The research team designed a high-performance polymer electret material using a deep-learning-based molecule generator, identifying the importance of hydroxyl groups in enhancing electron gain energy and successfully creating a molecule with superior performance. The new material shows great potential for application in vibration-based energy harvesting.
APPLIED PHYSICS LETTERS
(2021)
Article
Microbiology
Hae-Jin Sohn, Jong-Hyun Kim, Kyongmin Kim, Sun Park, Ho-Joon Shin
Summary: Naegleria fowleri is a pathogenic amoeba commonly found in warm water and soil, and it can infect humans by entering the brain through the nose. Recent advances in genomics and bioinformatics have allowed for the identification of pathogen-related and environmental resistance in N. fowleri. Transcriptome sequencing revealed differential gene expression between trophozoites and cysts, providing new insights into the pathogenesis of N. fowleri.
Article
Forestry
Peng-Le Li, Mo-Hua Yang, Xiao-Long Jiang, Huan Xiong, Hui-Liang Duan, Feng-Lan Zou, Qian-Yu Xu, Wei Wang, Yong-Hui Hong, Neng-Qing Lin
Summary: This study used genotyping-by-sequencing to discover and genotype SNPs in 299 Masson pine trees. Filtering and validation of the results identified 20,055 precise and reliable SNPs. These SNPs were found to be informative for studying genetic diversity and structure, and have implications for genomic research and genomics-assisted breeding of Masson pine.
Article
Biochemistry & Molecular Biology
Devin Rocks, Ivana Jaric, Lydia Tesfa, John M. Greally, Masako Suzuki, Marija Kundakovic
Summary: ATAC-seq is a popular method in neuroscience research, offering advantages of requiring minimal material and capturing a variety of gene regulatory elements. Different freezing methods can impact the results but overall, ATAC-seq coupled with FANS generates consistent and robust data for studying neuronal chromatin accessibility.
Article
Genetics & Heredity
Nathaniel M. Pearson, Christian Stolte, Kevin Shi, Faygel Beren, Noura S. Abul-Husn, Gabrielle Bertier, Kaitlyn Brown, George A. Diaz, Jacqueline A. Odgis, Sabrina A. Suckiel, Carol R. Horowitz, Melissa Wasserstein, Bruce D. Gelb, Eimear E. Kenny, Charles Gagnon, Vaidehi Jobanputra, Toby Bloom, John M. Greally
Summary: GenomeDiver facilitates collaboration between clinicians and diagnostic laboratories by utilizing HPO terms to enrich structured phenotype data, ultimately improving the outcome of genomic diagnostic testing.
GENETICS IN MEDICINE
(2021)
Article
Nutrition & Dietetics
Masako Suzuki, Tao Wang, Diana Garretto, Carmen R. Isasi, Wellington V. Cardoso, John M. Greally, Loredana Quadro
Summary: The prevalence of vitamin A deficiency varies among different ethnic groups, potentially linked to single nucleotide polymorphism (SNP) allele frequencies associated with vitamin A metabolism. Significant differences were found in the VAD prevalence for Hispanic pregnant women between datasets. Genetic variants conferring risk for low retinol levels showed higher frequencies in populations with more VAD.
Article
Genetics & Heredity
Christelle Alexa Garcia Perez, Shungo Adachi, Quang Dang Nong, Nikko Adhitama, Tomoaki Matsuura, Toru Natsume, Tadashi Wada, Yasuhiko Kato, Hajime Watanabe, John M. Greally
Summary: Long noncoding RNAs (lncRNAs) are extensively transcribed and studied, but those overlapping with mRNA in the sense orientation have been less explored. We investigated the lncRNA DAPALR overlapping with the 5' UTR of the male determining gene Doublesex1 (Dsx1) in Daphnia magna. Through affinity purification, we identified an RNA binding protein, Shep, as a DAPALR binding protein. Shep binds to Dsx1 5' UTR by recognizing the overlapping sequence and suppresses mRNA translation. In vitro and in vivo analyses indicated that DAPALR enhances Dsx1 translation efficiency by sequestering Shep. This mechanism may play a significant role in displaying dimorphic gene expressions, such as sex determination, and could explain binary expression in various developmental processes.
Article
Oncology
Parvathi A. Myer, Jessica K. Lee, Russell W. Madison, Kith Pradhan, Justin Y. Newberg, Carmen R. Isasi, Samuel J. Klempner, Garrett M. Frampton, Jeffery S. Ross, Jeffrey M. Venstrom, Alexa B. Schrock, Sudipto Das, Leonard Augenlicht, Amit Verma, John M. Greally, Srilakshmi M. Raj, Sanjay Goel, Siraj M. Ali
Summary: Black people have a higher incidence and worse survival rates for colorectal cancer compared to white people. African descent patients have more frequent genetic alterations, particularly in KRAS, APC, and PIK3CA genes. In young-onset colorectal cancer, there are significant differences in APC mutations between African descent and European descent patients.
Article
Endocrinology & Metabolism
Kassidy Lundy, John F. Greally, Grace Essilfie-Bondzie, Josephine B. Olivier, Reanna Dona-Termine, John M. M. Greally, Masako Suzuki
Summary: Vitamin D plays a critical role in calcium homeostasis, the immune system, and normal development. Many global epidemiological studies have found high prevalence rates of vitamin D deficiency and insufficiency, particularly in reproductive age and pregnant women. This study using a mouse model found that prenatal vitamin D deficiency increases the occurrence of liver histopathological changes and alters gene expression profiles, potentially contributing to offspring health risks.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Genetics & Heredity
Jamie M. Ellingford, Joo Wook Ahn, Richard D. Bagnall, Diana Baralle, Stephanie Barton, Chris Campbell, Kate Downes, Sian Ellard, Celia Duff-Farrier, David R. FitzPatrick, John M. Greally, Jodie Ingles, Neesha Krishnan, Jenny Lord, Hilary C. Martin, William G. Newman, Anne O'Donnell-Luria, Simon C. Ramsden, Heidi L. Rehm, Ebony Richardson, Moriel Singer-Berk, Jenny C. Taylor, Maggie Williams, Jordan C. Wood, Caroline F. Wright, Steven M. Harrison, Nicola Whiffin
Summary: This article discusses genetic variants in non-coding regions and proposes guidelines for defining and interpreting these variants. The aim of these guidelines is to increase the number and range of non-coding region variants that can be clinically interpreted, leading to new diagnoses and the discovery of novel disease mechanisms.
Review
Hematology
Patricia A. Shi, Larry L. Luchsinger, John M. Greally, Colleen S. Delaney
Summary: This review discusses the decline in the use of umbilical cord blood (UCB) as a source of donor hematopoietic stem cells (HSC) for transplantation and emphasizes the potential of UCB and related birthing tissues for a wide range of therapies. When best practices are followed, UCB transplant can provide better survival and decreased risks compared to other donor sources. The review suggests that the potential of UCB for transplant and other cell-based therapies is undervalued and underutilized.
CURRENT OPINION IN HEMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Stacey R. McGee, Shivakumar Rajamanickam, Sandeep Adhikari, Oluwatosin C. Falayi, Theresa A. Wilson, Brian J. Shayota, Jessica A. Cooley Coleman, Cindy Skinner, Raymond C. Caylor, Roger E. Stevenson, Caio Robledo D' Angioli Costa Quaio, Berenice Cunha Wilke, Jennifer M. Bain, Kwame Anyane-Yeboa, Kaitlyn Brown, John M. Greally, Emilia K. Bijlsma, Claudia A. L. Ruivenkamp, Keren Politi, Lydia A. Arbogast, Michael W. Collard, Jodi Huggenvik, Sarah H. Elsea, Philip J. Jensik
Summary: De novo deleterious and heritable biallelic mutations in the DNA binding domain of DEAF1 result in a phenotypic spectrum of neurodevelopmental disorders, affecting genes involved in neuronal function and dendritic spine maintenance. This study expands the clinical spectrum of individuals with DEAF1-associated neurodevelopmental disorders, enhances our understanding of DEAF1's potential roles in neuronal function, and demonstrates the dominant negative activity of de novo variants.
HUMAN MOLECULAR GENETICS
(2023)
Article
Multidisciplinary Sciences
Netha Ulahannan, Ronald Cutler, Reanna Dona-Termine, Claudia A. Simoes-Pires, N. Ari Wijetunga, Matthew McKnight Croken, Andrew D. Johnston, Yu Kong, Shahina B. Maqbool, Masako Suzuki, John M. Greally
Summary: By studying the gene expression and chromatin states of human fibroblasts infected with Toxoplasma gondii, we gained insights into the molecular interactions between the intracellular pathogen and its host cell. We found that host cell genes were activated to regulate cellular processes, some of which were protective of the host cell while others were advantageous to the pathogen. Analysis of the host and parasite genomic information allowed us to annotate the T. gondii genome more accurately and discover new genes and cis-regulatory elements. By inferring the involved transcription factors and cell signaling responses in the host cell, we could understand how T. gondii perturbs host cell physiology.
Meeting Abstract
Hematology
Caner Saygin, Jacob Stauber, Ibrahim Aldoss, Adam S. Sperling, Lachelle D. Weeks, Marlise R. Luskin, Todd C. Knepper, Pankhuri Wanjari, Peng Wang, Angela Lager, Jeremy Segal, Benjamin Kaumeyer, Sandeep Gurbuxani, Girish Venkataraman, Jason Xiaojun Cheng, Bartholomew Eisfelder, Oliver Bohorquez, Anand Ashwin Patel, Olatoyosi Odenike, Richard A. Larson, Lucy A. Godley, Daniel A. Arber, Benjamin L. Ebert, John M. Greally, Ulrich G. Steidl, Bijal D. Shah, Wendy Stock
Article
Genetics & Heredity
Kevin M. Bowling, Michelle L. Thompson, Melissa A. Kelly, Sarah Scollon, Anne M. Slavotinek, Bradford C. Powell, Brian M. Kirmse, Laura G. Hendon, Kyle B. Brothers, Bruce R. Korf, Gregory M. Cooper, John M. Greally, Anna C. E. Hurst
Summary: The uptake of exome/genome sequencing has introduced challenges related to unexpected testing results, especially for pediatric patients, sparking debate on whether incidental findings should be returned. Identification and return of non-ACMG-recommended incidental findings in pediatric patients can be complex and difficult. While returning incidental genetic findings can benefit patients and providers, challenges and risks are also present.
Review
Genetics & Heredity
Julia J. Wattacheril, Srilakshmi Raj, David A. Knowles, John M. Greally
Summary: It is believed that environmental influences can affect gene expression by altering epigenetic regulators of transcription. These epigenetic changes can be maintained long term and through cell division, resulting in a prolonged effect of the exposure. The evidence supporting this model comes from the observation of changes in molecular regulators of transcription following exposures. However, this model may be oversimplistic, and further research is needed to fully understand the complex associations between environmental exposures and phenotypes.
Correction
Biotechnology & Applied Microbiology
Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W. Langhorst, V. K. Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M. Greally, Masako Suzuki, Mark Menor, Masaki Nasu, Alicia Alonso, Caroline Sheridan, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Agata Muszynska, Pawel P. Labaj, Matthew A. Campbell, Frank Wos, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Zhong Chen, Zhaowei Yang, Jing Li, Xiaopeng Yang, Hongwei Wang, Ari Melnick, Shang Guo, Alexander Blume, Vedran Franke, Inmaculada Ibanez de Caceres, Carlos Rodriguez-Antolin, Rocio Rosas, Justin Wade Davis, Jennifer Ishii, Dalila B. Megherbi, Wenming Xiao, Will Liao, Joshua Xu, Huixiao Hong, Baitang Ning, Weida Tong, Altuna Akalin, Yunliang Wang, Youping Deng, Christopher E. Mason
Article
Biotechnology & Applied Microbiology
Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W. Langhorst, V. K. Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M. Greally, Masako Suzuki, Mark Menor, Masaki Nasu, Alicia Alonso, Caroline Sheridan, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Agata Muszynska, Pawel P. Labaj, Matthew A. Campbell, Frank Wos, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Zhong Chen, Zhaowei Yang, Jing Li, Xiaopeng Yang, Hongwei Wang, Ari Melnick, Shang Guo, Alexander Blume, Vedran Franke, Inmaculada Ibanez de Caceres, Carlos Rodriguez-Antolin, Rocio Rosas, Justin Wade Davis, Jennifer Ishii, Dalila B. Megherbi, Wenming Xiao, Will Liao, Joshua Xu, Huixiao Hong, Baitang Ning, Weida Tong, Altuna Akalin, Yunliang Wang, Youping Deng, Christopher E. Mason
Summary: The study presents a multi-platform assessment and cross-validated resource for epigenetics research, showing overall high concordance between assays but also some differences. The data provided can guide the use of DNA reference materials in epigenomics research and offer best practices for future studies.
