Editorial Material
Chemistry, Multidisciplinary
Yingyu Liu, Yajun Wang
Summary: Amino-containing four-carbon threose nucleic acids (TNAs) have long been considered irrelevant to prebiotic chemistry due to their challenging formation process. However, a new prebiotically plausible method for synthesizing 3'-amino-TNA nucleoside triphosphate has been developed, suggesting the potential role of 3'-amino-TNA as a non-canonical nucleic acid in the origin of life.
Article
Engineering, Biomedical
Fei Wang, Ling Sum Liu, Pan Li, Cia Hin Lau, Hoi Man Leung, Y. Rebecca Chin, Chung Tin, Pik Kwan Lo
Summary: Compared with siRNAs or other ASOs, TNA has the advantages of chemical simplicity, DNA/RNA binding capability, folding ability of tertiary structure, and excellent physiological stability, which make it a promising tool in biomedical applications. This study investigates the pharmacokinetics and biosafety of TNAs in living organisms, finding that they exhibit excellent stability, low cytotoxicity, and substantial uptake in living cells without transfection. TNAs also show the ability to efficiently penetrate multicellular spheroids and can be safely administered in mice without causing pathological changes in the kidneys.
MATERIALS TODAY BIO
(2022)
Article
Medicine, Research & Experimental
YaGuang Han, Jun Wu, ZhenYu Gong, YiQin Zhou, HaoBo Li, Bo Wang, QiRong Qian
Summary: The study found that the immune score in OA samples was significantly higher than in normal samples. Through WGCNA, a co-expression module positively correlated with OA was identified, and 5 final hub genes were discovered. A diagnostic model based on these 5 genes showed good performance.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Lin Li, Kejia Kan, Prama Pallavi, Michael Keese
Summary: This study identified significant genes and regulatory mechanisms in patients with abdominal aortic aneurysm (AAA), and predicted potential therapeutic compounds for these genes. The findings provide new insights into potential AAA-related protein targets and compound predictions for two of these targets.
Article
Biochemistry & Molecular Biology
Florencia Haase, Brian S. Gloss, Patrick P. L. Tam, Wendy A. Gold
Summary: Rett Syndrome is an X linked neurodevelopmental disorder caused by mutations in the MECP2 gene, with symptoms typically appearing between 6 to 18 months of age. Recent studies have found subtle cellular and molecular changes in neural cells before symptoms onset, suggesting global translational dysregulation may start prior to neuronal lineage commitment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yongjun He, Zhaowei Wang, Haiyan Ge, Yang Liu, Huoying Chen
Summary: The study identified the key genes and pathways related to anthocyanin biosynthesis in eggplant through WGCNA analysis and highlighted the significant role of the hub gene SmWRKY44. Research showed that SmWRKY44 interacted with other key genes to promote anthocyanin biosynthesis.
Article
Biochemical Research Methods
Esau Medina, Eric J. Yik, Piet Herdewijn, John C. Chaput
Summary: XNA polymerases have great potential in synthetic biology, but little is known about their biochemical properties. This study compared various evolved polymerases and found that mutations for XNA synthesis increased substrate tolerance but could affect protein folding stability. Additionally, reverse transcriptase activity on different XNA substrates varied among polymerases. These findings can help in the development of new polymerase variants with improved activity and specificity.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Huijie Li, Yefeng Hu, Yongyong Zhang, Zheng Ma, Andreas Bechthold, Xiaoping Yu
Summary: In this study, a protein called RimR2 was identified as a positive regulator of rimocidin biosynthesis in Streptomyces rimosus M527. RimR2 plays a crucial role in the production of rimocidin by influencing the transcriptional levels of rim genes and binding to their promoter regions. Moreover, overexpression of the RimR2 gene leads to an increase in rimocidin production.
MICROBIAL CELL FACTORIES
(2023)
Article
Chemistry, Multidisciplinary
Ben W. F. Colville, Matthew W. Powner
Summary: The debate over the structure of life's first genetic polymer continues, with the RNA world theory proposing RNA as the first nucleic acid. However, simpler nucleic acids like TNA could also have carried genetic information. The study demonstrates a high-yielding, selective prebiotic synthesis of a key component of TNA, suggesting that TNA may have coexisted with RNA during the emergence of life.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Adriana Lozoya-Colinas, Yutong Yu, John C. Chaput
Summary: This study presents a single-round screening approach for aptamer discovery, using function-enhancing chemotypes to increase the distribution of high-affinity sequences in a random-sequence library. The study demonstrates the successful de novo discovery of aptamers against the receptor binding domain of the S1 protein from SARS-CoV-2, with binding affinity values comparable to those produced by conventional methods.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Alexis M. Ceasrine, Lauren A. Green, Staci D. Bilbo
Summary: Endotoxin accumulation has been widely observed in various diseases, and the use of limulus amebocyte lysate (LAL) assays for endotoxin detection has been the most reliable method. However, there is still a lack of optimized assays for detecting endotoxin in opaque tissues. This study optimized a sensitive Kinetic LAL assay for endotoxin detection in murine tissues.
Article
Biochemistry & Molecular Biology
Liping Tan, Rufei Gao, Xuemei Chen, Yanqing Geng, Xin Yin, Chuan Peng, Xinyi Mu, Yan Su, Yan Zhang, Fangfang Li, Junlin He
Summary: This study identified a novel lncRNA, RP24-315D19.10, that is highly expressed during endometrial decidualization. Knockdown of RP24-315D19.10 inhibited decidualization in mouse endometrial stromal cells. The study also found that RP24-315D19.10 regulates hnRNPA2B1, which may be a new marker for decidualization-related spontaneous abortion.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Article
Medicine, Research & Experimental
Liyu Yang, Jiamei Liu, Yuanqi Yu, Shengye Liu
Summary: This study aimed to identify autophagy-related markers for immunophenotyping in osteoarthritis (OA) using microarray expression profiling and autophagy database screening. A weighted gene co-expression network analysis (WGCNA) was performed to identify key modules associated with OA clinical information. Three autophagy hub genes (HSPA5, HSP90AA1, and ITPKB) were identified and their differential expression was validated. These markers may facilitate the diagnosis of OA and the design of immunotherapies and individualized medical treatments.
Article
Chemistry, Multidisciplinary
Fatemeh Seifikar, Saeid Azizian, Atefeh Nasri, Babak Jaleh
Summary: This study introduces a nanofluid without the disadvantages of instability and time-consuming preparation. Two colloidal systems of vanadium (V/PEG and V/H2O nanofluids) were synthesized and used in light-to-heat conversion. V/PEG is more stable and shows higher heat generation due to the different morphologies and sizes of vanadium nanoparticles.
JOURNAL OF INDUSTRIAL AND ENGINEERING CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Florencia Haase, Rachna Singh, Brian Gloss, Patrick Tam, Wendy Gold
Summary: Rett syndrome is a rare disorder that causes intellectual disabilities in females, primarily due to mutations in the MeCP2 gene. The molecular pathways from genotype to phenotype are not yet fully understood. Treatment options for Rett syndrome are limited, and there is a lack of common disease drivers, biomarkers, or therapeutic targets. In this study, a meta-analysis of transcriptomic studies identified a module of genes common to multiple datasets, with ten hub genes driving their expression. These genes have the potential to be therapeutic targets for Rett syndrome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Edward D. Barker, Alex Ing, Francesca Biondo, Tianye Jia, Jean-Baptiste Pingault, Ebba Du Rietz, Yuning Zhang, Barbara Ruggeri, Tobias Banaschewski, Sarah Hohmann, Arun L. W. Bokde, Uli Bromberg, Christian Buechel, Erin Burke Quinlan, Edmund Sounga-Barke, April B. Bowling, Sylvane Desrivieres, Herta Flor, Vincent Frouin, Hugh Garavan, Philip Asherson, Penny Gowland, Andreas Heinz, Bernd Ittermann, Jean-Luc Martinot, Marie-Laure Paillere Martinot, Frauke Nees, Dimitri Papadopoulos-Orfanos, Luise Poustka, Michael N. Smolka, Nora C. Vetter, Henrik Walter, Robert Whelan, Gunter Schumann
Summary: There is a clear link between ADHD, impulsivity features, and overweight/obesity, with neural and polygenic correlates playing a role in this association. The study found shared neural substrate associated with impulsivity symptoms, BMI, and their respective polygenic risk scores, indicating a common genetic liability for ADHD and BMI. Impulsivity symptoms and BMI were also mediated by neuroimaging substrate, revealing a potential underlying mechanism for their phenotypic association.
MOLECULAR PSYCHIATRY
(2021)
Article
Biology
Eilis Hannon, Emma L. Dempster, Georgina Mansell, Joe Burrage, Nick Bass, Marc M. Bohlken, Aiden Corvin, Charles J. Curtis, David Dempster, Marta Di Forti, Timothy G. Dinan, Gary Donohoe, Fiona Gaughran, Michael Gill, Amy Gillespie, Cerisse Gunasinghe, Hilleke E. Hulshoff, Christina M. Hultman, Viktoria Johansson, Rene S. Kahn, Jaakko Kaprio, Gunter Kenis, Kaarina Kowalec, James MacCabe, Colm McDonald, Andrew McQuillin, Derek W. Morris, Kieran C. Murphy, Colette J. Mustard, Igor Nenadic, Michael C. O'Donovan, Diego Quattrone, Alexander L. Richards, Bart Pf Rutten, David St Clair, Sebastian Therman, Timothea Toulopoulou, Jim Van Os, John L. Waddington, Patrick Sullivan, Evangelos Vassos, Gerome Breen, David Andrew Collier, Robin M. Murray, Leonard S. Schalkwyk, Jonathan Mill
Summary: The study identified differentially methylated positions (DMPs) in blood DNA methylation profiles associated with psychosis, schizophrenia, and treatment-resistant schizophrenia. Analysis across datasets revealed DMPs with evidence of colocalization to regions nominated by genetic association studies of the diseases. The findings suggest that DNA methylation data can serve as molecular biomarkers for treatment-resistant schizophrenia and reveal environmental factors associated with psychosis.
Article
Clinical Neurology
Le Zhang, Ebba Du Rietz, Ralf Kuja-Halkola, Maja Dobrosavljevic, Kristina Johnell, Nancy L. Pedersen, Henrik Larsson, Zheng Chang
Summary: The study found an intergenerational association between attention-deficit/hyperactivity disorder (ADHD) and Alzheimer's disease (AD) and other forms of dementia and neurodegenerative diseases, with the association weakening with decreasing genetic relatedness.
ALZHEIMERS & DEMENTIA
(2022)
Article
Biotechnology & Applied Microbiology
Yucheng Wang, Eilis Hannon, Olivia A. Grant, Tyler J. Gorrie-Stone, Meena Kumari, Jonathan Mill, Xiaojun Zhai, Klaus D. McDonald-Maier, Leonard C. Schalkwyk
Summary: A novel method for predicting sex using DNA methylation beta values was presented, which can be applied to various formats of DNA methylation datasets. The sex classifier based on sex-associated CpG sites demonstrates good performance across different tissues and can be used to identify samples with sex chromosome aneuploidy.
Article
Genetics & Heredity
Josine L. Min, Gibran Hemani, Eilis Hannon, Koen F. Dekkers, Juan Castillo-Fernandez, Rene Luijk, Elena Carnero-Montoro, Daniel J. Lawson, Kimberley Burrows, Matthew Suderman, Andrew D. Bretherick, Tom G. Richardson, Johanna Klughammer, Valentina Iotchkova, Gemma Sharp, Ahmad Al Khleifat, Aleksey Shatunov, Alfredo Iacoangeli, Wendy L. McArdle, Karen M. Ho, Ashish Kumar, Cilia Soderhall, Carolina Soriano-Tarraga, Eva Giralt-Steinhauer, Nabila Kazmi, Dan Mason, Allan F. McRae, David L. Corcoran, Karen Sugden, Silva Kasela, Alexia Cardona, Felix R. Day, Giovanni Cugliari, Clara Viberti, Simonetta Guarrera, Michael Lerro, Richa Gupta, Sailalitha Bollepalli, Pooja Mandaviya, Yanni Zeng, Toni-Kim Clarke, Rosie M. Walker, Vanessa Schmoll, Darina Czamara, Carlos Ruiz-Arenas, Faisal Rezwan, Riccardo E. Marioni, Tian Lin, Yvonne Awaloff, Marine Germain, Dylan Aissi, Ramona Zwamborn, Kristel van Eijk, Annelot Dekker, Jenny van Dongen, Jouke-Jan Hottenga, Gonneke Willemsen, Cheng-Jian Xu, Guillermo Barturen, Francesc Catala-Moll, Martin Kerick, Carol Wang, Phillip Melton, Hannah R. Elliott, Jean Shin, Manon Bernard, Idil Yet, Melissa Smarts, Tyler Gorrie-Stone, Chris Shaw, Ammar Al Chalabi, Susan M. Ring, Goran Pershagen, Erik Melen, Jordi Jimenez-Conde, Jaume Roquer, Deborah A. Lawlor, John Wright, Nicholas G. Martin, Grant W. Montgomery, Terrie E. Moffitt, Richie Poulton, Tonu Esko, Lili Milani, Andres Metspalu, John R. B. Perry, Ken K. Ong, Nicholas J. Wareham, Giuseppe Matullo, Carlotta Sacerdote, Salvatore Panico, Avshalom Caspi, Louise Arseneault, France Gagnon, Miina Ollikainen, Jaakko Kaprio, Janine F. Felix, Fernando Rivadeneira, Henning Tiemeier, Marinus H. van IJzendoorn, Andre G. Uitterlinden, Vincent W. V. Jaddoe, Chris Hale, Andrew M. McIntosh, Kathryn L. Evans, Alison Murray, Katri Raikkonen, Jari Lahti, Ellen A. Nohr, Thorkild I. A. Sorensen, Torben Hansen, Camilla S. Morgen, Elisabeth B. Binder, Susanne Lucae, Juan Ramon Gonzalez, Mariona Bustamante, Jordi Sunyer, John W. Holloway, Wilfried Karmaus, Hongmei Zhang, Ian J. Deary, Naomi R. Wray, John M. Starr, Marian Beekman, Diana VanHeemst, P. Eline Slagboom, Pierre-Emmanuel Morange, David-Alexandre Tregouet, Jan H. Veldink, Gareth E. Davies, Eco J. C. de Geus, Dorret Boomsma, Judith M. Vonk, Bert Brunekreef, Gerard H. Koppelman, Marta E. Alarcon-Riquelme, Rae-Chi Huang, Craig E. Pennell, Joyce van Meurs, M. Arfan Ikram, Alun D. Hughes, Therese Tillin, Nish Chaturvedi, Zdenka Pausova, Tomas Paus, Timothy D. Spector, Meena Kumari, Leonard C. Schalkwyk, Peter M. Visscher, George Davey Smith, Christoph Bock, Tom R. Gaunt, Jordana T. Bell, Bastiaan T. Heijmans, Jonathan Mill, Caroline L. Relton
Summary: In this study, DNA methylation quantitative trait locus (mQTL) analyses were conducted on 32,851 participants, revealing genetic variants associated with DNA methylation at 420,509 sites in blood and generating a database of over 270,000 independent mQTLs. The genetic architecture of DNA methylation levels was shown to be highly polygenic, with some genetic variants linked to both DNA methylation levels and complex diseases, indicating a complex genotype-phenotype map.
Article
Pediatrics
Bezawit E. Kase, Nanda Rommelse, Qi Chen, Lin Li, Anneli Andersson, Ebba Du Rietz, Melissa Vos, Samuele Cortese, Henrik Larsson, Catharina A. Hartman
Summary: This study found a stable link between ADHD symptoms and BMI during adolescence, primarily with hyperactive and impulsive symptoms rather than inattention. No direct effects were found between ADHD symptoms and BMI increase or enhanced ADHD symptoms due to BMI during this period.
Article
Psychiatry
Maja Dobrosavljevic, Le Zhang, Miguel Garcia-Argibay, Ebba Du Rietz, Henrik Andershed, Zheng Chang, Stephen Faraone, Henrik Larsson
Summary: Previous research has shown that there is an association between ADHD and an increased risk for dementia and MCI, particularly stronger in men. The association significantly attenuates after controlling for psychiatric disorders such as depression, anxiety, substance use disorder, and bipolar disorder.
EUROPEAN PSYCHIATRY
(2021)
Article
Biochemistry & Molecular Biology
Robert Flynn, Sam Washer, Aaron R. Jeffries, Alexandria Andrayas, Gemma Shireby, Meena Kumari, Leonard C. Schalkwyk, Jonathan Mill, Eilis Hannon
Summary: Most epigenetic epidemiology studies have used microarrays, which only cover less than 3% of DNA methylation sites. Nanopore sequencing has the potential to provide genuine genome-wide coverage and profile epigenetic modifications directly from native DNA. This study demonstrates the viability of using Nanopore sequencing in epidemiology and its potential to advance our understanding of complex diseases.
HUMAN MOLECULAR GENETICS
(2022)
Article
Oncology
Olivia A. Grant, Yucheng Wang, Meena Kumari, Nicolae Radu Zabet, Leonard Schalkwyk
Summary: This study analyzed for the first time the autosomal sex differences in DNA methylation using human whole blood samples. The researchers identified and validated 396 sex-associated differentially methylated CpG sites, with the majority being female-biased CpGs. They also discovered 266 significant sex-associated differentially methylated regions overlapping genes, including novel genes.
CLINICAL EPIGENETICS
(2022)
Article
Psychiatry
Miguel Garcia-Argibay, Ebba du Rietz, Yi Lu, Joanna Martin, Elis Haan, Kelli Letho, Sarah E. Bergen, Paul Lichtenstein, Henrik Larsson, Isabell Brikell
Summary: Growing evidence suggests that ADHD is associated with poor somatic health in adulthood, but the mechanisms underlying these associations are poorly understood. This study found that ADHD polygenic risk scores (PRS) are associated with multiple somatic health problems in mid-to-late life, particularly in the cardiometabolic domain. These associations were observed in the general population and appear to be partially mediated by life-course risk factors.
TRANSLATIONAL PSYCHIATRY
(2022)
Article
Biochemical Research Methods
Yucheng Wang, Tyler J. Gorrie-Stone, Olivia A. Grant, Alexandria D. Andrayas, Xiaojun Zhai, Klaus D. McDonald-Maier, Leonard C. Schalkwyk
Summary: This article presents a new two-step strategy to address the bias issue in normalizing sex chromosome data, and proposes a concept to quantitatively measure the normalization effect. The method can be applied to all quantile-based and non-quantile-based normalization methods, as well as other array-based data types.
Article
Psychiatry
Miguel Garcia-Argibay, Ebba Du Rietz, Catharina A. Hartman, Paul Lichtenstein, Zheng Chang, Cristiano Fava, Samuele Cortese, Henrik Larsson
Summary: This study found that there is an association between cardiovascular risk factors and ADHD, and this association is not influenced by medication treatment for ADHD, but is partly due to shared familial risk factors.
INTERNATIONAL JOURNAL OF METHODS IN PSYCHIATRIC RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Dorothea Seiler Vellame, Gemma Shireby, Ailsa MacCalman, Emma L. Dempster, Joe Burrage, Tyler Gorrie-Stone, Leonard S. Schalkwyk, Jonathan Mill, Eilis Hannon
Summary: Most epigenetic epidemiology studies have used bulk tissues for genome-wide profiling, but these can be confounded by variation in cellular composition. In this study, researchers developed a metric called CETYGO score to assess the accuracy of derived cellular heterogeneity variables. They found that the CETYGO score can distinguish inaccurate deconvolutions when applied to whole blood profiles. The study also revealed that estimating accurate cellular composition is influenced by technical and biological factors, such as gender, age, and smoking status.
Article
Multidisciplinary Sciences
Yanchun Bao, Tyler Gorrie-Stone, Eilis Hannon, Amanda Hughes, Alexandria Andrayas, Grant Neilson, Joe Burrage, Jonathon Mill, Leonard Schalkwyk, Meena Kumari
Summary: This study investigated the relationship between social mobility and positive age acceleration. The findings showed that disadvantaged socioeconomic position in early life was associated with positive age acceleration for three out of the four measures examined. Social mobility was only associated with age acceleration measured by Hannum, and upward mobility was associated with greater age independent of socioeconomic position. Downward mobility was associated with positive age acceleration for two measures, while upward mobility was associated with negative age acceleration compared to continually disadvantaged groups. The study suggests that disadvantaged socioeconomic position across the lifecourse is consistently related to positive age acceleration.
SCIENTIFIC REPORTS
(2022)
Article
Endocrinology & Metabolism
Matthew Devall, Darren M. Soanes, Adam R. Smith, Emma L. Dempster, Rebecca G. Smith, Joe Burrage, Artemis Iatrou, Eilis Hannon, Claire Troakes, Karen Moore, Paul O'Neill, Safa Al-Sarraj, Leonard Schalkwyk, Jonathan Mill, Michael Weedon, Katie Lunnon
Summary: This study presents a novel approach to investigate the patterns of mitochondrial DNA methylation in human brain tissue. The results show relatively low but conserved patterns of mitochondrial DNA methylation, with peaks observed in the D-LOOP and several genes in a non-CpG context. Differential methylation patterns associated with age, sex, and brain region were also identified. This study provides detailed annotation of DNA methylation in the mitochondrial genome and highlights the potential role of mitochondrial epigenetic mechanisms in disorders characterized by mitochondrial dysfunction.
FRONTIERS IN ENDOCRINOLOGY
(2023)