Article
Genetics & Heredity
Tingyi Cao, Marcella E. O'Reilly, Caitlin Selvaggi, Esther Cynn, Heidi Lumish, Chenyi Xue, Anjali Jha, Muredach P. Reilly, Andrea S. Foulkes
Summary: The genetically regulated expression of non-conserved lincRNAs shows similar rates of association with complex cardiometabolic traits as conserved lincRNAs, challenging the conventional notion of conservation and highlighting the need for comprehensive strategies to study non-conserved lincRNAs in human disease.
JOURNAL OF HUMAN GENETICS
(2022)
Article
Genetics & Heredity
Neta Degani, Yoav Lubelsky, Rotem Ben-Tov Perry, Elena Ainbinder, Igor Ulitsky
Summary: The highly conserved lncRNAs HOXA-AS3 and HOXB-AS3, transcribed antisense to Hox protein-coding genes, play a role in regulating gene expression in the endoderm lineage and during differentiation of human embryonic stem cells. Their expression patterns are similar across vertebrates, suggesting a potential impact on embryonic development in humans.
Article
Biochemistry & Molecular Biology
Rhondene Wint, Asaf Salamov, Igor Grigoriev
Summary: Protein-coding genes have evolved a preference for codon usage as a result of both adaptive and nonadaptive influences. Comparative genomics analysis of over 450 species suggests that codon usage and tRNAs are coadapted for translation speed, likely a form of convergent evolution. Phylogenetic reconstruction indicates that adaptive radiation is a better explanation for the variation in interspecific codon usage bias than genetic drift.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Cell Biology
Anthony Beucher, Irene Miguel-Escalada, Diego Balboa, Matias G. De Vas, Miguel Angel Maestro, Javier Garcia-Hurtado, Aina Bernal, Roser Gonzalez-Franco, Pierfrancesco Vargiu, Holger Heyn, Philippe Ravassard, Sagrario Ortega, Jorge Ferrer
Summary: This study reveals that HASTER plays a role in maintaining the normal concentration of HNF1A through positive and negative feedback loops. Mutations in Haster lead to silencing or overexpression of HNF1A in pancreatic beta cells, resulting in hyperglycemia. The HASTER-dependent negative feedback is essential for preventing inappropriate binding of HNF1A to genomic regions.
NATURE CELL BIOLOGY
(2022)
Article
Entomology
Xiao-Qing Hou, Zhongqiang Jia, Dan-Dan Zhang, Guirong Wang
Summary: Insects' odorant receptor (OR) multigene family evolves through the birth-and-death evolutionary model. The ORs in moths are genetically conserved across species and specifically respond to cis-jasmone. These findings suggest the high conservation of OR for ecologically important compounds in Heterocera.
Article
Multidisciplinary Sciences
Yu H. Sun, Anqi Wang, Chi Song, Goutham Shankar, Rajesh K. Srivastava, Kin Fai Au, Xin Zhiguo Li
Summary: This study successfully identified thousands of intact RNA species in mouse and human sperm, including both mRNAs and long non-coding RNAs, using single molecule long-read sequencing. These spiRNAs show evolutionary conservation between mice and humans.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Toshiyuki Imaizumi, Kaworu Ebana, Yoshihiro Kawahara, Chiaki Muto, Hiroyuki Kobayashi, Akira Koarai, Kenneth M. Olsen
Summary: The study explores the origin and adaptation mechanism of Japanese weedy rice through whole-genome sequence analysis, revealing different genetic mechanisms between weed types and the importance of hybridization between weedy and cultivated rice in weedy rice evolution. Hybridization with cultivated rice not only confers crop-like adaptive traits but also weedy-like traits to weedy rice, promoting its persistence and proliferation.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Guilian Xiao, Junzhi Zhou, Zhiheng Huo, Tong Wu, Yingchun Li, Yajing Li, Yanxia Wang, Mengcheng Wang
Summary: The domestication of rice is accompanied by genomic variation, including synonymous codon usage bias (SCUB). SCUB characteristics differ between cultivated and wild rice, and the differences become more significant with the increase in exon numbers. Studying the differences in SCUB frequencies can provide insight into the possible association between genomic and epigenetic variation during rice domestication.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Swapnil C. Devarkar, Michael Vetick, Shravani Balaji, Ivan B. Lomakin, Luojia Yang, Danni Jin, Wendy V. Gilbert, Sidi Chen, Yong Xiong
Summary: Research has found that MERS-CoV Nsp1 directly interacts with the 40S ribosomal subunit to restrict host gene expression through translation inhibition. The extensive interactions between MERS-CoV Nsp1 and the mRNA entry channel of the 40S ribosomal subunit are critical for its translation inhibition function, and this mechanism is strikingly similar to SARS-CoV and SARS-CoV-2 Nsp1.
Article
Multidisciplinary Sciences
Jose M. G. Vilar, Leonor Saiz
Summary: The prevalent one-dimensional alignment of genomic signals to a reference landmark is prone to mask potential relations among multiple DNA elements. We developed a systematic approach to align genomic signals to multiple locations simultaneously by expanding the dimensionality of the genomic-coordinate space. Our results reveal a conserved hierarchy of alternative TSS usage within a previously unrecognized level of genomic organization and provide a general methodology to analyze complex functional relationships among multiple types of DNA elements.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Huilin Hong, Zhiguang Zhao, Xiahe Huang, Chao Guo, Hui Zhao, Guo-Dong Wang, Ya-Ping Zhang, Jian-Ping Zhao, Jianhui Shi, Qing-Feng Wu, Yong-Hui Jiang, Yingchun Wang, Lei M. Li, Zhuo Du, Yong Q. Zhang, Ying Xiong
Summary: This study analyzed proteomes from six regions of the postnatal brain at three developmental stages of domestic dogs, revealing the correlation between myelination and hippocampus-related proteins in dogs and humans. The global expression patterns of disease-associated proteins in the brain of dogs resemble those in humans more than in mice. These findings provide insights into brain development and function, and can guide mechanistic and translational research using appropriate animal models.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Oncology
Ali S. Ropri, Rebecca S. DeVaux, Jonah Eng, Sridar Chittur, Jason Herschkowitz
Summary: Increased breast cancer screening has led to a rise in DCIS diagnosis, emphasizing the need to identify factors influencing DCIS progression to IDC. SE-lncRNAs, which can regulate nearby gene expression, represent novel therapeutic targets. Integrative analysis and cross-referencing with databases revealed differential expression of SE-lncRNAs and alterations in super-enhancers associated with breast cancer progression.
BREAST CANCER RESEARCH
(2021)
Article
Microbiology
Zhonghua Liu, Shriya Raj, Norman van Rhijn, Marcin Fraczek, Jean-Philippe Michel, Odile Sismeiro, Rachel Legendre, Hugo Varet, Thierry Fontaine, Michael Bromley, Jean-Paul Latge
Summary: The study explores the inhibition of fungal growth by Congo red and the discovery of Quasimodo cells in resistant mutants that facilitate the absorption of the drug and promote the growth of remaining fungi. It also reveals a novel drug-induced growth stimulation effect after long-term exposure to Congo red.
Article
Multidisciplinary Sciences
Kate Megquier, Jason Turner-Maier, Kathleen Morrill, Xue Li, Jeremy Johnson, Elinor K. Karlsson, Cheryl A. London, Heather L. Gardner
Summary: The whole genome characterization of canine osteosarcoma cell lines reveals that many alterations previously characterized in primary canine osteosarcoma tissue are also present in these cell lines. This provides a new framework for incorporating in vitro findings into the design of future clinical studies on spontaneous canine osteosarcoma.
Article
Genetics & Heredity
Chenkang Yang, Qi Zhao, Ying Wang, Jiajia Zhao, Ling Qiao, Bangbang Wu, Suxian Yan, Jun Zheng, Xingwei Zheng
Summary: The usage of synonymous codons varies among different organisms, with a bias towards G/C-ending codons observed in hexaploid wheat compared to its progenitor species. Mutation has a limited effect on codon usage, with selection playing a larger role in shaping the preferences. High GC content, gene length, chromosomal distribution density, and tRNA abundance all influence codon usage in these species. Gene Ontology enrichment analysis reveals that genes with GC bias are enriched in physiological processes, such as photosynthesis and response to acid chemical in hexaploid wheat. Additionally, certain gene families in hexaploid wheat show changes in codon usage during evolution.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Julia R. Gog, Andrew M. L. Lever, Jordan P. Skittrall
Article
Infectious Diseases
Petra Klepac, Stephen Kissler, Julia Gog
Article
Multidisciplinary Sciences
Benjamin D. Dalziel, Stephen Kissler, Julia R. Gog, Cecile Viboud, Ottar N. Bjornstad, C. Jessica E. Metcalf, Bryan T. Grenfell
Article
Infectious Diseases
Stephen M. Kissler, Julia R. Gog, Cecile Viboud, Vivek Charu, Ottar N. Bjornstad, Lone Simonsen, Bryan T. Grenfell
Article
Biochemical Research Methods
Jordan P. Skittrall, Carin K. Ingemarsdotter, Julia R. Gog, Andrew M. L. Lever
PLOS COMPUTATIONAL BIOLOGY
(2019)
Editorial Material
Ecology
Viggo Andreasen, Julia R. Gog
THEORETICAL POPULATION BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Stephen M. Kissler, Cecile Viboud, Bryan T. Grenfell, Julia R. Gog
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2020)
Article
Infectious Diseases
Adam J. Kucharski, Petra Klepac, Andrew J. K. Conlan, Stephen M. Kissler, Maria L. Tang, Hannah Fry, Julia R. Gog, W. John Edmunds
LANCET INFECTIOUS DISEASES
(2020)
Article
Biology
Robin N. Thompson, T. Deirdre Hollingsworth, Valerie Isham, Daniel Arribas-Bel, Ben Ashby, Tom Britton, Peter Challenor, Lauren H. K. Chappell, Hannah Clapham, Nik J. Cunniffe, A. Philip Dawid, Christl A. Donnelly, Rosalind M. Eggo, Sebastian Funk, Nigel Gilbert, Paul Glendinning, Julia R. Gog, William S. Hart, Hans Heesterbeek, Thomas House, Matt Keeling, Istvan Z. Kiss, Mirjam E. Kretzschmar, Alun L. Lloyd, Emma S. McBryde, James M. McCaw, Trevelyan J. McKinley, Joel C. Miller, Martina Morris, Philip D. O'Neill, Kris Parag, Carl A. B. Pearson, Lorenzo Pellis, Juliet R. C. Pulliam, Joshua Ross, Gianpaolo Scalia Tomba, Bernard W. Silverman, Claudio J. Struchiner, Michael J. Tildesley, Pieter Trapman, Cerian R. Webb, Denis Mollison, Olivier Restif
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Letter
Infectious Diseases
Robin N. Thompson, Edward M. Hill, Julia R. Gog
LANCET INFECTIOUS DISEASES
(2021)
Article
Biology
Tim C. D. Lucas, Emma L. Davis, Diepreye Ayabina, Anna Borlase, Thomas Crellen, Li Pi, Graham F. Medley, Lucy Yardley, Petra Klepac, Julia Gog, T. Deirdre Hollingsworth
Summary: Contact tracing is crucial for easing lockdown policies, but strict self-isolation measures may deter self-reporting, leading to potential risks of large outbreaks. Policies to increase self-isolation adherence should be implemented carefully to avoid reducing self-reporting rates.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biology
Julia R. Gog, T. Deirdre Hollingsworth
Summary: Analytical expressions and approximations from simple models have played a crucial role in understanding infectious disease epidemiology during the COVID-19 pandemic. Basic models continue to provide a core framework for our thinking and policy decisions, offering valuable benchmarks for comparison with outputs of more complex modelling approaches.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Jessica Enright, Edward M. Hill, Helena B. Stage, Kirsty J. Bolton, Emily J. Nixon, Emma L. Fairbanks, Maria L. Tang, Ellen Brooks-Pollock, Louise Dyson, Chris J. Budd, Rebecca B. Hoyle, Lars Schewe, Julia R. Gog, Michael J. Tildesley
Summary: The study found that university outbreaks in late 2020 were consistent with infections brought by arriving students. In terms of control measures, student adherence to testing and self-isolation was deemed more important than staggering the return of students to reduce transmission. In the context of a more transmissible variant, frequent testing would be necessary to prevent a major outbreak.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Multidisciplinary Sciences
Julia R. Gog, Edward M. Hill, Leon Danon, Robin N. Thompson
Summary: As vaccination programs against the SARS-CoV-2 pandemic roll out, there is a concern that they may exert selection pressure on the virus, potentially leading to vaccine escape. Careful targeting of vaccines towards specific population groups could effectively reduce disease transmission while minimizing the risk of vaccine escape.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Health Care Sciences & Services
Carolin Vegvari, Sam Abbott, Frank Ball, Ellen Brooks-Pollock, Robert Challen, Benjamin S. Collyer, Ciara Dangerfield, Julia R. Gog, Katelyn M. Gostic, Jane M. Heffernan, T. Deirdre Hollingsworth, Valerie Isham, Eben Kenah, Denis Mollison, Jasmina Panovska-Griffiths, Lorenzo Pellis, Michael G. Roberts, Gianpaolo Scalia Tomba, Robin N. Thompson, Pieter Trapman
Summary: The reproduction number R has become a popular epidemiological metric during the COVID-19 pandemic, but its interpretation and estimation can vary significantly depending on the definition and statistical methods used. The availability and type of data also play a crucial role in estimating R accurately. Careful consideration and analysis are required when using R as an indicator for managing the epidemic effectively.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2022)