Article
Endocrinology & Metabolism
Manuela Wuelling, Christoph Neu, Andrea M. Thiesen, Simo Kitanovski, Yingying Cao, Anja Lange, Astrid M. Westendorf, Daniel Hoffmann, Andrea Vortkamp
Summary: Research has shown that specific differentiation steps during endochondral ossification are regulated by specific epigenetic modifications. Differences in gene expression and enhancer profiles between cell types are significant, with metabolic pathways playing a key role in cell differentiation.
JOURNAL OF BONE AND MINERAL RESEARCH
(2021)
Review
Plant Sciences
Samir C. Debnath, Amrita Ghosh
Summary: This review provides an in-depth study on various aspects of phenotypic variation in micropropagated berry plants and the epigenetic effects on these variations along with the role of DNA methylation, to fill the existing gap in literature.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Daniel Richard, Terence D. Capellini
Summary: This paper discusses the effects of epigenetic changes on gene regulation during aging, emphasizing their impact on disease pathomechanism. The study found that developmental epigenetic changes have less influence on genetic risk associations, while variants with increased local accessibility in adult tissues have stronger effects, especially in young adults compared to the elderly.
Article
Cell Biology
Marta Marchini, Mitchell R. Ashkin, Melina Bellini, Margaret Man-Ger Sun, Matthew Lloyd Workentine, Hamza Malik Okuyan, Roman Krawetz, Frank Beier, Campbell Rolian
Summary: The genetic and developmental mechanisms of limb formation are well understood, but how chondrocyte physiology modulates these mechanisms to produce differences in limb bone length is unclear. Through RNA sequencing and cell culture experiments, it was found that NKA plays a key role in chondrocyte differentiation and regulation of bone length, with implications for limb length diversity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Thanvi Srikant, Anjar Tri Wibowo
Summary: This article focuses on epiallelic variations in plants, particularly on methylated regions. It is still uncertain whether variations at individual methylated cytosines serve any regulatory function. Most epialleles in the form of methylated regions have not been assigned any biological function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Raquel Garcia-Perez, Paula Esteller-Cucala, Gloria Mas, Irene Lobon, Valerio Di Carlo, Meritxell Riera, Martin Kuhlwilm, Arcadi Navarro, Antoine Blancher, Luciano Di Croce, Jose Luis Gomez-Skarmeta, David Juan, Tomas Marques-Bonet
Summary: This study highlights the importance of epigenetic regulation in gene expression evolution across primates. The research reveals that epigenetic conservation in primates is dependent on the activity state of regulatory elements, with most changes occurring in weakly active elements. Human-specific regulatory elements with weak activities are enriched in genes associated with human adaptation, suggesting their role in recent human evolution.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Yanjie Hou, Xianquan Qin, Hongye Qiu, Dongbo Li, Ning Xu, Shuwei Zhang, Chen Fang, Hongli Li
Summary: Litchi is an important commercial fruit crop, but graft incompatibility is a major obstacle for its large-scale cultivation. This study analyzed the metabolic and transcriptomic differences between graft compatible and incompatible rootstock-scion combinations of litchi. The results provide insights into the molecular mechanism of graft incompatibility in litchi.
FRONTIERS IN GENETICS
(2023)
Review
Environmental Sciences
Fernando Uriel Rojas-Rojas, Julio C. Vega-Arreguin
Summary: The article discusses the adaptive lifestyle and molecular mechanisms of the phytopathogenic genus Phytophthora in different hosts and environmental changes, emphasizing the potential role of chromatin covalent modifications in this process.
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Magdalena Ewa Pawelkowicz, Agnieszka Skarzynska, Tomasz Mroz, Estelle Bystrzycki, Wojciech Plader
Summary: The research analyzed the fruit transcriptome of three independent cucumber lines using RNA-sequencing technology and found that somaclonal variation altered the expression of key genes, likely due to polymorphism in genic regions and interactions among molecular networks.
PLANT CELL TISSUE AND ORGAN CULTURE
(2021)
Article
Multidisciplinary Sciences
Sarah Rubin, Ankit Agrawal, Johannes Stegmaier, Sharon Krief, Neta Felsenthal, Jonathan Svorai, Yoseph Addadi, Paul Villoutreix, Tomer Stern, Elazar Zelzer
Summary: The 3D MAPs pipeline allows for the characterization of morphogenetic behaviors of chondrocytes while retaining spatial context, aiding in the study of bone development. The analysis revealed a wide range of morphological changes, growth strategies, and cell organizations in bones, as well as abnormalities in Gdf5 KO tibias, providing insights into cellular mechanisms regulating the differentiation process.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Xin Wu, Neharika Bhatia, Christina M. Grozinger, Soojin Yi
Summary: Different genomic features have varying effects on gene expression variability. Highly expressed genes tend to have less expression variability, while genes with TATA box tend to have increased expression variability. DNA methylation of transcriptional units is associated with reduced gene expression variability, except in certain insect lineages like Drosophila melanogaster. Our analysis of large-scale data sets in D. melanogaster and honey bee shows that increased gene expression levels and the presence of TATA box consistently influence gene expression variability in both species, while gene body DNA methylation has a negative association with gene expression variability only in honey bees.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Magdalena Ewa Pawelkowicz, Agnieszka Skarzynska, Marek Daniel Koter, Szymon Turek, Wojciech Plader
Summary: This study investigates the potential role of miRNAs in the multi-omics regulatory pathways in cucumber somaclonal lines. It suggests that miRNAs may indirectly influence molecular networks and contribute to somaclonal variation in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
B. Zhou, T. R. Stueve, E. A. Mihalakakos, L. Miao, D. Mullen, Y. Wang, Y. Liu, J. Luo, E. Tran, K. D. Siegmund, S. K. Lynch, A. L. Ryan, I. A. Offringa, Z. Borok, C. N. Marconett
Summary: This study comprehensively profiles the epigenomic alterations in enhancer regions during AEC differentiation, and reveals that the differentiation process is regulated by dynamic networks of transcription factors acting in concert, rather than individually. The findings provide insight into the relationship between disruption of the epigenetic state during AEC differentiation and development of lung diseases, potentially offering therapeutic strategies.
Article
Optics
Wonjun Bae, Yangjin Kim, Young Hoon Moon, Kenichi Hibino, Naohiko Sugita, Mamoru Mitsuishi
Summary: In this study, two 19-frame phase extraction formulas were derived to simultaneously measure the thickness variation and surface profile of glass plates, effectively eliminating offset phase errors. The Fourier description in the frequency domain was utilized to visualize the new formulas, and numerical error analysis confirmed their ability to eliminate offset errors. Using these new formulas with a large-aperture Fizeau interferometer, the standard deviations for thickness variation and surface profiling were lower compared to other phase extraction methods.
OPTICS COMMUNICATIONS
(2021)
Article
Plant Sciences
Amandeep Kaur, Kashmir Singh, Santosh Kumar Upadhyay
Summary: This study identified 14 TaAAO genes in the bread wheat genome and found that these genes play important roles in growth, development, phytohormone responses, light responses, and stress responses. Most TaAAOs showed higher expression in roots and were upregulated under salt stress. Some genes also showed modulated expression in other tissues and under heat stress, drought stress, and fungal infestations. The interaction of TaAAO proteins with antioxidant enzymes and related molecules revealed their synchronized functioning in redox homeostasis.
PLANT GROWTH REGULATION
(2023)
Article
Genetics & Heredity
Michael H. Guo, Anthony R. Gregg
GENETICS IN MEDICINE
(2019)
Article
Multidisciplinary Sciences
Karolina Kania, Fabio Colella, Anna H. K. Riemen, Hui Wang, Kenneth A. Howard, Thomas Aigner, Francesco Dell'Accio, Terence D. Capellini, Anke J. Roelofs, Cosimo De Bari
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Daniel Richard, Zun Liu, Jiaxue Cao, Ata M. Kiapour, Jessica Willen, Siddharth Yarlagadda, Evelyn Jagoda, Vijaya B. Kolachalama, Jakob T. Sieker, Gary H. Chang, Pushpanathan Muthuirulan, Mariel Young, Anand Masson, Johannes Konrad, Shayan Hosseinzadeh, David E. Maridas, Vicki Rosen, Roman Krawetz, Neil Roach, Terence D. Capellini
Article
Multidisciplinary Sciences
Arinjay Banerjee, Nader El-Sayes, Patrick Budylowski, Rajesh Abraham Jacob, Daniel Richard, Hassaan Maan, Jennifer A. Aguiar, Wael L. Demian, Kaushal Baid, Michael R. D'Agostino, Jann Catherine Ang, Tetyana Murdza, Benjamin J-M Tremblay, Sam Afkhami, Mehran Karimzadeh, Aaron T. Irving, Lily Yip, Mario Ostrowski, Jeremy A. Hirota, Robert Kozak, Terence D. Capellini, Matthew S. Miller, Bo Wang, Samira Mubareka, Allison J. McGeer, Andrew G. McArthur, Andrew C. Doxey, Karen Mossman
Summary: Recent studies have shown that SARS-CoV-2 proteins can inhibit human type I interferon responses, and the timing and extent of interferon production are associated with COVID-19 severity. SARS-CoV-2 infection induces a type I interferon response in vitro and in moderate cases of COVID-19, with physiological levels of IFNa being sufficient to suppress SARS-CoV-2 replication in human airway cells.
Article
Genetics & Heredity
Michael H. Guo, Tanya M. Bardakjian, Morgan R. Brzozowski, Steven S. Scherer, Colin Quinn, Lauren Elman, Jennifer Orthmann-Murphy, Thomas F. Tropea, Colin A. Ellis, Pedro Gonzalez-Alegre
Summary: Genetics evaluation is increasingly used in adult neurology patients, but its utilization and effectiveness are not well characterized. Our study of 1461 patients in an adult neurogenetics clinic showed that genetic testing yielded a causal genetic diagnosis in 30.7% of patients, with higher rates in certain diagnostic categories such as neuromuscular and epilepsy. Further research is needed to determine optimal genetic testing strategies and cost effectiveness in adult neurogenetics evaluation.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2021)
Article
Multidisciplinary Sciences
Pushpanathan Muthuirulan, Dewei Zhao, Mariel Young, Daniel Richard, Zun Liu, Alireza Emami, Gabriela Portilla, Shayan Hosseinzadeh, Jiaxue Cao, David Maridas, Mary Sedlak, Danilo Menghini, Liangliang Cheng, Lu Li, Xinjia Ding, Yan Ding, Vicki Rosen, Ata M. Kiapour, Terence D. Capellini
Summary: Non-coding sequences may hold disease-specificity, with loci such as GDF5 showing multiple associations in joint disorders. By identifying causal variants for hip dysplasia and knee osteoarthritis, researchers pinpointed variants residing in site-specific enhancers. The study also found modularity patterns at GDF5 and other loci with multiple GWAS disease associations, suggesting common regulatory mechanisms for joint-specific diseases.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Daniel E. Lieberman, Timothy M. Kistner, Daniel Richard, I-Min Lee, Aaron L. Baggish
Summary: Research has shown that lifelong physical activity helps slow aging and reduce disease risk, but there is a lack of ultimate evolutionary explanation for how it promotes health. Integrating evolutionary and biomedical perspectives can provide insights into why lifelong physical activity is beneficial for health and longevity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Correction
Multidisciplinary Sciences
Pushpanathan Muthuirulan, Dewei Zhao, Mariel Young, Daniel Richard, Zun Liu, Alireza Emami, Gabriela Portilla, Shayan Hosseinzadeh, Jiaxue Cao, David Maridas, Mary Sedlak, Danilo Menghini, Liangliang Cheng, Lu Li, Xinjia Ding, Yan Ding, Vicki Rosen, Ata M. Kiapour, Terence D. Capellini
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Mariel Young, Daniel Richard, Mark Grabowski, Benjamin M. Auerbach, Bernadette S. de Bakker, Jaco Hagoort, Pushpanathan Muthuirulan, Vismaya Kharkar, Helen K. Kurki, Lia Betti, Lyena Birkenstock, Kristi L. Lewton, Terence D. Capellini
Summary: In this study, researchers used functional genomics to investigate the developmental genetic mechanisms of human pelvic shape and identified a key gestational window when human-specific morphology becomes recognizable. They found evidence of ancient selection and genetic constraint on regulatory sequences involved in ilium expansion and growth, and showed that variation in iliac traits is reduced in humans compared to African apes.
Article
Multidisciplinary Sciences
Daniel Richard, Pushpanathan Muthuirulan, Jennifer Aguiar, Andrew C. Doxey, Arinjay Banerjee, Karen Mossman, Jeremy Hirota, Terence D. Capellini
Summary: This study makes use of bioinformatic analysis to propose hypotheses for ACE2 gene regulation and validates these hypotheses through functional experiments. It identifies regulatory elements associated with immune signaling and oxidative stress pathways. The findings contribute to our understanding of ACE2 gene regulation under normal conditions and immune challenges, supporting further research on these regulatory mechanisms in the context of current and future SARS-related virus infection/disease.
Article
Biology
Evelyn Jagoda, Davide Marnetto, Gayani Senevirathne, Victoria Gonzalez, Kaushal Baid, Francesco Montinaro, Daniel Richard, Darryl Falzarano, Emmanuelle LeBlanc, Che C. Colpitts, Arinjay Banerjee, Luca Pagani, Terence D. Capellini
Summary: Individuals infected with the SARS-CoV-2 virus display a wide range of symptoms. Previous research has identified a genetic haplotype on chromosome 3 as a strong risk factor for severe COVID-19 outcomes. However, the specific variants and biological mechanisms behind this remain unclear.
Article
Biology
Daniel Richard, Steven Pregizer, Divya Venkatasubramanian, Rosanne M. Raftery, Pushpanathan Muthuirulan, Zun Liu, Terence D. Capellini, April M. Craft
Summary: To fill in the knowledge gaps of molecular regulation in human articular and growth plate cartilage development, researchers used directed differentiation approach to generate these cartilage tissues from human embryonic stem cells. The transcriptomic profiles of the resulting cartilage cells were similar to fetal chondrocytes, in terms of both known and unknown genes related to cartilage biology. By mapping chromatin accessibility in the chondrocyte lineages, researchers identified lineage-specific gene regulatory networks, and validated the functional interactions of two transcription factors with their predicted genomic targets. This work provides a framework for studying chondrocyte differentiation and sheds new light on human cartilage development and biology.
Article
Biotechnology & Applied Microbiology
Michael H. Guo, Prashanth Sama, Brenna A. LaBarre, Hrishikesh Lokhande, John Balibalos, Ci Chu, Xiaomi Du, Pouya Kheradpour, Charles C. Kim, Taylor Oniskey, Thomas Snyder, Damien Z. Soghoian, Howard L. Weiner, Tanuja Chitnis, Nikolaos A. Patsopoulos
Summary: This study utilizes chromatin accessibility data to identify cell type-specific enrichments of multiple sclerosis (MS) genetic signals, finding that CD4 T cells and B cells independently drive the genetic signals of MS. The study also identifies driver subsets and proposes potential causal genes through fine-mapping and chromatin interactions.
Article
Cell Biology
Daniel Richard, Terence D. Capellini
Summary: This paper discusses the effects of epigenetic changes on gene regulation during aging, emphasizing their impact on disease pathomechanism. The study found that developmental epigenetic changes have less influence on genetic risk associations, while variants with increased local accessibility in adult tissues have stronger effects, especially in young adults compared to the elderly.
Meeting Abstract
Anthropology
Terence D. Capellini, Mariel Young, Pushpanathan Muthuirulan, Vismaya Kharkar, Daniel Richard
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2020)