Article
Ecology
Ewa Pikus, Peter O. Dunn, Piotr Minias
Summary: This study examined the relationship between MHC gene diversity and fitness-related traits in a population of Eurasian coot. The results showed that high MHC gene diversity was associated with poorer condition, weaker ornament expression, later onset of breeding, and smaller clutches. The study suggests that the costs of high MHC diversity outweighed the benefits in an urban landscape.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Cell Biology
Wenyue Wang, Tessa Sherry, Xinran Cheng, Qi Fan, Rebecca Cornell, Jie Liu, Zhicheng Xiao, Roger Pocock
Summary: Wang et al. found that intestinal sphingosine-1-phosphate is transferred to oocytes and affects the sphingolipid metabolism in the next generations. This sphingosine-1-phosphate protects Caenorhabditis elegans neurons against axon fragility. It was also discovered that feeding C. elegans with ursolic acid improves axon transport and reduces axon fragility across generations by enhancing sphingosine-1-phosphate provisioning.
NATURE CELL BIOLOGY
(2023)
Article
Biology
Alex J. Veglia, Kalia S. I. Bistolas, Christian R. Voolstra, Benjamin C. C. Hume, Hans-Joachim Ruscheweyh, Serge Planes, Denis Allemand, Emilie Boissin, Patrick Wincker, Julie Poulain, Clementine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Fabien Lombard, Stephane Pesant, Stephanie Reynaud, Shinichi Sunagawa, Olivier P. Thomas, Romain Trouble, Didier Zoccola, Adrienne M. S. Correa, Rebecca L. Vega L. Thurber
Summary: A study on newly sequenced and publicly available metagenomes and genomes revealed the presence of endogenous +ssRNA viral elements within coral symbionts. These findings provide insight into the evolutionary history and hosts of contemporary viruses. This study highlights the importance of +ssRNA viruses in nested symbioses and their implications for host evolution, exaptation, and immunity in the context of reef health and disease.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Gongyu Tang, Minsu Cho, Xiaowei Wang
Summary: OncoDB is an online database resource that integrates multi-omics data from TCGA and GTEx studies to study gene expression dysregulation and viral infection in cancer, providing valuable insights into clinical features and outcomes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Yajun Wang, Michael Abrouk, Spyridon Gourdoupis, Dal-Hoe Koo, Miroslava Karafiatova, Istvan Molnar, Katerina Holusova, Jaroslav Dolezel, Naveenkumar Athiyannan, Emile Cavalet-Giorsa, Lukasz Jaremko, Jesse Poland, Simon G. Krattinger
Summary: To enrich crop germplasm with disease-resistance genes, we successfully cloned the leaf rust resistance gene Lr9 through mutagenesis and transcriptome sequencing, and found that Lr9 encodes an unusual tandem kinase fusion protein. By utilizing long-read sequencing, we identified the Lr9 translocation of approximately 28.4-Mb and the translocation breakpoint in a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor. We also discovered a homologous gene Lr58 with the same coding sequence as Lr9, which was reportedly introgressed from Aegilops triuncialis, indicating a common translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.
Article
Multidisciplinary Sciences
Maria E. Diaz-Ortiz, Yunji Seo, Marijan Posavi, Marc Carceles Cordon, Elisia Clark, Nimansha Jain, Rakshita Charan, Michael D. Gallagher, Travis L. Unger, Noor Amari, R. Tyler Skrinak, Roseanne Davila-Rivera, Eliza M. Brody, Noah Han, Rebecca Zack, Vivianna M. Van Deerlin, Thomas F. Tropea, Kelvin C. Luk, Edward B. Lee, Daniel Weintraub, Alice S. Chen-Plotkin
Summary: Through genome-wide association studies, a risk gene called GPNMB has been identified for Parkinson's disease, and its interaction and function with α-synuclein have been discovered. In PD patients, elevated levels of GPNMB in plasma are associated with disease severity.
Article
Gastroenterology & Hepatology
Randy J. Chandler, Leah E. Venturoni, Jing Liao, Brandon T. Hubbard, Jessica L. Schneller, Victoria Hoffmann, Susana Gordo, Shengwen Zang, Chih-Wei Ko, Nelson Chau, Kyle Chiang, Mark A. Kay, Adi Barzel, Charles P. Venditti
Summary: This study tested a novel AAV vector in mouse models of methylmalonic acidemia, showing sustained hepatic transgene expression with reduced toxicity compared to traditional AAV therapy. Promoterless, nuclease-free genome editing at the albumin locus provided safe and durable therapeutic benefit in neonatally treated MMA mice, without adverse events like hepatocellular carcinoma.
Article
Multidisciplinary Sciences
Deepak Mishra, Tristan Bepler, Brian Teague, Bonnie Berger, Jim Broach, Ron Weiss
Summary: The research team created a bistable toggle switch in Saccharomyces cerevisiae using a cross-repression topology, and developed a computational framework to search for and validate other large and similar bistable networks. This highlights the potential of building synthetic protein-protein networks.
Article
Plant Sciences
Celymar Angela Solis, Miing-Tiem Yong, Gayatri Venkataraman, Paul Milham, Meixue Zhou, Lana Shabala, Paul Holford, Sergey Shabala, Zhong-Hua Chen
Summary: Comparison between wild rice O. rufipogon and cultivated rice O. sativa revealed the former's superior photosynthetic efficiency and lesser leaf tissue damage under salinity stress. Additionally, O. rufipogon showed significantly higher tissue Na+ accumulation achieved through vacuolar sequestration. High expression of genes involved in ion transport and sequestration in O. rufipogon suggests its potential for improving salinity tolerance in cultivated rice.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biochemistry & Molecular Biology
Merrit Romeike, Stephanie Spach, Marie Huber, Songjie Feng, Gintautas Vainorius, Ulrich Elling, Gjis A. Versteeg, Christa Buecker
Summary: Stem cells express a subset of genes related to interferon stimulation and innate immune response. The expression of these genes in stem cells is independent of external stimuli like viral infection. Irf1, controlled by the pluripotency gene network, is transiently upregulated during the transition from naive to formative pluripotency. It binds to regulatory regions of certain interferon-stimulated genes and is necessary for their accurate expression after exiting naive pluripotency. The absence of Irf1 makes cells more susceptible to viral infection, highlighting its role in connecting the formative pluripotency network, regulation of innate immunity genes, and defense against viral infections.
Article
Multidisciplinary Sciences
Thomas A. O'Shea-Wheller, Frank D. Rinkevich, Robert G. Danka, Michael Simone-Finstrom, Philip G. Tokarz, Kristen B. Healy
Summary: This study characterizes the parasite and viral dynamics of a Varroa-resistant honey bee stock through a large-scale longitudinal study. The results show significantly reduced levels of Varroa mites in this stock, decreased titres of major viruses, and an increase in survival. A fourth virus that is not associated with Varroa does not differ between stocks. The study also suggests that viral titres alone are not strong independent predictors of colony mortality risk.
SCIENTIFIC REPORTS
(2022)
Article
Medicine, Research & Experimental
Agnese Padula, Michele Spinelli, Edoardo Nusco, Xabier Bujanda Cundin, Filomena Capolongo, Severo Campione, Claudia Perna, Amy Bastille, Megan Ericson, Chih-Chieh Wang, Shengwen Zhang, Angela Amoresano, Mariana Nacht, Pasquale Piccolo
Summary: A liver-directed, nuclease-free genome editing approach was applied to treat Wilson disease by restoring ATP7B function. The study showed that targeted integration of mini-ATP7B cDNA into the albumin locus resulted in extensive liver repopulation and improved liver injury and copper metabolism. Combination of genome editing with a copper chelator achieved even greater disease improvement.
Article
Chemistry, Multidisciplinary
Wen-Jing Zhou, Hua Li, Ke-Ke Zhang, Fenglin Wang, Xia Chu, Jian-Hui Jiang
Summary: Genetically encoded molecular tools are crucial for live cell RNA imaging, and this study develops a new sensor system using conformation switching RNA induced fluorogenic proteins that enable multicolor imaging and signal amplification of endogenous RNAs. The sensor is designed with an RNA sensing module and a degron-fused fluorescent protein reporter for high-contrast imaging of RNA abundance and dynamics in live cells. Furthermore, the sensor system is extended to a multicolor palette and engineered into a signal amplifier, providing a valuable platform for RNA imaging in biomedical research and clinical theranostics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Liam C. Hunt, Vishwajeeth Pagala, Anna Stephan, Boer Xie, Kiran Kodali, Kanisha Kavdia, Yong-Dong Wang, Abbas Shirinifard, Michelle Curley, Flavia A. Graca, Yingxue Fu, Suresh Poudel, Yuxin Li, Xusheng Wang, Haiyan Tan, Junmin Peng, Fabio Demontis
Summary: This study investigates the effects of decreased ubiquitination on cellular processes and organelle adaptations. The researchers identified a compensatory upregulation of other proteins in response to decreased ubiquitination, which helps maintain protein import in organelles.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Paula Rozo-Lopez, William Brewer, Simon Kaefer, McKayla M. Martin, Benjamin J. Parker
Summary: Insects are an important reservoir of viral biodiversity, but the majority of insect-associated viruses remain undiscovered. This study used multiple sequencing methods to investigate the virome of the potato aphid and found insect-specific viruses, parasitoid virus, plant pathogenic virus, and phages. However, the analysis of the insect's genome assembly revealed that some of the "virome" could be attributed to endogenous viral elements.
Article
Biochemistry & Molecular Biology
Maike M. K. Hansen, Winnie Y. Wen, Elena Ingerman, Brandon S. Razooky, Cassandra E. Thompson, Roy D. Dar, Charles W. Chin, Michael L. Simpson, Leor S. Weinberger
Article
Biochemical Research Methods
S. Elizabeth Norred, Patrick M. Caveney, Gaurav Chauhan, Lauren K. Collier, C. Patrick Collier, Steven M. Abel, Michael L. Simpson
ACS SYNTHETIC BIOLOGY
(2018)
Article
Chemistry, Physical
William T. McClintic, Graham J. Taylor, Michael L. Simpson, C. Patrick Collier
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Multidisciplinary Sciences
Tarun Mahajan, Roy D. Dar
Summary: The study reveals that the transcriptional regulatory network (TRN) and protein-protein interaction (PPI) network are non-randomly coupled in five different eukaryotic species, with gene degrees in TRN positively correlated with protein degrees in PPI. The interactions in TRN and PPI also non-randomly overlap, and this coupling determines the robustness of the TRN-PPI multiplex. Important genes and proteins are preferentially situated in key parts of the human multiplex, indicating a conserved design principle across eukaryotic species.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Yiyang Lu, Kathrin Bohn-Wippert, Patrick J. Pazerunas, Jennifer M. Moy, Harpal Singh, Roy D. Dar
Summary: By screening gene expression noise, new latency-promoting agents have been identified to control HIV reactivation from latency, offering new strategies for treating HIV.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Yiyang Lu, Harpal Singh, Abhyudai Singh, Roy D. Dar
Summary: Reactivation of individual latent cells may be a deterministic outcome of underlying cell states rather than a stochastic process. A transient heritable memory regulates HIV-1 reactivation, with single cells responsive to LRAs for a few weeks before switching back to an unresponsive state.
Article
Virology
Alexandra Blanco, Tarun Mahajan, Robert A. Coronado, Kelly Ma, Dominic R. Demma, Roy D. Dar
Summary: This study investigates the effects of latency reversal agents on HIV latent reactivation and cell migration in monocytes, demonstrating the synergy between drug treatments and activation of the HIV promoter. The findings suggest that epigenetic mechanisms in monocytes, similar to T-cells, play a role in controlling the relationship between latent reactivation and cell migration, highlighting the need for targeted therapies in a complex latency milieu.
Article
Multidisciplinary Sciences
Neha Goswami, Yiyang Lu, Mikhail E. Kandel, Michael J. Fanous, Kathrin Bohn-Wippert, Erin N. Tevonian, Roy D. Dar, Gabriel Popescu
Summary: This study utilizes GLIM to reveal the changes in dry mass, diameter, and dry mass density of HIV-infected cells during reactivation, and discovers the impact of cell dry mass and diameter on latent reactivation.
Article
Engineering, Biomedical
Onur Aydin, Austin P. Passaro, Ritu Raman, Samantha E. Spellicy, Robert P. Weinberg, Roger D. Kamm, Matthew Sample, George A. Truskey, Jeremiah Zartman, Roy D. Dar, Sebastian Palacios, Jason Wang, Jesse Tordoff, Nuria Montserrat, Rashid Bashir, M. Taher A. Saif, Ron Weiss
Summary: Remarkable progress in bioengineering has enabled the formulation of design principles for multicellular engineered living systems (M-CELS), integrating biological parts into functional modules within living machines. These design principles involve genetic circuit manipulation, self-assembly, cell communication, and artificial tissues/organs enabled through various technologies. The review introduces a blueprint for forward production of robust M-CELS and provides practical and theoretical frameworks for their design, control, and optimization. Potential applications range from biopharmaceuticals to environmental bioremediation.
APL BIOENGINEERING
(2022)
Proceedings Paper
Automation & Control Systems
Tarun Mahajan, Michael Saint-Antoine, Roy D. Dar, Abhyudai Singh
Summary: Inferring gene regulatory networks from single-cell expression data is a popular problem in computational biology, but remains unsolved due to measurement errors, lack of perturbation data, or difficulty in causal inference. This study shows that the relative stability of mRNA and protein can hinder the inference process. A more stable protein than mRNA deteriorates the correlation between the mRNA of a transcription factor and its target gene, even when mRNA and protein are on the same timescale. The relative difference in timescales has a stronger effect on true interactions than false positives.
2022 IEEE 61ST CONFERENCE ON DECISION AND CONTROL (CDC)
(2022)
Correction
Multidisciplinary Sciences
Yiyang Lu, Kathrin Bohn-Wippert, Patrick J. Pazerunas, Jennifer M. Moy, Harpal Singh, Roy D. Dar
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Biomedical
Roy D. Dar, Ron Weiss
APL BIOENGINEERING
(2018)
Article
Engineering, Biomedical
Melina R. Megaridis, Yiyang Lu, Erin N. Tevonian, Kendall M. Junger, Jennifer M. Moy, Kathrin Bohn-Wippert, Roy D. Dar
APL BIOENGINEERING
(2018)
Article
Engineering, Biomedical
Roger D. Kamm, Rashid Bashir, Natasha Arora, Roy D. Dar, Martha U. Gillette, Linda G. Griffith, Melissa L. Kemp, Kathy Kinlaw, Michael Levin, Adam C. Martin, Todd C. McDevitt, Robert M. Nerem, Mark J. Powers, Taher A. Saif, James Sharpe, Shuichi Takayama, Shoji Takeuchi, Ron Weiss, Kaiming Ye, Hannah G. Yevick, Muhammad H. Zaman
APL BIOENGINEERING
(2018)