Article
Development Studies
Mai Hassan, Ahmed Kodouda
Summary: Bureaucratic actions can hinder civil service reform in post-uprising contexts, as bureaucrats can leverage their knowledge of state processes to establish clientelistic ties with the new political elites, prompting politicians to block the creation of more rational and legal agencies.
Article
Infectious Diseases
Alexandra Tabaran, Virginie Soulageon, Flore Chirila, Oana Lucia Reget, Marian Mihaiu, Mihai Borzan, Sorin Daniel Dan
Summary: Antimicrobial resistance is a global concern and this study found that bovines in Romania may serve as reservoirs for multi-drug resistant E. coli, highlighting the need for surveillance of antimicrobial usage in farm animals.
Article
Multidisciplinary Sciences
Negin Malekian, Amay A. Agrawal, Thomas U. Berendonk, Ali Al-Fatlawi, Michael Schroeder
Summary: This study investigates the positively selected genes in wastewater E. coli and finds that some of them are functionally associated with antibiotic resistance. Mutations associated with antibiotic resistance are also identified. The findings provide novel insights into the mechanisms driving antibiotic resistance.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Christopher H. Connor, Amanda Z. Zucoloto, John T. Munnoch, Ian-Ling Yu, Jukka Corander, Paul A. Hoskisson, Braedon McDonald, Alan Mcnally
Summary: This study demonstrates that MDR E. coli ST131 can compete and displace non-MDR E. coli in vivo, even without antibiotic treatment. The study also reveals that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes.
Article
Gastroenterology & Hepatology
Rahul Gomes, Ashleigh Denison Kroschel, Stephanie Day, Rick Jansen
Summary: By analyzing RNA-seq data of three pathogenic E. coli hybrid isolates, researchers have identified differences in gene interactions caused by different virulent factors, especially in metabolism-related biological pathways. This suggests potential variations in resource allocation or energy generation among these isolates based on genomic variation.
Article
Microbiology
Dalmasso Guillaume, Beyrouthy Racha, Brugiroux Sandrine, Ruppe Etienne, Guillouard Laurent, Bonnin Virginie, Saint-Sardos Pierre, Ghozlane Amine, Gaumet Vincent, Barnich Nicolas, Delmas Julien, Bonnet Richard
Summary: Without the use of antibiotics, the plasmid-mediated resistance gene mcr-1 enhances the colonization ability of Escherichia coli in the gut, but impairs its lethal effect. This improvement in gut fitness is associated with a downregulation of intestinal inflammatory markers and the preservation of intestinal microbiota composition.
Article
Fisheries
Wen-Hong Liu, Johonsan Fabilane, Wen-Kai Hsu
Summary: The abundance of fisheries resources in the waters of northern Philippines bordering southern Taiwan has been shown by studies. However, collaboration is complex due to discrepancies in legal frameworks, enforcement mechanisms, cultural practices, and maritime boundary issues. This paper highlights the importance of establishing fisheries cooperation under the legal framework of the WCPFC for managing and conserving fishery resources in disputed areas.
Article
Cell Biology
Martijn Wehrens, Laurens H. J. Krah, Benjamin D. Towbin, Rutger Hermsen, Sander J. Tans
Summary: This study reveals that catabolic enzyme expression in E. coli cells continuously responds to metabolic fluctuations, which is regulated by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) system. The study uses single-cell microscopy, genetic constructs, and mathematical modeling to show how fluctuations circulate through the metabolic and genetic network at sub-cell-cycle timescales. The findings suggest that the cAMP-CRP system may have evolved to control both internal metabolic fluctuations and external growth conditions.
Article
Multidisciplinary Sciences
Jude Fonbah Leinyuy, Innocent Mbulli Ali, Karimo Ousenu, Christopher B. Tume
Summary: This study analyzed 200 Enterobacteriaceae isolates resistant and susceptible to ESBL, quinolones, and aminoglycosides. It found a high carriage of resistance genes, but the carriage of resistance genes may not always be correlated with phenotypic expression.
Article
Infectious Diseases
Momna Rubab, Deog-Hwan Oh
Summary: The study investigated the antibiotic resistance of Shiga toxin-producing Escherichia coli (STEC) isolates, finding that most strains exhibited phenotypic resistance, with common resistant genes including ere(A), aadA1, and aac(3)-I. These results underscore the importance of monitoring multidrug resistance globally.
Article
Environmental Sciences
Laura M. Rubeck, James E. Wells, Kathryn J. Hanford, Lisa M. Durso, Walter H. Schacht, Elaine D. Berry
Summary: The study evaluated the impacts of management-intensive grazing (MIG) on water quality, specifically the concentrations of total Escherichia coli, total suspended solids (TSS), and nitrate-nitrite nitrogen (NO3 + NO2-N), as well as the occurrence of E. coli O157:H7 and antibiotic resistance genes (ARGs). The results showed that grazing increased the concentrations of total E. coli and TSS in downstream water, while reducing the concentration of NO3 + NO2-N. furthermore, precipitation and overwintering mallard ducks were found to also affect water quality. Overall, MIG was found to have a positive effect in reducing the negative impacts of cattle grazing on stream water quality.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Xiaomei Liu, Dan Wang, Jingchun Tang, Feng Liu, Lan Wang
Summary: The study found that dissolved biochar can promote the transfer of antibiotic resistance genes in bacteria, with humic acid-like substances playing an important role. However, increasing the concentration of dissolved biochar weakens this transfer effect, leading to a decrease in the frequency of antibiotic resistance gene transfer.
ENVIRONMENTAL POLLUTION
(2021)
Article
Environmental Sciences
Haowen Chen
Summary: This paper investigates the impact of the interaction between strategic flexibility and managerial ties on green innovation in new firms, and explores ways to match strategic flexibility and managerial ties that are more appropriate for conducting green innovation practices. The results of the empirical study indicate that different types of strategic flexibility and managerial ties can generate different synergies and thus have different impacts on green innovation.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2022)
Article
Microbiology
Amira M. Sultan, Ghada F. Amer, Yasmin Nabiel
Summary: This study found a significantly higher prevalence of quinolone resistance genetic determinants as well as gyrA gene mutation among biofilm-forming uropathogenic Escherichia coli. The coexistence of these different resistance mechanisms may exacerbate quinolone resistance, highlighting the importance of monitoring resistance mechanisms and implementing proper stewardship programs.
JOURNAL OF MEDICAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Matthew P. Grindle, Ben Carter, John Paul Alao, Katherine Connors, Riina Tehver, Andrea N. Kravats
Summary: This study investigated the allosteric communication between Hsp90(Ec) and DnaK, as well as how the chaperones couple their conformational cycles. The findings support an asymmetric binding of DnaK to Hsp90(Ec), suggesting that the chaperone cycles of Hsp90(Ec) and DnaK operate independently.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Hidenori Tanaka, Jason F. Kreisberg, Trey Ideker
Summary: Using a machine learning system and hierarchical biological knowledge, researchers found associations between genetic mutations and specific phenotypic traits; although mostly novel loci were identified, they still failed to explain all heritable variations; this approach demonstrates the potential of amplifying and interpreting signals in population genetic studies.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Leah Schaffer, Trey Ideker
Summary: Biological systems are inherently multiscale, allowing for the application of diverse technologies to characterize units at different levels and create networks of proximities. By using network proximity measures to build hierarchical maps of biological systems, functionalizing them to create predictive models, and addressing challenges in multiscale modeling, a unified hierarchical approach to biological data can be achieved, spanning from the molecular to macroscopic level.
Article
Biochemistry & Molecular Biology
Sara Brin Rosenthal, Helen Rankin Willsey, Yuxiao Xu, Yuan Mei, Jeanselle Dea, Sheng Wang, Charlotte Curtis, Emily Sempou, Mustafa K. Khokha, Neil C. Chi, Arthur Jeremy Willsey, Kathleen M. Fisch, Trey Ideker
Summary: Using network genetics, this study identified a convergent molecular network underlying autism and congenital heart disease, pinpointing 101 genes with shared genetic risk. Additionally, previously unidentified genes for autism and congenital heart disease were implicated, providing insights into the pathological mechanisms of co-morbid conditions. The study also confirmed heart and brain developmental abnormalities in Xenopus tropicalis, highlighting the role of ion channels like SCN2A in early heart and brain development.
Article
Microbiology
Laura Martin-Sancho, Shashank Tripathi, Ariel Rodriguez-Frandsen, Lars Pache, Maite Sanchez-Aparicio, Michael J. McGregor, Kelsey M. Haas, Danielle L. Swaney, Thong T. Nguyen, Joao Mamede, Christopher Churas, Dexter Pratt, Sara B. Rosenthal, Laura Riva, Courtney Nguyen, Nish Beltran-Raygoza, Stephen Soonthornvacharin, Guojun Wang, David Jimenez-Morales, Paul D. De Jesus, Hong M. Moulton, David A. Stein, Max W. Chang, Chris Benner, Trey Ideker, Randy A. Albrecht, Judd F. Hultquist, Nevan J. Krogan, Adolfo Garcia-Sastre, Sumit K. Chanda
Summary: Multi-omics analysis revealed a range of both IFN-dependent and independent cellular defence mechanisms that inhibit IAV replication, with TBC1D5 playing a key role in controlling IAV replication and promoting lysosomal targeting of IAV M2 protein through interaction with Rab7. Additionally, the study found that IAV M2 protein can escape lysosomal degradation by abrogating TBC1D5-Rab7 binding via physical interaction.
NATURE MICROBIOLOGY
(2021)
Editorial Material
Oncology
Samson H. Fong, Brenton P. Munson, Trey Ideker
Summary: The study explores the complex gene networks that give rise to tumorigenesis by using CRISPR-Cas9 system to knockout pairwise combinations of tumor suppressor genes and identifying clear cooperation among NF2, PTEN, and TP53. Further characterization of strongly synergistic interactions is done through single-cell transcriptomic profiling. This methodology provides a scalable approach to move beyond single-gene drivers in mapping the complex gene networks involved in cancer development.
Article
Multidisciplinary Sciences
Yue Qin, Edward L. Huttlin, Casper F. Winsnes, Maya L. Gosztyla, Ludivine Wacheul, Marcus R. Kelly, Steven M. Blue, Fan Zheng, Michael Chen, Leah Schaffer, Katherine Licon, Anna Backstrom, Laura Pontano Vaites, John J. Lee, Wei Ouyang, Sophie N. Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason F. Kreisberg, Steven P. Gygi, Jianzhu Ma, J. Wade Harper, Gene W. Yeo, Denis L. J. Lafontaine, Emma Lundberg, Trey Ideker
Summary: This study integrates protein fluorescent imaging and protein biophysical association data to create a unified hierarchical map of human cell architecture, revealing 69 subcellular systems. By calibrating the measures from these two different approaches using machine learning, the resolution of imaging is enhanced while giving protein interactions a spatial dimension.
Article
Biotechnology & Applied Microbiology
Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki, Nozomu Yachie
Summary: This study proposes a deep distributed computing framework, FRACTAL, for inferring large-scale cell lineages. The framework constructs lineages from a large number of input sequences through recursive iteration, significantly enhancing scalability, and demonstrates its utility in different experiments.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Fan Zheng, Marcus R. Kelly, Dana J. Ramms, Marissa L. Heintschel, Kai Tao, Beril Tutuncuoglu, John J. Lee, Keiichiro Ono, Helene Foussard, Michael Chen, Kari A. Herrington, Erica Silva, Sophie N. Liu, Jing Chen, Christopher Churas, Nicholas Wilson, Anton Kratz, Rudolf T. Pillich, Devin N. Patel, Jisoo Park, Brent Kuenzi, Michael K. Yu, Katherine Licon, Dexter Pratt, Jason F. Kreisberg, Minkyu Kim, Danielle L. Swaney, Xiaolin Nan, Stephanie Fraley, J. Silvio Gutkind, Nevan J. Krogan, Trey Ideker
Summary: This study successfully created a comprehensive map of cancer protein systems called NeST and identified 395 specific systems under mutational selection, contributing to the understanding of how disparate tumor mutations converge on protein assemblies at different scales.
Article
Biology
Sabine Ottilie, Madeline R. Luth, Erich Hellemann, Gregory M. Goldgof, Eddy Vigil, Prianka Kumar, Andrea L. Cheung, Miranda Song, Karla P. Godinez-Macias, Krypton Carolino, Jennifer Yang, Gisel Lopez, Matthew Abraham, Maureen Tarsio, Emmanuelle LeBlanc, Luke Whitesell, Jake Schenken, Felicia Gunawan, Reysha Patel, Joshua Smith, Melissa S. Love, Roy M. Williams, Case W. McNamara, William H. Gerwick, Trey Ideker, Yo Suzuki, Dyann F. Wirth, Amanda K. Lukens, Patricia M. Kane, Leah E. Cowen, Jacob D. Durrant, Elizabeth A. Winzeler
Summary: Ottilie et al. used an experimental evolution approach to investigate the role of transcription factors in yeast chemical resistance. They found that most emergent mutations in resistant strains were enriched in transcription factor coding genes, highlighting their importance in drug resistance. Through in vitro evolution and whole genome analysis, they comprehensively identified the genetic determinants of chemical resistance in Saccharomyces cerevisiae. This work emphasizes the important role of transcription factors in the evolution of antifungal xenobiotic resistance and poses challenges to the development of effective antifungal treatments.
COMMUNICATIONS BIOLOGY
(2022)
Letter
Biotechnology & Applied Microbiology
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
NATURE BIOTECHNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber
Review
Medicine, General & Internal
Adam Li, Zane Koch, Trey Ideker
Summary: Numerous studies have shown that epigenetic age is associated with various factors and can be computed based on DNA methylation patterns. The focus of research needs to shift from accurate age prediction to understanding the links between the epigenome and aging mechanisms. Current research areas include epigenetic clocks and investigation of the epigenome to build a mechanistic theory of aging and inform clinical practice.
JOURNAL OF INTERNAL MEDICINE
(2022)
Article
Neurosciences
Richard Karlsson Linner, Travis T. Mallard, Peter B. Barr, Sandra Sanchez-Roige, James W. Madole, Morgan N. Driver, Holly E. Poore, Ronald de Vlaming, Andrew D. Grotzinger, Jorim J. Tielbeek, Emma C. Johnson, Mengzhen Liu, Sara Brin Rosenthal, Trey Ideker, Hang Zhou, Rachel L. Kember, Joelle A. Pasman, Karin J. H. Verweij, Dajiang J. Liu, Scott Vrieze, Henry R. Kranzler, Joel Gelernter, Kathleen Mullan Harris, Elliot M. Tucker-Drob, Irwin D. Waldman, Abraham A. Palmer, K. Paige Harden, Philipp D. Koellinger, Danielle M. Dick
Summary: Research shows that persistent difficulties in self-regulation may be conceptualized as a neurodevelopmental trait with complex and far-reaching social and health correlates. By leveraging genetic correlations, over 500 genetic loci related to externalizing traits were identified, enriched for genes expressed in the brain and related to nervous system development.
NATURE NEUROSCIENCE
(2021)
Correction
Oncology
Brent M. Kuenzi, Trey Ideker
Summary: The correction to this paper has been published.
NATURE REVIEWS CANCER
(2021)
Article
Biotechnology & Applied Microbiology
Fan Zheng, She Zhang, Christopher Churas, Dexter Pratt, Ivet Bahar, Trey Ideker
Summary: In this study, a new method called HiDeF is introduced, which utilizes the concept of persistent homology from mathematical topology to identify robust structures in data at all scales simultaneously. The application of HiDeF to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, and the analysis of SARS-COV-2 protein interactions suggests hijacking of the WNT pathway. The HiDeF method is available through Python and Cytoscape.
