Article
Multidisciplinary Sciences
Sahar Gelfman, Arden Moscati, Santiago Mendez Huergo, Rujin Wang, Veera Rajagopal, Neelroop Parikshak, Vijay Kumar Pounraja, Esteban Chen, Michelle Leblanc, Ralph Hazlewood, Jan Freudenberg, Blerta Cooper, Ann J. Ligocki, Charles G. Miller, Tave Van Zyl, Jonathan Weyne, Carmelo Romano, Botir Sagdullaev, Olle Melander, Aris Baras, Eli A. Stahl, Giovanni Coppola
Summary: In this study, the authors performed genome-wide association analysis and whole-exome analysis to uncover the underlying genetics of HLA-B*27 positive and negative forms of anterior uveitis (AU).
NATURE COMMUNICATIONS
(2023)
Review
Ecology
Adam Z. Hasik, Daniela de Angeli Dutra, Jean-Francois Doherty, Meghan A. Duffy, Robert Poulin, Adam M. Siepielski
Summary: The study found that parasitism did not significantly affect the mean or variance of host-species interaction outcomes. Infected hosts could experience both strongly detrimental and strongly beneficial effects. The impact of parasites on host species interactions varied depending on the environment.
Article
Nanoscience & Nanotechnology
Arjun Rana, Chen-Ting Liao, Ezio Iacocca, Ji Zou, Minh Pham, Xingyuan Lu, Emma-Elizabeth Cating Subramanian, Yuan Hung Lo, Sinead A. Ryan, Charles S. Bevis, Robert M. M. Karl Jr, Andrew J. Glaid, Jeffrey Rable, Pratibha Mahale, Joel Hirst, Thomas Ostler, William Liu, Colum M. O'Leary, Young-Sang Yu, Karen Bustillo, Hendrik Ohldag, David A. Shapiro, Sadegh Yazdi, Thomas E. Mallouk, Stanley J. Osher, Henry C. Kapteyn, Vincent H. Crespi, John V. Badding, Yaroslav Tserkovnyak, Margaret M. Murnane, Jianwei Miao
Summary: The researchers successfully created 138 stable magnetic monopoles on a ferromagnetic meta-lattice and used soft X-ray vector ptycho-tomography to determine their magnetization vector and emergent magnetic field. The study found that the distances between monopole-anti-monopole pairs, monopole-monopole pairs, and anti-monopole-anti-monopole pairs were 18.3 +/- 1.6 nm, 36.1 +/- 2.4 nm, and 43.1 +/- 2.0 nm, respectively. This work demonstrates the potential of ferromagnetic meta-lattices as a platform for studying the interactions and dynamics of magnetic monopoles, and the broad application of soft X-ray vector ptycho-tomography for quantitatively imaging 3D vector fields in magnetic and anisotropic materials at the nanoscale.
NATURE NANOTECHNOLOGY
(2023)
Article
Genetics & Heredity
Kyoko Watanabe, Philip R. Jansen, Jeanne E. Savage, Priyanka Nandakumar, Xin Wang, David A. Hinds, Joel Gelernter, Daniel F. Levey, Renato Polimanti, Murray B. Stein, Eus J. W. Van Someren, August B. Smit, Danielle Posthuma
Summary: Genome-wide association meta-analysis identified 554 risk loci for insomnia in a sample size of almost 600,000 cases and 1.8 million controls, and implicated specific biological pathways through gene prioritization.
Article
Ecology
Huei-Yi Lai, Yen-Hsin Yu, Yu-Ting Jhou, Chia-Wei Liao, Jun-Yi Leu
Summary: By replacing 86 essential genes in Saccharomyces cerevisiae with orthologues from species with different diverging times, the authors demonstrate that intermolecular epistasis is crucial in their evolution and that co-evolution of interacting components maintains conserved physiological functions.
NATURE ECOLOGY & EVOLUTION
(2023)
Review
Engineering, Environmental
Imran Azeem, Muhammad Adeel, Muhammad Arslan Ahmad, Noman Shakoor, Muhammad Zain, Naglaa Yousef, Zhao Yinghai, Kamran Azeem, Pingfan Zhou, Jason C. White, Xu Ming, Yukui Rui
Summary: The study found that the effects of MPx/NPx exposure on different plant species vary, with staple crops showing insignificant responses. Nano-sized plastics negatively affected plant development parameters, photosynthetic pigments, and biochemical indicators more than microplastics, while microplastics had negative impacts on germination and root morphology.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Payal Trivedi, Manmohan Pandey, Pankaj Kumar Rai, Pradyumn Singh, Prachi Srivastava
Summary: This study performed a meta-analysis to identify differentially expressed genes (DEGs) and analyzed regulatory genes in autism spectrum disorder (ASD). The study found that certain genes are upregulated or downregulated in ASD patients and identified significant pathways associated with the disorder. The research highlights the importance of specific genes in neurobiological regulations related to ASD.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Environmental Sciences
Maria Luiza S. Suhadolnik, Patricia S. Costa, Giovanni M. Castro, Francisco P. Lobo, Andrea M. A. Nascimento
Summary: The meta-analysis revealed the widespread presence of arsenic and iron redox genes in various environmental conditions, with specific genes playing important roles in different environments. The diversity and taxonomy of gene carriers were also found to be extensive. However, almost all AsRGs and FeRGs were not carried by plasmid sequences.
ENVIRONMENT INTERNATIONAL
(2021)
Review
Immunology
Amber Park, Laura K. Harris
Summary: The study used a meta-analysis approach to analyze mRNA expression data from SARS infections, potentially identifying therapeutic targets associated with major SARS infections. By comparing gene signatures from different sources, genes associated with SARS infection were identified, providing potential targets for future therapeutic research.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Pablo L. Hunicken, Carolina L. Morales, Ana E. De Villalobos, Lucas A. Garibaldi
Summary: Approximately 75% of global crop productivity relies on insect pollination, but wild pollinator populations are declining. Research shows that crop productivity is similar between honeybees and other managed pollinators, and using both honeybees and other pollinators can increase crop yield. The study also suggests that increasing pollinator diversity can improve pollination service, particularly in systems with a low abundance of pollinators.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2022)
Article
Behavioral Sciences
Kai Lin, Shaohua Sui, Jing Zhao, Liyong Zhang, Kun Chen
Summary: This study revealed that direct and combined bypass surgeries have a lower recurrence rate of stroke compared to indirect bypass surgery in treating MMD. Additionally, cases undergoing direct bypass surgery showed better angiographic changes than those undergoing an indirect bypass.
BRAIN AND BEHAVIOR
(2021)
Review
Surgery
Marliza O'Dwyer, Cristina A. Fleming, Shane Ahern, Sean Barrett, Nicola B. Raftery, Tara Ni Dhonnchu, Kishore Doddakula
Summary: Simulation-based training in coronary artery anastomosis improves time efficiency and overall performance, particularly for novice cardiothoracic surgeons. The fidelity of the simulator does not significantly affect the improvement rates. Further studies are needed to determine the optimal timing for trainees to transition from simulation training to live operating.
Article
Biochemistry & Molecular Biology
Cui-Ping Li, Yu-Xin Song, Zi-Jun Lin, Mei-Lin Ma, Lian-Ping He
Summary: This study explores the relationship between serum trace elements and lipid metabolism. It found no significant association between serum zinc and dyslipidemia, while other serum trace elements (iron, selenium, copper, chromium, and manganese) were associated with hyperlipidemia. The study suggests that zinc, copper, and calcium content in the human body may be related to lipid metabolism, but further research is needed.
CURRENT MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Min Wu, Holger Wille, Maria Stepanova
Summary: This study investigates the structure and dynamics of misfolded aggregates of alpha-synuclein using molecular dynamics simulations. The results indicate that monomeric alpha-synuclein tends to form aggregates with fibrillar seeds. Analysis reveals the impact of long-range interactions on the stability of these aggregates.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Review
Engineering, Environmental
Han Dong, Yuliang Chen, Jun Wang, Yue Zhang, Pan Zhang, Xiang Li, Jixing Zou, Aiguo Zhou
Summary: This review discusses the ecological effects of microplastics and antibiotic resistance genes in aquaculture environments. The widespread use of antibiotics in agricultural production leads to the presence of antibiotic residues in water and the emergence of antibiotic-resistant bacteria. Additionally, water microplastics act as carriers of environmental microbes and antibiotic-resistant bacteria, potentially entering aquaculture environments and eventually the human body through food chains.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Multidisciplinary Sciences
Katja Luck, Dae-Kyum Kim, Luke Lambourne, Kerstin Spirohn, Bridget E. Begg, Wenting Bian, Ruth Brignall, Tiziana Cafarelli, Francisco J. Campos-Laborie, Benoit Charloteaux, Dongsic Choi, Atina G. Cote, Meaghan Daley, Steven Deimling, Alice Desbuleux, Amelie Dricot, Marinella Gebbia, Madeleine F. Hardy, Nishka Kishore, Jennifer J. Knapp, Istvan A. Kovacs, Irma Lemmens, Miles W. Mee, Joseph C. Mellor, Carl Pollis, Carles Pons, Aaron D. Richardson, Sadie Schlabach, Bridget Teeking, Anupama Yadav, Mariana Babor, Dawit Balcha, Omer Basha, Christian Bowman-Colin, Suet-Feung Chin, Soon Gang Choi, Claudia Colabella, Georges Coppin, Cassandra D'Amata, David De Ridder, Steffi De Rouck, Miquel Duran-Frigola, Hanane Ennajdaoui, Florian Goebels, Liana Goehring, Anjali Gopal, Ghazal Haddad, Elodie Hatchi, Mohamed Helmy, Yves Jacob, Yoseph Kassa, Serena Landini, Roujia Li, Natascha van Lieshout, Andrew MacWilliams, Dylan Markey, Joseph N. Paulson, Sudharshan Rangarajan, John Rasla, Ashyad Rayhan, Thomas Rolland, Adriana San-Miguel, Yun Shen, Dayag Sheykhkarimli, Gloria M. Sheynkman, Eyal Simonovsky, Murat Tasan, Alexander Tejeda, Vincent Tropepe, Jean-Claude Twizere, Yang Wang, Robert J. Weatheritt, Jochen Weile, Yu Xia, Xinping Yang, Esti Yeger-Lotem, Quan Zhong, Patrick Aloy, Gary D. Bader, Javier De las Rivas, Suzanne Gaudet, Tong Hao, Janusz Rak, Jan Tavernier, David E. Hill, Marc Vidal, Frederick P. Roth, Michael A. Calderwood
Article
Multidisciplinary Sciences
Elena Kuzmin, Benjamin VanderSluis, Alex N. Nguyen Ba, Wen Wang, Elizabeth N. Koch, Matej Usaj, Anton Khmelinskii, Mojca Mattiazzi Usaj, Jolanda van Leeuwen, Oren Kraus, Amy Tresenrider, Michael Pryszlak, Ming-Che Hu, Brenda Varriano, Michael Costanzo, Michael Knop, Alan Moses, Chad L. Myers, Brenda J. Andrews, Charles Boone
Article
Biochemistry & Molecular Biology
Jolanda van Leeuwen, Carles Pons, Guihong Tan, Jason Zi Wang, Jing Hou, Jochen Weile, Marinella Gebbia, Wendy Liang, Ermira Shuteriqi, Zhijian Li, Maykel Lopes, Matej Usaj, Andreia Dos Santos Lopes, Natascha van Lieshout, Chad L. Myers, Frederick P. Roth, Patrick Aloy, Brenda J. Andrews, Charles Boone
MOLECULAR SYSTEMS BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Birgit H. M. Meldal, Carles Pons, Livia Perfetto, Noemi Del-Toro, Edith Wong, Patrick Aloy, Henning Hermjakob, Sandra Orchard, Pablo Porras
Summary: The EMBL-EBI Complex Portal is a knowledgebase of macromolecular complexes that provides persistent stable identifiers, with data freely available and downloadable. In collaboration with other databases, the yeast complexome was curated, leading to an increase in curated complexes compared to the previous dataset. The analysis showed that genes in complexes have more genetic interactions, are more multifunctional, and are often involved in nucleic acid-related metabolic processes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Michael Costanzo, Jing Hou, Vincent Messier, Justin Nelson, Mahfuzur Rahman, Benjamin VanderSluis, Wen Wang, Carles Pons, Catherine Ross, Matej Usaj, Bryan-Joseph San Luis, Emira Shuteriqi, Elizabeth N. Koch, Patrick Aloy, Chad L. Myers, Charles Boone, Brenda Andrews
Summary: Through analyzing the rewiring of genetic networks in yeast under different environmental conditions, new differential interactions were discovered, highlighting functional connections between different gene pairs. However, the majority of genetic interactions remained stable across different conditions, suggesting that the global yeast genetic interaction network is robust to environmental perturbations and reflects the fundamental functional architecture of a eukaryotic cell.
Article
Biology
Amandine Batte, Sophie C. van der Horst, Mireille Tittel-Elmer, Su Ming Sun, Sushma Sharma, Jolanda van Leeuwen, Andrei Chabes, Haico van Attikum
Summary: MRC1 and CHL1 have distinct roles in the replication stress response, with Mrc1 facilitating the restart of stalled replication forks and Chl1 controlling replication fork rate by regulating dNTP levels. The Chl1 helicase affects RPA-dependent checkpoint activation in response to replication fork arrest.
LIFE SCIENCE ALLIANCE
(2022)
Article
Biochemistry & Molecular Biology
Ananth Pallaseni, Elin Madli Peets, Jonas Koeppel, Juliane Weller, Thomas Vanderstichele, Uyen Linh Ho, Luca Crepaldi, Jolanda van Leeuwen, Felicity Allen, Leopold Parts
Summary: CRISPR/Cas base editors offer precise control over DNA sequences, but their activity is not fully understood. This study reveals sequence biases in base editing activity, with the flanking nucleotides playing a major role. A machine learning model is developed to predict editing activity, allowing more efficient planning of editing campaigns.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Nuria Bosch-Guiteras, Jolanda van Leeuwen
Summary: Gene essentiality is crucial for the survival of organisms and can be categorized into core essential genes and conditional essential genes. Core essential genes are always required, while conditional essential genes vary in their essentiality depending on genetic and environmental contexts.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2022)
Editorial Material
Biochemistry & Molecular Biology
Lucia Trastulla, Aurora Savino, Pedro Beltrao, Isidro Cortes Ciriano, Peter Fenici, Mathew J. J. Garnett, Ilaria Guerini, Nuria Lopez Bigas, Iain Mattaj, Evangelia Petsalaki, Laura Riva, Christopher J. J. Tape, Sumana Sharma, Francisca Vazquez, Francesco Iorio
Summary: The systematic identification of tumour vulnerabilities through perturbational experiments on cancer models, including genome editing and drug screens, known as the Cancer Dependency Map (DepMap), is crucial in combating cancer. The 1st European Cancer Dependency Map Symposium (EuroDepMap) held in Milan last May showcased the latest discoveries and future challenges related to DepMap, aiming to facilitate interactions among participants, encourage idea exchange with leading experts, and discuss future endeavors.
Article
Genetics & Heredity
Betul Unlu, Carles Pons, Uyen Linh Ho, Amandine Batte, Patrick Aloy, Jolanda van Leeuwen
Summary: The study identified 476 unique suppression interactions between human genes, covering a wide spectrum of diseases and biological functions. The suppressors were enriched for genes involved in stress response or signaling, suggesting a potential protective role in modulating signaling cascades or immune responses. This research formulated mechanisms of genetic suppression that explained 71% of interactions and predicted suppressor genes in the human genome.
Article
Biochemistry & Molecular Biology
Leopold Parts, Amandine Batte, Maykel Lopes, Michael W. Yuen, Meredith Laver, Bryan-Joseph San Luis, Jia-Xing Yue, Carles Pons, Elise Eray, Patrick Aloy, Gianni Liti, Jolanda van Leeuwen
Summary: The consequences of mutations depend on the genetic background in which they occur, with gene function loss being tolerated in some backgrounds but lethal in others. Genetic variation in different yeast strains can suppress fitness defects in certain genes, driven by gain-of-function of a single modifier gene. This suggests that a significant portion of monogenic diseases may be managed by modulating other gene products.
MOLECULAR SYSTEMS BIOLOGY
(2021)
