Review
Microbiology
J. Diez, A. Lopez-Lozano, M. A. Dominguez-Martin, G. Gomez-Baena, M. C. Munoz-Marin, Y. Melero-Rubio, J. M. Garcia-Fernandez
Summary: Marine picocyanobacteria, such as Prochlorococcus and Synechococcus, have developed unique adaptive mechanisms in nitrogen metabolism to thrive in oligotrophic oceans, including strategies such as reducing GC and protein contents, utilizing truncated proteins, and perceiving nanomolar nitrate concentrations. These adaptations contrast with the knowledge obtained in freshwater cyanobacteria and are essential for the ecological success of these microorganisms.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Alireza Karbalayghareh, Merve Sahin, Christina S. Leslie
Summary: This study presents a new deep learning approach called GraphReg that utilizes 3D chromatin interaction data to predict gene expression. GraphReg outperforms other deep learning methods in accurately modeling gene regulation and predicting functional enhancers and transcription factor targets.
Article
Chemistry, Multidisciplinary
Yao Lu, Yang Gao, Junjie Jia, Shuoyue Wang, Kun Sun, Xianrui Ha, Zhaoxi Li
Summary: The water-air interface is the most active area for lake carbon emissions. The study found that the C exchange status at the water-air interface is regulated by the coupled connective effect of the water regime-water quality-GPP-pCO(2) effect. Additionally, in water conveyance-type lake systems, C emissions were highest during the intermediate-water-level period.
ACS EARTH AND SPACE CHEMISTRY
(2022)
Article
Microbiology
Mario L. Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Serdar Turkarslan, Wei-Ju Wu, Brintha P. Girinathan, Jay N. Worley, Nicholas DiBenedetto, Olga Soutourina, Johann Peltier, Bruno Dupuy, Lynn Bry, Nitin S. Baliga
Summary: By leveraging published transcriptomes and metabolic models, we developed a predictive model for comprehensive systems analysis of Clostridioides difficile, shedding light on gene organization and metabolic requirements, as well as the role of transcription factors in growth and ecological adaptation.
CELL HOST & MICROBE
(2021)
Article
Multidisciplinary Sciences
Agneesh Barua, Alexander S. Mikheyev
Summary: Research has found that the gene expression pattern of venom glands in snakes is surprisingly well conserved compared to the salivary glands of other amniotes. A network called the metavenom network, consisting of around 3,000 nonsecreted housekeeping genes, is strongly coexpressed with toxins and primarily involved in protein folding and modification. This network, conserved across amniotes, was coopted for venom evolution by utilizing existing members and recruiting new toxin genes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Multidisciplinary Sciences
Federico Riva, Caio Graco-Roza, Gergana N. Daskalova, Emma J. Hudgins, Jayme M. M. Lewthwaite, Erica A. Newman, Masahiro Ryo, Stefano Mammola
Summary: Ecological systems are complex and understanding complexity is crucial for progress in ecology and conservation. However, multiple definitions of complexity and excessive reliance on traditional scientific approaches hinder conceptual advances. By analyzing articles referring to ecological complexity, we find that the study of complexity in ecology is diverse and weakly related to complex system science. Current research trends focus on basic theory, scaling, and macroecology. We propose a more coherent and cohesive approach to studying complexity in ecology based on our review and generalities identified.
Review
Cell Biology
Isabella Schember, Marc S. Halfon
Summary: This study reviews two insect pigmentation gene regulatory networks (GRNs) and discusses common themes in GRN evolution, as well as the challenges of studying GRN changes across different evolutionary distances. The study finds that alterations in pigmentation GRNs in species like fruit flies and butterflies can occur through the co-option and rewiring of trans-acting factors.
Article
Genetics & Heredity
Md Bulbul Ahmed, Ahmad Humayan Kabir
Summary: This article provides an overview of recent advances in the development of gene regulatory networks (GRNs) in plant research, highlighting their applications in physiological responses regulation, genome and transcriptome research, and crop improvement. It also discusses different approaches for GRN predictions and their roles in crop yield enhancement and stress resistance.
Article
Genetics & Heredity
Md Bulbul Ahmed, Ahmad Humayan Kabir
Summary: This article introduces the hierarchical relationship in gene regulatory networks, explaining how plant genotype and environment control downstream physiological responses, discussing recent advances in basic and applied plant research, and exploring the role of GRNs in crop improvement and stress responses.
Article
Biochemical Research Methods
Lirong Zhang, Yanchao Yang, Lu Chai, Qianzhong Li, Junjie Liu, Hao Lin, Li Liu
Summary: This study quantitatively analyzed the correlation between transcription factors (TFs) and gene expression and identified TF modules associated with gene expression. A convolutional neural network model, TFCNN, was constructed to predict gene expression levels based on the enrichment characteristics of TFs. Results showed that TFCNN achieved high prediction performance and outperformed other models by better extracting combinatorial interactions among TFs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Erik K. Zhivkoplias, Oleg Vavulov, Thomas Hillerton, Erik L. L. Sonnhammer
Summary: The regulatory relationships between genes and proteins in a cell form a gene regulatory network (GRN) that controls cellular response. Methods have been developed to reverse engineer GRNs from expression data, but realistic simulations are necessary due to the lack of ground-truth GRNs. Analysis shows that the feed-forward loop (FFL) motif is significantly enriched in real GRNs, leading to the development of a novel preferential attachment algorithm, FFLatt, for network generation.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Emanuelle I. Grody, Ajay Abraham, Vipul Shukla, Yogesh Goyal
Summary: Cancer is a genetic disease that evolves through both genetic and non-genetic mechanisms, involving complex interactions between cell-intrinsic and extrinsic factors. Recent single-cell profiling of tumors has revealed unprecedented heterogeneity, supporting the existence of both branched and neutral evolution models. This perspective discusses the role of these factors in shaping clonal behaviors during tumor progression, metastasis, and drug resistance, focusing on pre-malignant states associated with hematological malignancies and esophageal cancer.
Article
Multidisciplinary Sciences
Bhargav R. R. Karamched, Christopher E. E. Miles
Summary: Delays and stochasticity play crucial roles in mathematical descriptions of control, physical and biological systems. This study investigates how explicitly dynamical stochasticity in delays modulates the effect of delayed feedback. A hybrid model is considered, where stochastic delays evolve by a continuous-time Markov chain, and between switching events, the system evolves via a deterministic delay equation. The main contribution is the calculation of an effective delay equation in the fast switching limit, which maintains the influence of all subsystem delays.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Multidisciplinary Sciences
Surama Biswas, Santosh Manicka, Erik Hoel, Michael Levin
Summary: Studies have shown that gene regulatory networks possess various types of memory, which is important for understanding the variability and time-dependent changes of drug action. Defining and identifying memory through a computational framework is beneficial for the biomedical field. Timed stimuli offer a powerful alternative for controlling complex in vivo dynamics.
Article
Biochemistry & Molecular Biology
Maxwell L. Neal, Ling Wei, Eliza Peterson, Mario L. Arrieta-Ortiz, Samuel A. Danziger, Nitin S. Baliga, Alexis Kaushansky, John D. Aitchison
Summary: Researchers developed a gene regulatory network model for Plasmodium falciparum using machine learning, which accurately predicted gene expression levels across diverse datasets. By investigating gene expression coherence, they found that artemisinin resistance in the parasite is associated with incoherent expression across multiple regulatory programs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Min Chen, Miguel A. Hernandez-Prieto, Patrick C. Loughlin, Yaqiong Li, Robert D. Willows
Article
Cell Biology
Jose Manuel Inacio, Joao von Gilsa Lopes, Ana Mafalda Silva, Fernando Cristo, Sara Marques, Matthias E. Futschik, Jose Antonio Belo
Summary: Deciphering the clues of a regenerative mechanism for the mammalian adult heart, particularly focusing on the role of DAND5, could potentially lead to the development of more effective treatment options for heart failure. Further research on the transcriptional profiling sequencing and quantitative RT-PCR assays of DAND5 may provide insights into the generation and expansion of pluripotent stem cell-derived cardiomyocytes systems for clinical applications.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Rui Machado, Agapios Sachinidis, Matthias E. Futschik
Summary: This study successfully identified conservatively expressed miRNA-mRNA interactions in vitro and in vivo, providing insights into gene regulation across differentiating murine ESCs. The comparative approach used in this study will be crucial for utilizing stem cells in cardiovascular research.
Article
Biochemistry & Molecular Biology
Martin Kuiper, Joseph Bonello, Jesualdo T. Fernandez-Breis, Philipp Bucher, Matthias E. Futschik, Pascale Gaudet, Ivan V. Kulakovskiy, Luana Licata, Colin Logie, Ruth C. Lovering, Vsevolod J. Makeev, Sandra Orchard, Simona Panni, Livia Perfetto, David Sant, Stefan Schulz, Steven Vercruysse, Daniel R. Zerbino, Astrid Laegreid
Summary: Following nine workshops organized by GREEKC, experts from around the world worked to improve the Gene Regulation Knowledge Commons (GRKC) by standardizing and updating workflows, as well as involving end-users in the design process, leading to significant achievements in enhancing the GRKC.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Genetics & Heredity
Matthias Riediger, Miguel A. Hernandez-Prieto, Kuo Song, Wolfgang R. Hess, Matthias E. Futschik
Summary: The Fur protein plays a crucial role in maintaining iron homeostasis and defending against reactive oxygen species in both pathogenic and non-pathogenic bacteria. By analyzing genome-wide transcriptional data, a high confidence regulon controlled by Fur was identified in Synechocystis sp. PCC 6803 and its close relative, strain 6714, consisting of 33 protein-coding genes primarily involved in iron ion transport and storage. The regulation of iron uptake, storage, and utilization involves interactions between the Fur regulon, various transcription factors, the FtsH3 protease, and the sRNA IsaR1.
Article
Neurosciences
Thomas Wallach, Zoe J. Mossmann, Michal Szczepek, Max Wetzel, Rui Machado, Martin Raden, Milad Miladi, Gunnar Kleinau, Christina Krueger, Paul Dembny, Drew Adler, Yuanyuan Zhai, Victor Kumbol, Omar Dzaye, Jutta Schueler, Matthias Futschik, Rolf Backofen, Patrick Scheerer, Seija Lehnardt
Summary: Specific miRNAs released from apoptotic cortical neurons can activate TLR7 and/or TLR8, leading to neuronal apoptosis in the CNS. This study highlights the role of miRNAs as extracellular signaling molecules in neurodegenerative diseases.
MOLECULAR NEURODEGENERATION
(2021)
Article
Plant Sciences
Miguel A. Hernandez-Prieto, Roger Hiller, Min Chen
Summary: Chlorophyll f, a new type of chlorophyll, allows oxygenic-photosynthetic organisms to thrive in environments with scarce white light but abundant far-red light. The study of its ligand properties and energy transfer characteristics reveals its role in extending the photosynthetic spectral range.
PHOTOSYNTHESIS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Catherine M. Francis, Matthias E. Futschik, Jian Huang, Wenjia Bai, Muralidharan Sargurupremraj, Alexander Teumer, Monique M. B. Breteler, Enrico Petretto, Amanda S. R. Ho, Philippe Amouyel, Stefan T. Engelter, Robin Buelow, Uwe Voelker, Henry Voelzke, Marcus Doerr, Mohammed-Aslam Imtiaz, N. Ahmad Aziz, Valerie Lohner, James S. Ware, Stephanie Debette, Paul Elliott, Abbas Dehghan, Paul M. Matthews
Summary: The study identifies genetic variants associated with aortic distensibility, highlighting the causal relationships between aortic distensibility and aortic aneurysms as well as brain small vessel disease. The findings provide new insights into the mechanisms related to cardiovascular development, extracellular matrix production, and smooth muscle cell contraction.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Fernando Bonet, Sabrina Brito Anez, Jose Manuel Inacio, Matthias E. Futschik, Jose Antonio Belo
Summary: Loss of CCBE1 leads to congenital heart defects, thinner myocardium, and hyper-trabeculation in mice. It also results in reduced proliferation of cardiomyocytes and epicardial cells, as well as impaired migration of epicardial-derived cells (EPDC) and decreased nonmyocyte/nonendothelial cells intramyocardially. Furthermore, CCBE1 deficiency causes deregulation of EMT-related genes during heart development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Dounia Djeghloul, Andrew Dimond, Sherry Cheriyamkunnel, Holger Kramer, Bhavik Patel, Karen Brown, Alex Montoya, Chad Whilding, Yi-Fang Wang, Matthias E. Futschik, Nicolas Veland, Thomas Montavon, Thomas Jenuwein, Matthias Merkenschlager, Amanda G. Fisher
Summary: Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and polycomb repressor complexes, binds to chromosomes throughout mitosis and their depletion results in increased chromosome size. In this study, the researchers found that enzymes that catalyze H3K9 methylation are also retained on mitotic chromosomes. Mutants lacking H3K9me3 display unusually small and compact mitotic chromosomes, but this phenotype can be rescued by providing exogenous protein lysine methyltransferase or inhibiting Ezh2 activity. These findings highlight the important role of H3K9me3 in maintaining chromosome architecture and epigenetic memory during cell division.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Tania Barata, Isabel Duarte, Matthias E. Futschik
Summary: Stem cells possess the ability to self-renew and differentiate, making them crucial in processes like development and aging. By comparing multiple stem cell samples, a significant overlap in gene signatures was found, leading to the identification of integrated stemness signatures (ISSs). These ISSs provide a more reliable basis for research by excluding false positives.
Article
Virology
Jamie Fagg, Rupert Beale, Matthias E. Futschik, Elena Turek, David Chapman, Susan Halstead, Marc Jones, Joanna Cole-Hamilton, Rory Gunson, Malur Sudhanva, Paul E. Klapper, Harper Vansteenhouse, Sarah Tunkel, Anna Dominiczak, Timothy E. A. Peto, Tom Fowler
Summary: This study demonstrates that swab pooling has high sensitivity and specificity, and high-throughput laboratories are capable of implementing this method immediately, making it an option for rapid upscaling of laboratory capacity during future pandemics.
JOURNAL OF CLINICAL VIROLOGY
(2023)
Article
Infectious Diseases
Olivia Kay, Matthias E. Futschik, Elena Turek, David Chapman, Simon Carr, Malur Sudhanva, Paul E. Klapper, Tony Cox, Michael Hill, Joanna Cole-Hamilton, Peter Marks, Sarah A. Tunkel, Timothy Peto, Lindsey Davies, Tom Fowler
Summary: This study aimed to explore the feasibility of using expectorated saliva (ES) and drooled saliva (DS) for community mass testing. The results showed that ES and DS tests had a high level of concordance with combined throat and nose (CTN) swab-based results. DS showed a significantly higher sensitivity than ES and CTN swab in detecting symptomatic cases. This study demonstrates that saliva-based SARS-CoV-2 RNA testing is highly accurate and can be considered as an alternative to swabbing.
JOURNAL OF CLINICAL VIROLOGY PLUS
(2023)
Article
Oncology
Jemma Dunn, Vasileios P. Lenis, David A. Hilton, Rolf Warta, Christel Herold-Mende, C. Oliver Hanemann, Matthias E. Futschik