Article
Biology
Fabien Duveau, Petra Vande Zande, Brian P. H. Metzger, Crisandra J. Diaz, Elizabeth A. Walker, Stephen Tryban, Mohammad A. Siddiq, Bing Yang, Patricia J. Wittkopp
Summary: The study found that mutations with trans-regulatory effects on the same focal gene were enriched in coding sequences of transcription factors predicted to regulate the gene, but also mapped to other types of genes involved in various biological processes. This shows how genetic changes in diverse types of genes can impact a gene's expression in trans and provide raw material for segregating trans-regulatory variation within natural populations.
Review
Neurosciences
Camila. D. D. Arcuschin, Marina Pinkasz, Ignacio. E. E. Schor
Summary: The functionality of living organisms is influenced by different types of perturbations, both internal and external, with functional effects and phenotypic impact. Multicellular organisms with complex body patterns and cell type heterogeneity rely on robustness to maintain the functionality of their genetic developmental programs. We discuss the molecular mechanisms of robustness in neurodevelopment and its implications for gene regulatory networks driving neural development, including transcriptional regulatory elements, miRNA-based regulation, and gene network topology.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2023)
Article
Computer Science, Theory & Methods
Satyaki Roy, Preetam Ghosh, Nirnay Ghosh, Sajal K. Das
Summary: The emergence of the edge computing network paradigm has improved network performance but faces optimization challenges related to the topological robustness of biological networks. The study of transcriptional regulatory networks as biological networks provides inspiration for the design of intelligent networking protocols and architectures.
ACM COMPUTING SURVEYS
(2021)
Article
Biochemical Research Methods
Yuridia S. Posadas-Garcia, Carlos Espinosa-Soto
Summary: This study investigates how gene duplication affects the behavior of gene regulatory networks and finds that gene duplication often mitigates the impact of new mutations, and this effect is not merely due to changes in the number of genes.
BMC BIOINFORMATICS
(2022)
Article
Biology
Stefan Landmann, Caroline M. Holmes, Mikhail Tikhonov
Summary: Bacteria can learn the structure of environmental fluctuations through evolution, while also inferring and acting upon environmental statistics through physiological mechanisms. Research shows that a common regulatory motif is sufficient for bacteria to learn the statistical structure of the environment and translate this information into predictive behavior, accomplishing these tasks near-optimally.
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
Multidisciplinary Sciences
Wencheng Yin, Luis Mendoza, Jimena Monzon-Sandoval, Araxi O. Urrutia, Humberto Gutierrez
Summary: Transcriptomes self-organize into gene co-expression clusters where genes display coordinated expression patterns across samples. Highly co-expressed gene groups are enriched in common functions and processes. Widespread co-expression naturally emerges in regulatory networks and serves as a reliable indicator of active co-regulation in cellular contexts.
Article
Biology
Milo S. Johnson, Michael M. Desai
Summary: The distribution of fitness effects in a population can change during evolution, affecting the rate of adaptation and accumulation of deleterious mutations. This study directly measures changes in the fitness landscape neighborhood during laboratory adaptation and finds differences in the distribution due to variations in patterns of epistasis at the level of individual mutations.
Review
Cell Biology
Jeanne M. C. McDonald, Robert D. Reed
Summary: Gene regulatory networks (GRNs) are essential for organismal development and understanding their structure is crucial for studying phenotypic change and evolution. However, the field of evolutionary developmental biology has largely overlooked the evolution of functional relationships within GRNs. This paper discusses the architecture of developmental GRNs, the variation in positive selection strength across GRNs, and proposes testable models and experimental approaches to study these patterns.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, Jianlin Cheng
Summary: GNET2 is an improved implementation of GNET as an integrated R package, providing more flexibility for parameter initialization and regulatory module construction, offering a convenient option for the inference of gene regulatory networks.
Article
Engineering, Industrial
Sebastian Wandelt, Yifan Xu, Xiaoqian Sun
Summary: This study uses complex network analysis techniques to evaluate the importance of airports in airline operations and proposes a recovery baseline model for airline recovery under node disruptions. The research found that existing node importance methods often underestimate the impact of node failures.
RELIABILITY ENGINEERING & SYSTEM SAFETY
(2023)
Article
Plant Sciences
Mimi Luo, Xiaoxia Liu, Hongyan Su, Meiling Li, Mengfei Li, Jianhe Wei
Summary: A transcriptomic analysis was conducted on Angelica sinensis using RNA-seq, revealing key genes involved in flowering regulation during vernalization and providing new insights into the regulatory networks of flowering in Angelica sinensis.
Article
Biotechnology & Applied Microbiology
Yongqing Zhang, Qingyuan Chen, Meiqin Gong, Yuanqi Zeng, Dongrui Gao
Summary: This study proposes constructing gene regulatory networks under different molecular subtypes of MIBC and analyzing the regulatory differences. Differential expression analysis and network analysis revealed significant differences in expression and regulatory relationships of genes such as SERPINI1, NOTUM, and FGFR1. Pathway enrichment analysis showed pathways like Neuroactive ligand-receptor interaction and Cytokine-cytokine receptor interaction are significantly enriched with diverse genes in bladder cancer subtypes.
Article
Biochemical Research Methods
Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho
Summary: ShareNet is a Bayesian framework that enhances the accuracy of cell type-specific gene regulatory networks by sharing information across related cell types. The method demonstrates significantly improved accuracy on three benchmark scRNA-seq datasets and reveals key changes in gene associations that support the complex rewiring of regulatory networks.
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)
Article
Plant Sciences
Esmer Jongedijk, Sebastian Muller, Aalt D. J. van Dijk, Elio Schijlen, Antoine Champagne, Marc Boutry, Mark Levisson, Sander van der Krol, Harro Bouwmeester, Jules Beekwilder
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Article
Genetics & Heredity
Sevgin Demirci, Roven Rommel Fuentes, Willem van Dooijeweert, Saulo Aflitos, Elio Schijlen, Thamara Hesselink, Dick de Ridder, Aalt D. J. van Dijk, Sander Peters
Summary: Melon, an important crop in the Cucurbitaceae family, has undergone cross pollination and domestication throughout its breeding history, resulting in a highly diverse genetic structure. Research on the genetic diversity and relationships among different melon cultivars has shed light on the breeding history of melon. Additionally, unique inversions and expanded resistance genes in cultivar genomes compared to wild relatives provide insights into the selective breeding that has shaped modern melon varieties.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Muhammad Farooq, Aalt D. J. van Dijk, Harm Nijveen, Mark G. M. Aarts, Willem Kruijer, Nguyen Thu-Phuong, Shahid Mansoor, Dick de Ridder
Summary: Prediction of growth-related complex traits in crop breeding has been revolutionized by technological advancements in genomics and phenomics. Incorporating prior biological knowledge can improve genomic prediction accuracy, with the effectiveness depending on the trait, type of knowledge, and trait heritability. Transcriptomics provides additional evidence for improvement when defining functional gene groups.
FRONTIERS IN GENETICS
(2021)
Review
Multidisciplinary Sciences
Aalt Dirk Jan van Dijk, Gert Kootstra, Willem Kruijer, Dick de Ridder
Summary: Machine learning has been widely applied in plant science and breeding to extract meaningful patterns from large, complex plant data sets, particularly in connecting genotypes to different levels of phenotypes such as biochemical traits and yield.
Article
Nutrition & Dietetics
Ying Deng, Coen Govers, Ellen ter Beest, Aalt-Jan van Dijk, Kasper Hettinga, Harry J. Wichers
Summary: In this study, macrophages and dendritic cells derived from THP-1 monocytes were used to investigate allergen recognition and processing. It was found that macrophages exhibited a stronger transcriptional response compared to dendritic cells, especially when exposed to severely structurally modified beta-lactoglobulin. These results indicate the importance of processing in the transcriptional response of innate immune cells towards beta-lactoglobulin.
FRONTIERS IN NUTRITION
(2021)
Article
Biochemical Research Methods
Janani Durairaj, Elena Melillo, Harro J. Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D. J. van Dijk
Summary: Predicting enzyme function is a challenging task, especially with the vast amount of protein sequences and limited experimental characterization. This study presents a computational approach using homology modeling, machine learning, and co-evolution analysis to predict carbocation specificity in sesquiterpene synthases. The results identify residues and structural regions influencing product specificity and can be applied to enzyme engineering in various enzyme classes.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Roven Rommel Fuentes, Dick de Ridder, Aalt D. J. van Dijk, Sander A. Peters
Summary: The study reveals that the recombination landscape is overall conserved between domesticated and wild tomato populations, with local changes in effective recombination rate in specific genomic regions. Dynamics of recombination hotspots resulting from domestication are also studied, showing that loss of such hotspots is associated with selective sweeps, particularly in the pericentromeric heterochromatin. This study detected footprints of genetic changes and structural variants, including transposable elements, linked with hotspot divergence during domestication, causing fine-scale alterations to recombination patterns and resulting in linkage drag.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Yanting Wang, Janani Durairaj, Hernando G. Suarez Duran, Robin van Velzen, Kristyna Flokova, Che-Yang Liao, Aleksandra Chojnacka, Stuart MacFarlane, M. Eric Schranz, Marnix H. Medema, Aalt D. J. van Dijk, Lemeng Dong, Harro J. Bouwmeester
Summary: By using root RNA-seq data and co-expression analysis, candidate genes involved in the biosynthesis of SLs in tomato, including several cytochrome P450 genes, were discovered. Experimental results demonstrated the catalytic activity of CYP712G1 in oxidizing orobanchol to form DDH isomers, which can be further converted to solanacol, a major component of tomato root exudate.
Review
Biochemical Research Methods
Selena Koene, Umidjon Shapulatov, Aalt D. J. van Dijk, Alexander R. van der Krol
Summary: The growth and defense of Arabidopsis are regulated by specific transcription factors and co-factors, with PIF4, BZR1, HY5, and MYC2 playing key roles. Negative feedback regulation is observed on PIF4, BZR1, and MYC2 activity by their respective co-factors, while positive feedback is observed on HY5 activity by its co-factors. The balance between growth and defense is maintained through direct cross-regulation between HY5 and MYC2, as well as potential transcriptional feedback between PIF4, BZR1, HY5 and MYC2 and their co-factor genes.
PLANT MOLECULAR BIOLOGY REPORTER
(2023)
Article
Biochemistry & Molecular Biology
Rumyana Karlova, Jeroen Busscher, Florence M. Schempp, Markus Buchhaupt, Aalt D. J. van Dijk, Jules Beekwilder
Summary: This study developed an approach to identify and characterize enzymes that can detoxify plant monoterpenes and found that glycosyltransferases can protect cells from the toxicity of these compounds.
Article
Biochemistry & Molecular Biology
Arman Beyraghdar Kashkooli, Aalt D. J. van Dijk, Harro Bouwmeester, Alexander van der Krol
Summary: This study describes the highly specialized function of individual LTPs for different products in the same terpenoid biosynthesis pathway, and investigates the function of a GPI anchor in LTPs. Eight non-specific Lipid transfer proteins (nsLTPs) genes expressed in feverfew trichomes were identified, and their role in the transport of lipophilic sesquiterpene lactones produced in feverfew trichomes was tested. The results showed that two nsLTPs (TpLTP1 and TpLTP2) improved extracellular accumulation of the sesquiterpene costunolide, while one nsLTP (TpLTP3) specifically exported parthenolide.
PLANT MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
C. Li, L. Dong, J. Durairaj, J. -C. Guan, M. Yoshimura, P. Quinodoz, R. Horber, K. Gaus, J. Li, Y. B. Setotaw, J. Qi, H. De Groote, Y. Wang, B. Thiombiano, K. Flokova, A. Walmsley, T. V. Charnikhova, A. Chojnacka, S. Correia de Lemos, Y. Ding, D. Skibbe, K. Hermann, C. Screpanti, A. De Mesmaeker, E. A. Schmelz, A. Menkir, M. Medema, A. D. J. Van Dijk, J. Wu, K. E. Koch, H. J. Bouwmeester
Summary: Maize, a major crop in Africa, is threatened by the parasitic witchweed Striga. Researchers have discovered two new strigolactones, zealactol and zealactonoic acid, which have weaker germination-inducing effects on Striga compared to the major strigolactone, zealactone. They also identified a key enzyme, ZmCYP706C37, in the maize strigolactone biosynthetic pathway, and reducing its activity, along with two others, can change strigolactone composition and reduce Striga germination and infection.
Article
Biochemistry & Molecular Biology
Janani Durairaj, Dick de Ridder, Aalt D. J. van Dijk
Summary: Recent breakthroughs in protein structure prediction indicate a new era in structural bioinformatics. Machine learning methods in protein bioinformatics are shifting from sequence-based approaches to utilizing structural information as input. This review explores the diversity of structure-based machine learning approaches, input methods, and typical applications in protein biology, while also discussing the current challenges and opportunities in this important and growing field.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Sam W. van Es, Aitor Munoz-Gasca, Francisco J. Romero-Campero, Eduardo Gonzalez-Grandio, Pedro de los Reyes, Carlos Tarancon, Aalt D. J. van Dijk, Wilma van Esse, Alberto Pascual-Garcia, Gerco C. Angenent, Richard G. H. Immink, Pilar Cubas
Summary: The study investigates the regulatory network of the transcription factor BRC1 in controlling shoot branching and promoting bud dormancy in Arabidopsis. The researchers constructed the BRC1 gene regulatory network by integrating multi-omics data and validated the role of a group of transcription factors in modulating the network and promoting bud dormancy.
Article
Plant Sciences
Miguel Correa Marrero, Sylvain Capdevielle, Weijie Huang, Ali M. Al-Subhi, Marco Busscher, Jacqueline Busscher-Lange, Froukje van Der Wal, Dick de Ridder, Aalt D. J. van Dijk, Saskia A. Hogenhout, Richard G. H. Immink
Summary: This study generated a protein-protein interaction network between phytoplasma effectors and Arabidopsis thaliana transcription factors. The results showed widespread interactions between phytoplasma effectors and host transcription factors, especially those involved in host developmental processes. Comparison with other host-pathogen protein interaction networks revealed that phytoplasma effectors have unusual targets, indicating a unique and unusual infection strategy employed by phytoplasmas.
