Article
Genetics & Heredity
Atsunori Yoshimura, Takashi Sutani, Katsuhiko Shirahige
Summary: The study shows that Eco1 in budding yeast physically interacts with the MCM complex, specifically binding to the Mcm2 subunit and stabilizing Eco1 through their interaction, promoting DNA replication-coupled SCC establishment.
Article
Biotechnology & Applied Microbiology
Michael A. Boemo
Summary: This paper introduces a new software, DNAscent v2, for high-throughput, single-molecule detection of DNA replication dynamics with fast and accurate detection of the thymidine analogue BrdU. The software excels in accuracy, speed, and versatility across different experimental protocols.
Review
Biochemistry & Molecular Biology
Magdalena Foltman, Alberto Sanchez-Diaz
Summary: This article focuses on the significance of the highly conserved TOR signaling pathway, particularly the connection between TORC1 complex in budding yeast and the cell cycle, and the importance of this connection for cell size and chromosome stability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Tim Hachigian, Drew Lysne, Elton Graugnard, Jeunghoon Lee
Summary: A novel aptamer transduction network was designed to release customizable output domains, eliminating the need for significant redesign of downstream DNA reaction networks. The aptamer transducer showed successful customizability and feed-forward capability in amplifying signal detection.
Article
Microbiology
Setsu Kato, Kenta Suzuki, Taiki Kenjo, Junya Kato, Yoshiteru Aoi, Yutaka Nakashimada
Summary: Saccharomyces cerevisiae is widely used as a model organism for aging and longevity studies. In a clonal population, cell death in the stationary phase is asynchronous, highlighting heterogeneity in survival at a single-cell level. Cell size heterogeneity and its correlation with death rate are observed, with cells shrinking upon death and a constant proportion between cell size and shrinkage noted in different strains. Further investigation is needed to understand the mechanisms behind this shrinkage event and its implications for cell death and survival heterogeneity.
Article
Biochemical Research Methods
Pascal A. Pieters, Bryan L. Nathalia, Ardjan J. van der Linden, Peng Yin, Jongmin Kim, Wilhelm T. S. Huck, Tom F. A. de Greef
Summary: Regulatory pathways in living cells use feed-forward architectures to process and interpret signals, with the ability to reduce noise and detect fold changes. Experimental study in bacterial cells using post-transcriptional regulation has implemented a synthetic feed-forward loop, showing effective repression of background activity but limited potential as a temporal filter.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Genetics & Heredity
Yulong Li, Alexander J. Hartemink, David M. MacAlpine
Summary: This study investigated the dynamic changes in chromatin organization at and surrounding replication origins in Saccharomyces cerevisiae. It found that the downstream repositioning of the origin-proximal +1 nucleosome and an increase in protected DNA fragments spanning the ARS consensus sequence are indicative of pre-RC assembly. The strongest correlation between chromatin occupancy at the ACS and origin efficiency occurred in early S phase, consistent with the rate-limiting formation of the CMG complex being a determinant of origin activity. Nucleosome disruption and disorganization were observed emanating from replication origins and traveling with the elongating replication forks in S phase, reflecting the disassembly and assembly of chromatin ahead of and behind the replication fork.
Article
Biochemical Research Methods
Andreas P. Cuny, Aaron Ponti, Tomas Kundig, Fabian Rudolf, Jorg Stelling
Summary: TracX improves the accuracy of single-cell tracking using a fingerprinting approach to measure cell similarity across consecutive images. It is applicable across different cell types and image modalities, aiding in accurate cell observation and biological discovery in single-cell biology.
Article
Biochemistry & Molecular Biology
Valentina Tosato, Beatrice Rossi, Jason Sims, Carlo V. Bruschi
Summary: This study investigates the cell uptake and genomic integration of exogenous linear DNA in the model organism Saccharomyces cerevisiae throughout the cell cycle. The researchers found that transformability increases in S phase regardless of sequence homologies, and the efficiency of chromosomal integration depends on the genomic targets during a specific phase. The Pol32 polymerase was found to control a specific translocation between chromosomes XV and VIII during DNA synthesis. The cell-cycle dependent regulation of DNA repair pathways under stress and the increase of ROS levels following translocation events were also discovered.
Article
Biology
Mark C. Johnson, Geylani Can, Miguel Monteiro Santos, Diana Alexander, Philip Zegerman
Summary: This study reveals that Rad53 phosphorylates the same substrates throughout the cell cycle, not just in S-phase, suggesting its roles beyond S-phase. By inhibiting 51d3 and Dbf4, Rad53 limits re-replication in G2/M, preventing gene amplification, and inhibiting these substrates in G1 prevents premature initiation at the G1/S transition. This redefinition of the 'S-phase checkpoint' has implications for understanding checkpoint function in cancers without proper cell cycle controls.
Article
Microbiology
Kathrin Alpers, Elisabeth Vatareck, Lothar Groebe, Mathias Muesken, Maren Scharfe, Susanne Haeussler, Jurgen Tomasch
Summary: Pseudomonas aeruginosa undergoes a transition from fast growth with overlapping cell cycles to sustained slow growth with non-overlapping cell cycles when cultivated under standard laboratory conditions. This transition is characterized by sequential changes in transcriptional activity along the chromosome and a shift in quorum sensing activity. RNA sequencing of subpopulations identified distinct gene expression patterns for replicating and nonreplicating cells.
Article
Biochemical Research Methods
Chen Jia, Abhyudai Singh, Ramon Grima
Summary: This study investigates the dynamics of cell size in fission yeast, revealing the relationship between different cell growth phases and size control strategies, as well as their effects under various growth conditions. By matching experimental data with theoretical models, the size control strategy and model parameters of cell size distribution are determined.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tadas Andriuskevicius, Anton Dubenko, Svetlana Makovets
Summary: The proper maintenance of genetic material is crucial for the survival of living organisms. In this study, it is shown that the regulation of Rad51 nucleoprotein filaments by Srs2 and Rad54 is essential for the inhibition of damage-associated DNA synthesis during DNA repair, as well as for cell survival under normal growth conditions. The lack of Srs2 and Rad54 impedes cell recovery from replication stress, resulting in genome instability features and the loss of genetic material.
Article
Biochemistry & Molecular Biology
Aneliya Ivanova, Aleksandar Atemin, Sonya Uzunova, Georgi Danovski, Radoslav Aleksandrov, Stoyno Stoynov, Marina Nedelcheva-Veleva
Summary: Cells have evolved mechanisms to regulate DNA replication and cell cycles in response to DNA damage and replication stress. The absence of Dia2 prolongs the cell cycle, increases cell size, and activates the S-phase checkpoint.
Editorial Material
Microbiology
Jacob L. Steenwyk
Summary: Cell cycle checkpoints and DNA repair pathways are crucial for maintaining genome integrity, but recent studies have revealed evolutionary diversity in eukaryotic DNA damage responses, with some fungi showing reduced activation of key kinases and downregulation of genome maintenance genes in response to DNA damage.
Article
Biotechnology & Applied Microbiology
Alberto Santos, Ana R. Colaco, Annelaura B. Nielsen, Lili Niu, Maximilian Strauss, Philipp E. Geyer, Fabian Coscia, Nicolai J. Wewer Albrechtsen, Filip Mundt, Lars Juhl Jensen, Matthias Mann
Summary: A knowledge graph platform integrates proteomics with other omics data and biomedical databases, providing support for precision medicine. The Clinical Knowledge Graph (CKG) is a flexible data model that can accommodate a large number of nodes and relationships, accelerating the analysis and interpretation of proteomics data. By incorporating CKG, clinical decision-making can be informed and proteomics data can be enriched.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Istvan Z. Reguly, David Csercsik, Janos Juhasz, Kalman Tornai, Zsofia Bujtar, Gergely Horvath, Bence Keoemley-Horvath, Tamas Kos, Gyoergy Cserey, Kristof Ivan, Sandor Pongor, Gabor Szederkenyi, Gergely Roest, Attila Csikasz-Nagy
Summary: Pandemic management requires reliable and efficient dynamical simulation to predict and control disease spreading. Vaccination strategies prioritising occupational risk groups can minimize infections, while prioritising vulnerable groups can minimize mortality. Intensive vaccination and non-pharmaceutical interventions can significantly suppress the spread of the virus.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Marcell Miski, Bence Mark Keomley-Horvath, Dorina Rakoczi Megyerine, Attila Csikasz-Nagy, Zoltan Gaspari
Summary: This study used large-scale stochastic simulations of protein binding events to predict the presence and distribution of PSD complexes. The results show that the relative ratio of emerging protein complexes is sensitive to subtle changes in protein abundances, highlighting the importance of explicit simulations in understanding protein availability and complex formation.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Haris Zafeiropoulos, Savvas Paragkamian, Stelios Ninidakis, Georgios A. Pavlopoulos, Lars Juhl Jensen, Evangelos Pafilis
Summary: PREGO is a comprehensive knowledge base that provides associations between what, where, and who through text mining and data integration techniques, assisting researchers in designing and interpreting experiments and their results.
Article
Biochemistry & Molecular Biology
Bela Novak, John J. Tyson
Summary: In 1996, Kim Nasmyth proposed that the eukaryotic cell cycle consists of alternating transitions between G1 and S-G2-M phases. These transitions are driven by helper proteins and are associated with high activity of CDKs and CDK antagonists. If the latch mechanism of CDK switches is broken, the biochemical reactions can swing back and forth across the transitions.
Article
Biochemical Research Methods
Xiangyu Yao, Benjamin L. Heidebrecht, Jing Chen, John J. Tyson
Summary: This paper explores mathematical models of genetic oscillators based on transcription-translation feedback and investigates modifications to improve the accuracy of the models. The study relaxes constraints by introducing multistep reaction chains and replacing rate laws, resulting in more realistic parameter values. Additionally, the addition of a supplementary positive feedback loop enhances the robustness of the oscillations. The results provide testable predictions for future experimental studies.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Mathematics, Applied
Dorjsuren Battogtokh, John J. Tyson
Summary: Shoot apical meristems (SAMs) are responsible for the development of above-ground tissues in plants. The growth and expansion of SAMs rely on the division of stem cells in a central zone, which is regulated by a transcription factor called WUSCHEL. WUSCHEL is self-activating and downregulated by a signaling pathway involving CLAVATA proteins. While most mathematical models of stem cell confinement in the SAM rely on Turing's mechanism, this study proposes a bistable-switch model based on interactions between WUSCHEL and CLAVATA. Comparisons between the two mechanisms demonstrate that the bistable-switch provides a better explanation for the nucleation and confinement of stem cells.
Article
Mathematical & Computational Biology
Suchana Chakravarty, Christian I. Hong, Attila Csikasz-Nagy
Summary: Temperature compensation and robustness to biological noise are key characteristics of the circadian clock. The circadian oscillators can maintain steady oscillations in a wide range of environmental conditions due to the presence of feedback loops. The negative feedback loop system performs the best in compensating temperature changes, while a positive feedback loop can reduce extrinsic noise in periods of circadian oscillators and negative feedback loops reduce intrinsic noise.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Biology
Rajat Singhania, John J. Tyson
Summary: When a perfume is released in a room, the initial occupants will smell it but become desensitized after a few minutes, while newcomers can still smell it. This adaptation behavior is studied in this paper, which focuses on the molecular basis behind it using an evolutionary search approach.
Article
Engineering, Environmental
Peter Polcz, Kalman Tornai, Janos Juhasz, Gyorgy Cserey, Gyorgy Surjan, Tamas Pandics, Eszter Roka, Marta Vargha, Istvan Z. Reguly, Attila Csikasz-Nagy Csikasz-Nagya, Sandor Pongor, Gabor Szederkeny
Summary: Wastewater-based epidemiology (WBE) is a cost-effective and reliable approach for monitoring the COVID-19 pandemic. Fusion of wastewater measurements with clinical data and other indicators is essential for future epidemic surveillance.
Proceedings Paper
Computer Science, Interdisciplinary Applications
Bence Keomley-Horvath, Gergely Horvath, Peter Polcz, Balint Siklosi, Kalman Tornai, Janos Juhasz, Gabor Szederkenyi, Gyorgy Cserey, Attila Csikasz-Nagy, Istvan Z. Reguly
Summary: The COVID-19 pandemic has created an urgent need for decision making, which requires integrating high-performance computing (HPC) into workflows for model calibration and decision space exploration. This paper presents the design of PanSim, a portable and efficient agent-based simulator used extensively for modeling and forecasting the pandemic in Hungary. The performance and scalability of PanSim on CPUs and GPUs are demonstrated, and the integrated workflows are discussed.
2022 FIRST COMBINED INTERNATIONAL WORKSHOP ON INTERACTIVE URGENT SUPERCOMPUTING (CIW-IUS)
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
T. Gaizer, B. Piller, L. David, N. Gorog, M. Metzig, B. Makove, E. Nagy, D. Pesti, J. Juhasz, C. I. Pongor, A. Csikasz-Nagy
Review
Biology
John J. Tyson, Bela Novak
Summary: Cell growth, DNA replication, mitosis, and division are fundamental processes for passing on life. The eukaryotic cell cycle is a periodic process that plays a crucial role in maintaining the integrity of the genome. Key factors in cell cycle control include mitosis promoting factor and cyclin-dependent kinases.
Article
Biochemistry & Molecular Biology
Timothy K. Sheils, Stephen L. Mathias, Keith J. Kelleher, Vishal B. Siramshetty, Dac-Trung Nguyen, Cristian G. Bologa, Lars Juhl Jensen, Dusica Vidovic, Amar Koleti, Stephan C. Schurer, Anna Waller, Jeremy J. Yang, Jayme Holmes, Giovanni Bocci, Noel Southall, Poorva Dharkar, Ewy Mathe, Anton Simeonov, Tudor Oprea
Summary: The NIH's IDG program aims to study poorly characterized proteins that can be modulated using small molecules or biologics. The program has produced the Target Central Resource Database (TCRD) and Pharos, which aggregate data from multiple sources and rank targets based on data availability, in machine learning ready format. Integrated data include protein interactions, disease associations, and gene signatures, among others, enabling new visualizations and sections to empower users in exploring the druggable genome.
NUCLEIC ACIDS RESEARCH
(2021)
