Article
Mathematics
Qian Xiao, Chao Ma, Shuailing Wang
Summary: In this paper, we study continued beta-fractions with golden ratio base beta and prove that if the continued beta-fraction expansion of a non-negative real number is periodic, then it is the root of a quadratic irreducible polynomial with coefficients in Z[beta].
Article
Ecology
Francisco Martinez-Hernandez, Awa Diop, Inmaculada Garcia-Heredia, Louis-Marie Bobay, Manuel Martinez-Garcia
Summary: Viral genetic microdiversity has critical impacts on the viral-host arms race, microbial community structure, and biogeochemical cycles. Single-virus genomics has discovered abundant microdiversity in an ocean virus infecting marine bacteria, with up to 1,500 viral strains and 30 related species found in a single sample. The maintenance of viral microdiversity over space and time, and the impact of recombination on virus and host speciation have been demonstrated.
Article
Mathematics
Yann Bugeaud, Dong Han Kim, Seul Bee Lee
Summary: The Levy constant of an irrational real number is defined by the exponential growth rate of the sequence of denominators of the principal convergents in its continued fraction expansion. The study shows that the set of Levy constants of irrational real numbers whose sequence of partial quotients is periodic or Sturmian is equal to the whole interval [log((1 + root 5)/2), +infinity). This suggests that the Levy constant is influenced by the Sturmian sequence and specific values of positive integers a, b.
PACIFIC JOURNAL OF MATHEMATICS
(2021)
Article
Multidisciplinary Sciences
Hatem M. Bahig, Dieaa Nassr, Mohammed A. Mahdi, Hazem M. Bahig
Summary: This paper presents a new technique that improves the attack on RSA with small private exponent using continued fractions and multicore systems. By finding an interval containing phi(n) and generating different points within the interval, the proposed technique enables the recovery of the private key. Experimental results show that the previous bound of the private key has been extended after three attacks on RSA with small private exponents.
Article
Automation & Control Systems
Xiaoming Duan, Saber Jafarpour, Francesco Bullo
Summary: This study investigates the stability of positive monotone systems using graph-theoretic conditions. Necessary and sufficient conditions for the stability of linear positive systems described by Metzler matrices are established, with novel graph-theoretic conditions obtained for the stability of Metzler systems. The results are also extended to nonlinear monotone systems with similar sufficient conditions for global asymptotic stability.
SIAM JOURNAL ON CONTROL AND OPTIMIZATION
(2021)
Article
Multidisciplinary Sciences
Victor Faundes, Martin D. Jennings, Siobhan Crilly, Sarah Legraie, Sarah E. Withers, Sara Cuvertino, Sally J. Davies, Andrew G. L. Douglas, Andrew E. Fry, Victoria Harrison, Jeanne Amiel, Daphne Lehalle, William G. Newman, Patricia Newkirk, Judith Ranells, Miranda Splitt, Laura A. Cross, Carol J. Saunders, Bonnie R. Sullivan, Jorge L. Granadillo, Christopher T. Gordon, Paul R. Kasher, Graham D. Pavitt, Siddharth Banka
Summary: The study uncovers the role of eIF5A in human development and disease, demonstrates the mechanistic complexity of EIF5A-related disorder, and raises possibilities for its treatment. Yeast and zebrafish experiments show that EIF5A variants cause a Mendelian disorder through reduced eIF5A-ribosome interactions, which can be partially corrected by spermidine supplementation.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Akshay J. J. Maheshwari, Alp M. M. Sunol, Emma Gonzalez, Drew Endy, Roseanna N. N. Zia
Summary: Faster-growing cells need to synthesize proteins more quickly, and the increased abundance of ribosomes alone cannot explain the increase in total protein synthesis rates. The productivity of individual ribosomes must also increase, almost doubling by an unknown mechanism. Physical crowding, transport, and stoichiometry together provide a more nuanced explanation.
Article
Biology
Hideyuki Nakanishi
Summary: Synthetic mRNAs produced by in vitro transcription can express any transgenes without the risk of insertional mutagenesis. Preclinical studies have developed translational regulation systems to ensure high efficacy and low adverse effects by producing the appropriate amount of therapeutic proteins.
Article
Biochemistry & Molecular Biology
Benjamin Tickman, Diego Alba Burbano, Venkata P. Chavali, Cholpisit Kiattisewee, Jason Fontana, Aset Khakimzhan, Vincent Noireaux, Jesse G. Zalatan, James M. Carothers
Summary: CRISPR-Cas transcriptional circuits are promising platforms for engineering metabolic networks and information processing circuits. This study develops design principles for CRISPRa/i circuits and establishes a framework for building scalable circuits.
Article
Biochemical Research Methods
Lori Van de Cauter, Federico Fanalista, Lennard van Buren, Nicola De Franceschi, Elisa Godino, Sharon Bouw, Christophe Danelon, Cees Dekker, Gijsje H. Koenderink, Kristina A. Ganzinger
Summary: Optimizing the continuous droplet interface crossing encapsulation (cDICE) method can produce defect-free GUVs, significantly improving reproducibility and encapsulation efficiency for various biological systems.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Materials Science, Biomaterials
Yang Zhang, Wentao Ding, Zhihui Wang, Huimin Zhao, Shuobo Shi
Summary: The importance of constructing host-orthogonal genetic systems, their potential applications in synthetic biology, and future challenges are discussed in this review.
Article
Mathematics, Applied
A. S. Chernikova, A. M. Nedashkovska
Summary: The importance of continued fractions in numerical methods is evident in various applications such as the development of the solar calendar, proving irrationality of numbers, calculating eigenvalues of matrices, and factorization algorithms. In this study, a simple scheme using matrix continued fractions was proposed for solving systems of nonlinear equations, with test problems confirming its convergence and effectiveness.
JOURNAL OF NUMERICAL AND APPLIED MATHEMATICS
(2021)
Article
Physics, Multidisciplinary
S. M. Khryashchev
Summary: This study examines the controllability of systems switched in discrete time, constructing controls using the theory of generalized multicomponent continued fractions and the congruences theory. The proposed control method is applied to specific systems to achieve the control goal of transferring a polysystem from an initial state to a final state.
NONLINEAR PHENOMENA IN COMPLEX SYSTEMS
(2021)
Article
Biochemical Research Methods
Maya Galili, Tamir Tuller
BMC BIOINFORMATICS
(2020)
Article
Genetics & Heredity
Yoram Zarai, Zohar Zafrir, Bunpote Siridechadilok, Amporn Suphatrakul, Modi Roopin, Justin Julander, Tamir Tuller
Review
Biochemistry & Molecular Biology
Shir Bahiri-Elitzur, Tamir Tuller
BIOCHEMICAL SOCIETY TRANSACTIONS
(2020)
Article
Biochemical Research Methods
Doron Levin, Tamir Tuller
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Genetics & Heredity
Tal Gutman, Guy Goren, Omri Efroni, Tamir Tuller
Summary: Silent mutations have significant predictive power over cancer classification and survival prognosis, likely due to their impact on gene expression. Combining both non-silent and silent mutations can achieve the best classification and survival estimation results for various cancer types. It is recommended to integrate silent mutations into cancer research to fully understand the genomic landscape of cancer and its implications on cancer fitness.
NPJ GENOMIC MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Tamar Neumann, Tamir Tuller
Summary: This study developed a predictive model of small subunit (SSU) density based on TCP-seq data and analyzed the effect of transcript features on SSU scanning dynamics. The results showed that the AUG context indeed affects the movement of the SSU, strong folding may cause the detachment of the SSU from the mRNA, and several novel sequence motifs can affect the SSU scan.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Itamar Menuhin-Gruman, Matan Arbel, Niv Amitay, Karin Sionov, Doron Naki, Itai Katzir, Omer Edgar, Shaked Bergman, Tamir Tuller
Summary: Modern synthetic biology relies on stable genetic constructs, but maintenance requires cell energy and natural selection can lead to loss of construct functionality. The ESO software tool automates the design of evolutionarily stable constructs while considering host organism characteristics to balance stability and gene expression.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
David Shallom, Danny Naiger, Shlomo Weiss, Tamir Tuller
Summary: In recent years, intracellular biophysical simulations have been increasingly used in both basic scientific research and synthetic biology. These simulations are time-consuming due to the complex networks of interactions between millions of components, and running them on parallel computers is not easy. This study presents a novel approach using dedicated hardware to address this issue, focusing specifically on simulating mRNA translation at a much faster rate than software solutions.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biology
Liyam Chitayat Levi, Ido Rippin, Moran Ben Tulila, Rotem Galron, Tamir Tuller
Summary: The development of computational biology methodologies has provided a comprehensive understanding of the complexity of microbiomes and their impact on the environment. However, current microbiome engineering techniques neglect the interactions between genetic information and bacterial populations. In this study, a generic computational method was developed to automatically tune gene expression in microbiomes based on user preferences. The method has been validated through computational and experimental tools.
Article
Biotechnology & Applied Microbiology
Arup Panda, Tamir Tuller
Summary: The environment may impact the codon and amino acid choice of microbial communities, and samples from similar environmental niches show similar codon and amino acid distribution compared to samples from other habitats. Factors like GC content, functional or taxonomic abundance cannot fully explain the trends observed at the codon or amino acid level, implying a direct environmental influence on them.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Review
Biotechnology & Applied Microbiology
Matan Arbel-Groissman, Itamar Menuhin-Gruman, Doron Naki, Shaked Bergman, Tamir Tuller
Summary: Evolutionary stability of synthetic constructs made of heterologous genes is a major challenge in synthetic biology, and the available tools to address this challenge are discussed in this review.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Rami Katz, Elad Attias, Tamir Tuller, Michael Margaliot
Summary: Research has shown that mRNAs compete for shared resources during translation, which can significantly impact the global dynamics of translation in the cell when resources are scarce. By modeling this competition using a network approach, it was found that adding a new mRNA has a complex effect on total protein production, with diminishing marginal utility as the number of mRNAs increases, leading to saturation of total protein production rate to a limiting value.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Biochemistry & Molecular Biology
Stav Carmel Ezra, Tamir Tuller
Summary: This study investigates the translation initiation process in chloroplasts and develops computational models to understand and model translation regulation. The folding energy of rRNA and mRNA is found to correlate with codon usage and protein levels. Additionally, the presence of various structural elements in chloroplast transcripts is reported.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Sophie Vinokour, Tamir Tuller
Summary: The study demonstrates the use of generic algorithms to introduce silent mutations for optimizing or reducing ribosomal traffic jams during mRNA translation. The cost of these algorithms includes factors such as computational time and the number of mutations introduced, enriching the methods for translation engineering.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Shir Bahiri-Elitzur, Tamir Tuller
Summary: Codon usage bias refers to the differing frequencies of synonymous codons in genes and organisms, believed to be a balance between mutational biases and natural selection. Various codon usage bias indices have been developed to estimate the fitness of coding sequences to different phenomena, with applications in biomedical fields. Despite the differences in aims, many indices tend to correlate, highlighting the importance of continuously developing new indices to capture additional aspects of gene expression steps.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)