Article
Multidisciplinary Sciences
Nahla A. Belal, Lenwood S. Heath
Summary: This method proposes using partial orders (posets) to detect horizontal gene transfer (HGT). Each species/gene pair is represented as a poset, and a phylogenetic tree compatible with the posets is constructed for each gene. The set of posets can also be derived from the constructed trees. The trees for each gene are compared and tested for contradicting information, indicating the occurrence of HGT.
Article
Biochemistry & Molecular Biology
Minkyu Park, Pascal-Antoine Christin, Jeffrey L. Bennetzen
Summary: Limited genome resources have hindered the study of horizontal transfer of DNA in plants. This study utilized low-depth sequencing data from 19 uncharacterized panicoid grasses to investigate horizontal transfer, revealing frequent transfers of LTR-retrotransposons between panicoids and rice. Additionally, analysis of Echinichloa and Oryza species showed recurrent horizontal transfers of diverse transposable element types at different points in Oryza history.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Operations Research & Management Science
Sandeep K. Singh, Brian D. Anderson, Ehsan Taheri, John L. Junkins
Summary: This paper investigates the manifolds of three Near-Rectilinear Halo Orbits (NRHOs) and optimal low-thrust transfer trajectories using a high-fidelity dynamical model. Time- and fuel-optimal low-thrust transfers to (and from) these NRHOs are generated leveraging their 'invariant' manifolds, which serve as long terminal coast arcs. Analyses are performed to identify suitable manifold entry/exit conditions based on inclination and minimum distance from the Earth, and the relative merits of the stable/unstable manifolds are studied with regard to time- and fuel-optimality criteria.
JOURNAL OF OPTIMIZATION THEORY AND APPLICATIONS
(2021)
Article
Multidisciplinary Sciences
Jeffrey J. Power, Fernanda Pinheiro, Simone Pompei, Viera Kovacova, Melih Yueksel, Isabel Rathmann, Mona Foerster, Michael Laessig, Berenike Maier
Summary: Horizontal gene transfer is an important factor in bacterial evolution, allowing for rapid evolution and increased adaptation in recipient organisms. Adaptive evolution mainly occurs in populations with increased fitness, with HGT selection having a broad genetic basis and showing different types of selection in functional gene networks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Genetics & Heredity
Megan L. Smith, Matthew W. Hahn
Summary: The availability of whole genome sequences was expected to provide unlimited data for phylogenetics, but reliance on single-copy genes has limited the amount of usable data. New methods that allow the inclusion of duplicated genes appear promising for maximizing the use of genomic data, with recent developments showing robustness to incomplete lineage sorting and inclusion of paralogs. Further research is needed to explore potential pitfalls and avenues for improvement.
TRENDS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Li-Bin Wang, Zhi-Kun Li, Le-Yun Wang, Kai Xu, Tian-Tian Ji, Yi-Huan Mao, Si-Nan Ma, Tao Liu, Cheng-Fang Tu, Qian Zhao, Xu-Ning Fan, Chao Liu, Li-Ying Wang, You-Jia Shu, Ning Yang, Qi Zhou, Wei Li
Summary: This study reports successful programmed chromosome ligation in mice, leading to the creation of new karyotypes. By fusing chromosomes 1 and 2, as well as chromosomes 4 and 5, using haploid embryonic stem cells and gene editing, the researchers were able to generate new chromosome combinations. The fused chromosome pairs had minimal impact on chromatin conformation and stem cell differentiation. However, the fused chromosomes 1 and 2 resulted in mitotic arrest, polyploidization, and embryonic lethality, while the smaller fused chromosome composed of chromosomes 4 and 5 could be passed on to homozygous offspring.
Article
Astronomy & Astrophysics
Benoit-Joseph Grea, Antoine Briard
Summary: By extending the potential approach to the magnetohydrodynamics equations, the authors found nonlinear solutions to the single-mode Rayleigh-Taylor instability and predicted the velocities of terminal bubble and spike under different Atwood numbers. In the nonlinear regime, the magnetic field can enhance the growth rate, leading to velocities faster than the Alfven speed. Furthermore, the solutions provide insights into inferring the orientation and intensity of the magnetic field.
ASTROPHYSICAL JOURNAL
(2023)
Article
Astronomy & Astrophysics
Chaitanya Afle, Duncan A. Brown
Summary: Galactic core-collapse supernovae are studied as potential sources of gravitational waves, with the ability of gravitational-wave observatories to extract properties of the collapsing progenitor being investigated through simulations of supernovae. Bayesian parameter inference and principal component analysis are used to calculate posterior probabilities for physical properties based on gravitational-wave observations, demonstrating the precision of estimating key parameters using this method.
Article
Biochemistry & Molecular Biology
Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu
Summary: The reconstruction of phylogenetic networks is a challenging task due to the vastness of the network space. One approach is to solve the minimum phylogenetic network problem by inferring phylogenetic trees first and then computing the smallest network that displays all the trees. A new method, named ALTS, was developed to infer the minimum tree-child network by aligning lineage taxon strings in the phylogenetic trees, overcoming the limitations of existing programs. ALTS is fast enough to handle large-scale networks with reticulations for a set of up to 50 phylogenetic trees with 50 taxa in about 15 minutes on average.
Article
Biochemistry & Molecular Biology
Paul Banse, Juliette Luiselli, David P. Parsons, Theotime Grohens, Marco Foley, Leonardo Trujillo, Jonathan Rouzaud-Cornabas, Carole Knibbe, Guillaume Beslon
Summary: While little is known about the evolutionary significance of chromosomal rearrangements, the study using Aevol simulation platform shows that chromosomal rearrangements make decisive contributions to evolutionary dynamics by expanding the gene repertoire, reducing the effect of diminishing-returns epistasis, and regulating the size of the genome through indirect selection for reproductive robustness.
Article
Biotechnology & Applied Microbiology
Irene M. Kaplow, Daniel E. Schaffer, Morgan E. Wirthlin, Alyssa J. Lawler, Ashley R. Brown, Michael Kleyman, Andreas R. Pfenning
Summary: This study proposes a machine learning-based approach to evaluate enhancer conservation, which leverages the combinatorial sequence code of enhancer activity instead of relying on individual nucleotide alignment. The researchers use a convolutional neural network model to predict tissue-specific open chromatin in mammals and demonstrate the model's high accuracy in predicting enhancer conservation and divergence. This framework provides a mechanism to annotate tissue-specific regulatory function across genomes and study enhancer evolution using predicted regulatory differences.
Article
Chemistry, Physical
Xiang Huang, Jiong Wang, Changming Zhao, Li-Yong Gan, Hu Xu
Summary: This paper proposes a PdTe2 bilayer as a promising electrocatalyst for the oxygen reduction reaction (ORR), based on extensive investigation of its electronic properties and atomic-level reaction kinetics. It is found that under electrochemical reducing conditions, the electron is directly transferred to the O-2 adsorbed on the PdTe2 bilayer, reducing the dissociation barrier of O-2 and promoting the ORR via a dissociative pathway. The electrochemical steps in this pathway have barriers less than 0.1 eV at the ORR limiting potential, indicating fast ORR kinetics at ambient conditions. It is considered a promising candidate for fuel cell applications due to its excellent energy efficiency and four-electron selectivity.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Astronomy & Astrophysics
Tim Cunningham, Pier-Emmanuel Tremblay, Evan B. Bauer, Odette Toloza, Elena Cukanovaite, Detlev Koester, Jay Farihi, Bernd Freytag, Boris T. Gansicke, Hans-Gunter Ludwig, Dimitri Veras
Summary: White dwarfs with warm hydrogen-rich atmospheres and helium-rich atmospheres above certain temperatures are unable to efficiently spread accreted metals across their surface, while cooler atmospheres show a largely homogeneous distribution of metals within a vertical diffusion time-scale. These results have significant implications for studies of the bulk composition of evolved planetary systems and models of accretion disc physics.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Haiyang Jiang, Tao Chen, Fengxin Kang, Fugang Wang, Liangliang Guo, Yanling Cao
Summary: The decomposition of clay minerals and the corrosion of rocks are important factors affecting the development of clay nanopores. Under conditions of no water and water immersion, with the increase of decomposition temperature or immersion time, the corrosion of clay minerals becomes more obvious, and the specific surface area of nanoscale pores also shows a decreasing trend. The corrosion of clay is closely related to the changes in the development of nanoscale pores.
Review
Biotechnology & Applied Microbiology
Rujia Chen, Liexiang Huangfu, Yue Lu, Huimin Fang, Yang Xu, Pengcheng Li, Yong Zhou, Chenwu Xu, Jinling Huang, Zefeng Yang
Summary: Horizontal gene transfer (HGT) plays a significant role in the evolution and adaptive innovations of green plants by facilitating the acquisition of genetic material from other organisms. The occurrence of HGT in major lineages of green plants can potentially be applied to crop breeding and improvement.
BIOTECHNOLOGY ADVANCES
(2021)
Review
Biochemistry & Molecular Biology
Shaked Bergman, Tamir Tuller
Article
Multidisciplinary Sciences
Yonatan Chemla, Michael Peeri, Mathias Luidor Heltberg, Jerry Eichler, Mogens Hogh Jensen, Tamir Tuller, Lital Alfonta
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Shaked Bergman, Alon Diament, Tamir Tuller
Article
Genetics & Heredity
Arup Panda, Tamir Tuller
GENOMICS PROTEOMICS & BIOINFORMATICS
(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)