Article
Evolutionary Biology
Masa-Aki Yoshida, Kazuki Hirota, Junichi Imoto, Miki Okuno, Hiroyuki Tanaka, Rei Kajitani, Atsushi Toyoda, Takehiko Itoh, Kazuho Ikeo, Takenori Sasaki, Davin H. E. Setiamarga
Summary: The paper nautilus, also known as the greater argonaut, has been sequenced to reveal its genomic background and adaptations. The genome size is 1.1 Gb, the smallest among cephalopods, and it contains genes related to the pelagic lifestyle and shell formation. Comparative genomics analysis also found similar genes in shell-less octopus and Nautilus. This study provides insights into the genetic background of the paper nautilus and its evolution.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Cell Biology
Pascal Schmidt, Eva Leman, Ronan Lagadec, Michael Schubert, Sylvie Mazan, Ram Reshef
Summary: This study investigates the role of retinoic acid (RA) in the regulation of chordate and vertebrate pronephros formation through a comparative developmental approach. The results show that the conservation of Pax2 and Lim1 expressions in chordate pronephros homologs is present, but the responsiveness to RA and Hox-dependent regulation is a novelty in gnathostomes.
Article
Biochemistry & Molecular Biology
Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang, Bo Dong
Summary: Evolutionary developmental biology (evo-devo) is an interdisciplinary field that aims to understand the origin and evolution of developmental processes in different animals. EDomics is a comparative multi-omics database that provides comprehensive genomic, transcriptomic, and single-cell data for 40 representative species. It offers valuable resources and customized datasets for evo-devo research, allowing researchers to decipher the history of developmental evolution across the tree of life.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Peter O. Mulhair, Liam Crowley, Douglas H. Boyes, Amber Harper, Owen T. Lewis, Peter W. H. Holland
Summary: Homeobox genes encode transcription factors that play essential roles in the patterning and cell fate of developing animal embryos. Most Lepidoptera species have around 100 homeobox loci, including a unique Hox gene cluster. The Shx genes are generally conserved, but some moth lineages have undergone dramatic duplication in the Hox gene cluster.
Editorial Material
Biochemistry & Molecular Biology
Samantha R. Royle, John J. Young
Summary: Most living tetrapods show postaxial dominance in digit formation, except for urodele amphibians which exhibit preaxial dominance. Recent research has uncovered genetic differences between these two modes of limb development, indicating that variations in 5'Hoxd expression, regulated by Gli3, could be responsible for the switch in axial polarity.
Editorial Material
Biochemistry & Molecular Biology
Narendra P. Singh
Summary: This study demonstrates how the Hox transcription factor Ultrabithorax acts as both a repressor and an activator in a cell type-specific manner to alter chromatin accessibility and gene regulation.
Editorial Material
Multidisciplinary Sciences
Chris Amemiya
Summary: Genome sequencing and analysis of genomic interactions have revealed new insights into the evolution of the wing shapes in skates and rays, dating back over 200 million years.
Article
Agriculture, Dairy & Animal Science
Marco Mendizabal-Castillero, Manuel Alejandro Merlo, Ismael Cross, Maria Esther Rodriguez, Laureana Rebordinos
Summary: In this study, hox gene clusters in the Senegalese sole were characterized to better understand the developmental and metamorphosis process in this species. Cytogenetic analysis revealed the localization of hox genes on specific chromosomes. Comparative and phylogenetic analysis showed conserved organization within each hox cluster, but different clustering patterns between clusters. Analysis of structural and repetitive sequences identified polymorphisms mediated by repetitive elements in the hoxba gene cluster, suggesting a possible loss of the hoxb7a gene in the Pleuronectiformes lineage. This work provides insights into the organization and regulation of hox clusters, and serves as a foundation for further studies on expression patterns.
Article
Cell Biology
Renate L. M. Jansen, Carlos Santana-Molina, Marco van den Noort, Damien P. Devos, Ida J. van der Klei
Summary: PEX genes encode proteins involved in peroxisome biogenesis and proliferation. A comparative genomics approach was used to clarify the evolutionary relationships between the 37 known PEX proteins in a representative set of eukaryotes, defining the core set of PEX proteins required for peroxisome formation. The molecular processes in peroxisome biogenesis in different organisms were analyzed, showing that peroxisomes are not static organelles in eukaryotic evolution.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Shane Denecke, Ivan Rankic, Olympia Driva, Megha Kalsi, Ngoc Bao Hang Luong, Benjamin Buer, Ralf Nauen, Sven Geibel, John Vontas
Summary: By annotating the ABC superfamily across more than 150 arthropod species with good quality protein annotations, specific expansions of ABC transporter families suggesting evolutionary adaptation were highlighted. Functional redundancy was observed in the transporters, with the exception of the highly conserved gene Snu, likely due to its role in cuticular formation. This analysis can be used as a resource for further understanding the ABC superfamily in arthropods.
Article
Environmental Sciences
Jun Min, Suyun Fang, Jian Peng, Xin Lv, Lingxue Xu, Yan Li, Xiaoke Hu
Summary: This study identified Cupriavidus sp. CNP-8 as a bacterium with a novel pathway for degrading TBP and characterized the molecular mechanisms involved in its degradation, revealing unique evolutionary patterns in acquiring TBP-degrading genes. The findings provide new insights into microbial detoxification of TBP and highlight the microbial adaptive evolution in halophenols-contaminated environments.
ENVIRONMENTAL RESEARCH
(2022)
Article
Microbiology
Xiaoqin Wu, Alexey E. Kazakov, Sara Gushgari-Doyle, Xingli Yu, Valentine Trotter, Rhona Kayra Stuart, Romy Chakraborty
Summary: This study investigated the genomic factors regulating violacein production in nine Janthinobacterium strains. Despite being closely related phylogenetically and containing essential genes for violacein biosynthesis, these strains showed variations in carbon usage and violacein production. Strains from sediment and groundwater exhibited weaker violacein production and fewer secondary metabolite biosynthesis genes than soil strains, indicating genome adaptation. The study also suggested that quorum sensing may play a role in regulating violacein in Janthinobacterium, with strains possessing both AHL QS and JQS systems showing stronger potential in violacein production.
MICROBIOLOGY SPECTRUM
(2021)
Article
Biotechnology & Applied Microbiology
Jun Chen, Yu Zang, Shuo Liang, Song Xue, Shuai Shang, Meiling Zhu, Ying Wang, Xuexi Tang
Summary: This study sequenced and compared the mitochondrial genomes of Zostera japonica and Phyllospadix iwatensis, providing new evidence of genome size reduction, gene loss, and adaptive evolution in seagrasses. It found a large number of repeat sequences and extensive loss of ribosomal protein genes in seagrass species. Additionally, it identified positive selection genes associated with seagrass adaptation to the marine environment.
Review
Cell Biology
James C. -G. Hombria, Mar Garcia-Ferres, Carlos Sanchez-Higueras
Summary: Bilateral animals have undergone a progressive process of cephalization during evolution, with the involvement of Hox genes in vertebrates and arthropods playing a key role in head innovation. This indicates that the control of cephalic structures by Hox genes was independently acquired during the evolution of vertebrates and invertebrates.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Microbiology
Ye Jin, Wangxiao Zhou, Qing Zhan, Beiwen Zheng, Yunbo Chen, Qixia Luo, Ping Shen, Yonghong Xiao
Summary: Since 2010, MRSA ST59 has gradually replaced ST239 to become the dominant clone in most hospitals in China. ST59 clones demonstrate higher susceptibility to antibiotics, and the detection of virulence factors suggests that sak and chp genes may contribute to their successful spread.
Article
Biochemical Research Methods
David Schaller, Manuela Geiss, Marc Hellmuth, Peter F. F. Stadler
Summary: We propose a near-cubic algorithm to determine if Best match graphs (BMG) can be explained by a fully resolved gene tree and to construct such a tree. We prove that all binary trees are refinements of the unique binary-refinable tree (BRT) which is a significant refinement of the least resolved tree of a BMG. Additionally, we demonstrate the NP-completeness of editing an arbitrary vertex-colored graph to a binary-explainable BMG and provide an integer linear program formulation for this task.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Mathematics
Anahy Santiago Arguello, Juan Jose Montellano-Ballesteros, Peter F. Stadler
Summary: This paper investigates the power graphs of a class of abelian groups and explores whether the power graph is Hamiltonian in this case.
JOURNAL OF ALGEBRAIC COMBINATORICS
(2023)
Article
Biochemical Research Methods
Fumiaki Sugahara, Juan Pascual-Anaya
Summary: High-purity total RNA extraction from animal embryos is essential for transcriptome analyses. Lampreys, as a key organism for EvoDevo studies, face challenges in extracting uncontaminated RNA from early-stage embryos. By modifying the RNA extraction protocol with precentrifugation and adding salts before isopropanol precipitation, RNA yield is significantly increased, contaminants are removed, and RNA integrity is improved. This technique proves particularly effective for early-stage embryos from single-cell to prehatching stages.
Article
Biochemical Research Methods
Lisa Fiedler, Matthias Bernt, Martin Middendorf, Peter F. Stadler
Summary: This study presents a novel method for detecting gene breakpoints in the nucleotide sequences of complete mitochondrial genomes, considering high substitution rates. The method uses a parallel program design and has been extensively tested for accuracy.
BMC BIOINFORMATICS
(2023)
Article
Mathematics, Applied
Carsten R. Seemann, Vincent Moulton, Peter F. Stadler, Marc Hellmuth
Summary: Median graphs are connected graphs where there is a unique vertex belonging to the shortest paths between any three vertices. This paper presents new characterizations of planar median graphs by using forbidden subgraphs, isometric cycles, and subgraphs contained inside and outside of 4-cycles. These characterizations lead to a new definition of planar median graphs called cubesquare-graphs, and also provide an O(n log n)-time recognition algorithm for computing the decomposition of a planar median graph into cubes and square-graphs.
DISCRETE APPLIED MATHEMATICS
(2023)
Article
Mathematics, Applied
Annachiara Korchmaros, David Schaller, Marc Hellmuth, Peter F. Stadler
Summary: Quasi-best match graphs (qBMGs) are directed, properly vertex-colored graphs that generalize best match graphs and represent the evolutionary closest relatedness of genes in multiple species. They can be explained by rooted trees where each leaf corresponds to a vertex. Compared to best match graphs, qBMGs only represent best matches within a restricted phylogenetic distance. We provide characterizations of qBMGs, including polynomial-time recognition algorithms, and identify best match graphs as color-sink-free qBMGs. Additionally, two-colored qBMGs are characterized as directed graphs satisfying three simple local conditions.
DISCRETE APPLIED MATHEMATICS
(2023)
Article
Mathematics
M. Hellmuth, K. T. Huber, V. Moulton, G. E. Scholz, P. F. Stadler
Summary: This paper studies the properties of split systems, with a focus on injective split systems that can be used to represent symbolic tree maps. The authors prove the existence of an injective split system on any set X and provide a characterization for when a split system is injective. They also introduce related concepts such as injective dimension and provide upper and lower bounds for these dimensions. An important motivation for studying injective split systems is their application in representing three-way symbolic maps.
GRAPHS AND COMBINATORICS
(2023)
Article
Biochemistry & Molecular Biology
Tim Kolberg, Sarah von Loehneysen, Iuliia Ozerova, Karolin Wellner, Roland K. Hartmann, Peter F. Stadler, Mario Moerl
Summary: Structural analysis of RNA is important in understanding its function. Led-Seq is a new approach based on lead-induced cleavage, which allows investigation of both resulting cleavage products. It provides accurate information about cleavage sites and is an improved method for studying RNA structures in vivo.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Andres M. Bran, Peter F. Stadler, Juergen Jost, Guillermo Restrepo
Summary: The periodic system encodes order and similarity among chemical elements. The system has converged towards its current stable structure through six stages by analyzing the space between 1800 and 2021. Given the limited chemical possibilities and low diversity of the chemical space, the periodic system is expected to remain largely unchanged.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Biochemical Research Methods
Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
Summary: This article presents the influence of salt ion concentration on RNA structure prediction algorithms and proposes an improved model for better predicting the structure and stability of RNA. By comparing with experimental data, it is found that the predicted free energy and melting temperature are in close agreement with the experiments. This new feature has been added to the ViennaRNA package, allowing for systematic study of the effects of salt concentration on RNA folding.
ALGORITHMS FOR MOLECULAR BIOLOGY
(2023)
Article
Biology
Sean Tsz Sum Law, Yifei Yu, Wenyan Nong, Wai Lok So, Yiqian Li, Thomas Swale, David E. K. Ferrier, Jianwen Qiu, Peiyuan Qian, Jerome Ho Lam Hui
Summary: This study reports the first chromosome-level deep-sea cnidarian genome from an Actinernus sp. anemone, revealing molecular adaptations to extreme environments such as a mega-array of homeobox genes and cnidarian-specific microRNA complements. Additionally, the loss of circadian rhythm genes suggests an adaptation to the dark deep-sea environment.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biology
Marc Hellmuth, David Schaller, Peter F. Stadler
Summary: Rooted acyclic graphs play a crucial role in modeling different types of evolutionary processes, and there are correspondences between different classes of networks and their clustering systems, revealing the mutual dependencies among various network types.
THEORY IN BIOSCIENCES
(2023)
Article
Mathematical & Computational Biology
John Anders, Peter F. Stadler
Summary: Differentiating regions with coding potential from non-coding regions is an important task in computational biology. RNAcode, a method that utilizes sequence conservation patterns, shows superior classification accuracy for short coding sequences compared to methods that rely on a single input sequence. However, obtaining suitable multiple sequence alignments can be tedious and challenging. To address this, a new web service called RNAcode_Web is introduced, which automates the process of collecting, selecting, and preparing homologous sequences from the NCBI database and constructing multiple sequence alignments needed for RNAcode input. This service simplifies the investigation of previously unannotated coding regions for non-expert users.
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Christopher Klapproth, Siegfried Zoetzsche, Felix Kuehnl, Joerg Fallmann, Peter F. Stadler, Sven Findeiss
Summary: This article introduces a software framework for in silico prediction of non-coding and protein-coding genetic loci, which allows for the alignment-based training, evaluation, and application of machine learning models with user-defined parameters. Instead of using the one-size-fits-all approach of pervasive in silico annotation pipelines, this framework focuses on the structured generation and evaluation of models based on arbitrary features and input data, aiming for stable and explainable results. Furthermore, the software package is applied to a full-genome screen of Drosophila melanogaster and evaluated against the well-known but less flexible program RNAz.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Marcos E. Gonzalez Laffitte, Nora Beier, Nico Domschke, Peter F. Stadler
Summary: The computation of reliable and chemically correct atom maps from educt/product pairs is a challenging task in cheminformatics. Various competing models have been developed and compared through extensive benchmarking studies. This study formalizes the equivalence of atom maps and demonstrates the use of Fujita's Imaginary Transition State for this purpose. Numerical experiments confirm the practical feasibility. The article also briefly discusses generalizations to subgraph matches, graph transformation rules, and multi-step reaction mechanisms.
MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY
(2023)
