Editorial Material
Biochemistry & Molecular Biology
Jonas Juan-Mateu, Juan Valcarcel
Summary: Elevated levels of U6atac snRNA are found to be associated with prostate cancer cell growth and may serve as a novel therapeutic target.
Article
Biochemistry & Molecular Biology
Jason W. Rausch, William F. Heinz, Matthew J. Payea, Chringma Sherpa, Myriam Gorospe, Stuart F. J. Le Grice
Summary: Custom circRNA can be synthesized in vitro using PIE transcription templates, which have been used to produce a variety of circRNA versions for various applications. Limitations of this approach include obligatory incorporation of small RNA segments and restrictions on the synthesis of therapeutics and RNA nanoparticles. Through mutagenesis and selection, guidelines for designing tailored PIE transcription templates have been established to efficiently synthesize synthetic circRNAs of almost any sequence.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Cheng-Hong Yang, Yu-Huei Cheng, Emirlyn Cheng Yang, Li-Yeh Chuang, Yu-Da Lin
Summary: This study designed new fitness functions based on user-specified parameters and used the functions in a primer design approach based on the multiobjective particle swarm optimization (MOPSO) algorithm to address the challenge of primer design with user-specified parameters. The algorithms based on fitness functions with user-specified parameters outperformed the algorithms based on general fitness functions for 11 primer constraints.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Ettaib El Marabti, Joel Malek, Ihab Younis
Summary: The article discusses the essential role of pre-mRNA splicing in gene expression, catalyzed by two machineries in eukaryotes - the major and minor spliceosomes. It highlights the significance of minor splicing and its regulatory role in alternative splicing, impacting the expression of host genes and potentially leading to tissue-specific pathologies when deregulated. Studies on minor spliceosome-associated diseases suggest a key regulatory pathway with implications for disease pathogenesis and potential novel therapies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Julian Vosseberg, Daan Stolker, Samuel H. A. von der Dunk, Berend Snel
Summary: This study uses phylogenetic analyses to infer the evolutionary history of 145 proteins in the spliceosome. The results show that an abundance of ribosome-related proteins were added to the prokaryotic-derived core, and duplications of these proteins increased the overall complexity of the spliceosome. Most of the spliceosomal complexity originated after the spread of introns in the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insights into the emergence of complexes with many proteins during eukaryogenesis.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Computer Science, Theory & Methods
Zijun Li, Linsong Guo, Jiagan Cheng, Quan Chen, Bingsheng He, Minyi Guo
Summary: This article surveys and elaborates on the research domains in the serverless context, highlighting the key implications and limitations of works in each layer. It emphasizes the potential of the serverless computing model while pointing out the challenges for further research.
ACM COMPUTING SURVEYS
(2022)
Article
Microbiology
Jigeesha Mukhopadhyay, Alvan Wai, Georg Hausner
Summary: This study examines the mitochondrial genomes of three members of the Leptographium sensu lato. The results show variations in genome size and gene arrangement, supporting the current classification of the Ophiostomatales and highlighting the potential of mitochondrial genomes in resolving evolutionary relationships within this order.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yanru Liu, Samuel DeMario, Kevin Hea, Michelle R. Gibbs, Keaton W. Barr, Guillaume F. Chanfreau
Summary: This study investigated the impact of splicing on the processing and fate of snoRNA. The researchers found that inactivation of splicing factors or mutation of splicing signals leads to the accumulation of partially processed hmsnoRNA transcripts. These hmsnoRNAs are processed to the mature 3' ends of the snoRNAs by the nuclear exosome and bound by small nucleolar ribonucleoproteins. However, due to their mRNA-like 5' extensions, hmsnoRNAs are degraded by the major cytoplasmic exonuclease Xrn1p.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Jeremy J. Baumberg
Summary: This article introduces the discovery and significance of sub-nanometer-scale optical cavities. We develop simple models for these picocavities and discuss what is known and unknown in this field, as well as the challenges faced in developing comprehensive theories. We also provide simple analytic expressions for key properties and discuss the importance of picocavities in various applications.
Editorial Material
Biochemical Research Methods
Alexander Derry, Martin Krzywinski, Naomi Altman
Summary: Nature is usually concealed, occasionally conquered, rarely eradicated.
Review
Chemistry, Analytical
Min Luo, Fei Lan, Wenbin Li, Siting Chen, Lifeng Zhang, Bo Situ, Bo Li, Chunchen Liu, Weilun Pan, Zhuowei Gao, Ye Zhang, Lei Zheng
Summary: Early disease diagnosis requires sensitive detection and imaging techniques. Primer exchange reaction (PER) is a novel signal amplification technique that is simple and sensitive. Currently, there are various PER-based signal amplification strategies available to improve detection sensitivity and promote the development of this field.
ANALYTICA CHIMICA ACTA
(2023)
Article
Multidisciplinary Sciences
Nina G. Xie, Michael X. Wang, Ping Song, Shiqi Mao, Yifan Wang, Yuxia Yang, Junfeng Luo, Shengxiang Ren, David Yu Zhang
Summary: One major challenge in designing highly multiplexed PCR primer sets is the increase in potential primer dimer species and the difficulty in computationally evaluating multiplex primer sequence selection. The researchers presented and validated a stochastic algorithm called SADDLE for designing multiplex PCR primer sets that minimize primer dimer formation. The experiment showed that the optimized primer set significantly reduced the fraction of primer dimers, even when scaling to a larger number of primers.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Ting-Hui Wu, Cing-Han Yang, Tun-Wen Pai, Li-Ping Ho, Jen-Leih Wu, Hsin-Yiu Chou
Summary: This study develops a practical strategy to discover unique primers for fish species identification by analyzing tRNA segments of COI genes. Through in silico analysis, exclusive primers for 2618 fish species were successfully discovered. The study provides a comprehensive list of primers for extracting COI barcode sequences of fish species, facilitating the verification of fish products and identification of unknown fish species.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Xiaoliang Ren, Yanwen Shao, Yiwen Zhang, Ying Ni, Yu Bi, Runsheng Li
Summary: The primerdiffer pipeline is introduced as a large-scale primer design tool that can differentiate haplotypes with precise false priming checking. It includes steps like greedy primer search, in silico PCR-based false priming checking, and automated best primer selection. The pipeline provides a command-line interface and flexibility for users to design primers with their own genome sequences and specific parameters.
Article
Biochemistry & Molecular Biology
Qusay Q. Omran, Olga Fedorova, Tianshuo Liu, Anna M. Pyle
Summary: The development of a molecular beacon assay for monitoring RNA splicing reactions allows for the analysis of kinetic characteristics and determination of inhibition constants for small molecules.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Multidisciplinary Sciences
Harris A. Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Miklos Balint, Katharine B. Barker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica DiPalma, Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer Marshall Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg, Sachiko Isobe, Kjetill Sigurd Jakobsen, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, Jin-Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, James H. Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose V. Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O'Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. Bradley Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano-Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, Guojie Zhang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Mara K. N. Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques Bonet, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xin Liu, Jose Victor Lopez, Eugene W. Myers, Olga Vinnere Pettersson, Adam M. Phillippy, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Francoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guojie Zhang, He Zhang, Harris A. Lewin, Stephen Richards
Summary: The Earth BioGenome Project (EBP) is a global international initiative that requires agreement and coordination on standards. To ensure rapid progress towards its goals, EBP has established five technical standards committees and made the current versions of the standards documents available on its website.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Mark Blaxter, John M. Archibald, Anna K. Childers, Jonathan A. Coddington, Keith A. Crandall, Federica Di Palma, Richard Durbin, Scott V. Edwards, Jennifer A. M. Graves, Kevin J. Hackett, Neil Hall, Erich D. Jarvis, Rebecca N. Johnson, Elinor K. Karlsson, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Kerstin Lindblad-Toh, Jose V. Lopez, Nancy A. Moran, Gene E. Robinson, Oliver A. Ryder, Beth Shapiro, Pamela S. Soltis, Tandy Warnow, Guojie Zhang, Harris A. Lewin
Summary: Life on Earth has evolved from simplicity to complexity, with bacteria and archaea excelling in metabolic diversification and eukaryotes displaying morphological innovation. The Earth BioGenome Project proposes sequencing the genomes of all known eukaryotic species to create a digital library of life, which will help address evolutionary and ecological questions and provide insights into speciation, adaptation, and organismal dependencies within ecosystems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Mark L. Blaxter
Summary: The Earth Biogenome Project aims to sequence the genomes of all eukaryotic life on earth, and the Darwin Tree of Life Project focuses on delivering high-quality genome sequences for the British and Irish islands. The collaboration between biodiversity organizations and genomics institutes has established a workflow that collects specimens, performs sequencing, generates curated assemblies, and openly releases the data for global use in future scientific and conservation efforts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Biochemistry & Molecular Biology
Jack C. Schultz, Graham N. Stone
Summary: Plant galls are plant organs initiated and controlled by parasitic microbes, nematodes, insects, and mites, providing a safe environment for arthropods and exhibiting complex anatomical and tissue variations. Recent research has shown significant transcriptional and anatomical differences in gall tissues.
Editorial Material
Multidisciplinary Sciences
ThankGod Echezona Ebenezer, Anne W. T. Muigai, Simplice Nouala, Bouabid Badaoui, Mark Blaxter, Alan G. Buddie, Erich D. Jarvis, Jonas Korlach, Josiah O. Kuja, Harris A. Lewin, Roksana Majewska, Ntanganedzeni Mapholi, Suresh Maslamoney, Michele Mbo'o-Tchouawou, Julian O. Osuji, Ole Seehausen, Oluwaseyi Shorinola, Christian Keambou Tiambo, Nicola Mulder, Cathrine Ziyomo, Appolinaire Djikeng
Article
Zoology
James A. Nicholls, George Melika, Scott C. Digweed, Graham N. Stone
Summary: This paper describes previously unknown generations for 12 Nearctic oak gallwasps. It provides descriptions and diagnoses for these taxa and summarizes what is known about their biology, including host associations. The relationships between alternate generations are supported by morphological and molecular data.
Article
Zoology
Victor Cuesta-Porta, George Melika, James A. Nicholls, Graham N. Stone, Juli Pujade-Villar
Summary: This study re-establishes the Nearctic cynipid oak gall wasp genus Druon Kinsey comb. rev., describing new species and previously classified species. Descriptions, diagnoses, DNA sequence data and analyses, as well as information on biology, phenology, and distribution are provided.
Article
Biochemistry & Molecular Biology
Yuanmeng M. Zhang, Sofia Sheikh, Anna K. G. Ward, Andrew A. Forbes, Kirsten M. Prior, Graham N. Stone, Michael W. Gates, Scott P. Egan, Linyi Zhang, Charles Davis, Kelly L. Weinersmith, George Melika, Andrea Lucky
Summary: Cryptic species diversity is a major challenge in parasitoids attacking oak gall wasps due to sexual dimorphism, morphological plasticity, small size, and poorly known biology. The study reveals that parasitoid wasps have adaptations allowing them to exploit specific host trait combinations and prefer larger galls. These findings have implications for evolutionary ecology and biocontrol, supporting the tritrophic niche concept in plant-herbivore-parasitoid communities.
Article
Plant Sciences
Suo Qiu, James M. Bradley, Peijun Zhang, Roy Chaudhuri, Mark Blaxter, Roger K. Butlin, Julie D. Scholes
Summary: This study reveals diverse strategies used by Striga hermonthica to overcome different layers of host resistance. Understanding the maintenance of variation at virulence loci by balancing selection is crucial for controlling the evolution of parasite virulence.
Article
Ecology
Nora Villamil, Karina Boege, Graham N. Stone
Summary: Ant guards do not affect pollinator community composition, but decrease flower visit duration and reduce pollen deposition and exports, while significantly increasing outcross pollen transfer.
Article
Zoology
Majid Tavakoli, Graham N. Stone, Juli Pujade-Villar, George Melika
Summary: Five new gall wasp species have been discovered in Lorestan, Iran, including Aulacidea koeiana Melika, Tavakoli & Stone, sp. nov., A. lorestanica Melika, Tavakoli & Stone, sp. nov., A. piroziae Melika, Stone & Pujade-Villar, sp. nov., Phanacis strigosa Melika, Stone & Tavakoli, sp. nov., P. tavakolii Melika, Stone & Pujade-Villar, sp. nov. Descriptions, diagnoses, and information on biology and host associations are provided for all new species, and the male of Isocolus beheni Melika & Karimpour, 2008 is described for the first time.
Article
Zoology
Irene Lobato-Vila, Alba Sala-Nishikawa, George Melika, Graham N. Stone, Chang-Ti Tang, Man-Miao Yang, Zhiqiang Fang, Ying Zhu, Yiping Wang, Sunghoon Jung, James A. Nicholls, Juli Pujade-Villar
Summary: Recent years have witnessed significant progress in the study of Fagaceae-associated gall wasps in the Eastern Palaearctic and the Oriental regions. However, this progress has also given rise to taxonomic errors and uncertainties. To establish a solid foundation for further research, this paper reviews the taxonomic status of the 212 species in these regions and provides comprehensive information on their taxonomy, distribution, and host associations.
Article
Biochemistry & Molecular Biology
Emmelien Vancaester, Mark Blaxter
Summary: The Darwin Tree of Life (DToL) project aims to sequence all described terrestrial and aquatic eukaryotic species found in Britain and Ireland. From data generated by the DToL project, 110 complete Wolbachia genomes from 93 host species spanning 92 families were identified and assembled. Different insect orders had distinct patterns of Wolbachia infection, with Lepidopteran hosts mostly infected with supergroup B, while infections in Diptera and Hymenoptera were dominated by A-type Wolbachia. Host and Wolbachia phylogenies revealed no (or very limited) cophylogeny, indicating frequent host switching events in the evolutionary history of Wolbachia. Mining raw genome data generated for reference genome assemblies is an effective way to analyze cobiont genomes and provide ecological context for their hosts.
Article
Evolutionary Biology
Jack Hearn, Erik Gobbo, Jose Luis Nieves-Aldrey, Antoine Branca, James A. Nicholls, Georgios Koutsovoulos, Nicolas Lartillot, Graham N. Stone, Fredrik Ronquist
Summary: This article analyzes the phylogenetic relationships of gall wasps using genome and transcriptome data. The results show that gall wasps are not monophyletic and can be divided into three families. The article also explores the evolution of gall wasp life histories, suggesting complex transitions.
SYSTEMATIC ENTOMOLOGY
(2023)