Article
Biochemistry & Molecular Biology
Hsin-Yen Larry Wu, Qiaoyun Ai, Rita Teresa Teixeira, Phong H. T. Nguyen, Gaoyuan Song, Christian Montes, J. Mitch Elmore, Justin W. Walley, Polly Yingshan Hsu
Summary: By improving the coverage of super-resolution Ribo-seq, previously uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes in Arabidopsis have been revealed. These events include untranslated ORFs in noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events.
Article
Biochemistry & Molecular Biology
Alexander Bartholomaeus, Baban Kolte, Ayten Mustafayeva, Ingrid Goebel, Stephan Fuchs, Dirk Benndorf, Susanne Engelmann, Zoya Ignatova
Summary: New evidence highlights the importance of small proteins in physiological processes, but their functional identification and genome annotation remain challenging. A new algorithm, smORFer, shows high accuracy in detecting putative smORFs in prokaryotic organisms.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Xiaoping Dong, Kun Zhang, Chengfeng Xun, Tianqi Chu, Songping Liang, Yong Zeng, Zhonghua Liu
Summary: Small open reading frames (sORFs) have been previously overlooked as noncoding or transcriptional noise, but recent evidence suggests they may encode small polypeptides (SEPs) involved in various biological processes. Advances in computational algorithms, ribosome profiling, and peptidome have aided in the prediction and identification of new SEPs. This review discusses the history, development, and challenges in studying sORFs and SEPs, providing valuable insights and tools for future research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Akshay Khanduja, Manish Kumar, Debasisa Mohanty
Summary: Small open reading frames (smORFs) encoding proteins less than 100 amino acids (aa) are important regulators of cellular processes. Computational identification of smORFs remains challenging. The ProsmORF-pred resource utilizes a machine learning-based method to predict smORFs in prokaryotic genomes, achieving comparable performance to other state-of-the-art approaches. It can also aid in functional annotation of predicted smORFs based on sequence similarity in ProsmORFDB.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Business
Juergen Kai-Uwe Brock, Ajay K. Kohli
Summary: This research utilizes two global surveys of IT service customers to identify the emergence of Digital Exploration services. In contrast to Traditional IT services and cloud-based Digital Exploitation services, Digital Exploration services involve adopting new digital technologies (e.g., blockchain, augmented reality, deep learning, IoT) to develop novel business strategies and processes. In-depth interviews with IT customers highlight the critical success factors for Digital Exploration, including customer selectivity, collaboration between IT providers and customers, strategic and systemic thinking, open innovation, and performance directionality. These interviews also shed light on the mindset and behavioral changes needed in business unit leaders and various functions within IT providers and customers to fully realize the potential of Digital Exploration services.
JOURNAL OF BUSINESS RESEARCH
(2023)
Article
Biochemical Research Methods
Eduardo Vieira de Souza, Pedro Ferrari Dalberto, Vinicius Pellisoli Machado, Adriana Canedo Miranda, Alan Saghatelian, Pablo Machado, Luiz Augusto Basso, Cristiano Valim Bizarro
Summary: We developed a proteogenomics pipeline, called mu ProtelnS, which combines genomics, transcriptomics, and proteomics to identify novel microproteins in bacteria. This pipeline overcomes the limitations of traditional approaches by filtering out low confidence spectra and including overlapping genes, leaderless transcripts, and non-conserved sequences that are common among small ORFs.
Article
Biochemistry & Molecular Biology
Christine Dozier, Audrey Montigny, Mireia Viladrich, Raphael Culerrier, Jean-Philippe Combier, Arnaud Besson, Serge Plaza
Summary: miRNAs are small regulatory non-coding RNAs generated from pri-miRNAs, with some hosted in lncRNAs containing translatable smORFs. This study demonstrates the involvement of smORFs in regulating pri-miRNAs and miRNAs expression in Human and Drosophila, independent of nucleotide and amino acid sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Thomas F. Martinez, Sally Lyons-Abbott, Angie L. Bookout, Eduardo V. De Souza, Cynthia Donaldson, Joan M. Vaughan, Calvin Lau, Ariel Abramov, Arian F. Baquero, Karalee Baquero, Dave Friedrich, Justin Huard, Ray Davis, Bong Kim, Ty Koch, Aaron J. Mercer, Ayesha Misquith, Sara A. Murray, Sakara Perry, Lindsay K. Pino, Christina Sanford, Alex Simon, Yu Zhang, Garrett Zipp, Cristiano V. Bizarro, Maxim N. Shokhirev, Andrew J. Whittle, Brian C. Searle, Michael J. MacCoss, Alan Saghatelian, Christopher A. Barnes
Summary: Microproteins (MPs) in adipocytes were identified using ribosome profiling. 3,877 unannotated MP-encoding small ORFs were curated, and 85 MPs were validated, including 33 circulating MPs in mouse plasma. The analysis revealed the regulation of MPs in adipose tissue and their co-expression with metabolic genes. One secreted MP Gm8773 was found to be highly expressed in the hypothalamus and showed orexigenic activity in obese mice.
Article
Multidisciplinary Sciences
Valdir C. Barth, Unnati Chauhan, Jumei Zeng, Xiaoyang Su, Haiyan Zheng, Robert N. Husson, Nancy A. Woychik
Summary: The VapBC4 toxin-antitoxin system in Mycobacterium tuberculosis triggers a series of stress survival pathways, activating virulence and controlling translation of messenger RNA by inactivating tRNACys through cleavage at a single site.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Jiafeng Yu, Wenwen Jiang, Sen-Bin Zhu, Zhen Liao, Xianghua Dou, Jian Liu, Feng-Biao Guo, Chuan Dong
Summary: This study presents a protein-coding sORFs prediction method solely based on integrative sequence-derived features, with prediction performance better or comparable to other prevalent methods. The method provides a relatively reliable research tool for predicting protein-coding sORFs. The study also demonstrates that the method allows estimation of the potential expression of a queried sORF, validated through correlation analysis with codon adaption index (CAI).
Editorial Material
Chemistry, Multidisciplinary
Fernando Gomollon-Bel, Javier Garcia-Martinez
Summary: Chemistry plays a crucial role in addressing current challenges and ensuring a sustainable future. IUPAC has been identifying technologies since 2019 that have the potential to advance society and improve quality of life.
Editorial Material
Agriculture, Dairy & Animal Science
Joao R. Mesquita
Summary: This article highlights the significance of zoonotic diseases, with over 61% of human pathogens being zoonotic and global warming providing ideal conditions for the spread of exotic infectious agents. The 2019 novel coronavirus epidemic and other examples emphasize the role of animal reservoirs in public health, stressing the importance of prevention and control of zoonotic diseases.
Review
Cell Biology
Xue Sun, Gebang Wang, Wenting Luo, Hui Gu, Wei Ma, Xiaowei Wei, Dan Liu, Shanshan Jia, Songying Cao, Yu Wang, Zhengwei Yuan
Summary: Cardiovascular diseases are the leading cause of death worldwide, and studies have shown that non-coding RNAs play a significant role in their development. Small nucleolar RNAs are a novel species of ncRNAs that may regulate different illnesses, including CVDs. Understanding the molecular processes and signaling pathways of snoRNAs in relation to CVDs is essential for further research and potential clinical applications.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Review
Environmental Studies
Sarah Rosenberg-Jansen
Summary: This paper explores the issue of energy in humanitarian settings and identifies the rapid development of research on this topic in existing literature. The study emphasizes the urgent need for new evidence in areas where there are significant gaps. It also highlights the importance of disciplinary diversity in fully understanding energy issues in humanitarian environments.
ENERGY RESEARCH & SOCIAL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Leonardo N. Ferreira, Inho Hong, Alex Rutherford, Manuel Cebrian
Summary: Protest diffusion is a cascade process that can spread over different regions of the planet, possibly spreading quickly through persistent temporal hubs. Empirical investigation using temporal networks with small-world structures showed that average path lengths are decreasing, indicating a shrinking world trend.
SCIENTIFIC REPORTS
(2021)
Review
Virology
Zacharie LeBlanc, Peter Waterhouse, Julia Bally
Summary: Severe virus outbreaks are happening frequently with rapid and widespread transmission. Preparedness plans based on past epidemics can help in controlling and treating new diseases, but there are gaps in current biologics production systems in responding to emergency situations. Plant-based biologics production systems have commercial viability, low production costs, high scalability, and flexibility, making them potential first responders in emergency pandemic situations.
Article
Genetics & Heredity
Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly K. W. Yuen, Nadia Warner, Brigid Betz-Stablein, Fabio Luciani, Peter A. Revill, Chris M. Brown
Summary: Hepatitis B virus (HBV) generates a variety of splice variants, some of which can predict liver cancer but their roles are not yet fully understood. Different HBV genotypes may express distinct splice transcript isoforms, and these splice variants show biological relevance in the context of viral infection.
MICROBIAL GENOMICS
(2021)
Review
Plant Sciences
Jiffinvir Khosa, Francesca Bellinazzo, Rina Kamenetsky Goldstein, Richard Macknight, Richard G. H. Immink
Summary: Geophytes use a dual reproduction system to adapt to harsh climatic conditions, with the PEBP gene family playing a crucial role in regulating both types of reproduction. Differential expression and protein complex formation give unique functions to members of the PEBP gene family, mediating the crosstalk between the two reproductive events in geophytes.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Samarth, Robyn Lee, Dave Kelly, Matthew H. Turnbull, Richard C. Macknight, Anthony M. Poole, Paula E. Jameson
Summary: Research on the alpine perennial herbaceous plant Celmisia lyallii (Asteraceae) found that warm summer conditions that promote flowering lead to differential regulation of genes, including promoters and repressors of flowering. Results suggest that plants may maintain a summer memory to induce flowering.
Article
Plant Sciences
Rowan Herridge, Samarth, Lynette Brownfield, Richard Macknight
Summary: The flowering of perennial ryegrass is crucial for both farmers and seed producers, as it affects metabolizable energy content and seed yield. Gene studies on flowering time regulation can provide insights into the growth and flowering processes of ryegrass.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemical Research Methods
Peter A. Crisp, Pooja Bhatnagar-Mathur, Penny Hundleby, Ian D. Godwin, Peter M. Waterhouse, Lee T. Hickey
Summary: Traditional plant breeding has achieved certain success, but it is facing the challenge of meeting the growing demand. To fill the yield gaps and meet consumer preferences, new breeding strategies and sources of genetic variation are needed, and it is important to go beyond the traditional gene-centric thinking and consider the roles of epigenetic variation and cis-regulatory variation in plant traits.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Samarth, Robyn Lee, Dave Kelly, Matthew H. Turnbull, Richard Macknight, Anthony M. Poole, Paula E. Jameson
Summary: A study on genes controlling flowering in masting plants found that a novel orthologue of TERMINAL FLOWER 1 promotes flowering induction. Global transcriptomic analysis indicated the importance of endogenous cues and epigenetic regulation in plants' responsiveness to initiate flowering.
Article
Plant Sciences
Soledad Perez-Santangelo, Nathanael Napier, Fran Robson, James L. Weller, Donna M. Bond, Richard C. Macknight
Summary: Plants use seasonal cues to initiate flowering at the optimal time for reproductive success, and this involves the integration of daily and seasonal cues with the circadian clock and light signals. Research on legume crops suggests that the phyA gene plays a crucial role in synchronizing the circadian clock and integrating light signals to precisely control the timing of flowering.
Article
Biochemistry & Molecular Biology
Saadlee Shehreen, Nils Birkholz, Peter C. Fineran, Chris M. Brown
Summary: Many bacteria use CRISPR-Cas systems to defend against invasive mobile genetic elements, and in response, these genetic elements have developed strategies to resist CRISPR-Cas. This study identified and analyzed Aca and AcrIIA1 homologs in bacterial genomes and demonstrated the widespread conservation of Aca proteins in repressing acr expression.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Daniel A. Careno, Soledad Perez Santangelo, Richard C. Macknight, Marcelo J. Yanovsky
Summary: Circadian rhythms are regulated by a set of clock genes, and this study identified LSM1 and XRN4 as factors involved in mRNA decay pathway that affects clock function in plants.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Somrutai Winichayakul, Richard Macknight, Liam Le Lievre, Zac Beechey-Gradwell, Robyn Lee, Luke Cooney, Hong Xue, Tracey Crowther, Philip Anderson, Kim Richardson, Xiuying Zou, Dorothy Maher, Gregory Bryan, Nick Roberts
Summary: This study demonstrates that perennial ryegrass engineered to accumulate high lipid in their leaves can enhance photosynthesis and growth under optimal conditions. However, the growth advantage is diminished in a dense canopy. The genetic regulatory network linking leaf lipid sinks and physiological changes remains unknown.
Article
Plant Sciences
Rowan Herridge, Tyler McCourt, Jeanne M. E. Jacobs, Peter Mace, Lynette Brownfield, Richard Macknight
Summary: Self-incompatibility is a characteristic of flowering plants, and grasses have a unique two-locus system to control self-recognition. By analyzing genome data from ryegrass and other grass species, it was found that DUF247 genes and SP/ZP genes are present at the S and Z loci in self-incompatibility species, acting as male and female components. These genes are highly variable, but key secondary structure features are conserved. The time of formation of specificity groups is related to the divergence of grass subfamilies.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Felipe F. de Felippes, Peter M. Waterhouse
Summary: To be properly expressed, genes require a terminator, a region downstream of the coding sequence that contains information for mRNA maturation. The addition of a poly(A) tail at the 3' end of the new transcript is a critical step in mRNA biology that affects gene expression levels. Different terminators can also impact gene expression and the production of regulatory small RNAs in plants, which are important for gene regulation.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Agronomy
Caitlin Harris, Madison Hall, Ruby Arrowfield, Rowan Herridge, Colin Eady, Richard Macknight, Lynette Brownfield
Summary: Perennial ryegrass, an important grass in temperate regions, has limited genetic improvement due to the self-incompatibility preventing inbreeding. However, a naturally occurring self-fertile (SF) locus has been identified, and this study successfully introduced it into an elite cultivar, producing a self-compatible population. Through genotyping-by-sequencing (GBS), researchers found that increased homozygosity did not necessarily affect growth and performance. This study concludes that self-compatible ryegrass can be a promising tool for hybrid breeding and agronomic improvement.
Article
Forestry
Rongmei Wu, Janine Cooney, Sumathi Tomes, Ria Rebstock, Sakuntala Karunairetnam, Andrew C. Allan, Richard C. Macknight, Erika Varkonyi-Gasic
Summary: The reduced expression of DAM/SVP genes in apple through RNAi resulted in plants that failed to enter dormancy, continued leaf growth, and exhibited precocious flowering. Changes in phytohormone composition, particularly increased levels of gibberellins and jasmonates, were observed in the transgenic plants, along with alterations in the expression of key genes related to flowering and dormancy.