Article
Biology
Kun Du, Yang Yang, Jinping Li, Ming Wang, Jinjin Jiang, Jian Wu, Yujie Fang, Yang Xiang, Youping Wang
Summary: Phosphorus stress is a significant factor limiting plant growth, and miRNA, specifically miR399, plays a role in regulating the response to nutrient stress. This study showed that overexpressing Bna-miR399c in rapeseed increased taproot length, lateral root number, biomass, and phosphorus accumulation while reducing anthocyanin content and improving chlorophyll content under low phosphorus stress. BnPHO2 was identified as one of the targets of Bna-miR399c, and its overexpression increased phosphorus rejection in rapeseed seedlings. This research provides insights into improving phosphorus uptake and transportation in rapeseed and has potential applications in germplasm innovation and the development of intelligent crops.
Article
Cell Biology
Scott Dindot, Sarah Christian, William J. Murphy, Allyson Berent, Jennifer Panagoulias, Annalise Schlafer, Johnathan Ballard, Kamelia Radeva, Ruth Robinson, Luke Myers, Thomas Jepp, Hillary Shaheen, Paul Hillman, Kranti Konganti, Andrew Hillhouse, Kevin R. Bredemeyer, Lauren Black, Julie Douville, FIRE Consortium
Summary: Angelman syndrome is a devastating neurogenetic disorder with no effective treatment. Researchers have developed an antisense oligonucleotide therapy that targets a specific region of the UBE3A-AS transcript, leading to the reactivation of the paternal UBE3A allele in neurons. They demonstrated the effectiveness of this therapy in both cell culture and primate models and propose advancing it to clinical development.
SCIENCE TRANSLATIONAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Terry R. Suk, Marilyn T. Tirard, Zoe A. Fisk, Miso Mitkovski, Haley M. Geertsma, Jean-Louis A. Parmasad, Meghan M. Heer, Steve M. Callaghan, Fritz Benseler, Nils Brose, Marilyn Tirard, Maxime W. C. Rousseaux
Summary: SUMOylation is a protein modification widely present in evolutionarily conserved eukaryotes and has broad biological significance. To differentiate between SUMO paralogs and uncover their specific functions in vivo, His6-HA-Sumo2 and HA-Sumo2 knockin mouse lines were generated, expanding upon the existing His6-HA-Sumo1 mouse line. By utilizing the specificity of the HA epitope, regional differences in Sumo1 and Sumo2 expression were observed through whole-brain imaging. Immunoprecipitation coupled with mass spectrometry identified shared and specific neuronal targets of Sumo1 and Sumo2, and proximity ligation assays provided insight into the subcellular distribution of neuronal Sumo2-conjugates. These mouse models and associated datasets provide a powerful framework to determine the native SUMO code in cells of the central nervous system.
Article
Plant Sciences
Zengke Ma, Juncheng Wang, Chengdao Li, Panrong Ren, Lirong Yao, Baochun Li, Yaxiong Meng, Xiaole Ma, Erjing Si, Ke Yang, Xunwu Shang, Huajun Wang
Summary: This study reveals the phosphorylation proteins in barley roots under P starvation and resupply conditions, and their functions in various metabolic pathways. The phosphorylated proteins show significant changes under P starvation and resupply conditions, mainly participating in carbohydrate metabolism, phytohormones, signal transduction, and other metabolic processes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Sciences
Awais Shakoor, Angela D. Bosch-Serra, Jose Ramon Olarieta Alberdi, Carmen Herrero
Summary: Intensive pig farming can lead to the production of large quantities of slurry, which is commonly used as fertilizer in agriculture. A 7-year field study was conducted to investigate the effects of pig slurry on soil properties and the accumulation of nutrients and heavy metals in a calcareous silty-loam soil and barley plants. The results showed that slurry application increased organic carbon, available phosphorus and potassium, and total phosphorus in the soil. There were no significant differences in concentrations of certain heavy metals in the soil, but slurry application increased the extraction and plant concentrations of copper, manganese, and zinc. Overall, the lowest slurry rate was found to maintain high grain yields while improving soil fertility.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Plant Sciences
Tingting Li, Yihan Li, Hongbin Shangguan, Jianxin Bian, Ruihan Luo, Yuan Tian, Zhimin Li, Xiaojun Nie, Licao Cui
Summary: BarleyExpDB is an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley for functional genomics research and crop molecular breeding. It provides a platform for querying gene expression data and visualizing it in various formats, along with functional annotations.
Article
Agronomy
C. Mariano Cossani, Jairo Palta, Victor O. Sadras
Summary: The aim of this study was to assess the rate of genetic gain and associated changes in phenotype in Australian barley cultivars bred over several decades. The results showed that grain yield increased at a rate of 16.0 kg/ha/yr or 0.43% yr/yr, and root traits and nutrient uptake also changed with the year of registration.
Review
Biochemistry & Molecular Biology
Adriana Volna, Martin Bartas, Petr Pecinka, Vladimir Spunda, Jiri Cerven
Summary: This paper reviews the current understanding of miRNAs in spring barley, discussing their roles in plant development, homeostasis, and immune processes, and proposing future research directions and unresolved questions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Ruiqing Cheng, Lei Yin, Rui Hu, Huijun Liu, Yao Wen, Chuansheng Liu, Jun He
Summary: This study reports the modulation of a unique NDR effect in ambipolar black phosphorus transistors, which exhibit high peak current density and operating temperature. The NDR peak current and voltage can be effectively modulated by the strong coupling between the channel and the gate electrode.
ADVANCED MATERIALS
(2021)
Article
Engineering, Environmental
Brian Rippey, Yvonne McElarney, James Thompson, Michelle Allen, Mary Gallagher, Richard Douglas
Summary: The framework, model and methods of Nurnberg were applied and evaluated in Lough Neagh and 19 other lakes to determine inflow phosphorus concentrations that support target lake values. Supporting concentrations were derived and the effect of uncertainty in the model retention co-efficient was relatively small. Other data also supported the model and methods. According to estimates of recovery time from multiple lakes, lakes with internal loads may take a long time to reach their target values.
Article
Plant Sciences
Emna Ghouili, Yassine Hidri, Hatem Cheikh M'Hamed, Anil Somenahally, Qingwu Xue, Ibrahim El Akram Znaidi, Moez Jebara, Rim Nefissi Ouertani, Yordan Muhovski, Jouhaina Riahi, Ghassen Abid, Khaled Sassi
Summary: Organic fertilizers have a promoting effect on the growth and yield of barley, increasing straw yield, biological yield, and the number of grains. They also enhance the content of photosynthesizing pigments and nutrient uptake in plants. Furthermore, real-time PCR analysis reveals differential expression of candidate genes involved in nitrogen and phosphorus metabolism in barley, suggesting their role in nutrient absorption and transport.
SOUTH AFRICAN JOURNAL OF BOTANY
(2022)
Article
Chemistry, Multidisciplinary
Carly K. Schissel, Somesh Mohapatra, Justin M. Wolfe, Colin M. Fadzen, Kamela Bellovoda, Chia-Ling Wu, Jenna A. Wood, Annika B. Malmberg, Andrei Loas, Rafael Gomez-Bombarelli, Bradley L. Pentelute
Summary: The study demonstrates that deep learning can decipher design principles to generate highly active biomolecules, such as Mach proteins, which are capable of delivering antisense cargo efficiently without toxicity in mice. This approach combines high-throughput experimentation with a deep-learning method inspired by directed evolution, representing molecular structures as topological fingerprints.
Article
Agronomy
L. Jordan-Meille, J. E. Holland, S. P. McGrath, M. J. Glendining, C. L. Thomas, S. M. Haefele
Summary: The study analyzed the effects of liming on the mineral concentrations in three main cereal crops, finding that pH has a significant impact on grain mineral concentrations, with factors including soil nutrient concentrations and P treatment. Different crops showed varied responses to pH, with differences in Cu and Zn concentrations mainly attributed to soil type.
EUROPEAN JOURNAL OF AGRONOMY
(2021)
Review
Medicine, Research & Experimental
Rong Dong, Bo Zhang, Biqin Tan, Nengming Lin
Summary: Macrophages play a crucial role in M2 polarization, which is regulated by various factors. Long non-coding RNAs (lncRNAs) are essential for the process, guiding macrophages towards an M2 phenotype through multiple mechanisms. Exosomal lncRNAs can also regulate polarization through paracrine action.
Article
Biochemistry & Molecular Biology
Habes Bilal Aydemir, Merve Nur Aydemir, Ertan Mahir Korkmaz
Summary: A study was conducted on the mitogenome of Syrista parreyssi (Hymenoptera: Cephidae) to investigate gene expression and encoding potential. It was discovered that there were differences in gene expression and the mitogenome had the ability to encode additional peptides, some of which were encoded in antisense transcript units. A unique finding was the potential open reading frame sequence within the antisense rrnL gene, which contained a conserved cox3 domain.
ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY
(2023)
Article
Agronomy
Vahid Rahimi Eichi, Mamoru Okamoto, Trevor Garnett, Paul Eckermann, Benoit Darrier, Matteo Riboni, Peter Langridge
Article
Plant Sciences
Satyvaldy Jatayev, Igor Sukhikh, Valeriya Vavilova, Svetlana E. Smolenskaya, Nikolay P. Goncharov, Akhylbek Kurishbayev, Lyudmila Zotova, Aiman Absattarova, Dauren Serikbay, Yin-Gang Hu, Nikolai Borisjuk, Narendra K. Gupta, Bertus Jacobs, Stephan de Groot, Francois Koekemoer, Badr Alharthi, Katso Lethola, Dan T. Cu, Carly Schramm, Peter Anderson, Colin L. D. Jenkins, Kathleen L. Soole, Yuri Shavrukov, Peter Langridge
PLANT CELL AND ENVIRONMENT
(2020)
Article
Plant Sciences
Akmaral Baidyussen, Maryam Aldammas, Akhylbek Kurishbayev, Malika Myrzabaeva, Askar Zhubatkanov, Grigory Sereda, Raisa Porkhun, Sergey Sereda, Satyvaldy Jatayev, Peter Langridge, Carly Schramm, Colin L. D. Jenkins, Kathleen L. Soole, Yuri Shavrukov
Article
Biochemistry & Molecular Biology
Charity Chidzanga, Delphine Fleury, Ute Baumann, Dan Mullan, Sayuri Watanabe, Priyanka Kalambettu, Robert Pontre, James Edwards, Kerrie Forrest, Debbie Wong, Peter Langridge, Ken Chalmers, Melissa Garcia
Summary: The importance of genetic diversity and efficient utilization of genetic resources in plant breeding was discussed in the article, along with the establishment process of Nested Association Mapping (NAM) populations and their applications in breeding programs. Through genetic typing and multi-environment trials, potential QTLs were identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
C. Gomez-Martin, E. Aparicio-Puerta, J. M. Medina, Guillermo Barturen, J. L. Oliver, M. Hackenberg
Summary: Genetic variation, gene expression, and DNA methylation influence each other in a complex way. The geno(5)mC database is created to study the impact of sequence variation and DNA methylation on gene expression. By analyzing SNP-CpG associations and correlations with gene expression levels, previously unknown interactions between disease-associated SNPs and their functional targets can be inferred.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Correction
Agronomy
Habtamu Tura, James Edwards, Vijay Gahlaut, Melissa Garcia, Beata Sznajder, Ute Baumann, Fahimeh Shahinnia, Matthew Reynolds, Peter Langridge, Harindra Singh Balyan, Pushpendra K. Gupta, Thorsten Schnurbusch, Delphine Fleury
THEORETICAL AND APPLIED GENETICS
(2021)
Review
Agronomy
Peter Langridge, Matthew Reynolds
Summary: The article evaluates various strategies used to enhance the heat and drought tolerance of wheat. While these strategies have expanded our knowledge of factors influencing yield under stress, not all have yielded the expected progress.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Plant Sciences
Judith Atieno, Timothy D. Colmer, Julian Taylor, Yongle Li, John Quealy, Lukasz Kotula, Dion Nicol, Duong T. Nguyen, Chris Brien, Peter Langridge, Janine Croser, Julie E. Hayes, Tim Sutton
Summary: By utilizing molecular markers and QTL analysis, this study identified multiple loci associated with salinity tolerance in chickpea, revealing the genetic basis of salt tolerance and its influence on growth and yield traits under salinity stress.
FRONTIERS IN PLANT SCIENCE
(2021)
Editorial Material
Agronomy
Peter Langridge, Hans Braun, Brent Hulke, Eric Ober, B. M. Prasanna
Summary: In order to enhance the resilience of crops to the impacts of climate change, breeders and agronomists need to broaden the adaptability of varieties grown, increase yield stability, and help farmers minimize the risks associated with climate change, ultimately building resilience in crops.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Cell Biology
Esther E. E. Drees, Margaretha G. M. Roemer, Nils J. Groenewegen, Jennifer Perez-Boza, Monique A. J. van Eijndhoven, Leah I. Prins, Sandra A. W. M. Verkuijlen, Xuan-Mai Tran, Julia Driessen, G. J. C. Zwezerijnen, Phylicia Stathi, Kevin Mol, Joey J. J. P. Karregat, Aikaterini Kalantidou, Andrea Valles-Marti, T. J. Molenaar, Ernesto Aparicio-Puerta, Erik van Dijk, Bauke Ylstra, Catharina G. M. Groothuis-Oudshoorn, Michael Hackenberg, Daphne de Jong, Josee M. Zijlstra, D. Michiel Pegtel
Summary: This study showed that miRNAs associated with tumour-secreted EVs in the circulation of cHL patients can improve response assessment. The levels of EV-miRNAs are predictive of metabolic tumour activity in cHL patients, and combining them with TARC protein levels increases the accuracy for predicting PET-status.
JOURNAL OF EXTRACELLULAR VESICLES
(2021)
Article
Oncology
Carlos Pedraz-Valdunciel, Stavros Giannoukakos, Nicolas Potie, Ana Gimenez-Capitan, Chung-Ying Huang, Michael Hackenberg, Alberto Fernandez-Hilario, Jill Bracht, Martyna Filipska, Erika Aldeguer, Sonia Rodriguez, Trever G. Bivona, Sarah Warren, Cristina Aguado, Masaoki Ito, Andres Aguilar-Hernandez, Miguel Angel Molina-Vila, Rafael Rosell
Summary: This study utilizes the nCounter platform and machine learning methods to identify two circRNA signatures with diagnostic potential for non-small cell lung cancer, providing new approaches and tools for its diagnosis.
MOLECULAR ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Bastian Fromm, Eirik Hoye, Diana Domanska, Xiangfu Zhong, Ernesto Aparicio-Puerta, Vladimir Ovchinnikov, Sinan U. Umu, Peter J. Chabot, Wenjing Kang, Morteza Aslanzadeh, Marcel Tarbier, Emilio Marmol-Sanchez, Gianvito Urgese, Morten Johansen, Eivind Hovig, Michael Hackenberg, Marc R. Friedlander, Kevin J. Peterson
Summary: The update of MirGeneDB to MirGeneDB 2.1 added 30 additional species, expanding the database to cover 75 species spanning over 800 million years of animal evolution and containing 16670 microRNAs. The update also improved performance and allowed the download of microRNA expression matrices for all tissues and species.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Agronomy
Peter Langridge, Michael Alaux, Nuno Felipe Almeida, Karim Ammar, Michael Baum, Faouzi Bekkaoui, Alison R. Bentley, Brian L. Beres, Bettina Berger, Hans-Joachim Braun, Gina Brown-Guedira, Christopher James Burt, Mario Jose Caccamo, Luigi Cattivelli, Gilles Charmet, Peter Civan, Sylvie Cloutier, Jean-Pierre Cohan, Pierre J. Devaux, Fiona M. Doohan, M. Fernanda Dreccer, Moha Ferrahi, Silvia E. German, Stephen B. Goodwin, Simon Griffiths, Carlos Guzman, Hirokazu Handa, Malcolm John Hawkesford, Zhonghu He, Eric Huttner, Tatsuya M. Ikeda, Benjamin Kilian, Ian Philip King, Julie King, John A. Kirkegaard, Jacob Lage, Jacques Le Gouis, Suchismita Mondal, Ewen Mullins, Frank Ordon, Jose Ivan Ortiz-Monasterio, Hakan Ozkan, Irfan Ozturk, Silvia A. Pereyra, Curtis J. Pozniak, Hadi Quesneville, Martin C. Quincke, Greg John Rebetzke, Jochen Christoph Reif, Teresa Saavedra-Bravo, Ulrich Schurr, Shivali Sharma, Sanjay Kumar Singh, Ravi P. Singh, John W. Snape, Wuletaw Tadesse, Hisashi Tsujimoto, Roberto Tuberosa, Tim G. Willis, Xueyong Zhang
Summary: Wheat plays a crucial role in global food security by providing carbohydrates and protein, but faces threats from climate change and rising resource costs. The international wheat research community is working to find solutions to ensure global wheat production can meet demand.
Meeting Abstract
Oncology
C. Pedraz-Valdunciel, M. Filipska, S. Giannoukakos, N. Potie, A. Fernandez-Hilario, M. Hackenberg, A. Aguilar-Hernandez, J. Valarezo, C. Huang, A. Gimenez Capitan, C. Aguado Esteban, S. Warren, M. A. Molina-Vila, R. Rosell
JOURNAL OF THORACIC ONCOLOGY
(2021)
Review
Cell Biology
Chaima Bensaoud, Larissa Almeida Martins, Hajer Aounallah, Michael Hackenberg, Michail Kotsyfakis
Summary: Non-coding RNAs play crucial roles in regulating protein activity, subcellular structures, and interactions between vectors, hosts, and pathogens. They are involved in various mechanisms to ensure vector and pathogen survival, and host defense responses against vector-borne diseases.
JOURNAL OF CELL SCIENCE
(2021)