Article
Plant Sciences
John Paul Bradican, Salvatore Tomasello, Francesco Boscutti, Kevin Karbstein, Elvira Hoerandl
Summary: The taxonomic status of many Southern European taxa of the Ranunculus auricomus complex remains uncertain. We found the majority of Mediterranean taxa to be tetraploid, with hybrid populations propagating primarily via apomixis. Phylogenomic analysis revealed that except for the progenitor species, the Mediterranean taxa are often polyphyletic.
Article
Plant Sciences
Kevin Karbstein, Salvatore Tomasello, Ladislav Hoda, Natascha Wagner, Pia Marincek, Birthe Hilkka Barke, Claudia Paetzold, Elvira Hoerandl
Summary: This study investigated the Eurasian Ranunculus auricomus species complex using a comprehensive workflow and multiple data analysis methods. The results revealed that the speciation process was mainly driven by allopolyploidization, involving different sexual progenitor species. The biodiversity of polyploid complexes can be attributed to multiple hybrid origins and subsequent evolution.
Article
Plant Sciences
Vladislav Kolarcik, Maria Mirkova, Vlastimil Mikolas
Summary: The remarkable species diversity of the genus Sorbus is a result of polyploidization and frequent hybridization between species of different cytotypes. Gametophytic apomixis plays an important role in the evolutionary stabilization of hybridogeneous genotypes. The reproduction modes and ploidy levels of selected Sorbus species in mixed-cytotype populations were investigated.
Article
Gastroenterology & Hepatology
Kara Wegermann, Melanie E. Garrett, Jiayin Zheng, Andrea Coviello, Cynthia A. Moylan, Manal F. Abdelmalek, Shein-Chung Chow, Cynthia D. Guy, Anna Mae Diehl, Allison Ashley-Koch, Ayako Suzuki
Summary: The study found that sex and menopausal status significantly influence the effect of metabolism-related single nucleotide polymorphisms (SNPs) on the development of fibrosis in nonalcoholic fatty liver disease (NAFLD), with 10 loci identified to be relevant to fibrosis progression.
HEPATOLOGY COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Christopher Oberc, Abootaleb Sedighi, Paul C. H. Li
Summary: Panax ginseng and Panax quinquefolius, commonly known as Chinese ginseng and American ginseng, have similar physical appearances, making it difficult to differentiate them. A molecular technique based on nucleic acid testing has been developed to accurately distinguish between the two ginseng species.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Veterinary Sciences
Ling Yang, Jiachen Bai, Zhihua Ju, Qiang Jiang, Jinpeng Wang, Yaping Gao, Yaran Zhang, Xiaochao Wei, Jinming Huang
Summary: This study identified an association between the APOA1 gene and ketosis in high-yielding dairy cows. A novel SNP (g.-572 A > G) in the core promoter region of the APOA1 gene was found, which may serve as a genetic marker for ketosis prevention. Furthermore, lower concentrations of blood beta-hydroxybutyrate were observed in cows with the genotype GG compared to cows with genotypes AA and AG.
RESEARCH IN VETERINARY SCIENCE
(2021)
Article
Chemistry, Analytical
Salvatore Petralia, Antonella Vigilanza, Emanuele Sciuto, Michele Maffia, Antonella Romanini, Sabrina Conoci
Summary: The study investigated single nucleotide polymorphisms in the MC1R gene using a miniaturized silicon-based microarray-chip, showing good sensitivity and high confidence level, paving the way for future development of portable genetic assays.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Biochemistry & Molecular Biology
Maria Radanova, Mariya Levkova, Galya Mihaylova, Rostislav Manev, Margarita Maneva, Rossen Hadgiev, Nikolay Conev, Ivan Donev
Summary: There is a growing interest in studying single nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, as they may be associated with susceptibility, prognosis, and treatment response in colorectal cancer (CRC). These miRNA-SNPs could serve as non-invasive biomarkers for early detection of CRC. However, contradictory findings have been reported when different research groups investigated the same SNP in a gene for a specific miRNA, highlighting the need for more case-control studies involving participants from different ethnic backgrounds. According to our review, three miRNA-SNPs - miR-146a rs2910164, miR-27a rs895819, and miR-608 rs4919510 - appear to be promising prognostic, diagnostic, and predictive biomarkers for CRC.
Review
Plant Sciences
Zheng Ying, Muhammad Awais, Reshmi Akter, Fengjiao Xu, Sul Baik, Daehyo Jung, Deok Chun Yang, Gi-Young Kwak, Wenying You
Summary: Discriminating plant species, cultivars, and landraces is challenging, but SNP markers have proven to be a reliable tool for differentiating Panax ginseng and similar species. This article provides a cost-effective guide for SNP marker analysis in a traditional laboratory setting.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cardiac & Cardiovascular Systems
Matthew R. Alexander, Samuel Hank, Bethany L. Dale, Lauren Himmel, Xue Zhong, Charles D. Smart, Daniel J. Fehrenbach, Yuhan Chen, Nitin Prabakaran, Brian Tirado, Megan Centrella, Mingfang Ao, Liping Du, Yu Shyr, Daniel Levy, Meena S. Madhur
Summary: Research suggests that the Trp encoding allele of rs3184504 may be causal for hypertension and renal dysfunction, in part due to the loss of SH2B3-mediated repression of T cell IL-12 signaling leading to enhanced IFNg production.
CIRCULATION RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Justyna Basak, Danuta Piotrzkowska, Ireneusz Majsterek, Ewa Kucharska
Summary: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system with no cure and unclear etiology. This study aimed to identify SNPs associated with an increased risk of developing MS. The findings suggest that the GG AGO1 rs636832 and AA GEMIN4 rs7813 genotypes are associated with an increased risk of MS.
Article
Immunology
Yan Li, Wei Li, Li Huang, Huijia Li, Peipeng He, Chao Xue
Summary: This study investigated the association between microscopic polyangiitis and the single nucleotide polymorphism rs807185 in autophagy-associated gene 4A (ATG4A) in the Chinese population. Using multiplex polymerase chain reaction and high-throughput sequencing, it was found that the control group had a higher frequency of the A allele of rs807185 compared to the microscopic polyangiitis group, suggesting that the A allele of rs807185 may have a protective effect against microscopic polyangiitis in the Chinese population. However, the molecular mechanisms remain unclear.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Cell Biology
Concetta Scimone, Luigi Donato, Simona Alibrandi, Concetta Alafaci, Angela D'Ascola, Sergio Vinci, Rosalia D'Angelo, Antonina Sidoti
Summary: This study reveals the importance of epitranscriptomic modifications in gene expression regulation and suggests the involvement of altered epitranscriptome profile in the development of CCM. These findings provide new insights for further investigation into the pathogenesis of CCM.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2022)
Review
Cell Biology
Farbod Bahreini, Elham Rayzan, Nima Rezaei
Summary: Breast cancer, a multifactorial disease, may have an increased risk due to alterations in microRNA sequences. miR-SNPs are potential biomarkers for early detection of breast cancer.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Anoja Megalathan, Kalani M. Wijesinghe, Soma Dhakal
Summary: The article presents a background-free ultrasensitive detection sensor on a simple platform for p53 tumor suppressor gene, showing continuous dynamic switching between low- and high-FRET states in the presence of a target and detecting down to low femtomolar (fM) concentration. The sensor is also highly effective in discriminating against single-nucleotide polymorphisms (SNPs), offering a wide range of nucleic acid sequences detection for early disease diagnosis and genetic disorder screening.
Article
Food Science & Technology
Olivier F. Vilpoux, Timothy F. Sharbel, Andres Posso-Terranova, Eulalia S. S. Hoogerheide, Marney P. Cereda
Summary: The study aimed to verify the potential of identifying different starches in Brazilian landraces of cassava using near and medium infrared analyses. Results showed that infrared analysis allows for rapid identification of different genetic variants chosen by small isolated producers. This demonstrates the potential of MIR analyses for in situ evaluation and appreciates the efforts made by small producers in developing important varieties.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Murukarthick Jayakodi, Sudharsan Padmarasu, Georg Haberer, Venkata Suresh Bonthala, Heidrun Gundlach, Ceecile Monat, Thomas Lux, Nadia Kamal, Daniel Lang, Axel Himmelbach, Jennifer Ens, Xiao-Qi Zhang, Tefera T. Angessa, Gaofeng Zhou, Cong Tan, Camilla Hill, Penghao Wang, Miriam Schreiber, Lori B. Boston, Christopher Plott, Jerry Jenkins, Yu Guo, Anne Fiebig, Hikmet Budak, Dongdong Xu, Jing Zhang, Chunchao Wang, Jane Grimwood, Jeremy Schmutz, Ganggang Guo, Guoping Zhang, Keiichi Mochida, Takashi Hirayama, Kazuhiro Sato, Kenneth J. Chalmers, Peter Langridge, Robbie Waugh, Curtis J. Pozniak, Uwe Scholz, Klaus F. X. Mayer, Manuel Spannagl, Chengdao Li, Martin Mascher, Nils Stein
Article
Multidisciplinary Sciences
Sean Walkowiak, Liangliang Gao, Cecile Monat, Georg Haberer, Mulualem T. Kassa, Jemima Brinton, Ricardo H. Ramirez-Gonzalez, Markus C. Kolodziej, Emily Delorean, Dinushika Thambugala, Valentyna Klymiuk, Brook Byrns, Heidrun Gundlach, Venkat Bandi, Jorge Nunez Siri, Kirby Nilsen, Catharine Aquino, Axel Himmelbach, Dario Copetti, Tomohiro Ban, Luca Venturini, Michael Bevan, Bernardo Clavijo, Dal-Hoe Koo, Jennifer Ens, Krystalee Wiebe, Amidou N'Diaye, Allen K. Fritz, Carl Gutwin, Anne Fiebig, Christine Fosker, Bin Xiao Fu, Gonzalo Garcia Accinelli, Keith A. Gardner, Nick Fradgley, Juan Gutierrez-Gonzalez, Gwyneth Halstead-Nussloch, Masaomi Hatakeyama, Chu Shin Koh, Jasline Deek, Alejandro C. Costamagna, Pierre Fobert, Darren Heavens, Hiroyuki Kanamori, Kanako Kawaura, Fuminori Kobayashi, Ksenia Krasileva, Tony Kuo, Neil McKenzie, Kazuki Murata, Yusuke Nabeka, Timothy Paape, Sudharsan Padmarasu, Lawrence Percival-Alwyn, Sateesh Kagale, Uwe Scholz, Jun Sese, Philomin Juliana, Ravi Singh, Rie Shimizu-Inatsugi, David Swarbreck, James Cockram, Hikmet Budak, Toshiaki Tameshige, Tsuyoshi Tanaka, Hiroyuki Tsuji, Jonathan Wright, Jianzhong Wu, Burkhard Steuernagel, Ian Small, Sylvie Cloutier, Gabriel Keeble-Gagnere, Gary Muehlbauer, Josquin Tibbets, Shuhei Nasuda, Joanna Melonek, Pierre J. Hucl, Andrew G. Sharpe, Matthew Clark, Erik Legg, Arvind Bharti, Peter Langridge, Anthony Hall, Cristobal Uauy, Martin Mascher, Simon G. Krattinger, Hirokazu Handa, Kentaro K. Shimizu, Assaf Distelfeld, Ken Chalmers, Beat Keller, Klaus F. X. Mayer, Jesse Poland, Nils Stein, Curt A. McCartney, Manuel Spannagl, Thomas Wicker, Curtis J. Pozniak
Article
Plant Sciences
Martin Mau, Tiina Liiving, Liza Fomenko, Richard Goertzen, Dorota Paczesniak, Laura Bottner, Timothy F. Sharbel
Summary: The study explored the reproductive diversity of the genus Boechera and found that hybridization can trigger the transition to apomixis, with the transmission of apomixis influenced by pollen type and mating system. Apomixis can occur through various pathways, leading to the formation of polyploids.
Article
Plant Sciences
Sebastian Zahn, Thomas Schmutzer, Klaus Pillen, Andreas Maurer
Summary: This study investigated the genetic control of barley peduncle morphology and identified three major QTL regions on chromosomes 2H and 3H impacting peduncle traits. The exotic allele at the QTL on chromosome 3H improved all three investigated traits, showing potential for enhancing plant stability and straw biomass production.
Article
Multidisciplinary Sciences
Mathias Ruben Gemmer, Chris Richter, Thomas Schmutzer, Manish L. Raorane, Bjoern Junker, Klaus Pillen, Andreas Maurer
Summary: Metabolites, especially sugars, play a key role in plant development and stress responses. A GWAS study in a wild barley NAM population identified multiple metabolic quantitative trait loci (mQTL) associated with sugars, linking them to plant growth, development, flowering, and disease resistance. The study highlights the natural genetic variation in sugar metabolites and their biological functions in barley.
Article
Biology
Matthias Lange, Blaise T. F. Alako, Guy Cochrane, Mehmood Ghaffar, Martin Mascher, Pia-Katharina Habekost, Upneet Hillebrand, Uwe Scholz, Florian Schorch, Jens Freitag, Amber Hartman Scholz
Summary: Linking nucleotide sequence data to scientific publication citations enhances understanding of data provenance, usage, and global trends in scientific knowledge gain. Data quality review, best practice recommendations for citation extraction, and construction of a data warehouse enable exploration of NSD use and statistics. This global provision and use of NSD allows scientists worldwide to engage with literature and sequence databases in a multidimensional manner.
Article
Plant Sciences
Daniel Arend, Dennis Psaroudakis, Junaid Altaf Memon, Elena Rey-Mazon, Danuta Schueler, Jedrzej Jakub Szymanski, Uwe Scholz, Astrid Junker, Matthias Lange
Summary: The research data life cycle is an integral part of current research, but its complexity often exceeds the expertise and infrastructure available to scientists. This article explores how data stewards can address the challenges in data-driven research, using concrete use cases and best practices from plant phenotyping. By enhancing the necessary digital transformation, data stewards can improve the quality of progressive research.
Article
Plant Sciences
Martin Mau, Terezie M. Mandakova, Xingliang Ma, Jana Ebersbach, Lifang Zou, Martin A. Lysak, Timothy F. Sharbel
Summary: This study investigates the molecular evolution, gene regulation, and chromosomal location of a male apomeiosis factor (UPG2) in Boechera, revealing its origin in the apomixis genome and demonstrating selective pressure to maintain its function for unreduced pollen formation in apomicts.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Mohammed A. Sayed, Andreas Maurer, Thomas Schmutzer, Thorsten Schnurbusch, Andreas Boerner, Mats Hansson, Klaus Pillen, Helmy M. Youssef
Summary: Increased salinity due to climatic change is a major factor affecting global crop production. This study identified SNP markers associated with germination and seedling development in barley under salinity treatment, as well as identified salt-tolerant accessions. The results provide a basis for improving salt tolerance breeding programs in barley.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Mathematical & Computational Biology
Manuel Feser, Patrick Koenig, Anne Fiebig, Daniel Arend, Matthias Lange, Uwe Scholz
Summary: In recent years, advancements in data collection in life science have increased the demand and opportunities for advanced bioinformatics. Good research data management strategies are crucial for the use and re-use of genotypic data. The development of reusable and maintainable tools and ecosystems is essential for sustainable software. Using established file formats improves tool reusability and overall interoperability. Building strong communities for tool maintenance is also important.
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2022)
Article
Plant Sciences
Antonia Lisker, Andreas Maurer, Thomas Schmutzer, Ebrahim Kazman, Hilmar Coester, Josef Holzapfel, Erhard Ebmeyer, Ahmad M. Alqudah, Wiebke Sannemann, Klaus Pillen
Summary: The multi-parent-advanced-generation-intercross population WM-800 was developed to enhance genetic diversity in wheat breeding. WM-800 lines showed significant differences between treatments and high heritabilities for agronomic traits. GWAS based on haplotypes identified multiple QTL associated with grain yield and other traits. A novel QTL on chromosome 2B exhibited pleiotropic effects on multiple yield components, possibly mediated by a nitrate transporter gene.
Article
Plant Sciences
Tanja Zahn, Zihao Zhu, Niklas Ritoff, Jonathan Krapf, Astrid Junker, Thomas Altmann, Thomas Schmutzer, Christian Tueting, Panagiotis L. Kastritis, Steve Babben, Marcel Quint, Klaus Pillen, Andreas Maurer
Summary: Novel exotic ELF3 alleles have been discovered and shown to be associated with agronomic traits in barley. These findings suggest a central role for ELF3 in barley adaptation.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biology
Patrick Koenig, Sebastian Beier, Martin Mascher, Nils Stein, Matthias Lange, Uwe Scholz
Summary: DivBrowse is a web application that allows interactive visualization and exploratory analysis of genomic diversity data stored in VCF files. It combines BLAST as an entry point with features like principal component analysis, providing a unique set of capabilities for studying genomic biodiversity datasets. The application also supports data interoperability and integration with existing web applications.
Article
Multidisciplinary Sciences
Phuong T. N. Hoang, Anne Fiebig, Petr Novak, Jiri Macas, Hieu X. Cao, Anton Stepanenko, Guimin Chen, Nikolai Borisjuk, Uwe Scholz, Ingo Schubert
SCIENTIFIC REPORTS
(2020)